From 66834f53c5ce608ffae5ee08f1e2c0d4b22bd419 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 16 Dec 2019 19:52:50 +0000 Subject: [PATCH 001/358] v1.4.1 (16/12/2019) (#275) - bug fix: in helpers/assign_stereochemistry.py - bug fix: auto-fitting of ligands - bug fix: add 'module load mx' to restraints generation script --- ChangeLog.txt | 5 +++++ gui_scripts/settings_preferences.py | 2 +- helpers/assign_stereochemistry.py | 30 ++++++++++++++++++----------- lib/XChemLog.py | 2 +- lib/XChemThread.py | 5 +++++ lib/XChemUtils.py | 6 ++++++ 6 files changed, 37 insertions(+), 13 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 70296500..ddd85415 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,8 @@ +v1.4.1 (16/12/2019) +- bug fix: in helpers/assign_stereochemistry.py; use CompoundSMILES instead of CompoundSMILESproduct (which need to be provided by user) +- bug fix: auto-fitting of ligands - use default ccp4 distribition and submission command +- bug fix: add 'module load mx' to restraints generation script; uses default ccp4 installation, otherwise CLIB path for GRADE broken + v1.4.0 (03/12/2019) - introduced simple semantic versioning according to https://semver.org diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 15a39ce7..724ffede 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.4.0' + xce_object.xce_version = 'v1.4.1' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/helpers/assign_stereochemistry.py b/helpers/assign_stereochemistry.py index a3b6db05..1c48d390 100755 --- a/helpers/assign_stereochemistry.py +++ b/helpers/assign_stereochemistry.py @@ -11,28 +11,34 @@ def enumerateStereoChem(compoundID,sampleDir,db,xtal): # which program was used to create the initial restrains # this is because funny things happen to aromatic rings in case the file was made with GRADE os.chdir(os.path.join(sampleDir,'compound')) - sql = "select CompoundSMILESproduct from mainTable where CrystalName = '%s'" % xtal + sql = "select CompoundSMILES from mainTable where CrystalName = '%s'" % xtal + print 'sqlite query:',sql query = db.execute_statement(sql) originalSMILES = query[0][0] + print originalSMILES cmd = 'phenix.elbow --smiles="%s" --id=LIG --output=tmp' % (originalSMILES) + print 'current working directory:',os.getcwd() + print 'runnning:',cmd os.system(cmd) stereosmiles = None + pdb = None if os.path.isfile(os.path.join(sampleDir,'compound','tmp.pdb')): pdb = os.path.join(sampleDir,'compound','tmp.pdb') else: print 'cannot find tmp.pdb' pass - mol = Chem.MolFromPDBFile(pdb) - Chem.AssignStereochemistry(mol,cleanIt=True,force=True,flagPossibleStereoCenters=True) - if Chem.FindMolChiralCenters(mol,includeUnassigned=True) == []: - print 'no chiral centres found' - db_dict = {} - db_dict['CompoundStereo'] = 'FALSE' - updateDB(db,db_dict,xtal) - else: - stereosmiles = Chem.MolToSmiles(mol,isomericSmiles=True) - generateRestraints(compoundID,sampleDir,db,stereosmiles,xtal) + if pdb: + mol = Chem.MolFromPDBFile(pdb) + Chem.AssignStereochemistry(mol,cleanIt=True,force=True,flagPossibleStereoCenters=True) + if Chem.FindMolChiralCenters(mol,includeUnassigned=True) == []: + print 'no chiral centres found' + db_dict = {} + db_dict['CompoundStereo'] = 'FALSE' + updateDB(db,db_dict,xtal) + else: + stereosmiles = Chem.MolToSmiles(mol,isomericSmiles=True) + generateRestraints(compoundID,sampleDir,db,stereosmiles,xtal) def generateRestraints(compoundID,sampleDir,db,stereosmiles,xtal): cmd = 'phenix.elbow --smiles="%s" --chiral=enumerate --id=LIG --output=%s' %(stereosmiles,compoundID) @@ -66,7 +72,9 @@ def updateDB(db,db_dict,xtal): compoundID = sys.argv[1] sampleDir = sys.argv[2] xtal = sampleDir[sampleDir.rfind('/')+1:] + print 'sampleID:',xtal database = sys.argv[3] + print 'database:',database db=XChemDB.data_source(database) enumerateStereoChem(compoundID,sampleDir,db,xtal) diff --git a/lib/XChemLog.py b/lib/XChemLog.py index d67d7213..0adef996 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 03/12/2019 #\n' + ' # Date: 16/12/2019 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 72df4e3c..b2edc9d7 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -930,6 +930,10 @@ def get_header(self,sampleID): else: top_line = '#!' + os.getenv('SHELL') + '\n' + module = '' + if os.path.isdir('/dls'): + module = 'module load mx\n' + cmd = ( '{0!s}\n'.format(top_line)+ '\n' @@ -937,6 +941,7 @@ def get_header(self,sampleID): '\n' 'cd %s\n' %os.path.join(self.initial_model_directory,sampleID,'autofit_ligand') + '\n' + + module ) return cmd diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 83c268cf..feb8f833 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -267,6 +267,10 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft strip_hydrogens = 'phenix.reduce {0!s}.pdb -trim > {0!s}_tmp.pdb'.format(compoundID.replace(' ', '')) + module = '' + if os.path.isdir('/dls'): + module = 'module load mx\n' + Cmds = ( header + @@ -275,6 +279,8 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft '\n' 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh' '\n' + + module + + '\n' '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py {0!s} {1!s} {2!s} {3!s}' .format(os.path.join(database_directory, data_source_file), sample, 'RefinementCIFStatus', 'running') + '\n' From 00526fc62fc30b41a14c017d75f33de8e355ce38 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 18 Dec 2019 06:43:28 +0000 Subject: [PATCH 002/358] v1.4.2 (17/12/2019) (#276) - bug fix: arbitrary clicking order for atoms making a new covalent link --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemRefine.py | 8 +++++++- 4 files changed, 12 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index ddd85415..0e1e6e7f 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.4.2 (17/12/2019) +- bug fix: arbitrary clicking order for atoms making a new covalent link + v1.4.1 (16/12/2019) - bug fix: in helpers/assign_stereochemistry.py; use CompoundSMILES instead of CompoundSMILESproduct (which need to be provided by user) - bug fix: auto-fitting of ligands - use default ccp4 distribition and submission command diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 724ffede..a76a3582 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.4.1' + xce_object.xce_version = 'v1.4.2' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 0adef996..acad9759 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 16/12/2019 #\n' + ' # Date: 17/12/2019 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 36ee10ee..3c7933a9 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -294,12 +294,18 @@ def GetSerial(self): def make_covalent_link(self,covLinkAtomSpec,Logfile): + residuesToModify = ['CYS','SER'] + atom1 = covLinkAtomSpec[1][5] atom2 = covLinkAtomSpec[2][5] residue_1 = covLinkAtomSpec[3] residue_2 = covLinkAtomSpec[4] - bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' %(residue_1,self.compoundID,atom1,residue_2,atom2) + if residue_2 in residuesToModify: + bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' %(residue_1,self.compoundID,atom1,residue_2,atom2) + else: + bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' % (residue_2, self.compoundID, atom2, residue_1, atom1) + os.chdir(os.path.join(self.ProjectPath,self.xtalID)) f = open('covalent_bond.txt','w') f.write(bond_text) From fc43cec33619b68f013078639d63bbb2304029c2 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 10 Jan 2020 16:46:51 +0000 Subject: [PATCH 003/358] v1.4.3 (10/10/2019) - added additional error message during pandda.export in case of missing ensemble model (#277) --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 3 +++ 4 files changed, 8 insertions(+), 2 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 0e1e6e7f..b93bf459 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.4.3 (10/10/2019) +- added additional error message during pandda.export in case of missing ensemble model + v1.4.2 (17/12/2019) - bug fix: arbitrary clicking order for atoms making a new covalent link diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index a76a3582..4cdbf6ec 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.4.2' + xce_object.xce_version = 'v1.4.3' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index acad9759..74f80ed0 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 17/12/2019 #\n' + ' # Date: 10/01/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 1d4ecafa..a116569a 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -111,6 +111,9 @@ def refine_exported_models(self,samples_to_export): # ' does not have a modelled structure. Check whether you expect this dataset to ' + # ' have a modelled structure, compare pandda.inspect and datasource,' # ' then tell XCHEMBB ') + else: + self.Logfile.error('%s: cannot find %s-ensemble-model.pdb; cannot start refinement...' %(xtal,xtal)) + self.Logfile.error('Please check terminal window for any PanDDA related tracebacks') elif xtal in samples_to_export and not os.path.isfile( os.path.join(self.initial_model_directory, xtal, xtal + '.free.mtz')): From f4b64fa03bcc73a42bc825eae47724c1917b1f57 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 10 Jan 2020 16:56:12 +0000 Subject: [PATCH 004/358] v1.4.4 (10/01/2019) - bug fix: corrected pandda.analyse keyword 'exclude_from_z_map_analysis' (#278) --- ChangeLog.txt | 5 ++++- gui_scripts/settings_preferences.py | 2 +- lib/XChemPANDDA.py | 2 +- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index b93bf459..621e56e3 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,4 +1,7 @@ -v1.4.3 (10/10/2019) +v1.4.4 (10/01/2019) +- bug fix: corrected pandda.analyse keyword 'exclude_from_z_map_analysis' + +v1.4.3 (10/01/2019) - added additional error message during pandda.export in case of missing ensemble model v1.4.2 (17/12/2019) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 4cdbf6ec..d848f82f 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.4.3' + xce_object.xce_version = 'v1.4.4' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index a116569a..d960c25a 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -510,7 +510,7 @@ def append_to_ignore_string(datasets_list, append_string): char_string = 'exclude_from_characterisation="' char_string = append_to_ignore_string(char, char_string) - zmap_string = 'exclude_from_zmap_analysis="' + zmap_string = 'exclude_from_z_map_analysis="' zmap_string = append_to_ignore_string(zmap, zmap_string) for i in range(number_of_cyles): From f0ecdce2a6bda5817865c0cf10805886b7d2805c Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 16 Jan 2020 16:08:39 +0000 Subject: [PATCH 005/358] v1.4.5 (16/01/2020) (#282) * v1.4.5 (16/01/2020) - bug fix: removing and re-parsing of folders from project directory does not need the DataProcessingAutoAssigned flag to be reset if the MTZ file does not exist --- ChangeLog.txt | 7 +++++-- gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemThread.py | 8 ++++++-- 4 files changed, 13 insertions(+), 6 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 621e56e3..0da4b39e 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,7 +1,10 @@ -v1.4.4 (10/01/2019) +v1.4.5 (16/01/2020) +- bug fix: removing and re-parsing of folders from project directory does not need the DataProcessingAutoAssigned flag to be reset if the MTZ file does not exist + +v1.4.4 (10/01/2020) - bug fix: corrected pandda.analyse keyword 'exclude_from_z_map_analysis' -v1.4.3 (10/01/2019) +v1.4.3 (10/01/2020) - added additional error message during pandda.export in case of missing ensemble model v1.4.2 (17/12/2019) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index d848f82f..e27dab42 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.4.4' + xce_object.xce_version = 'v1.4.5' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 74f80ed0..b9465804 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 10/01/2020 #\n' + ' # Date: 16/01/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemThread.py b/lib/XChemThread.py index b2edc9d7..dd59c4c7 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2228,8 +2228,12 @@ def __init__(self, def run(self): for sample in sorted(self.allSamples): if self.db.autoprocessing_result_user_assigned(sample) and not self.rescore: - self.Logfile.warning('{0!s}: user has manually selected auto-processing result; will NOT auto-select!'.format(sample)) - continue + if os.path.isfile(os.path.join(self.projectDir,sample,sample+'.mtz')): + self.Logfile.warning('{0!s}: user has manually selected auto-processing result; will NOT auto-select!'.format(sample)) + continue + else: + self.Logfile.warning('{0!s}: user has manually selected auto-processing result before, but {1!s}.mtz does not exist'.format(sample,sample)) + self.Logfile.insert('%s: selecting autoprocessing result' % sample) elif self.rescore: self.Logfile.warning('{0!s}: rescore selected -> might overwrite user selection!'.format(sample)) else: From 12921956fdec80c1b4b1e6564d49c1be7fbfcd23 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 31 Jan 2020 13:21:06 +0000 Subject: [PATCH 006/358] v1.4.6 (21/01/2020) (#284) - added xia2-* wildcard to read_write_autoprocessing_results_from_to_disc because autoprocessing folder names changed - added parsing of DIALS JSON merging statistics file and MMCIF cell parameter file - added 'recollect' folder for parsing of auto-collections --- ChangeLog.txt | 5 + gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemThread.py | 64 +++++-- lib/XChemUtils.py | 285 +++++++++++++++++++--------- 5 files changed, 255 insertions(+), 103 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 0da4b39e..fa3cd8bc 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,8 @@ +v1.4.6 (21/01/2020) +- added xia2-* wildcard to read_write_autoprocessing_results_from_to_disc because autoprocessing folder names changed +- added parsing of DIALS JSON merging statistics file and MMCIF cell parameter file +- added 'recollect' folder for parsing of auto-collections + v1.4.5 (16/01/2020) - bug fix: removing and re-parsing of folders from project directory does not need the DataProcessingAutoAssigned flag to be reset if the MTZ file does not exist diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index e27dab42..fc066470 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.4.5' + xce_object.xce_version = 'v1.4.6' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index b9465804..201ee71d 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 16/01/2020 #\n' + ' # Date: 21/01/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemThread.py b/lib/XChemThread.py index dd59c4c7..3ca259bc 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2432,6 +2432,12 @@ def __init__(self, [ os.path.join('xia2', '*'), os.path.join('LogFiles', '*aimless.log'), os.path.join('DataFiles', '*free.mtz')], + [ os.path.join('xia2-3*'), + os.path.join('LogFiles', '*aimless.log'), + os.path.join('DataFiles', '*free.mtz')], + [ os.path.join('xia2-dials*'), + os.path.join('LogFiles', '*merging-statistics.json'), + os.path.join('DataFiles', '*free.mtz')], [ os.path.join('multi-xia2', '*'), os.path.join('LogFiles', '*aimless.log'), os.path.join('DataFiles', '*free.mtz')], @@ -2498,6 +2504,10 @@ def copyMTZandLOGfiles(self,xtal,run,autoproc,mtzfile,logfile): if not os.path.isfile(mtzfile[mtzfile.rfind('/') + 1:]): self.Logfile.insert('%s: copying %s' % (xtal, mtzfile)) os.system('/bin/cp ' + mtzfile + ' .') + for mmcif in glob.glob(os.path.join(mtzfile[:mtzfile.rfind('/')],'*')): + if mmcif.endswith('.mmcif'): + self.Logfile.insert('%s: copying %s' %(xtal,mmcif)) + os.system('/bin/cp ' + mmcif + ' .') if os.path.isfile(mtzfile[mtzfile.rfind('/')+1:]) and not os.path.isfile(xtal+'.mtz'): os.symlink(mtzfile[mtzfile.rfind('/')+1:], xtal + '.mtz') if os.path.isfile(mtzfile[mtzfile.rfind('/') + 1:]): @@ -2536,7 +2546,7 @@ def copyJPGs(self,xtal,run,auto): for img in glob.glob(os.path.join(self.processedDir.replace(proposal,self.visit),'jpegs',auto,self.target,xtal,run + '*.0.png')): if not os.path.isfile(os.path.join(self.projectDir,xtal,'jpg', self.visit +'-'+ run,img[img.rfind('/')+1:])): self.Logfile.insert('%s: copying %s' % (xtal, img)) - os.system('/bin/cp %s %s' %(img,os.path.join(self.projectDir,xtal,'jpg', self.visit + '-' + run))) + os.system('/bin/cp %s %s' %(img,os.path.join(self.projectDir,xtal,'jpg', self.visit + '-' + auto+'_'+ run))) else: for img in glob.glob(os.path.join(self.processedDir.replace('processed', 'jpegs'), run + '*.0.png')): found = True @@ -2561,8 +2571,12 @@ def findJPGs(self,xtal,run): def readProcessingUpdateResults(self,xtal,folder,log,mtz,timestamp,current_run,autoproc): db_dict = {} + self.Logfile.warning('%s: looking for %s' %(xtal,os.path.join(folder, mtz))) for mtzfile in glob.glob(os.path.join(folder,mtz)): + self.Logfile.insert('%s: found %s' %(xtal,mtzfile)) + self.Logfile.warning('%s: looking for %s' %(xtal,os.path.join(folder, log))) for logfile in glob.glob(os.path.join(folder, log)): + self.Logfile.insert('%s: found %s' % (xtal, logfile)) self.createAutoprocessingDir(xtal, current_run, autoproc) mtzNew,logNew = self.copyMTZandLOGfiles(xtal,current_run,autoproc,mtzfile,logfile) if self.target == '=== project directory ===': @@ -2582,11 +2596,18 @@ def readProcessingUpdateResults(self,xtal,folder,log,mtz,timestamp,current_run,a # return db_dict def getAutoProc(self,folder): - autoproc='unkown' + autoproc='unknown' if 'ap-run' in folder: autoproc = 'autoPROC' + elif 'autoPROC' in folder: + autoproc = 'autoPROC' else: - autoproc = folder.split('/')[len(folder.split('/'))-1] + for f in folder.split('/'): + print f + if ('xia2' or 'dials' or 'autoPROC') in f: + autoproc = f + break +# autoproc = folder.split('/')[len(folder.split('/'))-1] return autoproc def update_data_collection_table(self,xtal,current_run,autoproc,db_dict): @@ -2672,8 +2693,13 @@ def parse_file_system(self): procDir = os.path.join(run,item[0]) logfile = item[1] mtzfile = item[2] + self.Logfile.insert('%s: search template: procDir - logfile - mtzfile' %xtal) + self.Logfile.insert('%s: procDir = %s' %(xtal,procDir)) + self.Logfile.insert('%s: logfile = %s' %(xtal,logfile)) + self.Logfile.insert('%s: mtzfile = %s' %(xtal,mtzfile)) for folder in glob.glob(procDir): + self.Logfile.insert('%s: searching %s' %(xtal,folder)) if self.junk(folder): continue if self.empty_folder(xtal,folder): @@ -2681,7 +2707,7 @@ def parse_file_system(self): if 'staraniso' in logfile or 'summary.tar.gz' in logfile: autoproc = 'aP_staraniso' else: - autoproc = self.getAutoProc(folder) + autoproc = self.getAutoProc(procDir) if self.alreadyParsed(xtal,current_run,autoproc): continue self.readProcessingUpdateResults(xtal,folder,logfile,mtzfile,timestamp,current_run,autoproc) @@ -2717,7 +2743,7 @@ def parse_agamemnon_file_system(self): runList = [] - autoDir = ['auto','agamemnon'] + autoDir = ['auto','agamemnon','recollect'] for auto in autoDir: for collected_xtals in sorted(glob.glob(os.path.join(self.processedDir+'-*','processed',auto,self.target,'*'))): @@ -2731,13 +2757,18 @@ def parse_agamemnon_file_system(self): if xtal.endswith('_'): continue # happened sometime during testing, but should not happen anymore - self.Logfile.insert('%s: checking auto-processing results' %xtal) + self.Logfile.insert('%s: checking auto-processing results in %s %s' %(xtal,self.visit,auto)) self.createSampleDir(xtal) + foundRun = False + self.Logfile.insert('%s: checking for runs in %s' %(xtal,os.path.join(collected_xtals,'*'))) for run in sorted(glob.glob(os.path.join(collected_xtals,'*'))): - current_run=run[run.rfind('/')+1:] + foundRun = True + self.Logfile.insert('%s: current run %s' %(xtal,run)) + current_run=auto+'_'+run[run.rfind('/')+1:] if current_run not in runList: - runList.append(current_run) + self.Logfile.insert('%s: found new run -> %s' %(xtal,current_run)) + runList.append(self.visit+'_'+auto+'_'+current_run) else: continue self.Logfile.insert('%s -> run: %s -> current run: %s' %(xtal,run,current_run)) @@ -2745,18 +2776,24 @@ def parse_agamemnon_file_system(self): # create directory for crystal aligment images in projectDir self.makeJPGdir(xtal,current_run) - self.copyJPGs(xtal, current_run, auto) + self.copyJPGs(xtal, run[run.rfind('/')+1:], auto) for item in self.toParse: procDir = os.path.join(run,item[0]) logfile = item[1] mtzfile = item[2] - for folder in glob.glob(procDir): - for mtz in glob.glob(os.path.join(procDir,mtzfile)): - print mtz + self.Logfile.insert('%s: search template: procDir - logfile - mtzfile' % xtal) + self.Logfile.insert('%s: procDir = %s' % (xtal, procDir)) + self.Logfile.insert('%s: logfile = %s' % (xtal, logfile)) + self.Logfile.insert('%s: mtzfile = %s' % (xtal, mtzfile)) + +# for folder in glob.glob(procDir): +# for mtz in glob.glob(os.path.join(procDir,mtzfile)): +# print mtz for folder in glob.glob(procDir): + self.Logfile.insert('%s: searching %s' % (xtal, folder)) if self.junk(folder): continue if self.empty_folder(xtal,folder): @@ -2776,6 +2813,9 @@ def parse_agamemnon_file_system(self): self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'parsing auto-processing results for '+collected_xtals) self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + if not foundRun: + self.Logfile.error('%s: could not find run' %xtal) + self.Logfile.insert('====== finished parsing beamline directory ======') self.emit(QtCore.SIGNAL('read_pinIDs_from_gda_logs')) self.emit(QtCore.SIGNAL("finished()")) diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index feb8f833..c719e0e0 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -10,7 +10,7 @@ import math import platform import tarfile - +import json from rdkit import Chem from rdkit.Chem import AllChem @@ -398,7 +398,7 @@ def __init__(self): '432': 24 } self.aimless = { 'DataProcessingProgram': 'n/a', - 'DataCollectionRun': 'n/a', +# 'DataCollectionRun': 'n/a', 'DataProcessingSpaceGroup': 'n/a', 'DataProcessingUnitCell': 'n/a', 'DataProcessingA': 'n/a', @@ -578,8 +578,12 @@ def read_aimless_logfile(self,logfile): self.aimless['DataProcessingProgram']='xia2 3d' elif '3dii-run' in logfile: self.aimless['DataProcessingProgram']='xia2 3dii' + elif 'xia2' in logfile: + self.aimless['DataProcessingProgram'] = 'xia2' elif 'dials-run' in logfile: self.aimless['DataProcessingProgram']='dials' + elif 'dials' in logfile: + self.aimless['DataProcessingProgram']='dials' elif 'autoPROC' in logfile: self.aimless['DataProcessingProgram']='autoPROC' elif 'staraniso' in logfile: @@ -589,81 +593,133 @@ def read_aimless_logfile(self,logfile): # Note: only works if file is in original directory, but not once it moved to 'inital_model' folder# ## print self.Logfile.split('/')[9].split('_')[1] ## if len(self.Logfile.split('/'))>8 and len(self.Logfile.split('/')[9].split('_'))==1: - try: - self.aimless['DataCollectionRun']=logfile.split('/')[9].split('_')[1] - except IndexError: - pass +# try: +# self.aimless['DataCollectionRun']=logfile.split('/')[9].split('_')[1] +# except IndexError: +# pass + + + if logfile.endswith('.log') or logfile.endswith('.table1'): + self.aimless_logile(logfile) + elif logfile.endswith('.json'): + self.json_logfile(logfile) + + + # Hex Color code: + # red: #FF0000 + # orange: #FF9900 + # green: #00FF00 + # gray: #E0E0E0 - resolution_at_15_sigma_line_overall_found=False - resolution_at_20_sigma_line_overall_found=False + if self.aimless['DataProcessingA'] != 'n/a' and self.aimless['DataProcessingB'] != 'n/a' and self.aimless['DataProcessingC'] != 'n/a' \ + and self.aimless['DataProcessingAlpha'] != 'n/a' and self.aimless['DataProcessingBeta'] != 'n/a' and self.aimless['DataProcessingGamma'] != 'n/a' \ + and self.aimless['DataProcessingLattice'] != 'n/a': + a = self.aimless['DataProcessingA'] + b = self.aimless['DataProcessingB'] + c = self.aimless['DataProcessingC'] + alpha = self.aimless['DataProcessingAlpha'] + beta = self.aimless['DataProcessingBeta'] + gamma = self.aimless['DataProcessingGamma'] + self.aimless['DataProcessingUnitCellVolume'] = str( + self.calc_unitcell_volume_from_logfile(float(a), float(b), float(c), + math.radians(float(alpha)), + math.radians(float(beta)), + math.radians(float(gamma)), + self.aimless['DataProcessingLattice'])) + try: + high_symmetry_boost = self.nr_asu_in_unitcell_for_point_group[ + self.aimless['DataProcessingPointGroup']] + self.aimless['DataProcessingScore'] = (float( + self.aimless['DataProcessingUniqueReflectionsOverall']) * float(self.aimless['DataProcessingCompletenessOverall']) * high_symmetry_boost * float(self.aimless['DataProcessingIsigOverall'])) / float( + self.aimless['DataProcessingUnitCellVolume']) + except ValueError: + self.aimless['DataProcessingScore'] = 0.0 + self.aimless['DataProcessingUnitCell'] = str(a) + ' ' + str(b) + ' ' + str(c) + ' ' + str(alpha) + ' ' + str( + beta) + ' ' + str(gamma) + self.aimless['DataProcessingResolutionOverall'] = str( + self.aimless['DataProcessingResolutionLow']) + ' - ' + str(self.aimless['DataProcessingResolutionHigh']) + + + if self.aimless['DataProcessingResolutionHigh']=='n/a' or self.aimless['DataProcessingRmergeLow'] =='n/a': + self.aimless['DataProcessingAlert'] = '#FF0000' + else: + if float(self.aimless['DataProcessingResolutionHigh']) > 3.5 or float(self.aimless['DataProcessingRmergeLow']) > 0.1: + self.aimless['DataProcessingAlert'] = '#FF0000' + if (3.5 >= float(self.aimless['DataProcessingResolutionHigh']) > 2.5) or \ + (0.1 >= float(self.aimless['DataProcessingRmergeLow']) > 0.05): + self.aimless['DataProcessingAlert'] = '#FF9900' + if float(self.aimless['DataProcessingResolutionHigh']) <= 2.5 and float(self.aimless['DataProcessingRmergeLow']) <= 0.05: + self.aimless['DataProcessingAlert'] = '#00FF00' + return self.aimless -# -# print '=====>',self.aimless['DataCollectionRun'],logfile -# - resolution_at_sigma_line_overall_found=False - for line_number,line in enumerate(open(logfile)): -# if 'Wavelength' in line: -# print 'here' -# print line.split() + def aimless_logile(self,logfile): + resolution_at_15_sigma_line_overall_found = False + resolution_at_20_sigma_line_overall_found = False + resolution_at_sigma_line_overall_found = False + for line_number, line in enumerate(open(logfile)): + # if 'Wavelength' in line: + # print 'here' + # print line.split() if 'Wavelength' in line and len(line.split()) >= 2: - self.aimless['DataCollectionWavelength']=line.split()[1] - if 'Low resolution limit' in line and len(line.split())==6: + self.aimless['DataCollectionWavelength'] = line.split()[1] + if 'Low resolution limit' in line and len(line.split()) == 6: self.aimless['DataProcessingResolutionLow'] = line.split()[3] self.aimless['DataProcessingResolutionHighOuterShell'] = line.split()[5] - if 'High resolution limit' in line and len(line.split())==6: + if 'High resolution limit' in line and len(line.split()) == 6: self.aimless['DataProcessingResolutionHigh'] = line.split()[3] self.aimless['DataProcessingResolutionLowInnerShell'] = line.split()[4] - if 'Rmerge (all I+ and I-)' in line and len(line.split())==8: + if 'Rmerge (all I+ and I-)' in line and len(line.split()) == 8: self.aimless['DataProcessingRmergeOverall'] = line.split()[5] self.aimless['DataProcessingRmergeLow'] = line.split()[6] - self.aimless['DataProcessingRmergeHigh'] = line.split()[7] - if 'Rmerge (all I+ & I-)' in line and len(line.split())==8: + self.aimless['DataProcessingRmergeHigh'] = line.split()[7] + if 'Rmerge (all I+ & I-)' in line and len(line.split()) == 8: self.aimless['DataProcessingRmergeOverall'] = line.split()[5] self.aimless['DataProcessingRmergeLow'] = line.split()[6] - self.aimless['DataProcessingRmergeHigh'] = line.split()[7] - if 'Mean((I)/sd(I))' in line and len(line.split())==4: + self.aimless['DataProcessingRmergeHigh'] = line.split()[7] + if 'Mean((I)/sd(I))' in line and len(line.split()) == 4: self.aimless['DataProcessingIsigOverall'] = line.split()[1] self.aimless['DataProcessingIsigHigh'] = line.split()[3] self.aimless['DataProcessingIsigLow'] = line.split()[2] - if 'Mean(I)/sd(I)' in line and len(line.split())==4: + if 'Mean(I)/sd(I)' in line and len(line.split()) == 4: self.aimless['DataProcessingIsigOverall'] = line.split()[1] self.aimless['DataProcessingIsigHigh'] = line.split()[3] self.aimless['DataProcessingIsigLow'] = line.split()[2] - if line.startswith('Completeness') and len(line.split())==4: + if line.startswith('Completeness') and len(line.split()) == 4: self.aimless['DataProcessingCompletenessOverall'] = line.split()[1] self.aimless['DataProcessingCompletenessHigh'] = line.split()[3] self.aimless['DataProcessingCompletenessLow'] = line.split()[2] - if 'Completeness (ellipsoidal)' in line and len(line.split())==5: + if 'Completeness (ellipsoidal)' in line and len(line.split()) == 5: self.aimless['DataProcessingCompletenessOverall'] = line.split()[2] self.aimless['DataProcessingCompletenessHigh'] = line.split()[4] self.aimless['DataProcessingCompletenessLow'] = line.split()[3] - if 'Multiplicity' in line and len(line.split())==4: + if 'Multiplicity' in line and len(line.split()) == 4: self.aimless['DataProcessingMultiplicityOverall'] = line.split()[1] self.aimless['DataProcessingMultiplicityHigh'] = line.split()[3] self.aimless['DataProcessingMultiplicityLow'] = line.split()[3] - if line.startswith('Mn(I) half-set correlation CC(1/2)') and len(line.split())==7: + if line.startswith('Mn(I) half-set correlation CC(1/2)') and len(line.split()) == 7: self.aimless['DataProcessingCChalfOverall'] = line.split()[4] self.aimless['DataProcessingCChalfLow'] = line.split()[5] self.aimless['DataProcessingCChalfHigh'] = line.split()[6] - if line.startswith(' CC(1/2)') and len(line.split())==4: + if line.startswith(' CC(1/2)') and len(line.split()) == 4: self.aimless['DataProcessingCChalfOverall'] = line.split()[1] self.aimless['DataProcessingCChalfLow'] = line.split()[2] self.aimless['DataProcessingCChalfHigh'] = line.split()[3] if line.startswith('Estimates of resolution limits: overall'): - resolution_at_15_sigma_line_overall_found=True - resolution_at_20_sigma_line_overall_found=True + resolution_at_15_sigma_line_overall_found = True + resolution_at_20_sigma_line_overall_found = True if resolution_at_15_sigma_line_overall_found: if 'from Mn(I/sd)' in line and len(line.split()) >= 7: if '1.5' in line.split()[3]: - self.aimless['DataProcessingResolutionHigh15sigma']=line.split()[6][:-1] - resolution_at_15_sigma_line_overall_found=False + self.aimless['DataProcessingResolutionHigh15sigma'] = line.split()[6][:-1] + resolution_at_15_sigma_line_overall_found = False if resolution_at_20_sigma_line_overall_found: if 'from Mn(I/sd)' in line and len(line.split()) >= 7: if '2.0' in line.split()[3]: - self.aimless['DataProcessingResolutionHigh20sigma']=line.split()[6][:-1] - resolution_at_20_sigma_line_overall_found=False - if (line.startswith('Average unit cell:') or line.startswith(' Unit cell parameters')) and len(line.split())==9: + self.aimless['DataProcessingResolutionHigh20sigma'] = line.split()[6][:-1] + resolution_at_20_sigma_line_overall_found = False + if (line.startswith('Average unit cell:') or line.startswith(' Unit cell parameters')) and len( + line.split()) == 9: tmp = [line.split()] a = int(float(tmp[0][3])) b = int(float(tmp[0][4])) @@ -671,62 +727,112 @@ def read_aimless_logfile(self,logfile): alpha = int(float(tmp[0][6])) beta = int(float(tmp[0][7])) gamma = int(float(tmp[0][8])) - self.aimless['DataProcessingA']=str(a) - self.aimless['DataProcessingB']=str(b) - self.aimless['DataProcessingC']=str(c) - self.aimless['DataProcessingAlpha']=str(alpha) - self.aimless['DataProcessingBeta']=str(beta) - self.aimless['DataProcessingGamma']=str(gamma) - if 'Total number unique' in line and len(line.split())==6: - self.aimless['DataProcessingUniqueReflectionsOverall']=line.split()[3] + self.aimless['DataProcessingA'] = str(a) + self.aimless['DataProcessingB'] = str(b) + self.aimless['DataProcessingC'] = str(c) + self.aimless['DataProcessingAlpha'] = str(alpha) + self.aimless['DataProcessingBeta'] = str(beta) + self.aimless['DataProcessingGamma'] = str(gamma) + if 'Total number unique' in line and len(line.split()) == 6: + self.aimless['DataProcessingUniqueReflectionsOverall'] = line.split()[3] if line.startswith('Space group:') or line.startswith(' Spacegroup name'): if 'Laue' in line: continue if 'Spacegroup name' in line: - self.aimless['DataProcessingSpaceGroup'] = line.replace(' Spacegroup name', '')[:-1].replace(' ','') + self.aimless['DataProcessingSpaceGroup'] = line.replace(' Spacegroup name', '')[:-1].replace(' ', + '') else: - self.aimless['DataProcessingSpaceGroup']=line.replace('Space group: ','')[:-1] - self.aimless['DataProcessingLattice']=self.get_lattice_from_space_group(self.aimless['DataProcessingSpaceGroup']) - self.aimless['DataProcessingPointGroup']=self.get_pointgroup_from_space_group(self.aimless['DataProcessingSpaceGroup']) -# print a,b,c,alpha,beta,gamma,self.aimless['DataProcessingLattice'] - if a != 'n/a' and b != 'n/a' and c != 'n/a' and \ - alpha != 'n/a' and beta != 'n/a' and gamma != 'n/a' and self.aimless['DataProcessingLattice'] != 'n/a': - self.aimless['DataProcessingUnitCellVolume']=str(self.calc_unitcell_volume_from_logfile(float(a),float(b),float(c), - math.radians(float(alpha)), - math.radians(float(beta)), - math.radians(float(gamma)), - self.aimless['DataProcessingLattice'])) - try: - high_symmetry_boost=self.nr_asu_in_unitcell_for_point_group[self.aimless['DataProcessingPointGroup']] - self.aimless['DataProcessingScore'] = (float(self.aimless['DataProcessingUniqueReflectionsOverall'])*\ - float(self.aimless['DataProcessingCompletenessOverall'])*\ - high_symmetry_boost*\ - float(self.aimless['DataProcessingIsigOverall']))/float(self.aimless['DataProcessingUnitCellVolume']) - except ValueError: - self.aimless['DataProcessingScore']=0.0 - self.aimless['DataProcessingUnitCell']=str(a)+' '+str(b)+' '+str(c)+' '+str(alpha)+' '+str(beta)+' '+str(gamma) - self.aimless['DataProcessingResolutionOverall']=str(self.aimless['DataProcessingResolutionLow'])+' - '+str(self.aimless['DataProcessingResolutionHigh']) - - # Hex Color code: - # red: #FF0000 - # orange: #FF9900 - # green: #00FF00 - # gray: #E0E0E0 - - if self.aimless['DataProcessingResolutionHigh']=='n/a' or self.aimless['DataProcessingRmergeLow'] =='n/a': - self.aimless['DataProcessingAlert'] = '#FF0000' - else: - if float(self.aimless['DataProcessingResolutionHigh']) > 3.5 or float(self.aimless['DataProcessingRmergeLow']) > 0.1: - self.aimless['DataProcessingAlert'] = '#FF0000' - if (3.5 >= float(self.aimless['DataProcessingResolutionHigh']) > 2.5) or \ - (0.1 >= float(self.aimless['DataProcessingRmergeLow']) > 0.05): - self.aimless['DataProcessingAlert'] = '#FF9900' - if float(self.aimless['DataProcessingResolutionHigh']) <= 2.5 and float(self.aimless['DataProcessingRmergeLow']) <= 0.05: - self.aimless['DataProcessingAlert'] = '#00FF00' - - return self.aimless - - + self.aimless['DataProcessingSpaceGroup'] = line.replace('Space group: ', '')[:-1] + self.aimless['DataProcessingLattice'] = self.get_lattice_from_space_group( + self.aimless['DataProcessingSpaceGroup']) + self.aimless['DataProcessingPointGroup'] = self.get_pointgroup_from_space_group( + self.aimless['DataProcessingSpaceGroup']) + # print a,b,c,alpha,beta,gamma,self.aimless['DataProcessingLattice'] +# if a != 'n/a' and b != 'n/a' and c != 'n/a' and \ +# alpha != 'n/a' and beta != 'n/a' and gamma != 'n/a' and self.aimless[ +# 'DataProcessingLattice'] != 'n/a': +# self.aimless['DataProcessingUnitCellVolume'] = str( +# self.calc_unitcell_volume_from_logfile(float(a), float(b), float(c), +# math.radians(float(alpha)), +# math.radians(float(beta)), +# math.radians(float(gamma)), +# self.aimless['DataProcessingLattice'])) +# try: +# high_symmetry_boost = self.nr_asu_in_unitcell_for_point_group[ +# self.aimless['DataProcessingPointGroup']] +# self.aimless['DataProcessingScore'] = (float( +# self.aimless['DataProcessingUniqueReflectionsOverall']) * float(self.aimless['DataProcessingCompletenessOverall']) * high_symmetry_boost * float(self.aimless['DataProcessingIsigOverall'])) / float( +# self.aimless['DataProcessingUnitCellVolume']) +# except ValueError: +# self.aimless['DataProcessingScore'] = 0.0 +# self.aimless['DataProcessingUnitCell'] = str(a) + ' ' + str(b) + ' ' + str(c) + ' ' + str(alpha) + ' ' + str( +# beta) + ' ' + str(gamma) +# self.aimless['DataProcessingResolutionOverall'] = str( +# self.aimless['DataProcessingResolutionLow']) + ' - ' + str(self.aimless['DataProcessingResolutionHigh']) + + def json_logfile(self,logfile): + with open(logfile, 'r') as log: + data = log.read() + obj = json.loads(data) + self.aimless['DataProcessingResolutionLow'] = str(round(math.sqrt(1/float(obj['d_star_sq_max'][0])),2)) + self.aimless['DataProcessingResolutionLowInnerShell'] = str(round(math.sqrt(1/float(obj['d_star_sq_max'][1])),2)) + self.aimless['DataProcessingResolutionHigh'] = str(round(math.sqrt(1/float(obj['d_star_sq_min'][len(obj['d_star_sq_min'])-1])),2)) + self.aimless['DataProcessingResolutionHighOuterShell'] = str(round(math.sqrt(1/float(obj['d_star_sq_min'][len(obj['d_star_sq_min'])-2])),2)) + self.aimless['DataProcessingResolutionOverall'] = self.aimless['DataProcessingResolutionLow'] + '-' + self.aimless['DataProcessingResolutionHigh'] + self.aimless['DataProcessingRmergeOverall'] = str(round(obj['overall']['r_merge'],3)) + self.aimless['DataProcessingRmergeLow'] = str(round(obj['r_merge'][0],3)) + self.aimless['DataProcessingRmergeHigh'] = str(round(obj['r_merge'][len(obj['r_merge'])-1],3)) + self.aimless['DataProcessingIsigOverall'] = str(round(obj['overall']['i_over_sigma_mean'],1)) + self.aimless['DataProcessingIsigLow'] = str(round(obj['i_over_sigma_mean'][0],1)) + self.aimless['DataProcessingIsigHigh'] = str(round(obj['i_over_sigma_mean'][len(obj['i_over_sigma_mean'])-1],1)) + self.aimless['DataProcessingCompletenessOverall'] = str(round(obj['overall']['completeness'],1)) + self.aimless['DataProcessingCompletenessLow'] = str(round(obj['completeness'][0],1)) + self.aimless['DataProcessingCompletenessHigh'] = str(round(obj['completeness'][len(obj['completeness'])-1],1)) + self.aimless['DataProcessingMultiplicityOverall'] = str(round(obj['overall']['multiplicity'],1)) + self.aimless['DataProcessingMultiplicityLow'] = str(round(obj['multiplicity'][0],1)) + self.aimless['DataProcessingMultiplicityHigh'] = str(round(obj['multiplicity'][len(obj['multiplicity'])-1],1)) + self.aimless['DataProcessingCChalfOverall'] = str(round(obj['overall']['cc_one_half'],2)) + self.aimless['DataProcessingCChalfLow'] = str(round(obj['cc_one_half'][0],2)) + self.aimless['DataProcessingCChalfHigh'] = str(round(obj['cc_one_half'][len(obj['cc_one_half'])-1],2)) +# self.aimless['DataProcessingResolutionHigh15sigma'] = + self.aimless['DataProcessingUniqueReflectionsOverall'] = str(obj['overall']['n_obs']) +# self.aimless['DataProcessingPointGroup'] = +# self.aimless['DataProcessingUnitCellVolume'] = +# self.aimless['DataProcessingAlert'] = +# self.aimless['DataProcessingScore'] = + json_name = logfile[logfile.rfind('/')+1:] + mmcif_file = logfile.replace('LogFiles','DataFiles').replace(json_name,'xia2.mmcif') + if os.path.isfile(mmcif_file): + self.read_mmcif(mmcif_file) + + + def read_mmcif(self,mmcif): + for line in open(mmcif): + if line.startswith('_cell.angle_alpha '): + self.aimless['DataProcessingAlpha'] = line.split()[1] + elif line.startswith('_cell.angle_beta '): + self.aimless['DataProcessingBeta'] = line.split()[1] + elif line.startswith('_cell.angle_gamma '): + self.aimless['DataProcessingGamma'] = line.split()[1] + elif line.startswith('_cell.length_a '): + self.aimless['DataProcessingA'] = line.split()[1] + elif line.startswith('_cell.length_b '): + self.aimless['DataProcessingB'] = line.split()[1] + elif line.startswith('_cell.length_c '): + self.aimless['DataProcessingC'] = line.split()[1] + elif line.startswith('_diffrn_radiation_wavelength.wavelength'): + self.aimless['DataCollectionWavelength'] = line.split()[1] + elif line.startswith('_symmetry.space_group_name_H-M'): + self.aimless['DataProcessingSpaceGroup'] = line[line.find("'")+1:line.rfind("'")].replace(' ','') + self.aimless['DataProcessingPointGroup'] = self.get_pointgroup_from_space_group( + self.aimless['DataProcessingSpaceGroup']) + elif line.startswith('_space_group.crystal_system'): + self.aimless['DataProcessingLattice'] = line.split()[1] + + self.aimless['DataProcessingUnitCell'] = self.aimless['DataProcessingA'] + ' ' + self.aimless[ + 'DataProcessingA'] + ' ' + self.aimless['DataProcessingA'] + ' ' + self.aimless[ + 'DataProcessingA'] + ' ' + self.aimless[ + 'DataProcessingA'] + ' ' + self.aimless['DataProcessingA'] def get_lattice_from_space_group(self,logfile_spacegroup): @@ -750,6 +856,7 @@ def get_pointgroup_from_space_group(self,logfile_spacegroup): def calc_unitcell_volume_from_logfile(self,a,b,c,alpha,beta,gamma,lattice): + print '>>>',a,b,c,alpha,beta,gamma,lattice unitcell_volume=0 if lattice=='triclinic': unitcell_volume=a*b*c* \ @@ -1010,7 +1117,7 @@ def __init__(self,mtzfile): '432': 24 } self.aimless = { 'DataProcessingProgram': 'n/a', - 'DataCollectionRun': 'n/a', +# 'DataCollectionRun': 'n/a', 'DataProcessingSpaceGroup': 'n/a', 'DataProcessingUnitCell': 'n/a', 'DataProcessingA': 'n/a', From 6bf08735eacbed275b903712006814d27607cb83 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 7 Feb 2020 14:48:55 +0000 Subject: [PATCH 007/358] v1.4.7 (07/02/2020) - added script to helpers which can replace residues in bound and ground state based on a new reference model (change_residues_in_ground_and_bound-state.py); cannot be called from GUI at the moment --- ChangeLog.txt | 3 + gui_scripts/settings_preferences.py | 2 +- ...ange_residues_in_ground_and_bound-state.py | 62 +++++++++++++++++++ lib/XChemLog.py | 2 +- 4 files changed, 67 insertions(+), 2 deletions(-) create mode 100755 helpers/change_residues_in_ground_and_bound-state.py diff --git a/ChangeLog.txt b/ChangeLog.txt index fa3cd8bc..e2de14dd 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.4.7 (07/02/2020) +- added script to helpers which can replace residues in bound and ground state based on a new reference model (change_residues_in_ground_and_bound-state.py); cannot be called from GUI at the moment + v1.4.6 (21/01/2020) - added xia2-* wildcard to read_write_autoprocessing_results_from_to_disc because autoprocessing folder names changed - added parsing of DIALS JSON merging statistics file and MMCIF cell parameter file diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index fc066470..0ea4440f 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.4.6' + xce_object.xce_version = 'v1.4.7' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/helpers/change_residues_in_ground_and_bound-state.py b/helpers/change_residues_in_ground_and_bound-state.py new file mode 100755 index 00000000..8e72b8dd --- /dev/null +++ b/helpers/change_residues_in_ground_and_bound-state.py @@ -0,0 +1,62 @@ +import glob,os +import sys + +def replace_residues(): + for dirs in glob.glob(os.path.join(projectDir,'*')): + xtal = dirs[dirs.rfind('/')+1:] + os.chdir(dirs) + if xtal == test: + continue + for mol in toEdit: + if os.path.isfile(mol): + if not os.path.isfile(mol+'_original'): + os.system('/bin/cp %s %s' %(mol,mol+'_original')) + print '%s: found %s' %(xtal,mol) + os.system('phenix.superpose_pdbs %s %s' %(mol,newModel)) + out = '' + changeResi = None + for line in open(mol): + if line.startswith('ATOM') or line.startswith('HETATM'): + chainID=str(line[21:23]).replace(' ','') + resseq=str(line[23:26]).replace(' ','') + occupancy=str(line[56:60]).replace(' ','') + resi = chainID + resseq + if changeResi != None: + if resi == changeResi: + print 'here',changeResi + continue + else: + changeResi = None + if resi in residues_to_change: + changeResi = resi + print 'changeResi',changeResi + for line in open(newModelName+'_fitted.pdb'): + if line.startswith('ATOM') or line.startswith('HETATM'): + chainIDFitted=str(line[21:23]).replace(' ','') + resseqFitted=str(line[23:26]).replace(' ','') + residFitted = chainIDFitted + resseqFitted + if residFitted == changeResi: + out += line[:56] + occupancy + line[60:] + else: + out += line + else: + out+=line + print 'saving file',mol,'...' + newFile = open(mol,'w') + newFile.write(out) + newFile.close() + + +if __name__ == '__main__': +# newModel = '/dls/labxchem/data/2019/lb22717-1/processing/INPP5DA/processing/reference/INPP5DA-x0080-ground-state-corrected.pdb' +# residues_to_change = ['A567', 'A812', 'A851'] +# projectDir = '/dls/labxchem/data/2019/lb22717-1/processing/INPP5DA/processing/analysis/model_building' +# toEdit = ['refine.split.ground-state.pdb', 'refine.split.bound-state.pdb'] +# test = 'INPP5DA-x0019' + + newModel = sys.argv[1] + residues_to_change = sys.argv[2] + projectDir = sys.argv[3] + toEdit = ['refine.split.ground-state.pdb', 'refine.split.bound-state.pdb'] + newModelName = newModel[newModel.rfind('/') + 1:] + diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 201ee71d..12c2e0bd 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 21/01/2020 #\n' + ' # Date: 07/02/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 7c44f38cca95d9483e9469a658a18edc5f7798d0 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 7 Feb 2020 15:10:56 +0000 Subject: [PATCH 008/358] v1.4.8 (07/02/2020) (#286) * v1.4.8 (07/02/2020) - bug fix: default folders are only selected if xce starts in /dls/labxchem/...; just having labxchem in current directory string is not sufficient --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 12 ++++++++---- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index e2de14dd..74330ce5 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.4.8 (07/02/2020) +- bug fix: default labxchem folders are only selected if xce starts in /dls/labxchem/...; just having labxchem in current directory string is not sufficient + v1.4.7 (07/02/2020) - added script to helpers which can replace residues in bound and ground state based on a new reference model (change_residues_in_ground_and_bound-state.py); cannot be called from GUI at the moment diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 0ea4440f..2a33e3aa 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.4.7' + xce_object.xce_version = 'v1.4.8' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -46,7 +46,8 @@ def settings(self, xce_object): xce_object.xce_logfile = os.path.join(xce_object.current_directory, 'xce.log') # if in the correct place, set the various directories - if 'labxchem' in xce_object.current_directory: + if xce_object.current_directory.startswith('/dls/labxchem'): +# if 'labxchem' in xce_object.current_directory: if len(xce_object.current_directory.split('/')) >= 9 and xce_object.current_directory.split('/')[6] == 'processing' and xce_object.current_directory.split('/')[8] == 'processing': xce_object.labxchem_directory = '/' + os.path.join( *xce_object.current_directory.split('/')[1:8]) # need splat operator: * @@ -70,8 +71,11 @@ def settings(self, xce_object): xce_object.database_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'database') xce_object.panddas_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'analysis', 'panddas') - xce_object.datasets_summary_file = os.path.join(xce_object.database_directory, - str(os.getcwd().split('/')[5]) + '_summary.pkl') + + + xce_object.datasets_summary_file = None +# xce_object.datasets_summary_file = os.path.join(xce_object.database_directory, +# str(os.getcwd().split('/')[5]) + '_summary.pkl') xce_object.data_source_file = '' xce_object.html_export_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'html') xce_object.group_deposit_directory = os.path.join(xce_object.labxchem_directory, 'processing', From 551e019631dd9502c31be74406b13f15488a83e4 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 13 Feb 2020 15:14:29 +0000 Subject: [PATCH 009/358] v1.4.9 (13/02/2020) (#288) * v1.4.9 (13/02/2020) - bug fix: corrected DataProcessingUnitCellVolume calculation from merging-statistics.json file for trigonal lattice * v1.4.9 (13/02/2020) - show only 'resolution high' in tables because formatting for resolution at 1.5 or 2.0 I/sig(I) inconsistent in aimless logfiles and not reported in dials scaling logile --- ChangeLog.txt | 4 ++++ gui_scripts/settings_preferences.py | 11 +++++++---- lib/XChemLog.py | 2 +- lib/XChemUtils.py | 5 +++-- 4 files changed, 15 insertions(+), 7 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 74330ce5..ba9428a9 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.4.9 (13/02/2020) +- bug fix: corrected DataProcessingUnitCellVolume calculation from merging-statistics.json file for trigonal lattice +- show only 'resolution high' in tables because formatting for resolution at 1.5 or 2.0 I/sig(I) inconsistent in aimless logfiles and not reported in dials scaling logile + v1.4.8 (07/02/2020) - bug fix: default labxchem folders are only selected if xce starts in /dls/labxchem/...; just having labxchem in current directory string is not sufficient diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 2a33e3aa..e036b895 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.4.8' + xce_object.xce_version = 'v1.4.9' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -305,7 +305,8 @@ def tables(self, xce_object): # - appears in create_widgets_for_autoprocessing_results_only() xce_object.datasets_summary_table_columns = ['Sample ID', - 'Resolution\n[Mn = 2.0]', +# 'Resolution\n[Mn = 2.0]', + 'Resolution\nHigh', 'DataProcessing\nSpaceGroup', 'DataProcessing\nRfree', 'SoakDB\nBarcode', @@ -349,7 +350,8 @@ def tables(self, xce_object): xce_object.datasets_reprocess_columns = ['Dataset ID', 'Sample ID', 'Run\nxia2', - 'Resolution\n[Mn = 1.5]', +# 'Resolution\n[Mn = 1.5]', + 'Resolution\nHigh', 'Rmerge\nLow', 'Dimple\nRfree', 'DataProcessing\nSpaceGroup', @@ -364,7 +366,8 @@ def tables(self, xce_object): 'Select', 'Compound ID', 'Smiles', - 'Resolution\n[Mn = 1.5]', +# 'Resolution\n[Mn = 1.5]', + 'Resolution\nHigh', 'Dimple\nRcryst', 'Dimple\nRfree', 'DataProcessing\nSpaceGroup', diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 12c2e0bd..d058df80 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 07/02/2020 #\n' + ' # Date: 13/02/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index c719e0e0..802be7c6 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -828,13 +828,13 @@ def read_mmcif(self,mmcif): self.aimless['DataProcessingSpaceGroup']) elif line.startswith('_space_group.crystal_system'): self.aimless['DataProcessingLattice'] = line.split()[1] - + if self.aimless['DataProcessingLattice'] == 'trigonal': + self.aimless['DataProcessingLattice'] = 'hexagonal' self.aimless['DataProcessingUnitCell'] = self.aimless['DataProcessingA'] + ' ' + self.aimless[ 'DataProcessingA'] + ' ' + self.aimless['DataProcessingA'] + ' ' + self.aimless[ 'DataProcessingA'] + ' ' + self.aimless[ 'DataProcessingA'] + ' ' + self.aimless['DataProcessingA'] - def get_lattice_from_space_group(self,logfile_spacegroup): lattice_type='n/a' for lattice in self.space_group_dict: @@ -862,6 +862,7 @@ def calc_unitcell_volume_from_logfile(self,a,b,c,alpha,beta,gamma,lattice): unitcell_volume=a*b*c* \ math.sqrt((1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2) \ +2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma))) + print 'unit cell volume',unitcell_volume # if lattice=='monoclinic': if 'monoclinic' in lattice: unitcell_volume=round(a*b*c*math.sin(beta),1) From bd17be88d4478987c9086ca318f30ec76d8cefca Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 20 Feb 2020 14:56:54 +0000 Subject: [PATCH 010/358] v1.4.10 (18/02/2020) (#289) * v1.4.10 (18/02/2020) - XChemDeposit: remove _pdbx_related_exp_data_set block because PanDDA ZENODO upload is not required - XChemDeposit: add _pdbx_contact_author.identifier_ORCID field - XChemDeposit: add pdbx_keywords dropdown - added helper script to reset occupancy of all protein residues with single conformer to 1.00 - XChemDeposit: add ligand cif file to structure mmcif file --- ChangeLog.txt | 7 + XChemExplorer.py | 191 +++++++++++++++++++--- gui_scripts/settings_preferences.py | 2 +- helpers/reset_occupancy_protein_to_one.py | 36 ++++ lib/XChemDB.py | 2 + lib/XChemDeposit.py | 120 ++++++++------ lib/XChemLog.py | 2 +- lib/XChemMain.py | 90 ++++++++++ 8 files changed, 375 insertions(+), 75 deletions(-) create mode 100644 helpers/reset_occupancy_protein_to_one.py diff --git a/ChangeLog.txt b/ChangeLog.txt index ba9428a9..8ecf404e 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,10 @@ +v1.4.10 (18/02/2020) +- XChemDeposit: remove _pdbx_related_exp_data_set block because PanDDA ZENODO upload is not required +- XChemDeposit: add _pdbx_contact_author.identifier_ORCID field +- XChemDeposit: add pdbx_keywords dropdown +- added helper script to reset occupancy of all protein residues with single conformer to 1.00 +- XChemDeposit: add ligand cif file to structure mmcif file + v1.4.9 (13/02/2020) - bug fix: corrected DataProcessingUnitCellVolume calculation from merging-statistics.json file for trigonal lattice - show only 'resolution high' in tables because formatting for resolution at 1.5 or 2.0 I/sig(I) inconsistent in aimless logfiles and not reported in dials scaling logile diff --git a/XChemExplorer.py b/XChemExplorer.py index b5eabe8a..0d453ffc 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -1203,6 +1203,12 @@ def deposition_data(self): self.contact_author_PI_phone_number.setFixedWidth(200) grid.addWidget(self.contact_author_PI_phone_number, 14, 1) + grid.addWidget(QtGui.QLabel('ORCID'), 15, 0) + self.contact_author_PI_ORCID = QtGui.QLineEdit() + self.contact_author_PI_ORCID.setText('') + self.contact_author_PI_ORCID.setFixedWidth(200) + grid.addWidget(self.contact_author_PI_ORCID, 15, 1) + frame.setLayout(grid) hbox.addWidget(frame) @@ -1298,6 +1304,12 @@ def deposition_data(self): self.contact_author_phone_number.setFixedWidth(200) grid.addWidget(self.contact_author_phone_number, 14, 1) + grid.addWidget(QtGui.QLabel('ORCID'), 15, 0) + self.contact_author_ORCID = QtGui.QLineEdit() + self.contact_author_ORCID.setText('') + self.contact_author_ORCID.setFixedWidth(200) + grid.addWidget(self.contact_author_ORCID, 15, 1) + frame.setLayout(grid) hbox.addWidget(frame) @@ -1505,7 +1517,7 @@ def deposition_data(self): self.molecule_name = QtGui.QLineEdit() self.molecule_name.setText('') self.molecule_name.setFixedWidth(300) - self.molecule_name.setStyleSheet("background-color: rgb(192, 192, 192);") +# self.molecule_name.setStyleSheet("background-color: rgb(192, 192, 192);") grid.addWidget(self.molecule_name, 2, 1) grid.addWidget(QtGui.QLabel('(e.g. RNA Hammerhead Ribozyme)'), 2, 2) @@ -1620,7 +1632,7 @@ def deposition_data(self): self.molecule_name_two = QtGui.QLineEdit() self.molecule_name_two.setText('') self.molecule_name_two.setFixedWidth(300) - self.molecule_name_two.setStyleSheet("background-color: rgb(192, 192, 192);") +# self.molecule_name_two.setStyleSheet("background-color: rgb(192, 192, 192);") grid.addWidget(self.molecule_name_two, 2, 1) grid.addWidget(QtGui.QLabel('(e.g. RNA Hammerhead Ribozyme)'), 2, 2) @@ -1747,57 +1759,68 @@ def deposition_data(self): grid.addWidget(self.structure_keywords, 1, 1) grid.addWidget(QtGui.QLabel('(e.g. beta barrel, protein-DNA complex)'), 1, 2) - grid.addWidget(QtGui.QLabel('Biological Assembly'), 2, 0) + grid.addWidget(QtGui.QLabel('Type'), 2, 0) + self.structure_keywords_type = QtGui.QComboBox() + for item in XChemMain.pdbx_keywords(): self.structure_keywords_type.addItem(item) + grid.addWidget(self.structure_keywords_type, 2, 1) +# self.structure_keywords = QtGui.QLineEdit() +# self.structure_keywords.setText('SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer') +# self.structure_keywords.setFixedWidth(300) +# grid.addWidget(self.structure_keywords, 1, 1) +# grid.addWidget(QtGui.QLabel('(e.g. beta barrel, protein-DNA complex)'), 1, 2) + + grid.addWidget(QtGui.QLabel('Biological Assembly'), 3, 0) self.biological_assembly_chain_number = QtGui.QLineEdit() self.biological_assembly_chain_number.setText('') self.biological_assembly_chain_number.setFixedWidth(300) - grid.addWidget(self.biological_assembly_chain_number, 2, 1) - grid.addWidget(QtGui.QLabel('(e.g. 1 for monomer, 2 for dimer ..)'), 2, 2) + grid.addWidget(self.biological_assembly_chain_number, 3, 1) + grid.addWidget(QtGui.QLabel('(e.g. 1 for monomer, 2 for dimer ..)'), 3, 2) - grid.addWidget(QtGui.QLabel('Sequence UNIPROT ID'), 3, 0) + grid.addWidget(QtGui.QLabel('Sequence UNIPROT ID'), 4, 0) self.molecule_one_letter_sequence_uniprot_id = QtGui.QLineEdit() self.molecule_one_letter_sequence_uniprot_id.setText('') self.molecule_one_letter_sequence_uniprot_id.setFixedWidth(300) - grid.addWidget(self.molecule_one_letter_sequence_uniprot_id, 3, 1) - grid.addWidget(QtGui.QLabel('(e.g. Q6B0I6)'), 3, 2) + grid.addWidget(self.molecule_one_letter_sequence_uniprot_id, 4, 1) + grid.addWidget(QtGui.QLabel('(e.g. Q6B0I6)'), 4, 2) - grid.addWidget(QtGui.QLabel('Sequence'), 4, 0) + grid.addWidget(QtGui.QLabel('Sequence'), 5, 0) self.molecule_one_letter_sequence = QtGui.QTextEdit() self.molecule_one_letter_sequence.setText('') self.molecule_one_letter_sequence.setFixedWidth(300) - grid.addWidget(self.molecule_one_letter_sequence, 4, 1, 7, 2) + grid.addWidget(self.molecule_one_letter_sequence, 5, 1, 8, 2) - grid.addWidget(QtGui.QLabel('Sequence information for entity 2 (Important: only fill in if you have a protein-protein complex'), 8, 0) + grid.addWidget(QtGui.QLabel('Sequence information for entity 2'), 10, 0) + grid.addWidget(QtGui.QLabel('(Important: only for protein-protein complex'), 10, 1) - grid.addWidget(QtGui.QLabel('Sequence UNIPROT ID (Entity 2)'), 9, 0) + grid.addWidget(QtGui.QLabel('Sequence UNIPROT ID (Entity 2)'), 13, 0) self.molecule_one_letter_sequence_uniprot_id_two = QtGui.QLineEdit() self.molecule_one_letter_sequence_uniprot_id_two.setText('') self.molecule_one_letter_sequence_uniprot_id_two.setFixedWidth(300) - grid.addWidget(self.molecule_one_letter_sequence_uniprot_id_two, 9, 1) - grid.addWidget(QtGui.QLabel('(e.g. Q6B0I6)'), 9, 2) + grid.addWidget(self.molecule_one_letter_sequence_uniprot_id_two, 13, 1) + grid.addWidget(QtGui.QLabel('(e.g. Q6B0I6)'), 13, 2) - grid.addWidget(QtGui.QLabel('Sequence (Entity 2)'), 10, 0) + grid.addWidget(QtGui.QLabel('Sequence (Entity 2)'), 14, 0) self.molecule_one_letter_sequence_two = QtGui.QTextEdit() self.molecule_one_letter_sequence_two.setText('') self.molecule_one_letter_sequence_two.setFixedWidth(300) - grid.addWidget(self.molecule_one_letter_sequence_two, 10, 1, 13, 2) + grid.addWidget(self.molecule_one_letter_sequence_two, 14, 1, 19, 2) - grid.addWidget(QtGui.QLabel('Structural Genomic (optional)'), 14, 0) + grid.addWidget(QtGui.QLabel('Structural Genomic (optional)'), 21, 0) - grid.addWidget(QtGui.QLabel('Project Name'), 15, 0) + grid.addWidget(QtGui.QLabel('Project Name'), 22, 0) self.SG_project_name = QtGui.QLineEdit() self.SG_project_name.setText('') self.SG_project_name.setFixedWidth(300) - grid.addWidget(self.SG_project_name, 15, 1) - grid.addWidget(QtGui.QLabel('(e.g. SGC, Structural Genomics Consortium)'), 15, 2) + grid.addWidget(self.SG_project_name, 22, 1) + grid.addWidget(QtGui.QLabel('(e.g. SGC, Structural Genomics Consortium)'), 22, 2) - grid.addWidget(QtGui.QLabel('Full Name'), 16, 0) + grid.addWidget(QtGui.QLabel('Full Name'), 23, 0) self.full_name_of_SG_center = QtGui.QLineEdit() self.full_name_of_SG_center.setText('') self.full_name_of_SG_center.setFixedWidth(300) - grid.addWidget(self.full_name_of_SG_center, 16, 1) - grid.addWidget(QtGui.QLabel('(e.g. Structural Genomics Consortium)'), 16, 2) + grid.addWidget(self.full_name_of_SG_center, 23, 1) + grid.addWidget(QtGui.QLabel('(e.g. Structural Genomics Consortium)'), 23, 2) frame.setLayout(grid) vb.addWidget(frame) @@ -1995,6 +2018,10 @@ def load_deposit_config_file(self): file_name = tuple(file_name_temp)[0] self.deposit_dict = pickle.load(open(file_name, "rb")) print self.deposit_dict + for key in self.get_deposit_dict_template(): + if key not in self.deposit_dict: + self.update_log.warning('field not in .deposit file: ' + str(key)) + self.deposit_dict[key] = '' self.update_deposit_input() def load_deposit_from_database(self): @@ -2039,6 +2066,7 @@ def update_deposit_input(self): self.contact_author_PI_Zip_Code.setText(self.deposit_dict['contact_author_PI_Zip_Code']) self.contact_author_PI_Country.setText(self.deposit_dict['contact_author_PI_Country']) self.contact_author_PI_phone_number.setText(self.deposit_dict['contact_author_PI_phone_number']) + self.contact_author_PI_ORCID.setText(self.deposit_dict['contact_author_PI_ORCID']) self.contact_author_salutation.setText(self.deposit_dict['contact_author_salutation']) self.contact_author_first_name.setText(self.deposit_dict['contact_author_first_name']) @@ -2058,6 +2086,7 @@ def update_deposit_input(self): self.contact_author_Zip_Code.setText(self.deposit_dict['contact_author_Zip_Code']) self.contact_author_Country.setText(self.deposit_dict['contact_author_Country']) self.contact_author_phone_number.setText(self.deposit_dict['contact_author_phone_number']) + self.contact_author_ORCID.setText(self.deposit_dict['contact_author_ORCID']) index = self.Release_status_for_coordinates.findText(self.deposit_dict['Release_status_for_coordinates'], QtCore.Qt.MatchFixedString) self.Release_status_for_coordinates.setCurrentIndex(index) @@ -2187,9 +2216,9 @@ def update_deposit_input(self): index = self.phasing_software.findText(self.deposit_dict['phasing_software'], QtCore.Qt.MatchFixedString) self.phasing_software.setCurrentIndex(index) - except ValueError: - self.update_status_bar('Sorry, this is not a XChemExplorer deposit file!') - self.update_log.insert('Sorry, this is not a XChemExplorer deposit file!') + except ValueError, e: +# self.update_status_bar('Sorry, this is not a XChemExplorer deposit file!') + self.update_log.error('file is not a valid .deposit file: ' + str(e)) def update_deposit_dict(self): self.deposit_dict = { @@ -2207,6 +2236,7 @@ def update_deposit_dict(self): 'contact_author_PI_Zip_Code': str(self.contact_author_PI_Zip_Code.text()), 'contact_author_PI_Country': str(self.contact_author_PI_Country.text()), 'contact_author_PI_phone_number': str(self.contact_author_PI_phone_number.text()), + 'contact_author_PI_ORCID': str(self.contact_author_PI_ORCID.text()), 'contact_author_salutation': str(self.contact_author_salutation.text()), 'contact_author_first_name': str(self.contact_author_first_name.text()), @@ -2222,6 +2252,7 @@ def update_deposit_dict(self): 'contact_author_Zip_Code': str(self.contact_author_Zip_Code.text()), 'contact_author_Country': str(self.contact_author_Country.text()), 'contact_author_phone_number': str(self.contact_author_phone_number.text()), + 'contact_author_ORCID': str(self.contact_author_ORCID.text()), 'Release_status_for_coordinates': str(self.Release_status_for_coordinates.currentText()), 'Release_status_for_sequence': str(self.Release_status_for_sequence.currentText()), @@ -2306,6 +2337,114 @@ def update_deposit_dict(self): primary_citation_author_name += str(widget.text()) + ';' self.deposit_dict['primary_citation_author_name'] = primary_citation_author_name[:-1] + def get_deposit_dict_template(self): + deposit_dict_template = { + 'contact_author_PI_salutation': None, + 'contact_author_PI_first_name': None, + 'contact_author_PI_last_name': None, + 'contact_author_PI_middle_name': None, + 'contact_author_PI_role': None, + 'contact_author_PI_organization_type': None, + 'contact_author_PI_organization_name': None, + 'contact_author_PI_email': None, + 'contact_author_PI_address': None, + 'contact_author_PI_city': None, + 'contact_author_PI_State_or_Province': None, + 'contact_author_PI_Zip_Code': None, + 'contact_author_PI_Country': None, + 'contact_author_PI_phone_number': None, + 'contact_author_PI_ORCID': None, + + 'contact_author_salutation': None, + 'contact_author_first_name': None, + 'contact_author_last_name': None, + 'contact_author_middle_name': None, + 'contact_author_role': None, + 'contact_author_organization_type': None, + 'contact_author_organization_name': None, + 'contact_author_email': None, + 'contact_author_address': None, + 'contact_author_city': None, + 'contact_author_State_or_Province': None, + 'contact_author_Zip_Code': None, + 'contact_author_Country': None, + 'contact_author_phone_number': None, + 'contact_author_ORCID': None, + + 'Release_status_for_coordinates': None, + 'Release_status_for_sequence': None, + + 'group_deposition_title': None, + 'group_description': None, + + 'structure_title': None, + 'structure_title_apo': None, + + 'primary_citation_id': None, + 'primary_citation_journal_abbrev': None, + 'primary_citation_title': None, + 'primary_citation_year': None, + 'primary_citation_journal_volume': None, + 'primary_citation_page_first': None, + 'primary_citation_page_last': None, + ### entity 1 + 'molecule_name': None, + 'Source_organism_scientific_name': None, + 'Source_organism_gene': None, + 'Source_organism_strain': None, + 'Expression_system_scientific_name': None, + 'Expression_system_strain': None, + 'Expression_system_plasmid_name': None, + 'Expression_system_vector_type': None, + 'Manipulated_source_details': None, + 'fragment_name_one_specific_mutation': None, + 'molecule_chain_one': None, + + ### entity 2 + 'molecule_name_two': None, + 'Source_organism_scientific_name_two': None, + 'Source_organism_gene_two': None, + 'Source_organism_strain_two': None, + 'Expression_system_scientific_name_two': None, + 'Expression_system_strain_two': None, + 'Expression_system_plasmid_name_two': None, + 'Expression_system_vector_type_two': None, + 'Manipulated_source_details_two': None, + 'fragment_name_two_specific_mutation': None, + 'molecule_chain_two': None, + + 'structure_keywords': None, + 'biological_assembly_chain_number': None, + 'molecule_one_letter_sequence_uniprot_id': None, + 'molecule_two_letter_sequence_uniprot_id': None, + 'SG_project_name': None, + 'full_name_of_SG_center': None, + 'molecule_one_letter_sequence': None, + 'molecule_two_letter_sequence': None, + + 'crystallization_method': None, + 'crystallization_pH': None, + 'crystallization_temperature': None, + 'crystallization_details': None, + + 'radiation_source': None, + 'radiation_source_type': None, + 'radiation_wavelengths': None, + 'radiation_detector': None, + 'radiation_detector_type': None, + 'data_collection_date': None, + 'data_collection_temperature': None, + 'data_collection_protocol': None, + 'pdbx_starting_model': None, + 'data_integration_software': None, + 'phasing_software': None, + 'structure_author_name': None, + 'primary_citation_author_name': None + + } + + return deposit_dict_template + def set_primary_citation_as_structure_authors(self, state): if state == QtCore.Qt.Checked: for n, entry in enumerate(self.structure_author_name_List): diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index e036b895..00515ee8 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.4.9' + xce_object.xce_version = 'v1.4.10' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/helpers/reset_occupancy_protein_to_one.py b/helpers/reset_occupancy_protein_to_one.py new file mode 100644 index 00000000..1d87fc39 --- /dev/null +++ b/helpers/reset_occupancy_protein_to_one.py @@ -0,0 +1,36 @@ +import glob,os +import sys + +def reset_residues(projectDir): + for dirs in glob.glob(os.path.join(projectDir,'*')): + xtal = dirs[dirs.rfind('/')+1:] + os.chdir(dirs) + for mol in toEdit: + if os.path.isfile(mol): + if not os.path.isfile(mol+'_original'): + os.system('/bin/cp %s %s' %(mol,mol+'_original')) + print '%s: found %s' %(xtal,mol) + out = '' + changeResi = None + for line in open(mol): + if line.startswith('ATOM'): + chainID=str(line[21:23]).replace(' ','') + resseq=str(line[23:26]).replace(' ','') + occupancy=str(line[56:60]).replace(' ','') + altLoc=str(line[16:17]).replace(' ','') + if altLoc != '': + out += line + else: + out += line[:56] + '1.00' + line[60:] + else: + out += line + print 'saving file',mol,'...' + newFile = open(mol,'w') + newFile.write(out) + newFile.close() + + +if __name__ == '__main__': + projectDir = sys.argv[1] + toEdit = ['refine.split.bound-state.pdb'] + reset_residues(projectDir) diff --git a/lib/XChemDB.py b/lib/XChemDB.py index 1a1b3e08..ee206833 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -296,6 +296,7 @@ def __init__(self,data_source_file): ['contact_author_PI_Country', 'contact_author_PI_Country', 'TEXT'], ['contact_author_PI_fax_number', 'contact_author_PI_fax_number', 'TEXT'], ['contact_author_PI_phone_number', 'contact_author_PI_phone_number', 'TEXT'], + ['contact_author_PI_ORCID', 'contact_author_PI_ORCID', 'TEXT'], ['contact_author_salutation', 'contact_author_salutation', 'TEXT'], ['contact_author_first_name', 'contact_author_first_name', 'TEXT'], @@ -312,6 +313,7 @@ def __init__(self,data_source_file): ['contact_author_Country', 'contact_author_Country', 'TEXT'], ['contact_author_fax_number', 'contact_author_fax_number', 'TEXT'], ['contact_author_phone_number', 'contact_author_phone_number', 'TEXT'], + ['contact_author_ORCID', 'contact_author_ORCID', 'TEXT'], ['Release_status_for_coordinates', 'Release_status_for_coordinates', 'TEXT'], ['Release_status_for_structure_factor', 'Release_status_for_structure_factor', 'TEXT'], diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index e5c5fff9..c0de5a49 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -109,37 +109,40 @@ def data_template_cif(self,depositDict): counter+=1 if depositDict['molecule_name_two'].replace(' ','') == '' or depositDict['molecule_name_two'].replace(' ','').lower() == 'none': - entity = ( - 'loop_\n' - '_entity.id\n' - '_entity.type\n' - '_entity.src_method\n' - '_entity.pdbx_description\n' - '_entity.pdbx_mutation\n' - '1 polymer man "%s" %s\n' % (depositDict['Source_organism_gene'], depositDict['fragment_name_one_specific_mutation']) + - '#\n' - 'loop_\n' - '_entity_poly.entity_id\n' - '_entity_poly.type\n' - '_entity_poly.pdbx_seq_one_letter_code\n' - '_entity_poly.pdbx_strand_id\n' - '_entity_poly.pdbx_seq_db_id\n' - '_entity_poly.pdbx_seq_db_name\n' - '1 "polypeptide(L)"\n' - + molecule_one_letter_sequence + '\n' - ';\n' - '%s %s UNP\n' %(depositDict['protein_chains'],depositDict['molecule_one_letter_sequence_uniprot_id'])+ - '#\n' - 'loop_\n' - '_entity_src_gen.entity_id\n' - '_entity_src_gen.gene_src_strain\n' - '_entity_src_gen.pdbx_gene_src_scientific_name\n' - '_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id\n' - '_entity_src_gen.pdbx_host_org_scientific_name\n' - '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n' - '1 ? "%s" %s "%s" %s\n' % (depositDict['Source_organism_scientific_name'], pdbx_gene_src_ncbi_taxonomy_id,depositDict['Expression_system_scientific_name'], pdbx_host_org_ncbi_taxonomy_id) + - '#\n' - ) + try: + entity = ( + 'loop_\n' + '_entity.id\n' + '_entity.type\n' + '_entity.src_method\n' + '_entity.pdbx_description\n' + '_entity.pdbx_mutation\n' + '1 polymer man "%s" %s\n' % (depositDict['Source_organism_gene'], depositDict['fragment_name_one_specific_mutation']) + + '#\n' + 'loop_\n' + '_entity_poly.entity_id\n' + '_entity_poly.type\n' + '_entity_poly.pdbx_seq_one_letter_code\n' + '_entity_poly.pdbx_strand_id\n' + '_entity_poly.pdbx_seq_db_id\n' + '_entity_poly.pdbx_seq_db_name\n' + '1 "polypeptide(L)"\n' + + molecule_one_letter_sequence + '\n' + ';\n' + '%s %s UNP\n' %(depositDict['protein_chains'],depositDict['molecule_one_letter_sequence_uniprot_id'])+ + '#\n' + 'loop_\n' + '_entity_src_gen.entity_id\n' + '_entity_src_gen.gene_src_strain\n' + '_entity_src_gen.pdbx_gene_src_scientific_name\n' + '_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id\n' + '_entity_src_gen.pdbx_host_org_scientific_name\n' + '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n' + '1 ? "%s" %s "%s" %s\n' % (depositDict['Source_organism_scientific_name'], pdbx_gene_src_ncbi_taxonomy_id,depositDict['Expression_system_scientific_name'], pdbx_host_org_ncbi_taxonomy_id) + + '#\n' + ) + except UnboundLocalError: + print 'Error: Something went wrong! Please check if you have saved the .deposit file to the database: Menu Deposition -> Edit Information' else: molecule_two_letter_sequence=';' counter=1 @@ -275,8 +278,9 @@ def data_template_cif(self,depositDict): '_pdbx_contact_author.phone \n' '_pdbx_contact_author.role \n' '_pdbx_contact_author.organization_type \n' - "1 '%s' '%s' '%s' '%s' '%s' %s %s '%s' '%s' '%s' '%s' %s\n" %(depositDict['contact_author_PI_address'],depositDict['contact_author_PI_organization_name'],depositDict['contact_author_PI_city'],depositDict['contact_author_PI_State_or_Province'],depositDict['contact_author_PI_Zip_Code'],depositDict['contact_author_PI_email'],depositDict['contact_author_PI_first_name'],depositDict['contact_author_PI_last_name'],depositDict['contact_author_PI_Country'],depositDict['contact_author_PI_phone_number'],depositDict['contact_author_PI_role'],depositDict['contact_author_PI_organization_type'])+ - "2 '{0!s}' '{1!s}' '{2!s}' '{3!s}' '{4!s}' {5!s} {6!s} '{7!s}' '{8!s}' '{9!s}' '{10!s}' {11!s}\n".format(depositDict['contact_author_address'], depositDict['contact_author_organization_name'], depositDict['contact_author_city'], depositDict['contact_author_State_or_Province'], depositDict['contact_author_Zip_Code'].replace(' ',''), depositDict['contact_author_email'], depositDict['contact_author_first_name'], depositDict['contact_author_last_name'], depositDict['contact_author_Country'], depositDict['contact_author_phone_number'], depositDict['contact_author_role'], depositDict['contact_author_organization_type'])+ + '_pdbx_contact_author.identifier_ORCID \n' + "1 '%s' '%s' '%s' '?' '%s' %s %s '%s' '%s' '%s' '%s' %s %s\n" %(depositDict['contact_author_PI_address'],depositDict['contact_author_PI_organization_name'],depositDict['contact_author_PI_city'],depositDict['contact_author_PI_Zip_Code'],depositDict['contact_author_PI_email'],depositDict['contact_author_PI_first_name'],depositDict['contact_author_PI_last_name'],depositDict['contact_author_PI_Country'],depositDict['contact_author_PI_phone_number'],depositDict['contact_author_PI_role'],depositDict['contact_author_PI_organization_type'],depositDict['contact_author_PI_ORCID'])+ + "2 '{0!s}' '{1!s}' '{2!s}' '?' '{3!s}' '{4!s}' {5!s} {6!s} '{7!s}' '{8!s}' '{9!s}' '{10!s}' {11!s}\n".format(depositDict['contact_author_address'], depositDict['contact_author_organization_name'], depositDict['contact_author_city'], depositDict['contact_author_Zip_Code'].replace(' ',''), depositDict['contact_author_email'], depositDict['contact_author_first_name'], depositDict['contact_author_last_name'], depositDict['contact_author_Country'], depositDict['contact_author_phone_number'], depositDict['contact_author_role'], depositDict['contact_author_organization_type'],depositDict['contact_author_ORCID'])+ '#\n' 'loop_\n' '_audit_author.name\n' @@ -495,6 +499,9 @@ def run(self): if not self.create_model_mmcif(xtal): continue + if not self.add_ligand_cif_to_model_mmcif(xtal): + continue + if not self.create_sf_mmcif(xtal): continue @@ -934,20 +941,21 @@ def update_model_mmcif_header(self,xtal): 'data_integration_software']) + '{0!s} {1!s} ? ? program ? ? phasing ? ?\n'.format(str(max(softwareEntry) + 2), self.data_template_dict[ - 'phasing_software']) + - '#\n' - "loop_\n" - "_pdbx_related_exp_data_set.ordinal\n" - "_pdbx_related_exp_data_set.data_reference\n" - "_pdbx_related_exp_data_set.metadata_reference\n" - "_pdbx_related_exp_data_set.data_set_type\n" - "_pdbx_related_exp_data_set.details\n" - " 1 " - " 'doi:%s' " %self.zenodo_dict['ZenodoDOI']+ - " 'doi:%s' " %self.zenodo_dict['ZenodoDOI']+ - " 'other data' " # 'other data' is only thing wwPDB accepts at the moment - " 'Complete PanDDA analysis'\n" - "\n" ) + 'phasing_software']) +# '#\n' +# "loop_\n" +# "_pdbx_related_exp_data_set.ordinal\n" +# "_pdbx_related_exp_data_set.data_reference\n" +# "_pdbx_related_exp_data_set.metadata_reference\n" +# "_pdbx_related_exp_data_set.data_set_type\n" +# "_pdbx_related_exp_data_set.details\n" +# " 1 " +# " 'doi:%s' " %self.zenodo_dict['ZenodoDOI']+ +# " 'doi:%s' " %self.zenodo_dict['ZenodoDOI']+ +# " 'other data' " # 'other data' is only thing wwPDB accepts at the moment +# " 'Complete PanDDA analysis'\n" +# "\n" + ) sys.stdout.write(cifItem) amendSoftwareBlock = False @@ -964,6 +972,24 @@ def update_model_mmcif_header(self,xtal): # elif '_refine.ls_d_res_low' in line and len(line.split()) == 2: # sys.stdout.write('_refine.ls_d_res_low {0!s}\n'.format(min(low_reso_list))) + def add_ligand_cif_to_model_mmcif(self,xtal): + filestatus = False + self.Logfile.insert('%s: looking for ligand restraints file...' %xtal) + os.chdir(os.path.join(self.projectDir, xtal)) + if os.path.isfile(self.db_dict['CompoundCode']+'.cif'): + self.Logfile.insert('%s: found ligand restraints file -> %s' %(xtal,self.db_dict['CompoundCode']+'.cif')) + self.Logfile.insert('%s: adding ligand restraints file to model mmcif' %xtal) + cif = '' + for line in open(self.db_dict['CompoundCode']+'.cif'): + cif += line + f = open(xtal+'.mmcif','a') + f.write(cif) + f.close() + filestatus = True + else: + self.Logfile.warning('%s: could not find %s' %(xtal,self.db_dict['CompoundCode']+'.cif')) + return filestatus + def make_table_one(self,xtal): os.chdir(os.path.join(self.projectDir, xtal)) diff --git a/lib/XChemLog.py b/lib/XChemLog.py index d058df80..616aba83 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 13/02/2020 #\n' + ' # Date: 18/02/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemMain.py b/lib/XChemMain.py index 629ca421..77132b2e 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -654,6 +654,96 @@ def phasing_software(): return software + +def pdbx_keywords(): + + keywords = [ + 'ALLERGEN', + 'ANTIBIOTIC', + 'ANTIFREEZE PROTEIN', + 'ANTIFUNGAL PROTEIN', + 'ANTIMICROBIAL PROTEIN', + 'ANTITOXIN', + 'ANTITUMOR PROTEIN', + 'ANTIVIRAL PROTEIN', + 'APOPTOSIS', + 'ATTRACTANT', + 'BIOSYNTHETIC PROTEIN', + 'BLOOD CLOTTING', + 'CARBOHYDRATE', + 'CELL ADHESION', + 'CELL CYCLE', + 'CELL INVASION', + 'CHAPERONE', + 'CHOLINE - BINDING PROTEIN', + 'CIRCADIAN CLOCK PROTEIN', + 'CONTRACTILE PROTEIN', + 'CYTOKINE', + 'CYTOSOLIC PROTEIN', + 'DE NOVO PROTEIN', + 'DNA', + 'DNA BINDING PROTEIN', + 'DNA - RNA HYBRID', + 'ELECTRON TRANSPORT', + 'ENDOCYTOSIS', + 'EXOCYTOSIS', + 'FLAVOPROTEIN', + 'FLUORESCENT PROTEIN', + 'GENE REGULATION', + 'HORMONE', + 'HYDROLASE', + 'IMMUNE SYSTEM', + 'IMMUNOSUPPRESSANT', + 'ISOMERASE', + 'LIGASE', + 'LIPID BINDING PROTEIN', + 'LIPID TRANSPORT', + 'LUMINESCENT PROTEIN', + 'LYASE', + 'MEMBRANE PROTEIN', + 'METAL BINDING PROTEIN', + 'METAL TRANSPORT', + 'MOTOR PROTEIN', + 'NEUROPEPTIDE', + 'NUCLEAR PROTEIN', + 'ONCOPROTEIN', + 'OXIDOREDUCTASE', + 'OXYGEN BINDING', + 'OXYGEN STORAGE', + 'OXYGEN TRANSPORT', + 'PEPTIDE BINDING PROTEIN', + 'PHOTOSYNTHESIS', + 'PLANT PROTEIN', + 'PROTEIN BINDING', + 'PROTEIN FIBRIL', + 'PROTEIN TRANSPORT', + 'PROTON TRANSPORT', + 'RECOMBINATION', + 'REPLICATION', + 'RIBOSOMAL PROTEIN', + 'RIBOSOME', + 'RNA', + 'RNA BINDING PROTEIN', + 'SIGNALING PROTEIN', + 'SPLICING', + 'STRUCTURAL GENOMICS', + 'STRUCTURAL PROTEIN', + 'SUGAR BINDING PROTEIN', + 'SURFACTANT PROTEIN', + 'TOXIN', + 'TRANSCRIPTION', + 'TRANSFERASE', + 'TRANSLATION', + 'TRANSLOCASE', + 'TRANSPORT PROTEIN', + 'UNKNOWN FUNCTION', + 'VIRAL PROTEIN', + 'VIRUS', + 'VIRUS LIKE PARTICLE' + ] + + return keywords + def html_header(): header = ( From 4cf4423350d32e476f70acdceed30e2a8ba311cc Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 21 Feb 2020 15:52:45 +0000 Subject: [PATCH 011/358] v1.5.0 (20/02/2020) (#290) * v1.5.0 (20/02/2020) - ground-state mean maps are EXCLUDED from apo deposition, because either map2mtz conversion was faulty or columns were missing; moreover, they are not required to reproduce the maps and users can deposit them separately on ZENODO if they want --- ChangeLog.txt | 3 + XChemExplorer.py | 110 +++++++++++++++++++++------- gui_scripts/deposition_tab.py | 43 +++++------ gui_scripts/settings_preferences.py | 2 +- lib/XChemDB.py | 13 ++-- lib/XChemDeposit.py | 47 ++++++++---- lib/XChemLog.py | 2 +- lib/XChemToolTips.py | 28 +++++-- lib/XChemUtils.py | 2 +- 9 files changed, 172 insertions(+), 78 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 8ecf404e..385a7268 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.0 (20/02/2020) +- ground-state mean maps are EXCLUDED from apo deposition, because either map2mtz conversion was faulty or columns were missing; moreover, they are not required to reproduce the maps and users can deposit them separately on ZENODO if they want + v1.4.10 (18/02/2020) - XChemDeposit: remove _pdbx_related_exp_data_set block because PanDDA ZENODO upload is not required - XChemDeposit: add _pdbx_contact_author.identifier_ORCID field diff --git a/XChemExplorer.py b/XChemExplorer.py index 0d453ffc..6eb01252 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -546,10 +546,10 @@ def export_to_html(self): # self.update_log.insert('be patient, this may take a while, depending on the number of events') # self.status_bar.showMessage('please check terminal window for further information') - def select_ground_state_pdb(self): - p = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', os.getcwd(),'*.pdb') - pdb = str(tuple(p)[0]) - self.ground_state_pdb_button_label.setText(pdb) +# def select_ground_state_pdb(self): +# p = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', os.getcwd(),'*.pdb') +# pdb = str(tuple(p)[0]) +# self.ground_state_pdb_button_label.setText(pdb) def select_ground_state_mtz(self): m = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', os.getcwd(),'*.mtz') @@ -557,15 +557,49 @@ def select_ground_state_mtz(self): self.ground_state_mtz_button_label.setText(mtz) def add_ground_state_db(self): - db_dict = {'DimplePANDDApath': self.panddas_directory, - 'PDB_file': str(self.ground_state_pdb_button_label.text()), - 'MTZ_file': str(self.ground_state_mtz_button_label.text())} - self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, 'ground_state', 'ground_state', + pdb, mtz = self.auto_select_ground_state_reference_PDB() + if pdb != None: + db_dict = {'DimplePANDDApath': self.panddas_directory, + 'PDB_file': pdb, + 'MTZ_file': mtz} + self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, 'ground_state', 'ground_state', db_dict) + else: + self.update_log.error('could not find a suitable reference file; see messages above!') + + def auto_select_ground_state_reference_PDB(self): + pdb = None + mtz = None + xtalList = [] + for dirs in glob.glob(os.path.join(self.panddas_directory,'processed_datasets','*')): + xtal = dirs[dirs.rfind('/')+1:] + if os.path.isfile(os.path.join(dirs,xtal+'-pandda-input.pdb')): + pdbHeader = parse().PDBheader(os.path.join(dirs,xtal+'-pandda-input.pdb')) + try: + xtalList.append( [xtal, float(pdbHeader['Rfree']) , float(pdbHeader['ResolutionHigh']) ] ) + except ValueError: + self.update_log.error('%s: cannot read Rfree or Resolution from PDB header; skipping...') + pass + self.update_log.insert('found %s PDB files in %s' %(str(len(xtalList)),os.path.join(self.panddas_directory,'processed_datasets'))) + if len(xtalList) >= 10: + self.update_log.insert('sorting PDBs by Rfree and selecting the 10 with lowest value') + rfree = sorted(xtalList, key=lambda x: x[1])[:10] + self.update_log.insert('top 10 PDB files with lowest Rfree:') + for item in rfree: + self.update_log.insert('%s: Rfree = %s | Resolution = %s' %(item[0],str(round(item[1],3)),str(round(item[2],2)))) + self.update_log.insert('selecting PDB with highest resolution') + reso = sorted(rfree, key=lambda x: x[2])[:1] + self.update_log.insert('selected the following PDB file: %s: Rfree = %s | Resolution = %s' %(reso[0][0],str(round(reso[0][1],3)),str(round(reso[0][2],2)))) + pdb = os.path.join(self.panddas_directory,'processed_datasets',reso[0][0],reso[0][0]+'-pandda-input.pdb') + mtz = os.path.join(self.panddas_directory,'processed_datasets',reso[0][0],reso[0][0]+'-pandda-input.mtz') + else: + self.update_log.error('found less than 10 valid PDB files in %s' %os.path.join(self.panddas_directory,'processed_datasets')) + return pdb, mtz + def prepare_ground_state_mmcif(self): self.update_log.insert('preparing mmcif file for apo structure deposition') - self.prepare_models_for_deposition_ligand_bound('ground-state') + self.prepare_models_for_deposition_ligand_bound('ground_state') def open_icm(self): self.update_log.insert('starting ICM...') @@ -1001,12 +1035,29 @@ def create_missing_apo_records_in_depositTable(self): # self.xce_logfile) def prepare_models_for_deposition_ligand_bound(self,structureType): - + start_thread = True + self.update_log.insert('preparing mmcif files for PDB group deposition...') ignore_event_map = False - if structureType == 'ground-state': - ground_state = [ str(self.ground_state_pdb_button_label.text()), - str(self.ground_state_mtz_button_label.text()), - self.panddas_directory ] + if structureType == 'ground_state': + try: + self.update_log.insert('ground-state deposition') + data_template_dict = self.db.get_deposit_dict_for_sample('ground_state') + pdb = data_template_dict['PDB_file'] + self.update_log.insert('looking for ground-state PDB: ' + pdb) + if not os.path.isfile(pdb): + self.update_log.error('ground-state PDB does not exist; stopping...') + start_thread = False + mtz = data_template_dict['MTZ_file'] + self.update_log.insert('looking for ground-state MTZ: ' + mtz) + if not os.path.isfile(mtz): + self.update_log.error('ground-state MTZ does not exist; stopping...') + start_thread = False + ground_state = [ pdb, + mtz, + self.panddas_directory ] + except KeyError: + self.update_log.error('seems like there is no entry for ground-state in database') + start_thread = False else: ground_state = [] if self.deposition_bounnd_state_preparation_ignore_event_map.isChecked(): @@ -1014,19 +1065,24 @@ def prepare_models_for_deposition_ligand_bound(self,structureType): # structureType = "ligand_bound" - overwrite_existing_mmcif = True - self.work_thread = XChemDeposit.prepare_mmcif_files_for_deposition( - os.path.join(self.database_directory, self.data_source_file), - self.xce_logfile, - overwrite_existing_mmcif, - self.initial_model_directory, - ground_state, - ignore_event_map) - self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) - self.work_thread.start() + if start_thread: + if ground_state != []: + self.update_log.insert('apo PDB: ' + ground_state[0]) + self.update_log.insert('apo MTZ: ' + ground_state[1]) + self.update_log.insert('pandda directory: ' + ground_state[2]) + overwrite_existing_mmcif = True + self.work_thread = XChemDeposit.prepare_mmcif_files_for_deposition( + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile, + overwrite_existing_mmcif, + self.initial_model_directory, + ground_state, + ignore_event_map) + self.explorer_active = 1 + self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.work_thread.start() def prepare_models_for_deposition_apo(self): diff --git a/gui_scripts/deposition_tab.py b/gui_scripts/deposition_tab.py index dfa5ded9..ba1dd873 100755 --- a/gui_scripts/deposition_tab.py +++ b/gui_scripts/deposition_tab.py @@ -82,6 +82,7 @@ def setup(self, xce_object): deposition_ground_state_heading = self.layout_funcs.add_depo_heading('Group deposition of ground-state model') deposition_ground_state_heading.setStyleSheet("font: bold 20pt Arial") + deposition_ground_state_preparation_step_one_text = self.layout_funcs.add_depo_text(XChemToolTips.notification_about_changes_to_apo_deposition()) deposition_ground_state_prerequisites = self.layout_funcs.add_depo_heading('Prerequisites') @@ -92,23 +93,23 @@ def setup(self, xce_object): deposition_ground_state_preparation = self.layout_funcs.add_depo_heading('Procedure') deposition_ground_state_preparation.setStyleSheet("font: italic bold 17pt Arial ") - deposition_ground_state_preparation_step_one_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_one_text()) +# deposition_ground_state_preparation_step_one_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_one_text()) - ground_state_pdb_button = QtGui.QPushButton('Select PDB file') - ground_state_pdb_button.clicked.connect(xce_object.select_ground_state_pdb) - ground_state_pdb_button.setMaximumWidth(200) - xce_object.ground_state_pdb_button_label = QtGui.QLabel('') - xce_object.ground_state_pdb_button_label.setStyleSheet('color: blue') - - deposition_ground_state_log_info = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_log_info()) - - deposition_ground_state_preparation_step_two_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_two_text()) - - ground_state_mtz_button = QtGui.QPushButton('Select MTZ file') - ground_state_mtz_button.clicked.connect(xce_object.select_ground_state_mtz) - ground_state_mtz_button.setMaximumWidth(200) - xce_object.ground_state_mtz_button_label = QtGui.QLabel('') - xce_object.ground_state_mtz_button_label.setStyleSheet('color: blue') +# ground_state_pdb_button = QtGui.QPushButton('Select PDB file') +# ground_state_pdb_button.clicked.connect(xce_object.select_ground_state_pdb) +# ground_state_pdb_button.setMaximumWidth(200) +# xce_object.ground_state_pdb_button_label = QtGui.QLabel('') +# xce_object.ground_state_pdb_button_label.setStyleSheet('color: blue') +# +# deposition_ground_state_log_info = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_log_info()) +# +# deposition_ground_state_preparation_step_two_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_two_text()) +# +# ground_state_mtz_button = QtGui.QPushButton('Select MTZ file') +# ground_state_mtz_button.clicked.connect(xce_object.select_ground_state_mtz) +# ground_state_mtz_button.setMaximumWidth(200) +# xce_object.ground_state_mtz_button_label = QtGui.QLabel('') +# xce_object.ground_state_mtz_button_label.setStyleSheet('color: blue') deposition_ground_state_preparation_step_three_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_three_text()) xce_object.ground_state_pandda_directory_label = QtGui.QLabel(xce_object.panddas_directory) @@ -192,14 +193,14 @@ def setup(self, xce_object): QtGui.QLabel(' \n\n\n '), deposition_ground_state_heading, QtGui.QLabel(' \n '), + deposition_ground_state_preparation_step_one_text, QtGui.QLabel(' \n '), deposition_ground_state_prerequisites, deposition_ground_state_prerequisites_text, QtGui.QLabel(' \n '), deposition_ground_state_preparation, - deposition_ground_state_preparation_step_one_text, - ground_state_pdb_button, xce_object.ground_state_pdb_button_label, - deposition_ground_state_log_info, - deposition_ground_state_preparation_step_two_text, - ground_state_mtz_button,xce_object.ground_state_mtz_button_label, +# ground_state_pdb_button, xce_object.ground_state_pdb_button_label, +# deposition_ground_state_log_info, +# deposition_ground_state_preparation_step_two_text, +# ground_state_mtz_button,xce_object.ground_state_mtz_button_label, deposition_ground_state_preparation_step_three_text, xce_object.ground_state_pandda_directory_label, deposition_ground_state_preparation_step_four_text, diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 00515ee8..1e903cc1 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.4.10' + xce_object.xce_version = 'v1.5.0' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDB.py b/lib/XChemDB.py index ee206833..1215e445 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -628,11 +628,11 @@ def get_deposit_dict_for_sample(self,sampleID): data=[] connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent cursor = connect.cursor() - if sampleID == 'ground-state': # just select first row in depositTable - cursor.execute("SELECT * FROM depositTable ORDER BY ROWID ASC LIMIT 1;") - else: - cursor.execute("select * from depositTable where CrystalName='{0!s}';".format(sampleID)) - +# if sampleID == 'ground-state': # just select first row in depositTable +# cursor.execute("SELECT * FROM depositTable ORDER BY ROWID ASC LIMIT 1;") +# else: +# cursor.execute("select * from depositTable where CrystalName='{0!s}';".format(sampleID)) + cursor.execute("select * from depositTable where CrystalName='{0!s}';".format(sampleID)) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() @@ -1617,6 +1617,9 @@ def create_or_remove_missing_records_in_depositTable(self,xce_logfile,xtal,type, Logfile.insert('entry for ground-state model in depositTable does not exist') else: Logfile.warning('entry for ground-state model in depositTable does already exist') + Logfile.warning('updating PDB, MTZ and DimplePANDDApath for ground-state entry') + cursor.execute("update depositTable set PDB_file='%s', MTZ_file='%s', DimplePANDDApath='%s' where StructureType='ground_state'" %(db_dict['PDB_file'],db_dict['MTZ_file'],db_dict['DimplePANDDApath'])) + connect.commit() return cursor.execute("select CrystalName,StructureType from depositTable where CrystalName is '{0!s}' and StructureType is '{1!s}'".format(xtal, type)) diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index c0de5a49..561206fa 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -393,20 +393,23 @@ def __init__(self,database,xce_logfile,overwrite_existing_mmcif,projectDir,groun self.zenodo_dict = None self.pdb = None self.mtz = None + self.logDir = None self.ground_state = False self.ground_state_pdb = '' - self.ground_state_mean_mtz = '' +# self.ground_state_mean_mtz = '' self.panddaDir = '' self.ignore_event_map = ignore_event_map if ground_state: self.ground_state = True self.ground_state_pdb = ground_state[0] - self.ground_state_mean_mtz = ground_state[1] + self.ground_state_mtz = ground_state[1] self.panddaDir = ground_state[2] + self.logDir = self.projectDir self.projectDir = self.panddaDir self.pdb = pdbtools(self.ground_state_pdb) - self.mtz = mtztools(self.ground_state_mean_mtz) + self.mtz = mtztools(self.ground_state_mtz) +# self.mtz = mtztools(self.ground_state_mean_mtz) def run(self): @@ -438,8 +441,8 @@ def run(self): if not self.data_template_dict_exists(xtal): continue - if not self.zenodo_dict_exists(xtal): - continue +# if not self.zenodo_dict_exists(xtal): +# continue if not self.save_data_template_dict(xtal): continue @@ -447,8 +450,8 @@ def run(self): if not self.create_model_mmcif(xtal): continue - if not self.create_sf_mmcif(xtal): - continue +# if not self.create_sf_mmcif(xtal): +# continue if not self.apo_mmcif_exists(): continue @@ -469,8 +472,8 @@ def run(self): if not self.db_dict_exists(xtal): continue - if not self.zenodo_dict_exists(xtal): - continue +# if not self.zenodo_dict_exists(xtal): +# continue if not self.refine_bound_exists(xtal): continue @@ -855,12 +858,15 @@ def create_model_mmcif(self,xtal): 'pdb_extract/pdb-extract-prod/bin/pdb_extract') if self.ground_state: + refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] + aimless = os.path.join(self.logDir,refXtal,refXtal+'.log') + self.Logfile.insert('aimless.log file: ' + aimless) Cmd = (pdb_extract_init + ' -r {0!s}'.format(refSoft) + ' -iPDB {0!s}'.format(self.ground_state_pdb) + ' -e MR' ' -s AIMLESS' - ' -iLOG {0!s}'.format(self.ground_state_pdb.replace('.pdb','.log')) + + ' -iLOG {0!s}'.format(aimless) + ' -iENT data_template.cif' ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) else: @@ -1031,8 +1037,8 @@ def create_sf_mmcif(self,xtal): for event in self.eventList: mtzin += event + ' ' - if self.ground_state: - mtzin = self.ground_state_mean_mtz +# if self.ground_state: +# mtzin = self.ground_state_mean_mtz if os.path.isdir('/dls'): pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n' @@ -1086,12 +1092,21 @@ def apo_mmcif_exists(self): def add_apo_sf_mmcif_to_ground_state_mmcif(self): os.chdir(self.projectDir) self.Logfile.insert('checking pandda directory for apo mmcif files: '+self.panddaDir) - f = open('ground_state_sf.mmcif','a') + f = open('ground_state_sf.mmcif','w') + + refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/'))-2] + xtalList = [refXtal] # make sure that mmcof belonging to ref PDB file is first + for dirs in glob.glob(os.path.join(self.panddaDir, 'processed_datasets', '*')): + xtal = dirs[dirs.rfind('/') + 1:] + if xtal not in xtalList: + xtalList.append(xtal) + counter = 1 - for dirs in glob.glob(os.path.join(self.panddaDir,'processed_datasets','*')): - if not os.path.isdir(dirs): # this is needed in case single files are in processed_datasets + for xtal in xtalList: + if not os.path.isdir(os.path.join(self.panddaDir, 'processed_datasets', xtal)): # this is needed in case single files are in processed_datasets continue - xtal = dirs[dirs.rfind('/')+1:] + else: + dirs = os.path.join(self.panddaDir, 'processed_datasets', xtal) self.Logfile.insert('%s: reading saoked compound information from database' %xtal) xtalDict = self.db.get_db_dict_for_sample(xtal) if xtalDict['CompoundSMILES'].lower().replace(' ','') == '': diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 616aba83..c6d4cf51 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 18/02/2020 #\n' + ' # Date: 20/02/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemToolTips.py b/lib/XChemToolTips.py index a4aa2df5..dea12a50 100755 --- a/lib/XChemToolTips.py +++ b/lib/XChemToolTips.py @@ -338,7 +338,7 @@ def deposition_ground_state_preparation_step_two_text(): def deposition_ground_state_preparation_step_three_text(): msg = ( - '3. Please check the settings tab that you have selected the correct pandda directory.\n' + '1. Please check the settings tab that you have selected the correct pandda directory.\n' ' (Note: we will take all the apo mmcif files from this directory)\n' ' Current PanDDA directory:' ) @@ -346,13 +346,13 @@ def deposition_ground_state_preparation_step_three_text(): def deposition_ground_state_preparation_step_four_text(): msg = ( - '4. Add the ground-state entry to the database.' + '2. Add the ground-state entry to the database.' ) return msg def deposition_ground_state_preparation_step_five_text(): msg = ( - '5. Enter meta-data for ground-state model:\n' + '3. Enter meta-data for ground-state model:\n' ' - Open "Deposition -> Edit information"\n' ' - Fill out form or load .deposit file\n' ' - Press "Save to Database"\n' @@ -362,21 +362,21 @@ def deposition_ground_state_preparation_step_five_text(): def deposition_ground_state_preparation_step_six_text(): msg = ( - '6. Prepare the ground-state mmcif file.\n' + '4. Prepare the ground-state mmcif file.\n' ' Note: the mmcif files are saved into the selected pandda directory' ) return msg def deposition_ground_state_preparation_step_seven_text(): msg = ( - '7. Press the button below to copy the structire and structure factor mmcif files into the "group deposition directory" (see settings tab).\n' + '5. Press the button below to copy the structire and structure factor mmcif files into the "group deposition directory" (see settings tab).\n' 'Both mmcif files will be bundled into a single, bzipped tar archive which can be uploaded into via the PDB group deposition website.' ) return msg def deposition_ground_state_preparation_step_eight_text(): msg = ( - '8. Go to the group deposition website, create a session and upload the ligand-bound.tar.bz2 file from the group deposition directory.' + '6. Go to the group deposition website, create a session and upload the ligand-bound.tar.bz2 file from the group deposition directory.' ) return msg @@ -425,4 +425,20 @@ def second_cif_file_not_exists(): 'It was either not selected or the file was deleted/ moved in the meantime. ' 'Please check Menu -> Preferences.' ) + return msg + +def notification_about_changes_to_apo_deposition(): + msg = ( + 'The ground-state deposition procedure has changes in XCE v1.5.0!\n\n' + 'Previously, users had to select a specific reference PDB file, which had to have a ground-state mean-map and logfile associated with it.\n' + 'However, there were two main problems: (i) the map to mtz conversion did sometimes lead to strange maps or maps in space group P1 only\n' + 'and (2) occasionally the resulting MTZ files had missing columns. This lead to errors and delays during deposition, while inclusion of\n' + 'ground-state mean maps has little benefit since the mean map can be calculated with the deposited apo datasets. Hence, there is really\n' + 'no need to include it in the deposition.\n\n' + 'All you need to do is to select the relevant PanDDA directory and XCE will arbitrarily select a high resolution structure with low Rfree\n' + 'as the model for the deposition bundle and then put all structure factor MMCIF files into a single file. Note that it does not matter\n' + 'which PDB file gets chosen at this point since the positional modifications during refinement with REFMAC will be minimal.\n' + 'If you still want to make the ground-state mean map available, we would recommend to deposit ground-state mean map and \n' + 'everything else you think is relevant on ZENODO and ask the PDB annotator to include the respective DOI in the deposition\n' + ) return msg \ No newline at end of file diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 802be7c6..7f5a3715 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -856,7 +856,7 @@ def get_pointgroup_from_space_group(self,logfile_spacegroup): def calc_unitcell_volume_from_logfile(self,a,b,c,alpha,beta,gamma,lattice): - print '>>>',a,b,c,alpha,beta,gamma,lattice +# print '>>>',a,b,c,alpha,beta,gamma,lattice unitcell_volume=0 if lattice=='triclinic': unitcell_volume=a*b*c* \ From 4ebafd8137ee9144dd37cdb989ad370376d98a23 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 24 Feb 2020 12:55:30 +0000 Subject: [PATCH 012/358] v1.5.1 (24/02/2020) (#291) * v1.5.1 (24/02/2020) - enable parsing of autoPROC/ staraniso auto-processing results with specific space groups applied (e.g. autoPROC-P21) --- ChangeLog.txt | 4 ++++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemThread.py | 26 ++++++++++++++++++++------ 4 files changed, 26 insertions(+), 8 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 385a7268..ea2c2e27 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.5.1 (24/02/2020) +- enable parsing of autoPROC/ staraniso auto-processing results with specific space groups applied (e.g. autoPROC-P21) +- bug fix: names of auto-processing pipelines get now correctly determined + v1.5.0 (20/02/2020) - ground-state mean maps are EXCLUDED from apo deposition, because either map2mtz conversion was faulty or columns were missing; moreover, they are not required to reproduce the maps and users can deposit them separately on ZENODO if they want diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 1e903cc1..f3f21501 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.0' + xce_object.xce_version = 'v1.5.1' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index c6d4cf51..ae121275 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 20/02/2020 #\n' + ' # Date: 24/02/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 3ca259bc..8763d402 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2453,6 +2453,12 @@ def __init__(self, [ os.path.join('autoPROC'), '*summary.tar.gz', # staraniso_alldata-unique.table1 only available in tar archive '*staraniso_alldata-unique.mtz'], + [ os.path.join('autoPROC-*'), + '*aimless.log', + '*truncate-unique.mtz'], + [ os.path.join('autoPROC-*'), + '*summary.tar.gz', + '*staraniso_alldata-unique.mtz'], [ os.path.join('*'), os.path.join('LogFiles', '*aimless.log'), os.path.join('DataFiles', '*free.mtz')] @@ -2481,11 +2487,15 @@ def createSampleDir(self,xtal): def createAutoprocessingDir(self,xtal,run,autoproc): # create all the directories if necessary + self.Logfile.insert('%s: checking if new directory needs to be created for %s' %(xtal,os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc))) if not os.path.isdir(os.path.join(self.projectDir,xtal,'autoprocessing')): os.mkdir(os.path.join(self.projectDir,xtal,'autoprocessing')) if not os.path.isdir( os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc)): + self.Logfile.insert('%s: making directory %s' %(xtal,os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc))) os.mkdir(os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc)) + else: + self.Logfile.warning('%s: directory exists; skipping...' %xtal) def cleanUpDir(self,xtal,run,autoproc,mtzfile,logfile): toKeep = ['staraniso_alldata-unique.mtz','staraniso_alldata-unique.table1', @@ -2596,18 +2606,22 @@ def readProcessingUpdateResults(self,xtal,folder,log,mtz,timestamp,current_run,a # return db_dict def getAutoProc(self,folder): + self.Logfile.insert('checking name of auto-processing pipeline...') autoproc='unknown' if 'ap-run' in folder: autoproc = 'autoPROC' - elif 'autoPROC' in folder: - autoproc = 'autoPROC' else: for f in folder.split('/'): - print f - if ('xia2' or 'dials' or 'autoPROC') in f: + if 'autoPROC' in f: + autoproc = f + break + elif 'xia2' in f: + autoproc = f + break + elif 'dials' in f: autoproc = f break -# autoproc = folder.split('/')[len(folder.split('/'))-1] + self.Logfile.insert('name of auto-processing pipeline: %s' %autoproc) return autoproc def update_data_collection_table(self,xtal,current_run,autoproc,db_dict): @@ -2707,7 +2721,7 @@ def parse_file_system(self): if 'staraniso' in logfile or 'summary.tar.gz' in logfile: autoproc = 'aP_staraniso' else: - autoproc = self.getAutoProc(procDir) + autoproc = self.getAutoProc(folder) if self.alreadyParsed(xtal,current_run,autoproc): continue self.readProcessingUpdateResults(xtal,folder,logfile,mtzfile,timestamp,current_run,autoproc) From ccf0ea11bf1992aaab28443225d0f7e58b1e0937 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 25 Feb 2020 16:22:30 +0000 Subject: [PATCH 013/358] v1.5.2 (25/02/2020) (#292) * v1.5.2 (25/02/2020) - bug fix: correct determination of staraniso runs for different space groups --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 8 ++++---- lib/XChemThread.py | 23 +++++++++++++---------- 4 files changed, 21 insertions(+), 15 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index ea2c2e27..7720300c 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.2 (25/02/2020) +- bug fix: correct determination of staraniso runs for different space groups + v1.5.1 (24/02/2020) - enable parsing of autoPROC/ staraniso auto-processing results with specific space groups applied (e.g. autoPROC-P21) - bug fix: names of auto-processing pipelines get now correctly determined diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index f3f21501..d7db58be 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.1' + xce_object.xce_version = 'v1.5.2' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index ae121275..d54a62d2 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 24/02/2020 #\n' + ' # Date: 25/02/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' @@ -111,17 +111,17 @@ def __init__(self,logfile): self.logfile=open(logfile, "a") def insert(self,message): - present_time=datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M:%S') + present_time=datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] print( str(present_time)+' ==> XCE: '+message, file = self.logfile) print('==> XCE: '+message) def warning(self,message): - present_time=datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M:%S') + present_time=datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] print( str(present_time)+' ==> XCE: WARNING! '+message, file = self.logfile) print('==> XCE: WARNING! '+message) def error(self,message): - present_time=datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M:%S') + present_time=datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] print( str(present_time)+' ==> XCE: ERROR!!! '+message, file = self.logfile) print('==> XCE: ERROR!!! '+message) diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 8763d402..9a28eeb3 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2293,6 +2293,8 @@ def selectResultsSimilarToReference(self,dbList): self.Logfile.insert('checking unit cell volume difference and point group:') for reference_file in self.reference_file_list: if not reference_file[4]==0: + self.Logfile.insert('unitcell volume reference:' + str(reference_file[4])) + self.Logfile.insert('unitcell volume dataset: ' + str(resultDict['DataProcessingUnitCellVolume'])) unitcell_difference=round((math.fabs(reference_file[4]-float(resultDict['DataProcessingUnitCellVolume']))/reference_file[4])*100,1) self.Logfile.insert(resultDict['DataProcessingProgram'] + ': ' + str(unitcell_difference) + '% difference -> pg(ref): ' + @@ -2350,6 +2352,7 @@ def selectHighestResolution(self,dbList): def selectSpecificPipelineOnly(self,dbList): tmp = [] + self.Logfile.insert('selecting datasets by auto-processing pipeline: ' + self.selection_mechanism) for resultDict in dbList: if self.selection_mechanism == 'dials - only' and 'dials' in resultDict['DataProcessingProgram']: tmp.append(resultDict) @@ -2357,9 +2360,9 @@ def selectSpecificPipelineOnly(self,dbList): tmp.append(resultDict) if self.selection_mechanism == 'xia2 3dii - only' and '3dii-run' in resultDict['DataProcessingProgram']: tmp.append(resultDict) - if self.selection_mechanism == 'autoProc - only' and resultDict['DataProcessingProgram'] == 'autoPROC': + if self.selection_mechanism == 'autoProc - only' and 'autoPROC' in resultDict['DataProcessingProgram'] and not 'staraniso' in resultDict['DataProcessingProgram']: tmp.append(resultDict) - if self.selection_mechanism == 'autoProc_staraniso - only' and resultDict['DataProcessingProgram'] == 'aP_staraniso': + if self.selection_mechanism == 'autoProc_staraniso - only' and 'autoPROC' in resultDict['DataProcessingProgram'] and 'staraniso' in resultDict['DataProcessingProgram']: tmp.append(resultDict) if not tmp: tmp = dbList @@ -2605,7 +2608,7 @@ def readProcessingUpdateResults(self,xtal,folder,log,mtz,timestamp,current_run,a self.update_data_collection_table(xtal,current_run,autoproc,db_dict) # return db_dict - def getAutoProc(self,folder): + def getAutoProc(self,folder,staraniso): self.Logfile.insert('checking name of auto-processing pipeline...') autoproc='unknown' if 'ap-run' in folder: @@ -2613,7 +2616,7 @@ def getAutoProc(self,folder): else: for f in folder.split('/'): if 'autoPROC' in f: - autoproc = f + autoproc = f + staraniso break elif 'xia2' in f: autoproc = f @@ -2713,15 +2716,15 @@ def parse_file_system(self): self.Logfile.insert('%s: mtzfile = %s' %(xtal,mtzfile)) for folder in glob.glob(procDir): + staraniso = '' self.Logfile.insert('%s: searching %s' %(xtal,folder)) if self.junk(folder): continue if self.empty_folder(xtal,folder): continue if 'staraniso' in logfile or 'summary.tar.gz' in logfile: - autoproc = 'aP_staraniso' - else: - autoproc = self.getAutoProc(folder) + staraniso = '_staraniso' + autoproc = self.getAutoProc(folder,staraniso) if self.alreadyParsed(xtal,current_run,autoproc): continue self.readProcessingUpdateResults(xtal,folder,logfile,mtzfile,timestamp,current_run,autoproc) @@ -2807,15 +2810,15 @@ def parse_agamemnon_file_system(self): # print mtz for folder in glob.glob(procDir): + staraniso = '' self.Logfile.insert('%s: searching %s' % (xtal, folder)) if self.junk(folder): continue if self.empty_folder(xtal,folder): continue if 'staraniso' in logfile or 'summary.tar.gz' in logfile: - autoproc = 'aP_staraniso' - else: - autoproc = self.getAutoProc(folder) + staraniso = '_staraniso' + autoproc = self.getAutoProc(folder, staraniso) if self.alreadyParsed(xtal,current_run,autoproc): continue self.readProcessingUpdateResults(xtal,folder,logfile,mtzfile,timestamp,current_run,autoproc) From 966bc49c5f69f28b736a13f69dcae138627fcfbd Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 26 Feb 2020 14:09:15 +0000 Subject: [PATCH 014/358] v1.5.3 (26/02/2020) (#293) --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemUtils.py | 4 ++++ 4 files changed, 9 insertions(+), 2 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 7720300c..724420f4 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.3 (26/02/2020) +- bug fix: read spacegroup as H32 from xia2.mmcif ('R 3 2 :H') + v1.5.2 (25/02/2020) - bug fix: correct determination of staraniso runs for different space groups diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index d7db58be..3f9f3f8f 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.2' + xce_object.xce_version = 'v1.5.3' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index d54a62d2..05026c63 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 25/02/2020 #\n' + ' # Date: 26/02/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 7f5a3715..48ea4a39 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -824,6 +824,10 @@ def read_mmcif(self,mmcif): self.aimless['DataCollectionWavelength'] = line.split()[1] elif line.startswith('_symmetry.space_group_name_H-M'): self.aimless['DataProcessingSpaceGroup'] = line[line.find("'")+1:line.rfind("'")].replace(' ','') + if 'R32:H' in self.aimless['DataProcessingSpaceGroup']: + self.aimless['DataProcessingSpaceGroup'] = 'H32' + if 'R3:H' in self.aimless['DataProcessingSpaceGroup']: + self.aimless['DataProcessingSpaceGroup'] = 'H3' self.aimless['DataProcessingPointGroup'] = self.get_pointgroup_from_space_group( self.aimless['DataProcessingSpaceGroup']) elif line.startswith('_space_group.crystal_system'): From 94e3fbfeb78059009da643924643958008f4d7dd Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 27 Feb 2020 10:58:29 +0000 Subject: [PATCH 015/358] v1.5.4 (27/02/2020) (#294) * v1.5.4 (27/02/2020) - bug fix: iotbx spg symbol for H32 needed changing for unique step of initial map calculation --- ChangeLog.txt | 3 + gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemThread.py | 512 ++++++++++++++-------------- 4 files changed, 264 insertions(+), 255 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 724420f4..ad33c745 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.4 (27/02/2020) +- bug fix: iotbx spg symbol for H32 needed changing for unique step of initial map calculation + v1.5.3 (26/02/2020) - bug fix: read spacegroup as H32 from xia2.mmcif ('R 3 2 :H') diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 3f9f3f8f..96fabd17 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.3' + xce_object.xce_version = 'v1.5.4' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 05026c63..99ee0081 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 26/02/2020 #\n' + ' # Date: 27/02/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 9a28eeb3..9c892b05 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -1123,264 +1123,268 @@ def run_libcheck(self,sampleID,compoundID): -class run_dimple_on_all_autoprocessing_files(QtCore.QThread): - def __init__(self,sample_list,initial_model_directory,external_software,ccp4_scratch_directory,database_directory, - data_source_file,max_queue_jobs,xce_logfile, remote_submission, remote_submission_string, - dimple_twin_mode,pipeline): - QtCore.QThread.__init__(self) - self.sample_list=sample_list - self.initial_model_directory=initial_model_directory - self.external_software=external_software - self.queueing_system_available=external_software['qsub'] - self.ccp4_scratch_directory=ccp4_scratch_directory - self.database_directory=database_directory - self.data_source_file=data_source_file - self.max_queue_jobs=max_queue_jobs - self.xce_logfile=xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) - self.pipeline=pipeline - self.using_remote_qsub_submission = remote_submission - self.remote_qsub_submission = remote_submission_string - self.dimple_twin_mode = dimple_twin_mode - - - def run(self): - progress_step=1 - if len(self.sample_list) != 0: - progress_step=100/float(len(self.sample_list)) - progress=0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - - os.chdir(self.ccp4_scratch_directory) - os.system('/bin/rm -f xce_dimple*sh') - - db=XChemDB.data_source(os.path.join(self.database_directory,self.data_source_file)) - database=os.path.join(self.database_directory,self.data_source_file) - -# print(self.sample_list) - - for n,item in enumerate(self.sample_list): - - xtal = item[0] - visit_run_autoproc = item[1] - mtzin = item[2] - ref_pdb = item[3] - ref_mtz = item[4] - ref_cif = item[5] - - # check if reference mtzfile has an Rfree column; if not, then ignore - # DIMPLE assumes an Rfree column and barfs if it is not present - # note: ref_mtz looks like this: ref mtz -R reference.mtz -# if os.path.isfile(ref_mtz.split()[len(ref_mtz.split())-1]): -# mtz_column_dict=mtztools(ref_mtz.split()[len(ref_mtz.split())-1]).get_all_columns_as_dict() - if os.path.isfile(ref_mtz): - if 'FreeR_flag' not in mtz.object(ref_mtz).column_labels(): -# mtz_column_dict=mtztools(ref_mtz).get_all_columns_as_dict() -# if 'FreeR_flag' not in mtz_column_dict['RFREE']: - self.Logfile.insert('cannot find FreeR_flag in reference mtz file: {0!s} -> ignoring reference mtzfile!!!'.format(ref_mtz)) - ref_mtz = '' -# if mtz_column_dict['RFREE'] != []: -# self.Logfile.insert('found Rfree set with other column name though: {0!s}'.format(str(mtz_column_dict['RFREE']))) -# self.Logfile.insert('try renaming Rfree column to FreeR_flag with CAD!') - -# uniqueify = '' -# if 'FreeR_flag' in mtz.object(mtzin).column_labels(): -# uniqueify = 'uniqueify -f FreeR_flag ' + mtzin + ' ' + xtal + '-unique.mtz' + '\n' +#class run_dimple_on_all_autoprocessing_files(QtCore.QThread): +# def __init__(self,sample_list,initial_model_directory,external_software,ccp4_scratch_directory,database_directory, +# data_source_file,max_queue_jobs,xce_logfile, remote_submission, remote_submission_string, +# dimple_twin_mode,pipeline): +# QtCore.QThread.__init__(self) +# self.sample_list=sample_list +# self.initial_model_directory=initial_model_directory +# self.external_software=external_software +# self.queueing_system_available=external_software['qsub'] +# self.ccp4_scratch_directory=ccp4_scratch_directory +# self.database_directory=database_directory +# self.data_source_file=data_source_file +# self.max_queue_jobs=max_queue_jobs +# self.xce_logfile=xce_logfile +# self.Logfile=XChemLog.updateLog(xce_logfile) +# self.pipeline=pipeline +# self.using_remote_qsub_submission = remote_submission +# self.remote_qsub_submission = remote_submission_string +# self.dimple_twin_mode = dimple_twin_mode +# +# +# def run(self): +# progress_step=1 +# if len(self.sample_list) != 0: +# progress_step=100/float(len(self.sample_list)) +# progress=0 +# self.emit(QtCore.SIGNAL('update_progress_bar'), progress) +# +# os.chdir(self.ccp4_scratch_directory) +# os.system('/bin/rm -f xce_dimple*sh') +# +# db=XChemDB.data_source(os.path.join(self.database_directory,self.data_source_file)) +# database=os.path.join(self.database_directory,self.data_source_file) +# +## print(self.sample_list) +# +# for n,item in enumerate(self.sample_list): +# +# xtal = item[0] +# visit_run_autoproc = item[1] +# mtzin = item[2] +# ref_pdb = item[3] +# ref_mtz = item[4] +# ref_cif = item[5] +# +# # check if reference mtzfile has an Rfree column; if not, then ignore +# # DIMPLE assumes an Rfree column and barfs if it is not present +# # note: ref_mtz looks like this: ref mtz -R reference.mtz +## if os.path.isfile(ref_mtz.split()[len(ref_mtz.split())-1]): +## mtz_column_dict=mtztools(ref_mtz.split()[len(ref_mtz.split())-1]).get_all_columns_as_dict() +# if os.path.isfile(ref_mtz): +# if 'FreeR_flag' not in mtz.object(ref_mtz).column_labels(): +## mtz_column_dict=mtztools(ref_mtz).get_all_columns_as_dict() +## if 'FreeR_flag' not in mtz_column_dict['RFREE']: +# self.Logfile.insert('cannot find FreeR_flag in reference mtz file: {0!s} -> ignoring reference mtzfile!!!'.format(ref_mtz)) +# ref_mtz = '' +## if mtz_column_dict['RFREE'] != []: +## self.Logfile.insert('found Rfree set with other column name though: {0!s}'.format(str(mtz_column_dict['RFREE']))) +## self.Logfile.insert('try renaming Rfree column to FreeR_flag with CAD!') +# +## uniqueify = '' +## if 'FreeR_flag' in mtz.object(mtzin).column_labels(): +## uniqueify = 'uniqueify -f FreeR_flag ' + mtzin + ' ' + xtal + '-unique.mtz' + '\n' +## else: +## uniqueify = 'uniqueify ' + mtzin + ' ' + xtal + '-unique.mtz' + '\n' +# +# db_dict= {'DimpleReferencePDB': ref_pdb} +# db.update_data_source(xtal,db_dict) +# +# self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'creating input script for '+xtal+' in '+visit_run_autoproc) +# +# if not os.path.isdir(os.path.join(self.initial_model_directory,xtal)): +# os.mkdir(os.path.join(self.initial_model_directory,xtal)) +# if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'dimple')): +# os.mkdir(os.path.join(self.initial_model_directory,xtal,'dimple')) +# if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc)): +# os.mkdir(os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc)) +# os.chdir(os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc)) +# os.system('touch dimple_run_in_progress') +# os.system('/bin/rm final.mtz 2> /dev/null') +# os.system('/bin/rm final.pdb 2> /dev/null') +# +# if self.queueing_system_available: +# top_line='#PBS -joe -N XCE_dimple\n' # else: -# uniqueify = 'uniqueify ' + mtzin + ' ' + xtal + '-unique.mtz' + '\n' - - db_dict= {'DimpleReferencePDB': ref_pdb} - db.update_data_source(xtal,db_dict) - - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'creating input script for '+xtal+' in '+visit_run_autoproc) - - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal)): - os.mkdir(os.path.join(self.initial_model_directory,xtal)) - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'dimple')): - os.mkdir(os.path.join(self.initial_model_directory,xtal,'dimple')) - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc)): - os.mkdir(os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc)) - os.chdir(os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc)) - os.system('touch dimple_run_in_progress') - os.system('/bin/rm final.mtz 2> /dev/null') - os.system('/bin/rm final.pdb 2> /dev/null') - - if self.queueing_system_available: - top_line='#PBS -joe -N XCE_dimple\n' - else: - top_line='#!'+os.getenv('SHELL')+'\n' - - if 'csh' in os.getenv('SHELL'): - ccp4_scratch='setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' - elif 'bash' in os.getenv('SHELL'): - ccp4_scratch='export CCP4_SCR='+self.ccp4_scratch_directory+'\n' - else: - ccp4_scratch='' - - if 'dimple_rerun_on_selected_file' in visit_run_autoproc: - additional_cmds = ( - 'cd {0!s}\n'.format(os.path.join(self.initial_model_directory,xtal)) + - '/bin/rm dimple.pdb\n' - 'ln -s dimple/dimple_rerun_on_selected_file/dimple/final.pdb dimple.pdb\n' - '/bin/rm dimple.mtz\n' - 'ln -s dimple/dimple_rerun_on_selected_file/dimple/final.mtz dimple.mtz\n' - '/bin/rm 2fofc.map\n' - 'ln -s dimple/dimple_rerun_on_selected_file/dimple/2fofc.map .\n' - '/bin/rm fofc.map\n' - 'ln -s dimple/dimple_rerun_on_selected_file/dimple/fofc.map .\n' - '\n' - '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_for_new_dimple_pdb.py')+ - ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory,self.data_source_file), xtal, self.initial_model_directory) ) - - else: - additional_cmds='' - -# resolution_high = 0.1 -# o = iotbx.mtz.object(mtzin) -# low, high = o.max_min_resolution() - hkl = any_reflection_file(file_name=mtzin) - miller_arrays = hkl.as_miller_arrays() - mtzFile = miller_arrays[0] - - if mtzFile.space_group_info().symbol_and_number() == 'R 3 :H (No. 146)': - symNoAbsence = 'H3' - else: - symNoAbsence = str([x[0] for x in str(mtzFile.space_group_info().symbol_and_number().split('(')[0]).split()]).replace('[','').replace(']','').replace("'","").replace(',','').replace(' ','') - - dls_stuff = '' - if os.path.isdir('/dls'): - dls_stuff = ( - 'module unload ccp4\n' - 'source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' - ) - - twin = '' - if self.dimple_twin_mode: - twin = "--refmac-key 'TWIN'" - - Cmds = ( - '{0!s}\n'.format(top_line)+ - '\n' - 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' - '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc) + - '\n' - 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' - '\n' - + dls_stuff + - '\n' - + ccp4_scratch + - '\n' - '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(database,xtal,'DimpleStatus','running') + - '\n' - 'unique hklout unique.mtz << eof\n' - ' cell %s\n' %str([round(float(i),2) for i in mtzFile.unit_cell().parameters()]).replace('[','').replace(']','')+ - ' symmetry %s\n' %symNoAbsence+ - ' resolution %s\n' %str(round(float(mtzFile.d_min()),3))+ - 'eof\n' - '\n' -# 'freerflag hklin unique.mtz hklout free.mtz > freerflag.log\n' - '\n' - 'sftools << eof > sftools.log\n' - ' read unique.mtz\n' - ' calc col F = 10.0\n' - ' calc col SIGF = 1.0\n' - ' write sftools.mtz\n' - 'eof\n' - '\n' - 'cad hklin1 sftools.mtz hklin2 %s hklout %s.999A.mtz << eof\n' %(mtzin,xtal) + - ' monitor BRIEF\n' - ' labin file 1 E1=F E2=SIGF\n' - ' labout file 1 E1=F_unique E2=SIGF_unique\n' - ' labin file 2 ALL\n' - ' resolution file 1 999.0 %s\n' %str(round(float(mtzFile.d_min()),2))+ - 'eof\n' - '\n' - "dimple --no-cleanup %s.999A.mtz %s %s %s %s dimple\n" %(xtal,ref_pdb,ref_mtz,ref_cif,twin) + - '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc,'dimple') + -# + uniqueify + +# top_line='#!'+os.getenv('SHELL')+'\n' +# +# if 'csh' in os.getenv('SHELL'): +# ccp4_scratch='setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' +# elif 'bash' in os.getenv('SHELL'): +# ccp4_scratch='export CCP4_SCR='+self.ccp4_scratch_directory+'\n' +# else: +# ccp4_scratch='' +# +# if 'dimple_rerun_on_selected_file' in visit_run_autoproc: +# additional_cmds = ( +# 'cd {0!s}\n'.format(os.path.join(self.initial_model_directory,xtal)) + +# '/bin/rm dimple.pdb\n' +# 'ln -s dimple/dimple_rerun_on_selected_file/dimple/final.pdb dimple.pdb\n' +# '/bin/rm dimple.mtz\n' +# 'ln -s dimple/dimple_rerun_on_selected_file/dimple/final.mtz dimple.mtz\n' +# '/bin/rm 2fofc.map\n' +# 'ln -s dimple/dimple_rerun_on_selected_file/dimple/2fofc.map .\n' +# '/bin/rm fofc.map\n' +# 'ln -s dimple/dimple_rerun_on_selected_file/dimple/fofc.map .\n' +# '\n' +# '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_for_new_dimple_pdb.py')+ +# ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory,self.data_source_file), xtal, self.initial_model_directory) ) +# +# else: +# additional_cmds='' +# +## resolution_high = 0.1 +## o = iotbx.mtz.object(mtzin) +## low, high = o.max_min_resolution() +# hkl = any_reflection_file(file_name=mtzin) +# miller_arrays = hkl.as_miller_arrays() +# mtzFile = miller_arrays[0] +# +# if mtzFile.space_group_info().symbol_and_number() == 'R 3 :H (No. 146)': +# symNoAbsence = 'H3' +# elif mtzFile.space_group_info().symbol_and_number() == 'R 3 2 :H (No. 155)': +# symNoAbsence = 'H32' +# else: +# symNoAbsence = str([x[0] for x in str(mtzFile.space_group_info().symbol_and_number().split('(')[0]).split()]).replace('[','').replace(']','').replace("'","").replace(',','').replace(' ','') +# if symNoAbsence.replace(' ','') == "R32:": +# symNoAbsence = 'H32' +# +# dls_stuff = '' +# if os.path.isdir('/dls'): +# dls_stuff = ( +# 'module unload ccp4\n' +# 'source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' +# ) +# +# twin = '' +# if self.dimple_twin_mode: +# twin = "--refmac-key 'TWIN'" +# +# Cmds = ( +# '{0!s}\n'.format(top_line)+ +# '\n' +# 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' # '\n' -# 'cad hklin1 %s hklout %s < freerflag.log\n' +# '\n' +# 'sftools << eof > sftools.log\n' +# ' read unique.mtz\n' +# ' calc col F = 10.0\n' +# ' calc col SIGF = 1.0\n' +# ' write sftools.mtz\n' +# 'eof\n' +# '\n' +# 'cad hklin1 sftools.mtz hklin2 %s hklout %s.999A.mtz << eof\n' %(mtzin,xtal) + +# ' monitor BRIEF\n' +# ' labin file 1 E1=F E2=SIGF\n' +# ' labout file 1 E1=F_unique E2=SIGF_unique\n' +# ' labin file 2 ALL\n' +# ' resolution file 1 999.0 %s\n' %str(round(float(mtzFile.d_min()),2))+ # 'eof\n' -# 'dimple --no-cleanup %s-unique-2.mtz %s %s %s dimple\n' %(xtal,ref_pdb,ref_mtz,ref_cif) + +# '\n' +# "dimple --no-cleanup %s.999A.mtz %s %s %s %s dimple\n" %(xtal,ref_pdb,ref_mtz,ref_cif,twin) + # '\n' # 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc,'dimple') + - '\n' - 'fft hklin final.mtz mapout 2fofc.map << EOF\n' - ' labin F1=FWT PHI=PHWT\n' - 'EOF\n' - '\n' - 'fft hklin final.mtz mapout fofc.map << EOF\n' - ' labin F1=DELFWT PHI=PHDELWT\n' - 'EOF\n' - '\n' - +additional_cmds+ - '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc) + - '\n' - '/bin/rm dimple_run_in_progress\n' - '\n' - 'ln -s dimple/final.pdb .\n' - 'ln -s dimple/final.mtz .\n' - ) - - # print(Cmds) - - os.chdir(self.ccp4_scratch_directory) - f = open('xce_dimple_{0!s}.sh'.format(str(n+1)),'w') - f.write(Cmds) - f.close() - os.system('chmod +x xce_dimple_{0!s}.sh'.format(str(n+1))) - db_dict= {'DimpleStatus': 'started'} - self.Logfile.insert('{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) - db.update_data_source(xtal,db_dict) - - - progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - - # submit job - self.Logfile.insert('created input scripts for '+str(n+1)+' in '+self.ccp4_scratch_directory) - os.chdir(self.ccp4_scratch_directory) - if os.path.isdir('/dls'): - if self.external_software['qsub_array']: - Cmds = ( - '#PBS -joe -N xce_dimple_master\n' - './xce_dimple_$SGE_TASK_ID.sh\n' - ) - f = open('dimple_master.sh','w') - f.write(Cmds) - f.close() - print(os.getcwd()) - self.Logfile.insert('submitting array job with maximal 100 jobs running on cluster') - self.Logfile.insert('using the following command:') - self.Logfile.insert('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} dimple_master.sh'.format(str(n+1), self.max_queue_jobs)) - if self.using_remote_qsub_submission: - os.system(str(self.remote_qsub_submission).replace("qsub'", str('cd ' + str(os.getcwd()) + '; ' + 'qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} dimple_master.sh' - .format(str(n+1), self.max_queue_jobs))) + "'") - - else: - os.system('qsub -P labxchem -t 1:{0!s} -tc {1!s} -N dimple-master dimple_master.sh'.format(str(n+1), self.max_queue_jobs)) - else: - self.Logfile.insert("cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") - elif self.external_software['qsub']: - self.Logfile.insert('submitting {0!s} individual jobs to cluster'.format((str(n+1)))) - self.Logfile.insert('WARNING: this could potentially lead to a crash...') - for i in range(n+1): - self.Logfile.insert('qsub -q medium.q -N dimple xce_dimple_{0!s}.sh'.format((str(i+1)))) - os.system('qsub -N dimple xce_dimple_{0!s}.sh'.format((str(i+1)))) - else: - self.Logfile.insert('running %s consecutive DIMPLE jobs on your local machine') - for i in range(n+1): - self.Logfile.insert('starting xce_dimple_{0!s}.sh'.format((str(i+1)))) - os.system('./xce_dimple_{0!s}.sh'.format((str(i+1)))) - - self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) +## + uniqueify + +## '\n' +## 'cad hklin1 %s hklout %s < Date: Thu, 27 Feb 2020 18:16:31 +0000 Subject: [PATCH 016/358] v1.5.5 (27/02/2020) (#295) * v1.5.5 (27/02/2020) - bug fix: update depositTable with ground_state_sf.mmcif if successfully created --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 13 +++++++++++-- lib/XChemPANDDA.py | 1 + 4 files changed, 16 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index ad33c745..9a0ff261 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.5 (27/02/2020) +- bug fix: update depositTable with ground_state_sf.mmcif if successfully created + v1.5.4 (27/02/2020) - bug fix: iotbx spg symbol for H32 needed changing for unique step of initial map calculation diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 96fabd17..d01587fc 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.4' + xce_object.xce_version = 'v1.5.5' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 561206fa..9aed0c42 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -1163,13 +1163,22 @@ def add_data_increment_to_apo_mmcif(self): datasetCounter += 1 f.write(newLine) a += 1 - if datasetCounter % 50 == 0: - self.Logfile.insert('%s data_rxxxxsf records edited...' %str(datasetCounter)) + self.Logfile.insert('new dataset block: %s -> %s' %(str(datasetCounter),newLine.replace('\n','').replace('\r',''))) +# if datasetCounter % 50 == 0: +# self.Logfile.insert('%s data_rxxxxsf records edited...' %str(datasetCounter)) else: f.write(line) f.close() os.chdir(self.panddaDir) os.system('/bin/mv ground_state_sf_tmp.mmcif ground_state_sf.mmcif') + + if os.path.isfile('ground_state_sf.mmcif') and os.path.getsize('ground_state_sf.mmcif') > 20000 : + self.Logfile.insert('ground_state: SF mmcif file successfully created') + self.db.execute_statement("update depositTable set mmCIF_SF_file='ground_state_sf.mmcif' where CrystalName is 'ground_state' and DimplePANDDApath is '{0!s}'".format(self.panddaDir)) + else: + self.Logfile.error('%s: SF mmcif file was not created successfully') + self.add_to_errorList(xtal) + return True diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index d960c25a..5455f1bd 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -1139,6 +1139,7 @@ def __init__(self,panddaDir,xce_logfile): self.Logfile=XChemLog.updateLog(xce_logfile) def sf_convert_environment(self): + pdb_extract_init = '' if os.path.isdir('/dls'): pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n' pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-prod/bin/sf_convert' From d88ba728035faa2b68421abd1ed3ffe9d909cd1e Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 2 Mar 2020 16:56:41 +0000 Subject: [PATCH 017/358] v1.5.6 (02/03/2020) - added Taxonomy ID for BAT SARS-LIKE CORONAVIRUS and COVID-19 (#296) --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemMain.py | 6 ++++-- 4 files changed, 9 insertions(+), 4 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 9a0ff261..68c00134 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.6 (02/03/2020) +- added Taxonomy ID for BAT SARS-LIKE CORONAVIRUS and COVID-19 + v1.5.5 (27/02/2020) - bug fix: update depositTable with ground_state_sf.mmcif if successfully created diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index d01587fc..c435151f 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.5' + xce_object.xce_version = 'v1.5.6' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 99ee0081..363c8d49 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 27/02/2020 #\n' + ' # Date: 02/03/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemMain.py b/lib/XChemMain.py index 77132b2e..dcaf97c2 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -617,9 +617,11 @@ def detectorType(): def NCBI_taxonomy_ID(): taxonomy_dict = { '9606': 'homo sapiens', - '562': 'escherichia coli', '7108': 'SPODOPTERA FRUGIPERDA', - '5693 ': 'Trypanosoma cruzi' } + '5693 ': 'Trypanosoma cruzi', + '1508227': 'BAT SARS-LIKE CORONAVIRUS', + '2697049': 'COVID-19', + '562': 'escherichia coli' } return taxonomy_dict From 4e3771a4d5cbcf0f1fe4014327de22a49e99f79f Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 3 Mar 2020 12:01:37 +0000 Subject: [PATCH 018/358] v1.5.7 (03/03/2020) (#297) * v1.5.7 (03/03/2020) - bug fix: capture all available event maps during html export --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- web/XChemWeb.py | 13 ++++++++----- 4 files changed, 13 insertions(+), 7 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 68c00134..5b56e657 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.7 (03/03/2020) +- bug fix: capture all available event maps during html export + v1.5.6 (02/03/2020) - added Taxonomy ID for BAT SARS-LIKE CORONAVIRUS and COVID-19 diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index c435151f..aba1d269 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.6' + xce_object.xce_version = 'v1.5.7' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 363c8d49..59215e5a 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 02/03/2020 #\n' + ' # Date: 03/03/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/web/XChemWeb.py b/web/XChemWeb.py index d80e23b0..bd1e6a23 100755 --- a/web/XChemWeb.py +++ b/web/XChemWeb.py @@ -53,7 +53,10 @@ def prepare(self): ligNumber = ligand.split('-')[2] eventMap = self.find_matching_event_map_from_database(xtal, ligand) if eventMap: + self.Logfile.insert('%s: using the following event map -> %s' %(xtal,eventMap)) self.cut_and_copy_map(xtal, ligand+'.pdb', eventMap, xtal + '_' + ligand + '_event.ccp4','F','PHIF') + else: + self.Logfile.error('%s: value of event map -> %s' %(xtal,eventMap)) x,y,z = self.pdb.get_centre_of_gravity_of_residue(ligand) self.copy_spider_plot(xtal,ligand) pdbID = self.db_dict['Deposition_PDB_ID'] @@ -272,15 +275,15 @@ def find_matching_event_map_from_database(self,xtal,ligID): ligNumber = ligID.split('-')[2] eventMAP = self.db.get_event_map_for_ligand(xtal, ligChain, ligNumber, ligName) self.Logfile.insert('%s: the database thinks the following event map belongs to %s: %s' %(xtal,ligID,eventMAP)) - print 'event map', eventMAP +# print 'event map', eventMAP if eventMAP == '' or 'none' in str(eventMAP).lower(): self.Logfile.warning('%s: the respective field in the DB is apparently emtpy' %xtal) self.Logfile.warning('%s: will try to determine ligand - event map relationship by checking CC...' %xtal) - eventMap = self.find_matching_event_map(xtal,ligID) + eventMAP = self.find_matching_event_map(xtal,ligID) elif not os.path.isfile(eventMAP): self.Logfile.warning('%s: event map file does not exist!' %xtal) self.Logfile.warning('%s: will try to determine ligand - event map relationship by checking CC...' %xtal) - eventMap = self.find_matching_event_map(xtal,ligID) + eventMAP = self.find_matching_event_map(xtal,ligID) else: self.Logfile.insert('%s: found matching event map!' %xtal) return eventMAP @@ -311,8 +314,8 @@ def find_matching_event_map(self,xtal,ligID): else: self.Logfile.insert('%s: selected event map -> CC(%s) = %s for %s' %(xtal,ligID,highestCC,mtz[mtz.rfind('/')+1:])) eventMAP = mtz[mtz.rfind('/')+1:].replace('.P1.mtz','.ccp4') - if not os.path.isfile(eventMAP): - eventMAP = [] +# if not os.path.isfile(eventMAP): +# eventMAP = [] # else: # self.cut_eventMAP(xtal,ligID,eventMAP) return eventMAP From d479006c91361bcbaf880d02efc1be96441c0266 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 4 Mar 2020 08:27:30 +0000 Subject: [PATCH 019/358] v1.5.8 (04/03/2020) - added Taxonomy ID for mus musculus (#298) --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemMain.py | 1 + 4 files changed, 6 insertions(+), 2 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 5b56e657..48f3bd9c 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.8 (04/03/2020) +- added Taxonomy ID for mus musculus + v1.5.7 (03/03/2020) - bug fix: capture all available event maps during html export diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index aba1d269..7a6934a7 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.7' + xce_object.xce_version = 'v1.5.8' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 59215e5a..57bcb6ca 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 03/03/2020 #\n' + ' # Date: 04/03/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemMain.py b/lib/XChemMain.py index dcaf97c2..ce16da17 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -617,6 +617,7 @@ def detectorType(): def NCBI_taxonomy_ID(): taxonomy_dict = { '9606': 'homo sapiens', + '10090': 'mus musculus', '7108': 'SPODOPTERA FRUGIPERDA', '5693 ': 'Trypanosoma cruzi', '1508227': 'BAT SARS-LIKE CORONAVIRUS', From 5dc0bcdcb57fe31a656f5bc0eaf24824e1f976f7 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 5 Mar 2020 08:05:04 +0000 Subject: [PATCH 020/358] v1.5.9 (05/03/2020) - bug fix: reading of .json scaling logfiles enabled during 'update database from filesystem (#299) --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemThread.py | 3 ++- 4 files changed, 7 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 48f3bd9c..5842c765 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.9 (05/03/2020) +- bug fix: reading of .json scaling logfiles enabled during 'update database from filesystem' + v1.5.8 (04/03/2020) - added Taxonomy ID for mus musculus diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 7a6934a7..f39daf56 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.8' + xce_object.xce_version = 'v1.5.9' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 57bcb6ca..82c3eb68 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 04/03/2020 #\n' + ' # Date: 05/03/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 9c892b05..b2a0dc07 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -220,7 +220,8 @@ def sync_data_processing(self,xtal,db_dict): db_dict['DataProcessingLOGfileName']=xtal+'.log' if db_dict['DataCollectionOutcome']=='None' or db_dict['DataCollectionOutcome']=='': db_dict['DataCollectionOutcome']='success' - aimless_results=parse().read_aimless_logfile(xtal+'.log') +# aimless_results=parse().read_aimless_logfile(xtal+'.log') + aimless_results=parse().read_aimless_logfile(db_dict['DataProcessingPathToLogfile']) db_dict.update(aimless_results) else: db_dict['DataProcessingPathToLogfile']='' From b12e881a641e4948bc05b32764e26d3120ef24c5 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 5 Mar 2020 15:34:55 +0000 Subject: [PATCH 021/358] v1.5.10 (05/03/2020) (#300) * v1.5.10 (05/03/2020) - bug fix: correct name of event map in files directory --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- web/XChemWeb.py | 5 +++++ 3 files changed, 9 insertions(+), 1 deletion(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 5842c765..ef9fe4c3 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.10 (05/03/2020) +- bug fix: correct name of event map in files directory + v1.5.9 (05/03/2020) - bug fix: reading of .json scaling logfiles enabled during 'update database from filesystem' diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index f39daf56..36f69063 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.9' + xce_object.xce_version = 'v1.5.10' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/web/XChemWeb.py b/web/XChemWeb.py index bd1e6a23..f9554aa4 100755 --- a/web/XChemWeb.py +++ b/web/XChemWeb.py @@ -55,6 +55,7 @@ def prepare(self): if eventMap: self.Logfile.insert('%s: using the following event map -> %s' %(xtal,eventMap)) self.cut_and_copy_map(xtal, ligand+'.pdb', eventMap, xtal + '_' + ligand + '_event.ccp4','F','PHIF') + eventMap = xtal + '_' + ligand + '_event.ccp4' else: self.Logfile.error('%s: value of event map -> %s' %(xtal,eventMap)) x,y,z = self.pdb.get_centre_of_gravity_of_residue(ligand) @@ -69,6 +70,10 @@ def prepare(self): resoHigh = self.db_dict['DataProcessingResolutionHigh'] spg = self.db_dict['RefinementSpaceGroup'] unitCell = self.db_dict['DataProcessingUnitCell'] + t = '' + for ax in unitCell.split(): + t += str(round(float(ax),1)) + ' ' + unitCell = t[:-1] os.chdir(os.path.join(self.projectDir,xtal)) FWT = xtal + '-' + ligand + '_2fofc.ccp4' self.cut_and_copy_map(xtal, ligand + '.pdb', '2fofc.map', FWT,'FWT','PHWT') From c8e28a0fd2db9ba65f3a2f0be28d5e50bd3a8b97 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 10 Mar 2020 13:57:42 +0000 Subject: [PATCH 022/358] v1.5.11 (10/03/2020) (#301) - added linking of covalent binders for PanDDA models (refine.split-bound.pdb) - remove links to refine.output... PDB files after refinement --- ChangeLog.txt | 4 + gui_scripts/settings_preferences.py | 2 +- lib/XChemCootNew.py | 7 +- lib/XChemLog.py | 2 +- lib/XChemRefine.py | 1148 ++++++++++++++------------- 5 files changed, 613 insertions(+), 550 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index ef9fe4c3..d21c91b6 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.5.11 (10/03/2020) +- added linking of covalent binders for PanDDA models (refine.split-bound.pdb) +- remove links to refine.output... PDB files after refinement + v1.5.10 (05/03/2020) - bug fix: correct name of event map in files directory diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 36f69063..811a5584 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.10' + xce_object.xce_version = 'v1.5.11' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemCootNew.py b/lib/XChemCootNew.py index 460b3bc5..e07e01c3 100755 --- a/lib/XChemCootNew.py +++ b/lib/XChemCootNew.py @@ -1400,7 +1400,7 @@ def start_refinement(self): XChemRefine.panddaRefine(self.project_directory, self.xtalID, self.compoundID, self.data_source).RunQuickRefine(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, - self.refinementProtocol) + self.refinementProtocol, self.covLinkAtomSpec) else: ####################################################### # create folder for new refinement cycle and check if free.mtz exists @@ -1458,7 +1458,10 @@ def show_potential_link(self,*clicks): imol_protein = None for imol in coot_utils_XChem.molecule_number_list(): print '>',coot.molecule_name(imol) - if coot.molecule_name(imol).endswith(self.pdb_style) or coot.molecule_name(imol).endswith('init.pdb') or coot.molecule_name(imol).endswith('dimple.pdb'): + if coot.molecule_name(imol).endswith(self.pdb_style) or \ + coot.molecule_name(imol).endswith('init.pdb') or \ + coot.molecule_name(imol).endswith('dimple.pdb') or \ + coot.molecule_name(imol).endswith(self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb'): imol_protein = imol break diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 82c3eb68..6ddff51a 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 05/03/2020 #\n' + ' # Date: 10/03/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 3c7933a9..d113d402 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -793,7 +793,41 @@ def __init__(self,ProjectPath,xtalID,compoundID,datasource): self.prefix = 'refine' self.datasource=datasource - def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refinementProtocol): + + def make_covalent_link(self,covLinkAtomSpec,Logfile): + residuesToModify = ['CYS','SER'] + + atom1 = covLinkAtomSpec[1][5] + atom2 = covLinkAtomSpec[2][5] + residue_1 = covLinkAtomSpec[3] + residue_2 = covLinkAtomSpec[4] + + if residue_2 in residuesToModify: + bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' %(residue_1,self.compoundID,atom1,residue_2,atom2) + else: + bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' % (residue_2, self.compoundID, atom2, residue_1, atom1) + + os.chdir(os.path.join(self.ProjectPath,self.xtalID)) + f = open('covalent_bond.txt','w') + f.write(bond_text) + f.close() + + # seems somewhat unncessary, but acedrg does not like some certain descriptions generated by phenix.elbow + os.system('acedrg -c %s.cif -o %s_acedrg' %(self.compoundID,self.compoundID)) + + os.system('acedrg -L covalent_bond.txt -o %s' %self.compoundID) + + if os.path.isfile('%s_link.cif' %self.compoundID): + Logfile.insert('succefully created link file %s_link.cif' %self.compoundID) + os.system('/bin/rm %s.cif' %self.compoundID) + os.system('ln -s %s_link.cif %s.cif' %(self.compoundID,self.compoundID)) + else: + Logfile.error('could not create linkfile; please check logs in %s/%s' %(self.ProjectPath,self.xtalID)) + + + + + def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refinementProtocol,covLinkAtomSpec): Logfile=XChemLog.updateLog(xce_logfile) Logfile.insert('preparing files for giant.quick_refine') # panddaSerial because giant.quick_refine writes Refine_0001 instead of Refine_1 @@ -802,6 +836,9 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine make_all_links = True add_links_line = '' + if covLinkAtomSpec is not None: + self.make_covalent_link(covLinkAtomSpec,Logfile) + # first check if refinement is ongoing and exit if yes if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'REFINEMENT_IN_PROGRESS')): # coot.info_dialog('*** REFINEMENT IN PROGRESS ***') @@ -869,6 +906,25 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine ) Logfile.insert(cmd+'\n') os.system(cmd) + link_line = '' + for line in open(bound_state): + if line.startswith('LINK'): + Logfile.insert('found LINK: ' + line[:-1]) + link_line += line + if link_line != '': + if os.path.isfile('multi-state-model.pdb'): + for line in open('multi-state-model.pdb'): + if line.startswith('CRYST'): + Logfile.insert('adding LINK lines to multi-state-model.pdb') + out = link_line + line + else: + out += line + Logfile.insert('writing updated multi-state-model.pdb') + f = open('multi-state-model.pdb','w') + f.write(out) + f.close() + else: + Logfile.error('cannot find multi-state-model.pdb') else: Logfile.error('cannot find modified version of bound state in %s' %os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) return None @@ -1031,9 +1087,9 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine if make_all_links: add_links_line = ( 'ln -s Refine_%s/refine_%s.split.bound-state.pdb ./refine.split.bound-state.pdb\n' %(panddaSerial,Serial)+ - 'ln -s Refine_%s/refine_%s.split.ground-state.pdb ./refine.split.ground-state.pdb\n' %(panddaSerial,Serial)+ - 'ln -s Refine_%s/refine_%s.output.bound-state.pdb ./refine.output.bound-state.pdb\n' %(panddaSerial,Serial)+ - 'ln -s Refine_%s/refine_%s.output.ground-state.pdb ./refine.output.ground-state.pdb\n' %(panddaSerial,Serial) + 'ln -s Refine_%s/refine_%s.split.ground-state.pdb ./refine.split.ground-state.pdb\n' %(panddaSerial,Serial) +# 'ln -s Refine_%s/refine_%s.output.bound-state.pdb ./refine.output.bound-state.pdb\n' %(panddaSerial,Serial)+ +# 'ln -s Refine_%s/refine_%s.output.ground-state.pdb ./refine.output.ground-state.pdb\n' %(panddaSerial,Serial) ) @@ -1326,550 +1382,550 @@ def GetRefinementHistory(self): return(sorted(RefinementCycle),RcrystList,RfreeList) -class RefineOld(object): - - def __init__(self,ProjectPath,xtalID,compoundID,datasource): - self.ProjectPath = ProjectPath - self.xtalID = xtalID - self.compoundID = compoundID - self.prefix = 'refine' - self.datasource=datasource - - def GetSerial(self): - # check if there were already previous refinements - # if no: create a folder Refine_1 - # if yes: create a folder Refine_ - temp = [] - found = 0 - if os.path.isdir(os.path.join(self.ProjectPath,self.xtalID)): - for item in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): - if item.startswith(os.path.join(self.ProjectPath,self.xtalID,'Refine_')): - print int(item[item.rfind('_')+1:]) - temp.append(int(item[item.rfind('_')+1:])) - found = 1 - if found: - Serial = max(temp) + 1 - else: - Serial=1 - return Serial - - - def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile): - Logfile=XChemLog.updateLog(xce_logfile) - Serial=str(Serial) - - # first check if refinement is ongoing and exit if yes - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'REFINEMENT_IN_PROGRESS')): -# coot.info_dialog('*** REFINEMENT IN PROGRESS ***') - Logfile.insert('cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' %self.xtalID) - return None - - ####################################################### - # HKLIN & HKLOUT - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz')): - RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz \\\n') - elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): - RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') - else: - Logfile.insert('%s: cannot find HKLIN for refinement; aborting...' %self.xtalID) - return None - RefmacParams['HKLOUT']='HKLOUT '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz \\\n') - - ####################################################### - # XYZIN & XYZOUT - RefmacParams['XYZIN']='XYZIN '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb \\\n') - RefmacParams['XYZOUT']='XYZOUT '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.pdb \\\n') - - ####################################################### - # LIBIN & LIBOUT - found_cif=False - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif')): - found_cif=True - # in cases where multiple liagnds are present (e.g. NOG, ATP) the user for now needs to put - # the respective dictionary into the xtalID folder - # need to think of a better mechanism in the future - additional_cif=False - additional_cif_file='' - for file in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): - if file.endswith('.cif'): - if self.compoundID not in file: - additional_cif_file=file -# additional_cif=True <- should be true, but need to check this part of the code! 16/11/2016 - additional_cif=False - if additional_cif: - Cmds = ( - '#!'+os.getenv('SHELL')+'\n' - '\n' - '$CCP4/bin/libcheck << eof \n' - '_Y\n' - '_FILE_L '+os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif')+'\n' - '_FILE_L2 '+additional_cif_file+'\n' - '_FILE_O '+os.path.join(self.ProjectPath,self.xtalID,'combined_cif')+'\n' - '_END\n' - 'eof\n' - ) - os.chdir(os.path.join(self.ProjectPath,self.xtalID)) - print Cmds - os.system(Cmds) - RefmacParams['LIBIN']='LIBIN '+self.ProjectPath+'/'+self.xtalID+'/combined_cif.lib \\\n' - else: - RefmacParams['LIBIN']='LIBIN '+self.ProjectPath+'/'+self.xtalID+'/'+self.compoundID+'.cif \\\n' - RefmacParams['LIBOUT']='LIBOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine_'+Serial+'.cif \\\n' - if not found_cif: - # this should actually not be necessary, but the following scenario can happen: - # if a new data source is created from a file system, but smiles and compoundID where not updated; - # so the ligand may still be in the structure, but since the compoundID is unknown to the datasource, - # its restraints won't be read in and refmac will fail - for file in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): - if file.endswith('.cif'): - RefmacParams['LIBIN']='LIBIN '+file+' \\\n' - RefmacParams['LIBOUT']='LIBOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine_'+Serial+'.cif \\\n' - break - - ####################################################### - # TLSIN & TLSOUT - findTLS='\n' - TLSphenix='' - if RefmacParams['TLS'].startswith('refi'): - if external_software['phenix.find_tls_groups']: - findTLS=os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','phenix_find_TLS_groups.py')+' in.pdb\n' - RefmacParams['TLSIN']='TLSIN '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refmac.tls \\\n' - RefmacParams['TLSOUT']='TLSOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine.tls \\\n' - TLSphenix=' phenix.tls ' - else: - RefmacParams['TLS']='\n' - - +#class RefineOld(object): +# +# def __init__(self,ProjectPath,xtalID,compoundID,datasource): +# self.ProjectPath = ProjectPath +# self.xtalID = xtalID +# self.compoundID = compoundID +# self.prefix = 'refine' +# self.datasource=datasource +# +# def GetSerial(self): +# # check if there were already previous refinements +# # if no: create a folder Refine_1 +# # if yes: create a folder Refine_ +# temp = [] +# found = 0 +# if os.path.isdir(os.path.join(self.ProjectPath,self.xtalID)): +# for item in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): +# if item.startswith(os.path.join(self.ProjectPath,self.xtalID,'Refine_')): +# print int(item[item.rfind('_')+1:]) +# temp.append(int(item[item.rfind('_')+1:])) +# found = 1 +# if found: +# Serial = max(temp) + 1 +# else: +# Serial=1 +# return Serial +# +# +# def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile): +# Logfile=XChemLog.updateLog(xce_logfile) +# Serial=str(Serial) +# +# # first check if refinement is ongoing and exit if yes +# if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'REFINEMENT_IN_PROGRESS')): +## coot.info_dialog('*** REFINEMENT IN PROGRESS ***') +# Logfile.insert('cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' %self.xtalID) +# return None +# # ####################################################### -# # create folder for new refinement cycle -# os.mkdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) +# # HKLIN & HKLOUT +# if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz')): +# RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz \\\n') +# elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): +# RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') +# else: +# Logfile.insert('%s: cannot find HKLIN for refinement; aborting...' %self.xtalID) +# return None +# RefmacParams['HKLOUT']='HKLOUT '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz \\\n') # # ####################################################### -# # write PDB file -# # now take protein pdb file and write it to newly create Refine_ folder -# # note: the user has to make sure that the ligand file was merged into main file -# for item in coot_utils_XChem.molecule_number_list(): -# if coot.molecule_name(item).endswith(self.prefix+'.pdb'): -# coot.write_pdb_file(item,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb')) - - ####################################################### - # PANDDAs stuff - # only use occupancy refinement if EVENT map is present - occupancy_refinement='' - if external_software['giant.create_occupancy_params']: - os.chdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) - cmd = ( '#!'+os.getenv('SHELL')+'\n' - 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-sh')+'\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' - "giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'\n" ) +# # XYZIN & XYZOUT +# RefmacParams['XYZIN']='XYZIN '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb \\\n') +# RefmacParams['XYZOUT']='XYZOUT '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.pdb \\\n') +# +# ####################################################### +# # LIBIN & LIBOUT +# found_cif=False +# if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif')): +# found_cif=True +# # in cases where multiple liagnds are present (e.g. NOG, ATP) the user for now needs to put +# # the respective dictionary into the xtalID folder +# # need to think of a better mechanism in the future +# additional_cif=False +# additional_cif_file='' +# for file in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): +# if file.endswith('.cif'): +# if self.compoundID not in file: +# additional_cif_file=file +## additional_cif=True <- should be true, but need to check this part of the code! 16/11/2016 +# additional_cif=False +# if additional_cif: +# Cmds = ( +# '#!'+os.getenv('SHELL')+'\n' +# '\n' +# '$CCP4/bin/libcheck << eof \n' +# '_Y\n' +# '_FILE_L '+os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif')+'\n' +# '_FILE_L2 '+additional_cif_file+'\n' +# '_FILE_O '+os.path.join(self.ProjectPath,self.xtalID,'combined_cif')+'\n' +# '_END\n' +# 'eof\n' +# ) +# os.chdir(os.path.join(self.ProjectPath,self.xtalID)) +# print Cmds +# os.system(Cmds) +# RefmacParams['LIBIN']='LIBIN '+self.ProjectPath+'/'+self.xtalID+'/combined_cif.lib \\\n' +# else: +# RefmacParams['LIBIN']='LIBIN '+self.ProjectPath+'/'+self.xtalID+'/'+self.compoundID+'.cif \\\n' +# RefmacParams['LIBOUT']='LIBOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine_'+Serial+'.cif \\\n' +# if not found_cif: +# # this should actually not be necessary, but the following scenario can happen: +# # if a new data source is created from a file system, but smiles and compoundID where not updated; +# # so the ligand may still be in the structure, but since the compoundID is unknown to the datasource, +# # its restraints won't be read in and refmac will fail +# for file in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): +# if file.endswith('.cif'): +# RefmacParams['LIBIN']='LIBIN '+file+' \\\n' +# RefmacParams['LIBOUT']='LIBOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine_'+Serial+'.cif \\\n' +# break +# +# ####################################################### +# # TLSIN & TLSOUT +# findTLS='\n' +# TLSphenix='' +# if RefmacParams['TLS'].startswith('refi'): +# if external_software['phenix.find_tls_groups']: +# findTLS=os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','phenix_find_TLS_groups.py')+' in.pdb\n' +# RefmacParams['TLSIN']='TLSIN '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refmac.tls \\\n' +# RefmacParams['TLSOUT']='TLSOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine.tls \\\n' +# TLSphenix=' phenix.tls ' +# else: +# RefmacParams['TLS']='\n' +# +# +## ####################################################### +## # create folder for new refinement cycle +## os.mkdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) +## +## ####################################################### +## # write PDB file +## # now take protein pdb file and write it to newly create Refine_ folder +## # note: the user has to make sure that the ligand file was merged into main file +## for item in coot_utils_XChem.molecule_number_list(): +## if coot.molecule_name(item).endswith(self.prefix+'.pdb'): +## coot.write_pdb_file(item,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb')) +# +# ####################################################### +# # PANDDAs stuff +# # only use occupancy refinement if EVENT map is present +# occupancy_refinement='' +# if external_software['giant.create_occupancy_params']: +# os.chdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) +# cmd = ( '#!'+os.getenv('SHELL')+'\n' +# 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' +# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-sh')+'\n' +# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' +# "giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'\n" ) +## os.system("giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'") +## os.system(cmd) +# print "==> XCE: running giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'" # os.system("giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'") -# os.system(cmd) - print "==> XCE: running giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'" - os.system("giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'") - # quick fix for the moment; need to talk to Nick since this should not be necessary - try: - params_file = fileinput.input('refmac_refine.params',inplace=True) - for line in params_file: - if 'incomplete' in line: - line=line.replace('incomplete','complete') - print line, -# elif 'occupancy refine' in line: -# line=line.replace('occupancy refine','occupancy refine ncycle 10\noccupancy refine') -# print line, - else: - print line, - params_file.close() - except OSError: - # this may happen in case giant.create_occupancy_params did not produce a params output file - pass - - print '==> XCE: waiting 5 seconds for giant.create_occupancy_params to finish...' - time.sleep(5) - print '==> XCE: done!' - - print '==> XCE: assembling refmac.csh' - - create_bound_conformation='' - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac_refine.params')): - occupancy_refinement='@refmac_refine.params\n' - create_bound_conformation="/bin/rm *bound.pdb\ngiant.strip_conformations pdb=refine.pdb suffix='.bound.pdb'\n" - - ####################################################### - # we write 'REFINEMENT_IN_PROGRESS' immediately to avoid unncessary refiment - os.chdir(os.path.join(self.ProjectPath,self.xtalID)) - os.system('touch REFINEMENT_IN_PROGRESS') - - ####################################################### - # clean up! - # and remove all files which will be re-created by current refinement cycle - os.system('/bin/rm refine.pdb refine.mtz validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log') - - if external_software['qsub']: - pbs_line='#PBS -joe -N XCE_refmac\n' - else: - pbs_line='\n' - - ####################################################### - # weight - if str(RefmacParams['MATRIX_WEIGHT']).lower() == 'auto': - weight='weight AUTO\n' - else: - weight='weight matrix '+str(RefmacParams['MATRIX_WEIGHT'])+'\n' - - ####################################################### - # PANDDA validation @ spider plot - spider_plot='' - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-ensemble-model.pdb')): - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): - pdb_two=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-ensemble-model.pdb') - mtz_two=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz') - pdb_one=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.pdb') - mtz_one=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz') - spider_plot='$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/resort_ligand_atoms.py %s %s\n\n' %(pdb_two,pdb_one) - spider_plot+='giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' %(pdb_one,mtz_one,pdb_two,mtz_two) -# spider_plot='giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' %(pdb_one,mtz_one,pdb_two,mtz_two) - - ####################################################### - # PHENIX stuff (if working at DLS) - module_load='' - if os.getcwd().startswith('/dls'): - module_load='module load phenix\n' - - source ='' - if 'bash' in os.getenv('SHELL'): - source = ( - 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' - '\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-sh')+'\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' ) - elif 'csh' in os.getenv('SHELL'): - source = ( - 'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n' - '\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-csh')+'\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh')+'\n' ) - - - refmacCmds = ( - '#!'+os.getenv('SHELL')+'\n' - +pbs_line+ - '\n' - + module_load + - '\n' - + source + - 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'\n' - '\n' - '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(self.datasource,self.xtalID,'RefinementStatus','running') + - '\n' - +findTLS+ - 'refmac5 ' - +RefmacParams['HKLIN'] - +RefmacParams['HKLOUT'] - +RefmacParams['XYZIN'] - +RefmacParams['XYZOUT'] - +RefmacParams['LIBIN'] - +RefmacParams['LIBOUT'] - +RefmacParams['TLSIN'] - +RefmacParams['TLSOUT']+ - ' << EOF > refmac.log\n' - 'make -\n' - ' hydrogen ALL -\n' - ' hout NO -\n' - ' peptide NO -\n' - ' cispeptide YES -\n' - ' ssbridge YES -\n' - ' symmetry YES -\n' - ' sugar YES -\n' - ' connectivity NO -\n' - ' link NO\n' - +RefmacParams['NCS']+ - 'refi -\n' - ' type REST -\n' - ' resi MLKF -\n' - ' meth CGMAT -\n' - +RefmacParams['BREF'] - +RefmacParams['TLS'] - +RefmacParams['TWIN']+ - 'ncyc '+RefmacParams['NCYCLES']+'\n' - 'scal -\n' - ' type SIMP -\n' - ' LSSC -\n' - ' ANISO -\n' - ' EXPE\n' - +weight+ - 'solvent YES\n' - +occupancy_refinement+ - 'monitor MEDIUM -\n' - ' torsion 10.0 -\n' - ' distance 10.0 -\n' - ' angle 10.0 -\n' - ' plane 10.0 -\n' - ' chiral 10.0 -\n' - ' bfactor 10.0 -\n' - ' bsphere 10.0 -\n' - ' rbond 10.0 -\n' - ' ncsr 10.0\n' - 'labin FP=F SIGFP=SIGF FREE=FreeR_flag\n' - 'labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM\n' - +RefmacParams['TLSADD']+'\n' - 'DNAME '+self.xtalID+'\n' - 'END\n' - 'EOF\n' - '\n' - +spider_plot+ - '\n' - 'phenix.molprobity refine_%s.pdb refine_%s.mtz\n' %(Serial,Serial)+ - '/bin/mv molprobity.out refine_molprobity.log\n' - 'mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n' %(Serial,Serial)+ - 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' - '#ln -s %s/%s/Refine_%s/refine_%s.pdb refine.pdb\n' %(self.ProjectPath,self.xtalID,Serial,Serial)+ - '#ln -s %s/%s/Refine_%s/refine_%s.mtz refine.mtz\n' %(self.ProjectPath,self.xtalID,Serial,Serial)+ - 'ln -s ./Refine_%s/refine_%s.pdb refine.pdb\n' %(Serial,Serial)+ - 'ln -s ./Refine_%s/refine_%s.mtz refine.mtz\n' %(Serial,Serial)+ - '\n' - +create_bound_conformation+ - '\n' - 'ln -s Refine_%s/validate_ligands.txt .\n' %Serial+ - 'ln -s Refine_%s/refine_molprobity.log .\n' %Serial+ - 'mmtbx.validation_summary refine.pdb > validation_summary.txt\n' - '\n' - 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' - 'labin F1=FWT PHI=PHWT\n' - 'EOF\n' - '\n' - 'fft hklin refine.mtz mapout fofc.map << EOF\n' - 'labin F1=DELFWT PHI=PHDELWT\n' - 'EOF\n' - '\n' - '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+ - ' %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial))+ - '\n' - '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' %(self.ProjectPath,self.xtalID)+ - '\n' - ) - - Logfile.insert('writing refinement shell script to'+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac.csh')) - cmd = open(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac.csh'),'w') - cmd.write(refmacCmds) - cmd.close() - - os.chdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) -# os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) - Logfile.insert('changing directory to %s' %(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial))) - if external_software['qsub']: - Logfile.insert('starting refinement on cluster') - os.system('qsub -P labxchem refmac.csh') - elif external_software['qsub_remote'] != '': - Logfile.insert('starting refinement on remote cluster') - remote_command=external_software['qsub_remote'].replace('qsub','cd %s; qsub' %os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) - os.system('%s -P labxchem refmac.csh' %remote_command) - print '%s -P labxchem refmac.csh' %remote_command - else: - Logfile.insert('changing permission of refmac.csh: chmod +x refmac.csh') - os.system('chmod +x refmac.csh') - Logfile.insert('starting refinement on local machine') - os.system('./refmac.csh &') -# if '/work/' in os.getcwd(): -# os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) -# else: -# os.system('./refmac.csh &') - - - - - def RefinementParams(self,RefmacParams): - self.RefmacParams=RefmacParams - self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) - self.window.connect("delete_event", gtk.main_quit) - self.window.set_border_width(10) - self.window.set_title("Refmac Parameters") - self.vbox = gtk.VBox() - - self.hbox1=gtk.HBox() - self.hbox1.add(gtk.Label('Refine')) - self.cb = gtk.combo_box_new_text() - self.cb.connect("changed", self.ChooseBfacRefinement) - for item in ['isotropic','anisotropic']: - self.cb.append_text(item) - if 'ISOT' in self.RefmacParams['BREF']: - self.cb.set_active(0) - if 'ANIS' in self.RefmacParams['BREF']: - self.cb.set_active(1) - self.hbox1.add(self.cb) - self.hbox1.add(gtk.Label('temperature factors')) - self.vbox.add(self.hbox1) - - self.hbox2=gtk.HBox() - self.hbox2.add(gtk.Label('Number of Cycles: ')) - self.Ncycles=gtk.Entry() - self.Ncycles.add_events(gtk.gdk.KEY_RELEASE_MASK) - self.Ncycles.connect("key-release-event", self.on_key_release_Ncycles) - self.Ncycles.set_text(self.RefmacParams['NCYCLES']) - self.hbox2.add(self.Ncycles) - self.vbox.add(self.hbox2) - - self.hbox3=gtk.HBox() - self.hbox3.add(gtk.Label('MATRIX WEIGHT: ')) - self.MATRIX_WEIGHT=gtk.Entry() - self.MATRIX_WEIGHT.add_events(gtk.gdk.KEY_RELEASE_MASK) - self.MATRIX_WEIGHT.connect("key-release-event", self.on_key_release_MATRIX_WEIGHT) - self.MATRIX_WEIGHT.set_text(self.RefmacParams['MATRIX_WEIGHT']) - self.hbox3.add(self.MATRIX_WEIGHT) - self.vbox.add(self.hbox3) - - self.TLS = gtk.CheckButton('TLS (find TLS groups with phenix.find_tls_groups)') - self.TLS.connect("toggled", self.TLSCallback) - if self.RefmacParams['TLS']=='refi tlsc 10\n': self.TLS.set_active(True) - self.vbox.pack_start(self.TLS,False) - - self.NCS = gtk.CheckButton('NCS (if applicable') - self.NCS.connect("toggled", self.NCSCallback) - if self.RefmacParams['NCS']=='NCSR LOCAL\n': self.NCS.set_active(True) - self.vbox.pack_start(self.NCS,False) - - self.TWIN = gtk.CheckButton('Twin?') - self.TWIN.connect("toggled", self.TWINCallback) - if self.RefmacParams['TWIN']=='TWIN\n': self.TWIN.set_active(True) - self.vbox.pack_start(self.TWIN,False) - - self.OKbutton = gtk.Button(label="OK") - self.OKbutton.connect("clicked",self.OK) - self.vbox.add(self.OKbutton) - - self.window.add(self.vbox) - self.window.show_all() - return self.RefmacParams - - - def TLSCallback(self, widget): - if widget.get_active(): - self.RefmacParams['TLS']='refi tlsc 10\n' - self.RefmacParams['TLSIN']='refmac.tls\n' - self.RefmacParams['TLSOUT']='out.tls\n' - self.RefmacParams['TLSADD']='TLSO ADDU\n' - else: - self.RefmacParams['TLS']='' - self.RefmacParams['TLSIN']='' - self.RefmacParams['TLSOUT']='' - self.RefmacParams['TLSADD']='' - return self.RefmacParams - - def NCSCallback(self, widget): - if widget.get_active(): - self.RefmacParams['NCS']='NCSR LOCAL\n' - else: - self.RefmacParams['NCS']='' - return self.RefmacParams - - def ChooseBfacRefinement(self,widget): - if widget.get_active_text()=='isotropic': - self.RefmacParams['BREF']=' bref ISOT\n' - if widget.get_active_text()=='anisotropic': - self.RefmacParams['BREF']=' bref ANIS\n' - return self.RefmacParams - - def on_key_release_Ncycles(self, widget, event): - print widget.get_text() - self.RefmacParams['NCYCLES'] = widget.get_text() - return self.RefmacParams - - def on_key_release_MATRIX_WEIGHT(self, widget, event): - self.RefmacParams['MATRIX_WEIGHT'] = widget.get_text() - return self.RefmacParams - - def TWINCallback(self, widget): - if widget.get_active(): - self.RefmacParams['TWIN']='TWIN\n' - else: - self.RefmacParams['TWIN']='' - return self.RefmacParams - - def OK(self,widget): - self.window.destroy() - - - def ParamsFromPreviousCycle(self,Serial): - - RefmacParams={ 'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '' } - - if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): - for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): - if line.startswith('refi tlsc'): - RefmacParams['TLS']=line - if line.startswith('TLSO'): - RefmacParams['TLSADD']=line - if line.startswith('NCSR LOCAL'): - RefmacParams['NCS']=line - if line.startswith(' bref '): - RefmacParams['BREF']=line - if line.startswith('ncyc'): - RefmacParams['Ncycles'] = line.split()[1] - if line.startswith('weight'): - RefmacParams['MATRIX_WEIGHT'] = line.split()[len(line.split())-1] - if line.startswith('TWIN'): - RefmacParams['TWIN']=line - - return RefmacParams - - def GetRefinementHistory(self): -# RefinementHistory='' - RefinementCycle = [] - RcrystList=[] - RfreeList=[] - - found = False - for item in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): - if item.startswith(os.path.join(self.ProjectPath,self.xtalID,'Refine_')): - print item[item.rfind('_')+1:] - RefinementCycle.append(int(item[item.rfind('_')+1:])) - found = True - if found: - for cycle in sorted(RefinementCycle): -# for cycle in RefinementCycle: -# Rcryst=0 -# Rfree=0 -# LigandCC=0 - try: - found_Rcryst=False - found_Rfree=False - newestPDB = max(glob.iglob(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/refine_'+str(cycle)+'.pdb'), key=os.path.getctime) - for line in open(newestPDB): - if line.startswith('REMARK 3 R VALUE (WORKING + TEST SET) :'): - Rcryst = line.split()[9] - RcrystList.append(float(Rcryst)) - found_Rcryst=True - if line.startswith('REMARK 3 FREE R VALUE :'): - Rfree = line.split()[6] - RfreeList.append(float(Rfree)) - found_Rfree=True - if not found_Rcryst: - RcrystList.append(0) - if not found_Rfree: - RfreeList.append(0) -# if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): -# for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): -# if line.startswith('| LIG'): LigandCC = line.split()[6] -# RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' - except ValueError: - RcrystList.append(0) - RfreeList.append(0) -# RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' - else: - RefinementCycle = [0] - RcrystList=[0] - RfreeList=[0] - print RefinementCycle,RcrystList,RfreeList - return(sorted(RefinementCycle),RcrystList,RfreeList) - +# # quick fix for the moment; need to talk to Nick since this should not be necessary +# try: +# params_file = fileinput.input('refmac_refine.params',inplace=True) +# for line in params_file: +# if 'incomplete' in line: +# line=line.replace('incomplete','complete') +# print line, +## elif 'occupancy refine' in line: +## line=line.replace('occupancy refine','occupancy refine ncycle 10\noccupancy refine') +## print line, +# else: +# print line, +# params_file.close() +# except OSError: +# # this may happen in case giant.create_occupancy_params did not produce a params output file +# pass +# +# print '==> XCE: waiting 5 seconds for giant.create_occupancy_params to finish...' +# time.sleep(5) +# print '==> XCE: done!' +# +# print '==> XCE: assembling refmac.csh' +# +# create_bound_conformation='' +# if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac_refine.params')): +# occupancy_refinement='@refmac_refine.params\n' +# create_bound_conformation="/bin/rm *bound.pdb\ngiant.strip_conformations pdb=refine.pdb suffix='.bound.pdb'\n" +# +# ####################################################### +# # we write 'REFINEMENT_IN_PROGRESS' immediately to avoid unncessary refiment +# os.chdir(os.path.join(self.ProjectPath,self.xtalID)) +# os.system('touch REFINEMENT_IN_PROGRESS') +# +# ####################################################### +# # clean up! +# # and remove all files which will be re-created by current refinement cycle +# os.system('/bin/rm refine.pdb refine.mtz validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log') +# +# if external_software['qsub']: +# pbs_line='#PBS -joe -N XCE_refmac\n' +# else: +# pbs_line='\n' +# +# ####################################################### +# # weight +# if str(RefmacParams['MATRIX_WEIGHT']).lower() == 'auto': +# weight='weight AUTO\n' +# else: +# weight='weight matrix '+str(RefmacParams['MATRIX_WEIGHT'])+'\n' +# +# ####################################################### +# # PANDDA validation @ spider plot +# spider_plot='' +# if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-ensemble-model.pdb')): +# if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): +# pdb_two=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-ensemble-model.pdb') +# mtz_two=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz') +# pdb_one=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.pdb') +# mtz_one=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz') +# spider_plot='$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/resort_ligand_atoms.py %s %s\n\n' %(pdb_two,pdb_one) +# spider_plot+='giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' %(pdb_one,mtz_one,pdb_two,mtz_two) +## spider_plot='giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' %(pdb_one,mtz_one,pdb_two,mtz_two) +# +# ####################################################### +# # PHENIX stuff (if working at DLS) +# module_load='' +# if os.getcwd().startswith('/dls'): +# module_load='module load phenix\n' +# +# source ='' +# if 'bash' in os.getenv('SHELL'): +# source = ( +# 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' +# '\n' +# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-sh')+'\n' +# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' ) +# elif 'csh' in os.getenv('SHELL'): +# source = ( +# 'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n' +# '\n' +# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-csh')+'\n' +# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh')+'\n' ) +# +# +# refmacCmds = ( +# '#!'+os.getenv('SHELL')+'\n' +# +pbs_line+ +# '\n' +# + module_load + +# '\n' +# + source + +# 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'\n' +# '\n' +# '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(self.datasource,self.xtalID,'RefinementStatus','running') + +# '\n' +# +findTLS+ +# 'refmac5 ' +# +RefmacParams['HKLIN'] +# +RefmacParams['HKLOUT'] +# +RefmacParams['XYZIN'] +# +RefmacParams['XYZOUT'] +# +RefmacParams['LIBIN'] +# +RefmacParams['LIBOUT'] +# +RefmacParams['TLSIN'] +# +RefmacParams['TLSOUT']+ +# ' << EOF > refmac.log\n' +# 'make -\n' +# ' hydrogen ALL -\n' +# ' hout NO -\n' +# ' peptide NO -\n' +# ' cispeptide YES -\n' +# ' ssbridge YES -\n' +# ' symmetry YES -\n' +# ' sugar YES -\n' +# ' connectivity NO -\n' +# ' link NO\n' +# +RefmacParams['NCS']+ +# 'refi -\n' +# ' type REST -\n' +# ' resi MLKF -\n' +# ' meth CGMAT -\n' +# +RefmacParams['BREF'] +# +RefmacParams['TLS'] +# +RefmacParams['TWIN']+ +# 'ncyc '+RefmacParams['NCYCLES']+'\n' +# 'scal -\n' +# ' type SIMP -\n' +# ' LSSC -\n' +# ' ANISO -\n' +# ' EXPE\n' +# +weight+ +# 'solvent YES\n' +# +occupancy_refinement+ +# 'monitor MEDIUM -\n' +# ' torsion 10.0 -\n' +# ' distance 10.0 -\n' +# ' angle 10.0 -\n' +# ' plane 10.0 -\n' +# ' chiral 10.0 -\n' +# ' bfactor 10.0 -\n' +# ' bsphere 10.0 -\n' +# ' rbond 10.0 -\n' +# ' ncsr 10.0\n' +# 'labin FP=F SIGFP=SIGF FREE=FreeR_flag\n' +# 'labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM\n' +# +RefmacParams['TLSADD']+'\n' +# 'DNAME '+self.xtalID+'\n' +# 'END\n' +# 'EOF\n' +# '\n' +# +spider_plot+ +# '\n' +# 'phenix.molprobity refine_%s.pdb refine_%s.mtz\n' %(Serial,Serial)+ +# '/bin/mv molprobity.out refine_molprobity.log\n' +# 'mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n' %(Serial,Serial)+ +# 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' +# '#ln -s %s/%s/Refine_%s/refine_%s.pdb refine.pdb\n' %(self.ProjectPath,self.xtalID,Serial,Serial)+ +# '#ln -s %s/%s/Refine_%s/refine_%s.mtz refine.mtz\n' %(self.ProjectPath,self.xtalID,Serial,Serial)+ +# 'ln -s ./Refine_%s/refine_%s.pdb refine.pdb\n' %(Serial,Serial)+ +# 'ln -s ./Refine_%s/refine_%s.mtz refine.mtz\n' %(Serial,Serial)+ +# '\n' +# +create_bound_conformation+ +# '\n' +# 'ln -s Refine_%s/validate_ligands.txt .\n' %Serial+ +# 'ln -s Refine_%s/refine_molprobity.log .\n' %Serial+ +# 'mmtbx.validation_summary refine.pdb > validation_summary.txt\n' +# '\n' +# 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' +# 'labin F1=FWT PHI=PHWT\n' +# 'EOF\n' +# '\n' +# 'fft hklin refine.mtz mapout fofc.map << EOF\n' +# 'labin F1=DELFWT PHI=PHDELWT\n' +# 'EOF\n' +# '\n' +# '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+ +# ' %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial))+ +# '\n' +# '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' %(self.ProjectPath,self.xtalID)+ +# '\n' +# ) +# +# Logfile.insert('writing refinement shell script to'+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac.csh')) +# cmd = open(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac.csh'),'w') +# cmd.write(refmacCmds) +# cmd.close() +# +# os.chdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) +## os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) +# Logfile.insert('changing directory to %s' %(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial))) +# if external_software['qsub']: +# Logfile.insert('starting refinement on cluster') +# os.system('qsub -P labxchem refmac.csh') +# elif external_software['qsub_remote'] != '': +# Logfile.insert('starting refinement on remote cluster') +# remote_command=external_software['qsub_remote'].replace('qsub','cd %s; qsub' %os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) +# os.system('%s -P labxchem refmac.csh' %remote_command) +# print '%s -P labxchem refmac.csh' %remote_command +# else: +# Logfile.insert('changing permission of refmac.csh: chmod +x refmac.csh') +# os.system('chmod +x refmac.csh') +# Logfile.insert('starting refinement on local machine') +# os.system('./refmac.csh &') +## if '/work/' in os.getcwd(): +## os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) +## else: +## os.system('./refmac.csh &') +# +# +# +# +# def RefinementParams(self,RefmacParams): +# self.RefmacParams=RefmacParams +# self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) +# self.window.connect("delete_event", gtk.main_quit) +# self.window.set_border_width(10) +# self.window.set_title("Refmac Parameters") +# self.vbox = gtk.VBox() +# +# self.hbox1=gtk.HBox() +# self.hbox1.add(gtk.Label('Refine')) +# self.cb = gtk.combo_box_new_text() +# self.cb.connect("changed", self.ChooseBfacRefinement) +# for item in ['isotropic','anisotropic']: +# self.cb.append_text(item) +# if 'ISOT' in self.RefmacParams['BREF']: +# self.cb.set_active(0) +# if 'ANIS' in self.RefmacParams['BREF']: +# self.cb.set_active(1) +# self.hbox1.add(self.cb) +# self.hbox1.add(gtk.Label('temperature factors')) +# self.vbox.add(self.hbox1) +# +# self.hbox2=gtk.HBox() +# self.hbox2.add(gtk.Label('Number of Cycles: ')) +# self.Ncycles=gtk.Entry() +# self.Ncycles.add_events(gtk.gdk.KEY_RELEASE_MASK) +# self.Ncycles.connect("key-release-event", self.on_key_release_Ncycles) +# self.Ncycles.set_text(self.RefmacParams['NCYCLES']) +# self.hbox2.add(self.Ncycles) +# self.vbox.add(self.hbox2) +# +# self.hbox3=gtk.HBox() +# self.hbox3.add(gtk.Label('MATRIX WEIGHT: ')) +# self.MATRIX_WEIGHT=gtk.Entry() +# self.MATRIX_WEIGHT.add_events(gtk.gdk.KEY_RELEASE_MASK) +# self.MATRIX_WEIGHT.connect("key-release-event", self.on_key_release_MATRIX_WEIGHT) +# self.MATRIX_WEIGHT.set_text(self.RefmacParams['MATRIX_WEIGHT']) +# self.hbox3.add(self.MATRIX_WEIGHT) +# self.vbox.add(self.hbox3) +# +# self.TLS = gtk.CheckButton('TLS (find TLS groups with phenix.find_tls_groups)') +# self.TLS.connect("toggled", self.TLSCallback) +# if self.RefmacParams['TLS']=='refi tlsc 10\n': self.TLS.set_active(True) +# self.vbox.pack_start(self.TLS,False) +# +# self.NCS = gtk.CheckButton('NCS (if applicable') +# self.NCS.connect("toggled", self.NCSCallback) +# if self.RefmacParams['NCS']=='NCSR LOCAL\n': self.NCS.set_active(True) +# self.vbox.pack_start(self.NCS,False) +# +# self.TWIN = gtk.CheckButton('Twin?') +# self.TWIN.connect("toggled", self.TWINCallback) +# if self.RefmacParams['TWIN']=='TWIN\n': self.TWIN.set_active(True) +# self.vbox.pack_start(self.TWIN,False) +# +# self.OKbutton = gtk.Button(label="OK") +# self.OKbutton.connect("clicked",self.OK) +# self.vbox.add(self.OKbutton) +# +# self.window.add(self.vbox) +# self.window.show_all() +# return self.RefmacParams +# +# +# def TLSCallback(self, widget): +# if widget.get_active(): +# self.RefmacParams['TLS']='refi tlsc 10\n' +# self.RefmacParams['TLSIN']='refmac.tls\n' +# self.RefmacParams['TLSOUT']='out.tls\n' +# self.RefmacParams['TLSADD']='TLSO ADDU\n' +# else: +# self.RefmacParams['TLS']='' +# self.RefmacParams['TLSIN']='' +# self.RefmacParams['TLSOUT']='' +# self.RefmacParams['TLSADD']='' +# return self.RefmacParams +# +# def NCSCallback(self, widget): +# if widget.get_active(): +# self.RefmacParams['NCS']='NCSR LOCAL\n' +# else: +# self.RefmacParams['NCS']='' +# return self.RefmacParams +# +# def ChooseBfacRefinement(self,widget): +# if widget.get_active_text()=='isotropic': +# self.RefmacParams['BREF']=' bref ISOT\n' +# if widget.get_active_text()=='anisotropic': +# self.RefmacParams['BREF']=' bref ANIS\n' +# return self.RefmacParams +# +# def on_key_release_Ncycles(self, widget, event): +# print widget.get_text() +# self.RefmacParams['NCYCLES'] = widget.get_text() +# return self.RefmacParams +# +# def on_key_release_MATRIX_WEIGHT(self, widget, event): +# self.RefmacParams['MATRIX_WEIGHT'] = widget.get_text() +# return self.RefmacParams +# +# def TWINCallback(self, widget): +# if widget.get_active(): +# self.RefmacParams['TWIN']='TWIN\n' +# else: +# self.RefmacParams['TWIN']='' +# return self.RefmacParams# +# +# def OK(self,widget): +# self.window.destroy() +# +# +# def ParamsFromPreviousCycle(self,Serial): +# +# RefmacParams={ 'HKLIN': '', 'HKLOUT': '', +# 'XYZIN': '', 'XYZOUT': '', +# 'LIBIN': '', 'LIBOUT': '', +# 'TLSIN': '', 'TLSOUT': '', +# 'TLSADD': '', +# 'NCYCLES': '10', +# 'MATRIX_WEIGHT': 'AUTO', +# 'BREF': ' bref ISOT\n', +# 'TLS': '', +# 'NCS': '', +# 'TWIN': '' } +# +# if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): +# for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): +# if line.startswith('refi tlsc'): +# RefmacParams['TLS']=line +# if line.startswith('TLSO'): +# RefmacParams['TLSADD']=line +# if line.startswith('NCSR LOCAL'): +# RefmacParams['NCS']=line +# if line.startswith(' bref '): +# RefmacParams['BREF']=line +# if line.startswith('ncyc'): +# RefmacParams['Ncycles'] = line.split()[1] +# if line.startswith('weight'): +# RefmacParams['MATRIX_WEIGHT'] = line.split()[len(line.split())-1] +# if line.startswith('TWIN'): +# RefmacParams['TWIN']=line +# +# return RefmacParams +# +# def GetRefinementHistory(self): +## RefinementHistory='' +# RefinementCycle = [] +# RcrystList=[] +# RfreeList=[] +# +# found = False +# for item in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): +# if item.startswith(os.path.join(self.ProjectPath,self.xtalID,'Refine_')): +# print item[item.rfind('_')+1:] +# RefinementCycle.append(int(item[item.rfind('_')+1:])) +# found = True +# if found: +# for cycle in sorted(RefinementCycle): +## for cycle in RefinementCycle: +## Rcryst=0 +## Rfree=0 +## LigandCC=0 +# try: +# found_Rcryst=False +# found_Rfree=False +# newestPDB = max(glob.iglob(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/refine_'+str(cycle)+'.pdb'), key=os.path.getctime) +# for line in open(newestPDB): +# if line.startswith('REMARK 3 R VALUE (WORKING + TEST SET) :'): +# Rcryst = line.split()[9] +# RcrystList.append(float(Rcryst)) +# found_Rcryst=True +# if line.startswith('REMARK 3 FREE R VALUE :'): +# Rfree = line.split()[6] +# RfreeList.append(float(Rfree)) +# found_Rfree=True +# if not found_Rcryst: +# RcrystList.append(0) +# if not found_Rfree: +# RfreeList.append(0) +## if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): +## for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): +## if line.startswith('| LIG'): LigandCC = line.split()[6] +## RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' +# except ValueError: +# RcrystList.append(0) +# RfreeList.append(0) +## RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' +# else: +# RefinementCycle = [0] +# RcrystList=[0] +# RfreeList=[0] +# print RefinementCycle,RcrystList,RfreeList +# return(sorted(RefinementCycle),RcrystList,RfreeList) +# From c296ce515ca424ecc85fb75d78427efa75080fda Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 10 Mar 2020 20:58:15 +0000 Subject: [PATCH 023/358] v1.5.12 (10/03/2020) (#302) - DIMPLE: added pointless step before dimple to reindex according to ref_pdb if necessary --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemThread.py | 4 +++- 3 files changed, 7 insertions(+), 2 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index d21c91b6..50d66ab8 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.12 (10/03/2020) +- DIMPLE: added pointless step before dimple to reindex according to ref_pdb if necessary + v1.5.11 (10/03/2020) - added linking of covalent binders for PanDDA models (refine.split-bound.pdb) - remove links to refine.output... PDB files after refinement diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 811a5584..a2b63c7b 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.11' + xce_object.xce_version = 'v1.5.12' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemThread.py b/lib/XChemThread.py index b2a0dc07..34b8e057 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -1773,7 +1773,9 @@ def prepare_dimple_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,ref_m ' resolution file 1 999.0 %s\n' %str(round(float(mtzFile.d_min()),2))+ 'eof\n' '\n' - "dimple --no-cleanup %s.999A.mtz %s %s %s %s dimple\n" % (xtal, ref_pdb, ref_mtz, ref_cif, twin) + + 'pointless hklin %s.999A.mtz hklout %s.999A.reind.mtz xyzin %s > pointless.reind.log\n' %(xtal,xtal,ref_pdb) + + '\n' + "dimple --no-cleanup %s.999A.reind.mtz %s %s %s %s dimple\n" % (xtal, ref_pdb, ref_mtz, ref_cif, twin) + '\n' 'fft hklin dimple/final.mtz mapout 2fofc.map << EOF\n' ' labin F1=FWT PHI=PHWT\n' From 6df53a5147a8f10213ded39083a81970023fe48e Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 11 Mar 2020 10:57:47 +0000 Subject: [PATCH 024/358] v1.5.13 (11/03/2020) (#303) - bug fix: include covlinks argument is None in XChemPANDDA quickRefine --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 2 +- 4 files changed, 6 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 50d66ab8..c1697cde 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.13 (11/03/2020) +- bug fix: include covlinks argument is None in XChemPANDDA quickRefine + v1.5.12 (10/03/2020) - DIMPLE: added pointless step before dimple to reindex according to ref_pdb if necessary diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index a2b63c7b..1113f668 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.12' + xce_object.xce_version = 'v1.5.13' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 6ddff51a..b4501700 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 10/03/2020 #\n' + ' # Date: 11/03/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 5455f1bd..33ab617f 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -103,7 +103,7 @@ def refine_exported_models(self,samples_to_export): os.chdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))) Refine=XChemRefine.panddaRefine(self.initial_model_directory,xtal,compoundID,self.datasource) os.symlink(os.path.join(self.initial_model_directory,xtal,xtal+'-ensemble-model.pdb'),xtal+'-ensemble-model.pdb') - Refine.RunQuickRefine(Serial,self.RefmacParams,self.external_software,self.xce_logfile,'pandda_refmac') + Refine.RunQuickRefine(Serial,self.RefmacParams,self.external_software,self.xce_logfile,'pandda_refmac',None) # elif xtal in os.path.join(self.panddas_directory,'processed_datasets',xtal,'modelled_structures', # '{}-pandda-model.pdb'.format(xtal)): From 85ed8498c2054c0bf0a8650a908af2d4e03511e3 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sat, 14 Mar 2020 11:09:04 +0000 Subject: [PATCH 025/358] v1.5.14 (14/03/2020) (#304) - HTML export: enable changing of contour level of event maps - HTML export: set ligand confidence to "not assigned" for deposition ready model that have "0 - no ligand bound" --- ChangeLog.txt | 4 ++++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemMain.py | 26 +++++++++++++++++++++++--- web/XChemWeb.py | 4 +++- 5 files changed, 32 insertions(+), 6 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index c1697cde..29313a15 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.5.14 (14/03/2020) +- HTML export: enable changing of contour level of event maps +- HTML export: set ligand confidence to "not assigned" for deposition ready model that have "0 - no ligand bound" + v1.5.13 (11/03/2020) - bug fix: include covlinks argument is None in XChemPANDDA quickRefine diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 1113f668..ce220002 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.13' + xce_object.xce_version = 'v1.5.14' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index b4501700..c2ab9d60 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 11/03/2020 #\n' + ' # Date: 14/03/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemMain.py b/lib/XChemMain.py index ce16da17..5cd4bf2d 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -879,6 +879,7 @@ def html_ngl(firstPDB,firstEvent,firstMap,firstDiffMap,ligID): ' useWorker: false,\n' ' wrap: false,\n' ' color: "purple",\n' + ' isolevel: 1.0,\n' ' contour: true\n' ' } );\n' ' \n' @@ -887,7 +888,7 @@ def html_ngl(firstPDB,firstEvent,firstMap,firstDiffMap,ligID): ' useWorker: false,\n' ' wrap: false,\n' ' color: "skyblue",\n' - ' isolevel: 1.0,\n' + ' isolevel: 0.9,\n' ' contour: true\n' ' } );\n' ' \n' @@ -943,6 +944,25 @@ def html_ngl(firstPDB,firstEvent,firstMap,firstDiffMap,ligID): ' struc.autoView("ligand and " + ligResid + " and " + ":" + ligChain)\n' ' stage.setFocus( 95 );\n' '\n' + + 'stage.mouseControls.remove("scroll-shift")\n' + '\n' + "stage.mouseControls.add('scroll-shift', function (stage, delta) {\n" + " if (eventMap) {\n" + " var d = Math.sign(delta) / 5\n" + " var l = eventMap.getParameters().isolevel\n" + "eventMap.setParameters({ isolevel: l + d })\n" + " }\n" + " if (fwtMap) {\n" + " var d = Math.sign(delta) / 5\n" + " var l = eventMap.getParameters().isolevel\n" + "fwtMap.setParameters({ isolevel: l + d })\n" + " }\n" + "});\n" + "\n" + 'stage.mouseControls.remove("scroll-alt")\n' + 'stage.mouseControls.add("scroll-alt", NGL.MouseActions.focusScroll);\n' + "\n" " stage.mouseControls.add('scroll', function () {\n" ' if (fwtMap) {\n' ' var level2fofc = fwtMap.getParameters().isolevel.toFixed(1);\n' @@ -1073,11 +1093,11 @@ def html_download(protein_name): download = ( '
\n' - '

Human %s - XChem results

\n' %protein_name + + '

%s - XChem results

\n' %protein_name + " \n" '
\n' '

\n' - '

Click event map in table to view a different crystal / compound pair

\n' + '

Click event map in table to view a different crystal / compound pair (press SHIFT and scroll mouse wheel to change contour level of event map)

\n' '
\n' '
\n' '
\n' diff --git a/web/XChemWeb.py b/web/XChemWeb.py index f9554aa4..58127fb3 100755 --- a/web/XChemWeb.py +++ b/web/XChemWeb.py @@ -82,7 +82,9 @@ def prepare(self): ligConfidence = self.db.get_ligand_confidence_for_ligand(xtal, ligChain, ligNumber, ligName) if ligConfidence.startswith('0'): self.Logfile.warning('%s: ligand confidence of %s-%s-%s is %s; ignoring...' %(xtal,ligChain,ligNumber,ligName,ligConfidence)) - continue + self.Logfile.warning('%s: this seems unlikely because this structure is apparently ready for deposition' %xtal) + self.Logfile.warning('%s: will set it to "not assigned" for now, but please update in soakDB' %xtal) + ligConfidence = 'not assigned' modelStatus = self.db_dict['RefinementOutcome'] if firstFile: html += XChemMain.html_ngl(pdb,eventMap.replace(self.projectDir,''),FWT,DELFWT,ligand) From 9583484e88b961ecd832987cafb82ef5ba2ac525 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 6 Apr 2020 21:58:07 +0100 Subject: [PATCH 026/358] v1.5.15 (06/04/2020) (#305) * bug fix: found instance in pandda_inspect_events.csv where sites/ events displayed as float instead of int; added fix --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 9 ++++++--- 4 files changed, 11 insertions(+), 5 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 29313a15..f392552e 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.15 (06/04/2020) +- bug fix: found instance in pandda_inspect_events.csv where sites/ events displayed as float instead of int; added fix + v1.5.14 (14/03/2020) - HTML export: enable changing of contour level of event maps - HTML export: set ligand confidence to "not assigned" for deposition ready model that have "0 - no ligand bound" diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index ce220002..7140f894 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.14' + xce_object.xce_version = 'v1.5.15' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index c2ab9d60..e255e772 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 14/03/2020 #\n' + ' # Date: 06/04/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 33ab617f..08dbf845 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -142,12 +142,14 @@ def import_samples_into_datasouce(self,samples_to_export): with open(os.path.join(self.panddas_directory,'analyses','pandda_inspect_sites.csv'),'rb') as csv_import: csv_dict = csv.DictReader(csv_import) + self.Logfile.insert('reding pandda_inspect_sites.csv') for i,line in enumerate(csv_dict): + self.Logfile.insert(str(line).replace('\n','').replace('\r','')) site_index=line['site_idx'] name=line['Name'].replace("'","") comment=line['Comment'] site_list.append([site_index,name,comment]) - + self.Logfile.insert('add to site_list_:' + str([site_index,name,comment])) progress_step=1 for i,line in enumerate(open(os.path.join(self.panddas_directory,'analyses','pandda_inspect_events.csv'))): @@ -171,8 +173,9 @@ def import_samples_into_datasouce(self,samples_to_export): continue if sampleID not in pandda_hit_list: pandda_hit_list.append(sampleID) - site_index=line['site_idx'] - event_index=line['event_idx'] + site_index=str(line['site_idx']).replace('.0','') + event_index=str(line['event_idx']).replace('.0','') + self.Logfile.insert(str(line)) self.Logfile.insert('reading {0!s} -> site {1!s} -> event {2!s}'.format(sampleID, site_index, event_index)) for entry in site_list: From 4e29b70b53fe27dc320ae6997b45db80bff6cefd Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 7 Apr 2020 00:56:16 +0100 Subject: [PATCH 027/358] v1.5.16 (06/04/2020) (#306) - XChemThread: copy un-merged MTZ file for xia2, dials & 3d(ii) - XChemThread: change parsing of auto-processing results to enable reading of multiple runs with same name, e.g. xia-3dii - bug fix: enable 3dii only selection of auto-processing results - remove xia2-3d only auto-processing selection option --- ChangeLog.txt | 6 ++ gui_scripts/settings_preferences.py | 4 +- lib/XChemDB.py | 2 + lib/XChemMain.py | 19 ++-- lib/XChemThread.py | 155 ++++++++++++++++++---------- 5 files changed, 121 insertions(+), 65 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index f392552e..3d89702f 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,9 @@ +v1.5.16 (06/04/2020) +- XChemThread: copy un-merged MTZ file for xia2, dials & 3d(ii) +- XChemThread: change parsing of auto-processing results to enable reading of multiple runs with same name, e.g. xia-3dii +- bug fix: enable 3dii only selection of auto-processing results +- remove xia2-3d only auto-processing selection option + v1.5.15 (06/04/2020) - bug fix: found instance in pandda_inspect_events.csv where sites/ events displayed as float instead of int; added fix diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 7140f894..d20b1546 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.15' + xce_object.xce_version = 'v1.5.16' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -226,7 +226,7 @@ def preferences(self, xce_object): 'highest_resolution', 'lowest_Rfree', 'dials - only', - 'xia2 3d - only', +# 'xia2 3d - only', 'xia2 3dii - only', 'autoProc - only', 'autoProc_staraniso - only'] diff --git a/lib/XChemDB.py b/lib/XChemDB.py index 1215e445..a7690ece 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -87,6 +87,7 @@ def __init__(self,data_source_file): ['DataCollectionDate', 'Data Collection\nDate', 'TEXT', 1], ['DataCollectionOutcome', 'DataCollection\nOutcome', 'TEXT', 1], ['DataCollectionRun', 'Run', 'TEXT', 0], + ['DataCollectionSubdir', 'SubDir', 'TEXT', 0], ['DataCollectionComment', 'DataCollection\nComment', 'TEXT', 0], ['DataCollectionWavelength', 'Wavelength', 'TEXT', 0], ['DataCollectionPinBarcode', 'GDA\nBarcode', 'TEXT', 1], @@ -413,6 +414,7 @@ def __init__(self,data_source_file): ['DataCollectionVisit', 'Visit', 'TEXT', 0], ['DataCollectionRun', 'Run', 'TEXT', 0], + ['DataCollectionSubdir', 'SubDir', 'TEXT', 0], ['DataCollectionBeamline', 'Beamline', 'TEXT', 0], ['DataCollectionOutcome', 'DataCollection\nOutcome', 'TEXT', 1], ['DataCollectionDate', 'Data Collection\nDate', 'TEXT', 1], diff --git a/lib/XChemMain.py b/lib/XChemMain.py index 5cd4bf2d..64b2d003 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -496,6 +496,11 @@ def linkAutoProcessingResult(xtal,dbDict,projectDir,xce_logfile): Logfile=XChemLog.updateLog(xce_logfile) run = dbDict['DataCollectionRun'] + subDir = dbDict['DataCollectionSubdir'] + if subDir != '': + procCode = '_' + subDir + else: + procCode = '' visit = dbDict['DataCollectionVisit'] autoproc = dbDict['DataProcessingProgram'] mtzFileAbs = dbDict['DataProcessingPathToMTZfile'] @@ -509,18 +514,18 @@ def linkAutoProcessingResult(xtal,dbDict,projectDir,xce_logfile): # MTZ file Logfile.warning('removing %s.mtz' %xtal) os.system('/bin/rm %s.mtz' %xtal) - print xtal,os.path.join('autoprocessing', visit + '-' + run + autoproc, mtzfile) - if os.path.isfile(os.path.join('autoprocessing', visit + '-' + run + autoproc, mtzfile)): - os.symlink(os.path.join('autoprocessing', visit + '-' + run + autoproc, mtzfile), xtal + '.mtz') + print xtal,os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile) + if os.path.isfile(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile)): + os.symlink(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile), xtal + '.mtz') Logfile.insert('linking MTZ file from different auto-processing pipeline:') - Logfile.insert('ln -s ' + os.path.join('autoprocessing', visit + '-' + run + autoproc, mtzfile) + ' ' + xtal + '.mtz') + Logfile.insert('ln -s ' + os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile) + ' ' + xtal + '.mtz') # LOG file Logfile.warning('removing %s.log' %xtal) os.system('/bin/rm %s.log' %xtal) - if os.path.isfile(os.path.join('autoprocessing', visit + '-' + run + autoproc, logfile)): - os.symlink(os.path.join('autoprocessing', visit + '-' + run + autoproc, logfile), xtal + '.log') + if os.path.isfile(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfile)): + os.symlink(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfile), xtal + '.log') Logfile.insert('linking LOG file from different auto-processing pipeline:') - Logfile.insert('ln -s ' + os.path.join('autoprocessing', visit + '-' + run + autoproc, logfile) + ' ' + xtal + '.log') + Logfile.insert('ln -s ' + os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfile) + ' ' + xtal + '.log') diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 34b8e057..1f7f012b 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2365,9 +2365,9 @@ def selectSpecificPipelineOnly(self,dbList): for resultDict in dbList: if self.selection_mechanism == 'dials - only' and 'dials' in resultDict['DataProcessingProgram']: tmp.append(resultDict) - if self.selection_mechanism == 'xia2 3d - only' and '3d-run' in resultDict['DataProcessingProgram']: + if self.selection_mechanism == 'xia2 3d - only' and '3d-' in resultDict['DataProcessingProgram']: tmp.append(resultDict) - if self.selection_mechanism == 'xia2 3dii - only' and '3dii-run' in resultDict['DataProcessingProgram']: + if self.selection_mechanism == 'xia2 3dii - only' and '3dii' in resultDict['DataProcessingProgram']: tmp.append(resultDict) if self.selection_mechanism == 'autoProc - only' and 'autoPROC' in resultDict['DataProcessingProgram'] and not 'staraniso' in resultDict['DataProcessingProgram']: tmp.append(resultDict) @@ -2441,13 +2441,10 @@ def __init__(self, self.exisitingSamples = self.getExistingSamples() self.toParse = [ - [ os.path.join('xia2', '*'), - os.path.join('LogFiles', '*aimless.log'), - os.path.join('DataFiles', '*free.mtz')], - [ os.path.join('xia2-3*'), + [ os.path.join('*'), os.path.join('LogFiles', '*aimless.log'), os.path.join('DataFiles', '*free.mtz')], - [ os.path.join('xia2-dials*'), + [ os.path.join('*'), os.path.join('LogFiles', '*merging-statistics.json'), os.path.join('DataFiles', '*free.mtz')], [ os.path.join('multi-xia2', '*'), @@ -2476,6 +2473,43 @@ def __init__(self, os.path.join('DataFiles', '*free.mtz')] ] +# self.toParse = [ +# [ os.path.join('xia2', '*'), +# os.path.join('LogFiles', '*aimless.log'), +# os.path.join('DataFiles', '*free.mtz')], +# [ os.path.join('xia2-3*'), +# os.path.join('LogFiles', '*aimless.log'), +# os.path.join('DataFiles', '*free.mtz')], +# [ os.path.join('xia2-dials*'), +# os.path.join('LogFiles', '*merging-statistics.json'), +# os.path.join('DataFiles', '*free.mtz')], +# [ os.path.join('multi-xia2', '*'), +# os.path.join('LogFiles', '*aimless.log'), +# os.path.join('DataFiles', '*free.mtz')], +# [ os.path.join('autoPROC', '*'), +# '*aimless.log', +# '*truncate-unique.mtz'], +# [ os.path.join('autoPROC', '*'), +# '*staraniso_alldata-unique.table1', +# '*staraniso_alldata-unique.mtz'], +# [ os.path.join('autoPROC'), +# '*aimless.log', +# '*truncate-unique.mtz'], +# [ os.path.join('autoPROC'), +# '*summary.tar.gz', # staraniso_alldata-unique.table1 only available in tar archive +# '*staraniso_alldata-unique.mtz'], +# [ os.path.join('autoPROC-*'), +# '*aimless.log', +# '*truncate-unique.mtz'], +# [ os.path.join('autoPROC-*'), +# '*summary.tar.gz', +# '*staraniso_alldata-unique.mtz'], +# [ os.path.join('*'), +# os.path.join('LogFiles', '*aimless.log'), +# os.path.join('DataFiles', '*free.mtz')] +# ] + + def run(self): if self.agamemnon: self.parse_agamemnon_file_system() @@ -2497,31 +2531,31 @@ def createSampleDir(self,xtal): if not os.path.isdir(os.path.join(self.projectDir,xtal)): os.mkdir(os.path.join(self.projectDir,xtal)) - def createAutoprocessingDir(self,xtal,run,autoproc): + def createAutoprocessingDir(self,xtal,run,autoproc,proc_code): # create all the directories if necessary - self.Logfile.insert('%s: checking if new directory needs to be created for %s' %(xtal,os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc))) + self.Logfile.insert('%s: checking if new directory needs to be created for %s' %(xtal,os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc + '_' + proc_code))) if not os.path.isdir(os.path.join(self.projectDir,xtal,'autoprocessing')): os.mkdir(os.path.join(self.projectDir,xtal,'autoprocessing')) if not os.path.isdir( - os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc)): - self.Logfile.insert('%s: making directory %s' %(xtal,os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc))) - os.mkdir(os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc)) + os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code)): + self.Logfile.insert('%s: making directory %s' %(xtal,os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code))) + os.mkdir(os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code)) else: self.Logfile.warning('%s: directory exists; skipping...' %xtal) - def cleanUpDir(self,xtal,run,autoproc,mtzfile,logfile): + def cleanUpDir(self,xtal,run,autoproc,mtzfile,logfile,proc_code): toKeep = ['staraniso_alldata-unique.mtz','staraniso_alldata-unique.table1', 'staraniso_alldata.log',xtal+'.mtz',xtal+'.log'] - os.chdir(os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc)) + os.chdir(os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code)) for files in glob.glob('*'): if files not in toKeep: os.system('/bin/rm -f ' + files) - def copyMTZandLOGfiles(self,xtal,run,autoproc,mtzfile,logfile): + def copyMTZandLOGfiles(self,xtal,run,autoproc,mtzfile,logfile,proc_code): mtzNew = '' logNew = '' - os.chdir(os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc)) + os.chdir(os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code)) # MTZ file if not os.path.isfile(mtzfile[mtzfile.rfind('/') + 1:]): self.Logfile.insert('%s: copying %s' % (xtal, mtzfile)) @@ -2533,7 +2567,13 @@ def copyMTZandLOGfiles(self,xtal,run,autoproc,mtzfile,logfile): if os.path.isfile(mtzfile[mtzfile.rfind('/')+1:]) and not os.path.isfile(xtal+'.mtz'): os.symlink(mtzfile[mtzfile.rfind('/')+1:], xtal + '.mtz') if os.path.isfile(mtzfile[mtzfile.rfind('/') + 1:]): - mtzNew=os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc, mtzfile[mtzfile.rfind('/')+1:]) + mtzNew=os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code, mtzfile[mtzfile.rfind('/')+1:]) + # MTZ file unmerged + if os.path.isfile(mtzfile.replace('_free.mtz','_scaled_unmerged.mtz')): + self.Logfile.insert('%s: found unmerged mtz file' %xtal) + if not os.path.isfile(xtal+'_unmerged.mtz'): + self.Logfile.insert('%s: copying %s' %(xtal,mtzfile.replace('_free.mtz','_scaled_unmerged.mtz'))) + os.system('/bin/cp ' + mtzfile.replace('_free.mtz','_scaled_unmerged.mtz') + ' .') # AIMLESS logfile if not os.path.isfile(logfile[logfile.rfind('/')+1:]): self.Logfile.insert('%s: copying %s' % (xtal, logfile)) @@ -2542,11 +2582,11 @@ def copyMTZandLOGfiles(self,xtal,run,autoproc,mtzfile,logfile): self.Logfile.insert('unpacking summary.tar.gz') os.system('tar -xzvf summary.tar.gz') logfile = logfile.replace('summary.tar.gz','staraniso_alldata-unique.table1') - self.cleanUpDir(xtal,run,autoproc,mtzfile,logfile) + self.cleanUpDir(xtal,run,autoproc,mtzfile,logfile,proc_code) if os.path.isfile(logfile[logfile.rfind('/')+1:]) and not os.path.isfile(xtal+'.log'): os.symlink(logfile[logfile.rfind('/')+1:], xtal + '.log') if os.path.isfile(logfile[logfile.rfind('/') + 1:]): - logNew=os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc, logfile[logfile.rfind('/') + 1:]) + logNew=os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code, logfile[logfile.rfind('/') + 1:]) return mtzNew,logNew def makeJPGdir(self,xtal,run): @@ -2591,7 +2631,7 @@ def findJPGs(self,xtal,run): return jpgDict - def readProcessingUpdateResults(self,xtal,folder,log,mtz,timestamp,current_run,autoproc): + def readProcessingUpdateResults(self,xtal,folder,log,mtz,timestamp,current_run,autoproc,proc_code): db_dict = {} self.Logfile.warning('%s: looking for %s' %(xtal,os.path.join(folder, mtz))) for mtzfile in glob.glob(os.path.join(folder,mtz)): @@ -2599,8 +2639,8 @@ def readProcessingUpdateResults(self,xtal,folder,log,mtz,timestamp,current_run,a self.Logfile.warning('%s: looking for %s' %(xtal,os.path.join(folder, log))) for logfile in glob.glob(os.path.join(folder, log)): self.Logfile.insert('%s: found %s' % (xtal, logfile)) - self.createAutoprocessingDir(xtal, current_run, autoproc) - mtzNew,logNew = self.copyMTZandLOGfiles(xtal,current_run,autoproc,mtzfile,logfile) + self.createAutoprocessingDir(xtal, current_run, autoproc,proc_code) + mtzNew,logNew = self.copyMTZandLOGfiles(xtal,current_run,autoproc,mtzfile,logfile,proc_code) if self.target == '=== project directory ===': target = 'unknown' else: @@ -2614,7 +2654,7 @@ def readProcessingUpdateResults(self,xtal,folder,log,mtz,timestamp,current_run,a db_dict.update(parse().read_aimless_logfile(logNew)) db_dict.update(self.findJPGs(xtal,current_run)) # image exist even if data processing failed db_dict['DataCollectionBeamline'] = self.beamline - self.update_data_collection_table(xtal,current_run,autoproc,db_dict) + self.update_data_collection_table(xtal,current_run,autoproc,db_dict,proc_code) # return db_dict def getAutoProc(self,folder,staraniso): @@ -2636,10 +2676,11 @@ def getAutoProc(self,folder,staraniso): self.Logfile.insert('name of auto-processing pipeline: %s' %autoproc) return autoproc - def update_data_collection_table(self,xtal,current_run,autoproc,db_dict): + def update_data_collection_table(self,xtal,current_run,autoproc,db_dict,proc_code): condition_dict = { 'CrystalName': xtal, 'DataCollectionVisit': self.visit, 'DataCollectionRun': current_run, + 'DataCollectionSubdir': proc_code, 'DataProcessingProgram': autoproc } self.db.update_insert_any_table('collectionTable', db_dict, condition_dict) @@ -2706,38 +2747,40 @@ def parse_file_system(self): for run in sorted(glob.glob(runDir)): current_run=run[run.rfind('/')+1:] - if current_run in runList: - continue - self.Logfile.insert('%s -> run: %s -> current run: %s' %(xtal,run,current_run)) - timestamp=datetime.fromtimestamp(os.path.getmtime(run)).strftime('%Y-%m-%d %H:%M:%S') - - # create directory for crystal aligment images in projectDir - self.makeJPGdir(xtal,current_run) - self.copyJPGs(xtal, current_run, 'non-auto') # 'non-auto' is irrelevant here - - for item in self.toParse: - procDir = os.path.join(run,item[0]) - logfile = item[1] - mtzfile = item[2] - self.Logfile.insert('%s: search template: procDir - logfile - mtzfile' %xtal) - self.Logfile.insert('%s: procDir = %s' %(xtal,procDir)) - self.Logfile.insert('%s: logfile = %s' %(xtal,logfile)) - self.Logfile.insert('%s: mtzfile = %s' %(xtal,mtzfile)) - - for folder in glob.glob(procDir): - staraniso = '' - self.Logfile.insert('%s: searching %s' %(xtal,folder)) - if self.junk(folder): - continue - if self.empty_folder(xtal,folder): - continue - if 'staraniso' in logfile or 'summary.tar.gz' in logfile: - staraniso = '_staraniso' - autoproc = self.getAutoProc(folder,staraniso) - if self.alreadyParsed(xtal,current_run,autoproc): - continue - self.readProcessingUpdateResults(xtal,folder,logfile,mtzfile,timestamp,current_run,autoproc) - runList.append(current_run) + for code in glob.glob(os.path.join(run,'*')): + proc_code = code[code.rfind('/')+1:] + if current_run+proc_code in runList: + continue + self.Logfile.insert('%s -> run: %s -> current run: %s -> %s' %(xtal,run,current_run,proc_code)) + timestamp=datetime.fromtimestamp(os.path.getmtime(run)).strftime('%Y-%m-%d %H:%M:%S') + # create directory for crystal aligment images in projectDir + self.makeJPGdir(xtal,current_run) + self.copyJPGs(xtal, current_run, 'non-auto') # 'non-auto' is irrelevant here + + + for item in self.toParse: + procDir = os.path.join(code,item[0]) + logfile = item[1] + mtzfile = item[2] + self.Logfile.insert('%s: search template: procDir - logfile - mtzfile' %xtal) + self.Logfile.insert('%s: procDir = %s' %(xtal,procDir)) + self.Logfile.insert('%s: logfile = %s' %(xtal,logfile)) + self.Logfile.insert('%s: mtzfile = %s' %(xtal,mtzfile)) + + for folder in glob.glob(procDir): + staraniso = '' + self.Logfile.insert('%s: searching %s' %(xtal,folder)) + if self.junk(folder): + continue + if self.empty_folder(xtal,folder): + continue + if 'staraniso' in logfile or 'summary.tar.gz' in logfile: + staraniso = '_staraniso' + autoproc = self.getAutoProc(folder,staraniso) + if self.alreadyParsed(xtal,current_run+proc_code,autoproc): + continue + self.readProcessingUpdateResults(xtal,folder,logfile,mtzfile,timestamp,current_run,autoproc,proc_code) + runList.append(current_run+proc_code) progress += progress_step self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'parsing auto-processing results for '+xtal) From 15cfc795e5eb5fd800fb7fa0a3899ac24a671df2 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 7 Apr 2020 13:39:28 +0100 Subject: [PATCH 028/358] v1.5.17 (07/04/2020) (#307) - added option to specify in structure deposition title --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 2 +- lib/XChemLog.py | 2 +- 4 files changed, 6 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 3d89702f..0274cfbd 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.5.17 (07/04/2020) +- add option to specify $SampleID in structure deposition title + v1.5.16 (06/04/2020) - XChemThread: copy un-merged MTZ file for xia2, dials & 3d(ii) - XChemThread: change parsing of auto-processing results to enable reading of multiple runs with same name, e.g. xia-3dii diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index d20b1546..52397dc3 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.16' + xce_object.xce_version = 'v1.5.17' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 9aed0c42..fde00028 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -789,7 +789,7 @@ def save_data_template_dict(self,xtal): # self.data_template_dict['radiation_wavelengths'] = self.mtz.get_wavelength() title = self.data_template_dict['structure_title'].replace('$ProteinName', self.data_template_dict[ - 'Source_organism_gene']).replace('$CompoundName', self.db_dict['CompoundCode']) + 'Source_organism_gene']).replace('$CompoundName', self.db_dict['CompoundCode']).replace('($SampleID)','('+xtal+')') self.data_template_dict['group_type'] = 'changed state' diff --git a/lib/XChemLog.py b/lib/XChemLog.py index e255e772..d1ab70d0 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 06/04/2020 #\n' + ' # Date: 07/04/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 092e45f92a3627e54e61a7240509f15aa4dd8d62 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 15 Apr 2020 09:44:44 +0100 Subject: [PATCH 029/358] v1.6.0 (14/04/2020) (#308) - new option: directly refine bound-state only after pandda.inspect with buster --- ChangeLog.txt | 3 + XChemExplorer.py | 23 + gui_scripts/settings_preferences.py | 6 +- lib/XChemCootBuster.py | 1675 +++++++++++++++++++++++++++ lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 162 +++ lib/XChemRefine.py | 209 +++- lib/XChemThread.py | 2 + 8 files changed, 2077 insertions(+), 5 deletions(-) create mode 100755 lib/XChemCootBuster.py diff --git a/ChangeLog.txt b/ChangeLog.txt index 0274cfbd..422ce07e 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.0 (14/04/2020) +- new option: directly refine bound-state only after pandda.inspect with buster + v1.5.17 (07/04/2020) - add option to specify $SampleID in structure deposition title diff --git a/XChemExplorer.py b/XChemExplorer.py index 6eb01252..370a9b5b 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -3447,6 +3447,12 @@ def prepare_and_run_task(self, instruction): which_models = 'all' self.run_pandda_export(update_datasource_only, which_models) + elif instruction == 'refine ALL bound-state models with BUSTER': + self.run_refine_bound_state_with_buster('all') + + elif instruction == 'refine NEW bound-state models with BUSTER': + self.run_refine_bound_state_with_buster('new') + elif instruction == 'cluster datasets': self.cluster_datasets_for_pandda() @@ -3478,6 +3484,8 @@ def prepare_and_run_task(self, instruction): interface = 'panddaV1' elif instruction == 'Build ground state model': interface = 'reference' + elif instruction == 'Open COOT - BUSTER refinement -': + interface = 'buster' else: interface = 'old' print self.settings @@ -3745,6 +3753,21 @@ def run_pandda_export(self, update_datasource_only, which_models): self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) self.work_thread.start() + def run_refine_bound_state_with_buster(self,which_models): + start_thread = True + if start_thread: + self.work_thread = XChemPANDDA.refine_bound_state_with_buster(self.panddas_directory, + os.path.join(self.database_directory, + self.data_source_file), + self.initial_model_directory, self.xce_logfile, + which_models) + self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.work_thread.start() + + + + + def show_pandda_html_summary(self): self.pandda_initial_html.load(QtCore.QUrl(self.pandda_initial_html_file)) self.pandda_initial_html.show() diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 52397dc3..73e68531 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.5.17' + xce_object.xce_version = 'v1.6.0' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -624,11 +624,13 @@ def dropdown_items(self, xce_object): 'Event Map -> SF', 'apo -> mmcif', 'check modelled ligands', + 'refine ALL bound-state models with BUSTER', + 'refine NEW bound-state models with BUSTER', 'pre-run for ground state model', 'Build ground state model'] xce_object.refine_file_tasks = ['Open COOT', - 'Open COOT - test -'] + 'Open COOT - BUSTER refinement -'] # xce_object.refine_file_tasks = ['Open COOT', # 'Open COOT for old PanDDA', diff --git a/lib/XChemCootBuster.py b/lib/XChemCootBuster.py new file mode 100755 index 00000000..31842f48 --- /dev/null +++ b/lib/XChemCootBuster.py @@ -0,0 +1,1675 @@ +# last edited: 08/08/2017 - 15:00 + +import gobject +import sys +import os +import pickle +import glob + +from matplotlib.figure import Figure + +# from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas + +# XCE libraries +sys.path.append(os.getenv('XChemExplorer_DIR') + '/lib') +import XChemDB +import XChemRefine +import XChemUtils +import XChemLog + +# libraries from COOT +import pygtk, gtk, pango +import coot + +# had to adapt the original coot_utils.py file +# otherwise unable to import the original file without complaints about missing modules etc. +# modified file is now in $XChemExplorer_DIR/lib +import coot_utils_XChem + + +class GUI(object): + """ + main class which opens the actual GUI + """ + + def __init__(self): + + ########################################################################################### + # read in settings file from XChemExplorer to set the relevant paths + self.settings = pickle.load(open(".xce_settings.pkl", "rb")) + + remote_qsub_submission = self.settings['remote_qsub'] + self.database_directory = self.settings['database_directory'] + self.xce_logfile = self.settings['xce_logfile'] + self.Logfile = XChemLog.updateLog(self.xce_logfile) + self.Logfile.insert('==> COOT: starting coot plugin...') + self.data_source = self.settings['data_source'] + self.db = XChemDB.data_source(self.data_source) + + print self.settings + + # checking for external software packages + self.external_software = XChemUtils.external_software(self.xce_logfile).check() + self.external_software['qsub_remote'] = remote_qsub_submission + + self.selection_criteria = ['0 - All Datasets', + '1 - Analysis Pending', + '2 - PANDDA model', + '3 - In Refinement', + '4 - CompChem ready', + '5 - Deposition ready', + '6 - Deposited', + '7 - Analysed & Rejected'] + + self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], + ['In Refinement', '3 - In Refinement', 65000, 0, 0], + ['Comp Chem Ready!', '4 - CompChem ready', 65000, 0, 0], + ['Ready for Deposition!', '5 - Deposition ready', 65000, 0, 0], + ['In PDB', '6 - Deposited', 65000, 0, 0], + ['Analysed & Rejected', '7 - Analysed & Rejected', 65000, 0, 0]] + + self.ligand_confidence_category = ['0 - no ligand present', + '1 - Low Confidence', + '2 - Correct ligand, weak density', + '3 - Clear density, unexpected ligand', + '4 - High Confidence'] + + self.ligand_site_information = self.db.get_list_of_pandda_sites_for_coot() + + # this decides which samples will be looked at + self.selection_mode = '' + # self.selected_site='' + self.pandda_index = -1 # refers to the number of sites + self.site_index = '0' + self.event_index = '0' + + # the Folder is kind of a legacy thing because my inital idea was to have separate folders + # for Data Processing and Refinement + self.project_directory = self.settings['initial_model_directory'] + self.Serial = 0 + self.panddaSerial = 0 + self.Refine = None + self.index = -1 + self.Todo = [] + self.siteDict = {} + + self.xtalID = '' + self.compoundID = '' + self.ground_state_mean_map = '' + self.spider_plot = '' + self.ligand_confidence = '' + self.refinement_folder = '' +# self.refinementProtocol = 'pandda_refmac' + # self.datasetOutcome='' + + self.pdb_style = 'refine.pdb' + self.mtz_style = 'refine.mtz' + + self.covLink = ['X', 'X', 'X', 'X'] + self.covLinkObject = coot.new_generic_object_number("covalent bond") + self.covLinkAtomSpec = None + + self.label = None + + # stores imol of currently loaded molecules and maps + self.mol_dict = {'protein': -1, + 'ligand': -1, + '2fofc': -1, + 'fofc': -1, + 'event': -1, + 'ligand_stereo': []} + + # two dictionaries which are flushed when a new crystal is loaded + # and which contain information to update the data source if necessary + self.db_dict_mainTable = {} + self.db_dict_panddaTable = {} + + self.label_button_list = [] + + + ########################################################################################### + # some COOT settings + coot.set_map_radius(17) + coot.set_colour_map_rotation_for_map(0) + # coot.set_colour_map_rotation_on_read_pdb_flag(21) + + self.QualityIndicators = {'RefinementRcryst': '-', + 'RefinementRfree': '-', + 'RefinementRfreeTraficLight': 'gray', + 'RefinementResolution': '-', + 'RefinementResolutionTL': 'gray', + 'RefinementMolProbityScore': '-', + 'RefinementMolProbityScoreTL': 'gray', + 'RefinementRamachandranOutliers': '-', + 'RefinementRamachandranOutliersTL': 'gray', + 'RefinementRamachandranFavored': '-', + 'RefinementRamachandranFavoredTL': 'gray', + 'RefinementRmsdBonds': '-', + 'RefinementRmsdBondsTL': 'gray', + 'RefinementRmsdAngles': '-', + 'RefinementRmsdAnglesTL': 'gray', + 'RefinementMatrixWeight': '-'} + + self.spider_plot_data = {'PANDDA_site_ligand_id': '-', + 'PANDDA_site_occupancy': '-', + 'PANDDA_site_B_average': '-', + 'PANDDA_site_B_ratio_residue_surroundings': '-', + 'PANDDA_site_RSCC': '-', + 'PANDDA_site_rmsd': '-', + 'PANDDA_site_RSR': '-', + 'PANDDA_site_RSZD': '-'} + + # default refmac parameters + self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', + 'XYZIN': '', 'XYZOUT': '', + 'LIBIN': '', 'LIBOUT': '', + 'TLSIN': '', 'TLSOUT': '', + 'TLSADD': '', + 'NCYCLES': '10', + 'MATRIX_WEIGHT': 'AUTO', + 'BREF': ' bref ISOT\n', + 'TLS': '', + 'NCS': '', + 'TWIN': ''} + + def StartGUI(self): + + self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) + self.window.connect("delete_event", gtk.main_quit) + self.window.set_border_width(10) + self.window.set_default_size(400, 800) + self.window.set_title("XChemExplorer") + self.vbox = gtk.VBox() # this is the main container + + ################################################################################# + # --- Sample Selection --- + # self.vbox.add(gtk.Label('Select Samples')) + + frame = gtk.Frame(label='Select Samples') + self.hbox_select_samples = gtk.HBox() + # vbox=gtk.VBox() + + self.cb_select_samples = gtk.combo_box_new_text() + self.cb_select_samples.connect("changed", self.set_selection_mode) + for citeria in self.selection_criteria: + self.cb_select_samples.append_text(citeria) + self.hbox_select_samples.add(self.cb_select_samples) + + # self.cb_select_sites = gtk.combo_box_new_text() + # self.cb_select_sites.connect("changed", self.set_site) + # for site in self.ligand_site_information: + # self.cb_select_sites.append_text(str(site[0])+' - '+str(site[1])) + # self.hbox_select_samples.add(self.cb_select_sites) + + self.select_samples_button = gtk.Button(label="GO") + self.select_samples_button.connect("clicked", self.get_samples_to_look_at) + self.hbox_select_samples.add(self.select_samples_button) + frame.add(self.hbox_select_samples) + self.vbox.pack_start(frame) + + ################################################################################# + # --- status window --- + frame = gtk.Frame() + self.status_label = gtk.Label() + frame.add(self.status_label) + self.vbox.pack_start(frame) + + ################################################################################# + # --- refinement protocol --- +# frame = gtk.Frame() +# self.refinementProtocolcheckbox = gtk.CheckButton('PanDDA model refinement)') +# # callback is defined later +## self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) +# self.refinementProtocolcheckbox.set_active(True) +# frame.add(self.refinementProtocolcheckbox) +# self.vbox.pack_start(frame) + + ################################################################################# + # --- refinement program --- +# frame = gtk.Frame() +# self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') +# self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) +# self.refinementProgramcheckbox.set_active(False) +# frame.add(self.refinementProgramcheckbox) +# self.vbox.pack_start(frame) + + # SPACER +# self.vbox.add(gtk.Label(' ')) + + ################################################################################# + # --- Refinement Statistics --- + # next comes a section which displays some global quality indicators + # a combination of labels and textview widgets, arranged in a table + + RRfreeLabel_frame = gtk.Frame() + self.RRfreeLabel = gtk.Label('R/Rfree') + RRfreeLabel_frame.add(self.RRfreeLabel) + self.RRfreeValue = gtk.Label( + self.QualityIndicators['RefinementRcryst'] + '/' + self.QualityIndicators['RefinementRfree']) + RRfreeBox_frame = gtk.Frame() + self.RRfreeBox = gtk.EventBox() + self.RRfreeBox.add(self.RRfreeValue) + RRfreeBox_frame.add(self.RRfreeBox) + + ResolutionLabel_frame = gtk.Frame() + self.ResolutionLabel = gtk.Label('Resolution') + ResolutionLabel_frame.add(self.ResolutionLabel) + self.ResolutionValue = gtk.Label(self.QualityIndicators['RefinementResolution']) + ResolutionBox_frame = gtk.Frame() + self.ResolutionBox = gtk.EventBox() + self.ResolutionBox.add(self.ResolutionValue) + ResolutionBox_frame.add(self.ResolutionBox) + + MolprobityScoreLabel_frame = gtk.Frame() + self.MolprobityScoreLabel = gtk.Label('MolprobityScore') + MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) + self.MolprobityScoreValue = gtk.Label(self.QualityIndicators['RefinementMolProbityScore']) + MolprobityScoreBox_frame = gtk.Frame() + self.MolprobityScoreBox = gtk.EventBox() + self.MolprobityScoreBox.add(self.MolprobityScoreValue) + MolprobityScoreBox_frame.add(self.MolprobityScoreBox) + + RamachandranOutliersLabel_frame = gtk.Frame() + self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') + RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) + self.RamachandranOutliersValue = gtk.Label(self.QualityIndicators['RefinementRamachandranOutliers']) + RamachandranOutliersBox_frame = gtk.Frame() + self.RamachandranOutliersBox = gtk.EventBox() + self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) + RamachandranOutliersBox_frame.add(self.RamachandranOutliersBox) + + RamachandranFavoredLabel_frame = gtk.Frame() + self.RamachandranFavoredLabel = gtk.Label('Rama Favored') + RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) + self.RamachandranFavoredValue = gtk.Label(self.QualityIndicators['RefinementRamachandranFavored']) + RamachandranFavoredBox_frame = gtk.Frame() + self.RamachandranFavoredBox = gtk.EventBox() + self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) + RamachandranFavoredBox_frame.add(self.RamachandranFavoredBox) + + rmsdBondsLabel_frame = gtk.Frame() + self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') + rmsdBondsLabel_frame.add(self.rmsdBondsLabel) + self.rmsdBondsValue = gtk.Label(self.QualityIndicators['RefinementRmsdBonds']) + rmsdBondsBox_frame = gtk.Frame() + self.rmsdBondsBox = gtk.EventBox() + self.rmsdBondsBox.add(self.rmsdBondsValue) + rmsdBondsBox_frame.add(self.rmsdBondsBox) + + rmsdAnglesLabel_frame = gtk.Frame() + self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') + rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) + self.rmsdAnglesValue = gtk.Label(self.QualityIndicators['RefinementRmsdAngles']) + rmsdAnglesBox_frame = gtk.Frame() + self.rmsdAnglesBox = gtk.EventBox() + self.rmsdAnglesBox.add(self.rmsdAnglesValue) + rmsdAnglesBox_frame.add(self.rmsdAnglesBox) + + MatrixWeightLabel_frame = gtk.Frame() + self.MatrixWeightLabel = gtk.Label('Matrix Weight') + MatrixWeightLabel_frame.add(self.MatrixWeightLabel) + self.MatrixWeightValue = gtk.Label(self.QualityIndicators['RefinementMatrixWeight']) + MatrixWeightBox_frame = gtk.Frame() + self.MatrixWeightBox = gtk.EventBox() + self.MatrixWeightBox.add(self.MatrixWeightValue) + MatrixWeightBox_frame.add(self.MatrixWeightBox) + + ligandIDLabel_frame = gtk.Frame() + self.ligandIDLabel = gtk.Label('Ligand ID') + ligandIDLabel_frame.add(self.ligandIDLabel) + self.ligandIDValue = gtk.Label(self.spider_plot_data['PANDDA_site_ligand_id']) + ligandIDBox_frame = gtk.Frame() + self.ligandIDBox = gtk.EventBox() + self.ligandIDBox.add(self.ligandIDValue) + ligandIDBox_frame.add(self.ligandIDBox) + + ligand_occupancyLabel_frame = gtk.Frame() + self.ligand_occupancyLabel = gtk.Label('occupancy') + ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) + self.ligand_occupancyValue = gtk.Label(self.spider_plot_data['PANDDA_site_occupancy']) + ligand_occupancyBox_frame = gtk.Frame() + self.ligand_occupancyBox = gtk.EventBox() + self.ligand_occupancyBox.add(self.ligand_occupancyValue) + ligand_occupancyBox_frame.add(self.ligand_occupancyBox) + + ligand_BaverageLabel_frame = gtk.Frame() + self.ligand_BaverageLabel = gtk.Label('B average') + ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) + self.ligand_BaverageValue = gtk.Label(self.spider_plot_data['PANDDA_site_B_average']) + ligand_BaverageBox_frame = gtk.Frame() + self.ligand_BaverageBox = gtk.EventBox() + self.ligand_BaverageBox.add(self.ligand_BaverageValue) + ligand_BaverageBox_frame.add(self.ligand_BaverageBox) + + ligand_BratioSurroundingsLabel_frame = gtk.Frame() + self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') + ligand_BratioSurroundingsLabel_frame.add(self.ligand_BratioSurroundingsLabel) + self.ligand_BratioSurroundingsValue = gtk.Label( + self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) + ligand_BratioSurroundingsBox_frame = gtk.Frame() + self.ligand_BratioSurroundingsBox = gtk.EventBox() + self.ligand_BratioSurroundingsBox.add(self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add(self.ligand_BratioSurroundingsBox) + + ligand_RSCCLabel_frame = gtk.Frame() + self.ligand_RSCCLabel = gtk.Label('RSCC') + ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) + self.ligand_RSCCValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSCC']) + ligand_RSCCBox_frame = gtk.Frame() + self.ligand_RSCCBox = gtk.EventBox() + self.ligand_RSCCBox.add(self.ligand_RSCCValue) + ligand_RSCCBox_frame.add(self.ligand_RSCCBox) + + ligand_rmsdLabel_frame = gtk.Frame() + self.ligand_rmsdLabel = gtk.Label('rmsd') + ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) + self.ligand_rmsdValue = gtk.Label(self.spider_plot_data['PANDDA_site_rmsd']) + ligand_rmsdBox_frame = gtk.Frame() + self.ligand_rmsdBox = gtk.EventBox() + self.ligand_rmsdBox.add(self.ligand_rmsdValue) + ligand_rmsdBox_frame.add(self.ligand_rmsdBox) + + ligand_RSRLabel_frame = gtk.Frame() + self.ligand_RSRLabel = gtk.Label('RSR') + ligand_RSRLabel_frame.add(self.ligand_RSRLabel) + self.ligand_RSRValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSR']) + ligand_RSRBox_frame = gtk.Frame() + self.ligand_RSRBox = gtk.EventBox() + self.ligand_RSRBox.add(self.ligand_RSRValue) + ligand_RSRBox_frame.add(self.ligand_RSRBox) + + ligand_RSZDLabel_frame = gtk.Frame() + self.ligand_RSZDLabel = gtk.Label('RSZD') + ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) + self.ligand_RSZDValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSZD']) + ligand_RSZDBox_frame = gtk.Frame() + self.ligand_RSZDBox = gtk.EventBox() + self.ligand_RSZDBox.add(self.ligand_RSZDValue) + ligand_RSZDBox_frame.add(self.ligand_RSZDBox) + + outer_frame = gtk.Frame() + hbox = gtk.HBox() + + frame = gtk.Frame() + self.table_left = gtk.Table(8, 2, False) + self.table_left.attach(RRfreeLabel_frame, 0, 1, 0, 1) + self.table_left.attach(ResolutionLabel_frame, 0, 1, 1, 2) + self.table_left.attach(MolprobityScoreLabel_frame, 0, 1, 2, 3) + self.table_left.attach(RamachandranOutliersLabel_frame, 0, 1, 3, 4) + self.table_left.attach(RamachandranFavoredLabel_frame, 0, 1, 4, 5) + self.table_left.attach(rmsdBondsLabel_frame, 0, 1, 5, 6) + self.table_left.attach(rmsdAnglesLabel_frame, 0, 1, 6, 7) + self.table_left.attach(MatrixWeightLabel_frame, 0, 1, 7, 8) + self.table_left.attach(RRfreeBox_frame, 1, 2, 0, 1) + self.table_left.attach(ResolutionBox_frame, 1, 2, 1, 2) + self.table_left.attach(MolprobityScoreBox_frame, 1, 2, 2, 3) + self.table_left.attach(RamachandranOutliersBox_frame, 1, 2, 3, 4) + self.table_left.attach(RamachandranFavoredBox_frame, 1, 2, 4, 5) + self.table_left.attach(rmsdBondsBox_frame, 1, 2, 5, 6) + self.table_left.attach(rmsdAnglesBox_frame, 1, 2, 6, 7) + self.table_left.attach(MatrixWeightBox_frame, 1, 2, 7, 8) + frame.add(self.table_left) + hbox.add(frame) + + frame = gtk.Frame() + self.table_right = gtk.Table(8, 2, False) + self.table_right.attach(ligandIDLabel_frame, 0, 1, 0, 1) + self.table_right.attach(ligand_occupancyLabel_frame, 0, 1, 1, 2) + self.table_right.attach(ligand_BaverageLabel_frame, 0, 1, 2, 3) + self.table_right.attach(ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach(ligand_RSCCLabel_frame, 0, 1, 4, 5) + self.table_right.attach(ligand_rmsdLabel_frame, 0, 1, 5, 6) + self.table_right.attach(ligand_RSRLabel_frame, 0, 1, 6, 7) + self.table_right.attach(ligand_RSZDLabel_frame, 0, 1, 7, 8) + self.table_right.attach(ligandIDBox_frame, 1, 2, 0, 1) + self.table_right.attach(ligand_occupancyBox_frame, 1, 2, 1, 2) + self.table_right.attach(ligand_BaverageBox_frame, 1, 2, 2, 3) + self.table_right.attach(ligand_BratioSurroundingsBox_frame, 1, 2, 3, 4) + self.table_right.attach(ligand_RSCCBox_frame, 1, 2, 4, 5) + self.table_right.attach(ligand_rmsdBox_frame, 1, 2, 5, 6) + self.table_right.attach(ligand_RSRBox_frame, 1, 2, 6, 7) + self.table_right.attach(ligand_RSZDBox_frame, 1, 2, 7, 8) + frame.add(self.table_right) + hbox.add(frame) + + outer_frame.add(hbox) + self.vbox.add(outer_frame) + + hbox = gtk.HBox() + button = gtk.Button(label="Show MolProbity to-do list") + button.connect("clicked", self.show_molprobity_to_do) + hbox.add(button) + # --- ground state mean map --- + self.ground_state_mean_map_button = gtk.Button(label="Show ground state mean map") + self.ground_state_mean_map_button.connect("clicked", self.show_ground_state_mean_map) + hbox.add(self.ground_state_mean_map_button) +# self.vbox.add(self.ground_state_mean_map_button) + self.vbox.add(hbox) + + self.vbox.pack_start(frame) + + # SPACER +# self.vbox.add(gtk.Label(' ')) + + ################################################################################# + # --- hbox for compound picture & spider_plot (formerly: refinement history) --- + frame = gtk.Frame() + self.hbox_for_info_graphics = gtk.HBox() + + # --- compound picture --- + compound_frame = gtk.Frame() + pic = gtk.gdk.pixbuf_new_from_file( + os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.image = gtk.Image() + self.image.set_from_pixbuf(self.pic) + compound_frame.add(self.image) + self.hbox_for_info_graphics.add(compound_frame) + + # --- Refinement History --- + # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) + # self.canvas.set_size_request(190, 190) + # self.hbox_for_info_graphics.add(self.canvas) + + # --- Spider Plot --- + spider_plot_frame = gtk.Frame() + spider_plot_pic = gtk.gdk.pixbuf_new_from_file( + os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + self.spider_plot_pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_image = gtk.Image() + self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) + spider_plot_frame.add(self.spider_plot_image) + self.hbox_for_info_graphics.add(spider_plot_frame) + + frame.add(self.hbox_for_info_graphics) + self.vbox.add(frame) + + ################################################################################# + # --- pandda.inspect user comments --- +# outer_frame = gtk.Frame(label='pandda.inspect comments') +# vbox = gtk.VBox() +# ligand_site_name_label_frame = gtk.Frame() +# ligand_site_name_label = gtk.Label('Site Name') +# ligand_site_name_label_frame.add(ligand_site_name_label) +# ligand_inspect_confidence_label_frame = gtk.Frame() +# ligand_inspect_confidence_label = gtk.Label('Confidence') +# ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) +# ligand_inspect_interesting_label_frame = gtk.Frame() +# ligand_inspect_interesting_label = gtk.Label('Interesting') +# ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) +# ligand_inspect_comment_label_frame = gtk.Frame() +# ligand_inspect_comment_label = gtk.Label('Comment') +# ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) +# ligand_site_name_value_frame = gtk.Frame() +# self.ligand_site_name_value = gtk.Label('-') +# ligand_site_name_value_frame.add(self.ligand_site_name_value) +# ligand_inspect_confidence_value_frame = gtk.Frame() +# self.ligand_inspect_confidence_value = gtk.Label('-') +# ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) +# ligand_inspect_interesting_value_frame = gtk.Frame() +# self.ligand_inspect_interesting_value = gtk.Label('-') +# ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) +# ligand_inspect_comment_value_frame = gtk.Frame() +# self.ligand_inspect_comment_value = gtk.Label('-') +# ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) +# +# frame_pandda_inspect_comments_table = gtk.Frame() +# pandda_inspect_comments_table = gtk.Table(2, 6, False) +# pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) +# pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) +# pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) +# pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) +# pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) +# pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) +# pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) +# pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) +# +# frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) +# vbox.add(frame_pandda_inspect_comments_table) +# outer_frame.add(vbox) +# self.vbox.pack_start(outer_frame) + + # # SPACER +# self.vbox.add(gtk.Label(' ')) + + ################################################################################# + outer_frame = gtk.Frame(label='Sample Navigator') + hboxSample = gtk.HBox() + + # --- crystal navigator combobox --- + frame = gtk.Frame() + self.vbox_sample_navigator = gtk.VBox() + self.cb = gtk.combo_box_new_text() + self.cb.connect("changed", self.ChooseXtal) + self.vbox_sample_navigator.add(self.cb) + # --- crystal navigator backward/forward button --- + self.PREVbutton = gtk.Button(label="<<<") + self.NEXTbutton = gtk.Button(label=">>>") + self.PREVbutton.connect("clicked", self.ChangeXtal, -1) + self.NEXTbutton.connect("clicked", self.ChangeXtal, +1) + hbox = gtk.HBox() + hbox.pack_start(self.PREVbutton) + hbox.pack_start(self.NEXTbutton) + self.vbox_sample_navigator.add(hbox) + frame.add(self.vbox_sample_navigator) + hboxSample.add(frame) + + # --- site navigator combobox --- + frame = gtk.Frame() + self.vbox_site_navigator = gtk.VBox() + self.cb_site = gtk.combo_box_new_text() + self.cb_site.connect("changed", self.ChooseSite) + self.vbox_site_navigator.add(self.cb_site) + # --- site navigator backward/forward button --- + self.PREVbuttonSite = gtk.Button(label="<<<") + self.NEXTbuttonSite = gtk.Button(label=">>>") + self.PREVbuttonSite.connect("clicked", self.ChangeSite, -1) + self.NEXTbuttonSite.connect("clicked", self.ChangeSite, +1) + hbox = gtk.HBox() + hbox.pack_start(self.PREVbuttonSite) + hbox.pack_start(self.NEXTbuttonSite) + self.vbox_site_navigator.add(hbox) + frame.add(self.vbox_site_navigator) + hboxSample.add(frame) + + outer_frame.add(hboxSample) + self.vbox.add(outer_frame) + + # # SPACER +# self.vbox.add(gtk.Label(' ')) + + ################################################################################# +# outer_frame = gtk.Frame(label='Label') +# hboxlabel = gtk.HBox() +# +# frame = gtk.Frame() +# hbox = gtk.HBox() +# self.vbox_label = gtk.VBox() +# labels = self.db.get_labels_from_db() +# if len(labels) > 5: +# print '==> sorry, too many labels; cannot display them in panel' +# labels = labels[:5] +# # with radiobuttons, one of them needs to be always on +# # but there will be cases when the user has not assigned a label yet +# # hence, the not_shown button is not shown but gets active +# # if the label has not been set yet +# labels.append('not_shown') +# for n, l in enumerate(labels): +# print n,l +# if n == 0: +# new_button = gtk.RadioButton(None, l) +# else: +# new_button = gtk.RadioButton(new_button, l) +# new_button.connect("toggled", self.label_button_clicked, l) +# if not l == 'not_shown': +# hbox.add(new_button) +# self.label_button_list.append(new_button) +# self.vbox_label.add(hbox) +# frame.add(self.vbox_label) +# +# hboxlabel.add(frame) +# +# outer_frame.add(hboxlabel) +# self.vbox.add(outer_frame) + + # SPACER +# self.vbox.add(gtk.Label(' ')) + + ################################################################################# + # --- current refinement stage --- + outer_frame = gtk.Frame() + hbox = gtk.HBox() + + frame = gtk.Frame(label='Analysis Status') + vbox = gtk.VBox() + self.experiment_stage_button_list = [] + for n, button in enumerate(self.experiment_stage): + if n == 0: + new_button = gtk.RadioButton(None, button[0]) + else: + new_button = gtk.RadioButton(new_button, button[0]) + new_button.connect("toggled", self.experiment_stage_button_clicked, button[1]) + vbox.pack_start(new_button,False,False,0) +# vbox.add(new_button) + self.experiment_stage_button_list.append(new_button) + frame.add(vbox) + hbox.pack_start(frame) + + # --- ligand confidence --- + frame = gtk.Frame(label='Ligand Confidence') + vbox = gtk.VBox() + self.ligand_confidence_button_list = [] + for n, criteria in enumerate(self.ligand_confidence_category): + if n == 0: + new_button = gtk.RadioButton(None, criteria) + else: + new_button = gtk.RadioButton(new_button, criteria) + new_button.connect("toggled", self.ligand_confidence_button_clicked, criteria) + vbox.pack_start(new_button,False,False,0) +# vbox.add(new_button) + self.ligand_confidence_button_list.append(new_button) + frame.add(vbox) + hbox.pack_start(frame) + +# # label section --> start +# frame = gtk.Frame(label='Label') +# vbox = gtk.VBox() +# labels = self.db.get_labels_from_db() +# if len(labels) > 5: +# print '==> sorry, too many labels; cannot display them in panel' +# labels = labels[:5] +# # with radiobuttons, one of them needs to be always on +# # but there will be cases when the user has not assigned a label yet +# # hence, the not_shown button is not shown but gets active +# # if the label has not been set yet +# labels.append('not_shown') +# for n, l in enumerate(labels): +# print n,l +# if n == 0: +# new_button = gtk.RadioButton(None, l) +# else: +# new_button = gtk.RadioButton(new_button, l) +# new_button.connect("toggled", self.label_button_clicked, l) +# if not l == 'not_shown': +# vbox.add(new_button) +# self.label_button_list.append(new_button) +# frame.add(vbox) +# hbox.pack_start(frame) +# # label section <-- end + + outer_frame.add(hbox) + self.vbox.pack_start(outer_frame) + + # SPACER +# self.vbox.add(gtk.Label(' ')) + + # --- ligand modeling --- + frame = gtk.Frame(label='Ligand Modeling') + self.hbox_for_modeling = gtk.HBox() + self.merge_ligand_button = gtk.Button(label="Merge Ligand") + self.place_ligand_here_button = gtk.Button(label="Place Ligand here") + self.hbox_for_modeling.add(self.place_ligand_here_button) + self.place_ligand_here_button.connect("clicked", self.place_ligand_here) + self.hbox_for_modeling.add(self.merge_ligand_button) + self.merge_ligand_button.connect("clicked", self.merge_ligand_into_protein) + self.select_cpd_cb = gtk.combo_box_new_text() + self.select_cpd_cb.connect("changed", self.select_cpd) + self.hbox_for_modeling.add(self.select_cpd_cb) + frame.add(self.hbox_for_modeling) + self.vbox.pack_start(frame) + + # # --- ligand confidence --- + # self.cb_ligand_confidence = gtk.combo_box_new_text() + # self.cb_ligand_confidence.connect("changed", self.set_ligand_confidence) + # for citeria in self.ligand_confidence: + # self.cb_ligand_confidence.append_text(citeria) + # self.vbox.add(self.cb_ligand_confidence) + + + # --- refinement & options --- + self.hbox_for_refinement = gtk.HBox() + self.REFINEbutton = gtk.Button(label="Refine") + self.RefinementParamsButton = gtk.Button(label="refinement parameters") + self.covalentLinksbutton = gtk.Button(label="covalent links\n-define-") + self.covalentLinksCreatebutton = gtk.Button(label="covalent links\n-create & refine-") + self.REFINEbutton.connect("clicked", self.REFINE) + self.hbox_for_refinement.add(self.REFINEbutton) + self.RefinementParamsButton.connect("clicked", self.RefinementParams) + self.covalentLinksbutton.connect("clicked", self.covalentLinkDef) + self.covalentLinksCreatebutton.connect("clicked", self.covalentLinkCreate) + self.hbox_for_refinement.add(self.RefinementParamsButton) + self.hbox_for_refinement.add(self.covalentLinksbutton) + self.hbox_for_refinement.add(self.covalentLinksCreatebutton) + self.vbox.add(self.hbox_for_refinement) + + # self.VALIDATEbutton = gtk.Button(label="validate structure") + # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") + + +# # need to put it here, because attributes within refinementProtocolCallback function +# # are defined after checkbox is defined +# self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) + + + # --- CANCEL button --- + self.CANCELbutton = gtk.Button(label="CANCEL") + self.CANCELbutton.connect("clicked", self.CANCEL) + self.vbox.add(self.CANCELbutton) + + self.window.add(self.vbox) + self.window.show_all() + + def CANCEL(self, widget): + self.window.destroy() + + def ChangeXtal(self, widget, data=None): + self.index = self.index + data + if self.index < 0: + self.index = 0 + if self.index >= len(self.Todo): + # self.index = len(self.Todo) + self.index = 0 + self.cb.set_active(self.index) + + def ChooseXtal(self, widget): + self.xtalID = str(widget.get_active_text()) + for n, item in enumerate(self.Todo): + if str(item[0]) == self.xtalID: + self.index = n + self.merge_ligand_button.set_sensitive(True) + self.place_ligand_here_button.set_sensitive(True) + +# self.ligand_site_name_value.set_label('-') +# self.ligand_inspect_confidence_value.set_label('-') +# self.ligand_inspect_interesting_value.set_label('-') +# self.ligand_inspect_comment_value.set_label('-') + + self.refresh_site_combobox() + self.db_dict_mainTable = {} + self.db_dict_panddaTable = {} + if str(self.Todo[self.index][0]) is not None: + self.compoundID = str(self.Todo[self.index][1]) + self.refinement_folder = str(self.Todo[self.index][4]) + self.refinement_outcome = str(self.Todo[self.index][5]) +# self.label = self.db.get_label_of_sample(self.xtalID) +# self.update_label_radiobutton() + self.update_RefinementOutcome_radiobutton() + if self.xtalID not in self.siteDict: # i.e. we are not working with a PanDDA model + self.ligand_confidence = str(self.Todo[self.index][6]) +# self.update_LigandConfidence_radiobutton() +# self.label = self.db.get_label_of_sample(self.xtalID) +# self.update_label_radiobutton() + + self.RefreshData() + + def select_cpd(self, widget): + cpd = str(widget.get_active_text()) + for imol in coot_utils_XChem.molecule_number_list(): + if imol not in self.mol_dict['ligand_stereo']: + continue + molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): + molNameCIF = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/') + 1:].replace('.pdb', '').replace('_phenix','').replace('_rhofit','') + else: + molNameCIF = molName + print cpd,'-',imol,'-',coot.molecule_name(imol) + if molName == cpd: + coot.set_mol_displayed(imol, 1) + print 'reading',os.path.join(self.project_directory,self.xtalID,'compound',molNameCIF+'.cif') + coot.read_cif_dictionary(os.path.join(self.project_directory,self.xtalID,'compound',molNameCIF+'.cif')) + else: + coot.set_mol_displayed(imol, 0) + + + def update_RefinementOutcome_radiobutton(self): + # updating dataset outcome radiobuttons + current_stage = 0 + for i, entry in enumerate(self.experiment_stage): + if entry[1].split()[0] == self.refinement_outcome.split()[0]: + current_stage = i + break + for i, button in enumerate(self.experiment_stage_button_list): + if i == current_stage: + button.set_active(True) + break + +# def update_label_radiobutton(self): +# found = False +# for button in self.label_button_list: +# if button.get_label() == self.label: +# button.set_active(True) +# found = True +# if not found: +# for button in self.label_button_list: +# if button.get_label() == 'not_shown': +# button.set_active(True) +# break + + def update_LigandConfidence_radiobutton(self): + # updating ligand confidence radiobuttons + current_stage = 0 + for i, entry in enumerate(self.ligand_confidence_category): + print '--->', entry, self.ligand_confidence + try: + if entry.split()[0] == self.ligand_confidence.split()[0]: + current_stage = i + break + except IndexError: + pass + for i, button in enumerate(self.ligand_confidence_button_list): + if i == current_stage: + button.set_active(True) + break + + def refresh_site_combobox(self): + # reset self.pandda_index + self.pandda_index = -1 + # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites + for n in range(-1, 100): + self.cb_site.remove_text(0) + self.site_index = '0' + self.event_index = '0' + # only repopulate if site exists + if self.xtalID in self.siteDict: + for item in sorted(self.siteDict[self.xtalID]): + self.cb_site.append_text('site: {0!s} - event: {1!s}'.format(item[5], item[6])) + + def ChangeSite(self, widget, data=None): + if self.xtalID in self.siteDict: + self.pandda_index = self.pandda_index + data + if self.pandda_index < 0: + self.pandda_index = 0 + if self.pandda_index >= len(self.siteDict[self.xtalID]): + self.pandda_index = 0 + self.cb_site.set_active(self.pandda_index) + + def ChooseSite(self, widget): + tmp = str(widget.get_active_text()) + print self.siteDict + print self.site_index + self.site_index = tmp.split()[1] + self.event_index = tmp.split()[4] + for n, item in enumerate(self.siteDict[self.xtalID]): + if item[5] == self.site_index and item[6] == self.event_index: + self.pandda_index = n + self.RefreshSiteData() + + def RefreshSiteData(self): + + if self.pandda_index == -1: + self.merge_ligand_button.set_sensitive(True) + self.place_ligand_here_button.set_sensitive(True) + else: + self.merge_ligand_button.set_sensitive(False) + self.place_ligand_here_button.set_sensitive(False) + # and remove ligand molecule so that there is no temptation to merge it + if len(coot_utils_XChem.molecule_number_list()) > 0: + for imol in coot_utils_XChem.molecule_number_list(): + if self.compoundID + '.pdb' in coot.molecule_name(imol): + coot.close_molecule(imol) + +# for w in self.label_button_list: +# w.set_active(False) + + + print 'pandda index', self.pandda_index + self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] + print 'new spider plot:', self.spider_plot + self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] + print 'new event map:', self.event_map + self.ligand_confidence = str(self.siteDict[self.xtalID][self.pandda_index][7]) + self.update_LigandConfidence_radiobutton() + site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) + site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) + site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) + print 'new site coordinates:', site_x, site_y, site_z + coot.set_rotation_centre(site_x, site_y, site_z) + +# self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) +# self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) +# self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) +# self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) + + self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, + self.event_index) + print '>>>>> spider plot data', self.spider_plot_data + self.ligandIDValue.set_label(self.spider_plot_data['PANDDA_site_ligand_id']) + try: + self.ligand_occupancyValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) + except ValueError: + self.ligand_occupancyValue.set_label('-') + + try: + self.ligand_BaverageValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) + except ValueError: + self.ligand_BaverageValue.set_label('-') + + try: + self.ligand_BratioSurroundingsValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']), 2))) + except ValueError: + self.ligand_BratioSurroundingsValue.set_label('-') + + try: + self.ligand_RSCCValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) + except ValueError: + self.ligand_RSCCValue.set_label('-') + + try: + self.ligand_rmsdValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) + except ValueError: + self.ligand_rmsdValue.set_label('-') + + try: + self.ligand_RSRValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) + except ValueError: + self.ligand_RSRValue.set_label('-') + + try: + self.ligand_RSZDValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) + except ValueError: + self.ligand_RSZDValue.set_label('-') + + ######################################################################################### + # delete old Event MAPs + if len(coot_utils_XChem.molecule_number_list()) > 0: + for imol in coot_utils_XChem.molecule_number_list(): + if 'map.native.ccp4' in coot.molecule_name(imol): + coot.close_molecule(imol) + + ######################################################################################### + # Spider plot + # Note: refinement history was shown instead previously + if os.path.isfile(self.spider_plot): + spider_plot_pic = gtk.gdk.pixbuf_new_from_file(self.spider_plot) + else: + spider_plot_pic = gtk.gdk.pixbuf_new_from_file( + os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) + + ######################################################################################### + # check for PANDDAs EVENT maps + if os.path.isfile(self.event_map): + coot.set_colour_map_rotation_on_read_pdb(0) + coot.handle_read_ccp4_map((self.event_map), 0) + for imol in coot_utils_XChem.molecule_number_list(): + if self.event_map in coot.molecule_name(imol): + coot.set_contour_level_in_sigma(imol, 2) + # coot.set_contour_level_absolute(imol,0.5) + # coot.set_last_map_colour(0.4,0,0.4) + coot.set_last_map_colour(0.74, 0.44, 0.02) + + def experiment_stage_button_clicked(self, widget, data=None): + self.db_dict_mainTable['RefinementOutcome'] = data + self.Logfile.insert('==> COOT: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( + data) + ' in mainTable of datasource') +# print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( +# data) + ' in mainTable of datasource' +# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile,self.xtalID,'ligand_bound',self.db_dict_mainTable) + + def ligand_confidence_button_clicked(self, widget, data=None): + print 'PANDDA_index', self.pandda_index + if self.pandda_index == -1: + self.db_dict_mainTable['RefinementLigandConfidence'] = data + self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( + data) + ' in mainTable of datasource') +# print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( +# data) + ' in mainTable of datasource' + self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + self.Todo[self.index][6] = data + else: + self.db_dict_panddaTable['PANDDA_site_confidence'] = data + self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( + self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( + data) + ' in panddaTable of datasource') +# print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( +# self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( +# data) + ' in panddaTable of datasource' + self.db.update_site_event_panddaTable(self.xtalID, self.site_index, self.event_index, + self.db_dict_panddaTable) + self.siteDict[self.xtalID][self.pandda_index][7] = data + +# def update_label(self, widget): +# print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' +# # widget.pressed() +# for w in self.label_button_list: +# print w.get_label(), w.get_active() +# if w != widget: +# w.set_active(False) +# print '<<<<<<<<<<<<<<<<<<<<<<<<<<' +# self.db_dict_mainTable['label'] = widget.get_label() +# print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( +# widget.get_label()) + ' in mainTable of datasource' +# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + +# def label_button_clicked(self, widget, data=None): +# print '............',data +# if data == 'not_shown': +# self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) +# else: +# self.db_dict_mainTable['label'] = data +# print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' +# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + + def RefreshData(self): + # reset spider plot image + spider_plot_pic = gtk.gdk.pixbuf_new_from_file( + os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) + + # reset ground state mean map + self.ground_state_mean_map = '' + self.ground_state_mean_map_button.set_sensitive(False) + self.ground_state_mean_map_button.set_label('Show ground state mean map') + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.xtalID + '-ground-state-mean-map.native.ccp4')): + self.ground_state_mean_map_button.set_sensitive(True) + self.ground_state_mean_map = os.path.join(self.project_directory, self.xtalID, + self.xtalID + '-ground-state-mean-map.native.ccp4') + + # initialize Refinement library +# self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) + self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) + self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) + self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * '0' + str(self.Serial) + # self.Serial=self.Refine.GetSerial() + if self.Serial == 1: + # i.e. no refinement has been done; data is probably straight out of dimple + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + print '==> XCE: updating quality indicators in data source for ' + self.xtalID + XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, + os.path.join(self.project_directory, self.xtalID, + self.pdb_style)) + XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, + '') # '' because file does not exist + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.pdb')): + print '==> XCE: updating quality indicators in data source for ' + self.xtalID + XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, + os.path.join(self.project_directory, self.xtalID, + 'init.pdb')) + XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, + '') # '' because file does not exist + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): + print '==> XCE: updating quality indicators in data source for ' + self.xtalID + XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, + os.path.join(self.project_directory, self.xtalID, + 'dimple.pdb')) + XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, + '') # '' because file does not exist + + # all this information is now updated in the datasource after each refinement cycle + self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) + + ######################################################################################### + # history + # if the structure was previously refined, try to read the parameters + # self.hbox_for_info_graphics.remove(self.canvas) + if self.Serial > 1: + self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) + print '==> REFMAC params:', self.RefmacParams + # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() + # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) + # else: + # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea + # self.canvas.set_size_request(190, 190) + # self.hbox_for_info_graphics.add(self.canvas) + # self.canvas.show() + + ######################################################################################### + # ligand files + # first remove old samples if present + print '>>>',self.mol_dict['ligand_stereo'] + for n, item in enumerate(self.mol_dict['ligand_stereo']): + print '__',item + self.select_cpd_cb.remove_text(0) + print 'done' + + ######################################################################################### + # remove potential generic line which indicates a possible covalent link + generic_object_clear(self.covLinkObject) + self.covLinkAtomSpec = None + + ######################################################################################### + # reset covalent links + self.covLinks = ['X', 'X', 'X', 'X'] + + ######################################################################################### + # update pdb & maps + + ######################################################################################### + # delete old PDB and MAP files + # - get a list of all molecules which are currently opened in COOT + # - remove all molecules/ maps before loading a new set + if len(coot_utils_XChem.molecule_number_list()) > 0: + for item in coot_utils_XChem.molecule_number_list(): + coot.close_molecule(item) + + ######################################################################################### + # read new PDB files + # read protein molecule after ligand so that this one is the active molecule + coot.set_nomenclature_errors_on_read("ignore") + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): + coot.set_colour_map_rotation_on_read_pdb(0) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb'), 0) + self.mol_dict['ligand'] = imol + coot.read_cif_dictionary(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) + self.select_cpd_cb.append_text(self.compoundID) + self.mol_dict['ligand_stereo'] = [] + self.mol_dict['ligand_stereo'].append(imol) + # ligands in compound directory + for cifFile in sorted(glob.glob(os.path.join(self.project_directory,self.xtalID,'compound',self.compoundID+'_*.pdb'))): + cif = cifFile[cifFile.rfind('/')+1:] + if '_with_H' in cif: + continue + self.select_cpd_cb.append_text(cif.replace('.pdb','')) + imol = coot.handle_read_draw_molecule_with_recentre(cifFile, 0) + self.mol_dict['ligand_stereo'].append(imol) + coot.set_mol_displayed(imol,0) + # autofitted ligands + for pdbFile in sorted(glob.glob(os.path.join(self.project_directory,self.xtalID,'autofit_ligand','*','*.pdb'))): + autofitRun = pdbFile.split('/')[len(pdbFile.split('/')) - 2] + if pdbFile.endswith(autofitRun+'.pdb'): + self.select_cpd_cb.append_text(autofitRun) + imol = coot.handle_read_draw_molecule_with_recentre(pdbFile, 0) + self.mol_dict['ligand_stereo'].append(imol) + coot.set_mol_displayed(imol, 0) + self.select_cpd_cb.set_sensitive(True) + self.select_cpd_cb.set_active(0) + else: + print 'no compound found in sample directory' +# self.select_cpd_cb.append_text('') + self.select_cpd_cb.set_sensitive(False) + + if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + +# if self.refinementProtocol.startswith('pandda'): +# self.Logfile.insert('==> COOT: looking for ground-state model ' + os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', +# '') + '.split.ground-state.pdb')) +## print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, +## self.pdb_style.replace('.pdb', +## '') + '.split.ground-state.pdb') +# if os.path.isfile(os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): +# self.Logfile.insert('==> COOT: found ground-state model') +## print '=> XCE: found ground-state model' +# os.chdir(os.path.join(self.project_directory, self.xtalID)) +# coot.set_colour_map_rotation_on_read_pdb(0) +# try: +# color_wheel_rotation = 160 / float(imol + 2) +# except UnboundLocalError: +# color_wheel_rotation = 80 +# coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) +# imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', +# '') + '.split.ground-state.pdb'), +# 0) +# coot.set_colour_by_molecule(imol) +# coot.set_mol_active(imol, 0) +# else: +# self.Logfile.error('==> COOT - cannot find ground-state model') +## print '=> XCE - ERROR: cannot find ground-state model' +# self.Logfile.insert('==> COOT: looking for bound-state model '+ os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', +# '') + '.split.bound-state.pdb')) +# print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', +# '') + '.split.bound-state.pdb') +# if os.path.isfile(os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb')): +# self.Logfile.insert('==> COOT: found bound-state model') +## print '=> XCE: found bound-state model' +# os.chdir(os.path.join(self.project_directory, self.xtalID)) +# coot.set_colour_map_rotation_on_read_pdb(0) +# color_wheel_rotation = 21 / float(imol + 2) +# coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) +# imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', +# '') + '.split.bound-state.pdb'), +# 0) +# self.mol_dict['protein'] = imol +# else: +# self.Logfile.error('==> COOT: cannot find bound-state model') +## print '=> XCE - ERROR: cannot find bound-state model' +# self.Logfile.warning('==> COOT: moving to next crystal...') +## print '=> XCE: moving to next crystal...' +# self.go_to_next_xtal() +# else: + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.pdb')): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join(self.project_directory, self.xtalID, 'init.pdb'), 0) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join(self.project_directory, self.xtalID, 'dimple.pdb'), 0) + else: + self.go_to_next_xtal() + self.mol_dict['protein'] = imol + + # read any one event map if present + for event_map in glob.glob( + os.path.join(self.project_directory, self.xtalID, self.xtalID + '-event_*.native.ccp4')): + coot.handle_read_ccp4_map((event_map), 0) + coot.set_contour_level_in_sigma(imol, 2) + coot.set_last_map_colour(0.74, 0.44, 0.02) + break + + for item in coot_utils_XChem.molecule_number_list(): + if coot.molecule_name(item).endswith( + self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( + item).endswith(self.pdb_style): + coot.set_show_symmetry_master(1) # master switch to show symmetry molecules + coot.set_show_symmetry_molecule(item, 1) # show symm for model + + ######################################################################################### + # read fofc maps + # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map + # read 2fofc map last so that one can change its contour level + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): + coot.set_colour_map_rotation_on_read_pdb(0) + coot.set_default_initial_contour_level_for_difference_map(3) + coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, 'fofc.map'), 1) + coot.set_default_initial_contour_level_for_map(1) + coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, '2fofc.map'), 0) + coot.set_last_map_colour(0, 0, 1) + else: + # try to open mtz file with same name as pdb file + coot.set_default_initial_contour_level_for_map(1) + # if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): + # os.chdir(os.path.join(self.project_directory,self.xtalID)) + # if not os.path.isfile('REFINEMENT_IN_PROGRESS'): + # if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-pandda-input.mtz')): + # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) + # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): + # os.symlink('dimple.mtz',self.mtz_style) + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): + coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, self.mtz_style)) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.mtz')): + coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, 'init.mtz')) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')): + coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')) + + ######################################################################################### + # update Quality Indicator table + try: + self.RRfreeValue.set_label(str(round(float(self.QualityIndicators['RefinementRcryst']), 3)) + ' / ' + str( + round(float(self.QualityIndicators['RefinementRfree']), 3))) + except ValueError: + self.RRfreeValue.set_label('-') + + try: + self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators['RefinementRfreeTraficLight'])) + except ValueError: + pass + self.ResolutionValue.set_label(self.QualityIndicators['RefinementResolution']) + try: + self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators['RefinementResolutionTL'])) + except ValueError: + pass + self.MolprobityScoreValue.set_label(self.QualityIndicators['RefinementMolProbityScore']) + try: + self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementMolProbityScoreTL'])) + except ValueError: + pass + self.RamachandranOutliersValue.set_label(self.QualityIndicators['RefinementRamachandranOutliers']) + try: + self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRamachandranOutliersTL'])) + except ValueError: + pass + self.RamachandranFavoredValue.set_label(self.QualityIndicators['RefinementRamachandranFavored']) + try: + self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRamachandranFavoredTL'])) + except ValueError: + pass + self.rmsdBondsValue.set_label(self.QualityIndicators['RefinementRmsdBonds']) + try: + self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdBondsTL'])) + except ValueError: + pass + self.rmsdAnglesValue.set_label(self.QualityIndicators['RefinementRmsdAngles']) + try: + self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdAnglesTL'])) + except ValueError: + pass + self.MatrixWeightValue.set_label(self.QualityIndicators['RefinementMatrixWeight']) + + try: + pic = gtk.gdk.pixbuf_new_from_file( + os.path.join(self.project_directory, self.xtalID, self.compoundID + '.png')) + except gobject.GError: + pic = gtk.gdk.pixbuf_new_from_file( + os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.image.set_from_pixbuf(self.pic) + + def go_to_next_xtal(self): + self.index += 1 + if self.index >= len(self.Todo): + self.index = len(self.Todo) + self.cb.set_active(self.index) + + def REFINE(self, widget): + self.start_refinement() + + def start_refinement(self): + # ####################################################### + # if not os.path.isdir(os.path.join(self.project_directory,self.xtalID,'cootOut')): + # os.mkdir(os.path.join(self.project_directory,self.xtalID,'cootOut')) + # # create folder for new refinement cycle + # os.mkdir(os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial))) + # + # ####################################################### + # # write PDB file + # # now take protein pdb file and write it to newly create Refine_ folder + # # note: the user has to make sure that the ligand file was merged into main file + # for item in coot_utils_XChem.molecule_number_list(): + # if coot.molecule_name(item).endswith(self.pdb_style.replace('.pdb','')+'.split.bound-state.pdb') or coot.molecule_name(item).endswith(self.pdb_style): + # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) + # break + # elif coot.molecule_name(item).endswith('dimple.pdb'): + # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) + # break + # + + ####################################################### +# if self.refinementProtocol.startswith('pandda'): +# +# ####################################################### +# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): +# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) +# # create folder for new refinement cycle +# try: +# self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) +# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) +# except OSError: +# self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') +## print '==> XCE: WARNING -> folder exists; will overwrite contents!' +# self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') +# +# ####################################################### +# # write PDB file +# # now take protein pdb file and write it to newly create Refine_ folder +# # note: the user has to make sure that the ligand file was merged into main file +# for item in coot_utils_XChem.molecule_number_list(): +# if coot.molecule_name(item).endswith( +# self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( +# item).endswith(self.pdb_style): +# coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', +# 'Refine_' + str(self.Serial), 'refine.modified.pdb')) +# break +# # elif coot.molecule_name(item).endswith('dimple.pdb'): +# # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) +# # break +# +# XChemRefine.panddaRefine(self.project_directory, self.xtalID, self.compoundID, +# self.data_source).RunQuickRefine(self.Serial, self.RefmacParams, +# self.external_software, self.xce_logfile, +# self.refinementProtocol, self.covLinkAtomSpec) +# else: + + ####################################################### + if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): + os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) + # create folder for new refinement cycle + try: + self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + except OSError: + self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') +# print '==> XCE: WARNING -> folder exists; will overwrite contents!' + self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') + + +# ####################################################### +# # create folder for new refinement cycle and check if free.mtz exists +# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): +# os.mkdir(os.path.join(self.project_directory, self.xtalID)) +# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): +# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) + + ####################################################### + # write PDB file + # now take protein pdb file and write it to newly create Refine_ folder + # note: the user has to make sure that the ligand file was merged into main file + foundPDB = False + for item in coot_utils_XChem.molecule_number_list(): + if coot.molecule_name(item).endswith(self.pdb_style): + foundPDB = True + break + elif coot.molecule_name(item).endswith('refine.split.bound-state.pdb'): + foundPDB = True + break + elif coot.molecule_name(item).endswith('init.pdb'): + foundPDB = True + break + elif coot.molecule_name(item).endswith('dimple.pdb'): + foundPDB = True + break + if foundPDB: + coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', + 'Refine_' + str(self.Serial), 'in.pdb')) + +# self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) + self.Refine.RunBuster(self.Serial, self.external_software, self.xce_logfile, self.covLinkAtomSpec) + self.index += 1 + if self.index >= len(self.Todo): + # self.index = len(self.Todo) + self.index = 0 + self.cb.set_active(self.index) + + def RefinementParams(self, widget): + print '\n==> XCE: changing refinement parameters' + self.RefmacParams = XChemRefine.RefineParams(self.project_directory, self.xtalID, self.compoundID, + self.data_source).RefmacRefinementParams(self.RefmacParams) + + def covalentLinkDef(self, widget): + coot.user_defined_click_py(2,self.show_potential_link) + + def show_potential_link(self,*clicks): + # first find imol of protein molecule + # it's a prerequisite that the ligand is merged into the protein + imol_protein = None + for imol in coot_utils_XChem.molecule_number_list(): + print '>',coot.molecule_name(imol) + if coot.molecule_name(imol).endswith(self.pdb_style) or \ + coot.molecule_name(imol).endswith('init.pdb') or \ + coot.molecule_name(imol).endswith('dimple.pdb') or \ + coot.molecule_name(imol).endswith(self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb'): + imol_protein = imol + break + + print 'please click on the two atoms you want to link' + if (len(clicks) == 2): + click_1 = clicks[0] + click_2 = clicks[1] + imol_1 = click_1[1] + imol_2 = click_2[1] + print 'imolp',imol,'imo11',imol_1,'imol2',imol_2 + if imol_1 == imol_2 and imol_1 == imol_protein: + print 'click_1',click_1 + self.covLinkAtomSpec = None + xyz_1 = atom_info_string(click_1[1],click_1[2],click_1[3],click_1[4],click_1[5],click_1[6]) + residue_1 = residue_name(click_1[1],click_1[2],click_1[3],click_1[4]) + xyz_2 = atom_info_string(click_2[1],click_2[2],click_2[3],click_2[4],click_2[5],click_2[6]) + residue_2 = residue_name(click_2[1],click_2[2],click_2[3],click_2[4]) + thick = 4 + to_generic_object_add_line(self.covLinkObject, "yellowtint", thick, xyz_1[3], xyz_1[4], xyz_1[5], xyz_2[3], xyz_2[4], xyz_2[5]) + set_display_generic_object(self.covLinkObject, 1) + self.covLinkAtomSpec = [imol_protein,click_1,click_2,residue_1,residue_2] + else: + print 'error: both atoms must belong to the same object; did you merge the ligand with your protein?' + + def covalentLinkCreate(self, widget): + if self.covLinkAtomSpec is not None: + imol = self.covLinkAtomSpec[0] + atom1 = self.covLinkAtomSpec[1][1:] + atom2 = self.covLinkAtomSpec[2][1:] + residue_1 = self.covLinkAtomSpec[3] + residue_2 = self.covLinkAtomSpec[4] + make_link(imol, atom1, atom2, residue_1+'-'+residue_2, 1.7) + generic_object_clear(self.covLinkObject) + self.start_refinement() + else: + print 'error: no covalent link defined' + + def set_selection_mode(self, widget): + self.selection_mode = widget.get_active_text() + + def get_samples_to_look_at(self, widget): + if self.selection_mode == '': + self.status_label.set_text('select model stage') + return + self.status_label.set_text('checking datasource for samples... ') + # first remove old samples if present + if len(self.Todo) != 0: + for n, item in enumerate(self.Todo): + self.cb.remove_text(0) + self.Todo = [] + self.siteDict = {} + self.Todo, self.siteDict = self.db.get_todoList_for_coot(self.selection_mode) + self.status_label.set_text('found {0!s} samples'.format(len(self.Todo))) + # refresh sample CB + for item in sorted(self.Todo): + self.cb.append_text('{0!s}'.format(item[0])) + if self.siteDict == {}: + self.cb_site.set_sensitive(False) + self.PREVbuttonSite.set_sensitive(False) + self.NEXTbuttonSite.set_sensitive(False) + else: + self.cb_site.set_sensitive(True) + self.PREVbuttonSite.set_sensitive(True) + self.NEXTbuttonSite.set_sensitive(True) + + def update_plot(self, refinement_cycle, Rfree, Rcryst): + fig = Figure(figsize=(2, 2), dpi=50) + Plot = fig.add_subplot(111) + Plot.set_ylim([0, max(Rcryst + Rfree)]) + Plot.set_xlabel('Refinement Cycle', fontsize=12) + Plot.plot(refinement_cycle, Rfree, label='Rfree', linewidth=2) + Plot.plot(refinement_cycle, Rcryst, label='Rcryst', linewidth=2) + Plot.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, + ncol=2, mode="expand", borderaxespad=0., fontsize=12) + return fig + + def place_ligand_here(self, widget): + cpd = str(self.select_cpd_cb.get_active_text()) + for imol in coot_utils_XChem.molecule_number_list(): + if imol not in self.mol_dict['ligand_stereo']: + continue + molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + if molName == cpd: + print '===> XCE: moving ligand to pointer' + coot_utils_XChem.move_molecule_here(imol) + print 'LIGAND: ', molName +# print '===> XCE: moving ligand to pointer' +# # coot.move_molecule_here() +# print 'LIGAND: ', self.mol_dict['ligand'] +# coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) + + + def merge_ligand_into_protein(self, widget): + cpd = str(self.select_cpd_cb.get_active_text()) + for imol in coot_utils_XChem.molecule_number_list(): + if imol not in self.mol_dict['ligand_stereo']: + continue + molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + if molName == cpd: + print '===> XCE: merge ligand into protein structure -->',cpd + coot.merge_molecules_py([imol], self.mol_dict['protein']) + if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): + molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/') + 1:].replace('.pdb', '').replace('_phenix','').replace('_rhofit','') + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')): + os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) + print 'XCE: changing directory', os.path.join(self.project_directory, self.xtalID) + os.chdir(os.path.join(self.project_directory, self.xtalID)) + print 'XCE: changing symlink ln -s %s %s.cif' % ( + os.path.join('compound', molName + '.cif'), self.compoundID) + os.system('ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): + os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')) + print 'XCE: changing directory', os.path.join(self.project_directory, self.xtalID) + os.chdir(os.path.join(self.project_directory, self.xtalID)) + print 'XCE: changing symlink ln -s %s %s.pdb' % ( + os.path.join('compound', molName + '.pdb'), self.compoundID) + os.system('ln -s %s %s.pdb' % (os.path.join('compound', molName + + '.pdb'), self.compoundID)) + print '===> XCE: deleting ligand molecule',molName + coot.close_molecule(imol) + + self.select_cpd_cb.set_sensitive(False) + +# print '===> XCE: merge ligand into protein structure' +# # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) +# coot.merge_molecules_py([self.mol_dict['ligand']], self.mol_dict['protein']) +# print '===> XCE: deleting ligand molecule' +# coot.close_molecule(self.mol_dict['ligand']) + + def show_molprobity_to_do(self, widget): + print self.panddaSerial + AdjPanddaSerial = (4 - len(str(self.Serial))) * '0' + str(int(self.panddaSerial) - 1) + print os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), + 'molprobity_coot.py') + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), + 'molprobity_coot.py')): + print '==> XCE: running MolProbity Summary for', self.xtalID + coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), + 'molprobity_coot.py')) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), + 'molprobity_coot.py')): + print '==> XCE: running MolProbity Summary for', self.xtalID + coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), + 'molprobity_coot.py')) + else: + print '==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, + 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py') + +# def refinementProtocolCallback(self, widget): +# if widget.get_active(): +# if self.refinementProtocolcheckbox.get_active(): +# self.refinementProtocol = 'pandda_phenix' +# else: +# self.refinementProtocol = 'pandda_refmac' +# self.PREVbuttonSite.set_sensitive(True) +# self.NEXTbuttonSite.set_sensitive(True) +# else: +# self.refinementProtocolcheckbox.set_active(False) +# self.refinementProtocol = 'refmac' +# self.PREVbuttonSite.set_sensitive(False) +# self.NEXTbuttonSite.set_sensitive(False) +# print self.refinementProtocol + +# def refinementProgramCallback(self, widget): +# if widget.get_active(): +# if self.refinementProtocolcheckbox.get_active(): +# self.refinementProtocol = 'pandda_phenix' +# self.RefinementParamsButton.set_sensitive(False) +# else: +# self.refinementProgramcheckbox.set_active(False) +# self.refinementProtocol = 'refmac' +# else: +# self.RefinementParamsButton.set_sensitive(True) +# if self.refinementProtocolcheckbox.get_active(): +# self.refinementProtocol = 'pandda_refmac' +# else: +# self.refinementProtocol = 'refmac' +# print self.refinementProtocol + + def show_ground_state_mean_map(self, widget): + if widget.get_label().startswith('Show'): + loaded = False + for imol in coot_utils_XChem.molecule_number_list(): + if 'ground-state-mean-map' in coot.molecule_name(imol): + coot.set_map_displayed(imol, 1) + loaded = True + break + if not loaded: + coot.set_default_initial_contour_level_for_map(1) + coot.handle_read_ccp4_map(self.ground_state_mean_map, 0) + coot.set_last_map_colour(0.6, 0.6, 0) + widget.set_label('Undisplay ground state mean map') + else: + for imol in coot_utils_XChem.molecule_number_list(): + if 'ground-state-mean-map' in coot.molecule_name(imol): + coot.set_map_displayed(imol, 0) + widget.set_label('Show ground state mean map') + + +if __name__ == '__main__': + GUI().StartGUI() diff --git a/lib/XChemLog.py b/lib/XChemLog.py index d1ab70d0..46a79f36 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 07/04/2020 #\n' + ' # Date: 14/04/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 08dbf845..2b9aff11 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -31,6 +31,168 @@ def get_names_of_current_clusters(xce_logfile,panddas_directory): return cluster_dict + +class refine_bound_state_with_buster(QtCore.QThread): + + def __init__(self,panddas_directory,datasource,initial_model_directory,xce_logfile,which_models): + QtCore.QThread.__init__(self) + self.panddas_directory=panddas_directory + self.datasource=datasource + self.initial_model_directory=initial_model_directory + self.db=XChemDB.data_source(self.datasource) + self.db.create_missing_columns() + self.db_list=self.db.get_empty_db_dict() + self.external_software=XChemUtils.external_software(xce_logfile).check() + self.xce_logfile=xce_logfile + self.Logfile=XChemLog.updateLog(xce_logfile) + self.which_models=which_models + self.already_exported_models=[] + + def run(self): + + samples_to_export=self.export_models() + + self.refine_exported_models(samples_to_export) + + + def refine_exported_models(self,samples_to_export): + self.Logfile.insert('will try to refine the following crystals:') + for xtal in sorted(samples_to_export): + self.Logfile.insert(xtal) + for xtal in sorted(samples_to_export): + self.Logfile.insert('%s: getting compound code from database' %xtal) + query=self.db.execute_statement("select CompoundCode from mainTable where CrystalName='%s';" %xtal) + compoundID=str(query[0][0]) + self.Logfile.insert('%s: compounds code = %s' %(xtal,compoundID)) +# compoundID=str(item[1]) + if os.path.isfile(os.path.join(self.initial_model_directory,xtal,xtal+'.free.mtz')): + if os.path.isfile(os.path.join(self.initial_model_directory,xtal,xtal+'-pandda-model.pdb')): + self.Logfile.insert('running inital refinement on PANDDA model of '+xtal) + Serial=XChemRefine.GetSerial(self.initial_model_directory,xtal) + ####################################################### + if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'cootOut')): + os.mkdir(os.path.join(self.initial_model_directory,xtal,'cootOut')) + # create folder for new refinement cycle + if os.path.isdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))): + os.chdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))) + else: + os.mkdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))) + os.chdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))) + os.system('/bin/cp %s in.pdb' %os.path.join(self.initial_model_directory,xtal,xtal+'-pandda-model.pdb')) + Refine=XChemRefine.Refine(self.initial_model_directory,xtal,compoundID,self.datasource) + Refine.RunBuster(str(Serial),self.external_software,self.xce_logfile,None) + else: + self.Logfile.error('%s: cannot find %s-pandda-model.pdb; cannot start refinement...' %(xtal,xtal)) + + elif xtal in samples_to_export and not os.path.isfile( + os.path.join(self.initial_model_directory, xtal, xtal + '.free.mtz')): + self.Logfile.error('%s: cannot start refinement because %s.free.mtz is missing in %s' % ( + xtal, xtal, os.path.join(self.initial_model_directory, xtal))) + else: + self.Logfile.insert('%s: nothing to refine' % (xtal)) + + + def export_models(self): + + self.Logfile.insert('finding out which PanDDA models need to be exported') + + # first find which samples are in interesting datasets and have a model + # and determine the timestamp + fileModelsDict={} + queryModels='' + for model in glob.glob(os.path.join(self.panddas_directory,'processed_datasets','*','modelled_structures','*-pandda-model.pdb')): + sample=model[model.rfind('/')+1:].replace('-pandda-model.pdb','') + timestamp=datetime.fromtimestamp(os.path.getmtime(model)).strftime('%Y-%m-%d %H:%M:%S') + self.Logfile.insert(sample+'-pandda-model.pdb was created on '+str(timestamp)) + queryModels+="'"+sample+"'," + fileModelsDict[sample]=timestamp + + # now get these models from the database and compare the datestamps + # Note: only get the models that underwent some form of refinement, + # because only if the model was updated in pandda.inspect will it be exported and refined + dbModelsDict={} + if queryModels != '': + dbEntries=self.db.execute_statement("select CrystalName,DatePanDDAModelCreated from mainTable where CrystalName in ("+queryModels[:-1]+") and (RefinementOutcome like '3%' or RefinementOutcome like '4%' or RefinementOutcome like '5%')") + for item in dbEntries: + xtal=str(item[0]) + timestamp=str(item[1]) + dbModelsDict[xtal]=timestamp + self.Logfile.insert('PanDDA model for '+xtal+' is in database and was created on '+str(timestamp)) + + # compare timestamps and only export the ones where the timestamp of the file is newer than the one in the DB + samples_to_export={} + self.Logfile.insert('checking which PanDDA models were newly created or updated') + if self.which_models=='all': + self.Logfile.insert('Note: you chose to export ALL available PanDDA!') + + for sample in fileModelsDict: + if self.which_models=='all': + self.Logfile.insert('exporting '+sample) + samples_to_export[sample]=fileModelsDict[sample] + else: + if sample in dbModelsDict: + try: + difference=(datetime.strptime(fileModelsDict[sample],'%Y-%m-%d %H:%M:%S') - datetime.strptime(dbModelsDict[sample],'%Y-%m-%d %H:%M:%S') ) + if difference.seconds != 0: + self.Logfile.insert('exporting '+sample+' -> was already refined, but newer PanDDA model available') + samples_to_export[sample]=fileModelsDict[sample] + except ValueError: + # this will be raised if timestamp is not properly formatted; + # which will usually be the case when respective field in database is blank + # these are hopefully legacy cases which are from before this extensive check was introduced (13/01/2017) + advice = ( 'The pandda model of '+xtal+' was changed, but it was already refined! ' + 'This is most likely because this was done with an older version of XCE. ' + 'If you really want to export and refine this model, you need to open the database ' + 'with DBbroweser (sqlitebrowser.org); then change the RefinementOutcome field ' + 'of the respective sample to "2 - PANDDA model", save the database and repeat the export prodedure.' ) + self.Logfile.insert(advice) + else: + self.Logfile.insert('exporting '+sample+' -> first time to be exported and refined') + samples_to_export[sample]=fileModelsDict[sample] + + # update the DB: + # set timestamp to current timestamp of file and set RefinementOutcome to '2-pandda...' + + if samples_to_export != {}: + select_dir_string='' + select_dir_string_new_pannda=' ' + for sample in samples_to_export: + self.Logfile.insert('changing directory to ' + os.path.join(self.initial_model_directory,sample)) + os.chdir(os.path.join(self.initial_model_directory,sample)) + self.Logfile.insert(sample + ': copying ' + os.path.join(self.panddas_directory,'processed_datasets',sample,'modelled_structures',sample+'-pandda-model.pdb')) + os.system('/bin/cp %s .' %os.path.join(self.panddas_directory,'processed_datasets',sample,'modelled_structures',sample+'-pandda-model.pdb')) + db_dict= {'RefinementOutcome': '2 - PANDDA model', 'DatePanDDAModelCreated': samples_to_export[sample]} + for old_event_map in glob.glob('*-BDC_*.ccp4'): + if not os.path.isdir('old_event_maps'): + os.mkdir('old_event_maps') + self.Logfile.warning(sample + ': moving ' + old_event_map + ' to old_event_maps folder') + os.system('/bin/mv %s old_event_maps' %old_event_map) + for event_map in glob.glob(os.path.join(self.panddas_directory,'processed_datasets',sample,'*-BDC_*.ccp4')): + self.Logfile.insert(sample + ': copying ' + event_map) + os.system('/bin/cp %s .' %event_map) + select_dir_string+="select_dir={0!s} ".format(sample) + select_dir_string_new_pannda+='{0!s} '.format(sample) + self.Logfile.insert('updating database for '+sample+' setting time model was created to '+db_dict['DatePanDDAModelCreated']+' and RefinementOutcome to '+db_dict['RefinementOutcome']) + self.db.update_data_source(sample,db_dict) + + + return samples_to_export + + + + + + + + + + + + + + + + class run_pandda_export(QtCore.QThread): def __init__(self,panddas_directory,datasource,initial_model_directory,xce_logfile,update_datasource_only,which_models): diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index d113d402..dad3b638 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -323,6 +323,211 @@ def make_covalent_link(self,covLinkAtomSpec,Logfile): else: Logfile.error('could not create linkfile; please check logs in %s/%s' %(self.ProjectPath,self.xtalID)) + def get_hklin_hklout(self,Serial): + ####################################################### + # HKLIN & HKLOUT + hklin = None + hklout = None + if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz')): + hklin=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz') +# elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): +# RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') + else: + Logfile.error('%s: cannot find HKLIN for refinement; aborting...' %self.xtalID) + return None + hklout=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz') + return hklin, hklout + + def get_xyzin_xyzout(self,Serial): + ####################################################### + # XYZIN & XYZOUT + xyzin = None + xyzout = None + if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb')): + xyzin = os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb') + xyzout = os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.pdb') + elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'in.pdb')): + xyzin = os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'in.pdb') + else: + print 'error' + return None + return xyzin, xyzout + + def get_libin_libout(self,Serial): + ####################################################### + # LIBIN & LIBOUT + libin = None + libout = None + if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif')): + libin = os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif') + libout = os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.cif') + else: + print 'error' + return None + return libin, libout + + def write_refinement_in_progress(self): + ####################################################### + # we write 'REFINEMENT_IN_PROGRESS' immediately to avoid unncessary refiment + os.chdir(os.path.join(self.ProjectPath,self.xtalID)) + os.system('touch REFINEMENT_IN_PROGRESS') + + def clean_up_before_refinement(self): + ####################################################### + # clean up! + # and remove all files which will be re-created by current refinement cycle + os.chdir(os.path.join(self.ProjectPath,self.xtalID)) + os.system('/bin/rm refine.pdb refine.mtz refine.split.bound-state.pdb validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log') + + def get_shebang(self,program,qsub): + cmd = '#!'+os.getenv('SHELL')+'\n' + if qsub: + cmd += '#PBS -joe -N xce_%s\n' %program + return cmd + + def load_modules(self,cmd): + ####################################################### + # PHENIX stuff (if working at DLS) + if os.getcwd().startswith('/dls'): + cmd += 'module load phenix\n' + cmd += 'module load buster\n' + return cmd + + def get_source_line(self,cmd): + if 'bash' in os.getenv('SHELL'): + cmd += 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' + elif 'csh' in os.getenv('SHELL'): + cmd += 'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n' + return cmd + + def set_refinement_status(self,cmd): + cmd += ('$CCP4/bin/ccp4-python ' + ' $XChemExplorer_DIR/helpers/update_status_flag.py ' + + self.datasource + ' ' + self.xtalID + ' RefinementStatus running\n') + return cmd + + def add_buster_command(self,cmd,xyzin,hklin,libin,Serial): + cmd += ( + 'refine ' + ' -p %s' %xyzin + + ' -m %s' %hklin + + ' -l %s' %libin + + ' -autoncs' + ' -M TLSbasic' + ' -WAT' + ' -d Refine_%s\n' %str(Serial) + ) + return cmd + + def add_validation(self,cmd,cycle,program): + if program == 'refmac': + Serial = '_' + cycle + elif program == 'buster': + Serial = '' + cmd += ( + 'phenix.molprobity refine%s.pdb refine%s.mtz\n' %(Serial,Serial)+ + '/bin/mv molprobity.out refine_molprobity.log\n' + 'mmtbx.validate_ligands refine%s.pdb refine%s.mtz LIG > validate_ligands.txt\n' %(Serial,Serial)+ + 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' + 'ln -s ./Refine_%s/refine%s.pdb refine.pdb\n' %(cycle,Serial)+ + 'ln -s ./Refine_%s/refine%s.mtz refine.mtz\n' %(cycle,Serial)+ + 'ln -s refine.pdb refine.split.bound-state.pdb\n' + '\n' + 'ln -s Refine_%s/validate_ligands.txt .\n' %cycle+ + 'ln -s Refine_%s/refine_molprobity.log .\n' %cycle+ + 'mmtbx.validation_summary refine.pdb > validation_summary.txt\n' + '\n' + ) + return cmd + + def calculate_maps(self,cmd,program): + if program == 'refmac': + FWT = 'FWT' + PHWT = 'PHWT' + DELFWT = 'DELFWT' + PHDELWT = 'PHDELWT' + elif program == 'buster': + FWT = '2FOFCWT' + PHWT = 'PH2FOFCWT' + DELFWT = 'FOFCWT' + PHDELWT = 'PHFOFCWT' + cmd += ( + 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' + 'labin F1=%s PHI=%s\n' %(FWT,PHWT) + + 'EOF\n' + '\n' + 'fft hklin refine.mtz mapout fofc.map << EOF\n' + 'labin F1=%s PHI=%s\n' %(DELFWT,PHDELWT) + + 'EOF\n' + ) + return cmd + + def update_database(self,cmd,Serial): + cmd += ( '$CCP4/bin/ccp4-python ' + +os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+ + ' %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) ) + cmd += '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' %(self.ProjectPath,self.xtalID) + + return cmd + + def write_refinement_script(self,cmd,program): + os.chdir(os.path.join(self.ProjectPath,self.xtalID)) + f = open(program + '.sh','w') + f.write(cmd) + f.close() + + def run_script(self,program,qsub): + os.chdir(os.path.join(self.ProjectPath,self.xtalID)) + if qsub and not os.uname()[1] == 'hestia': + os.system("qsub -P labxchem -q medium.q %s.sh" %program) + else: + os.system('chmod +x %s.sh' %program) + os.system('./%s.sh &' %program) + + + + def RunBuster(self,Serial,external_software,xce_logfile,covLinkAtomSpec): + + if os.path.isfile(xce_logfile): Logfile=XChemLog.updateLog(xce_logfile) + Serial=str(Serial) + + if covLinkAtomSpec is not None: + self.make_covalent_link(covLinkAtomSpec,Logfile) + + # first check if refinement is ongoing and exit if yes + if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'REFINEMENT_IN_PROGRESS')): + Logfile.insert('cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' %self.xtalID) + return None + + hklin, hklout = self.get_hklin_hklout(Serial) + + xyzin, xyzout = self.get_xyzin_xyzout(Serial) + + libin, libout = self.get_libin_libout(Serial) + + self.clean_up_before_refinement() + + self.write_refinement_in_progress() + + cmd = self.get_shebang('buster',external_software['qsub']) + + cmd = self.load_modules(cmd) + + cmd = self.get_source_line(cmd) + + cmd = self.set_refinement_status(cmd) + + cmd = self.add_buster_command(cmd,xyzin,hklin,libin,Serial) + + cmd = self.add_validation(cmd,Serial,'buster') + + cmd = self.calculate_maps(cmd,'buster') + + cmd = self.update_database(cmd,Serial) + + self.write_refinement_script(cmd,'buster') + + self.run_script('buster',external_software['qsub']) def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtomSpec): @@ -345,7 +550,7 @@ def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom # elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): # RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') else: - Logfile.insert('%s: cannot find HKLIN for refinement; aborting...' %self.xtalID) + Logfile.error('%s: cannot find HKLIN for refinement; aborting...' %self.xtalID) return None RefmacParams['HKLOUT']='HKLOUT '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz \\\n') @@ -852,7 +1057,7 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): RefmacParams['HKLIN']=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz') else: - Logfile.insert('%s: cannot find HKLIN for refinement; aborting...' %self.xtalID) + Logfile.error('%s: cannot find HKLIN for refinement; aborting...' %self.xtalID) return None ####################################################### diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 1f7f012b..cd0a43a8 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2066,6 +2066,8 @@ def __init__(self,settings,interface): self.pylib='XChemCootOld.py' elif interface=='reference': self.pylib='XChemCootReference.py' + elif interface=='buster': + self.pylib='XChemCootBuster.py' def run(self): cwd=os.getcwd() From 599d3949892e27b7db9e97c18aed80b425e592aa Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 17 Apr 2020 11:27:17 +0100 Subject: [PATCH 030/358] v1.6.1 (17/04/2020) (#310) - added 7 - Analysed & Rejected' to refinement table combobox --- ChangeLog.txt | 3 +++ XChemExplorer.py | 2 +- gui_scripts/settings_preferences.py | 5 +++-- lib/XChemDB.py | 6 ++++-- lib/XChemLog.py | 2 +- 5 files changed, 12 insertions(+), 6 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 422ce07e..526c3ca9 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.1 (17/04/2020) +- added 7 - Analysed & Rejected' to refinement table combobox + v1.6.0 (14/04/2020) - new option: directly refine bound-state only after pandda.inspect with buster diff --git a/XChemExplorer.py b/XChemExplorer.py index 370a9b5b..68d1d1da 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -5136,7 +5136,7 @@ def populate_and_update_refinement_table(self): except IndexError: stage = 0 - if stage >= 3: + if stage >= 3 and stage < 7: row = self.refinement_table.rowCount() if xtal not in self.refinement_table_dict: self.refinement_table.insertRow(row) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 73e68531..73ad4284 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.0' + xce_object.xce_version = 'v1.6.1' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -186,7 +186,8 @@ def settings(self, xce_object): '3 - In Refinement', '4 - CompChem ready', '5 - Deposition ready', - '6 - Deposited'] + '6 - Deposited', + '7 - Analysed & Rejected'] self.set_xce_logfile(xce_object) diff --git a/lib/XChemDB.py b/lib/XChemDB.py index a7690ece..384036e7 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -1606,6 +1606,7 @@ def create_or_remove_missing_records_in_depositTable(self,xce_logfile,xtal,type, connect=sqlite3.connect(self.data_source_file) cursor = connect.cursor() Logfile=XChemLog.updateLog(xce_logfile) + oldRefiStage = '' if type == 'ligand_bound': cursor.execute("select RefinementOutcome from mainTable where CrystalName is '{0!s}'".format(xtal)) tmp = cursor.fetchall() @@ -1633,9 +1634,10 @@ def create_or_remove_missing_records_in_depositTable(self,xce_logfile,xtal,type, cursor.execute(sqlite) connect.commit() else: - if int(db_dict['RefinementOutcome'].split()[0]) < 5: + if int(db_dict['RefinementOutcome'].split()[0]) != 5: sqlite="delete from depositTable where CrystalName is '{0!s}' and StructureType is '{1!s}'".format(xtal, type) - Logfile.insert('removing entry for '+str(type)+' structure of '+xtal+' from depositTable') + if oldRefiStage.startswith('5'): + Logfile.insert('removing entry for '+str(type)+' structure of '+xtal+' from depositTable') cursor.execute(sqlite) connect.commit() elif type == 'ground_state': diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 46a79f36..013680c6 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 14/04/2020 #\n' + ' # Date: 17/04/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From eb783edf3d1312f58fdba38dc05685f9556d64b5 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 24 Apr 2020 21:31:42 +0100 Subject: [PATCH 031/358] v1.6.2 (24/04/2020) (#311) - restraints generation: use program name in script name for easier trouble-shooting - assign_stereochemistry.py option removed from restraints generation --- ChangeLog.txt | 4 ++++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemThread.py | 20 ++++++++++---------- lib/XChemUtils.py | 10 +++++----- 5 files changed, 21 insertions(+), 17 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 526c3ca9..960c882b 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.6.2 (24/04/2020) +- restraints generation: use program name in script name for easier trouble-shooting +- assign_stereochemistry.py option removed from restraints generation + v1.6.1 (17/04/2020) - added 7 - Analysed & Rejected' to refinement table combobox diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 73ad4284..29095122 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.1' + xce_object.xce_version = 'v1.6.2' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 013680c6..8e24d931 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 17/04/2020 #\n' + ' # Date: 24/04/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemThread.py b/lib/XChemThread.py index cd0a43a8..33ff5e6b 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -868,29 +868,29 @@ def run(self): if os.path.isdir('/dls'): if self.external_software['qsub_array']: Cmds = ( - '#PBS -joe -N xce_acedrg_master\n' - './xce_acedrg_$SGE_TASK_ID.sh\n' + '#PBS -joe -N xce_%s_master\n' %self.restraints_program + + './xce_%s_$SGE_TASK_ID.sh\n' %self.restraints_program ) - f = open('acedrg_master.sh','w') + f = open('%s_master.sh' %self.restraints_program,'w') f.write(Cmds) f.close() self.Logfile.insert('submitting array job with maximal 100 jobs running on cluster') self.Logfile.insert('using the following command:') - self.Logfile.insert(' qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} acedrg_master.sh'.format(str(counter), self.max_queue_jobs)) - os.system('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} -N acedrg acedrg_master.sh'.format(str(counter), self.max_queue_jobs)) + self.Logfile.insert(' qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh'.format(str(counter), self.max_queue_jobs,self.restraints_program)) + os.system('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} -N {2!s} {3!s}_master.sh'.format(str(counter), self.max_queue_jobs,self.restraints_program,self.restraints_program)) else: self.Logfile.insert("cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") elif self.external_software['qsub']: self.Logfile.insert('submitting {0!s} individual jobs to cluster'.format((str(counter)))) self.Logfile.insert('WARNING: this could potentially lead to a crash...') for i in range(counter): - self.Logfile.insert('qsub -q medium.q -N acedrg xce_acedrg_{0!s}.sh'.format((str(i+1)))) - os.system('qsub -N acedrg xce_acedrg_{0!s}.sh'.format((str(i+1)))) + self.Logfile.insert('qsub -q medium.q -N {0!s} xce_{1!s}_{2!s}.sh'.format(self.restraints_program,self.restraints_program,(str(i+1)))) + os.system('qsub -N {0!s} xce_{1!s}_{2!s}.sh'.format(self.restraints_program,self.restraints_program,(str(i+1)))) else: - self.Logfile.insert('running %s consecutive ACEDRG jobs on your local machine') + self.Logfile.insert('running %s consecutive %s jobs on your local machine' %self.restraints_program) for i in range(counter): - self.Logfile.insert('starting xce_acedrg_{0!s}.sh'.format((str(i+1)))) - os.system('./xce_acedrg_{0!s}.sh'.format((str(i+1)))) + self.Logfile.insert('starting xce_{0!s}_{1!s}.sh'.format(self.restraints_program,(str(i+1)))) + os.system('./xce_{0!s}_{1!s}.sh'.format(self.restraints_program,(str(i+1)))) # self.emit(QtCore.SIGNAL("finished()")) self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 48ea4a39..9973beee 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -292,9 +292,9 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft '\n' + software + '\n' - '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/assign_stereochemistry.py {0!s} {1!s} {2!s}' - .format(compoundID.replace(' ',''),os.path.join(initial_model_directory,sample), os.path.join(database_directory,data_source_file)) + - '\n' +# '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/assign_stereochemistry.py {0!s} {1!s} {2!s}' +# .format(compoundID.replace(' ',''),os.path.join(initial_model_directory,sample), os.path.join(database_directory,data_source_file)) + +# '\n' + copy_with_hydrogens + '\n' + strip_hydrogens + @@ -322,10 +322,10 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft Logfile.insert('creating ACEDRG shell script for {0!s},{1!s} in {2!s}'.format(sample, compoundID, ccp4_scratch_directory)) print Cmds print 'ccp4_scratch',ccp4_scratch_directory - f = open('xce_acedrg_{0!s}.sh'.format(str(counter)),'w') + f = open('xce_{0!s}_{1!s}.sh'.format(restraints_program,str(counter)),'w') f.write(Cmds) f.close() - os.system('chmod +x xce_acedrg_{0!s}.sh'.format(str(counter))) + os.system('chmod +x xce_{0!s}_{1!s}.sh'.format(restraints_program,str(counter))) From 975fa6324f7ad0c890b02495b73c4bd67d94bec6 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 27 Apr 2020 17:00:46 +0100 Subject: [PATCH 032/358] =?UTF-8?q?v1.6.3=20(25/04/2020)=E2=80=A8=20(#312)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - grade will use mogul for restraints generation if program available --- ChangeLog.txt | 3 +++ XChemExplorer_dmd.sh | 13 +++++++---- gui_scripts/settings_preferences.py | 4 ++-- lib/XChemLog.py | 6 ++++- lib/XChemUtils.py | 34 ++++++++++++++++++++++++----- 5 files changed, 48 insertions(+), 12 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 960c882b..9688f48e 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.3 (25/04/2020)
 +- grade will use mogul for restraints generation if program available
 + v1.6.2 (24/04/2020) - restraints generation: use program name in script name for easier trouble-shooting - assign_stereochemistry.py option removed from restraints generation diff --git a/XChemExplorer_dmd.sh b/XChemExplorer_dmd.sh index 80167bfe..243e29a2 100755 --- a/XChemExplorer_dmd.sh +++ b/XChemExplorer_dmd.sh @@ -1,8 +1,13 @@ #!/bin/bash -export XChemExplorer_DIR="/dls/science/groups/i04-1/software/XChemExplorer_new/XChemExplorer" -source $XChemExplorer_DIR/setup-scripts/xce.setup-sh -module unload ccp4 -source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh +if [ -d "/dls/labxchem" ] + then + export XChemExplorer_DIR="/dls/science/groups/i04-1/software/XChemExplorer_new/XChemExplorer" + source $XChemExplorer_DIR/setup-scripts/xce.setup-sh + module unload ccp4 + source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh + module load mx + export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul +fi ccp4-python $XChemExplorer_DIR/XChemExplorer.py diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 29095122..cb43e350 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.2' + xce_object.xce_version = 'v1.6.3' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -214,7 +214,7 @@ def settings(self, xce_object): ' restraints') else: xce_object.restraints_program = '' - xce_object.update_log.insert( + xce_object.update_log.warning( 'No program for generation of ligand coordinates and restraints available!') def preferences(self, xce_object): diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 8e24d931..0a0462f8 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 24/04/2020 #\n' + ' # Date: 27/04/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' @@ -125,4 +125,8 @@ def error(self,message): print( str(present_time)+' ==> XCE: ERROR!!! '+message, file = self.logfile) print('==> XCE: ERROR!!! '+message) + def hint(self,message): + present_time=datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] + print( str(present_time)+' ==> XCE: HINT -> '+message, file = self.logfile) + print('==> XCE: HINT -> '+message) diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 9973beee..c78348b9 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -249,14 +249,19 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft .format(productSmiles, compoundID.replace(' ','')) elif restraints_program=='grade': if os.getcwd().startswith('/dls'): - software+='module load buster\n' + software += 'module load buster\n' + software += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' software+="export BDG_TOOL_OBABEL='none'\n" + if external_software['mogul']: + mogul = '' + else: + mogul = '-nomogul' if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): - software+='grade -resname LIG -nomogul -in ../old.cif -ocif {0!s}.cif -opdb {1!s}.pdb\n'\ - .format(compoundID.replace(' ',''), compoundID.replace(' ','')) + software+='grade -resname LIG {0!s} -in ../old.cif -ocif {1!s}.cif -opdb {2!s}.pdb\n'\ + .format(mogul, compoundID.replace(' ',''), compoundID.replace(' ','')) else: - software+='grade -resname LIG -nomogul "{0!s}" -ocif {1!s}.cif -opdb {2!s}.pdb\n'\ - .format(productSmiles, compoundID.replace(' ',''), compoundID.replace(' ','')) + software+='grade -resname LIG {0!s} "{1!s}" -ocif {2!s}.cif -opdb {3!s}.pdb\n'\ + .format(mogul, productSmiles, compoundID.replace(' ',''), compoundID.replace(' ','')) # Removal of the hydrogen atoms in PDB files is required for REFMAC 5 run. With hydrogens some ligands fail to # pass the external restraints in pandda.giant.make_restraints. # Copy the file with hydrogens to retain in case needed @@ -1587,6 +1592,25 @@ def check(self): status='not found' self.Logfile.insert('{0:50} {1:10}'.format('checking for giant.create_occupancy_params:', status)) + self.Logfile.insert('checking if MOGUL is configured...') + self.available_programs['mogul']=False + if "BDG_TOOL_MOGUL" in os.environ: + self.Logfile.insert('BDG_TOOL_MOGUL is set to ' + os.environ['BDG_TOOL_MOGUL']) + if str(os.environ['BDG_TOOL_MOGUL']).lower() == 'none': + self.Logfile.warning('BDG_TOOL_MOGUL is not properly configured!') + self.Logfile.hint('try adding "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul" to your .bashrc file') + else: + if os.path.isfile(os.getenv('BDG_TOOL_MOGUL')): + self.available_programs['mogul']=True + status='found' + else: + status='not found' + self.Logfile.hint('try adding "export PATH=/dls_sw/apps/ccdc/CSD_2020/bin:$PATH" to your .bashrc file') + else: + self.Logfile.warning('BDG_TOOL_MOGUL is not set!') + self.Logfile.hint('try adding "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul" to your .bashrc file') + status='not found' + self.Logfile.insert('{0:50} {1:10}'.format('checking for mogul:', status)) return self.available_programs From 71b6e5d357f1bce5945732e9400498ec21edbedf Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 28 Apr 2020 13:48:45 +0100 Subject: [PATCH 033/358] v1.6.4 (28/04/2020) (#313) * v1.6.4 (28/04/2020) - added validation with buster-reports after refinement with buster --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemRefine.py | 21 ++++++++++++++++----- 4 files changed, 21 insertions(+), 7 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 9688f48e..1fa8ed84 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.4 (28/04/2020) +- added validation with buster-reports after refinement with buster + v1.6.3 (25/04/2020)
 - grade will use mogul for restraints generation if program available
 diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index cb43e350..181a0013 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.3' + xce_object.xce_version = 'v1.6.4' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 0a0462f8..5a049bfd 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 27/04/2020 #\n' + ' # Date: 28/04/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index dad3b638..eb3802e0 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -420,21 +420,32 @@ def add_buster_command(self,cmd,xyzin,hklin,libin,Serial): return cmd def add_validation(self,cmd,cycle,program): + buster_report = '' if program == 'refmac': Serial = '_' + cycle elif program == 'buster': Serial = '' + if os.getcwd().startswith('/dls'): + buster_report += 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+cycle+'\n' + buster_report += 'corr -p refine.pdb -m refine.mtz -F 2FOFCWT -P PH2FOFCWT\n' + buster_report += 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' + buster_report += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' + buster_report += 'buster-report -d Refine_%s\n' %cycle + cmd += ( - 'phenix.molprobity refine%s.pdb refine%s.mtz\n' %(Serial,Serial)+ - '/bin/mv molprobity.out refine_molprobity.log\n' - 'mmtbx.validate_ligands refine%s.pdb refine%s.mtz LIG > validate_ligands.txt\n' %(Serial,Serial)+ + '\n' + + buster_report + 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' 'ln -s ./Refine_%s/refine%s.pdb refine.pdb\n' %(cycle,Serial)+ 'ln -s ./Refine_%s/refine%s.mtz refine.mtz\n' %(cycle,Serial)+ 'ln -s refine.pdb refine.split.bound-state.pdb\n' '\n' - 'ln -s Refine_%s/validate_ligands.txt .\n' %cycle+ - 'ln -s Refine_%s/refine_molprobity.log .\n' %cycle+ + 'phenix.molprobity refine%s.pdb refine%s.mtz\n' %(Serial,Serial)+ + '/bin/mv molprobity.out refine_molprobity.log\n' + 'mmtbx.validate_ligands refine%s.pdb refine%s.mtz LIG > validate_ligands.txt\n' %(Serial,Serial)+ + '\n' +# 'ln -s Refine_%s/validate_ligands.txt .\n' %cycle+ +# 'ln -s Refine_%s/refine_molprobity.log .\n' %cycle+ 'mmtbx.validation_summary refine.pdb > validation_summary.txt\n' '\n' ) From 0852a4e2d3c62a10088085a583f0e0d005d7516e Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 28 Apr 2020 22:44:19 +0100 Subject: [PATCH 034/358] v1.6.5 (28/04/2020) (#314) * v1.6.5 (28/04/2020) - more verbose error messages in buster refine module --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemRefine.py | 37 +++++++++++++++++++---------- 3 files changed, 29 insertions(+), 13 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 1fa8ed84..4d25d79b 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.5 (28/04/2020) +- more verbose error messages in buster refine module + v1.6.4 (28/04/2020) - added validation with buster-reports after refinement with buster diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 181a0013..8452919f 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.4' + xce_object.xce_version = 'v1.6.5' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index eb3802e0..db5f175b 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -30,8 +30,12 @@ def GetSerial(ProjectPath,xtalID): if os.path.isdir(os.path.join(ProjectPath,xtalID)): for item in glob.glob(os.path.join(ProjectPath,xtalID,'*')): if item.startswith(os.path.join(ProjectPath,xtalID,'Refine_')): - print int(item[item.rfind('_')+1:]) - temp.append(int(item[item.rfind('_')+1:])) + if item.endswith('-report'): + continue + try: + temp.append(int(item[item.rfind('_')+1:])) + except ValueError: + continue found = 1 if found: Serial = max(temp) + 1 @@ -273,6 +277,8 @@ def __init__(self,ProjectPath,xtalID,compoundID,datasource): self.compoundID = compoundID self.prefix = 'refine' self.datasource=datasource + self.error = False + self.Logfile = None def GetSerial(self): # check if there were already previous refinements @@ -333,8 +339,8 @@ def get_hklin_hklout(self,Serial): # elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): # RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') else: - Logfile.error('%s: cannot find HKLIN for refinement; aborting...' %self.xtalID) - return None + self.Logfile.error('%s: cannot find HKLIN for refinement' %self.xtalID) + self.error = True hklout=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz') return hklin, hklout @@ -349,8 +355,8 @@ def get_xyzin_xyzout(self,Serial): elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'in.pdb')): xyzin = os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'in.pdb') else: - print 'error' - return None + self.Logfile.error('%s: cannot find XYZIN for refinement' %self.xtalID) + self.error = True return xyzin, xyzout def get_libin_libout(self,Serial): @@ -362,8 +368,8 @@ def get_libin_libout(self,Serial): libin = os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif') libout = os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.cif') else: - print 'error' - return None + self.Logfile.error('%s: cannot find CIF file for refinement' %self.xtalID) + self.error = True return libin, libout def write_refinement_in_progress(self): @@ -499,7 +505,10 @@ def run_script(self,program,qsub): def RunBuster(self,Serial,external_software,xce_logfile,covLinkAtomSpec): - if os.path.isfile(xce_logfile): Logfile=XChemLog.updateLog(xce_logfile) + self.error = False + + if os.path.isfile(xce_logfile): + self.Logfile=XChemLog.updateLog(xce_logfile) Serial=str(Serial) if covLinkAtomSpec is not None: @@ -536,9 +545,13 @@ def RunBuster(self,Serial,external_software,xce_logfile,covLinkAtomSpec): cmd = self.update_database(cmd,Serial) - self.write_refinement_script(cmd,'buster') - - self.run_script('buster',external_software['qsub']) + if self.error: + self.Logfile.error('%s: cannot start refinement; check error message above' %self.xtalID) + else: + self.Logfile.insert('%s: writing buster.sh file in %s' %(self.xtalID,os.path.join(self.ProjectPath,self.xtalID))) + self.write_refinement_script(cmd,'buster') + self.Logfile.insert('%s: starting refinement...' %self.xtalID) + self.run_script('buster',external_software['qsub']) def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtomSpec): From a2520fa83909cb13b29b32eae9a8d509ca03f6c0 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 28 Apr 2020 23:02:04 +0100 Subject: [PATCH 035/358] v1.6.6 (28/04/2020) (#315) - bug fix: NameError in XChemRefine --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemRefine.py | 4 ++-- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 4d25d79b..44caacb5 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.6 (28/04/2020) +- bug fix: NameError in XChemRefine + v1.6.5 (28/04/2020) - more verbose error messages in buster refine module diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 8452919f..a11691a4 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.5' + xce_object.xce_version = 'v1.6.6' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index db5f175b..90d8885e 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -512,11 +512,11 @@ def RunBuster(self,Serial,external_software,xce_logfile,covLinkAtomSpec): Serial=str(Serial) if covLinkAtomSpec is not None: - self.make_covalent_link(covLinkAtomSpec,Logfile) + self.make_covalent_link(covLinkAtomSpec,self.Logfile) # first check if refinement is ongoing and exit if yes if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'REFINEMENT_IN_PROGRESS')): - Logfile.insert('cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' %self.xtalID) + self.Logfile.insert('cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' %self.xtalID) return None hklin, hklout = self.get_hklin_hklout(Serial) From 994d8b47b93cc9c01d477481c2c307f108df1373 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 29 Apr 2020 13:28:11 +0100 Subject: [PATCH 036/358] v1.6.7 (29/04/2020) (#316) - initial twin refinement with dimple in separate folder and additional fields in XChemDB --- ChangeLog.txt | 3 + gui_scripts/settings_preferences.py | 2 +- ...ate_data_source_for_new_dimple_twin_pdb.py | 109 ++++++++++++++++++ lib/XChemDB.py | 14 +++ lib/XChemLog.py | 2 +- lib/XChemThread.py | 98 +++++++++------- lib/XChemUtils.py | 10 +- 7 files changed, 191 insertions(+), 47 deletions(-) create mode 100755 helpers/update_data_source_for_new_dimple_twin_pdb.py diff --git a/ChangeLog.txt b/ChangeLog.txt index 44caacb5..8b480252 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.7 (29/04/2020) +- initial twin refinement with dimple in separate folder and additional fields in XChemDB + v1.6.6 (28/04/2020) - bug fix: NameError in XChemRefine diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index a11691a4..6d4181c8 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.6' + xce_object.xce_version = 'v1.6.7' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/helpers/update_data_source_for_new_dimple_twin_pdb.py b/helpers/update_data_source_for_new_dimple_twin_pdb.py new file mode 100755 index 00000000..09dcd219 --- /dev/null +++ b/helpers/update_data_source_for_new_dimple_twin_pdb.py @@ -0,0 +1,109 @@ +# last edited: 15/11/2016, 15:00 + +import os,sys +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) +import glob + +from iotbx import mtz + +from XChemUtils import parse +import XChemDB + +if __name__=='__main__': + db_file=sys.argv[1] + xtal=sys.argv[2] + inital_model_directory=sys.argv[3] + + db=XChemDB.data_source(db_file) + if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin.pdb')): + db_dict= {'DimpleTwinPathToPDB': os.path.join(inital_model_directory, xtal, 'dimple_twin.pdb')} + dimple_ran_successfully=False + if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin.mtz')): + db_dict['DimpleTwinPathToMTZ']=os.path.join(inital_model_directory,xtal,'dimple_twin.mtz') + dimple_ran_successfully=True + db_dict['DataProcessingDimpleTwinSuccessful']='True' + db_dict['DimpleTwinStatus'] = 'finished' + if not dimple_ran_successfully: + db_dict['DataProcessingDimpleTwinSuccessful']='False' + db_dict['DimpleTwinStatus'] = 'failed' + pdb=parse().PDBheader(os.path.join(inital_model_directory,xtal,'dimple_twin.pdb')) + db_dict['DimpleTwinRcryst']=pdb['Rcryst'] + db_dict['DimpleTwinRfree']=pdb['Rfree'] + db_dict['RefinementOutcome']='1 - Analysis Pending' + db_dict['RefinementSpaceGroup']=pdb['SpaceGroup'] + db_dict['DimpleTwinFraction'] = pdb['TwinFraction'] +# if not os.path.isfile(xtal+'.free.mtz'): +# os.chdir(os.path.join(inital_model_directory,xtal)) +# os.system('/bin/rm '+xtal+'.free.mtz') +# if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz')): +# os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz'),xtal+'.free.mtz') +# db_dict['RefinementMTZfree']=xtal+'.free.mtz' +# elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz')): +# os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz'),xtal+'.free.mtz') +# db_dict['RefinementMTZfree']=xtal+'.free.mtz' + + # setting free.mtz file + + os.chdir(os.path.join(inital_model_directory,xtal)) + os.system('/bin/rm -f %s.free.mtz' %xtal) + mtzFree = None + db_dict['RefinementTwinMTZfree'] = '' + if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_rerun_on_selected_file','dimple_twin','prepared2.mtz')): + mtzFree = os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_rerun_on_selected_file','dimple_twin','prepared2.mtz') + elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_rerun_on_selected_file','dimple_twin','prepared.mtz')): + mtzFree = os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_rerun_on_selected_file','dimple_twin','prepared.mtz') + elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_twin','prepared.mtz')): + mtzFree = os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_twin','prepared.mtz') + elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_twin','prepared2.mtz')): + mtzFree = os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_twin','prepared2.mtz') + elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_rerun_on_selected_file','dimple_twin','free.mtz')): + mtzFree = os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_rerun_on_selected_file','dimple_twin','free.mtz') + elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_twin','free.mtz')): + mtzFree = os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_twin','free.mtz') + + if mtzFree is not None: + if 'F_unique' in mtz.object(mtzFree).column_labels(): + cmd = ( 'cad hklin1 %s hklout %s.free.mtz << eof\n' %(mtzFree,xtal) + + ' monitor BRIEF\n' + ' labin file 1 E1=F E2=SIGF E3=FreeR_flag\n' + ' labout file 1 E1=F E2=SIGF E3=FreeR_flag\n' + 'eof\n' ) + + os.system(cmd) + else: + os.symlink(mtzFree,xtal+'.free.mtz') + + db_dict['RefinementTwinMTZfree']=xtal+'.free.mtz' + + + + + # if no refinement was carried out yet, then we also want to link the dimple files to refine.pdb/refine.log + # so that we can look at them with the COOT plugin + # 15/11/2016: obsolete since COOT will now read dimple.pdb/dimple.mtz if no refine.pdb/refine.mtz is present +# found_previous_refinement=False +# os.chdir(os.path.join(inital_model_directory,xtal)) +# for dirs in glob.glob('*'): +# if os.path.isdir(dirs) and dirs.startswith('Refine_'): +# found_previous_refinement=True +# break +# if not found_previous_refinement: +# # first delete possible old symbolic links +# if os.path.isfile('refine.pdb'): os.system('/bin/rm refine.pdb') +# os.symlink('dimple.pdb','refine.pdb') +# if os.path.isfile('refine.mtz'): os.system('/bin/rm refine.mtz') +# os.symlink('dimple.mtz','refine.mtz') + + # finally, update data source + print '==> xce: updating data source after DIMPLE run' + db.update_data_source(xtal,db_dict) + + else: + # the actual dimple script creates symbolic links regardless if dimple was successful or not + # python os.path.isfile is False if symbolic link points to non existing file + # so we remove all of them! + os.chdir(os.path.join(inital_model_directory,xtal)) + os.system('/bin/rm dimple_twin.pdb') + os.system('/bin/rm dimple_twin.mtz') + os.system('/bin/rm 2fofc_twin.map') + os.system('/bin/rm fofc_twin.map') diff --git a/lib/XChemDB.py b/lib/XChemDB.py index 384036e7..b4110352 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -167,6 +167,17 @@ def __init__(self,data_source_file): ['DimpleReferencePDB', 'Dimple\nReference PDB', 'TEXT', 1], ['DimpleStatus', 'Dimple\nStatus', 'TEXT', 1], + ['DimpleTwinResolutionHigh', 'Dimple - twin\nResolution High', 'TEXT', 1], + ['DimpleTwinRcryst', 'Dimple - twin\nRcryst', 'TEXT', 1], + ['DimpleTwinRfree', 'Dimple - twin\nRfree', 'TEXT', 1], + ['DimpleTwinPathToPDB', 'Dimple - twin\nPath to PDB file', 'TEXT', 1], + ['DimpleTwinPathToMTZ', 'Dimple - twin\nPath to MTZ file', 'TEXT', 1], + ['DimpleTwinReferencePDB', 'Dimple - twin\nReference PDB', 'TEXT', 1], + ['DimpleTwinStatus', 'Dimple - twin\nStatus', 'TEXT', 1], + ['DimpleTwinFraction', 'Dimple - twin\nFraction', 'TEXT', 1], + ['DataProcessingDimpleTwinSuccessful', 'DataProcessingDimpleTwinSuccessful', 'TEXT', 0], + + ['DimplePANDDAwasRun', 'PanDDA\nlaunched?', 'TEXT', 1], ['DimplePANDDAhit', 'PanDDA\nhit?', 'TEXT', 1], ['DimplePANDDAreject', 'PanDDA\nreject?', 'TEXT', 1], @@ -188,7 +199,10 @@ def __init__(self,data_source_file): ['RefinementRmsdAngles', 'RefinementRmsdAngles', 'TEXT', 1], ['RefinementRmsdAnglesTL', 'RefinementRmsdAnglesTL', 'TEXT', 0], ['RefinementOutcome', 'Refinement\nOutcome', 'TEXT', 1], + ['RefinementMTZfree', 'RefinementMTZfree', 'TEXT', 1], + ['RefinementTwinMTZfree', 'RefinementTwinMTZfree', 'TEXT', 1], + ['RefinementCIF', 'RefinementCIF', 'TEXT', 1], ['RefinementCIFStatus', 'Compound\nStatus', 'TEXT', 1], ['RefinementCIFprogram', 'RefinementCIFprogram', 'TEXT', 1], diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 5a049bfd..655594b7 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 28/04/2020 #\n' + ' # Date: 29/04/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 33ff5e6b..b0e5a61c 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -1434,18 +1434,18 @@ def run(self): if 'dimple_rerun_on_selected_file' in visit_run_autoproc: if self.pipeline=='dimple': - self.prepare_dimple_shell_script(xtal,visit_run_autoproc,mtzin,ref_pdb,ref_mtz,ref_cif) + twin = self.prepare_dimple_shell_script(xtal,visit_run_autoproc,mtzin,ref_pdb,ref_mtz,ref_cif) elif self.pipeline=='pipedream': - self.prepare_pipedream_shell_script(xtal,visit_run_autoproc,mtzin,ref_pdb,ref_mtz,ref_cif) + twin = self.prepare_pipedream_shell_script(xtal,visit_run_autoproc,mtzin,ref_pdb,ref_mtz,ref_cif) elif self.pipeline=='phenix.ligand_pipeline': - self.prepare_phenix_ligand_pipeline_shell_script(xtal,visit_run_autoproc,mtzin,ref_pdb,ref_mtz,ref_cif) + twin = self.prepare_phenix_ligand_pipeline_shell_script(xtal,visit_run_autoproc,mtzin,ref_pdb,ref_mtz,ref_cif) else: - self.prepare_dimple_shell_script(xtal,visit_run_autoproc,mtzin,ref_pdb,ref_mtz,ref_cif) + twin = self.prepare_dimple_shell_script(xtal,visit_run_autoproc,mtzin,ref_pdb,ref_mtz,ref_cif) progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - self.run_script() + self.run_script(twin) self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) @@ -1571,6 +1571,8 @@ def prepare_phenix_ligand_pipeline_shell_script(self,xtal,visit_run_autoproc,mtz db_dict= {'DimpleStatus': 'started'} self.Logfile.insert('{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) self.db.update_data_source(xtal,db_dict) + twin = '' + return twin def prepare_pipedream_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,ref_mtz,ref_cif): @@ -1669,7 +1671,8 @@ def prepare_pipedream_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,re db_dict= {'DimpleStatus': 'started'} self.Logfile.insert('{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) self.db.update_data_source(xtal,db_dict) - + twin = '' + return twin @@ -1698,10 +1701,21 @@ def prepare_dimple_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,ref_m if not os.path.isdir(os.path.join(self.initial_model_directory,xtal)): os.mkdir(os.path.join(self.initial_model_directory,xtal)) os.chdir(os.path.join(self.initial_model_directory,xtal)) - if os.path.isdir(os.path.join(self.initial_model_directory,xtal,'dimple')): - os.system('/bin/rm -fr dimple') - os.mkdir(os.path.join(self.initial_model_directory,xtal,'dimple')) - os.system('touch dimple_run_in_progress') + + twin = '' + twinRefmac = "" + if self.dimple_twin_mode: + twinRefmac = "--refmac-key 'TWIN'" + twin = '_twin' + if os.path.isdir(os.path.join(self.initial_model_directory,xtal,'dimple_twin')): + os.system('/bin/rm -fr dimple_twin') + os.mkdir(os.path.join(self.initial_model_directory,xtal,'dimple_twin')) + os.system('touch dimple_twin_run_in_progress') + else: + if os.path.isdir(os.path.join(self.initial_model_directory,xtal,'dimple')): + os.system('/bin/rm -fr dimple') + os.mkdir(os.path.join(self.initial_model_directory,xtal,'dimple')) + os.system('touch dimple_run_in_progress') os.system('/bin/rm final.mtz 2> /dev/null') os.system('/bin/rm final.pdb 2> /dev/null') @@ -1731,16 +1745,12 @@ def prepare_dimple_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,ref_m else: symNoAbsence = str([x[0] for x in str(mtzFile.space_group_info().symbol_and_number().split('(')[0]).split()]).replace('[','').replace(']','').replace("'","").replace(',','').replace(' ','') - twin = '' - if self.dimple_twin_mode: - twin = "--refmac-key 'TWIN'" - Cmds = ( '{0!s}\n'.format(top_line)+ '\n' 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple') + + 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple%s' %twin) + '\n' 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' '\n' @@ -1748,7 +1758,7 @@ def prepare_dimple_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,ref_m '\n' '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(os.path.join(self.database_directory,self.data_source_file),xtal,'DimpleStatus','running') + '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple') + + 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple%s' %twin) + '\n' 'unique hklout unique.mtz << eof\n' ' cell %s\n' %str([round(float(i),2) for i in mtzFile.unit_cell().parameters()]).replace('[','').replace(']','')+ @@ -1775,37 +1785,37 @@ def prepare_dimple_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,ref_m '\n' 'pointless hklin %s.999A.mtz hklout %s.999A.reind.mtz xyzin %s > pointless.reind.log\n' %(xtal,xtal,ref_pdb) + '\n' - "dimple --no-cleanup %s.999A.reind.mtz %s %s %s %s dimple\n" % (xtal, ref_pdb, ref_mtz, ref_cif, twin) + + "dimple --no-cleanup %s.999A.reind.mtz %s %s %s %s dimple%s\n" % (xtal, ref_pdb, ref_mtz, ref_cif, twinRefmac, twin) + '\n' - 'fft hklin dimple/final.mtz mapout 2fofc.map << EOF\n' + 'fft hklin dimple%s/final.mtz mapout 2fofc%s.map << EOF\n' %(twin,twin) + ' labin F1=FWT PHI=PHWT\n' 'EOF\n' '\n' - 'fft hklin dimple/final.mtz mapout fofc.map << EOF\n' + 'fft hklin dimple%s/final.mtz mapout fofc%s.map << EOF\n' %(twin,twin) + ' labin F1=DELFWT PHI=PHDELWT\n' 'EOF\n' '\n' 'cd %s\n' %os.path.join(self.initial_model_directory,xtal) + '\n' - '/bin/rm dimple.pdb\n' - '/bin/rm dimple.mtz\n' + '/bin/rm dimple%s.pdb\n' %twin + + '/bin/rm dimple%s.mtz\n' %twin + '\n' - 'ln -s dimple/dimple/final.pdb dimple.pdb\n' - 'ln -s dimple/dimple/final.mtz dimple.mtz\n' + 'ln -s dimple%s/dimple%s/final.pdb dimple%s.pdb\n' %(twin,twin,twin) + + 'ln -s dimple%s/dimple%s/final.mtz dimple%s.mtz\n' %(twin,twin,twin) + '\n' - '/bin/rm init.pdb\n' - '/bin/rm init.mtz\n' + '/bin/rm init%s.pdb\n' %twin + + '/bin/rm init%s.mtz\n' %twin + '\n' - 'ln -s dimple.pdb init.pdb\n' - 'ln -s dimple.mtz init.mtz\n' + 'ln -s dimple%s.pdb init%s.pdb\n' %(twin,twin) + + 'ln -s dimple%s.mtz init%s.mtz\n' %(twin,twin) + '\n' - '/bin/rm 2fofc.map\n' - '/bin/rm fofc.map\n' + '/bin/rm 2fofc%s.map\n' %twin + + '/bin/rm fofc%s.map\n' %twin + '\n' - 'ln -s dimple/2fofc.map .\n' - 'ln -s dimple/fofc.map .\n' + 'ln -s dimple%s/2fofc%s.map .\n' %(twin,twin) + + 'ln -s dimple%s/fofc%s.map .\n' %(twin,twin) + '\n' - '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_for_new_dimple_pdb.py')+ + '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_for_new_dimple%s_pdb.py' %twin)+ ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory,self.data_source_file), xtal, self.initial_model_directory) + '\n' '/bin/rm dimple_run_in_progress\n' @@ -1813,46 +1823,46 @@ def prepare_dimple_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,ref_m ) os.chdir(self.ccp4_scratch_directory) - f = open('xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n)),'w') + f = open('xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline,twin, str(self.n)),'w') f.write(Cmds) f.close() - os.system('chmod +x xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n))) + os.system('chmod +x xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline, twin, str(self.n))) self.n+=1 db_dict= {'DimpleStatus': 'started'} self.Logfile.insert('{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) self.db.update_data_source(xtal,db_dict) + return twin - - def run_script(self): + def run_script(self,twin): # submit job self.Logfile.insert('created input scripts for '+str(self.n)+' in '+self.ccp4_scratch_directory) os.chdir(self.ccp4_scratch_directory) if os.path.isdir('/dls'): if self.external_software['qsub_array']: Cmds = ( - '#PBS -joe -N xce_{0!s}_master\n'.format(self.pipeline)+ - './xce_{0!s}_$SGE_TASK_ID.sh\n'.format(self.pipeline) + '#PBS -joe -N xce_{0!s}{1!s}_master\n'.format(self.pipeline,twin)+ + './xce_{0!s}{1!s}_$SGE_TASK_ID.sh\n'.format(self.pipeline,twin) ) - f = open('{0!s}_master.sh'.format(self.pipeline),'w') + f = open('{0!s}{1!s}_master.sh'.format(self.pipeline,twin),'w') f.write(Cmds) f.close() self.Logfile.insert('submitting array job with maximal 100 jobs running on cluster') self.Logfile.insert('using the following command:') self.Logfile.insert('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh'.format(str(self.n), self.max_queue_jobs, self.pipeline)) - os.system('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh'.format(str(self.n-1), self.max_queue_jobs, self.pipeline)) + os.system('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}{3!s}_master.sh'.format(str(self.n-1), self.max_queue_jobs, self.pipeline,twin)) else: self.Logfile.insert("cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") elif self.external_software['qsub']: self.Logfile.insert('submitting {0!s} individual jobs to cluster'.format((str(self.n)))) self.Logfile.insert('WARNING: this could potentially lead to a crash...') for i in range(1,self.n): - self.Logfile.insert('qsub -q medium.q xce_{0!s}_{1!s}.sh'.format(self.pipeline,str(i))) - os.system('qsub -q medium.q xce_{0!s}_{1!s}.sh'.format(self.pipeline,str(i))) + self.Logfile.insert('qsub -q medium.q xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline,twin,str(i))) + os.system('qsub -q medium.q xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline,twin,str(i))) else: self.Logfile.insert('running {0!s} consecutive {1!s} jobs on your local machine'.format(str(self.n-1),self.pipeline)) for i in range(1,self.n): - self.Logfile.insert('starting xce_{0!s}_{1!s}.sh'.format(self.pipeline,str(i))) - os.system('./xce_{0!s}_{1!s}.sh'.format(self.pipeline,str(i))) + self.Logfile.insert('starting xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline,twin,str(i))) + os.system('./xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline,twin,str(i))) diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index c78348b9..374e77bb 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -907,7 +907,8 @@ def PDBheader(self,pdbfile): 'rmsdBonds': 'n/a', 'rmsdBondsTL': 'gray', 'rmsdAngles': 'n/a', - 'rmsdAnglesTL': 'gray'} + 'rmsdAnglesTL': 'gray', + 'TwinFraction': 'n/a' } a='n/a' b='n/a' @@ -969,6 +970,13 @@ def PDBheader(self,pdbfile): except ValueError: pass + if line.startswith('REMARK 3 TWIN FRACTION'): + try: + PDBinfo['TwinFraction'] = line.split()[5] + except IndexError: + pass + + if line.startswith('CRYST1'): a=int(float(line.split()[1])) b=int(float(line.split()[2])) From e7ace38491ea97b700790af833aace72e583e3c4 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 30 Apr 2020 17:06:37 +0100 Subject: [PATCH 037/358] =?UTF-8?q?v1.6.8=20(30/04/2020)=E2=80=A8=20(#317)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - enable html export of '4 - CompChem ready' structures only --- ChangeLog.txt | 3 +++ XChemExplorer.py | 8 +++++++- gui_scripts/settings_preferences.py | 3 ++- lib/XChemDB.py | 11 +++++++---- lib/XChemLog.py | 2 +- web/XChemWeb.py | 4 ++-- 6 files changed, 22 insertions(+), 9 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 8b480252..df3d2ef8 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.8 (30/04/2020)
 +- enable html export of '4 - CompChem ready' structures only
 + v1.6.7 (29/04/2020) - initial twin refinement with dimple in separate folder and additional fields in XChemDB diff --git a/XChemExplorer.py b/XChemExplorer.py index 68d1d1da..df71480c 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -529,7 +529,13 @@ def export_to_html(self): XChemWeb.export_to_html(self.html_export_directory, self.initial_model_directory, os.path.join(self.database_directory, self.data_source_file), - self.xce_logfile).prepare() + self.xce_logfile).prepare(None) + + def export_to_html_CompChem(self): + XChemWeb.export_to_html(self.html_export_directory, + self.initial_model_directory, + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile).prepare('4') # self.update_log.insert('exporting contents of SQLite database into ' + self.html_export_directory) # os.system( diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 6d4181c8..469a793b 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.7' + xce_object.xce_version = 'v1.6.8' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -450,6 +450,7 @@ def top_menu_dict(self, xce_object): [ ['Edit information', '', xce_object.deposition_data], ['Export to HTML', '', xce_object.export_to_html], + ['Export to HTML - CompChem', '', xce_object.export_to_html_CompChem], # ['Find PanDDA apo structures', '', # xce_object.create_missing_apo_records_in_depositTable], # ['Update file info of apo structures', '', diff --git a/lib/XChemDB.py b/lib/XChemDB.py index b4110352..8ce8dc0d 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -1877,12 +1877,15 @@ def getCrystalImageDict(self,visit,xtalList): imageDict[xtal]=[str(img[1]),str(img[2]),str(img[3]),str(img[4])] return imageDict - def samples_for_html_summary(self): + def samples_for_html_summary(self,whichSamples): connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent cursor = connect.cursor() - cursor.execute("select CrystalName from mainTable where RefinementOutcome like '4%' or " - "RefinementOutcome like '5%' or " - "RefinementOutcome like '6%' order by CrystalName ASC") + if whichSamples.startswith('4'): + cursor.execute("select CrystalName from mainTable where RefinementOutcome like '4%' order by CrystalName ASC") + else: + cursor.execute("select CrystalName from mainTable where RefinementOutcome like '4%' or " + "RefinementOutcome like '5%' or " + "RefinementOutcome like '6%' order by CrystalName ASC") xtalList=[] samples = cursor.fetchall() for sample in samples: diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 655594b7..faf521af 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 29/04/2020 #\n' + ' # Date: 30/04/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/web/XChemWeb.py b/web/XChemWeb.py index 58127fb3..01bbf00b 100755 --- a/web/XChemWeb.py +++ b/web/XChemWeb.py @@ -23,13 +23,13 @@ def __init__(self,htmlDir,projectDir,database,xce_logfile): self.pdb = None self.protein_name = None - def prepare(self): + def prepare(self,whichSamples): self.Logfile.insert('======== preparing HTML summary ========') self.makeFolders() self.copy_jscss() html = XChemMain.html_header() firstFile = True - for xtal in self.db.samples_for_html_summary(): + for xtal in self.db.samples_for_html_summary(whichSamples): self.db_dict = self.db.get_db_dict_for_sample(xtal) if firstFile: if self.db_dict['ProteinName'] == 'None': From de2ce626dbdf09026f3533baf609fb6fdd6bf917 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 4 May 2020 14:26:05 +0100 Subject: [PATCH 038/358] =?UTF-8?q?v1.6.9=20(04/05/2020)=E2=80=A8=20(#318)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - added COOT command to open dimple_twin maps --- ChangeLog.txt | 3 + XChemExplorer.py | 2 + gui_scripts/settings_preferences.py | 5 +- lib/XChemCootTwin.py | 1675 +++++++++++++++++++++++++++ lib/XChemLog.py | 2 +- lib/XChemThread.py | 2 + 6 files changed, 1686 insertions(+), 3 deletions(-) create mode 100755 lib/XChemCootTwin.py diff --git a/ChangeLog.txt b/ChangeLog.txt index df3d2ef8..f5ad6d4a 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.9 (04/05/2020)
 +- added COOT command to open dimple_twin maps + v1.6.8 (30/04/2020)
 - enable html export of '4 - CompChem ready' structures only
 diff --git a/XChemExplorer.py b/XChemExplorer.py index df71480c..9183bd32 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -3492,6 +3492,8 @@ def prepare_and_run_task(self, instruction): interface = 'reference' elif instruction == 'Open COOT - BUSTER refinement -': interface = 'buster' + elif instruction == 'Open COOT - dimple_twin -': + interface = 'dimple_twin' else: interface = 'old' print self.settings diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 469a793b..8cea2607 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.8' + xce_object.xce_version = 'v1.6.9' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -632,7 +632,8 @@ def dropdown_items(self, xce_object): 'Build ground state model'] xce_object.refine_file_tasks = ['Open COOT', - 'Open COOT - BUSTER refinement -'] + 'Open COOT - BUSTER refinement -', + 'Open COOT - dimple_twin -' ] # xce_object.refine_file_tasks = ['Open COOT', # 'Open COOT for old PanDDA', diff --git a/lib/XChemCootTwin.py b/lib/XChemCootTwin.py new file mode 100755 index 00000000..85fe52f0 --- /dev/null +++ b/lib/XChemCootTwin.py @@ -0,0 +1,1675 @@ +# last edited: 08/08/2017 - 15:00 + +import gobject +import sys +import os +import pickle +import glob + +from matplotlib.figure import Figure + +# from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas + +# XCE libraries +sys.path.append(os.getenv('XChemExplorer_DIR') + '/lib') +import XChemDB +import XChemRefine +import XChemUtils +import XChemLog + +# libraries from COOT +import pygtk, gtk, pango +import coot + +# had to adapt the original coot_utils.py file +# otherwise unable to import the original file without complaints about missing modules etc. +# modified file is now in $XChemExplorer_DIR/lib +import coot_utils_XChem + + +class GUI(object): + """ + main class which opens the actual GUI + """ + + def __init__(self): + + ########################################################################################### + # read in settings file from XChemExplorer to set the relevant paths + self.settings = pickle.load(open(".xce_settings.pkl", "rb")) + + remote_qsub_submission = self.settings['remote_qsub'] + self.database_directory = self.settings['database_directory'] + self.xce_logfile = self.settings['xce_logfile'] + self.Logfile = XChemLog.updateLog(self.xce_logfile) + self.Logfile.insert('==> COOT: starting coot plugin...') + self.data_source = self.settings['data_source'] + self.db = XChemDB.data_source(self.data_source) + + print self.settings + + # checking for external software packages + self.external_software = XChemUtils.external_software(self.xce_logfile).check() + self.external_software['qsub_remote'] = remote_qsub_submission + + self.selection_criteria = ['0 - All Datasets', + '1 - Analysis Pending', + '2 - PANDDA model', + '3 - In Refinement', + '4 - CompChem ready', + '5 - Deposition ready', + '6 - Deposited', + '7 - Analysed & Rejected'] + + self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], + ['In Refinement', '3 - In Refinement', 65000, 0, 0], + ['Comp Chem Ready!', '4 - CompChem ready', 65000, 0, 0], + ['Ready for Deposition!', '5 - Deposition ready', 65000, 0, 0], + ['In PDB', '6 - Deposited', 65000, 0, 0], + ['Analysed & Rejected', '7 - Analysed & Rejected', 65000, 0, 0]] + + self.ligand_confidence_category = ['0 - no ligand present', + '1 - Low Confidence', + '2 - Correct ligand, weak density', + '3 - Clear density, unexpected ligand', + '4 - High Confidence'] + + self.ligand_site_information = self.db.get_list_of_pandda_sites_for_coot() + + # this decides which samples will be looked at + self.selection_mode = '' + # self.selected_site='' + self.pandda_index = -1 # refers to the number of sites + self.site_index = '0' + self.event_index = '0' + + # the Folder is kind of a legacy thing because my inital idea was to have separate folders + # for Data Processing and Refinement + self.project_directory = self.settings['initial_model_directory'] + self.Serial = 0 + self.panddaSerial = 0 + self.Refine = None + self.index = -1 + self.Todo = [] + self.siteDict = {} + + self.xtalID = '' + self.compoundID = '' + self.ground_state_mean_map = '' + self.spider_plot = '' + self.ligand_confidence = '' + self.refinement_folder = '' +# self.refinementProtocol = 'pandda_refmac' + # self.datasetOutcome='' + + self.pdb_style = 'refine.pdb' + self.mtz_style = 'refine.mtz' + + self.covLink = ['X', 'X', 'X', 'X'] + self.covLinkObject = coot.new_generic_object_number("covalent bond") + self.covLinkAtomSpec = None + + self.label = None + + # stores imol of currently loaded molecules and maps + self.mol_dict = {'protein': -1, + 'ligand': -1, + '2fofc': -1, + 'fofc': -1, + 'event': -1, + 'ligand_stereo': []} + + # two dictionaries which are flushed when a new crystal is loaded + # and which contain information to update the data source if necessary + self.db_dict_mainTable = {} + self.db_dict_panddaTable = {} + + self.label_button_list = [] + + + ########################################################################################### + # some COOT settings + coot.set_map_radius(17) + coot.set_colour_map_rotation_for_map(0) + # coot.set_colour_map_rotation_on_read_pdb_flag(21) + + self.QualityIndicators = {'RefinementRcryst': '-', + 'RefinementRfree': '-', + 'RefinementRfreeTraficLight': 'gray', + 'RefinementResolution': '-', + 'RefinementResolutionTL': 'gray', + 'RefinementMolProbityScore': '-', + 'RefinementMolProbityScoreTL': 'gray', + 'RefinementRamachandranOutliers': '-', + 'RefinementRamachandranOutliersTL': 'gray', + 'RefinementRamachandranFavored': '-', + 'RefinementRamachandranFavoredTL': 'gray', + 'RefinementRmsdBonds': '-', + 'RefinementRmsdBondsTL': 'gray', + 'RefinementRmsdAngles': '-', + 'RefinementRmsdAnglesTL': 'gray', + 'RefinementMatrixWeight': '-'} + + self.spider_plot_data = {'PANDDA_site_ligand_id': '-', + 'PANDDA_site_occupancy': '-', + 'PANDDA_site_B_average': '-', + 'PANDDA_site_B_ratio_residue_surroundings': '-', + 'PANDDA_site_RSCC': '-', + 'PANDDA_site_rmsd': '-', + 'PANDDA_site_RSR': '-', + 'PANDDA_site_RSZD': '-'} + + # default refmac parameters + self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', + 'XYZIN': '', 'XYZOUT': '', + 'LIBIN': '', 'LIBOUT': '', + 'TLSIN': '', 'TLSOUT': '', + 'TLSADD': '', + 'NCYCLES': '10', + 'MATRIX_WEIGHT': 'AUTO', + 'BREF': ' bref ISOT\n', + 'TLS': '', + 'NCS': '', + 'TWIN': ''} + + def StartGUI(self): + + self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) + self.window.connect("delete_event", gtk.main_quit) + self.window.set_border_width(10) + self.window.set_default_size(400, 800) + self.window.set_title("XChemExplorer") + self.vbox = gtk.VBox() # this is the main container + + ################################################################################# + # --- Sample Selection --- + # self.vbox.add(gtk.Label('Select Samples')) + + frame = gtk.Frame(label='Select Samples') + self.hbox_select_samples = gtk.HBox() + # vbox=gtk.VBox() + + self.cb_select_samples = gtk.combo_box_new_text() + self.cb_select_samples.connect("changed", self.set_selection_mode) + for citeria in self.selection_criteria: + self.cb_select_samples.append_text(citeria) + self.hbox_select_samples.add(self.cb_select_samples) + + # self.cb_select_sites = gtk.combo_box_new_text() + # self.cb_select_sites.connect("changed", self.set_site) + # for site in self.ligand_site_information: + # self.cb_select_sites.append_text(str(site[0])+' - '+str(site[1])) + # self.hbox_select_samples.add(self.cb_select_sites) + + self.select_samples_button = gtk.Button(label="GO") + self.select_samples_button.connect("clicked", self.get_samples_to_look_at) + self.hbox_select_samples.add(self.select_samples_button) + frame.add(self.hbox_select_samples) + self.vbox.pack_start(frame) + + ################################################################################# + # --- status window --- + frame = gtk.Frame() + self.status_label = gtk.Label() + frame.add(self.status_label) + self.vbox.pack_start(frame) + + ################################################################################# + # --- refinement protocol --- +# frame = gtk.Frame() +# self.refinementProtocolcheckbox = gtk.CheckButton('PanDDA model refinement)') +# # callback is defined later +## self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) +# self.refinementProtocolcheckbox.set_active(True) +# frame.add(self.refinementProtocolcheckbox) +# self.vbox.pack_start(frame) + + ################################################################################# + # --- refinement program --- +# frame = gtk.Frame() +# self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') +# self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) +# self.refinementProgramcheckbox.set_active(False) +# frame.add(self.refinementProgramcheckbox) +# self.vbox.pack_start(frame) + + # SPACER +# self.vbox.add(gtk.Label(' ')) + + ################################################################################# + # --- Refinement Statistics --- + # next comes a section which displays some global quality indicators + # a combination of labels and textview widgets, arranged in a table + + RRfreeLabel_frame = gtk.Frame() + self.RRfreeLabel = gtk.Label('R/Rfree') + RRfreeLabel_frame.add(self.RRfreeLabel) + self.RRfreeValue = gtk.Label( + self.QualityIndicators['RefinementRcryst'] + '/' + self.QualityIndicators['RefinementRfree']) + RRfreeBox_frame = gtk.Frame() + self.RRfreeBox = gtk.EventBox() + self.RRfreeBox.add(self.RRfreeValue) + RRfreeBox_frame.add(self.RRfreeBox) + + ResolutionLabel_frame = gtk.Frame() + self.ResolutionLabel = gtk.Label('Resolution') + ResolutionLabel_frame.add(self.ResolutionLabel) + self.ResolutionValue = gtk.Label(self.QualityIndicators['RefinementResolution']) + ResolutionBox_frame = gtk.Frame() + self.ResolutionBox = gtk.EventBox() + self.ResolutionBox.add(self.ResolutionValue) + ResolutionBox_frame.add(self.ResolutionBox) + + MolprobityScoreLabel_frame = gtk.Frame() + self.MolprobityScoreLabel = gtk.Label('MolprobityScore') + MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) + self.MolprobityScoreValue = gtk.Label(self.QualityIndicators['RefinementMolProbityScore']) + MolprobityScoreBox_frame = gtk.Frame() + self.MolprobityScoreBox = gtk.EventBox() + self.MolprobityScoreBox.add(self.MolprobityScoreValue) + MolprobityScoreBox_frame.add(self.MolprobityScoreBox) + + RamachandranOutliersLabel_frame = gtk.Frame() + self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') + RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) + self.RamachandranOutliersValue = gtk.Label(self.QualityIndicators['RefinementRamachandranOutliers']) + RamachandranOutliersBox_frame = gtk.Frame() + self.RamachandranOutliersBox = gtk.EventBox() + self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) + RamachandranOutliersBox_frame.add(self.RamachandranOutliersBox) + + RamachandranFavoredLabel_frame = gtk.Frame() + self.RamachandranFavoredLabel = gtk.Label('Rama Favored') + RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) + self.RamachandranFavoredValue = gtk.Label(self.QualityIndicators['RefinementRamachandranFavored']) + RamachandranFavoredBox_frame = gtk.Frame() + self.RamachandranFavoredBox = gtk.EventBox() + self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) + RamachandranFavoredBox_frame.add(self.RamachandranFavoredBox) + + rmsdBondsLabel_frame = gtk.Frame() + self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') + rmsdBondsLabel_frame.add(self.rmsdBondsLabel) + self.rmsdBondsValue = gtk.Label(self.QualityIndicators['RefinementRmsdBonds']) + rmsdBondsBox_frame = gtk.Frame() + self.rmsdBondsBox = gtk.EventBox() + self.rmsdBondsBox.add(self.rmsdBondsValue) + rmsdBondsBox_frame.add(self.rmsdBondsBox) + + rmsdAnglesLabel_frame = gtk.Frame() + self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') + rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) + self.rmsdAnglesValue = gtk.Label(self.QualityIndicators['RefinementRmsdAngles']) + rmsdAnglesBox_frame = gtk.Frame() + self.rmsdAnglesBox = gtk.EventBox() + self.rmsdAnglesBox.add(self.rmsdAnglesValue) + rmsdAnglesBox_frame.add(self.rmsdAnglesBox) + + MatrixWeightLabel_frame = gtk.Frame() + self.MatrixWeightLabel = gtk.Label('Matrix Weight') + MatrixWeightLabel_frame.add(self.MatrixWeightLabel) + self.MatrixWeightValue = gtk.Label(self.QualityIndicators['RefinementMatrixWeight']) + MatrixWeightBox_frame = gtk.Frame() + self.MatrixWeightBox = gtk.EventBox() + self.MatrixWeightBox.add(self.MatrixWeightValue) + MatrixWeightBox_frame.add(self.MatrixWeightBox) + + ligandIDLabel_frame = gtk.Frame() + self.ligandIDLabel = gtk.Label('Ligand ID') + ligandIDLabel_frame.add(self.ligandIDLabel) + self.ligandIDValue = gtk.Label(self.spider_plot_data['PANDDA_site_ligand_id']) + ligandIDBox_frame = gtk.Frame() + self.ligandIDBox = gtk.EventBox() + self.ligandIDBox.add(self.ligandIDValue) + ligandIDBox_frame.add(self.ligandIDBox) + + ligand_occupancyLabel_frame = gtk.Frame() + self.ligand_occupancyLabel = gtk.Label('occupancy') + ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) + self.ligand_occupancyValue = gtk.Label(self.spider_plot_data['PANDDA_site_occupancy']) + ligand_occupancyBox_frame = gtk.Frame() + self.ligand_occupancyBox = gtk.EventBox() + self.ligand_occupancyBox.add(self.ligand_occupancyValue) + ligand_occupancyBox_frame.add(self.ligand_occupancyBox) + + ligand_BaverageLabel_frame = gtk.Frame() + self.ligand_BaverageLabel = gtk.Label('B average') + ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) + self.ligand_BaverageValue = gtk.Label(self.spider_plot_data['PANDDA_site_B_average']) + ligand_BaverageBox_frame = gtk.Frame() + self.ligand_BaverageBox = gtk.EventBox() + self.ligand_BaverageBox.add(self.ligand_BaverageValue) + ligand_BaverageBox_frame.add(self.ligand_BaverageBox) + + ligand_BratioSurroundingsLabel_frame = gtk.Frame() + self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') + ligand_BratioSurroundingsLabel_frame.add(self.ligand_BratioSurroundingsLabel) + self.ligand_BratioSurroundingsValue = gtk.Label( + self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) + ligand_BratioSurroundingsBox_frame = gtk.Frame() + self.ligand_BratioSurroundingsBox = gtk.EventBox() + self.ligand_BratioSurroundingsBox.add(self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add(self.ligand_BratioSurroundingsBox) + + ligand_RSCCLabel_frame = gtk.Frame() + self.ligand_RSCCLabel = gtk.Label('RSCC') + ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) + self.ligand_RSCCValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSCC']) + ligand_RSCCBox_frame = gtk.Frame() + self.ligand_RSCCBox = gtk.EventBox() + self.ligand_RSCCBox.add(self.ligand_RSCCValue) + ligand_RSCCBox_frame.add(self.ligand_RSCCBox) + + ligand_rmsdLabel_frame = gtk.Frame() + self.ligand_rmsdLabel = gtk.Label('rmsd') + ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) + self.ligand_rmsdValue = gtk.Label(self.spider_plot_data['PANDDA_site_rmsd']) + ligand_rmsdBox_frame = gtk.Frame() + self.ligand_rmsdBox = gtk.EventBox() + self.ligand_rmsdBox.add(self.ligand_rmsdValue) + ligand_rmsdBox_frame.add(self.ligand_rmsdBox) + + ligand_RSRLabel_frame = gtk.Frame() + self.ligand_RSRLabel = gtk.Label('RSR') + ligand_RSRLabel_frame.add(self.ligand_RSRLabel) + self.ligand_RSRValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSR']) + ligand_RSRBox_frame = gtk.Frame() + self.ligand_RSRBox = gtk.EventBox() + self.ligand_RSRBox.add(self.ligand_RSRValue) + ligand_RSRBox_frame.add(self.ligand_RSRBox) + + ligand_RSZDLabel_frame = gtk.Frame() + self.ligand_RSZDLabel = gtk.Label('RSZD') + ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) + self.ligand_RSZDValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSZD']) + ligand_RSZDBox_frame = gtk.Frame() + self.ligand_RSZDBox = gtk.EventBox() + self.ligand_RSZDBox.add(self.ligand_RSZDValue) + ligand_RSZDBox_frame.add(self.ligand_RSZDBox) + + outer_frame = gtk.Frame() + hbox = gtk.HBox() + + frame = gtk.Frame() + self.table_left = gtk.Table(8, 2, False) + self.table_left.attach(RRfreeLabel_frame, 0, 1, 0, 1) + self.table_left.attach(ResolutionLabel_frame, 0, 1, 1, 2) + self.table_left.attach(MolprobityScoreLabel_frame, 0, 1, 2, 3) + self.table_left.attach(RamachandranOutliersLabel_frame, 0, 1, 3, 4) + self.table_left.attach(RamachandranFavoredLabel_frame, 0, 1, 4, 5) + self.table_left.attach(rmsdBondsLabel_frame, 0, 1, 5, 6) + self.table_left.attach(rmsdAnglesLabel_frame, 0, 1, 6, 7) + self.table_left.attach(MatrixWeightLabel_frame, 0, 1, 7, 8) + self.table_left.attach(RRfreeBox_frame, 1, 2, 0, 1) + self.table_left.attach(ResolutionBox_frame, 1, 2, 1, 2) + self.table_left.attach(MolprobityScoreBox_frame, 1, 2, 2, 3) + self.table_left.attach(RamachandranOutliersBox_frame, 1, 2, 3, 4) + self.table_left.attach(RamachandranFavoredBox_frame, 1, 2, 4, 5) + self.table_left.attach(rmsdBondsBox_frame, 1, 2, 5, 6) + self.table_left.attach(rmsdAnglesBox_frame, 1, 2, 6, 7) + self.table_left.attach(MatrixWeightBox_frame, 1, 2, 7, 8) + frame.add(self.table_left) + hbox.add(frame) + + frame = gtk.Frame() + self.table_right = gtk.Table(8, 2, False) + self.table_right.attach(ligandIDLabel_frame, 0, 1, 0, 1) + self.table_right.attach(ligand_occupancyLabel_frame, 0, 1, 1, 2) + self.table_right.attach(ligand_BaverageLabel_frame, 0, 1, 2, 3) + self.table_right.attach(ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach(ligand_RSCCLabel_frame, 0, 1, 4, 5) + self.table_right.attach(ligand_rmsdLabel_frame, 0, 1, 5, 6) + self.table_right.attach(ligand_RSRLabel_frame, 0, 1, 6, 7) + self.table_right.attach(ligand_RSZDLabel_frame, 0, 1, 7, 8) + self.table_right.attach(ligandIDBox_frame, 1, 2, 0, 1) + self.table_right.attach(ligand_occupancyBox_frame, 1, 2, 1, 2) + self.table_right.attach(ligand_BaverageBox_frame, 1, 2, 2, 3) + self.table_right.attach(ligand_BratioSurroundingsBox_frame, 1, 2, 3, 4) + self.table_right.attach(ligand_RSCCBox_frame, 1, 2, 4, 5) + self.table_right.attach(ligand_rmsdBox_frame, 1, 2, 5, 6) + self.table_right.attach(ligand_RSRBox_frame, 1, 2, 6, 7) + self.table_right.attach(ligand_RSZDBox_frame, 1, 2, 7, 8) + frame.add(self.table_right) + hbox.add(frame) + + outer_frame.add(hbox) + self.vbox.add(outer_frame) + + hbox = gtk.HBox() + button = gtk.Button(label="Show MolProbity to-do list") + button.connect("clicked", self.show_molprobity_to_do) + hbox.add(button) + # --- ground state mean map --- + self.ground_state_mean_map_button = gtk.Button(label="Show ground state mean map") + self.ground_state_mean_map_button.connect("clicked", self.show_ground_state_mean_map) + hbox.add(self.ground_state_mean_map_button) +# self.vbox.add(self.ground_state_mean_map_button) + self.vbox.add(hbox) + + self.vbox.pack_start(frame) + + # SPACER +# self.vbox.add(gtk.Label(' ')) + + ################################################################################# + # --- hbox for compound picture & spider_plot (formerly: refinement history) --- + frame = gtk.Frame() + self.hbox_for_info_graphics = gtk.HBox() + + # --- compound picture --- + compound_frame = gtk.Frame() + pic = gtk.gdk.pixbuf_new_from_file( + os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.image = gtk.Image() + self.image.set_from_pixbuf(self.pic) + compound_frame.add(self.image) + self.hbox_for_info_graphics.add(compound_frame) + + # --- Refinement History --- + # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) + # self.canvas.set_size_request(190, 190) + # self.hbox_for_info_graphics.add(self.canvas) + + # --- Spider Plot --- + spider_plot_frame = gtk.Frame() + spider_plot_pic = gtk.gdk.pixbuf_new_from_file( + os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + self.spider_plot_pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_image = gtk.Image() + self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) + spider_plot_frame.add(self.spider_plot_image) + self.hbox_for_info_graphics.add(spider_plot_frame) + + frame.add(self.hbox_for_info_graphics) + self.vbox.add(frame) + + ################################################################################# + # --- pandda.inspect user comments --- +# outer_frame = gtk.Frame(label='pandda.inspect comments') +# vbox = gtk.VBox() +# ligand_site_name_label_frame = gtk.Frame() +# ligand_site_name_label = gtk.Label('Site Name') +# ligand_site_name_label_frame.add(ligand_site_name_label) +# ligand_inspect_confidence_label_frame = gtk.Frame() +# ligand_inspect_confidence_label = gtk.Label('Confidence') +# ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) +# ligand_inspect_interesting_label_frame = gtk.Frame() +# ligand_inspect_interesting_label = gtk.Label('Interesting') +# ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) +# ligand_inspect_comment_label_frame = gtk.Frame() +# ligand_inspect_comment_label = gtk.Label('Comment') +# ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) +# ligand_site_name_value_frame = gtk.Frame() +# self.ligand_site_name_value = gtk.Label('-') +# ligand_site_name_value_frame.add(self.ligand_site_name_value) +# ligand_inspect_confidence_value_frame = gtk.Frame() +# self.ligand_inspect_confidence_value = gtk.Label('-') +# ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) +# ligand_inspect_interesting_value_frame = gtk.Frame() +# self.ligand_inspect_interesting_value = gtk.Label('-') +# ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) +# ligand_inspect_comment_value_frame = gtk.Frame() +# self.ligand_inspect_comment_value = gtk.Label('-') +# ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) +# +# frame_pandda_inspect_comments_table = gtk.Frame() +# pandda_inspect_comments_table = gtk.Table(2, 6, False) +# pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) +# pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) +# pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) +# pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) +# pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) +# pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) +# pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) +# pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) +# +# frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) +# vbox.add(frame_pandda_inspect_comments_table) +# outer_frame.add(vbox) +# self.vbox.pack_start(outer_frame) + + # # SPACER +# self.vbox.add(gtk.Label(' ')) + + ################################################################################# + outer_frame = gtk.Frame(label='Sample Navigator') + hboxSample = gtk.HBox() + + # --- crystal navigator combobox --- + frame = gtk.Frame() + self.vbox_sample_navigator = gtk.VBox() + self.cb = gtk.combo_box_new_text() + self.cb.connect("changed", self.ChooseXtal) + self.vbox_sample_navigator.add(self.cb) + # --- crystal navigator backward/forward button --- + self.PREVbutton = gtk.Button(label="<<<") + self.NEXTbutton = gtk.Button(label=">>>") + self.PREVbutton.connect("clicked", self.ChangeXtal, -1) + self.NEXTbutton.connect("clicked", self.ChangeXtal, +1) + hbox = gtk.HBox() + hbox.pack_start(self.PREVbutton) + hbox.pack_start(self.NEXTbutton) + self.vbox_sample_navigator.add(hbox) + frame.add(self.vbox_sample_navigator) + hboxSample.add(frame) + + # --- site navigator combobox --- + frame = gtk.Frame() + self.vbox_site_navigator = gtk.VBox() + self.cb_site = gtk.combo_box_new_text() + self.cb_site.connect("changed", self.ChooseSite) + self.vbox_site_navigator.add(self.cb_site) + # --- site navigator backward/forward button --- + self.PREVbuttonSite = gtk.Button(label="<<<") + self.NEXTbuttonSite = gtk.Button(label=">>>") + self.PREVbuttonSite.connect("clicked", self.ChangeSite, -1) + self.NEXTbuttonSite.connect("clicked", self.ChangeSite, +1) + hbox = gtk.HBox() + hbox.pack_start(self.PREVbuttonSite) + hbox.pack_start(self.NEXTbuttonSite) + self.vbox_site_navigator.add(hbox) + frame.add(self.vbox_site_navigator) + hboxSample.add(frame) + + outer_frame.add(hboxSample) + self.vbox.add(outer_frame) + + # # SPACER +# self.vbox.add(gtk.Label(' ')) + + ################################################################################# +# outer_frame = gtk.Frame(label='Label') +# hboxlabel = gtk.HBox() +# +# frame = gtk.Frame() +# hbox = gtk.HBox() +# self.vbox_label = gtk.VBox() +# labels = self.db.get_labels_from_db() +# if len(labels) > 5: +# print '==> sorry, too many labels; cannot display them in panel' +# labels = labels[:5] +# # with radiobuttons, one of them needs to be always on +# # but there will be cases when the user has not assigned a label yet +# # hence, the not_shown button is not shown but gets active +# # if the label has not been set yet +# labels.append('not_shown') +# for n, l in enumerate(labels): +# print n,l +# if n == 0: +# new_button = gtk.RadioButton(None, l) +# else: +# new_button = gtk.RadioButton(new_button, l) +# new_button.connect("toggled", self.label_button_clicked, l) +# if not l == 'not_shown': +# hbox.add(new_button) +# self.label_button_list.append(new_button) +# self.vbox_label.add(hbox) +# frame.add(self.vbox_label) +# +# hboxlabel.add(frame) +# +# outer_frame.add(hboxlabel) +# self.vbox.add(outer_frame) + + # SPACER +# self.vbox.add(gtk.Label(' ')) + + ################################################################################# + # --- current refinement stage --- + outer_frame = gtk.Frame() + hbox = gtk.HBox() + + frame = gtk.Frame(label='Analysis Status') + vbox = gtk.VBox() + self.experiment_stage_button_list = [] + for n, button in enumerate(self.experiment_stage): + if n == 0: + new_button = gtk.RadioButton(None, button[0]) + else: + new_button = gtk.RadioButton(new_button, button[0]) + new_button.connect("toggled", self.experiment_stage_button_clicked, button[1]) + vbox.pack_start(new_button,False,False,0) +# vbox.add(new_button) + self.experiment_stage_button_list.append(new_button) + frame.add(vbox) + hbox.pack_start(frame) + + # --- ligand confidence --- + frame = gtk.Frame(label='Ligand Confidence') + vbox = gtk.VBox() + self.ligand_confidence_button_list = [] + for n, criteria in enumerate(self.ligand_confidence_category): + if n == 0: + new_button = gtk.RadioButton(None, criteria) + else: + new_button = gtk.RadioButton(new_button, criteria) + new_button.connect("toggled", self.ligand_confidence_button_clicked, criteria) + vbox.pack_start(new_button,False,False,0) +# vbox.add(new_button) + self.ligand_confidence_button_list.append(new_button) + frame.add(vbox) + hbox.pack_start(frame) + +# # label section --> start +# frame = gtk.Frame(label='Label') +# vbox = gtk.VBox() +# labels = self.db.get_labels_from_db() +# if len(labels) > 5: +# print '==> sorry, too many labels; cannot display them in panel' +# labels = labels[:5] +# # with radiobuttons, one of them needs to be always on +# # but there will be cases when the user has not assigned a label yet +# # hence, the not_shown button is not shown but gets active +# # if the label has not been set yet +# labels.append('not_shown') +# for n, l in enumerate(labels): +# print n,l +# if n == 0: +# new_button = gtk.RadioButton(None, l) +# else: +# new_button = gtk.RadioButton(new_button, l) +# new_button.connect("toggled", self.label_button_clicked, l) +# if not l == 'not_shown': +# vbox.add(new_button) +# self.label_button_list.append(new_button) +# frame.add(vbox) +# hbox.pack_start(frame) +# # label section <-- end + + outer_frame.add(hbox) + self.vbox.pack_start(outer_frame) + + # SPACER +# self.vbox.add(gtk.Label(' ')) + + # --- ligand modeling --- + frame = gtk.Frame(label='Ligand Modeling') + self.hbox_for_modeling = gtk.HBox() + self.merge_ligand_button = gtk.Button(label="Merge Ligand") + self.place_ligand_here_button = gtk.Button(label="Place Ligand here") + self.hbox_for_modeling.add(self.place_ligand_here_button) + self.place_ligand_here_button.connect("clicked", self.place_ligand_here) + self.hbox_for_modeling.add(self.merge_ligand_button) + self.merge_ligand_button.connect("clicked", self.merge_ligand_into_protein) + self.select_cpd_cb = gtk.combo_box_new_text() + self.select_cpd_cb.connect("changed", self.select_cpd) + self.hbox_for_modeling.add(self.select_cpd_cb) + frame.add(self.hbox_for_modeling) + self.vbox.pack_start(frame) + + # # --- ligand confidence --- + # self.cb_ligand_confidence = gtk.combo_box_new_text() + # self.cb_ligand_confidence.connect("changed", self.set_ligand_confidence) + # for citeria in self.ligand_confidence: + # self.cb_ligand_confidence.append_text(citeria) + # self.vbox.add(self.cb_ligand_confidence) + + + # --- refinement & options --- + self.hbox_for_refinement = gtk.HBox() + self.REFINEbutton = gtk.Button(label="Refine") + self.RefinementParamsButton = gtk.Button(label="refinement parameters") + self.covalentLinksbutton = gtk.Button(label="covalent links\n-define-") + self.covalentLinksCreatebutton = gtk.Button(label="covalent links\n-create & refine-") + self.REFINEbutton.connect("clicked", self.REFINE) + self.hbox_for_refinement.add(self.REFINEbutton) + self.RefinementParamsButton.connect("clicked", self.RefinementParams) + self.covalentLinksbutton.connect("clicked", self.covalentLinkDef) + self.covalentLinksCreatebutton.connect("clicked", self.covalentLinkCreate) + self.hbox_for_refinement.add(self.RefinementParamsButton) + self.hbox_for_refinement.add(self.covalentLinksbutton) + self.hbox_for_refinement.add(self.covalentLinksCreatebutton) + self.vbox.add(self.hbox_for_refinement) + + # self.VALIDATEbutton = gtk.Button(label="validate structure") + # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") + + +# # need to put it here, because attributes within refinementProtocolCallback function +# # are defined after checkbox is defined +# self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) + + + # --- CANCEL button --- + self.CANCELbutton = gtk.Button(label="CANCEL") + self.CANCELbutton.connect("clicked", self.CANCEL) + self.vbox.add(self.CANCELbutton) + + self.window.add(self.vbox) + self.window.show_all() + + def CANCEL(self, widget): + self.window.destroy() + + def ChangeXtal(self, widget, data=None): + self.index = self.index + data + if self.index < 0: + self.index = 0 + if self.index >= len(self.Todo): + # self.index = len(self.Todo) + self.index = 0 + self.cb.set_active(self.index) + + def ChooseXtal(self, widget): + self.xtalID = str(widget.get_active_text()) + for n, item in enumerate(self.Todo): + if str(item[0]) == self.xtalID: + self.index = n + self.merge_ligand_button.set_sensitive(True) + self.place_ligand_here_button.set_sensitive(True) + +# self.ligand_site_name_value.set_label('-') +# self.ligand_inspect_confidence_value.set_label('-') +# self.ligand_inspect_interesting_value.set_label('-') +# self.ligand_inspect_comment_value.set_label('-') + + self.refresh_site_combobox() + self.db_dict_mainTable = {} + self.db_dict_panddaTable = {} + if str(self.Todo[self.index][0]) is not None: + self.compoundID = str(self.Todo[self.index][1]) + self.refinement_folder = str(self.Todo[self.index][4]) + self.refinement_outcome = str(self.Todo[self.index][5]) +# self.label = self.db.get_label_of_sample(self.xtalID) +# self.update_label_radiobutton() + self.update_RefinementOutcome_radiobutton() + if self.xtalID not in self.siteDict: # i.e. we are not working with a PanDDA model + self.ligand_confidence = str(self.Todo[self.index][6]) +# self.update_LigandConfidence_radiobutton() +# self.label = self.db.get_label_of_sample(self.xtalID) +# self.update_label_radiobutton() + + self.RefreshData() + + def select_cpd(self, widget): + cpd = str(widget.get_active_text()) + for imol in coot_utils_XChem.molecule_number_list(): + if imol not in self.mol_dict['ligand_stereo']: + continue + molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): + molNameCIF = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/') + 1:].replace('.pdb', '').replace('_phenix','').replace('_rhofit','') + else: + molNameCIF = molName + print cpd,'-',imol,'-',coot.molecule_name(imol) + if molName == cpd: + coot.set_mol_displayed(imol, 1) + print 'reading',os.path.join(self.project_directory,self.xtalID,'compound',molNameCIF+'.cif') + coot.read_cif_dictionary(os.path.join(self.project_directory,self.xtalID,'compound',molNameCIF+'.cif')) + else: + coot.set_mol_displayed(imol, 0) + + + def update_RefinementOutcome_radiobutton(self): + # updating dataset outcome radiobuttons + current_stage = 0 + for i, entry in enumerate(self.experiment_stage): + if entry[1].split()[0] == self.refinement_outcome.split()[0]: + current_stage = i + break + for i, button in enumerate(self.experiment_stage_button_list): + if i == current_stage: + button.set_active(True) + break + +# def update_label_radiobutton(self): +# found = False +# for button in self.label_button_list: +# if button.get_label() == self.label: +# button.set_active(True) +# found = True +# if not found: +# for button in self.label_button_list: +# if button.get_label() == 'not_shown': +# button.set_active(True) +# break + + def update_LigandConfidence_radiobutton(self): + # updating ligand confidence radiobuttons + current_stage = 0 + for i, entry in enumerate(self.ligand_confidence_category): + print '--->', entry, self.ligand_confidence + try: + if entry.split()[0] == self.ligand_confidence.split()[0]: + current_stage = i + break + except IndexError: + pass + for i, button in enumerate(self.ligand_confidence_button_list): + if i == current_stage: + button.set_active(True) + break + + def refresh_site_combobox(self): + # reset self.pandda_index + self.pandda_index = -1 + # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites + for n in range(-1, 100): + self.cb_site.remove_text(0) + self.site_index = '0' + self.event_index = '0' + # only repopulate if site exists + if self.xtalID in self.siteDict: + for item in sorted(self.siteDict[self.xtalID]): + self.cb_site.append_text('site: {0!s} - event: {1!s}'.format(item[5], item[6])) + + def ChangeSite(self, widget, data=None): + if self.xtalID in self.siteDict: + self.pandda_index = self.pandda_index + data + if self.pandda_index < 0: + self.pandda_index = 0 + if self.pandda_index >= len(self.siteDict[self.xtalID]): + self.pandda_index = 0 + self.cb_site.set_active(self.pandda_index) + + def ChooseSite(self, widget): + tmp = str(widget.get_active_text()) + print self.siteDict + print self.site_index + self.site_index = tmp.split()[1] + self.event_index = tmp.split()[4] + for n, item in enumerate(self.siteDict[self.xtalID]): + if item[5] == self.site_index and item[6] == self.event_index: + self.pandda_index = n + self.RefreshSiteData() + + def RefreshSiteData(self): + + if self.pandda_index == -1: + self.merge_ligand_button.set_sensitive(True) + self.place_ligand_here_button.set_sensitive(True) + else: + self.merge_ligand_button.set_sensitive(False) + self.place_ligand_here_button.set_sensitive(False) + # and remove ligand molecule so that there is no temptation to merge it + if len(coot_utils_XChem.molecule_number_list()) > 0: + for imol in coot_utils_XChem.molecule_number_list(): + if self.compoundID + '.pdb' in coot.molecule_name(imol): + coot.close_molecule(imol) + +# for w in self.label_button_list: +# w.set_active(False) + + + print 'pandda index', self.pandda_index + self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] + print 'new spider plot:', self.spider_plot + self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] + print 'new event map:', self.event_map + self.ligand_confidence = str(self.siteDict[self.xtalID][self.pandda_index][7]) + self.update_LigandConfidence_radiobutton() + site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) + site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) + site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) + print 'new site coordinates:', site_x, site_y, site_z + coot.set_rotation_centre(site_x, site_y, site_z) + +# self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) +# self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) +# self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) +# self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) + + self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, + self.event_index) + print '>>>>> spider plot data', self.spider_plot_data + self.ligandIDValue.set_label(self.spider_plot_data['PANDDA_site_ligand_id']) + try: + self.ligand_occupancyValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) + except ValueError: + self.ligand_occupancyValue.set_label('-') + + try: + self.ligand_BaverageValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) + except ValueError: + self.ligand_BaverageValue.set_label('-') + + try: + self.ligand_BratioSurroundingsValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']), 2))) + except ValueError: + self.ligand_BratioSurroundingsValue.set_label('-') + + try: + self.ligand_RSCCValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) + except ValueError: + self.ligand_RSCCValue.set_label('-') + + try: + self.ligand_rmsdValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) + except ValueError: + self.ligand_rmsdValue.set_label('-') + + try: + self.ligand_RSRValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) + except ValueError: + self.ligand_RSRValue.set_label('-') + + try: + self.ligand_RSZDValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) + except ValueError: + self.ligand_RSZDValue.set_label('-') + + ######################################################################################### + # delete old Event MAPs + if len(coot_utils_XChem.molecule_number_list()) > 0: + for imol in coot_utils_XChem.molecule_number_list(): + if 'map.native.ccp4' in coot.molecule_name(imol): + coot.close_molecule(imol) + + ######################################################################################### + # Spider plot + # Note: refinement history was shown instead previously + if os.path.isfile(self.spider_plot): + spider_plot_pic = gtk.gdk.pixbuf_new_from_file(self.spider_plot) + else: + spider_plot_pic = gtk.gdk.pixbuf_new_from_file( + os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) + + ######################################################################################### + # check for PANDDAs EVENT maps + if os.path.isfile(self.event_map): + coot.set_colour_map_rotation_on_read_pdb(0) + coot.handle_read_ccp4_map((self.event_map), 0) + for imol in coot_utils_XChem.molecule_number_list(): + if self.event_map in coot.molecule_name(imol): + coot.set_contour_level_in_sigma(imol, 2) + # coot.set_contour_level_absolute(imol,0.5) + # coot.set_last_map_colour(0.4,0,0.4) + coot.set_last_map_colour(0.74, 0.44, 0.02) + + def experiment_stage_button_clicked(self, widget, data=None): + self.db_dict_mainTable['RefinementOutcome'] = data + self.Logfile.insert('==> COOT: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( + data) + ' in mainTable of datasource') +# print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( +# data) + ' in mainTable of datasource' +# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile,self.xtalID,'ligand_bound',self.db_dict_mainTable) + + def ligand_confidence_button_clicked(self, widget, data=None): + print 'PANDDA_index', self.pandda_index + if self.pandda_index == -1: + self.db_dict_mainTable['RefinementLigandConfidence'] = data + self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( + data) + ' in mainTable of datasource') +# print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( +# data) + ' in mainTable of datasource' + self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + self.Todo[self.index][6] = data + else: + self.db_dict_panddaTable['PANDDA_site_confidence'] = data + self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( + self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( + data) + ' in panddaTable of datasource') +# print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( +# self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( +# data) + ' in panddaTable of datasource' + self.db.update_site_event_panddaTable(self.xtalID, self.site_index, self.event_index, + self.db_dict_panddaTable) + self.siteDict[self.xtalID][self.pandda_index][7] = data + +# def update_label(self, widget): +# print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' +# # widget.pressed() +# for w in self.label_button_list: +# print w.get_label(), w.get_active() +# if w != widget: +# w.set_active(False) +# print '<<<<<<<<<<<<<<<<<<<<<<<<<<' +# self.db_dict_mainTable['label'] = widget.get_label() +# print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( +# widget.get_label()) + ' in mainTable of datasource' +# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + +# def label_button_clicked(self, widget, data=None): +# print '............',data +# if data == 'not_shown': +# self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) +# else: +# self.db_dict_mainTable['label'] = data +# print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' +# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + + def RefreshData(self): + # reset spider plot image + spider_plot_pic = gtk.gdk.pixbuf_new_from_file( + os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) + + # reset ground state mean map + self.ground_state_mean_map = '' + self.ground_state_mean_map_button.set_sensitive(False) + self.ground_state_mean_map_button.set_label('Show ground state mean map') + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.xtalID + '-ground-state-mean-map.native.ccp4')): + self.ground_state_mean_map_button.set_sensitive(True) + self.ground_state_mean_map = os.path.join(self.project_directory, self.xtalID, + self.xtalID + '-ground-state-mean-map.native.ccp4') + + # initialize Refinement library +# self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) + self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) + self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) + self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * '0' + str(self.Serial) + # self.Serial=self.Refine.GetSerial() + if self.Serial == 1: + # i.e. no refinement has been done; data is probably straight out of dimple + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + print '==> XCE: updating quality indicators in data source for ' + self.xtalID + XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, + os.path.join(self.project_directory, self.xtalID, + self.pdb_style)) + XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, + '') # '' because file does not exist + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init_twin.pdb')): + print '==> XCE: updating quality indicators in data source for ' + self.xtalID + XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, + os.path.join(self.project_directory, self.xtalID, + 'init_twin.pdb')) + XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, + '') # '' because file does not exist + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple_twin.pdb')): + print '==> XCE: updating quality indicators in data source for ' + self.xtalID + XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, + os.path.join(self.project_directory, self.xtalID, + 'dimple_twin.pdb')) + XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, + '') # '' because file does not exist + + # all this information is now updated in the datasource after each refinement cycle + self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) + + ######################################################################################### + # history + # if the structure was previously refined, try to read the parameters + # self.hbox_for_info_graphics.remove(self.canvas) + if self.Serial > 1: + self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) + print '==> REFMAC params:', self.RefmacParams + # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() + # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) + # else: + # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea + # self.canvas.set_size_request(190, 190) + # self.hbox_for_info_graphics.add(self.canvas) + # self.canvas.show() + + ######################################################################################### + # ligand files + # first remove old samples if present + print '>>>',self.mol_dict['ligand_stereo'] + for n, item in enumerate(self.mol_dict['ligand_stereo']): + print '__',item + self.select_cpd_cb.remove_text(0) + print 'done' + + ######################################################################################### + # remove potential generic line which indicates a possible covalent link + generic_object_clear(self.covLinkObject) + self.covLinkAtomSpec = None + + ######################################################################################### + # reset covalent links + self.covLinks = ['X', 'X', 'X', 'X'] + + ######################################################################################### + # update pdb & maps + + ######################################################################################### + # delete old PDB and MAP files + # - get a list of all molecules which are currently opened in COOT + # - remove all molecules/ maps before loading a new set + if len(coot_utils_XChem.molecule_number_list()) > 0: + for item in coot_utils_XChem.molecule_number_list(): + coot.close_molecule(item) + + ######################################################################################### + # read new PDB files + # read protein molecule after ligand so that this one is the active molecule + coot.set_nomenclature_errors_on_read("ignore") + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): + coot.set_colour_map_rotation_on_read_pdb(0) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb'), 0) + self.mol_dict['ligand'] = imol + coot.read_cif_dictionary(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) + self.select_cpd_cb.append_text(self.compoundID) + self.mol_dict['ligand_stereo'] = [] + self.mol_dict['ligand_stereo'].append(imol) + # ligands in compound directory + for cifFile in sorted(glob.glob(os.path.join(self.project_directory,self.xtalID,'compound',self.compoundID+'_*.pdb'))): + cif = cifFile[cifFile.rfind('/')+1:] + if '_with_H' in cif: + continue + self.select_cpd_cb.append_text(cif.replace('.pdb','')) + imol = coot.handle_read_draw_molecule_with_recentre(cifFile, 0) + self.mol_dict['ligand_stereo'].append(imol) + coot.set_mol_displayed(imol,0) + # autofitted ligands + for pdbFile in sorted(glob.glob(os.path.join(self.project_directory,self.xtalID,'autofit_ligand','*','*.pdb'))): + autofitRun = pdbFile.split('/')[len(pdbFile.split('/')) - 2] + if pdbFile.endswith(autofitRun+'.pdb'): + self.select_cpd_cb.append_text(autofitRun) + imol = coot.handle_read_draw_molecule_with_recentre(pdbFile, 0) + self.mol_dict['ligand_stereo'].append(imol) + coot.set_mol_displayed(imol, 0) + self.select_cpd_cb.set_sensitive(True) + self.select_cpd_cb.set_active(0) + else: + print 'no compound found in sample directory' +# self.select_cpd_cb.append_text('') + self.select_cpd_cb.set_sensitive(False) + + if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + +# if self.refinementProtocol.startswith('pandda'): +# self.Logfile.insert('==> COOT: looking for ground-state model ' + os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', +# '') + '.split.ground-state.pdb')) +## print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, +## self.pdb_style.replace('.pdb', +## '') + '.split.ground-state.pdb') +# if os.path.isfile(os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): +# self.Logfile.insert('==> COOT: found ground-state model') +## print '=> XCE: found ground-state model' +# os.chdir(os.path.join(self.project_directory, self.xtalID)) +# coot.set_colour_map_rotation_on_read_pdb(0) +# try: +# color_wheel_rotation = 160 / float(imol + 2) +# except UnboundLocalError: +# color_wheel_rotation = 80 +# coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) +# imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', +# '') + '.split.ground-state.pdb'), +# 0) +# coot.set_colour_by_molecule(imol) +# coot.set_mol_active(imol, 0) +# else: +# self.Logfile.error('==> COOT - cannot find ground-state model') +## print '=> XCE - ERROR: cannot find ground-state model' +# self.Logfile.insert('==> COOT: looking for bound-state model '+ os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', +# '') + '.split.bound-state.pdb')) +# print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', +# '') + '.split.bound-state.pdb') +# if os.path.isfile(os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb')): +# self.Logfile.insert('==> COOT: found bound-state model') +## print '=> XCE: found bound-state model' +# os.chdir(os.path.join(self.project_directory, self.xtalID)) +# coot.set_colour_map_rotation_on_read_pdb(0) +# color_wheel_rotation = 21 / float(imol + 2) +# coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) +# imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', +# '') + '.split.bound-state.pdb'), +# 0) +# self.mol_dict['protein'] = imol +# else: +# self.Logfile.error('==> COOT: cannot find bound-state model') +## print '=> XCE - ERROR: cannot find bound-state model' +# self.Logfile.warning('==> COOT: moving to next crystal...') +## print '=> XCE: moving to next crystal...' +# self.go_to_next_xtal() +# else: + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init_twin.pdb')): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join(self.project_directory, self.xtalID, 'init_twin.pdb'), 0) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple_twin.pdb')): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join(self.project_directory, self.xtalID, 'dimple_twin.pdb'), 0) + else: + self.go_to_next_xtal() + self.mol_dict['protein'] = imol + + # read any one event map if present + for event_map in glob.glob( + os.path.join(self.project_directory, self.xtalID, self.xtalID + '-event_*.native.ccp4')): + coot.handle_read_ccp4_map((event_map), 0) + coot.set_contour_level_in_sigma(imol, 2) + coot.set_last_map_colour(0.74, 0.44, 0.02) + break + + for item in coot_utils_XChem.molecule_number_list(): + if coot.molecule_name(item).endswith( + self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( + item).endswith(self.pdb_style): + coot.set_show_symmetry_master(1) # master switch to show symmetry molecules + coot.set_show_symmetry_molecule(item, 1) # show symm for model + + ######################################################################################### + # read fofc maps + # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map + # read 2fofc map last so that one can change its contour level + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): + coot.set_colour_map_rotation_on_read_pdb(0) + coot.set_default_initial_contour_level_for_difference_map(3) + coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, 'fofc.map'), 1) + coot.set_default_initial_contour_level_for_map(1) + coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, '2fofc.map'), 0) + coot.set_last_map_colour(0, 0, 1) + else: + # try to open mtz file with same name as pdb file + coot.set_default_initial_contour_level_for_map(1) + # if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): + # os.chdir(os.path.join(self.project_directory,self.xtalID)) + # if not os.path.isfile('REFINEMENT_IN_PROGRESS'): + # if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-pandda-input.mtz')): + # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) + # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): + # os.symlink('dimple.mtz',self.mtz_style) + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): + coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, self.mtz_style)) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init_twin.mtz')): + coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, 'init_twin.mtz')) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple_twin.mtz')): + coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, 'dimple_twin.mtz')) + + ######################################################################################### + # update Quality Indicator table + try: + self.RRfreeValue.set_label(str(round(float(self.QualityIndicators['RefinementRcryst']), 3)) + ' / ' + str( + round(float(self.QualityIndicators['RefinementRfree']), 3))) + except ValueError: + self.RRfreeValue.set_label('-') + + try: + self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators['RefinementRfreeTraficLight'])) + except ValueError: + pass + self.ResolutionValue.set_label(self.QualityIndicators['RefinementResolution']) + try: + self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators['RefinementResolutionTL'])) + except ValueError: + pass + self.MolprobityScoreValue.set_label(self.QualityIndicators['RefinementMolProbityScore']) + try: + self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementMolProbityScoreTL'])) + except ValueError: + pass + self.RamachandranOutliersValue.set_label(self.QualityIndicators['RefinementRamachandranOutliers']) + try: + self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRamachandranOutliersTL'])) + except ValueError: + pass + self.RamachandranFavoredValue.set_label(self.QualityIndicators['RefinementRamachandranFavored']) + try: + self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRamachandranFavoredTL'])) + except ValueError: + pass + self.rmsdBondsValue.set_label(self.QualityIndicators['RefinementRmsdBonds']) + try: + self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdBondsTL'])) + except ValueError: + pass + self.rmsdAnglesValue.set_label(self.QualityIndicators['RefinementRmsdAngles']) + try: + self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdAnglesTL'])) + except ValueError: + pass + self.MatrixWeightValue.set_label(self.QualityIndicators['RefinementMatrixWeight']) + + try: + pic = gtk.gdk.pixbuf_new_from_file( + os.path.join(self.project_directory, self.xtalID, self.compoundID + '.png')) + except gobject.GError: + pic = gtk.gdk.pixbuf_new_from_file( + os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.image.set_from_pixbuf(self.pic) + + def go_to_next_xtal(self): + self.index += 1 + if self.index >= len(self.Todo): + self.index = len(self.Todo) + self.cb.set_active(self.index) + + def REFINE(self, widget): + self.start_refinement() + + def start_refinement(self): + # ####################################################### + # if not os.path.isdir(os.path.join(self.project_directory,self.xtalID,'cootOut')): + # os.mkdir(os.path.join(self.project_directory,self.xtalID,'cootOut')) + # # create folder for new refinement cycle + # os.mkdir(os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial))) + # + # ####################################################### + # # write PDB file + # # now take protein pdb file and write it to newly create Refine_ folder + # # note: the user has to make sure that the ligand file was merged into main file + # for item in coot_utils_XChem.molecule_number_list(): + # if coot.molecule_name(item).endswith(self.pdb_style.replace('.pdb','')+'.split.bound-state.pdb') or coot.molecule_name(item).endswith(self.pdb_style): + # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) + # break + # elif coot.molecule_name(item).endswith('dimple.pdb'): + # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) + # break + # + + ####################################################### +# if self.refinementProtocol.startswith('pandda'): +# +# ####################################################### +# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): +# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) +# # create folder for new refinement cycle +# try: +# self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) +# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) +# except OSError: +# self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') +## print '==> XCE: WARNING -> folder exists; will overwrite contents!' +# self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') +# +# ####################################################### +# # write PDB file +# # now take protein pdb file and write it to newly create Refine_ folder +# # note: the user has to make sure that the ligand file was merged into main file +# for item in coot_utils_XChem.molecule_number_list(): +# if coot.molecule_name(item).endswith( +# self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( +# item).endswith(self.pdb_style): +# coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', +# 'Refine_' + str(self.Serial), 'refine.modified.pdb')) +# break +# # elif coot.molecule_name(item).endswith('dimple.pdb'): +# # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) +# # break +# +# XChemRefine.panddaRefine(self.project_directory, self.xtalID, self.compoundID, +# self.data_source).RunQuickRefine(self.Serial, self.RefmacParams, +# self.external_software, self.xce_logfile, +# self.refinementProtocol, self.covLinkAtomSpec) +# else: + + ####################################################### + if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): + os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) + # create folder for new refinement cycle + try: + self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + except OSError: + self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') +# print '==> XCE: WARNING -> folder exists; will overwrite contents!' + self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') + + +# ####################################################### +# # create folder for new refinement cycle and check if free.mtz exists +# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): +# os.mkdir(os.path.join(self.project_directory, self.xtalID)) +# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): +# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) + + ####################################################### + # write PDB file + # now take protein pdb file and write it to newly create Refine_ folder + # note: the user has to make sure that the ligand file was merged into main file + foundPDB = False + for item in coot_utils_XChem.molecule_number_list(): + if coot.molecule_name(item).endswith(self.pdb_style): + foundPDB = True + break + elif coot.molecule_name(item).endswith('refine.split.bound-state.pdb'): + foundPDB = True + break + elif coot.molecule_name(item).endswith('init_twin.pdb'): + foundPDB = True + break + elif coot.molecule_name(item).endswith('dimple_twin.pdb'): + foundPDB = True + break + if foundPDB: + coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', + 'Refine_' + str(self.Serial), 'in.pdb')) + +# self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) + self.Refine.RunBuster(self.Serial, self.external_software, self.xce_logfile, self.covLinkAtomSpec) + self.index += 1 + if self.index >= len(self.Todo): + # self.index = len(self.Todo) + self.index = 0 + self.cb.set_active(self.index) + + def RefinementParams(self, widget): + print '\n==> XCE: changing refinement parameters' + self.RefmacParams = XChemRefine.RefineParams(self.project_directory, self.xtalID, self.compoundID, + self.data_source).RefmacRefinementParams(self.RefmacParams) + + def covalentLinkDef(self, widget): + coot.user_defined_click_py(2,self.show_potential_link) + + def show_potential_link(self,*clicks): + # first find imol of protein molecule + # it's a prerequisite that the ligand is merged into the protein + imol_protein = None + for imol in coot_utils_XChem.molecule_number_list(): + print '>',coot.molecule_name(imol) + if coot.molecule_name(imol).endswith(self.pdb_style) or \ + coot.molecule_name(imol).endswith('init_twin.pdb') or \ + coot.molecule_name(imol).endswith('dimple_twin.pdb') or \ + coot.molecule_name(imol).endswith(self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb'): + imol_protein = imol + break + + print 'please click on the two atoms you want to link' + if (len(clicks) == 2): + click_1 = clicks[0] + click_2 = clicks[1] + imol_1 = click_1[1] + imol_2 = click_2[1] + print 'imolp',imol,'imo11',imol_1,'imol2',imol_2 + if imol_1 == imol_2 and imol_1 == imol_protein: + print 'click_1',click_1 + self.covLinkAtomSpec = None + xyz_1 = atom_info_string(click_1[1],click_1[2],click_1[3],click_1[4],click_1[5],click_1[6]) + residue_1 = residue_name(click_1[1],click_1[2],click_1[3],click_1[4]) + xyz_2 = atom_info_string(click_2[1],click_2[2],click_2[3],click_2[4],click_2[5],click_2[6]) + residue_2 = residue_name(click_2[1],click_2[2],click_2[3],click_2[4]) + thick = 4 + to_generic_object_add_line(self.covLinkObject, "yellowtint", thick, xyz_1[3], xyz_1[4], xyz_1[5], xyz_2[3], xyz_2[4], xyz_2[5]) + set_display_generic_object(self.covLinkObject, 1) + self.covLinkAtomSpec = [imol_protein,click_1,click_2,residue_1,residue_2] + else: + print 'error: both atoms must belong to the same object; did you merge the ligand with your protein?' + + def covalentLinkCreate(self, widget): + if self.covLinkAtomSpec is not None: + imol = self.covLinkAtomSpec[0] + atom1 = self.covLinkAtomSpec[1][1:] + atom2 = self.covLinkAtomSpec[2][1:] + residue_1 = self.covLinkAtomSpec[3] + residue_2 = self.covLinkAtomSpec[4] + make_link(imol, atom1, atom2, residue_1+'-'+residue_2, 1.7) + generic_object_clear(self.covLinkObject) + self.start_refinement() + else: + print 'error: no covalent link defined' + + def set_selection_mode(self, widget): + self.selection_mode = widget.get_active_text() + + def get_samples_to_look_at(self, widget): + if self.selection_mode == '': + self.status_label.set_text('select model stage') + return + self.status_label.set_text('checking datasource for samples... ') + # first remove old samples if present + if len(self.Todo) != 0: + for n, item in enumerate(self.Todo): + self.cb.remove_text(0) + self.Todo = [] + self.siteDict = {} + self.Todo, self.siteDict = self.db.get_todoList_for_coot(self.selection_mode) + self.status_label.set_text('found {0!s} samples'.format(len(self.Todo))) + # refresh sample CB + for item in sorted(self.Todo): + self.cb.append_text('{0!s}'.format(item[0])) + if self.siteDict == {}: + self.cb_site.set_sensitive(False) + self.PREVbuttonSite.set_sensitive(False) + self.NEXTbuttonSite.set_sensitive(False) + else: + self.cb_site.set_sensitive(True) + self.PREVbuttonSite.set_sensitive(True) + self.NEXTbuttonSite.set_sensitive(True) + + def update_plot(self, refinement_cycle, Rfree, Rcryst): + fig = Figure(figsize=(2, 2), dpi=50) + Plot = fig.add_subplot(111) + Plot.set_ylim([0, max(Rcryst + Rfree)]) + Plot.set_xlabel('Refinement Cycle', fontsize=12) + Plot.plot(refinement_cycle, Rfree, label='Rfree', linewidth=2) + Plot.plot(refinement_cycle, Rcryst, label='Rcryst', linewidth=2) + Plot.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, + ncol=2, mode="expand", borderaxespad=0., fontsize=12) + return fig + + def place_ligand_here(self, widget): + cpd = str(self.select_cpd_cb.get_active_text()) + for imol in coot_utils_XChem.molecule_number_list(): + if imol not in self.mol_dict['ligand_stereo']: + continue + molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + if molName == cpd: + print '===> XCE: moving ligand to pointer' + coot_utils_XChem.move_molecule_here(imol) + print 'LIGAND: ', molName +# print '===> XCE: moving ligand to pointer' +# # coot.move_molecule_here() +# print 'LIGAND: ', self.mol_dict['ligand'] +# coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) + + + def merge_ligand_into_protein(self, widget): + cpd = str(self.select_cpd_cb.get_active_text()) + for imol in coot_utils_XChem.molecule_number_list(): + if imol not in self.mol_dict['ligand_stereo']: + continue + molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + if molName == cpd: + print '===> XCE: merge ligand into protein structure -->',cpd + coot.merge_molecules_py([imol], self.mol_dict['protein']) + if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): + molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/') + 1:].replace('.pdb', '').replace('_phenix','').replace('_rhofit','') + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')): + os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) + print 'XCE: changing directory', os.path.join(self.project_directory, self.xtalID) + os.chdir(os.path.join(self.project_directory, self.xtalID)) + print 'XCE: changing symlink ln -s %s %s.cif' % ( + os.path.join('compound', molName + '.cif'), self.compoundID) + os.system('ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): + os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')) + print 'XCE: changing directory', os.path.join(self.project_directory, self.xtalID) + os.chdir(os.path.join(self.project_directory, self.xtalID)) + print 'XCE: changing symlink ln -s %s %s.pdb' % ( + os.path.join('compound', molName + '.pdb'), self.compoundID) + os.system('ln -s %s %s.pdb' % (os.path.join('compound', molName + + '.pdb'), self.compoundID)) + print '===> XCE: deleting ligand molecule',molName + coot.close_molecule(imol) + + self.select_cpd_cb.set_sensitive(False) + +# print '===> XCE: merge ligand into protein structure' +# # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) +# coot.merge_molecules_py([self.mol_dict['ligand']], self.mol_dict['protein']) +# print '===> XCE: deleting ligand molecule' +# coot.close_molecule(self.mol_dict['ligand']) + + def show_molprobity_to_do(self, widget): + print self.panddaSerial + AdjPanddaSerial = (4 - len(str(self.Serial))) * '0' + str(int(self.panddaSerial) - 1) + print os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), + 'molprobity_coot.py') + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), + 'molprobity_coot.py')): + print '==> XCE: running MolProbity Summary for', self.xtalID + coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), + 'molprobity_coot.py')) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), + 'molprobity_coot.py')): + print '==> XCE: running MolProbity Summary for', self.xtalID + coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), + 'molprobity_coot.py')) + else: + print '==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, + 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py') + +# def refinementProtocolCallback(self, widget): +# if widget.get_active(): +# if self.refinementProtocolcheckbox.get_active(): +# self.refinementProtocol = 'pandda_phenix' +# else: +# self.refinementProtocol = 'pandda_refmac' +# self.PREVbuttonSite.set_sensitive(True) +# self.NEXTbuttonSite.set_sensitive(True) +# else: +# self.refinementProtocolcheckbox.set_active(False) +# self.refinementProtocol = 'refmac' +# self.PREVbuttonSite.set_sensitive(False) +# self.NEXTbuttonSite.set_sensitive(False) +# print self.refinementProtocol + +# def refinementProgramCallback(self, widget): +# if widget.get_active(): +# if self.refinementProtocolcheckbox.get_active(): +# self.refinementProtocol = 'pandda_phenix' +# self.RefinementParamsButton.set_sensitive(False) +# else: +# self.refinementProgramcheckbox.set_active(False) +# self.refinementProtocol = 'refmac' +# else: +# self.RefinementParamsButton.set_sensitive(True) +# if self.refinementProtocolcheckbox.get_active(): +# self.refinementProtocol = 'pandda_refmac' +# else: +# self.refinementProtocol = 'refmac' +# print self.refinementProtocol + + def show_ground_state_mean_map(self, widget): + if widget.get_label().startswith('Show'): + loaded = False + for imol in coot_utils_XChem.molecule_number_list(): + if 'ground-state-mean-map' in coot.molecule_name(imol): + coot.set_map_displayed(imol, 1) + loaded = True + break + if not loaded: + coot.set_default_initial_contour_level_for_map(1) + coot.handle_read_ccp4_map(self.ground_state_mean_map, 0) + coot.set_last_map_colour(0.6, 0.6, 0) + widget.set_label('Undisplay ground state mean map') + else: + for imol in coot_utils_XChem.molecule_number_list(): + if 'ground-state-mean-map' in coot.molecule_name(imol): + coot.set_map_displayed(imol, 0) + widget.set_label('Show ground state mean map') + + +if __name__ == '__main__': + GUI().StartGUI() diff --git a/lib/XChemLog.py b/lib/XChemLog.py index faf521af..a13b6d9c 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 30/04/2020 #\n' + ' # Date: 04/05/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemThread.py b/lib/XChemThread.py index b0e5a61c..f6d1cc7e 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2078,6 +2078,8 @@ def __init__(self,settings,interface): self.pylib='XChemCootReference.py' elif interface=='buster': self.pylib='XChemCootBuster.py' + elif interface=='dimple_twin': + self.pylib='XChemCootTwin.py' def run(self): cwd=os.getcwd() From 74f82ac42cf5c20b0bad71cbb765d5b30b8f4eb2 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 4 May 2020 14:58:17 +0100 Subject: [PATCH 039/358] =?UTF-8?q?v1.6.10=20(04/05/2020)=E2=80=A8=20(#319?= =?UTF-8?q?)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - bug fix: only read (2)fofc_twin.map during dimple_twin map review --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemCootTwin.py | 6 +++--- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index f5ad6d4a..542af957 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.10 (04/05/2020)
 +- bug fix: only read (2)fofc_twin.map during dimple_twin map review + v1.6.9 (04/05/2020)
 - added COOT command to open dimple_twin maps diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 8cea2607..1c4689e5 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.9' + xce_object.xce_version = 'v1.6.10' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemCootTwin.py b/lib/XChemCootTwin.py index 85fe52f0..d102f4ba 100755 --- a/lib/XChemCootTwin.py +++ b/lib/XChemCootTwin.py @@ -1255,12 +1255,12 @@ def RefreshData(self): # read fofc maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc_twin.map')): coot.set_colour_map_rotation_on_read_pdb(0) coot.set_default_initial_contour_level_for_difference_map(3) - coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, 'fofc.map'), 1) + coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, 'fofc_twin.map'), 1) coot.set_default_initial_contour_level_for_map(1) - coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, '2fofc.map'), 0) + coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, '2fofc_twin.map'), 0) coot.set_last_map_colour(0, 0, 1) else: # try to open mtz file with same name as pdb file From 764df53a21dc44346644d2eba21b86a1b539d203 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sat, 9 May 2020 14:14:22 +0100 Subject: [PATCH 040/358] v1.6.11 (04/05/2020) (#324) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - added giant.score_model after buster refinement 
- added field and capture of path to buster-reports in DB --- ChangeLog.txt | 4 ++++ gui_scripts/settings_preferences.py | 2 +- helpers/update_data_source_after_refinement.py | 8 +++++++- lib/XChemDB.py | 1 + lib/XChemRefine.py | 15 +++++++++++++++ 5 files changed, 28 insertions(+), 2 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 542af957..aea3e0e2 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.6.11 (04/05/2020)
 +- added giant.score_model after buster refinement +- added field and capture of path to buster-reports in DB + v1.6.10 (04/05/2020)
 - bug fix: only read (2)fofc_twin.map during dimple_twin map review diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 1c4689e5..4849eb1c 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.10' + xce_object.xce_version = 'v1.6.11' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/helpers/update_data_source_after_refinement.py b/helpers/update_data_source_after_refinement.py index 7aca6e3e..ffe5e2e4 100755 --- a/helpers/update_data_source_after_refinement.py +++ b/helpers/update_data_source_after_refinement.py @@ -209,6 +209,12 @@ def update_data_source(db_dict): ) db.execute_statement(sqlite) + +def update_buster_report_index_html(refinement_directory,db_dict): + if os.path.isfile(refinement_directory+'-report/index.html'): + db_dict['RefinementBusterReportHTML'] = refinement_directory+'-report/index.html' + return db_dict + if __name__=='__main__': print 'hallo' @@ -226,7 +232,7 @@ def update_data_source(db_dict): db_dict=check_refmac_matrix_weight(refinement_directory,db_dict) db_dict=parse_molprobity_output(inital_model_directory,xtal,db_dict) db_dict=check_refmac_logfile(refinement_directory,db_dict) - + db_dict=update_buster_report_index_html(refinement_directory,db_dict) update_ligand_information_in_panddaTable(inital_model_directory,xtal) parse_ligand_validation(inital_model_directory,refinement_directory,xtal) diff --git a/lib/XChemDB.py b/lib/XChemDB.py index 8ce8dc0d..aae1d032 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -222,6 +222,7 @@ def __init__(self,data_source_file): ['RefinementRamachandranFavoredTL', 'RefinementRamachandranFavoredTL', 'TEXT', 0], ['RefinementProgram', 'RefinementProgram', 'TEXT', 1], ['RefinementStatus', 'Refinement\nStatus', 'TEXT', 1], + ['RefinementBusterReportHTML', 'RefinementBusterReportHTML', 'TEXT', 1], ['Deposition_PDB_ID', 'Deposition_PDB_ID', 'TEXT', 1], ['Deposition_PDB_file', 'Deposition_PDB_file', 'TEXT', 0], diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 90d8885e..852da0e6 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -425,6 +425,18 @@ def add_buster_command(self,cmd,xyzin,hklin,libin,Serial): ) return cmd + def run_giant_score_model(self,cmd,cycle): + if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-model.pdb')): + cmd += ( 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+cycle+'\n' + 'giant.score_model ' + ' pdb1=../%s-pandda-model.pdb ' %self.xtalID + + ' mtz1=../dimple.mtz ' + ' pdb2=refine.pdb ' + ' mtz2=refine.mtz\n' ) + return cmd + + + def add_validation(self,cmd,cycle,program): buster_report = '' if program == 'refmac': @@ -479,6 +491,7 @@ def calculate_maps(self,cmd,program): ) return cmd + def update_database(self,cmd,Serial): cmd += ( '$CCP4/bin/ccp4-python ' +os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+ @@ -539,6 +552,8 @@ def RunBuster(self,Serial,external_software,xce_logfile,covLinkAtomSpec): cmd = self.add_buster_command(cmd,xyzin,hklin,libin,Serial) + cmd = self.run_giant_score_model(cmd,Serial) + cmd = self.add_validation(cmd,Serial,'buster') cmd = self.calculate_maps(cmd,'buster') From 6080effc7705681910f87fc97d6bf401b300060d Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sat, 9 May 2020 16:20:50 +0100 Subject: [PATCH 041/358] v1.6.12 (09/05/2020) (#325) - capture refinement mmcif file location in DB after refinement (if available) --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- helpers/update_data_source_after_refinement.py | 9 +++++++++ lib/XChemDB.py | 3 +++ lib/XChemLog.py | 2 +- 5 files changed, 17 insertions(+), 2 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index aea3e0e2..a6711890 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.12 (09/05/2020) +- capture refinement mmcif file location in DB after refinement (if available) + v1.6.11 (04/05/2020)
 - added giant.score_model after buster refinement - added field and capture of path to buster-reports in DB diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 4849eb1c..cabe1abe 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.11' + xce_object.xce_version = 'v1.6.12' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/helpers/update_data_source_after_refinement.py b/helpers/update_data_source_after_refinement.py index ffe5e2e4..79aeac42 100755 --- a/helpers/update_data_source_after_refinement.py +++ b/helpers/update_data_source_after_refinement.py @@ -30,6 +30,7 @@ def parse_pdb(inital_model_directory,xtal,db_dict): else: db_dict['RefinementStatus'] = 'failed' + if os.path.isfile(os.path.join(inital_model_directory,xtal,'refine.bound.pdb')): db_dict['RefinementBoundConformation']=os.path.realpath(os.path.join(inital_model_directory,xtal,'refine.bound.pdb')) elif os.path.isfile(os.path.join(inital_model_directory,xtal,'refine.split.bound-state.pdb')): @@ -215,6 +216,13 @@ def update_buster_report_index_html(refinement_directory,db_dict): db_dict['RefinementBusterReportHTML'] = refinement_directory+'-report/index.html' return db_dict +def update_mmcif_file_location(refinement_directory,db_dict): + if os.path.isfile(os.path.join(refinement_directory,'BUSTER_model.cif')): + db_dict['RefinementMMCIFmodel_latest'] = os.path.join(refinement_directory,'BUSTER_model.cif') + if os.path.isfile(os.path.join(refinement_directory,'BUSTER_refln.cif')): + db_dict['RefinementMMCIFreflections_latest'] = os.path.join(refinement_directory,'BUSTER_refln.cif') + return db_dict + if __name__=='__main__': print 'hallo' @@ -233,6 +241,7 @@ def update_buster_report_index_html(refinement_directory,db_dict): db_dict=parse_molprobity_output(inital_model_directory,xtal,db_dict) db_dict=check_refmac_logfile(refinement_directory,db_dict) db_dict=update_buster_report_index_html(refinement_directory,db_dict) + db_dict=update_mmcif_file_location(refinement_directory,db_dict) update_ligand_information_in_panddaTable(inital_model_directory,xtal) parse_ligand_validation(inital_model_directory,refinement_directory,xtal) diff --git a/lib/XChemDB.py b/lib/XChemDB.py index aae1d032..6ef4df77 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -208,6 +208,9 @@ def __init__(self,data_source_file): ['RefinementCIFprogram', 'RefinementCIFprogram', 'TEXT', 1], ['RefinementPDB_latest', 'RefinementPDB_latest', 'TEXT', 1], ['RefinementMTZ_latest', 'RefinementMTZ_latest', 'TEXT', 1], + ['RefinementMMCIFmodel_latest', 'RefinementMMCIFmodel_latest', 'TEXT', 1], + ['RefinementMMCIFreflections_latest', 'RefinementMMCIFreflections_latest', 'TEXT', 1], + ['RefinementMatrixWeight', 'RefinementMatrixWeight', 'TEXT', 0], ['RefinementComment', 'RefinementComment', 'TEXT', 0], ['RefinementPathToRefinementFolder', 'RefinementPathToRefinementFolder', 'TEXT', 0], diff --git a/lib/XChemLog.py b/lib/XChemLog.py index a13b6d9c..d421bfd9 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 04/05/2020 #\n' + ' # Date: 09/05/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 0bfe153f885f8fd30642e957177adae7cc7a22ee Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sun, 10 May 2020 22:46:57 +0100 Subject: [PATCH 042/358] v1.6.13 (10/05/2020) (#326) - XChemDeposit: use RefinementMMCIFmodel_latest (if available) instead of refine.split.bound-state.pdb --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 27 +++++++++++++++++++-------- lib/XChemLog.py | 2 +- 4 files changed, 24 insertions(+), 10 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index a6711890..d517023c 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.13 (10/05/2020) +- XChemDeposit: use RefinementMMCIFmodel_latest (if available) instead of refine.split.bound-state.pdb + v1.6.12 (09/05/2020) - capture refinement mmcif file location in DB after refinement (if available) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index cabe1abe..bda4833e 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.12' + xce_object.xce_version = 'v1.6.13' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index fde00028..a5edff8f 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -870,14 +870,25 @@ def create_model_mmcif(self,xtal): ' -iENT data_template.cif' ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) else: - Cmd = (pdb_extract_init + - ' -r {0!s}'.format(refSoft) + - ' -iPDB {0!s}'.format('refine.split.bound-state.pdb') + - ' -e MR' - ' -s AIMLESS' - ' -iLOG {0!s}.log'.format(xtal) + - ' -iENT data_template.cif' - ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) + if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): + self.Logfile.insert('%s: found MMCIF file; will use instead of PDB: %s' %(xtal,self.db_dict['RefinementMMCIFmodel_latest'])) + Cmd = (pdb_extract_init + + ' -r {0!s}'.format(refSoft) + + ' -iCIF {0!s}'.format(self.db_dict['RefinementMMCIFmodel_latest']) + + ' -e MR' + ' -s AIMLESS' + ' -iLOG {0!s}.log'.format(xtal) + + ' -iENT data_template.cif' + ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) + else: + Cmd = (pdb_extract_init + + ' -r {0!s}'.format(refSoft) + + ' -iPDB {0!s}'.format('refine.split.bound-state.pdb') + + ' -e MR' + ' -s AIMLESS' + ' -iLOG {0!s}.log'.format(xtal) + + ' -iENT data_template.cif' + ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) self.Logfile.insert(xtal + ': running pdb_extract: ' + Cmd) os.system(Cmd) diff --git a/lib/XChemLog.py b/lib/XChemLog.py index d421bfd9..de24f0ea 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 09/05/2020 #\n' + ' # Date: 10/05/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 6330522f0be2a805a63c2fa1b2dfe740e4ba1fdd Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 12 May 2020 08:20:01 +0100 Subject: [PATCH 043/358] v1.6.14 (11/05/2020) (#327) - XChemUtils: get BUSTER from PROGRAM REMARK - XChemDeposit: usage of model mmcif file disabled because of unclear errors during group deposition - XChemDeposit: do not add ligand cif to model mmcif because Buster does already include it - XChemDeposit: use pdb_extract v3.26 when using mmcif instead of pdb files --- ChangeLog.txt | 6 ++++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 52 +++++++++++++++++------------ lib/XChemLog.py | 2 +- lib/XChemUtils.py | 2 ++ 5 files changed, 40 insertions(+), 24 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index d517023c..f6011bc3 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,9 @@ +v1.6.14 (11/05/2020) +- XChemUtils: get BUSTER from PROGRAM REMARK +- XChemDeposit: usage of model mmcif file disabled because of unclear errors during group deposition +- XChemDeposit: do not add ligand cif to model mmcif because Buster does already include it +- XChemDeposit: use pdb_extract v3.26 when using mmcif instead of pdb files + v1.6.13 (10/05/2020) - XChemDeposit: use RefinementMMCIFmodel_latest (if available) instead of refine.split.bound-state.pdb diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index bda4833e..23b13ba7 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.13' + xce_object.xce_version = 'v1.6.14' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index a5edff8f..0be9dc19 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -849,6 +849,10 @@ def create_model_mmcif(self,xtal): refSoft = self.pdb.get_refinement_program() if os.path.isdir('/dls'): +# if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): +# pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-v3.26/pdb-extract-v3.26-prod-src/setup.sh\n' +# pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-v3.26/pdb-extract-v3.26-prod-src/bin/pdb_extract' +# else: pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n' pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-prod/bin/pdb_extract' else: @@ -870,18 +874,18 @@ def create_model_mmcif(self,xtal): ' -iENT data_template.cif' ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) else: - if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): - self.Logfile.insert('%s: found MMCIF file; will use instead of PDB: %s' %(xtal,self.db_dict['RefinementMMCIFmodel_latest'])) - Cmd = (pdb_extract_init + - ' -r {0!s}'.format(refSoft) + - ' -iCIF {0!s}'.format(self.db_dict['RefinementMMCIFmodel_latest']) + - ' -e MR' - ' -s AIMLESS' - ' -iLOG {0!s}.log'.format(xtal) + - ' -iENT data_template.cif' - ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) - else: - Cmd = (pdb_extract_init + +# if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): +# self.Logfile.insert('%s: found MMCIF file; will use instead of PDB: %s' %(xtal,self.db_dict['RefinementMMCIFmodel_latest'])) +# Cmd = (pdb_extract_init + +# ' -r {0!s}'.format(refSoft) + +# ' -iCIF {0!s}'.format(self.db_dict['RefinementMMCIFmodel_latest']) + +# ' -e MR' +# ' -s AIMLESS' +# ' -iLOG {0!s}.log'.format(xtal) + +# ' -iENT data_template.cif' +# ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) +# else: + Cmd = (pdb_extract_init + ' -r {0!s}'.format(refSoft) + ' -iPDB {0!s}'.format('refine.split.bound-state.pdb') + ' -e MR' @@ -993,18 +997,22 @@ def add_ligand_cif_to_model_mmcif(self,xtal): filestatus = False self.Logfile.insert('%s: looking for ligand restraints file...' %xtal) os.chdir(os.path.join(self.projectDir, xtal)) - if os.path.isfile(self.db_dict['CompoundCode']+'.cif'): - self.Logfile.insert('%s: found ligand restraints file -> %s' %(xtal,self.db_dict['CompoundCode']+'.cif')) - self.Logfile.insert('%s: adding ligand restraints file to model mmcif' %xtal) - cif = '' - for line in open(self.db_dict['CompoundCode']+'.cif'): - cif += line - f = open(xtal+'.mmcif','a') - f.write(cif) - f.close() + if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): + self.Logfile.insert('%s: found %s; assuming that ligand cif dictionary is already included...' %(xtal,self.db_dict['RefinementMMCIFmodel_latest'])) filestatus = True else: - self.Logfile.warning('%s: could not find %s' %(xtal,self.db_dict['CompoundCode']+'.cif')) + if os.path.isfile(self.db_dict['CompoundCode']+'.cif'): + self.Logfile.insert('%s: found ligand restraints file -> %s' %(xtal,self.db_dict['CompoundCode']+'.cif')) + self.Logfile.insert('%s: adding ligand restraints file to model mmcif' %xtal) + cif = '' + for line in open(self.db_dict['CompoundCode']+'.cif'): + cif += line + f = open(xtal+'.mmcif','a') + f.write(cif) + f.close() + filestatus = True + else: + self.Logfile.warning('%s: could not find %s' %(xtal,self.db_dict['CompoundCode']+'.cif')) return filestatus diff --git a/lib/XChemLog.py b/lib/XChemLog.py index de24f0ea..0f9f84f0 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 10/05/2020 #\n' + ' # Date: 11/05/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 374e77bb..2e8c107f 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -1828,6 +1828,8 @@ def get_refinement_program(self): program = 'REFMAC' elif 'phenix' in remark.lower(): program = 'PHENIX' + elif 'buster' in remark.lower(): + program = 'BUSTER' return program def get_residues_with_resname(self,resname): From e35fc61a3108e6300f0d7dfa0d651c866c59a673 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 12 May 2020 14:44:52 +0100 Subject: [PATCH 044/358] v1.6.15 (12/05/2020) (#328) - added html summary for all '5-deposition ready' structures - HTML summary: show NO_SPIDER_PLOT_AVAILABLE.png if spider plot is missing --- ChangeLog.txt | 4 ++++ XChemExplorer.py | 8 +++++++- gui_scripts/settings_preferences.py | 3 ++- lib/XChemDB.py | 2 ++ lib/XChemLog.py | 2 +- web/XChemWeb.py | 3 +++ 6 files changed, 19 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index f6011bc3..10d4128c 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.6.15 (12/05/2020) +- added html summary for all '5-deposition ready' structures +- HTML summary: show NO_SPIDER_PLOT_AVAILABLE.png if spider plot is missing + v1.6.14 (11/05/2020) - XChemUtils: get BUSTER from PROGRAM REMARK - XChemDeposit: usage of model mmcif file disabled because of unclear errors during group deposition diff --git a/XChemExplorer.py b/XChemExplorer.py index 9183bd32..4c7d88ee 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -529,7 +529,7 @@ def export_to_html(self): XChemWeb.export_to_html(self.html_export_directory, self.initial_model_directory, os.path.join(self.database_directory, self.data_source_file), - self.xce_logfile).prepare(None) + self.xce_logfile).prepare('0') def export_to_html_CompChem(self): XChemWeb.export_to_html(self.html_export_directory, @@ -537,6 +537,12 @@ def export_to_html_CompChem(self): os.path.join(self.database_directory, self.data_source_file), self.xce_logfile).prepare('4') + def export_to_html_deposition_ready(self): + XChemWeb.export_to_html(self.html_export_directory, + self.initial_model_directory, + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile).prepare('5') + # self.update_log.insert('exporting contents of SQLite database into ' + self.html_export_directory) # os.system( # 'ccp4-python ' + os.getenv('XChemExplorer_DIR') + '/web/process_sqlite.py -t Summary -s ' + os.path.join( diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 23b13ba7..6b39c6c7 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.14' + xce_object.xce_version = 'v1.6.15' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -451,6 +451,7 @@ def top_menu_dict(self, xce_object): ['Edit information', '', xce_object.deposition_data], ['Export to HTML', '', xce_object.export_to_html], ['Export to HTML - CompChem', '', xce_object.export_to_html_CompChem], + ['Export to HTML - deposition ready', '', xce_object.export_to_html_deposition_ready], # ['Find PanDDA apo structures', '', # xce_object.create_missing_apo_records_in_depositTable], # ['Update file info of apo structures', '', diff --git a/lib/XChemDB.py b/lib/XChemDB.py index 6ef4df77..49168b8e 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -1886,6 +1886,8 @@ def samples_for_html_summary(self,whichSamples): cursor = connect.cursor() if whichSamples.startswith('4'): cursor.execute("select CrystalName from mainTable where RefinementOutcome like '4%' order by CrystalName ASC") + elif whichSamples.startswith('5'): + cursor.execute("select CrystalName from mainTable where RefinementOutcome like '5%' order by CrystalName ASC") else: cursor.execute("select CrystalName from mainTable where RefinementOutcome like '4%' or " "RefinementOutcome like '5%' or " diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 0f9f84f0..afb3208c 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 11/05/2020 #\n' + ' # Date: 12/05/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/web/XChemWeb.py b/web/XChemWeb.py index 01bbf00b..ae57891f 100755 --- a/web/XChemWeb.py +++ b/web/XChemWeb.py @@ -255,6 +255,9 @@ def copy_spider_plot(self,xtal,ligID): os.system('/bin/cp %s %s_%s.png' % (plot, xtal, ligID)) else: self.Logfile.error('%s: cannot find spider plot for %s' %(xtal,ligID.replace('LIG-','')+'.png')) + self.Logfile.warning('%s: using %s instead' %(xtal,'NO_SPIDER_PLOT_AVAILABLE.png')) + os.system('/bin/cp %s %s_%s.png' % (os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png'), xtal, ligID)) + # else: self.Logfile.error('%s: cannot find refine.pdb, i.e. cannot start looking for spider plots...' %xtal) From a04f8e15e71b595528b0614e33921faaa420e55c Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sun, 17 May 2020 16:30:41 +0100 Subject: [PATCH 045/358] v1.6.16 (12/05/2020) (#329) - XChemExplorer.py removed unused 'import gtk' statement which is incompatible with ccp4 7.1 --- ChangeLog.txt | 3 +++ XChemExplorer.py | 5 +++-- gui_scripts/settings_preferences.py | 2 +- lib/XChemPANDDA.py | 3 +++ 4 files changed, 10 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 10d4128c..0aab98d2 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.16 (12/05/2020) +- XChemExplorer.py removed unused 'import gtk' statement which is incompatible with ccp4 7.1 + v1.6.15 (12/05/2020) - added html summary for all '5-deposition ready' structures - HTML summary: show NO_SPIDER_PLOT_AVAILABLE.png if spider plot is missing diff --git a/XChemExplorer.py b/XChemExplorer.py index 4c7d88ee..c2a3e992 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -15,9 +15,9 @@ ######################################################################################################################## # solve gtk startup error -import gtk +#import gtk -gtk.set_interactive(False) +#gtk.set_interactive(False) import base64 import getpass @@ -52,6 +52,7 @@ import XChemDeposit import XChemWeb + import matplotlib.pyplot as plt from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 6b39c6c7..9a6e1c94 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.15' + xce_object.xce_version = 'v1.6.16' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 2b9aff11..22bf31ba 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -586,6 +586,7 @@ def run(self): number_of_cyles=int(self.number_of_datasets)/int(self.max_new_datasets) if int(self.number_of_datasets) % int(self.max_new_datasets) != 0: # modulo gives remainder after integer division number_of_cyles+=1 + self.Logfile.insert('will run %s rounds of pandda.analyse' %str(number_of_cyles)) if os.path.isfile(os.path.join(self.panddas_directory,'pandda.running')): self.Logfile.insert('it looks as if a pandda.analyse job is currently running in: '+self.panddas_directory) @@ -737,6 +738,8 @@ def append_to_ignore_string(datasets_list, append_string): # #>>> for testing # self.submit_mode='local machine' + self.Logfile.insert('trying to run pandda.analyse on ' + str(self.submit_mode)) + if self.submit_mode=='local machine': self.Logfile.insert('running PANDDA on local machine') os.system('chmod +x pandda.sh') From 0a2d27c99ba12f6d0c51bf46bd309b72b21b8f2e Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sun, 17 May 2020 17:49:26 +0100 Subject: [PATCH 046/358] v1.6.17 (17/05/2020) (#330) - DIMPLE: added 'tolerance 5' keyword to pointless step to allow reindexing in case of slightly larger unit cell differences --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemThread.py | 4 +++- 4 files changed, 8 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 0aab98d2..c54d01a8 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.17 (17/05/2020) +- DIMPLE: added 'tolerance 5' keyword to pointless step to allow reindexing in case of slightly larger unit cell differences + v1.6.16 (12/05/2020) - XChemExplorer.py removed unused 'import gtk' statement which is incompatible with ccp4 7.1 diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 9a6e1c94..0ea02d21 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.16' + xce_object.xce_version = 'v1.6.17' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index afb3208c..17c63d94 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 12/05/2020 #\n' + ' # Date: 17/05/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemThread.py b/lib/XChemThread.py index f6d1cc7e..f4513b27 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -1783,7 +1783,9 @@ def prepare_dimple_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,ref_m ' resolution file 1 999.0 %s\n' %str(round(float(mtzFile.d_min()),2))+ 'eof\n' '\n' - 'pointless hklin %s.999A.mtz hklout %s.999A.reind.mtz xyzin %s > pointless.reind.log\n' %(xtal,xtal,ref_pdb) + + 'pointless hklin %s.999A.mtz hklout %s.999A.reind.mtz xyzin %s << eof > pointless.reind.log\n' %(xtal,xtal,ref_pdb) + + ' tolerance 5\n' + 'eof\n' '\n' "dimple --no-cleanup %s.999A.reind.mtz %s %s %s %s dimple%s\n" % (xtal, ref_pdb, ref_mtz, ref_cif, twinRefmac, twin) + '\n' From dc6cd99a3bbd9a9854ebc968d0eb3dbd99ca4436 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sun, 17 May 2020 23:02:35 +0100 Subject: [PATCH 047/358] v1.6.18 (17/05/2020) (#331) - removed dls specific source files from pandda.analyse script when running on local machine --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemPANDDA.py | 10 ++++++++-- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index c54d01a8..690a7199 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.18 (17/05/2020) +- removed dls specific source files from pandda.analyse script when running on local machine + v1.6.17 (17/05/2020) - DIMPLE: added 'tolerance 5' keyword to pointless step to allow reindexing in case of slightly larger unit cell differences diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 0ea02d21..69467a6c 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.17' + xce_object.xce_version = 'v1.6.18' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 22bf31ba..e215c54d 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -632,11 +632,17 @@ def run(self): # note: copied latest pandda.setup-sh from XCE2 installation (08/08/2017) + dls = '' + if self.data_directory.startswith('/dls'): + dls = ( + source_file + + '\n' + 'module load pymol/1.8.2.0' + ' \n' + ) + Cmds = ( '#!'+os.getenv('SHELL')+'\n' + '\n' + - source_file + - '\n' + 'module load pymol/1.8.2.0' + ' \n' + + dls + 'cd ' + self.panddas_directory + '\n' + '\n' ) From 29fd628474b84e28717fd3cc7e7a20d605d34649 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 2 Jun 2020 15:31:21 +0100 Subject: [PATCH 048/358] Update README.md --- README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/README.md b/README.md index 72593cbd..efda63b7 100755 --- a/README.md +++ b/README.md @@ -135,3 +135,8 @@ ccp4-python -m pip install panddas (Note, this is not supported – you really are on your own! Recommended only for geeks.) 3. If your IT team doesn’t want to help you, try setting up a virtual machine – then you have root permissions and can do whatever you like. Performance ought to be okay. + + +## Requirements + +XChemExplorer is licensed under the MIT license. From 1ab58ea34c686686384c121c91d9f5019c0f493c Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 2 Jun 2020 15:32:05 +0100 Subject: [PATCH 049/358] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index efda63b7..1893ce41 100755 --- a/README.md +++ b/README.md @@ -137,6 +137,6 @@ ccp4-python -m pip install panddas 3. If your IT team doesn’t want to help you, try setting up a virtual machine – then you have root permissions and can do whatever you like. Performance ought to be okay. -## Requirements +## License XChemExplorer is licensed under the MIT license. From 8411b1bd8126542b2ac6ab282f4bfd0b0155acdf Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 3 Jun 2020 09:04:45 +0100 Subject: [PATCH 050/358] v1.6.19 (28/05/2020) (#336) * v1.6.19 (28/05/2020) - combined parsing of 'agamemnon' auto-collection into single function --- ChangeLog.txt | 3 + XChemExplorer.py | 12 +- gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemMain.py | 47 +++--- lib/XChemThread.py | 253 +++++++++++++++------------- 6 files changed, 174 insertions(+), 145 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 690a7199..5a1e6eaa 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.19 (28/05/2020) +- combined parsing of 'agamemnon' auto-collection into single function + v1.6.18 (17/05/2020) - removed dls specific source files from pandda.analyse script when running on local machine diff --git a/XChemExplorer.py b/XChemExplorer.py index c2a3e992..7fec0044 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -338,12 +338,12 @@ def check_for_new_autoprocessing_results(self): elif self.target == '=== project directory ===': processedDir = self.initial_model_directory start_thread = True - elif self.read_agamemnon.isChecked(): - tmp = '/'.join(self.beamline_directory.split('/')[:6]) - processedDir = tmp[:tmp.rfind('-')] -# processedDir = os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*/processed/agamemnon/'+self.target) -# processedDir = os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*/processed/*/'+self.target) - start_thread = True +# elif self.read_agamemnon.isChecked(): +# tmp = '/'.join(self.beamline_directory.split('/')[:6]) +# processedDir = tmp[:tmp.rfind('-')] +## processedDir = os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*/processed/agamemnon/'+self.target) +## processedDir = os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*/processed/*/'+self.target) +# start_thread = True else: processedDir = os.path.join(self.beamline_directory, 'processed', self.target) start_thread = True diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 69467a6c..514ff4ac 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.18' + xce_object.xce_version = 'v1.6.19' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 17c63d94..859f453a 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 17/05/2020 #\n' + ' # Date: 28/05/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemMain.py b/lib/XChemMain.py index 64b2d003..765e301a 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -39,28 +39,35 @@ def get_target_and_visit_list(beamline_directory,agamemnon): visit_list=[] # the beamline directory could be a the real directory or # a directory where the visits are linked into - if agamemnon: - # /dls/i03/data/2019/lb18145-136 - for target in glob.glob(beamline_directory[:beamline_directory.rfind('-') + 1] + '*/agamemnon/*'): - visit_list.append(beamline_directory[:beamline_directory.rfind('/')].replace('/agamemnon','')) - if target[target.rfind('/') + 1:] not in ['results', 'README-log', 'edna-latest.html']: - if target[target.rfind('/') + 1:] not in target_list: - target_list.append(target[target.rfind('/') + 1:]) - for target in glob.glob(beamline_directory[:beamline_directory.rfind('-') + 1] + '*/auto/*'): - visit_list.append(beamline_directory[:beamline_directory.rfind('/')].replace('/auto', '')) - if target[target.rfind('/') + 1:] not in ['results', 'README-log', 'edna-latest.html']: - if target[target.rfind('/') + 1:] not in target_list: - target_list.append(target[target.rfind('/') + 1:]) +# if agamemnon: +# # /dls/i03/data/2019/lb18145-136 +# for target in glob.glob(beamline_directory[:beamline_directory.rfind('-') + 1] + '*/agamemnon/*'): +# visit_list.append(beamline_directory[:beamline_directory.rfind('/')].replace('/agamemnon','')) +# if target[target.rfind('/') + 1:] not in ['results', 'README-log', 'edna-latest.html']: +# if target[target.rfind('/') + 1:] not in target_list: +# target_list.append(target[target.rfind('/') + 1:]) +# for target in glob.glob(beamline_directory[:beamline_directory.rfind('-') + 1] + '*/auto/*'): +# visit_list.append(beamline_directory[:beamline_directory.rfind('/')].replace('/auto', '')) +# if target[target.rfind('/') + 1:] not in ['results', 'README-log', 'edna-latest.html']: +# if target[target.rfind('/') + 1:] not in target_list: +# target_list.append(target[target.rfind('/') + 1:]) +# else: + if len(beamline_directory.split('/')) and \ + beamline_directory.split('/')[1]=='dls' and beamline_directory.split('/')[3]=='data' \ + and not 'labxchem' in beamline_directory: + visit_list.append(beamline_directory) else: - if len(beamline_directory.split('/')) and \ - beamline_directory.split('/')[1]=='dls' and beamline_directory.split('/')[3]=='data' \ - and not 'labxchem' in beamline_directory: - visit_list.append(beamline_directory) - else: - visit_list.append(os.path.realpath(beamline_directory)) + visit_list.append(os.path.realpath(beamline_directory)) - for visit in visit_list: - print '-->',os.path.join(visit,'processed','*') + for visit in visit_list: + print '-->',os.path.join(visit,'processed','*') + if agamemnon: + for target in glob.glob(os.path.join(visit,'processed','auto','*')): + print target + if target[target.rfind('/')+1:] not in ['results','README-log','edna-latest.html']: + if target[target.rfind('/')+1:] not in target_list: + target_list.append(target[target.rfind('/')+1:]) + else: for target in glob.glob(os.path.join(visit,'processed','*')): print target if target[target.rfind('/')+1:] not in ['results','README-log','edna-latest.html']: diff --git a/lib/XChemThread.py b/lib/XChemThread.py index f4513b27..0b08a4ae 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2446,12 +2446,12 @@ def __init__(self, self.Logfile = XChemLog.updateLog(xce_logfile) self.target = target self.agamemnon = agamemnon - if self.agamemnon: -# print 'procDir',self.processedDir -# if len(procDir.split('/')) >= 8: -# if procDir.split('/')[7] == 'agamemnon' -# quit() - self.visit = 'agamemnon' # this is for trouble-shooting only +# if self.agamemnon: +## print 'procDir',self.processedDir +## if len(procDir.split('/')) >= 8: +## if procDir.split('/')[7] == 'agamemnon' +## quit() +# self.visit = 'agamemnon' # this is for trouble-shooting only self.db = XChemDB.data_source(os.path.join(database)) self.exisitingSamples = self.getExistingSamples() @@ -2527,10 +2527,12 @@ def __init__(self, def run(self): - if self.agamemnon: - self.parse_agamemnon_file_system() - else: - self.parse_file_system() +# if self.agamemnon: +# self.parse_agamemnon_file_system() +# else: +# self.parse_file_system() + self.parse_file_system() + def getExistingSamples(self): existingSamples={} @@ -2731,12 +2733,29 @@ def junk(self,folder): return do_not_parse def parse_file_system(self): - self.Logfile.insert('checking for new data processing results in '+self.processedDir) + if self.agamemnon: + d = self.processedDir[:self.processedDir.rfind('/')] + t = self.processedDir[self.processedDir.rfind('/')+1:] + autoDir = os.path.join(d,'auto',t) + else: + autoDir = self.processedDir + + self.Logfile.insert('checking for new data processing results in '+autoDir) progress = 0 - progress_step = XChemMain.getProgressSteps(len(glob.glob(os.path.join(self.processedDir,'*')))) + progress_step = XChemMain.getProgressSteps(len(glob.glob(os.path.join(autoDir,'*')))) runList = [] - for collected_xtals in sorted(glob.glob(os.path.join(self.processedDir,'*'))): +# for auto in autoDir: + self.Logfile.insert('--> ' + os.path.join(autoDir,'*')) + for nx,collected_xtals in enumerate(sorted(glob.glob(os.path.join(autoDir,'*')))): + self.Logfile.insert('%s: %s' %(nx,collected_xtals)) + self.visit = collected_xtals.split('/')[5] + if 'tmp' in collected_xtals or 'results' in collected_xtals or 'scre' in collected_xtals: + continue + if not os.path.isdir(collected_xtals): + continue + +# for collected_xtals in sorted(glob.glob(os.path.join(self.processedDir,'*'))): # why is this here? self.visit is derived in init function through XChemMain.getVisitAndBeamline # self.visit = collected_xtals.split('/')[5] if 'tmp' in collected_xtals or 'results' in collected_xtals or 'scre' in collected_xtals: @@ -2746,20 +2765,21 @@ def parse_file_system(self): continue xtal = collected_xtals[collected_xtals.rfind('/')+1:] - if self.agamemnon: - tmp = xtal[:xtal.rfind('_')] - xtal = tmp[:tmp.rfind('_')] +# if self.agamemnon: +# tmp = xtal[:xtal.rfind('_')] +# xtal = tmp[:tmp.rfind('_')] self.Logfile.insert('%s: checking auto-processing results' %xtal) self.createSampleDir(xtal) if self.target == '=== project directory ===': runDir = os.path.join(collected_xtals,'processed','*') - elif self.agamemnon: - tmpDir = collected_xtals[:collected_xtals.rfind('/')] - runDir = os.path.join(tmpDir,xtal+'_*_') +# elif self.agamemnon: +# tmpDir = collected_xtals[:collected_xtals.rfind('/')] +# runDir = os.path.join(tmpDir,xtal+'_*_') else: runDir = os.path.join(collected_xtals,'*') + self.Logfile.insert('current runDir: ' + runDir) for run in sorted(glob.glob(runDir)): current_run=run[run.rfind('/')+1:] @@ -2773,7 +2793,6 @@ def parse_file_system(self): self.makeJPGdir(xtal,current_run) self.copyJPGs(xtal, current_run, 'non-auto') # 'non-auto' is irrelevant here - for item in self.toParse: procDir = os.path.join(code,item[0]) logfile = item[1] @@ -2806,102 +2825,102 @@ def parse_file_system(self): self.emit(QtCore.SIGNAL('read_pinIDs_from_gda_logs')) self.emit(QtCore.SIGNAL("finished()")) - def parse_agamemnon_file_system(self): - self.Logfile.insert('checking for new data processing results in '+self.processedDir) - progress = 0 - progress_step = 1 - - autoDir = ['auto','agamemnon'] - - c = 0 - for auto in autoDir: - for collected_xtals in sorted(glob.glob(os.path.join(self.processedDir+'-*','processed',auto,self.target,'*'))): - if 'tmp' in collected_xtals or 'results' in collected_xtals or 'scre' in collected_xtals: - continue - c += 1 - - if c > 0: - progress_step = 100/float(c) - self.Logfile.insert('found %s samples of target %s' %(str(c),self.target)) - else: - self.Logfile.warning('found %s samples of target %s' %(str(c),self.target)) - - runList = [] - - autoDir = ['auto','agamemnon','recollect'] - - for auto in autoDir: - for collected_xtals in sorted(glob.glob(os.path.join(self.processedDir+'-*','processed',auto,self.target,'*'))): - self.visit = collected_xtals.split('/')[5] - if 'tmp' in collected_xtals or 'results' in collected_xtals or 'scre' in collected_xtals: - continue - if not os.path.isdir(collected_xtals): - continue - - xtal = collected_xtals[collected_xtals.rfind('/')+1:] - if xtal.endswith('_'): - continue # happened sometime during testing, but should not happen anymore - - self.Logfile.insert('%s: checking auto-processing results in %s %s' %(xtal,self.visit,auto)) - self.createSampleDir(xtal) - - foundRun = False - self.Logfile.insert('%s: checking for runs in %s' %(xtal,os.path.join(collected_xtals,'*'))) - for run in sorted(glob.glob(os.path.join(collected_xtals,'*'))): - foundRun = True - self.Logfile.insert('%s: current run %s' %(xtal,run)) - current_run=auto+'_'+run[run.rfind('/')+1:] - if current_run not in runList: - self.Logfile.insert('%s: found new run -> %s' %(xtal,current_run)) - runList.append(self.visit+'_'+auto+'_'+current_run) - else: - continue - self.Logfile.insert('%s -> run: %s -> current run: %s' %(xtal,run,current_run)) - timestamp=datetime.fromtimestamp(os.path.getmtime(run)).strftime('%Y-%m-%d %H:%M:%S') - - # create directory for crystal aligment images in projectDir - self.makeJPGdir(xtal,current_run) - self.copyJPGs(xtal, run[run.rfind('/')+1:], auto) - - for item in self.toParse: - procDir = os.path.join(run,item[0]) - logfile = item[1] - mtzfile = item[2] - - self.Logfile.insert('%s: search template: procDir - logfile - mtzfile' % xtal) - self.Logfile.insert('%s: procDir = %s' % (xtal, procDir)) - self.Logfile.insert('%s: logfile = %s' % (xtal, logfile)) - self.Logfile.insert('%s: mtzfile = %s' % (xtal, mtzfile)) - +# def parse_agamemnon_file_system(self): +# self.Logfile.insert('checking for new data processing results in '+self.processedDir) +# progress = 0 +# progress_step = 1 +# +# autoDir = ['auto','agamemnon'] +# +# c = 0 +# for auto in autoDir: +# for collected_xtals in sorted(glob.glob(os.path.join(self.processedDir+'-*','processed',auto,self.target,'*'))): +# if 'tmp' in collected_xtals or 'results' in collected_xtals or 'scre' in collected_xtals: +# continue +# c += 1 +# +# if c > 0: +# progress_step = 100/float(c) +# self.Logfile.insert('found %s samples of target %s' %(str(c),self.target)) +# else: +# self.Logfile.warning('found %s samples of target %s' %(str(c),self.target)) +# +# runList = [] +# +# autoDir = ['auto','agamemnon','recollect'] +# +# for auto in autoDir: +# for collected_xtals in sorted(glob.glob(os.path.join(self.processedDir+'-*','processed',auto,self.target,'*'))): +# self.visit = collected_xtals.split('/')[5] +# if 'tmp' in collected_xtals or 'results' in collected_xtals or 'scre' in collected_xtals: +# continue +# if not os.path.isdir(collected_xtals): +# continue +# +# xtal = collected_xtals[collected_xtals.rfind('/')+1:] +# if xtal.endswith('_'): +# continue # happened sometime during testing, but should not happen anymore +# +# self.Logfile.insert('%s: checking auto-processing results in %s %s' %(xtal,self.visit,auto)) +# self.createSampleDir(xtal) +# +# foundRun = False +# self.Logfile.insert('%s: checking for runs in %s' %(xtal,os.path.join(collected_xtals,'*'))) +# for run in sorted(glob.glob(os.path.join(collected_xtals,'*'))): +# foundRun = True +# self.Logfile.insert('%s: current run %s' %(xtal,run)) +# current_run=auto+'_'+run[run.rfind('/')+1:] +# if current_run not in runList: +# self.Logfile.insert('%s: found new run -> %s' %(xtal,current_run)) +# runList.append(self.visit+'_'+auto+'_'+current_run) +# else: +# continue +# self.Logfile.insert('%s -> run: %s -> current run: %s' %(xtal,run,current_run)) +# timestamp=datetime.fromtimestamp(os.path.getmtime(run)).strftime('%Y-%m-%d %H:%M:%S') +# +# # create directory for crystal aligment images in projectDir +# self.makeJPGdir(xtal,current_run) +# self.copyJPGs(xtal, run[run.rfind('/')+1:], auto) +# +# for item in self.toParse: +# procDir = os.path.join(run,item[0]) +# logfile = item[1] +# mtzfile = item[2] +# +# self.Logfile.insert('%s: search template: procDir - logfile - mtzfile' % xtal) +# self.Logfile.insert('%s: procDir = %s' % (xtal, procDir)) +# self.Logfile.insert('%s: logfile = %s' % (xtal, logfile)) +# self.Logfile.insert('%s: mtzfile = %s' % (xtal, mtzfile)) +# +## for folder in glob.glob(procDir): +## for mtz in glob.glob(os.path.join(procDir,mtzfile)): +## print mtz +# # for folder in glob.glob(procDir): -# for mtz in glob.glob(os.path.join(procDir,mtzfile)): -# print mtz - - for folder in glob.glob(procDir): - staraniso = '' - self.Logfile.insert('%s: searching %s' % (xtal, folder)) - if self.junk(folder): - continue - if self.empty_folder(xtal,folder): - continue - if 'staraniso' in logfile or 'summary.tar.gz' in logfile: - staraniso = '_staraniso' - autoproc = self.getAutoProc(folder, staraniso) - if self.alreadyParsed(xtal,current_run,autoproc): - continue - self.readProcessingUpdateResults(xtal,folder,logfile,mtzfile,timestamp,current_run,autoproc) - - - - - progress += progress_step - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'parsing auto-processing results for '+collected_xtals) - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - - if not foundRun: - self.Logfile.error('%s: could not find run' %xtal) - - self.Logfile.insert('====== finished parsing beamline directory ======') - self.emit(QtCore.SIGNAL('read_pinIDs_from_gda_logs')) - self.emit(QtCore.SIGNAL("finished()")) +# staraniso = '' +# self.Logfile.insert('%s: searching %s' % (xtal, folder)) +# if self.junk(folder): +# continue +# if self.empty_folder(xtal,folder): +# continue +# if 'staraniso' in logfile or 'summary.tar.gz' in logfile: +# staraniso = '_staraniso' +# autoproc = self.getAutoProc(folder, staraniso) +# if self.alreadyParsed(xtal,current_run,autoproc): +# continue +# self.readProcessingUpdateResults(xtal,folder,logfile,mtzfile,timestamp,current_run,autoproc) +# +# +# +# +# progress += progress_step +# self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'parsing auto-processing results for '+collected_xtals) +# self.emit(QtCore.SIGNAL('update_progress_bar'), progress) +# +# if not foundRun: +# self.Logfile.error('%s: could not find run' %xtal) +# +# self.Logfile.insert('====== finished parsing beamline directory ======') +# self.emit(QtCore.SIGNAL('read_pinIDs_from_gda_logs')) +# self.emit(QtCore.SIGNAL("finished()")) From 0f5278eb5c0ab462cbce2d16741ee77104cdc9e0 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 3 Jun 2020 15:24:41 +0100 Subject: [PATCH 051/358] v1.6.20 (03/06/2020) (#337) - enable remote cluster submission of (Buster) refinement jobs --- ChangeLog.txt | 3 +++ XChemExplorer.py | 2 +- gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemRefine.py | 13 ++++++++++--- 5 files changed, 16 insertions(+), 6 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 5a1e6eaa..37755428 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.20 (03/06/2020) +- enable remote cluster submission of (Buster) refinement jobs + v1.6.19 (28/05/2020) - combined parsing of 'agamemnon' auto-collection into single function diff --git a/XChemExplorer.py b/XChemExplorer.py index 7fec0044..837fb52a 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -867,7 +867,7 @@ def show_preferences(self): remote_qsub_label = QtGui.QLabel('remote qsub:') settings_hbox_remote_qsub.addWidget(remote_qsub_label) self.remote_qsub_checkbox = QtGui.QCheckBox('use') - #self.remote_qsub_checkbox.toggled.connect(self.run_qsub_remotely) + self.remote_qsub_checkbox.toggled.connect(self.run_qsub_remotely) settings_hbox_dimple_twin_mode = QtGui.QHBoxLayout() self.dimple_twin_mode_label_checkbox = QtGui.QCheckBox('run DIMPLE in TWIN mode') diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 514ff4ac..d65225e6 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.19' + xce_object.xce_version = 'v1.6.20' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 859f453a..06dacc37 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 28/05/2020 #\n' + ' # Date: 03/06/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 852da0e6..873ed988 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -506,11 +506,18 @@ def write_refinement_script(self,cmd,program): f.write(cmd) f.close() - def run_script(self,program,qsub): + def run_script(self,program,external_software): os.chdir(os.path.join(self.ProjectPath,self.xtalID)) - if qsub and not os.uname()[1] == 'hestia': + if external_software['qsub'] and not os.uname()[1] == 'hestia': + self.Logfile.insert('starting refinement with command: qsub -P labxchem -q medium.q %s.sh' %program) os.system("qsub -P labxchem -q medium.q %s.sh" %program) + elif external_software['qsub_remote'] != '': + Logfile.insert('starting refinement on remote cluster') + remote_command=external_software['qsub_remote'].replace('qsub','cd %s; qsub' %os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) + self.Logfile.insert('starting refinement with command: %s' %remote_command) + os.system('%s -P labxchem refmac.csh' %remote_command) else: + self.Logfile.insert('starting refinement with command: ./%s.sh &' %program) os.system('chmod +x %s.sh' %program) os.system('./%s.sh &' %program) @@ -566,7 +573,7 @@ def RunBuster(self,Serial,external_software,xce_logfile,covLinkAtomSpec): self.Logfile.insert('%s: writing buster.sh file in %s' %(self.xtalID,os.path.join(self.ProjectPath,self.xtalID))) self.write_refinement_script(cmd,'buster') self.Logfile.insert('%s: starting refinement...' %self.xtalID) - self.run_script('buster',external_software['qsub']) + self.run_script('buster',external_software) def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtomSpec): From b323c480bb4ece4739efc7503f5722a7242c059e Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 5 Jun 2020 00:00:43 +0100 Subject: [PATCH 052/358] v1.6.21 (04/06/2020) (#338) - source ccp4 7.0 at Diamond before running giant.score_model during Buster refinement --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemRefine.py | 5 +++++ 4 files changed, 10 insertions(+), 2 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 37755428..22247086 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.21 (04/06/2020) +- source ccp4 7.0 at Diamond before running giant.score_model during Buster refinement + v1.6.20 (03/06/2020) - enable remote cluster submission of (Buster) refinement jobs diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index d65225e6..63c4668e 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.20' + xce_object.xce_version = 'v1.6.21' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 06dacc37..5da191b8 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 03/06/2020 #\n' + ' # Date: 04/06/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 873ed988..7b65126b 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -426,8 +426,13 @@ def add_buster_command(self,cmd,xyzin,hklin,libin,Serial): return cmd def run_giant_score_model(self,cmd,cycle): + old_ccp4 = '' + if os.path.isfile('/dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh'): + # giant.score_model does not work with ccp4 7.1-000 + old_ccp4 = 'source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-model.pdb')): cmd += ( 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+cycle+'\n' + + old_ccp4 + 'giant.score_model ' ' pdb1=../%s-pandda-model.pdb ' %self.xtalID + ' mtz1=../dimple.mtz ' From b5f9196b8ee93ea591c6fc75744daeb240fd20aa Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 11 Jun 2020 15:03:14 +0100 Subject: [PATCH 053/358] v1.6.22 (11/06/2020) (#340) * added mapmask step after map calculation in buster refinement in order to cover entire molecule (required for nglview) --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemRefine.py | 16 ++++++++++++++-- 4 files changed, 19 insertions(+), 4 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 22247086..aac90b3f 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.22 (11/06/2020) +- added mapmask step after map calculation in buster refinement in order to cover entire molecule (required for nglview) + v1.6.21 (04/06/2020) - source ccp4 7.0 at Diamond before running giant.score_model during Buster refinement diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 63c4668e..24d80eb3 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.21' + xce_object.xce_version = 'v1.6.22' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 5da191b8..b8bb9946 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 04/06/2020 #\n' + ' # Date: 11/06/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 7b65126b..6a126c87 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -486,13 +486,25 @@ def calculate_maps(self,cmd,program): DELFWT = 'FOFCWT' PHDELWT = 'PHFOFCWT' cmd += ( - 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' + 'fft hklin refine.mtz mapout 2fofc_asu.map << EOF\n' 'labin F1=%s PHI=%s\n' %(FWT,PHWT) + 'EOF\n' '\n' - 'fft hklin refine.mtz mapout fofc.map << EOF\n' + 'mapmask mapin 2fofc_asu.map xyzin refine.pdb mapout 2fofc.map << EOF\n' + ' border 5\n' + 'EOF\n' + '\n' + '/bin/rm 2fofc_asu.map\n' + '\n' + 'fft hklin refine.mtz mapout fofc_asu.map << EOF\n' 'labin F1=%s PHI=%s\n' %(DELFWT,PHDELWT) + 'EOF\n' + '\n' + 'mapmask mapin fofc_asu.map xyzin refine.pdb mapout fofc.map << EOF\n' + ' border 5\n' + 'EOF\n' + '\n' + '/bin/rm fofc_asu.map' ) return cmd From e0f82da9066700ccc419bd4ea2d341ad68d5a2f1 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 12 Jun 2020 19:48:51 +0100 Subject: [PATCH 054/358] v1.6.23 (12/06/2020) (#342) * use gemmi (if available) to convert event maps to mtz --- ChangeLog.txt | 3 ++ XChemExplorer.py | 2 +- gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 49 ++++++++++++++++++++++++----- lib/XChemUtils.py | 9 ++++++ 6 files changed, 57 insertions(+), 10 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index aac90b3f..4510c46f 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.23 (12/06/2020) +- use gemmi (if available) to convert event maps to mtz + v1.6.22 (11/06/2020) - added mapmask step after map calculation in buster refinement in order to cover entire molecule (required for nglview) diff --git a/XChemExplorer.py b/XChemExplorer.py index 837fb52a..bd53cfbe 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -3699,7 +3699,7 @@ def convert_event_maps_to_SF(self): # os.path.join(self.database_directory, # self.data_source_file)) self.work_thread = XChemPANDDA.find_event_map_for_ligand(self.initial_model_directory, - self.xce_logfile) + self.xce_logfile,self.external_software) self.explorer_active = 1 self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 24d80eb3..92d91181 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.22' + xce_object.xce_version = 'v1.6.23' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index b8bb9946..30fec23f 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 11/06/2020 #\n' + ' # Date: 12/06/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index e215c54d..e8d14c37 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -12,6 +12,11 @@ import XChemToolTips import csv +try: + import gemmi +except ImportError: + pass + def get_names_of_current_clusters(xce_logfile,panddas_directory): Logfile=XChemLog.updateLog(xce_logfile) Logfile.insert('parsing {0!s}/cluster_analysis'.format(panddas_directory)) @@ -1549,10 +1554,17 @@ def run(self): class find_event_map_for_ligand(QtCore.QThread): - def __init__(self,project_directory,xce_logfile): + def __init__(self,project_directory,xce_logfile,external_software): QtCore.QThread.__init__(self) self.Logfile=XChemLog.updateLog(xce_logfile) self.project_directory=project_directory + self.external_software=external_software + try: + import gemmi + self.Logfile.insert('found gemmi library in ccp4-python') + except ImportError: + self.external_software['gemmi'] = False + self.Logfile.warning('cannot import gemmi; will use phenix.map_to_structure_factors instead') def run(self): self.Logfile.insert('======== checking ligand CC in event maps ========') @@ -1562,20 +1574,34 @@ def run(self): os.path.isfile(os.path.join(dirs,'refine.mtz')): self.Logfile.insert('%s: found refine.pdb' %xtal) os.chdir(dirs) + try: + p = gemmi.read_structure('refine.pdb') + except: + self.Logfile.error('gemmi library not available') + self.external_software['gemmi'] = False reso = XChemUtils.mtztools('refine.mtz').get_dmin() ligList = XChemUtils.pdbtools('refine.pdb').save_residues_with_resname(dirs,'LIG') self.Logfile.insert('%s: found %s ligands of type LIG in refine.pdb' %(xtal,str(len(ligList)))) for maps in glob.glob(os.path.join(dirs,'*event*.native.ccp4')): - self.expand_map_to_p1(maps) - self.convert_map_to_sf(maps.replace('.ccp4','.P1.ccp4'),reso) + if self.external_software['gemmi']: + self.convert_map_to_sf_with_gemmi(maps,p) + else: + self.expand_map_to_p1(maps) + self.convert_map_to_sf(maps.replace('.ccp4','.P1.ccp4'),reso) summary = '' for lig in sorted(ligList): - for mtz in sorted(glob.glob(os.path.join(dirs,'*event*.native*P1.mtz'))): - self.get_lig_cc(mtz,lig) - cc = self.check_lig_cc(mtz.replace('.mtz', '_CC.log')) - summary += '%s: %s LIG CC = %s (%s)\n' %(xtal,lig,cc,mtz[mtz.rfind('/')+1:]) + if self.external_software['gemmi']: + for mtz in sorted(glob.glob(os.path.join(dirs,'*event*.native.mtz'))): + self.get_lig_cc(mtz,lig) + cc = self.check_lig_cc(mtz.replace('.mtz', '_CC.log')) + summary += '%s: %s LIG CC = %s (%s)\n' %(xtal,lig,cc,mtz[mtz.rfind('/')+1:]) + else: + for mtz in sorted(glob.glob(os.path.join(dirs,'*event*.native*P1.mtz'))): + self.get_lig_cc(mtz,lig) + cc = self.check_lig_cc(mtz.replace('.mtz', '_CC.log')) + summary += '%s: %s LIG CC = %s (%s)\n' %(xtal,lig,cc,mtz[mtz.rfind('/')+1:]) self.Logfile.insert('\nsummary of CC analysis:\n======================:\n'+summary) def expand_map_to_p1(self,emap): @@ -1618,3 +1644,12 @@ def check_lig_cc(self,log): else: self.Logfile.error('logfile does not exist: %s' %log) return cc + + def convert_map_to_sf_with_gemmi(self,emap,p): + self.Logfile.insert('converting ccp4 map to mtz with gemmi map2sf: %s' %emap) + if os.path.isfile(emap.replace('.ccp4','.mtz')): + self.Logfile.warning('mtz file of event map exists; skipping...') + return + cmd = 'gemmi map2sf %s %s FWT PHWT --dmin=%s' %(emap,emap.replace('.ccp4','.mtz'),p.resolution) + self.Logfile.insert('converting map with command:\n' + cmd) + os.system(cmd) \ No newline at end of file diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 2e8c107f..5bc378b7 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -1620,6 +1620,15 @@ def check(self): status='not found' self.Logfile.insert('{0:50} {1:10}'.format('checking for mogul:', status)) + try: + subprocess.call(['gemmi'], stdout=FNULL, stderr=subprocess.STDOUT) + self.available_programs['gemmi']=True + status='found' + except OSError: + self.available_programs['gemmi']=False + status='not found' + self.Logfile.insert('{0:50} {1:10}'.format('checking for gemmi:', status)) + return self.available_programs From 7695d46fe05a7807fa80b66a15dfdd103e824c8c Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 22 Jun 2020 15:55:13 +0100 Subject: [PATCH 055/358] v1.6.24 (22/06/2020) (#351) - bug fix: missing '\n' in calculate_maps (XChemRefine) deleted soakDB file --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemRefine.py | 3 ++- 4 files changed, 7 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 4510c46f..4ba93660 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.24 (22/06/2020) +- bug fix: missing '\n' in calculate_maps (XChemRefine) deleted soakDB file + v1.6.23 (12/06/2020) - use gemmi (if available) to convert event maps to mtz diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 92d91181..e5e18f42 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.23' + xce_object.xce_version = 'v1.6.24' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 30fec23f..ffd01f89 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 12/06/2020 #\n' + ' # Date: 22/06/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 6a126c87..0d227f23 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -504,7 +504,8 @@ def calculate_maps(self,cmd,program): ' border 5\n' 'EOF\n' '\n' - '/bin/rm fofc_asu.map' + '/bin/rm fofc_asu.map\n' + '\n' ) return cmd From 6be44bfc46aea5dd574c00ebae0953972d1b1294 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 23 Jun 2020 06:43:42 +0100 Subject: [PATCH 056/358] v1.6.25 (22/06/2020) (#352) - backup soakDB after restart and 'update database from filesystem' --- ChangeLog.txt | 3 + XChemExplorer.py | 6 ++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 114 ++++++++++++++-------------- lib/XChemMain.py | 5 ++ lib/XChemThread.py | 3 + 6 files changed, 75 insertions(+), 58 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 4ba93660..70e39e68 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.25 (22/06/2020) +- backup soakDB after restart and 'update database from filesystem' + v1.6.24 (22/06/2020) - bug fix: missing '\n' in calculate_maps (XChemRefine) deleted soakDB file diff --git a/XChemExplorer.py b/XChemExplorer.py index bd53cfbe..c5b7c14a 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -93,6 +93,12 @@ def start_GUI(self): self.checkLabXChemDir() + if os.path.isfile(os.path.join(self.database_directory, self.data_source_file)): + self.backup_soakDB() + + def backup_soakDB(self): + XChemMain.backup_soakDB(os.path.join(self.database_directory, self.data_source_file),self.xce_logfile) + def checkLabXChemDir(self): dirCheck = QtGui.QMessageBox() dirCheckLayout = dirCheck.layout() diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index e5e18f42..a22b0464 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.24' + xce_object.xce_version = 'v1.6.25' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index ffd01f89..d1d26e83 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -47,63 +47,63 @@ def create_logfile(self,version): updateLog(self.logfile).insert(message) #print(message) -class depositLog: - - def __init__(self,logfile): - self.logfile=logfile - self.suffixes = ['B', 'KB', 'MB', 'GB', 'TB', 'PB'] - - def humansize(self,nbytes): - if nbytes == 0: return '0 B' - i = 0 - while nbytes >= 1024 and i < len(self.suffixes)-1: - nbytes /= 1024. - i += 1 - f = ('{0:.2f}'.format(nbytes)).rstrip('0').rstrip('.') - return '{0!s} {1!s}'.format(f, self.suffixes[i]) - - def modelInfo(self,xtal,structureType): - message=(xtal+' @ '+structureType) - updateLog(self.logfile).insert(message) - - def nEvents(self,xtal,n_eventMtz): - updateLog(self.logfile).insert(xtal+' contains '+str(n_eventMtz)+ ' sites which are ready for deposition') - - def site_xml(self,xtal,xml): - updateLog(self.logfile).insert('site description for '+xtal) - updateLog(self.logfile).insert(xml) - - def text(self,message): - updateLog(self.logfile).insert(message) - - def summary(self,n_toDeposit,success,failureDict,structureType,successDict): - message= ( '\n' - '==========================================================================\n' - 'SUMMARY:\n' - '--------------------------------------------------------------------------\n' - ' - structure type: %s\n' %structureType+ - ' - n(structures to deposit): {0!s}\n'.format(str(n_toDeposit))+ - ' - n(successful mmcif): {0!s}\n'.format(str(success))+ - '--------------------------------------------------------------------------\n' ) - - if successDict != {}: - message+='\n => the following structures were successfully created:\n' - message+='--------------------------------------------------------------------------\n' - for key in sorted(successDict): - message+='{0:20} {1:5} {2:25} {3:10} {4:25} {5:10}\n'.format(key,'->',successDict[key][0],str(self.humansize(successDict[key][1])),successDict[key][2],str(self.humansize(successDict[key][3]))) - - - if failureDict != {}: - message+='--------------------------------------------------------------------------\n' - message+='\n => the following structures had a problem:\n' - message+='--------------------------------------------------------------------------\n' - for key in failureDict: - for entry in failureDict[key]: - message+='{0!s} -> {1!s}\n'.format(key, entry) - - message+='==========================================================================\n\n' - - updateLog(self.logfile).insert(message) +#class depositLog: +# +# def __init__(self,logfile): +# self.logfile=logfile +# self.suffixes = ['B', 'KB', 'MB', 'GB', 'TB', 'PB'] +# +# def humansize(self,nbytes): +# if nbytes == 0: return '0 B' +# i = 0 +# while nbytes >= 1024 and i < len(self.suffixes)-1: +# nbytes /= 1024. +# i += 1 +# f = ('{0:.2f}'.format(nbytes)).rstrip('0').rstrip('.') +# return '{0!s} {1!s}'.format(f, self.suffixes[i]) +# +# def modelInfo(self,xtal,structureType): +# message=(xtal+' @ '+structureType) +# updateLog(self.logfile).insert(message) +# +# def nEvents(self,xtal,n_eventMtz): +# updateLog(self.logfile).insert(xtal+' contains '+str(n_eventMtz)+ ' sites which are ready for deposition') +# +# def site_xml(self,xtal,xml): +# updateLog(self.logfile).insert('site description for '+xtal) +# updateLog(self.logfile).insert(xml) +# +# def text(self,message): +# updateLog(self.logfile).insert(message) +# +# def summary(self,n_toDeposit,success,failureDict,structureType,successDict): +# message= ( '\n' +# '==========================================================================\n' +# 'SUMMARY:\n' +# '--------------------------------------------------------------------------\n' +# ' - structure type: %s\n' %structureType+ +# ' - n(structures to deposit): {0!s}\n'.format(str(n_toDeposit))+ +# ' - n(successful mmcif): {0!s}\n'.format(str(success))+ +# '--------------------------------------------------------------------------\n' ) +# +# if successDict != {}: +# message+='\n => the following structures were successfully created:\n' +# message+='--------------------------------------------------------------------------\n' +# for key in sorted(successDict): +# message+='{0:20} {1:5} {2:25} {3:10} {4:25} {5:10}\n'.format(key,'->',successDict[key][0],str(self.humansize(successDict[key][1])),successDict[key][2],str(self.humansize(successDict[key][3]))) +# +# +# if failureDict != {}: +# message+='--------------------------------------------------------------------------\n' +# message+='\n => the following structures had a problem:\n' +# message+='--------------------------------------------------------------------------\n' +# for key in failureDict: +# for entry in failureDict[key]: +# message+='{0!s} -> {1!s}\n'.format(key, entry) +# +# message+='==========================================================================\n\n' +# +# updateLog(self.logfile).insert(message) class updateLog: diff --git a/lib/XChemMain.py b/lib/XChemMain.py index 765e301a..c46cee9b 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -1284,6 +1284,11 @@ def make_thumbnail(xtal,ligID,sampleDir): os.chdir(sampleDir) os.system('convert -thumbnail 150x150 %s_%s.png %s_%s_thumb.png' %(xtal,ligID,xtal,ligID)) +def backup_soakDB(database,xce_logfile): + Logfile=XChemLog.updateLog(xce_logfile) + Logfile.insert('backing up soakDB: ' + database+str(datetime.now()).replace(' ','_')) + os.system('/bin/cp %s %s' %(database,database+'.'+str(datetime.now()).replace(' ','_'))) + class find_diffraction_image_directory(QtCore.QThread): def __init__(self,diffraction_data_directory): QtCore.QThread.__init__(self) diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 0b08a4ae..df4cafa1 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -50,6 +50,7 @@ def __init__(self,initial_model_directory,datasource,panddas_directory,xce_logfi self.db=XChemDB.data_source(self.datasource) self.all_samples_in_datasource=self.db.get_all_samples_in_data_source_as_list() self.panddas_directory=panddas_directory + self.xce_logfile = xce_logfile self.Logfile=XChemLog.updateLog(xce_logfile) self.mode=mode @@ -57,6 +58,8 @@ def run(self): self.Logfile.insert('synchronising database and filesystem') self.Logfile.insert('current project directory: '+self.initial_model_directory) + XChemMain.backup_soakDB(self.datasource,self.xce_logfile) + # # get list of xtals # From ae8c45746bfdc53df1a1b174d283792684e6b58f Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 24 Jun 2020 18:30:39 +0100 Subject: [PATCH 057/358] v1.6.26 (24/06/2020) (#353) - added option for anisotropic B-factor refinement with Buster --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemCootBuster.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemMain.py | 2 +- lib/XChemRefine.py | 13 +++++++++---- 6 files changed, 16 insertions(+), 8 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 70e39e68..2b0ce4aa 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.26 (24/06/2020) +- added option for anisotropic B-factor refinement with Buster + v1.6.25 (22/06/2020) - backup soakDB after restart and 'update database from filesystem' diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index a22b0464..4ed33dc1 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.25' + xce_object.xce_version = 'v1.6.26' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemCootBuster.py b/lib/XChemCootBuster.py index 31842f48..2eb96482 100755 --- a/lib/XChemCootBuster.py +++ b/lib/XChemCootBuster.py @@ -1447,7 +1447,7 @@ def start_refinement(self): 'Refine_' + str(self.Serial), 'in.pdb')) # self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) - self.Refine.RunBuster(self.Serial, self.external_software, self.xce_logfile, self.covLinkAtomSpec) + self.Refine.RunBuster(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) self.index += 1 if self.index >= len(self.Todo): # self.index = len(self.Todo) diff --git a/lib/XChemLog.py b/lib/XChemLog.py index d1d26e83..3a73727a 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 22/06/2020 #\n' + ' # Date: 24/06/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemMain.py b/lib/XChemMain.py index c46cee9b..18657025 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -1287,7 +1287,7 @@ def make_thumbnail(xtal,ligID,sampleDir): def backup_soakDB(database,xce_logfile): Logfile=XChemLog.updateLog(xce_logfile) Logfile.insert('backing up soakDB: ' + database+str(datetime.now()).replace(' ','_')) - os.system('/bin/cp %s %s' %(database,database+'.'+str(datetime.now()).replace(' ','_'))) + os.system('/bin/cp %s %s' %(database,database+'.'+str(datetime.now()).replace(' ','_').replace(':','-'))) class find_diffraction_image_directory(QtCore.QThread): def __init__(self,diffraction_data_directory): diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 0d227f23..aa19fda1 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -412,14 +412,14 @@ def set_refinement_status(self,cmd): + self.datasource + ' ' + self.xtalID + ' RefinementStatus running\n') return cmd - def add_buster_command(self,cmd,xyzin,hklin,libin,Serial): + def add_buster_command(self,cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor): cmd += ( 'refine ' ' -p %s' %xyzin + ' -m %s' %hklin + ' -l %s' %libin + ' -autoncs' - ' -M TLSbasic' + + anisotropic_Bfactor + ' -WAT' ' -d Refine_%s\n' %str(Serial) ) @@ -541,7 +541,12 @@ def run_script(self,program,external_software): - def RunBuster(self,Serial,external_software,xce_logfile,covLinkAtomSpec): + def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtomSpec): + + if 'ANIS' in RefmacParams['BREF']: + anisotropic_Bfactor = ' -M ADP ' + else: + anisotropic_Bfactor = ' -M TLSbasic ' self.error = False @@ -575,7 +580,7 @@ def RunBuster(self,Serial,external_software,xce_logfile,covLinkAtomSpec): cmd = self.set_refinement_status(cmd) - cmd = self.add_buster_command(cmd,xyzin,hklin,libin,Serial) + cmd = self.add_buster_command(cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor) cmd = self.run_giant_score_model(cmd,Serial) From ed777c9805d2cd473f14a37b357df03740c2080e Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sun, 28 Jun 2020 21:22:11 +0100 Subject: [PATCH 058/358] v1.6.27 (28/06/2020) (#354) - made water update optional when refining with with Buster --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemCootBuster.py | 4 +++- lib/XChemLog.py | 2 +- lib/XChemRefine.py | 30 +++++++++++++++++++++++------ 5 files changed, 32 insertions(+), 9 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 2b0ce4aa..f0d515e7 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.27 (28/06/2020) +- made water update optional when refining with with Buster + v1.6.26 (24/06/2020) - added option for anisotropic B-factor refinement with Buster diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 4ed33dc1..df0a4bdf 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.26' + xce_object.xce_version = 'v1.6.27' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemCootBuster.py b/lib/XChemCootBuster.py index 2eb96482..97b33ff3 100755 --- a/lib/XChemCootBuster.py +++ b/lib/XChemCootBuster.py @@ -170,7 +170,8 @@ def __init__(self): 'BREF': ' bref ISOT\n', 'TLS': '', 'NCS': '', - 'TWIN': ''} + 'TWIN': '', + 'WATER': '' } def StartGUI(self): @@ -1458,6 +1459,7 @@ def RefinementParams(self, widget): print '\n==> XCE: changing refinement parameters' self.RefmacParams = XChemRefine.RefineParams(self.project_directory, self.xtalID, self.compoundID, self.data_source).RefmacRefinementParams(self.RefmacParams) + print self.RefmacParams def covalentLinkDef(self, widget): coot.user_defined_click_py(2,self.show_potential_link) diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 3a73727a..105381f4 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 24/06/2020 #\n' + ' # Date: 28/06/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index aa19fda1..7d2a4c99 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -110,6 +110,11 @@ def RefmacRefinementParams(self,RefmacParams): if self.RefmacParams['TWIN']=='TWIN\n': self.TWIN.set_active(True) self.vbox.pack_start(self.TWIN,False) + self.WATER = gtk.CheckButton('Update waters (BUSTER)') + self.WATER.connect("toggled", self.WATERCallback) + if self.RefmacParams['WATER']=='WATER\n': self.WATER.set_active(True) + self.vbox.pack_start(self.WATER,False) + self.OKbutton = gtk.Button(label="OK") self.OKbutton.connect("clicked",self.OK) self.vbox.add(self.OKbutton) @@ -162,6 +167,13 @@ def TWINCallback(self, widget): self.RefmacParams['TWIN']='' return self.RefmacParams + def WATERCallback(self, widget): + if widget.get_active(): + self.RefmacParams['WATER']='WATER\n' + else: + self.RefmacParams['WATER']='' + return self.RefmacParams + def OK(self,widget): self.window.destroy() @@ -178,7 +190,8 @@ def ParamsFromPreviousCycle(self,Serial): 'BREF': ' bref ISOT\n', 'TLS': '', 'NCS': '', - 'TWIN': '' } + 'TWIN': '', + 'WATER': '' } if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): @@ -412,15 +425,14 @@ def set_refinement_status(self,cmd): + self.datasource + ' ' + self.xtalID + ' RefinementStatus running\n') return cmd - def add_buster_command(self,cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor): + def add_buster_command(self,cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water): cmd += ( 'refine ' ' -p %s' %xyzin + ' -m %s' %hklin + ' -l %s' %libin + ' -autoncs' - + anisotropic_Bfactor + - ' -WAT' + + anisotropic_Bfactor + update_water + ' -d Refine_%s\n' %str(Serial) ) return cmd @@ -548,6 +560,11 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom else: anisotropic_Bfactor = ' -M TLSbasic ' + if 'WATER' in RefmacParams['WATER']: + update_water = ' -WAT ' + else: + update_water = '' + self.error = False if os.path.isfile(xce_logfile): @@ -580,7 +597,7 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom cmd = self.set_refinement_status(cmd) - cmd = self.add_buster_command(cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor) + cmd = self.add_buster_command(cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water) cmd = self.run_giant_score_model(cmd,Serial) @@ -968,7 +985,8 @@ def ParamsFromPreviousCycle(self,Serial): 'BREF': ' bref ISOT\n', 'TLS': '', 'NCS': '', - 'TWIN': '' } + 'TWIN': '', + 'WATER': '' } if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): From aa4a1bcf6f862458d25d8fda8c7bc8a45e2a2974 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sun, 28 Jun 2020 23:02:26 +0100 Subject: [PATCH 059/358] v1.6.28 (28/06/2020) (#355) - added capture of refiner and date of refinement in DB after refinement --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- helpers/update_data_source_after_refinement.py | 4 ++++ lib/XChemDB.py | 3 +++ lib/XChemRefine.py | 13 ++++++++++--- 5 files changed, 21 insertions(+), 4 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index f0d515e7..ec13100b 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.28 (28/06/2020) +- added capture of refiner and date of refinement in DB after refinement + v1.6.27 (28/06/2020) - made water update optional when refining with with Buster diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index df0a4bdf..41cb273b 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.27' + xce_object.xce_version = 'v1.6.28' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/helpers/update_data_source_after_refinement.py b/helpers/update_data_source_after_refinement.py index 79aeac42..3d16db2a 100755 --- a/helpers/update_data_source_after_refinement.py +++ b/helpers/update_data_source_after_refinement.py @@ -231,9 +231,13 @@ def update_mmcif_file_location(refinement_directory,db_dict): xtal=sys.argv[2] inital_model_directory=sys.argv[3] refinement_directory=sys.argv[4] + refiner = sys.argv[5] + date = sys.argv[6] db=XChemDB.data_source(db_file) db_dict={} + db_dict['RefinementRefiner'] = refiner + db_dict['RefinementDate'] = date db_dict=parse_pdb(inital_model_directory,xtal,db_dict) db_dict=parse_mtz(inital_model_directory,xtal,db_dict) diff --git a/lib/XChemDB.py b/lib/XChemDB.py index 49168b8e..20bb14bd 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -226,6 +226,9 @@ def __init__(self,data_source_file): ['RefinementProgram', 'RefinementProgram', 'TEXT', 1], ['RefinementStatus', 'Refinement\nStatus', 'TEXT', 1], ['RefinementBusterReportHTML', 'RefinementBusterReportHTML', 'TEXT', 1], + ['RefinementRefiner', 'RefinementRefiner', 'TEXT', 1], + ['RefinementDate', 'RefinementDate', 'TEXT', 1], + ['Deposition_PDB_ID', 'Deposition_PDB_ID', 'TEXT', 1], ['Deposition_PDB_file', 'Deposition_PDB_file', 'TEXT', 0], diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 7d2a4c99..802db104 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -11,6 +11,7 @@ import getpass import fileinput import time +from datetime import datetime #sys.path.append(os.path.join(os.getenv('CCP4'),'lib/python2.7/site-packages')) #import coot #sys.path.append('/usr/local/coot/SoakProc/lib') @@ -523,9 +524,11 @@ def calculate_maps(self,cmd,program): def update_database(self,cmd,Serial): + date = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] + user = getpass.getuser() cmd += ( '$CCP4/bin/ccp4-python ' +os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+ - ' %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) ) + ' %s %s %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial),user,date) ) cmd += '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' %(self.ProjectPath,self.xtalID) return cmd @@ -677,10 +680,12 @@ def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom # no DB will be specified when a reference model is built and refined refinementStatus='' updateDB='' + date = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] + user = getpass.getuser() if os.path.isfile(self.datasource): refinementStatus='$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(self.datasource,self.xtalID,'RefinementStatus','running') updateDB = ( '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+ - ' %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) ) + ' %s %s %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial),user,date) ) ####################################################### @@ -1384,6 +1389,8 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine # 'ln -s Refine_%s/refine_%s.output.ground-state.pdb ./refine.output.ground-state.pdb\n' %(panddaSerial,Serial) ) + date = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] + user = getpass.getuser() refmacCmds = ( '#!'+os.getenv('SHELL')+'\n' @@ -1442,7 +1449,7 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine + mapCalculation + '\n' '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+ - ' %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+str(panddaSerial)))+ + ' %s %s %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+str(panddaSerial)),user,date)+ '\n' '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' %(self.ProjectPath,self.xtalID)+ '\n' From 768808db25cb4c09080e7bec18fda905d96b9400 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 29 Jun 2020 00:03:29 +0100 Subject: [PATCH 060/358] v1.6.29 (28/06/2020) (#357) - added capture of person (and date) changing RefinementOutcome field in DB --- ChangeLog.txt | 3 +++ XChemExplorer.py | 6 +++++- gui_scripts/settings_preferences.py | 2 +- lib/XChemCootBuster.py | 7 +++++++ lib/XChemCootNew.py | 5 +++++ lib/XChemDB.py | 2 ++ 6 files changed, 23 insertions(+), 2 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index ec13100b..a81bc0f6 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.6.29 (28/06/2020) +- added capture of person (and date) changing RefinementOutcome field in DB + v1.6.28 (28/06/2020) - added capture of refiner and date of refinement in DB after refinement diff --git a/XChemExplorer.py b/XChemExplorer.py index c5b7c14a..7730cf1b 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -4330,7 +4330,11 @@ def preferences_restraints_generation_combobox_changed(self): def refinement_outcome_combobox_changed(self): for xtal in self.refinement_table_dict: if self.sender() == self.refinement_table_dict[xtal]: - db_dict = {'RefinementOutcome': str(self.sender().currentText())} +# db_dict = {'RefinementOutcome': str(self.sender().currentText())} + db_dict = {} + db_dict['RefinementOutcome'] = str(self.sender().currentText()) + db_dict['RefinementOutcomePerson'] = getpass.getuser() + db_dict['RefinementOutcomeDate'] = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, xtal, 'ligand_bound', db_dict) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 41cb273b..af75843f 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.28' + xce_object.xce_version = 'v1.6.29' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemCootBuster.py b/lib/XChemCootBuster.py index 97b33ff3..77a72ed7 100755 --- a/lib/XChemCootBuster.py +++ b/lib/XChemCootBuster.py @@ -6,6 +6,9 @@ import pickle import glob +import getpass +from datetime import datetime + from matplotlib.figure import Figure # from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas @@ -983,6 +986,10 @@ def RefreshSiteData(self): def experiment_stage_button_clicked(self, widget, data=None): self.db_dict_mainTable['RefinementOutcome'] = data + self.db_dict_mainTable['RefinementOutcomePerson'] = getpass.getuser() + self.db_dict_mainTable['RefinementOutcomeDate'] = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] + + self.Logfile.insert('==> COOT: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( data) + ' in mainTable of datasource') # print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( diff --git a/lib/XChemCootNew.py b/lib/XChemCootNew.py index e07e01c3..92024bf7 100755 --- a/lib/XChemCootNew.py +++ b/lib/XChemCootNew.py @@ -6,6 +6,9 @@ import pickle import glob +import getpass +from datetime import datetime + from matplotlib.figure import Figure # from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas @@ -982,6 +985,8 @@ def RefreshSiteData(self): def experiment_stage_button_clicked(self, widget, data=None): self.db_dict_mainTable['RefinementOutcome'] = data + self.db_dict_mainTable['RefinementOutcomePerson'] = getpass.getuser() + self.db_dict_mainTable['RefinementOutcomeDate'] = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] self.Logfile.insert('==> COOT: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( data) + ' in mainTable of datasource') # print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( diff --git a/lib/XChemDB.py b/lib/XChemDB.py index 20bb14bd..bbe5bf6f 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -199,6 +199,8 @@ def __init__(self,data_source_file): ['RefinementRmsdAngles', 'RefinementRmsdAngles', 'TEXT', 1], ['RefinementRmsdAnglesTL', 'RefinementRmsdAnglesTL', 'TEXT', 0], ['RefinementOutcome', 'Refinement\nOutcome', 'TEXT', 1], + ['RefinementOutcomePerson', 'RefinementOutcomePerson', 'TEXT', 1], + ['RefinementOutcomeDate', 'RefinementOutcomeDate', 'TEXT', 1], ['RefinementMTZfree', 'RefinementMTZfree', 'TEXT', 1], ['RefinementTwinMTZfree', 'RefinementTwinMTZfree', 'TEXT', 1], From 77bbe7021d103970e69b5ef46b07bfa312946f24 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sun, 12 Jul 2020 17:17:38 +0100 Subject: [PATCH 061/358] v1.7.0 (29/06/2020) (#359) - implemented new pandda export routine which takes advantage of gemmi - updated html export accordingly - bug fix: order of commands changed in buster.sh to enable buster-report run on DLS cluster - added links to buster-reports in refinement table - calculate (2)fofc maps around ligand with ending _cut.ccp4 - calculate ligand CC with EDSTATS and display in refinement table --- ChangeLog.txt | 8 + XChemExplorer.py | 87 +++-- gui_scripts/settings_preferences.py | 6 +- .../update_data_source_after_refinement.py | 38 ++- lib/XChemDB.py | 4 +- lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 302 ++++++++++++++++- lib/XChemRefine.py | 75 ++-- lib/XChemToolTips.py | 11 + lib/XChemUtils.py | 237 ++++++++++--- web/XChemWeb.py | 320 ++++++++++-------- 11 files changed, 827 insertions(+), 263 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index a81bc0f6..fc124809 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,11 @@ +v1.7.0 (29/06/2020) +- implemented new pandda export routine which takes advantage of gemmi +- updated html export accordingly +- bug fix: order of commands changed in buster.sh to enable buster-report run on DLS cluster +- added links to buster-reports in refinement table +- calculate (2)fofc maps around ligand with ending _cut.ccp4 +- calculate ligand CC with EDSTATS and display in refinement table + v1.6.29 (28/06/2020) - added capture of person (and date) changing RefinementOutcome field in DB diff --git a/XChemExplorer.py b/XChemExplorer.py index 7730cf1b..ec763433 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -3472,6 +3472,9 @@ def prepare_and_run_task(self, instruction): elif instruction == 'refine NEW bound-state models with BUSTER': self.run_refine_bound_state_with_buster('new') +# elif instruction == 'refine NEW bound-state models with BUSTER - NEW': +# self.run_refine_bound_state_with_buster_new('new') + elif instruction == 'cluster datasets': self.cluster_datasets_for_pandda() @@ -3774,10 +3777,21 @@ def run_pandda_export(self, update_datasource_only, which_models): self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) self.work_thread.start() +# def run_refine_bound_state_with_buster(self,which_models): +# start_thread = True +# if start_thread: +# self.work_thread = XChemPANDDA.refine_bound_state_with_buster(self.panddas_directory, +# os.path.join(self.database_directory, +# self.data_source_file), +# self.initial_model_directory, self.xce_logfile, +# which_models) +# self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) +# self.work_thread.start() + def run_refine_bound_state_with_buster(self,which_models): start_thread = True if start_thread: - self.work_thread = XChemPANDDA.refine_bound_state_with_buster(self.panddas_directory, + self.work_thread = XChemPANDDA.export_and_refine_ligand_bound_models(self.panddas_directory, os.path.join(self.database_directory, self.data_source_file), self.initial_model_directory, self.xce_logfile, @@ -5140,14 +5154,14 @@ def select_sample_for_pandda(self, option): def populate_and_update_refinement_table(self): - panddaList = self.db.execute_statement( - "select CrystalName,PANDDA_site_index,PANDDA_site_name,RefinementOutcome " - "from panddaTable where CrystalName is not '' and PANDDA_site_ligand_placed is 'True';") - panddaDict = {} - for item in panddaList: - if str(item[0]) not in panddaDict: - panddaDict[str(item[0])] = [] - panddaDict[str(item[0])].append([str(item[1]), str(item[2]), str(item[3])]) +# panddaList = self.db.execute_statement( +# "select CrystalName,PANDDA_site_index,PANDDA_site_name,RefinementOutcome " +# "from panddaTable where CrystalName is not '' and PANDDA_site_ligand_placed is 'True';") +# panddaDict = {} +# for item in panddaList: +# if str(item[0]) not in panddaDict: +# panddaDict[str(item[0])] = [] +# panddaDict[str(item[0])].append([str(item[1]), str(item[2]), str(item[3])]) column_name = self.db.translate_xce_column_list_to_sqlite(self.refinement_table_columns) for xtal in sorted(self.xtal_db_dict): @@ -5191,27 +5205,40 @@ def populate_and_update_refinement_table(self): refinement_outcome_combobox.currentIndexChanged.connect( self.refinement_outcome_combobox_changed) - elif header[0] == 'PanDDA site details': - try: - panddaDict[xtal].insert(0, ['Index', 'Name', 'Status']) - outerFrame = QtGui.QFrame() - outerFrame.setFrameShape(QtGui.QFrame.Box) - grid = QtGui.QGridLayout() - for y, entry in enumerate(panddaDict[xtal]): - for x, info in enumerate(entry): - frame = QtGui.QFrame() - frame.setFrameShape(QtGui.QFrame.Box) - vbox = QtGui.QVBoxLayout() - vbox.addWidget(QtGui.QLabel(str(entry[x]))) - frame.setLayout(vbox) - grid.addWidget(frame, y, x) - outerFrame.setLayout(grid) - self.refinement_table.setCellWidget(current_row, column, outerFrame) - except KeyError: - cell_text = QtGui.QTableWidgetItem() - cell_text.setText('*** N/A ***') - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.refinement_table.setItem(current_row, column, cell_text) + elif header[0] == 'buster-reports': + #"'NAME'".format(db_dict['RefinementBusterReportHTML']) + # db_dict['RefinementBusterReportHTML'] = 'www.google.com' + buster_report = db_dict['RefinementBusterReportHTML'] + ref_name = buster_report.split('/')[len(buster_report.split('/'))-2] + buster_report_link = QtGui.QLabel("{1!s}".format(buster_report,ref_name)) + buster_report_link.setOpenExternalLinks(True) +# buster_report_link.setTextInteractionFlags(QtCore.Qt.TextBrowserInteraction) +# buster_report_link.setTextFormat(QtCore.Qt.RichText) +# self.refinement_table.setItem(current_row, column, buster_report_link) + self.refinement_table.setCellWidget(current_row, column, buster_report_link) + + +# elif header[0] == 'PanDDA site details': +# try: +# panddaDict[xtal].insert(0, ['Index', 'Name', 'Status']) +# outerFrame = QtGui.QFrame() +# outerFrame.setFrameShape(QtGui.QFrame.Box) +# grid = QtGui.QGridLayout() +# for y, entry in enumerate(panddaDict[xtal]): +# for x, info in enumerate(entry): +# frame = QtGui.QFrame() +# frame.setFrameShape(QtGui.QFrame.Box) +# vbox = QtGui.QVBoxLayout() +# vbox.addWidget(QtGui.QLabel(str(entry[x]))) +# frame.setLayout(vbox) +# grid.addWidget(frame, y, x) +# outerFrame.setLayout(grid) +# self.refinement_table.setCellWidget(current_row, column, outerFrame) +# except KeyError: +# cell_text = QtGui.QTableWidgetItem() +# cell_text.setText('*** N/A ***') +# cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) +# self.refinement_table.setItem(current_row, column, cell_text) else: cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(db_dict[header[1]])) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index af75843f..e6cab2f7 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.6.29' + xce_object.xce_version = 'v1.7.0' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -406,7 +406,8 @@ def tables(self, xce_object): 'Refinement\nRcryst', 'Refinement\nRfree', 'Refinement\nOutcome', - 'PanDDA site details', + 'buster-reports', + 'Ligand CC', 'Refinement\nStatus'] def top_menu_dict(self, xce_object): @@ -629,6 +630,7 @@ def dropdown_items(self, xce_object): 'check modelled ligands', 'refine ALL bound-state models with BUSTER', 'refine NEW bound-state models with BUSTER', +# 'refine NEW bound-state models with BUSTER - NEW', 'pre-run for ground state model', 'Build ground state model'] diff --git a/helpers/update_data_source_after_refinement.py b/helpers/update_data_source_after_refinement.py index 3d16db2a..4dffe008 100755 --- a/helpers/update_data_source_after_refinement.py +++ b/helpers/update_data_source_after_refinement.py @@ -7,6 +7,8 @@ from XChemUtils import parse from XChemUtils import pdbtools from XChemUtils import misc +from XChemUtils import pdbtools_gemmi +from XChemUtils import maptools import XChemDB import csv @@ -223,9 +225,38 @@ def update_mmcif_file_location(refinement_directory,db_dict): db_dict['RefinementMMCIFreflections_latest'] = os.path.join(refinement_directory,'BUSTER_refln.cif') return db_dict -if __name__=='__main__': +def generate_cut_maps_around_ligand(xtal): + if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.pdb')) and \ + os.path.isfile(os.path.join(inital_model_directory, xtal, '2fofc.map')) and \ + os.path.isfile(os.path.join(inital_model_directory, xtal, 'fofc.map')): + ligandDict = pdbtools_gemmi('refine.pdb').center_of_mass_ligand_dict('LIG') + pdbtools_gemmi('refine.pdb').save_ligands_to_pdb('LIG') + for ligand in ligandDict: + maptools().cut_map_around_ligand('2fofc.map',ligand+'.pdb','7') + os.system('/bin/mv 2fofc_mapmask.map %s_%s_2fofc_cut.ccp4' %(xtal,ligand)) + maptools().cut_map_around_ligand('fofc.map',ligand+'.pdb','7') + os.system('/bin/mv fofc_mapmask.map %s_%s_fofc_cut.ccp4' %(xtal,ligand)) + +def read_ligand_cc_from_edstats(xtal,db_dict): + ligCC = '' + if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.edstats')): + ligandDict = pdbtools_gemmi('refine.pdb').center_of_mass_ligand_dict('LIG') + for ligand in ligandDict: + lig = ligand.split('-')[0] + chain = ligand.split('-')[1] + resn = ligand.split('-')[2] + for line in open('refine.edstats'): + if line.startswith(lig) and line.split()[1] == chain and line.split()[2] == str(resn): + try: + cc = line.split()[8] + ligCC += ligand + ': ' + cc + '\n' + except IndexError: + continue + break + db_dict['RefinementLigandCC'] = ligCC.rstrip() + return db_dict - print 'hallo' +if __name__=='__main__': db_file=sys.argv[1] xtal=sys.argv[2] @@ -246,8 +277,11 @@ def update_mmcif_file_location(refinement_directory,db_dict): db_dict=check_refmac_logfile(refinement_directory,db_dict) db_dict=update_buster_report_index_html(refinement_directory,db_dict) db_dict=update_mmcif_file_location(refinement_directory,db_dict) + db_dict=read_ligand_cc_from_edstats(xtal,db_dict) update_ligand_information_in_panddaTable(inital_model_directory,xtal) parse_ligand_validation(inital_model_directory,refinement_directory,xtal) update_data_source(db_dict) + + generate_cut_maps_around_ligand(xtal) \ No newline at end of file diff --git a/lib/XChemDB.py b/lib/XChemDB.py index bbe5bf6f..4a90b529 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -193,7 +193,7 @@ def __init__(self,data_source_file): ['RefinementRfree', 'Refinement\nRfree', 'TEXT', 1], ['RefinementRfreeTraficLight', 'RefinementRfreeTraficLight', 'TEXT', 0], ['RefinementSpaceGroup', 'Refinement\nSpace Group', 'TEXT', 1], - ['RefinementLigandCC', 'RefinementLigandCC', 'TEXT', 0], + ['RefinementLigandCC', 'Ligand CC', 'TEXT', 0], ['RefinementRmsdBonds', 'RefinementRmsdBonds', 'TEXT', 1], ['RefinementRmsdBondsTL', 'RefinementRmsdBondsTL', 'TEXT', 0], ['RefinementRmsdAngles', 'RefinementRmsdAngles', 'TEXT', 1], @@ -227,7 +227,7 @@ def __init__(self,data_source_file): ['RefinementRamachandranFavoredTL', 'RefinementRamachandranFavoredTL', 'TEXT', 0], ['RefinementProgram', 'RefinementProgram', 'TEXT', 1], ['RefinementStatus', 'Refinement\nStatus', 'TEXT', 1], - ['RefinementBusterReportHTML', 'RefinementBusterReportHTML', 'TEXT', 1], + ['RefinementBusterReportHTML', 'buster-reports', 'TEXT', 1], ['RefinementRefiner', 'RefinementRefiner', 'TEXT', 1], ['RefinementDate', 'RefinementDate', 'TEXT', 1], diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 105381f4..68eeb0a0 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 28/06/2020 #\n' + ' # Date: 29/06/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index e8d14c37..381ce82a 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -14,26 +14,294 @@ try: import gemmi + import pandas except ImportError: pass -def get_names_of_current_clusters(xce_logfile,panddas_directory): - Logfile=XChemLog.updateLog(xce_logfile) - Logfile.insert('parsing {0!s}/cluster_analysis'.format(panddas_directory)) - os.chdir('{0!s}/cluster_analysis'.format(panddas_directory)) - cluster_dict={} - for out_dir in sorted(glob.glob('*')): - if os.path.isdir(out_dir): - cluster_dict[out_dir]=[] - found_first_pdb=False - for folder in glob.glob(os.path.join(out_dir,'pdbs','*')): - xtal=folder[folder.rfind('/')+1:] - if not found_first_pdb: - if os.path.isfile(os.path.join(panddas_directory,'cluster_analysis',out_dir,'pdbs',xtal,xtal+'.pdb') ): - cluster_dict[out_dir].append(os.path.join(panddas_directory,'cluster_analysis',out_dir,'pdbs',xtal,xtal+'.pdb')) - found_first_pdb=True - cluster_dict[out_dir].append(xtal) - return cluster_dict +#def get_names_of_current_clusters(xce_logfile,panddas_directory): +# Logfile=XChemLog.updateLog(xce_logfile) +# Logfile.insert('parsing {0!s}/cluster_analysis'.format(panddas_directory)) +# os.chdir('{0!s}/cluster_analysis'.format(panddas_directory)) +# cluster_dict={} +# for out_dir in sorted(glob.glob('*')): +# if os.path.isdir(out_dir): +# cluster_dict[out_dir]=[] +# found_first_pdb=False +# for folder in glob.glob(os.path.join(out_dir,'pdbs','*')): +# xtal=folder[folder.rfind('/')+1:] +# if not found_first_pdb: +# if os.path.isfile(os.path.join(panddas_directory,'cluster_analysis',out_dir,'pdbs',xtal,xtal+'.pdb') ): +# cluster_dict[out_dir].append(os.path.join(panddas_directory,'cluster_analysis',out_dir,'pdbs',xtal,xtal+'.pdb')) +# found_first_pdb=True +# cluster_dict[out_dir].append(xtal) +# return cluster_dict + + + +class export_and_refine_ligand_bound_models(QtCore.QThread): + + def __init__(self,PanDDA_directory,datasource,project_directory,xce_logfile,which_models): + QtCore.QThread.__init__(self) + self.PanDDA_directory = PanDDA_directory + self.datasource = datasource + self.db = XChemDB.data_source(self.datasource) + self.Logfile = XChemLog.updateLog(xce_logfile) + self.xce_logfile = xce_logfile + self.project_directory = project_directory + self.which_models=which_models + self.external_software=XChemUtils.external_software(xce_logfile).check() + +# self.initial_model_directory=initial_model_directory +# self.db.create_missing_columns() +# self.db_list=self.db.get_empty_db_dict() +# self.external_software=XChemUtils.external_software(xce_logfile).check() +# self.xce_logfile=xce_logfile + +# self.already_exported_models=[] + + def run(self): + + self.Logfile.warning(XChemToolTips.pandda_export_ligand_bound_models_only_disclaimer()) + + # find all folders with *-pandda-model.pdb + modelsDict = self.find_modeled_structures_and_timestamps() + + # if only NEW models shall be exported, check timestamps + if self.which_models != 'all': + modelsDict = self.find_new_models(modelsDict) + + # find pandda_inspect_events.csv and read in as pandas dataframe + inspect_csv = None + if os.path.isfile(os.path.join(self.PanDDA_directory,'analyses','pandda_inspect_events.csv')): + inspect_csv = pandas.read_csv(os.path.join(self.PanDDA_directory,'analyses','pandda_inspect_events.csv')) + + progress = 0 + try: + progress_step = float(1/len(modelsDict)) + except TypeError: + self.Logfile.error('DID NOT FIND ANY MODELS TO EXPORT') + return None + + for xtal in sorted(modelsDict): + + os.chdir(os.path.join(self.PanDDA_directory,'processed_datasets',xtal)) + pandda_model = os.path.join('modelled_structures',xtal + '-pandda-model.pdb') + pdb = gemmi.read_structure(pandda_model) + + # find out ligand event map relationship + ligandDict = XChemUtils.pdbtools_gemmi(pandda_model).center_of_mass_ligand_dict('LIG') + if ligandDict == {}: + self.Logfile.error(xtal + ': cannot find ligand of type LIG; skipping...') + continue + self.show_ligands_in_model(xtal,ligandDict) + emapLigandDict = self.find_ligands_matching_event_map(inspect_csv,xtal,ligandDict) + + self.Logfile.warning('emapLigandDict' + str(emapLigandDict)) + + # convert event map to SF + self.event_map_to_sf(pdb.resolution,emapLigandDict) + + # move existing event maps in project directory to old folder + self.move_old_event_to_backup_folder(xtal) + + # copy event MTZ to project directory + self.copy_event_mtz_to_project_directory(xtal) + + # copy pandda-model to project directory + self.copy_pandda_model_to_project_directory(xtal) + + # make map from MTZ and cut around ligand + self.make_and_cut_map(xtal,emapLigandDict) + + # update database + self.update_database(xtal,modelsDict) + + # refine models + self.refine_exported_model(xtal) + + progress += progress_step + self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + + def update_database(self,xtal,modelsDict): + db_dict = {} + timestamp_file = modelsDict[xtal] + db_dict['DatePanDDAModelCreated'] = timestamp_file + db_dict['RefinementOutcome'] = '3 - In Refinement' + self.Logfile.insert('updating database for '+xtal+' setting time model was created to '+db_dict['DatePanDDAModelCreated']) + self.db.update_data_source(xtal,db_dict) + + + + def make_and_cut_map(self,xtal,emapLigandDict): + self.Logfile.insert('changing directory to ' + os.path.join(self.project_directory,xtal)) + os.chdir(os.path.join(self.project_directory,xtal)) + XChemUtils.pdbtools_gemmi(xtal + '-pandda-model.pdb').save_ligands_to_pdb('LIG') + for ligID in emapLigandDict: + m = emapLigandDict[ligID] + emtz = m.replace('.ccp4','_' + ligID + '.mtz') + emap = m.replace('.ccp4','_' + ligID + '.ccp4') + XChemUtils.maptools().calculate_map(emtz,'FWT','PHWT') + XChemUtils.maptools().cut_map_around_ligand(emap,ligID+'.pdb','7') + if os.path.isfile(emap.replace('.ccp4','_mapmask.ccp4')): + os.system('/bin/mv %s %s_%s_event.ccp4' %(emap.replace('.ccp4','_mapmask.ccp4'),xtal,ligID)) + os.system('ln -s %s_%s_event.ccp4 %s_%s_event_cut.ccp4' %(xtal,ligID,xtal,ligID)) + + + def copy_pandda_model_to_project_directory(self,xtal): + os.chdir(os.path.join(self.project_directory,xtal)) + model = os.path.join(self.PanDDA_directory,'processed_datasets',xtal,'modelled_structures',xtal+'-pandda-model.pdb') + self.Logfile.insert('copying %s to project directory' %model) + os.system('/bin/cp %s .' %model) + + def copy_event_mtz_to_project_directory(self,xtal): + self.Logfile.insert('changing directory to ' + os.path.join(self.PanDDA_directory,'processed_datasets',xtal)) + os.chdir(os.path.join(self.PanDDA_directory,'processed_datasets',xtal)) + for emap in glob.glob('*-BDC_*.mtz'): + self.Logfile.insert('copying %s to %s...' %(emap,os.path.join(self.project_directory,xtal))) + os.system('/bin/cp %s %s' %(emap,os.path.join(self.project_directory,xtal))) + + + def move_old_event_to_backup_folder(self,xtal): + self.Logfile.insert('changing directory to ' + os.path.join(self.project_directory,xtal)) + os.chdir(os.path.join(self.project_directory,xtal)) + if not os.path.isdir('event_map_backup'): + os.mkdir('event_map_backup') + self.Logfile.insert('moving existing event maps to event_map_backup') + for emap in glob.glob('*-BDC_*.ccp4'): + os.system('/bin/mv %s event_map_backup/%s' %(emap,emap+'.'+str(datetime.now()).replace(' ','_').replace(':','-'))) + + def show_ligands_in_model(self,xtal,ligandDict): + self.Logfile.insert(xtal + ': found the following ligands...') + for lig in ligandDict: + self.Logfile.insert(lig + ' -> coordinates ' + str(ligandDict[lig])) + + + def find_modeled_structures_and_timestamps(self): + self.Logfile.insert('finding out modelled structures in ' + self.PanDDA_directory) + modelsDict={} + for model in sorted(glob.glob(os.path.join(self.PanDDA_directory,'processed_datasets','*','modelled_structures','*-pandda-model.pdb'))): + sample=model[model.rfind('/')+1:].replace('-pandda-model.pdb','') + timestamp=datetime.fromtimestamp(os.path.getmtime(model)).strftime('%Y-%m-%d %H:%M:%S') + self.Logfile.insert(sample+'-pandda-model.pdb was created on '+str(timestamp)) + modelsDict[sample]=timestamp + return modelsDict + + def find_new_models(self,modelsDict): + samples_to_export = {} + self.Logfile.hint('XCE will never export/ refine models that are "5-deposition ready" or "6-deposited"') + self.Logfile.hint('Please change the RefinementOutcome flag in the Refinement table if you wish to re-export them') + self.Logfile.insert('checking timestamps of models in database...') + for xtal in modelsDict: + timestamp_file = modelsDict[xtal] + db_query=self.db.execute_statement("select DatePanDDAModelCreated from mainTable where CrystalName is '"+xtal+"' and (RefinementOutcome like '3%' or RefinementOutcome like '4%')") + try: + timestamp_db=str(db_query[0][0]) + except IndexError: + self.Logfile.warning('%s: database query gave no results for DatePanDDAModelCreated; skipping...' %xtal) + self.Logfile.warning('%s: this might be a brand new model; will continue with export!' %xtal) + samples_to_export[xtal]=timestamp_file + timestamp_db = "2100-01-01 00:00:00" # some time in the future... + try: + difference=(datetime.strptime(timestamp_file,'%Y-%m-%d %H:%M:%S') - datetime.strptime(timestamp_db,'%Y-%m-%d %H:%M:%S') ) + if difference.seconds != 0: + self.Logfile.insert('exporting '+xtal+' -> was already refined, but newer PanDDA model available') + samples_to_export[xtal]=timestamp_file + else: + self.Logfile.insert('%s: model has not changed since it was created on %s' %(xtal,timestamp_db)) + except (ValueError, IndexError), e: + self.Logfile.error(str(e)) + return samples_to_export + + def event_map_to_sf(self,resolution,emapLigandDict): + for lig in emapLigandDict: + emap = emapLigandDict[lig] + emtz = emap.replace('.ccp4','.mtz') + emtz_ligand = emap.replace('.ccp4','_' + lig + '.mtz') + self.Logfile.insert('trying to convert %s to SF -> %s' %(emap,emtz_ligand)) + self.Logfile.insert('>>> ' + emtz) + XChemUtils.maptools_gemmi(emap).map_to_sf(resolution) + if os.path.isfile(emtz): + os.system('/bin/mv %s %s' %(emtz,emtz_ligand)) + self.Logfile.insert('success; %s exists' %emtz_ligand) + else: + self.Logfile.warning('something went wrong; %s could not be created...' %emtz_ligand) + + def find_ligands_matching_event_map(self,inspect_csv,xtal,ligandDict): + emapLigandDict = {} + for index, row in inspect_csv.iterrows(): + if row['dtag'] == xtal: + for emap in glob.glob('*-BDC_*.ccp4'): + self.Logfile.insert('checking if event and ligand are within 7A of each other') + x = float(row['x']) + y = float(row['y']) + z = float(row['z']) + matching_ligand = self.calculate_distance_to_ligands(ligandDict,x,y,z) + if matching_ligand is not None: + emapLigandDict[matching_ligand] = emap + self.Logfile.insert('found matching ligand (%s) for %s' %(matching_ligand,emap)) + break + else: + self.Logfile.warning('current ligand not close to event...') + if emapLigandDict == {}: + self.Logfile.error('could not find ligands within 7A of PanDDA events') + return emapLigandDict + + def calculate_distance_to_ligands(self,ligandDict,x,y,z): + matching_ligand = None + p_event = gemmi.Position(x, y, z) + for ligand in ligandDict: + c = ligandDict[ligand] + p_ligand = gemmi.Position(c[0], c[1], c[2]) + self.Logfile.insert('coordinates ligand: ' + str(c[0])+' '+ str(c[1])+' '+str(c[2])) + self.Logfile.insert('coordinates event: ' + str(x)+' '+ str(y)+' '+str(z)) + distance = p_event.dist(p_ligand) + self.Logfile.insert('distance between ligand and event: %s A' %str(distance)) + if distance < 7: + matching_ligand = ligand + break + return matching_ligand + + + + + def refine_exported_model(self,xtal): + self.Logfile.insert('trying to refine ' + xtal + '...') + self.Logfile.insert('%s: getting compound code from database' %xtal) + query=self.db.execute_statement("select CompoundCode from mainTable where CrystalName='%s';" %xtal) + compoundID=str(query[0][0]) + self.Logfile.insert('%s: compounds code = %s' %(xtal,compoundID)) + if os.path.isfile(os.path.join(self.project_directory,xtal,xtal+'.free.mtz')): + if os.path.isfile(os.path.join(self.project_directory,xtal,xtal+'-pandda-model.pdb')): + self.Logfile.insert('running inital refinement on PANDDA model of '+xtal) + Serial=XChemRefine.GetSerial(self.project_directory,xtal) + if not os.path.isdir(os.path.join(self.project_directory,xtal,'cootOut')): + os.mkdir(os.path.join(self.project_directory,xtal,'cootOut')) + # create folder for new refinement cycle + if os.path.isdir(os.path.join(self.project_directory,xtal,'cootOut','Refine_'+str(Serial))): + os.chdir(os.path.join(self.project_directory,xtal,'cootOut','Refine_'+str(Serial))) + else: + os.mkdir(os.path.join(self.project_directory,xtal,'cootOut','Refine_'+str(Serial))) + os.chdir(os.path.join(self.project_directory,xtal,'cootOut','Refine_'+str(Serial))) + os.system('/bin/cp %s in.pdb' %os.path.join(self.project_directory,xtal,xtal+'-pandda-model.pdb')) + Refine=XChemRefine.Refine(self.project_directory,xtal,compoundID,self.datasource) + Refine.RunBuster(str(Serial),None,self.external_software,self.xce_logfile,None) + else: + self.Logfile.error('%s: cannot find %s-pandda-model.pdb; cannot start refinement...' %(xtal,xtal)) + + else: + self.Logfile.error('%s: cannot start refinement because %s.free.mtz is missing in %s' % ( + xtal, xtal, os.path.join(self.project_directory, xtal))) + + + + + + + + + + + diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 802db104..2ed821d3 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -20,7 +20,7 @@ sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') import XChemLog from XChemUtils import pdbtools - +from XChemUtils import mtztools_gemmi def GetSerial(ProjectPath,xtalID): # check if there were already previous refinements @@ -499,25 +499,40 @@ def calculate_maps(self,cmd,program): DELFWT = 'FOFCWT' PHDELWT = 'PHFOFCWT' cmd += ( - 'fft hklin refine.mtz mapout 2fofc_asu.map << EOF\n' - 'labin F1=%s PHI=%s\n' %(FWT,PHWT) + - 'EOF\n' + 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' '\n' - 'mapmask mapin 2fofc_asu.map xyzin refine.pdb mapout 2fofc.map << EOF\n' - ' border 5\n' + 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' + ' labin F1=%s PHI=%s\n' %(FWT,PHWT) + + ' grid samp 4.5\n' 'EOF\n' '\n' - '/bin/rm 2fofc_asu.map\n' - '\n' - 'fft hklin refine.mtz mapout fofc_asu.map << EOF\n' - 'labin F1=%s PHI=%s\n' %(DELFWT,PHDELWT) + +# 'mapmask mapin 2fofc_asu.map xyzin refine.pdb mapout 2fofc.map << EOF\n' +# ' border 5\n' +# 'EOF\n' +# '\n' +# '/bin/rm 2fofc_asu.map\n' +# '\n' + 'fft hklin refine.mtz mapout fofc.map << EOF\n' + ' labin F1=%s PHI=%s\n' %(DELFWT,PHDELWT) + + ' grid samp 4.5\n' 'EOF\n' '\n' - 'mapmask mapin fofc_asu.map xyzin refine.pdb mapout fofc.map << EOF\n' - ' border 5\n' - 'EOF\n' +# 'mapmask mapin fofc_asu.map xyzin refine.pdb mapout fofc.map << EOF\n' +# ' border 5\n' +# 'EOF\n' +# '\n' +# '/bin/rm fofc_asu.map\n' '\n' - '/bin/rm fofc_asu.map\n' + ) + return cmd + + def run_edstats(self,cmd,resh,resl): + cmd += ( + '\n' + 'edstats XYZIN refine.pdb MAPIN1 2fofc.map MAPIN2 fofc.map OUT refine.edstats << eof\n' + ' resl={0!s}\n'.format(resl) + + ' resh={0!s}\n'.format(resh) + + 'eof\n' '\n' ) return cmd @@ -526,7 +541,13 @@ def calculate_maps(self,cmd,program): def update_database(self,cmd,Serial): date = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] user = getpass.getuser() - cmd += ( '$CCP4/bin/ccp4-python ' + ccp4_module = '' # need to source again, because giant.score_model still needs outdated version which does not have gemmi + if self.ProjectPath.startswith('/dls'): + ccp4_module = 'module load ccp4' + cmd += ('\n' + + ccp4_module + + '\n' + '$CCP4/bin/ccp4-python ' +os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+ ' %s %s %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial),user,date) ) cmd += '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' %(self.ProjectPath,self.xtalID) @@ -558,15 +579,19 @@ def run_script(self,program,external_software): def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtomSpec): - if 'ANIS' in RefmacParams['BREF']: + if RefmacParams == None: anisotropic_Bfactor = ' -M ADP ' + update_water = '' else: - anisotropic_Bfactor = ' -M TLSbasic ' + if 'ANIS' in RefmacParams['BREF']: + anisotropic_Bfactor = ' -M ADP ' + else: + anisotropic_Bfactor = ' -M TLSbasic ' - if 'WATER' in RefmacParams['WATER']: - update_water = ' -WAT ' - else: - update_water = '' + if 'WATER' in RefmacParams['WATER']: + update_water = ' -WAT ' + else: + update_water = '' self.error = False @@ -584,6 +609,8 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom hklin, hklout = self.get_hklin_hklout(Serial) + resh, resl = mtztools_gemmi(hklin).get_high_low_resolution_limits() + xyzin, xyzout = self.get_xyzin_xyzout(Serial) libin, libout = self.get_libin_libout(Serial) @@ -602,12 +629,14 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom cmd = self.add_buster_command(cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water) - cmd = self.run_giant_score_model(cmd,Serial) - cmd = self.add_validation(cmd,Serial,'buster') + cmd = self.run_giant_score_model(cmd,Serial) + cmd = self.calculate_maps(cmd,'buster') + cmd = self.run_edstats(cmd,resh,resl) + cmd = self.update_database(cmd,Serial) if self.error: diff --git a/lib/XChemToolTips.py b/lib/XChemToolTips.py index dea12a50..7ca1eecb 100755 --- a/lib/XChemToolTips.py +++ b/lib/XChemToolTips.py @@ -441,4 +441,15 @@ def notification_about_changes_to_apo_deposition(): 'If you still want to make the ground-state mean map available, we would recommend to deposit ground-state mean map and \n' 'everything else you think is relevant on ZENODO and ask the PDB annotator to include the respective DOI in the deposition\n' ) + return msg + +def pandda_export_ligand_bound_models_only_disclaimer(): + msg = ( + 'You have chosen to export and refine the ligand-bound model only. ' + 'This is different to the original procedure described by Pearce et al. (doi 10.1107/S2059798317003412), ' + 'which is based on refinement of an ensemble model consisting of ligand-bound state and confounding ground-state.' + 'Please note that working with the ligand-bound model only usually works well for reasonably well-defined ' + 'ligands and conformational changes, but it may not be ideal for weakly bound fragments and corresponding ' + 'conformational changes.' + ) return msg \ No newline at end of file diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 5bc378b7..226282f9 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -1,5 +1,3 @@ -# last edited: 07/07/2017, 17:00 - import sys import os import glob @@ -11,6 +9,10 @@ import platform import tarfile import json +import time + +from datetime import datetime +import gemmi from rdkit import Chem from rdkit.Chem import AllChem @@ -2701,56 +2703,185 @@ def ElementDict(self): return ElementDict class maptools(object): - def __init__(self,map): - self.translate_spg_to_number_dict = { - 'p1': 1, 'p2': 3, 'p121': 4, 'c2': 5, 'c121': 5, 'p222': 16, - 'p2122': 17, 'p2212': 17, 'p2221': 17, 'p21212': 18, 'p21221': 18, 'p22121': 18, - 'p212121': 19, 'c2221': 20, 'c222': 21, 'f222': 22, 'i222': 23, 'i212121': 24, - 'p4': 75, 'p41': 76, 'p42': 77, 'p43': 78, 'i4': 79, 'i41': 80, - 'p422': 89, 'p4212': 90, 'p4122': 91, 'p41212': 92, 'p4222': 93, 'p42212': 94, - 'p4322': 95, 'p43212': 96, 'i422': 97, 'i4122': 98, - 'p3': 143, 'p31': 144, 'p32': 145, 'p312': 149, 'p321': 150, 'p3112': 151, 'p3121': 152, - 'p3212': 153, 'p3221': 154, 'p6': 168, 'p61': 169, 'p65': 170, 'p62': 171, 'p64': 172, 'p63': 173, - 'p622': 177, 'p6122': 178, 'p6522': 179, 'p6222': 180, 'p6422': 181, 'p6322': 182, - 'r3': 146, 'h3': 146, 'r32': 155, 'h32': 155, - 'p23': 195, 'f23': 196, 'i23': 197, 'p213': 198, 'i213': 199, - 'p432': 207, 'p4232': 208, 'f432': 209, 'f4132': 210, 'i432': 211, 'p4332': 212, - 'p4132': 213, 'i4132': 214 } - - self.map=map - cmd = ( 'mapdump mapin {0!s} << eof\n'.format(self.map)+ - 'end\n' - 'eof' ) - mapdump=subprocess.Popen(cmd,shell=True,stdout=subprocess.PIPE) - self.grid_sampling=[0,0,0] - self.cell_dimensions=[] - self.space_group_number=0 - for line in iter(mapdump.stdout.readline,''): - if 'Grid sampling on x, y, z' in line: - if len(line.split()) == 10: - self.grid_sampling=[line.split()[7],line.split()[8],line.split()[9]] - if 'Cell dimensions' in line: - if len(line.split()) == 9: - self.cell_dimensions=[line.split()[3],line.split()[4],line.split()[5],line.split()[6],line.split()[7],line.split()[8]] - if 'Space-group' in line: - if len(line.split()) == 3: - self.space_group_number=line.split()[2] - - def grid_sampling(self): - return self.grid_sampling - - def cell_dimensions(self): - return self.cell_dimensions - - def space_group_number(self): - return self.space_group_number - - def space_group(self): - space_group='' - space_group_number=self.space_group_number - for spg in self.translate_spg_to_number_dict: - if str(self.translate_spg_to_number_dict[spg]) == str(space_group_number): - space_group=str(spg) - return space_group + def calculate_map(self,mtz,F,PH): + cmd = ( + 'fft hklin %s mapout %s << EOF\n' %(mtz,mtz.replace('.mtz','.ccp4')) + + 'labin F1=%s PHI=%s\n' %(F,PH) + + 'EOF\n' + ) + os.system(cmd) +# print(cmd) + + def cut_map_around_ligand(self,map,ligPDB,border): + if map.endswith('.map'): + map_extension = '.map' + elif map.endswith('.ccp4'): + map_extension = '.ccp4' + else: + map_extension = '' + + cmd = ( + 'mapmask mapin %s mapout %s xyzin %s << eof\n' %(map,map.replace(map_extension,'_mapmask'+map_extension),ligPDB) + + ' border %s\n' %border + + ' end\n' + 'eof' + ) + os.system(cmd) +# print(cmd) + +# self.translate_spg_to_number_dict = { +# 'p1': 1, 'p2': 3, 'p121': 4, 'c2': 5, 'c121': 5, 'p222': 16, +# 'p2122': 17, 'p2212': 17, 'p2221': 17, 'p21212': 18, 'p21221': 18, 'p22121': 18, +# 'p212121': 19, 'c2221': 20, 'c222': 21, 'f222': 22, 'i222': 23, 'i212121': 24, +# 'p4': 75, 'p41': 76, 'p42': 77, 'p43': 78, 'i4': 79, 'i41': 80, +# 'p422': 89, 'p4212': 90, 'p4122': 91, 'p41212': 92, 'p4222': 93, 'p42212': 94, +# 'p4322': 95, 'p43212': 96, 'i422': 97, 'i4122': 98, +# 'p3': 143, 'p31': 144, 'p32': 145, 'p312': 149, 'p321': 150, 'p3112': 151, 'p3121': 152, +# 'p3212': 153, 'p3221': 154, 'p6': 168, 'p61': 169, 'p65': 170, 'p62': 171, 'p64': 172, 'p63': 173, +# 'p622': 177, 'p6122': 178, 'p6522': 179, 'p6222': 180, 'p6422': 181, 'p6322': 182, +# 'r3': 146, 'h3': 146, 'r32': 155, 'h32': 155, +# 'p23': 195, 'f23': 196, 'i23': 197, 'p213': 198, 'i213': 199, +# 'p432': 207, 'p4232': 208, 'f432': 209, 'f4132': 210, 'i432': 211, 'p4332': 212, +# 'p4132': 213, 'i4132': 214 } +# +# self.map=map +# cmd = ( 'mapdump mapin {0!s} << eof\n'.format(self.map)+ +# 'end\n' +# 'eof' ) +# mapdump=subprocess.Popen(cmd,shell=True,stdout=subprocess.PIPE) +# self.grid_sampling=[0,0,0] +# self.cell_dimensions=[] +# self.space_group_number=0 +# for line in iter(mapdump.stdout.readline,''): +# if 'Grid sampling on x, y, z' in line: +# if len(line.split()) == 10: +# self.grid_sampling=[line.split()[7],line.split()[8],line.split()[9]] +# if 'Cell dimensions' in line: +# if len(line.split()) == 9: +# self.cell_dimensions=[line.split()[3],line.split()[4],line.split()[5],line.split()[6],line.split()[7],line.split()[8]] +# if 'Space-group' in line: +# if len(line.split()) == 3: +# self.space_group_number=line.split()[2] +# +# def grid_sampling(self): +# return self.grid_sampling +# +# def cell_dimensions(self): +# return self.cell_dimensions +# +# def space_group_number(self): +# return self.space_group_number +# +# def space_group(self): +# space_group='' +# space_group_number=self.space_group_number +# for spg in self.translate_spg_to_number_dict: +# if str(self.translate_spg_to_number_dict[spg]) == str(space_group_number): +# space_group=str(spg) +# return space_group +# + + +class mtztools_gemmi: + + def __init__(self,mtz): + self.mtz = gemmi.read_mtz_file(mtz) + + def get_map_labels(self): + labelList = [] + for l in self.mtz.columns: + labelList.append(l.label) + FWT = None + PHWT = None + DELFWT = None + PHDELWT = None + + if 'FWT' in labelList and 'PHWT' in labelList: + FWT = 'FWT' + PHWT = 'PHWT' + + if 'DELFWT' in labelList and 'PHDELWT' in labelList: + DELFWT = 'DELFWT' + PHDELWT = 'PHDELWT' + + if '2FOFCWT' in labelList and 'PH2FOFCWT' in labelList: + FWT = '2FOFCWT' + PHWT = 'PH2FOFCWT' + + if 'FOFCWT' in labelList and 'PHFOFCWT' in labelList: + DELFWT = 'FOFCWT' + PHDELWT = 'PHFOFCWT' + + return FWT, PHWT, DELFWT, PHDELWT + + def get_high_low_resolution_limits(self): + resl = self.mtz.resolution_low() + resh = self.mtz.resolution_high() + return resh, resl + + +class maptools_gemmi: + + def __init__(self,emap): + self.emap = emap + self.emtz = emap.replace('.ccp4','.mtz').replace('.map','.mtz') + + def map_to_sf(self,resolution): + if os.path.isfile(self.emtz): + print('mtz file of event map exists; skipping...') + return + cmd = 'gemmi map2sf %s %s FWT PHWT --dmin=%s' %(self.emap,self.emtz,resolution) + print('converting map with command:\n' + cmd) + os.system(cmd) + if os.path.isfile(self.emtz): + print('event map to SF conversion successful') + mtz = gemmi.read_mtz_file(self.emtz) + mtz.history += ['date created: ' + time.ctime(os.path.getmtime(self.emap))] + mtz.history += ['folder: ' + os.getcwd()] + mtz.history += ['file name: ' + self.emap] + if 'BDC' in self.emap: + mtz.history += ['BDC value: ' + self.emap[self.emap.find('BDC')+4:self.emap.find('BDC')+4+self.emap[self.emap.find('BDC')+4:].find('_')]] +# mtz.write_to_file(self.emtz) + else: + print('failed to convert event map to SF') + + +class pdbtools_gemmi: + + def __init__(self,pdb): + self.pdb = gemmi.read_structure(pdb) + + def get_ligand_models_as_dict(self,ligandID): + ligandDict = {} + for model in self.pdb: + for chain in model: + for residue in chain: + if residue.name == ligandID: + if str(residue.name + '-' + chain.name + '-' + str(residue.seqid.num)) not in ligandDict: + ligandDict[str(residue.name + '-' + chain.name + '-' + str(residue.seqid.num))] = None + m = gemmi.Model('1') + m.add_chain(gemmi.Chain('X')) + c = m['X'].get_polymer() + c.add_residue(gemmi.Residue(), 0) + c[0].name = residue.name + for n,atom in enumerate(residue): + c[0].add_atom(atom, n) + ligandDict[str(residue.name + '-' + chain.name + '-' + str(residue.seqid.num))] = m + return ligandDict + + def center_of_mass_ligand_dict(self,ligandID): + ligandDict = self.get_ligand_models_as_dict(ligandID) + ligandPositionDict = {} + for ligand in ligandDict: + pos = ligandDict[ligand].calculate_center_of_mass() + ligandPositionDict[ligand] = [pos.x, pos.y, pos.z] + return ligandPositionDict + + def save_ligands_to_pdb(self,ligandID): + ligandDict = self.get_ligand_models_as_dict(ligandID) + for ligand in ligandDict: + s = gemmi.Structure() + s.add_model(ligandDict[ligand]) + s.write_pdb(ligand + '.pdb') diff --git a/web/XChemWeb.py b/web/XChemWeb.py index ae57891f..a0950646 100755 --- a/web/XChemWeb.py +++ b/web/XChemWeb.py @@ -10,7 +10,7 @@ from XChemUtils import pdbtools from XChemUtils import mtztools - +import XChemUtils class export_to_html: @@ -47,18 +47,35 @@ def prepare(self,whichSamples): self.copy_mtz(xtal) # self.copy_electron_density(xtal) self.copy_ligand_files(xtal) - for ligand in self.ligands_in_pdbFile(xtal): + os.chdir(os.path.join(self.projectDir,xtal)) + ligandDict = XChemUtils.pdbtools_gemmi('refine.pdb').center_of_mass_ligand_dict('LIG') + self.Logfile.insert(xtal + ': saving ligand(s) of type LIG in refine.pdb as PDB files...') + XChemUtils.pdbtools_gemmi('refine.pdb').save_ligands_to_pdb('LIG') + for ligand in ligandDict: + self.Logfile.insert(xtal + ': current ligand -> ' + ligand) + os.chdir(os.path.join(self.projectDir,xtal)) +# for ligand in self.ligands_in_pdbFile(xtal): ligName = ligand.split('-')[0] ligChain = ligand.split('-')[1] ligNumber = ligand.split('-')[2] - eventMap = self.find_matching_event_map_from_database(xtal, ligand) - if eventMap: - self.Logfile.insert('%s: using the following event map -> %s' %(xtal,eventMap)) - self.cut_and_copy_map(xtal, ligand+'.pdb', eventMap, xtal + '_' + ligand + '_event.ccp4','F','PHIF') +# eventMap = self.find_matching_event_map_from_database(xtal, ligand) +# if eventMap: +# self.Logfile.insert('%s: using the following event map -> %s' %(xtal,eventMap)) +# self.cut_and_copy_map(xtal, ligand+'.pdb', eventMap, xtal + '_' + ligand + '_event.ccp4','F','PHIF') +# eventMap = xtal + '_' + ligand + '_event.ccp4' +# else: +# self.Logfile.error('%s: value of event map -> %s' %(xtal,eventMap)) + eventMap = '' +# self.Logfile.insert(xtal + ': looking for' + xtal + '_' + ligand + '_event.ccp4') + if os.path.isfile(xtal + '_' + ligand + '_event.ccp4'): eventMap = xtal + '_' + ligand + '_event.ccp4' - else: - self.Logfile.error('%s: value of event map -> %s' %(xtal,eventMap)) - x,y,z = self.pdb.get_centre_of_gravity_of_residue(ligand) +# self.Logfile.insert(xtal + ': found ' + eventMap) +# else: +# self.Logfile.error(xtal + ': cannot find' + xtal + '_' + ligand + '_event.ccp4') +# x,y,z = self.pdb.get_centre_of_gravity_of_residue(ligand) + x = ligandDict[ligand][0] + y = ligandDict[ligand][1] + z = ligandDict[ligand][2] self.copy_spider_plot(xtal,ligand) pdbID = self.db_dict['Deposition_PDB_ID'] compoundImage = xtal + '_' + self.db_dict['CompoundCode'] + '.png' @@ -75,10 +92,14 @@ def prepare(self,whichSamples): t += str(round(float(ax),1)) + ' ' unitCell = t[:-1] os.chdir(os.path.join(self.projectDir,xtal)) - FWT = xtal + '-' + ligand + '_2fofc.ccp4' - self.cut_and_copy_map(xtal, ligand + '.pdb', '2fofc.map', FWT,'FWT','PHWT') - DELFWT = xtal + '-' + ligand + '_fofc.ccp4' - self.cut_and_copy_map(xtal, ligand + '.pdb', 'fofc.map', DELFWT,'DELFWT','PHDELWT') +# FWT = xtal + '-' + ligand + '_2fofc.ccp4' +# self.cut_and_copy_map(xtal, ligand + '.pdb', '2fofc.map', FWT,'FWT','PHWT') +# DELFWT = xtal + '-' + ligand + '_fofc.ccp4' +# self.cut_and_copy_map(xtal, ligand + '.pdb', 'fofc.map', DELFWT,'DELFWT','PHDELWT') + if os.path.isfile('refine.mtz'): + self.Logfile.insert('%s: found refine.mtz' %xtal) + FWTmap, DELFWTmap = self.prepare_e_density_maps(xtal,ligand) + self.copy_electron_density(xtal,ligand,eventMap) ligConfidence = self.db.get_ligand_confidence_for_ligand(xtal, ligChain, ligNumber, ligName) if ligConfidence.startswith('0'): self.Logfile.warning('%s: ligand confidence of %s-%s-%s is %s; ignoring...' %(xtal,ligChain,ligNumber,ligName,ligConfidence)) @@ -87,14 +108,14 @@ def prepare(self,whichSamples): ligConfidence = 'not assigned' modelStatus = self.db_dict['RefinementOutcome'] if firstFile: - html += XChemMain.html_ngl(pdb,eventMap.replace(self.projectDir,''),FWT,DELFWT,ligand) + html += XChemMain.html_ngl(pdb,eventMap.replace(self.projectDir,''),FWTmap,DELFWTmap,ligand) html += XChemMain.html_download(self.protein_name) html += XChemMain.html_guide() html += XChemMain.html_table_header() firstFile = False html += XChemMain.html_table_row(xtal,pdbID,ligand,compoundImage,residuePlot,pdb,event, - thumbNail,resoHigh,spg,unitCell,FWT,DELFWT,ligConfidence,modelStatus) + thumbNail,resoHigh,spg,unitCell,FWTmap,DELFWTmap,ligConfidence,modelStatus) self.make_thumbnail(xtal,x,y,z,ligand,eventMap) self.prepare_for_download(xtal, pdb, event, compoundCIF, ligand) self.prepare_zip_archives() @@ -103,6 +124,30 @@ def prepare(self,whichSamples): self.Logfile.insert('======== finished preparing HTML summary ========') + def prepare_e_density_maps(self,xtal,ligand): + FWT, PHWT, DELFWT, PHDELWT = XChemUtils.mtztools_gemmi('refine.mtz').get_map_labels() + self.Logfile.insert(xtal + ': calculating 2fofc map...') + XChemUtils.maptools().calculate_map('refine.mtz',FWT,PHWT) + if os.path.isfile('refine.ccp4'): + self.Logfile.insert(xtal + ': 2fofc map successfully calculated') + else: + self.Logfile.error(xtal + ': 2fofc map could not be calculated') + self.Logfile.insert(xtal + ': cutting 2fofc map 7A around ' + ligand) + XChemUtils.maptools().cut_map_around_ligand('refine.ccp4',ligand+'.pdb','7') + if os.path.isfile('refine_mapmask.ccp4'): + self.Logfile.insert(xtal + ': 2fofc map around ' + ligand + ' successfully created') + else: + self.Logfile.error(xtal + ': 2fofc map around ' + ligand + ' could not be created') + os.system('/bin/mv %s %s_%s_2fofc.ccp4' %('refine_mapmask.ccp4',xtal,ligand)) + FWTmap = xtal + '_' + ligand + '_2fofc.ccp4' + self.Logfile.insert(xtal + ': current 2fofc map -> ' + xtal + '_' + ligand + '_2fofc.ccp4') + XChemUtils.maptools().calculate_map('refine.mtz',DELFWT,PHDELWT) + XChemUtils.maptools().cut_map_around_ligand('refine.ccp4',ligand+'.pdb','7') + os.system('/bin/mv %s %s_%s_fofc.ccp4' %('refine_mapmask.ccp4',xtal,ligand)) + DELFWTmap = xtal + '_' + ligand + '_fofc.ccp4' + return FWTmap, DELFWTmap + + def prepare_zip_archives(self): os.chdir(os.path.join(self.htmlDir,'files')) self.Logfile.insert('%s: preparing ZIP archive of all PDB files' %self.protein_name) @@ -209,20 +254,29 @@ def copy_mtz(self,xtal): else: self.Logfile.error('%s: cannot find %s.free.mtz' %(xtal,xtal)) - def copy_electron_density(self,xtal): + def copy_electron_density(self,xtal,ligand,eventMap): os.chdir(os.path.join(self.htmlDir, 'files')) - if os.path.isfile(os.path.join(self.projectDir,xtal,'2fofc.map')): - self.Logfile.insert('%s: copying 2fofc.map to html directory' %xtal) - os.system('/bin/cp %s/2fofc.map %s_2fofc.ccp4' %(os.path.join(self.projectDir,xtal),xtal)) + emap = xtal+'_'+ligand+'_2fofc.ccp4' + if os.path.isfile(os.path.join(self.projectDir,xtal,emap)): + self.Logfile.insert('%s: copying %s to html directory' %(xtal,emap)) + os.system('/bin/cp %s/%s %s' %(os.path.join(self.projectDir,xtal),emap,emap)) else: - self.Logfile.error('%s: cannot find 2fofc.map' %xtal) + self.Logfile.error('%s: cannot find %s' %(xtal,emap)) - if os.path.isfile(os.path.join(self.projectDir,xtal,'fofc.map')): - self.Logfile.insert('%s: copying fofc.map to html directory' %xtal) - os.system('/bin/cp %s/fofc.map %s_fofc.ccp4' %(os.path.join(self.projectDir,xtal),xtal)) + emap = xtal+'_'+ligand+'_fofc.ccp4' + if os.path.isfile(os.path.join(self.projectDir,xtal,emap)): + self.Logfile.insert('%s: copying %s to html directory' %(xtal,emap)) + os.system('/bin/cp %s/%s %s' %(os.path.join(self.projectDir,xtal),emap,emap)) else: - self.Logfile.error('%s: cannot find fofc.map' %xtal) + self.Logfile.error('%s: cannot find %s' %(xtal,emap)) + + self.Logfile.insert('%s: looking for %s' %(xtal,os.path.join(self.projectDir,xtal,eventMap))) + if os.path.isfile(os.path.join(self.projectDir,xtal,eventMap)): + self.Logfile.insert('%s: copying %s to html directory' %(xtal,eventMap)) + os.system('/bin/cp %s/%s %s' %(os.path.join(self.projectDir,xtal),eventMap,eventMap)) + else: + self.Logfile.error('%s: cannot find %s' %(xtal,eventMap)) def copy_ligand_files(self,xtal): os.chdir(os.path.join(self.htmlDir,'files')) @@ -262,89 +316,89 @@ def copy_spider_plot(self,xtal,ligID): self.Logfile.error('%s: cannot find refine.pdb, i.e. cannot start looking for spider plots...' %xtal) - def ligands_in_pdbFile(self,xtal): - os.chdir(os.path.join(self.projectDir,xtal)) - ligPDB = [] - ligList = [] - self.Logfile.insert('%s: reading ligands to type LIG in refine.split.bound-state.pdb' %xtal) - if os.path.isfile('refine.split.bound-state.pdb'): - ligPDB = self.pdb.save_residues_with_resname(os.path.join(self.projectDir, xtal), 'LIG') - else: - self.Logfile.error('%s: cannot find refine.split.bound-state.pdb' %xtal) - if not ligPDB: - self.Logfile.error('%s; cannot find any ligands of type LIG in refine.split.bound-state.pdb' %xtal) - else: - for lig in sorted(ligPDB): - ligList.append(lig.replace('.pdb', '')) - return ligList - - - def find_matching_event_map_from_database(self,xtal,ligID): - ligName = ligID.split('-')[0] - ligChain = ligID.split('-')[1] - ligNumber = ligID.split('-')[2] - eventMAP = self.db.get_event_map_for_ligand(xtal, ligChain, ligNumber, ligName) - self.Logfile.insert('%s: the database thinks the following event map belongs to %s: %s' %(xtal,ligID,eventMAP)) -# print 'event map', eventMAP - if eventMAP == '' or 'none' in str(eventMAP).lower(): - self.Logfile.warning('%s: the respective field in the DB is apparently emtpy' %xtal) - self.Logfile.warning('%s: will try to determine ligand - event map relationship by checking CC...' %xtal) - eventMAP = self.find_matching_event_map(xtal,ligID) - elif not os.path.isfile(eventMAP): - self.Logfile.warning('%s: event map file does not exist!' %xtal) - self.Logfile.warning('%s: will try to determine ligand - event map relationship by checking CC...' %xtal) - eventMAP = self.find_matching_event_map(xtal,ligID) - else: - self.Logfile.insert('%s: found matching event map!' %xtal) - return eventMAP - - def find_matching_event_map(self,xtal,ligID): - os.chdir(os.path.join(self.projectDir, xtal)) - eventMAP = [] - self.Logfile.insert('%s: trying to find fitting event maps for modelled ligands' %xtal) - if os.path.isfile('no_pandda_analysis_performed'): - self.Logfile.warning('%s: no pandda analysis performed; skipping this step...' %xtal) - return - ligCC = [] - for mtz in sorted(glob.glob('*event*.native*P1.mtz')): - self.get_lig_cc(xtal, mtz, ligID+'.pdb') - cc = self.check_lig_cc(mtz.replace('.mtz', '_CC'+ligID+'.log')) - self.Logfile.insert('%s: %s -> CC = %s for %s' %(xtal,ligID,cc,mtz)) - try: - ligCC.append([mtz,float(cc)]) - except ValueError: - ligCC.append([mtz, 0.00]) - try: - highestCC = max(ligCC, key=lambda x: x[0])[1] - except ValueError: - self.Logfile.error('%s: event maps are not yet converted to mtz files...' %xtal) - return - if highestCC == 0.00 or ligCC is []: - self.Logfile.error('%s: best CC of ligand %s for any event map is 0!' %(xtal,ligID)) - else: - self.Logfile.insert('%s: selected event map -> CC(%s) = %s for %s' %(xtal,ligID,highestCC,mtz[mtz.rfind('/')+1:])) - eventMAP = mtz[mtz.rfind('/')+1:].replace('.P1.mtz','.ccp4') +# def ligands_in_pdbFile(self,xtal): +# os.chdir(os.path.join(self.projectDir,xtal)) +# ligPDB = [] +# ligList = [] +# self.Logfile.insert('%s: reading ligands to type LIG in refine.split.bound-state.pdb' %xtal) +# if os.path.isfile('refine.split.bound-state.pdb'): +# ligPDB = self.pdb.save_residues_with_resname(os.path.join(self.projectDir, xtal), 'LIG') +# else: +# self.Logfile.error('%s: cannot find refine.split.bound-state.pdb' %xtal) +# if not ligPDB: +# self.Logfile.error('%s; cannot find any ligands of type LIG in refine.split.bound-state.pdb' %xtal) +# else: +# for lig in sorted(ligPDB): +# ligList.append(lig.replace('.pdb', '')) +# return ligList + + +# def find_matching_event_map_from_database(self,xtal,ligID): +# ligName = ligID.split('-')[0] +# ligChain = ligID.split('-')[1] +# ligNumber = ligID.split('-')[2] +# eventMAP = self.db.get_event_map_for_ligand(xtal, ligChain, ligNumber, ligName) +# self.Logfile.insert('%s: the database thinks the following event map belongs to %s: %s' %(xtal,ligID,eventMAP)) +## print 'event map', eventMAP +# if eventMAP == '' or 'none' in str(eventMAP).lower(): +# self.Logfile.warning('%s: the respective field in the DB is apparently emtpy' %xtal) +# self.Logfile.warning('%s: will try to determine ligand - event map relationship by checking CC...' %xtal) +# eventMAP = self.find_matching_event_map(xtal,ligID) +# elif not os.path.isfile(eventMAP): +# self.Logfile.warning('%s: event map file does not exist!' %xtal) +# self.Logfile.warning('%s: will try to determine ligand - event map relationship by checking CC...' %xtal) +# eventMAP = self.find_matching_event_map(xtal,ligID) +# else: +# self.Logfile.insert('%s: found matching event map!' %xtal) +# return eventMAP + +# def find_matching_event_map(self,xtal,ligID): +# os.chdir(os.path.join(self.projectDir, xtal)) +# eventMAP = [] +# self.Logfile.insert('%s: trying to find fitting event maps for modelled ligands' %xtal) +# if os.path.isfile('no_pandda_analysis_performed'): +# self.Logfile.warning('%s: no pandda analysis performed; skipping this step...' %xtal) +# return +# ligCC = [] +# for mtz in sorted(glob.glob('*event*.native*P1.mtz')): +# self.get_lig_cc(xtal, mtz, ligID+'.pdb') +# cc = self.check_lig_cc(mtz.replace('.mtz', '_CC'+ligID+'.log')) +# self.Logfile.insert('%s: %s -> CC = %s for %s' %(xtal,ligID,cc,mtz)) +# try: +# ligCC.append([mtz,float(cc)]) +# except ValueError: +# ligCC.append([mtz, 0.00]) +# try: +# highestCC = max(ligCC, key=lambda x: x[0])[1] +# except ValueError: +# self.Logfile.error('%s: event maps are not yet converted to mtz files...' %xtal) +# return +# if highestCC == 0.00 or ligCC is []: +# self.Logfile.error('%s: best CC of ligand %s for any event map is 0!' %(xtal,ligID)) +# else: +# self.Logfile.insert('%s: selected event map -> CC(%s) = %s for %s' %(xtal,ligID,highestCC,mtz[mtz.rfind('/')+1:])) +# eventMAP = mtz[mtz.rfind('/')+1:].replace('.P1.mtz','.ccp4') # if not os.path.isfile(eventMAP): # eventMAP = [] # else: # self.cut_eventMAP(xtal,ligID,eventMAP) - return eventMAP - - def cut_and_copy_map(self,xtal,pdbCentre,mapin,mapout,F,PHI): - os.chdir(os.path.join(self.projectDir, xtal)) - self.Logfile.insert('%s: cutting density of %s around %s' %(xtal,mapin.replace('.ccp4','.P1.ccp4'),pdbCentre)) - if os.path.isfile(mapout): - self.Logfile.warning('%s: removing map -> %s' %(xtal,mapout)) - os.system('/bin/rm '+mapout) -# else: +# return eventMAP - if mapin.endswith('.map') or mapin.endswith('.ccp4'): - cmd = ( - 'mapmask mapin %s mapout %s xyzin %s << eof\n' %(mapin.replace('.ccp4','.P1.ccp4'),mapout,pdbCentre) + - ' border 12\n' - ' end\n' - 'eof' - ) +# def cut_and_copy_map(self,xtal,pdbCentre,mapin,mapout,F,PHI): +# os.chdir(os.path.join(self.projectDir, xtal)) +# self.Logfile.insert('%s: cutting density of %s around %s' %(xtal,mapin.replace('.ccp4','.P1.ccp4'),pdbCentre)) +# if os.path.isfile(mapout): +# self.Logfile.warning('%s: removing map -> %s' %(xtal,mapout)) +# os.system('/bin/rm '+mapout) +## else: +# +# if mapin.endswith('.map') or mapin.endswith('.ccp4'): +# cmd = ( +# 'mapmask mapin %s mapout %s xyzin %s << eof\n' %(mapin.replace('.ccp4','.P1.ccp4'),mapout,pdbCentre) + +# ' border 12\n' +# ' end\n' +# 'eof' +# ) # cmd = ( # 'cmapcut -mapin %s -pdbin %s -mapout %s' %(mtzin,pdbCentre,mapout) @@ -353,14 +407,14 @@ def cut_and_copy_map(self,xtal,pdbCentre,mapin,mapout,F,PHI): # cmd = ( # "phenix.cut_out_density %s %s map_coeff_labels='%s,%s' cutout_model_radius=6 cutout_map_file_name=%s cutout_as_map=True" %(pdbCentre,mtzin,F,PHI,mapout) # ) - self.Logfile.insert(xtal+': running command:\n'+cmd) - os.system(cmd) - if os.path.isfile(mapout): - self.Logfile.insert(xtal+': reduced event map successfully created') - self.Logfile.insert('%s: copying %s to %s/files' % (xtal, mapout, self.htmlDir)) - os.system('/bin/cp %s %s/files' % (mapout, self.htmlDir)) - else: - self.Logfile.error(xtal+': creation of event map failed') +# self.Logfile.insert(xtal+': running command:\n'+cmd) +# os.system(cmd) +# if os.path.isfile(mapout): +# self.Logfile.insert(xtal+': reduced event map successfully created') +# self.Logfile.insert('%s: copying %s to %s/files' % (xtal, mapout, self.htmlDir)) +# os.system('/bin/cp %s %s/files' % (mapout, self.htmlDir)) +# else: +# self.Logfile.error(xtal+': creation of event map failed') @@ -382,29 +436,29 @@ def cut_and_copy_map(self,xtal,pdbCentre,mapin,mapout,F,PHI): # self.Logfile.insert('%s: copying event map for %s' %(xtal,ligID)) # os.system('/bin/mv %s/%s_%s.ccp4 .' %(os.path.join(self.projectDir,xtal),xtal,ligID)) - def get_lig_cc(self, xtal, mtz, lig): - ligID = lig.replace('.pdb','') - ccLog = mtz.replace('.mtz', '_CC'+ligID+'.log') - self.Logfile.insert('%s: calculating CC for %s in %s' %(xtal,lig,mtz)) -# if os.path.isfile(mtz.replace('.mtz', '_CC'+ligID+'.log')): - if os.path.isfile(ccLog) and os.path.getsize(ccLog) != 0: - self.Logfile.warning('logfile of CC analysis exists; skipping...') - return -# cmd = ( 'module load phenix\n' -# 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log')) ) - os.system('/bin/rm %s' %mtz.replace('.mtz', '_CC'+ligID+'.log') ) - cmd = ( 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log')) ) - os.system(cmd) - - def check_lig_cc(self,log): - cc = 'n/a' - if os.path.isfile(log): - for line in open(log): - if line.startswith('local'): - cc = line.split()[len(line.split()) - 1] - else: - self.Logfile.error('logfile does not exist: %s' %log) - return cc +# def get_lig_cc(self, xtal, mtz, lig): +# ligID = lig.replace('.pdb','') +# ccLog = mtz.replace('.mtz', '_CC'+ligID+'.log') +# self.Logfile.insert('%s: calculating CC for %s in %s' %(xtal,lig,mtz)) +## if os.path.isfile(mtz.replace('.mtz', '_CC'+ligID+'.log')): +# if os.path.isfile(ccLog) and os.path.getsize(ccLog) != 0: +# self.Logfile.warning('logfile of CC analysis exists; skipping...') +# return +## cmd = ( 'module load phenix\n' +## 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log')) ) +# os.system('/bin/rm %s' %mtz.replace('.mtz', '_CC'+ligID+'.log') ) +# cmd = ( 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log')) ) +# os.system(cmd) + +# def check_lig_cc(self,log): +# cc = 'n/a' +# if os.path.isfile(log): +# for line in open(log): +# if line.startswith('local'): +# cc = line.split()[len(line.split()) - 1] +# else: +# self.Logfile.error('logfile does not exist: %s' %log) +# return cc def write_html_file(self,html): os.chdir(self.htmlDir) From 3e4c66d4f102dd14472b0e3bbbfef39331776f83 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 13 Jul 2020 22:14:48 +0100 Subject: [PATCH 062/358] v1.7.1 (13/07/2020) (#360) - select auto-refinement from action box not from preferences --- ChangeLog.txt | 3 + XChemExplorer.py | 106 ++++++++++++++++++++-------- gui_scripts/settings_preferences.py | 23 ++++-- lib/XChemLog.py | 2 +- 4 files changed, 100 insertions(+), 34 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index fc124809..86072d84 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.1 (13/07/2020) +- select auto-refinement from action box not from preferences + v1.7.0 (29/06/2020) - implemented new pandda export routine which takes advantage of gemmi - updated html export accordingly diff --git a/XChemExplorer.py b/XChemExplorer.py index ec763433..4b534c41 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -818,17 +818,17 @@ def show_preferences(self): vbox_select.addWidget(self.preferences_selection_mechanism_combobox) vbox.addLayout(vbox_select) - vbox_inital_refinement = QtGui.QVBoxLayout() - vbox_inital_refinement.addWidget(QtGui.QLabel('Initial Refinement Pipeline:')) - self.preferences_initial_refinement_combobox = QtGui.QComboBox() - for item in self.preferences_initial_refinement_pipeline: - self.preferences_initial_refinement_combobox.addItem(item) - self.preferences_initial_refinement_combobox.currentIndexChanged.connect( - self.preferences_initial_refinement_combobox_changed) - index = self.preferences_initial_refinement_combobox.findText(self.preferences['initial_refinement_pipeline'], QtCore.Qt.MatchFixedString) - self.preferences_initial_refinement_combobox.setCurrentIndex(index) - vbox_inital_refinement.addWidget(self.preferences_initial_refinement_combobox) - vbox.addLayout(vbox_inital_refinement) +# vbox_inital_refinement = QtGui.QVBoxLayout() +# vbox_inital_refinement.addWidget(QtGui.QLabel('Initial Refinement Pipeline:')) +# self.preferences_initial_refinement_combobox = QtGui.QComboBox() +# for item in self.preferences_initial_refinement_pipeline: +# self.preferences_initial_refinement_combobox.addItem(item) +# self.preferences_initial_refinement_combobox.currentIndexChanged.connect( +# self.preferences_initial_refinement_combobox_changed) +# index = self.preferences_initial_refinement_combobox.findText(self.preferences['initial_refinement_pipeline'], QtCore.Qt.MatchFixedString) +# self.preferences_initial_refinement_combobox.setCurrentIndex(index) +# vbox_inital_refinement.addWidget(self.preferences_initial_refinement_combobox) +# vbox.addLayout(vbox_inital_refinement) vbox_restraints = QtGui.QVBoxLayout() vbox_restraints.addWidget(QtGui.QLabel('Restraints generation program:')) @@ -2867,7 +2867,7 @@ def rerun_dimple_on_all_autoprocessing_files(self): self.update_log.insert('trying to run DIMPLE on ALL auto-processing files') self.check_before_running_dimple(job_list) - def run_dimple_on_selected_autoprocessing_file(self): + def run_dimple_on_selected_autoprocessing_file(self, instruction): job_list = [] for xtal in sorted(self.initial_model_dimple_dict): # print(xtal) @@ -2939,9 +2939,16 @@ def run_dimple_on_selected_autoprocessing_file(self): if job_list: self.update_log.insert('trying to run DIMPLE on SELECTED auto-processing files') - self.check_before_running_dimple(job_list) + self.check_before_running_dimple(job_list,instruction) + + def remove_selected_dimple_files(self,instruction): + if 'dimple' in instruction.lower(): + pipeline = 'dimple' + elif 'pipedream' in instruction.lower(): + pipeline = 'pipedream' + elif 'phenix' in instruction.lower(): + pipeline = 'phenix.ligand_pipeline' - def remove_selected_dimple_files(self): job_list = [] for xtal in sorted(self.initial_model_dimple_dict): if self.initial_model_dimple_dict[xtal][0].isChecked(): @@ -2955,14 +2962,14 @@ def remove_selected_dimple_files(self): reply = msgBox.exec_(); if reply == 0: - self.status_bar.showMessage('preparing to remove DIMPLE files') - self.update_log.insert('preparing to remove DIMPLE files') + self.status_bar.showMessage('preparing to remove {0!s} files'.format(pipeline)) + self.update_log.insert('preparing to remove {0!s} files'.format(pipeline)) self.work_thread = XChemThread.remove_selected_dimple_files(job_list, self.initial_model_directory, self.xce_logfile, self.database_directory, self.data_source_file, - self.preferences['initial_refinement_pipeline']) + pipeline) self.explorer_active = 1 self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) @@ -2972,8 +2979,15 @@ def remove_selected_dimple_files(self): self.datasource_menu_reload_samples) self.work_thread.start() - def set_results_from_selected_pipeline(self): - self.update_log.warning('selecting initial refinement results from '+self.preferences['initial_refinement_pipeline']) + def set_results_from_selected_pipeline(self,instruction): + if 'dimple' in instruction.lower(): + pipeline = 'dimple' + elif 'pipedream' in instruction.lower(): + pipeline = 'pipedream' + elif 'phenix' in instruction.lower(): + pipeline = 'phenix.ligand_pipeline' + + self.update_log.warning('selecting initial refinement results from '+pipeline) job_list = [] for xtal in sorted(self.initial_model_dimple_dict): @@ -2985,7 +2999,7 @@ def set_results_from_selected_pipeline(self): self.xce_logfile, self.database_directory, self.data_source_file, - self.preferences['initial_refinement_pipeline']) + pipeline) self.explorer_active = 1 self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) @@ -3122,7 +3136,7 @@ def get_job_list_for_dimple_rerun(self, xtal, job_list, db_dict, entry): self.status_bar.showMessage('idle') return job_list - def check_before_running_dimple(self, job_list): + def check_before_running_dimple(self, job_list,instruction): msgBox = QtGui.QMessageBox() msgBox.setText( @@ -3133,6 +3147,13 @@ def check_before_running_dimple(self, job_list): reply = msgBox.exec_(); if reply == 0: + if 'dimple' in instruction.lower(): + pipeline = 'dimple' + elif 'pipedream' in instruction.lower(): + pipeline = 'pipedream' + elif 'phenix' in instruction.lower(): + pipeline = 'phenix.ligand_pipeline' + self.status_bar.showMessage('preparing {0!s} DIMPLE jobs'.format(len(job_list))) self.update_log.insert('preparing to run {0!s} DIMPLE jobs'.format(len(job_list))) if self.external_software['qsub_array']: @@ -3154,7 +3175,7 @@ def check_before_running_dimple(self, job_list): self.using_remote_qsub_submission, self.remote_qsub_submission, self.preferences['dimple_twin_mode'], - self.preferences['initial_refinement_pipeline']) + pipeline ) self.explorer_active = 1 self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) @@ -3417,14 +3438,43 @@ def prepare_and_run_task(self, instruction): # elif instruction == 'Run DIMPLE on All Autoprocessing MTZ files': # self.rerun_dimple_on_all_autoprocessing_files() - elif instruction == 'Run initial refinement on selected MTZ files': - self.run_dimple_on_selected_autoprocessing_file() +# elif instruction == 'Run initial refinement on selected MTZ files': +# self.run_dimple_on_selected_autoprocessing_file() + + elif instruction == 'Run DIMPLE on selected MTZ files': + self.run_dimple_on_selected_autoprocessing_file(instruction) + + elif instruction == 'Run PIPEDREAM on selected MTZ files': + self.run_dimple_on_selected_autoprocessing_file(instruction) + + elif instruction == 'Run PHENIX.LIGAND_PIPELINE on selected MTZ files': + self.run_dimple_on_selected_autoprocessing_file(instruction) + + +# elif instruction == 'Remove selected initial refinement files': +# self.remove_selected_dimple_files() + + elif instruction == 'Remove selected DIMPLE files': + self.remove_selected_dimple_files(instruction) + + elif instruction == 'Remove selected PIPEDREAM files': + self.remove_selected_dimple_files(instruction) + + elif instruction == 'Remove selected PHENIX.LIGAND_PIPELINE files': + self.remove_selected_dimple_files(instruction) + +# elif instruction == 'Set only results from selected pipeline': +# self.set_results_from_selected_pipeline() + + elif instruction == 'Set DIMPLE output': + self.set_results_from_selected_pipeline(instruction) + + elif instruction == 'Set PIPEDREAM output': + self.set_results_from_selected_pipeline(instruction) - elif instruction == 'Remove selected initial refinement files': - self.remove_selected_dimple_files() + elif instruction == 'Set PHENIX.LIGAND_PIPELINE output': + self.set_results_from_selected_pipeline(instruction) - elif instruction == 'Set only results from selected pipeline': - self.set_results_from_selected_pipeline() # elif instruction == 'Create CIF/PDB/PNG file of ALL compounds': # self.create_cif_pdb_png_files('ALL') diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index e6cab2f7..3aaf8d84 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.0' + xce_object.xce_version = 'v1.7.1' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -606,15 +606,28 @@ def dropdown_items(self, xce_object): 'Run xia2 on selected datasets', 'Run xia2 on selected datasets - overwrite'] - xce_object.map_cif_file_tasks = ['Run initial refinement on selected MTZ files', - 'Remove selected initial refinement files', - 'Set only results from selected pipeline', + xce_object.map_cif_file_tasks = [ +# 'Run initial refinement on selected MTZ files', +# 'Remove selected initial refinement files', + 'Run DIMPLE on selected MTZ files', + 'Remove selected DIMPLE files', + 'Set DIMPLE output', +# 'Set only results from selected pipeline', # 'Create CIF/PDB/PNG file of ALL compounds', # 'Create CIF/PDB/PNG file of NEW compounds', + '------------------------------------------', 'Create CIF/PDB/PNG file of SELECTED compounds', 'Merge ligand CIF file with selected compounds', 'Restore original CIF file of selected compounds', - 'Fit ligands into maps after initial refinement' + 'Fit ligands into maps after initial refinement', + '------------------------------------------', + 'Run PIPEDREAM on selected MTZ files', + 'Remove selected PIPEDREAM files', + 'Set PIPEDREAM output', + '------------------------------------------', + 'Run PHENIX.LIGAND_PIPELINE on selected MTZ files', + 'Remove selected PHENIX.LIGAND_PIPELINE files', + 'Set PHENIX.LIGAND_PIPELINE output' ] xce_object.panddas_file_tasks = ['pandda.analyse', diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 68eeb0a0..95117397 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 29/06/2020 #\n' + ' # Date: 13/07/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From a28ce858c33321308ab7a98924ece04d125a4bb6 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 16 Jul 2020 18:32:01 +0100 Subject: [PATCH 063/358] v1.7.2 (16/07/2020) (#361) - show molprobity to-do list generated by buster-report in XCE COOT interface --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemCootBuster.py | 23 ++++++++++++----------- lib/XChemLog.py | 2 +- 4 files changed, 17 insertions(+), 13 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 86072d84..f963685a 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.2 (16/07/2020) +- show molprobity to-do list generated by buster-report in XCE COOT interface + v1.7.1 (13/07/2020) - select auto-refinement from action box not from preferences diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 3aaf8d84..4aa11844 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.1' + xce_object.xce_version = 'v1.7.2' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemCootBuster.py b/lib/XChemCootBuster.py index 77a72ed7..98eaf401 100755 --- a/lib/XChemCootBuster.py +++ b/lib/XChemCootBuster.py @@ -1613,18 +1613,19 @@ def merge_ligand_into_protein(self, widget): def show_molprobity_to_do(self, widget): print self.panddaSerial AdjPanddaSerial = (4 - len(str(self.Serial))) * '0' + str(int(self.panddaSerial) - 1) - print os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), - 'molprobity_coot.py') - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), - 'molprobity_coot.py')): - print '==> XCE: running MolProbity Summary for', self.xtalID - coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), - 'molprobity_coot.py')) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), - 'molprobity_coot.py')): + + print '==> XCE COOT: trying to find ' + os.path.join(self.project_directory, self.xtalID, + 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py') + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, + 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py')): print '==> XCE: running MolProbity Summary for', self.xtalID - coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), - 'molprobity_coot.py')) + coot.run_script(os.path.join(self.project_directory, self.xtalID, + 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py')) +# elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), +# 'molprobity_coot.py')): +# print '==> XCE: running MolProbity Summary for', self.xtalID +# coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), +# 'molprobity_coot.py')) else: print '==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py') diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 95117397..42dce92a 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 13/07/2020 #\n' + ' # Date: 16/07/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From c8d21087d0f68635b9ea2e7c17c5b1b02070ac73 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 21 Jul 2020 08:13:44 +0100 Subject: [PATCH 064/358] v1.7.3 (20/07/2020) (#363) - bug fix: ignore large temporary files in get_gda_barcodes which lead to memory errors - removed obsolete PROASIS menu item - bug fix: xce now reads already parsed auto-processing results correctly to speed up parsing --- ChangeLog.txt | 5 ++++ gui_scripts/settings_preferences.py | 12 ++++----- lib/XChemLog.py | 2 +- lib/XChemMain.py | 3 +++ lib/XChemThread.py | 41 ++++++++++++++++++++++------- 5 files changed, 47 insertions(+), 16 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index f963685a..9d82f27c 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,8 @@ +v1.7.3 (20/07/2020) +- bug fix: ignore large temporary files in get_gda_barcodes which lead to memory errors +- removed obsolete PROASIS menu item +- bug fix: xce now reads already parsed auto-processing results correctly to speed up parsing + v1.7.2 (16/07/2020) - show molprobity to-do list generated by buster-report in XCE COOT interface diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 4aa11844..9ce21835 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.2' + xce_object.xce_version = 'v1.7.3' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -468,11 +468,11 @@ def top_menu_dict(self, xce_object): ['Update DB with PDB codes', '', xce_object.enter_pdb_codes], ['Check SMILES', '', xce_object.check_smiles_in_db_and_pdb] ]], - 'E: proasis': ["Proasis", - [ - ['Launch Proasis in browser', '', partial(webbrowser.open, - url='http://cs04r-sc-vserv-137.diamond.ac.uk/Proasis4_2017/')] - ]], +# 'E: proasis': ["Proasis", +# [ +# ['Launch Proasis in browser', '', partial(webbrowser.open, +# url='http://cs04r-sc-vserv-137.diamond.ac.uk/Proasis4_2017/')] +# ]], 'F: help': ["&Help", [ ['Open XCE manual', '', diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 42dce92a..447df179 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 16/07/2020 #\n' + ' # Date: 20/07/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemMain.py b/lib/XChemMain.py index 18657025..2f45e4f0 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -457,6 +457,9 @@ def get_gda_barcodes(sampleList,gzipped_logs_parsed,gda_log_start_line,beamline, pinDict = {} found_barcode_entry=False for gdaLogFile in glob.glob(os.path.join('/dls_sw',beamline,'logs','gda-server*log*')): + if gdaLogFile.endswith('tmp'): + Logfile.warning('ignoring temporary file ' + gdaLogFile) + continue Logfile.insert('parsing {0!s}'.format(gdaLogFile)) if gzipped_logs_parsed and gdaLogFile.endswith('.gz'): Logfile.insert('{0!s} was already parsed during this visit'.format(gdaLogFile)) diff --git a/lib/XChemThread.py b/lib/XChemThread.py index df4cafa1..856f990f 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2459,6 +2459,12 @@ def __init__(self, self.db = XChemDB.data_source(os.path.join(database)) self.exisitingSamples = self.getExistingSamples() +# for xtal in self.exisitingSamples: +# print self.exisitingSamples[xtal] +# break +# quit() + + self.toParse = [ [ os.path.join('*'), os.path.join('LogFiles', '*aimless.log'), @@ -2540,12 +2546,13 @@ def run(self): def getExistingSamples(self): existingSamples={} self.Logfile.insert('reading existing samples from collectionTable') - allEntries = self.db.execute_statement('select CrystalName,DataCollectionVisit,DataCollectionRun,DataProcessingProgram from collectionTable where DataCollectionOutcome = "success"') + allEntries = self.db.execute_statement('select CrystalName,DataCollectionVisit,DataCollectionRun,DataProcessingProgram, DataCollectionSubdir from collectionTable where DataCollectionOutcome = "success"') for item in allEntries: if str(item[0]) not in existingSamples: existingSamples[str(item[0])]=[] - self.Logfile.insert('%s: adding %s' %(str(item[0]),str(item[1]))) - existingSamples[str(item[0])].append(str(item[1])+ '-' + str(item[2])+str(item[3])) + self.Logfile.insert('%s: adding %s' %(str(item[0]),str(item[1]))) + # visit-runautoproc-subdir + existingSamples[str(item[0])].append(str(item[1])+ '-' + str(item[2])+str(item[3])+'-'+str(item[4])) return existingSamples def createSampleDir(self,xtal): @@ -2678,8 +2685,10 @@ def readProcessingUpdateResults(self,xtal,folder,log,mtz,timestamp,current_run,a self.update_data_collection_table(xtal,current_run,autoproc,db_dict,proc_code) # return db_dict - def getAutoProc(self,folder,staraniso): + def getAutoProc(self,folder_rel,staraniso): self.Logfile.insert('checking name of auto-processing pipeline...') + folder = os.path.realpath(folder_rel) + self.Logfile.insert('folder: ' + folder) autoproc='unknown' if 'ap-run' in folder: autoproc = 'autoPROC' @@ -2705,11 +2714,19 @@ def update_data_collection_table(self,xtal,current_run,autoproc,db_dict,proc_cod 'DataProcessingProgram': autoproc } self.db.update_insert_any_table('collectionTable', db_dict, condition_dict) - def alreadyParsed(self,xtal,current_run,autoproc): + def alreadyParsed(self,xtal,current_run,proc_code,autoproc): parsed=False + self.Logfile.insert('checking if this processed directory was already parsed') if xtal in self.exisitingSamples: - if self.visit + '-' + current_run + autoproc in self.exisitingSamples[xtal]: - self.Logfile.insert( + self.Logfile.insert(xtal + ' exists in collectionTable') + self.Logfile.insert('current identifier:') + self.Logfile.insert(self.visit + '-' + current_run + autoproc + '-' + proc_code) + self.Logfile.insert('indentifier in collectionTable') + for x in self.exisitingSamples[xtal]: + self.Logfile.insert(x) + # visit-runautoproc-subdir + if self.visit + '-' + current_run + autoproc + '-' + proc_code in self.exisitingSamples[xtal]: + self.Logfile.warning( '%s: results from %s already parsed; skipping...' % ( xtal, self.visit + '-' + current_run + autoproc)) parsed=True @@ -2787,7 +2804,12 @@ def parse_file_system(self): for run in sorted(glob.glob(runDir)): current_run=run[run.rfind('/')+1:] for code in glob.glob(os.path.join(run,'*')): - proc_code = code[code.rfind('/')+1:] + if os.path.islink(code): + continue +# else: +# proc_code = code[code.rfind('/')+1:] + proc_code = code.split('/')[len(code.split('/'))-1] + self.Logfile.insert(xtal + ': processed directory -> ' + proc_code) if current_run+proc_code in runList: continue self.Logfile.insert('%s -> run: %s -> current run: %s -> %s' %(xtal,run,current_run,proc_code)) @@ -2815,11 +2837,12 @@ def parse_file_system(self): if 'staraniso' in logfile or 'summary.tar.gz' in logfile: staraniso = '_staraniso' autoproc = self.getAutoProc(folder,staraniso) - if self.alreadyParsed(xtal,current_run+proc_code,autoproc): + if self.alreadyParsed(xtal,current_run,proc_code,autoproc): continue self.readProcessingUpdateResults(xtal,folder,logfile,mtzfile,timestamp,current_run,autoproc,proc_code) runList.append(current_run+proc_code) +# quit() progress += progress_step self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'parsing auto-processing results for '+xtal) self.emit(QtCore.SIGNAL('update_progress_bar'), progress) From 8f1c08915dbb3b5bef6eba2c303777afc64e79ce Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 21 Jul 2020 13:34:48 +0100 Subject: [PATCH 065/358] v1.7.4 (21/07/2020) (#365) - bug fix: selected results not linked after parsing of auto-processing results - enabled updates of message & progress bar during scoring of auto-processing results - enabled updates of message & progress bar during DB update of pinIDs --- ChangeLog.txt | 5 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemMain.py | 3 +- lib/XChemThread.py | 63 +++++++++++++++++++++++++++++ 5 files changed, 72 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 9d82f27c..ec053649 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,8 @@ +v1.7.4 (21/07/2020) +- bug fix: selected results not linked after parsing of auto-processing results +- enabled updates of message & progress bar during scoring of auto-processing results +- enabled updates of message & progress bar during DB update of pinIDs + v1.7.3 (20/07/2020) - bug fix: ignore large temporary files in get_gda_barcodes which lead to memory errors - removed obsolete PROASIS menu item diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 9ce21835..83e27cde 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.3' + xce_object.xce_version = 'v1.7.4' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 447df179..2032f96d 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 20/07/2020 #\n' + ' # Date: 21/07/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemMain.py b/lib/XChemMain.py index 2f45e4f0..e6d2fd58 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -524,7 +524,7 @@ def linkAutoProcessingResult(xtal,dbDict,projectDir,xce_logfile): # MTZ file Logfile.warning('removing %s.mtz' %xtal) os.system('/bin/rm %s.mtz' %xtal) - print xtal,os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile) + Logfile.insert(xtal+': looking for '+os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile)) if os.path.isfile(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile)): os.symlink(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile), xtal + '.mtz') Logfile.insert('linking MTZ file from different auto-processing pipeline:') @@ -532,6 +532,7 @@ def linkAutoProcessingResult(xtal,dbDict,projectDir,xce_logfile): # LOG file Logfile.warning('removing %s.log' %xtal) os.system('/bin/rm %s.log' %xtal) + Logfile.insert(xtal+': looking for '+os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfile)) if os.path.isfile(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfile)): os.symlink(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfile), xtal + '.log') Logfile.insert('linking LOG file from different auto-processing pipeline:') diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 856f990f..18c9559e 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2210,11 +2210,18 @@ def run(self): def update_database(self,pinDict): self.Logfile.insert('updating database with pinDIs from GDA logfiles') + + progress = 0 + progress_step = XChemMain.getProgressSteps(len(pinDict)) + for sample in pinDict: + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'updating pinID in DB for ' + sample) dbDict = {} dbDict['DataCollectionPinBarcode'] = pinDict[sample] # self.db.update_data_source(sample,dbDict) self.db.update_specified_table(sample,dbDict,'collectionTable') + progress += progress_step + self.emit(QtCore.SIGNAL('update_progress_bar'), progress) class choose_autoprocessing_outcome(QtCore.QThread): @@ -2254,6 +2261,10 @@ def __init__(self, def run(self): + + progress = 0 + progress_step = XChemMain.getProgressSteps(len(self.allSamples)) + for sample in sorted(self.allSamples): if self.db.autoprocessing_result_user_assigned(sample) and not self.rescore: if os.path.isfile(os.path.join(self.projectDir,sample,sample+'.mtz')): @@ -2269,6 +2280,13 @@ def run(self): dbList = self.db.all_autoprocessing_results_for_xtal_as_dict(sample) self.Logfile.insert('%s: found %s different autoprocessing results' %(sample,str(len(dbList)))) + # 0.) first check for which results files actually exist + # + dbList = self.checkExistingFiles(dbList,sample) + if not dbList: + self.Logfile.error(sample + ': cannot find any MTZ & LOG files; skipping...') + continue + # 1.) if posssible, only carry forward samples with similar UCvolume and same point group dbList = self.selectResultsSimilarToReference(dbList) @@ -2294,6 +2312,11 @@ def run(self): dbDict['DataProcessingAutoAssigned'] = 'True' self.updateDB(sample,dbDict) + progress += progress_step + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'scoring auto-processing results for '+sample) + self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + + self.Logfile.insert('====== finished scoring data processing results ======') self.emit(QtCore.SIGNAL('populate_datasets_summary_table_NEW')) self.emit(QtCore.SIGNAL("finished()")) @@ -2312,6 +2335,46 @@ def report_forward_carried_pipelines(self,dbListOut,dbList): resultDict['DataProcessingScore'])) return dbListOut + def checkExistingFiles(self,dbList,xtal): + self.Logfile.insert('checking if MTZ & LOG files exisit') + os.chdir(os.path.join(self.projectDir,xtal)) + self.Logfile.insert(xtal + ': changing directory ' + os.path.join(self.projectDir,xtal)) + dbListOut = [] + for resultDict in dbList: + try: + run = resultDict['DataCollectionRun'] + subDir = resultDict['DataCollectionSubdir'] + if subDir != '': + procCode = '_' + subDir + else: + procCode = '' + visit = resultDict['DataCollectionVisit'] + autoproc = resultDict['DataProcessingProgram'] + mtzFileAbs = resultDict['DataProcessingPathToMTZfile'] + mtzfileName = mtzFileAbs[mtzFileAbs.rfind('/')+1:] + logFileAbs = resultDict['DataProcessingPathToLogfile'] + logfileName = logFileAbs[logFileAbs.rfind('/')+1:] + + mtzfile = os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfileName) + logfile = os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfileName) + + + if os.path.isfile(mtzfile): + self.Logfile.insert(xtal + ': found ' + mtzfile) + if os.path.isfile(logfile): + self.Logfile.insert(xtal + ': found ' + logfile) + dbListOut.append(resultDict) + else: + self.Logfile.error(xtal + ': cannot find ' + logfile + ' ; skipping...') + else: + self.Logfile.error(xtal + ': cannot find ' + mtzfile + ' ; skipping...') + + except ValueError: + pass + return dbListOut + + + def selectResultsSimilarToReference(self,dbList): self.Logfile.insert('checking if MTZ files are similar to supplied reference files') dbListOut = [] From 68399f9df088e6fa807bf37f170f93d155d53cea Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 21 Jul 2020 15:19:49 +0100 Subject: [PATCH 066/358] v1.7.5 (21/07/2020) (#366) - bug fix: remove obsolete 'module load mx' statement from xce_ script which currently loads a gemmi incompatible ccp4 version --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemUtils.py | 12 ++++++------ 3 files changed, 10 insertions(+), 7 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index ec053649..d79c0ef0 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.5 (21/07/2020) +- bug fix: remove obsolete 'module load mx' statement from xce_ script which currently loads a gemmi incompatible ccp4 version + v1.7.4 (21/07/2020) - bug fix: selected results not linked after parsing of auto-processing results - enabled updates of message & progress bar during scoring of auto-processing results diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 83e27cde..1132ef88 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.4' + xce_object.xce_version = 'v1.7.5' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 226282f9..de78380a 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -274,9 +274,9 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft strip_hydrogens = 'phenix.reduce {0!s}.pdb -trim > {0!s}_tmp.pdb'.format(compoundID.replace(' ', '')) - module = '' - if os.path.isdir('/dls'): - module = 'module load mx\n' +# module = '' +# if os.path.isdir('/dls'): +# module = 'module load mx\n' Cmds = ( @@ -284,9 +284,9 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft '\n' 'export XChemExplorer_DIR="' + os.getenv('XChemExplorer_DIR') + '"' + '\n' - 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh' - '\n' - + module + +# 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh' +# '\n' +# + module + '\n' '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py {0!s} {1!s} {2!s} {3!s}' .format(os.path.join(database_directory, data_source_file), sample, 'RefinementCIFStatus', 'running') + From 938e466052a529548bdfd964d3e390f8af4ccbbd Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 23 Jul 2020 09:46:07 +0100 Subject: [PATCH 067/358] v1.7.6 (22/07/2020) (#367) - bug fix: added 'module load ccp4/phenix' to restraints script in case not part of user bashrc file --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemUtils.py | 4 ++++ 4 files changed, 9 insertions(+), 2 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index d79c0ef0..af6def06 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.6 (22/07/2020) +- bug fix: added 'module load ccp4/phenix' to restraints script in case not part of user bashrc file + v1.7.5 (21/07/2020) - bug fix: remove obsolete 'module load mx' statement from xce_ script which currently loads a gemmi incompatible ccp4 version diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 1132ef88..db0b9572 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.5' + xce_object.xce_version = 'v1.7.6' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 2032f96d..e354ec5f 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 21/07/2020 #\n' + ' # Date: 22/07/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index de78380a..417741c9 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -239,11 +239,15 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft software='' if restraints_program=='acedrg': + if os.getcwd().startswith('/dls'): + software += 'module load ccp4\n' if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): software='acedrg --res LIG -c ../old.cif -o {0!s}\n'.format((compoundID.replace(' ',''))) else: software='acedrg --res LIG -i "{0!s}" -o {1!s}\n'.format(productSmiles, compoundID.replace(' ','')) elif restraints_program=='phenix.elbow': + if os.getcwd().startswith('/dls'): + software += 'module load phenix\n' if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): software='phenix.elbow --file=../old.cif --id LIG --output {0!s}\n'.format((compoundID.replace(' ',''))) else: From 0aaa895f2f693ad3a8d4e6eb6d4a602f9fe854a2 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sun, 26 Jul 2020 10:01:45 +0100 Subject: [PATCH 068/358] v1.7.7 (22/07/2020) (#368) - bug fix: logical error in creation of restraints script when adding 'module load ccp4/phenix' command - removed phenix.reduce step from restraints generation --- ChangeLog.txt | 4 ++++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemUtils.py | 32 ++++++++++++++--------------- 4 files changed, 22 insertions(+), 18 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index af6def06..becc2001 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.7.7 (22/07/2020) +- bug fix: logical error in creation of restraints script when adding 'module load ccp4/phenix' command +- removed phenix.reduce step from restraints generation + v1.7.6 (22/07/2020) - bug fix: added 'module load ccp4/phenix' to restraints script in case not part of user bashrc file diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index db0b9572..490ea81b 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.6' + xce_object.xce_version = 'v1.7.7' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index e354ec5f..964d1a35 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 22/07/2020 #\n' + ' # Date: 24/07/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 417741c9..ed9a6cfd 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -242,16 +242,16 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft if os.getcwd().startswith('/dls'): software += 'module load ccp4\n' if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): - software='acedrg --res LIG -c ../old.cif -o {0!s}\n'.format((compoundID.replace(' ',''))) + software+='acedrg --res LIG -c ../old.cif -o {0!s}\n'.format((compoundID.replace(' ',''))) else: - software='acedrg --res LIG -i "{0!s}" -o {1!s}\n'.format(productSmiles, compoundID.replace(' ','')) + software+='acedrg --res LIG -i "{0!s}" -o {1!s}\n'.format(productSmiles, compoundID.replace(' ','')) elif restraints_program=='phenix.elbow': if os.getcwd().startswith('/dls'): software += 'module load phenix\n' if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): - software='phenix.elbow --file=../old.cif --id LIG --output {0!s}\n'.format((compoundID.replace(' ',''))) + software+='phenix.elbow --file=../old.cif --id LIG --output {0!s}\n'.format((compoundID.replace(' ',''))) else: - software='phenix.elbow --smiles="{0!s}" --id LIG --output {1!s}\n'\ + software+='phenix.elbow --smiles="{0!s}" --id LIG --output {1!s}\n'\ .format(productSmiles, compoundID.replace(' ','')) elif restraints_program=='grade': if os.getcwd().startswith('/dls'): @@ -274,10 +274,10 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft check_stereochemistry = '' - copy_with_hydrogens = 'cp {0!s}.pdb {0!s}_with_H.pdb'.format(compoundID.replace(' ', '')) - - strip_hydrogens = 'phenix.reduce {0!s}.pdb -trim > {0!s}_tmp.pdb'.format(compoundID.replace(' ', '')) - +# copy_with_hydrogens = 'cp {0!s}.pdb {0!s}_with_H.pdb'.format(compoundID.replace(' ', '')) +# +# strip_hydrogens = 'phenix.reduce {0!s}.pdb -trim > {0!s}_tmp.pdb'.format(compoundID.replace(' ', '')) +# # module = '' # if os.path.isdir('/dls'): # module = 'module load mx\n' @@ -306,14 +306,14 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft # '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/assign_stereochemistry.py {0!s} {1!s} {2!s}' # .format(compoundID.replace(' ',''),os.path.join(initial_model_directory,sample), os.path.join(database_directory,data_source_file)) + # '\n' - + copy_with_hydrogens + - '\n' - + strip_hydrogens + - '\n' - 'mv {0!s}_tmp.pdb {0!s}.pdb'.format(compoundID.replace(' ', '')) + - '\n' - 'rm -f {0!s}_tmp.pdb'.format(compoundID.replace(' ', '')) + - '\n' +# + copy_with_hydrogens + +# '\n' +# + strip_hydrogens + +# '\n' +# 'mv {0!s}_tmp.pdb {0!s}.pdb'.format(compoundID.replace(' ', '')) + +# '\n' +# 'rm -f {0!s}_tmp.pdb'.format(compoundID.replace(' ', '')) + +# '\n' 'cd ' + os.path.join(initial_model_directory, sample) + '\n' 'ln -s compound/%s.cif .\n' % compoundID.replace(' ', '') + From 8c595e75ddd0de8a6574bd41ea3030b73953cab8 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 2 Sep 2020 13:54:10 +0100 Subject: [PATCH 069/358] v1.7.8 (01/09/2020) (#369) - bug fix: string formatting error during restraints generation on local machine - added scanchirals option to rhofit command in fit_ligands function - bug fix: added 'module load buster' to fit_ligands function --- ChangeLog.txt | 5 +++++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemThread.py | 7 +++---- 4 files changed, 10 insertions(+), 6 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index becc2001..e58caeb6 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,8 @@ +v1.7.8 (01/09/2020) +- bug fix: string formatting error during restraints generation on local machine +- added scanchirals option to rhofit command in fit_ligands function +- bug fix: added 'module load buster' to fit_ligands function + v1.7.7 (22/07/2020) - bug fix: logical error in creation of restraints script when adding 'module load ccp4/phenix' command - removed phenix.reduce step from restraints generation diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 490ea81b..b9feea48 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.7' + xce_object.xce_version = 'v1.7.8' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 964d1a35..75f78795 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 24/07/2020 #\n' + ' # Date: 01/09/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 18c9559e..74dc4483 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -890,7 +890,7 @@ def run(self): self.Logfile.insert('qsub -q medium.q -N {0!s} xce_{1!s}_{2!s}.sh'.format(self.restraints_program,self.restraints_program,(str(i+1)))) os.system('qsub -N {0!s} xce_{1!s}_{2!s}.sh'.format(self.restraints_program,self.restraints_program,(str(i+1)))) else: - self.Logfile.insert('running %s consecutive %s jobs on your local machine' %self.restraints_program) + self.Logfile.insert('running %s consecutive %s jobs on your local machine' %(str(counter),self.restraints_program)) for i in range(counter): self.Logfile.insert('starting xce_{0!s}_{1!s}.sh'.format(self.restraints_program,(str(i+1)))) os.system('./xce_{0!s}_{1!s}.sh'.format(self.restraints_program,(str(i+1)))) @@ -918,7 +918,7 @@ def __init__(self,external_software,initial_model_directory,compound_list,databa def prepareInput(self,cmd,ligList): for cif in ligList: - cmd += 'rhofit -m ../init.mtz -p ../init.pdb -l ../compound/%s.cif -d %s_rhofit\n' %(cif,cif) + cmd += 'rhofit -m ../init.mtz -p ../init.pdb -l ../compound/%s.cif -scanchirals -d %s_rhofit\n' %(cif,cif) cmd += 'phenix.ligandfit data=../init.mtz model=../init.pdb ligand=../compound/%s.cif clean_up=True\n' %cif cmd += '/bin/mv LigandFit_run_1_ %s_phenix\n' %cif cmd += '/bin/rm -fr PDS\n\n' @@ -937,6 +937,7 @@ def get_header(self,sampleID): module = '' if os.path.isdir('/dls'): module = 'module load mx\n' + module += 'module load buster\n' cmd = ( '{0!s}\n'.format(top_line)+ @@ -2092,8 +2093,6 @@ def run(self): pickle.dump(self.settings,open(os.path.join(os.getenv('HOME'),'.xce_settings.pkl'),'wb')) os.system('cd {0!s}\ncoot --no-guano --no-state-script --script {1!s}'.format(os.getenv('HOME'), os.path.join(os.getenv('XChemExplorer_DIR'),'lib',self.pylib))) - - class start_ICM(QtCore.QThread): def __init__(self,html_export_directory): From 4167ee7e26431f4baf0bb8dabbe53c83517ffb40 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 7 Sep 2020 11:36:34 +0100 Subject: [PATCH 070/358] v1.7.9 (03/09/2020) (#370) - change 'Open COOT' to 'Open COOT - REFMAC refinement -' in Refinement action box --- ChangeLog.txt | 3 +++ XChemExplorer.py | 2 ++ gui_scripts/settings_preferences.py | 6 +++--- lib/XChemLog.py | 2 +- 4 files changed, 9 insertions(+), 4 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index e58caeb6..7722f854 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.9 (03/09/2020) +- change 'Open COOT' to 'Open COOT - REFMAC refinement -' in Refinement action box + v1.7.8 (01/09/2020) - bug fix: string formatting error during restraints generation on local machine - added scanchirals option to rhofit command in fit_ligands function diff --git a/XChemExplorer.py b/XChemExplorer.py index 4b534c41..2b81a610 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -3550,6 +3550,8 @@ def prepare_and_run_task(self, instruction): self.update_log.insert('starting coot...') if instruction == "Open COOT": interface = 'new' + elif instruction == "Open COOT - REFMAC refinement -": + interface = 'new' elif instruction == "Open COOT - test -": interface = 'test' elif instruction == "Open COOT for old PanDDA": diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index b9feea48..eea48a51 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.8' + xce_object.xce_version = 'v1.7.9' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -647,8 +647,8 @@ def dropdown_items(self, xce_object): 'pre-run for ground state model', 'Build ground state model'] - xce_object.refine_file_tasks = ['Open COOT', - 'Open COOT - BUSTER refinement -', + xce_object.refine_file_tasks = ['Open COOT - BUSTER refinement -', + 'Open COOT - REFMAC refinement -', 'Open COOT - dimple_twin -' ] # xce_object.refine_file_tasks = ['Open COOT', diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 75f78795..344d5010 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 01/09/2020 #\n' + ' # Date: 03/09/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 6bf2a37a10ecf008618369b0efce26682eb76eff Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 8 Sep 2020 17:20:43 +0100 Subject: [PATCH 071/358] v1.7.10 (08/09/2020) (#371) - bug fix - preparation of mmcif files for deposition: enable usage of event mtz files which were generated during 'BUSTER' export routine --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 13 +++++++++++++ lib/XChemLog.py | 2 +- 4 files changed, 18 insertions(+), 2 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 7722f854..d4e5a37f 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.10 (08/09/2020) +- bug fix - preparation of mmcif files for deposition: enable usage of event mtz files which were generated during 'BUSTER' export routine + v1.7.9 (03/09/2020) - change 'Open COOT' to 'Open COOT - REFMAC refinement -' in Refinement action box diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index eea48a51..2ae2a6c5 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.9' + xce_object.xce_version = 'v1.7.10' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 0be9dc19..9e9ef9ed 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -700,6 +700,7 @@ def find_matching_event_map(self,xtal): self.Logfile.warning('%s: found empty file named "no_pandda_analysis_performed" which suggests we will ignore event maps for this sample' %xtal) foundMatchingMap = True ligList = [] + for lig in sorted(ligList): ligID = lig.replace('.pdb','') # if os.path.isfile('no_pandda_analysis_performed'): @@ -707,6 +708,18 @@ def find_matching_event_map(self,xtal): # foundMatchingMap = True # break ligCC = [] + + # for newer BUSTER export + print '>>>> %s-event_*.native_%s.mtz' %(xtal,lig.replace('.pdb','')) + for mtz in glob.glob(('%s-event_*.native_%s.mtz' %(xtal,lig.replace('.pdb','')))): + self.Logfile.insert(xtal + ': found ' + mtz) + foundMatchingMap = True + self.eventList.append(mtz) + break + + if foundMatchingMap: + continue + for mtz in sorted(glob.glob('*event*.native*P1.mtz')): self.get_lig_cc(xtal, mtz, lig) cc = self.check_lig_cc(mtz.replace('.mtz', '_CC'+ligID+'.log')) diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 344d5010..4bde941a 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 03/09/2020 #\n' + ' # Date: 08/09/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 4b351e9915fc7cd58e5ca6ee3b3b99ec5aa88ee1 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 10 Sep 2020 06:49:46 +0100 Subject: [PATCH 072/358] v1.7.11 (09/09/2020) (#372) - bug fix: preparation of mmcif files: run aimless in onlymerge mode if only json file available --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 38 +++++++++++++++++++++++++++-- lib/XChemLog.py | 2 +- 4 files changed, 41 insertions(+), 4 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index d4e5a37f..6c2afe30 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.11 (09/09/2020) +- bug fix: preparation of mmcif files: run aimless in onlymerge mode if only json file available + v1.7.10 (08/09/2020) - bug fix - preparation of mmcif files for deposition: enable usage of event mtz files which were generated during 'BUSTER' export routine diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 2ae2a6c5..95d8493e 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.10' + xce_object.xce_version = 'v1.7.11' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 9e9ef9ed..20f84cca 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -633,16 +633,50 @@ def refine_mtz_exists(self,xtal): self.add_to_errorList(xtal) return fileStatus + def run_aimless_merge_only(self,xtal,unmerged,APpath): + cmd = ( + 'aimless hklin %s hklout mergeonly.mtz << eof > %s\n' %(unmerged, unmerged.replace('.mtz','.log')) + + ' onlymerge\n' + 'eof' + ) + self.Logfile.insert('%s: running AIMLESS in onlymerge mode...' %xtal) + os.system(cmd) + os.chdir(os.path.join(self.projectDir, xtal)) + os.system('/bin/rm %s.log' %xtal) + os.system('ln -s %s/%s %s.log' %(APpath,unmerged.replace('.mtz','.log'),xtal)) + + + def aimless_logfile_exists(self,xtal): self.Logfile.insert('%s: checking if aimless logfile, i.e. %s.log, exists' %(xtal,xtal)) fileStatus = False if os.path.isfile('%s.log' %xtal): self.Logfile.insert('%s: found %s.log' %(xtal,xtal)) - fileStatus = True + for line in open('%s.log' %xtal): + if 'AIMLESS' in line: + fileStatus = True + break + if not fileStatus: + self.Logfile.warning('%s: this does not seem to be an AIMLESS logfile' %xtal) + Filepath = os.path.relpath(os.path.realpath('%s.log' %xtal)) + APpath = Filepath[:Filepath.rfind('/')] + self.Logfile.insert('%s: relative path to logfile %s' %(xtal,APpath)) + self.Logfile.insert('%s: file path to logfile %s' %(xtal,Filepath)) + os.chdir(APpath) + foundUnmerged = False + for unmerged in glob.glob('*_scaled_unmerged.mtz'): + self.Logfile.insert('%s: found %s in %s' %(xtal,unmerged,APpath)) + self.run_aimless_merge_only(xtal,unmerged,APpath) + foundUnmerged = True + break + if not foundUnmerged: + self.Logfile.error('%s: cannot find a suitable AIMLESS logfile' %xtal) + self.add_to_errorList(xtal) +# fileStatus = True else: self.Logfile.error('%s: cannot find %s.log; moving to next dataset...' %(xtal,xtal)) self.add_to_errorList(xtal) - return fileStatus + return fileStatus def mtzFree_exists(self,xtal): diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 4bde941a..d1c6e2cc 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 08/09/2020 #\n' + ' # Date: 09/09/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From a4f83b9de3751d9ecdd8d3f4462cd4c1e182e3b7 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 16 Sep 2020 16:12:14 +0100 Subject: [PATCH 073/358] v1.7.12 (14/09/2020) (#373) - bug fix: problem with recognizing AIMLESS logfiles during preparation of MMCIF files - bug fix: try finding experimental wavelength from .free.mtz file if it is 0.0 in refine.mtz during MMCIF file preparation - preparation of mmcif files: catch and report missing event mtz files --- ChangeLog.txt | 5 ++++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 42 ++++++++++++++++++++++------- lib/XChemLog.py | 2 +- 4 files changed, 39 insertions(+), 12 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 6c2afe30..35d97435 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,8 @@ +v1.7.12 (14/09/2020) +- bug fix: problem with recognizing AIMLESS logfiles during preparation of MMCIF files +- bug fix: try finding experimental wavelength from .free.mtz file if it is 0.0 in refine.mtz during MMCIF file preparation +- preparation of mmcif files: catch and report missing event mtz files + v1.7.11 (09/09/2020) - bug fix: preparation of mmcif files: run aimless in onlymerge mode if only json file available diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 95d8493e..7a490295 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.11' + xce_object.xce_version = 'v1.7.12' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 20f84cca..0a58e8b2 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -644,6 +644,11 @@ def run_aimless_merge_only(self,xtal,unmerged,APpath): os.chdir(os.path.join(self.projectDir, xtal)) os.system('/bin/rm %s.log' %xtal) os.system('ln -s %s/%s %s.log' %(APpath,unmerged.replace('.mtz','.log'),xtal)) + self.Logfile.insert('%s: finished running AIMLESS' %xtal) + if os.path.isfile(xtal+'.log'): + self.Logfile.insert('%s: AIMLESS logfile successfully created' %xtal) + else: + self.Logfile.error('%s: cannot find AIMLESS logfile...' %xtal) @@ -652,16 +657,19 @@ def aimless_logfile_exists(self,xtal): fileStatus = False if os.path.isfile('%s.log' %xtal): self.Logfile.insert('%s: found %s.log' %(xtal,xtal)) - for line in open('%s.log' %xtal): + for n,line in enumerate(open('%s.log' %xtal)): if 'AIMLESS' in line: fileStatus = True break - if not fileStatus: - self.Logfile.warning('%s: this does not seem to be an AIMLESS logfile' %xtal) - Filepath = os.path.relpath(os.path.realpath('%s.log' %xtal)) - APpath = Filepath[:Filepath.rfind('/')] - self.Logfile.insert('%s: relative path to logfile %s' %(xtal,APpath)) - self.Logfile.insert('%s: file path to logfile %s' %(xtal,Filepath)) +# if n < 10: +# print line + if not fileStatus: + self.Logfile.warning('%s: this does not seem to be an AIMLESS logfile' %xtal) + Filepath = os.path.relpath(os.path.realpath('%s.log' %xtal)) + APpath = Filepath[:Filepath.rfind('/')] + self.Logfile.insert('%s: relative path to logfile %s' %(xtal,APpath)) + self.Logfile.insert('%s: file path to logfile %s' %(xtal,Filepath)) + if os.path.isdir(APpath): os.chdir(APpath) foundUnmerged = False for unmerged in glob.glob('*_scaled_unmerged.mtz'): @@ -672,6 +680,10 @@ def aimless_logfile_exists(self,xtal): if not foundUnmerged: self.Logfile.error('%s: cannot find a suitable AIMLESS logfile' %xtal) self.add_to_errorList(xtal) + else: + self.Logfile.error('%s: %s is not a directory' %(xtal,APpath)) + self.add_to_errorList(xtal) + # fileStatus = True else: self.Logfile.error('%s: cannot find %s.log; moving to next dataset...' %(xtal,xtal)) @@ -714,7 +726,7 @@ def eventMTZ_exists(self,xtal): self.Logfile.warning('%s: user selected to not include event map in SF mmcif file' %xtal) eventMTZexists = True else: - for mtz in glob.glob('*event*.native*P1.mtz'): + for mtz in glob.glob('*event*.native*.mtz'): eventMTZlist.append(mtz[mtz.rfind('/')+1:]) if eventMTZlist is []: self.Logfile.error('%s: MTZ files of event maps do not exists! Go to PANDDA tab and run "Event Map -> SF"' %xtal) @@ -735,6 +747,7 @@ def find_matching_event_map(self,xtal): foundMatchingMap = True ligList = [] + self.Logfile.insert('%s: looking for event maps for the following ligands -> %s' %(xtal,str(ligList))) for lig in sorted(ligList): ligID = lig.replace('.pdb','') # if os.path.isfile('no_pandda_analysis_performed'): @@ -744,7 +757,7 @@ def find_matching_event_map(self,xtal): ligCC = [] # for newer BUSTER export - print '>>>> %s-event_*.native_%s.mtz' %(xtal,lig.replace('.pdb','')) +# print '>>>> %s-event_*.native_%s.mtz' %(xtal,lig.replace('.pdb','')) for mtz in glob.glob(('%s-event_*.native_%s.mtz' %(xtal,lig.replace('.pdb','')))): self.Logfile.insert(xtal + ': found ' + mtz) foundMatchingMap = True @@ -762,7 +775,10 @@ def find_matching_event_map(self,xtal): ligCC.append([mtz,float(cc)]) except ValueError: ligCC.append([mtz, 0.00]) - highestCC = max(ligCC, key=lambda x: x[0])[1] + try: + highestCC = max(ligCC, key=lambda x: x[0])[1] + except ValueError: + highestCC = 0.00 if highestCC == 0.00 or ligCC is []: self.Logfile.error('%s: best CC of ligand %s for any event map is 0!' %(xtal,lig)) self.add_to_errorList(xtal) @@ -818,6 +834,12 @@ def save_data_template_dict(self,xtal): self.Logfile.insert('%s: preparing data_template.cif file' %xtal) if self.overwrite_existing_mmcif: self.data_template_dict['radiation_wavelengths'] = self.mtz.get_wavelength() + if str(self.data_template_dict['radiation_wavelengths']).startswith('0.0'): + self.Logfile.error('%s: this does not seem to be the true experimental wavelength: %s' %(xtal,str(self.data_template_dict['radiation_wavelengths']))) + self.Logfile.insert('%s: trying to find it from %s.free.mtz...' %(xtal,xtal)) + if os.path.isfile('%s.free.mtz' %xtal): + self.data_template_dict['radiation_wavelengths'] = mtztools(xtal+'.free.mtz').get_wavelength() + self.Logfile.warning('%s: found the following wavelength -> %s' %(xtal,str(self.data_template_dict['radiation_wavelengths']))) self.Logfile.insert('%s: experimental wavelength according to %s is %s' %(xtal,self.mtz,self.data_template_dict['radiation_wavelengths'])) if self.ground_state: os.chdir(self.projectDir) diff --git a/lib/XChemLog.py b/lib/XChemLog.py index d1c6e2cc..2bb8ecf8 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 09/09/2020 #\n' + ' # Date: 14/09/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 393f6daf1f67c6f4fd2fc82f730c590ec6ae7e85 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 23 Sep 2020 16:09:01 +0100 Subject: [PATCH 074/358] v1.7.13 (23/09/2020) (#374) - bug fix: use wavelength read from (.free).mtz during model MMCIF preparation when updating SF MMCIF --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 4 ++-- lib/XChemLog.py | 2 +- 4 files changed, 7 insertions(+), 4 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 35d97435..dad8e06e 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.13 (23/09/2020) +- bug fix: use wavelength read from (.free).mtz during model MMCIF preparation when updating SF MMCIF + v1.7.12 (14/09/2020) - bug fix: problem with recognizing AIMLESS logfiles during preparation of MMCIF files - bug fix: try finding experimental wavelength from .free.mtz file if it is 0.0 in refine.mtz during MMCIF file preparation diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 7a490295..133b3b28 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.12' + xce_object.xce_version = 'v1.7.13' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 0a58e8b2..7a3a19b8 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -1302,7 +1302,7 @@ def update_sf_mmcif_file(self,xtal): block = -1 - self.Logfile.insert('%s: reading wavelength from mtz file; lambda = %s' %(xtal,self.mtz.get_wavelength())) + self.Logfile.insert('%s: reading wavelength from mtz file; lambda = %s' %(xtal,str(self.data_template_dict['radiation_wavelengths']))) if os.path.isfile('no_pandda_analysis_performed'): self.Logfile.warning('%s: apparently not a pandda deposition; will skip this step...' %xtal) @@ -1324,7 +1324,7 @@ def update_sf_mmcif_file(self,xtal): '_diffrn.details "%s"\n' % bound[n]).replace('$',str(block-1)) sys.stdout.write(newLines) elif line.startswith('_diffrn_radiation_wavelength.wavelength'): - sys.stdout.write('_diffrn_radiation_wavelength.wavelength {0!s}\n'.format(self.mtz.get_wavelength())) + sys.stdout.write('_diffrn_radiation_wavelength.wavelength {0!s}\n'.format(str(self.data_template_dict['radiation_wavelengths']))) else: sys.stdout.write(line) diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 2bb8ecf8..953f4d75 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 14/09/2020 #\n' + ' # Date: 23/09/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 181d34bfb7294ed9022acd5f0c862cf743422436 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 25 Sep 2020 11:57:37 +0100 Subject: [PATCH 075/358] v1.7.14 (24/09/2020) (#376) - added option for ligand occupancy refinement in BUSTER - XChemCootBuster: reading of (2)fofc.maps disabled because Coot 0.9 does not handle P1 maps well --- ChangeLog.txt | 4 ++ gui_scripts/settings_preferences.py | 2 +- lib/XChemCootBuster.py | 11 ++++-- lib/XChemLog.py | 2 +- lib/XChemRefine.py | 58 ++++++++++++++++++++++++++--- 5 files changed, 67 insertions(+), 10 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index dad8e06e..ab07aeee 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.7.14 (24/09/2020) +- added option for ligand occupancy refinement in BUSTER +- XChemCootBuster: reading of (2)fofc.maps disabled because Coot 0.9 does not handle P1 maps well + v1.7.13 (23/09/2020) - bug fix: use wavelength read from (.free).mtz during model MMCIF preparation when updating SF MMCIF diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 133b3b28..f3221ed9 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.13' + xce_object.xce_version = 'v1.7.14' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemCootBuster.py b/lib/XChemCootBuster.py index 98eaf401..31b0c863 100755 --- a/lib/XChemCootBuster.py +++ b/lib/XChemCootBuster.py @@ -174,7 +174,8 @@ def __init__(self): 'TLS': '', 'NCS': '', 'TWIN': '', - 'WATER': '' } + 'WATER': '', + 'LIGOCC': '' } def StartGUI(self): @@ -1263,7 +1264,10 @@ def RefreshData(self): # read fofc maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): +# if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): + # coot 0.9 does not handle P1 maps well, so now looking for non-existent map in order to trigger + # map calculation from mtz file + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc_??????.map')): coot.set_colour_map_rotation_on_read_pdb(0) coot.set_default_initial_contour_level_for_difference_map(3) coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, 'fofc.map'), 1) @@ -1272,7 +1276,8 @@ def RefreshData(self): coot.set_last_map_colour(0, 0, 1) else: # try to open mtz file with same name as pdb file - coot.set_default_initial_contour_level_for_map(1) +# coot.set_default_initial_contour_level_for_map(1) + coot.set_colour_map_rotation_on_read_pdb(0) # if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): # os.chdir(os.path.join(self.project_directory,self.xtalID)) # if not os.path.isfile('REFINEMENT_IN_PROGRESS'): diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 953f4d75..72c60f57 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 23/09/2020 #\n' + ' # Date: 24/09/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 2ed821d3..044fce36 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -116,6 +116,11 @@ def RefmacRefinementParams(self,RefmacParams): if self.RefmacParams['WATER']=='WATER\n': self.WATER.set_active(True) self.vbox.pack_start(self.WATER,False) + self.LIGOCC = gtk.CheckButton('Refine ligand occupancy (BUSTER)') + self.LIGOCC.connect("toggled", self.LIGOCCCallback) + if self.RefmacParams['LIGOCC']=='LIGOCC\n': self.LIGOCC.set_active(True) + self.vbox.pack_start(self.LIGOCC,False) + self.OKbutton = gtk.Button(label="OK") self.OKbutton.connect("clicked",self.OK) self.vbox.add(self.OKbutton) @@ -175,6 +180,13 @@ def WATERCallback(self, widget): self.RefmacParams['WATER']='' return self.RefmacParams + def LIGOCCCallback(self, widget): + if widget.get_active(): + self.RefmacParams['LIGOCC']='LIGOCC\n' + else: + self.RefmacParams['LIGOCC']='' + return self.RefmacParams + def OK(self,widget): self.window.destroy() @@ -192,7 +204,8 @@ def ParamsFromPreviousCycle(self,Serial): 'TLS': '', 'NCS': '', 'TWIN': '', - 'WATER': '' } + 'WATER': '', + 'LIGOCC': '' } if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): @@ -426,14 +439,14 @@ def set_refinement_status(self,cmd): + self.datasource + ' ' + self.xtalID + ' RefinementStatus running\n') return cmd - def add_buster_command(self,cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water): + def add_buster_command(self,cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water,refine_ligand_occupancy): cmd += ( 'refine ' ' -p %s' %xyzin + ' -m %s' %hklin + ' -l %s' %libin + ' -autoncs' - + anisotropic_Bfactor + update_water + + + anisotropic_Bfactor + update_water + refine_ligand_occupancy + ' -d Refine_%s\n' %str(Serial) ) return cmd @@ -593,6 +606,7 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom else: update_water = '' + self.error = False if os.path.isfile(xce_logfile): @@ -613,6 +627,13 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom xyzin, xyzout = self.get_xyzin_xyzout(Serial) + refine_ligand_occupancy = '' + if RefmacParams != None: + if 'LIGOCC' in RefmacParams['LIGOCC']: + ligand_info = pdbtools(xyzin).get_residues_with_resname('LIG') + if self.prepare_gelly_dat(ligand_info): + refine_ligand_occupancy = ' -B user -Gelly gelly.dat ' + libin, libout = self.get_libin_libout(Serial) self.clean_up_before_refinement() @@ -627,7 +648,7 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom cmd = self.set_refinement_status(cmd) - cmd = self.add_buster_command(cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water) + cmd = self.add_buster_command(cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water,refine_ligand_occupancy) cmd = self.add_validation(cmd,Serial,'buster') @@ -647,6 +668,32 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom self.Logfile.insert('%s: starting refinement...' %self.xtalID) self.run_script('buster',external_software) + def prepare_gelly_dat(self,ligand_info): + found_ligand = False + gelly = 'NOTE BUSTER_SET Ligand = ' + for n,lig in enumerate(ligand_info): + resseq = lig[1] + chain = lig[2] + if n == 0: + gelly += '{ %s|%s }' %(chain.replace(' ',''),resseq.replace(' ','')) + else: + gelly += ' + { %s|%s }' %(chain.replace(' ',''),resseq.replace(' ','')) + found_ligand = True + if '{' in gelly: + gelly += '\n' + gelly += ( + 'NOTE BUSTER_SET NotLigand = \ Ligand\n' + 'NOTE BUSTER_CONSTANT OCC NotLigand \n' + 'NOTE BUSTER_COMBINE OCC Ligand \n' + 'NOTE BUSTER_COMBINE B Ligand \n' + ) + os.chdir(os.path.join(self.ProjectPath,self.xtalID)) + f = open('gelly.dat','w') + f.write(gelly) + f.close() + return found_ligand + + def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtomSpec): if os.path.isfile(xce_logfile): Logfile=XChemLog.updateLog(xce_logfile) @@ -1020,7 +1067,8 @@ def ParamsFromPreviousCycle(self,Serial): 'TLS': '', 'NCS': '', 'TWIN': '', - 'WATER': '' } + 'WATER': '', + 'LIGOCC': '' } if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): From ddb0e1129ea480013ea6da94a7146f3e4a3d45d6 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 25 Sep 2020 14:33:49 +0100 Subject: [PATCH 076/358] v1.7.15 (25/09/2020) (#377) - added option to ignore GELLY sanity check in BUSTER - added option to ignore GELLY sanity check during pandda export with BUSTER --- ChangeLog.txt | 4 ++++ XChemExplorer.py | 6 ++++++ gui_scripts/settings_preferences.py | 7 ++++++- lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 23 +++++++++++++++++++++-- lib/XChemRefine.py | 29 ++++++++++++++++++++++++----- 6 files changed, 62 insertions(+), 9 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index ab07aeee..c59b729f 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.7.15 (25/09/2020) +- added option to ignore GELLY sanity check in BUSTER +- added option to ignore GELLY sanity check during pandda export with BUSTER + v1.7.14 (24/09/2020) - added option for ligand occupancy refinement in BUSTER - XChemCootBuster: reading of (2)fofc.maps disabled because Coot 0.9 does not handle P1 maps well diff --git a/XChemExplorer.py b/XChemExplorer.py index 2b81a610..52e4dcab 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -3522,6 +3522,12 @@ def prepare_and_run_task(self, instruction): elif instruction == 'refine NEW bound-state models with BUSTER': self.run_refine_bound_state_with_buster('new') + elif instruction == 'refine ALL bound-state models with BUSTER (no sanity check)': + self.run_refine_bound_state_with_buster('allnocheck') + + elif instruction == 'refine NEW bound-state models with BUSTER (no sanity check)': + self.run_refine_bound_state_with_buster('newnocheck') + # elif instruction == 'refine NEW bound-state models with BUSTER - NEW': # self.run_refine_bound_state_with_buster_new('new') diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index f3221ed9..012c714f 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.14' + xce_object.xce_version = 'v1.7.15' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -641,8 +641,13 @@ def dropdown_items(self, xce_object): 'Event Map -> SF', 'apo -> mmcif', 'check modelled ligands', + '------------------------------------------', 'refine ALL bound-state models with BUSTER', 'refine NEW bound-state models with BUSTER', + '------------------------------------------', + 'refine ALL bound-state models with BUSTER (no sanity check)', + 'refine NEW bound-state models with BUSTER (no sanity check)', + '------------------------------------------', # 'refine NEW bound-state models with BUSTER - NEW', 'pre-run for ground state model', 'Build ground state model'] diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 72c60f57..8015c9ed 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 24/09/2020 #\n' + ' # Date: 25/09/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 381ce82a..8e9412c5 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -67,7 +67,7 @@ def run(self): modelsDict = self.find_modeled_structures_and_timestamps() # if only NEW models shall be exported, check timestamps - if self.which_models != 'all': + if not self.which_models.startswith('all'): modelsDict = self.find_new_models(modelsDict) # find pandda_inspect_events.csv and read in as pandas dataframe @@ -265,6 +265,25 @@ def calculate_distance_to_ligands(self,ligandDict,x,y,z): def refine_exported_model(self,xtal): + + RefmacParams={ 'HKLIN': '', 'HKLOUT': '', + 'XYZIN': '', 'XYZOUT': '', + 'LIBIN': '', 'LIBOUT': '', + 'TLSIN': '', 'TLSOUT': '', + 'TLSADD': '', + 'NCYCLES': '10', + 'MATRIX_WEIGHT': 'AUTO', + 'BREF': ' bref ISOT\n', + 'TLS': '', + 'NCS': '', + 'TWIN': '', + 'WATER': '', + 'LIGOCC': '', + 'SANITY': '' } + + if 'nocheck' in self.which_models: + RefmacParams['SANITY'] = 'off' + self.Logfile.insert('trying to refine ' + xtal + '...') self.Logfile.insert('%s: getting compound code from database' %xtal) query=self.db.execute_statement("select CompoundCode from mainTable where CrystalName='%s';" %xtal) @@ -284,7 +303,7 @@ def refine_exported_model(self,xtal): os.chdir(os.path.join(self.project_directory,xtal,'cootOut','Refine_'+str(Serial))) os.system('/bin/cp %s in.pdb' %os.path.join(self.project_directory,xtal,xtal+'-pandda-model.pdb')) Refine=XChemRefine.Refine(self.project_directory,xtal,compoundID,self.datasource) - Refine.RunBuster(str(Serial),None,self.external_software,self.xce_logfile,None) + Refine.RunBuster(str(Serial),RefmacParams,self.external_software,self.xce_logfile,None) else: self.Logfile.error('%s: cannot find %s-pandda-model.pdb; cannot start refinement...' %(xtal,xtal)) diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 044fce36..3da9e4ee 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -121,6 +121,11 @@ def RefmacRefinementParams(self,RefmacParams): if self.RefmacParams['LIGOCC']=='LIGOCC\n': self.LIGOCC.set_active(True) self.vbox.pack_start(self.LIGOCC,False) + self.SANITY = gtk.CheckButton('Ignore sanity checks (BUSTER)') + self.SANITY.connect("toggled", self.SANITYCallback) + if self.RefmacParams['SANITY']=='off\n': self.SANITY.set_active(True) + self.vbox.pack_start(self.SANITY,False) + self.OKbutton = gtk.Button(label="OK") self.OKbutton.connect("clicked",self.OK) self.vbox.add(self.OKbutton) @@ -187,6 +192,13 @@ def LIGOCCCallback(self, widget): self.RefmacParams['LIGOCC']='' return self.RefmacParams + def SANITYCallback(self, widget): + if widget.get_active(): + self.RefmacParams['SANITY']='off\n' + else: + self.RefmacParams['SANITY']='' + return self.RefmacParams + def OK(self,widget): self.window.destroy() @@ -205,7 +217,8 @@ def ParamsFromPreviousCycle(self,Serial): 'NCS': '', 'TWIN': '', 'WATER': '', - 'LIGOCC': '' } + 'LIGOCC': '', + 'SANITY': '' } if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): @@ -439,14 +452,14 @@ def set_refinement_status(self,cmd): + self.datasource + ' ' + self.xtalID + ' RefinementStatus running\n') return cmd - def add_buster_command(self,cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water,refine_ligand_occupancy): + def add_buster_command(self,cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water,refine_ligand_occupancy,ignore_sanity_check): cmd += ( 'refine ' ' -p %s' %xyzin + ' -m %s' %hklin + ' -l %s' %libin + ' -autoncs' - + anisotropic_Bfactor + update_water + refine_ligand_occupancy + + + anisotropic_Bfactor + update_water + refine_ligand_occupancy + ignore_sanity_check + ' -d Refine_%s\n' %str(Serial) ) return cmd @@ -606,6 +619,11 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom else: update_water = '' + if 'off' in RefmacParams['SANITY']: + ignore_sanity_check = ' StopOnGellySanityCheckError=no ' + else: + ignore_sanity_check = '' + self.error = False @@ -648,7 +666,7 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom cmd = self.set_refinement_status(cmd) - cmd = self.add_buster_command(cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water,refine_ligand_occupancy) + cmd = self.add_buster_command(cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water,refine_ligand_occupancy,ignore_sanity_check) cmd = self.add_validation(cmd,Serial,'buster') @@ -1068,7 +1086,8 @@ def ParamsFromPreviousCycle(self,Serial): 'NCS': '', 'TWIN': '', 'WATER': '', - 'LIGOCC': '' } + 'LIGOCC': '', + 'SANITY': '' } if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): From 97a622bc8d4d458294646fb578d7c011a84cb788 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 8 Oct 2020 11:12:10 +0100 Subject: [PATCH 077/358] v1.7.16 (08/10/2020) (#378) - enable export of selected datasets with pandda.export - glitch fix: remove hydrogens before saving model for buster refinement (causes problems during ligand occupancy refinement) - XChemRefine: removed "-q medium.q" option for non-DLS refinement - added helper script to which reverts to last successful non-pandda refinement - XChemCoot (pandda refinement): reading of (2)fofc.maps disabled because Coot 0.9 does not handle P1 maps well - pandda.analyse: stopped sourcing obsolete pandda v0.2.12 at DLS --- ChangeLog.txt | 8 +++ XChemExplorer.py | 44 +++++++++++++-- gui_scripts/settings_preferences.py | 11 +++- .../reset_to_last_successful_refinement.py | 55 +++++++++++++++++++ lib/XChemCootBuster.py | 1 + lib/XChemCootNew.py | 12 +++- lib/XChemDB.py | 4 ++ lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 14 ++++- lib/XChemRefine.py | 17 ++++-- 10 files changed, 152 insertions(+), 16 deletions(-) create mode 100644 helpers/reset_to_last_successful_refinement.py diff --git a/ChangeLog.txt b/ChangeLog.txt index c59b729f..9530c793 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,11 @@ +v1.7.16 (08/10/2020) +- enable export of selected datasets with pandda.export +- glitch fix: remove hydrogens before saving model for buster refinement (causes problems during ligand occupancy refinement) +- XChemRefine: removed "-q medium.q" option for non-DLS refinement +- added helper script to which reverts to last successful non-pandda refinement +- XChemCoot (pandda refinement): reading of (2)fofc.maps disabled because Coot 0.9 does not handle P1 maps well +- pandda.analyse: stopped sourcing obsolete pandda v0.2.12 at DLS + v1.7.15 (25/09/2020) - added option to ignore GELLY sanity check in BUSTER - added option to ignore GELLY sanity check during pandda export with BUSTER diff --git a/XChemExplorer.py b/XChemExplorer.py index 52e4dcab..9577c85b 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -3516,6 +3516,11 @@ def prepare_and_run_task(self, instruction): which_models = 'all' self.run_pandda_export(update_datasource_only, which_models) + elif instruction == 'Export SELECTED PANDDA models': + update_datasource_only = False + which_models = 'selected' + self.run_pandda_export(update_datasource_only, which_models) + elif instruction == 'refine ALL bound-state models with BUSTER': self.run_refine_bound_state_with_buster('all') @@ -3799,6 +3804,31 @@ def compare_modelled_ligands_and_panddaTable(self): self.work_thread.start() def run_pandda_export(self, update_datasource_only, which_models): + + pandda_params = { + 'data_dir': str(self.pandda_input_data_dir_entry.text()), + 'out_dir': str(self.pandda_output_data_dir_entry.text()), + 'submit_mode': str(self.pandda_submission_mode_selection_combobox.currentText()), + 'nproc': str(self.pandda_nproc_entry.text()), + 'min_build_datasets': str(self.pandda_min_build_dataset_entry.text()), + 'pdb_style': str(self.pandda_pdb_style_entry.text()), + 'mtz_style': str(self.pandda_mtz_style_entry.text()), + 'sort_event': str(self.pandda_sort_event_combobox.currentText()), + 'average_map': str(self.pandda_calc_map_combobox.currentText()), + 'max_new_datasets': str(self.pandda_max_new_datasets_entry.text()), + 'grid_spacing': str(self.pandda_grid_spacing_entry.text()), + 'pandda_dir_structure': str(self.pandda_input_data_dir_entry.text()), + 'perform_diffraction_data_scaling': str(self.wilson_checkbox.isChecked()), + 'filter_pdb': str(self.pandda_reference_file_selection_combobox.currentText()), + 'reference_dir': self.reference_directory, + 'appendix': '', + 'N_datasets': len(glob.glob(os.path.join(self.initial_model_directory, '*', 'dimple.pdb'))), + 'write_mean_map': 'interesting', + 'pandda_table': self.pandda_analyse_data_table, + 'use_remote': self.using_remote_qsub_submission, + 'remote_string': self.remote_qsub_submission + } + self.settings['panddas_directory'] = str(self.pandda_output_data_dir_entry.text()) if update_datasource_only: self.update_log.insert('updating data source with results from pandda.inspect') @@ -3831,7 +3861,7 @@ def run_pandda_export(self, update_datasource_only, which_models): os.path.join(self.database_directory, self.data_source_file), self.initial_model_directory, self.xce_logfile, - update_datasource_only, which_models) + update_datasource_only, which_models, pandda_params) self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) self.work_thread.start() @@ -5124,9 +5154,10 @@ def populate_and_update_datasource_table(self): def kill_other_pandda_options(self): for i in range(0, self.pandda_analyse_data_table.rowCount()): - checkbox1 = self.pandda_analyse_data_table.cellWidget(i,6) - checkbox2 = self.pandda_analyse_data_table.cellWidget(i,7) - checkbox3 = self.pandda_analyse_data_table.cellWidget(i,8) + checkbox0 = self.pandda_analyse_data_table.cellWidget(i,1) + checkbox1 = self.pandda_analyse_data_table.cellWidget(i,7) + checkbox2 = self.pandda_analyse_data_table.cellWidget(i,8) + checkbox3 = self.pandda_analyse_data_table.cellWidget(i,9) if checkbox1.isChecked(): checkbox2.setChecked(False) checkbox3.setChecked(False) @@ -5164,6 +5195,11 @@ def populate_pandda_analyse_input_table(self): deselect_button.stateChanged.connect(self.kill_other_pandda_options) self.pandda_analyse_data_table.setCellWidget(current_row, column, deselect_button) + elif header[0]=='Export': + deselect_button = QtGui.QCheckBox() + deselect_button.stateChanged.connect(self.kill_other_pandda_options) + self.pandda_analyse_data_table.setCellWidget(current_row, column, deselect_button) + elif header[0] == 'Sample ID': cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(xtal)) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 012c714f..38b82daf 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.15' + xce_object.xce_version = 'v1.7.16' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -386,6 +386,7 @@ def tables(self, xce_object): xce_object.pandda_table_columns = [ 'Sample ID', + 'Export\nSelected', 'Refinement\nSpace Group', 'Resolution\n[Mn = 1.5]', 'Dimple\nRcryst', @@ -633,8 +634,11 @@ def dropdown_items(self, xce_object): xce_object.panddas_file_tasks = ['pandda.analyse', 'pandda.inspect', 'run pandda.inspect at home', + '------------------------------------------', 'Export NEW PANDDA models', 'Export ALL PANDDA models', + 'Export SELECTED PANDDA models', + '------------------------------------------', 'Show HTML summary', # 'Update datasource with results from pandda.inspect', 'cluster datasets', @@ -654,7 +658,10 @@ def dropdown_items(self, xce_object): xce_object.refine_file_tasks = ['Open COOT - BUSTER refinement -', 'Open COOT - REFMAC refinement -', - 'Open COOT - dimple_twin -' ] + 'Open COOT - dimple_twin -', +# '-------------------------------', +# 'Reset to last successful refinement (BUSTER or REFMAC)', + ''] # xce_object.refine_file_tasks = ['Open COOT', # 'Open COOT for old PanDDA', diff --git a/helpers/reset_to_last_successful_refinement.py b/helpers/reset_to_last_successful_refinement.py new file mode 100644 index 00000000..152a2f38 --- /dev/null +++ b/helpers/reset_to_last_successful_refinement.py @@ -0,0 +1,55 @@ +import os,glob +import sys + +def find_refine_folder(projectDir): + for xtalDir in sorted(glob.glob(os.path.join(projectDir,'*'))): + xtal = xtalDir[xtalDir.rfind('/')+1:] + os.chdir(xtalDir) + dirList = [] + for dirs in sorted(glob.glob('*')): + if dirs.startswith('Refine_') and os.path.isdir(dirs): + if not os.path.isfile('refine.pdb'): + dirList.append([dirs,os.path.getctime(dirs)]) + if dirList != []: + find_refine_pdb(xtal, dirList) + +def find_refine_pdb(xtal, dirList): + sorted_list = sorted(dirList, key=lambda x: x[1], reverse = True) + foundRefinePDB = False + for d in sorted_list: + serial = int(d[0].split('_')[1]) + if os.path.isfile(os.path.join(d[0],'refine.pdb')): + print xtal + ': found refine.pdb in ' + d[0] + pdbLink = os.path.join(d[0],'refine.pdb') + mtzLink = os.path.join(d[0],'refine.mtz') + foundRefinePDB = True + break + elif os.path.isfile(os.path.join(d[0],'refine_%s.pdb' %str(serial))): + print xtal + ': found refine_%s.pdb in %s' %(str(serial),d[0]) + foundRefinePDB = True + pdbLink = os.path.join(d[0],'refine_%s.pdb' %str(serial)) + mtzLink = os.path.join(d[0],'refine_%s.mtz' %str(serial)) + break + if not foundRefinePDB: + print xtal + ': ERROR -> cannot find refine.pdb' + else: + print os.getcwd(),pdbLink, mtzLink + reset_links(xtal, pdbLink, mtzLink) + +def find_pandda_refine_pdb(xtal, dirList): + print 'hallp' + +def reset_links(xtal, pdbLink, mtzLink): + print xtal + ': resetting links...' + os.system('/bin/rm refine.pdb') + os.system('/bin/rm refine.mtz') + os.system('/bin/rm refine.split.bound-state.pdb') + os.system('ln -s %s refine.pdb' %pdbLink) + os.system('ln -s %s refine.mtz' %mtzLink) + os.system('ln -s refine.pdb refine.split.bound-state.pdb') + + + +if __name__ == '__main__': + projectDir = sys.argv[1] + find_refine_folder(projectDir) \ No newline at end of file diff --git a/lib/XChemCootBuster.py b/lib/XChemCootBuster.py index 31b0c863..244b0681 100755 --- a/lib/XChemCootBuster.py +++ b/lib/XChemCootBuster.py @@ -1456,6 +1456,7 @@ def start_refinement(self): foundPDB = True break if foundPDB: + coot.delete_hydrogens(item) coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial), 'in.pdb')) diff --git a/lib/XChemCootNew.py b/lib/XChemCootNew.py index 92024bf7..f8a13ab8 100755 --- a/lib/XChemCootNew.py +++ b/lib/XChemCootNew.py @@ -1259,7 +1259,9 @@ def RefreshData(self): # read fofc maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): + # coot 0.9 does not handle P1 maps well, so now looking for non-existent map in order to trigger + # map calculation from mtz file + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc_??????.map')): coot.set_colour_map_rotation_on_read_pdb(0) coot.set_default_initial_contour_level_for_difference_map(3) coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, 'fofc.map'), 1) @@ -1373,6 +1375,14 @@ def start_refinement(self): # ####################################################### + +# ####################################################### +# # create folder for new refinement cycle and check if free.mtz exists +# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): +# os.mkdir(os.path.join(self.project_directory, self.xtalID)) +# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): +# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) + if self.refinementProtocol.startswith('pandda'): ####################################################### diff --git a/lib/XChemDB.py b/lib/XChemDB.py index 4a90b529..8a436de2 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -1439,6 +1439,10 @@ def translate_xce_column_list_to_sqlite(self,column_list): # if item.startswith('img'): # out_list.append([item,item]) # continue + if item.startswith('Export'): +# out_list.append('Export') + out_list.append(['Export',item]) + continue if item.startswith('Show'): out_list.append([item,item]) continue diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 8015c9ed..10b54fa2 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 25/09/2020 #\n' + ' # Date: 08/10/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 8e9412c5..7acbfa5b 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -487,7 +487,7 @@ def export_models(self): class run_pandda_export(QtCore.QThread): - def __init__(self,panddas_directory,datasource,initial_model_directory,xce_logfile,update_datasource_only,which_models): + def __init__(self,panddas_directory,datasource,initial_model_directory,xce_logfile,update_datasource_only,which_models,pandda_params): QtCore.QThread.__init__(self) self.panddas_directory=panddas_directory self.datasource=datasource @@ -501,6 +501,7 @@ def __init__(self,panddas_directory,datasource,initial_model_directory,xce_logfi self.update_datasource_only=update_datasource_only self.which_models=which_models self.already_exported_models=[] + self.pandda_analyse_data_table = pandda_params['pandda_table'] self.RefmacParams={ 'HKLIN': '', 'HKLOUT': '', 'XYZIN': '', 'XYZOUT': '', @@ -746,6 +747,13 @@ def export_models(self): if self.which_models=='all': self.Logfile.insert('exporting '+sample) samples_to_export[sample]=fileModelsDict[sample] + elif self.which_models == 'selected': + for i in range(0, self.pandda_analyse_data_table.rowCount()): + if str(self.pandda_analyse_data_table.item(i, 0).text()) == sample: + if self.pandda_analyse_data_table.cellWidget(i, 1).isChecked(): + self.Logfile.insert('Dataset selected by user -> exporting '+sample) + samples_to_export[sample]=fileModelsDict[sample] + break else: if sample in dbModelsDict: try: @@ -899,7 +907,9 @@ def run(self): # else: # source_file='' # v1.2.1 - pandda.setup files should be obsolete now that pandda is part of ccp4 - source_file='source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' + # 08/10/2020 - pandda v0.2.12 installation at DLS is obsolete +# source_file='source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' + source_file = '' source_file += 'export XChemExplorer_DIR="' + os.getenv('XChemExplorer_DIR') + '"\n' if os.path.isfile(self.filter_pdb + '.pdb'): diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 3da9e4ee..71ef0a2d 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -588,9 +588,12 @@ def write_refinement_script(self,cmd,program): def run_script(self,program,external_software): os.chdir(os.path.join(self.ProjectPath,self.xtalID)) - if external_software['qsub'] and not os.uname()[1] == 'hestia': + if external_software['qsub'] and os.path.isdir('/dls'): self.Logfile.insert('starting refinement with command: qsub -P labxchem -q medium.q %s.sh' %program) os.system("qsub -P labxchem -q medium.q %s.sh" %program) + elif external_software['qsub'] and not os.path.isdir('/dls'): + self.Logfile.insert('starting refinement with command: qsub %s.sh' %program) + os.system("qsub %s.sh" %program) elif external_software['qsub_remote'] != '': Logfile.insert('starting refinement on remote cluster') remote_command=external_software['qsub_remote'].replace('qsub','cd %s; qsub' %os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) @@ -950,10 +953,12 @@ def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom os.system("%s -P labxchem -q medium.q refmac.csh'" %remote_command) print '%s -P labxchem -q medium.q refmac.csh' %remote_command - elif external_software['qsub'] and not os.uname()[1] == 'hestia': - Logfile.insert('starting refinement on cluster') + elif external_software['qsub'] and os.path.isdir('/dls'): + Logfile.insert('starting refinement on cluster with command "qsub -P labxchem -q medium.q refmac.csh"') os.system("qsub -P labxchem -q medium.q refmac.csh") - + elif external_software['qsub'] and not os.path.isdir('/dls'): + Logfile.insert('starting refinement on cluster with command "qsub refmac.csh"') + os.system("qsub refmac.csh") else: os.system('chmod +x refmac.csh') if os.path.isfile(xce_logfile): Logfile.insert('starting refinement on local machine') @@ -1495,7 +1500,7 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine + module_load + '\n' +source+ - 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' + 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'\n' '\n' '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(self.datasource,self.xtalID,'RefinementStatus','running') + '\n' @@ -1510,7 +1515,7 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine " split_conformations='False'" '\n' 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'\n' - + '\n' 'ln -s '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'/refine_'+str(Serial)+'_001.pdb ' +self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'/refine_'+str(Serial)+'.pdb' +'\n' From 8828d9e6c019938801e1d9a9f59281137ce98381 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 9 Oct 2020 14:05:06 +0100 Subject: [PATCH 078/358] v1.7.17 (09/10/2020) (#379) - bug fix: corrected positions of ignore checkboxes in pandda.analyse --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 6 +++--- 4 files changed, 8 insertions(+), 5 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 9530c793..48bbd6cc 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.17 (09/10/2020) +- bug fix: corrected positions of ignore checkboxes in pandda.analyse + v1.7.16 (08/10/2020) - enable export of selected datasets with pandda.export - glitch fix: remove hydrogens before saving model for buster refinement (causes problems during ligand occupancy refinement) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 38b82daf..4bfb8cca 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.16' + xce_object.xce_version = 'v1.7.17' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 10b54fa2..02f73c06 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 08/10/2020 #\n' + ' # Date: 09/10/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 7acbfa5b..e543d8c4 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -954,9 +954,9 @@ def run(self): zmap = [] for i in range(0, self.pandda_analyse_data_table.rowCount()): - ignore_all_checkbox = self.pandda_analyse_data_table.cellWidget(i, 6) - ignore_characterisation_checkbox = self.pandda_analyse_data_table.cellWidget(i, 7) - ignore_zmap_checkbox = self.pandda_analyse_data_table.cellWidget(i, 8) + ignore_all_checkbox = self.pandda_analyse_data_table.cellWidget(i, 7) + ignore_characterisation_checkbox = self.pandda_analyse_data_table.cellWidget(i, 8) + ignore_zmap_checkbox = self.pandda_analyse_data_table.cellWidget(i, 9) if ignore_all_checkbox.isChecked(): ignore.append(str(self.pandda_analyse_data_table.item(i, 0).text())) From a9e42e4a8eb3938b1710f7ded7d1a51ff4c6c982 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 12 Oct 2020 12:31:52 +0100 Subject: [PATCH 079/358] v1.7.18 (12/10/2020) (#380) - bug fix: added missing 'module load ccp4' statement when generating pandda.analyse shell script at DLS --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 6 +++++- 4 files changed, 10 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 48bbd6cc..6c0d172d 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.18 (12/10/2020) +- bug fix: added missing 'module load ccp4' statement when generating pandda.analyse shell script at DLS + v1.7.17 (09/10/2020) - bug fix: corrected positions of ignore checkboxes in pandda.analyse diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 4bfb8cca..8e1bd200 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.17' + xce_object.xce_version = 'v1.7.18' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 02f73c06..769f3e23 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 09/10/2020 #\n' + ' # Date: 12/10/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index e543d8c4..edd96c0a 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -938,7 +938,11 @@ def run(self): if self.data_directory.startswith('/dls'): dls = ( source_file + - '\n' + 'module load pymol/1.8.2.0' + ' \n' + '\n' + 'module load pymol/1.8.2.0\n' + '\n' + 'module load ccp4\n' + '\n' ) Cmds = ( From 9067a962cc35bcdd166bf3b4a356918db3a77aaf Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 12 Oct 2020 15:47:18 +0100 Subject: [PATCH 080/358] v1.7.19 (12/10/2020) (#381) - bug fix: use 'module load ccp4/7.0.072' for pandda.analyse, but 'module load ccp4' (i.e. v7.1) for pre-run ground-state selection at DLS --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemPANDDA.py | 6 ++++-- 3 files changed, 8 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 6c0d172d..b5d5d116 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.19 (12/10/2020) +- bug fix: use 'module load ccp4/7.0.072' for pandda.analyse, but 'module load ccp4' (i.e. v7.1) for pre-run ground-state selection at DLS + v1.7.18 (12/10/2020) - bug fix: added missing 'module load ccp4' statement when generating pandda.analyse shell script at DLS diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 8e1bd200..c3595b62 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.18' + xce_object.xce_version = 'v1.7.19' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index edd96c0a..fe87ead9 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -861,7 +861,9 @@ def __init__(self,pandda_params,xce_logfile,datasource): if os.path.isdir(self.panddas_directory): os.system('/bin/rm -fr %s' %self.panddas_directory) os.mkdir(self.panddas_directory) - self.select_ground_state_model='$CCP4/bin/ccp4-python %s %s\n' %(os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','select_ground_state_dataset.py'),self.panddas_directory) + if self.data_directory.startswith('/dls'): + self.select_ground_state_model = 'module load ccp4\n' + self.select_ground_state_model +='$CCP4/bin/ccp4-python %s %s\n' %(os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','select_ground_state_dataset.py'),self.panddas_directory) self.make_ligand_links='' def run(self): @@ -941,7 +943,7 @@ def run(self): '\n' 'module load pymol/1.8.2.0\n' '\n' - 'module load ccp4\n' + 'module load ccp4/7.0.072\n' '\n' ) From 50dd9c3ce5e8f486d477c9dd9ded808bb0dbf738 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Fri, 16 Oct 2020 13:56:17 +0100 Subject: [PATCH 081/358] v1.7.20 (16/10/2020) (#382) - bug fix: remove undocumented and faulty changes to RunQuickRefine --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemRefine.py | 6 +++--- 4 files changed, 8 insertions(+), 5 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index b5d5d116..061d3e75 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.20 (16/10/2020) +- bug fix: remove undocumented and faulty changes to RunQuickRefine + v1.7.19 (12/10/2020) - bug fix: use 'module load ccp4/7.0.072' for pandda.analyse, but 'module load ccp4' (i.e. v7.1) for pre-run ground-state selection at DLS diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index c3595b62..3b2f9eda 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.19' + xce_object.xce_version = 'v1.7.20' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 769f3e23..509f2673 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 12/10/2020 #\n' + ' # Date: 16/10/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 71ef0a2d..ce0b74d3 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -1500,7 +1500,7 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine + module_load + '\n' +source+ - 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'\n' + 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' '\n' '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(self.datasource,self.xtalID,'RefinementStatus','running') + '\n' @@ -1515,10 +1515,10 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine " split_conformations='False'" '\n' 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'\n' - '\n' + 'ln -s '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'/refine_'+str(Serial)+'_001.pdb ' +self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'/refine_'+str(Serial)+'.pdb' +'\n' - + 'ln -s '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'/refine_'+str(Serial)+'_001.mtz ' +self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'/refine_'+str(Serial)+'.mtz' +'\n' From b078310ab0cec156fab1077e7f9a0f937ffb3c10 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 19 Oct 2020 16:43:32 +0100 Subject: [PATCH 082/358] v1.7.21 (19/10/2020) (#383) - bug fix: use default CCP4 for giant.merge_conformations --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemRefine.py | 3 ++- 4 files changed, 7 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 061d3e75..20127c29 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.21 (19/10/2020) +- bug fix: use default CCP4 for giant.merge_conformations + v1.7.20 (16/10/2020) - bug fix: remove undocumented and faulty changes to RunQuickRefine diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 3b2f9eda..e36968e7 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.20' + xce_object.xce_version = 'v1.7.21' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 509f2673..83167371 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 16/10/2020 #\n' + ' # Date: 19/10/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index ce0b74d3..dca36727 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -1295,7 +1295,8 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine if os.getcwd().startswith('/dls'): cmd = ( 'export XChemExplorer_DIR="%s"\n' %os.getenv('XChemExplorer_DIR')+ - 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') + +# 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') + + 'module load ccp4\n' 'giant.merge_conformations major=%s minor=%s reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0' %(ground_state,bound_state) ) else: From 351a764f21cfbb8bffadb56a86a3f4665bdda84c Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 28 Oct 2020 19:28:54 +0000 Subject: [PATCH 083/358] v1.7.22 (28/10/2020) (#384) - cosmetic changes to deposition interface - bug fix: make event map assignment during MMCIF preparation backward compatible - bug fix: finding of event map with highest CC for given ligand --- ChangeLog.txt | 5 +++++ XChemExplorer.py | 14 +++++++++---- gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 31 ++++++++++++++++++++++++----- lib/XChemLog.py | 2 +- lib/XChemMain.py | 1 + 6 files changed, 44 insertions(+), 11 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 20127c29..ba4a4a03 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,8 @@ +v1.7.22 (28/10/2020) +- cosmetic changes to deposition interface +- bug fix: make event map assignment during MMCIF preparation backward compatible +- bug fix: finding of event map with highest CC for given ligand + v1.7.21 (19/10/2020) - bug fix: use default CCP4 for giant.merge_conformations diff --git a/XChemExplorer.py b/XChemExplorer.py index 9577c85b..7f20e98c 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -1836,6 +1836,7 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Type'), 2, 0) self.structure_keywords_type = QtGui.QComboBox() + self.structure_keywords_type.setStyleSheet("background-color: rgb(192, 192, 192);") for item in XChemMain.pdbx_keywords(): self.structure_keywords_type.addItem(item) grid.addWidget(self.structure_keywords_type, 2, 1) # self.structure_keywords = QtGui.QLineEdit() @@ -1860,21 +1861,24 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Sequence'), 5, 0) self.molecule_one_letter_sequence = QtGui.QTextEdit() + self.molecule_one_letter_sequence.setStyleSheet("background-color: rgb(255, 255, 255);") +# self.molecule_one_letter_sequence.setStyleSheet("background-color: rgb(192, 192, 192);") self.molecule_one_letter_sequence.setText('') self.molecule_one_letter_sequence.setFixedWidth(300) grid.addWidget(self.molecule_one_letter_sequence, 5, 1, 8, 2) - grid.addWidget(QtGui.QLabel('Sequence information for entity 2'), 10, 0) - grid.addWidget(QtGui.QLabel('(Important: only for protein-protein complex'), 10, 1) +# grid.addWidget(QtGui.QLabel('Sequence information for entity 2'), 10, 0) +# grid.addWidget(QtGui.QLabel('(Important: only for protein-protein complex'), 10, 1) - grid.addWidget(QtGui.QLabel('Sequence UNIPROT ID (Entity 2)'), 13, 0) + grid.addWidget(QtGui.QLabel('Sequence UNIPROT ID (Entity 2) - optional'), 13, 0) self.molecule_one_letter_sequence_uniprot_id_two = QtGui.QLineEdit() self.molecule_one_letter_sequence_uniprot_id_two.setText('') + self.molecule_one_letter_sequence_uniprot_id_two.setStyleSheet("background-color: rgb(192, 192, 192);") self.molecule_one_letter_sequence_uniprot_id_two.setFixedWidth(300) grid.addWidget(self.molecule_one_letter_sequence_uniprot_id_two, 13, 1) grid.addWidget(QtGui.QLabel('(e.g. Q6B0I6)'), 13, 2) - grid.addWidget(QtGui.QLabel('Sequence (Entity 2)'), 14, 0) + grid.addWidget(QtGui.QLabel('Sequence (Entity 2) - optional'), 14, 0) self.molecule_one_letter_sequence_two = QtGui.QTextEdit() self.molecule_one_letter_sequence_two.setText('') self.molecule_one_letter_sequence_two.setFixedWidth(300) @@ -1886,6 +1890,7 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Project Name'), 22, 0) self.SG_project_name = QtGui.QLineEdit() self.SG_project_name.setText('') + self.SG_project_name.setStyleSheet("background-color: rgb(192, 192, 192);") self.SG_project_name.setFixedWidth(300) grid.addWidget(self.SG_project_name, 22, 1) grid.addWidget(QtGui.QLabel('(e.g. SGC, Structural Genomics Consortium)'), 22, 2) @@ -1893,6 +1898,7 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Full Name'), 23, 0) self.full_name_of_SG_center = QtGui.QLineEdit() self.full_name_of_SG_center.setText('') + self.full_name_of_SG_center.setStyleSheet("background-color: rgb(192, 192, 192);") self.full_name_of_SG_center.setFixedWidth(300) grid.addWidget(self.full_name_of_SG_center, 23, 1) grid.addWidget(QtGui.QLabel('(e.g. Structural Genomics Consortium)'), 23, 2) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index e36968e7..e48c963f 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.21' + xce_object.xce_version = 'v1.7.22' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 7a3a19b8..6e6c6741 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -767,6 +767,16 @@ def find_matching_event_map(self,xtal): if foundMatchingMap: continue + for mtz in sorted(glob.glob('*event*.native.mtz')): + self.get_lig_cc(xtal, mtz, lig) + cc = self.check_lig_cc(mtz.replace('.mtz', '_CC'+ligID+'.log')) + self.Logfile.insert('%s: %s -> CC = %s for %s' %(xtal,ligID,cc,mtz)) + try: + ligCC.append([mtz,float(cc)]) + except ValueError: + ligCC.append([mtz, 0.00]) + + for mtz in sorted(glob.glob('*event*.native*P1.mtz')): self.get_lig_cc(xtal, mtz, lig) cc = self.check_lig_cc(mtz.replace('.mtz', '_CC'+ligID+'.log')) @@ -776,17 +786,28 @@ def find_matching_event_map(self,xtal): except ValueError: ligCC.append([mtz, 0.00]) try: - highestCC = max(ligCC, key=lambda x: x[0])[1] + for cm in ligCC: + self.Logfile.insert('%s: cc = %s - %s' %(xtal,cm[1],cm[0])) +# highestCC = max(ligCC, key=lambda x: x[0])[1] + highestCCeventmap = max(ligCC, key=lambda x: float(x[1]))[0] except ValueError: highestCC = 0.00 - if highestCC == 0.00 or ligCC is []: + highestCCeventmap = None + +# if highestCC == 0.00 or ligCC is []: + if highestCCeventmap is None or ligCC is []: self.Logfile.error('%s: best CC of ligand %s for any event map is 0!' %(xtal,lig)) self.add_to_errorList(xtal) foundMatchingMap = False else: - self.Logfile.insert('%s: selected event map -> CC(%s) = %s for %s' %(xtal,lig,highestCC,mtz[mtz.rfind('/')+1:])) - if mtz not in self.eventList: - self.eventList.append(mtz) + self.Logfile.insert('%s: selected event map for ligand %s is %s' %(xtal,lig,highestCCeventmap)) + if os.path.isfile(highestCCeventmap.replace('.mtz','_'+ligID+'.mtz')): + self.Logfile.warning('%s: symlink exists %s' %(xtal,highestCCeventmap.replace('.mtz','_'+ligID+'.mtz'))) + else: + self.Logfile.insert('%s: making symlink %s' %(xtal,highestCCeventmap.replace('.mtz','_'+ligID+'.mtz'))) + os.system('ln -s %s %s' %(highestCCeventmap,highestCCeventmap.replace('.mtz','_'+ligID+'.mtz'))) + if highestCCeventmap not in self.eventList: + self.eventList.append(highestCCeventmap) if foundMatchingMap is None: foundMatchingMap = True return foundMatchingMap diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 83167371..68056163 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 19/10/2020 #\n' + ' # Date: 28/10/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemMain.py b/lib/XChemMain.py index e6d2fd58..892ff250 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -677,6 +677,7 @@ def phasing_software(): def pdbx_keywords(): keywords = [ + '', 'ALLERGEN', 'ANTIBIOTIC', 'ANTIFREEZE PROTEIN', From bddae96b12ac23c799efcf1ec8aae307b529e6c7 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 2 Nov 2020 16:17:15 +0000 Subject: [PATCH 084/358] v1.7.23 (02/11/2020) (#385) - pandda refinement: stopped sourcing obsolete pandda v0.2.12 at DLS (otherwise refinement update script fails due to missing gemmi library) --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemRefine.py | 10 ++++++---- 4 files changed, 11 insertions(+), 6 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index ba4a4a03..9c4ef16f 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.23 (02/11/2020) +- pandda refinement: stopped sourcing obsolete pandda v0.2.12 at DLS (otherwise refinement update script fails due to missing gemmi library) + v1.7.22 (28/10/2020) - cosmetic changes to deposition interface - bug fix: make event map assignment during MMCIF preparation backward compatible diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index e48c963f..130bbbb0 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.22' + xce_object.xce_version = 'v1.7.23' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 68056163..4147b040 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 28/10/2020 #\n' + ' # Date: 02/11/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index dca36727..53644101 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -1435,24 +1435,26 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine spider_plot+='giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' %(pdb_one,mtz_one,pdb_two,mtz_two) ####################################################### - # PHENIX stuff (if working at DLS) + # CCP4 & PHENIX stuff (if working at DLS) module_load='' if os.getcwd().startswith('/dls'): - module_load='module load phenix\n' + module_load = 'module load ccp4\n' + module_load += 'module load phenix\n' # 2017-07-20: for the time being this will explicitly source pandda since version 0.2 really only works at DLS + # 2020-11-02: will start using default ccp4 installation at DLS otherwise gemmi does not work source ='' if 'bash' in os.getenv('SHELL'): source = ( 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' '\n' - 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') +# 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') ) elif 'csh' in os.getenv('SHELL'): source = ( 'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n' '\n' - 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh\n') +# 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh\n') ) From faea58daf82af8860d1546ae01afa528129d8932 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 3 Nov 2020 12:05:23 +0000 Subject: [PATCH 085/358] v1.7.24 (02/11/2020) (#386) - capitalized organism names in NCBI_taxonomy_ID dictionary --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemMain.py | 6 +++--- 4 files changed, 8 insertions(+), 5 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 9c4ef16f..1efd3434 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.24 (02/11/2020) +- capitalized organism names in NCBI_taxonomy_ID dictionary + v1.7.23 (02/11/2020) - pandda refinement: stopped sourcing obsolete pandda v0.2.12 at DLS (otherwise refinement update script fails due to missing gemmi library) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 130bbbb0..f580f272 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.23' + xce_object.xce_version = 'v1.7.24' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 4147b040..4a0bc53b 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 02/11/2020 #\n' + ' # Date: 03/11/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemMain.py b/lib/XChemMain.py index 892ff250..9b7e3b61 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -632,13 +632,13 @@ def detectorType(): def NCBI_taxonomy_ID(): - taxonomy_dict = { '9606': 'homo sapiens', - '10090': 'mus musculus', + taxonomy_dict = { '9606': 'Homo sapiens', + '10090': 'Mus musculus', '7108': 'SPODOPTERA FRUGIPERDA', '5693 ': 'Trypanosoma cruzi', '1508227': 'BAT SARS-LIKE CORONAVIRUS', '2697049': 'COVID-19', - '562': 'escherichia coli' } + '562': 'Escherichia coli' } return taxonomy_dict From efc153bad94502bcb3049abca954ca051237b009 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 11 Nov 2020 15:22:20 +0000 Subject: [PATCH 086/358] v1.7.25 (11/11/2020) (#387) - convert json logfile from dials into pseudo aimless file for mmcif file preparation (required for pdb-extract) --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 28 ++++++++++++++++----- lib/XChemLog.py | 2 +- lib/XChemUtils.py | 38 ++++++++++++++++++++++++++++- 5 files changed, 64 insertions(+), 9 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 1efd3434..9f7d833f 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.25 (11/11/2020) +- convert json logfile from dials into pseudo aimless file for mmcif file preparation (required for pdb-extract) + v1.7.24 (02/11/2020) - capitalized organism names in NCBI_taxonomy_ID dictionary diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index f580f272..1ecff9d2 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.24' + xce_object.xce_version = 'v1.7.25' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 6e6c6741..e903491f 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -17,7 +17,7 @@ from XChemUtils import pdbtools from XChemUtils import mtztools from XChemUtils import smilestools - +from XChemUtils import parse def create_SF_mmcif(outDir,mtzList): print 'hallo' @@ -650,7 +650,8 @@ def run_aimless_merge_only(self,xtal,unmerged,APpath): else: self.Logfile.error('%s: cannot find AIMLESS logfile...' %xtal) - + def prepare_aimless_log(self,xtal): + parse().make_pseudo_aimless_log_from_json(xtal + '.log') def aimless_logfile_exists(self,xtal): self.Logfile.insert('%s: checking if aimless logfile, i.e. %s.log, exists' %(xtal,xtal)) @@ -671,13 +672,19 @@ def aimless_logfile_exists(self,xtal): self.Logfile.insert('%s: file path to logfile %s' %(xtal,Filepath)) if os.path.isdir(APpath): os.chdir(APpath) - foundUnmerged = False for unmerged in glob.glob('*_scaled_unmerged.mtz'): self.Logfile.insert('%s: found %s in %s' %(xtal,unmerged,APpath)) self.run_aimless_merge_only(xtal,unmerged,APpath) - foundUnmerged = True + fileStatus = True break - if not foundUnmerged: + if not fileStatus: + os.chdir(os.path.join(self.projectDir,xtal)) + self.Logfile.insert('%s: trying to prepare a pseudo-aimless file from json file...' %xtal) + self.prepare_aimless_log(xtal) + if os.path.isfile('aimless_dials.log'): + self.Logfile.insert('%s: found aimless_dials.log' %xtal) + fileStatus = True + if not fileStatus: self.Logfile.error('%s: cannot find a suitable AIMLESS logfile' %xtal) self.add_to_errorList(xtal) else: @@ -951,6 +958,15 @@ def create_model_mmcif(self,xtal): pdb_extract_init += +os.path.join(os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/bin/pdb_extract') + aimless = None + for n,line in enumerate(open('%s.log' %xtal)): + if 'AIMLESS' in line: + aimless = '%s.log' %xtal + break + if not aimless: + if os.path.isfile('aimless_dials.log'): + aimless = 'aimless_dials.log' + if self.ground_state: refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] aimless = os.path.join(self.logDir,refXtal,refXtal+'.log') @@ -980,7 +996,7 @@ def create_model_mmcif(self,xtal): ' -iPDB {0!s}'.format('refine.split.bound-state.pdb') + ' -e MR' ' -s AIMLESS' - ' -iLOG {0!s}.log'.format(xtal) + + ' -iLOG {0!s}'.format(aimless) + ' -iENT data_template.cif' ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 4a0bc53b..8fedb5a8 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 03/11/2020 #\n' + ' # Date: 11/11/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index ed9a6cfd..456206ef 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -438,7 +438,9 @@ def __init__(self): 'DataProcessingCChalfOverall': 'n/a', 'DataProcessingCChalfLow': 'n/a', 'DataProcessingCChalfHigh': 'n/a', - 'DataProcessingResolutionHigh15sigma': 'n/a', + 'DataProcessingResolutionHigh15sigma': 'n/a', + 'DataProcessingUniqueReflectionsLow': 'n/a', + 'DataProcessingUniqueReflectionsHigh': 'n/a', 'DataProcessingUniqueReflectionsOverall': 'n/a', 'DataProcessingLattice': 'n/a', 'DataProcessingPointGroup': 'n/a', @@ -806,6 +808,10 @@ def json_logfile(self,logfile): self.aimless['DataProcessingCChalfLow'] = str(round(obj['cc_one_half'][0],2)) self.aimless['DataProcessingCChalfHigh'] = str(round(obj['cc_one_half'][len(obj['cc_one_half'])-1],2)) # self.aimless['DataProcessingResolutionHigh15sigma'] = + + self.aimless['DataProcessingUniqueReflectionsLow'] = str(obj['n_uniq'][0]) + self.aimless['DataProcessingUniqueReflectionsHigh'] = str(obj['n_uniq'][len(obj['n_uniq'])-1]) + self.aimless['DataProcessingUniqueReflectionsOverall'] = str(obj['overall']['n_obs']) # self.aimless['DataProcessingPointGroup'] = # self.aimless['DataProcessingUnitCellVolume'] = @@ -816,6 +822,36 @@ def json_logfile(self,logfile): if os.path.isfile(mmcif_file): self.read_mmcif(mmcif_file) + def make_pseudo_aimless_log_from_json(self,logfile): + self.json_logfile(logfile) + template = ( + '==============================================================\n' + '\n' + ' $TEXT:Result: $$ $$\n' + 'Summary data for Project: nt11175v63 Crystal: xPHIPAx17245 Dataset: SAD\n' + '\n' + ' Overall InnerShell OuterShell\n' + 'Low resolution limit {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingResolutionLow'],self.aimless['DataProcessingResolutionLow'],self.aimless['DataProcessingResolutionHighOuterShell'])+ + 'High resolution limit {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingResolutionHigh'],self.aimless['DataProcessingResolutionLowInnerShell'],self.aimless['DataProcessingResolutionHigh'])+ + '\n' + 'Rmerge (within I+/I-) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingRmergeOverall'],self.aimless['DataProcessingRmergeLow'],self.aimless['DataProcessingRmergeHigh']) + + 'Rmerge (all I+ and I-) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingRmergeOverall'],self.aimless['DataProcessingRmergeLow'],self.aimless['DataProcessingRmergeHigh']) + + 'Rmeas (within I+/I-) - - - \n' + 'Rmeas (all I+ & I-) - - - \n' + 'Rpim (within I+/I-) - - - \n' + 'Rpim (all I+ & I-) - - - \n' + 'Rmerge in top intensity bin - - - \n' + 'Total number of observations - - - \n' + 'Total number unique {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingUniqueReflectionsOverall'],self.aimless['DataProcessingUniqueReflectionsLow'],self.aimless['DataProcessingUniqueReflectionsHigh']) + + 'Mean((I)/sd(I)) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingIsigOverall'],self.aimless['DataProcessingIsigLow'],self.aimless['DataProcessingIsigHigh']) + + 'Mn(I) half-set correlation CC(1/2) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingCChalfOverall'],self.aimless['DataProcessingCChalfLow'],self.aimless['DataProcessingCChalfHigh']) + + 'Completeness {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingCompletenessOverall'],self.aimless['DataProcessingCompletenessLow'],self.aimless['DataProcessingCompletenessHigh']) + + 'Multiplicity {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingMultiplicityOverall'],self.aimless['DataProcessingMultiplicityLow'],self.aimless['DataProcessingMultiplicityHigh']) + ) + f = open('aimless_dials.log','w') + f.write(template) + f.close() + def read_mmcif(self,mmcif): for line in open(mmcif): From 9f05e2b4acd7a9c53d596b9d31825bfe2e0c1fb6 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 12 Nov 2020 17:36:51 +0000 Subject: [PATCH 087/358] v1.7.26 (12/11/2020) (#388) - XChemDeposit: remove \n and \r from smiles string in _diffrn.details --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 32 ++++++++++++++++++++++------- lib/XChemLog.py | 2 +- 4 files changed, 30 insertions(+), 9 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 9f7d833f..3d8854a8 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.26 (12/11/2020) +- XChemDeposit: remove \n and \r from smiles string in _diffrn.details + v1.7.25 (11/11/2020) - convert json logfile from dials into pseudo aimless file for mmcif file preparation (required for pdb-extract) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 1ecff9d2..d053f841 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.25' + xce_object.xce_version = 'v1.7.26' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index e903491f..27fa4527 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -958,18 +958,36 @@ def create_model_mmcif(self,xtal): pdb_extract_init += +os.path.join(os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/bin/pdb_extract') - aimless = None - for n,line in enumerate(open('%s.log' %xtal)): + if self.ground_state: + refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] + aimless = os.path.join(self.logDir,refXtal,refXtal+'.log') + else: + aimless = '%s.log' %xtal + + isAimlessFile = False + for n,line in enumerate(open(aimless)): if 'AIMLESS' in line: - aimless = '%s.log' %xtal + isAimlessFile = True break - if not aimless: + if not isAimlessFile: if os.path.isfile('aimless_dials.log'): aimless = 'aimless_dials.log' + else: + parse().make_pseudo_aimless_log_from_json(aimless) + aimless = 'aimless_dials.log' + +# aimless = None +# for n,line in enumerate(open('%s.log' %xtal)): +# if 'AIMLESS' in line: +# aimless = '%s.log' %xtal +# break +# if not aimless: +# if os.path.isfile('aimless_dials.log'): +# aimless = 'aimless_dials.log' if self.ground_state: - refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] - aimless = os.path.join(self.logDir,refXtal,refXtal+'.log') +# refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] +# aimless = os.path.join(self.logDir,refXtal,refXtal+'.log') self.Logfile.insert('aimless.log file: ' + aimless) Cmd = (pdb_extract_init + ' -r {0!s}'.format(refSoft) + @@ -1250,7 +1268,7 @@ def add_apo_sf_mmcif_to_ground_state_mmcif(self): newLine = line newLine += '#\n' newLine += '_diffrn.id 1\n' - newLine += '_diffrn.details "diffraction data from crystal %s; soaked compound: %s"\n' %(str(counter),smiles) + newLine += '_diffrn.details "diffraction data from crystal %s; soaked compound: %s"\n' %(str(counter),smiles.replace('\n','').replace('\r','')) f.write(newLine) counter += 1 else: diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 8fedb5a8..dce43685 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 11/11/2020 #\n' + ' # Date: 12/11/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From f7e120a9e58ee389e31928e75f8a9762f54add36 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 24 Nov 2020 12:36:05 +0000 Subject: [PATCH 088/358] v1.7.27 (24/11/2020) (#389) - bug fix: add missing DataProcessingUniqueReflectionsLow/High column to db --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDB.py | 6 +++++- lib/XChemLog.py | 2 +- 4 files changed, 10 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 3d8854a8..ba732c71 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.27 (24/11/2020) +- bug fix: add missing DataProcessingUniqueReflectionsLow/High column to db + v1.7.26 (12/11/2020) - XChemDeposit: remove \n and \r from smiles string in _diffrn.details diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index d053f841..51a24821 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.26' + xce_object.xce_version = 'v1.7.27' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDB.py b/lib/XChemDB.py index 8a436de2..d419696c 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -143,14 +143,16 @@ def __init__(self,data_source_file): ['DataProcessingLOGfileName', 'DataProcessingLOGfileName', 'TEXT', 0], ['DataProcessingMTZfileName', 'DataProcessingMTZfileName', 'TEXT', 0], ['DataProcessingDirectoryOriginal', 'DataProcessingDirectoryOriginal', 'TEXT', 0], - ['DataProcessingUniqueReflectionsOverall', 'Unique Reflections\nOverall', 'TEXT', 1], + ['DataProcessingUniqueReflectionsLow', 'Unique Reflections\nlow', 'TEXT', 1], + ['DataProcessingUniqueReflectionsHigh', 'Unique Reflections\nhigh', 'TEXT', 1], ['DataProcessingLattice', 'DataProcessing\nLattice', 'TEXT', 0], ['DataProcessingPointGroup', 'DataProcessing\nPointGroup', 'TEXT', 0], ['DataProcessingUnitCellVolume', 'DataProcessing\nUnit Cell Volume', 'TEXT', 0], ['DataProcessingAlert', 'DataProcessing\nAlert', 'TEXT', 0], ['DataProcessingScore', 'DataProcessing\nScore', 'TEXT', 1], + ['DataProcessingStatus', 'DataProcessing\nStatus', 'TEXT', 1], ['DataProcessingRcryst', 'DataProcessing\nRcryst', 'TEXT', 0], @@ -488,6 +490,8 @@ def __init__(self,data_source_file): ['DataProcessingMTZfileName', 'DataProcessingMTZfileName', 'TEXT', 0], ['DataProcessingDirectoryOriginal', 'DataProcessingDirectoryOriginal', 'TEXT', 0], ['DataProcessingUniqueReflectionsOverall', 'Unique Reflections\nOverall', 'TEXT', 1], + ['DataProcessingUniqueReflectionsLow', 'Unique Reflections\nlow', 'TEXT', 1], + ['DataProcessingUniqueReflectionsHigh', 'Unique Reflections\nhigh', 'TEXT', 1], ['DataProcessingLattice', 'DataProcessing\nLattice', 'TEXT', 0], ['DataProcessingPointGroup', 'DataProcessing\nPointGroup', 'TEXT', 0], ['DataProcessingUnitCellVolume', 'DataProcessing\nUnit Cell Volume', 'TEXT', 0], diff --git a/lib/XChemLog.py b/lib/XChemLog.py index dce43685..7718e9be 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 12/11/2020 #\n' + ' # Date: 24/11/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 162e162b157aa7c57e2d4b60e2c87be15754ca5a Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 25 Nov 2020 14:59:47 +0000 Subject: [PATCH 089/358] v1.7.28 (25/11/2020) (#390) - added exception to catch 'Cannot allocate memory' error in XChemMain.get_gda_barcodes --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemMain.py | 28 ++++++++++++++++------------ 4 files changed, 21 insertions(+), 14 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index ba732c71..eda4fca1 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.28 (25/11/2020) +- added exception to catch 'Cannot allocate memory' error in XChemMain.get_gda_barcodes + v1.7.27 (24/11/2020) - bug fix: add missing DataProcessingUniqueReflectionsLow/High column to db diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 51a24821..0df19aad 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.27' + xce_object.xce_version = 'v1.7.28' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 7718e9be..2605424d 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 24/11/2020 #\n' + ' # Date: 25/11/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' diff --git a/lib/XChemMain.py b/lib/XChemMain.py index 9b7e3b61..a15fa095 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -482,18 +482,22 @@ def get_gda_barcodes(sampleList,gzipped_logs_parsed,gda_log_start_line,beamline, except IOError: Logfile.warning('cannot open file %s' %gdaLogFile) else: - for n,line in enumerate(open(gdaLogFile).readlines()[gda_log_start_line:]): - if 'BART SampleChanger - getBarcode() returning' in line: - barcode = line.split()[len(line.split()) - 1] - found_barcode_entry = True - if found_barcode_entry: - if 'Snapshots will be saved' in line: - sampleID = line.split()[len(line.split()) - 1].split('/')[-1] - if sampleID in sampleList: - pinDict[sampleID] = barcode - Logfile.insert( - 'found: sample={0!s}, barcode={1!s}, file={2!s}'.format(sampleID, barcode, gdaLogFile)) - found_barcode_entry = False + try: + for n,line in enumerate(open(gdaLogFile).readlines()[gda_log_start_line:]): + if 'BART SampleChanger - getBarcode() returning' in line: + barcode = line.split()[len(line.split()) - 1] + found_barcode_entry = True + if found_barcode_entry: + if 'Snapshots will be saved' in line: + sampleID = line.split()[len(line.split()) - 1].split('/')[-1] + if sampleID in sampleList: + pinDict[sampleID] = barcode + Logfile.insert( + 'found: sample={0!s}, barcode={1!s}, file={2!s}'.format(sampleID, barcode, gdaLogFile)) + found_barcode_entry = False + except IOError: + Logfile.error('IOError -> ' + gdaLogFile) + try: gda_log_start_line = gda_log_start_line + n -1 except UnboundLocalError: From 8157be438391262d4f5c88fce67bd3663aaa0188 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 9 Dec 2020 13:42:16 +0000 Subject: [PATCH 090/358] v1.7.29 (09/12/2020) (#392) - bug fix: syntax error in XChemDeposit - XChemDeposit: use default pdb_extract if no installation in XChemExplorer_dir --- ChangeLog.txt | 4 ++++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 17 ++++++++++------- lib/XChemLog.py | 2 +- 4 files changed, 16 insertions(+), 9 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index eda4fca1..97bcdb3f 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.7.29 (09/12/2020) +- bug fix: syntax error in XChemDeposit +- XChemDeposit: use default pdb_extract if no installation in XChemExplorer_dir + v1.7.28 (25/11/2020) - added exception to catch 'Cannot allocate memory' error in XChemMain.get_gda_barcodes diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 0df19aad..0716be84 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.28' + xce_object.xce_version = 'v1.7.29' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 27fa4527..0098e0a5 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -953,10 +953,11 @@ def create_model_mmcif(self,xtal): pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n' pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-prod/bin/pdb_extract' else: - pdb_extract_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' - pdb_extract_init += +os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/bin/pdb_extract') + if os.path.isfile(os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/bin/pdb_extract')): + pdb_extract_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/setup.sh') + '\n' + pdb_extract_init += os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/bin/pdb_extract') + else: + pdb_extract_init += 'pdb_extract' if self.ground_state: refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] @@ -1150,7 +1151,7 @@ def make_table_one(self,xtal): else: extract_table_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' - extract_table_init += +os.path.join(os.getenv('XChemExplorer_DIR'), + extract_table_init += os.path.join(os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/bin/extract_table') Cmd = extract_table_init + ' ' + xtal + '.mmcif' @@ -1189,8 +1190,10 @@ def create_sf_mmcif(self,xtal): else: pdb_extract_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' - pdb_extract_init += +os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/bin/sf_convert') + if os.path.isfile(os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/bin/sf_convert')): + pdb_extract_init += os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/bin/sf_convert') + else: + pdb_extract_init += 'sf_convert' Cmd = (pdb_extract_init + ' -o mmcif' diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 2605424d..413cbe22 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 25/11/2020 #\n' + ' # Date: 09/12/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 0326eb9cb560fd1f9caeeaa3c205f76a0f4fbe4e Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 17 Dec 2020 21:45:31 +0000 Subject: [PATCH 091/358] v1.7.30 (17/12/2020) (#393) - bug fix in XChemDeposit --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 16 ++++++++-------- lib/XChemLog.py | 2 +- 4 files changed, 13 insertions(+), 10 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 97bcdb3f..57681b9f 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.30 (17/12/2020) +- bug fix in XChemDeposit + v1.7.29 (09/12/2020) - bug fix: syntax error in XChemDeposit - XChemDeposit: use default pdb_extract if no installation in XChemExplorer_dir diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 0716be84..83dcd334 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.29' + xce_object.xce_version = 'v1.7.30' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 0098e0a5..8fdb1606 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -726,7 +726,7 @@ def eventMTZ_exists(self,xtal): self.Logfile.insert('%s: checking if mtz of event maps exists' %xtal) eventMTZlist = [] eventMTZexists = False - if os.path.isfile('no_pandda_analysis_performed'): + if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: self.Logfile.warning('%s: found empty file named "no_pandda_analysis_performed" which suggests we will ignore event maps for this sample' %xtal) eventMTZexists = True elif self.ignore_event_map: @@ -957,7 +957,7 @@ def create_model_mmcif(self,xtal): pdb_extract_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/setup.sh') + '\n' pdb_extract_init += os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/bin/pdb_extract') else: - pdb_extract_init += 'pdb_extract' + pdb_extract_init = 'pdb_extract' if self.ground_state: refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] @@ -1174,7 +1174,7 @@ def create_sf_mmcif(self,xtal): else: os.chdir(os.path.join(self.projectDir, xtal)) - if os.path.isfile('no_pandda_analysis_performed'): + if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: mtzin = 'refine.mtz ' else: mtzin = 'refine.mtz ' + xtal + '.free.mtz ' @@ -1188,12 +1188,12 @@ def create_sf_mmcif(self,xtal): pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n' pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-prod/bin/sf_convert' else: - pdb_extract_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' if os.path.isfile(os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/bin/sf_convert')): + pdb_extract_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'), + 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' pdb_extract_init += os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/bin/sf_convert') else: - pdb_extract_init += 'sf_convert' + pdb_extract_init = 'sf_convert' Cmd = (pdb_extract_init + ' -o mmcif' @@ -1331,7 +1331,7 @@ def add_data_increment_to_apo_mmcif(self): def event_maps_exist_in_sf_mmcif(self,xtal): fileOK = False n_eventMTZ_found = -2 # set to -2 since first two data blocks are initial/final.mtz and data.mtz - if os.path.isfile('no_pandda_analysis_performed'): + if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: self.Logfile.warning('%s: no pandda analysis performed; skipping this step...' %xtal) fileOK = True else: @@ -1362,7 +1362,7 @@ def update_sf_mmcif_file(self,xtal): self.Logfile.insert('%s: reading wavelength from mtz file; lambda = %s' %(xtal,str(self.data_template_dict['radiation_wavelengths']))) - if os.path.isfile('no_pandda_analysis_performed'): + if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: self.Logfile.warning('%s: apparently not a pandda deposition; will skip this step...' %xtal) return None diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 413cbe22..60c92463 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 09/12/2020 #\n' + ' # Date: 17/12/2020 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 01b5f53023ac6cbe325be89677d20c6080447446 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 20 Jan 2021 22:20:50 +0100 Subject: [PATCH 092/358] v1.7.31 (20/01/2021) (#394) - bug fix: XChemDeposit - enable reading of staraniso .table1 file --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 8 ++++++++ lib/XChemLog.py | 2 +- 4 files changed, 13 insertions(+), 2 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 57681b9f..d88cdd4a 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.31 (20/01/2021) +- bug fix: XChemDeposit - enable reading of staraniso .table1 file + v1.7.30 (17/12/2020) - bug fix in XChemDeposit diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 83dcd334..a253ffd7 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.30' + xce_object.xce_version = 'v1.7.31' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 8fdb1606..a1b2452a 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -664,6 +664,10 @@ def aimless_logfile_exists(self,xtal): break # if n < 10: # print line + if not fileStatus: + if os.path.realpath('%s.log' %xtal).endswith('.table1'): + self.Logfile.warning('{0!s}: {1!s}.log seems to be a staraniso .table1 file'.format(xtal,xtal)) + fileStatus = True if not fileStatus: self.Logfile.warning('%s: this does not seem to be an AIMLESS logfile' %xtal) Filepath = os.path.relpath(os.path.realpath('%s.log' %xtal)) @@ -970,6 +974,10 @@ def create_model_mmcif(self,xtal): if 'AIMLESS' in line: isAimlessFile = True break + if not isAimlessFile: + if os.path.realpath('%s.log' %xtal).endswith('.table1'): + self.Logfile.warning('{0!s}: {1!s}.log seems to be a staraniso .table1 file'.format(xtal,xtal)) + isAimlessFile = True if not isAimlessFile: if os.path.isfile('aimless_dials.log'): aimless = 'aimless_dials.log' diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 60c92463..da6512a6 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 17/12/2020 #\n' + ' # Date: 20/01/2021 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 1c26b76c354059c364464e7622a2a05b2dfe21ee Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 25 Jan 2021 06:03:16 +0100 Subject: [PATCH 093/358] v1.7.32 (24/01/2021) (#395) - bug fix: XChemDeposit - enable reading of not symlinked logfiles --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemDeposit.py | 20 ++++++++++---------- lib/XChemLog.py | 2 +- 4 files changed, 15 insertions(+), 12 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index d88cdd4a..eb5f906a 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.32 (24/01/2021) +- bug fix: XChemDeposit - enable reading of not symlinked logfiles + v1.7.31 (20/01/2021) - bug fix: XChemDeposit - enable reading of staraniso .table1 file diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index a253ffd7..579cd993 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.31' + xce_object.xce_version = 'v1.7.32' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index a1b2452a..43b86ff7 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -681,19 +681,19 @@ def aimless_logfile_exists(self,xtal): self.run_aimless_merge_only(xtal,unmerged,APpath) fileStatus = True break - if not fileStatus: - os.chdir(os.path.join(self.projectDir,xtal)) - self.Logfile.insert('%s: trying to prepare a pseudo-aimless file from json file...' %xtal) - self.prepare_aimless_log(xtal) - if os.path.isfile('aimless_dials.log'): - self.Logfile.insert('%s: found aimless_dials.log' %xtal) - fileStatus = True - if not fileStatus: - self.Logfile.error('%s: cannot find a suitable AIMLESS logfile' %xtal) - self.add_to_errorList(xtal) else: self.Logfile.error('%s: %s is not a directory' %(xtal,APpath)) self.add_to_errorList(xtal) + if not fileStatus: + os.chdir(os.path.join(self.projectDir,xtal)) + self.Logfile.insert('%s: trying to prepare a pseudo-aimless file from json file...' %xtal) + self.prepare_aimless_log(xtal) + if os.path.isfile('aimless_dials.log'): + self.Logfile.insert('%s: found aimless_dials.log' %xtal) + fileStatus = True + if not fileStatus: + self.Logfile.error('%s: cannot find a suitable AIMLESS logfile' %xtal) + self.add_to_errorList(xtal) # fileStatus = True else: diff --git a/lib/XChemLog.py b/lib/XChemLog.py index da6512a6..c4bc3452 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 20/01/2021 #\n' + ' # Date: 24/01/2021 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 80aa2b28eb0ab676683159a98b9e18154eed4b14 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Tue, 2 Feb 2021 11:00:51 +0100 Subject: [PATCH 094/358] v1.7.33 (02/02/2021) (#398) - bug fix: enable RefinementParameters button in XChemCOOT --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemCootBuster.py | 3 ++- lib/XChemCootNew.py | 5 ++++- lib/XChemLog.py | 2 +- 5 files changed, 11 insertions(+), 4 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index eb5f906a..6425cca7 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.33 (02/02/2021) +- bug fix: enable RefinementParameters button in XChemCOOT + v1.7.32 (24/01/2021) - bug fix: XChemDeposit - enable reading of not symlinked logfiles diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 579cd993..28f8f883 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.32' + xce_object.xce_version = 'v1.7.33' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemCootBuster.py b/lib/XChemCootBuster.py index 244b0681..9f71f122 100755 --- a/lib/XChemCootBuster.py +++ b/lib/XChemCootBuster.py @@ -175,7 +175,8 @@ def __init__(self): 'NCS': '', 'TWIN': '', 'WATER': '', - 'LIGOCC': '' } + 'LIGOCC': '', + 'SANITY': '' } def StartGUI(self): diff --git a/lib/XChemCootNew.py b/lib/XChemCootNew.py index f8a13ab8..3e60410b 100755 --- a/lib/XChemCootNew.py +++ b/lib/XChemCootNew.py @@ -173,7 +173,10 @@ def __init__(self): 'BREF': ' bref ISOT\n', 'TLS': '', 'NCS': '', - 'TWIN': ''} + 'TWIN': '', + 'WATER': '', + 'LIGOCC': '', + 'SANITY': '' } def StartGUI(self): diff --git a/lib/XChemLog.py b/lib/XChemLog.py index c4bc3452..fb97134b 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 24/01/2021 #\n' + ' # Date: 02/02/2021 #\n' ' # #\n' ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' ' # tobias.krojer@sgc.ox.ac.uk #\n' From 7b0779387705ab37074d80f77baf22891eb56907 Mon Sep 17 00:00:00 2001 From: Graeme Winter Date: Tue, 23 Feb 2021 09:33:04 +0000 Subject: [PATCH 095/358] Putative patch set for bzip2 compressed mmCIF --- lib/XChemThread.py | 4 ++++ lib/XChemUtils.py | 17 ++++++++++++++++- 2 files changed, 20 insertions(+), 1 deletion(-) diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 74dc4483..792eaec1 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2654,6 +2654,10 @@ def copyMTZandLOGfiles(self,xtal,run,autoproc,mtzfile,logfile,proc_code): if mmcif.endswith('.mmcif'): self.Logfile.insert('%s: copying %s' %(xtal,mmcif)) os.system('/bin/cp ' + mmcif + ' .') + elif mmcif.endswith('.mmcif.bz2'): + self.Logfile.insert('%s: copying and decompressing %s' %(xtal,mmcif)) + os.system('/bin/cp ' + mmcif + ' .') + os.system('bzip2 -d ./' + mmcif) if os.path.isfile(mtzfile[mtzfile.rfind('/')+1:]) and not os.path.isfile(xtal+'.mtz'): os.symlink(mtzfile[mtzfile.rfind('/')+1:], xtal + '.mtz') if os.path.isfile(mtzfile[mtzfile.rfind('/') + 1:]): diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 456206ef..f2d05e1a 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -11,6 +11,9 @@ import json import time +import gzip +import bz2 + from datetime import datetime import gemmi @@ -27,6 +30,16 @@ import XChemDB import XChemLog +def open_decompress_file(filename, mode="rb"): + """Open file for reading, decompressing silently if necessary.""" + + if filename.endswith(".bz2"): + return bz2.BZ2File(filename, mode=mode) + + elif filename.endswith(".gz"): + return gzip.GzipFile(filename, mode=mode) + + return open(filename, mode=mode) class process: @@ -821,6 +834,8 @@ def json_logfile(self,logfile): mmcif_file = logfile.replace('LogFiles','DataFiles').replace(json_name,'xia2.mmcif') if os.path.isfile(mmcif_file): self.read_mmcif(mmcif_file) + elif os.path.isfile("%s.bz2" % mmcif_file): + self.read_mmcif("%s.bz2" % mmcif_file) def make_pseudo_aimless_log_from_json(self,logfile): self.json_logfile(logfile) @@ -854,7 +869,7 @@ def make_pseudo_aimless_log_from_json(self,logfile): def read_mmcif(self,mmcif): - for line in open(mmcif): + for line in open_decompress_file(mmcif): if line.startswith('_cell.angle_alpha '): self.aimless['DataProcessingAlpha'] = line.split()[1] elif line.startswith('_cell.angle_beta '): From 298580fd41831e4e1912e0f0afba0510dc9c5b32 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sat, 26 Jun 2021 00:33:22 +0200 Subject: [PATCH 096/358] v1.7.34 (25/06/2021) (#404) - added pdbx_audit_support category for funding agency now required for PDB deposition --- ChangeLog.txt | 3 + XChemExplorer.py | 169 +++++++++++++++++++++++++++- gui_scripts/settings_preferences.py | 2 +- lib/XChemDB.py | 15 +++ lib/XChemDeposit.py | 53 ++++++++- lib/XChemLog.py | 6 +- lib/XChemMain.py | 81 +++++++++++++ 7 files changed, 320 insertions(+), 9 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 6425cca7..ac91ea54 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.34 (25/06/2021) +- added pdbx_audit_support category for funding agency now required for PDB deposition + v1.7.33 (02/02/2021) - bug fix: enable RefinementParameters button in XChemCOOT diff --git a/XChemExplorer.py b/XChemExplorer.py index 7f20e98c..27bc7d16 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -1172,7 +1172,8 @@ def deposition_data(self): 'Molecule', 'Misc', 'Methods', - 'Software'] + 'Software', + 'Funding' ] deposit_tab_dict = {} for page in deposit_tab_list: @@ -2043,6 +2044,96 @@ def deposition_data(self): deposit_tab_dict['Software'][1].addLayout(vb) + ## Funding + + vb = QtGui.QVBoxLayout() + + frame = QtGui.QFrame() + frame.setFrameShape(QtGui.QFrame.StyledPanel) + + grid = QtGui.QGridLayout() + + grid.addWidget(QtGui.QLabel('Funding Organization'), 1, 0) + self.pdbx_funding_organization_one = QtGui.QLineEdit() + self.pdbx_funding_organization_one.setText('') + self.pdbx_funding_organization_one.setFixedWidth(700) + grid.addWidget(self.pdbx_funding_organization_one, 1, 1) + + grid.addWidget(QtGui.QLabel('Grant Number'), 2, 0) + self.pdbx_grant_number_one = QtGui.QLineEdit() + self.pdbx_grant_number_one.setText('') + self.pdbx_grant_number_one.setFixedWidth(700) + grid.addWidget(self.pdbx_grant_number_one, 2, 1) + + grid.addWidget(QtGui.QLabel('Country'), 3, 0) + self.pdbx_grant_country_one = QtGui.QComboBox() + for item in XChemMain.pdbx_country(): self.pdbx_grant_country_one.addItem(item) + grid.addWidget(self.pdbx_grant_country_one, 3, 1) + + frame.setLayout(grid) + vb.addWidget(frame) + + frame = QtGui.QFrame() + frame.setFrameShape(QtGui.QFrame.StyledPanel) + + grid = QtGui.QGridLayout() + + grid.addWidget(QtGui.QLabel('Funding Organization'), 1, 0) + self.pdbx_funding_organization_two = QtGui.QLineEdit() + self.pdbx_funding_organization_two.setText('') + self.pdbx_funding_organization_two.setFixedWidth(700) + grid.addWidget(self.pdbx_funding_organization_two, 1, 1) + + grid.addWidget(QtGui.QLabel('Grant Number'), 2, 0) + self.pdbx_grant_number_two = QtGui.QLineEdit() + self.pdbx_grant_number_two.setText('') + self.pdbx_grant_number_two.setFixedWidth(700) + grid.addWidget(self.pdbx_grant_number_two, 2, 1) + + grid.addWidget(QtGui.QLabel('Country'), 3, 0) + self.pdbx_grant_country_two = QtGui.QComboBox() + for item in XChemMain.pdbx_country(): self.pdbx_grant_country_two.addItem(item) + grid.addWidget(self.pdbx_grant_country_two, 3, 1) + + frame.setLayout(grid) + vb.addWidget(frame) + + frame = QtGui.QFrame() + frame.setFrameShape(QtGui.QFrame.StyledPanel) + + grid = QtGui.QGridLayout() + + grid.addWidget(QtGui.QLabel('Funding Organization'), 1, 0) + self.pdbx_funding_organization_three = QtGui.QLineEdit() + self.pdbx_funding_organization_three.setText('') + self.pdbx_funding_organization_three.setFixedWidth(700) + grid.addWidget(self.pdbx_funding_organization_three, 1, 1) + + grid.addWidget(QtGui.QLabel('Grant Number'), 2, 0) + self.pdbx_grant_number_three = QtGui.QLineEdit() + self.pdbx_grant_number_three.setText('') + self.pdbx_grant_number_three.setFixedWidth(700) + grid.addWidget(self.pdbx_grant_number_three, 2, 1) + + grid.addWidget(QtGui.QLabel('Country'), 3, 0) + self.pdbx_grant_country_three = QtGui.QComboBox() + for item in XChemMain.pdbx_country(): self.pdbx_grant_country_three.addItem(item) + grid.addWidget(self.pdbx_grant_country_three, 3, 1) + + frame.setLayout(grid) + vb.addWidget(frame) + + + vb.addStretch(1) + + deposit_tab_dict['Funding'][1].addLayout(vb) + + + + + + + vbox.addWidget(deposit_tab_widget) hbox = QtGui.QHBoxLayout() @@ -2297,11 +2388,59 @@ def update_deposit_input(self): index = self.phasing_software.findText(self.deposit_dict['phasing_software'], QtCore.Qt.MatchFixedString) self.phasing_software.setCurrentIndex(index) + self.pdbx_funding_organization_one.setText(self.deposit_dict['pdbx_funding_organization_one']) + self.pdbx_grant_number_one.setText(self.deposit_dict['pdbx_grant_number_one']) + index = self.pdbx_grant_country_one.findText( + self.deposit_dict['pdbx_grant_country_one'], QtCore.Qt.MatchFixedString) + self.pdbx_grant_country_one.setCurrentIndex(index) + + self.pdbx_funding_organization_two.setText(self.deposit_dict['pdbx_funding_organization_two']) + self.pdbx_grant_number_two.setText(self.deposit_dict['pdbx_grant_number_two']) + index = self.pdbx_grant_country_two.findText( + self.deposit_dict['pdbx_grant_country_two'], QtCore.Qt.MatchFixedString) + self.pdbx_grant_country_two.setCurrentIndex(index) + + self.pdbx_funding_organization_three.setText(self.deposit_dict['pdbx_funding_organization_three']) + self.pdbx_grant_number_three.setText(self.deposit_dict['pdbx_grant_number_three']) + index = self.pdbx_grant_country_three.findText( + self.deposit_dict['pdbx_grant_country_three'], QtCore.Qt.MatchFixedString) + self.pdbx_grant_country_three.setCurrentIndex(index) + except ValueError, e: # self.update_status_bar('Sorry, this is not a XChemExplorer deposit file!') self.update_log.error('file is not a valid .deposit file: ' + str(e)) def update_deposit_dict(self): + pdbx_funding_ordinal_one = '' + pdbx_funding_organization_one = '' + pdbx_grant_number_one = '' + pdbx_grant_country_one = '' + if str(self.pdbx_funding_organization_one.text()).replace(' ','') != '': + pdbx_funding_ordinal_one = '1' + pdbx_funding_organization_one = str(self.pdbx_funding_organization_one.text()) + pdbx_grant_number_one = str(self.pdbx_grant_number_one.text()) + pdbx_grant_country_one = str(self.pdbx_grant_country_one.currentText()) + + pdbx_funding_ordinal_two = '' + pdbx_funding_organization_two = '' + pdbx_grant_number_two = '' + pdbx_grant_country_two = '' + if str(self.pdbx_funding_organization_two.text()).replace(' ','') != '': + pdbx_funding_ordinal_two = '2' + pdbx_funding_organization_two = str(self.pdbx_funding_organization_two.text()) + pdbx_grant_number_two = str(self.pdbx_grant_number_two.text()) + pdbx_grant_country_two = str(self.pdbx_grant_country_two.currentText()) + + pdbx_funding_ordinal_three = '' + pdbx_funding_organization_three = '' + pdbx_grant_number_three = '' + pdbx_grant_country_three = '' + if str(self.pdbx_funding_organization_three.text()).replace(' ','') != '': + pdbx_funding_ordinal_three = '3' + pdbx_funding_organization_three = str(self.pdbx_funding_organization_three.text()) + pdbx_grant_number_three = str(self.pdbx_grant_number_three.text()) + pdbx_grant_country_three = str(self.pdbx_grant_country_three.currentText()) + self.deposit_dict = { 'contact_author_PI_salutation': str(self.contact_author_PI_salutation.text()), 'contact_author_PI_first_name': str(self.contact_author_PI_first_name.text()), @@ -2405,7 +2544,21 @@ def update_deposit_dict(self): 'data_collection_protocol': str(self.data_collection_protocol.text()), 'pdbx_starting_model': str(self.pdbx_starting_model.text()), 'data_integration_software': str(self.data_integration_software.currentText()), - 'phasing_software': str(self.phasing_software.currentText()) + 'phasing_software': str(self.phasing_software.currentText()), + + 'pdbx_funding_ordinal_one': pdbx_funding_ordinal_one, + 'pdbx_funding_organization_one': pdbx_funding_organization_one, + 'pdbx_grant_number_one': pdbx_grant_number_one, + 'pdbx_grant_country_one': pdbx_grant_country_one, + 'pdbx_funding_ordinal_two': pdbx_funding_ordinal_two, + 'pdbx_funding_organization_two': pdbx_funding_organization_two, + 'pdbx_grant_number_two': pdbx_grant_number_two, + 'pdbx_grant_country_two': pdbx_grant_country_two, + 'pdbx_funding_ordinal_three': pdbx_funding_ordinal_three, + 'pdbx_funding_organization_three': pdbx_funding_organization_three, + 'pdbx_grant_number_three': pdbx_grant_number_three, + 'pdbx_grant_country_three': pdbx_grant_country_three + } structure_author_name = '' @@ -2520,7 +2673,17 @@ def get_deposit_dict_template(self): 'data_integration_software': None, 'phasing_software': None, 'structure_author_name': None, - 'primary_citation_author_name': None + 'primary_citation_author_name': None, + + 'pdbx_funding_organization_one': '', + 'pdbx_grant_number_one': '', + 'pdbx_grant_country_one': '', + 'pdbx_funding_organization_two': '', + 'pdbx_grant_number_two': '', + 'pdbx_grant_country_two': '', + 'pdbx_funding_organization_three': '', + 'pdbx_grant_number_three': '', + 'pdbx_grant_country_three': '' } diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 28f8f883..7fd9231d 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.33' + xce_object.xce_version = 'v1.7.34' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemDB.py b/lib/XChemDB.py index d419696c..775db8d6 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -426,6 +426,21 @@ def __init__(self,data_source_file): ['data_integration_software', 'data_integration_software', 'TEXT'], ['phasing_software', 'phasing_software', 'TEXT'], + ['pdbx_funding_ordinal_one', 'pdbx_funding_ordinal_one', 'TEXT'], + ['pdbx_funding_organization_one', 'pdbx_funding_organization_one', 'TEXT'], + ['pdbx_grant_number_one', 'pdbx_grant_number_one', 'TEXT'], + ['pdbx_grant_country_one', 'pdbx_grant_country_one', 'TEXT'], + + ['pdbx_funding_ordinal_two', 'pdbx_funding_ordinal_two', 'TEXT'], + ['pdbx_funding_organization_two', 'pdbx_funding_organization_two', 'TEXT'], + ['pdbx_grant_number_two', 'pdbx_grant_number_two', 'TEXT'], + ['pdbx_grant_country_two', 'pdbx_grant_country_two', 'TEXT'], + + ['pdbx_funding_ordinal_three', 'pdbx_funding_ordinal_three', 'TEXT'], + ['pdbx_funding_organization_three', 'pdbx_funding_organization_three', 'TEXT'], + ['pdbx_grant_number_three', 'pdbx_grant_number_three', 'TEXT'], + ['pdbx_grant_country_three', 'pdbx_grant_country_three', 'TEXT'], + ['LastUpdated', 'LastUpdated', 'TEXT'], ['LastUpdated_by', 'LastUpdated_by', 'TEXT'] ] diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 43b86ff7..f1d3775d 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -309,8 +309,7 @@ def data_template_cif(self,depositDict): '_pdbx_struct_assembly_depositor_info.id 1\n' "_pdbx_struct_assembly_depositor_info.method_details PISA\n" '_pdbx_struct_assembly_depositor_info.oligomeric_count %s\n' %depositDict['biological_assembly_chain_number']+ - '#\n' - '#\n' + '#\n' ) return data_template_cif @@ -450,6 +449,8 @@ def run(self): if not self.create_model_mmcif(xtal): continue + self.add_funding_information(xtal) + # if not self.create_sf_mmcif(xtal): # continue @@ -502,6 +503,8 @@ def run(self): if not self.create_model_mmcif(xtal): continue + self.add_funding_information(xtal) + if not self.add_ligand_cif_to_model_mmcif(xtal): continue @@ -1126,6 +1129,52 @@ def update_model_mmcif_header(self,xtal): # elif '_refine.ls_d_res_low' in line and len(line.split()) == 2: # sys.stdout.write('_refine.ls_d_res_low {0!s}\n'.format(min(low_reso_list))) + def add_funding_information(self,xtal): + pdbx_funding_ordinal_one = self.data_template_dict['pdbx_funding_ordinal_one'] + if pdbx_funding_ordinal_one.lower().replace(' ', '').replace('none', '').replace('null', '') == '': + self.data_template_dict['pdbx_funding_ordinal_one'] = '' + self.data_template_dict['pdbx_funding_organization_one'] = '' + self.data_template_dict['pdbx_grant_number_one'] = '' + self.data_template_dict['pdbx_grant_country_one'] = '' + funding_one = '' + else: + funding_one = "%s '%s' '%s' '%s'\n" %(self.data_template_dict['pdbx_funding_ordinal_one'],self.data_template_dict['pdbx_funding_organization_one'],self.data_template_dict['pdbx_grant_number_one'],self.data_template_dict['pdbx_grant_country_one']) + + pdbx_funding_ordinal_two = self.data_template_dict['pdbx_funding_ordinal_two'] + if pdbx_funding_ordinal_two.lower().replace(' ', '').replace('none', '').replace('null', '') == '': + self.data_template_dict['pdbx_funding_ordinal_two'] = '' + self.data_template_dict['pdbx_funding_organization_two'] = '' + self.data_template_dict['pdbx_grant_number_two'] = '' + self.data_template_dict['pdbx_grant_country_two'] = '' + funding_two = '' + else: + funding_two = "%s '%s' '%s' '%s'\n" %(self.data_template_dict['pdbx_funding_ordinal_two'],self.data_template_dict['pdbx_funding_organization_two'],self.data_template_dict['pdbx_grant_number_two'],self.data_template_dict['pdbx_grant_country_two']) + + pdbx_funding_ordinal_three = self.data_template_dict['pdbx_funding_ordinal_three'] + if pdbx_funding_ordinal_three.lower().replace(' ', '').replace('none', '').replace('null', '') == '': + self.data_template_dict['pdbx_funding_ordinal_three'] = '' + self.data_template_dict['pdbx_funding_organization_three'] = '' + self.data_template_dict['pdbx_grant_number_three'] = '' + self.data_template_dict['pdbx_grant_country_three'] = '' + funding_three = '' + else: + funding_three = "%s '%s' '%s' '%s'\n" %(self.data_template_dict['pdbx_funding_ordinal_three'],self.data_template_dict['pdbx_funding_organization_three'],self.data_template_dict['pdbx_grant_number_three'],self.data_template_dict['pdbx_grant_country_three']) + + funding_info = ( + '#\n' + 'loop\n' + '_pdbx_audit_support.ordinal \n' + '_pdbx_audit_support.funding_organization \n' + '_pdbx_audit_support.grant_number \n' + '_pdbx_audit_support.country \n' + + funding_one + funding_two + funding_three + + '#\n' + ) + + f = open(xtal + '.mmcif', 'a') + f.write(funding_info) + f.close() + def add_ligand_cif_to_model_mmcif(self,xtal): filestatus = False self.Logfile.insert('%s: looking for ligand restraints file...' %xtal) diff --git a/lib/XChemLog.py b/lib/XChemLog.py index fb97134b..ebd988ec 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,10 +26,10 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 02/02/2021 #\n' + ' # Date: 25/06/2021 #\n' ' # #\n' - ' # Authors: Tobias Krojer, Structural Genomics Consortium, Oxford, UK #\n' - ' # tobias.krojer@sgc.ox.ac.uk #\n' + ' # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n' + ' # tobias.krojer@maxiv.lu.se #\n' ' # #\n' ' # Rachael Skyner, Diamond Light Source, UK #\n' ' # rachael.skyner@diamond.ac.uk #\n' diff --git a/lib/XChemMain.py b/lib/XChemMain.py index a15fa095..0ec14c9b 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -768,6 +768,87 @@ def pdbx_keywords(): return keywords +def pdbx_country(): + + countries = [ + 'United Kingdom', + 'United States', + 'Japan', + 'Albania', + 'Andorra', + 'Argentina', + 'Armenia', + 'Australia', + 'Austria', + 'Azerbaijan', + 'Bahamas', + 'Bangladesh', + 'Barbados', + 'Belarus', + 'Belgium', + 'Brazil', + 'Bulgaria', + 'Canada', + 'Chile', + 'China', + 'Croatia', + 'Cuba', + 'Cyprus', + 'Czech Republic', + 'Denmark', + 'Estonia', + 'Finland', + 'France', + 'Germany', + 'Greece', + 'Hungary', + 'Iceland', + 'India', + 'Indonesia', + 'Iran, Islamic Republic Of', + 'Iraq', + 'Ireland', + 'Israel', + 'Italy', + 'Jamaica', + 'Jordan', + 'Kazakhstan', + 'Kenya', + 'Kiribati', + 'Korea, Republic Of', + 'Latvia', + 'Lithuania', + 'Luxembourg', + 'Malta', + 'Mexico', + 'Netherlands', + 'New Zealand', + 'Norway', + 'Pakistan', + 'Paraguay', + 'Peru', + 'Philippines', + 'Poland', + 'Portugal', + 'Romania', + 'Russian Federation', + 'Serbia', + 'Singapore', + 'Slovakia', + 'Slovenia', + 'South Africa', + 'Spain', + 'Sweden', + 'Switzerland', + 'Taiwan', + 'Thailand', + 'Turkey', + 'Ukraine', + 'United Arab Emirates', + 'Uruguay' + ] + return countries + def html_header(): header = ( From 5128a25302312c9a55fb9c2d1e667420c98ccfdd Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 13 Oct 2021 23:59:25 +0200 Subject: [PATCH 097/358] v1.7.35 (13/10/2021) (#408) - ignore json merging statistics and xia2.mmcif if aimless.log exists --- ChangeLog.txt | 3 +++ XChemExplorer.py | 2 ++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemThread.py | 6 ++++++ 5 files changed, 13 insertions(+), 2 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index ac91ea54..0a9dd9d0 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.7.35 (13/10/2021) +- ignore json merging statistics and xia2.mmcif if aimless.log exists + v1.7.34 (25/06/2021) - added pdbx_audit_support category for funding agency now required for PDB deposition diff --git a/XChemExplorer.py b/XChemExplorer.py index 27bc7d16..b2116036 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -5140,6 +5140,8 @@ def update_outcome_datasets_summary_table(self, sample, outcome): def user_update_selected_autoproc_datasets_summary_table(self): for key in self.data_collection_column_three_dict: if self.data_collection_column_three_dict[key][0] == self.sender(): + self.update_log.insert('here: ' + self.sender()) + self.update_log.insert('herere' + str(self.data_collection_column_three_dict)) dbTmp = self.xtal_db_dict[key] stage = dbTmp['RefinementOutcome'].split()[0] print('===>', key, stage) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 7fd9231d..4fcb6578 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.34' + xce_object.xce_version = 'v1.7.35' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index ebd988ec..195a5ae6 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 25/06/2021 #\n' + ' # Date: 13/10/2021 #\n' ' # #\n' ' # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n' ' # tobias.krojer@maxiv.lu.se #\n' diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 792eaec1..b8e60dd2 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2681,6 +2681,12 @@ def copyMTZandLOGfiles(self,xtal,run,autoproc,mtzfile,logfile,proc_code): os.symlink(logfile[logfile.rfind('/')+1:], xtal + '.log') if os.path.isfile(logfile[logfile.rfind('/') + 1:]): logNew=os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code, logfile[logfile.rfind('/') + 1:]) + # September 2021: xia2 does not also output a xia2.mmcif and json merging statistics file, even if aimless was used + # for scaling, however, the xia2.mmcif file is differently formatted than the one from dials + # hence, if xtal.log file already exists, use this one + if 'aimless' in os.readlink(xtal + '.log'): + logNew = os.path.join(self.projectDir, xtal, 'autoprocessing', + self.visit + '-' + run + autoproc + '_' + proc_code, xtal + '.log') return mtzNew,logNew def makeJPGdir(self,xtal,run): From 9edcee4dc86bb554bcb12e1842dac33247efcd30 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 14 Oct 2021 21:40:29 +0200 Subject: [PATCH 098/358] v1.7.36 (13/10/2021) (#409) - bug fix: manual selection of different auto-processing results with same pipeline - removed obsolete paths used for parsing of auto-processing results --- ChangeLog.txt | 4 +++ XChemExplorer.py | 15 +++++++-- gui_scripts/settings_preferences.py | 7 ++-- lib/XChemDB.py | 24 ++++++++++++++ lib/XChemThread.py | 51 ++++++++++++++++++++++++----- lib/XChemUtils.py | 8 ++--- 6 files changed, 90 insertions(+), 19 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 0a9dd9d0..fbb20d38 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.7.36 (13/10/2021) +- bug fix: manual selection of different auto-processing results with same pipeline +- removed obsolete paths used for parsing of auto-processing results + v1.7.35 (13/10/2021) - ignore json merging statistics and xia2.mmcif if aimless.log exists diff --git a/XChemExplorer.py b/XChemExplorer.py index b2116036..84b7d045 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -4994,7 +4994,8 @@ def update_row_in_table(self,sample,row,db_dict,table,columns_to_show): # cell_text.setText('') cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) table.setItem(row, column, cell_text) - + print('row: {0!s} column: {1!s} value: {2!s} header: {3!s}'.format(row, column, cell_text, header[0])) + print('column_name {0!s}'.format(column_name)) def populate_datasets_summary_table_NEW(self): self.status_bar.showMessage( @@ -5055,7 +5056,8 @@ def show_results_from_all_pipelines(self): self.update_row_in_table(xtal, row, db_dict, self.data_collection_table, self.data_collection_table_columns) if selectedResultDict['DataCollectionVisit'] == db_dict['DataCollectionVisit'] \ and selectedResultDict['DataCollectionRun'] == db_dict['DataCollectionRun'] \ - and selectedResultDict['DataProcessingProgram'] == db_dict['DataProcessingProgram']: + and selectedResultDict['DataProcessingProgram'] == db_dict['DataProcessingProgram'] \ + and selectedResultDict['DataProcessingScore'] == db_dict['DataProcessingScore']: self.current_row = row self.data_collection_table.selectRow(row) self.data_collection_table.cellClicked.connect(self.select_different_autoprocessing_result) @@ -5096,8 +5098,15 @@ def select_different_autoprocessing_result(self): visit = self.data_collection_table.item(selected_row, 1).text() run = self.data_collection_table.item(selected_row, 2).text() autoproc = self.data_collection_table.item(selected_row, 3).text() + score = self.data_collection_table.item(selected_row, 12).text() + for q in range(13): + try: + print('--> {0!s}: {1!s}'.format(q, self.data_collection_table.item(selected_row, q).text())) + except AttributeError: + print('--> {0!s}: None'.format(q)) # get db_dict from collectionTable for visit, run, autoproc - dbDict = self.db.get_db_dict_for_visit_run_autoproc(xtal,visit,run,autoproc) +# dbDict = self.db.get_db_dict_for_visit_run_autoproc(xtal,visit,run,autoproc) + dbDict = self.db.get_db_dict_for_visit_run_autoproc_score(xtal, visit, run, autoproc, score) dbDict['DataProcessingAutoAssigned'] = 'False' self.update_log.insert('%s: changing selected autoprocessing result to %s %s %s' %(xtal,visit,run,autoproc)) # xtal is QString -> str(xtal) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 4fcb6578..e27ee52b 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.35' + xce_object.xce_version = 'v1.7.36' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -339,8 +339,9 @@ def tables(self, xce_object): 'Rmerge\nLow', 'Completeness\nOverall', 'DataProcessing\nUnitCell', - 'DataProcessing\nRfree' - 'DataProcessing\nScore'] + 'DataProcessing\nRfree', + 'DataProcessing\nScore' + ] diff --git a/lib/XChemDB.py b/lib/XChemDB.py index 775db8d6..43a0631c 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -659,9 +659,11 @@ def get_db_dict_for_sample(self,sampleID): connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent cursor = connect.cursor() cursor.execute("select * from mainTable where CrystalName='{0!s}';".format(sampleID)) + print("SQLITE: select * from mainTable where CrystalName='{0!s}';".format(sampleID)) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() + print("DATA: {0!s}".format(data)) for n,item in enumerate(data[0]): db_dict[header[n]]=str(item) return db_dict @@ -1870,6 +1872,28 @@ def get_db_dict_for_visit_run_autoproc(self,xtal,visit,run,autoproc): db_dict[header[n]] = str(item) return db_dict + def get_db_dict_for_visit_run_autoproc_score(self,xtal,visit,run,autoproc,score): + db_dict = {} + header=[] + connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + cursor = connect.cursor() + sqlite = ( 'select * ' + 'from collectionTable ' + "where CrystalName ='%s' and" %xtal + + " DataCollectionVisit = '%s' and" %visit + + " DataCollectionRun = '%s' and" %run + + " DataProcessingProgram = '%s' and" %autoproc + + " DataProcessingScore = '%s'" %score ) + cursor.execute(sqlite) + for column in cursor.description: + header.append(column[0]) + data = cursor.fetchall() + print('SQLITE: {0!s}'.format(sqlite)) + print('DATA: {0!s}'.format(data)) + for n, item in enumerate(data[0]): + db_dict[header[n]] = str(item) + return db_dict + def xtals_collected_during_visit_as_dict(self,visitID): # first get all collected xtals as list if isinstance(visitID,list): # for Agamemnon data structure diff --git a/lib/XChemThread.py b/lib/XChemThread.py index b8e60dd2..4f89d255 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -2537,12 +2537,12 @@ def __init__(self, [ os.path.join('multi-xia2', '*'), os.path.join('LogFiles', '*aimless.log'), os.path.join('DataFiles', '*free.mtz')], - [ os.path.join('autoPROC', '*'), - '*aimless.log', - '*truncate-unique.mtz'], - [ os.path.join('autoPROC', '*'), - '*staraniso_alldata-unique.table1', - '*staraniso_alldata-unique.mtz'], +# [ os.path.join('autoPROC', '*'), +# '*aimless.log', +# '*truncate-unique.mtz'], +# [ os.path.join('autoPROC', '*'), +# '*staraniso_alldata-unique.table1', +# '*staraniso_alldata-unique.mtz'], [ os.path.join('autoPROC'), '*aimless.log', '*truncate-unique.mtz'], @@ -2555,11 +2555,44 @@ def __init__(self, [ os.path.join('autoPROC-*'), '*summary.tar.gz', '*staraniso_alldata-unique.mtz'], - [ os.path.join('*'), - os.path.join('LogFiles', '*aimless.log'), - os.path.join('DataFiles', '*free.mtz')] +# [ os.path.join('*'), +# os.path.join('LogFiles', '*aimless.log'), +# os.path.join('DataFiles', '*free.mtz')] ] +# self.toParse = [ +# [ os.path.join('*'), +# os.path.join('LogFiles', '*aimless.log'), +# os.path.join('DataFiles', '*free.mtz')], +# [ os.path.join('*'), +# os.path.join('LogFiles', '*merging-statistics.json'), +# os.path.join('DataFiles', '*free.mtz')], +# [ os.path.join('multi-xia2', '*'), +# os.path.join('LogFiles', '*aimless.log'), +# os.path.join('DataFiles', '*free.mtz')], +# [ os.path.join('autoPROC', '*'), +# '*aimless.log', +# '*truncate-unique.mtz'], +# [ os.path.join('autoPROC', '*'), +# '*staraniso_alldata-unique.table1', +# '*staraniso_alldata-unique.mtz'], +# [ os.path.join('autoPROC'), +# '*aimless.log', +# '*truncate-unique.mtz'], +# [ os.path.join('autoPROC'), +# '*summary.tar.gz', # staraniso_alldata-unique.table1 only available in tar archive +# '*staraniso_alldata-unique.mtz'], +# [ os.path.join('autoPROC-*'), +# '*aimless.log', +# '*truncate-unique.mtz'], +# [ os.path.join('autoPROC-*'), +# '*summary.tar.gz', +# '*staraniso_alldata-unique.mtz'], +# [ os.path.join('*'), +# os.path.join('LogFiles', '*aimless.log'), +# os.path.join('DataFiles', '*free.mtz')] +# ] + # self.toParse = [ # [ os.path.join('xia2', '*'), # os.path.join('LogFiles', '*aimless.log'), diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index f2d05e1a..7f859e2b 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -601,11 +601,11 @@ def read_aimless_logfile(self,logfile): if 'fast_dp' in logfile: self.aimless['DataProcessingProgram']='fast_dp' elif '3d-run' in logfile: - self.aimless['DataProcessingProgram']='xia2 3d' + self.aimless['DataProcessingProgram']='xia2-3d' elif '3dii-run' in logfile: - self.aimless['DataProcessingProgram']='xia2 3dii' - elif 'xia2' in logfile: - self.aimless['DataProcessingProgram'] = 'xia2' + self.aimless['DataProcessingProgram']='xia2-3dii' + elif 'xia2-3dii' in logfile: + self.aimless['DataProcessingProgram'] = 'xia2-3dii' elif 'dials-run' in logfile: self.aimless['DataProcessingProgram']='dials' elif 'dials' in logfile: From 42ec9bc8d9bd99fcfb4a62c61043597001b7e888 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 20 Jan 2022 11:51:42 +0100 Subject: [PATCH 099/358] v1.8.2 (20/01/2022) (#411) v1.8.2 (20/01/2022) - added 'Porphyromonas gingivalis' to NCBI taxonomy id - fixed SARS-CoV-2 name in NCBI taxonomy id table - bug fix: XChemDeposit - added missing underscore to loop statement in _pdbx_audit_support block - XChemDeposit: issue warning and do not add empty xtal string to error list - bug fix: XChemDeposit - recognition of staraniso logfile v1.8.1 (19/01/2022) - fix: event map to sf conversion; ignore existing ligand pdb files v1.8.0 (17/12/2021) - added feature for working with cocktails/ combi-soaks: multiple compounds/ smiles separated by semi-colon in db are recognised during restraint generation --- ChangeLog.txt | 13 +++ gui_scripts/settings_preferences.py | 2 +- helpers/merge_ligand_cif_files.py | 17 +++ lib/XChemDeposit.py | 15 ++- lib/XChemLog.py | 5 +- lib/XChemMain.py | 6 +- lib/XChemUtils.py | 169 ++++++++++++++++------------ 7 files changed, 146 insertions(+), 81 deletions(-) create mode 100644 helpers/merge_ligand_cif_files.py diff --git a/ChangeLog.txt b/ChangeLog.txt index fbb20d38..c2c25afb 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,16 @@ +v1.8.2 (20/01/2022) +- added 'Porphyromonas gingivalis' to NCBI taxonomy id +- fixed SARS-CoV-2 name in NCBI taxonomy id table +- bug fix: XChemDeposit - added missing underscore to loop statement in _pdbx_audit_support block +- XChemDeposit: issue warning and do not add empty xtal string to error list +- bug fix: XChemDeposit - recognition of staraniso logfile + +v1.8.1 (19/01/2022) +- fix: event map to sf conversion; ignore existing ligand pdb files + +v1.8.0 (17/12/2021) +- added feature for working with cocktails/ combi-soaks: multiple compounds/ smiles separated by semi-colon in db are recognised during restraint generation + v1.7.36 (13/10/2021) - bug fix: manual selection of different auto-processing results with same pipeline - removed obsolete paths used for parsing of auto-processing results diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index e27ee52b..d174b8fc 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.7.36' + xce_object.xce_version = 'v1.8.2' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/helpers/merge_ligand_cif_files.py b/helpers/merge_ligand_cif_files.py new file mode 100644 index 00000000..a3c050da --- /dev/null +++ b/helpers/merge_ligand_cif_files.py @@ -0,0 +1,17 @@ +import os +import glob +import sys + +def merge_cifs(cpdDir): + os.chdir(cpdDir) + out = '' + for cif in glob.glob('*.cif'): + for line in open(cif): + out += line + f = open('merged.cif', 'w') + f.write(out) + f.close() + +if __name__ == '__main__': + cpdDir = sys.argv[1] + merge_cifs(cpdDir) \ No newline at end of file diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index f1d3775d..9258a0fd 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -849,8 +849,11 @@ def check_lig_cc(self,log): def add_to_errorList(self,xtal): - if xtal not in self.errorList: - self.errorList.append(xtal) + if xtal.replace(' ','') == '': + self.Logfile.warning('trying to add xtal to error list, but xtal string is empty') + else: + if xtal not in self.errorList: + self.errorList.append(xtal) def print_errorlist(self): if not self.errorList: @@ -968,6 +971,7 @@ def create_model_mmcif(self,xtal): if self.ground_state: refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] + self.Logfile.insert('ground_state deposition reference dataset: {0!s}'.format(refXtal)) aimless = os.path.join(self.logDir,refXtal,refXtal+'.log') else: aimless = '%s.log' %xtal @@ -978,9 +982,12 @@ def create_model_mmcif(self,xtal): isAimlessFile = True break if not isAimlessFile: - if os.path.realpath('%s.log' %xtal).endswith('.table1'): + self.Logfile.warning('processing log file does not seem to be an aimless file: {0!s}'.format(aimless)) + self.Logfile.insert('realpath of processing logfile: {0!s}'.format(os.path.realpath(aimless))) + if os.path.realpath(aimless).endswith('.table1'): self.Logfile.warning('{0!s}: {1!s}.log seems to be a staraniso .table1 file'.format(xtal,xtal)) isAimlessFile = True + self.Logfile.warning('it does not seem to originate from staraniso either') if not isAimlessFile: if os.path.isfile('aimless_dials.log'): aimless = 'aimless_dials.log' @@ -1162,7 +1169,7 @@ def add_funding_information(self,xtal): funding_info = ( '#\n' - 'loop\n' + 'loop_\n' '_pdbx_audit_support.ordinal \n' '_pdbx_audit_support.funding_organization \n' '_pdbx_audit_support.grant_number \n' diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 195a5ae6..7f93ed58 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,14 +26,11 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 13/10/2021 #\n' + ' # Date: 20/01/2022 #\n' ' # #\n' ' # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n' ' # tobias.krojer@maxiv.lu.se #\n' ' # #\n' - ' # Rachael Skyner, Diamond Light Source, UK #\n' - ' # rachael.skyner@diamond.ac.uk #\n' - ' # #\n' ' #######################################################################\n' '\n' ) diff --git a/lib/XChemMain.py b/lib/XChemMain.py index 0ec14c9b..695c3beb 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -641,8 +641,10 @@ def NCBI_taxonomy_ID(): '7108': 'SPODOPTERA FRUGIPERDA', '5693 ': 'Trypanosoma cruzi', '1508227': 'BAT SARS-LIKE CORONAVIRUS', - '2697049': 'COVID-19', - '562': 'Escherichia coli' } + '2697049': 'SARS-CoV-2', + '562': 'Escherichia coli', + '837': 'Porphyromonas gingivalis' + } return taxonomy_dict diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 7f859e2b..9b0340c3 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -233,68 +233,105 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft if not external_software['qsub_array']: header='#PBS -joe -N xce_acedrg\n' - # check if CompoundSMILEScovalent field is not Null - # CompoundSMILESproduct can be used to create only a CIF file for the product to make fitting easier - # however, the complete smiles string will be used to make the png file - productSmiles = None - db = XChemDB.data_source(os.path.join(database_directory,data_source_file)) - sql = "select CompoundSMILESproduct from mainTable where CrystalName = '%s'" %sample - query = db.execute_statement(sql) - productSmiles = query[0][0] - if str(productSmiles).replace(' ','') == '': - productSmiles = smiles - elif 'none' in str(productSmiles).lower(): - productSmiles = smiles - elif 'null' in str(productSmiles).lower(): - productSmiles = smiles - else: - productSmiles = str(productSmiles) - - software='' - if restraints_program=='acedrg': - if os.getcwd().startswith('/dls'): - software += 'module load ccp4\n' - if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): - software+='acedrg --res LIG -c ../old.cif -o {0!s}\n'.format((compoundID.replace(' ',''))) - else: - software+='acedrg --res LIG -i "{0!s}" -o {1!s}\n'.format(productSmiles, compoundID.replace(' ','')) - elif restraints_program=='phenix.elbow': - if os.getcwd().startswith('/dls'): - software += 'module load phenix\n' - if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): - software+='phenix.elbow --file=../old.cif --id LIG --output {0!s}\n'.format((compoundID.replace(' ',''))) - else: - software+='phenix.elbow --smiles="{0!s}" --id LIG --output {1!s}\n'\ - .format(productSmiles, compoundID.replace(' ','')) - elif restraints_program=='grade': - if os.getcwd().startswith('/dls'): - software += 'module load buster\n' - software += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' - software+="export BDG_TOOL_OBABEL='none'\n" - if external_software['mogul']: - mogul = '' + # check for combisoaks/ cocktails + # note: compoundIDs and smiles are semi-colon separated + if len(compoundID.split(';')) > 1: + Logfile.insert('looks like you are working with cocktails; found the following IDs and smiles:') + if len(compoundID.split(';')) != len(smiles.split(';')): + Logfile.error('Number of compoundIDs and SMILES does not match:') + Logfile.error('N(compoundID): {0!s} -> {1!s}'.format(len(compoundID.split(';')), compoundID.split(';'))) + Logfile.error('N(SMILES): {0!s} -> {1!s}'.format(len(smiles.split(';')), smiles.split(';'))) + Logfile.error('aborting...') + return else: - mogul = '-nomogul' - if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): - software+='grade -resname LIG {0!s} -in ../old.cif -ocif {1!s}.cif -opdb {2!s}.pdb\n'\ - .format(mogul, compoundID.replace(' ',''), compoundID.replace(' ','')) + software = '' + if restraints_program == 'acedrg': + if os.getcwd().startswith('/dls'): + software += 'module load ccp4\n' + elif restraints_program == 'phenix.elbow': + if os.getcwd().startswith('/dls'): + software += 'module load phenix\n' + elif restraints_program == 'grade': + if os.getcwd().startswith('/dls'): + software += 'module load buster\n' + software += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' + software += "export BDG_TOOL_OBABEL='none'\n" + + for i in range(len(compoundID.split(';'))): + Logfile.insert('{0!s} - {1!s}'.format(compoundID.split(';')[i], smiles.split(';')[i])) + cID = 'L' + (2 - len(str(i))) * '0' + str(i) + if restraints_program=='acedrg': + software += 'acedrg --res {0!s} -i "{1!s}" -o {2!s}\n'.format(cID, smiles.split(';')[i], compoundID.split(';')[i].replace(' ', '')) + elif restraints_program=='phenix.elbow': + software+='phenix.elbow --smiles="{0!s}" --id {1!s}} --output {2!s}\n'.format(smiles.split(';')[i], cID, compoundID.split(';')[i].replace(' ','')) + elif restraints_program=='grade': + if external_software['mogul']: + mogul = '' + else: + mogul = '-nomogul' + software+='grade -resname {0!s} {1!s} "{2!s}" -ocif {3!s}.cif -opdb {4!s}.pdb\n'.format( + cID, mogul, smiles.split(';')[i], compoundID.split(';')[i].replace(' ',''), compoundID.split(';')[i].replace(' ','')) + + else: + # check if CompoundSMILEScovalent field is not Null + # CompoundSMILESproduct can be used to create only a CIF file for the product to make fitting easier + # however, the complete smiles string will be used to make the png file + productSmiles = None + db = XChemDB.data_source(os.path.join(database_directory,data_source_file)) + sql = "select CompoundSMILESproduct from mainTable where CrystalName = '%s'" %sample + query = db.execute_statement(sql) + productSmiles = query[0][0] + if str(productSmiles).replace(' ','') == '': + productSmiles = smiles + elif 'none' in str(productSmiles).lower(): + productSmiles = smiles + elif 'null' in str(productSmiles).lower(): + productSmiles = smiles else: - software+='grade -resname LIG {0!s} "{1!s}" -ocif {2!s}.cif -opdb {3!s}.pdb\n'\ - .format(mogul, productSmiles, compoundID.replace(' ',''), compoundID.replace(' ','')) + productSmiles = str(productSmiles) + + software='' + if restraints_program=='acedrg': + if os.getcwd().startswith('/dls'): + software += 'module load ccp4\n' + if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): + software+='acedrg --res LIG -c ../old.cif -o {0!s}\n'.format((compoundID.replace(' ',''))) + else: + software+='acedrg --res LIG -i "{0!s}" -o {1!s}\n'.format(productSmiles, compoundID.replace(' ','')) + elif restraints_program=='phenix.elbow': + if os.getcwd().startswith('/dls'): + software += 'module load phenix\n' + if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): + software+='phenix.elbow --file=../old.cif --id LIG --output {0!s}\n'.format((compoundID.replace(' ',''))) + else: + software+='phenix.elbow --smiles="{0!s}" --id LIG --output {1!s}\n'\ + .format(productSmiles, compoundID.replace(' ','')) + elif restraints_program=='grade': + if os.getcwd().startswith('/dls'): + software += 'module load buster\n' + software += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' + software+="export BDG_TOOL_OBABEL='none'\n" + if external_software['mogul']: + mogul = '' + else: + mogul = '-nomogul' + if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): + software+='grade -resname LIG {0!s} -in ../old.cif -ocif {1!s}.cif -opdb {2!s}.pdb\n'\ + .format(mogul, compoundID.replace(' ',''), compoundID.replace(' ','')) + else: + software+='grade -resname LIG {0!s} "{1!s}" -ocif {2!s}.cif -opdb {3!s}.pdb\n'\ + .format(mogul, productSmiles, compoundID.replace(' ',''), compoundID.replace(' ','')) + + # merge all compound CIFs into 1 file called merged.cif + software += '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/merge_ligand_cif_files.py {0!s}\n'.format(os.path.join(initial_model_directory, sample, 'compound')) + + # Removal of the hydrogen atoms in PDB files is required for REFMAC 5 run. With hydrogens some ligands fail to # pass the external restraints in pandda.giant.make_restraints. # Copy the file with hydrogens to retain in case needed check_stereochemistry = '' -# copy_with_hydrogens = 'cp {0!s}.pdb {0!s}_with_H.pdb'.format(compoundID.replace(' ', '')) -# -# strip_hydrogens = 'phenix.reduce {0!s}.pdb -trim > {0!s}_tmp.pdb'.format(compoundID.replace(' ', '')) -# -# module = '' -# if os.path.isdir('/dls'): -# module = 'module load mx\n' - Cmds = ( header + @@ -316,17 +353,6 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft '\n' + software + '\n' -# '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/assign_stereochemistry.py {0!s} {1!s} {2!s}' -# .format(compoundID.replace(' ',''),os.path.join(initial_model_directory,sample), os.path.join(database_directory,data_source_file)) + -# '\n' -# + copy_with_hydrogens + -# '\n' -# + strip_hydrogens + -# '\n' -# 'mv {0!s}_tmp.pdb {0!s}.pdb'.format(compoundID.replace(' ', '')) + -# '\n' -# 'rm -f {0!s}_tmp.pdb'.format(compoundID.replace(' ', '')) + -# '\n' 'cd ' + os.path.join(initial_model_directory, sample) + '\n' 'ln -s compound/%s.cif .\n' % compoundID.replace(' ', '') + @@ -344,8 +370,8 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft os.chdir(ccp4_scratch_directory) Logfile.insert('creating ACEDRG shell script for {0!s},{1!s} in {2!s}'.format(sample, compoundID, ccp4_scratch_directory)) - print Cmds - print 'ccp4_scratch',ccp4_scratch_directory +# print Cmds +# print 'ccp4_scratch',ccp4_scratch_directory f = open('xce_{0!s}_{1!s}.sh'.format(restraints_program,str(counter)),'w') f.write(Cmds) f.close() @@ -1946,9 +1972,12 @@ def save_residues_with_resname(self,outDir,resname): ligName = (l[0] + '-' + l[2] + '-' + l[1] + '.pdb').replace(' ', '') ligList.append(ligName) - f = open(os.path.join(outDir,ligName), "w") - f.write(hierarchy_lig.as_pdb_string(crystal_symmetry=self.pdb_inp.crystal_symmetry())) - f.close() + try: + f = open(os.path.join(outDir,ligName), "w") + f.write(hierarchy_lig.as_pdb_string(crystal_symmetry=self.pdb_inp.crystal_symmetry())) + f.close() + except IOError: + print('ERROR: {0!s} exists; skipping...') return ligList From a0060e0041c3886f0ed3e2b8c40d3a7940420714 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Sat, 11 Jun 2022 16:39:43 +0200 Subject: [PATCH 100/358] v1.9.0 (22/04/2022) (#413) - add functionality for running PanDDA2 at Diamond Light Source - fixed hyperlink to PanDDA manual --- ChangeLog.txt | 4 ++ XChemExplorer.py | 22 +++--- gui_scripts/pandda_tab.py | 10 ++- gui_scripts/settings_preferences.py | 7 +- lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 106 ++++++++++++++++++++++++---- 6 files changed, 127 insertions(+), 24 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index c2c25afb..2c2027de 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.9.0 (22/04/2022) +- add functionality for running PanDDA2 at Diamond Light Source +- fixed hyperlink to PanDDA manual + v1.8.2 (20/01/2022) - added 'Porphyromonas gingivalis' to NCBI taxonomy id - fixed SARS-CoV-2 name in NCBI taxonomy id table diff --git a/XChemExplorer.py b/XChemExplorer.py index 84b7d045..47b8ff45 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -2180,16 +2180,16 @@ def update_database_with_labelInfo(self): for n,l in enumerate(self.labelList): label = str(l[0].text()) description = str(l[1].text()) - print "update labelTable set Label='%s',Description='%s' where ID=%s" %(label,description,str(n+1)) +# print "update labelTable set Label='%s',Description='%s' where ID=%s" %(label,description,str(n+1)) self.db.execute_statement("update labelTable set Label='%s',Description='%s' where ID=%s" %(label,description,str(n+1))) - print label,description +# print label,description def load_deposit_config_file(self): file_name_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Open file', self.current_directory, '*.deposit') file_name = tuple(file_name_temp)[0] self.deposit_dict = pickle.load(open(file_name, "rb")) - print self.deposit_dict +# print self.deposit_dict for key in self.get_deposit_dict_template(): if key not in self.deposit_dict: self.update_log.warning('field not in .deposit file: ' + str(key)) @@ -2992,7 +2992,7 @@ def open_config_file(self): self.update_log.insert('Sorry, this is not a XChemExplorer config file!') except: - print "Unexpected error:", sys.exc_info()[0] + print("Unexpected error:", sys.exc_info()[0]) raise def save_config_file(self): @@ -3666,6 +3666,9 @@ def prepare_and_run_task(self, instruction): elif instruction == 'pandda.analyse': self.run_pandda_analyse('production_run') + elif instruction == 'pandda.analyse (PanDDA2)': + self.run_pandda_analyse('production_run_pandda_two') + elif instruction == 'pre-run for ground state model': self.run_pandda_analyse('pre_run') @@ -3744,7 +3747,7 @@ def prepare_and_run_task(self, instruction): interface = 'dimple_twin' else: interface = 'old' - print self.settings +# print self.settings self.work_thread = XChemThread.start_COOT(self.settings, interface) self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) self.work_thread.start() @@ -3851,6 +3854,7 @@ def run_pandda_analyse(self, run): 'average_map': str(self.pandda_calc_map_combobox.currentText()), 'max_new_datasets': str(self.pandda_max_new_datasets_entry.text()), 'grid_spacing': str(self.pandda_grid_spacing_entry.text()), + 'keyword_arguments': str(self.pandda_keyword_arguments_entry.text()), 'pandda_dir_structure': str(self.pandda_input_data_dir_entry.text()), 'perform_diffraction_data_scaling': str(self.wilson_checkbox.isChecked()), 'filter_pdb': str(self.pandda_reference_file_selection_combobox.currentText()), @@ -3889,9 +3893,11 @@ def run_pandda_analyse(self, run): return None self.update_log.insert('preparing pandda.analyse input script') - self.work_thread = XChemPANDDA.run_pandda_analyse(pandda_params, self.xce_logfile, + if run == 'production_run_pandda_two': + self.work_thread = XChemPANDDA.run_pandda_two_analyse(pandda_params, self.xce_logfile, os.path.join(self.database_directory, self.data_source_file)) - self.work_thread = XChemPANDDA.run_pandda_analyse(pandda_params, self.xce_logfile, + else: + self.work_thread = XChemPANDDA.run_pandda_analyse(pandda_params, self.xce_logfile, os.path.join(self.database_directory, self.data_source_file)) #self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), #self.datasource_menu_reload_samples) @@ -5119,7 +5125,7 @@ def select_different_autoprocessing_result(self): self.update_row_in_table(xtal, row, dbDict, self.datasets_summary_table, self.datasets_summary_table_columns) else: - print 'nothing to change' + print('nothing to change') self.msgBox.done(1) diff --git a/gui_scripts/pandda_tab.py b/gui_scripts/pandda_tab.py index a2cef139..f8b33fa3 100755 --- a/gui_scripts/pandda_tab.py +++ b/gui_scripts/pandda_tab.py @@ -172,7 +172,7 @@ def copy_ligands(obj): label.setFont(header_font) params_hbox.addWidget(label) - url_html = "For docs: click here" + url_html = "For docs: click here" label = QtGui.QLabel() label.setText(url_html) label.setOpenExternalLinks(True) @@ -237,6 +237,14 @@ def copy_ligands(obj): xce_object.pandda_grid_spacing_entry = QtGui.QLineEdit() xce_object.pandda_grid_spacing_entry.setText('0.5') xce_object.pandda_analyse_input_params_vbox.addWidget(xce_object.pandda_grid_spacing_entry) + + # keyword arguments (pandda2) + label = QtGui.QLabel('keyword arguments (pandda2 only)') + xce_object.pandda_analyse_input_params_vbox.addWidget(label) + xce_object.pandda_keyword_arguments_entry = QtGui.QLineEdit() + xce_object.pandda_keyword_arguments_entry.setText('') + xce_object.pandda_analyse_input_params_vbox.addWidget(xce_object.pandda_keyword_arguments_entry) + frame_right.setLayout(xce_object.pandda_analyse_input_params_vbox) grid_pandda.addWidget(frame_right, 0, 1, 5, 5) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index d174b8fc..2ffc4325 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.8.2' + xce_object.xce_version = 'v1.9.0' # general settings xce_object.allowed_unitcell_difference_percent = 12 @@ -655,7 +655,10 @@ def dropdown_items(self, xce_object): '------------------------------------------', # 'refine NEW bound-state models with BUSTER - NEW', 'pre-run for ground state model', - 'Build ground state model'] + 'Build ground state model', + '------------------------------------------', + 'pandda.analyse (PanDDA2)' + ] xce_object.refine_file_tasks = ['Open COOT - BUSTER refinement -', 'Open COOT - REFMAC refinement -', diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 7f93ed58..85823f97 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 20/01/2022 #\n' + ' # Date: 22/04/2022 #\n' ' # #\n' ' # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n' ' # tobias.krojer@maxiv.lu.se #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index fe87ead9..1b9c9d04 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -923,7 +923,6 @@ def run(self): stat_command = self.remote_string.replace("qsub'", str('stat ' + self.filter_pdb + "'")) output = subprocess.Popen(stat_command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = output.communicate() - print out if 'cannot stat' in out: filter_pdb = '' else: @@ -971,8 +970,6 @@ def run(self): if ignore_zmap_checkbox.isChecked(): zmap.append(str(self.pandda_analyse_data_table.item(i, 0).text())) - print ignore - def append_to_ignore_string(datasets_list, append_string): if len(datasets_list)==0: append_string = '' @@ -1075,6 +1072,98 @@ def append_to_ignore_string(datasets_list, append_string): +class run_pandda_two_analyse(QtCore.QThread): + + def __init__(self,pandda_params,xce_logfile,datasource): + QtCore.QThread.__init__(self) + self.data_directory=pandda_params['data_dir'] + self.panddas_directory=pandda_params['out_dir'] + self.submit_mode=pandda_params['submit_mode'] + + self.pandda_analyse_data_table = pandda_params['pandda_table'] + self.nproc=pandda_params['nproc'] + self.min_build_datasets=pandda_params['min_build_datasets'] + self.pdb_style=pandda_params['pdb_style'] + self.mtz_style=pandda_params['mtz_style'] + self.sort_event=pandda_params['sort_event'] + self.number_of_datasets=pandda_params['N_datasets'] + self.max_new_datasets=pandda_params['max_new_datasets'] + self.grid_spacing=pandda_params['grid_spacing'] + self.keyword_arguments = pandda_params['keyword_arguments'] + self.reference_dir=pandda_params['reference_dir'] + self.filter_pdb=os.path.join(self.reference_dir,pandda_params['filter_pdb']) + self.wilson_scaling = pandda_params['perform_diffraction_data_scaling'] + self.Logfile=XChemLog.updateLog(xce_logfile) + self.datasource=datasource + self.db=XChemDB.data_source(datasource) + self.appendix=pandda_params['appendix'] + self.write_mean_maps=pandda_params['write_mean_map'] + self.calc_map_by = pandda_params['average_map'] + self.select_ground_state_model='' + + def run(self): + + if not self.data_directory.startswith('/dls'): + self.Logfile.error('Sorry, you need to be at DLS for pandda2 to work!') + return None + + os.chdir(self.panddas_directory) + + cmd = ( + '#/bin/sh\n' + 'module load ccp4\n' + 'module load phenix\n' + 'module load buster\n' + '__conda_setup="$(\'/dls/science/groups/i04-1/conor_dev/conda/anaconda/bin/conda\' \'shell.bash\' \'hook\' 2> /dev/null)"\n' + 'if [ $? -eq 0 ]; then\n' + ' eval "$__conda_setup"\n' + 'else\n' + ' if [ -f "/dls/science/groups/i04-1/conor_dev/conda/anaconda/etc/profile.d/conda.sh" ]; then\n' + ' . "/dls/science/groups/i04-1/conor_dev/conda/anaconda/etc/profile.d/conda.sh"\n' + ' else\n' + ' export PATH="/dls/science/groups/i04-1/conor_dev/conda/anaconda/bin:$PATH"\n' + ' fi\n' + 'fi\n' + 'unset __conda_setup\n' + 'export PYTHONPATH=""\n' + 'conda activate pandda2_ray\n' + 'python -u /dls/science/groups/i04-1/conor_dev/pandda_2_gemmi/pandda_gemmi/analyse.py' + ' --data_dirs={0!s}'.format(self.data_directory.replace('/*','')) + + ' --out_dir={0!s}'.format(self.panddas_directory) + + ' --pdb_regex="{0!s}" '.format(self.pdb_style) + + ' --mtz_regex="{0!s}" '.format(self.mtz_style) + + ' --autobuild=True ' + ' --global_processing="serial" ' + ' --local_cpus=6 ' + ' --local_processing="ray" ' + ' --rank_method=autobuild ' + ' --comparison_strategy="hybrid" ' + ' --min_characterisation_datasets=25 ' + ' {0!s} '.format(self.keyword_arguments) + + ' --debug=True --memory_availability="low" | tee livelog_20220324_event_class_old_score\n' + ) + + self.Logfile.insert('running pandda.analyse with the following command:\n' + cmd) + + f = open('pandda2.sh','w') + f.write(cmd) + f.close() + + self.Logfile.warning('ignoring selected submission option') + + self.Logfile.insert('running PANDDA on cluster, using qsub...') + os.system('qsub -pe smp 6 -l m_mem_free=30G -q medium.q -o log.out -e log.err pandda2.sh') + + self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) + + + + + + + + + class giant_cluster_datasets(QtCore.QThread): def __init__(self,initial_model_directory,pandda_params,xce_logfile,datasource,): @@ -1333,9 +1422,9 @@ def run(self): 'from panddaTable ' 'where PANDDA_site_event_map not like "event%"' ) - print sqlite + query=self.db.execute_statement(sqlite) - print query + progress_step=1 if len(query) != 0: progress_step=100/float(len(query)) @@ -1345,7 +1434,6 @@ def run(self): self.emit(QtCore.SIGNAL('update_progress_bar'), progress) for item in query: - print item xtalID=str(item[0]) event_map=str(item[1]) resname=str(item[2]) @@ -1359,7 +1447,6 @@ def run(self): XChemUtils.pdbtools(os.path.join(self.initial_model_directory,xtalID,'refine.pdb')).save_specific_ligands_to_pdb(resname,chainID,resseq,altLoc) if os.path.isfile('ligand_{0!s}_{1!s}_{2!s}_{3!s}.pdb'.format(str(resname), str(chainID), str(resseq), str(altLoc))): ligand_pdb='ligand_{0!s}_{1!s}_{2!s}_{3!s}.pdb'.format(str(resname), str(chainID), str(resseq), str(altLoc)) - print os.path.join(self.initial_model_directory,xtalID,ligand_pdb) else: self.Logfile.insert('could not extract ligand; trying next...') continue @@ -1729,11 +1816,6 @@ def insert_new_row_in_panddaTable(self,xtal,ligand,site,dbDict): 'PANDDA_site_y': y_site, 'PANDDA_site_z': z_site } - print xtal,db_dict - - - - def run(self): From 333b075b6a65dfc91fa7acbd3494d99a2312dc54 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Thu, 16 Jun 2022 15:01:35 +0200 Subject: [PATCH 101/358] v1.9.1 (16/06/2022) (#414) - changed add instances of 'module load ccp4' to 'module load ccp4/7.1.018', except for the pandda2 function --- ChangeLog.txt | 3 +++ XChemExplorer_dmd.sh | 7 +++---- gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 2 +- lib/XChemProcess.py | 2 +- lib/XChemRefine.py | 6 +++--- lib/XChemThread.py | 6 +++--- lib/XChemUtils.py | 4 ++-- 9 files changed, 18 insertions(+), 16 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 2c2027de..0cfad35c 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.9.1 (16/06/2022) +- changed add instances of 'module load ccp4' to 'module load ccp4/7.1.018', except for the pandda2 function + v1.9.0 (22/04/2022) - add functionality for running PanDDA2 at Diamond Light Source - fixed hyperlink to PanDDA manual diff --git a/XChemExplorer_dmd.sh b/XChemExplorer_dmd.sh index 243e29a2..763ea60a 100755 --- a/XChemExplorer_dmd.sh +++ b/XChemExplorer_dmd.sh @@ -2,11 +2,10 @@ if [ -d "/dls/labxchem" ] then + module load buster/20211020 + module load phenix/1.20 + module load ccp4/7.1.018 export XChemExplorer_DIR="/dls/science/groups/i04-1/software/XChemExplorer_new/XChemExplorer" - source $XChemExplorer_DIR/setup-scripts/xce.setup-sh - module unload ccp4 - source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh - module load mx export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul fi diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 2ffc4325..5280ed23 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.9.0' + xce_object.xce_version = 'v1.9.1' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 85823f97..6562ee4e 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 22/04/2022 #\n' + ' # Date: 16/06/2022 #\n' ' # #\n' ' # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n' ' # tobias.krojer@maxiv.lu.se #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 1b9c9d04..f85fe6d1 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -862,7 +862,7 @@ def __init__(self,pandda_params,xce_logfile,datasource): os.system('/bin/rm -fr %s' %self.panddas_directory) os.mkdir(self.panddas_directory) if self.data_directory.startswith('/dls'): - self.select_ground_state_model = 'module load ccp4\n' + self.select_ground_state_model = 'module load ccp4/7.1.018\n' self.select_ground_state_model +='$CCP4/bin/ccp4-python %s %s\n' %(os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','select_ground_state_dataset.py'),self.panddas_directory) self.make_ligand_links='' diff --git a/lib/XChemProcess.py b/lib/XChemProcess.py index 1182230d..0b18b03a 100755 --- a/lib/XChemProcess.py +++ b/lib/XChemProcess.py @@ -49,7 +49,7 @@ def run(self): script += 'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n' if os.getcwd().startswith('/dls'): - script += 'module load ccp4\n' + script += 'module load ccp4/7.1.018\n' script += 'module load XDS\n' # script += 'module load phenix\n' diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index 53644101..a34a7785 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -569,7 +569,7 @@ def update_database(self,cmd,Serial): user = getpass.getuser() ccp4_module = '' # need to source again, because giant.score_model still needs outdated version which does not have gemmi if self.ProjectPath.startswith('/dls'): - ccp4_module = 'module load ccp4' + ccp4_module = 'module load ccp4/7.1.018' cmd += ('\n' + ccp4_module + '\n' @@ -1296,7 +1296,7 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine cmd = ( 'export XChemExplorer_DIR="%s"\n' %os.getenv('XChemExplorer_DIR')+ # 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') + - 'module load ccp4\n' + 'module load ccp4/7.1.018\n' 'giant.merge_conformations major=%s minor=%s reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0' %(ground_state,bound_state) ) else: @@ -1438,7 +1438,7 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine # CCP4 & PHENIX stuff (if working at DLS) module_load='' if os.getcwd().startswith('/dls'): - module_load = 'module load ccp4\n' + module_load = 'module load ccp4/7.1.018\n' module_load += 'module load phenix\n' # 2017-07-20: for the time being this will explicitly source pandda since version 0.2 really only works at DLS diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 4f89d255..30c3bd5b 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -1501,7 +1501,7 @@ def prepare_phenix_ligand_pipeline_shell_script(self,xtal,visit_run_autoproc,mtz if os.path.isdir('/dls'): ccp4_scratch+='module load phenix\n' - ccp4_scratch+='module load ccp4\n' + ccp4_scratch+='module load ccp4/7.1.018\n' mtz_column_list=mtztools(mtzin).get_all_columns_as_list() rfree = '' @@ -1603,7 +1603,7 @@ def prepare_pipedream_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,re if os.path.isdir('/dls'): ccp4_scratch+='module load buster\n' - ccp4_scratch+='module load ccp4\n' + ccp4_scratch+='module load ccp4/7.1.018\n' if os.path.isfile(ref_mtz): hklref_line=' -hklref {0!s}'.format(ref_mtz) @@ -1736,7 +1736,7 @@ def prepare_dimple_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,ref_m ccp4_scratch='' if os.path.isdir('/dls'): - ccp4_scratch+='module load ccp4\n' + ccp4_scratch+='module load ccp4/7.1.018\n' hkl = any_reflection_file(file_name=mtzin) miller_arrays = hkl.as_miller_arrays() diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 9b0340c3..0dc911a3 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -247,7 +247,7 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft software = '' if restraints_program == 'acedrg': if os.getcwd().startswith('/dls'): - software += 'module load ccp4\n' + software += 'module load ccp4/7.1.018\n' elif restraints_program == 'phenix.elbow': if os.getcwd().startswith('/dls'): software += 'module load phenix\n' @@ -293,7 +293,7 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft software='' if restraints_program=='acedrg': if os.getcwd().startswith('/dls'): - software += 'module load ccp4\n' + software += 'module load ccp4/7.1.018\n' if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): software+='acedrg --res LIG -c ../old.cif -o {0!s}\n'.format((compoundID.replace(' ',''))) else: From afc8d9ff04fa0bfbafa1e45b8210ef6aac0fbcdb Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 29 Jun 2022 15:26:41 +0200 Subject: [PATCH 102/358] v1.9.2 (28/06/2022) (#415) replace obsolete 'source /dls/science/groups/i04-1/software/pandda-update/ccp4/ccp4-7.0/bin/ccp4.setup-sh' with 'module load ccp4/7.1.016' before running pandda.export --- ChangeLog.txt | 4 ++++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemPANDDA.py | 3 ++- 4 files changed, 8 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 0cfad35c..70037d18 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,7 @@ +v1.9.2 (28/06/2022) +- replace obsolete 'source /dls/science/groups/i04-1/software/pandda-update/ccp4/ccp4-7.0/bin/ccp4.setup-sh' with 'module load ccp4/7.1.016' before running pandda.export + + v1.9.1 (16/06/2022) - changed add instances of 'module load ccp4' to 'module load ccp4/7.1.018', except for the pandda2 function diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 5280ed23..86142485 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.9.1' + xce_object.xce_version = 'v1.9.2' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 6562ee4e..c5493502 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 16/06/2022 #\n' + ' # Date: 28/06/2022 #\n' ' # #\n' ' # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n' ' # tobias.krojer@maxiv.lu.se #\n' diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index f85fe6d1..3b9fcf26 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -804,7 +804,8 @@ def export_models(self): else: Cmds = ( - 'source /dls/science/groups/i04-1/software/pandda-update/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' + 'module load ccp4/7.1.016\n' +# 'source /dls/science/groups/i04-1/software/pandda-update/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' # 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' 'pandda.export' ' pandda_dir=%s' %self.panddas_directory+ From 7aeb58640aad80d21ffd1b6d7c1a7a84a018c6d6 Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Wed, 29 Jun 2022 18:44:38 +0200 Subject: [PATCH 103/358] v1.9.3 (29/06/2022) (#416) - added 'module load ccp4/7.1.018' to grade script otherwise the helper script will run with python3 --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemUtils.py | 10 +++++----- 4 files changed, 10 insertions(+), 7 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 70037d18..968b56c5 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.9.3 (29/06/2022) +- added 'module load ccp4/7.1.018' to grade script otherwise the helper script will run with python3 + v1.9.2 (28/06/2022) - replace obsolete 'source /dls/science/groups/i04-1/software/pandda-update/ccp4/ccp4-7.0/bin/ccp4.setup-sh' with 'module load ccp4/7.1.016' before running pandda.export diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 86142485..2a9f0db6 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.9.2' + xce_object.xce_version = 'v1.9.3' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index c5493502..7c38f341 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 28/06/2022 #\n' + ' # Date: 29/06/2022 #\n' ' # #\n' ' # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n' ' # tobias.krojer@maxiv.lu.se #\n' diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 0dc911a3..e730ff90 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -250,9 +250,11 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft software += 'module load ccp4/7.1.018\n' elif restraints_program == 'phenix.elbow': if os.getcwd().startswith('/dls'): + software += 'module load ccp4/7.1.018\n' software += 'module load phenix\n' elif restraints_program == 'grade': if os.getcwd().startswith('/dls'): + software += 'module load ccp4/7.1.018\n' software += 'module load buster\n' software += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' software += "export BDG_TOOL_OBABEL='none'\n" @@ -300,6 +302,7 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft software+='acedrg --res LIG -i "{0!s}" -o {1!s}\n'.format(productSmiles, compoundID.replace(' ','')) elif restraints_program=='phenix.elbow': if os.getcwd().startswith('/dls'): + software += 'module load ccp4/7.1.018\n' software += 'module load phenix\n' if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): software+='phenix.elbow --file=../old.cif --id LIG --output {0!s}\n'.format((compoundID.replace(' ',''))) @@ -308,6 +311,7 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft .format(productSmiles, compoundID.replace(' ','')) elif restraints_program=='grade': if os.getcwd().startswith('/dls'): + software += 'module load ccp4/7.1.018\n' software += 'module load buster\n' software += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' software+="export BDG_TOOL_OBABEL='none'\n" @@ -338,10 +342,6 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft '\n' 'export XChemExplorer_DIR="' + os.getenv('XChemExplorer_DIR') + '"' + '\n' -# 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh' -# '\n' -# + module + - '\n' '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py {0!s} {1!s} {2!s} {3!s}' .format(os.path.join(database_directory, data_source_file), sample, 'RefinementCIFStatus', 'running') + '\n' @@ -954,7 +954,7 @@ def calc_unitcell_volume_from_logfile(self,a,b,c,alpha,beta,gamma,lattice): unitcell_volume=a*b*c* \ math.sqrt((1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2) \ +2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma))) - print 'unit cell volume',unitcell_volume +# print 'unit cell volume',unitcell_volume # if lattice=='monoclinic': if 'monoclinic' in lattice: unitcell_volume=round(a*b*c*math.sin(beta),1) From 7f69bded55dabd7d00f3e231f1c6798700b795bb Mon Sep 17 00:00:00 2001 From: Tobias Krojer Date: Mon, 10 Oct 2022 16:44:28 +0200 Subject: [PATCH 104/358] v1.9.4 (10/10/2022) (#417) - catch unusual space group names in PDB CRYST card --- ChangeLog.txt | 3 +++ gui_scripts/settings_preferences.py | 2 +- lib/XChemLog.py | 2 +- lib/XChemUtils.py | 3 ++- 4 files changed, 7 insertions(+), 3 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 968b56c5..55980017 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -1,3 +1,6 @@ +v1.9.4 (10/10/2022) +- catch unusual space group names in PDB CRYST card + v1.9.3 (29/06/2022) - added 'module load ccp4/7.1.018' to grade script otherwise the helper script will run with python3 diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 2a9f0db6..f9d40e03 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -30,7 +30,7 @@ def set_xce_logfile(self, xce_object): def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.9.3' + xce_object.xce_version = 'v1.9.4' # general settings xce_object.allowed_unitcell_difference_percent = 12 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 7c38f341..94ebc741 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -26,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # Version: %s #\n' %pasteVersion+ ' # #\n' - ' # Date: 29/06/2022 #\n' + ' # Date: 10/10/2022 #\n' ' # #\n' ' # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n' ' # tobias.krojer@maxiv.lu.se #\n' diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index e730ff90..798d9f3c 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -684,7 +684,8 @@ def read_aimless_logfile(self,logfile): self.aimless['DataProcessingScore'] = (float( self.aimless['DataProcessingUniqueReflectionsOverall']) * float(self.aimless['DataProcessingCompletenessOverall']) * high_symmetry_boost * float(self.aimless['DataProcessingIsigOverall'])) / float( self.aimless['DataProcessingUnitCellVolume']) - except ValueError: + # When P-6 was accidentally used self.aimless['DataProcessingPointGroup'] through a KeyError, so handling this + except (ValueError, KeyError): self.aimless['DataProcessingScore'] = 0.0 self.aimless['DataProcessingUnitCell'] = str(a) + ' ' + str(b) + ' ' + str(c) + ' ' + str(alpha) + ' ' + str( beta) + ' ' + str(gamma) From 6c4a449aff322fd1354432c33cf7eb7aed7c8f2f Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Fri, 21 Oct 2022 15:50:03 +0000 Subject: [PATCH 105/358] Setup development environment --- .devcontainer/Dockerfile | 22 + .devcontainer/devcontainer.json | 21 + .../library-scripts/common-debian.sh | 454 ++++++++++++++++++ .dockerignore | 3 + .gitignore | 1 + .travis.yml | 4 - Dockerfile | 23 +- XChemExplorer | 1 - XChemExplorer_dmd.sh | 12 - XChemExplorer_local.sh | 10 - compile_test.py | 19 - run_tests | 3 - setup-scripts/pandda.setup-sh | 3 - setup-scripts/xce.setup-csh | 2 - setup-scripts/xce.setup-sh | 12 - setupssh.sh | 24 - test_build.sh | 22 - 17 files changed, 517 insertions(+), 119 deletions(-) create mode 100644 .devcontainer/Dockerfile create mode 100644 .devcontainer/devcontainer.json create mode 100644 .devcontainer/library-scripts/common-debian.sh create mode 100644 .dockerignore delete mode 100755 .travis.yml delete mode 120000 XChemExplorer delete mode 100755 XChemExplorer_dmd.sh delete mode 100755 XChemExplorer_local.sh delete mode 100755 compile_test.py delete mode 100755 run_tests delete mode 100755 setup-scripts/pandda.setup-sh delete mode 100755 setup-scripts/xce.setup-csh delete mode 100755 setup-scripts/xce.setup-sh delete mode 100755 setupssh.sh delete mode 100755 test_build.sh diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile new file mode 100644 index 00000000..58bf1fd6 --- /dev/null +++ b/.devcontainer/Dockerfile @@ -0,0 +1,22 @@ +FROM localhost/ccp4-7.1 + +ARG INSTALL_ZSH="true" +ARG UPGRADE_PACKAGES="true" +ARG USERNAME=vscode +ARG USER_UID=1000 +ARG USER_GID=$USER_UID + +COPY library-scripts/*.sh library-scripts/*.env /tmp/library-scripts/ +RUN bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" "true" "true" \ + && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts + +RUN apt-get update \ + && apt-get upgrade -y \ + && apt-get install -y \ + libxrender1 libfontconfig libxext6 \ + libglib2.0-0 libsm6 libxi6 libxrandr2 libxfixes3 libxcursor1 libxinerama1 \ + libgomp1 libxdamage1 libxcb-shm0 libxcb-render0 \ + && apt-get clean -y && rm -rf /var/lib/apt/lists/* + +ENV QT_X11_NO_MITSHM=1 \ + XChemExplorer_DIR=/workspace/ diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 00000000..7e26138c --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,21 @@ +{ + "name": "XChemExplorer", + "build": { + "dockerfile": "Dockerfile" + }, + "remoteEnv": { + "DISPLAY": "${localEnv:DISPLAY}" + }, + "features": { + "git": "os-provided" + }, + "workspaceMount": "src=${localWorkspaceFolder},dst=/workspace,type=bind", + "workspaceFolder": "/workspace", + "runArgs": [ + "--pid=host", + "--net=host" + ], + "mounts": [ + "src=/dls/labxchem/data/,dst=/dls/labxchem/data/,type=bind" + ] +} \ No newline at end of file diff --git a/.devcontainer/library-scripts/common-debian.sh b/.devcontainer/library-scripts/common-debian.sh new file mode 100644 index 00000000..bf1f9e2e --- /dev/null +++ b/.devcontainer/library-scripts/common-debian.sh @@ -0,0 +1,454 @@ +#!/usr/bin/env bash +#------------------------------------------------------------------------------------------------------------- +# Copyright (c) Microsoft Corporation. All rights reserved. +# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information. +#------------------------------------------------------------------------------------------------------------- +# +# Docs: https://github.com/microsoft/vscode-dev-containers/blob/main/script-library/docs/common.md +# Maintainer: The VS Code and Codespaces Teams +# +# Syntax: ./common-debian.sh [install zsh flag] [username] [user UID] [user GID] [upgrade packages flag] [install Oh My Zsh! flag] [Add non-free packages] + +set -e + +INSTALL_ZSH=${1:-"true"} +USERNAME=${2:-"automatic"} +USER_UID=${3:-"automatic"} +USER_GID=${4:-"automatic"} +UPGRADE_PACKAGES=${5:-"true"} +INSTALL_OH_MYS=${6:-"true"} +ADD_NON_FREE_PACKAGES=${7:-"false"} +SCRIPT_DIR="$(cd $(dirname "${BASH_SOURCE[0]}") && pwd)" +MARKER_FILE="/usr/local/etc/vscode-dev-containers/common" + +if [ "$(id -u)" -ne 0 ]; then + echo -e 'Script must be run as root. Use sudo, su, or add "USER root" to your Dockerfile before running this script.' + exit 1 +fi + +# Ensure that login shells get the correct path if the user updated the PATH using ENV. +rm -f /etc/profile.d/00-restore-env.sh +echo "export PATH=${PATH//$(sh -lc 'echo $PATH')/\$PATH}" > /etc/profile.d/00-restore-env.sh +chmod +x /etc/profile.d/00-restore-env.sh + +# If in automatic mode, determine if a user already exists, if not use vscode +if [ "${USERNAME}" = "auto" ] || [ "${USERNAME}" = "automatic" ]; then + USERNAME="" + POSSIBLE_USERS=("vscode" "node" "codespace" "$(awk -v val=1000 -F ":" '$3==val{print $1}' /etc/passwd)") + for CURRENT_USER in ${POSSIBLE_USERS[@]}; do + if id -u ${CURRENT_USER} > /dev/null 2>&1; then + USERNAME=${CURRENT_USER} + break + fi + done + if [ "${USERNAME}" = "" ]; then + USERNAME=vscode + fi +elif [ "${USERNAME}" = "none" ]; then + USERNAME=root + USER_UID=0 + USER_GID=0 +fi + +# Load markers to see which steps have already run +if [ -f "${MARKER_FILE}" ]; then + echo "Marker file found:" + cat "${MARKER_FILE}" + source "${MARKER_FILE}" +fi + +# Ensure apt is in non-interactive to avoid prompts +export DEBIAN_FRONTEND=noninteractive + +# Function to call apt-get if needed +apt_get_update_if_needed() +{ + if [ ! -d "/var/lib/apt/lists" ] || [ "$(ls /var/lib/apt/lists/ | wc -l)" = "0" ]; then + echo "Running apt-get update..." + apt-get update + else + echo "Skipping apt-get update." + fi +} + +# Run install apt-utils to avoid debconf warning then verify presence of other common developer tools and dependencies +if [ "${PACKAGES_ALREADY_INSTALLED}" != "true" ]; then + + package_list="apt-utils \ + openssh-client \ + gnupg2 \ + dirmngr \ + iproute2 \ + procps \ + lsof \ + htop \ + net-tools \ + psmisc \ + curl \ + wget \ + rsync \ + ca-certificates \ + unzip \ + zip \ + nano \ + vim-tiny \ + less \ + jq \ + lsb-release \ + apt-transport-https \ + dialog \ + libc6 \ + libgcc1 \ + libkrb5-3 \ + libgssapi-krb5-2 \ + libicu[0-9][0-9] \ + liblttng-ust[0-9] \ + libstdc++6 \ + zlib1g \ + locales \ + sudo \ + ncdu \ + man-db \ + strace \ + manpages \ + manpages-dev \ + init-system-helpers" + + # Needed for adding manpages-posix and manpages-posix-dev which are non-free packages in Debian + if [ "${ADD_NON_FREE_PACKAGES}" = "true" ]; then + # Bring in variables from /etc/os-release like VERSION_CODENAME + . /etc/os-release + sed -i -E "s/deb http:\/\/(deb|httpredir)\.debian\.org\/debian ${VERSION_CODENAME} main/deb http:\/\/\1\.debian\.org\/debian ${VERSION_CODENAME} main contrib non-free/" /etc/apt/sources.list + sed -i -E "s/deb-src http:\/\/(deb|httredir)\.debian\.org\/debian ${VERSION_CODENAME} main/deb http:\/\/\1\.debian\.org\/debian ${VERSION_CODENAME} main contrib non-free/" /etc/apt/sources.list + sed -i -E "s/deb http:\/\/(deb|httpredir)\.debian\.org\/debian ${VERSION_CODENAME}-updates main/deb http:\/\/\1\.debian\.org\/debian ${VERSION_CODENAME}-updates main contrib non-free/" /etc/apt/sources.list + sed -i -E "s/deb-src http:\/\/(deb|httpredir)\.debian\.org\/debian ${VERSION_CODENAME}-updates main/deb http:\/\/\1\.debian\.org\/debian ${VERSION_CODENAME}-updates main contrib non-free/" /etc/apt/sources.list + sed -i "s/deb http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}\/updates main/deb http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}\/updates main contrib non-free/" /etc/apt/sources.list + sed -i "s/deb-src http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}\/updates main/deb http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}\/updates main contrib non-free/" /etc/apt/sources.list + sed -i "s/deb http:\/\/deb\.debian\.org\/debian ${VERSION_CODENAME}-backports main/deb http:\/\/deb\.debian\.org\/debian ${VERSION_CODENAME}-backports main contrib non-free/" /etc/apt/sources.list + sed -i "s/deb-src http:\/\/deb\.debian\.org\/debian ${VERSION_CODENAME}-backports main/deb http:\/\/deb\.debian\.org\/debian ${VERSION_CODENAME}-backports main contrib non-free/" /etc/apt/sources.list + # Handle bullseye location for security https://www.debian.org/releases/bullseye/amd64/release-notes/ch-information.en.html + sed -i "s/deb http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}-security main/deb http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}-security main contrib non-free/" /etc/apt/sources.list + sed -i "s/deb-src http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}-security main/deb http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}-security main contrib non-free/" /etc/apt/sources.list + echo "Running apt-get update..." + apt-get update + package_list="${package_list} manpages-posix manpages-posix-dev" + else + apt_get_update_if_needed + fi + + # Install libssl1.1 if available + if [[ ! -z $(apt-cache --names-only search ^libssl1.1$) ]]; then + package_list="${package_list} libssl1.1" + fi + + # Install appropriate version of libssl1.0.x if available + libssl_package=$(dpkg-query -f '${db:Status-Abbrev}\t${binary:Package}\n' -W 'libssl1\.0\.?' 2>&1 || echo '') + if [ "$(echo "$LIlibssl_packageBSSL" | grep -o 'libssl1\.0\.[0-9]:' | uniq | sort | wc -l)" -eq 0 ]; then + if [[ ! -z $(apt-cache --names-only search ^libssl1.0.2$) ]]; then + # Debian 9 + package_list="${package_list} libssl1.0.2" + elif [[ ! -z $(apt-cache --names-only search ^libssl1.0.0$) ]]; then + # Ubuntu 18.04, 16.04, earlier + package_list="${package_list} libssl1.0.0" + fi + fi + + echo "Packages to verify are installed: ${package_list}" + apt-get -y install --no-install-recommends ${package_list} 2> >( grep -v 'debconf: delaying package configuration, since apt-utils is not installed' >&2 ) + + # Install git if not already installed (may be more recent than distro version) + if ! type git > /dev/null 2>&1; then + apt-get -y install --no-install-recommends git + fi + + PACKAGES_ALREADY_INSTALLED="true" +fi + +# Get to latest versions of all packages +if [ "${UPGRADE_PACKAGES}" = "true" ]; then + apt_get_update_if_needed + apt-get -y upgrade --no-install-recommends + apt-get autoremove -y +fi + +# Ensure at least the en_US.UTF-8 UTF-8 locale is available. +# Common need for both applications and things like the agnoster ZSH theme. +if [ "${LOCALE_ALREADY_SET}" != "true" ] && ! grep -o -E '^\s*en_US.UTF-8\s+UTF-8' /etc/locale.gen > /dev/null; then + echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen + locale-gen + LOCALE_ALREADY_SET="true" +fi + +# Create or update a non-root user to match UID/GID. +group_name="${USERNAME}" +if id -u ${USERNAME} > /dev/null 2>&1; then + # User exists, update if needed + if [ "${USER_GID}" != "automatic" ] && [ "$USER_GID" != "$(id -g $USERNAME)" ]; then + group_name="$(id -gn $USERNAME)" + groupmod --gid $USER_GID ${group_name} + usermod --gid $USER_GID $USERNAME + fi + if [ "${USER_UID}" != "automatic" ] && [ "$USER_UID" != "$(id -u $USERNAME)" ]; then + usermod --uid $USER_UID $USERNAME + fi +else + # Create user + if [ "${USER_GID}" = "automatic" ]; then + groupadd $USERNAME + else + groupadd --gid $USER_GID $USERNAME + fi + if [ "${USER_UID}" = "automatic" ]; then + useradd -s /bin/bash --gid $USERNAME -m $USERNAME + else + useradd -s /bin/bash --uid $USER_UID --gid $USERNAME -m $USERNAME + fi +fi + +# Add sudo support for non-root user +if [ "${USERNAME}" != "root" ] && [ "${EXISTING_NON_ROOT_USER}" != "${USERNAME}" ]; then + echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME + chmod 0440 /etc/sudoers.d/$USERNAME + EXISTING_NON_ROOT_USER="${USERNAME}" +fi + +# ** Shell customization section ** +if [ "${USERNAME}" = "root" ]; then + user_rc_path="/root" +else + user_rc_path="/home/${USERNAME}" +fi + +# Restore user .bashrc defaults from skeleton file if it doesn't exist or is empty +if [ ! -f "${user_rc_path}/.bashrc" ] || [ ! -s "${user_rc_path}/.bashrc" ] ; then + cp /etc/skel/.bashrc "${user_rc_path}/.bashrc" +fi + +# Restore user .profile defaults from skeleton file if it doesn't exist or is empty +if [ ! -f "${user_rc_path}/.profile" ] || [ ! -s "${user_rc_path}/.profile" ] ; then + cp /etc/skel/.profile "${user_rc_path}/.profile" +fi + +# .bashrc/.zshrc snippet +rc_snippet="$(cat << 'EOF' + +if [ -z "${USER}" ]; then export USER=$(whoami); fi +if [[ "${PATH}" != *"$HOME/.local/bin"* ]]; then export PATH="${PATH}:$HOME/.local/bin"; fi + +# Display optional first run image specific notice if configured and terminal is interactive +if [ -t 1 ] && [[ "${TERM_PROGRAM}" = "vscode" || "${TERM_PROGRAM}" = "codespaces" ]] && [ ! -f "$HOME/.config/vscode-dev-containers/first-run-notice-already-displayed" ]; then + if [ -f "/usr/local/etc/vscode-dev-containers/first-run-notice.txt" ]; then + cat "/usr/local/etc/vscode-dev-containers/first-run-notice.txt" + elif [ -f "/workspaces/.codespaces/shared/first-run-notice.txt" ]; then + cat "/workspaces/.codespaces/shared/first-run-notice.txt" + fi + mkdir -p "$HOME/.config/vscode-dev-containers" + # Mark first run notice as displayed after 10s to avoid problems with fast terminal refreshes hiding it + ((sleep 10s; touch "$HOME/.config/vscode-dev-containers/first-run-notice-already-displayed") &) +fi + +# Set the default git editor if not already set +if [ -z "$(git config --get core.editor)" ] && [ -z "${GIT_EDITOR}" ]; then + if [ "${TERM_PROGRAM}" = "vscode" ]; then + if [[ -n $(command -v code-insiders) && -z $(command -v code) ]]; then + export GIT_EDITOR="code-insiders --wait" + else + export GIT_EDITOR="code --wait" + fi + fi +fi + +EOF +)" + +# code shim, it fallbacks to code-insiders if code is not available +cat << 'EOF' > /usr/local/bin/code +#!/bin/sh + +get_in_path_except_current() { + which -a "$1" | grep -A1 "$0" | grep -v "$0" +} + +code="$(get_in_path_except_current code)" + +if [ -n "$code" ]; then + exec "$code" "$@" +elif [ "$(command -v code-insiders)" ]; then + exec code-insiders "$@" +else + echo "code or code-insiders is not installed" >&2 + exit 127 +fi +EOF +chmod +x /usr/local/bin/code + +# systemctl shim - tells people to use 'service' if systemd is not running +cat << 'EOF' > /usr/local/bin/systemctl +#!/bin/sh +set -e +if [ -d "/run/systemd/system" ]; then + exec /bin/systemctl "$@" +else + echo '\n"systemd" is not running in this container due to its overhead.\nUse the "service" command to start services instead. e.g.: \n\nservice --status-all' +fi +EOF +chmod +x /usr/local/bin/systemctl + +# Codespaces bash and OMZ themes - partly inspired by https://github.com/ohmyzsh/ohmyzsh/blob/master/themes/robbyrussell.zsh-theme +codespaces_bash="$(cat \ +<<'EOF' + +# Codespaces bash prompt theme +__bash_prompt() { + local userpart='`export XIT=$? \ + && [ ! -z "${GITHUB_USER}" ] && echo -n "\[\033[0;32m\]@${GITHUB_USER} " || echo -n "\[\033[0;32m\]\u " \ + && [ "$XIT" -ne "0" ] && echo -n "\[\033[1;31m\]➜" || echo -n "\[\033[0m\]➜"`' + local gitbranch='`\ + if [ "$(git config --get codespaces-theme.hide-status 2>/dev/null)" != 1 ]; then \ + export BRANCH=$(git symbolic-ref --short HEAD 2>/dev/null || git rev-parse --short HEAD 2>/dev/null); \ + if [ "${BRANCH}" != "" ]; then \ + echo -n "\[\033[0;36m\](\[\033[1;31m\]${BRANCH}" \ + && if git ls-files --error-unmatch -m --directory --no-empty-directory -o --exclude-standard ":/*" > /dev/null 2>&1; then \ + echo -n " \[\033[1;33m\]✗"; \ + fi \ + && echo -n "\[\033[0;36m\]) "; \ + fi; \ + fi`' + local lightblue='\[\033[1;34m\]' + local removecolor='\[\033[0m\]' + PS1="${userpart} ${lightblue}\w ${gitbranch}${removecolor}\$ " + unset -f __bash_prompt +} +__bash_prompt + +EOF +)" + +codespaces_zsh="$(cat \ +<<'EOF' +# Codespaces zsh prompt theme +__zsh_prompt() { + local prompt_username + if [ ! -z "${GITHUB_USER}" ]; then + prompt_username="@${GITHUB_USER}" + else + prompt_username="%n" + fi + PROMPT="%{$fg[green]%}${prompt_username} %(?:%{$reset_color%}➜ :%{$fg_bold[red]%}➜ )" # User/exit code arrow + PROMPT+='%{$fg_bold[blue]%}%(5~|%-1~/…/%3~|%4~)%{$reset_color%} ' # cwd + PROMPT+='$([ "$(git config --get codespaces-theme.hide-status 2>/dev/null)" != 1 ] && git_prompt_info)' # Git status + PROMPT+='%{$fg[white]%}$ %{$reset_color%}' + unset -f __zsh_prompt +} +ZSH_THEME_GIT_PROMPT_PREFIX="%{$fg_bold[cyan]%}(%{$fg_bold[red]%}" +ZSH_THEME_GIT_PROMPT_SUFFIX="%{$reset_color%} " +ZSH_THEME_GIT_PROMPT_DIRTY=" %{$fg_bold[yellow]%}✗%{$fg_bold[cyan]%})" +ZSH_THEME_GIT_PROMPT_CLEAN="%{$fg_bold[cyan]%})" +__zsh_prompt + +EOF +)" + +# Add RC snippet and custom bash prompt +if [ "${RC_SNIPPET_ALREADY_ADDED}" != "true" ]; then + echo "${rc_snippet}" >> /etc/bash.bashrc + echo "${codespaces_bash}" >> "${user_rc_path}/.bashrc" + echo 'export PROMPT_DIRTRIM=4' >> "${user_rc_path}/.bashrc" + if [ "${USERNAME}" != "root" ]; then + echo "${codespaces_bash}" >> "/root/.bashrc" + echo 'export PROMPT_DIRTRIM=4' >> "/root/.bashrc" + fi + chown ${USERNAME}:${group_name} "${user_rc_path}/.bashrc" + RC_SNIPPET_ALREADY_ADDED="true" +fi + +# Optionally install and configure zsh and Oh My Zsh! +if [ "${INSTALL_ZSH}" = "true" ]; then + if ! type zsh > /dev/null 2>&1; then + apt_get_update_if_needed + apt-get install -y zsh + fi + if [ "${ZSH_ALREADY_INSTALLED}" != "true" ]; then + echo "${rc_snippet}" >> /etc/zsh/zshrc + ZSH_ALREADY_INSTALLED="true" + fi + + # Adapted, simplified inline Oh My Zsh! install steps that adds, defaults to a codespaces theme. + # See https://github.com/ohmyzsh/ohmyzsh/blob/master/tools/install.sh for official script. + oh_my_install_dir="${user_rc_path}/.oh-my-zsh" + if [ ! -d "${oh_my_install_dir}" ] && [ "${INSTALL_OH_MYS}" = "true" ]; then + template_path="${oh_my_install_dir}/templates/zshrc.zsh-template" + user_rc_file="${user_rc_path}/.zshrc" + umask g-w,o-w + mkdir -p ${oh_my_install_dir} + git clone --depth=1 \ + -c core.eol=lf \ + -c core.autocrlf=false \ + -c fsck.zeroPaddedFilemode=ignore \ + -c fetch.fsck.zeroPaddedFilemode=ignore \ + -c receive.fsck.zeroPaddedFilemode=ignore \ + "https://github.com/ohmyzsh/ohmyzsh" "${oh_my_install_dir}" 2>&1 + echo -e "$(cat "${template_path}")\nDISABLE_AUTO_UPDATE=true\nDISABLE_UPDATE_PROMPT=true" > ${user_rc_file} + sed -i -e 's/ZSH_THEME=.*/ZSH_THEME="codespaces"/g' ${user_rc_file} + + mkdir -p ${oh_my_install_dir}/custom/themes + echo "${codespaces_zsh}" > "${oh_my_install_dir}/custom/themes/codespaces.zsh-theme" + # Shrink git while still enabling updates + cd "${oh_my_install_dir}" + git repack -a -d -f --depth=1 --window=1 + # Copy to non-root user if one is specified + if [ "${USERNAME}" != "root" ]; then + cp -rf "${user_rc_file}" "${oh_my_install_dir}" /root + chown -R ${USERNAME}:${group_name} "${user_rc_path}" + fi + fi +fi + +# Persist image metadata info, script if meta.env found in same directory +meta_info_script="$(cat << 'EOF' +#!/bin/sh +. /usr/local/etc/vscode-dev-containers/meta.env + +# Minimal output +if [ "$1" = "version" ] || [ "$1" = "image-version" ]; then + echo "${VERSION}" + exit 0 +elif [ "$1" = "release" ]; then + echo "${GIT_REPOSITORY_RELEASE}" + exit 0 +elif [ "$1" = "content" ] || [ "$1" = "content-url" ] || [ "$1" = "contents" ] || [ "$1" = "contents-url" ]; then + echo "${CONTENTS_URL}" + exit 0 +fi + +#Full output +echo +echo "Development container image information" +echo +if [ ! -z "${VERSION}" ]; then echo "- Image version: ${VERSION}"; fi +if [ ! -z "${DEFINITION_ID}" ]; then echo "- Definition ID: ${DEFINITION_ID}"; fi +if [ ! -z "${VARIANT}" ]; then echo "- Variant: ${VARIANT}"; fi +if [ ! -z "${GIT_REPOSITORY}" ]; then echo "- Source code repository: ${GIT_REPOSITORY}"; fi +if [ ! -z "${GIT_REPOSITORY_RELEASE}" ]; then echo "- Source code release/branch: ${GIT_REPOSITORY_RELEASE}"; fi +if [ ! -z "${BUILD_TIMESTAMP}" ]; then echo "- Timestamp: ${BUILD_TIMESTAMP}"; fi +if [ ! -z "${CONTENTS_URL}" ]; then echo && echo "More info: ${CONTENTS_URL}"; fi +echo +EOF +)" +if [ -f "${SCRIPT_DIR}/meta.env" ]; then + mkdir -p /usr/local/etc/vscode-dev-containers/ + cp -f "${SCRIPT_DIR}/meta.env" /usr/local/etc/vscode-dev-containers/meta.env + echo "${meta_info_script}" > /usr/local/bin/devcontainer-info + chmod +x /usr/local/bin/devcontainer-info +fi + +# Write marker file +mkdir -p "$(dirname "${MARKER_FILE}")" +echo -e "\ + PACKAGES_ALREADY_INSTALLED=${PACKAGES_ALREADY_INSTALLED}\n\ + LOCALE_ALREADY_SET=${LOCALE_ALREADY_SET}\n\ + EXISTING_NON_ROOT_USER=${EXISTING_NON_ROOT_USER}\n\ + RC_SNIPPET_ALREADY_ADDED=${RC_SNIPPET_ALREADY_ADDED}\n\ + ZSH_ALREADY_INSTALLED=${ZSH_ALREADY_INSTALLED}" > "${MARKER_FILE}" + +echo "Done!" \ No newline at end of file diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 00000000..c4d71aff --- /dev/null +++ b/.dockerignore @@ -0,0 +1,3 @@ +Dockerfile +/.devcontainer +/.git \ No newline at end of file diff --git a/.gitignore b/.gitignore index 6ed3aa79..5d993efb 100755 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,4 @@ *.pyc XChemExplorer_dmd.sh .idea +/libraries \ No newline at end of file diff --git a/.travis.yml b/.travis.yml deleted file mode 100755 index ae77ee17..00000000 --- a/.travis.yml +++ /dev/null @@ -1,4 +0,0 @@ -sudo: required -services: docker -install: docker build -t reskyner/xce . -script: docker run reskyner/xce /bin/bash -c "/ccp4/bin/ccp4-python /XChemExplorer/compile_test.py" diff --git a/Dockerfile b/Dockerfile index e6c7441f..6f093f96 100755 --- a/Dockerfile +++ b/Dockerfile @@ -1,7 +1,16 @@ -FROM reskyner/ccp4 -#RUN apt-get install -f libxcursor-dev -ADD ./run_tests . -ADD ./compile_test.py . -RUN mkdir XChemExplorer -ADD * /XChemExplorer/ -#CMD ccp4-python ./compile_tests.py +FROM localhost/ccp4-7.1 + +COPY . /xce + +RUN apt-get update \ + && apt-get upgrade -y \ + && apt-get install -y \ + libxrender1 libfontconfig libxext6 \ + libglib2.0-0 libsm6 libxi6 libxrandr2 libxfixes3 libxcursor1 libxinerama1 \ + libgomp1 libxdamage1 libxcb-shm0 libxcb-render0 \ + && apt-get clean -y && rm -rf /var/lib/apt/lists/* + +ENV QT_X11_NO_MITSHM=1 \ + XChemExplorer_DIR=/xce/ + +ENTRYPOINT /ccp4-7.1/bin/ccp4-python /xce/XChemExplorer.py diff --git a/XChemExplorer b/XChemExplorer deleted file mode 120000 index 05c692a5..00000000 --- a/XChemExplorer +++ /dev/null @@ -1 +0,0 @@ -XChemExplorer_dmd.sh \ No newline at end of file diff --git a/XChemExplorer_dmd.sh b/XChemExplorer_dmd.sh deleted file mode 100755 index 763ea60a..00000000 --- a/XChemExplorer_dmd.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/bash - -if [ -d "/dls/labxchem" ] - then - module load buster/20211020 - module load phenix/1.20 - module load ccp4/7.1.018 - export XChemExplorer_DIR="/dls/science/groups/i04-1/software/XChemExplorer_new/XChemExplorer" - export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul -fi - -ccp4-python $XChemExplorer_DIR/XChemExplorer.py diff --git a/XChemExplorer_local.sh b/XChemExplorer_local.sh deleted file mode 100755 index 6cb172d7..00000000 --- a/XChemExplorer_local.sh +++ /dev/null @@ -1,10 +0,0 @@ -#!/bin/bash - -export XChemExplorer_DIR=$( dirname "${BASH_SOURCE[0]}" ) -echo $XChemExplorer_DIR - -source $XChemExplorer_DIR/setup-scripts/xce.setup-sh -module unload ccp4 -source $XChemExplorer_DIR/../ccp4/bin/ccp4.setup-sh - -ccp4-python $XChemExplorer_DIR/XChemExplorer.py diff --git a/compile_test.py b/compile_test.py deleted file mode 100755 index 82081743..00000000 --- a/compile_test.py +++ /dev/null @@ -1,19 +0,0 @@ -import os, sys - -# set XCE environment variables -os.environ['XChemExplorer_DIR'] = os.path.join(os.getcwd(), 'XChemExplorer/') - -print('XCE path = ' + os.environ['XChemExplorer_DIR']) - -# Append all directories to path -sys.path.append(os.environ['XChemExplorer_DIR']) - -# print PATH to check -print('Current path:- ') -for p in sys.path: - print(p) - -# try to import all of XCE stuff -from XChemExplorer import * - -print('Successfully imported XCE... compile was succesful') diff --git a/run_tests b/run_tests deleted file mode 100755 index 5f8ff34f..00000000 --- a/run_tests +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -echo "Docker is working bro!" diff --git a/setup-scripts/pandda.setup-sh b/setup-scripts/pandda.setup-sh deleted file mode 100755 index c2844986..00000000 --- a/setup-scripts/pandda.setup-sh +++ /dev/null @@ -1,3 +0,0 @@ -# module load pymol -module load buster -source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh diff --git a/setup-scripts/xce.setup-csh b/setup-scripts/xce.setup-csh deleted file mode 100755 index 22eca627..00000000 --- a/setup-scripts/xce.setup-csh +++ /dev/null @@ -1,2 +0,0 @@ -unsetenv PYTHONPATH - diff --git a/setup-scripts/xce.setup-sh b/setup-scripts/xce.setup-sh deleted file mode 100755 index 75477e49..00000000 --- a/setup-scripts/xce.setup-sh +++ /dev/null @@ -1,12 +0,0 @@ -unset PYTHONPATH - -# --- DLS specific settings --- -for dir in /* - do - if [ $dir = "/dls" ]; then - module load global/cluster - module load phenix - module load coot - module load buster - fi - done; diff --git a/setupssh.sh b/setupssh.sh deleted file mode 100755 index ab8f0438..00000000 --- a/setupssh.sh +++ /dev/null @@ -1,24 +0,0 @@ -#!/bin/bash - -echo "Please enter your fedID:" -echo " " -read fedid -echo "Now generating ssh key..." -echo " " -rm ~/.ssh/* -ssh-keygen -t rsa -ssh-copy-id $fedid@nx.diamond.ac.uk - - -echo "Please enter the full path to the directory where you want to mount the diamond file system:" -echo " " - -read mountdir - -string="sshfs -o Ciphers=arcfour -o Compression=no -o allow_other -o reconnect -o workaround=rename ${fedid}@nx.diamond.ac.uk:/dls/labxchem/data ${mountdir}" - -echo $string > mount_diamond.sh - -string2="cd ${mountdir}" - -echo $string2 >> mount_diamond.sh diff --git a/test_build.sh b/test_build.sh deleted file mode 100755 index 6eabb450..00000000 --- a/test_build.sh +++ /dev/null @@ -1,22 +0,0 @@ -#!/bin/bash - -if [[ "$OSTYPE" == "linux-gnu" ]]; then - wget http://devtools.fg.oisin.rc-harwell.ac.uk/nightly/ccp4-linux64-latest.tar.bz2 - bunzip2 ccp4-linux64-latest.tar.bz2 - mkdir ./ccp4 - tar -xf ccp4-linux64-latest.tar -C ./ccp4 --strip-components=1 -elif [[ "$OSTYPE" == "darwin"* ]]; then - wget http://devtools.fg.oisin.rc-harwell.ac.uk/nightly/ccp4-osx-clang-latest.tar.gz - gunzip ccp4-osx-clang-latest.tar.gz - mkdir ./ccp4 - tar -xf ccp4-osx-clang-latest.tar -C ./ccp4 --strip-components=1 -fi -cd ccp4 -echo "changed directory to ccp4" -echo "running setup" -yes y | ./BINARY.setup > /dev/null 2>&1 -echo "finishing some other stuff..." -source bin/ccp4.setup-sh -yes y | ccp4-python -m pip uninstall panddas -ccp4-python -m pip install panddas -#git clone https://www.github.com/xchem/XChemExplorer From 0e6aa8cb5328164eb7c06e03ea65cbd70410e803 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 26 Oct 2022 09:54:49 +0000 Subject: [PATCH 106/358] Update dockerfile to use ccp4 from gcr --- Dockerfile | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 6f093f96..144b7689 100755 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,13 @@ -FROM localhost/ccp4-7.1 +FROM gcr.io/diamond-privreg/xchem/ccp4:7.1 as ccp4 -COPY . /xce +FROM registry.hub.docker.com/library/debian:bullseye as xce + +COPY --from=ccp4 /ccp4-7.1 /ccp4-7.1 + +ARG XCE_DIR=/xce +WORKDIR ${XCE_DIR} + +COPY . ${XCE_DIR} RUN apt-get update \ && apt-get upgrade -y \ @@ -10,7 +17,7 @@ RUN apt-get update \ libgomp1 libxdamage1 libxcb-shm0 libxcb-render0 \ && apt-get clean -y && rm -rf /var/lib/apt/lists/* -ENV QT_X11_NO_MITSHM=1 \ - XChemExplorer_DIR=/xce/ +ENV QT_X11_NO_MITSHM=1 + XChemExplorer_DIR=${XCE_DIR} ENTRYPOINT /ccp4-7.1/bin/ccp4-python /xce/XChemExplorer.py From 742055a5039f867d18d06137a3c70090223cbc5c Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 26 Oct 2022 09:57:28 +0000 Subject: [PATCH 107/358] Update devcontainer to use ccp4 from gcr --- .devcontainer/Dockerfile | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 58bf1fd6..e132ce0a 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -1,14 +1,6 @@ -FROM localhost/ccp4-7.1 +FROM gcr.io/diamond-privreg/xchem/ccp4:7.1 as ccp4 -ARG INSTALL_ZSH="true" -ARG UPGRADE_PACKAGES="true" -ARG USERNAME=vscode -ARG USER_UID=1000 -ARG USER_GID=$USER_UID - -COPY library-scripts/*.sh library-scripts/*.env /tmp/library-scripts/ -RUN bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" "true" "true" \ - && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts +FROM mcr.microsoft.com/vscode/devcontainers/base:bullseye RUN apt-get update \ && apt-get upgrade -y \ From c25a92ae9371249c66503cca12257f3405fe52cf Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 26 Oct 2022 10:06:34 +0000 Subject: [PATCH 108/358] Fix devcontainer --- .devcontainer/Dockerfile | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index e132ce0a..2424e540 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -2,13 +2,16 @@ FROM gcr.io/diamond-privreg/xchem/ccp4:7.1 as ccp4 FROM mcr.microsoft.com/vscode/devcontainers/base:bullseye +COPY --from=ccp4 /ccp4-7.1 /ccp4-7.1 + RUN apt-get update \ && apt-get upgrade -y \ && apt-get install -y \ libxrender1 libfontconfig libxext6 \ libglib2.0-0 libsm6 libxi6 libxrandr2 libxfixes3 libxcursor1 libxinerama1 \ libgomp1 libxdamage1 libxcb-shm0 libxcb-render0 \ - && apt-get clean -y && rm -rf /var/lib/apt/lists/* + && apt-get clean -y && rm -rf /var/lib/apt/lists/* \ + && echo . /ccp4-7.1/bin/ccp4.setup-sh | tee ~/.bashrc ~/.zshrc ENV QT_X11_NO_MITSHM=1 \ XChemExplorer_DIR=/workspace/ From 02c8c50b79845947fe458bc90c74d8cd56443ed4 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 26 Oct 2022 10:19:54 +0000 Subject: [PATCH 109/358] Fix dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 144b7689..59bfa419 100755 --- a/Dockerfile +++ b/Dockerfile @@ -17,7 +17,7 @@ RUN apt-get update \ libgomp1 libxdamage1 libxcb-shm0 libxcb-render0 \ && apt-get clean -y && rm -rf /var/lib/apt/lists/* -ENV QT_X11_NO_MITSHM=1 +ENV QT_X11_NO_MITSHM=1 \ XChemExplorer_DIR=${XCE_DIR} ENTRYPOINT /ccp4-7.1/bin/ccp4-python /xce/XChemExplorer.py From 4644f62f7bd6402ba6731ed0d9667d4459935fff Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 10:58:13 +0000 Subject: [PATCH 110/358] Git ignore xce.log --- .gitignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 5d993efb..ad920278 100755 --- a/.gitignore +++ b/.gitignore @@ -2,4 +2,5 @@ *.pyc XChemExplorer_dmd.sh .idea -/libraries \ No newline at end of file +/libraries +xce.log \ No newline at end of file From d42298f37944fa400e07fc72c6275171ead49314 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 10:58:35 +0000 Subject: [PATCH 111/358] Add python extension to dev container --- .devcontainer/devcontainer.json | 9 ++++++++- .vscode/settings.json | 3 +++ 2 files changed, 11 insertions(+), 1 deletion(-) create mode 100644 .vscode/settings.json diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 7e26138c..791994bf 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -17,5 +17,12 @@ ], "mounts": [ "src=/dls/labxchem/data/,dst=/dls/labxchem/data/,type=bind" - ] + ], + "customizations": { + "vscode": { + "extensions": [ + "ms-python.python@2021.9.1246542782" + ] + } + } } \ No newline at end of file diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 00000000..acc2526f --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,3 @@ +{ + "python.pythonPath": "/ccp4-7.1/bin/ccp4-python" +} \ No newline at end of file From d60cc8c0b81454f058e10d56ed53827df9712310 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 10:58:45 +0000 Subject: [PATCH 112/358] Setup debug launch task --- .vscode/launch.json | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 .vscode/launch.json diff --git a/.vscode/launch.json b/.vscode/launch.json new file mode 100644 index 00000000..93a5a7fb --- /dev/null +++ b/.vscode/launch.json @@ -0,0 +1,15 @@ +{ + // Use IntelliSense to learn about possible attributes. + // Hover to view descriptions of existing attributes. + // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 + "version": "0.2.0", + "configurations": [ + { + "name": "XCE", + "type": "python", + "request": "launch", + "module": "XChemExplorer", + "justMyCode": true + } + ] +} \ No newline at end of file From ad5aeb1c2a018bb8f0ad00ff6b92b974b8dc9c16 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 12:09:22 +0000 Subject: [PATCH 113/358] Add pip to dev container --- .devcontainer/Dockerfile | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 2424e540..65233439 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -11,7 +11,9 @@ RUN apt-get update \ libglib2.0-0 libsm6 libxi6 libxrandr2 libxfixes3 libxcursor1 libxinerama1 \ libgomp1 libxdamage1 libxcb-shm0 libxcb-render0 \ && apt-get clean -y && rm -rf /var/lib/apt/lists/* \ - && echo . /ccp4-7.1/bin/ccp4.setup-sh | tee ~/.bashrc ~/.zshrc + && echo . /ccp4-7.1/bin/ccp4.setup-sh | tee ~/.bashrc ~/.zshrc \ + && curl https://bootstrap.pypa.io/pip/2.7/get-pip.py -o /tmp/get-pip.py \ + && /ccp4-7.1/bin/ccp4-python /tmp/get-pip.py ENV QT_X11_NO_MITSHM=1 \ XChemExplorer_DIR=/workspace/ From 2196322a27f220f37c181cce2a399d2479d246a0 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 12:18:37 +0000 Subject: [PATCH 114/358] Format with autopep8 --- XChemExplorer.py | 2415 ++++++++----- gui_scripts/datasets_tab.py | 144 +- gui_scripts/deposition_tab.py | 176 +- gui_scripts/layout.py | 152 +- gui_scripts/maps_tab.py | 42 +- gui_scripts/overview_tab.py | 16 +- gui_scripts/pandda_tab.py | 173 +- gui_scripts/refinement_tab.py | 13 +- gui_scripts/settings_preferences.py | 403 +-- gui_scripts/settings_tab.py | 132 +- gui_scripts/stylesheet.py | 3 +- helpers/assign_stereochemistry.py | 64 +- ...ange_residues_in_ground_and_bound-state.py | 48 +- helpers/create_png_of_compound.py | 24 +- helpers/find_best_fitting_ligand.py | 54 +- helpers/make_ligand_links_after_pandda.py | 38 +- helpers/merge_ligand_cif_files.py | 4 +- helpers/phenix_find_TLS_groups.py | 51 +- helpers/prepare_for_zenodo_upload.py | 118 +- helpers/reset_interesting_datasets.py | 41 +- helpers/reset_occupancy_protein_to_one.py | 22 +- .../reset_to_last_successful_refinement.py | 36 +- helpers/resort_ligand_atoms.py | 107 +- helpers/select_ground_state_dataset.py | 122 +- .../update_data_source_after_refinement.py | 258 +- .../update_data_source_for_new_cif_files.py | 47 +- .../update_data_source_for_new_dimple_pdb.py | 111 +- ...ate_data_source_for_new_dimple_twin_pdb.py | 111 +- helpers/update_pandda_status_flag.py | 26 +- helpers/update_status_flag.py | 15 +- lib/PuckDB.py | 10 +- lib/XChemCoot.py | 286 +- lib/XChemCootBuster.py | 417 ++- lib/XChemCootNew.py | 376 ++- lib/XChemCootOld.py | 957 +++--- lib/XChemCootReference.py | 490 +-- lib/XChemCootTwin.py | 405 ++- lib/XChemDB.py | 2632 +++++++++------ lib/XChemDeposit.py | 1314 +++---- lib/XChemDialogs.py | 40 +- lib/XChemLigand.py | 6 +- lib/XChemLog.py | 64 +- lib/XChemMain.py | 1836 +++++----- lib/XChemPANDDA.py | 2134 ++++++------ lib/XChemPlots.py | 101 +- lib/XChemProcess.py | 211 +- lib/XChemRefine.py | 1565 +++++---- lib/XChemThread.py | 2624 +++++++------- lib/XChemToolTips.py | 316 +- lib/XChemUtils.py | 3006 +++++++++-------- lib/coot_utils_XChem.py | 1248 ++++--- web/XChemWeb.py | 354 +- web/process_sqlite.py | 614 ++-- 53 files changed, 14598 insertions(+), 11374 deletions(-) diff --git a/XChemExplorer.py b/XChemExplorer.py index 47b8ff45..40ce78ec 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -17,8 +17,24 @@ # solve gtk startup error #import gtk -#gtk.set_interactive(False) +# gtk.set_interactive(False) +from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas +import matplotlib.pyplot as plt +import XChemWeb +import XChemDeposit +import XChemProcess +import XChemLog +import XChemPlots +import XChemMain +import XChemToolTips +import XChemPANDDA +import XChemDB +import XChemThread +from XChemUtils import parse +from stylesheet import set_stylesheet +from layout import * +from settings_preferences import * import base64 import getpass import glob @@ -26,7 +42,8 @@ import multiprocessing import pickle import subprocess -import sys, os +import sys +import os import webbrowser from datetime import datetime from PyQt4 import QtGui, QtCore, QtWebKit @@ -35,26 +52,6 @@ sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'web')) sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) -from settings_preferences import * -from layout import * -from stylesheet import set_stylesheet - - -from XChemUtils import parse -import XChemThread -import XChemDB -import XChemPANDDA -import XChemToolTips -import XChemMain -import XChemPlots -import XChemLog -import XChemProcess -import XChemDeposit -import XChemWeb - - -import matplotlib.pyplot as plt -from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas class XChemExplorer(QtGui.QApplication): def __init__(self, args): @@ -97,7 +94,8 @@ def start_GUI(self): self.backup_soakDB() def backup_soakDB(self): - XChemMain.backup_soakDB(os.path.join(self.database_directory, self.data_source_file),self.xce_logfile) + XChemMain.backup_soakDB(os.path.join( + self.database_directory, self.data_source_file), self.xce_logfile) def checkLabXChemDir(self): dirCheck = QtGui.QMessageBox() @@ -105,18 +103,18 @@ def checkLabXChemDir(self): vbox = QtGui.QVBoxLayout() try: warning = ( - 'Are you sure you want to launch XCE here:\n\n' - +self.labxchem_directory_current+'\n\n' - 'If this is not where you should be running XCE, please close!\n' - ) + 'Are you sure you want to launch XCE here:\n\n' + + self.labxchem_directory_current+'\n\n' + 'If this is not where you should be running XCE, please close!\n' + ) except AttributeError: return vbox.addWidget(QtGui.QLabel(warning)) dirCheckLayout.addLayout(vbox, 0, 0) - dirCheck.exec_(); - + dirCheck.exec_() # function to update datasource + def datasource_menu_reload_samples(self): self.update_log.insert( 'reading samples from data source: ' + os.path.join(self.database_directory, self.data_source_file)) @@ -128,7 +126,8 @@ def datasource_menu_reload_samples(self): # function to create new datasource def create_new_data_source(self): - file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'Save file', self.database_directory)) + file_name = str(QtGui.QFileDialog.getSaveFileName( + self.window, 'Save file', self.database_directory)) # make sure that the file always has .sqlite extension if file_name.rfind('.') != -1: file_name = file_name[:file_name.rfind('.')] + '.sqlite' @@ -140,18 +139,19 @@ def create_new_data_source(self): self.db.create_missing_columns() self.database_directory = file_name[:file_name.rfind('/')] self.data_source_file = file_name[file_name.rfind('/') + 1:] - self.data_source_file_label.setText(os.path.join(self.database_directory, self.data_source_file)) + self.data_source_file_label.setText(os.path.join( + self.database_directory, self.data_source_file)) self.settings['database_directory'] = self.database_directory self.settings['data_source'] = self.data_source_file self.data_source_set = True self.datasource_menu_reload_samples() - #################################################################################################################### # # # DATASETS TAB # # # #################################################################################################################### + def continously_check_for_new_data_collection(self, state): self.timer_to_check_for_new_data_collection.timeout.connect( lambda: self.check_for_new_autoprocessing_or_rescore(False)) @@ -166,22 +166,30 @@ def target_selection_combobox_activated(self, text): self.target = str(text) def select_diffraction_data_directory(self): - self.diffraction_data_directory = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) - self.diffraction_data_dir_label.setText(self.diffraction_data_directory) + self.diffraction_data_directory = str( + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) + self.diffraction_data_dir_label.setText( + self.diffraction_data_directory) self.settings['diffraction_data_directory'] = self.diffraction_data_directory - self.update_log.insert('setting diffraction data directory to ' + self.diffraction_data_directory) + self.update_log.insert( + 'setting diffraction data directory to ' + self.diffraction_data_directory) def search_for_datasets(self): - self.update_log.insert('search diffraction data directory for datasets...') + self.update_log.insert( + 'search diffraction data directory for datasets...') print('will search ' + str(self.diffraction_data_directory)) - self.work_thread = XChemMain.find_diffraction_image_directory_fast(self.diffraction_data_directory) + self.work_thread = XChemMain.find_diffraction_image_directory_fast( + self.diffraction_data_directory) self.explorer_active = 1 self.connect(self.work_thread, QtCore.SIGNAL("update_datasets_reprocess_table"), self.update_datasets_reprocess_table) - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() @@ -193,14 +201,17 @@ def translate_datasetID_to_sampleID(self): self.translate_datasetID_to_sampleID_file = '-' vbox = QtGui.QVBoxLayout() button = QtGui.QPushButton('Open CSV') - button.clicked.connect(self.open_csv_file_translate_datasetID_to_sampleID) + button.clicked.connect( + self.open_csv_file_translate_datasetID_to_sampleID) vbox.addWidget(button) - self.translate_datasetID_to_sampleID_csv_label = QtGui.QLabel(self.translate_datasetID_to_sampleID_file) + self.translate_datasetID_to_sampleID_csv_label = QtGui.QLabel( + self.translate_datasetID_to_sampleID_file) vbox.addWidget(self.translate_datasetID_to_sampleID_csv_label) translateLayout.addLayout(vbox, 0, 0) translate.addButton(QtGui.QPushButton('OK'), QtGui.QMessageBox.YesRole) - translate.addButton(QtGui.QPushButton('Cancel'), QtGui.QMessageBox.RejectRole) - reply = translate.exec_(); + translate.addButton(QtGui.QPushButton('Cancel'), + QtGui.QMessageBox.RejectRole) + reply = translate.exec_() if reply == 0: if os.path.isfile(self.translate_datasetID_to_sampleID_file): trans_dict = {} @@ -212,13 +223,17 @@ def translate_datasetID_to_sampleID(self): if len(trans_dict) >= 1: allRows = self.datasets_reprocess_table.rowCount() for row in xrange(0, allRows): - dataset_id = str(self.datasets_reprocess_table.item(row, 0).text()) - sample_id = str(self.datasets_reprocess_table.item(row, 1).text()) + dataset_id = str( + self.datasets_reprocess_table.item(row, 0).text()) + sample_id = str( + self.datasets_reprocess_table.item(row, 1).text()) if dataset_id in trans_dict: cell_text = QtGui.QTableWidgetItem() cell_text.setText(trans_dict[dataset_id]) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.datasets_reprocess_table.setItem(row, 1, cell_text) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + self.datasets_reprocess_table.setItem( + row, 1, cell_text) self.update_log.insert( 'dataset: {0!s} -> changing sampleID to: {1!s}'.format(dataset_id, trans_dict[dataset_id])) @@ -226,22 +241,28 @@ def translate_datasetID_to_sampleID(self): def select_sample_for_xia2(self): indexes = self.datasets_reprocess_table.selectionModel().selectedRows() for index in sorted(indexes): - xtal = str(self.datasets_reprocess_table.item(index.row(), 1).text()) + xtal = str(self.datasets_reprocess_table.item( + index.row(), 1).text()) print(xtal, self.diffraction_data_table_dict[xtal][0]) - self.update_log.insert('{0!s} marked for reprocessing'.format(index.row())) + self.update_log.insert( + '{0!s} marked for reprocessing'.format(index.row())) self.diffraction_data_table_dict[xtal][0].setChecked(True) def select_reprocess_reference_mtz(self): - self.update_log.insert('trying to set new reference mtz file for reprocessing with xia2') - file_name = str(QtGui.QFileDialog.getOpenFileName(self.window, 'Select file', self.database_directory)) + self.update_log.insert( + 'trying to set new reference mtz file for reprocessing with xia2') + file_name = str(QtGui.QFileDialog.getOpenFileName( + self.window, 'Select file', self.database_directory)) if os.path.isfile(file_name): if file_name.endswith('.mtz'): self.diffraction_data_reference_mtz = file_name self.update_log.insert( 'new reference file for data processing with xia2: ' + self.diffraction_data_reference_mtz) - self.reprocess_reference_mtz_file_label.setText(self.diffraction_data_reference_mtz) + self.reprocess_reference_mtz_file_label.setText( + self.diffraction_data_reference_mtz) else: - self.update_log.insert('this does not seem to be a mtz file: ' + file_name) + self.update_log.insert( + 'this does not seem to be a mtz file: ' + file_name) def check_for_new_autoprocessing_or_rescore(self, rescore_only): self.update_log.insert('checking for new data collection') @@ -249,10 +270,13 @@ def check_for_new_autoprocessing_or_rescore(self, rescore_only): if rescore_only: # first pop up a warning message as this will overwrite all user selections msgBox = QtGui.QMessageBox() - msgBox.setText("*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?") - msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) - reply = msgBox.exec_(); + msgBox.setText( + "*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?") + msgBox.addButton(QtGui.QPushButton('Yes'), + QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton( + 'No'), QtGui.QMessageBox.RejectRole) + reply = msgBox.exec_() if reply == 0: start_thread = True else: @@ -267,7 +291,7 @@ def check_for_new_autoprocessing_or_rescore(self, rescore_only): 'Please select a target or\n' 'select "=== project directory ===" if you want to read reprocessed results\n' 'In case target list is empty, make sure that you have selected the actual\n' - 'data collection visit (e.g. /dls/i04-1/data/2018/lb18145-70)' ) + 'data collection visit (e.g. /dls/i04-1/data/2018/lb18145-70)') msgBox.setText(warning) start_thread = False @@ -297,14 +321,16 @@ def check_for_new_autoprocessing_or_rescore(self, rescore_only): self.data_source_file), self.xce_logfile) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("create_widgets_for_autoprocessing_results_only"), self.create_widgets_for_autoprocessing_results_only) self.work_thread.start() - ################################################################################################################# # # @@ -318,7 +344,8 @@ def update_gdaLog_parsing_instructions_and_score(self, gdaLogInstructions): def read_pinIDs_from_gda_logs(self): self.update_log.insert('reading pinIDs from gda logfiles...') - visit, beamline = XChemMain.getVisitAndBeamline(self.beamline_directory) + visit, beamline = XChemMain.getVisitAndBeamline( + self.beamline_directory) self.work_thread = XChemThread.read_pinIDs_from_gda_logs(beamline, visit, os.path.join( @@ -328,18 +355,21 @@ def read_pinIDs_from_gda_logs(self): self.xce_logfile) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("update_gdaLog_parsing_instructions_and_score"), self.update_gdaLog_parsing_instructions_and_score) self.work_thread.start() - def check_for_new_autoprocessing_results(self): self.update_log.insert('checking for new data collection') if self.target == '=== SELECT TARGET ===': - self.update_log.error('NO TARGET SELECTED, PLEASE SELECT A TARGET AND TRY AGAIN!') + self.update_log.error( + 'NO TARGET SELECTED, PLEASE SELECT A TARGET AND TRY AGAIN!') start_thread = False elif self.target == '=== project directory ===': processedDir = self.initial_model_directory @@ -351,11 +381,12 @@ def check_for_new_autoprocessing_results(self): ## processedDir = os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*/processed/*/'+self.target) # start_thread = True else: - processedDir = os.path.join(self.beamline_directory, 'processed', self.target) + processedDir = os.path.join( + self.beamline_directory, 'processed', self.target) start_thread = True if start_thread: -# processedDir=os.path.join(self.beamline_directory,'processed',self.target) + # processedDir=os.path.join(self.beamline_directory,'processed',self.target) self.work_thread = XChemThread.read_write_autoprocessing_results_from_to_disc(processedDir, os.path.join( self.database_directory, @@ -366,9 +397,12 @@ def check_for_new_autoprocessing_results(self): self.read_agamemnon.isChecked()) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("read_pinIDs_from_gda_logs"), self.read_pinIDs_from_gda_logs) self.work_thread.start() @@ -377,10 +411,13 @@ def select_best_autoprocessing_result(self): if self.rescore: # first pop up a warning message as this will overwrite all user selections msgBox = QtGui.QMessageBox() - msgBox.setText("*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?") - msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) - reply = msgBox.exec_(); + msgBox.setText( + "*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?") + msgBox.addButton(QtGui.QPushButton('Yes'), + QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton( + 'No'), QtGui.QMessageBox.RejectRole) + reply = msgBox.exec_() if reply != 0: start_thread = False else: @@ -390,14 +427,16 @@ def select_best_autoprocessing_result(self): if start_thread: self.update_log.insert('selecting best autoprocessing result') - self.update_log.insert('samples where user made manual changes will be ignored!') + self.update_log.insert( + 'samples where user made manual changes will be ignored!') if self.target == '=== project directory ===': processedDir = self.initial_model_directory else: - processedDir = os.path.join(self.beamline_directory, 'processed', self.target) + processedDir = os.path.join( + self.beamline_directory, 'processed', self.target) - visit,beamline = XChemMain.getVisitAndBeamline(processedDir) + visit, beamline = XChemMain.getVisitAndBeamline(processedDir) if self.read_agamemnon.isChecked(): visit = [] @@ -407,34 +446,38 @@ def select_best_autoprocessing_result(self): self.work_thread = XChemThread.choose_autoprocessing_outcome(os.path.join(self.database_directory, self.data_source_file), - visit, - self.reference_file_list, - self.preferences, - self.initial_model_directory, - self.rescore, - self.xce_logfile, - self.read_agamemnon.isChecked()) + visit, + self.reference_file_list, + self.preferences, + self.initial_model_directory, + self.rescore, + self.xce_logfile, + self.read_agamemnon.isChecked()) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("populate_datasets_summary_table_NEW"), - self.populate_datasets_summary_table_NEW) + self.populate_datasets_summary_table_NEW) self.work_thread.start() # < end ################################################################################################################### - #################################################################################################################### # # # MAPS TAB # # # #################################################################################################################### + def set_new_reference_if_applicable(self): print('hallo') - reference_root = str(self.reference_file_selection_combobox.currentText()) + reference_root = str( + self.reference_file_selection_combobox.currentText()) pg_ref = '' ucVol_ref = 0.0 for reference in self.reference_file_list: @@ -444,7 +487,8 @@ def set_new_reference_if_applicable(self): ucVol_ref = reference[4] break if ucVol_ref == 0.0: - self.update_log.insert('cannot set reference file since unit cell volume of reference pdb is 0!') + self.update_log.insert( + 'cannot set reference file since unit cell volume of reference pdb is 0!') return for xtal in self.initial_model_dimple_dict: @@ -455,20 +499,25 @@ def set_new_reference_if_applicable(self): ucVol_xtal = db_dict['DataProcessingUnitCellVolume'] try: - difference = math.fabs(1 - (float(ucVol_xtal) / float(ucVol_ref))) * 100 + difference = math.fabs( + 1 - (float(ucVol_xtal) / float(ucVol_ref))) * 100 except ValueError: - self.update_log.insert(xtal + ' -> cannot calculate unit cell volume difference') + self.update_log.insert( + xtal + ' -> cannot calculate unit cell volume difference') continue if pg_xtal == pg_ref and difference < self.allowed_unitcell_difference_percent: print(xtal, pg_xtal, ucVol_xtal) - index = reference_file_selection_combobox.findText(reference_root, QtCore.Qt.MatchFixedString) + index = reference_file_selection_combobox.findText( + reference_root, QtCore.Qt.MatchFixedString) reference_file_selection_combobox.setCurrentIndex(index) - self.update_log.insert(xtal + ' -> setting ' + reference_root + ' as input PDB file for DIMPLE') + self.update_log.insert( + xtal + ' -> setting ' + reference_root + ' as input PDB file for DIMPLE') def refresh_reference_file_list(self): self.reference_file_list = self.get_reference_file_list(' ') - self.populate_reference_combobox(self.reference_file_selection_combobox) + self.populate_reference_combobox( + self.reference_file_selection_combobox) def on_context_menu_initial_model(self, point): # show context menu @@ -504,7 +553,7 @@ def select_pandda_input_template(self): self.pandda_input_data_dir_entry.setText( '/'+os.path.join(*filepath.split('/')[0:len(filepath.split('/'))-2])) except TypeError: - self.update_log.error('directory selection invalid') + self.update_log.error('directory selection invalid') # if len(filepath.split('/')) - len(self.initial_model_directory.split('/')) == 2: # self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*')) # elif len(filepath.split('/')) - len(self.initial_model_directory.split('/')) > 2: @@ -517,7 +566,8 @@ def select_pandda_input_template(self): self.pandda_mtz_style_entry.setText(mtzin) def change_pandda_spg_label(self): - combo_text = str(self.pandda_reference_file_selection_combobox.currentText()) + combo_text = str( + self.pandda_reference_file_selection_combobox.currentText()) for file in self.reference_file_list: if file[0] == combo_text: self.pandda_reference_file_spg_label.setText(file[1]) @@ -535,19 +585,22 @@ def on_context_menu_pandda(self, point): def export_to_html(self): XChemWeb.export_to_html(self.html_export_directory, self.initial_model_directory, - os.path.join(self.database_directory, self.data_source_file), + os.path.join(self.database_directory, + self.data_source_file), self.xce_logfile).prepare('0') def export_to_html_CompChem(self): XChemWeb.export_to_html(self.html_export_directory, self.initial_model_directory, - os.path.join(self.database_directory, self.data_source_file), + os.path.join(self.database_directory, + self.data_source_file), self.xce_logfile).prepare('4') def export_to_html_deposition_ready(self): XChemWeb.export_to_html(self.html_export_directory, self.initial_model_directory, - os.path.join(self.database_directory, self.data_source_file), + os.path.join(self.database_directory, + self.data_source_file), self.xce_logfile).prepare('5') # self.update_log.insert('exporting contents of SQLite database into ' + self.html_export_directory) @@ -571,7 +624,8 @@ def export_to_html_deposition_ready(self): # self.ground_state_pdb_button_label.setText(pdb) def select_ground_state_mtz(self): - m = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', os.getcwd(),'*.mtz') + m = QtGui.QFileDialog.getOpenFileNameAndFilter( + self.window, 'Select File', os.getcwd(), '*.mtz') mtz = str(tuple(m)[0]) self.ground_state_mtz_button_label.setText(mtz) @@ -582,48 +636,59 @@ def add_ground_state_db(self): 'PDB_file': pdb, 'MTZ_file': mtz} self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, 'ground_state', 'ground_state', - db_dict) + db_dict) else: - self.update_log.error('could not find a suitable reference file; see messages above!') + self.update_log.error( + 'could not find a suitable reference file; see messages above!') def auto_select_ground_state_reference_PDB(self): pdb = None mtz = None xtalList = [] - for dirs in glob.glob(os.path.join(self.panddas_directory,'processed_datasets','*')): + for dirs in glob.glob(os.path.join(self.panddas_directory, 'processed_datasets', '*')): xtal = dirs[dirs.rfind('/')+1:] - if os.path.isfile(os.path.join(dirs,xtal+'-pandda-input.pdb')): - pdbHeader = parse().PDBheader(os.path.join(dirs,xtal+'-pandda-input.pdb')) + if os.path.isfile(os.path.join(dirs, xtal+'-pandda-input.pdb')): + pdbHeader = parse().PDBheader(os.path.join(dirs, xtal+'-pandda-input.pdb')) try: - xtalList.append( [xtal, float(pdbHeader['Rfree']) , float(pdbHeader['ResolutionHigh']) ] ) + xtalList.append( + [xtal, float(pdbHeader['Rfree']), float(pdbHeader['ResolutionHigh'])]) except ValueError: - self.update_log.error('%s: cannot read Rfree or Resolution from PDB header; skipping...') + self.update_log.error( + '%s: cannot read Rfree or Resolution from PDB header; skipping...') pass - self.update_log.insert('found %s PDB files in %s' %(str(len(xtalList)),os.path.join(self.panddas_directory,'processed_datasets'))) + self.update_log.insert('found %s PDB files in %s' % ( + str(len(xtalList)), os.path.join(self.panddas_directory, 'processed_datasets'))) if len(xtalList) >= 10: - self.update_log.insert('sorting PDBs by Rfree and selecting the 10 with lowest value') + self.update_log.insert( + 'sorting PDBs by Rfree and selecting the 10 with lowest value') rfree = sorted(xtalList, key=lambda x: x[1])[:10] self.update_log.insert('top 10 PDB files with lowest Rfree:') for item in rfree: - self.update_log.insert('%s: Rfree = %s | Resolution = %s' %(item[0],str(round(item[1],3)),str(round(item[2],2)))) + self.update_log.insert('%s: Rfree = %s | Resolution = %s' % ( + item[0], str(round(item[1], 3)), str(round(item[2], 2)))) self.update_log.insert('selecting PDB with highest resolution') reso = sorted(rfree, key=lambda x: x[2])[:1] - self.update_log.insert('selected the following PDB file: %s: Rfree = %s | Resolution = %s' %(reso[0][0],str(round(reso[0][1],3)),str(round(reso[0][2],2)))) - pdb = os.path.join(self.panddas_directory,'processed_datasets',reso[0][0],reso[0][0]+'-pandda-input.pdb') - mtz = os.path.join(self.panddas_directory,'processed_datasets',reso[0][0],reso[0][0]+'-pandda-input.mtz') + self.update_log.insert('selected the following PDB file: %s: Rfree = %s | Resolution = %s' % ( + reso[0][0], str(round(reso[0][1], 3)), str(round(reso[0][2], 2)))) + pdb = os.path.join(self.panddas_directory, 'processed_datasets', + reso[0][0], reso[0][0]+'-pandda-input.pdb') + mtz = os.path.join(self.panddas_directory, 'processed_datasets', + reso[0][0], reso[0][0]+'-pandda-input.mtz') else: - self.update_log.error('found less than 10 valid PDB files in %s' %os.path.join(self.panddas_directory,'processed_datasets')) + self.update_log.error('found less than 10 valid PDB files in %s' % os.path.join( + self.panddas_directory, 'processed_datasets')) return pdb, mtz - def prepare_ground_state_mmcif(self): - self.update_log.insert('preparing mmcif file for apo structure deposition') + self.update_log.insert( + 'preparing mmcif file for apo structure deposition') self.prepare_models_for_deposition_ligand_bound('ground_state') def open_icm(self): self.update_log.insert('starting ICM...') self.work_thread = XChemThread.start_ICM(self.html_export_directory) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() def prepare_files_for_zenodo_upload(self): @@ -649,12 +714,16 @@ def update_html_for_zenodo_upload(self): #################################################################################################################### def settings_button_clicked(self): if self.sender().text() == 'Select Project Directory': - self.initial_model_directory = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) - self.initial_model_directory_label.setText(self.initial_model_directory) - self.pandda_input_data_dir_entry.setText(self.initial_model_directory) + self.initial_model_directory = str( + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) + self.initial_model_directory_label.setText( + self.initial_model_directory) + self.pandda_input_data_dir_entry.setText( + self.initial_model_directory) self.settings['initial_model_directory'] = self.initial_model_directory if self.sender().text() == 'Select Reference Structure Directory': - reference_directory_temp = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) + reference_directory_temp = str( + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) if reference_directory_temp != self.reference_directory: self.reference_directory = reference_directory_temp self.update_reference_files(' ') @@ -667,22 +736,28 @@ def settings_button_clicked(self): self.data_source_file = filepath.split('/')[-1] self.database_directory = filepath[:filepath.rfind('/')] self.settings['database_directory'] = self.database_directory - self.settings['data_source'] = os.path.join(self.database_directory, self.data_source_file) + self.settings['data_source'] = os.path.join( + self.database_directory, self.data_source_file) write_enabled = self.check_write_permissions_of_data_source() if not write_enabled: self.data_source_set = False else: self.data_source_set = True - self.data_source_file_label.setText(os.path.join(self.database_directory, self.data_source_file)) - self.db = XChemDB.data_source(os.path.join(self.database_directory, self.data_source_file)) + self.data_source_file_label.setText(os.path.join( + self.database_directory, self.data_source_file)) + self.db = XChemDB.data_source(os.path.join( + self.database_directory, self.data_source_file)) self.db.create_missing_columns() self.datasource_menu_reload_samples() if self.sender().text() == 'Select Data Collection Directory': - dir_name = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) + dir_name = str(QtGui.QFileDialog.getExistingDirectory( + self.window, "Select Directory")) if dir_name != self.beamline_directory: self.beamline_directory = dir_name - self.target_list, self.visit_list = XChemMain.get_target_and_visit_list(self.beamline_directory,self.read_agamemnon.isChecked()) - self.populate_target_selection_combobox(self.target_selection_combobox) + self.target_list, self.visit_list = XChemMain.get_target_and_visit_list( + self.beamline_directory, self.read_agamemnon.isChecked()) + self.populate_target_selection_combobox( + self.target_selection_combobox) self.beamline_directory_label.setText(self.beamline_directory) self.settings['beamline_directory'] = self.beamline_directory @@ -690,66 +765,77 @@ def settings_button_clicked(self): if self.datasets_summary_file != '': filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', self.datasets_summary_file[ - :self.datasets_summary_file.rfind( - '/')], '*.pkl') + :self.datasets_summary_file.rfind( + '/')], '*.pkl') else: filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', os.getcwd(), '*.pkl') filepath = str(tuple(filepath_temp)[0]) self.datasets_summary_file = filepath - self.datasets_summary_file_label.setText(self.datasets_summary_file) + self.datasets_summary_file_label.setText( + self.datasets_summary_file) self.settings['datasets_summary'] = self.datasets_summary_file if self.sender().text() == 'Assign New\nCollection Summary File': if self.datasets_summary_file != '': file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'New file', self.datasets_summary_file[ - :self.datasets_summary_file.rfind('/')])) + :self.datasets_summary_file.rfind('/')])) else: - file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'New file', self.current_directory)) + file_name = str(QtGui.QFileDialog.getSaveFileName( + self.window, 'New file', self.current_directory)) # make sure that the file always has .pkl extension if str(file_name).rfind('.') != -1: file_name = file_name[:file_name.rfind('.')] + '.pkl' else: file_name = file_name + '.pkl' self.datasets_summary_file = file_name - self.datasets_summary_file_label.setText(self.datasets_summary_file) + self.datasets_summary_file_label.setText( + self.datasets_summary_file) self.settings['datasets_summary'] = self.datasets_summary_file if self.sender().text() == 'Select CCP4_SCR Directory': - self.ccp4_scratch_directory = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) - self.ccp4_scratch_directory_label.setText(self.ccp4_scratch_directory) + self.ccp4_scratch_directory = str( + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) + self.ccp4_scratch_directory_label.setText( + self.ccp4_scratch_directory) self.settings['ccp4_scratch'] = self.ccp4_scratch_directory if self.sender().text() == 'Select PanDDA Directory': - self.panddas_directory = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) + self.panddas_directory = str( + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) self.panddas_directory_label.setText(self.panddas_directory) self.pandda_output_data_dir_entry.setText(self.panddas_directory) - self.ground_state_pandda_directory_label.setText(self.panddas_directory) + self.ground_state_pandda_directory_label.setText( + self.panddas_directory) print('PANDDA', self.panddas_directory) self.settings['panddas_directory'] = self.panddas_directory self.layout_funcs.pandda_html(self) if self.sender().text() == 'Select HTML Export Directory': - self.html_export_directory = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) - self.html_export_directory_label.setText(self.html_export_directory) + self.html_export_directory = str( + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) + self.html_export_directory_label.setText( + self.html_export_directory) self.settings['html_export_directory'] = self.html_export_directory if self.sender().text() == 'Select Group deposition Directory': - self.group_deposit_directory = str(QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) - self.group_deposition_directory_label.setText(self.group_deposit_directory) + self.group_deposit_directory = str( + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) + self.group_deposition_directory_label.setText( + self.group_deposit_directory) self.settings['group_deposit_directory'] = self.group_deposit_directory - #self.datasource_menu_reload_samples() - - + # self.datasource_menu_reload_samples() ######################################### sort stuff below here #################################################### + def select_sample_for_dimple(self): indexes = self.maps_table.selectionModel().selectedRows() for index in sorted(indexes): xtal = str(self.maps_table.item(index.row(), 0).text()) - self.update_log.insert('{0!s} is marked for DIMPLE'.format(index.row())) + self.update_log.insert( + '{0!s} is marked for DIMPLE'.format(index.row())) self.initial_model_dimple_dict[xtal][0].setChecked(True) def update_summary_plot(self): @@ -776,23 +862,31 @@ def show_preferences(self): settings_hbox_adjust_allowed_unit_cell_difference = QtGui.QHBoxLayout() adjust_allowed_unit_cell_difference_label = QtGui.QLabel( 'Max. Allowed Unit Cell Difference between Reference and Target (%):') - settings_hbox_adjust_allowed_unit_cell_difference.addWidget(adjust_allowed_unit_cell_difference_label) + settings_hbox_adjust_allowed_unit_cell_difference.addWidget( + adjust_allowed_unit_cell_difference_label) adjust_allowed_unit_cell_difference = QtGui.QLineEdit() adjust_allowed_unit_cell_difference.setFixedWidth(200) - adjust_allowed_unit_cell_difference.setText(str(self.allowed_unitcell_difference_percent)) - adjust_allowed_unit_cell_difference.textChanged[str].connect(self.change_allowed_unitcell_difference_percent) - settings_hbox_adjust_allowed_unit_cell_difference.addWidget(adjust_allowed_unit_cell_difference) + adjust_allowed_unit_cell_difference.setText( + str(self.allowed_unitcell_difference_percent)) + adjust_allowed_unit_cell_difference.textChanged[str].connect( + self.change_allowed_unitcell_difference_percent) + settings_hbox_adjust_allowed_unit_cell_difference.addWidget( + adjust_allowed_unit_cell_difference) vbox.addLayout(settings_hbox_adjust_allowed_unit_cell_difference) settings_hbox_acceptable_low_resolution_limit = QtGui.QHBoxLayout() adjust_acceptable_low_resolution_limit_label = QtGui.QLabel( 'Acceptable low resolution limit for datasets (in Angstrom):') - settings_hbox_acceptable_low_resolution_limit.addWidget(adjust_acceptable_low_resolution_limit_label) + settings_hbox_acceptable_low_resolution_limit.addWidget( + adjust_acceptable_low_resolution_limit_label) adjust_acceptable_low_resolution_limit = QtGui.QLineEdit() adjust_acceptable_low_resolution_limit.setFixedWidth(200) - adjust_acceptable_low_resolution_limit.setText(str(self.acceptable_low_resolution_limit_for_data)) - adjust_acceptable_low_resolution_limit.textChanged[str].connect(self.change_acceptable_low_resolution_limit) - settings_hbox_acceptable_low_resolution_limit.addWidget(adjust_acceptable_low_resolution_limit) + adjust_acceptable_low_resolution_limit.setText( + str(self.acceptable_low_resolution_limit_for_data)) + adjust_acceptable_low_resolution_limit.textChanged[str].connect( + self.change_acceptable_low_resolution_limit) + settings_hbox_acceptable_low_resolution_limit.addWidget( + adjust_acceptable_low_resolution_limit) vbox.addLayout(settings_hbox_acceptable_low_resolution_limit) vbox_data = QtGui.QVBoxLayout() @@ -813,7 +907,8 @@ def show_preferences(self): self.preferences_selection_mechanism_combobox.addItem(item) self.preferences_selection_mechanism_combobox.currentIndexChanged.connect( self.preferences_selection_mechanism_combobox_changed) - index = self.preferences_selection_mechanism_combobox.findText(self.preferences['dataset_selection_mechanism'], QtCore.Qt.MatchFixedString) + index = self.preferences_selection_mechanism_combobox.findText( + self.preferences['dataset_selection_mechanism'], QtCore.Qt.MatchFixedString) self.preferences_selection_mechanism_combobox.setCurrentIndex(index) vbox_select.addWidget(self.preferences_selection_mechanism_combobox) vbox.addLayout(vbox_select) @@ -831,15 +926,18 @@ def show_preferences(self): # vbox.addLayout(vbox_inital_refinement) vbox_restraints = QtGui.QVBoxLayout() - vbox_restraints.addWidget(QtGui.QLabel('Restraints generation program:')) + vbox_restraints.addWidget(QtGui.QLabel( + 'Restraints generation program:')) self.preferences_restraints_generation_combobox = QtGui.QComboBox() program_list = [] if self.external_software['acedrg']: program_list.append('acedrg') self.restraints_program = 'acedrg' - if self.external_software['phenix.elbow']: program_list.append('phenix.elbow') - if self.external_software['grade']: program_list.append('grade') + if self.external_software['phenix.elbow']: + program_list.append('phenix.elbow') + if self.external_software['grade']: + program_list.append('grade') for item in program_list: self.preferences_restraints_generation_combobox.addItem(item) self.preferences_restraints_generation_combobox.currentIndexChanged.connect( @@ -847,7 +945,8 @@ def show_preferences(self): index = self.preferences_restraints_generation_combobox.findText(self.restraints_program, QtCore.Qt.MatchFixedString) self.preferences_restraints_generation_combobox.setCurrentIndex(index) - vbox_restraints.addWidget(self.preferences_restraints_generation_combobox) + vbox_restraints.addWidget( + self.preferences_restraints_generation_combobox) vbox.addLayout(vbox_restraints) hbox = QtGui.QHBoxLayout() @@ -860,12 +959,14 @@ def show_preferences(self): vbox.addLayout(hbox) settings_hbox_max_queue_jobs = QtGui.QHBoxLayout() - adjust_max_queue_jobs_label = QtGui.QLabel('Max. number of jobs running at once on DLS cluster:') + adjust_max_queue_jobs_label = QtGui.QLabel( + 'Max. number of jobs running at once on DLS cluster:') settings_hbox_max_queue_jobs.addWidget(adjust_max_queue_jobs_label) adjust_max_queue_jobs = QtGui.QLineEdit() adjust_max_queue_jobs.setFixedWidth(200) adjust_max_queue_jobs.setText(str(self.max_queue_jobs)) - adjust_max_queue_jobs.textChanged[str].connect(self.change_max_queue_jobs) + adjust_max_queue_jobs.textChanged[str].connect( + self.change_max_queue_jobs) settings_hbox_max_queue_jobs.addWidget(adjust_max_queue_jobs) vbox.addLayout(settings_hbox_max_queue_jobs) @@ -876,11 +977,14 @@ def show_preferences(self): self.remote_qsub_checkbox.toggled.connect(self.run_qsub_remotely) settings_hbox_dimple_twin_mode = QtGui.QHBoxLayout() - self.dimple_twin_mode_label_checkbox = QtGui.QCheckBox('run DIMPLE in TWIN mode') + self.dimple_twin_mode_label_checkbox = QtGui.QCheckBox( + 'run DIMPLE in TWIN mode') if self.preferences['dimple_twin_mode']: self.dimple_twin_mode_label_checkbox.setChecked(True) - self.dimple_twin_mode_label_checkbox.toggled.connect(self.dimple_change_twin_mode) - settings_hbox_dimple_twin_mode.addWidget(self.dimple_twin_mode_label_checkbox) + self.dimple_twin_mode_label_checkbox.toggled.connect( + self.dimple_change_twin_mode) + settings_hbox_dimple_twin_mode.addWidget( + self.dimple_twin_mode_label_checkbox) vbox.addLayout(settings_hbox_dimple_twin_mode) if self.using_remote_qsub_submission: @@ -893,7 +997,8 @@ def show_preferences(self): vbox.addLayout(settings_hbox_remote_qsub) hbox = QtGui.QHBoxLayout() - hbox.addWidget(QtGui.QLabel('Additional CIF file for non-standard ligand:')) + hbox.addWidget(QtGui.QLabel( + 'Additional CIF file for non-standard ligand:')) self.second_cif_file_label = QtGui.QLabel(self.second_cif_file) hbox.addWidget(self.second_cif_file_label) button = QtGui.QPushButton("Select") @@ -914,10 +1019,9 @@ def show_preferences(self): # apply_button.clicked.connect(self.run_qsub_remotely) # settings_hbox_remote_qsub.addWidget(apply_button) - preferencesLayout.addLayout(vbox, 0, 0) - preferences.exec_(); + preferences.exec_() # def set_second_cif_file(self): # mb = QtGui.QMessageBox() @@ -934,21 +1038,22 @@ def show_preferences(self): # mb.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) # reply = mb.exec_(); - - def dimple_change_twin_mode(self): if self.preferences['dimple_twin_mode']: - self.update_log.insert('changing preferences: turning off DIMPLE in TWIN mode') + self.update_log.insert( + 'changing preferences: turning off DIMPLE in TWIN mode') self.preferences['dimple_twin_mode'] = False else: - self.update_log.insert('changing preferences: changing DIMPLE to TWIN mode') + self.update_log.insert( + 'changing preferences: changing DIMPLE to TWIN mode') self.preferences['dimple_twin_mode'] = True def run_qsub_remotely(self): self.remote_qsub_submission = str(self.remote_qsub_command.text()) print(str(self.remote_qsub_submission)) if self.remote_qsub_checkbox.isChecked(): - self.update_log.insert('submitting jobs to remote machine with: %s' % self.remote_qsub_submission) + self.update_log.insert( + 'submitting jobs to remote machine with: %s' % self.remote_qsub_submission) self.external_software['qsub_remote'] = self.remote_qsub_submission self.using_remote_qsub_submission = True self.settings['remote_qsub'] = self.remote_qsub_submission @@ -985,8 +1090,7 @@ def enter_pdb_codes(self): vbox.addLayout(hbox) pdbID_entryLayout.addLayout(vbox, 0, 0) - pdbID_entry.exec_(); - + pdbID_entry.exec_() def add_label_information(self): label_entry = QtGui.QMessageBox() @@ -1025,7 +1129,7 @@ def add_label_information(self): descriptionEdit.setText('') labelEdit.setFixedWidth(100) descriptionEdit.setFixedWidth(500) - self.labelList.append([labelEdit,descriptionEdit]) + self.labelList.append([labelEdit, descriptionEdit]) frame.setLayout(grid) vbox.addWidget(frame) @@ -1036,13 +1140,7 @@ def add_label_information(self): vbox.addLayout(hbox) label_entryLayout.addLayout(vbox, 0, 0) - label_entry.exec_(); - - - - - - + label_entry.exec_() def create_missing_apo_records_in_depositTable(self): self.db.create_missing_apo_records_for_all_structures_in_depositTable(self.initial_model_directory, @@ -1053,29 +1151,34 @@ def create_missing_apo_records_in_depositTable(self): # os.path.join(self.database_directory, self.data_source_file), self.initial_model_directory, # self.xce_logfile) - def prepare_models_for_deposition_ligand_bound(self,structureType): + def prepare_models_for_deposition_ligand_bound(self, structureType): start_thread = True - self.update_log.insert('preparing mmcif files for PDB group deposition...') + self.update_log.insert( + 'preparing mmcif files for PDB group deposition...') ignore_event_map = False if structureType == 'ground_state': try: self.update_log.insert('ground-state deposition') - data_template_dict = self.db.get_deposit_dict_for_sample('ground_state') + data_template_dict = self.db.get_deposit_dict_for_sample( + 'ground_state') pdb = data_template_dict['PDB_file'] self.update_log.insert('looking for ground-state PDB: ' + pdb) if not os.path.isfile(pdb): - self.update_log.error('ground-state PDB does not exist; stopping...') + self.update_log.error( + 'ground-state PDB does not exist; stopping...') start_thread = False mtz = data_template_dict['MTZ_file'] self.update_log.insert('looking for ground-state MTZ: ' + mtz) if not os.path.isfile(mtz): - self.update_log.error('ground-state MTZ does not exist; stopping...') + self.update_log.error( + 'ground-state MTZ does not exist; stopping...') start_thread = False - ground_state = [ pdb, - mtz, - self.panddas_directory ] + ground_state = [pdb, + mtz, + self.panddas_directory] except KeyError: - self.update_log.error('seems like there is no entry for ground-state in database') + self.update_log.error( + 'seems like there is no entry for ground-state in database') start_thread = False else: ground_state = [] @@ -1098,9 +1201,12 @@ def prepare_models_for_deposition_ligand_bound(self,structureType): ground_state, ignore_event_map) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() def prepare_models_for_deposition_apo(self): @@ -1115,9 +1221,12 @@ def prepare_models_for_deposition_apo(self): self.initial_model_directory, structureType) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() def prepare_for_group_deposition_upload_ligand_bound(self): @@ -1125,11 +1234,14 @@ def prepare_for_group_deposition_upload_ligand_bound(self): self.work_thread = XChemDeposit.prepare_for_group_deposition_upload( os.path.join(self.database_directory, self.data_source_file), self.xce_logfile, - self.group_deposit_directory,self.initial_model_directory,'ligand_bound') + self.group_deposit_directory, self.initial_model_directory, 'ligand_bound') self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() def prepare_for_group_deposition_upload_ground_state(self): @@ -1137,11 +1249,14 @@ def prepare_for_group_deposition_upload_ground_state(self): self.work_thread = XChemDeposit.prepare_for_group_deposition_upload( os.path.join(self.database_directory, self.data_source_file), self.xce_logfile, - self.group_deposit_directory,self.initial_model_directory,'ground_state') + self.group_deposit_directory, self.initial_model_directory, 'ground_state') self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() def check_smiles_in_db_and_pdb(self): @@ -1151,10 +1266,14 @@ def check_smiles_in_db_and_pdb(self): self.data_source_file), self.xce_logfile) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("show_error_dict"), self.show_error_dict) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "show_error_dict"), self.show_error_dict) self.work_thread.start() def deposition_data(self): @@ -1173,7 +1292,7 @@ def deposition_data(self): 'Misc', 'Methods', 'Software', - 'Funding' ] + 'Funding'] deposit_tab_dict = {} for page in deposit_tab_list: @@ -1182,7 +1301,7 @@ def deposition_data(self): deposit_tab_widget.addTab(tab, page) deposit_tab_dict[page] = [tab, vb] - ## PI and scientist info + # PI and scientist info vb = QtGui.QVBoxLayout() hbox = QtGui.QHBoxLayout() @@ -1214,20 +1333,23 @@ def deposition_data(self): self.contact_author_PI_middle_name = QtGui.QLineEdit() self.contact_author_PI_middle_name.setText('') self.contact_author_PI_middle_name.setFixedWidth(200) - self.contact_author_PI_middle_name.setStyleSheet("background-color: rgb(192, 192, 192);") + self.contact_author_PI_middle_name.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.contact_author_PI_middle_name, 4, 1) grid.addWidget(QtGui.QLabel('PI role'), 5, 0) self.contact_author_PI_role = QtGui.QComboBox() # PIroles = ['group leader', 'principal investigator/group leader', 'investigator'] PIroles = ['principal investigator/group leader'] - for item in PIroles: self.contact_author_PI_role.addItem(item) + for item in PIroles: + self.contact_author_PI_role.addItem(item) grid.addWidget(self.contact_author_PI_role, 5, 1) grid.addWidget(QtGui.QLabel('Organization type'), 6, 0) self.contact_author_PI_organization_type = QtGui.QComboBox() Organizations = ['academic', 'commercial', 'government'] - for item in Organizations: self.contact_author_PI_organization_type.addItem(item) + for item in Organizations: + self.contact_author_PI_organization_type.addItem(item) grid.addWidget(self.contact_author_PI_organization_type, 6, 1) grid.addWidget(QtGui.QLabel('Organization Name'), 7, 0) @@ -1258,7 +1380,8 @@ def deposition_data(self): self.contact_author_PI_State_or_Province = QtGui.QLineEdit() self.contact_author_PI_State_or_Province.setText('') self.contact_author_PI_State_or_Province.setFixedWidth(200) - self.contact_author_PI_State_or_Province.setStyleSheet("background-color: rgb(192, 192, 192);") + self.contact_author_PI_State_or_Province.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.contact_author_PI_State_or_Province, 11, 1) grid.addWidget(QtGui.QLabel('ZIP code'), 12, 0) @@ -1315,20 +1438,23 @@ def deposition_data(self): self.contact_author_middle_name = QtGui.QLineEdit() self.contact_author_middle_name.setText('') self.contact_author_middle_name.setFixedWidth(200) - self.contact_author_middle_name.setStyleSheet("background-color: rgb(192, 192, 192);") + self.contact_author_middle_name.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.contact_author_middle_name, 4, 1) grid.addWidget(QtGui.QLabel('Role'), 5, 0) self.contact_author_role = QtGui.QComboBox() ScientistRoles = ['responsible scientist', 'investigator'] - for item in ScientistRoles: self.contact_author_role.addItem(item) + for item in ScientistRoles: + self.contact_author_role.addItem(item) grid.addWidget(self.contact_author_role, 5, 1) grid.addWidget(QtGui.QLabel('Organization type'), 6, 0) self.contact_author_organization_type = QtGui.QComboBox() - for item in Organizations: self.contact_author_organization_type.addItem(item) + for item in Organizations: + self.contact_author_organization_type.addItem(item) grid.addWidget(self.contact_author_organization_type, 6, 1) grid.addWidget(QtGui.QLabel('Organization Name'), 7, 0) @@ -1359,7 +1485,8 @@ def deposition_data(self): self.contact_author_State_or_Province = QtGui.QLineEdit() self.contact_author_State_or_Province.setText('') self.contact_author_State_or_Province.setFixedWidth(200) - self.contact_author_State_or_Province.setStyleSheet("background-color: rgb(192, 192, 192);") + self.contact_author_State_or_Province.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.contact_author_State_or_Province, 11, 1) grid.addWidget(QtGui.QLabel('ZIP code'), 12, 0) @@ -1395,7 +1522,7 @@ def deposition_data(self): deposit_tab_dict['Contact'][1].addLayout(vb) - ## release status + # release status vb = QtGui.QVBoxLayout() frame = QtGui.QFrame() @@ -1408,14 +1535,17 @@ def deposition_data(self): self.Release_status_for_sequence = QtGui.QComboBox() codeStatus = ['RELEASE NOW', 'HOLD FOR RELEASE'] - for item in codeStatus: self.Release_status_for_sequence.addItem(item) + for item in codeStatus: + self.Release_status_for_sequence.addItem(item) grid.addWidget(self.Release_status_for_sequence, 4, 1) - grid.addWidget(QtGui.QLabel('Release Status for coordinates/ SF'), 8, 0) + grid.addWidget(QtGui.QLabel( + 'Release Status for coordinates/ SF'), 8, 0) self.Release_status_for_coordinates = QtGui.QComboBox() coordStatus = ['RELEASE NOW', 'HOLD FOR PUBLICATION', 'HOLD FOR 4 WEEKS', 'HOLD FOR 6 MONTHS', 'HOLD FOR 1 YEAR'] - for item in coordStatus: self.Release_status_for_coordinates.addItem(item) + for item in coordStatus: + self.Release_status_for_coordinates.addItem(item) grid.addWidget(self.Release_status_for_coordinates, 8, 1) frame.setLayout(grid) @@ -1446,7 +1576,8 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Structure Title (ligand bound)'), 4, 0) self.structure_title = QtGui.QLineEdit() - self.structure_title.setText('Crystal Structure of $ProteinName in complex with $CompoundName') + self.structure_title.setText( + 'Crystal Structure of $ProteinName in complex with $CompoundName') self.structure_title.setFixedWidth(600) grid.addWidget(self.structure_title, 4, 1) @@ -1467,14 +1598,15 @@ def deposition_data(self): deposit_tab_dict['General'][1].addLayout(vb) - ## authors + # authors vb = QtGui.QVBoxLayout() frame = QtGui.QFrame() frame.setFrameShape(QtGui.QFrame.StyledPanel) grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Deposition authors (e.g. Surname, F.M.)'), 0, 0) + grid.addWidget(QtGui.QLabel( + 'Deposition authors (e.g. Surname, F.M.)'), 0, 0) self.structure_author_name_List = [] @@ -1493,7 +1625,7 @@ def deposition_data(self): deposit_tab_dict['Authors'][1].addLayout(vb) - ## primary citation + # primary citation vb = QtGui.QVBoxLayout() frame = QtGui.QFrame() @@ -1518,46 +1650,52 @@ def deposition_data(self): self.primary_citation_title = QtGui.QLineEdit() self.primary_citation_title.setText('') self.primary_citation_title.setFixedWidth(500) - self.primary_citation_title.setStyleSheet("background-color: rgb(192, 192, 192);") + self.primary_citation_title.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.primary_citation_title, 3, 1) grid.addWidget(QtGui.QLabel('Year'), 4, 0) self.primary_citation_year = QtGui.QLineEdit() self.primary_citation_year.setText('') self.primary_citation_year.setFixedWidth(500) - self.primary_citation_year.setStyleSheet("background-color: rgb(192, 192, 192);") + self.primary_citation_year.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.primary_citation_year, 4, 1) grid.addWidget(QtGui.QLabel('Volume'), 5, 0) self.primary_citation_journal_volume = QtGui.QLineEdit() self.primary_citation_journal_volume.setText('') self.primary_citation_journal_volume.setFixedWidth(500) - self.primary_citation_journal_volume.setStyleSheet("background-color: rgb(192, 192, 192);") + self.primary_citation_journal_volume.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.primary_citation_journal_volume, 5, 1) grid.addWidget(QtGui.QLabel('Page, first'), 6, 0) self.primary_citation_page_first = QtGui.QLineEdit() self.primary_citation_page_first.setText('') self.primary_citation_page_first.setFixedWidth(500) - self.primary_citation_page_first.setStyleSheet("background-color: rgb(192, 192, 192);") + self.primary_citation_page_first.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.primary_citation_page_first, 6, 1) grid.addWidget(QtGui.QLabel('Page, last'), 7, 0) self.primary_citation_page_last = QtGui.QLineEdit() self.primary_citation_page_last.setText('') self.primary_citation_page_last.setFixedWidth(500) - self.primary_citation_page_last.setStyleSheet("background-color: rgb(192, 192, 192);") + self.primary_citation_page_last.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.primary_citation_page_last, 7, 1) frame.setLayout(grid) vb.addWidget(frame) - ## citation authors + # citation authors frame = QtGui.QFrame() frame.setFrameShape(QtGui.QFrame.StyledPanel) grid = QtGui.QGridLayout() - self.set_primary_citation_authors = QtGui.QCheckBox('same as deposition authors') + self.set_primary_citation_authors = QtGui.QCheckBox( + 'same as deposition authors') self.layout_funcs.add_checkbox(self, self.set_primary_citation_authors, 'xce_object.set_primary_citation_as_structure_authors') grid.addWidget(self.set_primary_citation_authors, 0, 0) @@ -1570,7 +1708,8 @@ def deposition_data(self): primary_citation_author_name.setText('') primary_citation_author_name.setFixedWidth(300) grid.addWidget(primary_citation_author_name, row, column) - self.primary_citation_author_name_List.append(primary_citation_author_name) + self.primary_citation_author_name_List.append( + primary_citation_author_name) frame.setLayout(grid) vb.addWidget(frame) @@ -1579,7 +1718,7 @@ def deposition_data(self): deposit_tab_dict['Citation'][1].addLayout(vb) - ## molecule info + # molecule info vb = QtGui.QVBoxLayout() frame = QtGui.QFrame() @@ -1601,15 +1740,18 @@ def deposition_data(self): self.fragment_name_one = QtGui.QLineEdit() self.fragment_name_one.setText('') self.fragment_name_one.setFixedWidth(300) - self.fragment_name_one.setStyleSheet("background-color: rgb(192, 192, 192);") + self.fragment_name_one.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.fragment_name_one, 3, 1) - grid.addWidget(QtGui.QLabel('(e.g. ligand binding domain, hairpin)'), 3, 2) + grid.addWidget(QtGui.QLabel( + '(e.g. ligand binding domain, hairpin)'), 3, 2) grid.addWidget(QtGui.QLabel('Specific Mutation'), 4, 0) self.fragment_name_one_specific_mutation = QtGui.QLineEdit() self.fragment_name_one_specific_mutation.setText('') self.fragment_name_one_specific_mutation.setFixedWidth(300) - self.fragment_name_one_specific_mutation.setStyleSheet("background-color: rgb(192, 192, 192);") + self.fragment_name_one_specific_mutation.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.fragment_name_one_specific_mutation, 4, 1) grid.addWidget(QtGui.QLabel('(e.g. C280S)'), 4, 2) @@ -1617,7 +1759,8 @@ def deposition_data(self): self.fragment_name_one_enzyme_comission_number = QtGui.QLineEdit() self.fragment_name_one_enzyme_comission_number.setText('') self.fragment_name_one_enzyme_comission_number.setFixedWidth(300) - self.fragment_name_one_enzyme_comission_number.setStyleSheet("background-color: rgb(192, 192, 192);") + self.fragment_name_one_enzyme_comission_number.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.fragment_name_one_enzyme_comission_number, 5, 1) grid.addWidget(QtGui.QLabel('(if known: e.g. 2.7.7.7)'), 5, 2) @@ -1642,11 +1785,13 @@ def deposition_data(self): self.Source_organism_strain = QtGui.QLineEdit() self.Source_organism_strain.setText('') self.Source_organism_strain.setFixedWidth(300) - self.Source_organism_strain.setStyleSheet("background-color: rgb(192, 192, 192);") + self.Source_organism_strain.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.Source_organism_strain, 9, 1) grid.addWidget(QtGui.QLabel('(e.g. BH10 ISOLATE, K-12...)'), 9, 2) - grid.addWidget(QtGui.QLabel('Expression system scientific name'), 10, 0) + grid.addWidget(QtGui.QLabel( + 'Expression system scientific name'), 10, 0) self.Expression_system_scientific_name = QtGui.QComboBox() for item in taxonomy_dict: @@ -1657,7 +1802,8 @@ def deposition_data(self): self.Expression_system_strain = QtGui.QLineEdit() self.Expression_system_strain.setText('') self.Expression_system_strain.setFixedWidth(300) - self.Expression_system_strain.setStyleSheet("background-color: rgb(192, 192, 192);") + self.Expression_system_strain.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.Expression_system_strain, 11, 1) grid.addWidget(QtGui.QLabel('(e.g. BL21(DE3))'), 11, 2) @@ -1665,7 +1811,8 @@ def deposition_data(self): self.Expression_system_vector_type = QtGui.QLineEdit() self.Expression_system_vector_type.setText('') self.Expression_system_vector_type.setFixedWidth(300) - self.Expression_system_vector_type.setStyleSheet("background-color: rgb(192, 192, 192);") + self.Expression_system_vector_type.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.Expression_system_vector_type, 12, 1) grid.addWidget(QtGui.QLabel('(e.g. plasmid)'), 12, 2) @@ -1673,7 +1820,8 @@ def deposition_data(self): self.Expression_system_plasmid_name = QtGui.QLineEdit() self.Expression_system_plasmid_name.setText('') self.Expression_system_plasmid_name.setFixedWidth(300) - self.Expression_system_plasmid_name.setStyleSheet("background-color: rgb(192, 192, 192);") + self.Expression_system_plasmid_name.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.Expression_system_plasmid_name, 13, 1) grid.addWidget(QtGui.QLabel('(e.g. pET26)'), 13, 2) @@ -1681,7 +1829,8 @@ def deposition_data(self): self.Manipulated_source_details = QtGui.QLineEdit() self.Manipulated_source_details.setText('') self.Manipulated_source_details.setFixedWidth(300) - self.Manipulated_source_details.setStyleSheet("background-color: rgb(192, 192, 192);") + self.Manipulated_source_details.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.Manipulated_source_details, 14, 1) grid.addWidget(QtGui.QLabel('(any other relevant information)'), 14, 2) @@ -1695,14 +1844,15 @@ def deposition_data(self): frame.setLayout(grid) vb.addWidget(frame) - ### entity 2 + # entity 2 frame = QtGui.QFrame() frame.setFrameShape(QtGui.QFrame.StyledPanel) grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Entity 2 (IMPORTANT: only fill in if you are working with a protein-protein complex!)'), 1, 0) + grid.addWidget(QtGui.QLabel( + 'Entity 2 (IMPORTANT: only fill in if you are working with a protein-protein complex!)'), 1, 0) grid.addWidget(QtGui.QLabel('Molecule Name'), 2, 0) self.molecule_name_two = QtGui.QLineEdit() @@ -1716,15 +1866,18 @@ def deposition_data(self): self.fragment_name_two = QtGui.QLineEdit() self.fragment_name_two.setText('') self.fragment_name_two.setFixedWidth(300) - self.fragment_name_two.setStyleSheet("background-color: rgb(192, 192, 192);") + self.fragment_name_two.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.fragment_name_two, 3, 1) - grid.addWidget(QtGui.QLabel('(e.g. ligand binding domain, hairpin)'), 3, 2) + grid.addWidget(QtGui.QLabel( + '(e.g. ligand binding domain, hairpin)'), 3, 2) grid.addWidget(QtGui.QLabel('Specific Mutation'), 4, 0) self.fragment_name_two_specific_mutation = QtGui.QLineEdit() self.fragment_name_two_specific_mutation.setText('') self.fragment_name_two_specific_mutation.setFixedWidth(300) - self.fragment_name_two_specific_mutation.setStyleSheet("background-color: rgb(192, 192, 192);") + self.fragment_name_two_specific_mutation.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.fragment_name_two_specific_mutation, 4, 1) grid.addWidget(QtGui.QLabel('(e.g. C280S)'), 4, 2) @@ -1732,7 +1885,8 @@ def deposition_data(self): self.fragment_name_two_enzyme_comission_number = QtGui.QLineEdit() self.fragment_name_two_enzyme_comission_number.setText('') self.fragment_name_two_enzyme_comission_number.setFixedWidth(300) - self.fragment_name_two_enzyme_comission_number.setStyleSheet("background-color: rgb(192, 192, 192);") + self.fragment_name_two_enzyme_comission_number.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.fragment_name_two_enzyme_comission_number, 5, 1) grid.addWidget(QtGui.QLabel('(if known: e.g. 2.7.7.7)'), 5, 2) @@ -1743,7 +1897,8 @@ def deposition_data(self): self.Source_organism_scientific_name_two = QtGui.QComboBox() taxonomy_dict = XChemMain.NCBI_taxonomy_ID() for item in taxonomy_dict: - self.Source_organism_scientific_name_two.addItem(taxonomy_dict[item]) + self.Source_organism_scientific_name_two.addItem( + taxonomy_dict[item]) grid.addWidget(self.Source_organism_scientific_name_two, 7, 1) grid.addWidget(QtGui.QLabel('Source organism gene'), 8, 0) @@ -1757,22 +1912,26 @@ def deposition_data(self): self.Source_organism_strain_two = QtGui.QLineEdit() self.Source_organism_strain_two.setText('') self.Source_organism_strain_two.setFixedWidth(300) - self.Source_organism_strain_two.setStyleSheet("background-color: rgb(192, 192, 192);") + self.Source_organism_strain_two.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.Source_organism_strain_two, 9, 1) grid.addWidget(QtGui.QLabel('(e.g. BH10 ISOLATE, K-12...)'), 9, 2) - grid.addWidget(QtGui.QLabel('Expression system scientific name'), 10, 0) + grid.addWidget(QtGui.QLabel( + 'Expression system scientific name'), 10, 0) self.Expression_system_scientific_name_two = QtGui.QComboBox() for item in taxonomy_dict: - self.Expression_system_scientific_name_two.addItem(taxonomy_dict[item]) + self.Expression_system_scientific_name_two.addItem( + taxonomy_dict[item]) grid.addWidget(self.Expression_system_scientific_name_two, 10, 1) grid.addWidget(QtGui.QLabel('Expression system strain'), 11, 0) self.Expression_system_strain_two = QtGui.QLineEdit() self.Expression_system_strain_two.setText('') self.Expression_system_strain_two.setFixedWidth(300) - self.Expression_system_strain_two.setStyleSheet("background-color: rgb(192, 192, 192);") + self.Expression_system_strain_two.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.Expression_system_strain_two, 11, 1) grid.addWidget(QtGui.QLabel('(e.g. BL21(DE3))'), 11, 2) @@ -1780,7 +1939,8 @@ def deposition_data(self): self.Expression_system_vector_type_two = QtGui.QLineEdit() self.Expression_system_vector_type_two.setText('') self.Expression_system_vector_type_two.setFixedWidth(300) - self.Expression_system_vector_type_two.setStyleSheet("background-color: rgb(192, 192, 192);") + self.Expression_system_vector_type_two.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.Expression_system_vector_type_two, 12, 1) grid.addWidget(QtGui.QLabel('(e.g. plasmid)'), 12, 2) @@ -1788,7 +1948,8 @@ def deposition_data(self): self.Expression_system_plasmid_name_two = QtGui.QLineEdit() self.Expression_system_plasmid_name_two.setText('') self.Expression_system_plasmid_name_two.setFixedWidth(300) - self.Expression_system_plasmid_name_two.setStyleSheet("background-color: rgb(192, 192, 192);") + self.Expression_system_plasmid_name_two.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.Expression_system_plasmid_name_two, 13, 1) grid.addWidget(QtGui.QLabel('(e.g. pET26)'), 13, 2) @@ -1796,7 +1957,8 @@ def deposition_data(self): self.Manipulated_source_details_two = QtGui.QLineEdit() self.Manipulated_source_details_two.setText('') self.Manipulated_source_details_two.setFixedWidth(300) - self.Manipulated_source_details_two.setStyleSheet("background-color: rgb(192, 192, 192);") + self.Manipulated_source_details_two.setStyleSheet( + "background-color: rgb(192, 192, 192);") grid.addWidget(self.Manipulated_source_details_two, 14, 1) grid.addWidget(QtGui.QLabel('(any other relevant information)'), 14, 2) @@ -1811,16 +1973,13 @@ def deposition_data(self): vb.addWidget(frame) - ### entity 2 --- END - - - + # entity 2 --- END vb.addStretch(1) deposit_tab_dict['Molecule'][1].addLayout(vb) - ## misc + # misc vb = QtGui.QVBoxLayout() frame = QtGui.QFrame() @@ -1830,15 +1989,19 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Keywords'), 1, 0) self.structure_keywords = QtGui.QLineEdit() - self.structure_keywords.setText('SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer') + self.structure_keywords.setText( + 'SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer') self.structure_keywords.setFixedWidth(300) grid.addWidget(self.structure_keywords, 1, 1) - grid.addWidget(QtGui.QLabel('(e.g. beta barrel, protein-DNA complex)'), 1, 2) + grid.addWidget(QtGui.QLabel( + '(e.g. beta barrel, protein-DNA complex)'), 1, 2) grid.addWidget(QtGui.QLabel('Type'), 2, 0) self.structure_keywords_type = QtGui.QComboBox() - self.structure_keywords_type.setStyleSheet("background-color: rgb(192, 192, 192);") - for item in XChemMain.pdbx_keywords(): self.structure_keywords_type.addItem(item) + self.structure_keywords_type.setStyleSheet( + "background-color: rgb(192, 192, 192);") + for item in XChemMain.pdbx_keywords(): + self.structure_keywords_type.addItem(item) grid.addWidget(self.structure_keywords_type, 2, 1) # self.structure_keywords = QtGui.QLineEdit() # self.structure_keywords.setText('SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer') @@ -1851,7 +2014,8 @@ def deposition_data(self): self.biological_assembly_chain_number.setText('') self.biological_assembly_chain_number.setFixedWidth(300) grid.addWidget(self.biological_assembly_chain_number, 3, 1) - grid.addWidget(QtGui.QLabel('(e.g. 1 for monomer, 2 for dimer ..)'), 3, 2) + grid.addWidget(QtGui.QLabel( + '(e.g. 1 for monomer, 2 for dimer ..)'), 3, 2) grid.addWidget(QtGui.QLabel('Sequence UNIPROT ID'), 4, 0) self.molecule_one_letter_sequence_uniprot_id = QtGui.QLineEdit() @@ -1862,7 +2026,8 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Sequence'), 5, 0) self.molecule_one_letter_sequence = QtGui.QTextEdit() - self.molecule_one_letter_sequence.setStyleSheet("background-color: rgb(255, 255, 255);") + self.molecule_one_letter_sequence.setStyleSheet( + "background-color: rgb(255, 255, 255);") # self.molecule_one_letter_sequence.setStyleSheet("background-color: rgb(192, 192, 192);") self.molecule_one_letter_sequence.setText('') self.molecule_one_letter_sequence.setFixedWidth(300) @@ -1871,10 +2036,12 @@ def deposition_data(self): # grid.addWidget(QtGui.QLabel('Sequence information for entity 2'), 10, 0) # grid.addWidget(QtGui.QLabel('(Important: only for protein-protein complex'), 10, 1) - grid.addWidget(QtGui.QLabel('Sequence UNIPROT ID (Entity 2) - optional'), 13, 0) + grid.addWidget(QtGui.QLabel( + 'Sequence UNIPROT ID (Entity 2) - optional'), 13, 0) self.molecule_one_letter_sequence_uniprot_id_two = QtGui.QLineEdit() self.molecule_one_letter_sequence_uniprot_id_two.setText('') - self.molecule_one_letter_sequence_uniprot_id_two.setStyleSheet("background-color: rgb(192, 192, 192);") + self.molecule_one_letter_sequence_uniprot_id_two.setStyleSheet( + "background-color: rgb(192, 192, 192);") self.molecule_one_letter_sequence_uniprot_id_two.setFixedWidth(300) grid.addWidget(self.molecule_one_letter_sequence_uniprot_id_two, 13, 1) grid.addWidget(QtGui.QLabel('(e.g. Q6B0I6)'), 13, 2) @@ -1885,24 +2052,27 @@ def deposition_data(self): self.molecule_one_letter_sequence_two.setFixedWidth(300) grid.addWidget(self.molecule_one_letter_sequence_two, 14, 1, 19, 2) - grid.addWidget(QtGui.QLabel('Structural Genomic (optional)'), 21, 0) grid.addWidget(QtGui.QLabel('Project Name'), 22, 0) self.SG_project_name = QtGui.QLineEdit() self.SG_project_name.setText('') - self.SG_project_name.setStyleSheet("background-color: rgb(192, 192, 192);") + self.SG_project_name.setStyleSheet( + "background-color: rgb(192, 192, 192);") self.SG_project_name.setFixedWidth(300) grid.addWidget(self.SG_project_name, 22, 1) - grid.addWidget(QtGui.QLabel('(e.g. SGC, Structural Genomics Consortium)'), 22, 2) + grid.addWidget(QtGui.QLabel( + '(e.g. SGC, Structural Genomics Consortium)'), 22, 2) grid.addWidget(QtGui.QLabel('Full Name'), 23, 0) self.full_name_of_SG_center = QtGui.QLineEdit() self.full_name_of_SG_center.setText('') - self.full_name_of_SG_center.setStyleSheet("background-color: rgb(192, 192, 192);") + self.full_name_of_SG_center.setStyleSheet( + "background-color: rgb(192, 192, 192);") self.full_name_of_SG_center.setFixedWidth(300) grid.addWidget(self.full_name_of_SG_center, 23, 1) - grid.addWidget(QtGui.QLabel('(e.g. Structural Genomics Consortium)'), 23, 2) + grid.addWidget(QtGui.QLabel( + '(e.g. Structural Genomics Consortium)'), 23, 2) frame.setLayout(grid) vb.addWidget(frame) @@ -1911,7 +2081,7 @@ def deposition_data(self): deposit_tab_dict['Misc'][1].addLayout(vb) - ## methods + # methods vb = QtGui.QVBoxLayout() frame = QtGui.QFrame() @@ -1924,7 +2094,8 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Method'), 2, 0) self.crystallization_method = QtGui.QComboBox() - for item in XChemMain.crystal_growth_methods(): self.crystallization_method.addItem(item) + for item in XChemMain.crystal_growth_methods(): + self.crystallization_method.addItem(item) grid.addWidget(self.crystallization_method, 2, 1) grid.addWidget(QtGui.QLabel('pH'), 3, 0) @@ -1957,13 +2128,15 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Source'), 8, 0) self.radiation_source = QtGui.QComboBox() - for item in XChemMain.radiationSource(): self.radiation_source.addItem(item) + for item in XChemMain.radiationSource(): + self.radiation_source.addItem(item) grid.addWidget(self.radiation_source, 8, 1) grid.addWidget(QtGui.QLabel('Source Type'), 9, 0) self.radiation_source_type = QtGui.QComboBox() - for item in XChemMain.wwBeamlines(): self.radiation_source_type.addItem(item) + for item in XChemMain.wwBeamlines(): + self.radiation_source_type.addItem(item) grid.addWidget(self.radiation_source_type, 9, 1) grid.addWidget(QtGui.QLabel('Wavelength'), 10, 0) @@ -1976,13 +2149,15 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Detector'), 11, 0) self.radiation_detector = QtGui.QComboBox() - for item in XChemMain.detector(): self.radiation_detector.addItem(item) + for item in XChemMain.detector(): + self.radiation_detector.addItem(item) grid.addWidget(self.radiation_detector, 11, 1) grid.addWidget(QtGui.QLabel('Detector Type'), 12, 0) self.radiation_detector_type = QtGui.QComboBox() - for item in XChemMain.detectorType(): self.radiation_detector_type.addItem(item) + for item in XChemMain.detectorType(): + self.radiation_detector_type.addItem(item) grid.addWidget(self.radiation_detector_type, 12, 1) grid.addWidget(QtGui.QLabel('Date'), 13, 0) @@ -2004,7 +2179,8 @@ def deposition_data(self): self.data_collection_protocol.setText('SINGLE WAVELENGTH') self.data_collection_protocol.setFixedWidth(300) grid.addWidget(self.data_collection_protocol, 15, 1) - grid.addWidget(QtGui.QLabel('(e.g. SINGLE WAVELENGTH, MAD, ...)'), 15, 2) + grid.addWidget(QtGui.QLabel( + '(e.g. SINGLE WAVELENGTH, MAD, ...)'), 15, 2) frame.setLayout(grid) vb.addWidget(frame) @@ -2013,7 +2189,7 @@ def deposition_data(self): deposit_tab_dict['Methods'][1].addLayout(vb) - ## software + # software vb = QtGui.QVBoxLayout() frame = QtGui.QFrame() @@ -2030,12 +2206,14 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Data reduction'), 2, 0) self.data_integration_software = QtGui.QComboBox() - for item in XChemMain.data_integration_software(): self.data_integration_software.addItem(item) + for item in XChemMain.data_integration_software(): + self.data_integration_software.addItem(item) grid.addWidget(self.data_integration_software, 2, 1) grid.addWidget(QtGui.QLabel('Phasing'), 3, 0) self.phasing_software = QtGui.QComboBox() - for item in XChemMain.phasing_software(): self.phasing_software.addItem(item) + for item in XChemMain.phasing_software(): + self.phasing_software.addItem(item) grid.addWidget(self.phasing_software, 3, 1) frame.setLayout(grid) @@ -2044,7 +2222,7 @@ def deposition_data(self): deposit_tab_dict['Software'][1].addLayout(vb) - ## Funding + # Funding vb = QtGui.QVBoxLayout() @@ -2067,7 +2245,8 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Country'), 3, 0) self.pdbx_grant_country_one = QtGui.QComboBox() - for item in XChemMain.pdbx_country(): self.pdbx_grant_country_one.addItem(item) + for item in XChemMain.pdbx_country(): + self.pdbx_grant_country_one.addItem(item) grid.addWidget(self.pdbx_grant_country_one, 3, 1) frame.setLayout(grid) @@ -2092,7 +2271,8 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Country'), 3, 0) self.pdbx_grant_country_two = QtGui.QComboBox() - for item in XChemMain.pdbx_country(): self.pdbx_grant_country_two.addItem(item) + for item in XChemMain.pdbx_country(): + self.pdbx_grant_country_two.addItem(item) grid.addWidget(self.pdbx_grant_country_two, 3, 1) frame.setLayout(grid) @@ -2117,23 +2297,17 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel('Country'), 3, 0) self.pdbx_grant_country_three = QtGui.QComboBox() - for item in XChemMain.pdbx_country(): self.pdbx_grant_country_three.addItem(item) + for item in XChemMain.pdbx_country(): + self.pdbx_grant_country_three.addItem(item) grid.addWidget(self.pdbx_grant_country_three, 3, 1) frame.setLayout(grid) vb.addWidget(frame) - vb.addStretch(1) deposit_tab_dict['Funding'][1].addLayout(vb) - - - - - - vbox.addWidget(deposit_tab_widget) hbox = QtGui.QHBoxLayout() @@ -2158,7 +2332,8 @@ def deposition_data(self): def save_deposit_config_file(self): self.update_deposit_dict() - file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'Save file', self.current_directory)) + file_name = str(QtGui.QFileDialog.getSaveFileName( + self.window, 'Save file', self.current_directory)) # make sure that the file always has .deposit extension if str(file_name).rfind('.') != -1: file_name = file_name[:file_name.rfind('.')] + '.deposit' @@ -2168,20 +2343,25 @@ def save_deposit_config_file(self): def update_database_with_pdb_codes(self): self.work_thread = XChemDeposit.import_PDB_IDs(str(self.pdb_code_entry.toPlainText()), - os.path.join(self.database_directory, self.data_source_file), + os.path.join( + self.database_directory, self.data_source_file), self.xce_logfile) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() def update_database_with_labelInfo(self): - for n,l in enumerate(self.labelList): + for n, l in enumerate(self.labelList): label = str(l[0].text()) description = str(l[1].text()) # print "update labelTable set Label='%s',Description='%s' where ID=%s" %(label,description,str(n+1)) - self.db.execute_statement("update labelTable set Label='%s',Description='%s' where ID=%s" %(label,description,str(n+1))) + self.db.execute_statement("update labelTable set Label='%s',Description='%s' where ID=%s" % ( + label, description, str(n+1))) # print label,description def load_deposit_config_file(self): @@ -2192,7 +2372,8 @@ def load_deposit_config_file(self): # print self.deposit_dict for key in self.get_deposit_dict_template(): if key not in self.deposit_dict: - self.update_log.warning('field not in .deposit file: ' + str(key)) + self.update_log.warning( + 'field not in .deposit file: ' + str(key)) self.deposit_dict[key] = '' self.update_deposit_input() @@ -2206,59 +2387,88 @@ def save_deposit_to_database(self): "*** WARNING ***\nAre you sure you want to update the database?\nThis will overwrite previous entries!") msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) - reply = msgBox.exec_(); + reply = msgBox.exec_() if reply == 0: self.work_thread = XChemDeposit.update_depositTable(self.deposit_dict, os.path.join(self.database_directory, self.data_source_file), self.xce_logfile) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() def update_deposit_input(self): try: - self.contact_author_PI_salutation.setText(self.deposit_dict['contact_author_PI_salutation']) - self.contact_author_PI_first_name.setText(self.deposit_dict['contact_author_PI_first_name']) - self.contact_author_PI_last_name.setText(self.deposit_dict['contact_author_PI_last_name']) - self.contact_author_PI_middle_name.setText(self.deposit_dict['contact_author_PI_middle_name']) + self.contact_author_PI_salutation.setText( + self.deposit_dict['contact_author_PI_salutation']) + self.contact_author_PI_first_name.setText( + self.deposit_dict['contact_author_PI_first_name']) + self.contact_author_PI_last_name.setText( + self.deposit_dict['contact_author_PI_last_name']) + self.contact_author_PI_middle_name.setText( + self.deposit_dict['contact_author_PI_middle_name']) index = self.contact_author_PI_role.findText(self.deposit_dict['contact_author_PI_role'], QtCore.Qt.MatchFixedString) self.contact_author_PI_role.setCurrentIndex(index) index = self.contact_author_PI_organization_type.findText( self.deposit_dict['contact_author_PI_organization_type'], QtCore.Qt.MatchFixedString) self.contact_author_PI_organization_type.setCurrentIndex(index) - self.contact_author_PI_organization_name.setText(self.deposit_dict['contact_author_PI_organization_name']) - self.contact_author_PI_email.setText(self.deposit_dict['contact_author_PI_email']) - self.contact_author_PI_address.setText(self.deposit_dict['contact_author_PI_address']) - self.contact_author_PI_city.setText(self.deposit_dict['contact_author_PI_city']) - self.contact_author_PI_State_or_Province.setText(self.deposit_dict['contact_author_PI_State_or_Province']) - self.contact_author_PI_Zip_Code.setText(self.deposit_dict['contact_author_PI_Zip_Code']) - self.contact_author_PI_Country.setText(self.deposit_dict['contact_author_PI_Country']) - self.contact_author_PI_phone_number.setText(self.deposit_dict['contact_author_PI_phone_number']) - self.contact_author_PI_ORCID.setText(self.deposit_dict['contact_author_PI_ORCID']) - - self.contact_author_salutation.setText(self.deposit_dict['contact_author_salutation']) - self.contact_author_first_name.setText(self.deposit_dict['contact_author_first_name']) - self.contact_author_last_name.setText(self.deposit_dict['contact_author_last_name']) - self.contact_author_middle_name.setText(self.deposit_dict['contact_author_middle_name']) + self.contact_author_PI_organization_name.setText( + self.deposit_dict['contact_author_PI_organization_name']) + self.contact_author_PI_email.setText( + self.deposit_dict['contact_author_PI_email']) + self.contact_author_PI_address.setText( + self.deposit_dict['contact_author_PI_address']) + self.contact_author_PI_city.setText( + self.deposit_dict['contact_author_PI_city']) + self.contact_author_PI_State_or_Province.setText( + self.deposit_dict['contact_author_PI_State_or_Province']) + self.contact_author_PI_Zip_Code.setText( + self.deposit_dict['contact_author_PI_Zip_Code']) + self.contact_author_PI_Country.setText( + self.deposit_dict['contact_author_PI_Country']) + self.contact_author_PI_phone_number.setText( + self.deposit_dict['contact_author_PI_phone_number']) + self.contact_author_PI_ORCID.setText( + self.deposit_dict['contact_author_PI_ORCID']) + + self.contact_author_salutation.setText( + self.deposit_dict['contact_author_salutation']) + self.contact_author_first_name.setText( + self.deposit_dict['contact_author_first_name']) + self.contact_author_last_name.setText( + self.deposit_dict['contact_author_last_name']) + self.contact_author_middle_name.setText( + self.deposit_dict['contact_author_middle_name']) index = self.contact_author_role.findText(self.deposit_dict['contact_author_role'], QtCore.Qt.MatchFixedString) self.contact_author_role.setCurrentIndex(index) index = self.contact_author_organization_type.findText( self.deposit_dict['contact_author_organization_type'], QtCore.Qt.MatchFixedString) self.contact_author_organization_type.setCurrentIndex(index) - self.contact_author_organization_name.setText(self.deposit_dict['contact_author_organization_name']) - self.contact_author_email.setText(self.deposit_dict['contact_author_email']) - self.contact_author_address.setText(self.deposit_dict['contact_author_address']) - self.contact_author_city.setText(self.deposit_dict['contact_author_city']) - self.contact_author_State_or_Province.setText(self.deposit_dict['contact_author_State_or_Province']) - self.contact_author_Zip_Code.setText(self.deposit_dict['contact_author_Zip_Code']) - self.contact_author_Country.setText(self.deposit_dict['contact_author_Country']) - self.contact_author_phone_number.setText(self.deposit_dict['contact_author_phone_number']) - self.contact_author_ORCID.setText(self.deposit_dict['contact_author_ORCID']) + self.contact_author_organization_name.setText( + self.deposit_dict['contact_author_organization_name']) + self.contact_author_email.setText( + self.deposit_dict['contact_author_email']) + self.contact_author_address.setText( + self.deposit_dict['contact_author_address']) + self.contact_author_city.setText( + self.deposit_dict['contact_author_city']) + self.contact_author_State_or_Province.setText( + self.deposit_dict['contact_author_State_or_Province']) + self.contact_author_Zip_Code.setText( + self.deposit_dict['contact_author_Zip_Code']) + self.contact_author_Country.setText( + self.deposit_dict['contact_author_Country']) + self.contact_author_phone_number.setText( + self.deposit_dict['contact_author_phone_number']) + self.contact_author_ORCID.setText( + self.deposit_dict['contact_author_ORCID']) index = self.Release_status_for_coordinates.findText(self.deposit_dict['Release_status_for_coordinates'], QtCore.Qt.MatchFixedString) self.Release_status_for_coordinates.setCurrentIndex(index) @@ -2266,67 +2476,95 @@ def update_deposit_input(self): QtCore.Qt.MatchFixedString) self.Release_status_for_sequence.setCurrentIndex(index) - self.group_deposition_title.setText(self.deposit_dict['group_deposition_title']) - self.group_description.setText(self.deposit_dict['group_description']) + self.group_deposition_title.setText( + self.deposit_dict['group_deposition_title']) + self.group_description.setText( + self.deposit_dict['group_description']) self.structure_title.setText(self.deposit_dict['structure_title']) - self.structure_title_apo.setText(self.deposit_dict['structure_title_apo']) + self.structure_title_apo.setText( + self.deposit_dict['structure_title_apo']) for n, name in enumerate(self.deposit_dict['structure_author_name'].split(';')): self.structure_author_name_List[n].setText(name) - self.primary_citation_id.setText(self.deposit_dict['primary_citation_id']) - self.primary_citation_journal_abbrev.setText(self.deposit_dict['primary_citation_journal_abbrev']) - self.primary_citation_title.setText(self.deposit_dict['primary_citation_title']) - self.primary_citation_year.setText(self.deposit_dict['primary_citation_year']) - self.primary_citation_journal_volume.setText(self.deposit_dict['primary_citation_journal_volume']) - self.primary_citation_page_first.setText(self.deposit_dict['primary_citation_page_first']) - self.primary_citation_page_last.setText(self.deposit_dict['primary_citation_page_last']) + self.primary_citation_id.setText( + self.deposit_dict['primary_citation_id']) + self.primary_citation_journal_abbrev.setText( + self.deposit_dict['primary_citation_journal_abbrev']) + self.primary_citation_title.setText( + self.deposit_dict['primary_citation_title']) + self.primary_citation_year.setText( + self.deposit_dict['primary_citation_year']) + self.primary_citation_journal_volume.setText( + self.deposit_dict['primary_citation_journal_volume']) + self.primary_citation_page_first.setText( + self.deposit_dict['primary_citation_page_first']) + self.primary_citation_page_last.setText( + self.deposit_dict['primary_citation_page_last']) for n, name in enumerate(self.deposit_dict['primary_citation_author_name'].split(';')): self.primary_citation_author_name_List[n].setText(name) - ### entity 1 + # entity 1 self.molecule_name.setText(self.deposit_dict['molecule_name']) - self.fragment_name_one_specific_mutation.setText(self.deposit_dict['fragment_name_one_specific_mutation']) + self.fragment_name_one_specific_mutation.setText( + self.deposit_dict['fragment_name_one_specific_mutation']) index = self.Source_organism_scientific_name.findText(self.deposit_dict['Source_organism_scientific_name'], QtCore.Qt.MatchFixedString) self.Source_organism_scientific_name.setCurrentIndex(index) - self.Source_organism_gene.setText(self.deposit_dict['Source_organism_gene']) - self.Source_organism_strain.setText(self.deposit_dict['Source_organism_strain']) + self.Source_organism_gene.setText( + self.deposit_dict['Source_organism_gene']) + self.Source_organism_strain.setText( + self.deposit_dict['Source_organism_strain']) index = self.Expression_system_scientific_name.findText( self.deposit_dict['Expression_system_scientific_name'], QtCore.Qt.MatchFixedString) self.Expression_system_scientific_name.setCurrentIndex(index) - self.Expression_system_strain.setText(self.deposit_dict['Expression_system_strain']) - self.Expression_system_vector_type.setText(self.deposit_dict['Expression_system_vector_type']) - self.Expression_system_plasmid_name.setText(self.deposit_dict['Expression_system_plasmid_name']) - self.Manipulated_source_details.setText(self.deposit_dict['Manipulated_source_details']) + self.Expression_system_strain.setText( + self.deposit_dict['Expression_system_strain']) + self.Expression_system_vector_type.setText( + self.deposit_dict['Expression_system_vector_type']) + self.Expression_system_plasmid_name.setText( + self.deposit_dict['Expression_system_plasmid_name']) + self.Manipulated_source_details.setText( + self.deposit_dict['Manipulated_source_details']) # try: - self.molecule_chain_one.setText(self.deposit_dict['molecule_chain_one']) - ### entity 2 - self.molecule_name_two.setText(self.deposit_dict['molecule_name_two']) - self.fragment_name_two_specific_mutation.setText(self.deposit_dict['fragment_name_two_specific_mutation']) + self.molecule_chain_one.setText( + self.deposit_dict['molecule_chain_one']) + # entity 2 + self.molecule_name_two.setText( + self.deposit_dict['molecule_name_two']) + self.fragment_name_two_specific_mutation.setText( + self.deposit_dict['fragment_name_two_specific_mutation']) index = self.Source_organism_scientific_name_two.findText(self.deposit_dict['Source_organism_scientific_name_two'], QtCore.Qt.MatchFixedString) self.Source_organism_scientific_name_two.setCurrentIndex(index) - self.Source_organism_gene_two.setText(self.deposit_dict['Source_organism_gene_two']) - self.Source_organism_strain_two.setText(self.deposit_dict['Source_organism_strain_two']) + self.Source_organism_gene_two.setText( + self.deposit_dict['Source_organism_gene_two']) + self.Source_organism_strain_two.setText( + self.deposit_dict['Source_organism_strain_two']) index = self.Expression_system_scientific_name_two.findText( - self.deposit_dict['Expression_system_scientific_name_two'], QtCore.Qt.MatchFixedString) + self.deposit_dict['Expression_system_scientific_name_two'], QtCore.Qt.MatchFixedString) self.Expression_system_scientific_name_two.setCurrentIndex(index) - self.Expression_system_strain_two.setText(self.deposit_dict['Expression_system_strain_two']) - self.Expression_system_vector_type_two.setText(self.deposit_dict['Expression_system_vector_type_two']) - self.Expression_system_plasmid_name_two.setText(self.deposit_dict['Expression_system_plasmid_name_two']) - self.Manipulated_source_details_two.setText(self.deposit_dict['Manipulated_source_details_two']) - self.molecule_chain_two.setText(self.deposit_dict['molecule_chain_two']) + self.Expression_system_strain_two.setText( + self.deposit_dict['Expression_system_strain_two']) + self.Expression_system_vector_type_two.setText( + self.deposit_dict['Expression_system_vector_type_two']) + self.Expression_system_plasmid_name_two.setText( + self.deposit_dict['Expression_system_plasmid_name_two']) + self.Manipulated_source_details_two.setText( + self.deposit_dict['Manipulated_source_details_two']) + self.molecule_chain_two.setText( + self.deposit_dict['molecule_chain_two']) self.molecule_one_letter_sequence_uniprot_id_two.setText( - self.deposit_dict['molecule_two_letter_sequence_uniprot_id']) - self.molecule_one_letter_sequence_two.setText(self.deposit_dict['molecule_two_letter_sequence']) + self.deposit_dict['molecule_two_letter_sequence_uniprot_id']) + self.molecule_one_letter_sequence_two.setText( + self.deposit_dict['molecule_two_letter_sequence']) # except KeyError: # self.molecule_chain_one.setText('') # ### entity 2 @@ -2346,29 +2584,38 @@ def update_deposit_input(self): ### - self.structure_keywords.setText(self.deposit_dict['structure_keywords']) - self.biological_assembly_chain_number.setText(self.deposit_dict['biological_assembly_chain_number']) + self.structure_keywords.setText( + self.deposit_dict['structure_keywords']) + self.biological_assembly_chain_number.setText( + self.deposit_dict['biological_assembly_chain_number']) self.molecule_one_letter_sequence_uniprot_id.setText( self.deposit_dict['molecule_one_letter_sequence_uniprot_id']) - self.molecule_one_letter_sequence.setText(self.deposit_dict['molecule_one_letter_sequence']) + self.molecule_one_letter_sequence.setText( + self.deposit_dict['molecule_one_letter_sequence']) self.SG_project_name.setText(self.deposit_dict['SG_project_name']) - self.full_name_of_SG_center.setText(self.deposit_dict['full_name_of_SG_center']) + self.full_name_of_SG_center.setText( + self.deposit_dict['full_name_of_SG_center']) index = self.crystallization_method.findText(self.deposit_dict['crystallization_method'], QtCore.Qt.MatchFixedString) self.crystallization_method.setCurrentIndex(index) - self.crystallization_pH.setText(self.deposit_dict['crystallization_pH']) - self.crystallization_temperature.setText(self.deposit_dict['crystallization_temperature']) - self.crystallization_details.setText(self.deposit_dict['crystallization_details']) - index = self.radiation_source.findText(self.deposit_dict['radiation_source'], QtCore.Qt.MatchFixedString) + self.crystallization_pH.setText( + self.deposit_dict['crystallization_pH']) + self.crystallization_temperature.setText( + self.deposit_dict['crystallization_temperature']) + self.crystallization_details.setText( + self.deposit_dict['crystallization_details']) + index = self.radiation_source.findText( + self.deposit_dict['radiation_source'], QtCore.Qt.MatchFixedString) self.radiation_source.setCurrentIndex(index) index = self.radiation_source_type.findText(self.deposit_dict['radiation_source_type'], QtCore.Qt.MatchFixedString) self.radiation_source_type.setCurrentIndex(index) - self.radiation_wavelengths.setText(self.deposit_dict['radiation_wavelengths']) + self.radiation_wavelengths.setText( + self.deposit_dict['radiation_wavelengths']) index = self.radiation_detector.findText(self.deposit_dict['radiation_detector'], QtCore.Qt.MatchFixedString) self.radiation_detector.setCurrentIndex(index) @@ -2377,69 +2624,87 @@ def update_deposit_input(self): QtCore.Qt.MatchFixedString) self.radiation_detector_type.setCurrentIndex(index) - self.data_collection_date.setText(self.deposit_dict['data_collection_date']) - self.data_collection_temperature.setText(self.deposit_dict['data_collection_temperature']) - self.data_collection_protocol.setText(self.deposit_dict['data_collection_protocol']) + self.data_collection_date.setText( + self.deposit_dict['data_collection_date']) + self.data_collection_temperature.setText( + self.deposit_dict['data_collection_temperature']) + self.data_collection_protocol.setText( + self.deposit_dict['data_collection_protocol']) - self.pdbx_starting_model.setText(self.deposit_dict['pdbx_starting_model']) + self.pdbx_starting_model.setText( + self.deposit_dict['pdbx_starting_model']) index = self.data_integration_software.findText(self.deposit_dict['data_integration_software'], QtCore.Qt.MatchFixedString) self.data_integration_software.setCurrentIndex(index) - index = self.phasing_software.findText(self.deposit_dict['phasing_software'], QtCore.Qt.MatchFixedString) + index = self.phasing_software.findText( + self.deposit_dict['phasing_software'], QtCore.Qt.MatchFixedString) self.phasing_software.setCurrentIndex(index) - self.pdbx_funding_organization_one.setText(self.deposit_dict['pdbx_funding_organization_one']) - self.pdbx_grant_number_one.setText(self.deposit_dict['pdbx_grant_number_one']) + self.pdbx_funding_organization_one.setText( + self.deposit_dict['pdbx_funding_organization_one']) + self.pdbx_grant_number_one.setText( + self.deposit_dict['pdbx_grant_number_one']) index = self.pdbx_grant_country_one.findText( self.deposit_dict['pdbx_grant_country_one'], QtCore.Qt.MatchFixedString) self.pdbx_grant_country_one.setCurrentIndex(index) - self.pdbx_funding_organization_two.setText(self.deposit_dict['pdbx_funding_organization_two']) - self.pdbx_grant_number_two.setText(self.deposit_dict['pdbx_grant_number_two']) + self.pdbx_funding_organization_two.setText( + self.deposit_dict['pdbx_funding_organization_two']) + self.pdbx_grant_number_two.setText( + self.deposit_dict['pdbx_grant_number_two']) index = self.pdbx_grant_country_two.findText( self.deposit_dict['pdbx_grant_country_two'], QtCore.Qt.MatchFixedString) self.pdbx_grant_country_two.setCurrentIndex(index) - self.pdbx_funding_organization_three.setText(self.deposit_dict['pdbx_funding_organization_three']) - self.pdbx_grant_number_three.setText(self.deposit_dict['pdbx_grant_number_three']) + self.pdbx_funding_organization_three.setText( + self.deposit_dict['pdbx_funding_organization_three']) + self.pdbx_grant_number_three.setText( + self.deposit_dict['pdbx_grant_number_three']) index = self.pdbx_grant_country_three.findText( self.deposit_dict['pdbx_grant_country_three'], QtCore.Qt.MatchFixedString) self.pdbx_grant_country_three.setCurrentIndex(index) except ValueError, e: -# self.update_status_bar('Sorry, this is not a XChemExplorer deposit file!') - self.update_log.error('file is not a valid .deposit file: ' + str(e)) + # self.update_status_bar('Sorry, this is not a XChemExplorer deposit file!') + self.update_log.error( + 'file is not a valid .deposit file: ' + str(e)) def update_deposit_dict(self): pdbx_funding_ordinal_one = '' pdbx_funding_organization_one = '' pdbx_grant_number_one = '' pdbx_grant_country_one = '' - if str(self.pdbx_funding_organization_one.text()).replace(' ','') != '': + if str(self.pdbx_funding_organization_one.text()).replace(' ', '') != '': pdbx_funding_ordinal_one = '1' - pdbx_funding_organization_one = str(self.pdbx_funding_organization_one.text()) + pdbx_funding_organization_one = str( + self.pdbx_funding_organization_one.text()) pdbx_grant_number_one = str(self.pdbx_grant_number_one.text()) - pdbx_grant_country_one = str(self.pdbx_grant_country_one.currentText()) + pdbx_grant_country_one = str( + self.pdbx_grant_country_one.currentText()) pdbx_funding_ordinal_two = '' pdbx_funding_organization_two = '' pdbx_grant_number_two = '' pdbx_grant_country_two = '' - if str(self.pdbx_funding_organization_two.text()).replace(' ','') != '': + if str(self.pdbx_funding_organization_two.text()).replace(' ', '') != '': pdbx_funding_ordinal_two = '2' - pdbx_funding_organization_two = str(self.pdbx_funding_organization_two.text()) + pdbx_funding_organization_two = str( + self.pdbx_funding_organization_two.text()) pdbx_grant_number_two = str(self.pdbx_grant_number_two.text()) - pdbx_grant_country_two = str(self.pdbx_grant_country_two.currentText()) + pdbx_grant_country_two = str( + self.pdbx_grant_country_two.currentText()) pdbx_funding_ordinal_three = '' pdbx_funding_organization_three = '' pdbx_grant_number_three = '' pdbx_grant_country_three = '' - if str(self.pdbx_funding_organization_three.text()).replace(' ','') != '': + if str(self.pdbx_funding_organization_three.text()).replace(' ', '') != '': pdbx_funding_ordinal_three = '3' - pdbx_funding_organization_three = str(self.pdbx_funding_organization_three.text()) + pdbx_funding_organization_three = str( + self.pdbx_funding_organization_three.text()) pdbx_grant_number_three = str(self.pdbx_grant_number_three.text()) - pdbx_grant_country_three = str(self.pdbx_grant_country_three.currentText()) + pdbx_grant_country_three = str( + self.pdbx_grant_country_three.currentText()) self.deposit_dict = { 'contact_author_PI_salutation': str(self.contact_author_PI_salutation.text()), @@ -2490,7 +2755,7 @@ def update_deposit_dict(self): 'primary_citation_journal_volume': str(self.primary_citation_journal_volume.text()), 'primary_citation_page_first': str(self.primary_citation_page_first.text()), 'primary_citation_page_last': str(self.primary_citation_page_last.text()), - ### entity 1 + # entity 1 'molecule_name': str(self.molecule_name.text()), 'Source_organism_scientific_name': str(self.Source_organism_scientific_name.currentText()), 'Source_organism_gene': str(self.Source_organism_gene.text()), @@ -2503,7 +2768,7 @@ def update_deposit_dict(self): 'fragment_name_one_specific_mutation': str(self.fragment_name_one_specific_mutation.text()), 'molecule_chain_one': str(self.molecule_chain_one.text()), - ### entity 2 + # entity 2 'molecule_name_two': str(self.molecule_name_two.text()), 'Source_organism_scientific_name_two': str(self.Source_organism_scientific_name_two.currentText()), 'Source_organism_gene_two': str(self.Source_organism_gene_two.text()), @@ -2526,7 +2791,7 @@ def update_deposit_dict(self): '').replace( '\n', '').replace('\r', ''), 'molecule_two_letter_sequence': str(self.molecule_one_letter_sequence_two.toPlainText()).replace(' ', - '').replace( + '').replace( '\n', '').replace('\r', ''), 'crystallization_method': str(self.crystallization_method.currentText()), @@ -2621,7 +2886,7 @@ def get_deposit_dict_template(self): 'primary_citation_journal_volume': None, 'primary_citation_page_first': None, 'primary_citation_page_last': None, - ### entity 1 + # entity 1 'molecule_name': None, 'Source_organism_scientific_name': None, 'Source_organism_gene': None, @@ -2634,7 +2899,7 @@ def get_deposit_dict_template(self): 'fragment_name_one_specific_mutation': None, 'molecule_chain_one': None, - ### entity 2 + # entity 2 'molecule_name_two': None, 'Source_organism_scientific_name_two': None, 'Source_organism_gene_two': None, @@ -2692,19 +2957,22 @@ def get_deposit_dict_template(self): def set_primary_citation_as_structure_authors(self, state): if state == QtCore.Qt.Checked: for n, entry in enumerate(self.structure_author_name_List): - self.primary_citation_author_name_List[n].setText(str(entry.text())) + self.primary_citation_author_name_List[n].setText( + str(entry.text())) else: for n, entry in enumerate(self.primary_citation_author_name_List): entry.setText('') def set_xce_logfile(self): - file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'Save file', self.current_directory)) + file_name = str(QtGui.QFileDialog.getSaveFileName( + self.window, 'Save file', self.current_directory)) self.xce_logfile = str(file_name) self.xce_logfile_label.setText(str(self.xce_logfile)) if self.xce_logfile == '' or self.xce_logfile[self.xce_logfile.rfind('/') + 1:] == '': print('==> XCE: invalid file format') else: - XChemLog.startLog(self.xce_logfile).create_logfile(self.xce_version) + XChemLog.startLog(self.xce_logfile).create_logfile( + self.xce_version) self.update_log = XChemLog.updateLog(self.xce_logfile) def set_second_cif_file(self): @@ -2713,7 +2981,8 @@ def set_second_cif_file(self): filepath = str(tuple(filepath_temp)[0]) self.second_cif_file = str(filepath) self.second_cif_file_label.setText(str(self.second_cif_file)) - self.update_log.insert('user selected %s as CIF file for merging into ligand CIF files' %self.second_cif_file) + self.update_log.insert( + 'user selected %s as CIF file for merging into ligand CIF files' % self.second_cif_file) def select_datasource_columns_to_display(self): columns_to_show = QtGui.QMessageBox() @@ -2736,7 +3005,8 @@ def select_datasource_columns_to_display(self): columns_to_ignore = self.db.columns_not_to_display() for entries_added in range(number_of_entries): if not columns_in_data_source[entries_added][1] in columns_to_ignore: - data_source_column = QtGui.QCheckBox(columns_in_data_source[entries_added][1]) + data_source_column = QtGui.QCheckBox( + columns_in_data_source[entries_added][1]) column_dict[entries_added] = data_source_column if columns_in_data_source[entries_added][1] in self.overview_datasource_table_columns: data_source_column.setChecked(True) @@ -2748,9 +3018,11 @@ def select_datasource_columns_to_display(self): vbox.addLayout(grid) columns_to_showLayout.addLayout(vbox, 0, 0) - columns_to_show.addButton(QtGui.QPushButton('OK'), QtGui.QMessageBox.YesRole) - columns_to_show.addButton(QtGui.QPushButton('Cancel'), QtGui.QMessageBox.RejectRole) - reply = columns_to_show.exec_(); + columns_to_show.addButton(QtGui.QPushButton( + 'OK'), QtGui.QMessageBox.YesRole) + columns_to_show.addButton(QtGui.QPushButton( + 'Cancel'), QtGui.QMessageBox.RejectRole) + reply = columns_to_show.exec_() if reply == 0: columns_to_show_list = ['Sample ID'] for key in column_dict: @@ -2760,14 +3032,17 @@ def select_datasource_columns_to_display(self): self.populate_and_update_datasource_table() def update_header_and_data_from_datasource(self): - self.update_log.insert('getting information for all samples from data source...') - self.db = XChemDB.data_source(os.path.join(self.database_directory, self.data_source_file)) + self.update_log.insert( + 'getting information for all samples from data source...') + self.db = XChemDB.data_source(os.path.join( + self.database_directory, self.data_source_file)) self.update_log.insert('creating missing columns in data source') self.db.create_missing_columns() self.update_log.insert('load header and data from data source') self.header, self.data = self.db.load_samples_from_data_source() self.update_log.insert('get all samples in data source') - all_samples_in_db = self.db.execute_statement("select CrystalName from mainTable where CrystalName is not '';") + all_samples_in_db = self.db.execute_statement( + "select CrystalName from mainTable where CrystalName is not '';") self.xtal_db_dict = {} sampleID_column = 0 @@ -2789,7 +3064,8 @@ def datasource_menu_save_samples(self): print('hallo') def datasource_menu_export_csv_file(self): - file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'Save file', self.database_directory)) + file_name = str(QtGui.QFileDialog.getSaveFileName( + self.window, 'Save file', self.database_directory)) if file_name.rfind('.') != -1: file_name = file_name[:file_name.rfind('.')] + '.csv' else: @@ -2798,7 +3074,8 @@ def datasource_menu_export_csv_file(self): def datasource_menu_import_csv_file(self): if self.data_source_set: - file_name = QtGui.QFileDialog.getOpenFileName(self.window, 'Open file', self.database_directory) + file_name = QtGui.QFileDialog.getOpenFileName( + self.window, 'Open file', self.database_directory) self.db.import_csv_file(file_name) else: self.update_status_bar('Please load a data source file first') @@ -2809,9 +3086,12 @@ def datasource_menu_update_datasource(self): self.data_source_file), self.panddas_directory, self.xce_logfile, 'project_directory') - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), self.datasource_menu_reload_samples) self.work_thread.start() @@ -2827,17 +3107,18 @@ def on_context_menu(self, point): self.dewar_label_active = key self.popMenu.exec_(self.sender().mapToGlobal(point)) - - def on_context_menu_reprocess_data(self, point): # show context menu - self.popMenu_for_datasets_reprocess_table.exec_(self.sender().mapToGlobal(point)) + self.popMenu_for_datasets_reprocess_table.exec_( + self.sender().mapToGlobal(point)) def flag_sample_for_recollection(self): - self.dewar_configuration_dict[self.dewar_label_active].setStyleSheet("background-color: yellow") + self.dewar_configuration_dict[self.dewar_label_active].setStyleSheet( + "background-color: yellow") def undo_flag_sample_for_recollection(self): - self.dewar_configuration_dict[self.dewar_label_active].setStyleSheet("background-color: gray") + self.dewar_configuration_dict[self.dewar_label_active].setStyleSheet( + "background-color: gray") def show_html_summary_in_firefox(self, xtal): html_summary = self.albula_button_dict[xtal][2] @@ -2847,40 +3128,40 @@ def show_html_summary_in_firefox(self, xtal): def update_pandda_crystal_from_combobox(self): self.pandda_analyse_crystal_from_selection_combobox.clear() - self.pandda_analyse_crystal_from_selection_combobox.addItem('use all datasets') + self.pandda_analyse_crystal_from_selection_combobox.addItem( + 'use all datasets') if os.path.isfile(os.path.join(self.database_directory, self.data_source_file)): self.load_crystal_form_from_datasource() if self.xtalform_dict != {}: print(self.xtalform_dict) for key in self.xtalform_dict: - self.pandda_analyse_crystal_from_selection_combobox.addItem(key) + self.pandda_analyse_crystal_from_selection_combobox.addItem( + key) def populate_reference_combobox(self, combobox): combobox.clear() for reference_file in self.reference_file_list: combobox.addItem(reference_file[0]) - - def populate_refinement_outcome_combobox(self, combobox): combobox.clear() for stage in self.refinement_stage: combobox.addItem(stage) - - def populate_target_selection_combobox(self, combobox): combobox.clear() for target in self.target_list: combobox.addItem(target) def combo_selected(self, text): - self.map_url = str(self.panddas_directory + '/analyses/html_summaries/pandda_map_' + text + '.html') + self.map_url = str(self.panddas_directory + + '/analyses/html_summaries/pandda_map_' + text + '.html') self.pandda_maps_html.load(QtCore.QUrl(self.map_url)) self.pandda_maps_html.show() def add_map_html(self): - self.map_list = glob.glob(str(self.panddas_directory + '/analyses/html_summaries/pandda_map_*.html')) + self.map_list = glob.glob( + str(self.panddas_directory + '/analyses/html_summaries/pandda_map_*.html')) self.list_options = [] for i in range(0, len(self.map_list)): string = self.map_list[i] @@ -2891,7 +3172,8 @@ def add_map_html(self): self.pandda_map_list.clear() for i in range(0, len(self.list_options)): self.pandda_map_list.addItem(self.list_options[i]) - self.connect(self.pandda_map_list, QtCore.SIGNAL('activated(QString)'), self.combo_selected) + self.connect(self.pandda_map_list, QtCore.SIGNAL( + 'activated(QString)'), self.combo_selected) def open_config_file(self): file_name_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Open file', self.current_directory, @@ -2902,28 +3184,30 @@ def open_config_file(self): pickled_settings = pickle.load(open(file_name, 'rb')) except: - print('==> XCE: failed to open config file...') - - key_list = {#'beamline_directory': 'beamline_directory', - 'initial_model_directory': 'initial_model_directory', - 'panddas_directory': 'panddas_directory', - 'html_export_directory': 'html_export_directory', - 'group_deposit_directory': 'group_deposit_directory', - 'database_directory': 'database_directory', - 'datasets_summary_file': 'datasets_summary', - #"'data_source_file': 'data_source', - 'ccp4_scratch_directory': 'ccp4_scratch', - 'allowed_unitcell_difference_percent': 'unitcell_difference', - 'acceptable_low_resolution_limit_for_data': 'too_low_resolution_data', - #'reference_directory_temp': 'reference_directory' - } + print('==> XCE: failed to open config file...') + + key_list = { # 'beamline_directory': 'beamline_directory', + 'initial_model_directory': 'initial_model_directory', + 'panddas_directory': 'panddas_directory', + 'html_export_directory': 'html_export_directory', + 'group_deposit_directory': 'group_deposit_directory', + 'database_directory': 'database_directory', + 'datasets_summary_file': 'datasets_summary', + # "'data_source_file': 'data_source', + 'ccp4_scratch_directory': 'ccp4_scratch', + 'allowed_unitcell_difference_percent': 'unitcell_difference', + 'acceptable_low_resolution_limit_for_data': 'too_low_resolution_data', + # 'reference_directory_temp': 'reference_directory' + } # self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*')) for current_key in key_list: try: - command = str('self.' + current_key + " = pickled_settings['" + key_list[current_key] +"']") + command = str( + 'self.' + current_key + " = pickled_settings['" + key_list[current_key] + "']") exec(command) - command = str('self.settings["' + key_list[current_key]+ '"]= self.' + current_key) + command = str( + 'self.settings["' + key_list[current_key] + '"]= self.' + current_key) exec(command) print('==> XCE: found ' + key_list[current_key]) except: @@ -2932,28 +3216,32 @@ def open_config_file(self): exec(str(current_key + " = ''")) continue - try: pickled_settings = pickle.load(open(file_name, "rb")) if pickled_settings['beamline_directory'] != self.beamline_directory: self.beamline_directory = pickled_settings['beamline_directory'] - self.target_list, self.visit_list = XChemMain.get_target_and_visit_list(self.beamline_directory,self.read_agamemnon.isChecked()) + self.target_list, self.visit_list = XChemMain.get_target_and_visit_list( + self.beamline_directory, self.read_agamemnon.isChecked()) self.settings['beamline_directory'] = self.beamline_directory - self.populate_target_selection_combobox(self.target_selection_combobox) - + self.populate_target_selection_combobox( + self.target_selection_combobox) self.layout_funcs.pandda_html(self) self.show_pandda_html_summary() - self.html_export_directory_label.setText(self.html_export_directory) + self.html_export_directory_label.setText( + self.html_export_directory) - self.group_deposition_directory_label.setText(self.group_deposit_directory) + self.group_deposition_directory_label.setText( + self.group_deposit_directory) - self.datasets_summary_file_label.setText(self.datasets_summary_file) + self.datasets_summary_file_label.setText( + self.datasets_summary_file) self.data_source_file = pickled_settings['data_source'] if self.data_source_file != '': - self.settings['data_source'] = os.path.join(self.database_directory, self.data_source_file) + self.settings['data_source'] = os.path.join( + self.database_directory, self.data_source_file) # this is probably not necessary if os.path.isfile(self.settings['data_source']): write_enabled = self.check_write_permissions_of_data_source() @@ -2964,7 +3252,8 @@ def open_config_file(self): self.data_source_file_label.setText( os.path.join(self.database_directory, self.data_source_file)) self.data_source_set = True - self.db = XChemDB.data_source(os.path.join(self.database_directory, self.data_source_file)) + self.db = XChemDB.data_source(os.path.join( + self.database_directory, self.data_source_file)) self.datasource_menu_reload_samples() reference_directory_temp = pickled_settings['reference_directory'] @@ -2974,29 +3263,36 @@ def open_config_file(self): self.update_reference_files(' ') for xtal in self.initial_model_dimple_dict: reference_file_selection_combobox = self.initial_model_dimple_dict[xtal][1] - self.populate_reference_combobox(reference_file_selection_combobox) + self.populate_reference_combobox( + reference_file_selection_combobox) - self.initial_model_directory_label.setText(self.initial_model_directory) + self.initial_model_directory_label.setText( + self.initial_model_directory) self.panddas_directory_label.setText(self.panddas_directory) self.pandda_output_data_dir_entry.setText(self.panddas_directory) self.reference_directory_label.setText(self.reference_directory) self.beamline_directory_label.setText(self.beamline_directory) - self.ccp4_scratch_directory_label.setText(self.ccp4_scratch_directory) + self.ccp4_scratch_directory_label.setText( + self.ccp4_scratch_directory) self.reference_file_list = self.get_reference_file_list(' ') - self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*')) + self.pandda_input_data_dir_entry.setText( + os.path.join(self.initial_model_directory, '*')) self.update_all_tables() except KeyError: - self.update_status_bar('Sorry, this is not a XChemExplorer config file!') - self.update_log.insert('Sorry, this is not a XChemExplorer config file!') + self.update_status_bar( + 'Sorry, this is not a XChemExplorer config file!') + self.update_log.insert( + 'Sorry, this is not a XChemExplorer config file!') except: print("Unexpected error:", sys.exc_info()[0]) raise def save_config_file(self): - file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'Save file', self.current_directory)) + file_name = str(QtGui.QFileDialog.getSaveFileName( + self.window, 'Save file', self.current_directory)) # make sure that the file always has .conf extension if str(file_name).rfind('.') != -1: file_name = file_name[:file_name.rfind('.')] + '.conf' @@ -3006,17 +3302,18 @@ def save_config_file(self): def update_reference_files(self, reference_root): self.reference_file_list = self.get_reference_file_list(reference_root) - self.populate_reference_combobox(self.reference_file_selection_combobox) - self.populate_reference_combobox(self.pandda_reference_file_selection_combobox) - - + self.populate_reference_combobox( + self.reference_file_selection_combobox) + self.populate_reference_combobox( + self.pandda_reference_file_selection_combobox) def check_status_rerun_dimple_on_all_autoprocessing_files(self): print('hallo') def rerun_dimple_on_all_autoprocessing_files(self): job_list = [] - self.update_log.insert('preparing to run DIMPLE on all autoprocessing files') + self.update_log.insert( + 'preparing to run DIMPLE on all autoprocessing files') for xtal in self.data_collection_dict: for entry in self.data_collection_dict[xtal]: if entry[0] == 'logfile': @@ -3025,15 +3322,18 @@ def rerun_dimple_on_all_autoprocessing_files(self): if os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'], db_dict['DataProcessingMTZfileName'])) or \ os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'])): - job_list = self.get_job_list_for_dimple_rerun(xtal, job_list, db_dict, entry) + job_list = self.get_job_list_for_dimple_rerun( + xtal, job_list, db_dict, entry) except KeyError: try: if os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'])): - job_list = self.get_job_list_for_dimple_rerun(xtal, job_list, db_dict, entry) + job_list = self.get_job_list_for_dimple_rerun( + xtal, job_list, db_dict, entry) except KeyError: continue if job_list: - self.update_log.insert('trying to run DIMPLE on ALL auto-processing files') + self.update_log.insert( + 'trying to run DIMPLE on ALL auto-processing files') self.check_before_running_dimple(job_list) def run_dimple_on_selected_autoprocessing_file(self, instruction): @@ -3060,7 +3360,8 @@ def run_dimple_on_selected_autoprocessing_file(self, instruction): mtzin = os.path.join(db_dict['DataProcessingPathToMTZfile'], db_dict['DataProcessingMTZfileName']) elif os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'])): - mtzin = os.path.join(db_dict['DataProcessingPathToMTZfile']) + mtzin = os.path.join( + db_dict['DataProcessingPathToMTZfile']) elif os.path.isfile( os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'], db_dict['DataProcessingMTZfileName'])): @@ -3068,17 +3369,22 @@ def run_dimple_on_selected_autoprocessing_file(self, instruction): db_dict['DataProcessingMTZfileName']) elif os.path.isfile( os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'])): - mtzin = os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile']) + mtzin = os.path.join( + db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile']) - reference_file = str(self.initial_model_dimple_dict[xtal][1].currentText()) + reference_file = str( + self.initial_model_dimple_dict[xtal][1].currentText()) - reference_file_pdb = os.path.join(self.reference_directory, reference_file + '.pdb') + reference_file_pdb = os.path.join( + self.reference_directory, reference_file + '.pdb') if not os.path.isfile(reference_file_pdb): continue if os.path.isfile(os.path.join(self.reference_directory, reference_file + '.mtz')): - reference_file_mtz = ' -R ' + os.path.join(self.reference_directory, reference_file + '.mtz') + reference_file_mtz = ' -R ' + \ + os.path.join(self.reference_directory, + reference_file + '.mtz') else: reference_file_mtz = '' @@ -3095,22 +3401,25 @@ def run_dimple_on_selected_autoprocessing_file(self, instruction): reference_file_mtz, reference_file_cif]) else: - print('WARNING: ' + xtal + ' has not been submitted to dimple because no files were found: ') + print( + 'WARNING: ' + xtal + ' has not been submitted to dimple because no files were found: ') if not os.path.isfile(os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'], - db_dict['DataProcessingMTZfileName'])): + db_dict['DataProcessingMTZfileName'])): print(' ' + str(os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'], - db_dict['DataProcessingMTZfileName'])) + ' is missing') + db_dict['DataProcessingMTZfileName'])) + ' is missing') if not os.path.isfile(os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'])): - print(' ' + str(os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'])) + ' is missing') + print(' ' + str(os.path.join( + db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'])) + ' is missing') if not os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'])): - print(' ' + str(os.path.join(db_dict['DataProcessingPathToMTZfile']) + ' is missing')) - + print( + ' ' + str(os.path.join(db_dict['DataProcessingPathToMTZfile']) + ' is missing')) if job_list: - self.update_log.insert('trying to run DIMPLE on SELECTED auto-processing files') - self.check_before_running_dimple(job_list,instruction) + self.update_log.insert( + 'trying to run DIMPLE on SELECTED auto-processing files') + self.check_before_running_dimple(job_list, instruction) - def remove_selected_dimple_files(self,instruction): + def remove_selected_dimple_files(self, instruction): if 'dimple' in instruction.lower(): pipeline = 'dimple' elif 'pipedream' in instruction.lower(): @@ -3125,14 +3434,19 @@ def remove_selected_dimple_files(self,instruction): if job_list: msgBox = QtGui.QMessageBox() - msgBox.setText("Do you really want to delete {0!s} {1!s} files?".format(len(job_list),self.preferences['initial_refinement_pipeline'])) - msgBox.addButton(QtGui.QPushButton('Go'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('Cancel'), QtGui.QMessageBox.RejectRole) - reply = msgBox.exec_(); + msgBox.setText("Do you really want to delete {0!s} {1!s} files?".format( + len(job_list), self.preferences['initial_refinement_pipeline'])) + msgBox.addButton(QtGui.QPushButton( + 'Go'), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton('Cancel'), + QtGui.QMessageBox.RejectRole) + reply = msgBox.exec_() if reply == 0: - self.status_bar.showMessage('preparing to remove {0!s} files'.format(pipeline)) - self.update_log.insert('preparing to remove {0!s} files'.format(pipeline)) + self.status_bar.showMessage( + 'preparing to remove {0!s} files'.format(pipeline)) + self.update_log.insert( + 'preparing to remove {0!s} files'.format(pipeline)) self.work_thread = XChemThread.remove_selected_dimple_files(job_list, self.initial_model_directory, self.xce_logfile, @@ -3140,15 +3454,19 @@ def remove_selected_dimple_files(self,instruction): self.data_source_file, pipeline) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), self.datasource_menu_reload_samples) self.work_thread.start() - def set_results_from_selected_pipeline(self,instruction): + def set_results_from_selected_pipeline(self, instruction): if 'dimple' in instruction.lower(): pipeline = 'dimple' elif 'pipedream' in instruction.lower(): @@ -3156,7 +3474,8 @@ def set_results_from_selected_pipeline(self,instruction): elif 'phenix' in instruction.lower(): pipeline = 'phenix.ligand_pipeline' - self.update_log.warning('selecting initial refinement results from '+pipeline) + self.update_log.warning( + 'selecting initial refinement results from '+pipeline) job_list = [] for xtal in sorted(self.initial_model_dimple_dict): @@ -3164,22 +3483,24 @@ def set_results_from_selected_pipeline(self,instruction): job_list.append(xtal) self.work_thread = XChemThread.set_results_from_selected_pipeline(job_list, - self.initial_model_directory, - self.xce_logfile, - self.database_directory, - self.data_source_file, - pipeline) + self.initial_model_directory, + self.xce_logfile, + self.database_directory, + self.data_source_file, + pipeline) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), - self.datasource_menu_reload_samples) + self.datasource_menu_reload_samples) self.work_thread.start() - - def run_xia2_on_selected_datasets(self, overwrite): # check which programs should be run @@ -3204,7 +3525,8 @@ def run_xia2_on_selected_datasets(self, overwrite): # resolution limit reso_limit = [] if str(self.reprocess_isigma_combobox.currentText()) != 'default': - reso_limit.append(str(self.reprocess_isigma_combobox.currentText())) + reso_limit.append( + str(self.reprocess_isigma_combobox.currentText())) # cc 1/2 cc_half = [] @@ -3231,17 +3553,24 @@ def run_xia2_on_selected_datasets(self, overwrite): self.external_software, self.ccp4_scratch_directory, self.max_queue_jobs, - os.path.join(self.database_directory, self.data_source_file), + os.path.join( + self.database_directory, self.data_source_file), overwrite) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() else: - self.update_log.insert('please select datasets and/ or data processing protocol') - self.update_status_bar('please select datasets and/ or data processing protocol') + self.update_log.insert( + 'please select datasets and/ or data processing protocol') + self.update_status_bar( + 'please select datasets and/ or data processing protocol') def update_reprocessing_table(self): allRows = self.datasets_reprocess_table.rowCount() @@ -3251,7 +3580,8 @@ def update_reprocessing_table(self): db_dict = self.xtal_db_dict[sample_id] cell_text = QtGui.QTableWidgetItem() cell_text.setText(db_dict['DataProcessingStatus']) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) if db_dict['DataProcessingStatus'] == 'running': cell_text.setBackground(QtGui.QColor(100, 230, 150)) elif db_dict['DataProcessingStatus'] == 'pending': @@ -3270,7 +3600,8 @@ def get_job_list_for_dimple_rerun(self, xtal, job_list, db_dict, entry): # first we need one in the same pointgroup if reference[5] == db_dict['DataProcessingPointGroup']: try: - difference = math.fabs(1 - (float(db_dict['DataProcessingUnitCellVolume']) / float(reference[4]))) + difference = math.fabs( + 1 - (float(db_dict['DataProcessingUnitCellVolume']) / float(reference[4]))) suitable_reference.append([reference[0], difference]) except ValueError: continue @@ -3280,22 +3611,29 @@ def get_job_list_for_dimple_rerun(self, xtal, job_list, db_dict, entry): run = entry[2] autoproc = entry[4] - reference_file_pdb = os.path.join(self.reference_directory, reference_file + '.pdb') + reference_file_pdb = os.path.join( + self.reference_directory, reference_file + '.pdb') if os.path.isfile(os.path.join(self.reference_directory, reference_file + '.mtz')): - reference_file_mtz = ' -R ' + os.path.join(self.reference_directory, reference_file + '.mtz') + reference_file_mtz = ' -R ' + \ + os.path.join(self.reference_directory, + reference_file + '.mtz') else: reference_file_mtz = '' if os.path.isfile(os.path.join(self.reference_directory, reference_file + '.cif')): - reference_file_cif = ' --libin ' + os.path.join(self.reference_directory, reference_file + '.cif') + reference_file_cif = ' --libin ' + \ + os.path.join(self.reference_directory, + reference_file + '.cif') else: reference_file_cif = '' - if os.path.isfile(os.path.join(self.initial_model_directory, xtal, xtal +'.mtz')): - mtzin = os.path.join(self.initial_model_directory, xtal, xtal +'.mtz') + if os.path.isfile(os.path.join(self.initial_model_directory, xtal, xtal + '.mtz')): + mtzin = os.path.join( + self.initial_model_directory, xtal, xtal + '.mtz') - self.update_log.insert('adding ' + xtal + visit + '-' + run + autoproc + ' to list') + self.update_log.insert( + 'adding ' + xtal + visit + '-' + run + autoproc + ' to list') job_list.append([xtal, visit + '-' + run + autoproc, mtzin, @@ -3305,15 +3643,16 @@ def get_job_list_for_dimple_rerun(self, xtal, job_list, db_dict, entry): self.status_bar.showMessage('idle') return job_list - def check_before_running_dimple(self, job_list,instruction): + def check_before_running_dimple(self, job_list, instruction): msgBox = QtGui.QMessageBox() msgBox.setText( "Do you really want to run {0!s} {1!s} jobs?\nNote: we will not run more than {2!s} at once on the cluster!".format( - len(job_list),self.preferences['initial_refinement_pipeline'],self.preferences['max_queue_jobs'])) + len(job_list), self.preferences['initial_refinement_pipeline'], self.preferences['max_queue_jobs'])) msgBox.addButton(QtGui.QPushButton('Go'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('Cancel'), QtGui.QMessageBox.RejectRole) - reply = msgBox.exec_(); + msgBox.addButton(QtGui.QPushButton('Cancel'), + QtGui.QMessageBox.RejectRole) + reply = msgBox.exec_() if reply == 0: if 'dimple' in instruction.lower(): @@ -3323,10 +3662,13 @@ def check_before_running_dimple(self, job_list,instruction): elif 'phenix' in instruction.lower(): pipeline = 'phenix.ligand_pipeline' - self.status_bar.showMessage('preparing {0!s} DIMPLE jobs'.format(len(job_list))) - self.update_log.insert('preparing to run {0!s} DIMPLE jobs'.format(len(job_list))) + self.status_bar.showMessage( + 'preparing {0!s} DIMPLE jobs'.format(len(job_list))) + self.update_log.insert( + 'preparing to run {0!s} DIMPLE jobs'.format(len(job_list))) if self.external_software['qsub_array']: - self.update_log.insert('we will be running an ARRAY job on the DLS computer cluster') + self.update_log.insert( + 'we will be running an ARRAY job on the DLS computer cluster') self.update_log.insert( 'please note that the maximum number of jobs that will be running at once is {0!s}'.format( self.max_queue_jobs)) @@ -3334,34 +3676,30 @@ def check_before_running_dimple(self, job_list,instruction): 'you can change this in the PREFERENCES menu, but be warned that to high a number might break the cluster!') self.update_log.insert('preparing input files for DIMPLE...') self.work_thread = XChemThread.run_dimple_on_all_autoprocessing_files_new(job_list, - self.initial_model_directory, - self.external_software, - self.ccp4_scratch_directory, - self.database_directory, - self.data_source_file, - self.max_queue_jobs, - self.xce_logfile, - self.using_remote_qsub_submission, - self.remote_qsub_submission, - self.preferences['dimple_twin_mode'], - pipeline ) + self.initial_model_directory, + self.external_software, + self.ccp4_scratch_directory, + self.database_directory, + self.data_source_file, + self.max_queue_jobs, + self.xce_logfile, + self.using_remote_qsub_submission, + self.remote_qsub_submission, + self.preferences['dimple_twin_mode'], + pipeline) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), self.datasource_menu_reload_samples) self.work_thread.start() - - - - - - - - def open_csv_file_translate_datasetID_to_sampleID(self): file_name_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Open file', self.current_directory, '*.csv') @@ -3369,20 +3707,21 @@ def open_csv_file_translate_datasetID_to_sampleID(self): self.translate_datasetID_to_sampleID_csv_label.setText(file_name) self.translate_datasetID_to_sampleID_file = file_name - - def update_datasets_reprocess_table(self, data_dict): self.update_log.insert('updating reprocess datasets table') print('updating reprocess datasets table') self.diffraction_data_table_dict = {} self.diffraction_data_dict = data_dict - self.diffraction_data_search_info = 'found ' + str(len(self.diffraction_data_dict)) + ' datasets' - self.diffraction_data_search_label.setText(self.diffraction_data_search_info) + self.diffraction_data_search_info = 'found ' + \ + str(len(self.diffraction_data_dict)) + ' datasets' + self.diffraction_data_search_label.setText( + self.diffraction_data_search_info) self.update_log.insert(self.diffraction_data_search_info) self.datasource_menu_reload_samples() # update table - column_name = self.db.translate_xce_column_list_to_sqlite(self.datasets_reprocess_columns) + column_name = self.db.translate_xce_column_list_to_sqlite( + self.datasets_reprocess_columns) # set rows to 0 self.datasets_reprocess_table.setRowCount(0) for entry in sorted(self.diffraction_data_dict): @@ -3397,12 +3736,15 @@ def update_datasets_reprocess_table(self, data_dict): if header[0] == 'Dataset ID' or header[0] == 'Sample ID': cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(entry)) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.datasets_reprocess_table.setItem(row, column, cell_text) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + self.datasets_reprocess_table.setItem( + row, column, cell_text) elif header[0] == 'Run\nxia2': run_xia2 = QtGui.QCheckBox() run_xia2.toggle() - self.datasets_reprocess_table.setCellWidget(row, column, run_xia2) + self.datasets_reprocess_table.setCellWidget( + row, column, run_xia2) run_xia2.setChecked(False) self.diffraction_data_table_dict[entry] = [run_xia2] else: @@ -3410,18 +3752,24 @@ def update_datasets_reprocess_table(self, data_dict): if db_dict != {}: if header[0] == 'DataProcessing\nStatus': if str(db_dict[header[1]]) == 'running': - cell_text.setBackground(QtGui.QColor(100, 230, 150)) + cell_text.setBackground( + QtGui.QColor(100, 230, 150)) elif str(db_dict[header[1]]) == 'pending': - cell_text.setBackground(QtGui.QColor(20, 100, 230)) + cell_text.setBackground( + QtGui.QColor(20, 100, 230)) elif str(db_dict[header[1]]) == 'started': - cell_text.setBackground(QtGui.QColor(230, 240, 110)) + cell_text.setBackground( + QtGui.QColor(230, 240, 110)) elif str(db_dict[header[1]]) == 'finished': - cell_text.setBackground(QtGui.QColor(255, 255, 255)) + cell_text.setBackground( + QtGui.QColor(255, 255, 255)) cell_text.setText(str(db_dict[header[1]])) else: cell_text.setText('') - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.datasets_reprocess_table.setItem(row, column, cell_text) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + self.datasets_reprocess_table.setItem( + row, column, cell_text) def update_all_tables(self): self.update_log.insert('checking for new reference files') @@ -3445,8 +3793,6 @@ def update_all_tables(self): self.update_status_bar('idle') self.update_summary_plot() - - def change_allowed_unitcell_difference_percent(self, text): try: self.allowed_unitcell_difference_percent = int(text) @@ -3456,7 +3802,8 @@ def change_allowed_unitcell_difference_percent(self, text): self.allowed_unitcell_difference_percent)) except ValueError: if str(text).find('.') != -1: - self.allowed_unitcell_difference_percent = int(str(text)[:str(text).find('.')]) + self.allowed_unitcell_difference_percent = int( + str(text)[:str(text).find('.')]) self.settings['unitcell_difference'] = self.allowed_unitcell_difference_percent self.update_log.insert( 'changing max allowed unit cell difference between reference and xtal to {0!s} percent'.format( @@ -3495,7 +3842,8 @@ def button_clicked(self): if not self.data_source_set: print('sender text bit') if self.sender().text() == "Create New Data\nSource (SQLite)": - file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'Save file', self.database_directory)) + file_name = str(QtGui.QFileDialog.getSaveFileName( + self.window, 'Save file', self.database_directory)) # make sure that the file always has .sqlite extension if file_name.rfind('.') != -1: file_name = file_name[:file_name.rfind('.')] + '.sqlite' @@ -3507,8 +3855,10 @@ def button_clicked(self): self.db.create_missing_columns() if self.data_source_file == '': self.database_directory = file_name[:file_name.rfind('/')] - self.data_source_file = file_name[file_name.rfind('/') + 1:] - self.data_source_file_label.setText(os.path.join(self.database_directory, self.data_source_file)) + self.data_source_file = file_name[file_name.rfind( + '/') + 1:] + self.data_source_file_label.setText(os.path.join( + self.database_directory, self.data_source_file)) self.settings['database_directory'] = self.database_directory self.settings['data_source'] = self.data_source_file self.data_source_set = True @@ -3524,27 +3874,34 @@ def button_clicked(self): # get index of item in self.workflow; Note this index should be the same as the index # of the self.main_tab_widget which belongs to this task task_index = self.workflow.index(item) - instruction = str(self.workflow_widget_dict[item][0].currentText()) + instruction = str( + self.workflow_widget_dict[item][0].currentText()) print(instruction) action = str(self.sender().text()) if self.main_tab_widget.currentIndex() == task_index: if self.explorer_active == 0 and self.data_source_set == True: if action == 'Run': - print('==> XCE: Remote submission status = ' + str(self.using_remote_qsub_submission)) + print('==> XCE: Remote submission status = ' + + str(self.using_remote_qsub_submission)) # print(instruction) self.prepare_and_run_task(instruction) elif action == 'Status': - self.get_status_of_workflow_milestone(instruction) + self.get_status_of_workflow_milestone( + instruction) if os.path.exists(str(self.panddas_directory + '/pandda.done')): self.pandda_status = 'Finished!' - self.pandda_status_label.setStyleSheet('color: green') + self.pandda_status_label.setStyleSheet( + 'color: green') if os.path.exists(str(self.panddas_directory + '/pandda.running')): self.pandda_status = 'Running...' - self.pandda_status_label.setStyleSheet('color: orange') + self.pandda_status_label.setStyleSheet( + 'color: orange') if os.path.exists(str(self.panddas_directory + '/pandda.errored')): self.pandda_status = 'Error encountered... please check the log files for pandda!' - self.pandda_status_label.setStyleSheet('color: red') - self.pandda_status_label.setText(str('STATUS: ' + self.pandda_status)) + self.pandda_status_label.setStyleSheet( + 'color: red') + self.pandda_status_label.setText( + str('STATUS: ' + self.pandda_status)) else: self.need_to_switch_main_tab(task_index) @@ -3556,25 +3913,32 @@ def get_status_of_workflow_milestone(self, instruction): self.update_log.insert('getting status updates...') - self.status_bar.showMessage('please check terminal window for further information') + self.status_bar.showMessage( + 'please check terminal window for further information') - self.update_log.insert('{0!s} samples are currently in database'.format(str(len(self.xtal_db_dict)))) + self.update_log.insert( + '{0!s} samples are currently in database'.format(str(len(self.xtal_db_dict)))) if 'DIMPLE' in instruction: - XChemMain.print_cluster_status_message('dimple', cluster_dict, self.xce_logfile) + XChemMain.print_cluster_status_message( + 'dimple', cluster_dict, self.xce_logfile) elif 'Create CIF/PDB/PNG file' in instruction: XChemMain.print_acedrg_status(self.xce_logfile, self.xtal_db_dict) - XChemMain.print_cluster_status_message('acedrg', cluster_dict, self.xce_logfile) + XChemMain.print_cluster_status_message( + 'acedrg', cluster_dict, self.xce_logfile) elif instruction.startswith('Run xia2 on selected datasets'): - XChemMain.print_cluster_status_message('xia2', cluster_dict, self.xce_logfile) + XChemMain.print_cluster_status_message( + 'xia2', cluster_dict, self.xce_logfile) elif 'pandda' in instruction.lower(): - XChemMain.print_cluster_status_message('pandda', cluster_dict, self.xce_logfile) + XChemMain.print_cluster_status_message( + 'pandda', cluster_dict, self.xce_logfile) elif 'coot' in instruction.lower(): - XChemMain.print_cluster_status_message('refmac', cluster_dict, self.xce_logfile) + XChemMain.print_cluster_status_message( + 'refmac', cluster_dict, self.xce_logfile) def prepare_and_run_task(self, instruction): @@ -3748,16 +4112,15 @@ def prepare_and_run_task(self, instruction): else: interface = 'old' # print self.settings - self.work_thread = XChemThread.start_COOT(self.settings, interface) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.work_thread = XChemThread.start_COOT( + self.settings, interface) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() - elif instruction == 'Update Deposition Table': self.update_deposition_table() - - def check_status_create_png_of_soaked_compound(self): number_of_samples = 0 running = 0 @@ -3781,8 +4144,6 @@ def check_status_create_png_of_soaked_compound(self): cif_file_generated) + ', last job submmitted: ' + str(last_timestamp) self.status_bar.showMessage(message) - - if start_thread: if self.target == '=== SELECT TARGET ===': msgBox = QtGui.QMessageBox() @@ -3792,9 +4153,11 @@ def check_status_create_png_of_soaked_compound(self): 'Please note that this option is usually only useful in case you reprocessed your data.\n' 'Do you want to continue?') msgBox.setText(warning) - msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) - reply = msgBox.exec_(); + msgBox.addButton(QtGui.QPushButton('Yes'), + QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton( + 'No'), QtGui.QMessageBox.RejectRole) + reply = msgBox.exec_() if reply == 0: start_thread = True else: @@ -3817,9 +4180,12 @@ def check_status_create_png_of_soaked_compound(self): self.data_source_file), self.xce_logfile) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("create_widgets_for_autoprocessing_results_only"), self.create_widgets_for_autoprocessing_results_only) self.work_thread.start() @@ -3835,10 +4201,14 @@ def save_files_to_initial_model_folder(self): self.preferences, self.datasets_summary_file) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() def run_pandda_analyse(self, run): @@ -3871,7 +4241,8 @@ def run_pandda_analyse(self, run): msgBox = QtGui.QMessageBox() msgBoxLayout = msgBox.layout() vbox = QtGui.QVBoxLayout() - vbox.addWidget(QtGui.QLabel(XChemToolTips.pandda_pre_run(self.reference_directory))) + vbox.addWidget(QtGui.QLabel( + XChemToolTips.pandda_pre_run(self.reference_directory))) hbox = QtGui.QHBoxLayout() hbox.addWidget(QtGui.QLabel('appendix:')) appendix = QtGui.QLineEdit() @@ -3881,9 +4252,11 @@ def run_pandda_analyse(self, run): vbox.addLayout(hbox) msgBoxLayout.addLayout(vbox, 0, 0) - msgBox.addButton(QtGui.QPushButton('Go'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('Cancel'), QtGui.QMessageBox.RejectRole) - reply = msgBox.exec_(); + msgBox.addButton(QtGui.QPushButton( + 'Go'), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton('Cancel'), + QtGui.QMessageBox.RejectRole) + reply = msgBox.exec_() if reply == 0: pandda_params['appendix'] = str(appendix.text()) pandda_params['max_new_datasets'] = '100' @@ -3895,13 +4268,14 @@ def run_pandda_analyse(self, run): self.update_log.insert('preparing pandda.analyse input script') if run == 'production_run_pandda_two': self.work_thread = XChemPANDDA.run_pandda_two_analyse(pandda_params, self.xce_logfile, - os.path.join(self.database_directory, self.data_source_file)) + os.path.join(self.database_directory, self.data_source_file)) else: self.work_thread = XChemPANDDA.run_pandda_analyse(pandda_params, self.xce_logfile, - os.path.join(self.database_directory, self.data_source_file)) - #self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), - #self.datasource_menu_reload_samples) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + os.path.join(self.database_directory, self.data_source_file)) + # self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), + # self.datasource_menu_reload_samples) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() def cluster_datasets_for_pandda(self): @@ -3917,65 +4291,87 @@ def cluster_datasets_for_pandda(self): self.data_source_file), run_pandda_analyse) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), self.datasource_menu_reload_samples) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() def run_pandda_inspect(self): - self.settings['panddas_directory'] = str(self.pandda_output_data_dir_entry.text()) + self.settings['panddas_directory'] = str( + self.pandda_output_data_dir_entry.text()) print('==> XCE: starting pandda.inspect') - self.work_thread = XChemThread.start_pandda_inspect(self.settings, self.xce_logfile) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.work_thread = XChemThread.start_pandda_inspect( + self.settings, self.xce_logfile) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() def run_pandda_inspect_at_home(self): - self.work_thread = XChemPANDDA.run_pandda_inspect_at_home(self.panddas_directory, self.xce_logfile) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.work_thread = XChemPANDDA.run_pandda_inspect_at_home( + self.panddas_directory, self.xce_logfile) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) def convert_event_maps_to_SF(self): - self.update_log.insert('converting all event maps in {0!s} to mtz files'.format(self.initial_model_directory)) + self.update_log.insert('converting all event maps in {0!s} to mtz files'.format( + self.initial_model_directory)) # self.work_thread = XChemPANDDA.convert_all_event_maps_in_database(self.initial_model_directory, # self.xce_logfile, # os.path.join(self.database_directory, # self.data_source_file)) self.work_thread = XChemPANDDA.find_event_map_for_ligand(self.initial_model_directory, - self.xce_logfile,self.external_software) + self.xce_logfile, self.external_software) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() def convert_apo_to_mmcif(self): self.work_thread = XChemPANDDA.convert_apo_structures_to_mmcif(self.panddas_directory, - self.xce_logfile) + self.xce_logfile) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() - def compare_modelled_ligands_and_panddaTable(self): - self.update_log.insert('checking agreement of ligands in refine.pdb and entries in panddaTable') + self.update_log.insert( + 'checking agreement of ligands in refine.pdb and entries in panddaTable') self.work_thread = XChemPANDDA.check_number_of_modelled_ligands(self.initial_model_directory, self.xce_logfile, os.path.join(self.database_directory, self.data_source_file)) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("show_error_dict"), self.show_error_dict) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "show_error_dict"), self.show_error_dict) self.work_thread.start() def run_pandda_export(self, update_datasource_only, which_models): @@ -4004,24 +4400,31 @@ def run_pandda_export(self, update_datasource_only, which_models): 'remote_string': self.remote_qsub_submission } - self.settings['panddas_directory'] = str(self.pandda_output_data_dir_entry.text()) + self.settings['panddas_directory'] = str( + self.pandda_output_data_dir_entry.text()) if update_datasource_only: - self.update_log.insert('updating data source with results from pandda.inspect') + self.update_log.insert( + 'updating data source with results from pandda.inspect') else: self.update_log.insert( 'exporting PANDDA models, updating data source and launching inital refinement for new models') start_thread = False if which_models == 'all': - self.update_log.insert('exporting ALL models! *** WARNING *** This may overwrite previous refinements!!!') + self.update_log.insert( + 'exporting ALL models! *** WARNING *** This may overwrite previous refinements!!!') msgBox = QtGui.QMessageBox() - msgBox.setText("*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?") - msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) - reply = msgBox.exec_(); + msgBox.setText( + "*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?") + msgBox.addButton(QtGui.QPushButton('Yes'), + QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton( + 'No'), QtGui.QMessageBox.RejectRole) + reply = msgBox.exec_() if reply == 0: if update_datasource_only: - self.update_log.insert('will update panddaTable in database only') + self.update_log.insert( + 'will update panddaTable in database only') else: self.update_log.insert('will export ALL models!') start_thread = True @@ -4037,7 +4440,8 @@ def run_pandda_export(self, update_datasource_only, which_models): self.data_source_file), self.initial_model_directory, self.xce_logfile, update_datasource_only, which_models, pandda_params) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() # def run_refine_bound_state_with_buster(self,which_models): @@ -4051,28 +4455,28 @@ def run_pandda_export(self, update_datasource_only, which_models): # self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) # self.work_thread.start() - def run_refine_bound_state_with_buster(self,which_models): + def run_refine_bound_state_with_buster(self, which_models): start_thread = True if start_thread: self.work_thread = XChemPANDDA.export_and_refine_ligand_bound_models(self.panddas_directory, - os.path.join(self.database_directory, - self.data_source_file), - self.initial_model_directory, self.xce_logfile, - which_models) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + os.path.join(self.database_directory, + self.data_source_file), + self.initial_model_directory, self.xce_logfile, + which_models) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.work_thread.start() - - - - def show_pandda_html_summary(self): - self.pandda_initial_html.load(QtCore.QUrl(self.pandda_initial_html_file)) + self.pandda_initial_html.load( + QtCore.QUrl(self.pandda_initial_html_file)) self.pandda_initial_html.show() - self.pandda_analyse_html.load(QtCore.QUrl(self.pandda_analyse_html_file)) + self.pandda_analyse_html.load( + QtCore.QUrl(self.pandda_analyse_html_file)) self.pandda_analyse_html.show() self.add_map_html() - self.pandda_inspect_html.load(QtCore.QUrl(self.pandda_inspect_html_file)) + self.pandda_inspect_html.load( + QtCore.QUrl(self.pandda_inspect_html_file)) self.pandda_inspect_html.show() def create_cif_pdb_png_files(self, todo): @@ -4089,11 +4493,13 @@ def create_cif_pdb_png_files(self, todo): compound_list.append([str(item[0]), compoundID, str(item[2])]) elif todo == 'NEW': if not os.path.isfile(os.path.join(self.initial_model_directory, str(item[0]), compoundID + '.cif')): - compound_list.append([str(item[0]), compoundID, str(item[2])]) + compound_list.append( + [str(item[0]), compoundID, str(item[2])]) elif todo == 'SELECTED': if str(item[0]) in self.initial_model_dimple_dict: if self.initial_model_dimple_dict[str(item[0])][0].isChecked(): - compound_list.append([str(item[0]), compoundID, str(item[2])]) + compound_list.append( + [str(item[0]), compoundID, str(item[2])]) if compound_list: self.update_log.insert( @@ -4119,9 +4525,12 @@ def create_cif_pdb_png_files(self, todo): self.xce_logfile, self.max_queue_jobs, self.restraints_program) - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), self.datasource_menu_reload_samples) self.work_thread.start() @@ -4138,7 +4547,8 @@ def fit_ligands_into_dimple_maps(self): if str(item[0]) in self.initial_model_dimple_dict: if self.initial_model_dimple_dict[str(item[0])][0].isChecked(): - compound_list.append([str(item[0]), compoundID, str(item[2])]) + compound_list.append( + [str(item[0]), compoundID, str(item[2])]) if compound_list: self.update_log.insert( @@ -4155,61 +4565,71 @@ def fit_ligands_into_dimple_maps(self): self.update_log.insert('this could take a while...') self.explorer_active = 1 self.work_thread = XChemThread.fit_ligands(self.external_software, - self.initial_model_directory, - compound_list, - self.database_directory, - self.data_source_file, - self.ccp4_scratch_directory, - self.xce_logfile, - self.max_queue_jobs) - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.initial_model_directory, + compound_list, + self.database_directory, + self.data_source_file, + self.ccp4_scratch_directory, + self.xce_logfile, + self.max_queue_jobs) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), self.datasource_menu_reload_samples) self.work_thread.start() - - - - def merge_cif_files(self,todo): + def merge_cif_files(self, todo): start_thread = False if todo == 'merge': - self.update_log.insert('trying to merge %s with ligand restraint files in project directory' %self.second_cif_file) + self.update_log.insert( + 'trying to merge %s with ligand restraint files in project directory' % self.second_cif_file) elif todo == 'restore': self.update_log.insert('restoring original CIF files') start_thread = True if todo == 'merge': if os.path.isfile(str(self.second_cif_file)): - self.update_log.insert('checking compound code of second CIF file (%s)' % self.second_cif_file) + self.update_log.insert( + 'checking compound code of second CIF file (%s)' % self.second_cif_file) self.update_log.insert('Note: LIG and DRG are not allowed!') import iotbx.cif - cif_model = iotbx.cif.reader(file_path=self.second_cif_file).model() + cif_model = iotbx.cif.reader( + file_path=self.second_cif_file).model() cif_block = cif_model["comp_list"] ligID = cif_block["_chem_comp.id"] - self.update_log.insert('found the following compound codes in the supplied CIF file: %s' % str(list(ligID))) + self.update_log.insert( + 'found the following compound codes in the supplied CIF file: %s' % str(list(ligID))) if 'LIG' in list(ligID) or 'DRG' in list(ligID): - self.update_log.error('please change compound code to something other than LIG or DRG') + self.update_log.error( + 'please change compound code to something other than LIG or DRG') start_thread = False else: start_thread = True else: - self.update_log.error(XChemToolTips.second_cif_file_not_exists()) + self.update_log.error( + XChemToolTips.second_cif_file_not_exists()) start_thread = False if start_thread: msgBox = QtGui.QMessageBox() - msgBox.setText(XChemToolTips.second_cif_file_info(self.second_cif_file)) - msgBox.addButton(QtGui.QPushButton('OK'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('Cancel'), QtGui.QMessageBox.RejectRole) - reply = msgBox.exec_(); + msgBox.setText(XChemToolTips.second_cif_file_info( + self.second_cif_file)) + msgBox.addButton(QtGui.QPushButton( + 'OK'), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton('Cancel'), + QtGui.QMessageBox.RejectRole) + reply = msgBox.exec_() if reply == 0: start_thread = True else: start_thread = False else: - self.status_bar.showMessage('Error. Please check terminal window for further information') + self.status_bar.showMessage( + 'Error. Please check terminal window for further information') tmp = self.db.execute_statement( "select CrystalName,CompoundCode from mainTable where CrystalName is not '' and CompoundSmiles is not '' and CompoundSmiles is not NULL;") @@ -4218,33 +4638,38 @@ def merge_cif_files(self,todo): xtal = str(item[0]) compoundID = str(item[1]) if compoundID == '' or compoundID == 'NULL': - self.update_log.warning('%s: no compound ID in database; skipping...' %xtal) + self.update_log.warning( + '%s: no compound ID in database; skipping...' % xtal) else: if str(item[0]) in self.initial_model_dimple_dict: if self.initial_model_dimple_dict[str(item[0])][0].isChecked(): - self.update_log.warning('%s: %s is flagged for merging' % (xtal, compoundID)) + self.update_log.warning( + '%s: %s is flagged for merging' % (xtal, compoundID)) compound_list.append([xtal, compoundID]) if compound_list == []: - self.update_log.error('Either no compound ID information in database or no sample selected!') + self.update_log.error( + 'Either no compound ID information in database or no sample selected!') start_thread = False if start_thread: self.explorer_active = 1 self.work_thread = XChemThread.merge_cif_files(self.initial_model_directory, - self.xce_logfile, - self.second_cif_file, - compound_list, - todo) - self.connect(self.work_thread, QtCore.SIGNAL("update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL("update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + self.xce_logfile, + self.second_cif_file, + compound_list, + todo) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_progress_bar"), self.update_progress_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "update_status_bar(QString)"), self.update_status_bar) + self.connect(self.work_thread, QtCore.SIGNAL( + "finished()"), self.thread_finished) self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), self.datasource_menu_reload_samples) self.work_thread.start() - def update_deposition_table(self): # check if PanDDA models are ready for deposition @@ -4254,10 +4679,13 @@ def update_deposition_table(self): toDeposit, mismatch = depositChecks.PanDDA_models_to_deposit() if mismatch != {}: - self.update_log.insert('The following samples contain ligand that are not ready for deposition:') + self.update_log.insert( + 'The following samples contain ligand that are not ready for deposition:') for entry in mismatch: - self.update_log.insert(entry[0] + ' -> site: ' + entry[1] + ' @ ' + entry[2] + ' => ' + entry[4]) - self.update_log.insert('You need to change this before you can continue!') + self.update_log.insert( + entry[0] + ' -> site: ' + entry[1] + ' @ ' + entry[2] + ' => ' + entry[4]) + self.update_log.insert( + 'You need to change this before you can continue!') return None for xtal in toDeposit: @@ -4271,10 +4699,11 @@ def show_html_summary_and_diffraction_image(self): def need_to_switch_main_tab(self, task_index): msgBox = QtGui.QMessageBox() - msgBox.setText("Need to switch main tab before you can launch this job") + msgBox.setText( + "Need to switch main tab before you can launch this job") msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) - reply = msgBox.exec_(); + reply = msgBox.exec_() if reply == 0: self.main_tab_widget.setCurrentIndex(task_index) @@ -4321,7 +4750,8 @@ def show_error_dict(self, errorDict): msgBox.exec_() def create_widgets_for_autoprocessing_results_only(self, data_dict): - self.status_bar.showMessage('Building details table for data processing results') + self.status_bar.showMessage( + 'Building details table for data processing results') self.data_collection_dict = data_dict column_name = ['Program', @@ -4350,28 +4780,33 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): tmp = [] for entry in self.data_collection_dict[xtal]: if entry[0] == 'image': - tmp.append([entry[3], datetime.strptime(entry[3], '%Y-%m-%d %H:%M:%S')]) + tmp.append([entry[3], datetime.strptime( + entry[3], '%Y-%m-%d %H:%M:%S')]) latest_run = max(tmp, key=lambda x: x[1])[0] # first check if it does already exist if xtal not in self.data_collection_column_three_dict: # generate all the widgets which can later be appended and add them to the dictionary - data_collection_table = QtGui.QTableWidget() # table with data processing results for each pipeline + # table with data processing results for each pipeline + data_collection_table = QtGui.QTableWidget() selection_changed_by_user = False - self.data_collection_column_three_dict[xtal] = [data_collection_table, selection_changed_by_user] + self.data_collection_column_three_dict[xtal] = [ + data_collection_table, selection_changed_by_user] xtal_in_table = True else: data_collection_table = self.data_collection_column_three_dict[xtal][0] selection_changed_by_user = self.data_collection_column_three_dict[xtal][1] - data_collection_table.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff) + data_collection_table.setVerticalScrollBarPolicy( + QtCore.Qt.ScrollBarAlwaysOff) data_collection_table.setColumnCount(len(column_name)) font = QtGui.QFont() font.setPointSize(8) data_collection_table.setFont(font) data_collection_table.setHorizontalHeaderLabels(column_name) data_collection_table.horizontalHeader().setFont(font) - data_collection_table.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows) + data_collection_table.setSelectionBehavior( + QtGui.QAbstractItemView.SelectRows) ############################################################################# # crystal images @@ -4401,7 +4836,8 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): # not if there is a run, but images are for whatever reason not present in self.data_collection_dict # then use image not available from $XChemExplorer_DIR/image/IMAGE_NOT_AVAILABLE.png # not sure how to do this at the moment; it will probably trigger an error that I can catch - self.data_collection_image_dict[xtal].append([entry[6], entry[1], entry[2], entry[3], entry[5]]) + self.data_collection_image_dict[xtal].append( + [entry[6], entry[1], entry[2], entry[3], entry[5]]) ############################################################################# # initialize dataset_outcome_dict for xtal @@ -4421,7 +4857,8 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): for entry in self.data_collection_dict[xtal]: if entry[0] == 'logfile': logfile_list.append(entry) - for entry in sorted(logfile_list, key=lambda x: x[7]): # sort by aimless_index and so make sure + # sort by aimless_index and so make sure + for entry in sorted(logfile_list, key=lambda x: x[7]): entry_already_in_table = False # that aimless_index == row for logfile in self.data_collection_table_dict[xtal]: if entry[1] == logfile[1] and entry[2] == logfile[2] and entry[3] == logfile[3] and entry[4] == \ @@ -4433,8 +4870,10 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): # entry[7]==aimless_index, i.e. row number cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(db_dict[header[1]])) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - data_collection_table.setItem(entry[7], column, cell_text) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + data_collection_table.setItem( + entry[7], column, cell_text) break break if not entry_already_in_table: @@ -4447,15 +4886,18 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): except KeyError: # this may happen if not score exists cell_text.setText('0') - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - data_collection_table.setItem(row_position, column, cell_text) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + data_collection_table.setItem( + row_position, column, cell_text) data_collection_table.setRowHeight(row_position, 20) row_position += 1 self.data_collection_table_dict[xtal].append( ['logfile', entry[1], entry[2], entry[3], entry[4]]) # 'logfile' is just added to have # same index numbers between lists - data_collection_table.cellClicked.connect(self.user_update_selected_autoproc_datasets_summary_table) + data_collection_table.cellClicked.connect( + self.user_update_selected_autoproc_datasets_summary_table) # select best resolution file + set data collection outcome # the assumption is that index in data_collection_dict and row number are identical @@ -4490,14 +4932,16 @@ def find_suitable_reference_file(self, db_dict): return reference_file def create_maps_table(self): - column_name = self.db.translate_xce_column_list_to_sqlite(self.maps_table_columns) + column_name = self.db.translate_xce_column_list_to_sqlite( + self.maps_table_columns) for xtal in sorted(self.xtal_db_dict): new_xtal = False db_dict = self.xtal_db_dict[xtal] if str(db_dict['DataCollectionOutcome']).lower().startswith('success'): reference_file = self.find_suitable_reference_file(db_dict) - smallest_uc_difference = min(reference_file, key=lambda x: x[1]) + smallest_uc_difference = min( + reference_file, key=lambda x: x[1]) row = self.maps_table.rowCount() if xtal not in self.initial_model_dimple_dict: self.maps_table.insertRow(row) @@ -4512,75 +4956,100 @@ def create_maps_table(self): if header[0] == 'Sample ID': cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(xtal)) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) self.maps_table.setItem(current_row, column, cell_text) elif header[0] == 'Select': if new_xtal: run_dimple = QtGui.QCheckBox() run_dimple.toggle() - self.maps_table.setCellWidget(current_row, column, run_dimple) + self.maps_table.setCellWidget( + current_row, column, run_dimple) run_dimple.setChecked(False) elif header[0] == 'Reference\nSpaceGroup': cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(smallest_uc_difference[0][1])) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) self.maps_table.setItem(current_row, column, cell_text) elif header[0] == 'Difference\nUC Volume (%)': cell_text = QtGui.QTableWidgetItem() - smallest_uc_difference = min(reference_file, key=lambda x: x[1]) - cell_text.setText(str(round(float(smallest_uc_difference[1]), 1))) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + smallest_uc_difference = min( + reference_file, key=lambda x: x[1]) + cell_text.setText( + str(round(float(smallest_uc_difference[1]), 1))) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) self.maps_table.setItem(current_row, column, cell_text) elif header[0] == 'Reference File': if new_xtal: reference_file_selection_combobox = QtGui.QComboBox() - self.populate_reference_combobox(reference_file_selection_combobox) + self.populate_reference_combobox( + reference_file_selection_combobox) if float(smallest_uc_difference[1]) < self.allowed_unitcell_difference_percent: index = reference_file_selection_combobox.findText(str(smallest_uc_difference[0][0]), QtCore.Qt.MatchFixedString) - reference_file_selection_combobox.setCurrentIndex(index) + reference_file_selection_combobox.setCurrentIndex( + index) else: - reference_file_selection_combobox.setCurrentIndex(0) + reference_file_selection_combobox.setCurrentIndex( + 0) self.maps_table.setCellWidget(current_row, column, reference_file_selection_combobox) else: - reference_file_selection_combobox = self.initial_model_dimple_dict[xtal][1] - self.populate_reference_combobox(reference_file_selection_combobox) + reference_file_selection_combobox = self.initial_model_dimple_dict[ + xtal][1] + self.populate_reference_combobox( + reference_file_selection_combobox) if float(smallest_uc_difference[1]) < self.allowed_unitcell_difference_percent: index = reference_file_selection_combobox.findText(str(smallest_uc_difference[0][0]), QtCore.Qt.MatchFixedString) - reference_file_selection_combobox.setCurrentIndex(index) + reference_file_selection_combobox.setCurrentIndex( + index) else: - reference_file_selection_combobox.setCurrentIndex(0) + reference_file_selection_combobox.setCurrentIndex( + 0) else: cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(db_dict[header[1]])) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) if header[0] == 'Dimple\nStatus': if str(db_dict[header[1]]) == 'running': - cell_text.setBackground(QtGui.QColor(100, 230, 150)) + cell_text.setBackground( + QtGui.QColor(100, 230, 150)) elif str(db_dict[header[1]]) == 'pending': - cell_text.setBackground(QtGui.QColor(20, 100, 230)) + cell_text.setBackground( + QtGui.QColor(20, 100, 230)) elif str(db_dict[header[1]]) == 'started': - cell_text.setBackground(QtGui.QColor(230, 240, 110)) + cell_text.setBackground( + QtGui.QColor(230, 240, 110)) elif str(db_dict[header[1]]) == 'finished': - cell_text.setBackground(QtGui.QColor(255, 255, 255)) + cell_text.setBackground( + QtGui.QColor(255, 255, 255)) if header[0] == 'Compound\nStatus': if str(db_dict[header[1]]) == 'running': - cell_text.setBackground(QtGui.QColor(100, 230, 150)) + cell_text.setBackground( + QtGui.QColor(100, 230, 150)) elif str(db_dict[header[1]]) == 'pending': - cell_text.setBackground(QtGui.QColor(20, 100, 230)) + cell_text.setBackground( + QtGui.QColor(20, 100, 230)) elif str(db_dict[header[1]]) == 'started': - cell_text.setBackground(QtGui.QColor(230, 240, 110)) + cell_text.setBackground( + QtGui.QColor(230, 240, 110)) elif str(db_dict[header[1]]) == 'restraints generated': - cell_text.setBackground(QtGui.QColor(255, 255, 255)) + cell_text.setBackground( + QtGui.QColor(255, 255, 255)) elif str(db_dict[header[1]]) == 'restraints failed': - cell_text.setBackground(QtGui.QColor(255, 0, 0)) + cell_text.setBackground( + QtGui.QColor(255, 0, 0)) elif str(db_dict[header[1]]) == 'missing smiles': - cell_text.setBackground(QtGui.QColor(240, 150, 20)) + cell_text.setBackground( + QtGui.QColor(240, 150, 20)) self.maps_table.setItem(current_row, column, cell_text) if new_xtal: - self.initial_model_dimple_dict[xtal] = [run_dimple, reference_file_selection_combobox] + self.initial_model_dimple_dict[xtal] = [ + run_dimple, reference_file_selection_combobox] def preferences_data_to_copy_combobox_changed(self, i): text = str(self.preferences_data_to_copy_combobox.currentText()) @@ -4592,26 +5061,30 @@ def preferences_data_to_copy_combobox_changed(self, i): def preferences_selection_mechanism_combobox_changed(self, i): text = str(self.preferences_selection_mechanism_combobox.currentText()) self.preferences['dataset_selection_mechanism'] = text - self.update_log.insert('setting datasets selection mechanism to ' + text) + self.update_log.insert( + 'setting datasets selection mechanism to ' + text) def preferences_initial_refinement_combobox_changed(self, i): text = str(self.preferences_initial_refinement_combobox.currentText()) self.preferences['initial_refinement_pipeline'] = text - self.update_log.insert('setting initial refinement pipeline to ' + text) + self.update_log.insert( + 'setting initial refinement pipeline to ' + text) def preferences_restraints_generation_combobox_changed(self): text = str(self.preferences_restraints_generation_combobox.currentText()) self.restraints_program = text - self.update_log.insert('will use {0!s} for generation of ligand coordinates and restraints'.format(text)) + self.update_log.insert( + 'will use {0!s} for generation of ligand coordinates and restraints'.format(text)) def refinement_outcome_combobox_changed(self): for xtal in self.refinement_table_dict: if self.sender() == self.refinement_table_dict[xtal]: -# db_dict = {'RefinementOutcome': str(self.sender().currentText())} + # db_dict = {'RefinementOutcome': str(self.sender().currentText())} db_dict = {} db_dict['RefinementOutcome'] = str(self.sender().currentText()) db_dict['RefinementOutcomePerson'] = getpass.getuser() - db_dict['RefinementOutcomeDate'] = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] + db_dict['RefinementOutcomeDate'] = datetime.strftime( + datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, xtal, 'ligand_bound', db_dict) @@ -4621,7 +5094,8 @@ def get_reference_file_list(self, reference_root): dummy = ['...', '', '', '', 0, '0'] reference_file_list.append(dummy) if os.path.isfile(os.path.join(self.reference_directory, reference_root + '.pdb')): - pdb_reference = parse().PDBheader(os.path.join(self.reference_directory, reference_root + '.pdb')) + pdb_reference = parse().PDBheader(os.path.join( + self.reference_directory, reference_root + '.pdb')) spg_reference = pdb_reference['SpaceGroup'] unitcell_reference = pdb_reference['UnitCell'] lattice_reference = pdb_reference['Lattice'] @@ -4636,7 +5110,8 @@ def get_reference_file_list(self, reference_root): else: for files in glob.glob(self.reference_directory + '/*'): if files.endswith('.pdb'): - reference_root = files[files.rfind('/') + 1:files.rfind('.')] + reference_root = files[files.rfind( + '/') + 1:files.rfind('.')] if os.path.isfile(os.path.join(self.reference_directory, reference_root + '.pdb')): # reference_file = reference_root + '.pdb' @@ -4654,7 +5129,8 @@ def get_reference_file_list(self, reference_root): unitcell_volume_reference, pointgroup_reference]) for n, file in enumerate(reference_file_list): - self.update_log.insert('reference file {0!s}: {1!s}'.format(n, file)) + self.update_log.insert( + 'reference file {0!s}: {1!s}'.format(n, file)) return reference_file_list def dataset_outcome_combobox_change_outcome(self, text): @@ -4663,24 +5139,26 @@ def dataset_outcome_combobox_change_outcome(self, text): for key in self.dataset_outcome_combobox_dict: if self.dataset_outcome_combobox_dict[key] == self.sender(): xtal = key - self.update_log.insert('user changed data collection outcome of {0!s} to {1!s}'.format(xtal, outcome)) + self.update_log.insert( + 'user changed data collection outcome of {0!s} to {1!s}'.format(xtal, outcome)) break self.dataset_outcome_dict[xtal] = outcome if xtal != '': -# # need to also update if not yet done -# user_already_changed_selection = False -# for n, entry in enumerate(self.data_collection_dict[xtal]): -# if entry[0] == 'user_changed_selection': -# user_already_changed_selection = True -# if entry[0] == 'logfile': -# db_dict = entry[6] -# db_dict['DataCollectionOutcome'] = outcome -# entry[6] = db_dict -# self.data_collection_dict[xtal][n] = entry -# if not user_already_changed_selection: -# self.data_collection_dict[xtal].append(['user_changed_selection']) -# # finally need to update outcome field in data source accordingly - self.update_log.insert('updating dataset outcome in datasource for {0!s}'.format(xtal)) + # # need to also update if not yet done + # user_already_changed_selection = False + # for n, entry in enumerate(self.data_collection_dict[xtal]): + # if entry[0] == 'user_changed_selection': + # user_already_changed_selection = True + # if entry[0] == 'logfile': + # db_dict = entry[6] + # db_dict['DataCollectionOutcome'] = outcome + # entry[6] = db_dict + # self.data_collection_dict[xtal][n] = entry + # if not user_already_changed_selection: + # self.data_collection_dict[xtal].append(['user_changed_selection']) + # # finally need to update outcome field in data source accordingly + self.update_log.insert( + 'updating dataset outcome in datasource for {0!s}'.format(xtal)) update_dict = {'DataCollectionOutcome': outcome} self.db.update_insert_data_source(xtal, update_dict) @@ -4692,7 +5170,6 @@ def set_run_dimple_flag(self, state): for key in self.initial_model_dimple_dict: self.initial_model_dimple_dict[key][0].setChecked(False) - def show_data_collection_details(self, state): # first remove currently displayed widget if self.data_collection_details_currently_on_display is not None: @@ -4702,7 +5179,8 @@ def show_data_collection_details(self, state): tmp = [] allRows = self.datasets_summary_table.rowCount() for table_row in range(allRows): - tmp.append([self.datasets_summary_table.item(table_row, 0).text(), table_row]) + tmp.append([self.datasets_summary_table.item( + table_row, 0).text(), table_row]) for key in self.datasets_summary_dict: if self.datasets_summary_dict[key][3] == self.sender(): @@ -4710,7 +5188,8 @@ def show_data_collection_details(self, state): for item in tmp: if item[0] == key: self.datasets_summary_table.selectRow(item[1]) - self.data_collection_details_currently_on_display = self.data_collection_column_three_dict[key][0] + self.data_collection_details_currently_on_display = self.data_collection_column_three_dict[ + key][0] self.datasets_summarys_vbox_for_details.addWidget( self.data_collection_details_currently_on_display) self.data_collection_details_currently_on_display.show() @@ -4902,7 +5381,7 @@ def show_data_collection_details(self, state): # => new data collection summary table # > start - def get_sample_list_from_table(self,table): + def get_sample_list_from_table(self, table): sampleList = [] allRows = table.rowCount() for row in xrange(0, allRows): @@ -4910,26 +5389,28 @@ def get_sample_list_from_table(self,table): sampleList.append(sample_id) return sorted(sampleList) - def get_row_of_sample_in_table(self,table,xtal): + def get_row_of_sample_in_table(self, table, xtal): allRows = table.rowCount() sampleRow = allRows - for n,row in enumerate(xrange(0, allRows)): + for n, row in enumerate(xrange(0, allRows)): sample_id = str(table.item(row, 0).text()) if sample_id == xtal: sampleRow = n break return sampleRow - def update_row_in_table(self,sample,row,db_dict,table,columns_to_show): + def update_row_in_table(self, sample, row, db_dict, table, columns_to_show): xtal = str(sample) - column_name = self.db.translate_xce_column_list_to_sqlite(columns_to_show) + column_name = self.db.translate_xce_column_list_to_sqlite( + columns_to_show) for column, header in enumerate(column_name): if header[0] == 'Sample ID': cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(xtal)) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) table.setItem(row, column, cell_text) elif header[0] == 'DataCollection\nOutcome': @@ -4937,10 +5418,12 @@ def update_row_in_table(self,sample,row,db_dict,table,columns_to_show): dataset_outcome_combobox = QtGui.QComboBox() for outcomeItem in self.dataset_outcome: dataset_outcome_combobox.addItem(outcomeItem) - dataset_outcome_combobox.activated[str].connect(self.dataset_outcome_combobox_change_outcome) + dataset_outcome_combobox.activated[str].connect( + self.dataset_outcome_combobox_change_outcome) self.dataset_outcome_combobox_dict[xtal] = dataset_outcome_combobox table.setCellWidget(row, column, dataset_outcome_combobox) - index = self.dataset_outcome_combobox_dict[xtal].findText(str(db_dict['DataCollectionOutcome']), QtCore.Qt.MatchFixedString) + index = self.dataset_outcome_combobox_dict[xtal].findText( + str(db_dict['DataCollectionOutcome']), QtCore.Qt.MatchFixedString) self.dataset_outcome_combobox_dict[xtal].setCurrentIndex(index) elif header[0].startswith('img'): @@ -4951,7 +5434,8 @@ def update_row_in_table(self,sample,row,db_dict,table,columns_to_show): os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'IMAGE_NOT_AVAILABLE.png')) image = QtGui.QLabel() image.resize(128, 80) - image.setPixmap(pixmap.scaled(image.size(), QtCore.Qt.KeepAspectRatio)) + image.setPixmap(pixmap.scaled( + image.size(), QtCore.Qt.KeepAspectRatio)) table.setCellWidget(row, column, image) elif header[0] == 'Select': @@ -4966,7 +5450,7 @@ def update_row_in_table(self,sample,row,db_dict,table,columns_to_show): table.setCellWidget(row, column, checkbox) checkbox.setChecked(False) - #elif header[0].startswith('SoakDB\nBarcode') or header[0].startswith('GDA\nBarcode'): + # elif header[0].startswith('SoakDB\nBarcode') or header[0].startswith('GDA\nBarcode'): # if new_xtal: # cell_text = QtGui.QTableWidgetItem() # if xtal in pinDict: @@ -4998,9 +5482,11 @@ def update_row_in_table(self,sample,row,db_dict,table,columns_to_show): # cell_text.setText('999') # else: # cell_text.setText('') - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) table.setItem(row, column, cell_text) - print('row: {0!s} column: {1!s} value: {2!s} header: {3!s}'.format(row, column, cell_text, header[0])) + print('row: {0!s} column: {1!s} value: {2!s} header: {3!s}'.format( + row, column, cell_text, header[0])) print('column_name {0!s}'.format(column_name)) def populate_datasets_summary_table_NEW(self): @@ -5008,23 +5494,28 @@ def populate_datasets_summary_table_NEW(self): 'Building summary table for data processing results; be patient this may take a while') # get information about all samples collected during the current visit - visit, beamline = XChemMain.getVisitAndBeamline(self.beamline_directory) + visit, beamline = XChemMain.getVisitAndBeamline( + self.beamline_directory) if self.read_agamemnon.isChecked(): visit = [] for v in glob.glob(os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*')): visit.append(v[v.rfind('/')+1:]) - self.update_log.insert('reading information about collected crystals from database...') - collectedXtalsDict = self.db.xtals_collected_during_visit_as_dict(visit) + self.update_log.insert( + 'reading information about collected crystals from database...') + collectedXtalsDict = self.db.xtals_collected_during_visit_as_dict( + visit) # instead of using dictionaries, query table of which crystals are in table - samples_in_table = self.get_sample_list_from_table(self.datasets_summary_table) + samples_in_table = self.get_sample_list_from_table( + self.datasets_summary_table) for xtal in sorted(collectedXtalsDict): if xtal not in samples_in_table: row = self.datasets_summary_table.rowCount() self.datasets_summary_table.insertRow(row) else: - row = self.get_row_of_sample_in_table(self.datasets_summary_table,xtal) + row = self.get_row_of_sample_in_table( + self.datasets_summary_table, xtal) db_dict = collectedXtalsDict[xtal] self.update_row_in_table(xtal, row, db_dict, self.datasets_summary_table, self.datasets_summary_table_columns) @@ -5036,54 +5527,60 @@ def populate_datasets_summary_table_NEW(self): self.status_bar.showMessage('idle') - - def get_selected_row(self,table): + def get_selected_row(self, table): indexes = table.selectionModel().selectedRows() for index in sorted(indexes): selected_row = index.row() return selected_row def show_results_from_all_pipelines(self): - selected_row=self.get_selected_row(self.datasets_summary_table) + selected_row = self.get_selected_row(self.datasets_summary_table) xtal = self.datasets_summary_table.item(selected_row, 0).text() # get details of currently selected autoprocessing result selectedResultDict = self.db.get_db_dict_for_sample(xtal) - dbList=self.db.all_autoprocessing_results_for_xtal_as_dict(xtal) + dbList = self.db.all_autoprocessing_results_for_xtal_as_dict(xtal) self.make_data_collection_table() - self.msgBox = QtGui.QMessageBox() # needs to be created here, otherwise the cellClicked function - # will reference it before it exists + # needs to be created here, otherwise the cellClicked function + self.msgBox = QtGui.QMessageBox() + # will reference it before it exists for db_dict in dbList: if str(db_dict['DataProcessingSpaceGroup']).lower() == 'null' or str(db_dict['DataProcessingSpaceGroup']).lower() == 'none': continue row = self.data_collection_table.rowCount() self.data_collection_table.insertRow(row) - self.update_row_in_table(xtal, row, db_dict, self.data_collection_table, self.data_collection_table_columns) + self.update_row_in_table( + xtal, row, db_dict, self.data_collection_table, self.data_collection_table_columns) if selectedResultDict['DataCollectionVisit'] == db_dict['DataCollectionVisit'] \ - and selectedResultDict['DataCollectionRun'] == db_dict['DataCollectionRun'] \ - and selectedResultDict['DataProcessingProgram'] == db_dict['DataProcessingProgram'] \ - and selectedResultDict['DataProcessingScore'] == db_dict['DataProcessingScore']: + and selectedResultDict['DataCollectionRun'] == db_dict['DataCollectionRun'] \ + and selectedResultDict['DataProcessingProgram'] == db_dict['DataProcessingProgram'] \ + and selectedResultDict['DataProcessingScore'] == db_dict['DataProcessingScore']: self.current_row = row self.data_collection_table.selectRow(row) - self.data_collection_table.cellClicked.connect(self.select_different_autoprocessing_result) + self.data_collection_table.cellClicked.connect( + self.select_different_autoprocessing_result) self.data_collection_table_popup() def make_data_collection_table(self): # this creates a new table widget every time # more elegant would be to delete or reset an existing widget... self.data_collection_table = QtGui.QTableWidget() - self.data_collection_table.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOff) - self.data_collection_table.setColumnCount(len(self.data_collection_table_columns)) + self.data_collection_table.setVerticalScrollBarPolicy( + QtCore.Qt.ScrollBarAlwaysOff) + self.data_collection_table.setColumnCount( + len(self.data_collection_table_columns)) font = QtGui.QFont() font.setPointSize(8) self.data_collection_table.setFont(font) - self.data_collection_table.setHorizontalHeaderLabels(self.data_collection_table_columns) + self.data_collection_table.setHorizontalHeaderLabels( + self.data_collection_table_columns) self.data_collection_table.horizontalHeader().setFont(font) - self.data_collection_table.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows) + self.data_collection_table.setSelectionBehavior( + QtGui.QAbstractItemView.SelectRows) def data_collection_table_popup(self): -# self.msgBox = QtGui.QMessageBox() + # self.msgBox = QtGui.QMessageBox() msgBoxLayout = self.msgBox.layout() qWid = QtGui.QWidget() qWid.setFixedWidth(3000) @@ -5093,57 +5590,51 @@ def data_collection_table_popup(self): qWid.setLayout(vbox) # msgBoxLayout.addLayout(vbox, 0, 0) msgBoxLayout.addWidget(qWid) - self.msgBox.addButton(QtGui.QPushButton('Cancel'), QtGui.QMessageBox.RejectRole) - self.msgBox.resize(1000,200) - self.msgBox.exec_(); + self.msgBox.addButton(QtGui.QPushButton( + 'Cancel'), QtGui.QMessageBox.RejectRole) + self.msgBox.resize(1000, 200) + self.msgBox.exec_() def select_different_autoprocessing_result(self): - selected_row=self.get_selected_row(self.data_collection_table) + selected_row = self.get_selected_row(self.data_collection_table) if selected_row != self.current_row: - xtal = self.data_collection_table.item(selected_row, 0).text() - visit = self.data_collection_table.item(selected_row, 1).text() - run = self.data_collection_table.item(selected_row, 2).text() + xtal = self.data_collection_table.item(selected_row, 0).text() + visit = self.data_collection_table.item(selected_row, 1).text() + run = self.data_collection_table.item(selected_row, 2).text() autoproc = self.data_collection_table.item(selected_row, 3).text() - score = self.data_collection_table.item(selected_row, 12).text() + score = self.data_collection_table.item(selected_row, 12).text() for q in range(13): try: - print('--> {0!s}: {1!s}'.format(q, self.data_collection_table.item(selected_row, q).text())) + print('--> {0!s}: {1!s}'.format(q, + self.data_collection_table.item(selected_row, q).text())) except AttributeError: print('--> {0!s}: None'.format(q)) # get db_dict from collectionTable for visit, run, autoproc # dbDict = self.db.get_db_dict_for_visit_run_autoproc(xtal,visit,run,autoproc) - dbDict = self.db.get_db_dict_for_visit_run_autoproc_score(xtal, visit, run, autoproc, score) + dbDict = self.db.get_db_dict_for_visit_run_autoproc_score( + xtal, visit, run, autoproc, score) dbDict['DataProcessingAutoAssigned'] = 'False' - self.update_log.insert('%s: changing selected autoprocessing result to %s %s %s' %(xtal,visit,run,autoproc)) + self.update_log.insert('%s: changing selected autoprocessing result to %s %s %s' % ( + xtal, visit, run, autoproc)) # xtal is QString -> str(xtal) - XChemMain.linkAutoProcessingResult(str(xtal), dbDict, self.initial_model_directory,self.xce_logfile) - self.update_log.insert('%s: updating row in Datasets table' %xtal) - self.db.update_data_source(str(xtal),dbDict) - self.update_log.insert('%s: getting updated information from DB mainTable' %xtal) + XChemMain.linkAutoProcessingResult( + str(xtal), dbDict, self.initial_model_directory, self.xce_logfile) + self.update_log.insert('%s: updating row in Datasets table' % xtal) + self.db.update_data_source(str(xtal), dbDict) + self.update_log.insert( + '%s: getting updated information from DB mainTable' % xtal) dbDict = self.db.get_db_dict_for_sample(xtal) - row = self.get_row_of_sample_in_table(self.datasets_summary_table,xtal) + row = self.get_row_of_sample_in_table( + self.datasets_summary_table, xtal) self.update_row_in_table(xtal, row, dbDict, self.datasets_summary_table, self.datasets_summary_table_columns) else: print('nothing to change') self.msgBox.done(1) - - # < end ################################################################################################################# - - - - - - - - - - - def update_outcome_datasets_summary_table(self, sample, outcome): rows_in_table = self.datasets_summary_table.rowCount() for row in range(rows_in_table): @@ -5156,7 +5647,8 @@ def user_update_selected_autoproc_datasets_summary_table(self): for key in self.data_collection_column_three_dict: if self.data_collection_column_three_dict[key][0] == self.sender(): self.update_log.insert('here: ' + self.sender()) - self.update_log.insert('herere' + str(self.data_collection_column_three_dict)) + self.update_log.insert( + 'herere' + str(self.data_collection_column_three_dict)) dbTmp = self.xtal_db_dict[key] stage = dbTmp['RefinementOutcome'].split()[0] print('===>', key, stage) @@ -5166,18 +5658,22 @@ def user_update_selected_autoproc_datasets_summary_table(self): "*** WARNING ***\n%s is currently %s\nIt will disappear from the Refinement table,\n" "when you refresh it next time.\nDo you want to continue?" % ( key, dbTmp['RefinementOutcome'])) - msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.RejectRole) - reply = msgBox.exec_(); + msgBox.addButton(QtGui.QPushButton( + 'No'), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton('Yes'), + QtGui.QMessageBox.RejectRole) + reply = msgBox.exec_() if reply == 0: - self.update_log.insert('will not change data processing selection') + self.update_log.insert( + 'will not change data processing selection') # restore previous selection for n, entry in enumerate(self.data_collection_dict[key]): print('==>', n) if entry[0] == 'logfile': if entry[8]: print('===> found:', n) - self.data_collection_column_three_dict[key][0].selectRow(n) + self.data_collection_column_three_dict[key][0].selectRow( + n) break indexes = self.sender().selectionModel().selectedRows() @@ -5213,7 +5709,8 @@ def user_update_selected_autoproc_datasets_summary_table(self): entry[6] = db_dict self.data_collection_dict[key][n] = entry if not user_already_changed_selection: - self.data_collection_dict[key].append(['user_changed_selection']) + self.data_collection_dict[key].append( + ['user_changed_selection']) XChemMain.change_links_to_selected_data_collection_outcome(key, self.data_collection_dict, self.data_collection_column_three_dict, self.dataset_outcome_dict, @@ -5241,9 +5738,12 @@ def user_update_selected_autoproc_datasets_summary_table(self): else: cell_text = QtGui.QTableWidgetItem() try: - cell_text.setText(str(db_dict_current[header[1]])) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.datasets_summary_table.setItem(row, column, cell_text) + cell_text.setText( + str(db_dict_current[header[1]])) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + self.datasets_summary_table.setItem( + row, column, cell_text) except KeyError: pass @@ -5293,20 +5793,25 @@ def update_selected_autoproc_datasets_summary_table(self): else: cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(db_dict[header[1]])) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.datasets_summary_table.setItem(row, column, cell_text) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + self.datasets_summary_table.setItem( + row, column, cell_text) def populate_and_update_datasource_table(self): - self.overview_datasource_table.setColumnCount(len(self.overview_datasource_table_columns)) + self.overview_datasource_table.setColumnCount( + len(self.overview_datasource_table_columns)) # first get a list of all the samples that are already in the table and which will be updated samples_in_table = [] current_row = self.overview_datasource_table.rowCount() for row in range(current_row): - sampleID = str(self.overview_datasource_table.item(row, 0).text()) # this must be the case + sampleID = str(self.overview_datasource_table.item( + row, 0).text()) # this must be the case samples_in_table.append(sampleID) - columns_to_show = self.get_columns_to_show(self.overview_datasource_table_columns) + columns_to_show = self.get_columns_to_show( + self.overview_datasource_table_columns) n_rows = self.get_rows_with_sample_id_not_null_from_datasource() sample_id_column = self.get_columns_to_show(['Sample ID']) @@ -5332,18 +5837,22 @@ def populate_and_update_datasource_table(self): cell_text.setText('') else: cell_text.setText(str(row[item])) - if self.overview_datasource_table_columns[y] == 'Sample ID': # assumption is that column 0 is always sampleID - cell_text.setFlags(QtCore.Qt.ItemIsEnabled) # and this field cannot be changed - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + # assumption is that column 0 is always sampleID + if self.overview_datasource_table_columns[y] == 'Sample ID': + # and this field cannot be changed + cell_text.setFlags(QtCore.Qt.ItemIsEnabled) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) self.overview_datasource_table.setItem(x, y, cell_text) - self.overview_datasource_table.setHorizontalHeaderLabels(self.overview_datasource_table_columns) + self.overview_datasource_table.setHorizontalHeaderLabels( + self.overview_datasource_table_columns) def kill_other_pandda_options(self): for i in range(0, self.pandda_analyse_data_table.rowCount()): - checkbox0 = self.pandda_analyse_data_table.cellWidget(i,1) - checkbox1 = self.pandda_analyse_data_table.cellWidget(i,7) - checkbox2 = self.pandda_analyse_data_table.cellWidget(i,8) - checkbox3 = self.pandda_analyse_data_table.cellWidget(i,9) + checkbox0 = self.pandda_analyse_data_table.cellWidget(i, 1) + checkbox1 = self.pandda_analyse_data_table.cellWidget(i, 7) + checkbox2 = self.pandda_analyse_data_table.cellWidget(i, 8) + checkbox3 = self.pandda_analyse_data_table.cellWidget(i, 9) if checkbox1.isChecked(): checkbox2.setChecked(False) checkbox3.setChecked(False) @@ -5354,7 +5863,8 @@ def kill_other_pandda_options(self): def populate_pandda_analyse_input_table(self): - column_name = self.db.translate_xce_column_list_to_sqlite(self.pandda_table_columns) + column_name = self.db.translate_xce_column_list_to_sqlite( + self.pandda_table_columns) print(column_name) for xtal in sorted(self.xtal_db_dict): new_xtal = False @@ -5371,42 +5881,57 @@ def populate_pandda_analyse_input_table(self): current_row = table_row break for column, header in enumerate(column_name): - if header[0]=='Exclude': + if header[0] == 'Exclude': deselect_button = QtGui.QCheckBox() - deselect_button.stateChanged.connect(self.kill_other_pandda_options) - self.pandda_analyse_data_table.setCellWidget(current_row, column, deselect_button) + deselect_button.stateChanged.connect( + self.kill_other_pandda_options) + self.pandda_analyse_data_table.setCellWidget( + current_row, column, deselect_button) - elif header[0]=='Ignore': + elif header[0] == 'Ignore': deselect_button = QtGui.QCheckBox() - deselect_button.stateChanged.connect(self.kill_other_pandda_options) - self.pandda_analyse_data_table.setCellWidget(current_row, column, deselect_button) + deselect_button.stateChanged.connect( + self.kill_other_pandda_options) + self.pandda_analyse_data_table.setCellWidget( + current_row, column, deselect_button) - elif header[0]=='Export': + elif header[0] == 'Export': deselect_button = QtGui.QCheckBox() - deselect_button.stateChanged.connect(self.kill_other_pandda_options) - self.pandda_analyse_data_table.setCellWidget(current_row, column, deselect_button) + deselect_button.stateChanged.connect( + self.kill_other_pandda_options) + self.pandda_analyse_data_table.setCellWidget( + current_row, column, deselect_button) elif header[0] == 'Sample ID': cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(xtal)) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.pandda_analyse_data_table.setItem(current_row, column, cell_text) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + self.pandda_analyse_data_table.setItem( + current_row, column, cell_text) else: cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(db_dict[header[1]])) if header[0] == 'PanDDA\nStatus': if str(db_dict[header[1]]) == 'running': - cell_text.setBackground(QtGui.QColor(100, 230, 150)) + cell_text.setBackground( + QtGui.QColor(100, 230, 150)) elif str(db_dict[header[1]]) == 'pending': - cell_text.setBackground(QtGui.QColor(20, 100, 230)) + cell_text.setBackground( + QtGui.QColor(20, 100, 230)) elif str(db_dict[header[1]]) == 'started': - cell_text.setBackground(QtGui.QColor(230, 240, 110)) + cell_text.setBackground( + QtGui.QColor(230, 240, 110)) elif str(db_dict[header[1]]) == 'finished': - cell_text.setBackground(QtGui.QColor(255, 255, 255)) + cell_text.setBackground( + QtGui.QColor(255, 255, 255)) elif 'problem' in str(db_dict[header[1]]): - cell_text.setBackground(QtGui.QColor(255, 0, 0)) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.pandda_analyse_data_table.setItem(current_row, column, cell_text) + cell_text.setBackground( + QtGui.QColor(255, 0, 0)) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + self.pandda_analyse_data_table.setItem( + current_row, column, cell_text) if new_xtal: self.pandda_analyse_input_table_dict[xtal] = [] @@ -5414,36 +5939,46 @@ def select_sample_for_pandda(self, option): indexes = self.pandda_analyse_data_table.selectionModel().selectedRows() if option == 'deselect': for index in sorted(indexes): - self.pandda_analyse_data_table.cellWidget(index.row(), 6).setChecked(False) - self.pandda_analyse_data_table.cellWidget(index.row(), 7).setChecked(False) - self.pandda_analyse_data_table.cellWidget(index.row(), 8).setChecked(False) + self.pandda_analyse_data_table.cellWidget( + index.row(), 6).setChecked(False) + self.pandda_analyse_data_table.cellWidget( + index.row(), 7).setChecked(False) + self.pandda_analyse_data_table.cellWidget( + index.row(), 8).setChecked(False) else: for index in sorted(indexes): - self.pandda_analyse_data_table.cellWidget(index.row(), 6).setChecked(False) - self.pandda_analyse_data_table.cellWidget(index.row(), 7).setChecked(False) - self.pandda_analyse_data_table.cellWidget(index.row(), 8).setChecked(False) - if option =='ignore': - checkbox = self.pandda_analyse_data_table.cellWidget(index.row(), 6) + self.pandda_analyse_data_table.cellWidget( + index.row(), 6).setChecked(False) + self.pandda_analyse_data_table.cellWidget( + index.row(), 7).setChecked(False) + self.pandda_analyse_data_table.cellWidget( + index.row(), 8).setChecked(False) + if option == 'ignore': + checkbox = self.pandda_analyse_data_table.cellWidget( + index.row(), 6) if option == 'char': - checkbox = self.pandda_analyse_data_table.cellWidget(index.row(), 7) + checkbox = self.pandda_analyse_data_table.cellWidget( + index.row(), 7) if option == 'zmap': - checkbox = self.pandda_analyse_data_table.cellWidget(index.row(), 8) + checkbox = self.pandda_analyse_data_table.cellWidget( + index.row(), 8) checkbox.setChecked(True) self.kill_other_pandda_options() def populate_and_update_refinement_table(self): -# panddaList = self.db.execute_statement( -# "select CrystalName,PANDDA_site_index,PANDDA_site_name,RefinementOutcome " -# "from panddaTable where CrystalName is not '' and PANDDA_site_ligand_placed is 'True';") -# panddaDict = {} -# for item in panddaList: -# if str(item[0]) not in panddaDict: -# panddaDict[str(item[0])] = [] -# panddaDict[str(item[0])].append([str(item[1]), str(item[2]), str(item[3])]) - - column_name = self.db.translate_xce_column_list_to_sqlite(self.refinement_table_columns) + # panddaList = self.db.execute_statement( + # "select CrystalName,PANDDA_site_index,PANDDA_site_name,RefinementOutcome " + # "from panddaTable where CrystalName is not '' and PANDDA_site_ligand_placed is 'True';") + # panddaDict = {} + # for item in panddaList: + # if str(item[0]) not in panddaDict: + # panddaDict[str(item[0])] = [] + # panddaDict[str(item[0])].append([str(item[1]), str(item[2]), str(item[3])]) + + column_name = self.db.translate_xce_column_list_to_sqlite( + self.refinement_table_columns) for xtal in sorted(self.xtal_db_dict): new_xtal = False db_dict = self.xtal_db_dict[xtal] @@ -5470,32 +6005,40 @@ def populate_and_update_refinement_table(self): if header[0] == 'Sample ID': cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(xtal)) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.refinement_table.setItem(current_row, column, cell_text) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + self.refinement_table.setItem( + current_row, column, cell_text) elif header[0] == 'Refinement\nOutcome': if new_xtal: refinement_outcome_combobox = QtGui.QComboBox() - self.populate_refinement_outcome_combobox(refinement_outcome_combobox) - self.refinement_table.setCellWidget(current_row, column, refinement_outcome_combobox) + self.populate_refinement_outcome_combobox( + refinement_outcome_combobox) + self.refinement_table.setCellWidget( + current_row, column, refinement_outcome_combobox) else: refinement_outcome_combobox = self.refinement_table_dict[xtal] - index = refinement_outcome_combobox.findText(refinementStage, QtCore.Qt.MatchFixedString) + index = refinement_outcome_combobox.findText( + refinementStage, QtCore.Qt.MatchFixedString) refinement_outcome_combobox.setCurrentIndex(index) refinement_outcome_combobox.currentIndexChanged.connect( self.refinement_outcome_combobox_changed) elif header[0] == 'buster-reports': - #"'NAME'".format(db_dict['RefinementBusterReportHTML']) - # db_dict['RefinementBusterReportHTML'] = 'www.google.com' + # "'NAME'".format(db_dict['RefinementBusterReportHTML']) + # db_dict['RefinementBusterReportHTML'] = 'www.google.com' buster_report = db_dict['RefinementBusterReportHTML'] - ref_name = buster_report.split('/')[len(buster_report.split('/'))-2] - buster_report_link = QtGui.QLabel("{1!s}".format(buster_report,ref_name)) + ref_name = buster_report.split( + '/')[len(buster_report.split('/'))-2] + buster_report_link = QtGui.QLabel( + "{1!s}".format(buster_report, ref_name)) buster_report_link.setOpenExternalLinks(True) # buster_report_link.setTextInteractionFlags(QtCore.Qt.TextBrowserInteraction) # buster_report_link.setTextFormat(QtCore.Qt.RichText) # self.refinement_table.setItem(current_row, column, buster_report_link) - self.refinement_table.setCellWidget(current_row, column, buster_report_link) + self.refinement_table.setCellWidget( + current_row, column, buster_report_link) # elif header[0] == 'PanDDA site details': @@ -5524,17 +6067,24 @@ def populate_and_update_refinement_table(self): cell_text.setText(str(db_dict[header[1]])) if header[0] == 'Refinement\nStatus': if str(db_dict[header[1]]) == 'running': - cell_text.setBackground(QtGui.QColor(100, 230, 150)) + cell_text.setBackground( + QtGui.QColor(100, 230, 150)) elif str(db_dict[header[1]]) == 'pending': - cell_text.setBackground(QtGui.QColor(20, 100, 230)) + cell_text.setBackground( + QtGui.QColor(20, 100, 230)) elif str(db_dict[header[1]]) == 'started': - cell_text.setBackground(QtGui.QColor(230, 240, 110)) + cell_text.setBackground( + QtGui.QColor(230, 240, 110)) elif str(db_dict[header[1]]) == 'finished': - cell_text.setBackground(QtGui.QColor(255, 255, 255)) + cell_text.setBackground( + QtGui.QColor(255, 255, 255)) elif 'problem' in str(db_dict[header[1]]): - cell_text.setBackground(QtGui.QColor(255, 0, 0)) - cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.refinement_table.setItem(current_row, column, cell_text) + cell_text.setBackground( + QtGui.QColor(255, 0, 0)) + cell_text.setTextAlignment( + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + self.refinement_table.setItem( + current_row, column, cell_text) if new_xtal: self.refinement_table_dict[xtal] = refinement_outcome_combobox @@ -5562,20 +6112,21 @@ def get_rows_with_sample_id_not_null_from_datasource(self): sample_id_column = self.get_columns_to_show(['Sample ID']) n_rows = 0 for row in self.data: - if not str(row[sample_id_column[0]]).lower() != 'none' or not str(row[sample_id_column[0]]).replace \ - (' ', '') == '': + if not str(row[sample_id_column[0]]).lower() != 'none' or not str(row[sample_id_column[0]]).replace(' ', '') == '': n_rows += 1 return n_rows def update_data_source(self, sample, db_dict): - data_source = XChemDB.data_source(os.path.join(self.database_directory, self.data_source_file)) + data_source = XChemDB.data_source(os.path.join( + self.database_directory, self.data_source_file)) def quit_xce(self): # save pkl file if self.data_collection_dict != {}: if os.path.isfile(self.datasets_summary_file): self.update_log.insert('saving results to PKL file') - pickle.dump(self.data_collection_dict, open(self.datasets_summary_file, 'wb')) + pickle.dump(self.data_collection_dict, open( + self.datasets_summary_file, 'wb')) self.update_log.insert('quitting XCE... bye,bye!') QtGui.qApp.quit() diff --git a/gui_scripts/datasets_tab.py b/gui_scripts/datasets_tab.py index 52d98955..0fa11007 100755 --- a/gui_scripts/datasets_tab.py +++ b/gui_scripts/datasets_tab.py @@ -1,13 +1,12 @@ -import sys, os +import XChemMain +import layout +import sys +import os from PyQt4 import QtGui, QtCore, QtWebKit sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) -import layout - -import XChemMain - class DatasetsTab(): def __init__(self): @@ -25,7 +24,8 @@ def setup(self, xce_object): xce_object.datasets_tab_dict = {} # make subtabs - self.layout_funcs.make_tab_dict(datasets_tab_list, xce_object.datasets_tab_widget, xce_object.datasets_tab_dict) + self.layout_funcs.make_tab_dict( + datasets_tab_list, xce_object.datasets_tab_widget, xce_object.datasets_tab_dict) # main body - things that are always displayed # add a container to hold everythting and add to main tab layout @@ -35,18 +35,24 @@ def setup(self, xce_object): xce_object.autocheck_hbox = QtGui.QHBoxLayout() # checkbox for autocollect - xce_object.check_for_new_data_collection = QtGui.QCheckBox('Check for new data collection every two minutes') - xce_object.check_for_new_data_collection = QtGui.QCheckBox('Check for new data collection every two minutes') + xce_object.check_for_new_data_collection = QtGui.QCheckBox( + 'Check for new data collection every two minutes') + xce_object.check_for_new_data_collection = QtGui.QCheckBox( + 'Check for new data collection every two minutes') self.layout_funcs.add_checkbox(xce_object, xce_object.check_for_new_data_collection, 'xce_object.continously_check_for_new_data_collection') # select target dropdown select_target_label = QtGui.QLabel('Select Target: ') - select_target_label.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter) + select_target_label.setAlignment( + QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter) xce_object.target_selection_combobox = QtGui.QComboBox() - xce_object.populate_target_selection_combobox(xce_object.target_selection_combobox) - xce_object.target_selection_combobox.activated[str].connect(xce_object.target_selection_combobox_activated) - xce_object.target = str(xce_object.target_selection_combobox.currentText()) + xce_object.populate_target_selection_combobox( + xce_object.target_selection_combobox) + xce_object.target_selection_combobox.activated[str].connect( + xce_object.target_selection_combobox_activated) + xce_object.target = str( + xce_object.target_selection_combobox.currentText()) # array defining order of xce_objects to add xce_object.autocheck_hbox_widgets = [xce_object.check_for_new_data_collection, select_target_label, @@ -56,7 +62,8 @@ def setup(self, xce_object): xce_object.autocheck_hbox_widgets) # add xce_objects in order # add target dropdown to top bar - xce_object.datasets_data_collection_vbox.addLayout(xce_object.autocheck_hbox) + xce_object.datasets_data_collection_vbox.addLayout( + xce_object.autocheck_hbox) # summary sub-tab # table @@ -64,22 +71,30 @@ def setup(self, xce_object): xce_object.datasets_summary_table.resizeRowsToContents() xce_object.datasets_summary_table.resizeColumnsToContents() - xce_object.datasets_summary_table.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows) - xce_object.datasets_summary_table.cellClicked.connect(xce_object.show_results_from_all_pipelines) - - self.layout_funcs.table_setup(xce_object.datasets_summary_table, xce_object.datasets_summary_table_columns) - xce_object.datasets_summarys_vbox_for_table = QtGui.QVBoxLayout() # setup layout to hold table - xce_object.datasets_summarys_vbox_for_table.addWidget(xce_object.datasets_summary_table) # add table to layout + xce_object.datasets_summary_table.setSelectionBehavior( + QtGui.QAbstractItemView.SelectRows) + xce_object.datasets_summary_table.cellClicked.connect( + xce_object.show_results_from_all_pipelines) + + self.layout_funcs.table_setup( + xce_object.datasets_summary_table, xce_object.datasets_summary_table_columns) + # setup layout to hold table + xce_object.datasets_summarys_vbox_for_table = QtGui.QVBoxLayout() + xce_object.datasets_summarys_vbox_for_table.addWidget( + xce_object.datasets_summary_table) # add table to layout xce_object.datasets_summarys_vbox_for_details = QtGui.QVBoxLayout() # vbox for details - xce_object.data_collection_details_currently_on_display = None # switch for displaying/updating table + # switch for displaying/updating table + xce_object.data_collection_details_currently_on_display = None - xce_object.datasets_data_collection_vbox.addWidget(xce_object.datasets_tab_widget) # add subtab to main tab + xce_object.datasets_data_collection_vbox.addWidget( + xce_object.datasets_tab_widget) # add subtab to main tab # reprocessing sub-tab # top options # data collection label dc_label = QtGui.QLabel('Data collection directory: ') - dc_label.setAlignment(QtCore.Qt.AlignLeft | QtCore.Qt.AlignVCenter) # align left and centre of container + # align left and centre of container + dc_label.setAlignment(QtCore.Qt.AlignLeft | QtCore.Qt.AlignVCenter) xce_object.diffraction_data_dir_label = QtGui.QLabel( xce_object.diffraction_data_directory) # add directory as text xce_object.diffraction_data_dir_label.setAlignment( @@ -87,23 +102,30 @@ def setup(self, xce_object): # select label select_button = QtGui.QPushButton("Select") - select_button.clicked.connect(xce_object.select_diffraction_data_directory) # attach file open dialogue + # attach file open dialogue + select_button.clicked.connect( + xce_object.select_diffraction_data_directory) # search button search_button = QtGui.QPushButton("Search Datasets") - search_button.clicked.connect(xce_object.search_for_datasets) # search for datasets in the selected directory + # search for datasets in the selected directory + search_button.clicked.connect(xce_object.search_for_datasets) # search info - xce_object.diffraction_data_search_label = QtGui.QLabel(xce_object.diffraction_data_search_info) + xce_object.diffraction_data_search_label = QtGui.QLabel( + xce_object.diffraction_data_search_info) # translate label - translate_label = QtGui.QLabel('Translate: datasetID -> sampleID') - translate_label.setAlignment(QtCore.Qt.AlignCenter) # align in centre of container + translate_label = QtGui.QLabel( + 'Translate: datasetID -> sampleID') + # align in centre of container + translate_label.setAlignment(QtCore.Qt.AlignCenter) # CSV button csv_button = QtGui.QPushButton('Open CSV') csv_button.setStyleSheet("QPushButton { padding: 1px; margin: 1px }") - csv_button.clicked.connect(xce_object.translate_datasetID_to_sampleID) # open the relevant csv file + # open the relevant csv file + csv_button.clicked.connect(xce_object.translate_datasetID_to_sampleID) # create hbox to hold everything and add widgets to it xce_object.hbox_select = QtGui.QHBoxLayout() # top options box @@ -111,11 +133,13 @@ def setup(self, xce_object): xce_object.diffraction_data_search_label, translate_label, csv_button] # array defining order of xce_objects to be added - self.layout_funcs.add_to_box(xce_object.hbox_select, xce_object.hbox_select_widgets) # add xce_objects in order + self.layout_funcs.add_to_box( + xce_object.hbox_select, xce_object.hbox_select_widgets) # add xce_objects in order # frame to hold everything frame_select = QtGui.QFrame() - frame_select.setLayout(xce_object.hbox_select) # apply to containing frame + # apply to containing frame + frame_select.setLayout(xce_object.hbox_select) # table - main body xce_object.datasets_reprocess_table = QtGui.QTableWidget() @@ -124,10 +148,14 @@ def setup(self, xce_object): # create context menu - no idea where this lives... xce_object.popMenu_for_datasets_reprocess_table = QtGui.QMenu() - run_xia2_on_selected = QtGui.QAction("mark selected for reprocessing", xce_object.window) - run_xia2_on_selected.triggered.connect(xce_object.select_sample_for_xia2) - xce_object.popMenu_for_datasets_reprocess_table.addAction(run_xia2_on_selected) - xce_object.datasets_reprocess_table.setContextMenuPolicy(QtCore.Qt.CustomContextMenu) + run_xia2_on_selected = QtGui.QAction( + "mark selected for reprocessing", xce_object.window) + run_xia2_on_selected.triggered.connect( + xce_object.select_sample_for_xia2) + xce_object.popMenu_for_datasets_reprocess_table.addAction( + run_xia2_on_selected) + xce_object.datasets_reprocess_table.setContextMenuPolicy( + QtCore.Qt.CustomContextMenu) xce_object.datasets_reprocess_table.customContextMenuRequested.connect( xce_object.on_context_menu_reprocess_data) @@ -154,11 +182,13 @@ def setup(self, xce_object): mtz_label = QtGui.QLabel('Reference MTZ:') # file label - xce_object.reprocess_reference_mtz_file_label = QtGui.QLabel(xce_object.diffraction_data_reference_mtz) + xce_object.reprocess_reference_mtz_file_label = QtGui.QLabel( + xce_object.diffraction_data_reference_mtz) # select button select_button = QtGui.QPushButton("Select") - select_button.clicked.connect(xce_object.select_reprocess_reference_mtz) + select_button.clicked.connect( + xce_object.select_reprocess_reference_mtz) # define order of widgets to be added to options hbox hbox_options_widgets = [label, xce_object.xia2_3d_checkbox, xce_object.xia2_3dii_checkbox, @@ -180,9 +210,11 @@ def setup(self, xce_object): # res limit isig dropdown menu xce_object.reprocess_isigma_combobox = QtGui.QComboBox() misigma = ['default', '4', '3', '2.5', '2', '1.5', '1', '0.5'] - self.layout_funcs.populate_combobox(misigma, xce_object.reprocess_isigma_combobox) + self.layout_funcs.populate_combobox( + misigma, xce_object.reprocess_isigma_combobox) xce_object.reprocess_isigma_combobox.setCurrentIndex(0) - xce_object.reprocess_isigma_combobox.setStyleSheet(" QComboBox { padding: 1px; margin: 1px }") + xce_object.reprocess_isigma_combobox.setStyleSheet( + " QComboBox { padding: 1px; margin: 1px }") # create vertical box to add labels and dropdowns to, create box and put in frame vbox_isigma = QtGui.QVBoxLayout() @@ -197,14 +229,18 @@ def setup(self, xce_object): # res limit cc half dropdown xce_object.reprocess_cc_half_combobox = QtGui.QComboBox() - cc_half = ['default', '0.9', '0.8', '0.7', '0.6', '0.5', '0.4', '0.3', '0.2', '0.1'] - self.layout_funcs.populate_combobox(cc_half, xce_object.reprocess_cc_half_combobox) + cc_half = ['default', '0.9', '0.8', '0.7', + '0.6', '0.5', '0.4', '0.3', '0.2', '0.1'] + self.layout_funcs.populate_combobox( + cc_half, xce_object.reprocess_cc_half_combobox) xce_object.reprocess_cc_half_combobox.setCurrentIndex(0) - xce_object.reprocess_cc_half_combobox.setStyleSheet(" QComboBox { padding: 1px; margin: 1px }") + xce_object.reprocess_cc_half_combobox.setStyleSheet( + " QComboBox { padding: 1px; margin: 1px }") # create a vbox for label and dropdown, and add items to it vbox_cc_half = QtGui.QVBoxLayout() - vbox_cc_half_widgets = [res_cc_label, xce_object.reprocess_cc_half_combobox] + vbox_cc_half_widgets = [res_cc_label, + xce_object.reprocess_cc_half_combobox] self.layout_funcs.add_to_box(vbox_cc_half, vbox_cc_half_widgets) # create frame to hold everything and add vbox @@ -213,19 +249,19 @@ def setup(self, xce_object): # create a hbox to hold the bottom frames and add everything data_protocol_hbox = QtGui.QHBoxLayout() - data_protocol_hbox_widgets = [frame_options, frame_isigma, frame_cc_half] - self.layout_funcs.add_to_box(data_protocol_hbox, data_protocol_hbox_widgets) + data_protocol_hbox_widgets = [ + frame_options, frame_isigma, frame_cc_half] + self.layout_funcs.add_to_box( + data_protocol_hbox, data_protocol_hbox_widgets) - bottom_options_frame = QtGui.QFrame() # create frame to hold everything (horizontal) + # create frame to hold everything (horizontal) + bottom_options_frame = QtGui.QFrame() bottom_options_frame.setLayout(data_protocol_hbox) # code below sets final layout for whole subtab - xce_object.reprocess_vbox = QtGui.QVBoxLayout() # box to hold reprocessing subtab content - xce_object.reprocess_hbox_widgets = [frame_select, xce_object.datasets_reprocess_table, bottom_options_frame] - self.layout_funcs.add_to_box(xce_object.reprocess_vbox, xce_object.reprocess_hbox_widgets) - - - - - - + # box to hold reprocessing subtab content + xce_object.reprocess_vbox = QtGui.QVBoxLayout() + xce_object.reprocess_hbox_widgets = [ + frame_select, xce_object.datasets_reprocess_table, bottom_options_frame] + self.layout_funcs.add_to_box( + xce_object.reprocess_vbox, xce_object.reprocess_hbox_widgets) diff --git a/gui_scripts/deposition_tab.py b/gui_scripts/deposition_tab.py index ba1dd873..b65f1890 100755 --- a/gui_scripts/deposition_tab.py +++ b/gui_scripts/deposition_tab.py @@ -1,12 +1,12 @@ -import sys, os +import XChemToolTips +import layout +import sys +import os from PyQt4 import QtGui, QtCore, QtWebKit sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) -import layout -import XChemToolTips - class DepositionTab(): def __init__(self): @@ -27,71 +27,95 @@ def setup(self, xce_object): scrollContent.setLayout(scrollLayout) # deposition page heading - deposition_page_heading = self.layout_funcs.add_depo_heading('Group deposition of bound-state structures & ground-state model') + deposition_page_heading = self.layout_funcs.add_depo_heading( + 'Group deposition of bound-state structures & ground-state model') deposition_page_heading.setStyleSheet("font: bold 40pt Arial") - deposition_page_introduction = QtGui.QLabel(XChemToolTips.deposition_introduction()) - deposition_page_introduction_link = QtGui.QLabel(XChemToolTips.deposition_introduction_link()) + deposition_page_introduction = QtGui.QLabel( + XChemToolTips.deposition_introduction()) + deposition_page_introduction_link = QtGui.QLabel( + XChemToolTips.deposition_introduction_link()) deposition_page_introduction_link.setOpenExternalLinks(True) # # bound-state depostion # - deposition_bound_state_heading = self.layout_funcs.add_depo_heading('Group deposition of bound-state structures') + deposition_bound_state_heading = self.layout_funcs.add_depo_heading( + 'Group deposition of bound-state structures') deposition_bound_state_heading.setStyleSheet("font: bold 20pt Arial") - deposition_bound_state_prerequisites = self.layout_funcs.add_depo_heading('Prerequisites') - deposition_bound_state_prerequisites.setStyleSheet("font: italic bold 17pt Arial") + deposition_bound_state_prerequisites = self.layout_funcs.add_depo_heading( + 'Prerequisites') + deposition_bound_state_prerequisites.setStyleSheet( + "font: italic bold 17pt Arial") - deposition_bound_state_prerequisites_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_bound_state_prerequisites()) + deposition_bound_state_prerequisites_text = self.layout_funcs.add_depo_text( + XChemToolTips.deposition_bound_state_prerequisites()) - deposition_bound_state_preparation = self.layout_funcs.add_depo_heading('Procedure') - deposition_bound_state_preparation.setStyleSheet("font: italic bold 17pt Arial ") + deposition_bound_state_preparation = self.layout_funcs.add_depo_heading( + 'Procedure') + deposition_bound_state_preparation.setStyleSheet( + "font: italic bold 17pt Arial ") - deposition_bound_state_preparation_step_one_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_bound_state_preparation_step_one_text()) + deposition_bound_state_preparation_step_one_text = self.layout_funcs.add_depo_text( + XChemToolTips.deposition_bound_state_preparation_step_one_text()) - xce_object.deposition_bounnd_state_preparation_ignore_event_map = QtGui.QCheckBox(XChemToolTips.deposition_bounnd_state_preparation_ignore_event_map()) + xce_object.deposition_bounnd_state_preparation_ignore_event_map = QtGui.QCheckBox( + XChemToolTips.deposition_bounnd_state_preparation_ignore_event_map()) prepare_mmcif_button = QtGui.QPushButton('prepare mmcif') - prepare_mmcif_button.clicked.connect(xce_object.prepare_models_for_deposition_ligand_bound) + prepare_mmcif_button.clicked.connect( + xce_object.prepare_models_for_deposition_ligand_bound) prepare_mmcif_button.setMaximumWidth(200) - deposition_bound_state_preparation_step_two_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_bound_state_preparation_step_two_text()) + deposition_bound_state_preparation_step_two_text = self.layout_funcs.add_depo_text( + XChemToolTips.deposition_bound_state_preparation_step_two_text()) copy_mmcif_button = QtGui.QPushButton('copy mmcif') - copy_mmcif_button.clicked.connect(xce_object.prepare_for_group_deposition_upload_ligand_bound) + copy_mmcif_button.clicked.connect( + xce_object.prepare_for_group_deposition_upload_ligand_bound) copy_mmcif_button.setMaximumWidth(200) - pdb_group_deposition_instruction_one = self.layout_funcs.add_depo_text(XChemToolTips.pdb_group_deposition_instruction_one()) + pdb_group_deposition_instruction_one = self.layout_funcs.add_depo_text( + XChemToolTips.pdb_group_deposition_instruction_one()) - pdb_group_deposition_link = QtGui.QLabel(XChemToolTips.pdb_group_deposition_link()) + pdb_group_deposition_link = QtGui.QLabel( + XChemToolTips.pdb_group_deposition_link()) pdb_group_deposition_link.setOpenExternalLinks(True) - pdb_group_deposition_link_two = QtGui.QLabel(XChemToolTips.pdb_group_deposition_link()) + pdb_group_deposition_link_two = QtGui.QLabel( + XChemToolTips.pdb_group_deposition_link()) pdb_group_deposition_link_two.setOpenExternalLinks(True) - pdb_group_deposition_instruction_two = self.layout_funcs.add_depo_text(XChemToolTips.pdb_group_deposition_instruction_two()) - pdb_group_deposition_instruction_two_two = self.layout_funcs.add_depo_text(XChemToolTips.pdb_group_deposition_instruction_two()) - + pdb_group_deposition_instruction_two = self.layout_funcs.add_depo_text( + XChemToolTips.pdb_group_deposition_instruction_two()) + pdb_group_deposition_instruction_two_two = self.layout_funcs.add_depo_text( + XChemToolTips.pdb_group_deposition_instruction_two()) # # ground-state depostion # - deposition_ground_state_heading = self.layout_funcs.add_depo_heading('Group deposition of ground-state model') + deposition_ground_state_heading = self.layout_funcs.add_depo_heading( + 'Group deposition of ground-state model') deposition_ground_state_heading.setStyleSheet("font: bold 20pt Arial") - deposition_ground_state_preparation_step_one_text = self.layout_funcs.add_depo_text(XChemToolTips.notification_about_changes_to_apo_deposition()) - + deposition_ground_state_preparation_step_one_text = self.layout_funcs.add_depo_text( + XChemToolTips.notification_about_changes_to_apo_deposition()) - deposition_ground_state_prerequisites = self.layout_funcs.add_depo_heading('Prerequisites') - deposition_ground_state_prerequisites.setStyleSheet("font: italic bold 17pt Arial") + deposition_ground_state_prerequisites = self.layout_funcs.add_depo_heading( + 'Prerequisites') + deposition_ground_state_prerequisites.setStyleSheet( + "font: italic bold 17pt Arial") - deposition_ground_state_prerequisites_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_prerequisites()) + deposition_ground_state_prerequisites_text = self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_prerequisites()) - deposition_ground_state_preparation = self.layout_funcs.add_depo_heading('Procedure') - deposition_ground_state_preparation.setStyleSheet("font: italic bold 17pt Arial ") + deposition_ground_state_preparation = self.layout_funcs.add_depo_heading( + 'Procedure') + deposition_ground_state_preparation.setStyleSheet( + "font: italic bold 17pt Arial ") # deposition_ground_state_preparation_step_one_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_one_text()) @@ -111,46 +135,57 @@ def setup(self, xce_object): # xce_object.ground_state_mtz_button_label = QtGui.QLabel('') # xce_object.ground_state_mtz_button_label.setStyleSheet('color: blue') - deposition_ground_state_preparation_step_three_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_three_text()) - xce_object.ground_state_pandda_directory_label = QtGui.QLabel(xce_object.panddas_directory) - xce_object.ground_state_pandda_directory_label.setStyleSheet('color: blue') + deposition_ground_state_preparation_step_three_text = self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_preparation_step_three_text()) + xce_object.ground_state_pandda_directory_label = QtGui.QLabel( + xce_object.panddas_directory) + xce_object.ground_state_pandda_directory_label.setStyleSheet( + 'color: blue') - deposition_ground_state_preparation_step_four_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_four_text()) + deposition_ground_state_preparation_step_four_text = self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_preparation_step_four_text()) add_ground_state_db_button = QtGui.QPushButton('Add to database') - add_ground_state_db_button.clicked.connect(xce_object.add_ground_state_db) + add_ground_state_db_button.clicked.connect( + xce_object.add_ground_state_db) add_ground_state_db_button.setMaximumWidth(200) - deposition_ground_state_preparation_step_five_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_five_text()) + deposition_ground_state_preparation_step_five_text = self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_preparation_step_five_text()) - deposition_ground_state_preparation_step_six_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_six_text()) + deposition_ground_state_preparation_step_six_text = self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_preparation_step_six_text()) prepare_ground_state_mmcif_button = QtGui.QPushButton('Prepare mmcif') - prepare_ground_state_mmcif_button.clicked.connect(xce_object.prepare_ground_state_mmcif) + prepare_ground_state_mmcif_button.clicked.connect( + xce_object.prepare_ground_state_mmcif) prepare_ground_state_mmcif_button.setMaximumWidth(200) - deposition_ground_state_preparation_step_seven_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_seven_text()) + deposition_ground_state_preparation_step_seven_text = self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_preparation_step_seven_text()) copy_apo_mmcif_button = QtGui.QPushButton('copy mmcif') - copy_apo_mmcif_button.clicked.connect(xce_object.prepare_for_group_deposition_upload_ground_state) + copy_apo_mmcif_button.clicked.connect( + xce_object.prepare_for_group_deposition_upload_ground_state) copy_apo_mmcif_button.setMaximumWidth(200) - deposition_ground_state_preparation_step_eight_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_eight_text()) - + deposition_ground_state_preparation_step_eight_text = self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_preparation_step_eight_text()) # # after ligand_bound depostion # - after_deposition_heading = self.layout_funcs.add_depo_heading('After deposition of ligand-bound structures') + after_deposition_heading = self.layout_funcs.add_depo_heading( + 'After deposition of ligand-bound structures') after_deposition_heading.setStyleSheet("font: bold 20pt Arial") - - - after_deposition_preparation = self.layout_funcs.add_depo_heading('Procedure') - after_deposition_preparation.setStyleSheet("font: italic bold 17pt Arial ") - after_deposition_preparation_text = self.layout_funcs.add_depo_text(XChemToolTips.after_deposition_step_one_text()) - + after_deposition_preparation = self.layout_funcs.add_depo_heading( + 'Procedure') + after_deposition_preparation.setStyleSheet( + "font: italic bold 17pt Arial ") + after_deposition_preparation_text = self.layout_funcs.add_depo_text( + XChemToolTips.after_deposition_step_one_text()) ############################################### @@ -164,16 +199,16 @@ def setup(self, xce_object): # html_export_button.clicked.connect(xce_object.export_to_html) # html_export_button.setMaximumWidth(200) - - deposition_widget_list = [deposition_page_heading, QtGui.QLabel(' \n '), - deposition_page_introduction,deposition_page_introduction_link, + deposition_page_introduction, deposition_page_introduction_link, QtGui.QLabel(' \n '), - deposition_bound_state_heading, QtGui.QLabel(' \n '), + deposition_bound_state_heading, QtGui.QLabel( + ' \n '), deposition_bound_state_prerequisites, - deposition_bound_state_prerequisites_text, QtGui.QLabel(' \n '), + deposition_bound_state_prerequisites_text, QtGui.QLabel( + ' \n '), deposition_bound_state_preparation, deposition_bound_state_preparation_step_one_text, xce_object.deposition_bounnd_state_preparation_ignore_event_map, @@ -186,21 +221,25 @@ def setup(self, xce_object): QtGui.QLabel(' \n\n\n '), - after_deposition_heading, QtGui.QLabel(' \n '), + after_deposition_heading, QtGui.QLabel( + ' \n '), after_deposition_preparation, after_deposition_preparation_text, QtGui.QLabel(' \n\n\n '), - deposition_ground_state_heading, QtGui.QLabel(' \n '), - deposition_ground_state_preparation_step_one_text, QtGui.QLabel(' \n '), + deposition_ground_state_heading, QtGui.QLabel( + ' \n '), + deposition_ground_state_preparation_step_one_text, QtGui.QLabel( + ' \n '), deposition_ground_state_prerequisites, - deposition_ground_state_prerequisites_text, QtGui.QLabel(' \n '), + deposition_ground_state_prerequisites_text, QtGui.QLabel( + ' \n '), deposition_ground_state_preparation, -# ground_state_pdb_button, xce_object.ground_state_pdb_button_label, -# deposition_ground_state_log_info, -# deposition_ground_state_preparation_step_two_text, -# ground_state_mtz_button,xce_object.ground_state_mtz_button_label, + # ground_state_pdb_button, xce_object.ground_state_pdb_button_label, + # deposition_ground_state_log_info, + # deposition_ground_state_preparation_step_two_text, + # ground_state_mtz_button,xce_object.ground_state_mtz_button_label, deposition_ground_state_preparation_step_three_text, xce_object.ground_state_pandda_directory_label, deposition_ground_state_preparation_step_four_text, @@ -216,9 +255,9 @@ def setup(self, xce_object): QtGui.QLabel(' \n\n\n ') -# after_deposition_heading, QtGui.QLabel(' \n '), -# after_deposition_preparation, -# after_deposition_preparation_text + # after_deposition_heading, QtGui.QLabel(' \n '), + # after_deposition_preparation, + # after_deposition_preparation_text ] @@ -227,7 +266,7 @@ def setup(self, xce_object): # deposition_html_heading, QtGui.QLabel(' \n '), # introduction_text, # html_export_button, QtGui.QLabel(' \n\n '), -#s QtGui.QLabel(' \n ')] +# s QtGui.QLabel(' \n ')] # # deposition_widget_list2 = [update_html_button, QtGui.QLabel(' '), # upload_html_heading, upload_html_text, QtGui.QLabel(' ')] @@ -239,4 +278,3 @@ def setup(self, xce_object): # container settings scrollLayout.addStretch(1) scroll.setWidget(scrollContent) - diff --git a/gui_scripts/layout.py b/gui_scripts/layout.py index 9eccbbff..05c825f1 100755 --- a/gui_scripts/layout.py +++ b/gui_scripts/layout.py @@ -1,6 +1,19 @@ +from settings_tab import SettingsTab +from deposition_tab import DepositionTab +from refinement_tab import RefinementTab +from pandda_tab import PanddaTab +from maps_tab import MapsTab +from datasets_tab import DatasetsTab +from overview_tab import OverviewTab +from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas +import matplotlib.pyplot as plt +import XChemMain +import XChemToolTips +from settings_preferences import setup import multiprocessing import subprocess -import sys, os +import sys +import os from PyQt4 import QtGui, QtCore, QtWebKit from functools import partial @@ -8,22 +21,6 @@ sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'web')) sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) -from settings_preferences import setup - -import XChemToolTips -import XChemMain - -import matplotlib.pyplot as plt -from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas - -from overview_tab import OverviewTab -from datasets_tab import DatasetsTab -from maps_tab import MapsTab -from pandda_tab import PanddaTab -from refinement_tab import RefinementTab -from deposition_tab import DepositionTab -from settings_tab import SettingsTab - class LayoutObjects(): def __init__(self, xce_object): @@ -44,7 +41,8 @@ def initialise_menu_bar(self, xce_object): setup().top_menu_dict(xce_object) # create menu from menu dictionary - menu_bar = self.layout_funcs.setup_menubar(xce_object, menu_bar, xce_object.menu_dict) + menu_bar = self.layout_funcs.setup_menubar( + xce_object, menu_bar, xce_object.menu_dict) # END OF MENU BAR - CODE BELOW: stuff removed from apo structure stuff that appears might have a funky # consequence - work out later. @@ -53,13 +51,13 @@ def initialise_menu_bar(self, xce_object): # xce_object.prepare_mmcif_files_dict['apo'] = prepare_mmcif_files_for_apo_structures # xce_object.prepare_mmcif_files_dict['ligand_bound'] = prepare_mmcif_files_for_ligand_bound_structures - return menu_bar # function containing setup for bottom boxes def initialise_bottom_boxes(self, xce_object): - icons_directory = os.path.join((os.getenv('XChemExplorer_DIR')), 'icons') + icons_directory = os.path.join( + (os.getenv('XChemExplorer_DIR')), 'icons') # import all buttons setup().bottom_box_buttons(xce_object) @@ -83,11 +81,12 @@ def initialise_bottom_boxes(self, xce_object): xce_object.dataset_task_status_button_dict) # array of both button xce_objects to apply to bottom box layout - dataset_buttons = [xce_object.dataset_task_run_button, xce_object.dataset_task_status_button] - + dataset_buttons = [xce_object.dataset_task_run_button, + xce_object.dataset_task_status_button] # label for the bottom box layout - dataset_label = str(" Datasets") + dataset_label = str(" Datasets") # return the frame and combobox from the bottom box setup function frame_dataset_task, xce_object.dataset_tasks_combobox = self.layout_funcs.bottom_box_setup(xce_object, @@ -122,10 +121,12 @@ def initialise_bottom_boxes(self, xce_object): xce_object.map_cif_file_task_status_button_dict) # array of both button xce_objects to apply to bottom box layout - map_cif_file_buttons = [xce_object.map_cif_file_task_run_button, xce_object.map_cif_file_task_status_button] + map_cif_file_buttons = [ + xce_object.map_cif_file_task_run_button, xce_object.map_cif_file_task_status_button] # label for the bottom box layout - map_cif_file_label = str(" Maps & Restraints") + map_cif_file_label = str( + " Maps & Restraints") # return the frame and combobox from the bottom box setup function frame_map_cif_file_task, xce_object.map_cif_file_tasks_combobox = \ @@ -161,10 +162,12 @@ def initialise_bottom_boxes(self, xce_object): xce_object.panddas_file_task_status_button_dict) # array of both button xce_objects to apply to bottom box layout - panddas_file_buttons = [xce_object.panddas_file_task_run_button, xce_object.panddas_file_task_status_button] + panddas_file_buttons = [ + xce_object.panddas_file_task_run_button, xce_object.panddas_file_task_status_button] # label for the bottom box layout - panddas_file_label = str(" Hit Identification") + panddas_file_label = str(" Hit Identification") # return the frame and combobox from the bottom box setup function frame_panddas_file_task, xce_object.panddas_file_tasks_combobox = \ @@ -191,17 +194,21 @@ def initialise_bottom_boxes(self, xce_object): # setup the run button with push button function xce_object.refine_file_task_run_button = \ - self.layout_funcs.setup_push_button(xce_object, xce_object.refine_file_task_run_button_dict) + self.layout_funcs.setup_push_button( + xce_object, xce_object.refine_file_task_run_button_dict) # setup the task button with push button function xce_object.refine_file_task_status_button = \ - self.layout_funcs.setup_push_button(xce_object, xce_object.refine_file_task_status_button_dict) + self.layout_funcs.setup_push_button( + xce_object, xce_object.refine_file_task_status_button_dict) # array of both button xce_objects to apply to bottom box layout - refine_file_buttons = [xce_object.refine_file_task_run_button, xce_object.refine_file_task_status_button] + refine_file_buttons = [ + xce_object.refine_file_task_run_button, xce_object.refine_file_task_status_button] # label for the bottom box layout - refine_file_label = str(" Refinement") + refine_file_label = str( + " Refinement") # return the frame and combobox from the bottom box setup function frame_refine_file_task, xce_object.refine_file_tasks_combobox = \ @@ -220,7 +227,7 @@ def initialise_bottom_boxes(self, xce_object): xce_object.refine_file_task_status_button] return update_from_datasource_button, frame_dataset_task, frame_map_cif_file_task, frame_panddas_file_task, \ - frame_refine_file_task + frame_refine_file_task def main_layout(self, xce_object): # initialise menu bar @@ -228,7 +235,7 @@ def main_layout(self, xce_object): # initialise bottom boxes update_from_datasource_button, frame_dataset_task, frame_map_cif_file_task, frame_panddas_file_task, \ - frame_refine_file_task = self.initialise_bottom_boxes(xce_object) + frame_refine_file_task = self.initialise_bottom_boxes(xce_object) # Tab layout & content # -------------------- @@ -282,7 +289,8 @@ def main_layout(self, xce_object): vbox_main = QtGui.QVBoxLayout() menu_bar.setMaximumWidth(xce_object.screen.width()) vbox_main.addWidget(menu_bar) - xce_object.main_tab_widget.setMaximumSize(xce_object.screen.width(), xce_object.screen.height() - 245) + xce_object.main_tab_widget.setMaximumSize( + xce_object.screen.width(), xce_object.screen.height() - 245) vbox_main.addWidget(xce_object.main_tab_widget) hboxTaskFrames = QtGui.QHBoxLayout() @@ -314,7 +322,6 @@ def workflow(self, xce_object): # # ################################################################################################################ - # workflow task container - order of tabs as they appear for the main window xce_object.workflow = ['Overview', # 0 'Datasets', # 1 @@ -338,7 +345,8 @@ def workflow(self, xce_object): # tab widget xce_object.main_tab_widget = QtGui.QTabWidget() xce_object.tab_dict = {} - self.layout_funcs.make_tab_dict(xce_object.workflow, xce_object.main_tab_widget, xce_object.tab_dict) + self.layout_funcs.make_tab_dict( + xce_object.workflow, xce_object.main_tab_widget, xce_object.tab_dict) class LayoutFuncs(): @@ -366,8 +374,10 @@ def table_setup(self, table, table_columns, sortingopt=True): def pandda_html(self, xce_object): if os.path.exists(str(xce_object.panddas_directory + '/interesting_datasets')): - print('WARNING: USING RESULTS FROM OLD PANDDA ANALYSE! THIS IS NOT FULLY SUPPORTED IN XCE2') - print('PLEASE CHANGE YOUR PANDDA DIRECTORY TO A NEW RUN, OR USE THE OLD VERSION OF XCE!') + print( + 'WARNING: USING RESULTS FROM OLD PANDDA ANALYSE! THIS IS NOT FULLY SUPPORTED IN XCE2') + print( + 'PLEASE CHANGE YOUR PANDDA DIRECTORY TO A NEW RUN, OR USE THE OLD VERSION OF XCE!') xce_object.pandda_initial_html_file = str( xce_object.panddas_directory + '/results_summareis/pandda_initial.html') xce_object.pandda_analyse_html_file = str( @@ -384,14 +394,17 @@ def setup_push_button(self, xce_object, button_dict): # use iterkeys to determine order of key by letter for name in sorted(button_dict.iterkeys()): # add current item to menu bar - button = eval('QtGui.QPushButton("' + str(button_dict[name][0]) + '")') + button = eval( + 'QtGui.QPushButton("' + str(button_dict[name][0]) + '")') # for each configuration item for button_config in button_dict[name][1]: eval(str('button.setToolTip(' + str(button_config[0]) + ')')) - eval(str('button.setStyleSheet("' + str(button_config[1] + '")'))) + eval( + str('button.setStyleSheet("' + str(button_config[1] + '")'))) if len(button_config[2]) > 1: eval(str('button.setFont(' + str(button_config[2]) + ')')) - eval(str('button.clicked.connect(' + str(button_config[3]) + ')')) + eval( + str('button.clicked.connect(' + str(button_config[3]) + ')')) return button @@ -436,14 +449,17 @@ def setup_menubar(self, xce_object, menu_bar, menu_items_dict): # use iterkeys to determine order of key by letter for config in sorted(menu_items_dict.iterkeys()): # add current item to menu bar - menu = eval('menu_bar.addMenu("' + str(menu_items_dict[config][0]) + '")') + menu = eval( + 'menu_bar.addMenu("' + str(menu_items_dict[config][0]) + '")') # for each configuration item for menu_item in menu_items_dict[config][1]: # add the drop down option - action = eval(str('QtGui.QAction("' + str(menu_item[0]) + '", xce_object.window)')) + action = eval( + str('QtGui.QAction("' + str(menu_item[0]) + '", xce_object.window)')) # add a shortcut if defined if len(menu_item[1]) > 1: - eval(str('action.setShortcut("' + str(menu_item[1]) + '")')) + eval( + str('action.setShortcut("' + str(menu_item[1]) + '")')) # connect the relevant function and add as an action try: action.triggered.connect(menu_item[2]) @@ -493,25 +509,41 @@ def settings_section_setup(self, vbox, label_text, directory, button_text, butto def add_widgets_layouts(self, xce_object): tab_add_widget = [ - [xce_object.tab_dict[xce_object.workflow_dict['Overview']][1], xce_object.overview_tab_widget], - [xce_object.overview_tab_dict['Data Source'][1], xce_object.overview_datasource_table], - [xce_object.overview_tab_dict['Summary'][1], xce_object.overview_canvas], - [xce_object.pandda_tab_dict['Dataset Summary'][1], xce_object.pandda_initial_html], - [xce_object.pandda_tab_dict['Processing Output'][1], xce_object.pandda_analyse_html], + [xce_object.tab_dict[xce_object.workflow_dict['Overview']] + [1], xce_object.overview_tab_widget], + [xce_object.overview_tab_dict['Data Source'] + [1], xce_object.overview_datasource_table], + [xce_object.overview_tab_dict['Summary'] + [1], xce_object.overview_canvas], + [xce_object.pandda_tab_dict['Dataset Summary'] + [1], xce_object.pandda_initial_html], + [xce_object.pandda_tab_dict['Processing Output'] + [1], xce_object.pandda_analyse_html], [xce_object.pandda_tab_dict['pandda.inspect'][1], xce_object.pandda_inspect_html]] tab_add_layout = [ - [xce_object.tab_dict[xce_object.workflow_dict['Datasets']][1], xce_object.datasets_data_collection_vbox], - [xce_object.datasets_tab_dict['Summary'][1], xce_object.datasets_summarys_vbox_for_table], - [xce_object.datasets_tab_dict['Summary'][1], xce_object.datasets_summarys_vbox_for_details], - [xce_object.datasets_tab_dict['Reprocess'][1], xce_object.reprocess_vbox], - [xce_object.tab_dict[xce_object.workflow_dict['Maps']][1], xce_object.maps_checkbutton_hbox], - [xce_object.tab_dict[xce_object.workflow_dict['Maps']][1], xce_object.initial_model_vbox_for_table], - [xce_object.pandda_tab_dict['Statistical Map Summaries'][1], xce_object.pandda_map_layout], - [xce_object.pandda_tab_dict['pandda.analyse'][1], xce_object.pandda_analyse_hbox], - [xce_object.tab_dict[xce_object.workflow_dict['PANDDAs']][1], xce_object.panddas_results_vbox], - [xce_object.tab_dict[xce_object.workflow_dict['Refinement']][1], xce_object.summary_vbox_for_table], - [xce_object.tab_dict[xce_object.workflow_dict['Deposition']][1], xce_object.deposition_vbox], + [xce_object.tab_dict[xce_object.workflow_dict['Datasets']] + [1], xce_object.datasets_data_collection_vbox], + [xce_object.datasets_tab_dict['Summary'][1], + xce_object.datasets_summarys_vbox_for_table], + [xce_object.datasets_tab_dict['Summary'][1], + xce_object.datasets_summarys_vbox_for_details], + [xce_object.datasets_tab_dict['Reprocess'] + [1], xce_object.reprocess_vbox], + [xce_object.tab_dict[xce_object.workflow_dict['Maps']] + [1], xce_object.maps_checkbutton_hbox], + [xce_object.tab_dict[xce_object.workflow_dict['Maps']] + [1], xce_object.initial_model_vbox_for_table], + [xce_object.pandda_tab_dict['Statistical Map Summaries'] + [1], xce_object.pandda_map_layout], + [xce_object.pandda_tab_dict['pandda.analyse'] + [1], xce_object.pandda_analyse_hbox], + [xce_object.tab_dict[xce_object.workflow_dict['PANDDAs']] + [1], xce_object.panddas_results_vbox], + [xce_object.tab_dict[xce_object.workflow_dict['Refinement']] + [1], xce_object.summary_vbox_for_table], + [xce_object.tab_dict[xce_object.workflow_dict['Deposition']] + [1], xce_object.deposition_vbox], [xce_object.tab_dict[xce_object.workflow_dict['Settings']][1], xce_object.settings_vbox]] for item in tab_add_widget: diff --git a/gui_scripts/maps_tab.py b/gui_scripts/maps_tab.py index b0bdba2a..89507e18 100755 --- a/gui_scripts/maps_tab.py +++ b/gui_scripts/maps_tab.py @@ -1,10 +1,10 @@ -import sys, os +import layout +import sys +import os from PyQt4 import QtGui, QtCore, QtWebKit sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) -import layout - class MapsTab(): def __init__(self): @@ -17,42 +17,54 @@ def setup(self, xce_object): # # ################################################################################################################ # select box for dimple - xce_object.select_sample_for_dimple_box = QtGui.QCheckBox('(de-)select all samples for DIMPLE') + xce_object.select_sample_for_dimple_box = QtGui.QCheckBox( + '(de-)select all samples for DIMPLE') self.layout_funcs.add_checkbox(xce_object, xce_object.select_sample_for_dimple_box, 'xce_object.set_run_dimple_flag') # set new reference button - set_new_reference_button = QtGui.QPushButton("Set New Reference (if applicable)") - set_new_reference_button.clicked.connect(xce_object.set_new_reference_if_applicable) + set_new_reference_button = QtGui.QPushButton( + "Set New Reference (if applicable)") + set_new_reference_button.clicked.connect( + xce_object.set_new_reference_if_applicable) # refresh button - refresh_reference_file_list_button = QtGui.QPushButton("Refresh reference file list") - refresh_reference_file_list_button.clicked.connect(xce_object.refresh_reference_file_list) + refresh_reference_file_list_button = QtGui.QPushButton( + "Refresh reference file list") + refresh_reference_file_list_button.clicked.connect( + xce_object.refresh_reference_file_list) # list and populate reference files - xce_object.reference_file_list = xce_object.get_reference_file_list(' ') + xce_object.reference_file_list = xce_object.get_reference_file_list( + ' ') xce_object.reference_file_selection_combobox = QtGui.QComboBox() - xce_object.populate_reference_combobox(xce_object.reference_file_selection_combobox) + xce_object.populate_reference_combobox( + xce_object.reference_file_selection_combobox) # setup hbox to hold everything and add widgets xce_object.maps_checkbutton_hbox = QtGui.QHBoxLayout() maps_checkbutton_widgets = [xce_object.select_sample_for_dimple_box, set_new_reference_button, refresh_reference_file_list_button, xce_object.reference_file_selection_combobox] - self.layout_funcs.add_to_box(xce_object.maps_checkbutton_hbox, maps_checkbutton_widgets) + self.layout_funcs.add_to_box( + xce_object.maps_checkbutton_hbox, maps_checkbutton_widgets) # table setup xce_object.maps_table = QtGui.QTableWidget() - self.layout_funcs.table_setup(xce_object.maps_table, xce_object.maps_table_columns) + self.layout_funcs.table_setup( + xce_object.maps_table, xce_object.maps_table_columns) # box for table, add to box, add to tab xce_object.initial_model_vbox_for_table = QtGui.QVBoxLayout() - xce_object.initial_model_vbox_for_table.addWidget(xce_object.maps_table) + xce_object.initial_model_vbox_for_table.addWidget( + xce_object.maps_table) # create context menu... no idea where this lives again. xce_object.popMenu_for_maps_table = QtGui.QMenu() - run_dimple = QtGui.QAction("mark selected for dimple run", xce_object.window) + run_dimple = QtGui.QAction( + "mark selected for dimple run", xce_object.window) run_dimple.triggered.connect(xce_object.select_sample_for_dimple) xce_object.popMenu_for_maps_table.addAction(run_dimple) xce_object.maps_table.setContextMenuPolicy(QtCore.Qt.CustomContextMenu) - xce_object.maps_table.customContextMenuRequested.connect(xce_object.on_context_menu_initial_model) + xce_object.maps_table.customContextMenuRequested.connect( + xce_object.on_context_menu_initial_model) diff --git a/gui_scripts/overview_tab.py b/gui_scripts/overview_tab.py index 10180a8f..7631e1e9 100755 --- a/gui_scripts/overview_tab.py +++ b/gui_scripts/overview_tab.py @@ -1,13 +1,12 @@ -import sys, os +from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas +import matplotlib.pyplot as plt +import layout +import sys +import os from PyQt4 import QtGui, QtCore, QtWebKit sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) -import layout - -import matplotlib.pyplot as plt -from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas - class OverviewTab(): def __init__(self): @@ -25,7 +24,8 @@ def setup(self, xce_object): xce_object.overview_tab_dict = {} # make subtabs - self.layout_funcs.make_tab_dict(overview_tab_list, xce_object.overview_tab_widget, xce_object.overview_tab_dict) + self.layout_funcs.make_tab_dict( + overview_tab_list, xce_object.overview_tab_widget, xce_object.overview_tab_dict) # initiate the table in overview/datasource xce_object.overview_datasource_table = QtGui.QTableWidget() @@ -35,4 +35,4 @@ def setup(self, xce_object): # initiate the graph in overview/summary xce_object.overview_figure, xce_object.overview_axes = plt.subplots() xce_object.overview_canvas = FigureCanvas(xce_object.overview_figure) - xce_object.update_summary_plot() \ No newline at end of file + xce_object.update_summary_plot() diff --git a/gui_scripts/pandda_tab.py b/gui_scripts/pandda_tab.py index f8b33fa3..43874381 100755 --- a/gui_scripts/pandda_tab.py +++ b/gui_scripts/pandda_tab.py @@ -1,12 +1,13 @@ -import sys, os, multiprocessing +import XChemPANDDA +import layout +import sys +import os +import multiprocessing from PyQt4 import QtGui, QtCore, QtWebKit sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) -import layout -import XChemPANDDA - class PanddaTab(): def __init__(self): @@ -28,7 +29,8 @@ def setup(self, xce_object): # setup tab widget, set up tab dict, and make tab dict xce_object.pandda_tab_widget = QtGui.QTabWidget() xce_object.pandda_tab_dict = {} - self.layout_funcs.make_tab_dict(pandda_tab_list, xce_object.pandda_tab_widget, xce_object.pandda_tab_dict) + self.layout_funcs.make_tab_dict( + pandda_tab_list, xce_object.pandda_tab_widget, xce_object.pandda_tab_dict) # pandda analyse subtab # setup a grid to hold everything @@ -38,7 +40,8 @@ def setup(self, xce_object): # table - left xce_object.pandda_analyse_data_table = QtGui.QTableWidget() - self.layout_funcs.table_setup(xce_object.pandda_analyse_data_table, xce_object.pandda_table_columns) + self.layout_funcs.table_setup( + xce_object.pandda_analyse_data_table, xce_object.pandda_table_columns) # add table to grid frame_pandda = QtGui.QFrame() @@ -60,8 +63,10 @@ def setup(self, xce_object): xce_object.pandda_status = option[1] xce_object.pandda_status_label.setStyleSheet(option[2]) - xce_object.pandda_status_label.setText(str('STATUS: ' + xce_object.pandda_status)) - xce_object.pandda_status_label.setFont(QtGui.QFont("Arial", 25, QtGui.QFont.Bold)) + xce_object.pandda_status_label.setText( + str('STATUS: ' + xce_object.pandda_status)) + xce_object.pandda_status_label.setFont( + QtGui.QFont("Arial", 25, QtGui.QFont.Bold)) grid_pandda.addWidget(xce_object.pandda_status_label, 3, 0) header_font = QtGui.QFont() @@ -78,12 +83,17 @@ def setup(self, xce_object): label.setFont(header_font) xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_input_data_dir_entry = QtGui.QLineEdit() - xce_object.pandda_input_data_dir_entry.setText(os.path.join(xce_object.initial_model_directory, '*')) + xce_object.pandda_input_data_dir_entry.setText( + os.path.join(xce_object.initial_model_directory, '*')) pandda_input_dir_hbox.addWidget(xce_object.pandda_input_data_dir_entry) - xce_object.select_pandda_input_dir_button = QtGui.QPushButton("Select Input Template") - xce_object.select_pandda_input_dir_button.clicked.connect(xce_object.select_pandda_input_template) - pandda_input_dir_hbox.addWidget(xce_object.select_pandda_input_dir_button) - xce_object.pandda_analyse_input_params_vbox.addLayout(pandda_input_dir_hbox) + xce_object.select_pandda_input_dir_button = QtGui.QPushButton( + "Select Input Template") + xce_object.select_pandda_input_dir_button.clicked.connect( + xce_object.select_pandda_input_template) + pandda_input_dir_hbox.addWidget( + xce_object.select_pandda_input_dir_button) + xce_object.pandda_analyse_input_params_vbox.addLayout( + pandda_input_dir_hbox) # pdb style section pandda_pdb_style_hbox = QtGui.QHBoxLayout() @@ -92,7 +102,8 @@ def setup(self, xce_object): xce_object.pandda_pdb_style_entry = QtGui.QLineEdit() xce_object.pandda_pdb_style_entry.setText('dimple.pdb') pandda_pdb_style_hbox.addWidget(xce_object.pandda_pdb_style_entry) - xce_object.pandda_analyse_input_params_vbox.addLayout(pandda_pdb_style_hbox) + xce_object.pandda_analyse_input_params_vbox.addLayout( + pandda_pdb_style_hbox) # mtz style section pandda_mtz_style_hbox = QtGui.QHBoxLayout() @@ -101,18 +112,19 @@ def setup(self, xce_object): xce_object.pandda_mtz_style_entry = QtGui.QLineEdit() xce_object.pandda_mtz_style_entry.setText('dimple.mtz') pandda_mtz_style_hbox.addWidget(xce_object.pandda_mtz_style_entry) - xce_object.pandda_analyse_input_params_vbox.addLayout(pandda_mtz_style_hbox) + xce_object.pandda_analyse_input_params_vbox.addLayout( + pandda_mtz_style_hbox) print(xce_object.initial_model_directory) data_dir_string = xce_object.initial_model_directory.replace('/*', '') def copy_ligands(obj): os.system(str( - 'find ' + data_dir_string + - '/*/compound -name "*.cif" | while read line; do echo ${line//"' + - data_dir_string + '"/"' + xce_object.panddas_directory + - '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' - 'done; done;')) + 'find ' + data_dir_string + + '/*/compound -name "*.cif" | while read line; do echo ${line//"' + + data_dir_string + '"/"' + xce_object.panddas_directory + + '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' + 'done; done;')) os.system(str( 'find ' + data_dir_string + @@ -129,16 +141,25 @@ def copy_ligands(obj): label.setFont(header_font) xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_output_data_dir_entry = QtGui.QLineEdit() - xce_object.pandda_output_data_dir_entry.setText(xce_object.panddas_directory) - pandda_output_dir_hbox.addWidget(xce_object.pandda_output_data_dir_entry) - xce_object.select_pandda_output_dir_button = QtGui.QPushButton("Select PanDDA Directory") - xce_object.select_pandda_output_dir_button.clicked.connect(xce_object.settings_button_clicked) - pandda_output_dir_hbox.addWidget(xce_object.select_pandda_output_dir_button) - xce_object.pandda_analyse_input_params_vbox.addLayout(pandda_output_dir_hbox) - - pandda_add_ligands_button = QtGui.QPushButton('Copy Ligand restraints for PanDDA') - pandda_add_ligands_button.clicked.connect(lambda: copy_ligands(xce_object)) - xce_object.pandda_analyse_input_params_vbox.addWidget(pandda_add_ligands_button) + xce_object.pandda_output_data_dir_entry.setText( + xce_object.panddas_directory) + pandda_output_dir_hbox.addWidget( + xce_object.pandda_output_data_dir_entry) + xce_object.select_pandda_output_dir_button = QtGui.QPushButton( + "Select PanDDA Directory") + xce_object.select_pandda_output_dir_button.clicked.connect( + xce_object.settings_button_clicked) + pandda_output_dir_hbox.addWidget( + xce_object.select_pandda_output_dir_button) + xce_object.pandda_analyse_input_params_vbox.addLayout( + pandda_output_dir_hbox) + + pandda_add_ligands_button = QtGui.QPushButton( + 'Copy Ligand restraints for PanDDA') + pandda_add_ligands_button.clicked.connect( + lambda: copy_ligands(xce_object)) + xce_object.pandda_analyse_input_params_vbox.addWidget( + pandda_add_ligands_button) # spacer to separate out sections spacer = QtGui.QLabel(' ') @@ -153,17 +174,22 @@ def copy_ligands(obj): xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_submission_mode_selection_combobox = QtGui.QComboBox() if xce_object.external_software['qsub']: - xce_object.pandda_submission_mode_selection_combobox.addItem('qsub') - xce_object.pandda_submission_mode_selection_combobox.addItem('local machine') - xce_object.pandda_analyse_input_params_vbox.addWidget(xce_object.pandda_submission_mode_selection_combobox) + xce_object.pandda_submission_mode_selection_combobox.addItem( + 'qsub') + xce_object.pandda_submission_mode_selection_combobox.addItem( + 'local machine') + xce_object.pandda_analyse_input_params_vbox.addWidget( + xce_object.pandda_submission_mode_selection_combobox) # number of processors section label = QtGui.QLabel('Number of processors:') xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_nproc = multiprocessing.cpu_count() - 1 xce_object.pandda_nproc_entry = QtGui.QLineEdit() - xce_object.pandda_nproc_entry.setText(str(xce_object.pandda_nproc).replace(' ', '')) - xce_object.pandda_analyse_input_params_vbox.addWidget(xce_object.pandda_nproc_entry) + xce_object.pandda_nproc_entry.setText( + str(xce_object.pandda_nproc).replace(' ', '')) + xce_object.pandda_analyse_input_params_vbox.addWidget( + xce_object.pandda_nproc_entry) xce_object.pandda_analyse_input_params_vbox.addWidget(spacer) @@ -183,8 +209,10 @@ def copy_ligands(obj): # checkbox for wilson scaling xce_object.wilson_checkbox = QtGui.QCheckBox('Wilson B-factor Scaling') - self.layout_funcs.add_checkbox(xce_object, xce_object.wilson_checkbox, 'xce_object.set_run_dimple_flag') - xce_object.pandda_analyse_input_params_vbox.addWidget(xce_object.wilson_checkbox) + self.layout_funcs.add_checkbox( + xce_object, xce_object.wilson_checkbox, 'xce_object.set_run_dimple_flag') + xce_object.pandda_analyse_input_params_vbox.addWidget( + xce_object.wilson_checkbox) # crystal form option label = QtGui.QLabel('Use space group of reference file as filter:') @@ -193,8 +221,10 @@ def copy_ligands(obj): hbox = QtGui.QHBoxLayout() # xce_object.reference_file_list = xce_object.get_reference_file_list('') xce_object.pandda_reference_file_selection_combobox = QtGui.QComboBox() - xce_object.populate_reference_combobox(xce_object.pandda_reference_file_selection_combobox) - xce_object.pandda_reference_file_selection_combobox.activated[str].connect(xce_object.change_pandda_spg_label) + xce_object.populate_reference_combobox( + xce_object.pandda_reference_file_selection_combobox) + xce_object.pandda_reference_file_selection_combobox.activated[str].connect( + xce_object.change_pandda_spg_label) hbox.addWidget(xce_object.pandda_reference_file_selection_combobox) xce_object.pandda_reference_file_spg_label = QtGui.QLabel() hbox.addWidget(xce_object.pandda_reference_file_spg_label) @@ -205,30 +235,36 @@ def copy_ligands(obj): xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_sort_event_combobox = QtGui.QComboBox() pandda_events = ['cluster_size', 'z_peak'] - self.layout_funcs.populate_combobox(pandda_events, xce_object.pandda_sort_event_combobox) - xce_object.pandda_analyse_input_params_vbox.addWidget(xce_object.pandda_sort_event_combobox) + self.layout_funcs.populate_combobox( + pandda_events, xce_object.pandda_sort_event_combobox) + xce_object.pandda_analyse_input_params_vbox.addWidget( + xce_object.pandda_sort_event_combobox) # how calculate mean map label = QtGui.QLabel('Calculate average map by:') xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_calc_map_combobox = QtGui.QComboBox() average_map = ['mean_map', 'median_map'] - self.layout_funcs.populate_combobox(average_map, xce_object.pandda_calc_map_combobox) - xce_object.pandda_analyse_input_params_vbox.addWidget(xce_object.pandda_calc_map_combobox) + self.layout_funcs.populate_combobox( + average_map, xce_object.pandda_calc_map_combobox) + xce_object.pandda_analyse_input_params_vbox.addWidget( + xce_object.pandda_calc_map_combobox) # minimum number of datasets label = QtGui.QLabel('min_build_datasets') xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_min_build_dataset_entry = QtGui.QLineEdit() xce_object.pandda_min_build_dataset_entry.setText('40') - xce_object.pandda_analyse_input_params_vbox.addWidget(xce_object.pandda_min_build_dataset_entry) + xce_object.pandda_analyse_input_params_vbox.addWidget( + xce_object.pandda_min_build_dataset_entry) # maximum number of datasets label = QtGui.QLabel('max_new_datasets') xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_max_new_datasets_entry = QtGui.QLineEdit() xce_object.pandda_max_new_datasets_entry.setText('300') - xce_object.pandda_analyse_input_params_vbox.addWidget(xce_object.pandda_max_new_datasets_entry) + xce_object.pandda_analyse_input_params_vbox.addWidget( + xce_object.pandda_max_new_datasets_entry) # grid spacing label = QtGui.QLabel( @@ -236,14 +272,16 @@ def copy_ligands(obj): xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_grid_spacing_entry = QtGui.QLineEdit() xce_object.pandda_grid_spacing_entry.setText('0.5') - xce_object.pandda_analyse_input_params_vbox.addWidget(xce_object.pandda_grid_spacing_entry) + xce_object.pandda_analyse_input_params_vbox.addWidget( + xce_object.pandda_grid_spacing_entry) # keyword arguments (pandda2) label = QtGui.QLabel('keyword arguments (pandda2 only)') xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_keyword_arguments_entry = QtGui.QLineEdit() xce_object.pandda_keyword_arguments_entry.setText('') - xce_object.pandda_analyse_input_params_vbox.addWidget(xce_object.pandda_keyword_arguments_entry) + xce_object.pandda_analyse_input_params_vbox.addWidget( + xce_object.pandda_keyword_arguments_entry) frame_right.setLayout(xce_object.pandda_analyse_input_params_vbox) @@ -256,45 +294,58 @@ def copy_ligands(obj): # statistical map summaries vbox, add to vbox and add to layout xce_object.pandda_map_layout = QtGui.QVBoxLayout() - pandda_map_layout_widgets = [xce_object.pandda_map_list, xce_object.pandda_maps_html] - self.layout_funcs.add_to_box(xce_object.pandda_map_layout, pandda_map_layout_widgets) + pandda_map_layout_widgets = [ + xce_object.pandda_map_list, xce_object.pandda_maps_html] + self.layout_funcs.add_to_box( + xce_object.pandda_map_layout, pandda_map_layout_widgets) xce_object.pandda_maps_html.show() xce_object.pandda_analyse_hbox = QtGui.QHBoxLayout() xce_object.pandda_analyse_hbox.addWidget(frame_pandda) - ## change to do select options + # change to do select options # create context menu... no idea where this lives again. xce_object.popMenu_for_pandda_table = QtGui.QMenu() ignore = QtGui.QAction("ignore selected", xce_object.window) - exclude_characterisation = QtGui.QAction("exclude selected from characterisation", xce_object.window) - exclude_zmap = QtGui.QAction("exclude selected from z-map analysis", xce_object.window) + exclude_characterisation = QtGui.QAction( + "exclude selected from characterisation", xce_object.window) + exclude_zmap = QtGui.QAction( + "exclude selected from z-map analysis", xce_object.window) deselect = QtGui.QAction("deselect highlighted", xce_object.window) - ignore.triggered.connect(lambda: xce_object.select_sample_for_pandda(option='ignore')) - exclude_characterisation.triggered.connect(lambda: xce_object.select_sample_for_pandda(option='char')) - exclude_zmap.triggered.connect(lambda: xce_object.select_sample_for_pandda(option='zmap')) - deselect.triggered.connect(lambda: xce_object.select_sample_for_pandda(option='deselect')) + ignore.triggered.connect( + lambda: xce_object.select_sample_for_pandda(option='ignore')) + exclude_characterisation.triggered.connect( + lambda: xce_object.select_sample_for_pandda(option='char')) + exclude_zmap.triggered.connect( + lambda: xce_object.select_sample_for_pandda(option='zmap')) + deselect.triggered.connect( + lambda: xce_object.select_sample_for_pandda(option='deselect')) xce_object.popMenu_for_pandda_table.addAction(ignore) xce_object.popMenu_for_pandda_table.addAction(exclude_characterisation) xce_object.popMenu_for_pandda_table.addAction(exclude_zmap) xce_object.popMenu_for_pandda_table.addAction(deselect) - xce_object.pandda_analyse_data_table.setContextMenuPolicy(QtCore.Qt.CustomContextMenu) - xce_object.pandda_analyse_data_table.customContextMenuRequested.connect(xce_object.on_context_menu_pandda) + xce_object.pandda_analyse_data_table.setContextMenuPolicy( + QtCore.Qt.CustomContextMenu) + xce_object.pandda_analyse_data_table.customContextMenuRequested.connect( + xce_object.on_context_menu_pandda) # next three blocks display html documents created by pandda.analyse self.layout_funcs.pandda_html(xce_object) xce_object.pandda_initial_html = QtWebKit.QWebView() - xce_object.pandda_initial_html.load(QtCore.QUrl(xce_object.pandda_initial_html_file)) + xce_object.pandda_initial_html.load( + QtCore.QUrl(xce_object.pandda_initial_html_file)) xce_object.pandda_initial_html.show() xce_object.pandda_analyse_html = QtWebKit.QWebView() - xce_object.pandda_analyse_html.load(QtCore.QUrl(xce_object.pandda_analyse_html_file)) + xce_object.pandda_analyse_html.load( + QtCore.QUrl(xce_object.pandda_analyse_html_file)) xce_object.pandda_analyse_html.show() xce_object.pandda_inspect_html = QtWebKit.QWebView() - xce_object.pandda_analyse_html.load(QtCore.QUrl(xce_object.pandda_inspect_html_file)) + xce_object.pandda_analyse_html.load( + QtCore.QUrl(xce_object.pandda_inspect_html_file)) xce_object.pandda_analyse_html.show() xce_object.panddas_results_vbox = QtGui.QVBoxLayout() diff --git a/gui_scripts/refinement_tab.py b/gui_scripts/refinement_tab.py index 71b50a5b..dd8c7578 100755 --- a/gui_scripts/refinement_tab.py +++ b/gui_scripts/refinement_tab.py @@ -1,10 +1,10 @@ -import sys, os +import layout +import sys +import os from PyQt4 import QtGui, QtCore, QtWebKit sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) -import layout - class RefinementTab(): def __init__(self): @@ -20,6 +20,7 @@ def setup(self, xce_object): # table xce_object.refinement_table = QtGui.QTableWidget() - self.layout_funcs.table_setup(xce_object.refinement_table, xce_object.refinement_table_columns) - xce_object.summary_vbox_for_table.addWidget(xce_object.refinement_table) - + self.layout_funcs.table_setup( + xce_object.refinement_table, xce_object.refinement_table_columns) + xce_object.summary_vbox_for_table.addWidget( + xce_object.refinement_table) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index f9d40e03..72cc11fe 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -1,4 +1,11 @@ -import os, sys, subprocess +import XChemDeposit +import XChemLog +import XChemMain +import XChemDB +import XChemUtils +import os +import sys +import subprocess from PyQt4 import QtCore, QtGui from functools import partial import webbrowser @@ -7,12 +14,6 @@ sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'web')) -import XChemUtils -import XChemDB -import XChemMain -import XChemLog -import XChemDeposit - class setup(): def __init__(self): @@ -25,7 +26,8 @@ def openFile(self, file): os.startfile(file) def set_xce_logfile(self, xce_object): - XChemLog.startLog(xce_object.xce_logfile).create_logfile(xce_object.xce_version) + XChemLog.startLog(xce_object.xce_logfile).create_logfile( + xce_object.xce_version) xce_object.update_log = XChemLog.updateLog(xce_object.xce_logfile) def settings(self, xce_object): @@ -39,57 +41,63 @@ def settings(self, xce_object): xce_object.data_source_set = False xce_object.max_queue_jobs = 100 - ## directory settings + # directory settings # set current directory and direct log to it xce_object.current_directory = os.getcwd() - xce_object.xce_logfile = os.path.join(xce_object.current_directory, 'xce.log') + xce_object.xce_logfile = os.path.join( + xce_object.current_directory, 'xce.log') # if in the correct place, set the various directories if xce_object.current_directory.startswith('/dls/labxchem'): -# if 'labxchem' in xce_object.current_directory: + # if 'labxchem' in xce_object.current_directory: if len(xce_object.current_directory.split('/')) >= 9 and xce_object.current_directory.split('/')[6] == 'processing' and xce_object.current_directory.split('/')[8] == 'processing': xce_object.labxchem_directory = '/' + os.path.join( - *xce_object.current_directory.split('/')[1:8]) # need splat operator: * + *xce_object.current_directory.split('/')[1:8]) # need splat operator: * xce_object.labxchem_directory_current = '/' + os.path.join( *xce_object.current_directory.split('/')[1:9]) # labxchem_directory_current is where they actually have write permission else: xce_object.labxchem_directory = '/' + os.path.join( - *xce_object.current_directory.split('/')[1:6]) # need splat operator: * + *xce_object.current_directory.split('/')[1:6]) # need splat operator: * xce_object.labxchem_directory_current = '/' + os.path.join( - *xce_object.current_directory.split('/')[1:7]) # need splat operator: * + *xce_object.current_directory.split('/')[1:7]) # need splat operator: * # xce_object.labxchem_directory = '/' + os.path.join( # *xce_object.current_directory.split('/')[1:6]) # need splat operator: * - xce_object.beamline_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'beamline') - if os.path.isdir(os.path.join(xce_object.labxchem_directory, 'processing', 'analysis','model_building')): + xce_object.beamline_directory = os.path.join( + xce_object.labxchem_directory, 'processing', 'beamline') + if os.path.isdir(os.path.join(xce_object.labxchem_directory, 'processing', 'analysis', 'model_building')): xce_object.initial_model_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'analysis', - 'model_building') + 'model_building') else: xce_object.initial_model_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'analysis', - 'initial_model') - xce_object.reference_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'reference') - xce_object.database_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'database') + 'initial_model') + xce_object.reference_directory = os.path.join( + xce_object.labxchem_directory, 'processing', 'reference') + xce_object.database_directory = os.path.join( + xce_object.labxchem_directory, 'processing', 'database') xce_object.panddas_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'analysis', 'panddas') - xce_object.datasets_summary_file = None # xce_object.datasets_summary_file = os.path.join(xce_object.database_directory, # str(os.getcwd().split('/')[5]) + '_summary.pkl') xce_object.data_source_file = '' - xce_object.html_export_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'html') + xce_object.html_export_directory = os.path.join( + xce_object.labxchem_directory, 'processing', 'html') xce_object.group_deposit_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'group_deposition') if os.path.isfile( os.path.join(xce_object.labxchem_directory, 'processing', 'database', 'soakDBDataFile.sqlite')): xce_object.data_source_file = 'soakDBDataFile.sqlite' - xce_object.database_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'database') + xce_object.database_directory = os.path.join( + xce_object.labxchem_directory, 'processing', 'database') xce_object.data_source_set = True xce_object.db = XChemDB.data_source( os.path.join(xce_object.database_directory, xce_object.data_source_file)) xce_object.db.create_missing_columns() - xce_object.ccp4_scratch_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'tmp') + xce_object.ccp4_scratch_directory = os.path.join( + xce_object.labxchem_directory, 'processing', 'tmp') directory_list = [xce_object.beamline_directory, os.path.join(xce_object.labxchem_directory, 'processing', 'analysis'), @@ -116,12 +124,11 @@ def settings(self, xce_object): xce_object.datasets_summary_file = '' xce_object.group_deposit_directory = xce_object.current_directory - - ## deposition + # deposition xce_object.deposit_dict = {} - ## internal lists and dictionaries + # internal lists and dictionaries xce_object.data_collection_list = [] xce_object.visit_list = [] @@ -132,13 +139,15 @@ def settings(self, xce_object): xce_object.pandda_analyse_input_table_dict = {} xce_object.dewar_configuration_dict = {} xce_object.data_collection_statistics_dict = {} - xce_object.initial_model_dimple_dict = {} # contains toggle button if dimple should be run + # contains toggle button if dimple should be run + xce_object.initial_model_dimple_dict = {} xce_object.reference_file_list = [] xce_object.all_columns_in_data_source = XChemDB.data_source(os.path.join (xce_object.database_directory, xce_object.data_source_file)) \ .return_column_list() - xce_object.albula_button_dict = {} # using dials.image_viewer instead of albula, but keep name for dictionary + # using dials.image_viewer instead of albula, but keep name for dictionary + xce_object.albula_button_dict = {} xce_object.xtalform_dict = {} xce_object.dataset_outcome_dict = {} # contains the dataset outcome buttons @@ -153,11 +162,11 @@ def settings(self, xce_object): xce_object.agamemnon = False xce_object.target_list, xce_object.visit_list = XChemMain.get_target_and_visit_list( - xce_object.beamline_directory,False) + xce_object.beamline_directory, False) xce_object.diffraction_data_dict = {} - ## internal switches and flags + # internal switches and flags xce_object.explorer_active = 0 xce_object.coot_running = 0 @@ -166,7 +175,7 @@ def settings(self, xce_object): xce_object.albula = None xce_object.albula_subframes = [] xce_object.show_diffraction_image = None - xce_object.gdaLogInstructions = [0,False] + xce_object.gdaLogInstructions = [0, False] # can be any widget to be displayed in data collection summary tab xce_object.data_collection_details_currently_on_display = None @@ -191,7 +200,7 @@ def settings(self, xce_object): self.set_xce_logfile(xce_object) - ## external software packages + # external software packages xce_object.using_remote_qsub_submission = False xce_object.remote_qsub_submission = "/usr/bin/ssh @nx.diamond.ac.uk 'module load global/cluster; qsub'" @@ -201,7 +210,8 @@ def settings(self, xce_object): xce_object.diffraction_data_search_info = 'n/a' xce_object.diffraction_data_reference_mtz = 'ignore' xce_object.html_export_directory = os.getcwd() - xce_object.external_software = XChemUtils.external_software(xce_object.xce_logfile).check() + xce_object.external_software = XChemUtils.external_software( + xce_object.xce_logfile).check() xce_object.second_cif_file = None @@ -218,16 +228,17 @@ def settings(self, xce_object): 'No program for generation of ligand coordinates and restraints available!') def preferences(self, xce_object): - ## preferences + # preferences - xce_object.preferences_data_to_copy = [['aimless logiles and merged mtz only', 'mtz_log_only'], ] + xce_object.preferences_data_to_copy = [ + ['aimless logiles and merged mtz only', 'mtz_log_only'], ] # ['All Files in the respective auto-processing directory','everything'], xce_object.preferences_selection_mechanism = ['IsigI*Comp*UniqueRefl', 'highest_resolution', 'lowest_Rfree', 'dials - only', -# 'xia2 3d - only', + # 'xia2 3d - only', 'xia2 3dii - only', 'autoProc - only', 'autoProc_staraniso - only'] @@ -238,10 +249,9 @@ def preferences(self, xce_object): xce_object.max_queue_jobs = 100 xce_object.dimple_twin_mode = False - - xce_object.preferences_initial_refinement_pipeline = [ 'dimple', - 'pipedream', - 'phenix.ligand_pipeline' ] + xce_object.preferences_initial_refinement_pipeline = ['dimple', + 'pipedream', + 'phenix.ligand_pipeline'] xce_object.preferences = {'processed_data_to_copy': 'mtz_log_only', 'dataset_selection_mechanism': 'IsigI*Comp*UniqueRefl', @@ -251,10 +261,9 @@ def preferences(self, xce_object): 'filename_root': '${samplename}', 'max_queue_jobs': 100, 'dimple_twin_mode': False, - 'initial_refinement_pipeline': 'dimple' } - + 'initial_refinement_pipeline': 'dimple'} - ## settings + # settings xce_object.settings = {'current_directory': xce_object.current_directory, 'beamline_directory': xce_object.beamline_directory, @@ -276,7 +285,7 @@ def preferences(self, xce_object): 'group_deposit_directory': xce_object.group_deposit_directory, 'remote_qsub': '', 'dimple_twin_mode': False, - 'agamemnon': False } + 'agamemnon': False} def tables(self, xce_object): # Table column settings @@ -306,7 +315,7 @@ def tables(self, xce_object): # - appears in create_widgets_for_autoprocessing_results_only() xce_object.datasets_summary_table_columns = ['Sample ID', -# 'Resolution\n[Mn = 2.0]', + # 'Resolution\n[Mn = 2.0]', 'Resolution\nHigh', 'DataProcessing\nSpaceGroup', 'DataProcessing\nRfree', @@ -319,9 +328,9 @@ def tables(self, xce_object): 'img2', 'img3', 'img4' -# 'img5', -# 'Show\nDetails', -# 'Show Diffraction\nImage' + # 'img5', + # 'Show\nDetails', + # 'Show Diffraction\nImage' ] # functions that use tables.data_collection_table_columns: @@ -343,8 +352,6 @@ def tables(self, xce_object): 'DataProcessing\nScore' ] - - # functions that use tables.datasets_reprocess_columns: # # - update_datasets_reprocess_table() - appears in search_for_datasets() @@ -352,7 +359,7 @@ def tables(self, xce_object): xce_object.datasets_reprocess_columns = ['Dataset ID', 'Sample ID', 'Run\nxia2', -# 'Resolution\n[Mn = 1.5]', + # 'Resolution\n[Mn = 1.5]', 'Resolution\nHigh', 'Rmerge\nLow', 'Dimple\nRfree', @@ -368,7 +375,7 @@ def tables(self, xce_object): 'Select', 'Compound ID', 'Smiles', -# 'Resolution\n[Mn = 1.5]', + # 'Resolution\n[Mn = 1.5]', 'Resolution\nHigh', 'Dimple\nRcryst', 'Dimple\nRfree', @@ -386,16 +393,16 @@ def tables(self, xce_object): # - populate_pandda_analyse_input_table() - appears in update_all_tables() xce_object.pandda_table_columns = [ - 'Sample ID', - 'Export\nSelected', - 'Refinement\nSpace Group', - 'Resolution\n[Mn = 1.5]', - 'Dimple\nRcryst', - 'Dimple\nRfree', - 'Crystal Form\nName', - 'Ignore\ncompletely', - 'Exclude from\n characterisation\n(binds)', - 'Exclude from\n z-map analysis\n(does not bind)'] + 'Sample ID', + 'Export\nSelected', + 'Refinement\nSpace Group', + 'Resolution\n[Mn = 1.5]', + 'Dimple\nRcryst', + 'Dimple\nRfree', + 'Crystal Form\nName', + 'Ignore\ncompletely', + 'Exclude from\n characterisation\n(binds)', + 'Exclude from\n z-map analysis\n(does not bind)'] # functions that use tables.refinement_table_columns: # @@ -423,9 +430,12 @@ def top_menu_dict(self, xce_object): # } xce_object.menu_dict = {'A: file': ["&File", [ - ['Open Config File', 'Ctrl+O', xce_object.open_config_file], - ['Save Config File', 'Ctrl+S', xce_object.save_config_file], - ['Quit', 'Ctrl+Q', xce_object.quit_xce] + ['Open Config File', 'Ctrl+O', + xce_object.open_config_file], + ['Save Config File', 'Ctrl+S', + xce_object.save_config_file], + ['Quit', 'Ctrl+Q', + xce_object.quit_xce] ]], 'B: datasource': ["&Datasource", [ @@ -443,38 +453,46 @@ def top_menu_dict(self, xce_object): xce_object.select_datasource_columns_to_display], ['Create New Datasource (SQLite)', '', xce_object.create_new_data_source], - ['Export CSV for wonka', '', xce_object.export_data_for_WONKA] + ['Export CSV for wonka', '', + xce_object.export_data_for_WONKA] ]], 'C: preferences': ["&Preferences", [ - ['Edit preferences', '', xce_object.show_preferences] + ['Edit preferences', '', + xce_object.show_preferences] ]], 'D: deposition': ["&Deposition", [ - ['Edit information', '', xce_object.deposition_data], - ['Export to HTML', '', xce_object.export_to_html], - ['Export to HTML - CompChem', '', xce_object.export_to_html_CompChem], - ['Export to HTML - deposition ready', '', xce_object.export_to_html_deposition_ready], -# ['Find PanDDA apo structures', '', -# xce_object.create_missing_apo_records_in_depositTable], -# ['Update file info of apo structures', '', -# xce_object.update_file_information_of_apo_records], -# ['Prepare mmcif for apo structures', '', -# xce_object.prepare_models_for_deposition_apo], -# ['Prepare mmcif for ligand bound structures', '', -# xce_object.prepare_models_for_deposition_ligand_bound], -# ['Copy files to group deposition directory (ligand bound)', '', -# xce_object.prepare_for_group_deposition_upload_ligand_bound], -# ['Copy files to group deposition directory (ground state)', '', -# xce_object.prepare_for_group_deposition_upload_ground_state], - ['Update DB with PDB codes', '', xce_object.enter_pdb_codes], - ['Check SMILES', '', xce_object.check_smiles_in_db_and_pdb] + ['Edit information', '', + xce_object.deposition_data], + ['Export to HTML', '', + xce_object.export_to_html], + ['Export to HTML - CompChem', '', + xce_object.export_to_html_CompChem], + ['Export to HTML - deposition ready', '', + xce_object.export_to_html_deposition_ready], + # ['Find PanDDA apo structures', '', + # xce_object.create_missing_apo_records_in_depositTable], + # ['Update file info of apo structures', '', + # xce_object.update_file_information_of_apo_records], + # ['Prepare mmcif for apo structures', '', + # xce_object.prepare_models_for_deposition_apo], + # ['Prepare mmcif for ligand bound structures', '', + # xce_object.prepare_models_for_deposition_ligand_bound], + # ['Copy files to group deposition directory (ligand bound)', '', + # xce_object.prepare_for_group_deposition_upload_ligand_bound], + # ['Copy files to group deposition directory (ground state)', '', + # xce_object.prepare_for_group_deposition_upload_ground_state], + ['Update DB with PDB codes', '', + xce_object.enter_pdb_codes], + ['Check SMILES', '', + xce_object.check_smiles_in_db_and_pdb] ]], -# 'E: proasis': ["Proasis", -# [ -# ['Launch Proasis in browser', '', partial(webbrowser.open, -# url='http://cs04r-sc-vserv-137.diamond.ac.uk/Proasis4_2017/')] -# ]], + # 'E: proasis': ["Proasis", + # [ + # ['Launch Proasis in browser', '', partial(webbrowser.open, + # url='http://cs04r-sc-vserv-137.diamond.ac.uk/Proasis4_2017/')] + # ]], 'F: help': ["&Help", [ ['Open XCE manual', '', @@ -490,9 +508,10 @@ def top_menu_dict(self, xce_object): "/dls/science/groups/i04-1/software/xce_troubleshooting.pdf")] ]], 'G: labels': ["&Labels", - [ - ['Edit label information', '', xce_object.add_label_information] - ]] + [ + ['Edit label information', '', + xce_object.add_label_information] + ]] } @@ -513,124 +532,125 @@ def bottom_box_buttons(self, xce_object): ]]} xce_object.dataset_task_run_button_dict = {'dataset_run_button': - [r"Run", - [ - ['XChemToolTips.dataset_task_run_button_tip()', # tooltip - 'QPushButton { padding: 1px; margin: 1px }', # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} + [r"Run", + [ + ['XChemToolTips.dataset_task_run_button_tip()', # tooltip + # stylesheet + 'QPushButton { padding: 1px; margin: 1px }', + '', # font + 'xce_object.button_clicked'] # action + ]]} xce_object.dataset_task_status_button_dict = {'dataset_status_button': - [r"Status", - [ - ['XChemToolTips.dataset_task_status_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} + [r"Status", + [ + ['XChemToolTips.dataset_task_status_button_tip()', + # tooltip + 'QPushButton { padding: 1px; margin: 1px }', + # stylesheet + '', # font + 'xce_object.button_clicked'] # action + ]]} xce_object.map_cif_file_task_run_button_dict = {'dataset_run_button': - [r"Run", - [ - ['XChemToolTips.map_cif_file_task_run_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} + [r"Run", + [ + ['XChemToolTips.map_cif_file_task_run_button_tip()', + # tooltip + 'QPushButton { padding: 1px; margin: 1px }', + # stylesheet + '', # font + 'xce_object.button_clicked'] # action + ]]} xce_object.map_cif_file_task_status_button_dict = {'dataset_status_button': - [r"Status", + [r"Status", + [ [ - [ - 'XChemToolTips.map_cif_file_task_status_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} + 'XChemToolTips.map_cif_file_task_status_button_tip()', + # tooltip + 'QPushButton { padding: 1px; margin: 1px }', + # stylesheet + '', # font + 'xce_object.button_clicked'] # action + ]]} xce_object.panddas_file_task_run_button_dict = {'dataset_run_button': - [r"Run", - [ - ['XChemToolTips.panddas_file_task_run_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} + [r"Run", + [ + ['XChemToolTips.panddas_file_task_run_button_tip()', + # tooltip + 'QPushButton { padding: 1px; margin: 1px }', + # stylesheet + '', # font + 'xce_object.button_clicked'] # action + ]]} xce_object.panddas_file_task_status_button_dict = {'dataset_status_button': - [r"Status", + [r"Status", + [ [ - [ - 'XChemToolTips.panddas_file_task_status_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} + 'XChemToolTips.panddas_file_task_status_button_tip()', + # tooltip + 'QPushButton { padding: 1px; margin: 1px }', + # stylesheet + '', # font + 'xce_object.button_clicked'] # action + ]]} xce_object.refine_file_task_run_button_dict = {'dataset_run_button': - [r"Run", - [ - ['XChemToolTips.refine_file_task_run_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} + [r"Run", + [ + ['XChemToolTips.refine_file_task_run_button_tip()', + # tooltip + 'QPushButton { padding: 1px; margin: 1px }', + # stylesheet + '', # font + 'xce_object.button_clicked'] # action + ]]} xce_object.refine_file_task_status_button_dict = {'dataset_status_button': - [r"Status", + [r"Status", + [ [ - [ - 'XChemToolTips.refine_file_task_status_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} + 'XChemToolTips.refine_file_task_status_button_tip()', + # tooltip + 'QPushButton { padding: 1px; margin: 1px }', + # stylesheet + '', # font + 'xce_object.button_clicked'] # action + ]]} def dropdown_items(self, xce_object): xce_object.dataset_tasks = ['Get New Results from Autoprocessing', -# 'Run DIMPLE on All Autoprocessing MTZ files', + # 'Run DIMPLE on All Autoprocessing MTZ files', 'Rescore Datasets', 'Run xia2 on selected datasets', 'Run xia2 on selected datasets - overwrite'] xce_object.map_cif_file_tasks = [ -# 'Run initial refinement on selected MTZ files', -# 'Remove selected initial refinement files', - 'Run DIMPLE on selected MTZ files', - 'Remove selected DIMPLE files', - 'Set DIMPLE output', -# 'Set only results from selected pipeline', -# 'Create CIF/PDB/PNG file of ALL compounds', -# 'Create CIF/PDB/PNG file of NEW compounds', - '------------------------------------------', - 'Create CIF/PDB/PNG file of SELECTED compounds', - 'Merge ligand CIF file with selected compounds', - 'Restore original CIF file of selected compounds', - 'Fit ligands into maps after initial refinement', - '------------------------------------------', - 'Run PIPEDREAM on selected MTZ files', - 'Remove selected PIPEDREAM files', - 'Set PIPEDREAM output', - '------------------------------------------', - 'Run PHENIX.LIGAND_PIPELINE on selected MTZ files', - 'Remove selected PHENIX.LIGAND_PIPELINE files', - 'Set PHENIX.LIGAND_PIPELINE output' - ] + # 'Run initial refinement on selected MTZ files', + # 'Remove selected initial refinement files', + 'Run DIMPLE on selected MTZ files', + 'Remove selected DIMPLE files', + 'Set DIMPLE output', + # 'Set only results from selected pipeline', + # 'Create CIF/PDB/PNG file of ALL compounds', + # 'Create CIF/PDB/PNG file of NEW compounds', + '------------------------------------------', + 'Create CIF/PDB/PNG file of SELECTED compounds', + 'Merge ligand CIF file with selected compounds', + 'Restore original CIF file of selected compounds', + 'Fit ligands into maps after initial refinement', + '------------------------------------------', + 'Run PIPEDREAM on selected MTZ files', + 'Remove selected PIPEDREAM files', + 'Set PIPEDREAM output', + '------------------------------------------', + 'Run PHENIX.LIGAND_PIPELINE on selected MTZ files', + 'Remove selected PHENIX.LIGAND_PIPELINE files', + 'Set PHENIX.LIGAND_PIPELINE output' + ] xce_object.panddas_file_tasks = ['pandda.analyse', 'pandda.inspect', @@ -641,7 +661,7 @@ def dropdown_items(self, xce_object): 'Export SELECTED PANDDA models', '------------------------------------------', 'Show HTML summary', -# 'Update datasource with results from pandda.inspect', + # 'Update datasource with results from pandda.inspect', 'cluster datasets', 'Event Map -> SF', 'apo -> mmcif', @@ -653,7 +673,7 @@ def dropdown_items(self, xce_object): 'refine ALL bound-state models with BUSTER (no sanity check)', 'refine NEW bound-state models with BUSTER (no sanity check)', '------------------------------------------', -# 'refine NEW bound-state models with BUSTER - NEW', + # 'refine NEW bound-state models with BUSTER - NEW', 'pre-run for ground state model', 'Build ground state model', '------------------------------------------', @@ -663,12 +683,11 @@ def dropdown_items(self, xce_object): xce_object.refine_file_tasks = ['Open COOT - BUSTER refinement -', 'Open COOT - REFMAC refinement -', 'Open COOT - dimple_twin -', -# '-------------------------------', -# 'Reset to last successful refinement (BUSTER or REFMAC)', + # '-------------------------------', + # 'Reset to last successful refinement (BUSTER or REFMAC)', ''] # xce_object.refine_file_tasks = ['Open COOT', # 'Open COOT for old PanDDA', # 'Update Deposition Table', # 'Prepare Group Deposition'] - diff --git a/gui_scripts/settings_tab.py b/gui_scripts/settings_tab.py index 2cf2e147..00c68e20 100755 --- a/gui_scripts/settings_tab.py +++ b/gui_scripts/settings_tab.py @@ -1,10 +1,10 @@ -import sys, os +import layout +import sys +import os from PyQt4 import QtGui, QtCore, QtWebKit sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) -import layout - class SettingsTab(): def __init__(self): @@ -30,41 +30,38 @@ def setup(self, xce_object): # Settings Tab xce_object.data_collection_vbox_for_settings = QtGui.QVBoxLayout() - xce_object.buttons_etc.setLayout(xce_object.data_collection_vbox_for_settings) + xce_object.buttons_etc.setLayout( + xce_object.data_collection_vbox_for_settings) xce_object.scroll.setWidget(xce_object.buttons_etc) - xce_object.initial_model_directory_label = self.layout_funcs.settings_section_setup \ - (xce_object.data_collection_vbox_for_settings, - '\n\nProject Directory: - REQUIRED -', - xce_object.initial_model_directory, - 'Select Project Directory', - xce_object.settings_button_clicked) + xce_object.initial_model_directory_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, + '\n\nProject Directory: - REQUIRED -', + xce_object.initial_model_directory, + 'Select Project Directory', + xce_object.settings_button_clicked) - xce_object.reference_directory_label = self.layout_funcs.settings_section_setup \ - (xce_object.data_collection_vbox_for_settings, - '\n\nReference Structure Directory: - OPTIONAL -', - xce_object.reference_directory, - 'Select Reference Structure Directory', - xce_object.settings_button_clicked) + xce_object.reference_directory_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, + '\n\nReference Structure Directory: - OPTIONAL -', + xce_object.reference_directory, + 'Select Reference Structure Directory', + xce_object.settings_button_clicked) if xce_object.data_source_file != '': xce_object.data_source_file_label_text = os.path.join(xce_object.database_directory, xce_object.data_source_file) - xce_object.data_source_file_label = self.layout_funcs.settings_section_setup \ - (xce_object.data_collection_vbox_for_settings, - '\n\nData Source: - REQUIRED -', - xce_object.data_source_file_label_text, - 'Select Data Source File', - xce_object.settings_button_clicked) + xce_object.data_source_file_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, + '\n\nData Source: - REQUIRED -', + xce_object.data_source_file_label_text, + 'Select Data Source File', + xce_object.settings_button_clicked) else: xce_object.data_source_file_label_text = '' - xce_object.data_source_file_label = self.layout_funcs.settings_section_setup \ - (xce_object.data_collection_vbox_for_settings, - '\n\nData Source: - REQUIRED -', - xce_object.data_source_file_label_text, - 'Select Data Source File', - xce_object.settings_button_clicked) + xce_object.data_source_file_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, + '\n\nData Source: - REQUIRED -', + xce_object.data_source_file_label_text, + 'Select Data Source File', + xce_object.settings_button_clicked) xce_object.data_collection_vbox_for_settings.addWidget( QtGui.QLabel('\n\nData Collection Directory: (e.g. /dls/i04-1/data/2017/lb18145-70) -')) @@ -74,20 +71,25 @@ def setup(self, xce_object): settings_beamline_vbox = QtGui.QVBoxLayout() settings_hbox_beamline_directory = QtGui.QHBoxLayout() - xce_object.beamline_directory_label = QtGui.QLabel(xce_object.beamline_directory) - settings_hbox_beamline_directory.addWidget(xce_object.beamline_directory_label) - settings_button_beamline_directory = QtGui.QPushButton('Select Data Collection Directory') + xce_object.beamline_directory_label = QtGui.QLabel( + xce_object.beamline_directory) + settings_hbox_beamline_directory.addWidget( + xce_object.beamline_directory_label) + settings_button_beamline_directory = QtGui.QPushButton( + 'Select Data Collection Directory') settings_button_beamline_directory.setMaximumWidth(500) - settings_button_beamline_directory.clicked.connect(xce_object.settings_button_clicked) + settings_button_beamline_directory.clicked.connect( + xce_object.settings_button_clicked) - settings_hbox_beamline_directory.addWidget(settings_button_beamline_directory) + settings_hbox_beamline_directory.addWidget( + settings_button_beamline_directory) settings_beamline_vbox.addLayout(settings_hbox_beamline_directory) - xce_object.read_agamemnon = QtGui.QCheckBox('Read Agamemnon data structure') + xce_object.read_agamemnon = QtGui.QCheckBox( + 'Read Agamemnon data structure') settings_beamline_vbox.addWidget(xce_object.read_agamemnon) - # settings_hbox_datasets_summary_file = QtGui.QHBoxLayout() # xce_object.datasets_summary_file_label = QtGui.QLabel(xce_object.datasets_summary_file) # settings_hbox_datasets_summary_file.addWidget(xce_object.datasets_summary_file_label) @@ -104,38 +106,36 @@ def setup(self, xce_object): # settings_beamline_vbox.addLayout(settings_hbox_datasets_summary_file) settings_beamline_frame.setLayout(settings_beamline_vbox) - xce_object.data_collection_vbox_for_settings.addWidget(settings_beamline_frame) - - xce_object.ccp4_scratch_directory_label = self.layout_funcs.settings_section_setup \ - (xce_object.data_collection_vbox_for_settings, - '\n\nCCP4_SCR Directory: - OPTIONAL -', - xce_object.ccp4_scratch_directory, - 'Select CCP4_SCR Directory', - xce_object.settings_button_clicked) - - xce_object.panddas_directory_label = self.layout_funcs.settings_section_setup \ - (xce_object.data_collection_vbox_for_settings, - '\n\nPANDDAs directory: - OPTIONAL -', - xce_object.panddas_directory, - 'Select PanDDA Directory', - xce_object.settings_button_clicked) - - xce_object.html_export_directory_label = self.layout_funcs.settings_section_setup \ - (xce_object.data_collection_vbox_for_settings, - '\n\nHTML export directory: - OPTIONAL -', - xce_object.html_export_directory, - 'Select HTML Export Directory', - xce_object.settings_button_clicked) - - xce_object.group_deposition_directory_label = self.layout_funcs.settings_section_setup \ - (xce_object.data_collection_vbox_for_settings, - '\n\nGroup deposition directory: - OPTIONAL -', - xce_object.group_deposit_directory, - 'Select Group deposition Directory', - xce_object.settings_button_clicked) + xce_object.data_collection_vbox_for_settings.addWidget( + settings_beamline_frame) + + xce_object.ccp4_scratch_directory_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, + '\n\nCCP4_SCR Directory: - OPTIONAL -', + xce_object.ccp4_scratch_directory, + 'Select CCP4_SCR Directory', + xce_object.settings_button_clicked) + + xce_object.panddas_directory_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, + '\n\nPANDDAs directory: - OPTIONAL -', + xce_object.panddas_directory, + 'Select PanDDA Directory', + xce_object.settings_button_clicked) + + xce_object.html_export_directory_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, + '\n\nHTML export directory: - OPTIONAL -', + xce_object.html_export_directory, + 'Select HTML Export Directory', + xce_object.settings_button_clicked) + + xce_object.group_deposition_directory_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, + '\n\nGroup deposition directory: - OPTIONAL -', + xce_object.group_deposit_directory, + 'Select Group deposition Directory', + xce_object.settings_button_clicked) # xce_object.data_collection_vbox_for_settings.setSpacing(0) - xce_object.data_collection_vbox_for_settings.setContentsMargins(30, 30, 30, 30) + xce_object.data_collection_vbox_for_settings.setContentsMargins( + 30, 30, 30, 30) xce_object.buttons_etc.resize(xce_object.buttons_etc.sizeHint().width() + 100, xce_object.buttons_etc.sizeHint() - .height()) \ No newline at end of file + .height()) diff --git a/gui_scripts/stylesheet.py b/gui_scripts/stylesheet.py index 0f97bdf2..87aa1807 100755 --- a/gui_scripts/stylesheet.py +++ b/gui_scripts/stylesheet.py @@ -1,6 +1,7 @@ from PyQt4 import QtGui import os + def set_stylesheet(xce_object): palette = QtGui.QPalette() @@ -77,4 +78,4 @@ def set_stylesheet(xce_object): } """) - QtGui.qApp.setStyle('Cleanlooks') \ No newline at end of file + QtGui.qApp.setStyle('Cleanlooks') diff --git a/helpers/assign_stereochemistry.py b/helpers/assign_stereochemistry.py index 1c48d390..a439533d 100755 --- a/helpers/assign_stereochemistry.py +++ b/helpers/assign_stereochemistry.py @@ -1,80 +1,86 @@ -import os,sys +import XChemDB +import os +import sys import glob from rdkit import Chem #from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) -import XChemDB +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) -def enumerateStereoChem(compoundID,sampleDir,db,xtal): + +def enumerateStereoChem(compoundID, sampleDir, db, xtal): # first need to recreate the original CIF file with phenix.elbow because we cannot be sure # which program was used to create the initial restrains # this is because funny things happen to aromatic rings in case the file was made with GRADE - os.chdir(os.path.join(sampleDir,'compound')) + os.chdir(os.path.join(sampleDir, 'compound')) sql = "select CompoundSMILES from mainTable where CrystalName = '%s'" % xtal - print 'sqlite query:',sql + print 'sqlite query:', sql query = db.execute_statement(sql) originalSMILES = query[0][0] print originalSMILES cmd = 'phenix.elbow --smiles="%s" --id=LIG --output=tmp' % (originalSMILES) - print 'current working directory:',os.getcwd() - print 'runnning:',cmd + print 'current working directory:', os.getcwd() + print 'runnning:', cmd os.system(cmd) stereosmiles = None pdb = None - if os.path.isfile(os.path.join(sampleDir,'compound','tmp.pdb')): - pdb = os.path.join(sampleDir,'compound','tmp.pdb') + if os.path.isfile(os.path.join(sampleDir, 'compound', 'tmp.pdb')): + pdb = os.path.join(sampleDir, 'compound', 'tmp.pdb') else: print 'cannot find tmp.pdb' pass if pdb: mol = Chem.MolFromPDBFile(pdb) - Chem.AssignStereochemistry(mol,cleanIt=True,force=True,flagPossibleStereoCenters=True) - if Chem.FindMolChiralCenters(mol,includeUnassigned=True) == []: + Chem.AssignStereochemistry( + mol, cleanIt=True, force=True, flagPossibleStereoCenters=True) + if Chem.FindMolChiralCenters(mol, includeUnassigned=True) == []: print 'no chiral centres found' db_dict = {} db_dict['CompoundStereo'] = 'FALSE' - updateDB(db,db_dict,xtal) + updateDB(db, db_dict, xtal) else: - stereosmiles = Chem.MolToSmiles(mol,isomericSmiles=True) - generateRestraints(compoundID,sampleDir,db,stereosmiles,xtal) + stereosmiles = Chem.MolToSmiles(mol, isomericSmiles=True) + generateRestraints(compoundID, sampleDir, db, stereosmiles, xtal) + -def generateRestraints(compoundID,sampleDir,db,stereosmiles,xtal): - cmd = 'phenix.elbow --smiles="%s" --chiral=enumerate --id=LIG --output=%s' %(stereosmiles,compoundID) +def generateRestraints(compoundID, sampleDir, db, stereosmiles, xtal): + cmd = 'phenix.elbow --smiles="%s" --chiral=enumerate --id=LIG --output=%s' % ( + stereosmiles, compoundID) os.system(cmd) - checkFiles(compoundID,sampleDir,db,stereosmiles,xtal) + checkFiles(compoundID, sampleDir, db, stereosmiles, xtal) -def checkFiles(compoundID,sampleDir,db,stereosmiles,xtal): +def checkFiles(compoundID, sampleDir, db, stereosmiles, xtal): foundCIF = False allCIF = '' for cif in glob.glob(os.path.join(compoundID + '_*.cif')): foundCIF = True allCIF += cif+';' - print '---',cif,'===',allCIF + print '---', cif, '===', allCIF if foundCIF: db_dict = {} db_dict['CompoundStereo'] = 'TRUE' db_dict['CompoundStereoSMILES'] = stereosmiles db_dict['CompoundStereoCIFprogram'] = 'phenix.elbow' db_dict['CompoundStereoCIFs'] = allCIF[:-1] - print '>>>',db_dict - updateDB(db,db_dict,xtal) + print '>>>', db_dict + updateDB(db, db_dict, xtal) -def updateDB(db,db_dict,xtal): + +def updateDB(db, db_dict, xtal): # update stereo field # update restraintsprogram field # update stereosmiles db.update_data_source(xtal, db_dict) -if __name__=='__main__': + +if __name__ == '__main__': compoundID = sys.argv[1] sampleDir = sys.argv[2] xtal = sampleDir[sampleDir.rfind('/')+1:] - print 'sampleID:',xtal + print 'sampleID:', xtal database = sys.argv[3] - print 'database:',database - db=XChemDB.data_source(database) - enumerateStereoChem(compoundID,sampleDir,db,xtal) - + print 'database:', database + db = XChemDB.data_source(database) + enumerateStereoChem(compoundID, sampleDir, db, xtal) diff --git a/helpers/change_residues_in_ground_and_bound-state.py b/helpers/change_residues_in_ground_and_bound-state.py index 8e72b8dd..dfd298b3 100755 --- a/helpers/change_residues_in_ground_and_bound-state.py +++ b/helpers/change_residues_in_ground_and_bound-state.py @@ -1,8 +1,10 @@ -import glob,os +import glob +import os import sys + def replace_residues(): - for dirs in glob.glob(os.path.join(projectDir,'*')): + for dirs in glob.glob(os.path.join(projectDir, '*')): xtal = dirs[dirs.rfind('/')+1:] os.chdir(dirs) if xtal == test: @@ -10,53 +12,55 @@ def replace_residues(): for mol in toEdit: if os.path.isfile(mol): if not os.path.isfile(mol+'_original'): - os.system('/bin/cp %s %s' %(mol,mol+'_original')) - print '%s: found %s' %(xtal,mol) - os.system('phenix.superpose_pdbs %s %s' %(mol,newModel)) + os.system('/bin/cp %s %s' % (mol, mol+'_original')) + print '%s: found %s' % (xtal, mol) + os.system('phenix.superpose_pdbs %s %s' % (mol, newModel)) out = '' changeResi = None for line in open(mol): if line.startswith('ATOM') or line.startswith('HETATM'): - chainID=str(line[21:23]).replace(' ','') - resseq=str(line[23:26]).replace(' ','') - occupancy=str(line[56:60]).replace(' ','') + chainID = str(line[21:23]).replace(' ', '') + resseq = str(line[23:26]).replace(' ', '') + occupancy = str(line[56:60]).replace(' ', '') resi = chainID + resseq if changeResi != None: if resi == changeResi: - print 'here',changeResi + print 'here', changeResi continue else: changeResi = None if resi in residues_to_change: changeResi = resi - print 'changeResi',changeResi + print 'changeResi', changeResi for line in open(newModelName+'_fitted.pdb'): if line.startswith('ATOM') or line.startswith('HETATM'): - chainIDFitted=str(line[21:23]).replace(' ','') - resseqFitted=str(line[23:26]).replace(' ','') + chainIDFitted = str( + line[21:23]).replace(' ', '') + resseqFitted = str( + line[23:26]).replace(' ', '') residFitted = chainIDFitted + resseqFitted if residFitted == changeResi: - out += line[:56] + occupancy + line[60:] + out += line[:56] + \ + occupancy + line[60:] else: out += line else: - out+=line - print 'saving file',mol,'...' - newFile = open(mol,'w') + out += line + print 'saving file', mol, '...' + newFile = open(mol, 'w') newFile.write(out) newFile.close() if __name__ == '__main__': -# newModel = '/dls/labxchem/data/2019/lb22717-1/processing/INPP5DA/processing/reference/INPP5DA-x0080-ground-state-corrected.pdb' -# residues_to_change = ['A567', 'A812', 'A851'] -# projectDir = '/dls/labxchem/data/2019/lb22717-1/processing/INPP5DA/processing/analysis/model_building' -# toEdit = ['refine.split.ground-state.pdb', 'refine.split.bound-state.pdb'] -# test = 'INPP5DA-x0019' + # newModel = '/dls/labxchem/data/2019/lb22717-1/processing/INPP5DA/processing/reference/INPP5DA-x0080-ground-state-corrected.pdb' + # residues_to_change = ['A567', 'A812', 'A851'] + # projectDir = '/dls/labxchem/data/2019/lb22717-1/processing/INPP5DA/processing/analysis/model_building' + # toEdit = ['refine.split.ground-state.pdb', 'refine.split.bound-state.pdb'] + # test = 'INPP5DA-x0019' newModel = sys.argv[1] residues_to_change = sys.argv[2] projectDir = sys.argv[3] toEdit = ['refine.split.ground-state.pdb', 'refine.split.bound-state.pdb'] newModelName = newModel[newModel.rfind('/') + 1:] - diff --git a/helpers/create_png_of_compound.py b/helpers/create_png_of_compound.py index c8caded2..421f377c 100755 --- a/helpers/create_png_of_compound.py +++ b/helpers/create_png_of_compound.py @@ -1,20 +1,20 @@ -import os,sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) - -from rdkit import Chem -from rdkit.Chem import AllChem from rdkit.Chem import Draw +from rdkit.Chem import AllChem +from rdkit import Chem +import os +import sys +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) -if __name__=='__main__': +if __name__ == '__main__': - smiles = sys.argv[1] - compoundID = sys.argv[2] - xtal = sys.argv[3] - inital_model_directory = sys.argv[4] + smiles = sys.argv[1] + compoundID = sys.argv[2] + xtal = sys.argv[3] + inital_model_directory = sys.argv[4] mol = Chem.MolFromSmiles(smiles) AllChem.Compute2DCoords(mol) - os.chdir(os.path.join(inital_model_directory,xtal,'compound')) - Draw.MolToFile(mol, "{0!s}.png".format(compoundID.replace(' ',''))) + os.chdir(os.path.join(inital_model_directory, xtal, 'compound')) + Draw.MolToFile(mol, "{0!s}.png".format(compoundID.replace(' ', ''))) diff --git a/helpers/find_best_fitting_ligand.py b/helpers/find_best_fitting_ligand.py index 5ad2985c..55afc17a 100755 --- a/helpers/find_best_fitting_ligand.py +++ b/helpers/find_best_fitting_ligand.py @@ -1,35 +1,40 @@ -import sys, os +import XChemDB +import sys +import os import glob -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) -import XChemDB +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) -def parse_autofit_folder(sampleDir,compoundID): - filenames = ['best.pdb','ligand_fit_1.pdb'] + +def parse_autofit_folder(sampleDir, compoundID): + filenames = ['best.pdb', 'ligand_fit_1.pdb'] pdbList = [] - for files in glob.glob(os.path.join(sampleDir,'autofit_ligand',compoundID+'_*','*')): + for files in glob.glob(os.path.join(sampleDir, 'autofit_ligand', compoundID+'_*', '*')): pdb = files[files.rfind('/')+1:] if pdb in filenames: pdbList.append(files) return pdbList + def find_input_mtz(sampleDir): - possibleMTZ = ['refine.mtz','init.mtz','dimple.mtz',] + possibleMTZ = ['refine.mtz', 'init.mtz', 'dimple.mtz', ] mtzin = None for mtz in possibleMTZ: - if os.path.isfile(os.path.join(sampleDir,mtz)): - mtzin = os.path.join(sampleDir,mtz) + if os.path.isfile(os.path.join(sampleDir, mtz)): + mtzin = os.path.join(sampleDir, mtz) break return mtzin -def calculate_cc(sampleDir,compoundID,db): + +def calculate_cc(sampleDir, compoundID, db): xtal = sampleDir[sampleDir.rfind('/') + 1:] - pdbList = parse_autofit_folder(sampleDir,compoundID) + pdbList = parse_autofit_folder(sampleDir, compoundID) mtzin = find_input_mtz(sampleDir) for pdb in pdbList: autofitDir = pdb[:pdb.rfind('/')] os.chdir(autofitDir) - os.system('phenix.get_cc_mtz_pdb %s %s > phenix.get_cc_mtz_pdb.log' %(pdb,mtzin)) + os.system( + 'phenix.get_cc_mtz_pdb %s %s > phenix.get_cc_mtz_pdb.log' % (pdb, mtzin)) new_file_links(pdbList) bestRun, bestCC = parse_cc_log(sampleDir, compoundID) changeLinks(sampleDir, pdbList, bestRun, compoundID) @@ -51,21 +56,24 @@ def new_file_links(pdbList): pdbFile = pdb[pdb.rfind('/')+1:] os.chdir(autofitDir) if not os.path.isfile(autofitRun+'.pdb'): - os.system('ln -s %s %s.pdb' %(pdbFile,autofitRun)) + os.system('ln -s %s %s.pdb' % (pdbFile, autofitRun)) + -def changeLinks(sampleDir,pdbList,bestRun,compoundID): +def changeLinks(sampleDir, pdbList, bestRun, compoundID): os.chdir(sampleDir) for pdb in pdbList: autofitDir = pdb.split('/')[len(pdb.split('/')) - 2] if autofitDir == bestRun: - if os.path.isfile(pdb.replace(sampleDir,'.')): - os.system('/bin/rm %s.pdb' %compoundID) - os.system('ln -s %s %s.pdb' %(pdb.replace(sampleDir,'.'),compoundID)) + if os.path.isfile(pdb.replace(sampleDir, '.')): + os.system('/bin/rm %s.pdb' % compoundID) + os.system('ln -s %s %s.pdb' % + (pdb.replace(sampleDir, '.'), compoundID)) + -def parse_cc_log(sampleDir,compoundID): +def parse_cc_log(sampleDir, compoundID): ccDict = {} ccList = [] - for ccLog in glob.glob(os.path.join(sampleDir,'autofit_ligand',compoundID+'_*','phenix.get_cc_mtz_pdb.log')): + for ccLog in glob.glob(os.path.join(sampleDir, 'autofit_ligand', compoundID+'_*', 'phenix.get_cc_mtz_pdb.log')): autofitDir = ccLog.split('/')[len(ccLog.split('/'))-2] for line in open(ccLog): if line.startswith('local CC:') and len(line.split()) > 2: @@ -77,7 +85,7 @@ def parse_cc_log(sampleDir,compoundID): try: bestCC = max(ccList) for ccRun in ccDict: - print ccRun,ccDict[ccRun],bestCC + print ccRun, ccDict[ccRun], bestCC if str(ccDict[ccRun]) == str(bestCC): bestRun = ccRun break @@ -86,7 +94,7 @@ def parse_cc_log(sampleDir,compoundID): return bestRun, bestCC -def updateDB(db,db_dict,xtal): +def updateDB(db, db_dict, xtal): db.update_data_source(xtal, db_dict) @@ -94,6 +102,6 @@ def updateDB(db,db_dict,xtal): compoundID = sys.argv[1] sampleDir = sys.argv[2] database = sys.argv[3] - db=XChemDB.data_source(database) + db = XChemDB.data_source(database) - calculate_cc(sampleDir, compoundID, db) \ No newline at end of file + calculate_cc(sampleDir, compoundID, db) diff --git a/helpers/make_ligand_links_after_pandda.py b/helpers/make_ligand_links_after_pandda.py index 878d42b7..a2ec0cc1 100755 --- a/helpers/make_ligand_links_after_pandda.py +++ b/helpers/make_ligand_links_after_pandda.py @@ -1,27 +1,29 @@ # last edited: 10/08/2017, 15:00 -import os,glob +import os +import glob import sys -#projectDir='/dls/labxchem/data/2017/lb13385-109/processing/analysis/initial_model_cov' -#panddaDir='/dls/labxchem/data/2017/lb13385-109/processing/analysis/panddas_cov' +# projectDir='/dls/labxchem/data/2017/lb13385-109/processing/analysis/initial_model_cov' +# panddaDir='/dls/labxchem/data/2017/lb13385-109/processing/analysis/panddas_cov' -def make_links(projectDir,panddaDir): - os.chdir(os.path.join(panddaDir,'processed_datasets')) +def make_links(projectDir, panddaDir): + os.chdir(os.path.join(panddaDir, 'processed_datasets')) for xtal in glob.glob('*'): -# for cif in glob.glob(os.path.join(xtal,'ligand_files','*.cif')): -# print cif -# os.system('/bin/rm %s' %cif) -# for pdb in glob.glob(os.path.join(xtal,'ligand_files','*.pdb')): -# print pdb -# os.system('/bin/rm %s' %pdb) + # for cif in glob.glob(os.path.join(xtal,'ligand_files','*.cif')): + # print cif + # os.system('/bin/rm %s' %cif) + # for pdb in glob.glob(os.path.join(xtal,'ligand_files','*.pdb')): + # print pdb + # os.system('/bin/rm %s' %pdb) - for pdb in glob.glob(os.path.join(projectDir,xtal,'compound','*.pdb')): - os.system('ln -s %s %s/ligand_files' %(pdb,xtal)) - for cif in glob.glob(os.path.join(projectDir,xtal,'compound','*.cif')): - os.system('ln -s %s %s/ligand_files' %(cif,xtal)) + for pdb in glob.glob(os.path.join(projectDir, xtal, 'compound', '*.pdb')): + os.system('ln -s %s %s/ligand_files' % (pdb, xtal)) + for cif in glob.glob(os.path.join(projectDir, xtal, 'compound', '*.cif')): + os.system('ln -s %s %s/ligand_files' % (cif, xtal)) -if __name__=='__main__': - projectDir=sys.argv[1] - panddaDir=sys.argv[2] \ No newline at end of file + +if __name__ == '__main__': + projectDir = sys.argv[1] + panddaDir = sys.argv[2] diff --git a/helpers/merge_ligand_cif_files.py b/helpers/merge_ligand_cif_files.py index a3c050da..db2116aa 100644 --- a/helpers/merge_ligand_cif_files.py +++ b/helpers/merge_ligand_cif_files.py @@ -2,6 +2,7 @@ import glob import sys + def merge_cifs(cpdDir): os.chdir(cpdDir) out = '' @@ -12,6 +13,7 @@ def merge_cifs(cpdDir): f.write(out) f.close() + if __name__ == '__main__': cpdDir = sys.argv[1] - merge_cifs(cpdDir) \ No newline at end of file + merge_cifs(cpdDir) diff --git a/helpers/phenix_find_TLS_groups.py b/helpers/phenix_find_TLS_groups.py index ec96ce1e..b85db6b4 100755 --- a/helpers/phenix_find_TLS_groups.py +++ b/helpers/phenix_find_TLS_groups.py @@ -2,43 +2,46 @@ import os import sys + def FindTLSgroups(pdbFile): print '\n==> XCE @ helpers: running phenix.find_tls_groups on new pdb file' - os.system('phenix.find_tls_groups {0!s} > phenix.find_tls_groups.out'.format(pdbFile)) - GroupNames = ['A','B','C','D','E','F','G','H','I','J','K','L','M', - 'N','O','P','Q','R','S','T','U','V','W','X','Y','Z'] - OutRefmac = '' - found = 0 - i = 0 - for line in open('phenix.find_tls_groups.out'): - if found: + os.system( + 'phenix.find_tls_groups {0!s} > phenix.find_tls_groups.out'.format(pdbFile)) + GroupNames = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', + 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'] + OutRefmac = '' + found = 0 + i = 0 + for line in open('phenix.find_tls_groups.out'): + if found: if line.startswith('}'): - break + break temp = [line.split()] OutRefmac = OutRefmac + '\nTLS {0!s}\nRANGE '.format((GroupNames)[i]) + str(temp[0][3])[:-1] + ' ' + \ - str(temp[0][6]) +'.\' ' + str(temp[0][3])[:-1] + ' ' + str(temp[0][8]) + '.\' ALL\n' + str(temp[0][6]) + '.\' ' + str(temp[0][3])[:-1] + \ + ' ' + str(temp[0][8]) + '.\' ALL\n' i += 1 if line.startswith('refinement.refine.adp {'): - found = 1 - f = open('refmac.tls','w') - f.write(OutRefmac) - f.close() + found = 1 + f = open('refmac.tls', 'w') + f.write(OutRefmac) + f.close() - OutPhenix='' - found=0 + OutPhenix = '' + found = 0 for line in open('phenix.find_tls_groups.out'): if found: - OutPhenix=OutPhenix+line - if line.startswith('}'): + OutPhenix = OutPhenix+line + if line.startswith('}'): break if line.startswith('refinement.refine.adp {'): - found=1 - OutPhenix=OutPhenix+line - f = open('phenix.tls','w') - f.write(OutPhenix) - f.close() + found = 1 + OutPhenix = OutPhenix+line + f = open('phenix.tls', 'w') + f.write(OutPhenix) + f.close() -if __name__=='__main__': +if __name__ == '__main__': pdbFile = sys.argv[1] FindTLSgroups(pdbFile) diff --git a/helpers/prepare_for_zenodo_upload.py b/helpers/prepare_for_zenodo_upload.py index a836c6f5..61376a62 100755 --- a/helpers/prepare_for_zenodo_upload.py +++ b/helpers/prepare_for_zenodo_upload.py @@ -1,102 +1,118 @@ # last edited: 13/01/2017, 15:00 -import os,sys +import os +import sys import glob + def copy_files(htmlDir): - os.chdir(htmlDir) - if not os.path.isdir('zenodo'): - os.mkdir('zenodo') - os.chdir(os.path.join(htmlDir,'zenodo')) + os.chdir(htmlDir) + if not os.path.isdir('zenodo'): + os.mkdir('zenodo') + os.chdir(os.path.join(htmlDir, 'zenodo')) + + print 'copying compoundImages' + os.system('/bin/cp ../compoundImages/* .') - print 'copying compoundImages' - os.system('/bin/cp ../compoundImages/* .') + print 'copying pdbs' + os.system('/bin/cp ../pdbs/* .') - print 'copying pdbs' - os.system('/bin/cp ../pdbs/* .') + print 'copying maps' + os.system('/bin/cp ../maps/* .') - print 'copying maps' - os.system('/bin/cp ../maps/* .') + print 'copying residueplots' + os.system('/bin/cp ../residueplots/* .') - print 'copying residueplots' - os.system('/bin/cp ../residueplots/* .') + print 'copying mapImages' + os.system('/bin/cp ../mapImages/* .') - print 'copying mapImages' - os.system('/bin/cp ../mapImages/* .') + print 'copying icbs' + os.system('/bin/cp ../icbs/* .') - print 'copying icbs' - os.system('/bin/cp ../icbs/* .') + print 'copying css' + os.system('/bin/cp ../css/* .') - print 'copying css' - os.system('/bin/cp ../css/* .') + print 'copying js' + os.system('/bin/cp ../js/* .') - print 'copying js' - os.system('/bin/cp ../js/* .') -def edit_index_html(htmlDir,uploadID): - os.chdir(os.path.join(htmlDir,'zenodo')) +def edit_index_html(htmlDir, uploadID): + os.chdir(os.path.join(htmlDir, 'zenodo')) - out='' + out = '' for line in open('../index.html'): if 'compoundImages/' in line: - line=line.replace('compoundImages/','https://zenodo.org/record/'+uploadID+'/files/') + line = line.replace( + 'compoundImages/', 'https://zenodo.org/record/'+uploadID+'/files/') if 'pdbs/' in line: - line=line.replace('pdbs/','https://zenodo.org/record/'+uploadID+'/files/') + line = line.replace( + 'pdbs/', 'https://zenodo.org/record/'+uploadID+'/files/') if 'maps/' in line: - line=line.replace('maps/','https://zenodo.org/record/'+uploadID+'/files/') + line = line.replace( + 'maps/', 'https://zenodo.org/record/'+uploadID+'/files/') if 'residueplots/' in line: - line=line.replace('residueplots/','https://zenodo.org/record/'+uploadID+'/files/') + line = line.replace( + 'residueplots/', 'https://zenodo.org/record/'+uploadID+'/files/') if 'mapImages/' in line: - line=line.replace('mapImages/','https://zenodo.org/record/'+uploadID+'/files/') + line = line.replace( + 'mapImages/', 'https://zenodo.org/record/'+uploadID+'/files/') if 'icbs/' in line: - line=line.replace('icbs/','https://zenodo.org/record/'+uploadID+'/files/') + line = line.replace( + 'icbs/', 'https://zenodo.org/record/'+uploadID+'/files/') if 'css/' in line: - line=line.replace('css/','https://zenodo.org/record/'+uploadID+'/files/') + line = line.replace( + 'css/', 'https://zenodo.org/record/'+uploadID+'/files/') if 'js/' in line: - line=line.replace('js/','https://zenodo.org/record/'+uploadID+'/files/') - out+=line + line = line.replace( + 'js/', 'https://zenodo.org/record/'+uploadID+'/files/') + out += line - print 'writing index.html to',os.path.join(htmlDir,'zenodo') - f=open('0_index.html','w') + print 'writing index.html to', os.path.join(htmlDir, 'zenodo') + f = open('0_index.html', 'w') f.write(out) f.close() -def edit_icb_html_files(htmlDir,uploadID): + +def edit_icb_html_files(htmlDir, uploadID): # https://zenodo.org/record/48768/files/README.txt - os.chdir(os.path.join(htmlDir,'zenodo')) + os.chdir(os.path.join(htmlDir, 'zenodo')) for file in glob.glob('*event*html'): - out='' + out = '' for line in open(file): if 'src="http://molsoft.com/lib/acticm.js">' in line: - line=line.replace('src="http://molsoft.com/lib/acticm.js">','src="https://molsoft.com/lib/acticm.js">') + line = line.replace('src="http://molsoft.com/lib/acticm.js">', + 'src="https://molsoft.com/lib/acticm.js">') if '../mapImages/' in line: - line=line.replace('../mapImages/','https://zenodo.org/record/'+uploadID+'/files/') + line = line.replace( + '../mapImages/', 'https://zenodo.org/record/'+uploadID+'/files/') if '../compoundImages/' in line: - line=line.replace('../compoundImages/','https://zenodo.org/record/'+uploadID+'/files/') + line = line.replace( + '../compoundImages/', 'https://zenodo.org/record/'+uploadID+'/files/') if ' act.projectFile = "' in line: - line=line.replace(' act.projectFile = "',' act.projectFile = "https://zenodo.org/record/'+uploadID+'/files/') - out+=line - print 'updating',file - f=open(file,'w') + line = line.replace( + ' act.projectFile = "', ' act.projectFile = "https://zenodo.org/record/'+uploadID+'/files/') + out += line + print 'updating', file + f = open(file, 'w') f.write(out) f.close() -if __name__=='__main__': +if __name__ == '__main__': print len(sys.argv) if len(sys.argv) == 2: - htmlDir=sys.argv[1] + htmlDir = sys.argv[1] if os.path.isdir(htmlDir): copy_files(htmlDir) elif len(sys.argv) == 3: - htmlDir=sys.argv[1] - uploadID=sys.argv[2] + htmlDir = sys.argv[1] + uploadID = sys.argv[2] if os.path.isdir(htmlDir): - edit_index_html(htmlDir,uploadID) - edit_icb_html_files(htmlDir,uploadID) + edit_index_html(htmlDir, uploadID) + edit_icb_html_files(htmlDir, uploadID) else: print 'wrong input!' diff --git a/helpers/reset_interesting_datasets.py b/helpers/reset_interesting_datasets.py index 9f89959c..f9589354 100755 --- a/helpers/reset_interesting_datasets.py +++ b/helpers/reset_interesting_datasets.py @@ -1,11 +1,13 @@ # last edited: 01/03/2017, 15:00 -import os,glob +import os +import glob import sys + def relink_interesting_datasets(panddaDir): - os.chdir(os.path.join(panddaDir,'interesting_datasets')) - dirList=[] + os.chdir(os.path.join(panddaDir, 'interesting_datasets')) + dirList = [] for dirs in glob.glob('*'): if os.path.isdir(dirs): dirList.append(dirs) @@ -16,23 +18,26 @@ def relink_interesting_datasets(panddaDir): print 'ln -s ../processed_datasets/{0!s} .'.format(dirs) os.system('ln -s ../processed_datasets/{0!s} .'.format(dirs)) + def check_interesting_datasets(panddaDir): - os.chdir(os.path.join(panddaDir,'interesting_datasets')) + os.chdir(os.path.join(panddaDir, 'interesting_datasets')) for xtal in sorted(glob.glob('*')): if not os.path.islink(xtal): -# print xtal -# print os.path.join(panddaDir,'interesting_datasets',xtal,'modelled_structures',xtal+'-pandda-model.pdb') - if os.path.isfile(os.path.join(panddaDir,'interesting_datasets',xtal,'modelled_structures',xtal+'-pandda-model.pdb')): - print 'mv --backup=numbered {0!s} {1!s}'.format(os.path.join(panddaDir,'interesting_datasets',xtal,'modelled_structures'), os.path.join(panddaDir,'processed_datasets',xtal)) - os.system('mv --backup=numbered {0!s} {1!s}'.format(os.path.join(panddaDir,'interesting_datasets',xtal,'modelled_structures'), os.path.join(panddaDir,'processed_datasets',xtal))) - print 'cp {0!s} {1!s}'.format(os.path.join(panddaDir,'interesting_datasets',xtal,'*params'), os.path.join(panddaDir,'processed_datasets',xtal)) - os.system('cp {0!s} {1!s}'.format(os.path.join(panddaDir,'interesting_datasets',xtal,'*params'), os.path.join(panddaDir,'processed_datasets',xtal))) - - - - -if __name__=='__main__': - panddaDir=sys.argv[1] + # print xtal + # print os.path.join(panddaDir,'interesting_datasets',xtal,'modelled_structures',xtal+'-pandda-model.pdb') + if os.path.isfile(os.path.join(panddaDir, 'interesting_datasets', xtal, 'modelled_structures', xtal+'-pandda-model.pdb')): + print 'mv --backup=numbered {0!s} {1!s}'.format(os.path.join( + panddaDir, 'interesting_datasets', xtal, 'modelled_structures'), os.path.join(panddaDir, 'processed_datasets', xtal)) + os.system('mv --backup=numbered {0!s} {1!s}'.format(os.path.join(panddaDir, 'interesting_datasets', + xtal, 'modelled_structures'), os.path.join(panddaDir, 'processed_datasets', xtal))) + print 'cp {0!s} {1!s}'.format(os.path.join( + panddaDir, 'interesting_datasets', xtal, '*params'), os.path.join(panddaDir, 'processed_datasets', xtal)) + os.system('cp {0!s} {1!s}'.format(os.path.join(panddaDir, 'interesting_datasets', + xtal, '*params'), os.path.join(panddaDir, 'processed_datasets', xtal))) + + +if __name__ == '__main__': + panddaDir = sys.argv[1] check_interesting_datasets(panddaDir) - relink_interesting_datasets(panddaDir) \ No newline at end of file + relink_interesting_datasets(panddaDir) diff --git a/helpers/reset_occupancy_protein_to_one.py b/helpers/reset_occupancy_protein_to_one.py index 1d87fc39..01f42e10 100644 --- a/helpers/reset_occupancy_protein_to_one.py +++ b/helpers/reset_occupancy_protein_to_one.py @@ -1,31 +1,33 @@ -import glob,os +import glob +import os import sys + def reset_residues(projectDir): - for dirs in glob.glob(os.path.join(projectDir,'*')): + for dirs in glob.glob(os.path.join(projectDir, '*')): xtal = dirs[dirs.rfind('/')+1:] os.chdir(dirs) for mol in toEdit: if os.path.isfile(mol): if not os.path.isfile(mol+'_original'): - os.system('/bin/cp %s %s' %(mol,mol+'_original')) - print '%s: found %s' %(xtal,mol) + os.system('/bin/cp %s %s' % (mol, mol+'_original')) + print '%s: found %s' % (xtal, mol) out = '' changeResi = None for line in open(mol): if line.startswith('ATOM'): - chainID=str(line[21:23]).replace(' ','') - resseq=str(line[23:26]).replace(' ','') - occupancy=str(line[56:60]).replace(' ','') - altLoc=str(line[16:17]).replace(' ','') + chainID = str(line[21:23]).replace(' ', '') + resseq = str(line[23:26]).replace(' ', '') + occupancy = str(line[56:60]).replace(' ', '') + altLoc = str(line[16:17]).replace(' ', '') if altLoc != '': out += line else: out += line[:56] + '1.00' + line[60:] else: out += line - print 'saving file',mol,'...' - newFile = open(mol,'w') + print 'saving file', mol, '...' + newFile = open(mol, 'w') newFile.write(out) newFile.close() diff --git a/helpers/reset_to_last_successful_refinement.py b/helpers/reset_to_last_successful_refinement.py index 152a2f38..57c7a6ae 100644 --- a/helpers/reset_to_last_successful_refinement.py +++ b/helpers/reset_to_last_successful_refinement.py @@ -1,55 +1,59 @@ -import os,glob +import os +import glob import sys + def find_refine_folder(projectDir): - for xtalDir in sorted(glob.glob(os.path.join(projectDir,'*'))): + for xtalDir in sorted(glob.glob(os.path.join(projectDir, '*'))): xtal = xtalDir[xtalDir.rfind('/')+1:] os.chdir(xtalDir) dirList = [] for dirs in sorted(glob.glob('*')): if dirs.startswith('Refine_') and os.path.isdir(dirs): if not os.path.isfile('refine.pdb'): - dirList.append([dirs,os.path.getctime(dirs)]) + dirList.append([dirs, os.path.getctime(dirs)]) if dirList != []: find_refine_pdb(xtal, dirList) + def find_refine_pdb(xtal, dirList): - sorted_list = sorted(dirList, key=lambda x: x[1], reverse = True) + sorted_list = sorted(dirList, key=lambda x: x[1], reverse=True) foundRefinePDB = False for d in sorted_list: serial = int(d[0].split('_')[1]) - if os.path.isfile(os.path.join(d[0],'refine.pdb')): + if os.path.isfile(os.path.join(d[0], 'refine.pdb')): print xtal + ': found refine.pdb in ' + d[0] - pdbLink = os.path.join(d[0],'refine.pdb') - mtzLink = os.path.join(d[0],'refine.mtz') + pdbLink = os.path.join(d[0], 'refine.pdb') + mtzLink = os.path.join(d[0], 'refine.mtz') foundRefinePDB = True break - elif os.path.isfile(os.path.join(d[0],'refine_%s.pdb' %str(serial))): - print xtal + ': found refine_%s.pdb in %s' %(str(serial),d[0]) + elif os.path.isfile(os.path.join(d[0], 'refine_%s.pdb' % str(serial))): + print xtal + ': found refine_%s.pdb in %s' % (str(serial), d[0]) foundRefinePDB = True - pdbLink = os.path.join(d[0],'refine_%s.pdb' %str(serial)) - mtzLink = os.path.join(d[0],'refine_%s.mtz' %str(serial)) + pdbLink = os.path.join(d[0], 'refine_%s.pdb' % str(serial)) + mtzLink = os.path.join(d[0], 'refine_%s.mtz' % str(serial)) break if not foundRefinePDB: print xtal + ': ERROR -> cannot find refine.pdb' else: - print os.getcwd(),pdbLink, mtzLink + print os.getcwd(), pdbLink, mtzLink reset_links(xtal, pdbLink, mtzLink) + def find_pandda_refine_pdb(xtal, dirList): print 'hallp' + def reset_links(xtal, pdbLink, mtzLink): print xtal + ': resetting links...' os.system('/bin/rm refine.pdb') os.system('/bin/rm refine.mtz') os.system('/bin/rm refine.split.bound-state.pdb') - os.system('ln -s %s refine.pdb' %pdbLink) - os.system('ln -s %s refine.mtz' %mtzLink) + os.system('ln -s %s refine.pdb' % pdbLink) + os.system('ln -s %s refine.mtz' % mtzLink) os.system('ln -s refine.pdb refine.split.bound-state.pdb') - if __name__ == '__main__': projectDir = sys.argv[1] - find_refine_folder(projectDir) \ No newline at end of file + find_refine_folder(projectDir) diff --git a/helpers/resort_ligand_atoms.py b/helpers/resort_ligand_atoms.py index 59d8d05a..c271ed58 100755 --- a/helpers/resort_ligand_atoms.py +++ b/helpers/resort_ligand_atoms.py @@ -1,80 +1,83 @@ # last edited: 07/06/2017, 17:00 -import os,sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) +import os +import sys +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + def get_atom_order_of_ensemble_model(ensembleModel): - ligandResnames = ['LIG','FRS','DRG','UNL'] + ligandResnames = ['LIG', 'FRS', 'DRG', 'UNL'] ensembleLIGdir = {} for line in open(ensembleModel): if line.startswith('ATOM') or line.startswith('HETATM'): - atomName_line= str(line[11:16]) - altLoc_line= str(line[16:17]) - resname_line= str(line[17:20]) - chainID_line= str(line[20:23]) - resseq_line= str(line[23:26]) - - residueID = resname_line.replace(' ','')+'-'+\ - chainID_line.replace(' ','')+'-'+\ - resseq_line.replace(' ','')+'-'+\ - chainID_line.replace(' ','')+'-'+\ - altLoc_line + atomName_line = str(line[11:16]) + altLoc_line = str(line[16:17]) + resname_line = str(line[17:20]) + chainID_line = str(line[20:23]) + resseq_line = str(line[23:26]) + + residueID = resname_line.replace(' ', '')+'-' +\ + chainID_line.replace(' ', '')+'-' +\ + resseq_line.replace(' ', '')+'-' +\ + chainID_line.replace(' ', '')+'-' +\ + altLoc_line if resname_line in ligandResnames: if residueID not in ensembleLIGdir: - ensembleLIGdir[residueID]=[] - ensembleLIGdir[residueID].append([atomName_line,altLoc_line,resname_line,chainID_line,resseq_line]) + ensembleLIGdir[residueID] = [] + ensembleLIGdir[residueID].append( + [atomName_line, altLoc_line, resname_line, chainID_line, resseq_line]) return ensembleLIGdir -def resort_ligand_atoms_in_refined_model(refinedModel,ensembleLIGdir): - ligandResnames = ['LIG','FRS','DRG','UNL'] - out='' - refineLIGDir={} - LIGlineAdditional='' - LIGlist=[] + +def resort_ligand_atoms_in_refined_model(refinedModel, ensembleLIGdir): + ligandResnames = ['LIG', 'FRS', 'DRG', 'UNL'] + out = '' + refineLIGDir = {} + LIGlineAdditional = '' + LIGlist = [] for line in open(refinedModel): if line.startswith('ATOM') or line.startswith('HETATM'): - altLoc_line= str(line[16:17]) - resname_line= str(line[17:20]) - chainID_line= str(line[20:23]) - resseq_line= str(line[23:26]) + altLoc_line = str(line[16:17]) + resname_line = str(line[17:20]) + chainID_line = str(line[20:23]) + resseq_line = str(line[23:26]) - residueID = resname_line.replace(' ','')+'-'+\ - chainID_line.replace(' ','')+'-'+\ - resseq_line.replace(' ','')+'-'+\ - chainID_line.replace(' ','')+'-'+\ - altLoc_line + residueID = resname_line.replace(' ', '')+'-' +\ + chainID_line.replace(' ', '')+'-' +\ + resseq_line.replace(' ', '')+'-' +\ + chainID_line.replace(' ', '')+'-' +\ + altLoc_line if residueID in ensembleLIGdir: if residueID not in refineLIGDir: - refineLIGDir[residueID]=[] + refineLIGDir[residueID] = [] else: # if a ligand was for modelled after pandda.inspect - LIGlineAdditional+=line + LIGlineAdditional += line refineLIGDir[residueID].append(line) - - LIGline='' + LIGline = '' for ligand in ensembleLIGdir: for atomLine in ensembleLIGdir[ligand]: - atomName=atomLine[0] + atomName = atomLine[0] for line in refineLIGDir[ligand]: - atomName_line=str(line[11:16]) - if atomName_line==atom: - LIGline+=line + atomName_line = str(line[11:16]) + if atomName_line == atom: + LIGline += line break for line in open(refinedModel): if line.startswith('ATOM') or line.startswith('HETATM'): - resname_line= str(line[17:20]) + resname_line = str(line[17:20]) if resname_line in ligandResnames: continue else: - out+=line + out += line elif line.startswith('END'): continue @@ -83,20 +86,20 @@ def resort_ligand_atoms_in_refined_model(refinedModel,ensembleLIGdir): continue else: - out+=line + out += line - out+=LIGline - out+='END\n' + out += LIGline + out += 'END\n' - os.system('/bin/mv %s %s' %(refinedModel,refinedModel.replace('.pdb','_original_atom_order.pdb'))) - f=open(refinedModel,'w') + os.system('/bin/mv %s %s' % (refinedModel, + refinedModel.replace('.pdb', '_original_atom_order.pdb'))) + f = open(refinedModel, 'w') f.write(out) f.close() - -if __name__=='__main__': - ensembleModel=sys.argv[1] - refinedModel=sys.argv[2] - ensembleLIGdir=get_atom_order_of_ensemble_model(ensembleModel) - resort_ligand_atoms_in_refined_model(refinedModel,ensembleLIGdir) \ No newline at end of file +if __name__ == '__main__': + ensembleModel = sys.argv[1] + refinedModel = sys.argv[2] + ensembleLIGdir = get_atom_order_of_ensemble_model(ensembleModel) + resort_ligand_atoms_in_refined_model(refinedModel, ensembleLIGdir) diff --git a/helpers/select_ground_state_dataset.py b/helpers/select_ground_state_dataset.py index 0527cf14..afc1d0c3 100755 --- a/helpers/select_ground_state_dataset.py +++ b/helpers/select_ground_state_dataset.py @@ -1,11 +1,11 @@ # last edited: 03/08/2017, 15:00 -import os,sys -import glob -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) - -from XChemUtils import parse from XChemUtils import mtztools +from XChemUtils import parse +import os +import sys +import glob +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) # - select datasets with highest resolution @@ -14,78 +14,91 @@ def find_highest_resolution_datasets(panddaDir): - found=False - datasetList=[] - for logFile in glob.glob(os.path.join(panddaDir,'logs','*.log')): - for n,line in enumerate(open(logFile)): + found = False + datasetList = [] + for logFile in glob.glob(os.path.join(panddaDir, 'logs', '*.log')): + for n, line in enumerate(open(logFile)): if line.startswith('Statistical Electron Density Characterisation') and len(line.split()) == 6: - resolution=line.split()[5] - found=True - foundLine=n - if found and n>=foundLine+3: + resolution = line.split()[5] + found = True + foundLine = n + if found and n >= foundLine+3: if line.startswith('---'): break else: - tmpLine=line.replace(' ','').replace('\t','').replace('\n','').replace('\r','') + tmpLine = line.replace(' ', '').replace( + '\t', '').replace('\n', '').replace('\r', '') for item in tmpLine.split(','): if item != '': datasetList.append(item) print datasetList return datasetList -def get_datasets_without_event_map(panddaDir,datasetList): - datasetListwithoutEvent=[] + +def get_datasets_without_event_map(panddaDir, datasetList): + datasetListwithoutEvent = [] for dataset in datasetList: - noEvent=True - for files in glob.glob(os.path.join(panddaDir,'processed_datasets',dataset,'*')): + noEvent = True + for files in glob.glob(os.path.join(panddaDir, 'processed_datasets', dataset, '*')): if 'event' in files: - noEvent=False + noEvent = False break if noEvent: datasetListwithoutEvent.append(dataset) print datasetListwithoutEvent return datasetListwithoutEvent -def select_dataset_with_lowest_Rfree(panddaDir,datasetListwithoutEvent): - datasetList=[] - lowestRfree='' + +def select_dataset_with_lowest_Rfree(panddaDir, datasetListwithoutEvent): + datasetList = [] + lowestRfree = '' for dataset in datasetListwithoutEvent: - if os.path.isfile(os.path.join(panddaDir,'processed_datasets',dataset,dataset+'-pandda-input.pdb')): - stats=parse().PDBheader(os.path.join(panddaDir,'processed_datasets',dataset,dataset+'-pandda-input.pdb')) - Rfree=stats['Rfree'] + if os.path.isfile(os.path.join(panddaDir, 'processed_datasets', dataset, dataset+'-pandda-input.pdb')): + stats = parse().PDBheader(os.path.join( + panddaDir, 'processed_datasets', dataset, dataset+'-pandda-input.pdb')) + Rfree = stats['Rfree'] try: - print dataset,Rfree,stats['ResolutionHigh'] - datasetList.append([dataset,float(Rfree)]) + print dataset, Rfree, stats['ResolutionHigh'] + datasetList.append([dataset, float(Rfree)]) except ValueError: pass if datasetList: - lowestRfree=min(datasetList,key=lambda x: x[1])[0] + lowestRfree = min(datasetList, key=lambda x: x[1])[0] return lowestRfree -def link_pdb_mtz_files(panddaDir,lowestRfree): - targetDir='/'.join(panddaDir.split('/')[:len(panddaDir.split('/'))-1]) - panddaFolder=panddaDir.split('/')[len(panddaDir.split('/'))-1] + +def link_pdb_mtz_files(panddaDir, lowestRfree): + targetDir = '/'.join(panddaDir.split('/')[:len(panddaDir.split('/'))-1]) + panddaFolder = panddaDir.split('/')[len(panddaDir.split('/'))-1] print targetDir print panddaFolder os.chdir(targetDir) - if os.path.isfile(os.path.join(panddaDir,'processed_datasets',lowestRfree,lowestRfree+'-pandda-input.pdb')): - os.system('/bin/rm %s-ground-state.pdb 2> /dev/null' %lowestRfree) - os.symlink(os.path.join(panddaFolder,'processed_datasets',lowestRfree,lowestRfree+'-pandda-input.pdb'),lowestRfree+'-ground-state.pdb') - if os.path.isfile(os.path.join(panddaDir,'processed_datasets',lowestRfree,lowestRfree+'-pandda-input.mtz')): - os.system('/bin/rm %s-ground-state.free.mtz 2> /dev/null' %lowestRfree) - os.symlink(os.path.join(panddaFolder,'processed_datasets',lowestRfree,lowestRfree+'-pandda-input.mtz'),lowestRfree+'-ground-state.free.mtz') + if os.path.isfile(os.path.join(panddaDir, 'processed_datasets', lowestRfree, lowestRfree+'-pandda-input.pdb')): + os.system('/bin/rm %s-ground-state.pdb 2> /dev/null' % lowestRfree) + os.symlink(os.path.join(panddaFolder, 'processed_datasets', lowestRfree, + lowestRfree+'-pandda-input.pdb'), lowestRfree+'-ground-state.pdb') + if os.path.isfile(os.path.join(panddaDir, 'processed_datasets', lowestRfree, lowestRfree+'-pandda-input.mtz')): + os.system('/bin/rm %s-ground-state.free.mtz 2> /dev/null' % + lowestRfree) + os.symlink(os.path.join(panddaFolder, 'processed_datasets', lowestRfree, + lowestRfree+'-pandda-input.mtz'), lowestRfree+'-ground-state.free.mtz') - if os.path.isfile(os.path.join(panddaDir,'processed_datasets',lowestRfree,lowestRfree+'-ground-state-mean-map.native.ccp4')): - os.system('/bin/rm %s-ground-state-mean-map.native.ccp4 2> /dev/null' %lowestRfree) - os.symlink(os.path.join(panddaFolder,'processed_datasets',lowestRfree,lowestRfree+'-ground-state-mean-map.native.ccp4'),lowestRfree+'-ground-state-mean-map.native.ccp4') - elif os.path.isfile(os.path.join(panddaDir,'processed_datasets',lowestRfree,lowestRfree+'-ground-state-average-map.native.ccp4')): - os.system('/bin/rm %s-ground-state-mean-map.native.ccp4 2> /dev/null' %lowestRfree) - os.symlink(os.path.join(panddaFolder,'processed_datasets',lowestRfree,lowestRfree+'-ground-state-average-map.native.ccp4'),lowestRfree+'-ground-state-mean-map.native.ccp4') + if os.path.isfile(os.path.join(panddaDir, 'processed_datasets', lowestRfree, lowestRfree+'-ground-state-mean-map.native.ccp4')): + os.system( + '/bin/rm %s-ground-state-mean-map.native.ccp4 2> /dev/null' % lowestRfree) + os.symlink(os.path.join(panddaFolder, 'processed_datasets', lowestRfree, lowestRfree + + '-ground-state-mean-map.native.ccp4'), lowestRfree+'-ground-state-mean-map.native.ccp4') + elif os.path.isfile(os.path.join(panddaDir, 'processed_datasets', lowestRfree, lowestRfree+'-ground-state-average-map.native.ccp4')): + os.system( + '/bin/rm %s-ground-state-mean-map.native.ccp4 2> /dev/null' % lowestRfree) + os.symlink(os.path.join(panddaFolder, 'processed_datasets', lowestRfree, lowestRfree + + '-ground-state-average-map.native.ccp4'), lowestRfree+'-ground-state-mean-map.native.ccp4') - convert_mean_map_to_mtz(lowestRfree+'-ground-state-mean-map.native.ccp4',lowestRfree+'-ground-state.free.mtz') + convert_mean_map_to_mtz( + lowestRfree+'-ground-state-mean-map.native.ccp4', lowestRfree+'-ground-state.free.mtz') -def convert_mean_map_to_mtz(emap,mtz): +def convert_mean_map_to_mtz(emap, mtz): print 'converting ground-state-mean-map to MTZ' cmd = ('mapmask MAPIN %s MAPOUT %s << eof\n' % (emap, emap.replace('.ccp4', '.P1.ccp4')) + ' XYZLIM CELL\n' @@ -94,18 +107,21 @@ def convert_mean_map_to_mtz(emap,mtz): 'eof\n') print cmd os.system(cmd) - print '--->',mtz + print '--->', mtz reso = mtztools(mtz).get_dmin() - print '-> resolution:',reso + print '-> resolution:', reso cmd = ('module load phenix\n' 'phenix.map_to_structure_factors %s d_min=%s\n' % (emap.replace('.ccp4', '.P1.ccp4'), reso) + '/bin/mv map_to_structure_factors.mtz %s' % emap.replace('.ccp4', '.mtz')) print cmd os.system(cmd) -if __name__=='__main__': - panddaDir=sys.argv[1] - datasetList=find_highest_resolution_datasets(panddaDir) - datasetListwithoutEvent=get_datasets_without_event_map(panddaDir,datasetList) - lowestRfree=select_dataset_with_lowest_Rfree(panddaDir,datasetListwithoutEvent) - link_pdb_mtz_files(panddaDir,lowestRfree) + +if __name__ == '__main__': + panddaDir = sys.argv[1] + datasetList = find_highest_resolution_datasets(panddaDir) + datasetListwithoutEvent = get_datasets_without_event_map( + panddaDir, datasetList) + lowestRfree = select_dataset_with_lowest_Rfree( + panddaDir, datasetListwithoutEvent) + link_pdb_mtz_files(panddaDir, lowestRfree) diff --git a/helpers/update_data_source_after_refinement.py b/helpers/update_data_source_after_refinement.py index 4dffe008..1715e59f 100755 --- a/helpers/update_data_source_after_refinement.py +++ b/helpers/update_data_source_after_refinement.py @@ -1,61 +1,67 @@ # last edited: 27/07/2016, 17:00 -import os,sys -import glob -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) - -from XChemUtils import parse -from XChemUtils import pdbtools -from XChemUtils import misc -from XChemUtils import pdbtools_gemmi -from XChemUtils import maptools -import XChemDB import csv +import XChemDB +from XChemUtils import maptools +from XChemUtils import pdbtools_gemmi +from XChemUtils import misc +from XChemUtils import pdbtools +from XChemUtils import parse +import os +import sys +import glob +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) -def parse_pdb(inital_model_directory,xtal,db_dict): - if os.path.isfile(os.path.join(inital_model_directory,xtal,'refine.pdb')): - db_dict['RefinementPDB_latest']=os.path.realpath(os.path.join(inital_model_directory,xtal,'refine.pdb')) - pdb=parse().PDBheader(os.path.join(inital_model_directory,xtal,'refine.pdb')) - db_dict['RefinementRcryst'] = pdb['Rcryst'] - db_dict['RefinementRcrystTraficLight'] = pdb['RcrystTL'] - db_dict['RefinementRfree']= pdb['Rfree'] - db_dict['RefinementRfreeTraficLight'] = pdb['RfreeTL'] - db_dict['RefinementRmsdBonds'] = pdb['rmsdBonds'] - db_dict['RefinementRmsdBondsTL'] = pdb['rmsdBondsTL'] - db_dict['RefinementRmsdAngles'] = pdb['rmsdAngles'] - db_dict['RefinementRmsdAnglesTL'] = pdb['rmsdAnglesTL'] - db_dict['RefinementSpaceGroup'] = pdb['SpaceGroup'] - db_dict['RefinementResolution'] = pdb['ResolutionHigh'] - db_dict['RefinementResolutionTL'] = pdb['ResolutionColor'] - db_dict['RefinementStatus'] = 'finished' +def parse_pdb(inital_model_directory, xtal, db_dict): + if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.pdb')): + db_dict['RefinementPDB_latest'] = os.path.realpath( + os.path.join(inital_model_directory, xtal, 'refine.pdb')) + pdb = parse().PDBheader(os.path.join(inital_model_directory, xtal, 'refine.pdb')) + db_dict['RefinementRcryst'] = pdb['Rcryst'] + db_dict['RefinementRcrystTraficLight'] = pdb['RcrystTL'] + db_dict['RefinementRfree'] = pdb['Rfree'] + db_dict['RefinementRfreeTraficLight'] = pdb['RfreeTL'] + db_dict['RefinementRmsdBonds'] = pdb['rmsdBonds'] + db_dict['RefinementRmsdBondsTL'] = pdb['rmsdBondsTL'] + db_dict['RefinementRmsdAngles'] = pdb['rmsdAngles'] + db_dict['RefinementRmsdAnglesTL'] = pdb['rmsdAnglesTL'] + db_dict['RefinementSpaceGroup'] = pdb['SpaceGroup'] + db_dict['RefinementResolution'] = pdb['ResolutionHigh'] + db_dict['RefinementResolutionTL'] = pdb['ResolutionColor'] + db_dict['RefinementStatus'] = 'finished' else: - db_dict['RefinementStatus'] = 'failed' - - - if os.path.isfile(os.path.join(inital_model_directory,xtal,'refine.bound.pdb')): - db_dict['RefinementBoundConformation']=os.path.realpath(os.path.join(inital_model_directory,xtal,'refine.bound.pdb')) - elif os.path.isfile(os.path.join(inital_model_directory,xtal,'refine.split.bound-state.pdb')): - db_dict['RefinementBoundConformation']=os.path.realpath(os.path.join(inital_model_directory,xtal,'refine.split.bound-state.pdb')) - elif os.path.isfile(os.path.join(inital_model_directory,xtal,'refine.pdb')): - db_dict['RefinementBoundConformation']=os.path.realpath(os.path.join(inital_model_directory,xtal,'refine.pdb')) + db_dict['RefinementStatus'] = 'failed' + + if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.bound.pdb')): + db_dict['RefinementBoundConformation'] = os.path.realpath( + os.path.join(inital_model_directory, xtal, 'refine.bound.pdb')) + elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.split.bound-state.pdb')): + db_dict['RefinementBoundConformation'] = os.path.realpath( + os.path.join(inital_model_directory, xtal, 'refine.split.bound-state.pdb')) + elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.pdb')): + db_dict['RefinementBoundConformation'] = os.path.realpath( + os.path.join(inital_model_directory, xtal, 'refine.pdb')) print db_dict return db_dict -def parse_mtz(inital_model_directory,xtal,db_dict): - if os.path.isfile(os.path.join(inital_model_directory,xtal,'refine.mtz')): - db_dict['RefinementMTZ_latest']=os.path.realpath(os.path.join(inital_model_directory,xtal,'refine.mtz')) + +def parse_mtz(inital_model_directory, xtal, db_dict): + if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.mtz')): + db_dict['RefinementMTZ_latest'] = os.path.realpath( + os.path.join(inital_model_directory, xtal, 'refine.mtz')) return db_dict -def check_refmac_matrix_weight(refinement_directory,db_dict): - if os.path.isfile(os.path.join(refinement_directory,'refmac.log')): - logFile=os.path.join(refinement_directory,'refmac.log') + +def check_refmac_matrix_weight(refinement_directory, db_dict): + if os.path.isfile(os.path.join(refinement_directory, 'refmac.log')): + logFile = os.path.join(refinement_directory, 'refmac.log') else: - logFile='' - for files in glob.glob(os.path.join(refinement_directory,'*refine.log')): - logFile=files + logFile = '' + for files in glob.glob(os.path.join(refinement_directory, '*refine.log')): + logFile = files break if os.path.isfile(logFile): for line in open(logFile): @@ -63,13 +69,14 @@ def check_refmac_matrix_weight(refinement_directory,db_dict): db_dict['RefinementMatrixWeight'] = line.split()[2] return db_dict -def check_refmac_logfile(refinement_directory,db_dict): - if os.path.isfile(os.path.join(refinement_directory,'refmac.log')): - logFile=os.path.join(refinement_directory,'refmac.log') + +def check_refmac_logfile(refinement_directory, db_dict): + if os.path.isfile(os.path.join(refinement_directory, 'refmac.log')): + logFile = os.path.join(refinement_directory, 'refmac.log') else: - logFile='' - for files in glob.glob(os.path.join(refinement_directory,'*refine.log')): - logFile=files + logFile = '' + for files in glob.glob(os.path.join(refinement_directory, '*refine.log')): + logFile = files break if os.path.isfile(logFile): for line in open(logFile): @@ -77,9 +84,10 @@ def check_refmac_logfile(refinement_directory,db_dict): db_dict['RefinementStatus'] = 'CIF problem' return db_dict -def parse_molprobity_output(inital_model_directory,xtal,db_dict): - if os.path.isfile(os.path.join(inital_model_directory,xtal,'validation_summary.txt')): - for line in open(os.path.join(inital_model_directory,xtal,'validation_summary.txt')): + +def parse_molprobity_output(inital_model_directory, xtal, db_dict): + if os.path.isfile(os.path.join(inital_model_directory, xtal, 'validation_summary.txt')): + for line in open(os.path.join(inital_model_directory, xtal, 'validation_summary.txt')): if 'molprobity score' in line.lower(): if len(line.split()) >= 4: db_dict['RefinementMolProbityScore'] = line.split()[3] @@ -114,35 +122,38 @@ def parse_molprobity_output(inital_model_directory,xtal,db_dict): return db_dict -def parse_ligand_validation(inital_model_directory,refinement_directory,xtal): +def parse_ligand_validation(inital_model_directory, refinement_directory, xtal): if os.path.isfile(os.path.join(refinement_directory, 'residue_scores.csv')): with open(os.path.join(refinement_directory, 'residue_scores.csv'), 'rb') as csv_import: csv_dict = csv.DictReader(csv_import) for i, line in enumerate(csv_dict): db_pandda_dict = {} - residue = line[''].replace(' ','') + residue = line[''].replace(' ', '') residueFilename = line[''] if len(residue.split('-')) == 2: -# residue_name = residue.split('-')[0] -# print residue_name + # residue_name = residue.split('-')[0] + # print residue_name residue_chain = residue.split('-')[0] residue_number = residue.split('-')[1] - residue_xyz = pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb')).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) - event = db.execute_statement("select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='{0!s}'".format(xtal)) + residue_xyz = pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb') + ).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) + event = db.execute_statement( + "select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='{0!s}'".format(xtal)) for coord in event: db_pandda_dict = {} event_x = float(str(coord[0])) event_y = float(str(coord[1])) event_z = float(str(coord[2])) site_index = str(coord[3]) - distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1],residue_xyz[2], - event_x, event_y,event_z) - print 'distance',distance + distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1], residue_xyz[2], + event_x, event_y, event_z) + print 'distance', distance # if coordinate of ligand and event are closer than 7A, then we assume they belong together if distance < 7: db_pandda_dict['PANDDA_site_ligand_id'] = residue db_pandda_dict['PANDDA_site_occupancy'] = line['Occupancy'] - db_pandda_dict['PANDDA_site_B_average'] = line['Average B-factor (Residue)'] + db_pandda_dict['PANDDA_site_B_average'] = line[ + 'Average B-factor (Residue)'] db_pandda_dict['PANDDA_site_B_ratio_residue_surroundings'] = line['Surroundings B-factor Ratio'] db_pandda_dict['PANDDA_site_rmsd'] = line['Model RMSD'] db_pandda_dict['PANDDA_site_RSCC'] = line['RSCC'] @@ -157,31 +168,36 @@ def parse_ligand_validation(inital_model_directory,refinement_directory,xtal): if db_pandda_dict != {}: print '==> XCE: updating pandda Table of data source' - db.update_panddaTable(xtal, site_index, db_pandda_dict) + db.update_panddaTable( + xtal, site_index, db_pandda_dict) + -def update_ligand_information_in_panddaTable(inital_model_directory,xtal): +def update_ligand_information_in_panddaTable(inital_model_directory, xtal): if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.pdb')): -# ligands_in_file=pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb')).find_xce_ligand_details() - ligands_in_file=pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb')).get_residues_with_resname('LIG') + # ligands_in_file=pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb')).find_xce_ligand_details() + ligands_in_file = pdbtools(os.path.join( + inital_model_directory, xtal, 'refine.pdb')).get_residues_with_resname('LIG') for ligand in ligands_in_file: -# residue_name= ligand[0] -# residue_chain= ligand[1] -# residue_number= ligand[2] -# residue_altLoc= ligand[3] - residue_name= ligand[0] - residue_chain= ligand[2] - residue_number= ligand[1] + # residue_name= ligand[0] + # residue_chain= ligand[1] + # residue_number= ligand[2] + # residue_altLoc= ligand[3] + residue_name = ligand[0] + residue_chain = ligand[2] + residue_number = ligand[1] residue_altLoc = 'X' - residue_xyz = pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb')).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) - event = db.execute_statement("select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='{0!s}'".format(xtal)) + residue_xyz = pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb') + ).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) + event = db.execute_statement( + "select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='{0!s}'".format(xtal)) for coord in event: db_pandda_dict = {} event_x = float(str(coord[0])) event_y = float(str(coord[1])) event_z = float(str(coord[2])) site_index = str(coord[3]) - distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1],residue_xyz[2], - event_x, event_y,event_z) + distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1], residue_xyz[2], + event_x, event_y, event_z) # if coordinate of ligand and event are closer than 7A, then we assume they belong together if distance < 7: db_pandda_dict['PANDDA_site_ligand_resname'] = residue_name @@ -194,53 +210,62 @@ def update_ligand_information_in_panddaTable(inital_model_directory,xtal): db.update_panddaTable(xtal, site_index, db_pandda_dict) - def update_data_source(db_dict): if db_dict != {}: print '==> xce: updating mainTable of data source' - db.update_data_source(xtal,db_dict) + db.update_data_source(xtal, db_dict) # update refinement outcome if necessary sqlite = ( - "update mainTable set RefinementOutcome = '3 - In Refinement' where CrystalName is '{0!s}' ".format(xtal)+ + "update mainTable set RefinementOutcome = '3 - In Refinement' where CrystalName is '{0!s}' ".format(xtal) + "and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending' or RefinementOutcome is '2 - PANDDA model')" - ) + ) db.execute_statement(sqlite) # now do the same for each site in the pandda table sqlite = ( - "update panddaTable set RefinementOutcome = '3 - In Refinement' where CrystalName is '{0!s}' ".format(xtal)+ + "update panddaTable set RefinementOutcome = '3 - In Refinement' where CrystalName is '{0!s}' ".format(xtal) + "and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending' or RefinementOutcome is '2 - PANDDA model')" - ) + ) db.execute_statement(sqlite) -def update_buster_report_index_html(refinement_directory,db_dict): +def update_buster_report_index_html(refinement_directory, db_dict): if os.path.isfile(refinement_directory+'-report/index.html'): - db_dict['RefinementBusterReportHTML'] = refinement_directory+'-report/index.html' + db_dict['RefinementBusterReportHTML'] = refinement_directory + \ + '-report/index.html' return db_dict -def update_mmcif_file_location(refinement_directory,db_dict): - if os.path.isfile(os.path.join(refinement_directory,'BUSTER_model.cif')): - db_dict['RefinementMMCIFmodel_latest'] = os.path.join(refinement_directory,'BUSTER_model.cif') - if os.path.isfile(os.path.join(refinement_directory,'BUSTER_refln.cif')): - db_dict['RefinementMMCIFreflections_latest'] = os.path.join(refinement_directory,'BUSTER_refln.cif') + +def update_mmcif_file_location(refinement_directory, db_dict): + if os.path.isfile(os.path.join(refinement_directory, 'BUSTER_model.cif')): + db_dict['RefinementMMCIFmodel_latest'] = os.path.join( + refinement_directory, 'BUSTER_model.cif') + if os.path.isfile(os.path.join(refinement_directory, 'BUSTER_refln.cif')): + db_dict['RefinementMMCIFreflections_latest'] = os.path.join( + refinement_directory, 'BUSTER_refln.cif') return db_dict + def generate_cut_maps_around_ligand(xtal): if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.pdb')) and \ os.path.isfile(os.path.join(inital_model_directory, xtal, '2fofc.map')) and \ os.path.isfile(os.path.join(inital_model_directory, xtal, 'fofc.map')): - ligandDict = pdbtools_gemmi('refine.pdb').center_of_mass_ligand_dict('LIG') + ligandDict = pdbtools_gemmi( + 'refine.pdb').center_of_mass_ligand_dict('LIG') pdbtools_gemmi('refine.pdb').save_ligands_to_pdb('LIG') for ligand in ligandDict: - maptools().cut_map_around_ligand('2fofc.map',ligand+'.pdb','7') - os.system('/bin/mv 2fofc_mapmask.map %s_%s_2fofc_cut.ccp4' %(xtal,ligand)) - maptools().cut_map_around_ligand('fofc.map',ligand+'.pdb','7') - os.system('/bin/mv fofc_mapmask.map %s_%s_fofc_cut.ccp4' %(xtal,ligand)) + maptools().cut_map_around_ligand('2fofc.map', ligand+'.pdb', '7') + os.system('/bin/mv 2fofc_mapmask.map %s_%s_2fofc_cut.ccp4' % + (xtal, ligand)) + maptools().cut_map_around_ligand('fofc.map', ligand+'.pdb', '7') + os.system('/bin/mv fofc_mapmask.map %s_%s_fofc_cut.ccp4' % + (xtal, ligand)) + -def read_ligand_cc_from_edstats(xtal,db_dict): +def read_ligand_cc_from_edstats(xtal, db_dict): ligCC = '' if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.edstats')): - ligandDict = pdbtools_gemmi('refine.pdb').center_of_mass_ligand_dict('LIG') + ligandDict = pdbtools_gemmi( + 'refine.pdb').center_of_mass_ligand_dict('LIG') for ligand in ligandDict: lig = ligand.split('-')[0] chain = ligand.split('-')[1] @@ -256,32 +281,33 @@ def read_ligand_cc_from_edstats(xtal,db_dict): db_dict['RefinementLigandCC'] = ligCC.rstrip() return db_dict -if __name__=='__main__': - db_file=sys.argv[1] - xtal=sys.argv[2] - inital_model_directory=sys.argv[3] - refinement_directory=sys.argv[4] +if __name__ == '__main__': + + db_file = sys.argv[1] + xtal = sys.argv[2] + inital_model_directory = sys.argv[3] + refinement_directory = sys.argv[4] refiner = sys.argv[5] date = sys.argv[6] - db=XChemDB.data_source(db_file) - db_dict={} + db = XChemDB.data_source(db_file) + db_dict = {} db_dict['RefinementRefiner'] = refiner db_dict['RefinementDate'] = date - db_dict=parse_pdb(inital_model_directory,xtal,db_dict) - db_dict=parse_mtz(inital_model_directory,xtal,db_dict) - db_dict=check_refmac_matrix_weight(refinement_directory,db_dict) - db_dict=parse_molprobity_output(inital_model_directory,xtal,db_dict) - db_dict=check_refmac_logfile(refinement_directory,db_dict) - db_dict=update_buster_report_index_html(refinement_directory,db_dict) - db_dict=update_mmcif_file_location(refinement_directory,db_dict) - db_dict=read_ligand_cc_from_edstats(xtal,db_dict) - update_ligand_information_in_panddaTable(inital_model_directory,xtal) + db_dict = parse_pdb(inital_model_directory, xtal, db_dict) + db_dict = parse_mtz(inital_model_directory, xtal, db_dict) + db_dict = check_refmac_matrix_weight(refinement_directory, db_dict) + db_dict = parse_molprobity_output(inital_model_directory, xtal, db_dict) + db_dict = check_refmac_logfile(refinement_directory, db_dict) + db_dict = update_buster_report_index_html(refinement_directory, db_dict) + db_dict = update_mmcif_file_location(refinement_directory, db_dict) + db_dict = read_ligand_cc_from_edstats(xtal, db_dict) + update_ligand_information_in_panddaTable(inital_model_directory, xtal) - parse_ligand_validation(inital_model_directory,refinement_directory,xtal) + parse_ligand_validation(inital_model_directory, refinement_directory, xtal) update_data_source(db_dict) - generate_cut_maps_around_ligand(xtal) \ No newline at end of file + generate_cut_maps_around_ligand(xtal) diff --git a/helpers/update_data_source_for_new_cif_files.py b/helpers/update_data_source_for_new_cif_files.py index 6322d63c..3ee2dba1 100755 --- a/helpers/update_data_source_for_new_cif_files.py +++ b/helpers/update_data_source_for_new_cif_files.py @@ -1,28 +1,33 @@ # last edited: 22/11/2016, 15:00 -import os,sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) - -from XChemUtils import parse import XChemDB +from XChemUtils import parse +import os +import sys +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + -if __name__=='__main__': - db_file=sys.argv[1] - xtal=sys.argv[2] - initial_model_directory=sys.argv[3] - compoundID=sys.argv[4] +if __name__ == '__main__': + db_file = sys.argv[1] + xtal = sys.argv[2] + initial_model_directory = sys.argv[3] + compoundID = sys.argv[4] - db=XChemDB.data_source(db_file) - db_dict={} - if os.path.isfile(os.path.join(initial_model_directory,xtal,'compound',compoundID+'.cif')) and \ - os.path.getsize(os.path.join(initial_model_directory,xtal,'compound',compoundID+'.cif')) > 20 : - db_dict['RefinementCIF']=os.path.join(initial_model_directory,xtal,'compound',compoundID+'.cif') - db_dict['RefinementCIFStatus']='restraints generated' + db = XChemDB.data_source(db_file) + db_dict = {} + if os.path.isfile(os.path.join(initial_model_directory, xtal, 'compound', compoundID+'.cif')) and \ + os.path.getsize(os.path.join(initial_model_directory, xtal, 'compound', compoundID+'.cif')) > 20: + db_dict['RefinementCIF'] = os.path.join( + initial_model_directory, xtal, 'compound', compoundID+'.cif') + db_dict['RefinementCIFStatus'] = 'restraints generated' else: - db_dict['RefinementCIF']='' - db_dict['RefinementCIFStatus']='restraints failed' - os.system('/bin/rm '+os.path.join(initial_model_directory,xtal,compoundID.replace(' ','')+'.pdb')) - os.system('/bin/rm '+os.path.join(initial_model_directory,xtal,compoundID.replace(' ','')+'.cif')) - os.system('/bin/rm '+os.path.join(initial_model_directory,xtal,compoundID.replace(' ','')+'.png')) + db_dict['RefinementCIF'] = '' + db_dict['RefinementCIFStatus'] = 'restraints failed' + os.system('/bin/rm '+os.path.join(initial_model_directory, + xtal, compoundID.replace(' ', '')+'.pdb')) + os.system('/bin/rm '+os.path.join(initial_model_directory, + xtal, compoundID.replace(' ', '')+'.cif')) + os.system('/bin/rm '+os.path.join(initial_model_directory, + xtal, compoundID.replace(' ', '')+'.png')) - db.update_data_source(xtal,db_dict) \ No newline at end of file + db.update_data_source(xtal, db_dict) diff --git a/helpers/update_data_source_for_new_dimple_pdb.py b/helpers/update_data_source_for_new_dimple_pdb.py index c7614b6a..890396cd 100755 --- a/helpers/update_data_source_for_new_dimple_pdb.py +++ b/helpers/update_data_source_for_new_dimple_pdb.py @@ -1,36 +1,38 @@ # last edited: 15/11/2016, 15:00 -import os,sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) -import glob - -from iotbx import mtz - -from XChemUtils import parse import XChemDB - -if __name__=='__main__': - db_file=sys.argv[1] - xtal=sys.argv[2] - inital_model_directory=sys.argv[3] - - db=XChemDB.data_source(db_file) - if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple.pdb')): - db_dict= {'DimplePathToPDB': os.path.join(inital_model_directory, xtal, 'dimple.pdb')} - dimple_ran_successfully=False - if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple.mtz')): - db_dict['DimplePathToMTZ']=os.path.join(inital_model_directory,xtal,'dimple.mtz') - dimple_ran_successfully=True - db_dict['DataProcessingDimpleSuccessful']='True' +from XChemUtils import parse +from iotbx import mtz +import glob +import os +import sys +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + + +if __name__ == '__main__': + db_file = sys.argv[1] + xtal = sys.argv[2] + inital_model_directory = sys.argv[3] + + db = XChemDB.data_source(db_file) + if os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple.pdb')): + db_dict = {'DimplePathToPDB': os.path.join( + inital_model_directory, xtal, 'dimple.pdb')} + dimple_ran_successfully = False + if os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple.mtz')): + db_dict['DimplePathToMTZ'] = os.path.join( + inital_model_directory, xtal, 'dimple.mtz') + dimple_ran_successfully = True + db_dict['DataProcessingDimpleSuccessful'] = 'True' db_dict['DimpleStatus'] = 'finished' if not dimple_ran_successfully: - db_dict['DataProcessingDimpleSuccessful']='False' + db_dict['DataProcessingDimpleSuccessful'] = 'False' db_dict['DimpleStatus'] = 'failed' - pdb=parse().PDBheader(os.path.join(inital_model_directory,xtal,'dimple.pdb')) - db_dict['DimpleRcryst']=pdb['Rcryst'] - db_dict['DimpleRfree']=pdb['Rfree'] - db_dict['RefinementOutcome']='1 - Analysis Pending' - db_dict['RefinementSpaceGroup']=pdb['SpaceGroup'] + pdb = parse().PDBheader(os.path.join(inital_model_directory, xtal, 'dimple.pdb')) + db_dict['DimpleRcryst'] = pdb['Rcryst'] + db_dict['DimpleRfree'] = pdb['Rfree'] + db_dict['RefinementOutcome'] = '1 - Analysis Pending' + db_dict['RefinementSpaceGroup'] = pdb['SpaceGroup'] # if not os.path.isfile(xtal+'.free.mtz'): # os.chdir(os.path.join(inital_model_directory,xtal)) # os.system('/bin/rm '+xtal+'.free.mtz') @@ -43,39 +45,42 @@ # setting free.mtz file - os.chdir(os.path.join(inital_model_directory,xtal)) - os.system('/bin/rm -f %s.free.mtz' %xtal) + os.chdir(os.path.join(inital_model_directory, xtal)) + os.system('/bin/rm -f %s.free.mtz' % xtal) mtzFree = None db_dict['RefinementMTZfree'] = '' - if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz')): - mtzFree = os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz') - elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz')): - mtzFree = os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz') - elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple','prepared.mtz')): - mtzFree = os.path.join(inital_model_directory,xtal,'dimple','dimple','prepared.mtz') - elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple','prepared2.mtz')): - mtzFree = os.path.join(inital_model_directory,xtal,'dimple','dimple','prepared2.mtz') - elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','free.mtz')): - mtzFree = os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','free.mtz') - elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple','free.mtz')): - mtzFree = os.path.join(inital_model_directory,xtal,'dimple','dimple','free.mtz') + if os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple', 'dimple_rerun_on_selected_file', 'dimple', 'prepared2.mtz')): + mtzFree = os.path.join(inital_model_directory, xtal, 'dimple', + 'dimple_rerun_on_selected_file', 'dimple', 'prepared2.mtz') + elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple', 'dimple_rerun_on_selected_file', 'dimple', 'prepared.mtz')): + mtzFree = os.path.join(inital_model_directory, xtal, 'dimple', + 'dimple_rerun_on_selected_file', 'dimple', 'prepared.mtz') + elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple', 'dimple', 'prepared.mtz')): + mtzFree = os.path.join( + inital_model_directory, xtal, 'dimple', 'dimple', 'prepared.mtz') + elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple', 'dimple', 'prepared2.mtz')): + mtzFree = os.path.join( + inital_model_directory, xtal, 'dimple', 'dimple', 'prepared2.mtz') + elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple', 'dimple_rerun_on_selected_file', 'dimple', 'free.mtz')): + mtzFree = os.path.join(inital_model_directory, xtal, 'dimple', + 'dimple_rerun_on_selected_file', 'dimple', 'free.mtz') + elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple', 'dimple', 'free.mtz')): + mtzFree = os.path.join( + inital_model_directory, xtal, 'dimple', 'dimple', 'free.mtz') if mtzFree is not None: if 'F_unique' in mtz.object(mtzFree).column_labels(): - cmd = ( 'cad hklin1 %s hklout %s.free.mtz << eof\n' %(mtzFree,xtal) + - ' monitor BRIEF\n' - ' labin file 1 E1=F E2=SIGF E3=FreeR_flag\n' - ' labout file 1 E1=F E2=SIGF E3=FreeR_flag\n' - 'eof\n' ) + cmd = ('cad hklin1 %s hklout %s.free.mtz << eof\n' % (mtzFree, xtal) + + ' monitor BRIEF\n' + ' labin file 1 E1=F E2=SIGF E3=FreeR_flag\n' + ' labout file 1 E1=F E2=SIGF E3=FreeR_flag\n' + 'eof\n') os.system(cmd) else: - os.symlink(mtzFree,xtal+'.free.mtz') - - db_dict['RefinementMTZfree']=xtal+'.free.mtz' - - + os.symlink(mtzFree, xtal+'.free.mtz') + db_dict['RefinementMTZfree'] = xtal+'.free.mtz' # if no refinement was carried out yet, then we also want to link the dimple files to refine.pdb/refine.log # so that we can look at them with the COOT plugin @@ -95,13 +100,13 @@ # finally, update data source print '==> xce: updating data source after DIMPLE run' - db.update_data_source(xtal,db_dict) + db.update_data_source(xtal, db_dict) else: # the actual dimple script creates symbolic links regardless if dimple was successful or not # python os.path.isfile is False if symbolic link points to non existing file # so we remove all of them! - os.chdir(os.path.join(inital_model_directory,xtal)) + os.chdir(os.path.join(inital_model_directory, xtal)) os.system('/bin/rm dimple.pdb') os.system('/bin/rm dimple.mtz') os.system('/bin/rm 2fofc.map') diff --git a/helpers/update_data_source_for_new_dimple_twin_pdb.py b/helpers/update_data_source_for_new_dimple_twin_pdb.py index 09dcd219..d9e2f9f7 100755 --- a/helpers/update_data_source_for_new_dimple_twin_pdb.py +++ b/helpers/update_data_source_for_new_dimple_twin_pdb.py @@ -1,36 +1,38 @@ # last edited: 15/11/2016, 15:00 -import os,sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) -import glob - -from iotbx import mtz - -from XChemUtils import parse import XChemDB - -if __name__=='__main__': - db_file=sys.argv[1] - xtal=sys.argv[2] - inital_model_directory=sys.argv[3] - - db=XChemDB.data_source(db_file) - if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin.pdb')): - db_dict= {'DimpleTwinPathToPDB': os.path.join(inital_model_directory, xtal, 'dimple_twin.pdb')} - dimple_ran_successfully=False - if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin.mtz')): - db_dict['DimpleTwinPathToMTZ']=os.path.join(inital_model_directory,xtal,'dimple_twin.mtz') - dimple_ran_successfully=True - db_dict['DataProcessingDimpleTwinSuccessful']='True' +from XChemUtils import parse +from iotbx import mtz +import glob +import os +import sys +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + + +if __name__ == '__main__': + db_file = sys.argv[1] + xtal = sys.argv[2] + inital_model_directory = sys.argv[3] + + db = XChemDB.data_source(db_file) + if os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin.pdb')): + db_dict = {'DimpleTwinPathToPDB': os.path.join( + inital_model_directory, xtal, 'dimple_twin.pdb')} + dimple_ran_successfully = False + if os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin.mtz')): + db_dict['DimpleTwinPathToMTZ'] = os.path.join( + inital_model_directory, xtal, 'dimple_twin.mtz') + dimple_ran_successfully = True + db_dict['DataProcessingDimpleTwinSuccessful'] = 'True' db_dict['DimpleTwinStatus'] = 'finished' if not dimple_ran_successfully: - db_dict['DataProcessingDimpleTwinSuccessful']='False' + db_dict['DataProcessingDimpleTwinSuccessful'] = 'False' db_dict['DimpleTwinStatus'] = 'failed' - pdb=parse().PDBheader(os.path.join(inital_model_directory,xtal,'dimple_twin.pdb')) - db_dict['DimpleTwinRcryst']=pdb['Rcryst'] - db_dict['DimpleTwinRfree']=pdb['Rfree'] - db_dict['RefinementOutcome']='1 - Analysis Pending' - db_dict['RefinementSpaceGroup']=pdb['SpaceGroup'] + pdb = parse().PDBheader(os.path.join(inital_model_directory, xtal, 'dimple_twin.pdb')) + db_dict['DimpleTwinRcryst'] = pdb['Rcryst'] + db_dict['DimpleTwinRfree'] = pdb['Rfree'] + db_dict['RefinementOutcome'] = '1 - Analysis Pending' + db_dict['RefinementSpaceGroup'] = pdb['SpaceGroup'] db_dict['DimpleTwinFraction'] = pdb['TwinFraction'] # if not os.path.isfile(xtal+'.free.mtz'): # os.chdir(os.path.join(inital_model_directory,xtal)) @@ -44,39 +46,42 @@ # setting free.mtz file - os.chdir(os.path.join(inital_model_directory,xtal)) - os.system('/bin/rm -f %s.free.mtz' %xtal) + os.chdir(os.path.join(inital_model_directory, xtal)) + os.system('/bin/rm -f %s.free.mtz' % xtal) mtzFree = None db_dict['RefinementTwinMTZfree'] = '' - if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_rerun_on_selected_file','dimple_twin','prepared2.mtz')): - mtzFree = os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_rerun_on_selected_file','dimple_twin','prepared2.mtz') - elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_rerun_on_selected_file','dimple_twin','prepared.mtz')): - mtzFree = os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_rerun_on_selected_file','dimple_twin','prepared.mtz') - elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_twin','prepared.mtz')): - mtzFree = os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_twin','prepared.mtz') - elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_twin','prepared2.mtz')): - mtzFree = os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_twin','prepared2.mtz') - elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_rerun_on_selected_file','dimple_twin','free.mtz')): - mtzFree = os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_rerun_on_selected_file','dimple_twin','free.mtz') - elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_twin','free.mtz')): - mtzFree = os.path.join(inital_model_directory,xtal,'dimple_twin','dimple_twin','free.mtz') + if os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin', 'dimple_rerun_on_selected_file', 'dimple_twin', 'prepared2.mtz')): + mtzFree = os.path.join(inital_model_directory, xtal, 'dimple_twin', + 'dimple_rerun_on_selected_file', 'dimple_twin', 'prepared2.mtz') + elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin', 'dimple_rerun_on_selected_file', 'dimple_twin', 'prepared.mtz')): + mtzFree = os.path.join(inital_model_directory, xtal, 'dimple_twin', + 'dimple_rerun_on_selected_file', 'dimple_twin', 'prepared.mtz') + elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin', 'dimple_twin', 'prepared.mtz')): + mtzFree = os.path.join( + inital_model_directory, xtal, 'dimple_twin', 'dimple_twin', 'prepared.mtz') + elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin', 'dimple_twin', 'prepared2.mtz')): + mtzFree = os.path.join( + inital_model_directory, xtal, 'dimple_twin', 'dimple_twin', 'prepared2.mtz') + elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin', 'dimple_rerun_on_selected_file', 'dimple_twin', 'free.mtz')): + mtzFree = os.path.join(inital_model_directory, xtal, 'dimple_twin', + 'dimple_rerun_on_selected_file', 'dimple_twin', 'free.mtz') + elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin', 'dimple_twin', 'free.mtz')): + mtzFree = os.path.join( + inital_model_directory, xtal, 'dimple_twin', 'dimple_twin', 'free.mtz') if mtzFree is not None: if 'F_unique' in mtz.object(mtzFree).column_labels(): - cmd = ( 'cad hklin1 %s hklout %s.free.mtz << eof\n' %(mtzFree,xtal) + - ' monitor BRIEF\n' - ' labin file 1 E1=F E2=SIGF E3=FreeR_flag\n' - ' labout file 1 E1=F E2=SIGF E3=FreeR_flag\n' - 'eof\n' ) + cmd = ('cad hklin1 %s hklout %s.free.mtz << eof\n' % (mtzFree, xtal) + + ' monitor BRIEF\n' + ' labin file 1 E1=F E2=SIGF E3=FreeR_flag\n' + ' labout file 1 E1=F E2=SIGF E3=FreeR_flag\n' + 'eof\n') os.system(cmd) else: - os.symlink(mtzFree,xtal+'.free.mtz') - - db_dict['RefinementTwinMTZfree']=xtal+'.free.mtz' - - + os.symlink(mtzFree, xtal+'.free.mtz') + db_dict['RefinementTwinMTZfree'] = xtal+'.free.mtz' # if no refinement was carried out yet, then we also want to link the dimple files to refine.pdb/refine.log # so that we can look at them with the COOT plugin @@ -96,13 +101,13 @@ # finally, update data source print '==> xce: updating data source after DIMPLE run' - db.update_data_source(xtal,db_dict) + db.update_data_source(xtal, db_dict) else: # the actual dimple script creates symbolic links regardless if dimple was successful or not # python os.path.isfile is False if symbolic link points to non existing file # so we remove all of them! - os.chdir(os.path.join(inital_model_directory,xtal)) + os.chdir(os.path.join(inital_model_directory, xtal)) os.system('/bin/rm dimple_twin.pdb') os.system('/bin/rm dimple_twin.mtz') os.system('/bin/rm 2fofc_twin.map') diff --git a/helpers/update_pandda_status_flag.py b/helpers/update_pandda_status_flag.py index a55ec20d..82a742a2 100755 --- a/helpers/update_pandda_status_flag.py +++ b/helpers/update_pandda_status_flag.py @@ -1,21 +1,23 @@ # last edited: 18/11/2016, 15:00 -import os,sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) - import XChemDB +import os +import sys +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) -def update_data_source(db_file,crystalString,status): - db=XChemDB.data_source(db_file) +def update_data_source(db_file, crystalString, status): + db = XChemDB.data_source(db_file) - print "update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format(status, "'"+crystalString.replace(",","','")+"'") - db.execute_statement("update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format(status, "'"+crystalString.replace(",","','")+"'")) + print "update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format( + status, "'"+crystalString.replace(",", "','")+"'") + db.execute_statement("update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format( + status, "'"+crystalString.replace(",", "','")+"'")) -if __name__=='__main__': - db_file=sys.argv[1] - crystalString=sys.argv[2] - status=sys.argv[3] +if __name__ == '__main__': + db_file = sys.argv[1] + crystalString = sys.argv[2] + status = sys.argv[3] - update_data_source(db_file,crystalString,status) + update_data_source(db_file, crystalString, status) diff --git a/helpers/update_status_flag.py b/helpers/update_status_flag.py index 3025cb0b..1ca8714f 100755 --- a/helpers/update_status_flag.py +++ b/helpers/update_status_flag.py @@ -1,15 +1,16 @@ # last edited: 15/11/2016, 15:00 -import os,sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) - import XChemDB +import os +import sys +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + +def update_data_source(db_file, xtal, db_column, status): + db = XChemDB.data_source(db_file) + db_dict = {db_column: status} + db.update_data_source(xtal, db_dict) -def update_data_source(db_file,xtal,db_column,status): - db=XChemDB.data_source(db_file) - db_dict= {db_column: status} - db.update_data_source(xtal,db_dict) if __name__ == '__main__': db_file = sys.argv[1] diff --git a/lib/PuckDB.py b/lib/PuckDB.py index beffd5a9..a6c25b2d 100755 --- a/lib/PuckDB.py +++ b/lib/PuckDB.py @@ -1,14 +1,15 @@ import sqlite3 -import os,sys +import os +import sys sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') -class puck_db(object): - def __init__(self,data_base): +class puck_db(object): - self.data_base=data_base + def __init__(self, data_base): + self.data_base = data_base def get_all_pucks_from_DB(self): print 'hello' @@ -24,4 +25,3 @@ def change_puck_location(self): def execute_sqlite(self): print 'hello' - diff --git a/lib/XChemCoot.py b/lib/XChemCoot.py index f367e923..4bba48df 100755 --- a/lib/XChemCoot.py +++ b/lib/XChemCoot.py @@ -1,5 +1,14 @@ # last edited: 08/08/2017 - 15:00 +import pango +import gtk +import pygtk +import coot_utils_XChem +import coot +import XChemLog +import XChemUtils +import XChemRefine +import XChemDB import gobject import sys import os @@ -12,19 +21,12 @@ # XCE libraries sys.path.append(os.getenv('XChemExplorer_DIR') + '/lib') -import XChemDB -import XChemRefine -import XChemUtils -import XChemLog # libraries from COOT -import pygtk, gtk, pango -import coot # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. # modified file is now in $XChemExplorer_DIR/lib -import coot_utils_XChem class GUI(object): @@ -49,7 +51,8 @@ def __init__(self): print self.settings # checking for external software packages - self.external_software = XChemUtils.external_software(self.xce_logfile).check() + self.external_software = XChemUtils.external_software( + self.xce_logfile).check() self.external_software['qsub_remote'] = remote_qsub_submission self.selection_criteria = ['0 - All Datasets', @@ -63,8 +66,10 @@ def __init__(self): self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], ['In Refinement', '3 - In Refinement', 65000, 0, 0], - ['Comp Chem Ready!', '4 - CompChem ready', 65000, 0, 0], - ['Ready for Deposition!', '5 - Deposition ready', 65000, 0, 0], + ['Comp Chem Ready!', + '4 - CompChem ready', 65000, 0, 0], + ['Ready for Deposition!', + '5 - Deposition ready', 65000, 0, 0], ['In PDB', '6 - Deposited', 65000, 0, 0], ['Analysed & Rejected', '7 - Analysed & Rejected', 65000, 0, 0]] @@ -121,7 +126,6 @@ def __init__(self): self.label_button_list = [] - ########################################################################################### # some COOT settings coot.set_map_radius(17) @@ -174,7 +178,6 @@ def __init__(self): menu, "set all occupanicies to 1", lambda func: self.reset_occupancy()) - def StartGUI(self): self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) @@ -205,7 +208,8 @@ def StartGUI(self): # self.hbox_select_samples.add(self.cb_select_sites) self.select_samples_button = gtk.Button(label="GO") - self.select_samples_button.connect("clicked", self.get_samples_to_look_at) + self.select_samples_button.connect( + "clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) @@ -220,7 +224,8 @@ def StartGUI(self): ################################################################################# # --- refinement protocol --- frame = gtk.Frame() - self.refinementProtocolcheckbox = gtk.CheckButton('PanDDA model refinement)') + self.refinementProtocolcheckbox = gtk.CheckButton( + 'PanDDA model refinement)') # callback is defined later # self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) self.refinementProtocolcheckbox.set_active(True) @@ -257,7 +262,8 @@ def StartGUI(self): ResolutionLabel_frame = gtk.Frame() self.ResolutionLabel = gtk.Label('Resolution') ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label(self.QualityIndicators['RefinementResolution']) + self.ResolutionValue = gtk.Label( + self.QualityIndicators['RefinementResolution']) ResolutionBox_frame = gtk.Frame() self.ResolutionBox = gtk.EventBox() self.ResolutionBox.add(self.ResolutionValue) @@ -266,7 +272,8 @@ def StartGUI(self): MolprobityScoreLabel_frame = gtk.Frame() self.MolprobityScoreLabel = gtk.Label('MolprobityScore') MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) - self.MolprobityScoreValue = gtk.Label(self.QualityIndicators['RefinementMolProbityScore']) + self.MolprobityScoreValue = gtk.Label( + self.QualityIndicators['RefinementMolProbityScore']) MolprobityScoreBox_frame = gtk.Frame() self.MolprobityScoreBox = gtk.EventBox() self.MolprobityScoreBox.add(self.MolprobityScoreValue) @@ -275,7 +282,8 @@ def StartGUI(self): RamachandranOutliersLabel_frame = gtk.Frame() self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) - self.RamachandranOutliersValue = gtk.Label(self.QualityIndicators['RefinementRamachandranOutliers']) + self.RamachandranOutliersValue = gtk.Label( + self.QualityIndicators['RefinementRamachandranOutliers']) RamachandranOutliersBox_frame = gtk.Frame() self.RamachandranOutliersBox = gtk.EventBox() self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) @@ -284,7 +292,8 @@ def StartGUI(self): RamachandranFavoredLabel_frame = gtk.Frame() self.RamachandranFavoredLabel = gtk.Label('Rama Favored') RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) - self.RamachandranFavoredValue = gtk.Label(self.QualityIndicators['RefinementRamachandranFavored']) + self.RamachandranFavoredValue = gtk.Label( + self.QualityIndicators['RefinementRamachandranFavored']) RamachandranFavoredBox_frame = gtk.Frame() self.RamachandranFavoredBox = gtk.EventBox() self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) @@ -293,7 +302,8 @@ def StartGUI(self): rmsdBondsLabel_frame = gtk.Frame() self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') rmsdBondsLabel_frame.add(self.rmsdBondsLabel) - self.rmsdBondsValue = gtk.Label(self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue = gtk.Label( + self.QualityIndicators['RefinementRmsdBonds']) rmsdBondsBox_frame = gtk.Frame() self.rmsdBondsBox = gtk.EventBox() self.rmsdBondsBox.add(self.rmsdBondsValue) @@ -302,7 +312,8 @@ def StartGUI(self): rmsdAnglesLabel_frame = gtk.Frame() self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) - self.rmsdAnglesValue = gtk.Label(self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue = gtk.Label( + self.QualityIndicators['RefinementRmsdAngles']) rmsdAnglesBox_frame = gtk.Frame() self.rmsdAnglesBox = gtk.EventBox() self.rmsdAnglesBox.add(self.rmsdAnglesValue) @@ -311,7 +322,8 @@ def StartGUI(self): MatrixWeightLabel_frame = gtk.Frame() self.MatrixWeightLabel = gtk.Label('Matrix Weight') MatrixWeightLabel_frame.add(self.MatrixWeightLabel) - self.MatrixWeightValue = gtk.Label(self.QualityIndicators['RefinementMatrixWeight']) + self.MatrixWeightValue = gtk.Label( + self.QualityIndicators['RefinementMatrixWeight']) MatrixWeightBox_frame = gtk.Frame() self.MatrixWeightBox = gtk.EventBox() self.MatrixWeightBox.add(self.MatrixWeightValue) @@ -320,7 +332,8 @@ def StartGUI(self): ligandIDLabel_frame = gtk.Frame() self.ligandIDLabel = gtk.Label('Ligand ID') ligandIDLabel_frame.add(self.ligandIDLabel) - self.ligandIDValue = gtk.Label(self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue = gtk.Label( + self.spider_plot_data['PANDDA_site_ligand_id']) ligandIDBox_frame = gtk.Frame() self.ligandIDBox = gtk.EventBox() self.ligandIDBox.add(self.ligandIDValue) @@ -329,7 +342,8 @@ def StartGUI(self): ligand_occupancyLabel_frame = gtk.Frame() self.ligand_occupancyLabel = gtk.Label('occupancy') ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) - self.ligand_occupancyValue = gtk.Label(self.spider_plot_data['PANDDA_site_occupancy']) + self.ligand_occupancyValue = gtk.Label( + self.spider_plot_data['PANDDA_site_occupancy']) ligand_occupancyBox_frame = gtk.Frame() self.ligand_occupancyBox = gtk.EventBox() self.ligand_occupancyBox.add(self.ligand_occupancyValue) @@ -338,7 +352,8 @@ def StartGUI(self): ligand_BaverageLabel_frame = gtk.Frame() self.ligand_BaverageLabel = gtk.Label('B average') ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) - self.ligand_BaverageValue = gtk.Label(self.spider_plot_data['PANDDA_site_B_average']) + self.ligand_BaverageValue = gtk.Label( + self.spider_plot_data['PANDDA_site_B_average']) ligand_BaverageBox_frame = gtk.Frame() self.ligand_BaverageBox = gtk.EventBox() self.ligand_BaverageBox.add(self.ligand_BaverageValue) @@ -346,18 +361,22 @@ def StartGUI(self): ligand_BratioSurroundingsLabel_frame = gtk.Frame() self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') - ligand_BratioSurroundingsLabel_frame.add(self.ligand_BratioSurroundingsLabel) + ligand_BratioSurroundingsLabel_frame.add( + self.ligand_BratioSurroundingsLabel) self.ligand_BratioSurroundingsValue = gtk.Label( self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) ligand_BratioSurroundingsBox_frame = gtk.Frame() self.ligand_BratioSurroundingsBox = gtk.EventBox() - self.ligand_BratioSurroundingsBox.add(self.ligand_BratioSurroundingsValue) - ligand_BratioSurroundingsBox_frame.add(self.ligand_BratioSurroundingsBox) + self.ligand_BratioSurroundingsBox.add( + self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add( + self.ligand_BratioSurroundingsBox) ligand_RSCCLabel_frame = gtk.Frame() self.ligand_RSCCLabel = gtk.Label('RSCC') ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) - self.ligand_RSCCValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSCC']) + self.ligand_RSCCValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSCC']) ligand_RSCCBox_frame = gtk.Frame() self.ligand_RSCCBox = gtk.EventBox() self.ligand_RSCCBox.add(self.ligand_RSCCValue) @@ -366,7 +385,8 @@ def StartGUI(self): ligand_rmsdLabel_frame = gtk.Frame() self.ligand_rmsdLabel = gtk.Label('rmsd') ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) - self.ligand_rmsdValue = gtk.Label(self.spider_plot_data['PANDDA_site_rmsd']) + self.ligand_rmsdValue = gtk.Label( + self.spider_plot_data['PANDDA_site_rmsd']) ligand_rmsdBox_frame = gtk.Frame() self.ligand_rmsdBox = gtk.EventBox() self.ligand_rmsdBox.add(self.ligand_rmsdValue) @@ -375,7 +395,8 @@ def StartGUI(self): ligand_RSRLabel_frame = gtk.Frame() self.ligand_RSRLabel = gtk.Label('RSR') ligand_RSRLabel_frame.add(self.ligand_RSRLabel) - self.ligand_RSRValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSR']) + self.ligand_RSRValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSR']) ligand_RSRBox_frame = gtk.Frame() self.ligand_RSRBox = gtk.EventBox() self.ligand_RSRBox.add(self.ligand_RSRValue) @@ -384,7 +405,8 @@ def StartGUI(self): ligand_RSZDLabel_frame = gtk.Frame() self.ligand_RSZDLabel = gtk.Label('RSZD') ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) - self.ligand_RSZDValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSZD']) + self.ligand_RSZDValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSZD']) ligand_RSZDBox_frame = gtk.Frame() self.ligand_RSZDBox = gtk.EventBox() self.ligand_RSZDBox.add(self.ligand_RSZDValue) @@ -419,7 +441,8 @@ def StartGUI(self): self.table_right.attach(ligandIDLabel_frame, 0, 1, 0, 1) self.table_right.attach(ligand_occupancyLabel_frame, 0, 1, 1, 2) self.table_right.attach(ligand_BaverageLabel_frame, 0, 1, 2, 3) - self.table_right.attach(ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach( + ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) self.table_right.attach(ligand_RSCCLabel_frame, 0, 1, 4, 5) self.table_right.attach(ligand_rmsdLabel_frame, 0, 1, 5, 6) self.table_right.attach(ligand_RSRLabel_frame, 0, 1, 6, 7) @@ -443,8 +466,10 @@ def StartGUI(self): button.connect("clicked", self.show_molprobity_to_do) hbox.add(button) # --- ground state mean map --- - self.ground_state_mean_map_button = gtk.Button(label="Show ground state mean map") - self.ground_state_mean_map_button.connect("clicked", self.show_ground_state_mean_map) + self.ground_state_mean_map_button = gtk.Button( + label="Show ground state mean map") + self.ground_state_mean_map_button.connect( + "clicked", self.show_ground_state_mean_map) hbox.add(self.ground_state_mean_map_button) # self.vbox.add(self.ground_state_mean_map_button) self.vbox.add(hbox) @@ -478,7 +503,8 @@ def StartGUI(self): spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_pic = pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image = gtk.Image() self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) spider_plot_frame.add(self.spider_plot_image) @@ -631,8 +657,9 @@ def StartGUI(self): new_button = gtk.RadioButton(None, button[0]) else: new_button = gtk.RadioButton(new_button, button[0]) - new_button.connect("toggled", self.experiment_stage_button_clicked, button[1]) - vbox.pack_start(new_button,False,False,0) + new_button.connect( + "toggled", self.experiment_stage_button_clicked, button[1]) + vbox.pack_start(new_button, False, False, 0) # vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) @@ -647,8 +674,9 @@ def StartGUI(self): new_button = gtk.RadioButton(None, criteria) else: new_button = gtk.RadioButton(new_button, criteria) - new_button.connect("toggled", self.ligand_confidence_button_clicked, criteria) - vbox.pack_start(new_button,False,False,0) + new_button.connect( + "toggled", self.ligand_confidence_button_clicked, criteria) + vbox.pack_start(new_button, False, False, 0) # vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) @@ -692,9 +720,11 @@ def StartGUI(self): self.merge_ligand_button = gtk.Button(label="Merge Ligand") self.place_ligand_here_button = gtk.Button(label="Place Ligand here") self.hbox_for_modeling.add(self.place_ligand_here_button) - self.place_ligand_here_button.connect("clicked", self.place_ligand_here) + self.place_ligand_here_button.connect( + "clicked", self.place_ligand_here) self.hbox_for_modeling.add(self.merge_ligand_button) - self.merge_ligand_button.connect("clicked", self.merge_ligand_into_protein) + self.merge_ligand_button.connect( + "clicked", self.merge_ligand_into_protein) frame.add(self.hbox_for_modeling) self.vbox.pack_start(frame) @@ -705,7 +735,6 @@ def StartGUI(self): # self.cb_ligand_confidence.append_text(citeria) # self.vbox.add(self.cb_ligand_confidence) - # --- refinement & options --- self.hbox_for_refinement = gtk.HBox() self.REFINEbutton = gtk.Button(label="Refine") @@ -719,11 +748,10 @@ def StartGUI(self): # self.VALIDATEbutton = gtk.Button(label="validate structure") # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") - # need to put it here, because attributes within refinementProtocolCallback function # are defined after checkbox is defined - self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) - + self.refinementProtocolcheckbox.connect( + "toggled", self.refinementProtocolCallback) # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") @@ -827,7 +855,8 @@ def refresh_site_combobox(self): # only repopulate if site exists if self.xtalID in self.siteDict: for item in sorted(self.siteDict[self.xtalID]): - self.cb_site.append_text('site: {0!s} - event: {1!s}'.format(item[5], item[6])) + self.cb_site.append_text( + 'site: {0!s} - event: {1!s}'.format(item[5], item[6])) def ChangeSite(self, widget, data=None): if self.xtalID in self.siteDict: @@ -866,13 +895,13 @@ def RefreshSiteData(self): for w in self.label_button_list: w.set_active(False) - print 'pandda index', self.pandda_index self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] print 'new spider plot:', self.spider_plot self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] print 'new event map:', self.event_map - self.ligand_confidence = str(self.siteDict[self.xtalID][self.pandda_index][7]) + self.ligand_confidence = str( + self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) @@ -888,14 +917,17 @@ def RefreshSiteData(self): self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, self.event_index) print '>>>>> spider plot data', self.spider_plot_data - self.ligandIDValue.set_label(self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue.set_label( + self.spider_plot_data['PANDDA_site_ligand_id']) try: - self.ligand_occupancyValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) + self.ligand_occupancyValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) except ValueError: self.ligand_occupancyValue.set_label('-') try: - self.ligand_BaverageValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) + self.ligand_BaverageValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) except ValueError: self.ligand_BaverageValue.set_label('-') @@ -906,22 +938,26 @@ def RefreshSiteData(self): self.ligand_BratioSurroundingsValue.set_label('-') try: - self.ligand_RSCCValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) + self.ligand_RSCCValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) except ValueError: self.ligand_RSCCValue.set_label('-') try: - self.ligand_rmsdValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) + self.ligand_rmsdValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) except ValueError: self.ligand_rmsdValue.set_label('-') try: - self.ligand_RSRValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) + self.ligand_RSRValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) except ValueError: self.ligand_RSRValue.set_label('-') try: - self.ligand_RSZDValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) + self.ligand_RSZDValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) except ValueError: self.ligand_RSZDValue.set_label('-') @@ -940,7 +976,8 @@ def RefreshSiteData(self): else: spider_plot_pic = gtk.gdk.pixbuf_new_from_file( os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_pic = spider_plot_pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) ######################################################################################### @@ -958,11 +995,13 @@ def RefreshSiteData(self): def experiment_stage_button_clicked(self, widget, data=None): if data == '4 - CompChem ready' and self.refinementProtocol.startswith('pandda'): print "==> XCE: removing refine.pdb and linking refine_.split.bound-state.pdb to refine.pdb" - os.chdir(os.path.join(self.project_directory,self.xtalID)) + os.chdir(os.path.join(self.project_directory, self.xtalID)) if os.path.realpath('refine.pdb').replace('.pdb', '.split.bound-state.pdb'): - newPDB = os.path.realpath('refine.pdb').replace('.pdb', '.split.bound-state.pdb') + newPDB = os.path.realpath('refine.pdb').replace( + '.pdb', '.split.bound-state.pdb') os.system('/bin/rm refine.pdb') - os.system('ln -s .%s refine.pdb' %newPDB.replace(os.getcwd(),'')) + os.system('ln -s .%s refine.pdb' % + newPDB.replace(os.getcwd(), '')) self.refinementProtocolcheckbox.set_active(False) self.refinementProtocol = 'refmac' else: @@ -970,11 +1009,10 @@ def experiment_stage_button_clicked(self, widget, data=None): pass self.db_dict_mainTable['RefinementOutcome'] = data print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( - data) + ' in mainTable of datasource' - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + data) + ' in mainTable of datasource' + # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, self.xtalID, 'ligand_bound', - self.db_dict_mainTable) - + self.db_dict_mainTable) def ligand_confidence_button_clicked(self, widget, data=None): print 'PANDDA_index', self.pandda_index @@ -1019,13 +1057,15 @@ def RefreshData(self): # reset spider plot image spider_plot_pic = gtk.gdk.pixbuf_new_from_file( os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_pic = spider_plot_pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) # reset ground state mean map self.ground_state_mean_map = '' self.ground_state_mean_map_button.set_sensitive(False) - self.ground_state_mean_map_button.set_label('Show ground state mean map') + self.ground_state_mean_map_button.set_label( + 'Show ground state mean map') if os.path.isfile( os.path.join(self.project_directory, self.xtalID, self.xtalID + '-ground-state-mean-map.native.ccp4')): self.ground_state_mean_map_button.set_sensitive(True) @@ -1033,9 +1073,12 @@ def RefreshData(self): self.xtalID + '-ground-state-mean-map.native.ccp4') # initialize Refinement library - self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) - self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) - self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * '0' + str(self.Serial) + self.Refine = XChemRefine.Refine( + self.project_directory, self.xtalID, self.compoundID, self.data_source) + self.Serial = XChemRefine.GetSerial( + self.project_directory, self.xtalID) + self.panddaSerial = panddaSerial = m = ( + 4 - len(str(self.Serial))) * '0' + str(self.Serial) # self.Serial=self.Refine.GetSerial() if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple @@ -1069,7 +1112,8 @@ def RefreshData(self): # if the structure was previously refined, try to read the parameters # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: - self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) + self.RefmacParams = self.Refine.ParamsFromPreviousCycle( + self.Serial - 1) print '==> REFMAC params:', self.RefmacParams # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) @@ -1099,7 +1143,8 @@ def RefreshData(self): imol = coot.handle_read_draw_molecule_with_recentre( os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb'), 0) self.mol_dict['ligand'] = imol - coot.read_cif_dictionary(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) + coot.read_cif_dictionary(os.path.join( + self.project_directory, self.xtalID, self.compoundID + '.cif')) if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): os.chdir(os.path.join(self.project_directory, self.xtalID)) @@ -1171,9 +1216,10 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( + self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( item).endswith(self.pdb_style): - coot.set_show_symmetry_master(1) # master switch to show symmetry molecules + # master switch to show symmetry molecules + coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model ######################################################################################### @@ -1183,9 +1229,11 @@ def RefreshData(self): if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): coot.set_colour_map_rotation_on_read_pdb(0) coot.set_default_initial_contour_level_for_difference_map(3) - coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, 'fofc.map'), 1) + coot.handle_read_ccp4_map(os.path.join( + self.project_directory, self.xtalID, 'fofc.map'), 1) coot.set_default_initial_contour_level_for_map(1) - coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, '2fofc.map'), 0) + coot.handle_read_ccp4_map(os.path.join( + self.project_directory, self.xtalID, '2fofc.map'), 0) coot.set_last_map_colour(0, 0, 1) else: # try to open mtz file with same name as pdb file @@ -1198,11 +1246,14 @@ def RefreshData(self): # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): # os.symlink('dimple.mtz',self.mtz_style) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, self.mtz_style)) + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, self.mtz_style)) elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, 'init.mtz')) + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, 'init.mtz')) elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')) + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, 'dimple.mtz')) ######################################################################################### # update Quality Indicator table @@ -1217,43 +1268,50 @@ def RefreshData(self): gtk.gdk.color_parse(self.QualityIndicators['RefinementRfreeTraficLight'])) except ValueError: pass - self.ResolutionValue.set_label(self.QualityIndicators['RefinementResolution']) + self.ResolutionValue.set_label( + self.QualityIndicators['RefinementResolution']) try: self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementResolutionTL'])) except ValueError: pass - self.MolprobityScoreValue.set_label(self.QualityIndicators['RefinementMolProbityScore']) + self.MolprobityScoreValue.set_label( + self.QualityIndicators['RefinementMolProbityScore']) try: self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( self.QualityIndicators['RefinementMolProbityScoreTL'])) except ValueError: pass - self.RamachandranOutliersValue.set_label(self.QualityIndicators['RefinementRamachandranOutliers']) + self.RamachandranOutliersValue.set_label( + self.QualityIndicators['RefinementRamachandranOutliers']) try: self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( self.QualityIndicators['RefinementRamachandranOutliersTL'])) except ValueError: pass - self.RamachandranFavoredValue.set_label(self.QualityIndicators['RefinementRamachandranFavored']) + self.RamachandranFavoredValue.set_label( + self.QualityIndicators['RefinementRamachandranFavored']) try: self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( self.QualityIndicators['RefinementRamachandranFavoredTL'])) except ValueError: pass - self.rmsdBondsValue.set_label(self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue.set_label( + self.QualityIndicators['RefinementRmsdBonds']) try: self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdBondsTL'])) except ValueError: pass - self.rmsdAnglesValue.set_label(self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue.set_label( + self.QualityIndicators['RefinementRmsdAngles']) try: self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdAnglesTL'])) except ValueError: pass - self.MatrixWeightValue.set_label(self.QualityIndicators['RefinementMatrixWeight']) + self.MatrixWeightValue.set_label( + self.QualityIndicators['RefinementMatrixWeight']) try: pic = gtk.gdk.pixbuf_new_from_file( @@ -1296,10 +1354,12 @@ def REFINE(self, widget): ####################################################### if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): - os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) + os.mkdir(os.path.join( + self.project_directory, self.xtalID, 'cootOut')) # create folder for new refinement cycle try: - os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + os.mkdir(os.path.join(self.project_directory, + self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) except OSError: print '==> XCE: WARNING -> folder exists; will overwrite contents!' @@ -1309,7 +1369,7 @@ def REFINE(self, widget): # note: the user has to make sure that the ligand file was merged into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( + self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( item).endswith(self.pdb_style): coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial), 'refine.modified.pdb')) @@ -1328,7 +1388,8 @@ def REFINE(self, widget): if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): os.mkdir(os.path.join(self.project_directory, self.xtalID)) if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): - os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) + os.mkdir(os.path.join(self.project_directory, + self.xtalID, 'Refine_' + str(self.Serial))) ####################################################### # write PDB file @@ -1343,8 +1404,9 @@ def REFINE(self, widget): elif coot.molecule_name(item).endswith('refine.split.bound-state.pdb'): coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial), - 'in.pdb')) + 'Refine_' + + str(self.Serial), + 'in.pdb')) break elif coot.molecule_name(item).endswith('init.pdb'): coot.write_pdb_file(item, @@ -1357,7 +1419,8 @@ def REFINE(self, widget): 'in.pdb')) break - self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile) + self.Refine.RunRefmac( + self.Serial, self.RefmacParams, self.external_software, self.xce_logfile) self.index += 1 if self.index >= len(self.Todo): @@ -1384,7 +1447,8 @@ def get_samples_to_look_at(self, widget): self.cb.remove_text(0) self.Todo = [] self.siteDict = {} - self.Todo, self.siteDict = self.db.get_todoList_for_coot(self.selection_mode) + self.Todo, self.siteDict = self.db.get_todoList_for_coot( + self.selection_mode) # self.status_label.set_text('found {0!s} samples'.format(len(self.Todo))) # refresh sample CB for item in sorted(self.Todo): @@ -1397,13 +1461,12 @@ def get_samples_to_look_at(self, widget): self.cb_site.set_sensitive(True) self.PREVbuttonSite.set_sensitive(True) self.NEXTbuttonSite.set_sensitive(True) - print '===========>',self.cb_select_samples.get_active_text() + print '===========>', self.cb_select_samples.get_active_text() if int(self.cb_select_samples.get_active_text().split()[0]) > 3: print '==> XCE: sorry cannot change refinement protocol since you are at a stage when we refine the ligand bound state only' self.refinementProtocol = 'refmac' self.refinementProtocolcheckbox.set_active(False) - def update_plot(self, refinement_cycle, Rfree, Rcryst): fig = Figure(figsize=(2, 2), dpi=50) Plot = fig.add_subplot(111) @@ -1424,13 +1487,15 @@ def place_ligand_here(self, widget): def merge_ligand_into_protein(self, widget): print '===> XCE: merge ligand into protein structure' # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) - coot.merge_molecules_py([self.mol_dict['ligand']], self.mol_dict['protein']) + coot.merge_molecules_py( + [self.mol_dict['ligand']], self.mol_dict['protein']) print '===> XCE: deleting ligand molecule' coot.close_molecule(self.mol_dict['ligand']) def show_molprobity_to_do(self, widget): print self.panddaSerial - AdjPanddaSerial = (4 - len(str(self.Serial))) * '0' + str(int(self.panddaSerial) - 1) + AdjPanddaSerial = (4 - len(str(self.Serial))) * \ + '0' + str(int(self.panddaSerial) - 1) print os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), 'molprobity_coot.py') if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), @@ -1502,22 +1567,26 @@ def show_ground_state_mean_map(self, widget): widget.set_label('Show ground state mean map') def reset_occupancy(self): - self.Logfile.warning('==> COOT: trying to set occupancies of all residues to 1.0') + self.Logfile.warning( + '==> COOT: trying to set occupancies of all residues to 1.0') if self.refinementProtocol.startswith('pandda'): - self.Logfile.warning('==> COOT: you cannot reset occupancies while working in PanDDA refine mode') + self.Logfile.warning( + '==> COOT: you cannot reset occupancies while working in PanDDA refine mode') else: for imol in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(imol).endswith(self.pdb_style) or \ coot.molecule_name(imol).endswith('refine.split.bound-state.pdb') or \ coot.molecule_name(imol).endswith('ini.pdb') or \ coot.molecule_name(imol).endswith('dimple.pdb'): - self.Logfile.warning('==> COOT: setting occupancies of all protein residues in %s to 1.0' %coot.molecule_name(imol)) + self.Logfile.warning( + '==> COOT: setting occupancies of all protein residues in %s to 1.0' % coot.molecule_name(imol)) # coot.fill_occupancy_residue_range(imol,"A",1,10000) chains = chain_ids(imol) resiDict = {} for chain in chains: resiDict[chain] = residues_in_chain(imol, chain) - amino_acids = XChemUtils.pdbtools(coot.molecule_name(imol)).amino_acids() + amino_acids = XChemUtils.pdbtools( + coot.molecule_name(imol)).amino_acids() resetDict = {} for chain in resiDict: @@ -1525,28 +1594,28 @@ def reset_occupancy(self): resid_prev = -1000 n_res = 0 for resid in resiDict[chain]: - if residue_name(imol,chain,resid[1],'') in amino_acids: + if residue_name(imol, chain, resid[1], '') in amino_acids: n_res += 1 counter = 0 - for n,resid in enumerate(resiDict[chain]): - if residue_name(imol,chain,resid[1],'') in amino_acids: + for n, resid in enumerate(resiDict[chain]): + if residue_name(imol, chain, resid[1], '') in amino_acids: counter += 1 if chain not in resetDict: resetDict[chain] = None if resid[1] != resid_prev + 1: if resid_prev != -1000: - residRange.append([start,resid_prev]) + residRange.append([start, resid_prev]) start = resid[1] resid_prev = resid[1] if counter == n_res: - residRange.append([start,resid[1]]) + residRange.append([start, resid[1]]) if chain in resetDict: resetDict[chain] = residRange for chain in resetDict: for resid_range in resetDict[chain]: - print 'setting occupancy to 1: ->',chain,resid_range[0],resid_range[1] - coot.fill_occupancy_residue_range(imol,chain,resid_range[0],resid_range[1]) - + print 'setting occupancy to 1: ->', chain, resid_range[0], resid_range[1] + coot.fill_occupancy_residue_range( + imol, chain, resid_range[0], resid_range[1]) # @@ -1555,6 +1624,5 @@ def reset_occupancy(self): # for residue in residues_in_chain(imol, chain): # print residue - if __name__ == '__main__': GUI().StartGUI() diff --git a/lib/XChemCootBuster.py b/lib/XChemCootBuster.py index 9f71f122..0dccc0c4 100755 --- a/lib/XChemCootBuster.py +++ b/lib/XChemCootBuster.py @@ -1,5 +1,14 @@ # last edited: 08/08/2017 - 15:00 +import pango +import gtk +import pygtk +import coot_utils_XChem +import coot +import XChemLog +import XChemUtils +import XChemRefine +import XChemDB import gobject import sys import os @@ -15,19 +24,12 @@ # XCE libraries sys.path.append(os.getenv('XChemExplorer_DIR') + '/lib') -import XChemDB -import XChemRefine -import XChemUtils -import XChemLog # libraries from COOT -import pygtk, gtk, pango -import coot # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. # modified file is now in $XChemExplorer_DIR/lib -import coot_utils_XChem class GUI(object): @@ -52,7 +54,8 @@ def __init__(self): print self.settings # checking for external software packages - self.external_software = XChemUtils.external_software(self.xce_logfile).check() + self.external_software = XChemUtils.external_software( + self.xce_logfile).check() self.external_software['qsub_remote'] = remote_qsub_submission self.selection_criteria = ['0 - All Datasets', @@ -66,8 +69,10 @@ def __init__(self): self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], ['In Refinement', '3 - In Refinement', 65000, 0, 0], - ['Comp Chem Ready!', '4 - CompChem ready', 65000, 0, 0], - ['Ready for Deposition!', '5 - Deposition ready', 65000, 0, 0], + ['Comp Chem Ready!', + '4 - CompChem ready', 65000, 0, 0], + ['Ready for Deposition!', + '5 - Deposition ready', 65000, 0, 0], ['In PDB', '6 - Deposited', 65000, 0, 0], ['Analysed & Rejected', '7 - Analysed & Rejected', 65000, 0, 0]] @@ -129,7 +134,6 @@ def __init__(self): self.label_button_list = [] - ########################################################################################### # some COOT settings coot.set_map_radius(17) @@ -176,7 +180,7 @@ def __init__(self): 'TWIN': '', 'WATER': '', 'LIGOCC': '', - 'SANITY': '' } + 'SANITY': ''} def StartGUI(self): @@ -208,7 +212,8 @@ def StartGUI(self): # self.hbox_select_samples.add(self.cb_select_sites) self.select_samples_button = gtk.Button(label="GO") - self.select_samples_button.connect("clicked", self.get_samples_to_look_at) + self.select_samples_button.connect( + "clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) @@ -260,7 +265,8 @@ def StartGUI(self): ResolutionLabel_frame = gtk.Frame() self.ResolutionLabel = gtk.Label('Resolution') ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label(self.QualityIndicators['RefinementResolution']) + self.ResolutionValue = gtk.Label( + self.QualityIndicators['RefinementResolution']) ResolutionBox_frame = gtk.Frame() self.ResolutionBox = gtk.EventBox() self.ResolutionBox.add(self.ResolutionValue) @@ -269,7 +275,8 @@ def StartGUI(self): MolprobityScoreLabel_frame = gtk.Frame() self.MolprobityScoreLabel = gtk.Label('MolprobityScore') MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) - self.MolprobityScoreValue = gtk.Label(self.QualityIndicators['RefinementMolProbityScore']) + self.MolprobityScoreValue = gtk.Label( + self.QualityIndicators['RefinementMolProbityScore']) MolprobityScoreBox_frame = gtk.Frame() self.MolprobityScoreBox = gtk.EventBox() self.MolprobityScoreBox.add(self.MolprobityScoreValue) @@ -278,7 +285,8 @@ def StartGUI(self): RamachandranOutliersLabel_frame = gtk.Frame() self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) - self.RamachandranOutliersValue = gtk.Label(self.QualityIndicators['RefinementRamachandranOutliers']) + self.RamachandranOutliersValue = gtk.Label( + self.QualityIndicators['RefinementRamachandranOutliers']) RamachandranOutliersBox_frame = gtk.Frame() self.RamachandranOutliersBox = gtk.EventBox() self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) @@ -287,7 +295,8 @@ def StartGUI(self): RamachandranFavoredLabel_frame = gtk.Frame() self.RamachandranFavoredLabel = gtk.Label('Rama Favored') RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) - self.RamachandranFavoredValue = gtk.Label(self.QualityIndicators['RefinementRamachandranFavored']) + self.RamachandranFavoredValue = gtk.Label( + self.QualityIndicators['RefinementRamachandranFavored']) RamachandranFavoredBox_frame = gtk.Frame() self.RamachandranFavoredBox = gtk.EventBox() self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) @@ -296,7 +305,8 @@ def StartGUI(self): rmsdBondsLabel_frame = gtk.Frame() self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') rmsdBondsLabel_frame.add(self.rmsdBondsLabel) - self.rmsdBondsValue = gtk.Label(self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue = gtk.Label( + self.QualityIndicators['RefinementRmsdBonds']) rmsdBondsBox_frame = gtk.Frame() self.rmsdBondsBox = gtk.EventBox() self.rmsdBondsBox.add(self.rmsdBondsValue) @@ -305,7 +315,8 @@ def StartGUI(self): rmsdAnglesLabel_frame = gtk.Frame() self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) - self.rmsdAnglesValue = gtk.Label(self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue = gtk.Label( + self.QualityIndicators['RefinementRmsdAngles']) rmsdAnglesBox_frame = gtk.Frame() self.rmsdAnglesBox = gtk.EventBox() self.rmsdAnglesBox.add(self.rmsdAnglesValue) @@ -314,7 +325,8 @@ def StartGUI(self): MatrixWeightLabel_frame = gtk.Frame() self.MatrixWeightLabel = gtk.Label('Matrix Weight') MatrixWeightLabel_frame.add(self.MatrixWeightLabel) - self.MatrixWeightValue = gtk.Label(self.QualityIndicators['RefinementMatrixWeight']) + self.MatrixWeightValue = gtk.Label( + self.QualityIndicators['RefinementMatrixWeight']) MatrixWeightBox_frame = gtk.Frame() self.MatrixWeightBox = gtk.EventBox() self.MatrixWeightBox.add(self.MatrixWeightValue) @@ -323,7 +335,8 @@ def StartGUI(self): ligandIDLabel_frame = gtk.Frame() self.ligandIDLabel = gtk.Label('Ligand ID') ligandIDLabel_frame.add(self.ligandIDLabel) - self.ligandIDValue = gtk.Label(self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue = gtk.Label( + self.spider_plot_data['PANDDA_site_ligand_id']) ligandIDBox_frame = gtk.Frame() self.ligandIDBox = gtk.EventBox() self.ligandIDBox.add(self.ligandIDValue) @@ -332,7 +345,8 @@ def StartGUI(self): ligand_occupancyLabel_frame = gtk.Frame() self.ligand_occupancyLabel = gtk.Label('occupancy') ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) - self.ligand_occupancyValue = gtk.Label(self.spider_plot_data['PANDDA_site_occupancy']) + self.ligand_occupancyValue = gtk.Label( + self.spider_plot_data['PANDDA_site_occupancy']) ligand_occupancyBox_frame = gtk.Frame() self.ligand_occupancyBox = gtk.EventBox() self.ligand_occupancyBox.add(self.ligand_occupancyValue) @@ -341,7 +355,8 @@ def StartGUI(self): ligand_BaverageLabel_frame = gtk.Frame() self.ligand_BaverageLabel = gtk.Label('B average') ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) - self.ligand_BaverageValue = gtk.Label(self.spider_plot_data['PANDDA_site_B_average']) + self.ligand_BaverageValue = gtk.Label( + self.spider_plot_data['PANDDA_site_B_average']) ligand_BaverageBox_frame = gtk.Frame() self.ligand_BaverageBox = gtk.EventBox() self.ligand_BaverageBox.add(self.ligand_BaverageValue) @@ -349,18 +364,22 @@ def StartGUI(self): ligand_BratioSurroundingsLabel_frame = gtk.Frame() self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') - ligand_BratioSurroundingsLabel_frame.add(self.ligand_BratioSurroundingsLabel) + ligand_BratioSurroundingsLabel_frame.add( + self.ligand_BratioSurroundingsLabel) self.ligand_BratioSurroundingsValue = gtk.Label( self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) ligand_BratioSurroundingsBox_frame = gtk.Frame() self.ligand_BratioSurroundingsBox = gtk.EventBox() - self.ligand_BratioSurroundingsBox.add(self.ligand_BratioSurroundingsValue) - ligand_BratioSurroundingsBox_frame.add(self.ligand_BratioSurroundingsBox) + self.ligand_BratioSurroundingsBox.add( + self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add( + self.ligand_BratioSurroundingsBox) ligand_RSCCLabel_frame = gtk.Frame() self.ligand_RSCCLabel = gtk.Label('RSCC') ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) - self.ligand_RSCCValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSCC']) + self.ligand_RSCCValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSCC']) ligand_RSCCBox_frame = gtk.Frame() self.ligand_RSCCBox = gtk.EventBox() self.ligand_RSCCBox.add(self.ligand_RSCCValue) @@ -369,7 +388,8 @@ def StartGUI(self): ligand_rmsdLabel_frame = gtk.Frame() self.ligand_rmsdLabel = gtk.Label('rmsd') ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) - self.ligand_rmsdValue = gtk.Label(self.spider_plot_data['PANDDA_site_rmsd']) + self.ligand_rmsdValue = gtk.Label( + self.spider_plot_data['PANDDA_site_rmsd']) ligand_rmsdBox_frame = gtk.Frame() self.ligand_rmsdBox = gtk.EventBox() self.ligand_rmsdBox.add(self.ligand_rmsdValue) @@ -378,7 +398,8 @@ def StartGUI(self): ligand_RSRLabel_frame = gtk.Frame() self.ligand_RSRLabel = gtk.Label('RSR') ligand_RSRLabel_frame.add(self.ligand_RSRLabel) - self.ligand_RSRValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSR']) + self.ligand_RSRValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSR']) ligand_RSRBox_frame = gtk.Frame() self.ligand_RSRBox = gtk.EventBox() self.ligand_RSRBox.add(self.ligand_RSRValue) @@ -387,7 +408,8 @@ def StartGUI(self): ligand_RSZDLabel_frame = gtk.Frame() self.ligand_RSZDLabel = gtk.Label('RSZD') ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) - self.ligand_RSZDValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSZD']) + self.ligand_RSZDValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSZD']) ligand_RSZDBox_frame = gtk.Frame() self.ligand_RSZDBox = gtk.EventBox() self.ligand_RSZDBox.add(self.ligand_RSZDValue) @@ -422,7 +444,8 @@ def StartGUI(self): self.table_right.attach(ligandIDLabel_frame, 0, 1, 0, 1) self.table_right.attach(ligand_occupancyLabel_frame, 0, 1, 1, 2) self.table_right.attach(ligand_BaverageLabel_frame, 0, 1, 2, 3) - self.table_right.attach(ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach( + ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) self.table_right.attach(ligand_RSCCLabel_frame, 0, 1, 4, 5) self.table_right.attach(ligand_rmsdLabel_frame, 0, 1, 5, 6) self.table_right.attach(ligand_RSRLabel_frame, 0, 1, 6, 7) @@ -446,8 +469,10 @@ def StartGUI(self): button.connect("clicked", self.show_molprobity_to_do) hbox.add(button) # --- ground state mean map --- - self.ground_state_mean_map_button = gtk.Button(label="Show ground state mean map") - self.ground_state_mean_map_button.connect("clicked", self.show_ground_state_mean_map) + self.ground_state_mean_map_button = gtk.Button( + label="Show ground state mean map") + self.ground_state_mean_map_button.connect( + "clicked", self.show_ground_state_mean_map) hbox.add(self.ground_state_mean_map_button) # self.vbox.add(self.ground_state_mean_map_button) self.vbox.add(hbox) @@ -481,7 +506,8 @@ def StartGUI(self): spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_pic = pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image = gtk.Image() self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) spider_plot_frame.add(self.spider_plot_image) @@ -634,8 +660,9 @@ def StartGUI(self): new_button = gtk.RadioButton(None, button[0]) else: new_button = gtk.RadioButton(new_button, button[0]) - new_button.connect("toggled", self.experiment_stage_button_clicked, button[1]) - vbox.pack_start(new_button,False,False,0) + new_button.connect( + "toggled", self.experiment_stage_button_clicked, button[1]) + vbox.pack_start(new_button, False, False, 0) # vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) @@ -650,8 +677,9 @@ def StartGUI(self): new_button = gtk.RadioButton(None, criteria) else: new_button = gtk.RadioButton(new_button, criteria) - new_button.connect("toggled", self.ligand_confidence_button_clicked, criteria) - vbox.pack_start(new_button,False,False,0) + new_button.connect( + "toggled", self.ligand_confidence_button_clicked, criteria) + vbox.pack_start(new_button, False, False, 0) # vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) @@ -695,9 +723,11 @@ def StartGUI(self): self.merge_ligand_button = gtk.Button(label="Merge Ligand") self.place_ligand_here_button = gtk.Button(label="Place Ligand here") self.hbox_for_modeling.add(self.place_ligand_here_button) - self.place_ligand_here_button.connect("clicked", self.place_ligand_here) + self.place_ligand_here_button.connect( + "clicked", self.place_ligand_here) self.hbox_for_modeling.add(self.merge_ligand_button) - self.merge_ligand_button.connect("clicked", self.merge_ligand_into_protein) + self.merge_ligand_button.connect( + "clicked", self.merge_ligand_into_protein) self.select_cpd_cb = gtk.combo_box_new_text() self.select_cpd_cb.connect("changed", self.select_cpd) self.hbox_for_modeling.add(self.select_cpd_cb) @@ -711,18 +741,19 @@ def StartGUI(self): # self.cb_ligand_confidence.append_text(citeria) # self.vbox.add(self.cb_ligand_confidence) - # --- refinement & options --- self.hbox_for_refinement = gtk.HBox() self.REFINEbutton = gtk.Button(label="Refine") self.RefinementParamsButton = gtk.Button(label="refinement parameters") self.covalentLinksbutton = gtk.Button(label="covalent links\n-define-") - self.covalentLinksCreatebutton = gtk.Button(label="covalent links\n-create & refine-") + self.covalentLinksCreatebutton = gtk.Button( + label="covalent links\n-create & refine-") self.REFINEbutton.connect("clicked", self.REFINE) self.hbox_for_refinement.add(self.REFINEbutton) self.RefinementParamsButton.connect("clicked", self.RefinementParams) self.covalentLinksbutton.connect("clicked", self.covalentLinkDef) - self.covalentLinksCreatebutton.connect("clicked", self.covalentLinkCreate) + self.covalentLinksCreatebutton.connect( + "clicked", self.covalentLinkCreate) self.hbox_for_refinement.add(self.RefinementParamsButton) self.hbox_for_refinement.add(self.covalentLinksbutton) self.hbox_for_refinement.add(self.covalentLinksCreatebutton) @@ -736,7 +767,6 @@ def StartGUI(self): # # are defined after checkbox is defined # self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) - # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") self.CANCELbutton.connect("clicked", self.CANCEL) @@ -793,20 +823,23 @@ def select_cpd(self, widget): for imol in coot_utils_XChem.molecule_number_list(): if imol not in self.mol_dict['ligand_stereo']: continue - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + molName = coot.molecule_name(imol)[coot.molecule_name( + imol).rfind('/')+1:].replace('.pdb', '') if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): - molNameCIF = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/') + 1:].replace('.pdb', '').replace('_phenix','').replace('_rhofit','') + molNameCIF = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( + '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') else: molNameCIF = molName - print cpd,'-',imol,'-',coot.molecule_name(imol) + print cpd, '-', imol, '-', coot.molecule_name(imol) if molName == cpd: coot.set_mol_displayed(imol, 1) - print 'reading',os.path.join(self.project_directory,self.xtalID,'compound',molNameCIF+'.cif') - coot.read_cif_dictionary(os.path.join(self.project_directory,self.xtalID,'compound',molNameCIF+'.cif')) + print 'reading', os.path.join( + self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif') + coot.read_cif_dictionary(os.path.join( + self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) else: coot.set_mol_displayed(imol, 0) - def update_RefinementOutcome_radiobutton(self): # updating dataset outcome radiobuttons current_stage = 0 @@ -858,7 +891,8 @@ def refresh_site_combobox(self): # only repopulate if site exists if self.xtalID in self.siteDict: for item in sorted(self.siteDict[self.xtalID]): - self.cb_site.append_text('site: {0!s} - event: {1!s}'.format(item[5], item[6])) + self.cb_site.append_text( + 'site: {0!s} - event: {1!s}'.format(item[5], item[6])) def ChangeSite(self, widget, data=None): if self.xtalID in self.siteDict: @@ -897,13 +931,13 @@ def RefreshSiteData(self): # for w in self.label_button_list: # w.set_active(False) - print 'pandda index', self.pandda_index self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] print 'new spider plot:', self.spider_plot self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] print 'new event map:', self.event_map - self.ligand_confidence = str(self.siteDict[self.xtalID][self.pandda_index][7]) + self.ligand_confidence = str( + self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) @@ -919,14 +953,17 @@ def RefreshSiteData(self): self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, self.event_index) print '>>>>> spider plot data', self.spider_plot_data - self.ligandIDValue.set_label(self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue.set_label( + self.spider_plot_data['PANDDA_site_ligand_id']) try: - self.ligand_occupancyValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) + self.ligand_occupancyValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) except ValueError: self.ligand_occupancyValue.set_label('-') try: - self.ligand_BaverageValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) + self.ligand_BaverageValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) except ValueError: self.ligand_BaverageValue.set_label('-') @@ -937,22 +974,26 @@ def RefreshSiteData(self): self.ligand_BratioSurroundingsValue.set_label('-') try: - self.ligand_RSCCValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) + self.ligand_RSCCValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) except ValueError: self.ligand_RSCCValue.set_label('-') try: - self.ligand_rmsdValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) + self.ligand_rmsdValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) except ValueError: self.ligand_rmsdValue.set_label('-') try: - self.ligand_RSRValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) + self.ligand_RSRValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) except ValueError: self.ligand_RSRValue.set_label('-') try: - self.ligand_RSZDValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) + self.ligand_RSZDValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) except ValueError: self.ligand_RSZDValue.set_label('-') @@ -971,7 +1012,8 @@ def RefreshSiteData(self): else: spider_plot_pic = gtk.gdk.pixbuf_new_from_file( os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_pic = spider_plot_pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) ######################################################################################### @@ -989,15 +1031,16 @@ def RefreshSiteData(self): def experiment_stage_button_clicked(self, widget, data=None): self.db_dict_mainTable['RefinementOutcome'] = data self.db_dict_mainTable['RefinementOutcomePerson'] = getpass.getuser() - self.db_dict_mainTable['RefinementOutcomeDate'] = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] - + self.db_dict_mainTable['RefinementOutcomeDate'] = datetime.strftime( + datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] self.Logfile.insert('==> COOT: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( data) + ' in mainTable of datasource') # print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( # data) + ' in mainTable of datasource' # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile,self.xtalID,'ligand_bound',self.db_dict_mainTable) + self.db.create_or_remove_missing_records_in_depositTable( + self.xce_logfile, self.xtalID, 'ligand_bound', self.db_dict_mainTable) def ligand_confidence_button_clicked(self, widget, data=None): print 'PANDDA_index', self.pandda_index @@ -1047,13 +1090,15 @@ def RefreshData(self): # reset spider plot image spider_plot_pic = gtk.gdk.pixbuf_new_from_file( os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_pic = spider_plot_pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) # reset ground state mean map self.ground_state_mean_map = '' self.ground_state_mean_map_button.set_sensitive(False) - self.ground_state_mean_map_button.set_label('Show ground state mean map') + self.ground_state_mean_map_button.set_label( + 'Show ground state mean map') if os.path.isfile( os.path.join(self.project_directory, self.xtalID, self.xtalID + '-ground-state-mean-map.native.ccp4')): self.ground_state_mean_map_button.set_sensitive(True) @@ -1062,9 +1107,12 @@ def RefreshData(self): # initialize Refinement library # self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) - self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) - self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) - self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * '0' + str(self.Serial) + self.Refine = XChemRefine.Refine( + self.project_directory, self.xtalID, self.compoundID, self.data_source) + self.Serial = XChemRefine.GetSerial( + self.project_directory, self.xtalID) + self.panddaSerial = panddaSerial = m = ( + 4 - len(str(self.Serial))) * '0' + str(self.Serial) # self.Serial=self.Refine.GetSerial() if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple @@ -1098,7 +1146,8 @@ def RefreshData(self): # if the structure was previously refined, try to read the parameters # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: - self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) + self.RefmacParams = self.Refine.ParamsFromPreviousCycle( + self.Serial - 1) print '==> REFMAC params:', self.RefmacParams # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) @@ -1111,9 +1160,9 @@ def RefreshData(self): ######################################################################################### # ligand files # first remove old samples if present - print '>>>',self.mol_dict['ligand_stereo'] + print '>>>', self.mol_dict['ligand_stereo'] for n, item in enumerate(self.mol_dict['ligand_stereo']): - print '__',item + print '__', item self.select_cpd_cb.remove_text(0) print 'done' @@ -1146,25 +1195,27 @@ def RefreshData(self): imol = coot.handle_read_draw_molecule_with_recentre( os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb'), 0) self.mol_dict['ligand'] = imol - coot.read_cif_dictionary(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) + coot.read_cif_dictionary(os.path.join( + self.project_directory, self.xtalID, self.compoundID + '.cif')) self.select_cpd_cb.append_text(self.compoundID) self.mol_dict['ligand_stereo'] = [] self.mol_dict['ligand_stereo'].append(imol) # ligands in compound directory - for cifFile in sorted(glob.glob(os.path.join(self.project_directory,self.xtalID,'compound',self.compoundID+'_*.pdb'))): + for cifFile in sorted(glob.glob(os.path.join(self.project_directory, self.xtalID, 'compound', self.compoundID+'_*.pdb'))): cif = cifFile[cifFile.rfind('/')+1:] if '_with_H' in cif: continue - self.select_cpd_cb.append_text(cif.replace('.pdb','')) + self.select_cpd_cb.append_text(cif.replace('.pdb', '')) imol = coot.handle_read_draw_molecule_with_recentre(cifFile, 0) self.mol_dict['ligand_stereo'].append(imol) - coot.set_mol_displayed(imol,0) + coot.set_mol_displayed(imol, 0) # autofitted ligands - for pdbFile in sorted(glob.glob(os.path.join(self.project_directory,self.xtalID,'autofit_ligand','*','*.pdb'))): + for pdbFile in sorted(glob.glob(os.path.join(self.project_directory, self.xtalID, 'autofit_ligand', '*', '*.pdb'))): autofitRun = pdbFile.split('/')[len(pdbFile.split('/')) - 2] if pdbFile.endswith(autofitRun+'.pdb'): self.select_cpd_cb.append_text(autofitRun) - imol = coot.handle_read_draw_molecule_with_recentre(pdbFile, 0) + imol = coot.handle_read_draw_molecule_with_recentre( + pdbFile, 0) self.mol_dict['ligand_stereo'].append(imol) coot.set_mol_displayed(imol, 0) self.select_cpd_cb.set_sensitive(True) @@ -1181,9 +1232,9 @@ def RefreshData(self): # self.Logfile.insert('==> COOT: looking for ground-state model ' + os.path.join(self.project_directory, self.xtalID, # self.pdb_style.replace('.pdb', # '') + '.split.ground-state.pdb')) -## print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, -## self.pdb_style.replace('.pdb', -## '') + '.split.ground-state.pdb') +# print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', +# '') + '.split.ground-state.pdb') # if os.path.isfile(os.path.join(self.project_directory, self.xtalID, # self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): # self.Logfile.insert('==> COOT: found ground-state model') @@ -1256,9 +1307,10 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( + self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( item).endswith(self.pdb_style): - coot.set_show_symmetry_master(1) # master switch to show symmetry molecules + # master switch to show symmetry molecules + coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model ######################################################################################### @@ -1271,13 +1323,15 @@ def RefreshData(self): if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc_??????.map')): coot.set_colour_map_rotation_on_read_pdb(0) coot.set_default_initial_contour_level_for_difference_map(3) - coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, 'fofc.map'), 1) + coot.handle_read_ccp4_map(os.path.join( + self.project_directory, self.xtalID, 'fofc.map'), 1) coot.set_default_initial_contour_level_for_map(1) - coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, '2fofc.map'), 0) + coot.handle_read_ccp4_map(os.path.join( + self.project_directory, self.xtalID, '2fofc.map'), 0) coot.set_last_map_colour(0, 0, 1) else: # try to open mtz file with same name as pdb file -# coot.set_default_initial_contour_level_for_map(1) + # coot.set_default_initial_contour_level_for_map(1) coot.set_colour_map_rotation_on_read_pdb(0) # if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): # os.chdir(os.path.join(self.project_directory,self.xtalID)) @@ -1287,11 +1341,14 @@ def RefreshData(self): # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): # os.symlink('dimple.mtz',self.mtz_style) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, self.mtz_style)) + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, self.mtz_style)) elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, 'init.mtz')) + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, 'init.mtz')) elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')) + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, 'dimple.mtz')) ######################################################################################### # update Quality Indicator table @@ -1306,43 +1363,50 @@ def RefreshData(self): gtk.gdk.color_parse(self.QualityIndicators['RefinementRfreeTraficLight'])) except ValueError: pass - self.ResolutionValue.set_label(self.QualityIndicators['RefinementResolution']) + self.ResolutionValue.set_label( + self.QualityIndicators['RefinementResolution']) try: self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementResolutionTL'])) except ValueError: pass - self.MolprobityScoreValue.set_label(self.QualityIndicators['RefinementMolProbityScore']) + self.MolprobityScoreValue.set_label( + self.QualityIndicators['RefinementMolProbityScore']) try: self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( self.QualityIndicators['RefinementMolProbityScoreTL'])) except ValueError: pass - self.RamachandranOutliersValue.set_label(self.QualityIndicators['RefinementRamachandranOutliers']) + self.RamachandranOutliersValue.set_label( + self.QualityIndicators['RefinementRamachandranOutliers']) try: self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( self.QualityIndicators['RefinementRamachandranOutliersTL'])) except ValueError: pass - self.RamachandranFavoredValue.set_label(self.QualityIndicators['RefinementRamachandranFavored']) + self.RamachandranFavoredValue.set_label( + self.QualityIndicators['RefinementRamachandranFavored']) try: self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( self.QualityIndicators['RefinementRamachandranFavoredTL'])) except ValueError: pass - self.rmsdBondsValue.set_label(self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue.set_label( + self.QualityIndicators['RefinementRmsdBonds']) try: self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdBondsTL'])) except ValueError: pass - self.rmsdAnglesValue.set_label(self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue.set_label( + self.QualityIndicators['RefinementRmsdAngles']) try: self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdAnglesTL'])) except ValueError: pass - self.MatrixWeightValue.set_label(self.QualityIndicators['RefinementMatrixWeight']) + self.MatrixWeightValue.set_label( + self.QualityIndicators['RefinementMatrixWeight']) try: pic = gtk.gdk.pixbuf_new_from_file( @@ -1383,52 +1447,56 @@ def start_refinement(self): # ####################################################### -# if self.refinementProtocol.startswith('pandda'): -# -# ####################################################### -# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): -# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) -# # create folder for new refinement cycle -# try: -# self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) -# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) -# except OSError: -# self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') -## print '==> XCE: WARNING -> folder exists; will overwrite contents!' -# self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') -# -# ####################################################### -# # write PDB file -# # now take protein pdb file and write it to newly create Refine_ folder -# # note: the user has to make sure that the ligand file was merged into main file -# for item in coot_utils_XChem.molecule_number_list(): -# if coot.molecule_name(item).endswith( -# self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( -# item).endswith(self.pdb_style): -# coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', -# 'Refine_' + str(self.Serial), 'refine.modified.pdb')) -# break -# # elif coot.molecule_name(item).endswith('dimple.pdb'): -# # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) -# # break -# -# XChemRefine.panddaRefine(self.project_directory, self.xtalID, self.compoundID, -# self.data_source).RunQuickRefine(self.Serial, self.RefmacParams, -# self.external_software, self.xce_logfile, -# self.refinementProtocol, self.covLinkAtomSpec) -# else: + # if self.refinementProtocol.startswith('pandda'): + # + # ####################################################### + # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): + # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) + # # create folder for new refinement cycle + # try: + # self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + # except OSError: + # self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') + ## print '==> XCE: WARNING -> folder exists; will overwrite contents!' + # self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') + # + # ####################################################### + # # write PDB file + # # now take protein pdb file and write it to newly create Refine_ folder + # # note: the user has to make sure that the ligand file was merged into main file + # for item in coot_utils_XChem.molecule_number_list(): + # if coot.molecule_name(item).endswith( + # self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( + # item).endswith(self.pdb_style): + # coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', + # 'Refine_' + str(self.Serial), 'refine.modified.pdb')) + # break + # # elif coot.molecule_name(item).endswith('dimple.pdb'): + # # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) + # # break + # + # XChemRefine.panddaRefine(self.project_directory, self.xtalID, self.compoundID, + # self.data_source).RunQuickRefine(self.Serial, self.RefmacParams, + # self.external_software, self.xce_logfile, + # self.refinementProtocol, self.covLinkAtomSpec) + # else: ####################################################### if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) # create folder for new refinement cycle try: - self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) - os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + self.Logfile.insert('==> COOT: trying to make folder: %s' % os.path.join( + self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + os.mkdir(os.path.join(self.project_directory, self.xtalID, + 'cootOut', 'Refine_' + str(self.Serial))) except OSError: - self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') + self.Logfile.warning( + '==> COOT: folder exists; will overwrite contents!') # print '==> XCE: WARNING -> folder exists; will overwrite contents!' - self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') + self.Logfile.warning( + '==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') # ####################################################### @@ -1459,10 +1527,11 @@ def start_refinement(self): if foundPDB: coot.delete_hydrogens(item) coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', - 'Refine_' + str(self.Serial), 'in.pdb')) + 'Refine_' + str(self.Serial), 'in.pdb')) # self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) - self.Refine.RunBuster(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) + self.Refine.RunBuster(self.Serial, self.RefmacParams, + self.external_software, self.xce_logfile, self.covLinkAtomSpec) self.index += 1 if self.index >= len(self.Todo): # self.index = len(self.Todo) @@ -1476,14 +1545,14 @@ def RefinementParams(self, widget): print self.RefmacParams def covalentLinkDef(self, widget): - coot.user_defined_click_py(2,self.show_potential_link) + coot.user_defined_click_py(2, self.show_potential_link) - def show_potential_link(self,*clicks): + def show_potential_link(self, *clicks): # first find imol of protein molecule # it's a prerequisite that the ligand is merged into the protein imol_protein = None for imol in coot_utils_XChem.molecule_number_list(): - print '>',coot.molecule_name(imol) + print '>', coot.molecule_name(imol) if coot.molecule_name(imol).endswith(self.pdb_style) or \ coot.molecule_name(imol).endswith('init.pdb') or \ coot.molecule_name(imol).endswith('dimple.pdb') or \ @@ -1497,18 +1566,24 @@ def show_potential_link(self,*clicks): click_2 = clicks[1] imol_1 = click_1[1] imol_2 = click_2[1] - print 'imolp',imol,'imo11',imol_1,'imol2',imol_2 + print 'imolp', imol, 'imo11', imol_1, 'imol2', imol_2 if imol_1 == imol_2 and imol_1 == imol_protein: - print 'click_1',click_1 + print 'click_1', click_1 self.covLinkAtomSpec = None - xyz_1 = atom_info_string(click_1[1],click_1[2],click_1[3],click_1[4],click_1[5],click_1[6]) - residue_1 = residue_name(click_1[1],click_1[2],click_1[3],click_1[4]) - xyz_2 = atom_info_string(click_2[1],click_2[2],click_2[3],click_2[4],click_2[5],click_2[6]) - residue_2 = residue_name(click_2[1],click_2[2],click_2[3],click_2[4]) + xyz_1 = atom_info_string( + click_1[1], click_1[2], click_1[3], click_1[4], click_1[5], click_1[6]) + residue_1 = residue_name( + click_1[1], click_1[2], click_1[3], click_1[4]) + xyz_2 = atom_info_string( + click_2[1], click_2[2], click_2[3], click_2[4], click_2[5], click_2[6]) + residue_2 = residue_name( + click_2[1], click_2[2], click_2[3], click_2[4]) thick = 4 - to_generic_object_add_line(self.covLinkObject, "yellowtint", thick, xyz_1[3], xyz_1[4], xyz_1[5], xyz_2[3], xyz_2[4], xyz_2[5]) + to_generic_object_add_line( + self.covLinkObject, "yellowtint", thick, xyz_1[3], xyz_1[4], xyz_1[5], xyz_2[3], xyz_2[4], xyz_2[5]) set_display_generic_object(self.covLinkObject, 1) - self.covLinkAtomSpec = [imol_protein,click_1,click_2,residue_1,residue_2] + self.covLinkAtomSpec = [imol_protein, + click_1, click_2, residue_1, residue_2] else: print 'error: both atoms must belong to the same object; did you merge the ligand with your protein?' @@ -1539,8 +1614,10 @@ def get_samples_to_look_at(self, widget): self.cb.remove_text(0) self.Todo = [] self.siteDict = {} - self.Todo, self.siteDict = self.db.get_todoList_for_coot(self.selection_mode) - self.status_label.set_text('found {0!s} samples'.format(len(self.Todo))) + self.Todo, self.siteDict = self.db.get_todoList_for_coot( + self.selection_mode) + self.status_label.set_text( + 'found {0!s} samples'.format(len(self.Todo))) # refresh sample CB for item in sorted(self.Todo): self.cb.append_text('{0!s}'.format(item[0])) @@ -1569,7 +1646,8 @@ def place_ligand_here(self, widget): for imol in coot_utils_XChem.molecule_number_list(): if imol not in self.mol_dict['ligand_stereo']: continue - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + molName = coot.molecule_name(imol)[coot.molecule_name( + imol).rfind('/')+1:].replace('.pdb', '') if molName == cpd: print '===> XCE: moving ligand to pointer' coot_utils_XChem.move_molecule_here(imol) @@ -1579,34 +1657,40 @@ def place_ligand_here(self, widget): # print 'LIGAND: ', self.mol_dict['ligand'] # coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) - def merge_ligand_into_protein(self, widget): cpd = str(self.select_cpd_cb.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): if imol not in self.mol_dict['ligand_stereo']: continue - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + molName = coot.molecule_name(imol)[coot.molecule_name( + imol).rfind('/')+1:].replace('.pdb', '') if molName == cpd: - print '===> XCE: merge ligand into protein structure -->',cpd + print '===> XCE: merge ligand into protein structure -->', cpd coot.merge_molecules_py([imol], self.mol_dict['protein']) if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/') + 1:].replace('.pdb', '').replace('_phenix','').replace('_rhofit','') + molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( + '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')): - os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) - print 'XCE: changing directory', os.path.join(self.project_directory, self.xtalID) + os.system('/bin/rm %s' % os.path.join(self.project_directory, + self.xtalID, self.compoundID + '.cif')) + print 'XCE: changing directory', os.path.join( + self.project_directory, self.xtalID) os.chdir(os.path.join(self.project_directory, self.xtalID)) print 'XCE: changing symlink ln -s %s %s.cif' % ( - os.path.join('compound', molName + '.cif'), self.compoundID) - os.system('ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) + os.path.join('compound', molName + '.cif'), self.compoundID) + os.system( + 'ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): - os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')) - print 'XCE: changing directory', os.path.join(self.project_directory, self.xtalID) + os.system('/bin/rm %s' % os.path.join(self.project_directory, + self.xtalID, self.compoundID + '.pdb')) + print 'XCE: changing directory', os.path.join( + self.project_directory, self.xtalID) os.chdir(os.path.join(self.project_directory, self.xtalID)) print 'XCE: changing symlink ln -s %s %s.pdb' % ( - os.path.join('compound', molName + '.pdb'), self.compoundID) + os.path.join('compound', molName + '.pdb'), self.compoundID) os.system('ln -s %s %s.pdb' % (os.path.join('compound', molName - + '.pdb'), self.compoundID)) - print '===> XCE: deleting ligand molecule',molName + + '.pdb'), self.compoundID)) + print '===> XCE: deleting ligand molecule', molName coot.close_molecule(imol) self.select_cpd_cb.set_sensitive(False) @@ -1619,15 +1703,16 @@ def merge_ligand_into_protein(self, widget): def show_molprobity_to_do(self, widget): print self.panddaSerial - AdjPanddaSerial = (4 - len(str(self.Serial))) * '0' + str(int(self.panddaSerial) - 1) + AdjPanddaSerial = (4 - len(str(self.Serial))) * \ + '0' + str(int(self.panddaSerial) - 1) print '==> XCE COOT: trying to find ' + os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py') if os.path.isfile(os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py')): + 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py')): print '==> XCE: running MolProbity Summary for', self.xtalID coot.run_script(os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py')) + 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py')) # elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), # 'molprobity_coot.py')): # print '==> XCE: running MolProbity Summary for', self.xtalID diff --git a/lib/XChemCootNew.py b/lib/XChemCootNew.py index 3e60410b..6bae8402 100755 --- a/lib/XChemCootNew.py +++ b/lib/XChemCootNew.py @@ -1,5 +1,14 @@ # last edited: 08/08/2017 - 15:00 +import pango +import gtk +import pygtk +import coot_utils_XChem +import coot +import XChemLog +import XChemUtils +import XChemRefine +import XChemDB import gobject import sys import os @@ -15,19 +24,12 @@ # XCE libraries sys.path.append(os.getenv('XChemExplorer_DIR') + '/lib') -import XChemDB -import XChemRefine -import XChemUtils -import XChemLog # libraries from COOT -import pygtk, gtk, pango -import coot # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. # modified file is now in $XChemExplorer_DIR/lib -import coot_utils_XChem class GUI(object): @@ -52,7 +54,8 @@ def __init__(self): print self.settings # checking for external software packages - self.external_software = XChemUtils.external_software(self.xce_logfile).check() + self.external_software = XChemUtils.external_software( + self.xce_logfile).check() self.external_software['qsub_remote'] = remote_qsub_submission self.selection_criteria = ['0 - All Datasets', @@ -66,8 +69,10 @@ def __init__(self): self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], ['In Refinement', '3 - In Refinement', 65000, 0, 0], - ['Comp Chem Ready!', '4 - CompChem ready', 65000, 0, 0], - ['Ready for Deposition!', '5 - Deposition ready', 65000, 0, 0], + ['Comp Chem Ready!', + '4 - CompChem ready', 65000, 0, 0], + ['Ready for Deposition!', + '5 - Deposition ready', 65000, 0, 0], ['In PDB', '6 - Deposited', 65000, 0, 0], ['Analysed & Rejected', '7 - Analysed & Rejected', 65000, 0, 0]] @@ -129,7 +134,6 @@ def __init__(self): self.label_button_list = [] - ########################################################################################### # some COOT settings coot.set_map_radius(17) @@ -176,7 +180,7 @@ def __init__(self): 'TWIN': '', 'WATER': '', 'LIGOCC': '', - 'SANITY': '' } + 'SANITY': ''} def StartGUI(self): @@ -208,7 +212,8 @@ def StartGUI(self): # self.hbox_select_samples.add(self.cb_select_sites) self.select_samples_button = gtk.Button(label="GO") - self.select_samples_button.connect("clicked", self.get_samples_to_look_at) + self.select_samples_button.connect( + "clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) @@ -223,7 +228,8 @@ def StartGUI(self): ################################################################################# # --- refinement protocol --- frame = gtk.Frame() - self.refinementProtocolcheckbox = gtk.CheckButton('PanDDA model refinement)') + self.refinementProtocolcheckbox = gtk.CheckButton( + 'PanDDA model refinement)') # callback is defined later # self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) self.refinementProtocolcheckbox.set_active(True) @@ -260,7 +266,8 @@ def StartGUI(self): ResolutionLabel_frame = gtk.Frame() self.ResolutionLabel = gtk.Label('Resolution') ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label(self.QualityIndicators['RefinementResolution']) + self.ResolutionValue = gtk.Label( + self.QualityIndicators['RefinementResolution']) ResolutionBox_frame = gtk.Frame() self.ResolutionBox = gtk.EventBox() self.ResolutionBox.add(self.ResolutionValue) @@ -269,7 +276,8 @@ def StartGUI(self): MolprobityScoreLabel_frame = gtk.Frame() self.MolprobityScoreLabel = gtk.Label('MolprobityScore') MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) - self.MolprobityScoreValue = gtk.Label(self.QualityIndicators['RefinementMolProbityScore']) + self.MolprobityScoreValue = gtk.Label( + self.QualityIndicators['RefinementMolProbityScore']) MolprobityScoreBox_frame = gtk.Frame() self.MolprobityScoreBox = gtk.EventBox() self.MolprobityScoreBox.add(self.MolprobityScoreValue) @@ -278,7 +286,8 @@ def StartGUI(self): RamachandranOutliersLabel_frame = gtk.Frame() self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) - self.RamachandranOutliersValue = gtk.Label(self.QualityIndicators['RefinementRamachandranOutliers']) + self.RamachandranOutliersValue = gtk.Label( + self.QualityIndicators['RefinementRamachandranOutliers']) RamachandranOutliersBox_frame = gtk.Frame() self.RamachandranOutliersBox = gtk.EventBox() self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) @@ -287,7 +296,8 @@ def StartGUI(self): RamachandranFavoredLabel_frame = gtk.Frame() self.RamachandranFavoredLabel = gtk.Label('Rama Favored') RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) - self.RamachandranFavoredValue = gtk.Label(self.QualityIndicators['RefinementRamachandranFavored']) + self.RamachandranFavoredValue = gtk.Label( + self.QualityIndicators['RefinementRamachandranFavored']) RamachandranFavoredBox_frame = gtk.Frame() self.RamachandranFavoredBox = gtk.EventBox() self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) @@ -296,7 +306,8 @@ def StartGUI(self): rmsdBondsLabel_frame = gtk.Frame() self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') rmsdBondsLabel_frame.add(self.rmsdBondsLabel) - self.rmsdBondsValue = gtk.Label(self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue = gtk.Label( + self.QualityIndicators['RefinementRmsdBonds']) rmsdBondsBox_frame = gtk.Frame() self.rmsdBondsBox = gtk.EventBox() self.rmsdBondsBox.add(self.rmsdBondsValue) @@ -305,7 +316,8 @@ def StartGUI(self): rmsdAnglesLabel_frame = gtk.Frame() self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) - self.rmsdAnglesValue = gtk.Label(self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue = gtk.Label( + self.QualityIndicators['RefinementRmsdAngles']) rmsdAnglesBox_frame = gtk.Frame() self.rmsdAnglesBox = gtk.EventBox() self.rmsdAnglesBox.add(self.rmsdAnglesValue) @@ -314,7 +326,8 @@ def StartGUI(self): MatrixWeightLabel_frame = gtk.Frame() self.MatrixWeightLabel = gtk.Label('Matrix Weight') MatrixWeightLabel_frame.add(self.MatrixWeightLabel) - self.MatrixWeightValue = gtk.Label(self.QualityIndicators['RefinementMatrixWeight']) + self.MatrixWeightValue = gtk.Label( + self.QualityIndicators['RefinementMatrixWeight']) MatrixWeightBox_frame = gtk.Frame() self.MatrixWeightBox = gtk.EventBox() self.MatrixWeightBox.add(self.MatrixWeightValue) @@ -323,7 +336,8 @@ def StartGUI(self): ligandIDLabel_frame = gtk.Frame() self.ligandIDLabel = gtk.Label('Ligand ID') ligandIDLabel_frame.add(self.ligandIDLabel) - self.ligandIDValue = gtk.Label(self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue = gtk.Label( + self.spider_plot_data['PANDDA_site_ligand_id']) ligandIDBox_frame = gtk.Frame() self.ligandIDBox = gtk.EventBox() self.ligandIDBox.add(self.ligandIDValue) @@ -332,7 +346,8 @@ def StartGUI(self): ligand_occupancyLabel_frame = gtk.Frame() self.ligand_occupancyLabel = gtk.Label('occupancy') ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) - self.ligand_occupancyValue = gtk.Label(self.spider_plot_data['PANDDA_site_occupancy']) + self.ligand_occupancyValue = gtk.Label( + self.spider_plot_data['PANDDA_site_occupancy']) ligand_occupancyBox_frame = gtk.Frame() self.ligand_occupancyBox = gtk.EventBox() self.ligand_occupancyBox.add(self.ligand_occupancyValue) @@ -341,7 +356,8 @@ def StartGUI(self): ligand_BaverageLabel_frame = gtk.Frame() self.ligand_BaverageLabel = gtk.Label('B average') ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) - self.ligand_BaverageValue = gtk.Label(self.spider_plot_data['PANDDA_site_B_average']) + self.ligand_BaverageValue = gtk.Label( + self.spider_plot_data['PANDDA_site_B_average']) ligand_BaverageBox_frame = gtk.Frame() self.ligand_BaverageBox = gtk.EventBox() self.ligand_BaverageBox.add(self.ligand_BaverageValue) @@ -349,18 +365,22 @@ def StartGUI(self): ligand_BratioSurroundingsLabel_frame = gtk.Frame() self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') - ligand_BratioSurroundingsLabel_frame.add(self.ligand_BratioSurroundingsLabel) + ligand_BratioSurroundingsLabel_frame.add( + self.ligand_BratioSurroundingsLabel) self.ligand_BratioSurroundingsValue = gtk.Label( self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) ligand_BratioSurroundingsBox_frame = gtk.Frame() self.ligand_BratioSurroundingsBox = gtk.EventBox() - self.ligand_BratioSurroundingsBox.add(self.ligand_BratioSurroundingsValue) - ligand_BratioSurroundingsBox_frame.add(self.ligand_BratioSurroundingsBox) + self.ligand_BratioSurroundingsBox.add( + self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add( + self.ligand_BratioSurroundingsBox) ligand_RSCCLabel_frame = gtk.Frame() self.ligand_RSCCLabel = gtk.Label('RSCC') ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) - self.ligand_RSCCValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSCC']) + self.ligand_RSCCValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSCC']) ligand_RSCCBox_frame = gtk.Frame() self.ligand_RSCCBox = gtk.EventBox() self.ligand_RSCCBox.add(self.ligand_RSCCValue) @@ -369,7 +389,8 @@ def StartGUI(self): ligand_rmsdLabel_frame = gtk.Frame() self.ligand_rmsdLabel = gtk.Label('rmsd') ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) - self.ligand_rmsdValue = gtk.Label(self.spider_plot_data['PANDDA_site_rmsd']) + self.ligand_rmsdValue = gtk.Label( + self.spider_plot_data['PANDDA_site_rmsd']) ligand_rmsdBox_frame = gtk.Frame() self.ligand_rmsdBox = gtk.EventBox() self.ligand_rmsdBox.add(self.ligand_rmsdValue) @@ -378,7 +399,8 @@ def StartGUI(self): ligand_RSRLabel_frame = gtk.Frame() self.ligand_RSRLabel = gtk.Label('RSR') ligand_RSRLabel_frame.add(self.ligand_RSRLabel) - self.ligand_RSRValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSR']) + self.ligand_RSRValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSR']) ligand_RSRBox_frame = gtk.Frame() self.ligand_RSRBox = gtk.EventBox() self.ligand_RSRBox.add(self.ligand_RSRValue) @@ -387,7 +409,8 @@ def StartGUI(self): ligand_RSZDLabel_frame = gtk.Frame() self.ligand_RSZDLabel = gtk.Label('RSZD') ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) - self.ligand_RSZDValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSZD']) + self.ligand_RSZDValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSZD']) ligand_RSZDBox_frame = gtk.Frame() self.ligand_RSZDBox = gtk.EventBox() self.ligand_RSZDBox.add(self.ligand_RSZDValue) @@ -422,7 +445,8 @@ def StartGUI(self): self.table_right.attach(ligandIDLabel_frame, 0, 1, 0, 1) self.table_right.attach(ligand_occupancyLabel_frame, 0, 1, 1, 2) self.table_right.attach(ligand_BaverageLabel_frame, 0, 1, 2, 3) - self.table_right.attach(ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach( + ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) self.table_right.attach(ligand_RSCCLabel_frame, 0, 1, 4, 5) self.table_right.attach(ligand_rmsdLabel_frame, 0, 1, 5, 6) self.table_right.attach(ligand_RSRLabel_frame, 0, 1, 6, 7) @@ -446,8 +470,10 @@ def StartGUI(self): button.connect("clicked", self.show_molprobity_to_do) hbox.add(button) # --- ground state mean map --- - self.ground_state_mean_map_button = gtk.Button(label="Show ground state mean map") - self.ground_state_mean_map_button.connect("clicked", self.show_ground_state_mean_map) + self.ground_state_mean_map_button = gtk.Button( + label="Show ground state mean map") + self.ground_state_mean_map_button.connect( + "clicked", self.show_ground_state_mean_map) hbox.add(self.ground_state_mean_map_button) # self.vbox.add(self.ground_state_mean_map_button) self.vbox.add(hbox) @@ -481,7 +507,8 @@ def StartGUI(self): spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_pic = pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image = gtk.Image() self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) spider_plot_frame.add(self.spider_plot_image) @@ -634,8 +661,9 @@ def StartGUI(self): new_button = gtk.RadioButton(None, button[0]) else: new_button = gtk.RadioButton(new_button, button[0]) - new_button.connect("toggled", self.experiment_stage_button_clicked, button[1]) - vbox.pack_start(new_button,False,False,0) + new_button.connect( + "toggled", self.experiment_stage_button_clicked, button[1]) + vbox.pack_start(new_button, False, False, 0) # vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) @@ -650,8 +678,9 @@ def StartGUI(self): new_button = gtk.RadioButton(None, criteria) else: new_button = gtk.RadioButton(new_button, criteria) - new_button.connect("toggled", self.ligand_confidence_button_clicked, criteria) - vbox.pack_start(new_button,False,False,0) + new_button.connect( + "toggled", self.ligand_confidence_button_clicked, criteria) + vbox.pack_start(new_button, False, False, 0) # vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) @@ -695,9 +724,11 @@ def StartGUI(self): self.merge_ligand_button = gtk.Button(label="Merge Ligand") self.place_ligand_here_button = gtk.Button(label="Place Ligand here") self.hbox_for_modeling.add(self.place_ligand_here_button) - self.place_ligand_here_button.connect("clicked", self.place_ligand_here) + self.place_ligand_here_button.connect( + "clicked", self.place_ligand_here) self.hbox_for_modeling.add(self.merge_ligand_button) - self.merge_ligand_button.connect("clicked", self.merge_ligand_into_protein) + self.merge_ligand_button.connect( + "clicked", self.merge_ligand_into_protein) self.select_cpd_cb = gtk.combo_box_new_text() self.select_cpd_cb.connect("changed", self.select_cpd) self.hbox_for_modeling.add(self.select_cpd_cb) @@ -711,18 +742,19 @@ def StartGUI(self): # self.cb_ligand_confidence.append_text(citeria) # self.vbox.add(self.cb_ligand_confidence) - # --- refinement & options --- self.hbox_for_refinement = gtk.HBox() self.REFINEbutton = gtk.Button(label="Refine") self.RefinementParamsButton = gtk.Button(label="refinement parameters") self.covalentLinksbutton = gtk.Button(label="covalent links\n-define-") - self.covalentLinksCreatebutton = gtk.Button(label="covalent links\n-create & refine-") + self.covalentLinksCreatebutton = gtk.Button( + label="covalent links\n-create & refine-") self.REFINEbutton.connect("clicked", self.REFINE) self.hbox_for_refinement.add(self.REFINEbutton) self.RefinementParamsButton.connect("clicked", self.RefinementParams) self.covalentLinksbutton.connect("clicked", self.covalentLinkDef) - self.covalentLinksCreatebutton.connect("clicked", self.covalentLinkCreate) + self.covalentLinksCreatebutton.connect( + "clicked", self.covalentLinkCreate) self.hbox_for_refinement.add(self.RefinementParamsButton) self.hbox_for_refinement.add(self.covalentLinksbutton) self.hbox_for_refinement.add(self.covalentLinksCreatebutton) @@ -731,11 +763,10 @@ def StartGUI(self): # self.VALIDATEbutton = gtk.Button(label="validate structure") # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") - # need to put it here, because attributes within refinementProtocolCallback function # are defined after checkbox is defined - self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) - + self.refinementProtocolcheckbox.connect( + "toggled", self.refinementProtocolCallback) # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") @@ -793,20 +824,23 @@ def select_cpd(self, widget): for imol in coot_utils_XChem.molecule_number_list(): if imol not in self.mol_dict['ligand_stereo']: continue - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + molName = coot.molecule_name(imol)[coot.molecule_name( + imol).rfind('/')+1:].replace('.pdb', '') if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): - molNameCIF = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/') + 1:].replace('.pdb', '').replace('_phenix','').replace('_rhofit','') + molNameCIF = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( + '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') else: molNameCIF = molName - print cpd,'-',imol,'-',coot.molecule_name(imol) + print cpd, '-', imol, '-', coot.molecule_name(imol) if molName == cpd: coot.set_mol_displayed(imol, 1) - print 'reading',os.path.join(self.project_directory,self.xtalID,'compound',molNameCIF+'.cif') - coot.read_cif_dictionary(os.path.join(self.project_directory,self.xtalID,'compound',molNameCIF+'.cif')) + print 'reading', os.path.join( + self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif') + coot.read_cif_dictionary(os.path.join( + self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) else: coot.set_mol_displayed(imol, 0) - def update_RefinementOutcome_radiobutton(self): # updating dataset outcome radiobuttons current_stage = 0 @@ -858,7 +892,8 @@ def refresh_site_combobox(self): # only repopulate if site exists if self.xtalID in self.siteDict: for item in sorted(self.siteDict[self.xtalID]): - self.cb_site.append_text('site: {0!s} - event: {1!s}'.format(item[5], item[6])) + self.cb_site.append_text( + 'site: {0!s} - event: {1!s}'.format(item[5], item[6])) def ChangeSite(self, widget, data=None): if self.xtalID in self.siteDict: @@ -897,13 +932,13 @@ def RefreshSiteData(self): # for w in self.label_button_list: # w.set_active(False) - print 'pandda index', self.pandda_index self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] print 'new spider plot:', self.spider_plot self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] print 'new event map:', self.event_map - self.ligand_confidence = str(self.siteDict[self.xtalID][self.pandda_index][7]) + self.ligand_confidence = str( + self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) @@ -919,14 +954,17 @@ def RefreshSiteData(self): self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, self.event_index) print '>>>>> spider plot data', self.spider_plot_data - self.ligandIDValue.set_label(self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue.set_label( + self.spider_plot_data['PANDDA_site_ligand_id']) try: - self.ligand_occupancyValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) + self.ligand_occupancyValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) except ValueError: self.ligand_occupancyValue.set_label('-') try: - self.ligand_BaverageValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) + self.ligand_BaverageValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) except ValueError: self.ligand_BaverageValue.set_label('-') @@ -937,22 +975,26 @@ def RefreshSiteData(self): self.ligand_BratioSurroundingsValue.set_label('-') try: - self.ligand_RSCCValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) + self.ligand_RSCCValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) except ValueError: self.ligand_RSCCValue.set_label('-') try: - self.ligand_rmsdValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) + self.ligand_rmsdValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) except ValueError: self.ligand_rmsdValue.set_label('-') try: - self.ligand_RSRValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) + self.ligand_RSRValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) except ValueError: self.ligand_RSRValue.set_label('-') try: - self.ligand_RSZDValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) + self.ligand_RSZDValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) except ValueError: self.ligand_RSZDValue.set_label('-') @@ -971,7 +1013,8 @@ def RefreshSiteData(self): else: spider_plot_pic = gtk.gdk.pixbuf_new_from_file( os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_pic = spider_plot_pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) ######################################################################################### @@ -989,13 +1032,15 @@ def RefreshSiteData(self): def experiment_stage_button_clicked(self, widget, data=None): self.db_dict_mainTable['RefinementOutcome'] = data self.db_dict_mainTable['RefinementOutcomePerson'] = getpass.getuser() - self.db_dict_mainTable['RefinementOutcomeDate'] = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] + self.db_dict_mainTable['RefinementOutcomeDate'] = datetime.strftime( + datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] self.Logfile.insert('==> COOT: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( data) + ' in mainTable of datasource') # print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( # data) + ' in mainTable of datasource' # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile,self.xtalID,'ligand_bound',self.db_dict_mainTable) + self.db.create_or_remove_missing_records_in_depositTable( + self.xce_logfile, self.xtalID, 'ligand_bound', self.db_dict_mainTable) def ligand_confidence_button_clicked(self, widget, data=None): print 'PANDDA_index', self.pandda_index @@ -1045,13 +1090,15 @@ def RefreshData(self): # reset spider plot image spider_plot_pic = gtk.gdk.pixbuf_new_from_file( os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_pic = spider_plot_pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) # reset ground state mean map self.ground_state_mean_map = '' self.ground_state_mean_map_button.set_sensitive(False) - self.ground_state_mean_map_button.set_label('Show ground state mean map') + self.ground_state_mean_map_button.set_label( + 'Show ground state mean map') if os.path.isfile( os.path.join(self.project_directory, self.xtalID, self.xtalID + '-ground-state-mean-map.native.ccp4')): self.ground_state_mean_map_button.set_sensitive(True) @@ -1059,9 +1106,12 @@ def RefreshData(self): self.xtalID + '-ground-state-mean-map.native.ccp4') # initialize Refinement library - self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) - self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) - self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * '0' + str(self.Serial) + self.Refine = XChemRefine.Refine( + self.project_directory, self.xtalID, self.compoundID, self.data_source) + self.Serial = XChemRefine.GetSerial( + self.project_directory, self.xtalID) + self.panddaSerial = panddaSerial = m = ( + 4 - len(str(self.Serial))) * '0' + str(self.Serial) # self.Serial=self.Refine.GetSerial() if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple @@ -1095,7 +1145,8 @@ def RefreshData(self): # if the structure was previously refined, try to read the parameters # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: - self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) + self.RefmacParams = self.Refine.ParamsFromPreviousCycle( + self.Serial - 1) print '==> REFMAC params:', self.RefmacParams # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) @@ -1108,9 +1159,9 @@ def RefreshData(self): ######################################################################################### # ligand files # first remove old samples if present - print '>>>',self.mol_dict['ligand_stereo'] + print '>>>', self.mol_dict['ligand_stereo'] for n, item in enumerate(self.mol_dict['ligand_stereo']): - print '__',item + print '__', item self.select_cpd_cb.remove_text(0) print 'done' @@ -1143,25 +1194,27 @@ def RefreshData(self): imol = coot.handle_read_draw_molecule_with_recentre( os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb'), 0) self.mol_dict['ligand'] = imol - coot.read_cif_dictionary(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) + coot.read_cif_dictionary(os.path.join( + self.project_directory, self.xtalID, self.compoundID + '.cif')) self.select_cpd_cb.append_text(self.compoundID) self.mol_dict['ligand_stereo'] = [] self.mol_dict['ligand_stereo'].append(imol) # ligands in compound directory - for cifFile in sorted(glob.glob(os.path.join(self.project_directory,self.xtalID,'compound',self.compoundID+'_*.pdb'))): + for cifFile in sorted(glob.glob(os.path.join(self.project_directory, self.xtalID, 'compound', self.compoundID+'_*.pdb'))): cif = cifFile[cifFile.rfind('/')+1:] if '_with_H' in cif: continue - self.select_cpd_cb.append_text(cif.replace('.pdb','')) + self.select_cpd_cb.append_text(cif.replace('.pdb', '')) imol = coot.handle_read_draw_molecule_with_recentre(cifFile, 0) self.mol_dict['ligand_stereo'].append(imol) - coot.set_mol_displayed(imol,0) + coot.set_mol_displayed(imol, 0) # autofitted ligands - for pdbFile in sorted(glob.glob(os.path.join(self.project_directory,self.xtalID,'autofit_ligand','*','*.pdb'))): + for pdbFile in sorted(glob.glob(os.path.join(self.project_directory, self.xtalID, 'autofit_ligand', '*', '*.pdb'))): autofitRun = pdbFile.split('/')[len(pdbFile.split('/')) - 2] if pdbFile.endswith(autofitRun+'.pdb'): self.select_cpd_cb.append_text(autofitRun) - imol = coot.handle_read_draw_molecule_with_recentre(pdbFile, 0) + imol = coot.handle_read_draw_molecule_with_recentre( + pdbFile, 0) self.mol_dict['ligand_stereo'].append(imol) coot.set_mol_displayed(imol, 0) self.select_cpd_cb.set_sensitive(True) @@ -1176,8 +1229,8 @@ def RefreshData(self): if self.refinementProtocol.startswith('pandda'): self.Logfile.insert('==> COOT: looking for ground-state model ' + os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', - '') + '.split.ground-state.pdb')) + self.pdb_style.replace('.pdb', + '') + '.split.ground-state.pdb')) # print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, # self.pdb_style.replace('.pdb', # '') + '.split.ground-state.pdb') @@ -1201,9 +1254,9 @@ def RefreshData(self): else: self.Logfile.error('==> COOT - cannot find ground-state model') # print '=> XCE - ERROR: cannot find ground-state model' - self.Logfile.insert('==> COOT: looking for bound-state model '+ os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', - '') + '.split.bound-state.pdb')) + self.Logfile.insert('==> COOT: looking for bound-state model ' + os.path.join(self.project_directory, self.xtalID, + self.pdb_style.replace('.pdb', + '') + '.split.bound-state.pdb')) # print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, # self.pdb_style.replace('.pdb', # '') + '.split.bound-state.pdb') @@ -1253,9 +1306,10 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( + self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( item).endswith(self.pdb_style): - coot.set_show_symmetry_master(1) # master switch to show symmetry molecules + # master switch to show symmetry molecules + coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model ######################################################################################### @@ -1267,9 +1321,11 @@ def RefreshData(self): if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc_??????.map')): coot.set_colour_map_rotation_on_read_pdb(0) coot.set_default_initial_contour_level_for_difference_map(3) - coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, 'fofc.map'), 1) + coot.handle_read_ccp4_map(os.path.join( + self.project_directory, self.xtalID, 'fofc.map'), 1) coot.set_default_initial_contour_level_for_map(1) - coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, '2fofc.map'), 0) + coot.handle_read_ccp4_map(os.path.join( + self.project_directory, self.xtalID, '2fofc.map'), 0) coot.set_last_map_colour(0, 0, 1) else: # try to open mtz file with same name as pdb file @@ -1282,11 +1338,14 @@ def RefreshData(self): # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): # os.symlink('dimple.mtz',self.mtz_style) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, self.mtz_style)) + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, self.mtz_style)) elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, 'init.mtz')) + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, 'init.mtz')) elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')) + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, 'dimple.mtz')) ######################################################################################### # update Quality Indicator table @@ -1301,43 +1360,50 @@ def RefreshData(self): gtk.gdk.color_parse(self.QualityIndicators['RefinementRfreeTraficLight'])) except ValueError: pass - self.ResolutionValue.set_label(self.QualityIndicators['RefinementResolution']) + self.ResolutionValue.set_label( + self.QualityIndicators['RefinementResolution']) try: self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementResolutionTL'])) except ValueError: pass - self.MolprobityScoreValue.set_label(self.QualityIndicators['RefinementMolProbityScore']) + self.MolprobityScoreValue.set_label( + self.QualityIndicators['RefinementMolProbityScore']) try: self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( self.QualityIndicators['RefinementMolProbityScoreTL'])) except ValueError: pass - self.RamachandranOutliersValue.set_label(self.QualityIndicators['RefinementRamachandranOutliers']) + self.RamachandranOutliersValue.set_label( + self.QualityIndicators['RefinementRamachandranOutliers']) try: self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( self.QualityIndicators['RefinementRamachandranOutliersTL'])) except ValueError: pass - self.RamachandranFavoredValue.set_label(self.QualityIndicators['RefinementRamachandranFavored']) + self.RamachandranFavoredValue.set_label( + self.QualityIndicators['RefinementRamachandranFavored']) try: self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( self.QualityIndicators['RefinementRamachandranFavoredTL'])) except ValueError: pass - self.rmsdBondsValue.set_label(self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue.set_label( + self.QualityIndicators['RefinementRmsdBonds']) try: self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdBondsTL'])) except ValueError: pass - self.rmsdAnglesValue.set_label(self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue.set_label( + self.QualityIndicators['RefinementRmsdAngles']) try: self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdAnglesTL'])) except ValueError: pass - self.MatrixWeightValue.set_label(self.QualityIndicators['RefinementMatrixWeight']) + self.MatrixWeightValue.set_label( + self.QualityIndicators['RefinementMatrixWeight']) try: pic = gtk.gdk.pixbuf_new_from_file( @@ -1379,26 +1445,31 @@ def start_refinement(self): ####################################################### -# ####################################################### -# # create folder for new refinement cycle and check if free.mtz exists -# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): -# os.mkdir(os.path.join(self.project_directory, self.xtalID)) -# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): -# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) + # ####################################################### + # # create folder for new refinement cycle and check if free.mtz exists + # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): + # os.mkdir(os.path.join(self.project_directory, self.xtalID)) + # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): + # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) if self.refinementProtocol.startswith('pandda'): ####################################################### if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): - os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) + os.mkdir(os.path.join( + self.project_directory, self.xtalID, 'cootOut')) # create folder for new refinement cycle try: - self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) - os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + self.Logfile.insert('==> COOT: trying to make folder: %s' % os.path.join( + self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + os.mkdir(os.path.join(self.project_directory, + self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) except OSError: - self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') + self.Logfile.warning( + '==> COOT: folder exists; will overwrite contents!') # print '==> XCE: WARNING -> folder exists; will overwrite contents!' - self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') + self.Logfile.warning( + '==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') ####################################################### # write PDB file @@ -1406,7 +1477,7 @@ def start_refinement(self): # note: the user has to make sure that the ligand file was merged into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( + self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( item).endswith(self.pdb_style): coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial), 'refine.modified.pdb')) @@ -1425,7 +1496,8 @@ def start_refinement(self): if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): os.mkdir(os.path.join(self.project_directory, self.xtalID)) if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): - os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) + os.mkdir(os.path.join(self.project_directory, + self.xtalID, 'Refine_' + str(self.Serial))) ####################################################### # write PDB file @@ -1440,8 +1512,9 @@ def start_refinement(self): elif coot.molecule_name(item).endswith('refine.split.bound-state.pdb'): coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial), - 'in.pdb')) + 'Refine_' + + str(self.Serial), + 'in.pdb')) break elif coot.molecule_name(item).endswith('init.pdb'): coot.write_pdb_file(item, @@ -1454,7 +1527,8 @@ def start_refinement(self): 'in.pdb')) break - self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) + self.Refine.RunRefmac(self.Serial, self.RefmacParams, + self.external_software, self.xce_logfile, self.covLinkAtomSpec) self.index += 1 if self.index >= len(self.Todo): @@ -1468,14 +1542,14 @@ def RefinementParams(self, widget): self.data_source).RefmacRefinementParams(self.RefmacParams) def covalentLinkDef(self, widget): - coot.user_defined_click_py(2,self.show_potential_link) + coot.user_defined_click_py(2, self.show_potential_link) - def show_potential_link(self,*clicks): + def show_potential_link(self, *clicks): # first find imol of protein molecule # it's a prerequisite that the ligand is merged into the protein imol_protein = None for imol in coot_utils_XChem.molecule_number_list(): - print '>',coot.molecule_name(imol) + print '>', coot.molecule_name(imol) if coot.molecule_name(imol).endswith(self.pdb_style) or \ coot.molecule_name(imol).endswith('init.pdb') or \ coot.molecule_name(imol).endswith('dimple.pdb') or \ @@ -1489,18 +1563,24 @@ def show_potential_link(self,*clicks): click_2 = clicks[1] imol_1 = click_1[1] imol_2 = click_2[1] - print 'imolp',imol,'imo11',imol_1,'imol2',imol_2 + print 'imolp', imol, 'imo11', imol_1, 'imol2', imol_2 if imol_1 == imol_2 and imol_1 == imol_protein: - print 'click_1',click_1 + print 'click_1', click_1 self.covLinkAtomSpec = None - xyz_1 = atom_info_string(click_1[1],click_1[2],click_1[3],click_1[4],click_1[5],click_1[6]) - residue_1 = residue_name(click_1[1],click_1[2],click_1[3],click_1[4]) - xyz_2 = atom_info_string(click_2[1],click_2[2],click_2[3],click_2[4],click_2[5],click_2[6]) - residue_2 = residue_name(click_2[1],click_2[2],click_2[3],click_2[4]) + xyz_1 = atom_info_string( + click_1[1], click_1[2], click_1[3], click_1[4], click_1[5], click_1[6]) + residue_1 = residue_name( + click_1[1], click_1[2], click_1[3], click_1[4]) + xyz_2 = atom_info_string( + click_2[1], click_2[2], click_2[3], click_2[4], click_2[5], click_2[6]) + residue_2 = residue_name( + click_2[1], click_2[2], click_2[3], click_2[4]) thick = 4 - to_generic_object_add_line(self.covLinkObject, "yellowtint", thick, xyz_1[3], xyz_1[4], xyz_1[5], xyz_2[3], xyz_2[4], xyz_2[5]) + to_generic_object_add_line( + self.covLinkObject, "yellowtint", thick, xyz_1[3], xyz_1[4], xyz_1[5], xyz_2[3], xyz_2[4], xyz_2[5]) set_display_generic_object(self.covLinkObject, 1) - self.covLinkAtomSpec = [imol_protein,click_1,click_2,residue_1,residue_2] + self.covLinkAtomSpec = [imol_protein, + click_1, click_2, residue_1, residue_2] else: print 'error: both atoms must belong to the same object; did you merge the ligand with your protein?' @@ -1531,8 +1611,10 @@ def get_samples_to_look_at(self, widget): self.cb.remove_text(0) self.Todo = [] self.siteDict = {} - self.Todo, self.siteDict = self.db.get_todoList_for_coot(self.selection_mode) - self.status_label.set_text('found {0!s} samples'.format(len(self.Todo))) + self.Todo, self.siteDict = self.db.get_todoList_for_coot( + self.selection_mode) + self.status_label.set_text( + 'found {0!s} samples'.format(len(self.Todo))) # refresh sample CB for item in sorted(self.Todo): self.cb.append_text('{0!s}'.format(item[0])) @@ -1561,7 +1643,8 @@ def place_ligand_here(self, widget): for imol in coot_utils_XChem.molecule_number_list(): if imol not in self.mol_dict['ligand_stereo']: continue - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + molName = coot.molecule_name(imol)[coot.molecule_name( + imol).rfind('/')+1:].replace('.pdb', '') if molName == cpd: print '===> XCE: moving ligand to pointer' coot_utils_XChem.move_molecule_here(imol) @@ -1571,34 +1654,40 @@ def place_ligand_here(self, widget): # print 'LIGAND: ', self.mol_dict['ligand'] # coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) - def merge_ligand_into_protein(self, widget): cpd = str(self.select_cpd_cb.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): if imol not in self.mol_dict['ligand_stereo']: continue - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + molName = coot.molecule_name(imol)[coot.molecule_name( + imol).rfind('/')+1:].replace('.pdb', '') if molName == cpd: - print '===> XCE: merge ligand into protein structure -->',cpd + print '===> XCE: merge ligand into protein structure -->', cpd coot.merge_molecules_py([imol], self.mol_dict['protein']) if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/') + 1:].replace('.pdb', '').replace('_phenix','').replace('_rhofit','') + molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( + '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')): - os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) - print 'XCE: changing directory', os.path.join(self.project_directory, self.xtalID) + os.system('/bin/rm %s' % os.path.join(self.project_directory, + self.xtalID, self.compoundID + '.cif')) + print 'XCE: changing directory', os.path.join( + self.project_directory, self.xtalID) os.chdir(os.path.join(self.project_directory, self.xtalID)) print 'XCE: changing symlink ln -s %s %s.cif' % ( - os.path.join('compound', molName + '.cif'), self.compoundID) - os.system('ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) + os.path.join('compound', molName + '.cif'), self.compoundID) + os.system( + 'ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): - os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')) - print 'XCE: changing directory', os.path.join(self.project_directory, self.xtalID) + os.system('/bin/rm %s' % os.path.join(self.project_directory, + self.xtalID, self.compoundID + '.pdb')) + print 'XCE: changing directory', os.path.join( + self.project_directory, self.xtalID) os.chdir(os.path.join(self.project_directory, self.xtalID)) print 'XCE: changing symlink ln -s %s %s.pdb' % ( - os.path.join('compound', molName + '.pdb'), self.compoundID) + os.path.join('compound', molName + '.pdb'), self.compoundID) os.system('ln -s %s %s.pdb' % (os.path.join('compound', molName - + '.pdb'), self.compoundID)) - print '===> XCE: deleting ligand molecule',molName + + '.pdb'), self.compoundID)) + print '===> XCE: deleting ligand molecule', molName coot.close_molecule(imol) self.select_cpd_cb.set_sensitive(False) @@ -1611,7 +1700,8 @@ def merge_ligand_into_protein(self, widget): def show_molprobity_to_do(self, widget): print self.panddaSerial - AdjPanddaSerial = (4 - len(str(self.Serial))) * '0' + str(int(self.panddaSerial) - 1) + AdjPanddaSerial = (4 - len(str(self.Serial))) * \ + '0' + str(int(self.panddaSerial) - 1) print os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), 'molprobity_coot.py') if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), diff --git a/lib/XChemCootOld.py b/lib/XChemCootOld.py index 73654740..224b826a 100755 --- a/lib/XChemCootOld.py +++ b/lib/XChemCootOld.py @@ -1,5 +1,13 @@ # last edited: 21/07/2017 - 15:00 +import pango +import gtk +import pygtk +import coot_utils_XChem +import coot +import XChemUtils +import XChemRefine +import XChemDB import gobject import sys import os @@ -10,18 +18,12 @@ # XCE libraries sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') -import XChemDB -import XChemRefine -import XChemUtils # libraries from COOT -import pygtk, gtk, pango -import coot # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. # modified file is now in $XChemExplorer_DIR/lib -import coot_utils_XChem class GUI(object): @@ -34,80 +36,83 @@ def __init__(self): ########################################################################################### # read in settings file from XChemExplorer to set the relevant paths - print 'current dir',os.getcwd() - self.settings = pickle.load(open(".xce_settings.pkl","rb")) - remote_qsub_submission=self.settings['remote_qsub'] - print 'setting',self.settings + print 'current dir', os.getcwd() + self.settings = pickle.load(open(".xce_settings.pkl", "rb")) + remote_qsub_submission = self.settings['remote_qsub'] + print 'setting', self.settings # self.refine_model_directory=self.settings['refine_model_directory'] - self.database_directory=self.settings['database_directory'] - self.xce_logfile=self.settings['xce_logfile'] - self.data_source=self.settings['data_source'] - self.db=XChemDB.data_source(self.data_source) + self.database_directory = self.settings['database_directory'] + self.xce_logfile = self.settings['xce_logfile'] + self.data_source = self.settings['data_source'] + self.db = XChemDB.data_source(self.data_source) # checking for external software packages - self.external_software=XChemUtils.external_software(self.xce_logfile).check() - self.external_software['qsub_remote']=remote_qsub_submission - - self.selection_criteria = [ '0 - All Datasets', - '1 - Analysis Pending', - '2 - PANDDA model', - '3 - In Refinement', - '4 - CompChem ready', - '5 - Deposition ready', - '6 - Deposited' ] - - self.experiment_stage = [ ['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], - ['In Refinement', '3 - In Refinement', 65000, 0, 0], - ['Comp Chem Ready!', '4 - CompChem ready', 65000, 0, 0], - ['Ready for Deposition!', '5 - Deposition ready', 65000, 0, 0], - ['In PDB', '6 - Deposited', 65000, 0, 0]] - - self.ligand_confidence_category = [ '0 - no ligand present', - '1 - Low Confidence', - '2 - Correct ligand, weak density', - '3 - Clear density, unexpected ligand', - '4 - High Confidence' ] - - self.ligand_site_information = self.db.get_list_of_pandda_sites_for_coot() - + self.external_software = XChemUtils.external_software( + self.xce_logfile).check() + self.external_software['qsub_remote'] = remote_qsub_submission + + self.selection_criteria = ['0 - All Datasets', + '1 - Analysis Pending', + '2 - PANDDA model', + '3 - In Refinement', + '4 - CompChem ready', + '5 - Deposition ready', + '6 - Deposited'] + + self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], + ['In Refinement', + '3 - In Refinement', 65000, 0, 0], + ['Comp Chem Ready!', + '4 - CompChem ready', 65000, 0, 0], + ['Ready for Deposition!', + '5 - Deposition ready', 65000, 0, 0], + ['In PDB', '6 - Deposited', 65000, 0, 0]] + + self.ligand_confidence_category = ['0 - no ligand present', + '1 - Low Confidence', + '2 - Correct ligand, weak density', + '3 - Clear density, unexpected ligand', + '4 - High Confidence'] + + self.ligand_site_information = self.db.get_list_of_pandda_sites_for_coot() # this decides which samples will be looked at self.selection_mode = '' # self.selected_site='' - self.pandda_index=-1 # refers to the number of sites - self.site_index='0' - self.event_index='0' + self.pandda_index = -1 # refers to the number of sites + self.site_index = '0' + self.event_index = '0' # the Folder is kind of a legacy thing because my inital idea was to have separate folders # for Data Processing and Refinement self.project_directory = self.settings['initial_model_directory'] - self.Serial=0 - self.Refine=None + self.Serial = 0 + self.Refine = None self.index = -1 - self.Todo=[] - self.siteDict={} - - self.xtalID='' - self.compoundID='' - self.spider_plot='' - self.ligand_confidence='' - self.refinement_folder='' + self.Todo = [] + self.siteDict = {} + + self.xtalID = '' + self.compoundID = '' + self.spider_plot = '' + self.ligand_confidence = '' + self.refinement_folder = '' # self.datasetOutcome='' - self.pdb_style='refine.pdb' - self.mtz_style='refine.mtz' + self.pdb_style = 'refine.pdb' + self.mtz_style = 'refine.mtz' # stores imol of currently loaded molecules and maps - self.mol_dict = { 'protein': -1, - 'ligand': -1, - '2fofc': -1, - 'fofc': -1, - 'event': -1 } + self.mol_dict = {'protein': -1, + 'ligand': -1, + '2fofc': -1, + 'fofc': -1, + 'event': -1} # two dictionaries which are flushed when a new crystal is loaded # and which contain information to update the data source if necessary - self.db_dict_mainTable={} - self.db_dict_panddaTable={} + self.db_dict_mainTable = {} + self.db_dict_panddaTable = {} ########################################################################################### # some COOT settings @@ -115,47 +120,44 @@ def __init__(self): coot.set_colour_map_rotation_for_map(0) coot.set_colour_map_rotation_on_read_pdb_flag(0) - self.QualityIndicators = { 'RefinementRcryst': '-', - 'RefinementRfree': '-', - 'RefinementRfreeTraficLight': 'gray', - 'RefinementResolution': '-', - 'RefinementResolutionTL': 'gray', - 'RefinementMolProbityScore': '-', - 'RefinementMolProbityScoreTL': 'gray', - 'RefinementRamachandranOutliers': '-', - 'RefinementRamachandranOutliersTL': 'gray', - 'RefinementRamachandranFavored': '-', - 'RefinementRamachandranFavoredTL': 'gray', - 'RefinementRmsdBonds': '-', - 'RefinementRmsdBondsTL': 'gray', - 'RefinementRmsdAngles': '-', - 'RefinementRmsdAnglesTL': 'gray', - 'RefinementMatrixWeight': '-' } - - self.spider_plot_data = { 'PANDDA_site_ligand_id': '-', - 'PANDDA_site_occupancy': '-', - 'PANDDA_site_B_average': '-', - 'PANDDA_site_B_ratio_residue_surroundings': '-', - 'PANDDA_site_RSCC': '-', - 'PANDDA_site_rmsd': '-', - 'PANDDA_site_RSR': '-', - 'PANDDA_site_RSZD': '-' } - + self.QualityIndicators = {'RefinementRcryst': '-', + 'RefinementRfree': '-', + 'RefinementRfreeTraficLight': 'gray', + 'RefinementResolution': '-', + 'RefinementResolutionTL': 'gray', + 'RefinementMolProbityScore': '-', + 'RefinementMolProbityScoreTL': 'gray', + 'RefinementRamachandranOutliers': '-', + 'RefinementRamachandranOutliersTL': 'gray', + 'RefinementRamachandranFavored': '-', + 'RefinementRamachandranFavoredTL': 'gray', + 'RefinementRmsdBonds': '-', + 'RefinementRmsdBondsTL': 'gray', + 'RefinementRmsdAngles': '-', + 'RefinementRmsdAnglesTL': 'gray', + 'RefinementMatrixWeight': '-'} + + self.spider_plot_data = {'PANDDA_site_ligand_id': '-', + 'PANDDA_site_occupancy': '-', + 'PANDDA_site_B_average': '-', + 'PANDDA_site_B_ratio_residue_surroundings': '-', + 'PANDDA_site_RSCC': '-', + 'PANDDA_site_rmsd': '-', + 'PANDDA_site_RSR': '-', + 'PANDDA_site_RSZD': '-'} # default refmac parameters - self.RefmacParams={ 'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '' } - - + self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', + 'XYZIN': '', 'XYZOUT': '', + 'LIBIN': '', 'LIBOUT': '', + 'TLSIN': '', 'TLSOUT': '', + 'TLSADD': '', + 'NCYCLES': '10', + 'MATRIX_WEIGHT': 'AUTO', + 'BREF': ' bref ISOT\n', + 'TLS': '', + 'NCS': '', + 'TWIN': ''} def StartGUI(self): @@ -171,7 +173,7 @@ def StartGUI(self): # self.vbox.add(gtk.Label('Select Samples')) frame = gtk.Frame(label='Select Samples') - self.hbox_select_samples=gtk.HBox() + self.hbox_select_samples = gtk.HBox() # vbox=gtk.VBox() self.cb_select_samples = gtk.combo_box_new_text() @@ -187,19 +189,19 @@ def StartGUI(self): # self.hbox_select_samples.add(self.cb_select_sites) self.select_samples_button = gtk.Button(label="GO") - self.select_samples_button.connect("clicked",self.get_samples_to_look_at) + self.select_samples_button.connect( + "clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) ################################################################################# # --- status window --- - frame=gtk.Frame() - self.status_label=gtk.Label() + frame = gtk.Frame() + self.status_label = gtk.Label() frame.add(self.status_label) self.vbox.pack_start(frame) - # SPACER self.vbox.add(gtk.Label(' ')) @@ -208,146 +210,165 @@ def StartGUI(self): # next comes a section which displays some global quality indicators # a combination of labels and textview widgets, arranged in a table - RRfreeLabel_frame=gtk.Frame() + RRfreeLabel_frame = gtk.Frame() self.RRfreeLabel = gtk.Label('R/Rfree') RRfreeLabel_frame.add(self.RRfreeLabel) - self.RRfreeValue = gtk.Label(self.QualityIndicators['RefinementRcryst']+'/'+self.QualityIndicators['RefinementRfree']) - RRfreeBox_frame=gtk.Frame() + self.RRfreeValue = gtk.Label( + self.QualityIndicators['RefinementRcryst']+'/'+self.QualityIndicators['RefinementRfree']) + RRfreeBox_frame = gtk.Frame() self.RRfreeBox = gtk.EventBox() self.RRfreeBox.add(self.RRfreeValue) RRfreeBox_frame.add(self.RRfreeBox) - ResolutionLabel_frame=gtk.Frame() + ResolutionLabel_frame = gtk.Frame() self.ResolutionLabel = gtk.Label('Resolution') ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label(self.QualityIndicators['RefinementResolution']) - ResolutionBox_frame=gtk.Frame() + self.ResolutionValue = gtk.Label( + self.QualityIndicators['RefinementResolution']) + ResolutionBox_frame = gtk.Frame() self.ResolutionBox = gtk.EventBox() self.ResolutionBox.add(self.ResolutionValue) ResolutionBox_frame.add(self.ResolutionBox) - MolprobityScoreLabel_frame=gtk.Frame() + MolprobityScoreLabel_frame = gtk.Frame() self.MolprobityScoreLabel = gtk.Label('MolprobityScore') MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) - self.MolprobityScoreValue = gtk.Label(self.QualityIndicators['RefinementMolProbityScore']) - MolprobityScoreBox_frame=gtk.Frame() + self.MolprobityScoreValue = gtk.Label( + self.QualityIndicators['RefinementMolProbityScore']) + MolprobityScoreBox_frame = gtk.Frame() self.MolprobityScoreBox = gtk.EventBox() self.MolprobityScoreBox.add(self.MolprobityScoreValue) MolprobityScoreBox_frame.add(self.MolprobityScoreBox) - RamachandranOutliersLabel_frame=gtk.Frame() + RamachandranOutliersLabel_frame = gtk.Frame() self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) - self.RamachandranOutliersValue = gtk.Label(self.QualityIndicators['RefinementRamachandranOutliers']) - RamachandranOutliersBox_frame=gtk.Frame() + self.RamachandranOutliersValue = gtk.Label( + self.QualityIndicators['RefinementRamachandranOutliers']) + RamachandranOutliersBox_frame = gtk.Frame() self.RamachandranOutliersBox = gtk.EventBox() self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) RamachandranOutliersBox_frame.add(self.RamachandranOutliersBox) - RamachandranFavoredLabel_frame=gtk.Frame() + RamachandranFavoredLabel_frame = gtk.Frame() self.RamachandranFavoredLabel = gtk.Label('Rama Favored') RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) - self.RamachandranFavoredValue = gtk.Label(self.QualityIndicators['RefinementRamachandranFavored']) - RamachandranFavoredBox_frame=gtk.Frame() + self.RamachandranFavoredValue = gtk.Label( + self.QualityIndicators['RefinementRamachandranFavored']) + RamachandranFavoredBox_frame = gtk.Frame() self.RamachandranFavoredBox = gtk.EventBox() self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) RamachandranFavoredBox_frame.add(self.RamachandranFavoredBox) - rmsdBondsLabel_frame=gtk.Frame() + rmsdBondsLabel_frame = gtk.Frame() self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') rmsdBondsLabel_frame.add(self.rmsdBondsLabel) - self.rmsdBondsValue = gtk.Label(self.QualityIndicators['RefinementRmsdBonds']) - rmsdBondsBox_frame=gtk.Frame() + self.rmsdBondsValue = gtk.Label( + self.QualityIndicators['RefinementRmsdBonds']) + rmsdBondsBox_frame = gtk.Frame() self.rmsdBondsBox = gtk.EventBox() self.rmsdBondsBox.add(self.rmsdBondsValue) rmsdBondsBox_frame.add(self.rmsdBondsBox) - rmsdAnglesLabel_frame=gtk.Frame() + rmsdAnglesLabel_frame = gtk.Frame() self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) - self.rmsdAnglesValue = gtk.Label(self.QualityIndicators['RefinementRmsdAngles']) - rmsdAnglesBox_frame=gtk.Frame() + self.rmsdAnglesValue = gtk.Label( + self.QualityIndicators['RefinementRmsdAngles']) + rmsdAnglesBox_frame = gtk.Frame() self.rmsdAnglesBox = gtk.EventBox() self.rmsdAnglesBox.add(self.rmsdAnglesValue) rmsdAnglesBox_frame.add(self.rmsdAnglesBox) - MatrixWeightLabel_frame=gtk.Frame() + MatrixWeightLabel_frame = gtk.Frame() self.MatrixWeightLabel = gtk.Label('Matrix Weight') MatrixWeightLabel_frame.add(self.MatrixWeightLabel) - self.MatrixWeightValue = gtk.Label(self.QualityIndicators['RefinementMatrixWeight']) - MatrixWeightBox_frame=gtk.Frame() + self.MatrixWeightValue = gtk.Label( + self.QualityIndicators['RefinementMatrixWeight']) + MatrixWeightBox_frame = gtk.Frame() self.MatrixWeightBox = gtk.EventBox() self.MatrixWeightBox.add(self.MatrixWeightValue) MatrixWeightBox_frame.add(self.MatrixWeightBox) - ligandIDLabel_frame=gtk.Frame() + ligandIDLabel_frame = gtk.Frame() self.ligandIDLabel = gtk.Label('Ligand ID') ligandIDLabel_frame.add(self.ligandIDLabel) - self.ligandIDValue = gtk.Label(self.spider_plot_data['PANDDA_site_ligand_id']) - ligandIDBox_frame=gtk.Frame() + self.ligandIDValue = gtk.Label( + self.spider_plot_data['PANDDA_site_ligand_id']) + ligandIDBox_frame = gtk.Frame() self.ligandIDBox = gtk.EventBox() self.ligandIDBox.add(self.ligandIDValue) ligandIDBox_frame.add(self.ligandIDBox) - ligand_occupancyLabel_frame=gtk.Frame() + ligand_occupancyLabel_frame = gtk.Frame() self.ligand_occupancyLabel = gtk.Label('occupancy') ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) - self.ligand_occupancyValue = gtk.Label(self.spider_plot_data['PANDDA_site_occupancy']) - ligand_occupancyBox_frame=gtk.Frame() + self.ligand_occupancyValue = gtk.Label( + self.spider_plot_data['PANDDA_site_occupancy']) + ligand_occupancyBox_frame = gtk.Frame() self.ligand_occupancyBox = gtk.EventBox() self.ligand_occupancyBox.add(self.ligand_occupancyValue) ligand_occupancyBox_frame.add(self.ligand_occupancyBox) - ligand_BaverageLabel_frame=gtk.Frame() + ligand_BaverageLabel_frame = gtk.Frame() self.ligand_BaverageLabel = gtk.Label('B average') ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) - self.ligand_BaverageValue = gtk.Label(self.spider_plot_data['PANDDA_site_B_average']) - ligand_BaverageBox_frame=gtk.Frame() + self.ligand_BaverageValue = gtk.Label( + self.spider_plot_data['PANDDA_site_B_average']) + ligand_BaverageBox_frame = gtk.Frame() self.ligand_BaverageBox = gtk.EventBox() self.ligand_BaverageBox.add(self.ligand_BaverageValue) ligand_BaverageBox_frame.add(self.ligand_BaverageBox) - ligand_BratioSurroundingsLabel_frame=gtk.Frame() + ligand_BratioSurroundingsLabel_frame = gtk.Frame() self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') - ligand_BratioSurroundingsLabel_frame.add(self.ligand_BratioSurroundingsLabel) - self.ligand_BratioSurroundingsValue = gtk.Label(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) - ligand_BratioSurroundingsBox_frame=gtk.Frame() + ligand_BratioSurroundingsLabel_frame.add( + self.ligand_BratioSurroundingsLabel) + self.ligand_BratioSurroundingsValue = gtk.Label( + self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) + ligand_BratioSurroundingsBox_frame = gtk.Frame() self.ligand_BratioSurroundingsBox = gtk.EventBox() - self.ligand_BratioSurroundingsBox.add(self.ligand_BratioSurroundingsValue) - ligand_BratioSurroundingsBox_frame.add(self.ligand_BratioSurroundingsBox) + self.ligand_BratioSurroundingsBox.add( + self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add( + self.ligand_BratioSurroundingsBox) - ligand_RSCCLabel_frame=gtk.Frame() + ligand_RSCCLabel_frame = gtk.Frame() self.ligand_RSCCLabel = gtk.Label('RSCC') ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) - self.ligand_RSCCValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSCC']) - ligand_RSCCBox_frame=gtk.Frame() + self.ligand_RSCCValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSCC']) + ligand_RSCCBox_frame = gtk.Frame() self.ligand_RSCCBox = gtk.EventBox() self.ligand_RSCCBox.add(self.ligand_RSCCValue) ligand_RSCCBox_frame.add(self.ligand_RSCCBox) - ligand_rmsdLabel_frame=gtk.Frame() + ligand_rmsdLabel_frame = gtk.Frame() self.ligand_rmsdLabel = gtk.Label('rmsd') ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) - self.ligand_rmsdValue = gtk.Label(self.spider_plot_data['PANDDA_site_rmsd']) - ligand_rmsdBox_frame=gtk.Frame() + self.ligand_rmsdValue = gtk.Label( + self.spider_plot_data['PANDDA_site_rmsd']) + ligand_rmsdBox_frame = gtk.Frame() self.ligand_rmsdBox = gtk.EventBox() self.ligand_rmsdBox.add(self.ligand_rmsdValue) ligand_rmsdBox_frame.add(self.ligand_rmsdBox) - ligand_RSRLabel_frame=gtk.Frame() + ligand_RSRLabel_frame = gtk.Frame() self.ligand_RSRLabel = gtk.Label('RSR') ligand_RSRLabel_frame.add(self.ligand_RSRLabel) - self.ligand_RSRValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSR']) - ligand_RSRBox_frame=gtk.Frame() + self.ligand_RSRValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSR']) + ligand_RSRBox_frame = gtk.Frame() self.ligand_RSRBox = gtk.EventBox() self.ligand_RSRBox.add(self.ligand_RSRValue) ligand_RSRBox_frame.add(self.ligand_RSRBox) - ligand_RSZDLabel_frame=gtk.Frame() + ligand_RSZDLabel_frame = gtk.Frame() self.ligand_RSZDLabel = gtk.Label('RSZD') ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) - self.ligand_RSZDValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSZD']) - ligand_RSZDBox_frame=gtk.Frame() + self.ligand_RSZDValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSZD']) + ligand_RSZDBox_frame = gtk.Frame() self.ligand_RSZDBox = gtk.EventBox() self.ligand_RSZDBox.add(self.ligand_RSZDValue) ligand_RSZDBox_frame.add(self.ligand_RSZDBox) @@ -356,7 +377,7 @@ def StartGUI(self): hbox = gtk.HBox() frame = gtk.Frame() - self.table_left = gtk.Table(8, 2, False) + self.table_left = gtk.Table(8, 2, False) self.table_left.attach(RRfreeLabel_frame, 0, 1, 0, 1) self.table_left.attach(ResolutionLabel_frame, 0, 1, 1, 2) self.table_left.attach(MolprobityScoreLabel_frame, 0, 1, 2, 3) @@ -376,24 +397,40 @@ def StartGUI(self): frame.add(self.table_left) hbox.add(frame) - frame=gtk.Frame() + frame = gtk.Frame() self.table_right = gtk.Table(8, 2, False) - self.table_right.attach(ligandIDLabel_frame, 0, 1, 0, 1) - self.table_right.attach(ligand_occupancyLabel_frame, 0, 1, 1, 2) - self.table_right.attach(ligand_BaverageLabel_frame, 0, 1, 2, 3) - self.table_right.attach(ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) - self.table_right.attach(ligand_RSCCLabel_frame, 0, 1, 4, 5) - self.table_right.attach(ligand_rmsdLabel_frame, 0, 1, 5, 6) - self.table_right.attach(ligand_RSRLabel_frame, 0, 1, 6, 7) - self.table_right.attach(ligand_RSZDLabel_frame, 0, 1, 7, 8) - self.table_right.attach(ligandIDBox_frame, 1, 2, 0, 1) - self.table_right.attach(ligand_occupancyBox_frame, 1, 2, 1, 2) - self.table_right.attach(ligand_BaverageBox_frame, 1, 2, 2, 3) - self.table_right.attach(ligand_BratioSurroundingsBox_frame, 1, 2, 3, 4) - self.table_right.attach(ligand_RSCCBox_frame, 1, 2, 4, 5) - self.table_right.attach(ligand_rmsdBox_frame, 1, 2, 5, 6) - self.table_right.attach(ligand_RSRBox_frame, 1, 2, 6, 7) - self.table_right.attach(ligand_RSZDBox_frame, 1, 2, 7, 8) + self.table_right.attach(ligandIDLabel_frame, + 0, 1, 0, 1) + self.table_right.attach( + ligand_occupancyLabel_frame, 0, 1, 1, 2) + self.table_right.attach( + ligand_BaverageLabel_frame, 0, 1, 2, 3) + self.table_right.attach( + ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach( + ligand_RSCCLabel_frame, 0, 1, 4, 5) + self.table_right.attach( + ligand_rmsdLabel_frame, 0, 1, 5, 6) + self.table_right.attach( + ligand_RSRLabel_frame, 0, 1, 6, 7) + self.table_right.attach( + ligand_RSZDLabel_frame, 0, 1, 7, 8) + self.table_right.attach(ligandIDBox_frame, + 1, 2, 0, 1) + self.table_right.attach( + ligand_occupancyBox_frame, 1, 2, 1, 2) + self.table_right.attach( + ligand_BaverageBox_frame, 1, 2, 2, 3) + self.table_right.attach( + ligand_BratioSurroundingsBox_frame, 1, 2, 3, 4) + self.table_right.attach( + ligand_RSCCBox_frame, 1, 2, 4, 5) + self.table_right.attach( + ligand_rmsdBox_frame, 1, 2, 5, 6) + self.table_right.attach(ligand_RSRBox_frame, + 1, 2, 6, 7) + self.table_right.attach( + ligand_RSZDBox_frame, 1, 2, 7, 8) frame.add(self.table_right) hbox.add(frame) @@ -401,22 +438,22 @@ def StartGUI(self): self.vbox.add(outer_frame) button = gtk.Button(label="Show MolProbity to-do list") - button.connect("clicked",self.show_molprobity_to_do) + button.connect("clicked", self.show_molprobity_to_do) self.vbox.add(button) self.vbox.pack_start(frame) - # SPACER self.vbox.add(gtk.Label(' ')) ################################################################################# # --- hbox for compound picture & spider_plot (formerly: refinement history) --- - frame=gtk.Frame() - self.hbox_for_info_graphics=gtk.HBox() + frame = gtk.Frame() + self.hbox_for_info_graphics = gtk.HBox() # --- compound picture --- - compound_frame=gtk.Frame() - pic = gtk.gdk.pixbuf_new_from_file(os.path.join(os.getenv('XChemExplorer_DIR'),'image','NO_COMPOUND_IMAGE_AVAILABLE.png')) + compound_frame = gtk.Frame() + pic = gtk.gdk.pixbuf_new_from_file(os.path.join( + os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.image = gtk.Image() self.image.set_from_pixbuf(self.pic) @@ -429,9 +466,11 @@ def StartGUI(self): # self.hbox_for_info_graphics.add(self.canvas) # --- Spider Plot --- - spider_plot_frame=gtk.Frame() - spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join(os.getenv('XChemExplorer_DIR'),'image','NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + spider_plot_frame = gtk.Frame() + spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join( + os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + self.spider_plot_pic = pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image = gtk.Image() self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) spider_plot_frame.add(self.spider_plot_image) @@ -440,47 +479,58 @@ def StartGUI(self): frame.add(self.hbox_for_info_graphics) self.vbox.add(frame) - - ################################################################################# # --- pandda.inspect user comments --- outer_frame = gtk.Frame(label='pandda.inspect comments') - vbox=gtk.VBox() - ligand_site_name_label_frame = gtk.Frame() - ligand_site_name_label = gtk.Label('Site Name') + vbox = gtk.VBox() + ligand_site_name_label_frame = gtk.Frame() + ligand_site_name_label = gtk.Label('Site Name') ligand_site_name_label_frame.add(ligand_site_name_label) - ligand_inspect_confidence_label_frame = gtk.Frame() - ligand_inspect_confidence_label = gtk.Label('Confidence') - ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) - ligand_inspect_interesting_label_frame = gtk.Frame() - ligand_inspect_interesting_label = gtk.Label('Interesting') - ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) - ligand_inspect_comment_label_frame = gtk.Frame() - ligand_inspect_comment_label = gtk.Label('Comment') + ligand_inspect_confidence_label_frame = gtk.Frame() + ligand_inspect_confidence_label = gtk.Label('Confidence') + ligand_inspect_confidence_label_frame.add( + ligand_inspect_confidence_label) + ligand_inspect_interesting_label_frame = gtk.Frame() + ligand_inspect_interesting_label = gtk.Label('Interesting') + ligand_inspect_interesting_label_frame.add( + ligand_inspect_interesting_label) + ligand_inspect_comment_label_frame = gtk.Frame() + ligand_inspect_comment_label = gtk.Label('Comment') ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) - ligand_site_name_value_frame = gtk.Frame() - self.ligand_site_name_value = gtk.Label('-') + ligand_site_name_value_frame = gtk.Frame() + self.ligand_site_name_value = gtk.Label('-') ligand_site_name_value_frame.add(self.ligand_site_name_value) - ligand_inspect_confidence_value_frame = gtk.Frame() - self.ligand_inspect_confidence_value = gtk.Label('-') - ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) - ligand_inspect_interesting_value_frame = gtk.Frame() - self.ligand_inspect_interesting_value = gtk.Label('-') - ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) - ligand_inspect_comment_value_frame = gtk.Frame() - self.ligand_inspect_comment_value = gtk.Label('-') - ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) + ligand_inspect_confidence_value_frame = gtk.Frame() + self.ligand_inspect_confidence_value = gtk.Label('-') + ligand_inspect_confidence_value_frame.add( + self.ligand_inspect_confidence_value) + ligand_inspect_interesting_value_frame = gtk.Frame() + self.ligand_inspect_interesting_value = gtk.Label('-') + ligand_inspect_interesting_value_frame.add( + self.ligand_inspect_interesting_value) + ligand_inspect_comment_value_frame = gtk.Frame() + self.ligand_inspect_comment_value = gtk.Label('-') + ligand_inspect_comment_value_frame.add( + self.ligand_inspect_comment_value) frame_pandda_inspect_comments_table = gtk.Frame() - pandda_inspect_comments_table = gtk.Table(2, 6, False) - pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0,1,0,1) - pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1,2,0,1) - pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2,3,0,1) - pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3,4,0,1) - pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4,5,0,1) - pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5,6,0,1) - pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0,1,1,2) - pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1,6,1,2) + pandda_inspect_comments_table = gtk.Table(2, 6, False) + pandda_inspect_comments_table.attach( + ligand_site_name_label_frame, 0, 1, 0, 1) + pandda_inspect_comments_table.attach( + ligand_site_name_value_frame, 1, 2, 0, 1) + pandda_inspect_comments_table.attach( + ligand_inspect_confidence_label_frame, 2, 3, 0, 1) + pandda_inspect_comments_table.attach( + ligand_inspect_confidence_value_frame, 3, 4, 0, 1) + pandda_inspect_comments_table.attach( + ligand_inspect_interesting_label_frame, 4, 5, 0, 1) + pandda_inspect_comments_table.attach( + ligand_inspect_interesting_value_frame, 5, 6, 0, 1) + pandda_inspect_comments_table.attach( + ligand_inspect_comment_label_frame, 0, 1, 1, 2) + pandda_inspect_comments_table.attach( + ligand_inspect_comment_value_frame, 1, 6, 1, 2) frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) vbox.add(frame_pandda_inspect_comments_table) @@ -492,19 +542,19 @@ def StartGUI(self): ################################################################################# outer_frame = gtk.Frame(label='Sample Navigator') - hboxSample=gtk.HBox() + hboxSample = gtk.HBox() # --- crystal navigator combobox --- frame = gtk.Frame() - self.vbox_sample_navigator=gtk.VBox() + self.vbox_sample_navigator = gtk.VBox() self.cb = gtk.combo_box_new_text() self.cb.connect("changed", self.ChooseXtal) self.vbox_sample_navigator.add(self.cb) # --- crystal navigator backward/forward button --- self.PREVbutton = gtk.Button(label="<<<") self.NEXTbutton = gtk.Button(label=">>>") - self.PREVbutton.connect("clicked", self.ChangeXtal,-1) - self.NEXTbutton.connect("clicked", self.ChangeXtal,+1) + self.PREVbutton.connect("clicked", self.ChangeXtal, -1) + self.NEXTbutton.connect("clicked", self.ChangeXtal, +1) hbox = gtk.HBox() hbox.pack_start(self.PREVbutton) hbox.pack_start(self.NEXTbutton) @@ -514,15 +564,15 @@ def StartGUI(self): # --- site navigator combobox --- frame = gtk.Frame() - self.vbox_site_navigator=gtk.VBox() + self.vbox_site_navigator = gtk.VBox() self.cb_site = gtk.combo_box_new_text() self.cb_site.connect("changed", self.ChooseSite) self.vbox_site_navigator.add(self.cb_site) # --- site navigator backward/forward button --- self.PREVbuttonSite = gtk.Button(label="<<<") self.NEXTbuttonSite = gtk.Button(label=">>>") - self.PREVbuttonSite.connect("clicked", self.ChangeSite,-1) - self.NEXTbuttonSite.connect("clicked", self.ChangeSite,+1) + self.PREVbuttonSite.connect("clicked", self.ChangeSite, -1) + self.NEXTbuttonSite.connect("clicked", self.ChangeSite, +1) hbox = gtk.HBox() hbox.pack_start(self.PREVbuttonSite) hbox.pack_start(self.NEXTbuttonSite) @@ -538,18 +588,19 @@ def StartGUI(self): ################################################################################# # --- current refinement stage --- - outer_frame=gtk.Frame() - hbox=gtk.HBox() + outer_frame = gtk.Frame() + hbox = gtk.HBox() frame = gtk.Frame(label='Analysis Status') - vbox=gtk.VBox() - self.experiment_stage_button_list=[] - for n,button in enumerate(self.experiment_stage): + vbox = gtk.VBox() + self.experiment_stage_button_list = [] + for n, button in enumerate(self.experiment_stage): if n == 0: new_button = gtk.RadioButton(None, button[0]) else: new_button = gtk.RadioButton(new_button, button[0]) - new_button.connect("toggled",self.experiment_stage_button_clicked,button[1]) + new_button.connect( + "toggled", self.experiment_stage_button_clicked, button[1]) vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) @@ -557,14 +608,15 @@ def StartGUI(self): # --- ligand confidence --- frame = gtk.Frame(label='Ligand Confidence') - vbox=gtk.VBox() - self.ligand_confidence_button_list=[] - for n,criteria in enumerate(self.ligand_confidence_category): + vbox = gtk.VBox() + self.ligand_confidence_button_list = [] + for n, criteria in enumerate(self.ligand_confidence_category): if n == 0: new_button = gtk.RadioButton(None, criteria) else: new_button = gtk.RadioButton(new_button, criteria) - new_button.connect("toggled",self.ligand_confidence_button_clicked,criteria) + new_button.connect( + "toggled", self.ligand_confidence_button_clicked, criteria) vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) @@ -578,13 +630,15 @@ def StartGUI(self): # --- ligand modeling --- frame = gtk.Frame(label='Ligand Modeling') - self.hbox_for_modeling=gtk.HBox() - self.merge_ligand_button=gtk.Button(label="Merge Ligand") - self.place_ligand_here_button=gtk.Button(label="Place Ligand here") + self.hbox_for_modeling = gtk.HBox() + self.merge_ligand_button = gtk.Button(label="Merge Ligand") + self.place_ligand_here_button = gtk.Button(label="Place Ligand here") self.hbox_for_modeling.add(self.place_ligand_here_button) - self.place_ligand_here_button.connect("clicked",self.place_ligand_here) + self.place_ligand_here_button.connect( + "clicked", self.place_ligand_here) self.hbox_for_modeling.add(self.merge_ligand_button) - self.merge_ligand_button.connect("clicked",self.merge_ligand_into_protein) + self.merge_ligand_button.connect( + "clicked", self.merge_ligand_into_protein) frame.add(self.hbox_for_modeling) self.vbox.pack_start(frame) @@ -596,21 +650,19 @@ def StartGUI(self): # self.cb_ligand_confidence.append_text(citeria) # self.vbox.add(self.cb_ligand_confidence) - # --- refinement & options --- - self.hbox_for_refinement=gtk.HBox() + self.hbox_for_refinement = gtk.HBox() self.REFINEbutton = gtk.Button(label="Refine") self.RefinementParamsButton = gtk.Button(label="refinement parameters") - self.REFINEbutton.connect("clicked",self.REFINE) + self.REFINEbutton.connect("clicked", self.REFINE) self.hbox_for_refinement.add(self.REFINEbutton) - self.RefinementParamsButton.connect("clicked",self.RefinementParams) + self.RefinementParamsButton.connect("clicked", self.RefinementParams) self.hbox_for_refinement.add(self.RefinementParamsButton) self.vbox.add(self.hbox_for_refinement) # self.VALIDATEbutton = gtk.Button(label="validate structure") # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") - # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") self.CANCELbutton.connect("clicked", self.CANCEL) @@ -619,22 +671,21 @@ def StartGUI(self): self.window.add(self.vbox) self.window.show_all() - def CANCEL(self,widget): + def CANCEL(self, widget): self.window.destroy() - - def ChangeXtal(self,widget,data=None): + def ChangeXtal(self, widget, data=None): self.index = self.index + data if self.index < 0: self.index = 0 if self.index >= len(self.Todo): -# self.index = len(self.Todo) + # self.index = len(self.Todo) self.index = 0 self.cb.set_active(self.index) def ChooseXtal(self, widget): self.xtalID = str(widget.get_active_text()) - for n,item in enumerate(self.Todo): + for n, item in enumerate(self.Todo): if str(item[0]) == self.xtalID: self.index = n self.merge_ligand_button.set_sensitive(True) @@ -646,77 +697,76 @@ def ChooseXtal(self, widget): self.ligand_inspect_comment_value.set_label('-') self.refresh_site_combobox() - self.db_dict_mainTable={} - self.db_dict_panddaTable={} + self.db_dict_mainTable = {} + self.db_dict_panddaTable = {} if str(self.Todo[self.index][0]) is not None: - self.compoundID=str(self.Todo[self.index][1]) - self.refinement_folder=str(self.Todo[self.index][4]) - self.refinement_outcome=str(self.Todo[self.index][5]) + self.compoundID = str(self.Todo[self.index][1]) + self.refinement_folder = str(self.Todo[self.index][4]) + self.refinement_outcome = str(self.Todo[self.index][5]) self.update_RefinementOutcome_radiobutton() if self.xtalID not in self.siteDict: # i.e. we are not working with a PanDDA model - self.ligand_confidence=str(self.Todo[self.index][6]) + self.ligand_confidence = str(self.Todo[self.index][6]) self.update_LigandConfidence_radiobutton() self.RefreshData() - def update_RefinementOutcome_radiobutton(self): # updating dataset outcome radiobuttons - current_stage=0 - for i,entry in enumerate(self.experiment_stage): + current_stage = 0 + for i, entry in enumerate(self.experiment_stage): if entry[1].split()[0] == self.refinement_outcome.split()[0]: - current_stage=i + current_stage = i break - for i,button in enumerate(self.experiment_stage_button_list): - if i==current_stage: + for i, button in enumerate(self.experiment_stage_button_list): + if i == current_stage: button.set_active(True) break def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons - current_stage=0 - for i,entry in enumerate(self.ligand_confidence_category): - print '--->',entry,self.ligand_confidence + current_stage = 0 + for i, entry in enumerate(self.ligand_confidence_category): + print '--->', entry, self.ligand_confidence try: if entry.split()[0] == self.ligand_confidence.split()[0]: - current_stage=i + current_stage = i break except IndexError: pass - for i,button in enumerate(self.ligand_confidence_button_list): - if i==current_stage: + for i, button in enumerate(self.ligand_confidence_button_list): + if i == current_stage: button.set_active(True) break - def refresh_site_combobox(self): # reset self.pandda_index - self.pandda_index=-1 + self.pandda_index = -1 # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites - for n in range(-1,100): + for n in range(-1, 100): self.cb_site.remove_text(0) - self.site_index='0' - self.event_index='0' + self.site_index = '0' + self.event_index = '0' # only repopulate if site exists if self.xtalID in self.siteDict: for item in sorted(self.siteDict[self.xtalID]): - self.cb_site.append_text('site: %s - event: %s' %(item[5],item[6])) + self.cb_site.append_text( + 'site: %s - event: %s' % (item[5], item[6])) - def ChangeSite(self, widget,data=None): + def ChangeSite(self, widget, data=None): if self.xtalID in self.siteDict: self.pandda_index = self.pandda_index + data if self.pandda_index < 0: - self.pandda_index=0 + self.pandda_index = 0 if self.pandda_index >= len(self.siteDict[self.xtalID]): - self.pandda_index=0 + self.pandda_index = 0 self.cb_site.set_active(self.pandda_index) def ChooseSite(self, widget): - tmp=str(widget.get_active_text()) - self.site_index=tmp.split()[1] - self.event_index=tmp.split()[4] - for n,item in enumerate(self.siteDict[self.xtalID]): - if item[5]==self.site_index and item[6]==self.event_index: + tmp = str(widget.get_active_text()) + self.site_index = tmp.split()[1] + self.event_index = tmp.split()[4] + for n, item in enumerate(self.siteDict[self.xtalID]): + if item[5] == self.site_index and item[6] == self.event_index: self.pandda_index = n self.RefreshSiteData() @@ -734,60 +784,73 @@ def RefreshSiteData(self): if self.compoundID+'.pdb' in coot.molecule_name(imol): coot.close_molecule(imol) - - print 'pandda index',self.pandda_index - self.spider_plot=self.siteDict[self.xtalID][self.pandda_index][4] - print 'new spider plot:',self.spider_plot - self.event_map=self.siteDict[self.xtalID][self.pandda_index][0] - print 'new event map:',self.event_map - self.ligand_confidence=str(self.siteDict[self.xtalID][self.pandda_index][7]) + print 'pandda index', self.pandda_index + self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] + print 'new spider plot:', self.spider_plot + self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] + print 'new event map:', self.event_map + self.ligand_confidence = str( + self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() - site_x=float(self.siteDict[self.xtalID][self.pandda_index][1]) - site_y=float(self.siteDict[self.xtalID][self.pandda_index][2]) - site_z=float(self.siteDict[self.xtalID][self.pandda_index][3]) - print 'new site coordinates:',site_x,site_y,site_z - coot.set_rotation_centre(site_x,site_y,site_z) - - self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) - self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) - self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) - self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) - - self.spider_plot_data=self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID,self.site_index,self.event_index) - print '>>>>> spider plot data',self.spider_plot_data - self.ligandIDValue.set_label(self.spider_plot_data['PANDDA_site_ligand_id']) + site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) + site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) + site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) + print 'new site coordinates:', site_x, site_y, site_z + coot.set_rotation_centre(site_x, site_y, site_z) + + self.ligand_site_name_value.set_label( + str(self.siteDict[self.xtalID][self.pandda_index][8])) + self.ligand_inspect_confidence_value.set_label( + str(self.siteDict[self.xtalID][self.pandda_index][9])) + self.ligand_inspect_interesting_value.set_label( + str(self.siteDict[self.xtalID][self.pandda_index][10])) + self.ligand_inspect_comment_value.set_label( + str(self.siteDict[self.xtalID][self.pandda_index][11])) + + self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event( + self.xtalID, self.site_index, self.event_index) + print '>>>>> spider plot data', self.spider_plot_data + self.ligandIDValue.set_label( + self.spider_plot_data['PANDDA_site_ligand_id']) try: - self.ligand_occupancyValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_occupancy']),2)) ) + self.ligand_occupancyValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) except ValueError: self.ligand_occupancyValue.set_label('-') try: - self.ligand_BaverageValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_B_average']),2)) ) + self.ligand_BaverageValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) except ValueError: self.ligand_BaverageValue.set_label('-') try: - self.ligand_BratioSurroundingsValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']),2)) ) + self.ligand_BratioSurroundingsValue.set_label(str(round( + float(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']), 2))) except ValueError: self.ligand_BratioSurroundingsValue.set_label('-') try: - self.ligand_RSCCValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_RSCC']),2)) ) + self.ligand_RSCCValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) except ValueError: self.ligand_RSCCValue.set_label('-') try: - self.ligand_rmsdValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_rmsd']),2)) ) + self.ligand_rmsdValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) except ValueError: self.ligand_rmsdValue.set_label('-') try: - self.ligand_RSRValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_RSR']),2)) ) + self.ligand_RSRValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) except ValueError: self.ligand_RSRValue.set_label('-') try: - self.ligand_RSZDValue.set_label( str(round(float(self.spider_plot_data['PANDDA_site_RSZD']),2)) ) + self.ligand_RSZDValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) except ValueError: self.ligand_RSZDValue.set_label('-') @@ -804,71 +867,83 @@ def RefreshSiteData(self): if os.path.isfile(self.spider_plot): spider_plot_pic = gtk.gdk.pixbuf_new_from_file(self.spider_plot) else: - spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join(os.getenv('XChemExplorer_DIR'),'image','NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join( + os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + self.spider_plot_pic = spider_plot_pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) ######################################################################################### # check for PANDDAs EVENT maps if os.path.isfile(self.event_map): - coot.handle_read_ccp4_map((self.event_map),0) + coot.handle_read_ccp4_map((self.event_map), 0) for imol in coot_utils_XChem.molecule_number_list(): if self.event_map in coot.molecule_name(imol): - coot.set_contour_level_in_sigma(imol,2) + coot.set_contour_level_in_sigma(imol, 2) # coot.set_contour_level_absolute(imol,0.5) # coot.set_last_map_colour(0.4,0,0.4) - coot.set_last_map_colour(0.74,0.44,0.02) - + coot.set_last_map_colour(0.74, 0.44, 0.02) + def experiment_stage_button_clicked(self, widget, data=None): + self.db_dict_mainTable['RefinementOutcome'] = data + print '==> XCE: setting Refinement Outcome for ' + \ + self.xtalID+' to '+str(data)+' in mainTable of datasource' + self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - def experiment_stage_button_clicked(self,widget, data=None): - self.db_dict_mainTable['RefinementOutcome']=data - print '==> XCE: setting Refinement Outcome for '+self.xtalID+' to '+str(data)+' in mainTable of datasource' - self.db.update_data_source(self.xtalID,self.db_dict_mainTable) - - - def ligand_confidence_button_clicked(self,widget,data=None): - print 'PANDDA_index',self.pandda_index + def ligand_confidence_button_clicked(self, widget, data=None): + print 'PANDDA_index', self.pandda_index if self.pandda_index == -1: - self.db_dict_mainTable['RefinementLigandConfidence']=data - print '==> XCE: setting Ligand Confidence for '+self.xtalID+' to '+str(data)+' in mainTable of datasource' - self.db.update_data_source(self.xtalID,self.db_dict_mainTable) - self.Todo[self.index][6]=data + self.db_dict_mainTable['RefinementLigandConfidence'] = data + print '==> XCE: setting Ligand Confidence for ' + \ + self.xtalID+' to '+str(data)+' in mainTable of datasource' + self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + self.Todo[self.index][6] = data else: - self.db_dict_panddaTable['PANDDA_site_confidence']=data - print '==> XCE: setting Ligand Confidence for '+self.xtalID+' (site='+str(self.site_index)+', event='+str(self.event_index)+') to '+str(data)+' in panddaTable of datasource' - self.db.update_site_event_panddaTable(self.xtalID,self.site_index,self.event_index,self.db_dict_panddaTable) - self.siteDict[self.xtalID][self.pandda_index][7]=data + self.db_dict_panddaTable['PANDDA_site_confidence'] = data + print '==> XCE: setting Ligand Confidence for '+self.xtalID + \ + ' (site='+str(self.site_index)+', event='+str(self.event_index) + \ + ') to '+str(data)+' in panddaTable of datasource' + self.db.update_site_event_panddaTable( + self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable) + self.siteDict[self.xtalID][self.pandda_index][7] = data def RefreshData(self): # reset spider plot image - spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join(os.getenv('XChemExplorer_DIR'),'image','NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join( + os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + self.spider_plot_pic = spider_plot_pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) # initialize Refinement library - self.Refine=XChemRefine.RefineOld(self.project_directory,self.xtalID,self.compoundID,self.data_source) - self.Serial=self.Refine.GetSerial() - if self.Serial==1: + self.Refine = XChemRefine.RefineOld( + self.project_directory, self.xtalID, self.compoundID, self.data_source) + self.Serial = self.Refine.GetSerial() + if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple - if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.pdb_style)): + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): print '==> XCE: updating quality indicators in data source for '+self.xtalID - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID,self.data_source,os.path.join(self.project_directory,self.xtalID,self.pdb_style)) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID,self.data_source,'') # '' because file does not exist - elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.pdb')): + XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, + os.path.join(self.project_directory, self.xtalID, self.pdb_style)) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, '') # '' because file does not exist + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): print '==> XCE: updating quality indicators in data source for '+self.xtalID - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID,self.data_source,os.path.join(self.project_directory,self.xtalID,'dimple.pdb')) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID,self.data_source,'') # '' because file does not exist + XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, + os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, '') # '' because file does not exist # all this information is now updated in the datasource after each refinement cycle - self.QualityIndicators=self.db.get_db_dict_for_sample(self.xtalID) + self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) ######################################################################################### # history # if the structure was previously refined, try to read the parameters # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: - self.RefmacParams=self.Refine.ParamsFromPreviousCycle(self.Serial-1) + self.RefmacParams = self.Refine.ParamsFromPreviousCycle( + self.Serial-1) # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) # else: @@ -892,12 +967,14 @@ def RefreshData(self): # read new PDB files # read protein molecule after ligand so that this one is the active molecule coot.set_nomenclature_errors_on_read("ignore") - if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.compoundID+'.pdb')): - imol=coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory,self.xtalID,self.compoundID+'.pdb'),0) - self.mol_dict['ligand']=imol - coot.read_cif_dictionary(os.path.join(self.project_directory,self.xtalID,self.compoundID+'.cif')) - if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.pdb_style)): - os.chdir(os.path.join(self.project_directory,self.xtalID)) + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID+'.pdb')): + imol = coot.handle_read_draw_molecule_with_recentre(os.path.join( + self.project_directory, self.xtalID, self.compoundID+'.pdb'), 0) + self.mol_dict['ligand'] = imol + coot.read_cif_dictionary(os.path.join( + self.project_directory, self.xtalID, self.compoundID+'.cif')) + if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + os.chdir(os.path.join(self.project_directory, self.xtalID)) # we want to be able to check dimple results immediately, but don't want to interfere with refinement # if not os.path.isfile('REFINEMENT_IN_PROGRESS'): # if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-ensemble-model.pdb')): @@ -906,30 +983,35 @@ def RefreshData(self): # os.symlink('dimple.pdb',self.pdb_style) # else: # self.go_to_next_xtal() - if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.pdb_style)): - os.chdir(os.path.join(self.project_directory,self.xtalID)) - imol=coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory,self.xtalID,self.pdb_style),0) - elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.pdb')): - os.chdir(os.path.join(self.project_directory,self.xtalID)) - imol=coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory,self.xtalID,'dimple.pdb'),0) + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join(self.project_directory, self.xtalID, 'dimple.pdb'), 0) else: self.go_to_next_xtal() - self.mol_dict['protein']=imol + self.mol_dict['protein'] = imol for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith(self.pdb_style): - coot.set_show_symmetry_master(1) # master switch to show symmetry molecules - coot.set_show_symmetry_molecule(item,1) # show symm for model + # master switch to show symmetry molecules + coot.set_show_symmetry_master(1) + coot.set_show_symmetry_molecule(item, 1) # show symm for model ######################################################################################### # read fofo maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level - if os.path.isfile(os.path.join(self.project_directory,self.xtalID,'2fofc.map')): + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): coot.set_default_initial_contour_level_for_difference_map(3) - coot.handle_read_ccp4_map(os.path.join(self.project_directory,self.xtalID,'fofc.map'),1) + coot.handle_read_ccp4_map(os.path.join( + self.project_directory, self.xtalID, 'fofc.map'), 1) coot.set_default_initial_contour_level_for_map(1) - coot.handle_read_ccp4_map(os.path.join(self.project_directory,self.xtalID,'2fofc.map'),0) - coot.set_last_map_colour(0,0,1) + coot.handle_read_ccp4_map(os.path.join( + self.project_directory, self.xtalID, '2fofc.map'), 0) + coot.set_last_map_colour(0, 0, 1) else: # try to open mtz file with same name as pdb file coot.set_default_initial_contour_level_for_map(1) @@ -940,73 +1022,92 @@ def RefreshData(self): # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): # os.symlink('dimple.mtz',self.mtz_style) - if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory,self.xtalID,self.mtz_style)) - elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')) + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, self.mtz_style)) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')): + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, 'dimple.mtz')) ######################################################################################### # update Quality Indicator table try: - self.RRfreeValue.set_label( str(round(float(self.QualityIndicators['RefinementRcryst']),3)) +' / '+str(round(float(self.QualityIndicators['RefinementRfree']),3))) + self.RRfreeValue.set_label(str(round(float(self.QualityIndicators['RefinementRcryst']), 3)) + ' / '+str( + round(float(self.QualityIndicators['RefinementRfree']), 3))) except ValueError: self.RRfreeValue.set_label('-') try: - self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRfreeTraficLight'])) + self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRfreeTraficLight'])) except ValueError: pass - self.ResolutionValue.set_label(self.QualityIndicators['RefinementResolution']) + self.ResolutionValue.set_label( + self.QualityIndicators['RefinementResolution']) try: - self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementResolutionTL'])) + self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementResolutionTL'])) except ValueError: pass - self.MolprobityScoreValue.set_label(self.QualityIndicators['RefinementMolProbityScore']) + self.MolprobityScoreValue.set_label( + self.QualityIndicators['RefinementMolProbityScore']) try: - self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementMolProbityScoreTL'])) + self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementMolProbityScoreTL'])) except ValueError: pass - self.RamachandranOutliersValue.set_label(self.QualityIndicators['RefinementRamachandranOutliers']) + self.RamachandranOutliersValue.set_label( + self.QualityIndicators['RefinementRamachandranOutliers']) try: - self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRamachandranOutliersTL'])) + self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRamachandranOutliersTL'])) except ValueError: pass - self.RamachandranFavoredValue.set_label(self.QualityIndicators['RefinementRamachandranFavored']) + self.RamachandranFavoredValue.set_label( + self.QualityIndicators['RefinementRamachandranFavored']) try: - self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRamachandranFavoredTL'])) + self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRamachandranFavoredTL'])) except ValueError: pass - self.rmsdBondsValue.set_label(self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue.set_label( + self.QualityIndicators['RefinementRmsdBonds']) try: - self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdBondsTL'])) + self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRmsdBondsTL'])) except ValueError: pass - self.rmsdAnglesValue.set_label(self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue.set_label( + self.QualityIndicators['RefinementRmsdAngles']) try: - self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdAnglesTL'])) + self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRmsdAnglesTL'])) except ValueError: pass - self.MatrixWeightValue.set_label(self.QualityIndicators['RefinementMatrixWeight']) + self.MatrixWeightValue.set_label( + self.QualityIndicators['RefinementMatrixWeight']) try: - pic = gtk.gdk.pixbuf_new_from_file(os.path.join(self.project_directory,self.xtalID,self.compoundID+'.png')) + pic = gtk.gdk.pixbuf_new_from_file(os.path.join( + self.project_directory, self.xtalID, self.compoundID+'.png')) except gobject.GError: - pic = gtk.gdk.pixbuf_new_from_file(os.path.join(os.getenv('XChemExplorer_DIR'),'image','NO_COMPOUND_IMAGE_AVAILABLE.png')) + pic = gtk.gdk.pixbuf_new_from_file(os.path.join( + os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.image.set_from_pixbuf(self.pic) def go_to_next_xtal(self): - self.index+=1 + self.index += 1 if self.index >= len(self.Todo): self.index = len(self.Todo) self.cb.set_active(self.index) - - def REFINE(self,widget): + def REFINE(self, widget): ####################################################### # create folder for new refinement cycle - os.mkdir(os.path.join(self.project_directory,self.xtalID,'Refine_'+str(self.Serial))) + os.mkdir(os.path.join(self.project_directory, + self.xtalID, 'Refine_'+str(self.Serial))) ####################################################### # write PDB file @@ -1014,48 +1115,49 @@ def REFINE(self,widget): # note: the user has to make sure that the ligand file was merged into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith(self.pdb_style): - coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'Refine_'+str(self.Serial),'in.pdb')) + coot.write_pdb_file(item, os.path.join( + self.project_directory, self.xtalID, 'Refine_'+str(self.Serial), 'in.pdb')) break elif coot.molecule_name(item).endswith('dimple.pdb'): - coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'Refine_'+str(self.Serial),'in.pdb')) + coot.write_pdb_file(item, os.path.join( + self.project_directory, self.xtalID, 'Refine_'+str(self.Serial), 'in.pdb')) break - ####################################################### # run REFMAC - self.Refine.RunRefmac(self.Serial,self.RefmacParams,self.external_software,self.xce_logfile) + self.Refine.RunRefmac(self.Serial, self.RefmacParams, + self.external_software, self.xce_logfile) - self.index+=1 + self.index += 1 if self.index >= len(self.Todo): -# self.index = len(self.Todo) + # self.index = len(self.Todo) self.index = 0 self.cb.set_active(self.index) - - def RefinementParams(self,widget): + def RefinementParams(self, widget): print '\n==> XCE: changing refinement parameters' - self.RefmacParams=self.Refine.RefinementParams(self.RefmacParams) - - def set_selection_mode(self,widget): - self.selection_mode=widget.get_active_text() + self.RefmacParams = self.Refine.RefinementParams(self.RefmacParams) + def set_selection_mode(self, widget): + self.selection_mode = widget.get_active_text() - def get_samples_to_look_at(self,widget): - if self.selection_mode=='': + def get_samples_to_look_at(self, widget): + if self.selection_mode == '': self.status_label.set_text('select model stage') return self.status_label.set_text('checking datasource for samples... ') # first remove old samples if present if len(self.Todo) != 0: - for n,item in enumerate(self.Todo): + for n, item in enumerate(self.Todo): self.cb.remove_text(0) - self.Todo=[] - self.siteDict={} - self.Todo,self.siteDict=self.db.get_todoList_for_coot(self.selection_mode) - self.status_label.set_text('found %s samples' %len(self.Todo)) + self.Todo = [] + self.siteDict = {} + self.Todo, self.siteDict = self.db.get_todoList_for_coot( + self.selection_mode) + self.status_label.set_text('found %s samples' % len(self.Todo)) # refresh sample CB for item in sorted(self.Todo): - self.cb.append_text('%s' %item[0]) + self.cb.append_text('%s' % item[0]) if self.siteDict == {}: self.cb_site.set_sensitive(False) self.PREVbuttonSite.set_sensitive(False) @@ -1065,43 +1167,44 @@ def get_samples_to_look_at(self,widget): self.PREVbuttonSite.set_sensitive(True) self.NEXTbuttonSite.set_sensitive(True) - - - - - def update_plot(self,refinement_cycle,Rfree,Rcryst): + def update_plot(self, refinement_cycle, Rfree, Rcryst): fig = Figure(figsize=(2, 2), dpi=50) Plot = fig.add_subplot(111) - Plot.set_ylim([0,max(Rcryst+Rfree)]) - Plot.set_xlabel('Refinement Cycle',fontsize=12) - Plot.plot(refinement_cycle,Rfree,label='Rfree',linewidth=2) - Plot.plot(refinement_cycle,Rcryst,label='Rcryst',linewidth=2) + Plot.set_ylim([0, max(Rcryst+Rfree)]) + Plot.set_xlabel('Refinement Cycle', fontsize=12) + Plot.plot(refinement_cycle, Rfree, label='Rfree', linewidth=2) + Plot.plot(refinement_cycle, Rcryst, label='Rcryst', linewidth=2) Plot.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, - ncol=2, mode="expand", borderaxespad=0.,fontsize=12) + ncol=2, mode="expand", borderaxespad=0., fontsize=12) return fig - def place_ligand_here(self,widget): + def place_ligand_here(self, widget): print '===> XCE: moving ligand to pointer' # coot.move_molecule_here() - print 'LIGAND: ',self.mol_dict['ligand'] + print 'LIGAND: ', self.mol_dict['ligand'] coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) - def merge_ligand_into_protein(self,widget): + def merge_ligand_into_protein(self, widget): print '===> XCE: merge ligand into protein structure' # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) - coot.merge_molecules_py([self.mol_dict['ligand']],self.mol_dict['protein']) + coot.merge_molecules_py( + [self.mol_dict['ligand']], self.mol_dict['protein']) print '===> XCE: deleting ligand molecule' coot.close_molecule(self.mol_dict['ligand']) - def show_molprobity_to_do(self,widget): - if os.path.isfile(os.path.join(self.project_directory,self.xtalID,'Refine_'+str(self.Serial-1),'molprobity_coot.py')): - print '==> XCE: running MolProbity Summary for',self.xtalID - coot.run_script(os.path.join(self.project_directory,self.xtalID,'Refine_'+str(self.Serial-1),'molprobity_coot.py')) + def show_molprobity_to_do(self, widget): + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')): + print '==> XCE: running MolProbity Summary for', self.xtalID + coot.run_script(os.path.join(self.project_directory, self.xtalID, + 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')) else: - print '==> XCE: cannot find '+os.path.join(self.project_directory,self.xtalID,'Refine_'+str(self.Serial-1),'molprobity_coot.py') + print '==> XCE: cannot find ' + \ + os.path.join(self.project_directory, self.xtalID, + 'Refine_'+str(self.Serial-1), 'molprobity_coot.py') # def fit_ligand(self,widget): # print 'fit' -if __name__=='__main__': + +if __name__ == '__main__': GUI().StartGUI() diff --git a/lib/XChemCootReference.py b/lib/XChemCootReference.py index 96412abb..0881566e 100755 --- a/lib/XChemCootReference.py +++ b/lib/XChemCootReference.py @@ -1,31 +1,32 @@ # last edited: 03/08/2017 - 15:00 -import sys,glob +import coot_utils_XChem +import coot +import XChemLog +import XChemUtils +import XChemRefine +import sys +import glob import os import pickle import time import gtk #import threading #import gobject -#gtk.gdk.threads_init() +# gtk.gdk.threads_init() from matplotlib.figure import Figure from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas # XCE libraries sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') -import XChemRefine -import XChemUtils -import XChemLog # libraries from COOT #import pygtk, gtk, pango -import coot # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. # modified file is now in $XChemExplorer_DIR/lib -import coot_utils_XChem class GUI(object): @@ -38,44 +39,45 @@ def __init__(self): ########################################################################################### # read in settings file from XChemExplorer to set the relevant paths - self.settings = pickle.load(open(".xce_settings.pkl","rb")) - remote_qsub_submission=self.settings['remote_qsub'] - self.database_directory=self.settings['database_directory'] - self.xce_logfile=self.settings['xce_logfile'] - self.Logfile=XChemLog.updateLog(self.xce_logfile) + self.settings = pickle.load(open(".xce_settings.pkl", "rb")) + remote_qsub_submission = self.settings['remote_qsub'] + self.database_directory = self.settings['database_directory'] + self.xce_logfile = self.settings['xce_logfile'] + self.Logfile = XChemLog.updateLog(self.xce_logfile) self.Logfile.insert('starting COOT gui for reference model refinement') - self.data_source=self.settings['data_source'] + self.data_source = self.settings['data_source'] # checking for external software packages - self.external_software=XChemUtils.external_software(self.xce_logfile).check() - self.external_software['qsub_remote']=remote_qsub_submission + self.external_software = XChemUtils.external_software( + self.xce_logfile).check() + self.external_software['qsub_remote'] = remote_qsub_submission # the Folder is kind of a legacy thing because my inital idea was to have separate folders # for Data Processing and Refinement self.reference_directory = self.settings['reference_directory'] self.refinementDir = '' - self.Serial=0 - self.Refine=None + self.Serial = 0 + self.Refine = None - self.xtalID='' - self.compoundID='' - self.spider_plot='' - self.refinement_folder='' - self.pdbFile='' - self.mtzFree='' + self.xtalID = '' + self.compoundID = '' + self.spider_plot = '' + self.refinement_folder = '' + self.pdbFile = '' + self.mtzFree = '' - self.pdb_style='refine.pdb' - self.mtz_style='refine.mtz' + self.pdb_style = 'refine.pdb' + self.mtz_style = 'refine.mtz' # stores imol of currently loaded molecules and maps - self.mol_dict = { 'protein': -1, - 'ligand': -1, - '2fofc': -1, - 'fofc': -1, - 'event': -1 } + self.mol_dict = {'protein': -1, + 'ligand': -1, + '2fofc': -1, + 'fofc': -1, + 'event': -1} self.ground_state_map_List = [] - self.job_running=False + self.job_running = False ########################################################################################### # some COOT settings @@ -83,37 +85,35 @@ def __init__(self): coot.set_colour_map_rotation_for_map(0) # coot.set_colour_map_rotation_on_read_pdb_flag(21) - self.QualityIndicators = { 'Rcryst': '-', - 'Rfree': '-', - 'RfreeTL': 'gray', - 'ResolutionHigh': '-', - 'ResolutionColor': 'gray', - 'MolprobityScore': '-', - 'MolprobityScoreColor': 'gray', - 'RamachandranOutliers': '-', - 'RamachandranOutliersColor': 'gray', - 'RamachandranFavored': '-', - 'RamachandranFavoredColor': 'gray', - 'rmsdBonds': '-', - 'rmsdBondsTL': 'gray', - 'rmsdAngles': '-', - 'rmsdAnglesTL': 'gray', - 'MatrixWeight': '-' } + self.QualityIndicators = {'Rcryst': '-', + 'Rfree': '-', + 'RfreeTL': 'gray', + 'ResolutionHigh': '-', + 'ResolutionColor': 'gray', + 'MolprobityScore': '-', + 'MolprobityScoreColor': 'gray', + 'RamachandranOutliers': '-', + 'RamachandranOutliersColor': 'gray', + 'RamachandranFavored': '-', + 'RamachandranFavoredColor': 'gray', + 'rmsdBonds': '-', + 'rmsdBondsTL': 'gray', + 'rmsdAngles': '-', + 'rmsdAnglesTL': 'gray', + 'MatrixWeight': '-'} # default refmac parameters - self.RefmacParams={ 'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '' } - - + self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', + 'XYZIN': '', 'XYZOUT': '', + 'LIBIN': '', 'LIBOUT': '', + 'TLSIN': '', 'TLSOUT': '', + 'TLSADD': '', + 'NCYCLES': '10', + 'MATRIX_WEIGHT': 'AUTO', + 'BREF': ' bref ISOT\n', + 'TLS': '', + 'NCS': '', + 'TWIN': ''} def StartGUI(self): @@ -127,12 +127,12 @@ def StartGUI(self): ################################################################################# # --- PDB file selection --- # checking for pdb files in reference directory - referenceFiles=[] - for files in glob.glob(os.path.join(self.reference_directory,'*-ground-state.pdb')): - pdbFile=files[files.rfind('/')+1:] + referenceFiles = [] + for files in glob.glob(os.path.join(self.reference_directory, '*-ground-state.pdb')): + pdbFile = files[files.rfind('/')+1:] referenceFiles.append(pdbFile) frame = gtk.Frame(label='Select PDB file') - hbox=gtk.HBox() + hbox = gtk.HBox() self.cb_select_pdb = gtk.combo_box_new_text() # self.cb_select_pdb.connect("changed", self.set_selection_mode) for pdbFile in referenceFiles: @@ -143,7 +143,7 @@ def StartGUI(self): self.load_pdb_file_button = gtk.Button(label="Load") # self.load_pdb_file_button.connect("clicked",self.get_samples_to_look_at) - self.load_pdb_file_button.connect("clicked",self.load_pdb_file) + self.load_pdb_file_button.connect("clicked", self.load_pdb_file) hbox.add(self.load_pdb_file_button) frame.add(hbox) self.vbox.pack_start(frame) @@ -152,9 +152,9 @@ def StartGUI(self): self.vbox.add(gtk.Label(' ')) frame = gtk.Frame(label='MTZ file to refine against') - hbox=gtk.HBox() - self.mtzFree='' - self.mtzFree_label=gtk.Label() + hbox = gtk.HBox() + self.mtzFree = '' + self.mtzFree_label = gtk.Label() hbox.add(self.mtzFree_label) frame.add(hbox) self.vbox.pack_start(frame) @@ -163,18 +163,15 @@ def StartGUI(self): self.vbox.add(gtk.Label(' ')) frame = gtk.Frame(label='MTZ file after refinement') - hbox=gtk.HBox() - self.mtzRefine_label=gtk.Label() + hbox = gtk.HBox() + self.mtzRefine_label = gtk.Label() hbox.add(self.mtzRefine_label) frame.add(hbox) self.vbox.pack_start(frame) - - # SPACER self.vbox.add(gtk.Label(' \n ')) - ################################################################################# # --- ground state mean map --- # checking for ground state mean map in reference folder @@ -204,11 +201,11 @@ def StartGUI(self): # self.cb_select_mean_map_by_resolution.connect("changed", self.show_selected_mean_map) # hbox.add(self.cb_select_mean_map_by_resolution) ## self.show_highres_ground_state_map_button = gtk.Button(label="Show Highest\nResolution Map") -## self.show_highres_ground_state_map_button.connect("clicked",self.show_highres_ground_state_map) -## hbox.add(self.show_highres_ground_state_map_button) +# self.show_highres_ground_state_map_button.connect("clicked",self.show_highres_ground_state_map) +# hbox.add(self.show_highres_ground_state_map_button) ## self.show_all_ground_state_map_button = gtk.Button(label="Show All Maps") -## self.show_all_ground_state_map_button.connect("clicked",self.show_all_ground_state_map) -## hbox.add(self.show_all_ground_state_map_button) +# self.show_all_ground_state_map_button.connect("clicked",self.show_all_ground_state_map) +# hbox.add(self.show_all_ground_state_map_button) # frame.add(hbox) # self.vbox.pack_start(frame) @@ -218,8 +215,8 @@ def StartGUI(self): ################################################################################# # --- Refinement History --- frame = gtk.Frame(label='Refinement History') - self.hbox_for_info_graphics=gtk.HBox() - self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) + self.hbox_for_info_graphics = gtk.HBox() + self.canvas = FigureCanvas(self.update_plot([0], [0], [0])) self.canvas.set_size_request(190, 190) self.hbox_for_info_graphics.add(self.canvas) frame.add(self.hbox_for_info_graphics) @@ -227,13 +224,13 @@ def StartGUI(self): ################################################################################# # --- status window --- - frame=gtk.Frame(label='Status') - vbox=gtk.VBox() - self.spinnerBox=gtk.VBox() - self.refinementRunning=gtk.Spinner() + frame = gtk.Frame(label='Status') + vbox = gtk.VBox() + self.spinnerBox = gtk.VBox() + self.refinementRunning = gtk.Spinner() vbox.add(self.spinnerBox) # hbox.add(self.refinementRunning) - self.status_label=gtk.Label() + self.status_label = gtk.Label() vbox.add(self.status_label) frame.add(vbox) self.status_label.set_text('idle') @@ -246,74 +243,80 @@ def StartGUI(self): # next comes a section which displays some global quality indicators # a combination of labels and textview widgets, arranged in a table - RRfreeLabel_frame=gtk.Frame() + RRfreeLabel_frame = gtk.Frame() self.RRfreeLabel = gtk.Label('R/Rfree') RRfreeLabel_frame.add(self.RRfreeLabel) - self.RRfreeValue = gtk.Label(self.QualityIndicators['Rcryst']+'/'+self.QualityIndicators['Rfree']) - RRfreeBox_frame=gtk.Frame() + self.RRfreeValue = gtk.Label( + self.QualityIndicators['Rcryst']+'/'+self.QualityIndicators['Rfree']) + RRfreeBox_frame = gtk.Frame() self.RRfreeBox = gtk.EventBox() self.RRfreeBox.add(self.RRfreeValue) RRfreeBox_frame.add(self.RRfreeBox) - ResolutionLabel_frame=gtk.Frame() + ResolutionLabel_frame = gtk.Frame() self.ResolutionLabel = gtk.Label('Resolution') ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label(self.QualityIndicators['ResolutionHigh']) - ResolutionBox_frame=gtk.Frame() + self.ResolutionValue = gtk.Label( + self.QualityIndicators['ResolutionHigh']) + ResolutionBox_frame = gtk.Frame() self.ResolutionBox = gtk.EventBox() self.ResolutionBox.add(self.ResolutionValue) ResolutionBox_frame.add(self.ResolutionBox) - MolprobityScoreLabel_frame=gtk.Frame() + MolprobityScoreLabel_frame = gtk.Frame() self.MolprobityScoreLabel = gtk.Label('MolprobityScore') MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) - self.MolprobityScoreValue = gtk.Label(self.QualityIndicators['MolprobityScore']) - MolprobityScoreBox_frame=gtk.Frame() + self.MolprobityScoreValue = gtk.Label( + self.QualityIndicators['MolprobityScore']) + MolprobityScoreBox_frame = gtk.Frame() self.MolprobityScoreBox = gtk.EventBox() self.MolprobityScoreBox.add(self.MolprobityScoreValue) MolprobityScoreBox_frame.add(self.MolprobityScoreBox) - RamachandranOutliersLabel_frame=gtk.Frame() + RamachandranOutliersLabel_frame = gtk.Frame() self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) - self.RamachandranOutliersValue = gtk.Label(self.QualityIndicators['RamachandranOutliers']) - RamachandranOutliersBox_frame=gtk.Frame() + self.RamachandranOutliersValue = gtk.Label( + self.QualityIndicators['RamachandranOutliers']) + RamachandranOutliersBox_frame = gtk.Frame() self.RamachandranOutliersBox = gtk.EventBox() self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) RamachandranOutliersBox_frame.add(self.RamachandranOutliersBox) - RamachandranFavoredLabel_frame=gtk.Frame() + RamachandranFavoredLabel_frame = gtk.Frame() self.RamachandranFavoredLabel = gtk.Label('Rama Favored') RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) - self.RamachandranFavoredValue = gtk.Label(self.QualityIndicators['RamachandranFavoredColor']) - RamachandranFavoredBox_frame=gtk.Frame() + self.RamachandranFavoredValue = gtk.Label( + self.QualityIndicators['RamachandranFavoredColor']) + RamachandranFavoredBox_frame = gtk.Frame() self.RamachandranFavoredBox = gtk.EventBox() self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) RamachandranFavoredBox_frame.add(self.RamachandranFavoredBox) - rmsdBondsLabel_frame=gtk.Frame() + rmsdBondsLabel_frame = gtk.Frame() self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') rmsdBondsLabel_frame.add(self.rmsdBondsLabel) self.rmsdBondsValue = gtk.Label(self.QualityIndicators['rmsdBonds']) - rmsdBondsBox_frame=gtk.Frame() + rmsdBondsBox_frame = gtk.Frame() self.rmsdBondsBox = gtk.EventBox() self.rmsdBondsBox.add(self.rmsdBondsValue) rmsdBondsBox_frame.add(self.rmsdBondsBox) - rmsdAnglesLabel_frame=gtk.Frame() + rmsdAnglesLabel_frame = gtk.Frame() self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) self.rmsdAnglesValue = gtk.Label(self.QualityIndicators['rmsdAngles']) - rmsdAnglesBox_frame=gtk.Frame() + rmsdAnglesBox_frame = gtk.Frame() self.rmsdAnglesBox = gtk.EventBox() self.rmsdAnglesBox.add(self.rmsdAnglesValue) rmsdAnglesBox_frame.add(self.rmsdAnglesBox) - MatrixWeightLabel_frame=gtk.Frame() + MatrixWeightLabel_frame = gtk.Frame() self.MatrixWeightLabel = gtk.Label('Matrix Weight') MatrixWeightLabel_frame.add(self.MatrixWeightLabel) - self.MatrixWeightValue = gtk.Label(self.QualityIndicators['MatrixWeight']) - MatrixWeightBox_frame=gtk.Frame() + self.MatrixWeightValue = gtk.Label( + self.QualityIndicators['MatrixWeight']) + MatrixWeightBox_frame = gtk.Frame() self.MatrixWeightBox = gtk.EventBox() self.MatrixWeightBox.add(self.MatrixWeightValue) MatrixWeightBox_frame.add(self.MatrixWeightBox) @@ -322,7 +325,7 @@ def StartGUI(self): hbox = gtk.HBox() frame = gtk.Frame() - self.table_left = gtk.Table(8, 2, False) + self.table_left = gtk.Table(8, 2, False) self.table_left.attach(RRfreeLabel_frame, 0, 1, 0, 1) self.table_left.attach(ResolutionLabel_frame, 0, 1, 1, 2) self.table_left.attach(MolprobityScoreLabel_frame, 0, 1, 2, 3) @@ -346,7 +349,7 @@ def StartGUI(self): self.vbox.add(outer_frame) button = gtk.Button(label="Show MolProbity to-do list") - button.connect("clicked",self.show_molprobity_to_do) + button.connect("clicked", self.show_molprobity_to_do) self.vbox.add(button) self.vbox.pack_start(frame) @@ -354,12 +357,12 @@ def StartGUI(self): self.vbox.add(gtk.Label(' ')) # --- refinement & options --- - self.hbox_for_refinement=gtk.HBox() + self.hbox_for_refinement = gtk.HBox() self.REFINEbutton = gtk.Button(label="Refine") self.RefinementParamsButton = gtk.Button(label="refinement parameters") - self.REFINEbutton.connect("clicked",self.REFINE) + self.REFINEbutton.connect("clicked", self.REFINE) self.hbox_for_refinement.add(self.REFINEbutton) - self.RefinementParamsButton.connect("clicked",self.RefinementParams) + self.RefinementParamsButton.connect("clicked", self.RefinementParams) self.hbox_for_refinement.add(self.RefinementParamsButton) self.vbox.add(self.hbox_for_refinement) @@ -371,27 +374,30 @@ def StartGUI(self): self.window.add(self.vbox) self.window.show_all() - def CANCEL(self,widget): + def CANCEL(self, widget): self.window.destroy() - def RefreshData(self): # initialize Refinement library - self.Refine=XChemRefine.Refine(self.reference_directory,self.refinementDir,'dummy_compound_ID','dummy_database') - self.Serial=self.Refine.GetSerial() - print '====> Serial',self.Serial + self.Refine = XChemRefine.Refine( + self.reference_directory, self.refinementDir, 'dummy_compound_ID', 'dummy_database') + self.Serial = self.Refine.GetSerial() + print '====> Serial', self.Serial ######################################################################################### # history # if the structure was previously refined, try to read the parameters self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: - self.RefmacParams=self.Refine.ParamsFromPreviousCycle(self.Serial-1) - refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() - self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) + self.RefmacParams = self.Refine.ParamsFromPreviousCycle( + self.Serial-1) + refinement_cycle, Rfree, Rcryst = self.Refine.GetRefinementHistory() + self.canvas = FigureCanvas( + self.update_plot(refinement_cycle, Rfree, Rcryst)) else: - self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea + self.canvas = FigureCanvas(self.update_plot( + [0], [0], [0])) # a gtk.DrawingArea self.canvas.set_size_request(190, 190) self.hbox_for_info_graphics.add(self.canvas) self.canvas.show() @@ -400,48 +406,60 @@ def RefreshData(self): # update Quality Indicator table print self.QualityIndicators try: - self.RRfreeValue.set_label( str(round(float(self.QualityIndicators['Rcryst']),3)) +' / '+str(round(float(self.QualityIndicators['Rfree']),3))) + self.RRfreeValue.set_label(str(round(float( + self.QualityIndicators['Rcryst']), 3)) + ' / '+str(round(float(self.QualityIndicators['Rfree']), 3))) except ValueError: self.RRfreeValue.set_label('-') try: - self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RfreeTL'])) + self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RfreeTL'])) except ValueError: pass - self.ResolutionValue.set_label(self.QualityIndicators['ResolutionHigh']) + self.ResolutionValue.set_label( + self.QualityIndicators['ResolutionHigh']) try: - self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['ResolutionColor'])) + self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['ResolutionColor'])) except ValueError: pass - self.MolprobityScoreValue.set_label(self.QualityIndicators['MolprobityScore']) + self.MolprobityScoreValue.set_label( + self.QualityIndicators['MolprobityScore']) try: - self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['MolprobityScoreColor'])) + self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['MolprobityScoreColor'])) except ValueError: pass - self.RamachandranOutliersValue.set_label(self.QualityIndicators['RamachandranOutliers']) + self.RamachandranOutliersValue.set_label( + self.QualityIndicators['RamachandranOutliers']) try: - self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RamachandranOutliersColor'])) + self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RamachandranOutliersColor'])) except ValueError: pass - self.RamachandranFavoredValue.set_label(self.QualityIndicators['RamachandranFavored']) + self.RamachandranFavoredValue.set_label( + self.QualityIndicators['RamachandranFavored']) try: - self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RamachandranFavoredColor'])) + self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RamachandranFavoredColor'])) except ValueError: pass self.rmsdBondsValue.set_label(self.QualityIndicators['rmsdBonds']) try: - self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['rmsdBondsTL'])) + self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['rmsdBondsTL'])) except ValueError: pass self.rmsdAnglesValue.set_label(self.QualityIndicators['rmsdAngles']) try: - self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['rmsdAnglesTL'])) + self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['rmsdAnglesTL'])) except ValueError: pass - self.MatrixWeightValue.set_label(self.QualityIndicators['MatrixWeight']) - + self.MatrixWeightValue.set_label( + self.QualityIndicators['MatrixWeight']) - def REFINE(self,widget): + def REFINE(self, widget): if self.job_running: coot.info_dialog('*** refinement in progress ***') @@ -449,13 +467,14 @@ def REFINE(self,widget): ####################################################### # create folder for new refinement cycle and check if free.mtz exists - if not os.path.isdir(os.path.join(self.reference_directory,self.refinementDir)): - os.mkdir(os.path.join(self.reference_directory,self.refinementDir)) - if not os.path.isdir(os.path.join(self.reference_directory,self.refinementDir,'Refine_'+str(self.Serial))): - os.mkdir(os.path.join(self.reference_directory,self.refinementDir,'Refine_'+str(self.Serial))) - if not os.path.isfile(os.path.join(self.reference_directory,self.refinementDir,self.refinementDir+'.free.mtz')): - os.chdir(os.path.join(self.reference_directory,self.refinementDir)) - os.symlink(self.mtzFree,self.refinementDir+'.free.mtz') + if not os.path.isdir(os.path.join(self.reference_directory, self.refinementDir)): + os.mkdir(os.path.join(self.reference_directory, self.refinementDir)) + if not os.path.isdir(os.path.join(self.reference_directory, self.refinementDir, 'Refine_'+str(self.Serial))): + os.mkdir(os.path.join(self.reference_directory, + self.refinementDir, 'Refine_'+str(self.Serial))) + if not os.path.isfile(os.path.join(self.reference_directory, self.refinementDir, self.refinementDir+'.free.mtz')): + os.chdir(os.path.join(self.reference_directory, self.refinementDir)) + os.symlink(self.mtzFree, self.refinementDir+'.free.mtz') ####################################################### # write PDB file @@ -463,23 +482,26 @@ def REFINE(self,widget): # note: the user has to make sure that the ligand file was merged into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item) in self.pdbFile: - coot.write_pdb_file(item,os.path.join(self.reference_directory,self.refinementDir,'Refine_'+str(self.Serial),'in.pdb')) + coot.write_pdb_file(item, os.path.join( + self.reference_directory, self.refinementDir, 'Refine_'+str(self.Serial), 'in.pdb')) break - self.Refine.RunRefmac(self.Serial,self.RefmacParams,self.external_software,self.xce_logfile,None) + self.Refine.RunRefmac(self.Serial, self.RefmacParams, + self.external_software, self.xce_logfile, None) # self.spinnerBox.add(self.refinementRunning) # self.refinementRunning.start() self.status_label.set_text('Refinement running...') - time.sleep(1) # waiting 1s to make sure that REFINEMENT_IN_PROGRESS is written + # waiting 1s to make sure that REFINEMENT_IN_PROGRESS is written + time.sleep(1) snooze = 0 - while os.path.exists(os.path.join(self.reference_directory,self.refinementDir,'REFINEMENT_IN_PROGRESS')): + while os.path.exists(os.path.join(self.reference_directory, self.refinementDir, 'REFINEMENT_IN_PROGRESS')): time.sleep(10) - print '==> XCE: waiting for refinement to finish; elapsed time = ' + str(snooze) + 's' + print '==> XCE: waiting for refinement to finish; elapsed time = ' + \ + str(snooze) + 's' snooze += 10 self.update_pdb_mtz_files('') - # launch refinement # time.sleep(1) # waiting 1s to make sure that REFINEMENT_IN_PROGRESS is written # self.source_id = gobject.timeout_add(100, self.wait_for_refined_pdb) @@ -501,91 +523,105 @@ def REFINE(self,widget): # if action=='update_pdb_mtz': # self.update_pdb_mtz_files('') - - - def RefinementParams(self,widget): + def RefinementParams(self, widget): print '\n==> XCE: changing refinement parameters' - self.RefmacParams=self.Refine.RefinementParams(self.RefmacParams) + self.RefmacParams = self.Refine.RefinementParams(self.RefmacParams) - def set_selection_mode(self,widget): - self.selection_mode=widget.get_active_text() + def set_selection_mode(self, widget): + self.selection_mode = widget.get_active_text() - - def load_pdb_file(self,widget): - pdbRoot=self.cb_select_pdb.get_active_text() + def load_pdb_file(self, widget): + pdbRoot = self.cb_select_pdb.get_active_text() if self.pdbFile != '': - self.Logfile.error('sorry, you need to close the current instance of COOT and start again') + self.Logfile.error( + 'sorry, you need to close the current instance of COOT and start again') return None - self.refinementDir=pdbRoot.replace('.pdb','') + self.refinementDir = pdbRoot.replace('.pdb', '') self.update_pdb_mtz_files(pdbRoot) - def update_pdb_mtz_files(self,pdbRoot): + def update_pdb_mtz_files(self, pdbRoot): # first remove all pdb and mtz files from memory self.Logfile.insert('removing all PDB and MTZ files from memory') if len(coot_utils_XChem.molecule_number_list()) > 0: for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith('.pdb') or '.mtz' in coot.molecule_name(item): - self.Logfile.insert('removing %s' %coot.molecule_name(item)) + self.Logfile.insert('removing %s' % + coot.molecule_name(item)) coot.close_molecule(item) coot.set_nomenclature_errors_on_read("ignore") # first we check if there is a refinement folder and the respective refine.pdb # from previous refinement cycles - Root=self.cb_select_pdb.get_active_text() - print 'ROOT',Root - print 'REFI_DIR',os.path.join(self.reference_directory,self.refinementDir,'refine.pdb') - if os.path.isfile(os.path.join(self.reference_directory,self.refinementDir,'refine.pdb')): + Root = self.cb_select_pdb.get_active_text() + print 'ROOT', Root + print 'REFI_DIR', os.path.join( + self.reference_directory, self.refinementDir, 'refine.pdb') + if os.path.isfile(os.path.join(self.reference_directory, self.refinementDir, 'refine.pdb')): os.chdir(self.reference_directory) - print 'CURRENT DIR',os.getcwd() - os.system('/bin/rm %s 2> /dev/null' %Root) - os.symlink(os.path.realpath(os.path.join(self.refinementDir,'refine.pdb')),'%s' %Root) - self.pdbFile=os.path.join(self.reference_directory,self.refinementDir,'refine.pdb') - elif os.path.isfile(os.path.join(self.reference_directory,Root)): - self.pdbFile=os.path.join(self.reference_directory,Root) + print 'CURRENT DIR', os.getcwd() + os.system('/bin/rm %s 2> /dev/null' % Root) + os.symlink(os.path.realpath(os.path.join( + self.refinementDir, 'refine.pdb')), '%s' % Root) + self.pdbFile = os.path.join( + self.reference_directory, self.refinementDir, 'refine.pdb') + elif os.path.isfile(os.path.join(self.reference_directory, Root)): + self.pdbFile = os.path.join(self.reference_directory, Root) else: self.Logfile.error('cannot find PDB file') if self.pdbFile != '': -# os.chdir(os.path.join(self.reference_directory,self.refinementDir)) + # os.chdir(os.path.join(self.reference_directory,self.refinementDir)) coot.set_colour_map_rotation_on_read_pdb(0) - imol=coot.handle_read_draw_molecule_with_recentre(self.pdbFile,0) - self.QualityIndicators=XChemUtils.parse().PDBheader(os.path.join(self.pdbFile)) - self.QualityIndicators.update(XChemUtils.logtools(os.path.join(self.reference_directory,self.refinementDir,'refine_molprobity.log')).phenix_molprobity()) - self.QualityIndicators.update(XChemUtils.logtools(os.path.join(self.reference_directory,self.refinementDir,'Refine_'+str(self.Serial),'refmac.log')).refmac_log()) - self.mol_dict['protein']=imol - - - if self.mtzFree=='': - print 'FREE',os.path.join(self.reference_directory,pdbRoot.replace('.pdb','')+'.free.mtz') - if os.path.isfile(os.path.join(self.reference_directory,pdbRoot.replace('.pdb','')+'.free.mtz')): - self.mtzFree=os.path.join(self.reference_directory,pdbRoot.replace('.pdb','')+'.free.mtz') - self.mtzFree_label.set_text(pdbRoot.replace('.pdb','')+'.free.mtz') + imol = coot.handle_read_draw_molecule_with_recentre( + self.pdbFile, 0) + self.QualityIndicators = XChemUtils.parse().PDBheader(os.path.join(self.pdbFile)) + self.QualityIndicators.update(XChemUtils.logtools(os.path.join( + self.reference_directory, self.refinementDir, 'refine_molprobity.log')).phenix_molprobity()) + self.QualityIndicators.update(XChemUtils.logtools(os.path.join( + self.reference_directory, self.refinementDir, 'Refine_'+str(self.Serial), 'refmac.log')).refmac_log()) + self.mol_dict['protein'] = imol + + if self.mtzFree == '': + print 'FREE', os.path.join( + self.reference_directory, pdbRoot.replace('.pdb', '')+'.free.mtz') + if os.path.isfile(os.path.join(self.reference_directory, pdbRoot.replace('.pdb', '')+'.free.mtz')): + self.mtzFree = os.path.join( + self.reference_directory, pdbRoot.replace('.pdb', '')+'.free.mtz') + self.mtzFree_label.set_text( + pdbRoot.replace('.pdb', '')+'.free.mtz') self.REFINEbutton.set_sensitive(True) else: self.mtzFree_label.set_text('missing file') - self.Logfile.error('cannot find file with F,SIGF and FreeR_flag; cannot start refinement') + self.Logfile.error( + 'cannot find file with F,SIGF and FreeR_flag; cannot start refinement') self.REFINEbutton.set_sensitive(False) - self.mtzRefine='' - if os.path.isfile(os.path.join(self.reference_directory,self.refinementDir,'refine.mtz')): - self.mtzRefine=os.path.join(self.reference_directory,self.refinementDir,'refine.mtz') - mtzRefineReal = os.path.realpath(os.path.join(self.reference_directory,self.refinementDir,'refine.mtz')) - mtzRefineCurrent = mtzRefineReal.replace(os.path.join(self.reference_directory,self.refinementDir+'/'),'') + self.mtzRefine = '' + if os.path.isfile(os.path.join(self.reference_directory, self.refinementDir, 'refine.mtz')): + self.mtzRefine = os.path.join( + self.reference_directory, self.refinementDir, 'refine.mtz') + mtzRefineReal = os.path.realpath(os.path.join( + self.reference_directory, self.refinementDir, 'refine.mtz')) + mtzRefineCurrent = mtzRefineReal.replace(os.path.join( + self.reference_directory, self.refinementDir+'/'), '') self.mtzRefine_label.set_text(mtzRefineCurrent) coot.set_default_initial_contour_level_for_map(1) - if os.path.isfile(os.path.join(self.reference_directory,self.refinementDir,self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join(self.reference_directory,self.refinementDir,self.mtz_style)) + if os.path.isfile(os.path.join(self.reference_directory, self.refinementDir, self.mtz_style)): + coot.auto_read_make_and_draw_maps(os.path.join( + self.reference_directory, self.refinementDir, self.mtz_style)) else: self.mtzRefine_label.set_text('missing file') - self.Logfile.warning('cannot find file with F,SIGF and FreeR_flag; cannot start refinement') + self.Logfile.warning( + 'cannot find file with F,SIGF and FreeR_flag; cannot start refinement') - groundStateMap = os.path.join(self.reference_directory,Root+'-mean-map.native.ccp4').replace('.pdb','') - print '===>',groundStateMap + groundStateMap = os.path.join( + self.reference_directory, Root+'-mean-map.native.ccp4').replace('.pdb', '') + print '===>', groundStateMap if os.path.isfile(groundStateMap): - imol=coot.handle_read_ccp4_map(groundStateMap,0) - coot.set_contour_level_in_sigma(imol,1) - coot.set_last_map_colour(0.6,0.6,0) + imol = coot.handle_read_ccp4_map(groundStateMap, 0) + coot.set_contour_level_in_sigma(imol, 1) + coot.set_last_map_colour(0.6, 0.6, 0) else: print '==> XCE: ERROR - cannot find ground state mean map!' @@ -654,52 +690,58 @@ def update_pdb_mtz_files(self,pdbRoot): # elif 'ground-state-mean-map' in coot.molecule_name(imol): # coot.set_map_displayed(imol,0) - def show_molprobity_to_do(self,widget): - if os.path.isfile(os.path.join(self.reference_directory,self.refinementDir,'Refine_'+str(self.Serial-1),'molprobity_coot.py')): - coot.run_script(os.path.join(self.reference_directory,self.refinementDir,'Refine_'+str(self.Serial-1),'molprobity_coot.py')) + + def show_molprobity_to_do(self, widget): + if os.path.isfile(os.path.join(self.reference_directory, self.refinementDir, 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')): + coot.run_script(os.path.join(self.reference_directory, self.refinementDir, + 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')) else: - print '==> XCE: cannot find '+os.path.join(self.reference_directory,self.xtalID,'Refine_'+str(self.Serial-1),'molprobity_coot.py') + print '==> XCE: cannot find ' + \ + os.path.join(self.reference_directory, self.xtalID, + 'Refine_'+str(self.Serial-1), 'molprobity_coot.py') - def update_plot(self,refinement_cycle,Rfree,Rcryst): + def update_plot(self, refinement_cycle, Rfree, Rcryst): fig = Figure(figsize=(2, 2), dpi=50) Plot = fig.add_subplot(111) - Plot.set_ylim([0,max(Rcryst+Rfree)]) - Plot.set_xlabel('Refinement Cycle',fontsize=12) - Plot.plot(refinement_cycle,Rfree,label='Rfree',linewidth=2) - Plot.plot(refinement_cycle,Rcryst,label='Rcryst',linewidth=2) + Plot.set_ylim([0, max(Rcryst+Rfree)]) + Plot.set_xlabel('Refinement Cycle', fontsize=12) + Plot.plot(refinement_cycle, Rfree, label='Rfree', linewidth=2) + Plot.plot(refinement_cycle, Rcryst, label='Rcryst', linewidth=2) Plot.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, - ncol=2, mode="expand", borderaxespad=0.,fontsize=12) + ncol=2, mode="expand", borderaxespad=0., fontsize=12) return fig def get_ground_state_maps_by_resolution(self): - found=False - mapList=[] - for logFile in glob.glob(os.path.join(self.reference_directory,str(self.cb_select_mean_map.get_active_text()),'logs','*.log')): - for n,line in enumerate(open(logFile)): + found = False + mapList = [] + for logFile in glob.glob(os.path.join(self.reference_directory, str(self.cb_select_mean_map.get_active_text()), 'logs', '*.log')): + for n, line in enumerate(open(logFile)): if line.startswith('Statistical Electron Density Characterisation') and len(line.split()) == 6: -# try: -# resolution=float(line.split()[5]) - resolution=line.split()[5] + # try: + # resolution=float(line.split()[5]) + resolution = line.split()[5] print resolution - found=True - foundLine=n + found = True + foundLine = n # except ValueError: # print 'error' # break - if found and n==foundLine+3: - xtal=line.split(',')[0].replace(' ','').replace('\t','') - meanmap=os.path.join(self.reference_directory,self.cb_select_mean_map.get_active_text(),'processed_datasets',xtal,xtal+'-ground-state-mean-map.native.ccp4') - mapList.append([resolution,meanmap]) - found=False + if found and n == foundLine+3: + xtal = line.split(',')[0].replace( + ' ', '').replace('\t', '') + meanmap = os.path.join(self.reference_directory, self.cb_select_mean_map.get_active_text( + ), 'processed_datasets', xtal, xtal+'-ground-state-mean-map.native.ccp4') + mapList.append([resolution, meanmap]) + found = False return mapList def get_highest_reso_ground_state_map(self): mapList = self.get_ground_state_maps_by_resolution() print mapList - self.ground_state_map_List=[] + self.ground_state_map_List = [] self.ground_state_map_List.append(min(mapList, key=lambda x: x[0])) return self.ground_state_map_List -if __name__=='__main__': +if __name__ == '__main__': GUI().StartGUI() diff --git a/lib/XChemCootTwin.py b/lib/XChemCootTwin.py index d102f4ba..405be291 100755 --- a/lib/XChemCootTwin.py +++ b/lib/XChemCootTwin.py @@ -1,5 +1,14 @@ # last edited: 08/08/2017 - 15:00 +import pango +import gtk +import pygtk +import coot_utils_XChem +import coot +import XChemLog +import XChemUtils +import XChemRefine +import XChemDB import gobject import sys import os @@ -12,19 +21,12 @@ # XCE libraries sys.path.append(os.getenv('XChemExplorer_DIR') + '/lib') -import XChemDB -import XChemRefine -import XChemUtils -import XChemLog # libraries from COOT -import pygtk, gtk, pango -import coot # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. # modified file is now in $XChemExplorer_DIR/lib -import coot_utils_XChem class GUI(object): @@ -49,7 +51,8 @@ def __init__(self): print self.settings # checking for external software packages - self.external_software = XChemUtils.external_software(self.xce_logfile).check() + self.external_software = XChemUtils.external_software( + self.xce_logfile).check() self.external_software['qsub_remote'] = remote_qsub_submission self.selection_criteria = ['0 - All Datasets', @@ -63,8 +66,10 @@ def __init__(self): self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], ['In Refinement', '3 - In Refinement', 65000, 0, 0], - ['Comp Chem Ready!', '4 - CompChem ready', 65000, 0, 0], - ['Ready for Deposition!', '5 - Deposition ready', 65000, 0, 0], + ['Comp Chem Ready!', + '4 - CompChem ready', 65000, 0, 0], + ['Ready for Deposition!', + '5 - Deposition ready', 65000, 0, 0], ['In PDB', '6 - Deposited', 65000, 0, 0], ['Analysed & Rejected', '7 - Analysed & Rejected', 65000, 0, 0]] @@ -126,7 +131,6 @@ def __init__(self): self.label_button_list = [] - ########################################################################################### # some COOT settings coot.set_map_radius(17) @@ -202,7 +206,8 @@ def StartGUI(self): # self.hbox_select_samples.add(self.cb_select_sites) self.select_samples_button = gtk.Button(label="GO") - self.select_samples_button.connect("clicked", self.get_samples_to_look_at) + self.select_samples_button.connect( + "clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) @@ -254,7 +259,8 @@ def StartGUI(self): ResolutionLabel_frame = gtk.Frame() self.ResolutionLabel = gtk.Label('Resolution') ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label(self.QualityIndicators['RefinementResolution']) + self.ResolutionValue = gtk.Label( + self.QualityIndicators['RefinementResolution']) ResolutionBox_frame = gtk.Frame() self.ResolutionBox = gtk.EventBox() self.ResolutionBox.add(self.ResolutionValue) @@ -263,7 +269,8 @@ def StartGUI(self): MolprobityScoreLabel_frame = gtk.Frame() self.MolprobityScoreLabel = gtk.Label('MolprobityScore') MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) - self.MolprobityScoreValue = gtk.Label(self.QualityIndicators['RefinementMolProbityScore']) + self.MolprobityScoreValue = gtk.Label( + self.QualityIndicators['RefinementMolProbityScore']) MolprobityScoreBox_frame = gtk.Frame() self.MolprobityScoreBox = gtk.EventBox() self.MolprobityScoreBox.add(self.MolprobityScoreValue) @@ -272,7 +279,8 @@ def StartGUI(self): RamachandranOutliersLabel_frame = gtk.Frame() self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) - self.RamachandranOutliersValue = gtk.Label(self.QualityIndicators['RefinementRamachandranOutliers']) + self.RamachandranOutliersValue = gtk.Label( + self.QualityIndicators['RefinementRamachandranOutliers']) RamachandranOutliersBox_frame = gtk.Frame() self.RamachandranOutliersBox = gtk.EventBox() self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) @@ -281,7 +289,8 @@ def StartGUI(self): RamachandranFavoredLabel_frame = gtk.Frame() self.RamachandranFavoredLabel = gtk.Label('Rama Favored') RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) - self.RamachandranFavoredValue = gtk.Label(self.QualityIndicators['RefinementRamachandranFavored']) + self.RamachandranFavoredValue = gtk.Label( + self.QualityIndicators['RefinementRamachandranFavored']) RamachandranFavoredBox_frame = gtk.Frame() self.RamachandranFavoredBox = gtk.EventBox() self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) @@ -290,7 +299,8 @@ def StartGUI(self): rmsdBondsLabel_frame = gtk.Frame() self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') rmsdBondsLabel_frame.add(self.rmsdBondsLabel) - self.rmsdBondsValue = gtk.Label(self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue = gtk.Label( + self.QualityIndicators['RefinementRmsdBonds']) rmsdBondsBox_frame = gtk.Frame() self.rmsdBondsBox = gtk.EventBox() self.rmsdBondsBox.add(self.rmsdBondsValue) @@ -299,7 +309,8 @@ def StartGUI(self): rmsdAnglesLabel_frame = gtk.Frame() self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) - self.rmsdAnglesValue = gtk.Label(self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue = gtk.Label( + self.QualityIndicators['RefinementRmsdAngles']) rmsdAnglesBox_frame = gtk.Frame() self.rmsdAnglesBox = gtk.EventBox() self.rmsdAnglesBox.add(self.rmsdAnglesValue) @@ -308,7 +319,8 @@ def StartGUI(self): MatrixWeightLabel_frame = gtk.Frame() self.MatrixWeightLabel = gtk.Label('Matrix Weight') MatrixWeightLabel_frame.add(self.MatrixWeightLabel) - self.MatrixWeightValue = gtk.Label(self.QualityIndicators['RefinementMatrixWeight']) + self.MatrixWeightValue = gtk.Label( + self.QualityIndicators['RefinementMatrixWeight']) MatrixWeightBox_frame = gtk.Frame() self.MatrixWeightBox = gtk.EventBox() self.MatrixWeightBox.add(self.MatrixWeightValue) @@ -317,7 +329,8 @@ def StartGUI(self): ligandIDLabel_frame = gtk.Frame() self.ligandIDLabel = gtk.Label('Ligand ID') ligandIDLabel_frame.add(self.ligandIDLabel) - self.ligandIDValue = gtk.Label(self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue = gtk.Label( + self.spider_plot_data['PANDDA_site_ligand_id']) ligandIDBox_frame = gtk.Frame() self.ligandIDBox = gtk.EventBox() self.ligandIDBox.add(self.ligandIDValue) @@ -326,7 +339,8 @@ def StartGUI(self): ligand_occupancyLabel_frame = gtk.Frame() self.ligand_occupancyLabel = gtk.Label('occupancy') ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) - self.ligand_occupancyValue = gtk.Label(self.spider_plot_data['PANDDA_site_occupancy']) + self.ligand_occupancyValue = gtk.Label( + self.spider_plot_data['PANDDA_site_occupancy']) ligand_occupancyBox_frame = gtk.Frame() self.ligand_occupancyBox = gtk.EventBox() self.ligand_occupancyBox.add(self.ligand_occupancyValue) @@ -335,7 +349,8 @@ def StartGUI(self): ligand_BaverageLabel_frame = gtk.Frame() self.ligand_BaverageLabel = gtk.Label('B average') ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) - self.ligand_BaverageValue = gtk.Label(self.spider_plot_data['PANDDA_site_B_average']) + self.ligand_BaverageValue = gtk.Label( + self.spider_plot_data['PANDDA_site_B_average']) ligand_BaverageBox_frame = gtk.Frame() self.ligand_BaverageBox = gtk.EventBox() self.ligand_BaverageBox.add(self.ligand_BaverageValue) @@ -343,18 +358,22 @@ def StartGUI(self): ligand_BratioSurroundingsLabel_frame = gtk.Frame() self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') - ligand_BratioSurroundingsLabel_frame.add(self.ligand_BratioSurroundingsLabel) + ligand_BratioSurroundingsLabel_frame.add( + self.ligand_BratioSurroundingsLabel) self.ligand_BratioSurroundingsValue = gtk.Label( self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) ligand_BratioSurroundingsBox_frame = gtk.Frame() self.ligand_BratioSurroundingsBox = gtk.EventBox() - self.ligand_BratioSurroundingsBox.add(self.ligand_BratioSurroundingsValue) - ligand_BratioSurroundingsBox_frame.add(self.ligand_BratioSurroundingsBox) + self.ligand_BratioSurroundingsBox.add( + self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add( + self.ligand_BratioSurroundingsBox) ligand_RSCCLabel_frame = gtk.Frame() self.ligand_RSCCLabel = gtk.Label('RSCC') ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) - self.ligand_RSCCValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSCC']) + self.ligand_RSCCValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSCC']) ligand_RSCCBox_frame = gtk.Frame() self.ligand_RSCCBox = gtk.EventBox() self.ligand_RSCCBox.add(self.ligand_RSCCValue) @@ -363,7 +382,8 @@ def StartGUI(self): ligand_rmsdLabel_frame = gtk.Frame() self.ligand_rmsdLabel = gtk.Label('rmsd') ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) - self.ligand_rmsdValue = gtk.Label(self.spider_plot_data['PANDDA_site_rmsd']) + self.ligand_rmsdValue = gtk.Label( + self.spider_plot_data['PANDDA_site_rmsd']) ligand_rmsdBox_frame = gtk.Frame() self.ligand_rmsdBox = gtk.EventBox() self.ligand_rmsdBox.add(self.ligand_rmsdValue) @@ -372,7 +392,8 @@ def StartGUI(self): ligand_RSRLabel_frame = gtk.Frame() self.ligand_RSRLabel = gtk.Label('RSR') ligand_RSRLabel_frame.add(self.ligand_RSRLabel) - self.ligand_RSRValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSR']) + self.ligand_RSRValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSR']) ligand_RSRBox_frame = gtk.Frame() self.ligand_RSRBox = gtk.EventBox() self.ligand_RSRBox.add(self.ligand_RSRValue) @@ -381,7 +402,8 @@ def StartGUI(self): ligand_RSZDLabel_frame = gtk.Frame() self.ligand_RSZDLabel = gtk.Label('RSZD') ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) - self.ligand_RSZDValue = gtk.Label(self.spider_plot_data['PANDDA_site_RSZD']) + self.ligand_RSZDValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSZD']) ligand_RSZDBox_frame = gtk.Frame() self.ligand_RSZDBox = gtk.EventBox() self.ligand_RSZDBox.add(self.ligand_RSZDValue) @@ -416,7 +438,8 @@ def StartGUI(self): self.table_right.attach(ligandIDLabel_frame, 0, 1, 0, 1) self.table_right.attach(ligand_occupancyLabel_frame, 0, 1, 1, 2) self.table_right.attach(ligand_BaverageLabel_frame, 0, 1, 2, 3) - self.table_right.attach(ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach( + ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) self.table_right.attach(ligand_RSCCLabel_frame, 0, 1, 4, 5) self.table_right.attach(ligand_rmsdLabel_frame, 0, 1, 5, 6) self.table_right.attach(ligand_RSRLabel_frame, 0, 1, 6, 7) @@ -440,8 +463,10 @@ def StartGUI(self): button.connect("clicked", self.show_molprobity_to_do) hbox.add(button) # --- ground state mean map --- - self.ground_state_mean_map_button = gtk.Button(label="Show ground state mean map") - self.ground_state_mean_map_button.connect("clicked", self.show_ground_state_mean_map) + self.ground_state_mean_map_button = gtk.Button( + label="Show ground state mean map") + self.ground_state_mean_map_button.connect( + "clicked", self.show_ground_state_mean_map) hbox.add(self.ground_state_mean_map_button) # self.vbox.add(self.ground_state_mean_map_button) self.vbox.add(hbox) @@ -475,7 +500,8 @@ def StartGUI(self): spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_pic = pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image = gtk.Image() self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) spider_plot_frame.add(self.spider_plot_image) @@ -628,8 +654,9 @@ def StartGUI(self): new_button = gtk.RadioButton(None, button[0]) else: new_button = gtk.RadioButton(new_button, button[0]) - new_button.connect("toggled", self.experiment_stage_button_clicked, button[1]) - vbox.pack_start(new_button,False,False,0) + new_button.connect( + "toggled", self.experiment_stage_button_clicked, button[1]) + vbox.pack_start(new_button, False, False, 0) # vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) @@ -644,8 +671,9 @@ def StartGUI(self): new_button = gtk.RadioButton(None, criteria) else: new_button = gtk.RadioButton(new_button, criteria) - new_button.connect("toggled", self.ligand_confidence_button_clicked, criteria) - vbox.pack_start(new_button,False,False,0) + new_button.connect( + "toggled", self.ligand_confidence_button_clicked, criteria) + vbox.pack_start(new_button, False, False, 0) # vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) @@ -689,9 +717,11 @@ def StartGUI(self): self.merge_ligand_button = gtk.Button(label="Merge Ligand") self.place_ligand_here_button = gtk.Button(label="Place Ligand here") self.hbox_for_modeling.add(self.place_ligand_here_button) - self.place_ligand_here_button.connect("clicked", self.place_ligand_here) + self.place_ligand_here_button.connect( + "clicked", self.place_ligand_here) self.hbox_for_modeling.add(self.merge_ligand_button) - self.merge_ligand_button.connect("clicked", self.merge_ligand_into_protein) + self.merge_ligand_button.connect( + "clicked", self.merge_ligand_into_protein) self.select_cpd_cb = gtk.combo_box_new_text() self.select_cpd_cb.connect("changed", self.select_cpd) self.hbox_for_modeling.add(self.select_cpd_cb) @@ -705,18 +735,19 @@ def StartGUI(self): # self.cb_ligand_confidence.append_text(citeria) # self.vbox.add(self.cb_ligand_confidence) - # --- refinement & options --- self.hbox_for_refinement = gtk.HBox() self.REFINEbutton = gtk.Button(label="Refine") self.RefinementParamsButton = gtk.Button(label="refinement parameters") self.covalentLinksbutton = gtk.Button(label="covalent links\n-define-") - self.covalentLinksCreatebutton = gtk.Button(label="covalent links\n-create & refine-") + self.covalentLinksCreatebutton = gtk.Button( + label="covalent links\n-create & refine-") self.REFINEbutton.connect("clicked", self.REFINE) self.hbox_for_refinement.add(self.REFINEbutton) self.RefinementParamsButton.connect("clicked", self.RefinementParams) self.covalentLinksbutton.connect("clicked", self.covalentLinkDef) - self.covalentLinksCreatebutton.connect("clicked", self.covalentLinkCreate) + self.covalentLinksCreatebutton.connect( + "clicked", self.covalentLinkCreate) self.hbox_for_refinement.add(self.RefinementParamsButton) self.hbox_for_refinement.add(self.covalentLinksbutton) self.hbox_for_refinement.add(self.covalentLinksCreatebutton) @@ -730,7 +761,6 @@ def StartGUI(self): # # are defined after checkbox is defined # self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) - # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") self.CANCELbutton.connect("clicked", self.CANCEL) @@ -787,20 +817,23 @@ def select_cpd(self, widget): for imol in coot_utils_XChem.molecule_number_list(): if imol not in self.mol_dict['ligand_stereo']: continue - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + molName = coot.molecule_name(imol)[coot.molecule_name( + imol).rfind('/')+1:].replace('.pdb', '') if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): - molNameCIF = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/') + 1:].replace('.pdb', '').replace('_phenix','').replace('_rhofit','') + molNameCIF = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( + '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') else: molNameCIF = molName - print cpd,'-',imol,'-',coot.molecule_name(imol) + print cpd, '-', imol, '-', coot.molecule_name(imol) if molName == cpd: coot.set_mol_displayed(imol, 1) - print 'reading',os.path.join(self.project_directory,self.xtalID,'compound',molNameCIF+'.cif') - coot.read_cif_dictionary(os.path.join(self.project_directory,self.xtalID,'compound',molNameCIF+'.cif')) + print 'reading', os.path.join( + self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif') + coot.read_cif_dictionary(os.path.join( + self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) else: coot.set_mol_displayed(imol, 0) - def update_RefinementOutcome_radiobutton(self): # updating dataset outcome radiobuttons current_stage = 0 @@ -852,7 +885,8 @@ def refresh_site_combobox(self): # only repopulate if site exists if self.xtalID in self.siteDict: for item in sorted(self.siteDict[self.xtalID]): - self.cb_site.append_text('site: {0!s} - event: {1!s}'.format(item[5], item[6])) + self.cb_site.append_text( + 'site: {0!s} - event: {1!s}'.format(item[5], item[6])) def ChangeSite(self, widget, data=None): if self.xtalID in self.siteDict: @@ -891,13 +925,13 @@ def RefreshSiteData(self): # for w in self.label_button_list: # w.set_active(False) - print 'pandda index', self.pandda_index self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] print 'new spider plot:', self.spider_plot self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] print 'new event map:', self.event_map - self.ligand_confidence = str(self.siteDict[self.xtalID][self.pandda_index][7]) + self.ligand_confidence = str( + self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) @@ -913,14 +947,17 @@ def RefreshSiteData(self): self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, self.event_index) print '>>>>> spider plot data', self.spider_plot_data - self.ligandIDValue.set_label(self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue.set_label( + self.spider_plot_data['PANDDA_site_ligand_id']) try: - self.ligand_occupancyValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) + self.ligand_occupancyValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) except ValueError: self.ligand_occupancyValue.set_label('-') try: - self.ligand_BaverageValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) + self.ligand_BaverageValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) except ValueError: self.ligand_BaverageValue.set_label('-') @@ -931,22 +968,26 @@ def RefreshSiteData(self): self.ligand_BratioSurroundingsValue.set_label('-') try: - self.ligand_RSCCValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) + self.ligand_RSCCValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) except ValueError: self.ligand_RSCCValue.set_label('-') try: - self.ligand_rmsdValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) + self.ligand_rmsdValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) except ValueError: self.ligand_rmsdValue.set_label('-') try: - self.ligand_RSRValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) + self.ligand_RSRValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) except ValueError: self.ligand_RSRValue.set_label('-') try: - self.ligand_RSZDValue.set_label(str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) + self.ligand_RSZDValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) except ValueError: self.ligand_RSZDValue.set_label('-') @@ -965,7 +1006,8 @@ def RefreshSiteData(self): else: spider_plot_pic = gtk.gdk.pixbuf_new_from_file( os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_pic = spider_plot_pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) ######################################################################################### @@ -987,7 +1029,8 @@ def experiment_stage_button_clicked(self, widget, data=None): # print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( # data) + ' in mainTable of datasource' # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile,self.xtalID,'ligand_bound',self.db_dict_mainTable) + self.db.create_or_remove_missing_records_in_depositTable( + self.xce_logfile, self.xtalID, 'ligand_bound', self.db_dict_mainTable) def ligand_confidence_button_clicked(self, widget, data=None): print 'PANDDA_index', self.pandda_index @@ -1037,13 +1080,15 @@ def RefreshData(self): # reset spider plot image spider_plot_pic = gtk.gdk.pixbuf_new_from_file( os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = spider_plot_pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_pic = spider_plot_pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) # reset ground state mean map self.ground_state_mean_map = '' self.ground_state_mean_map_button.set_sensitive(False) - self.ground_state_mean_map_button.set_label('Show ground state mean map') + self.ground_state_mean_map_button.set_label( + 'Show ground state mean map') if os.path.isfile( os.path.join(self.project_directory, self.xtalID, self.xtalID + '-ground-state-mean-map.native.ccp4')): self.ground_state_mean_map_button.set_sensitive(True) @@ -1052,9 +1097,12 @@ def RefreshData(self): # initialize Refinement library # self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) - self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) - self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) - self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * '0' + str(self.Serial) + self.Refine = XChemRefine.Refine( + self.project_directory, self.xtalID, self.compoundID, self.data_source) + self.Serial = XChemRefine.GetSerial( + self.project_directory, self.xtalID) + self.panddaSerial = panddaSerial = m = ( + 4 - len(str(self.Serial))) * '0' + str(self.Serial) # self.Serial=self.Refine.GetSerial() if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple @@ -1088,7 +1136,8 @@ def RefreshData(self): # if the structure was previously refined, try to read the parameters # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: - self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) + self.RefmacParams = self.Refine.ParamsFromPreviousCycle( + self.Serial - 1) print '==> REFMAC params:', self.RefmacParams # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) @@ -1101,9 +1150,9 @@ def RefreshData(self): ######################################################################################### # ligand files # first remove old samples if present - print '>>>',self.mol_dict['ligand_stereo'] + print '>>>', self.mol_dict['ligand_stereo'] for n, item in enumerate(self.mol_dict['ligand_stereo']): - print '__',item + print '__', item self.select_cpd_cb.remove_text(0) print 'done' @@ -1136,25 +1185,27 @@ def RefreshData(self): imol = coot.handle_read_draw_molecule_with_recentre( os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb'), 0) self.mol_dict['ligand'] = imol - coot.read_cif_dictionary(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) + coot.read_cif_dictionary(os.path.join( + self.project_directory, self.xtalID, self.compoundID + '.cif')) self.select_cpd_cb.append_text(self.compoundID) self.mol_dict['ligand_stereo'] = [] self.mol_dict['ligand_stereo'].append(imol) # ligands in compound directory - for cifFile in sorted(glob.glob(os.path.join(self.project_directory,self.xtalID,'compound',self.compoundID+'_*.pdb'))): + for cifFile in sorted(glob.glob(os.path.join(self.project_directory, self.xtalID, 'compound', self.compoundID+'_*.pdb'))): cif = cifFile[cifFile.rfind('/')+1:] if '_with_H' in cif: continue - self.select_cpd_cb.append_text(cif.replace('.pdb','')) + self.select_cpd_cb.append_text(cif.replace('.pdb', '')) imol = coot.handle_read_draw_molecule_with_recentre(cifFile, 0) self.mol_dict['ligand_stereo'].append(imol) - coot.set_mol_displayed(imol,0) + coot.set_mol_displayed(imol, 0) # autofitted ligands - for pdbFile in sorted(glob.glob(os.path.join(self.project_directory,self.xtalID,'autofit_ligand','*','*.pdb'))): + for pdbFile in sorted(glob.glob(os.path.join(self.project_directory, self.xtalID, 'autofit_ligand', '*', '*.pdb'))): autofitRun = pdbFile.split('/')[len(pdbFile.split('/')) - 2] if pdbFile.endswith(autofitRun+'.pdb'): self.select_cpd_cb.append_text(autofitRun) - imol = coot.handle_read_draw_molecule_with_recentre(pdbFile, 0) + imol = coot.handle_read_draw_molecule_with_recentre( + pdbFile, 0) self.mol_dict['ligand_stereo'].append(imol) coot.set_mol_displayed(imol, 0) self.select_cpd_cb.set_sensitive(True) @@ -1171,9 +1222,9 @@ def RefreshData(self): # self.Logfile.insert('==> COOT: looking for ground-state model ' + os.path.join(self.project_directory, self.xtalID, # self.pdb_style.replace('.pdb', # '') + '.split.ground-state.pdb')) -## print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, -## self.pdb_style.replace('.pdb', -## '') + '.split.ground-state.pdb') +# print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, +# self.pdb_style.replace('.pdb', +# '') + '.split.ground-state.pdb') # if os.path.isfile(os.path.join(self.project_directory, self.xtalID, # self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): # self.Logfile.insert('==> COOT: found ground-state model') @@ -1246,9 +1297,10 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( + self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( item).endswith(self.pdb_style): - coot.set_show_symmetry_master(1) # master switch to show symmetry molecules + # master switch to show symmetry molecules + coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model ######################################################################################### @@ -1258,9 +1310,11 @@ def RefreshData(self): if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc_twin.map')): coot.set_colour_map_rotation_on_read_pdb(0) coot.set_default_initial_contour_level_for_difference_map(3) - coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, 'fofc_twin.map'), 1) + coot.handle_read_ccp4_map(os.path.join( + self.project_directory, self.xtalID, 'fofc_twin.map'), 1) coot.set_default_initial_contour_level_for_map(1) - coot.handle_read_ccp4_map(os.path.join(self.project_directory, self.xtalID, '2fofc_twin.map'), 0) + coot.handle_read_ccp4_map(os.path.join( + self.project_directory, self.xtalID, '2fofc_twin.map'), 0) coot.set_last_map_colour(0, 0, 1) else: # try to open mtz file with same name as pdb file @@ -1273,11 +1327,14 @@ def RefreshData(self): # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): # os.symlink('dimple.mtz',self.mtz_style) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, self.mtz_style)) + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, self.mtz_style)) elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init_twin.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, 'init_twin.mtz')) + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, 'init_twin.mtz')) elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple_twin.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join(self.project_directory, self.xtalID, 'dimple_twin.mtz')) + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, 'dimple_twin.mtz')) ######################################################################################### # update Quality Indicator table @@ -1292,43 +1349,50 @@ def RefreshData(self): gtk.gdk.color_parse(self.QualityIndicators['RefinementRfreeTraficLight'])) except ValueError: pass - self.ResolutionValue.set_label(self.QualityIndicators['RefinementResolution']) + self.ResolutionValue.set_label( + self.QualityIndicators['RefinementResolution']) try: self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementResolutionTL'])) except ValueError: pass - self.MolprobityScoreValue.set_label(self.QualityIndicators['RefinementMolProbityScore']) + self.MolprobityScoreValue.set_label( + self.QualityIndicators['RefinementMolProbityScore']) try: self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( self.QualityIndicators['RefinementMolProbityScoreTL'])) except ValueError: pass - self.RamachandranOutliersValue.set_label(self.QualityIndicators['RefinementRamachandranOutliers']) + self.RamachandranOutliersValue.set_label( + self.QualityIndicators['RefinementRamachandranOutliers']) try: self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( self.QualityIndicators['RefinementRamachandranOutliersTL'])) except ValueError: pass - self.RamachandranFavoredValue.set_label(self.QualityIndicators['RefinementRamachandranFavored']) + self.RamachandranFavoredValue.set_label( + self.QualityIndicators['RefinementRamachandranFavored']) try: self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( self.QualityIndicators['RefinementRamachandranFavoredTL'])) except ValueError: pass - self.rmsdBondsValue.set_label(self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue.set_label( + self.QualityIndicators['RefinementRmsdBonds']) try: self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdBondsTL'])) except ValueError: pass - self.rmsdAnglesValue.set_label(self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue.set_label( + self.QualityIndicators['RefinementRmsdAngles']) try: self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdAnglesTL'])) except ValueError: pass - self.MatrixWeightValue.set_label(self.QualityIndicators['RefinementMatrixWeight']) + self.MatrixWeightValue.set_label( + self.QualityIndicators['RefinementMatrixWeight']) try: pic = gtk.gdk.pixbuf_new_from_file( @@ -1369,52 +1433,56 @@ def start_refinement(self): # ####################################################### -# if self.refinementProtocol.startswith('pandda'): -# -# ####################################################### -# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): -# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) -# # create folder for new refinement cycle -# try: -# self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) -# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) -# except OSError: -# self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') -## print '==> XCE: WARNING -> folder exists; will overwrite contents!' -# self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') -# -# ####################################################### -# # write PDB file -# # now take protein pdb file and write it to newly create Refine_ folder -# # note: the user has to make sure that the ligand file was merged into main file -# for item in coot_utils_XChem.molecule_number_list(): -# if coot.molecule_name(item).endswith( -# self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( -# item).endswith(self.pdb_style): -# coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', -# 'Refine_' + str(self.Serial), 'refine.modified.pdb')) -# break -# # elif coot.molecule_name(item).endswith('dimple.pdb'): -# # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) -# # break -# -# XChemRefine.panddaRefine(self.project_directory, self.xtalID, self.compoundID, -# self.data_source).RunQuickRefine(self.Serial, self.RefmacParams, -# self.external_software, self.xce_logfile, -# self.refinementProtocol, self.covLinkAtomSpec) -# else: + # if self.refinementProtocol.startswith('pandda'): + # + # ####################################################### + # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): + # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) + # # create folder for new refinement cycle + # try: + # self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + # except OSError: + # self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') + ## print '==> XCE: WARNING -> folder exists; will overwrite contents!' + # self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') + # + # ####################################################### + # # write PDB file + # # now take protein pdb file and write it to newly create Refine_ folder + # # note: the user has to make sure that the ligand file was merged into main file + # for item in coot_utils_XChem.molecule_number_list(): + # if coot.molecule_name(item).endswith( + # self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( + # item).endswith(self.pdb_style): + # coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', + # 'Refine_' + str(self.Serial), 'refine.modified.pdb')) + # break + # # elif coot.molecule_name(item).endswith('dimple.pdb'): + # # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) + # # break + # + # XChemRefine.panddaRefine(self.project_directory, self.xtalID, self.compoundID, + # self.data_source).RunQuickRefine(self.Serial, self.RefmacParams, + # self.external_software, self.xce_logfile, + # self.refinementProtocol, self.covLinkAtomSpec) + # else: ####################################################### if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) # create folder for new refinement cycle try: - self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) - os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + self.Logfile.insert('==> COOT: trying to make folder: %s' % os.path.join( + self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + os.mkdir(os.path.join(self.project_directory, self.xtalID, + 'cootOut', 'Refine_' + str(self.Serial))) except OSError: - self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') + self.Logfile.warning( + '==> COOT: folder exists; will overwrite contents!') # print '==> XCE: WARNING -> folder exists; will overwrite contents!' - self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') + self.Logfile.warning( + '==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') # ####################################################### @@ -1444,10 +1512,11 @@ def start_refinement(self): break if foundPDB: coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', - 'Refine_' + str(self.Serial), 'in.pdb')) + 'Refine_' + str(self.Serial), 'in.pdb')) # self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) - self.Refine.RunBuster(self.Serial, self.external_software, self.xce_logfile, self.covLinkAtomSpec) + self.Refine.RunBuster( + self.Serial, self.external_software, self.xce_logfile, self.covLinkAtomSpec) self.index += 1 if self.index >= len(self.Todo): # self.index = len(self.Todo) @@ -1460,14 +1529,14 @@ def RefinementParams(self, widget): self.data_source).RefmacRefinementParams(self.RefmacParams) def covalentLinkDef(self, widget): - coot.user_defined_click_py(2,self.show_potential_link) + coot.user_defined_click_py(2, self.show_potential_link) - def show_potential_link(self,*clicks): + def show_potential_link(self, *clicks): # first find imol of protein molecule # it's a prerequisite that the ligand is merged into the protein imol_protein = None for imol in coot_utils_XChem.molecule_number_list(): - print '>',coot.molecule_name(imol) + print '>', coot.molecule_name(imol) if coot.molecule_name(imol).endswith(self.pdb_style) or \ coot.molecule_name(imol).endswith('init_twin.pdb') or \ coot.molecule_name(imol).endswith('dimple_twin.pdb') or \ @@ -1481,18 +1550,24 @@ def show_potential_link(self,*clicks): click_2 = clicks[1] imol_1 = click_1[1] imol_2 = click_2[1] - print 'imolp',imol,'imo11',imol_1,'imol2',imol_2 + print 'imolp', imol, 'imo11', imol_1, 'imol2', imol_2 if imol_1 == imol_2 and imol_1 == imol_protein: - print 'click_1',click_1 + print 'click_1', click_1 self.covLinkAtomSpec = None - xyz_1 = atom_info_string(click_1[1],click_1[2],click_1[3],click_1[4],click_1[5],click_1[6]) - residue_1 = residue_name(click_1[1],click_1[2],click_1[3],click_1[4]) - xyz_2 = atom_info_string(click_2[1],click_2[2],click_2[3],click_2[4],click_2[5],click_2[6]) - residue_2 = residue_name(click_2[1],click_2[2],click_2[3],click_2[4]) + xyz_1 = atom_info_string( + click_1[1], click_1[2], click_1[3], click_1[4], click_1[5], click_1[6]) + residue_1 = residue_name( + click_1[1], click_1[2], click_1[3], click_1[4]) + xyz_2 = atom_info_string( + click_2[1], click_2[2], click_2[3], click_2[4], click_2[5], click_2[6]) + residue_2 = residue_name( + click_2[1], click_2[2], click_2[3], click_2[4]) thick = 4 - to_generic_object_add_line(self.covLinkObject, "yellowtint", thick, xyz_1[3], xyz_1[4], xyz_1[5], xyz_2[3], xyz_2[4], xyz_2[5]) + to_generic_object_add_line( + self.covLinkObject, "yellowtint", thick, xyz_1[3], xyz_1[4], xyz_1[5], xyz_2[3], xyz_2[4], xyz_2[5]) set_display_generic_object(self.covLinkObject, 1) - self.covLinkAtomSpec = [imol_protein,click_1,click_2,residue_1,residue_2] + self.covLinkAtomSpec = [imol_protein, + click_1, click_2, residue_1, residue_2] else: print 'error: both atoms must belong to the same object; did you merge the ligand with your protein?' @@ -1523,8 +1598,10 @@ def get_samples_to_look_at(self, widget): self.cb.remove_text(0) self.Todo = [] self.siteDict = {} - self.Todo, self.siteDict = self.db.get_todoList_for_coot(self.selection_mode) - self.status_label.set_text('found {0!s} samples'.format(len(self.Todo))) + self.Todo, self.siteDict = self.db.get_todoList_for_coot( + self.selection_mode) + self.status_label.set_text( + 'found {0!s} samples'.format(len(self.Todo))) # refresh sample CB for item in sorted(self.Todo): self.cb.append_text('{0!s}'.format(item[0])) @@ -1553,7 +1630,8 @@ def place_ligand_here(self, widget): for imol in coot_utils_XChem.molecule_number_list(): if imol not in self.mol_dict['ligand_stereo']: continue - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + molName = coot.molecule_name(imol)[coot.molecule_name( + imol).rfind('/')+1:].replace('.pdb', '') if molName == cpd: print '===> XCE: moving ligand to pointer' coot_utils_XChem.move_molecule_here(imol) @@ -1563,34 +1641,40 @@ def place_ligand_here(self, widget): # print 'LIGAND: ', self.mol_dict['ligand'] # coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) - def merge_ligand_into_protein(self, widget): cpd = str(self.select_cpd_cb.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): if imol not in self.mol_dict['ligand_stereo']: continue - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/')+1:].replace('.pdb','') + molName = coot.molecule_name(imol)[coot.molecule_name( + imol).rfind('/')+1:].replace('.pdb', '') if molName == cpd: - print '===> XCE: merge ligand into protein structure -->',cpd + print '===> XCE: merge ligand into protein structure -->', cpd coot.merge_molecules_py([imol], self.mol_dict['protein']) if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind('/') + 1:].replace('.pdb', '').replace('_phenix','').replace('_rhofit','') + molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( + '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')): - os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) - print 'XCE: changing directory', os.path.join(self.project_directory, self.xtalID) + os.system('/bin/rm %s' % os.path.join(self.project_directory, + self.xtalID, self.compoundID + '.cif')) + print 'XCE: changing directory', os.path.join( + self.project_directory, self.xtalID) os.chdir(os.path.join(self.project_directory, self.xtalID)) print 'XCE: changing symlink ln -s %s %s.cif' % ( - os.path.join('compound', molName + '.cif'), self.compoundID) - os.system('ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) + os.path.join('compound', molName + '.cif'), self.compoundID) + os.system( + 'ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): - os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')) - print 'XCE: changing directory', os.path.join(self.project_directory, self.xtalID) + os.system('/bin/rm %s' % os.path.join(self.project_directory, + self.xtalID, self.compoundID + '.pdb')) + print 'XCE: changing directory', os.path.join( + self.project_directory, self.xtalID) os.chdir(os.path.join(self.project_directory, self.xtalID)) print 'XCE: changing symlink ln -s %s %s.pdb' % ( - os.path.join('compound', molName + '.pdb'), self.compoundID) + os.path.join('compound', molName + '.pdb'), self.compoundID) os.system('ln -s %s %s.pdb' % (os.path.join('compound', molName - + '.pdb'), self.compoundID)) - print '===> XCE: deleting ligand molecule',molName + + '.pdb'), self.compoundID)) + print '===> XCE: deleting ligand molecule', molName coot.close_molecule(imol) self.select_cpd_cb.set_sensitive(False) @@ -1603,7 +1687,8 @@ def merge_ligand_into_protein(self, widget): def show_molprobity_to_do(self, widget): print self.panddaSerial - AdjPanddaSerial = (4 - len(str(self.Serial))) * '0' + str(int(self.panddaSerial) - 1) + AdjPanddaSerial = (4 - len(str(self.Serial))) * \ + '0' + str(int(self.panddaSerial) - 1) print os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), 'molprobity_coot.py') if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), diff --git a/lib/XChemDB.py b/lib/XChemDB.py index 43a0631c..f2926d27 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -1,583 +1,1005 @@ # last edited: 21/07/2017, 15:00 +import XChemLog import sqlite3 -import os,sys,glob +import os +import sys +import glob import csv from datetime import datetime import getpass sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') #from XChemUtils import parse -import XChemLog class data_source: - def __init__(self,data_source_file): + def __init__(self, data_source_file): - self.data_source_file=data_source_file + self.data_source_file = data_source_file # [column_name in DB, column_name shown in XCE, SQLite column type (Integer,Text,PKEY...)] - self.column_list=[ + self.column_list = [ # SQLite column name XCE column name SQLite type display in overview tab # from Lab36 - ['ID', 'ID', 'INTEGER PRIMARY KEY', 0], - ['LabVisit', 'LabVisit', 'TEXT', 1], - ['LibraryPlate', 'LibraryPlate', 'TEXT', 0], - ['SourceWell', 'SourceWell', 'TEXT', 0], - ['LibraryName', 'LibraryName', 'TEXT', 1], - ['CompoundSMILES', 'Smiles', 'TEXT', 1], - ['CompoundSMILESproduct', 'Smiles - Product', 'TEXT', 1], - ['CompoundCode', 'Compound ID', 'TEXT', 1], - ['CompoundStereo', 'Compound Stereo', 'TEXT', 1], - ['CompoundStereoSMILES', 'Stereo SMILES', 'TEXT', 1], - ['CompoundStereoCIFprogram', 'Stereo CIF program', 'TEXT', 1], - ['CompoundStereoCIFs', 'Compound Stereo IDs', 'TEXT', 1], - ['CompoundAutofitCC', 'autofit CC', 'TEXT', 1], - ['CompoundAutofitprogram', 'autofit program', 'TEXT', 1], - ['CrystalPlate', 'CrystalPlate', 'TEXT', 1], - ['CrystalWell', 'CrystalWell', 'TEXT', 1], - ['EchoX', 'EchoX', 'TEXT', 0], - ['EchoY', 'EchoY', 'TEXT', 0], - ['DropVolume', 'DropVolume', 'TEXT', 0], - ['ProteinName', 'ProteinName', 'TEXT', 1], - ['BatchNumber', 'BatchNumber', 'TEXT', 0], - ['CompoundStockConcentration', 'CompoundStockConcentration', 'TEXT', 0], - ['CompoundConcentration', 'CompoundConcentration', 'TEXT', 1], - ['SolventFraction', 'SolventFraction', 'TEXT', 1], - ['SoakTransferVol', 'SoakTransferVol', 'TEXT', 0], - ['SoakStatus', 'SoakStatus', 'TEXT', 0], - ['SoakTimestamp', 'SoakTimestamp', 'TEXT', 0], - ['CryoStockFraction', 'CryoStockFraction', 'TEXT', 0], - ['CryoFraction', 'CryoFraction', 'TEXT', 0], - ['CryoWell', 'CryoWell', 'TEXT', 0], - ['CryoTransferVolume', 'CryoTransferVolume', 'TEXT', 0], - ['CryoStatus', 'CryoStatus', 'TEXT', 0], - ['CryoTimestamp', 'CryoTimestamp', 'TEXT', 0], - ['SoakingTime', 'SoakingTime', 'TEXT', 1], - ['HarvestStatus', 'HarvestStatus', 'TEXT', 0], - ['CrystalName', 'Sample ID', 'TEXT', 0], - ['Puck', 'Puck', 'TEXT', 1], - ['PuckPosition', 'PuckPosition', 'TEXT', 1], - ['PinBarcode', 'SoakDB\nBarcode', 'TEXT', 1], - ['MountingResult', 'MountingResult', 'TEXT', 0], - ['MountingArrivalTime', 'MountingArrivalTime', 'TEXT', 0], - ['MountedTimestamp', 'MountedTimestamp', 'TEXT', 0], - ['MountingTime', 'MountingTime', 'TEXT', 0], - ['ispybStatus', 'ispybStatus', 'TEXT', 0], - ['DataCollectionVisit', 'Visit', 'TEXT', 1], + ['ID', 'ID', + 'INTEGER PRIMARY KEY', 0], + ['LabVisit', 'LabVisit', + 'TEXT', 1], + ['LibraryPlate', 'LibraryPlate', + 'TEXT', 0], + ['SourceWell', 'SourceWell', + 'TEXT', 0], + ['LibraryName', 'LibraryName', + 'TEXT', 1], + ['CompoundSMILES', 'Smiles', + 'TEXT', 1], + ['CompoundSMILESproduct', 'Smiles - Product', + 'TEXT', 1], + ['CompoundCode', 'Compound ID', + 'TEXT', 1], + ['CompoundStereo', 'Compound Stereo', + 'TEXT', 1], + ['CompoundStereoSMILES', 'Stereo SMILES', + 'TEXT', 1], + ['CompoundStereoCIFprogram', 'Stereo CIF program', + 'TEXT', 1], + ['CompoundStereoCIFs', 'Compound Stereo IDs', + 'TEXT', 1], + ['CompoundAutofitCC', 'autofit CC', + 'TEXT', 1], + ['CompoundAutofitprogram', 'autofit program', + 'TEXT', 1], + ['CrystalPlate', 'CrystalPlate', + 'TEXT', 1], + ['CrystalWell', 'CrystalWell', + 'TEXT', 1], + ['EchoX', 'EchoX', + 'TEXT', 0], + ['EchoY', 'EchoY', + 'TEXT', 0], + ['DropVolume', 'DropVolume', + 'TEXT', 0], + ['ProteinName', 'ProteinName', + 'TEXT', 1], + ['BatchNumber', 'BatchNumber', + 'TEXT', 0], + ['CompoundStockConcentration', 'CompoundStockConcentration', + 'TEXT', 0], + ['CompoundConcentration', 'CompoundConcentration', + 'TEXT', 1], + ['SolventFraction', 'SolventFraction', + 'TEXT', 1], + ['SoakTransferVol', 'SoakTransferVol', + 'TEXT', 0], + ['SoakStatus', 'SoakStatus', + 'TEXT', 0], + ['SoakTimestamp', 'SoakTimestamp', + 'TEXT', 0], + ['CryoStockFraction', 'CryoStockFraction', + 'TEXT', 0], + ['CryoFraction', 'CryoFraction', + 'TEXT', 0], + ['CryoWell', 'CryoWell', + 'TEXT', 0], + ['CryoTransferVolume', 'CryoTransferVolume', + 'TEXT', 0], + ['CryoStatus', 'CryoStatus', + 'TEXT', 0], + ['CryoTimestamp', 'CryoTimestamp', + 'TEXT', 0], + ['SoakingTime', 'SoakingTime', + 'TEXT', 1], + ['HarvestStatus', 'HarvestStatus', + 'TEXT', 0], + ['CrystalName', 'Sample ID', + 'TEXT', 0], + ['Puck', 'Puck', + 'TEXT', 1], + ['PuckPosition', 'PuckPosition', + 'TEXT', 1], + ['PinBarcode', 'SoakDB\nBarcode', + 'TEXT', 1], + ['MountingResult', 'MountingResult', + 'TEXT', 0], + ['MountingArrivalTime', 'MountingArrivalTime', + 'TEXT', 0], + ['MountedTimestamp', 'MountedTimestamp', + 'TEXT', 0], + ['MountingTime', 'MountingTime', + 'TEXT', 0], + ['ispybStatus', 'ispybStatus', + 'TEXT', 0], + ['DataCollectionVisit', 'Visit', + 'TEXT', 1], # from XChemExplorer - ['ProjectDirectory', 'ProjectDirectory', 'TEXT', 0], - - ['CrystalTag', 'Tag', 'TEXT', 0], - ['CrystalFormName', 'Crystal Form\nName', 'TEXT', 0], - ['CrystalFormSpaceGroup', 'Space\nGroup', 'TEXT', 0], - ['CrystalFormPointGroup', 'Point\nGroup', 'TEXT', 0], - ['CrystalFormA', 'a', 'TEXT', 0], - ['CrystalFormB', 'b', 'TEXT', 0], - ['CrystalFormC', 'c', 'TEXT', 0], - ['CrystalFormAlpha', 'alpha', 'TEXT', 0], - ['CrystalFormBeta', 'beta', 'TEXT', 0], - ['CrystalFormGamma', 'gamma', 'TEXT', 0], - ['CrystalFormVolume', 'Crystal Form\nVolume', 'TEXT', 0], - - ['DataCollectionBeamline', 'Beamline', 'TEXT', 0], - ['DataCollectionDate', 'Data Collection\nDate', 'TEXT', 1], - ['DataCollectionOutcome', 'DataCollection\nOutcome', 'TEXT', 1], - ['DataCollectionRun', 'Run', 'TEXT', 0], - ['DataCollectionSubdir', 'SubDir', 'TEXT', 0], - ['DataCollectionComment', 'DataCollection\nComment', 'TEXT', 0], - ['DataCollectionWavelength', 'Wavelength', 'TEXT', 0], - ['DataCollectionPinBarcode', 'GDA\nBarcode', 'TEXT', 1], + ['ProjectDirectory', 'ProjectDirectory', + 'TEXT', 0], + + ['CrystalTag', 'Tag', + 'TEXT', 0], + ['CrystalFormName', 'Crystal Form\nName', + 'TEXT', 0], + ['CrystalFormSpaceGroup', 'Space\nGroup', + 'TEXT', 0], + ['CrystalFormPointGroup', 'Point\nGroup', + 'TEXT', 0], + ['CrystalFormA', 'a', + 'TEXT', 0], + ['CrystalFormB', 'b', + 'TEXT', 0], + ['CrystalFormC', 'c', + 'TEXT', 0], + ['CrystalFormAlpha', 'alpha', + 'TEXT', 0], + ['CrystalFormBeta', 'beta', + 'TEXT', 0], + ['CrystalFormGamma', 'gamma', + 'TEXT', 0], + ['CrystalFormVolume', 'Crystal Form\nVolume', + 'TEXT', 0], + + ['DataCollectionBeamline', 'Beamline', + 'TEXT', 0], + ['DataCollectionDate', 'Data Collection\nDate', + 'TEXT', 1], + ['DataCollectionOutcome', 'DataCollection\nOutcome', + 'TEXT', 1], + ['DataCollectionRun', 'Run', + 'TEXT', 0], + ['DataCollectionSubdir', 'SubDir', + 'TEXT', 0], + ['DataCollectionComment', 'DataCollection\nComment', + 'TEXT', 0], + ['DataCollectionWavelength', 'Wavelength', + 'TEXT', 0], + ['DataCollectionPinBarcode', 'GDA\nBarcode', + 'TEXT', 1], ['DataCollectionCrystalImage1', 'img1', 'TEXT', 1], ['DataCollectionCrystalImage2', 'img2', 'TEXT', 1], ['DataCollectionCrystalImage3', 'img3', 'TEXT', 1], ['DataCollectionCrystalImage4', 'img4', 'TEXT', 1], - ['DataProcessingPathToImageFiles', 'Path to diffraction\nimage files', 'TEXT', 1], - ['DataProcessingProgram', 'Program', 'TEXT', 1], - ['DataProcessingSpaceGroup', 'DataProcessing\nSpaceGroup', 'TEXT', 1], - ['DataProcessingUnitCell', 'DataProcessing\nUnitCell', 'TEXT', 0], - ['DataProcessingAutoAssigned', 'auto-assigned', 'TEXT', 0], - - ['DataProcessingA', 'DataProcessing\nA', 'TEXT', 0], - ['DataProcessingB', 'DataProcessing\nB', 'TEXT', 0], - ['DataProcessingC', 'DataProcessing\nC', 'TEXT', 0], - ['DataProcessingAlpha', 'DataProcessing\nAlpha', 'TEXT', 0], - ['DataProcessingBeta', 'DataProcessing\nBeta', 'TEXT', 0], - ['DataProcessingGamma', 'DataProcessing\nGamma', 'TEXT', 0], - - # True or False depending on whether user changed automatic selection -# ['DataProcessingUserSelected', 'DataProcessingUserSelected', 'TEXT', 0], - - ['DataProcessingResolutionOverall', 'Resolution\nOverall', 'TEXT', 0], - ['DataProcessingResolutionLow', 'Resolution\nLow', 'TEXT', 0], - ['DataProcessingResolutionLowInnerShell', 'Resolution\nLow (Inner Shell)', 'TEXT', 0], - ['DataProcessingResolutionHigh', 'Resolution\nHigh', 'TEXT', 1], - ['DataProcessingResolutionHigh15sigma', 'Resolution\n[Mn = 1.5]', 'TEXT', 1], - ['DataProcessingResolutionHigh20sigma', 'Resolution\n[Mn = 2.0]', 'TEXT', 1], - ['DataProcessingResolutionHighOuterShell', 'Resolution\nHigh (Outer Shell)', 'TEXT', 0], - ['DataProcessingRmergeOverall', 'Rmerge\nOverall', 'TEXT', 1], - ['DataProcessingRmergeLow', 'Rmerge\nLow', 'TEXT', 1], - ['DataProcessingRmergeHigh', 'Rmerge\nHigh', 'TEXT', 1], - ['DataProcessingIsigOverall', 'Mn\nOverall', 'TEXT', 1], - ['DataProcessingIsigLow', 'Mn\nLow', 'TEXT', 1], - ['DataProcessingIsigHigh', 'Mn\nHigh', 'TEXT', 1], - ['DataProcessingCompletenessOverall', 'Completeness\nOverall', 'TEXT', 1], - ['DataProcessingCompletenessLow', 'Completeness\nLow', 'TEXT', 1], - ['DataProcessingCompletenessHigh', 'Completeness\nHigh', 'TEXT', 1], - ['DataProcessingMultiplicityOverall', 'Multiplicity\nOverall', 'TEXT', 1], - ['DataProcessingMultiplicityLow', 'Multiplicity\nLow', 'TEXT', 1], - ['DataProcessingMultiplicityHigh', 'Multiplicity\nHigh', 'TEXT', 1], - ['DataProcessingCChalfOverall', 'CC(1/2)\nOverall', 'TEXT', 1], - ['DataProcessingCChalfLow', 'CC(1/2)\nLow', 'TEXT', 1], - ['DataProcessingCChalfHigh', 'CC(1/2)\nHigh', 'TEXT', 1], + ['DataProcessingPathToImageFiles', + 'Path to diffraction\nimage files', 'TEXT', 1], + ['DataProcessingProgram', 'Program', + 'TEXT', 1], + ['DataProcessingSpaceGroup', 'DataProcessing\nSpaceGroup', + 'TEXT', 1], + ['DataProcessingUnitCell', 'DataProcessing\nUnitCell', + 'TEXT', 0], + ['DataProcessingAutoAssigned', 'auto-assigned', + 'TEXT', 0], + + ['DataProcessingA', 'DataProcessing\nA', + 'TEXT', 0], + ['DataProcessingB', 'DataProcessing\nB', + 'TEXT', 0], + ['DataProcessingC', 'DataProcessing\nC', + 'TEXT', 0], + ['DataProcessingAlpha', 'DataProcessing\nAlpha', + 'TEXT', 0], + ['DataProcessingBeta', 'DataProcessing\nBeta', + 'TEXT', 0], + ['DataProcessingGamma', 'DataProcessing\nGamma', + 'TEXT', 0], + + # True or False depending on whether user changed automatic selection + # ['DataProcessingUserSelected', 'DataProcessingUserSelected', 'TEXT', 0], + + ['DataProcessingResolutionOverall', 'Resolution\nOverall', + 'TEXT', 0], + ['DataProcessingResolutionLow', 'Resolution\nLow', + 'TEXT', 0], + ['DataProcessingResolutionLowInnerShell', + 'Resolution\nLow (Inner Shell)', 'TEXT', 0], + ['DataProcessingResolutionHigh', 'Resolution\nHigh', + 'TEXT', 1], + ['DataProcessingResolutionHigh15sigma', + 'Resolution\n[Mn = 1.5]', 'TEXT', 1], + ['DataProcessingResolutionHigh20sigma', + 'Resolution\n[Mn = 2.0]', 'TEXT', 1], + ['DataProcessingResolutionHighOuterShell', + 'Resolution\nHigh (Outer Shell)', 'TEXT', 0], + ['DataProcessingRmergeOverall', 'Rmerge\nOverall', + 'TEXT', 1], + ['DataProcessingRmergeLow', 'Rmerge\nLow', + 'TEXT', 1], + ['DataProcessingRmergeHigh', 'Rmerge\nHigh', + 'TEXT', 1], + ['DataProcessingIsigOverall', + 'Mn\nOverall', 'TEXT', 1], + ['DataProcessingIsigLow', + 'Mn\nLow', 'TEXT', 1], + ['DataProcessingIsigHigh', + 'Mn\nHigh', 'TEXT', 1], + ['DataProcessingCompletenessOverall', 'Completeness\nOverall', + 'TEXT', 1], + ['DataProcessingCompletenessLow', 'Completeness\nLow', + 'TEXT', 1], + ['DataProcessingCompletenessHigh', 'Completeness\nHigh', + 'TEXT', 1], + ['DataProcessingMultiplicityOverall', 'Multiplicity\nOverall', + 'TEXT', 1], + ['DataProcessingMultiplicityLow', 'Multiplicity\nLow', + 'TEXT', 1], + ['DataProcessingMultiplicityHigh', 'Multiplicity\nHigh', + 'TEXT', 1], + ['DataProcessingCChalfOverall', + 'CC(1/2)\nOverall', 'TEXT', 1], + ['DataProcessingCChalfLow', + 'CC(1/2)\nLow', 'TEXT', 1], + ['DataProcessingCChalfHigh', + 'CC(1/2)\nHigh', 'TEXT', 1], # the data source is a bit exploding with entries like the ones below, # but the many different filenames and folder structures of Diamond autoprocessing makes it necessary - ['DataProcessingPathToLogfile', 'DataProcessingPathToLogfile', 'TEXT', 1], - ['DataProcessingPathToMTZfile', 'DataProcessingPathToMTZfile', 'TEXT', 1], - ['DataProcessingLOGfileName', 'DataProcessingLOGfileName', 'TEXT', 0], - ['DataProcessingMTZfileName', 'DataProcessingMTZfileName', 'TEXT', 0], - ['DataProcessingDirectoryOriginal', 'DataProcessingDirectoryOriginal', 'TEXT', 0], - ['DataProcessingUniqueReflectionsOverall', 'Unique Reflections\nOverall', 'TEXT', 1], - ['DataProcessingUniqueReflectionsLow', 'Unique Reflections\nlow', 'TEXT', 1], - ['DataProcessingUniqueReflectionsHigh', 'Unique Reflections\nhigh', 'TEXT', 1], - ['DataProcessingLattice', 'DataProcessing\nLattice', 'TEXT', 0], - ['DataProcessingPointGroup', 'DataProcessing\nPointGroup', 'TEXT', 0], - ['DataProcessingUnitCellVolume', 'DataProcessing\nUnit Cell Volume', 'TEXT', 0], - ['DataProcessingAlert', 'DataProcessing\nAlert', 'TEXT', 0], - ['DataProcessingScore', 'DataProcessing\nScore', 'TEXT', 1], - - - ['DataProcessingStatus', 'DataProcessing\nStatus', 'TEXT', 1], - - ['DataProcessingRcryst', 'DataProcessing\nRcryst', 'TEXT', 0], - ['DataProcessingRfree', 'DataProcessing\nRfree', 'TEXT', 0], - ['DataProcessingPathToDimplePDBfile', 'DataProcessingPathToDimplePDBfile', 'TEXT', 0], - ['DataProcessingPathToDimpleMTZfile', 'DataProcessingPathToDimpleMTZfile', 'TEXT', 0], - ['DataProcessingDimpleSuccessful', 'DataProcessingDimpleSuccessful', 'TEXT', 0], - - ['DimpleResolutionHigh', 'Dimple\nResolution High', 'TEXT', 1], - ['DimpleRcryst', 'Dimple\nRcryst', 'TEXT', 1], - ['DimpleRfree', 'Dimple\nRfree', 'TEXT', 1], - ['DimplePathToPDB', 'Dimple\nPath to PDB file', 'TEXT', 1], - ['DimplePathToMTZ', 'Dimple\nPath to MTZ file', 'TEXT', 1], - ['DimpleReferencePDB', 'Dimple\nReference PDB', 'TEXT', 1], - ['DimpleStatus', 'Dimple\nStatus', 'TEXT', 1], - - ['DimpleTwinResolutionHigh', 'Dimple - twin\nResolution High', 'TEXT', 1], - ['DimpleTwinRcryst', 'Dimple - twin\nRcryst', 'TEXT', 1], - ['DimpleTwinRfree', 'Dimple - twin\nRfree', 'TEXT', 1], - ['DimpleTwinPathToPDB', 'Dimple - twin\nPath to PDB file', 'TEXT', 1], - ['DimpleTwinPathToMTZ', 'Dimple - twin\nPath to MTZ file', 'TEXT', 1], - ['DimpleTwinReferencePDB', 'Dimple - twin\nReference PDB', 'TEXT', 1], - ['DimpleTwinStatus', 'Dimple - twin\nStatus', 'TEXT', 1], - ['DimpleTwinFraction', 'Dimple - twin\nFraction', 'TEXT', 1], - ['DataProcessingDimpleTwinSuccessful', 'DataProcessingDimpleTwinSuccessful', 'TEXT', 0], - - - ['DimplePANDDAwasRun', 'PanDDA\nlaunched?', 'TEXT', 1], - ['DimplePANDDAhit', 'PanDDA\nhit?', 'TEXT', 1], - ['DimplePANDDAreject', 'PanDDA\nreject?', 'TEXT', 1], - ['DimplePANDDApath', 'PanDDA\npath?', 'TEXT', 1], - ['PANDDAStatus', 'PanDDA\nStatus', 'TEXT', 1], - - ['DatePanDDAModelCreated', 'DatePanDDAModelCreated', 'TEXT', 0], - - ['RefinementResolution', 'Refinement\nResolution', 'TEXT', 1], - ['RefinementResolutionTL', 'RefinementResolutionTL', 'TEXT', 0], - ['RefinementRcryst', 'Refinement\nRcryst', 'TEXT', 1], - ['RefinementRcrystTraficLight', 'RefinementRcrystTraficLight', 'TEXT', 0], - ['RefinementRfree', 'Refinement\nRfree', 'TEXT', 1], - ['RefinementRfreeTraficLight', 'RefinementRfreeTraficLight', 'TEXT', 0], - ['RefinementSpaceGroup', 'Refinement\nSpace Group', 'TEXT', 1], - ['RefinementLigandCC', 'Ligand CC', 'TEXT', 0], - ['RefinementRmsdBonds', 'RefinementRmsdBonds', 'TEXT', 1], - ['RefinementRmsdBondsTL', 'RefinementRmsdBondsTL', 'TEXT', 0], - ['RefinementRmsdAngles', 'RefinementRmsdAngles', 'TEXT', 1], - ['RefinementRmsdAnglesTL', 'RefinementRmsdAnglesTL', 'TEXT', 0], - ['RefinementOutcome', 'Refinement\nOutcome', 'TEXT', 1], - ['RefinementOutcomePerson', 'RefinementOutcomePerson', 'TEXT', 1], - ['RefinementOutcomeDate', 'RefinementOutcomeDate', 'TEXT', 1], - - ['RefinementMTZfree', 'RefinementMTZfree', 'TEXT', 1], - ['RefinementTwinMTZfree', 'RefinementTwinMTZfree', 'TEXT', 1], - - ['RefinementCIF', 'RefinementCIF', 'TEXT', 1], - ['RefinementCIFStatus', 'Compound\nStatus', 'TEXT', 1], - ['RefinementCIFprogram', 'RefinementCIFprogram', 'TEXT', 1], - ['RefinementPDB_latest', 'RefinementPDB_latest', 'TEXT', 1], - ['RefinementMTZ_latest', 'RefinementMTZ_latest', 'TEXT', 1], - ['RefinementMMCIFmodel_latest', 'RefinementMMCIFmodel_latest', 'TEXT', 1], - ['RefinementMMCIFreflections_latest', 'RefinementMMCIFreflections_latest', 'TEXT', 1], - - ['RefinementMatrixWeight', 'RefinementMatrixWeight', 'TEXT', 0], - ['RefinementComment', 'RefinementComment', 'TEXT', 0], - ['RefinementPathToRefinementFolder', 'RefinementPathToRefinementFolder', 'TEXT', 0], - ['RefinementLigandConfidence', 'Ligand\nConfidence', 'TEXT', 0], - ['RefinementLigandBoundConformation', 'RefinementLigandBoundConformation', 'TEXT', 0], - ['RefinementBoundConformation', 'RefinementBoundConformation', 'TEXT', 0], - ['RefinementMolProbityScore', 'MolProbity Score', 'TEXT', 1], - ['RefinementMolProbityScoreTL', 'RefinementMolProbityScoreTL', 'TEXT', 0], - ['RefinementRamachandranOutliers', 'Ramachandran\nOutliers', 'TEXT', 1], - ['RefinementRamachandranOutliersTL', 'RefinementRamachandranOutliersTL', 'TEXT', 0], - ['RefinementRamachandranFavored', 'Ramachandran\nFavored', 'TEXT', 1], - ['RefinementRamachandranFavoredTL', 'RefinementRamachandranFavoredTL', 'TEXT', 0], - ['RefinementProgram', 'RefinementProgram', 'TEXT', 1], - ['RefinementStatus', 'Refinement\nStatus', 'TEXT', 1], - ['RefinementBusterReportHTML', 'buster-reports', 'TEXT', 1], - ['RefinementRefiner', 'RefinementRefiner', 'TEXT', 1], - ['RefinementDate', 'RefinementDate', 'TEXT', 1], - - - ['Deposition_PDB_ID', 'Deposition_PDB_ID', 'TEXT', 1], - ['Deposition_PDB_file', 'Deposition_PDB_file', 'TEXT', 0], - ['Deposition_Date', 'Deposition_Date', 'TEXT', 1], - ['Deposition_mmCIF_model_file', 'Deposition_mmCIF_model_file', 'TEXT', 0], - ['Deposition_mmCIF_SF_file', 'Deposition_mmCIF_SF_file', 'TEXT', 0], - - ['Label', 'Label', 'TEXT', 0], - ['table_one', 'table_one', 'TEXT', 0], - - ['AssayIC50', 'AssayIC50', 'TEXT', 0], - ['LastUpdated', 'LastUpdated', 'TEXT', 0], - ['LastUpdated_by', 'LastUpdated_by', 'TEXT', 0] + ['DataProcessingPathToLogfile', + 'DataProcessingPathToLogfile', 'TEXT', 1], + ['DataProcessingPathToMTZfile', + 'DataProcessingPathToMTZfile', 'TEXT', 1], + ['DataProcessingLOGfileName', 'DataProcessingLOGfileName', + 'TEXT', 0], + ['DataProcessingMTZfileName', 'DataProcessingMTZfileName', + 'TEXT', 0], + ['DataProcessingDirectoryOriginal', + 'DataProcessingDirectoryOriginal', 'TEXT', 0], + ['DataProcessingUniqueReflectionsOverall', + 'Unique Reflections\nOverall', 'TEXT', 1], + ['DataProcessingUniqueReflectionsLow', 'Unique Reflections\nlow', + 'TEXT', 1], + ['DataProcessingUniqueReflectionsHigh', + 'Unique Reflections\nhigh', 'TEXT', 1], + ['DataProcessingLattice', 'DataProcessing\nLattice', + 'TEXT', 0], + ['DataProcessingPointGroup', + 'DataProcessing\nPointGroup', 'TEXT', 0], + ['DataProcessingUnitCellVolume', + 'DataProcessing\nUnit Cell Volume', 'TEXT', 0], + ['DataProcessingAlert', 'DataProcessing\nAlert', + 'TEXT', 0], + ['DataProcessingScore', 'DataProcessing\nScore', + 'TEXT', 1], + + + ['DataProcessingStatus', 'DataProcessing\nStatus', + 'TEXT', 1], + + ['DataProcessingRcryst', 'DataProcessing\nRcryst', + 'TEXT', 0], + ['DataProcessingRfree', 'DataProcessing\nRfree', + 'TEXT', 0], + ['DataProcessingPathToDimplePDBfile', + 'DataProcessingPathToDimplePDBfile', 'TEXT', 0], + ['DataProcessingPathToDimpleMTZfile', + 'DataProcessingPathToDimpleMTZfile', 'TEXT', 0], + ['DataProcessingDimpleSuccessful', + 'DataProcessingDimpleSuccessful', 'TEXT', 0], + + ['DimpleResolutionHigh', 'Dimple\nResolution High', + 'TEXT', 1], + ['DimpleRcryst', 'Dimple\nRcryst', + 'TEXT', 1], + ['DimpleRfree', 'Dimple\nRfree', + 'TEXT', 1], + ['DimplePathToPDB', 'Dimple\nPath to PDB file', + 'TEXT', 1], + ['DimplePathToMTZ', 'Dimple\nPath to MTZ file', + 'TEXT', 1], + ['DimpleReferencePDB', 'Dimple\nReference PDB', + 'TEXT', 1], + ['DimpleStatus', 'Dimple\nStatus', + 'TEXT', 1], + + ['DimpleTwinResolutionHigh', + 'Dimple - twin\nResolution High', 'TEXT', 1], + ['DimpleTwinRcryst', 'Dimple - twin\nRcryst', + 'TEXT', 1], + ['DimpleTwinRfree', 'Dimple - twin\nRfree', + 'TEXT', 1], + ['DimpleTwinPathToPDB', + 'Dimple - twin\nPath to PDB file', 'TEXT', 1], + ['DimpleTwinPathToMTZ', + 'Dimple - twin\nPath to MTZ file', 'TEXT', 1], + ['DimpleTwinReferencePDB', + 'Dimple - twin\nReference PDB', 'TEXT', 1], + ['DimpleTwinStatus', 'Dimple - twin\nStatus', + 'TEXT', 1], + ['DimpleTwinFraction', 'Dimple - twin\nFraction', + 'TEXT', 1], + ['DataProcessingDimpleTwinSuccessful', + 'DataProcessingDimpleTwinSuccessful', 'TEXT', 0], + + + ['DimplePANDDAwasRun', 'PanDDA\nlaunched?', + 'TEXT', 1], + ['DimplePANDDAhit', 'PanDDA\nhit?', + 'TEXT', 1], + ['DimplePANDDAreject', 'PanDDA\nreject?', + 'TEXT', 1], + ['DimplePANDDApath', 'PanDDA\npath?', + 'TEXT', 1], + ['PANDDAStatus', 'PanDDA\nStatus', + 'TEXT', 1], + + ['DatePanDDAModelCreated', 'DatePanDDAModelCreated', + 'TEXT', 0], + + ['RefinementResolution', 'Refinement\nResolution', + 'TEXT', 1], + ['RefinementResolutionTL', 'RefinementResolutionTL', + 'TEXT', 0], + ['RefinementRcryst', 'Refinement\nRcryst', + 'TEXT', 1], + ['RefinementRcrystTraficLight', + 'RefinementRcrystTraficLight', 'TEXT', 0], + ['RefinementRfree', 'Refinement\nRfree', + 'TEXT', 1], + ['RefinementRfreeTraficLight', + 'RefinementRfreeTraficLight', 'TEXT', 0], + ['RefinementSpaceGroup', 'Refinement\nSpace Group', + 'TEXT', 1], + ['RefinementLigandCC', 'Ligand CC', + 'TEXT', 0], + ['RefinementRmsdBonds', 'RefinementRmsdBonds', + 'TEXT', 1], + ['RefinementRmsdBondsTL', 'RefinementRmsdBondsTL', + 'TEXT', 0], + ['RefinementRmsdAngles', 'RefinementRmsdAngles', + 'TEXT', 1], + ['RefinementRmsdAnglesTL', 'RefinementRmsdAnglesTL', + 'TEXT', 0], + ['RefinementOutcome', 'Refinement\nOutcome', + 'TEXT', 1], + ['RefinementOutcomePerson', 'RefinementOutcomePerson', + 'TEXT', 1], + ['RefinementOutcomeDate', 'RefinementOutcomeDate', + 'TEXT', 1], + + ['RefinementMTZfree', 'RefinementMTZfree', + 'TEXT', 1], + ['RefinementTwinMTZfree', 'RefinementTwinMTZfree', + 'TEXT', 1], + + ['RefinementCIF', 'RefinementCIF', + 'TEXT', 1], + ['RefinementCIFStatus', 'Compound\nStatus', + 'TEXT', 1], + ['RefinementCIFprogram', 'RefinementCIFprogram', + 'TEXT', 1], + ['RefinementPDB_latest', 'RefinementPDB_latest', + 'TEXT', 1], + ['RefinementMTZ_latest', 'RefinementMTZ_latest', + 'TEXT', 1], + ['RefinementMMCIFmodel_latest', + 'RefinementMMCIFmodel_latest', 'TEXT', 1], + ['RefinementMMCIFreflections_latest', + 'RefinementMMCIFreflections_latest', 'TEXT', 1], + + ['RefinementMatrixWeight', 'RefinementMatrixWeight', + 'TEXT', 0], + ['RefinementComment', 'RefinementComment', + 'TEXT', 0], + ['RefinementPathToRefinementFolder', + 'RefinementPathToRefinementFolder', 'TEXT', 0], + ['RefinementLigandConfidence', 'Ligand\nConfidence', + 'TEXT', 0], + ['RefinementLigandBoundConformation', + 'RefinementLigandBoundConformation', 'TEXT', 0], + ['RefinementBoundConformation', + 'RefinementBoundConformation', 'TEXT', 0], + ['RefinementMolProbityScore', 'MolProbity Score', + 'TEXT', 1], + ['RefinementMolProbityScoreTL', + 'RefinementMolProbityScoreTL', 'TEXT', 0], + ['RefinementRamachandranOutliers', 'Ramachandran\nOutliers', + 'TEXT', 1], + ['RefinementRamachandranOutliersTL', + 'RefinementRamachandranOutliersTL', 'TEXT', 0], + ['RefinementRamachandranFavored', 'Ramachandran\nFavored', + 'TEXT', 1], + ['RefinementRamachandranFavoredTL', + 'RefinementRamachandranFavoredTL', 'TEXT', 0], + ['RefinementProgram', 'RefinementProgram', + 'TEXT', 1], + ['RefinementStatus', 'Refinement\nStatus', + 'TEXT', 1], + ['RefinementBusterReportHTML', 'buster-reports', + 'TEXT', 1], + ['RefinementRefiner', 'RefinementRefiner', + 'TEXT', 1], + ['RefinementDate', 'RefinementDate', + 'TEXT', 1], + + + ['Deposition_PDB_ID', 'Deposition_PDB_ID', + 'TEXT', 1], + ['Deposition_PDB_file', 'Deposition_PDB_file', + 'TEXT', 0], + ['Deposition_Date', 'Deposition_Date', + 'TEXT', 1], + ['Deposition_mmCIF_model_file', + 'Deposition_mmCIF_model_file', 'TEXT', 0], + ['Deposition_mmCIF_SF_file', 'Deposition_mmCIF_SF_file', + 'TEXT', 0], + + ['Label', 'Label', + 'TEXT', 0], + ['table_one', 'table_one', + 'TEXT', 0], + + ['AssayIC50', 'AssayIC50', + 'TEXT', 0], + ['LastUpdated', 'LastUpdated', + 'TEXT', 0], + ['LastUpdated_by', 'LastUpdated_by', + 'TEXT', 0] ] self.pandda_table_columns = [ - ['ID', 'ID', 'INTEGER PRIMARY KEY'], - ['CrystalName', 'Sample ID', 'TEXT'], - ['PANDDApath', 'PANDDApath', 'TEXT'], - ['PANDDA_site_index', 'PANDDA_site_index', 'TEXT'], - ['PANDDA_site_name', 'PANDDA_site_name', 'TEXT'], - ['PANDDA_site_comment', 'PANDDA_site_comment', 'TEXT'], - ['PANDDA_site_event_index', 'PANDDA_site_event_index', 'TEXT'], - ['PANDDA_site_event_comment', 'PANDDA_site_event_comment', 'TEXT'], - ['PANDDA_site_confidence', 'PANDDA_site_confidence', 'TEXT'], - ['PANDDA_site_InspectConfidence', 'PANDDA_site_InspectConfidence', 'TEXT'], - ['PANDDA_site_ligand_placed', 'PANDDA_site_ligand_placed', 'TEXT'], - ['PANDDA_site_viewed', 'PANDDA_site_viewed', 'TEXT'], - ['PANDDA_site_interesting', 'PANDDA_site_interesting', 'TEXT'], - ['PANDDA_site_z_peak', 'PANDDA_site_z_peak', 'TEXT'], - ['PANDDA_site_x', 'PANDDA_site_x', 'TEXT'], - ['PANDDA_site_y', 'PANDDA_site_y', 'TEXT'], - ['PANDDA_site_z', 'PANDDA_site_z', 'TEXT'], - ['PANDDA_site_ligand_id', 'PANDDA_site_ligand_id', 'TEXT'], - - ['PANDDA_site_ligand_resname', 'PANDDA_site_ligand_resname', 'TEXT'], - ['PANDDA_site_ligand_chain', 'PANDDA_site_ligand_chain', 'TEXT'], - ['PANDDA_site_ligand_sequence_number', 'PANDDA_site_ligand_sequence_number', 'TEXT'], - ['PANDDA_site_ligand_altLoc', 'PANDDA_site_ligand_altLoc', 'TEXT'], - - ['PANDDA_site_event_map', 'PANDDA_site_event_map', 'TEXT'], - ['PANDDA_site_event_map_mtz', 'PANDDA_site_event_map_mtz', 'TEXT'], - ['PANDDA_site_initial_model', 'PANDDA_site_initial_model', 'TEXT'], - ['PANDDA_site_initial_mtz', 'PANDDA_site_initial_mtz', 'TEXT'], - ['PANDDA_site_spider_plot', 'PANDDA_site_spider_plot', 'TEXT'], - ['PANDDA_site_occupancy', 'PANDDA_site_occupancy', 'TEXT'], - ['PANDDA_site_B_average', 'PANDDA_site_B_average', 'TEXT'], - ['PANDDA_site_B_ratio_residue_surroundings', 'PANDDA_site_B_ratio_residue_surroundings', 'TEXT'], - ['PANDDA_site_RSCC', 'PANDDA_site_RSCC', 'TEXT'], - ['PANDDA_site_RSR', 'PANDDA_site_RSR', 'TEXT'], - ['PANDDA_site_RSZD', 'PANDDA_site_RSZD', 'TEXT'], - ['PANDDA_site_rmsd', 'PANDDA_site_rmsd', 'TEXT'], - ['RefinementOutcome', 'RefinementOutcome', 'TEXT'], - ['ApoStructures', 'ApoStructures', 'TEXT'], - ['LastUpdated', 'LastUpdated', 'TEXT'], - ['LastUpdated_by', 'LastUpdated_by', 'TEXT'] - ] + ['ID', 'ID', + 'INTEGER PRIMARY KEY'], + ['CrystalName', + 'Sample ID', 'TEXT'], + ['PANDDApath', + 'PANDDApath', 'TEXT'], + ['PANDDA_site_index', + 'PANDDA_site_index', 'TEXT'], + ['PANDDA_site_name', + 'PANDDA_site_name', 'TEXT'], + ['PANDDA_site_comment', + 'PANDDA_site_comment', 'TEXT'], + ['PANDDA_site_event_index', + 'PANDDA_site_event_index', 'TEXT'], + ['PANDDA_site_event_comment', + 'PANDDA_site_event_comment', 'TEXT'], + ['PANDDA_site_confidence', + 'PANDDA_site_confidence', 'TEXT'], + ['PANDDA_site_InspectConfidence', + 'PANDDA_site_InspectConfidence', 'TEXT'], + ['PANDDA_site_ligand_placed', + 'PANDDA_site_ligand_placed', 'TEXT'], + ['PANDDA_site_viewed', + 'PANDDA_site_viewed', 'TEXT'], + ['PANDDA_site_interesting', + 'PANDDA_site_interesting', 'TEXT'], + ['PANDDA_site_z_peak', + 'PANDDA_site_z_peak', 'TEXT'], + ['PANDDA_site_x', + 'PANDDA_site_x', 'TEXT'], + ['PANDDA_site_y', + 'PANDDA_site_y', 'TEXT'], + ['PANDDA_site_z', + 'PANDDA_site_z', 'TEXT'], + ['PANDDA_site_ligand_id', + 'PANDDA_site_ligand_id', 'TEXT'], + + ['PANDDA_site_ligand_resname', + 'PANDDA_site_ligand_resname', 'TEXT'], + ['PANDDA_site_ligand_chain', + 'PANDDA_site_ligand_chain', 'TEXT'], + ['PANDDA_site_ligand_sequence_number', + 'PANDDA_site_ligand_sequence_number', 'TEXT'], + ['PANDDA_site_ligand_altLoc', + 'PANDDA_site_ligand_altLoc', 'TEXT'], + + ['PANDDA_site_event_map', + 'PANDDA_site_event_map', 'TEXT'], + ['PANDDA_site_event_map_mtz', + 'PANDDA_site_event_map_mtz', 'TEXT'], + ['PANDDA_site_initial_model', + 'PANDDA_site_initial_model', 'TEXT'], + ['PANDDA_site_initial_mtz', + 'PANDDA_site_initial_mtz', 'TEXT'], + ['PANDDA_site_spider_plot', + 'PANDDA_site_spider_plot', 'TEXT'], + ['PANDDA_site_occupancy', + 'PANDDA_site_occupancy', 'TEXT'], + ['PANDDA_site_B_average', + 'PANDDA_site_B_average', 'TEXT'], + ['PANDDA_site_B_ratio_residue_surroundings', + 'PANDDA_site_B_ratio_residue_surroundings', 'TEXT'], + ['PANDDA_site_RSCC', + 'PANDDA_site_RSCC', 'TEXT'], + ['PANDDA_site_RSR', + 'PANDDA_site_RSR', 'TEXT'], + ['PANDDA_site_RSZD', + 'PANDDA_site_RSZD', 'TEXT'], + ['PANDDA_site_rmsd', + 'PANDDA_site_rmsd', 'TEXT'], + ['RefinementOutcome', + 'RefinementOutcome', 'TEXT'], + ['ApoStructures', + 'ApoStructures', 'TEXT'], + ['LastUpdated', + 'LastUpdated', 'TEXT'], + ['LastUpdated_by', + 'LastUpdated_by', 'TEXT'] + ] self.deposition_table_columns = [ - ['ID', 'ID', 'INTEGER PRIMARY KEY'], - - ['CrystalName', 'Sample ID', 'TEXT'], - ['StructureType', 'StructureType', 'TEXT'], # apo/model - - ['PDB_file', 'PDB_file', 'TEXT'], - ['MTZ_file', 'MTZ_file', 'TEXT'], - - ['mmCIF_model_file', 'mmCIF_model_file', 'TEXT'], - ['mmCIF_SF_file', 'mmCIF_SF_file', 'TEXT'], - ['label', 'label', 'TEXT'], # for index.txt - ['description', 'description', 'TEXT'], # for index.txt - - ['DimplePANDDApath', 'DimplePANDDApath', 'TEXT'], - - ['contact_author_PI_salutation', 'contact_author_PI_salutation', 'TEXT'], - ['contact_author_PI_first_name', 'contact_author_PI_first_name', 'TEXT'], - ['contact_author_PI_last_name', 'contact_author_PI_last_name', 'TEXT'], - ['contact_author_PI_middle_name', 'contact_author_PI_middle_name', 'TEXT'], - ['contact_author_PI_role', 'contact_author_PI_role', 'TEXT'], - ['contact_author_PI_organization_type', 'contact_author_PI_organization_type', 'TEXT'], - ['contact_author_PI_organization_name', 'contact_author_PI_organization_name', 'TEXT'], - ['contact_author_PI_email', 'contact_author_PI_email', 'TEXT'], - ['contact_author_PI_address', 'contact_author_PI_address', 'TEXT'], - ['contact_author_PI_city', 'contact_author_PI_city', 'TEXT'], - ['contact_author_PI_State_or_Province', 'contact_author_PI_State_or_Province', 'TEXT'], - ['contact_author_PI_Zip_Code', 'contact_author_PI_Zip_Code', 'TEXT'], - ['contact_author_PI_Country', 'contact_author_PI_Country', 'TEXT'], - ['contact_author_PI_fax_number', 'contact_author_PI_fax_number', 'TEXT'], - ['contact_author_PI_phone_number', 'contact_author_PI_phone_number', 'TEXT'], - ['contact_author_PI_ORCID', 'contact_author_PI_ORCID', 'TEXT'], - - ['contact_author_salutation', 'contact_author_salutation', 'TEXT'], - ['contact_author_first_name', 'contact_author_first_name', 'TEXT'], - ['contact_author_last_name', 'contact_author_last_name', 'TEXT'], - ['contact_author_middle_name', 'contact_author_middle_name', 'TEXT'], - ['contact_author_role', 'contact_author_role', 'TEXT'], - ['contact_author_organization_type', 'contact_author_organization_type', 'TEXT'], - ['contact_author_organization_name', 'contact_author_organization_name', 'TEXT'], - ['contact_author_email', 'contact_author_email', 'TEXT'], - ['contact_author_address', 'contact_author_address', 'TEXT'], - ['contact_author_city', 'contact_author_city', 'TEXT'], - ['contact_author_State_or_Province', 'contact_author_State_or_Province', 'TEXT'], - ['contact_author_Zip_Code', 'contact_author_Zip_Code', 'TEXT'], - ['contact_author_Country', 'contact_author_Country', 'TEXT'], - ['contact_author_fax_number', 'contact_author_fax_number', 'TEXT'], - ['contact_author_phone_number', 'contact_author_phone_number', 'TEXT'], - ['contact_author_ORCID', 'contact_author_ORCID', 'TEXT'], - - ['Release_status_for_coordinates', 'Release_status_for_coordinates', 'TEXT'], - ['Release_status_for_structure_factor', 'Release_status_for_structure_factor', 'TEXT'], - ['Release_status_for_sequence', 'Release_status_for_sequence', 'TEXT'], - - ['group_deposition_title', 'group_deposition_title', 'TEXT'], - ['group_description', 'group_description', 'TEXT'], - ['structure_title', 'structure_title', 'TEXT'], - ['structure_details', 'structure_details', 'TEXT'], - ['group_deposition_title_apo', 'group_deposition_title_apo', 'TEXT'], - ['structure_title_apo', 'structure_title_apo', 'TEXT'], - - ['structure_author_name', 'structure_author_name', 'TEXT'], - ['primary_citation_author_name', 'primary_citation_author_name', 'TEXT'], - - ['primary_citation_id', 'primary_citation_id', 'TEXT'], - ['primary_citation_journal_abbrev', 'primary_citation_journal_abbrev', 'TEXT'], - ['primary_citation_title', 'primary_citation_title', 'TEXT'], - ['primary_citation_year', 'primary_citation_year', 'TEXT'], - ['primary_citation_journal_volume', 'primary_citation_journal_volume', 'TEXT'], - ['primary_citation_page_first', 'primary_citation_page_first', 'TEXT'], - ['primary_citation_page_last', 'primary_citation_page_last', 'TEXT'], - - ['molecule_name', 'molecule_name', 'TEXT'], - ['Fragment_name', 'Fragment_name', 'TEXT'], - ['Specific_mutation', 'Specific_mutation', 'TEXT'], - ['Enzyme_Comission_number', 'Enzyme_Comission_number', 'TEXT'], - ['Source_organism_scientific_name', 'Source_organism_scientific_name', 'TEXT'], - ['Source_organism_gene', 'Source_organism_gene', 'TEXT'], - ['Source_organism_strain', 'Source_organism_strain', 'TEXT'], - ['Expression_system_scientific_name', 'Expression_system_scientific_name', 'TEXT'], - ['Expression_system_strain', 'Expression_system_strain', 'TEXT'], - ['Expression_system_vector_type', 'Expression_system_vector_type', 'TEXT'], - ['Expression_system_plasmid_name', 'Expression_system_plasmid_name', 'TEXT'], - ['Manipulated_source_details', 'Manipulated_source_details', 'TEXT'], - ['fragment_name_one_specific_mutation', 'fragment_name_one_specific_mutation', 'TEXT'], - ['molecule_chain_one', 'molecule_chain_one', 'TEXT'], - - ['molecule_name_two', 'molecule_name_two', 'TEXT'], - ['Fragment_name_two', 'Fragment_name_two', 'TEXT'], - ['Specific_mutation_two', 'Specific_mutation_two', 'TEXT'], - ['Enzyme_Comission_number_two', 'Enzyme_Comission_number_two', 'TEXT'], - ['Source_organism_scientific_name_two', 'Source_organism_scientific_name_two', 'TEXT'], - ['Source_organism_gene_two', 'Source_organism_gene_two', 'TEXT'], - ['Source_organism_strain_two', 'Source_organism_strain_two', 'TEXT'], - ['Expression_system_scientific_name_two', 'Expression_system_scientific_name_two', 'TEXT'], - ['Expression_system_strain_two', 'Expression_system_strain_two', 'TEXT'], - ['Expression_system_vector_type_two', 'Expression_system_vector_type_two', 'TEXT'], - ['Expression_system_plasmid_name_two', 'Expression_system_plasmid_name_two', 'TEXT'], - ['Manipulated_source_details_two', 'Manipulated_source_details_two', 'TEXT'], - ['fragment_name_two_specific_mutation', 'fragment_name_one_specific_mutation_two', 'TEXT'], - ['molecule_chain_two', 'molecule_chain_two', 'TEXT'], - - ['structure_keywords', 'structure_keywords', 'TEXT'], - ['biological_assembly_chain_number', 'biological_assembly_chain_number', 'TEXT'], - - - ['crystallization_id', 'crystallization_id', 'TEXT'], - ['crystallization_method', 'crystallization_method', 'TEXT'], - ['crystallization_pH', 'crystallization_pH', 'TEXT'], - ['crystallization_temperature', 'crystallization_temperature', 'TEXT'], - ['crystallization_details', 'crystallization_details', 'TEXT'], - - ['radiation_source', 'radiation_source', 'TEXT'], - ['radiation_source_type', 'radiation_source_type', 'TEXT'], - ['radiation_wavelengths', 'radiation_wavelengths', 'TEXT'], - ['radiation_detector', 'radiation_detector', 'TEXT'], - ['radiation_detector_type', 'radiation_detector_type', 'TEXT'], - ['data_collection_date', 'data_collection_date', 'TEXT'], - ['data_collection_temperature', 'data_collection_temperature', 'TEXT'], - ['data_collection_protocol', 'data_collection_protocol', 'TEXT'], - - ['SG_project_name', 'SG_project_name', 'TEXT'], - ['full_name_of_SG_center', 'full_name_of_SG_center', 'TEXT'], - - ['molecule_one_letter_sequence', 'molecule_one_letter_sequence', 'TEXT'], - ['molecule_one_letter_sequence_uniprot_id', 'molecule_one_letter_sequence_uniprot_id', 'TEXT'], - ['molecule_two_letter_sequence', 'molecule_two_letter_sequence', 'TEXT'], - ['molecule_two_letter_sequence_uniprot_id', 'molecule_two_letter_sequence_uniprot_id', 'TEXT'], - - ['CrystalName_of_pandda_input', 'CrystalName_of_pandda_input', 'TEXT'], - - ['pdbx_starting_model', 'pdbx_starting_model', 'TEXT'], - ['data_integration_software', 'data_integration_software', 'TEXT'], - ['phasing_software', 'phasing_software', 'TEXT'], - - ['pdbx_funding_ordinal_one', 'pdbx_funding_ordinal_one', 'TEXT'], - ['pdbx_funding_organization_one', 'pdbx_funding_organization_one', 'TEXT'], - ['pdbx_grant_number_one', 'pdbx_grant_number_one', 'TEXT'], - ['pdbx_grant_country_one', 'pdbx_grant_country_one', 'TEXT'], - - ['pdbx_funding_ordinal_two', 'pdbx_funding_ordinal_two', 'TEXT'], - ['pdbx_funding_organization_two', 'pdbx_funding_organization_two', 'TEXT'], - ['pdbx_grant_number_two', 'pdbx_grant_number_two', 'TEXT'], - ['pdbx_grant_country_two', 'pdbx_grant_country_two', 'TEXT'], - - ['pdbx_funding_ordinal_three', 'pdbx_funding_ordinal_three', 'TEXT'], - ['pdbx_funding_organization_three', 'pdbx_funding_organization_three', 'TEXT'], - ['pdbx_grant_number_three', 'pdbx_grant_number_three', 'TEXT'], - ['pdbx_grant_country_three', 'pdbx_grant_country_three', 'TEXT'], - - ['LastUpdated', 'LastUpdated', 'TEXT'], - ['LastUpdated_by', 'LastUpdated_by', 'TEXT'] - ] - - + ['ID', 'ID', + 'INTEGER PRIMARY KEY'], + + ['CrystalName', + 'Sample ID', 'TEXT'], + ['StructureType', 'StructureType', + 'TEXT'], # apo/model + + ['PDB_file', + 'PDB_file', 'TEXT'], + ['MTZ_file', + 'MTZ_file', 'TEXT'], + + ['mmCIF_model_file', + 'mmCIF_model_file', 'TEXT'], + ['mmCIF_SF_file', + 'mmCIF_SF_file', 'TEXT'], + ['label', 'label', + 'TEXT'], # for index.txt + ['description', 'description', + 'TEXT'], # for index.txt + + ['DimplePANDDApath', + 'DimplePANDDApath', 'TEXT'], + + ['contact_author_PI_salutation', + 'contact_author_PI_salutation', 'TEXT'], + ['contact_author_PI_first_name', + 'contact_author_PI_first_name', 'TEXT'], + ['contact_author_PI_last_name', + 'contact_author_PI_last_name', 'TEXT'], + ['contact_author_PI_middle_name', + 'contact_author_PI_middle_name', 'TEXT'], + ['contact_author_PI_role', + 'contact_author_PI_role', 'TEXT'], + ['contact_author_PI_organization_type', + 'contact_author_PI_organization_type', 'TEXT'], + ['contact_author_PI_organization_name', + 'contact_author_PI_organization_name', 'TEXT'], + ['contact_author_PI_email', + 'contact_author_PI_email', 'TEXT'], + ['contact_author_PI_address', + 'contact_author_PI_address', 'TEXT'], + ['contact_author_PI_city', + 'contact_author_PI_city', 'TEXT'], + ['contact_author_PI_State_or_Province', + 'contact_author_PI_State_or_Province', 'TEXT'], + ['contact_author_PI_Zip_Code', + 'contact_author_PI_Zip_Code', 'TEXT'], + ['contact_author_PI_Country', + 'contact_author_PI_Country', 'TEXT'], + ['contact_author_PI_fax_number', + 'contact_author_PI_fax_number', 'TEXT'], + ['contact_author_PI_phone_number', + 'contact_author_PI_phone_number', 'TEXT'], + ['contact_author_PI_ORCID', + 'contact_author_PI_ORCID', 'TEXT'], + + ['contact_author_salutation', + 'contact_author_salutation', 'TEXT'], + ['contact_author_first_name', + 'contact_author_first_name', 'TEXT'], + ['contact_author_last_name', + 'contact_author_last_name', 'TEXT'], + ['contact_author_middle_name', + 'contact_author_middle_name', 'TEXT'], + ['contact_author_role', + 'contact_author_role', 'TEXT'], + ['contact_author_organization_type', + 'contact_author_organization_type', 'TEXT'], + ['contact_author_organization_name', + 'contact_author_organization_name', 'TEXT'], + ['contact_author_email', + 'contact_author_email', 'TEXT'], + ['contact_author_address', + 'contact_author_address', 'TEXT'], + ['contact_author_city', + 'contact_author_city', 'TEXT'], + ['contact_author_State_or_Province', + 'contact_author_State_or_Province', 'TEXT'], + ['contact_author_Zip_Code', + 'contact_author_Zip_Code', 'TEXT'], + ['contact_author_Country', + 'contact_author_Country', 'TEXT'], + ['contact_author_fax_number', + 'contact_author_fax_number', 'TEXT'], + ['contact_author_phone_number', + 'contact_author_phone_number', 'TEXT'], + ['contact_author_ORCID', + 'contact_author_ORCID', 'TEXT'], + + ['Release_status_for_coordinates', + 'Release_status_for_coordinates', 'TEXT'], + ['Release_status_for_structure_factor', + 'Release_status_for_structure_factor', 'TEXT'], + ['Release_status_for_sequence', + 'Release_status_for_sequence', 'TEXT'], + + ['group_deposition_title', + 'group_deposition_title', 'TEXT'], + ['group_description', + 'group_description', 'TEXT'], + ['structure_title', + 'structure_title', 'TEXT'], + ['structure_details', + 'structure_details', 'TEXT'], + ['group_deposition_title_apo', + 'group_deposition_title_apo', 'TEXT'], + ['structure_title_apo', + 'structure_title_apo', 'TEXT'], + + ['structure_author_name', + 'structure_author_name', 'TEXT'], + ['primary_citation_author_name', + 'primary_citation_author_name', 'TEXT'], + + ['primary_citation_id', + 'primary_citation_id', 'TEXT'], + ['primary_citation_journal_abbrev', + 'primary_citation_journal_abbrev', 'TEXT'], + ['primary_citation_title', + 'primary_citation_title', 'TEXT'], + ['primary_citation_year', + 'primary_citation_year', 'TEXT'], + ['primary_citation_journal_volume', + 'primary_citation_journal_volume', 'TEXT'], + ['primary_citation_page_first', + 'primary_citation_page_first', 'TEXT'], + ['primary_citation_page_last', + 'primary_citation_page_last', 'TEXT'], + + ['molecule_name', + 'molecule_name', 'TEXT'], + ['Fragment_name', + 'Fragment_name', 'TEXT'], + ['Specific_mutation', + 'Specific_mutation', 'TEXT'], + ['Enzyme_Comission_number', + 'Enzyme_Comission_number', 'TEXT'], + ['Source_organism_scientific_name', + 'Source_organism_scientific_name', 'TEXT'], + ['Source_organism_gene', + 'Source_organism_gene', 'TEXT'], + ['Source_organism_strain', + 'Source_organism_strain', 'TEXT'], + ['Expression_system_scientific_name', + 'Expression_system_scientific_name', 'TEXT'], + ['Expression_system_strain', + 'Expression_system_strain', 'TEXT'], + ['Expression_system_vector_type', + 'Expression_system_vector_type', 'TEXT'], + ['Expression_system_plasmid_name', + 'Expression_system_plasmid_name', 'TEXT'], + ['Manipulated_source_details', + 'Manipulated_source_details', 'TEXT'], + ['fragment_name_one_specific_mutation', + 'fragment_name_one_specific_mutation', 'TEXT'], + ['molecule_chain_one', + 'molecule_chain_one', 'TEXT'], + + ['molecule_name_two', + 'molecule_name_two', 'TEXT'], + ['Fragment_name_two', + 'Fragment_name_two', 'TEXT'], + ['Specific_mutation_two', + 'Specific_mutation_two', 'TEXT'], + ['Enzyme_Comission_number_two', + 'Enzyme_Comission_number_two', 'TEXT'], + ['Source_organism_scientific_name_two', + 'Source_organism_scientific_name_two', 'TEXT'], + ['Source_organism_gene_two', + 'Source_organism_gene_two', 'TEXT'], + ['Source_organism_strain_two', + 'Source_organism_strain_two', 'TEXT'], + ['Expression_system_scientific_name_two', + 'Expression_system_scientific_name_two', 'TEXT'], + ['Expression_system_strain_two', + 'Expression_system_strain_two', 'TEXT'], + ['Expression_system_vector_type_two', + 'Expression_system_vector_type_two', 'TEXT'], + ['Expression_system_plasmid_name_two', + 'Expression_system_plasmid_name_two', 'TEXT'], + ['Manipulated_source_details_two', + 'Manipulated_source_details_two', 'TEXT'], + ['fragment_name_two_specific_mutation', + 'fragment_name_one_specific_mutation_two', 'TEXT'], + ['molecule_chain_two', + 'molecule_chain_two', 'TEXT'], + + ['structure_keywords', + 'structure_keywords', 'TEXT'], + ['biological_assembly_chain_number', + 'biological_assembly_chain_number', 'TEXT'], + + + ['crystallization_id', + 'crystallization_id', 'TEXT'], + ['crystallization_method', + 'crystallization_method', 'TEXT'], + ['crystallization_pH', + 'crystallization_pH', 'TEXT'], + ['crystallization_temperature', + 'crystallization_temperature', 'TEXT'], + ['crystallization_details', + 'crystallization_details', 'TEXT'], + + ['radiation_source', + 'radiation_source', 'TEXT'], + ['radiation_source_type', + 'radiation_source_type', 'TEXT'], + ['radiation_wavelengths', + 'radiation_wavelengths', 'TEXT'], + ['radiation_detector', + 'radiation_detector', 'TEXT'], + ['radiation_detector_type', + 'radiation_detector_type', 'TEXT'], + ['data_collection_date', + 'data_collection_date', 'TEXT'], + ['data_collection_temperature', + 'data_collection_temperature', 'TEXT'], + ['data_collection_protocol', + 'data_collection_protocol', 'TEXT'], + + ['SG_project_name', + 'SG_project_name', 'TEXT'], + ['full_name_of_SG_center', + 'full_name_of_SG_center', 'TEXT'], + + ['molecule_one_letter_sequence', + 'molecule_one_letter_sequence', 'TEXT'], + ['molecule_one_letter_sequence_uniprot_id', + 'molecule_one_letter_sequence_uniprot_id', 'TEXT'], + ['molecule_two_letter_sequence', + 'molecule_two_letter_sequence', 'TEXT'], + ['molecule_two_letter_sequence_uniprot_id', + 'molecule_two_letter_sequence_uniprot_id', 'TEXT'], + + ['CrystalName_of_pandda_input', + 'CrystalName_of_pandda_input', 'TEXT'], + + ['pdbx_starting_model', + 'pdbx_starting_model', 'TEXT'], + ['data_integration_software', + 'data_integration_software', 'TEXT'], + ['phasing_software', + 'phasing_software', 'TEXT'], + + ['pdbx_funding_ordinal_one', + 'pdbx_funding_ordinal_one', 'TEXT'], + ['pdbx_funding_organization_one', + 'pdbx_funding_organization_one', 'TEXT'], + ['pdbx_grant_number_one', + 'pdbx_grant_number_one', 'TEXT'], + ['pdbx_grant_country_one', + 'pdbx_grant_country_one', 'TEXT'], + + ['pdbx_funding_ordinal_two', + 'pdbx_funding_ordinal_two', 'TEXT'], + ['pdbx_funding_organization_two', + 'pdbx_funding_organization_two', 'TEXT'], + ['pdbx_grant_number_two', + 'pdbx_grant_number_two', 'TEXT'], + ['pdbx_grant_country_two', + 'pdbx_grant_country_two', 'TEXT'], + + ['pdbx_funding_ordinal_three', + 'pdbx_funding_ordinal_three', 'TEXT'], + ['pdbx_funding_organization_three', + 'pdbx_funding_organization_three', 'TEXT'], + ['pdbx_grant_number_three', + 'pdbx_grant_number_three', 'TEXT'], + ['pdbx_grant_country_three', + 'pdbx_grant_country_three', 'TEXT'], + + ['LastUpdated', + 'LastUpdated', 'TEXT'], + ['LastUpdated_by', + 'LastUpdated_by', 'TEXT'] + ] self.data_collection_columns = [ - ['ID', 'ID', 'INTEGER PRIMARY KEY'], - ['CrystalName', 'Sample ID', 'TEXT', 0], - ['ProteinName', 'ProteinName', 'TEXT', 1], - - ['DataCollectionVisit', 'Visit', 'TEXT', 0], - ['DataCollectionRun', 'Run', 'TEXT', 0], - ['DataCollectionSubdir', 'SubDir', 'TEXT', 0], - ['DataCollectionBeamline', 'Beamline', 'TEXT', 0], - ['DataCollectionOutcome', 'DataCollection\nOutcome', 'TEXT', 1], - ['DataCollectionDate', 'Data Collection\nDate', 'TEXT', 1], - ['DataCollectionWavelength', 'Wavelength', 'TEXT', 0], - ['DataCollectionPinBarcode', 'GDA\nBarcode', 'TEXT', 1], - - ['DataCollectionCrystalImage1', 'img1', 'TEXT', 1], - ['DataCollectionCrystalImage2', 'img2', 'TEXT', 1], - ['DataCollectionCrystalImage3', 'img3', 'TEXT', 1], - ['DataCollectionCrystalImage4', 'img4', 'TEXT', 1], - - ['DataProcessingPathToImageFiles', 'Path to diffraction\nimage files', 'TEXT', 1], - ['DataProcessingProgram', 'Program', 'TEXT', 1], - ['DataProcessingSpaceGroup', 'DataProcessing\nSpaceGroup', 'TEXT', 1], - ['DataProcessingUnitCell', 'DataProcessing\nUnitCell', 'TEXT', 0], - ['DataProcessingAutoAssigned', 'auto-assigned', 'TEXT', 0], - ['DataProcessingA', 'DataProcessing\nA', 'TEXT', 0], - ['DataProcessingB', 'DataProcessing\nB', 'TEXT', 0], - ['DataProcessingC', 'DataProcessing\nC', 'TEXT', 0], - ['DataProcessingAlpha', 'DataProcessing\nAlpha', 'TEXT', 0], - ['DataProcessingBeta', 'DataProcessing\nBeta', 'TEXT', 0], - ['DataProcessingGamma', 'DataProcessing\nGamma', 'TEXT', 0], - ['DataProcessingResolutionOverall', 'Resolution\nOverall', 'TEXT', 0], - ['DataProcessingResolutionLow', 'Resolution\nLow', 'TEXT', 0], - ['DataProcessingResolutionLowInnerShell', 'Resolution\nLow (Inner Shell)', 'TEXT', 0], - ['DataProcessingResolutionHigh', 'Resolution\nHigh', 'TEXT', 1], - ['DataProcessingResolutionHigh15sigma', 'Resolution\n[Mn = 1.5]', 'TEXT', 1], - ['DataProcessingResolutionHigh20sigma', 'Resolution\n[Mn = 2.0]', 'TEXT', 1], - ['DataProcessingResolutionHighOuterShell', 'Resolution\nHigh (Outer Shell)', 'TEXT', 0], - ['DataProcessingRmergeOverall', 'Rmerge\nOverall', 'TEXT', 1], - ['DataProcessingRmergeLow', 'Rmerge\nLow', 'TEXT', 1], - ['DataProcessingRmergeHigh', 'Rmerge\nHigh', 'TEXT', 1], - ['DataProcessingIsigOverall', 'Mn\nOverall', 'TEXT', 1], - ['DataProcessingIsigLow', 'Mn\nLow', 'TEXT', 1], - ['DataProcessingIsigHigh', 'Mn\nHigh', 'TEXT', 1], - ['DataProcessingCompletenessOverall', 'Completeness\nOverall', 'TEXT', 1], - ['DataProcessingCompletenessLow', 'Completeness\nLow', 'TEXT', 1], - ['DataProcessingCompletenessHigh', 'Completeness\nHigh', 'TEXT', 1], - ['DataProcessingMultiplicityOverall', 'Multiplicity\nOverall', 'TEXT', 1], - ['DataProcessingMultiplicityLow', 'Multiplicity\nLow', 'TEXT', 1], - ['DataProcessingMultiplicityHigh', 'Multiplicity\nHigh', 'TEXT', 1], - ['DataProcessingCChalfOverall', 'CC(1/2)\nOverall', 'TEXT', 1], - ['DataProcessingCChalfLow', 'CC(1/2)\nLow', 'TEXT', 1], - ['DataProcessingCChalfHigh', 'CC(1/2)\nHigh', 'TEXT', 1], - ['DataProcessingPathToLogfile', 'DataProcessingPathToLogfile', 'TEXT', 1], - ['DataProcessingPathToMTZfile', 'DataProcessingPathToMTZfile', 'TEXT', 1], - ['DataProcessingLOGfileName', 'DataProcessingLOGfileName', 'TEXT', 0], - ['DataProcessingMTZfileName', 'DataProcessingMTZfileName', 'TEXT', 0], - ['DataProcessingDirectoryOriginal', 'DataProcessingDirectoryOriginal', 'TEXT', 0], - ['DataProcessingUniqueReflectionsOverall', 'Unique Reflections\nOverall', 'TEXT', 1], - ['DataProcessingUniqueReflectionsLow', 'Unique Reflections\nlow', 'TEXT', 1], - ['DataProcessingUniqueReflectionsHigh', 'Unique Reflections\nhigh', 'TEXT', 1], - ['DataProcessingLattice', 'DataProcessing\nLattice', 'TEXT', 0], - ['DataProcessingPointGroup', 'DataProcessing\nPointGroup', 'TEXT', 0], - ['DataProcessingUnitCellVolume', 'DataProcessing\nUnit Cell Volume', 'TEXT', 0], - ['DataProcessingAlert', 'DataProcessing\nAlert', 'TEXT', 0], - ['DataProcessingScore', 'DataProcessing\nScore', 'TEXT', 1], - ['DataProcessingStatus', 'DataProcessing\nStatus', 'TEXT', 1], - ['LastUpdated', 'LastUpdated', 'TEXT', 0], - ['LastUpdated_by', 'LastUpdated_by', 'TEXT', 0] + ['ID', 'ID', + 'INTEGER PRIMARY KEY'], + ['CrystalName', 'Sample ID', + 'TEXT', 0], + ['ProteinName', 'ProteinName', + 'TEXT', 1], + + ['DataCollectionVisit', 'Visit', + 'TEXT', 0], + ['DataCollectionRun', 'Run', + 'TEXT', 0], + ['DataCollectionSubdir', 'SubDir', + 'TEXT', 0], + ['DataCollectionBeamline', 'Beamline', + 'TEXT', 0], + ['DataCollectionOutcome', 'DataCollection\nOutcome', + 'TEXT', 1], + ['DataCollectionDate', 'Data Collection\nDate', + 'TEXT', 1], + ['DataCollectionWavelength', 'Wavelength', + 'TEXT', 0], + ['DataCollectionPinBarcode', 'GDA\nBarcode', + 'TEXT', 1], + + ['DataCollectionCrystalImage1', 'img1', + 'TEXT', 1], + ['DataCollectionCrystalImage2', 'img2', + 'TEXT', 1], + ['DataCollectionCrystalImage3', 'img3', + 'TEXT', 1], + ['DataCollectionCrystalImage4', 'img4', + 'TEXT', 1], + + ['DataProcessingPathToImageFiles', + 'Path to diffraction\nimage files', 'TEXT', 1], + ['DataProcessingProgram', 'Program', + 'TEXT', 1], + ['DataProcessingSpaceGroup', 'DataProcessing\nSpaceGroup', + 'TEXT', 1], + ['DataProcessingUnitCell', 'DataProcessing\nUnitCell', + 'TEXT', 0], + ['DataProcessingAutoAssigned', 'auto-assigned', + 'TEXT', 0], + ['DataProcessingA', 'DataProcessing\nA', + 'TEXT', 0], + ['DataProcessingB', 'DataProcessing\nB', + 'TEXT', 0], + ['DataProcessingC', 'DataProcessing\nC', + 'TEXT', 0], + ['DataProcessingAlpha', 'DataProcessing\nAlpha', + 'TEXT', 0], + ['DataProcessingBeta', 'DataProcessing\nBeta', + 'TEXT', 0], + ['DataProcessingGamma', 'DataProcessing\nGamma', + 'TEXT', 0], + ['DataProcessingResolutionOverall', 'Resolution\nOverall', + 'TEXT', 0], + ['DataProcessingResolutionLow', 'Resolution\nLow', + 'TEXT', 0], + ['DataProcessingResolutionLowInnerShell', + 'Resolution\nLow (Inner Shell)', 'TEXT', 0], + ['DataProcessingResolutionHigh', 'Resolution\nHigh', + 'TEXT', 1], + ['DataProcessingResolutionHigh15sigma', + 'Resolution\n[Mn = 1.5]', 'TEXT', 1], + ['DataProcessingResolutionHigh20sigma', + 'Resolution\n[Mn = 2.0]', 'TEXT', 1], + ['DataProcessingResolutionHighOuterShell', + 'Resolution\nHigh (Outer Shell)', 'TEXT', 0], + ['DataProcessingRmergeOverall', 'Rmerge\nOverall', + 'TEXT', 1], + ['DataProcessingRmergeLow', 'Rmerge\nLow', + 'TEXT', 1], + ['DataProcessingRmergeHigh', 'Rmerge\nHigh', + 'TEXT', 1], + ['DataProcessingIsigOverall', + 'Mn\nOverall', 'TEXT', 1], + ['DataProcessingIsigLow', + 'Mn\nLow', 'TEXT', 1], + ['DataProcessingIsigHigh', + 'Mn\nHigh', 'TEXT', 1], + ['DataProcessingCompletenessOverall', 'Completeness\nOverall', + 'TEXT', 1], + ['DataProcessingCompletenessLow', 'Completeness\nLow', + 'TEXT', 1], + ['DataProcessingCompletenessHigh', 'Completeness\nHigh', + 'TEXT', 1], + ['DataProcessingMultiplicityOverall', 'Multiplicity\nOverall', + 'TEXT', 1], + ['DataProcessingMultiplicityLow', 'Multiplicity\nLow', + 'TEXT', 1], + ['DataProcessingMultiplicityHigh', 'Multiplicity\nHigh', + 'TEXT', 1], + ['DataProcessingCChalfOverall', + 'CC(1/2)\nOverall', 'TEXT', 1], + ['DataProcessingCChalfLow', + 'CC(1/2)\nLow', 'TEXT', 1], + ['DataProcessingCChalfHigh', + 'CC(1/2)\nHigh', 'TEXT', 1], + ['DataProcessingPathToLogfile', + 'DataProcessingPathToLogfile', 'TEXT', 1], + ['DataProcessingPathToMTZfile', + 'DataProcessingPathToMTZfile', 'TEXT', 1], + ['DataProcessingLOGfileName', 'DataProcessingLOGfileName', + 'TEXT', 0], + ['DataProcessingMTZfileName', 'DataProcessingMTZfileName', + 'TEXT', 0], + ['DataProcessingDirectoryOriginal', + 'DataProcessingDirectoryOriginal', 'TEXT', 0], + ['DataProcessingUniqueReflectionsOverall', + 'Unique Reflections\nOverall', 'TEXT', 1], + ['DataProcessingUniqueReflectionsLow', 'Unique Reflections\nlow', + 'TEXT', 1], + ['DataProcessingUniqueReflectionsHigh', + 'Unique Reflections\nhigh', 'TEXT', 1], + ['DataProcessingLattice', 'DataProcessing\nLattice', + 'TEXT', 0], + ['DataProcessingPointGroup', + 'DataProcessing\nPointGroup', 'TEXT', 0], + ['DataProcessingUnitCellVolume', + 'DataProcessing\nUnit Cell Volume', 'TEXT', 0], + ['DataProcessingAlert', 'DataProcessing\nAlert', + 'TEXT', 0], + ['DataProcessingScore', 'DataProcessing\nScore', + 'TEXT', 1], + ['DataProcessingStatus', 'DataProcessing\nStatus', + 'TEXT', 1], + ['LastUpdated', 'LastUpdated', + 'TEXT', 0], + ['LastUpdated_by', 'LastUpdated_by', + 'TEXT', 0] ] - self.zenodo_table_columns = [ - ['ID', 'ID', 'INTEGER PRIMARY KEY' ], - ['DimplePANDDApath', 'DimplePANDDApath', 'TEXT' ], - ['ZenodoTitle', 'ZenodoTitle', 'TEXT' ], - ['ZenodoHTTPS', 'ZenodoHTTPS', 'TEXT' ], - ['ZenodoDOI', 'ZenodoDOI', 'TEXT' ], - ['LastUpdated', 'LastUpdated', 'TEXT' ], - ['LastUpdated_by', 'LastUpdated_by', 'TEXT' ] + ['ID', 'ID', + 'INTEGER PRIMARY KEY'], + ['DimplePANDDApath', 'DimplePANDDApath', 'TEXT'], + ['ZenodoTitle', 'ZenodoTitle', 'TEXT'], + ['ZenodoHTTPS', 'ZenodoHTTPS', 'TEXT'], + ['ZenodoDOI', 'ZenodoDOI', 'TEXT'], + ['LastUpdated', 'LastUpdated', 'TEXT'], + ['LastUpdated_by', 'LastUpdated_by', 'TEXT'] ] self.label_table_columns = [ - ['ID', 'ID', 'INTEGER PRIMARY KEY' ], - ['Label', 'Label', 'TEXT' ], - ['Description', 'Description', 'TEXT' ], + ['ID', 'ID', + 'INTEGER PRIMARY KEY'], + ['Label', 'Label', 'TEXT'], + ['Description', 'Description', 'TEXT'], ] - def columns_not_to_display(self): do_not_display = [] for column in self.column_list: - if column[3]==0: + if column[3] == 0: do_not_display.append(column[1]) return do_not_display - + def get_empty_db_dict(self): - db_dict={} + db_dict = {} for column in self.column_list: if column[0] != 'ID': - db_dict[column[0]]='' + db_dict[column[0]] = '' return db_dict def create_missing_columns(self): - existing_columns=[] - connect=sqlite3.connect(self.data_source_file) + existing_columns = [] + connect = sqlite3.connect(self.data_source_file) connect.row_factory = sqlite3.Row cursor = connect.cursor() - tableDict = { 'mainTable': self.column_list, - 'panddaTable': self.pandda_table_columns, - 'depositTable': self.deposition_table_columns, - 'collectionTable': self.data_collection_columns, - 'zenodoTable': self.zenodo_table_columns, - 'labelTable': self.label_table_columns } + tableDict = {'mainTable': self.column_list, + 'panddaTable': self.pandda_table_columns, + 'depositTable': self.deposition_table_columns, + 'collectionTable': self.data_collection_columns, + 'zenodoTable': self.zenodo_table_columns, + 'labelTable': self.label_table_columns} for table in tableDict: - cursor.execute("create table if not exists "+table+" (ID INTEGER);") + cursor.execute("create table if not exists " + + table+" (ID INTEGER);") existing_columns = [] cursor.execute("SELECT * FROM "+table) for column in cursor.description: existing_columns.append(column[0]) for column in tableDict[table]: if column[0] not in existing_columns: - cursor.execute("alter table " + table + " add column '" + column[0] + "' '" + column[2] + "'") + cursor.execute( + "alter table " + table + " add column '" + column[0] + "' '" + column[2] + "'") connect.commit() if table == 'labelTable': cursor.execute('select ID from labelTable') id = cursor.fetchall() if id == []: for idx in range(5): - cursor.execute("insert into labelTable (ID) Values (%s)" %str(idx+1)) + cursor.execute( + "insert into labelTable (ID) Values (%s)" % str(idx+1)) # existing_columns=[] # connect=sqlite3.connect(self.data_source_file) @@ -611,19 +1033,20 @@ def create_missing_columns(self): # cursor.execute("alter table depositTable add column '"+column[0]+"' '"+column[2]+"'") # connect.commit() - def return_column_list(self): return self.column_list - def create_empty_data_source_file(self): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) with connect: cursor = connect.cursor() - cursor.execute("CREATE TABLE mainTable("+self.column_list[0][0]+' '+self.column_list[0][2]+")") - for i in range(1,len(self.column_list)): - cursor.execute("alter table mainTable add column '"+self.column_list[i][0]+"' '"+self.column_list[i][2]+"'") + cursor.execute( + "CREATE TABLE mainTable("+self.column_list[0][0]+' '+self.column_list[0][2]+")") + for i in range(1, len(self.column_list)): + cursor.execute("alter table mainTable add column '" + + self.column_list[i][0]+"' '"+self.column_list[i][2]+"'") connect.commit() # Don't need to create panddaTable at this point, because table will be created by create_missing_columns # which is called the first time a data source in specified in XCE @@ -635,135 +1058,147 @@ def create_empty_data_source_file(self): # connect.commit() def get_all_samples_in_data_source_as_list(self): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute("SELECT CrystalName FROM mainTable") - existing_samples_in_db=[] + existing_samples_in_db = [] samples = cursor.fetchall() for sample in samples: existing_samples_in_db.append(str(sample[0])) return existing_samples_in_db - def execute_statement(self,cmd): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def execute_statement(self, cmd): + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute(cmd) - output=cursor.fetchall() + output = cursor.fetchall() connect.commit() return output - def get_db_dict_for_sample(self,sampleID): - db_dict={} - header=[] - data=[] - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def get_db_dict_for_sample(self, sampleID): + db_dict = {} + header = [] + data = [] + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("select * from mainTable where CrystalName='{0!s}';".format(sampleID)) - print("SQLITE: select * from mainTable where CrystalName='{0!s}';".format(sampleID)) + cursor.execute( + "select * from mainTable where CrystalName='{0!s}';".format(sampleID)) + print( + "SQLITE: select * from mainTable where CrystalName='{0!s}';".format(sampleID)) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() print("DATA: {0!s}".format(data)) - for n,item in enumerate(data[0]): - db_dict[header[n]]=str(item) + for n, item in enumerate(data[0]): + db_dict[header[n]] = str(item) return db_dict - def get_deposit_dict_for_sample(self,sampleID): - db_dict={} - header=[] - data=[] - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def get_deposit_dict_for_sample(self, sampleID): + db_dict = {} + header = [] + data = [] + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() # if sampleID == 'ground-state': # just select first row in depositTable # cursor.execute("SELECT * FROM depositTable ORDER BY ROWID ASC LIMIT 1;") # else: # cursor.execute("select * from depositTable where CrystalName='{0!s}';".format(sampleID)) - cursor.execute("select * from depositTable where CrystalName='{0!s}';".format(sampleID)) + cursor.execute( + "select * from depositTable where CrystalName='{0!s}';".format(sampleID)) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() try: - for n,item in enumerate(data[0]): - db_dict[header[n]]=str(item) + for n, item in enumerate(data[0]): + db_dict[header[n]] = str(item) except IndexError: pass return db_dict - def get_zenodo_dict_for_pandda_analysis(self,panddaPath): - db_dict={} - header=[] - data=[] - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def get_zenodo_dict_for_pandda_analysis(self, panddaPath): + db_dict = {} + header = [] + data = [] + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() try: - cursor.execute("select * from zenodoTable where DimplePANDDApath='{0!s}';".format(panddaPath)) + cursor.execute( + "select * from zenodoTable where DimplePANDDApath='{0!s}';".format(panddaPath)) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() try: - for n,item in enumerate(data[0]): - db_dict[header[n]]=str(item) + for n, item in enumerate(data[0]): + db_dict[header[n]] = str(item) except IndexError: pass except sqlite3.OperationalError: db_dict = {} return db_dict - - - def get_db_pandda_dict_for_sample_and_site(self,sampleID,site_index): - db_dict={} - header=[] - data=[] - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def get_db_pandda_dict_for_sample_and_site(self, sampleID, site_index): + db_dict = {} + header = [] + data = [] + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("select * from panddaTable where CrystalName='{0!s}' and PANDDA_site_index='{1!s}';".format(sampleID, site_index)) + cursor.execute( + "select * from panddaTable where CrystalName='{0!s}' and PANDDA_site_index='{1!s}';".format(sampleID, site_index)) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() - for n,item in enumerate(data[0]): - db_dict[header[n]]=str(item) + for n, item in enumerate(data[0]): + db_dict[header[n]] = str(item) return db_dict - def get_db_pandda_dict_for_sample_and_site_and_event(self,sampleID,site_index,event_index): - db_dict={} - header=[] - data=[] - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def get_db_pandda_dict_for_sample_and_site_and_event(self, sampleID, site_index, event_index): + db_dict = {} + header = [] + data = [] + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("select * from panddaTable where CrystalName='{0!s}' and PANDDA_site_index='{1!s}' and PANDDA_site_event_index='{2!s}' and PANDDA_site_ligand_placed='True';".format(sampleID, site_index, event_index)) + cursor.execute("select * from panddaTable where CrystalName='{0!s}' and PANDDA_site_index='{1!s}' and PANDDA_site_event_index='{2!s}' and PANDDA_site_ligand_placed='True';".format( + sampleID, site_index, event_index)) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() - for n,item in enumerate(data[0]): - db_dict[header[n]]=str(item) + for n, item in enumerate(data[0]): + db_dict[header[n]] = str(item) return db_dict - def check_if_sample_exists_in_data_source(self,sampleID): - sample_exists=False - existing_samples_in_db=self.get_all_samples_in_data_source_as_list() + def check_if_sample_exists_in_data_source(self, sampleID): + sample_exists = False + existing_samples_in_db = self.get_all_samples_in_data_source_as_list() if sampleID in existing_samples_in_db: - sample_exists=True + sample_exists = True return sample_exists - def import_csv_file(self,csv_file): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def import_csv_file(self, csv_file): + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - available_columns=[] + available_columns = [] cursor.execute("SELECT * FROM mainTable") for column in cursor.description: # only update existing columns in data source available_columns.append(column[0]) - with open(csv_file,'rb') as csv_import: # `with` statement available in 2.5+ + with open(csv_file, 'rb') as csv_import: # `with` statement available in 2.5+ # csv.DictReader uses first line in file for column headings by default - csv_dict = csv.DictReader(csv_import) # comma is default delimiter + csv_dict = csv.DictReader(csv_import) # comma is default delimiter for line in csv_dict: - sampleID=line['CrystalName'] - if str(sampleID).replace(' ','')=='': + sampleID = line['CrystalName'] + if str(sampleID).replace(' ', '') == '': continue if self.check_if_sample_exists_in_data_source(sampleID): - update_string='' - for key,value in line.iteritems(): - if key=='ID' or key=='CrystalName': + update_string = '' + for key, value in line.iteritems(): + if key == 'ID' or key == 'CrystalName': continue if key not in available_columns: continue @@ -775,216 +1210,235 @@ def import_csv_file(self,csv_file): # print "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';" # cursor.execute("UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';") # now try this instead; not sure what will break now... - update_string+=str(key)+'='+"'"+str(value)+"'"+',' + update_string += str(key)+'='+"'"+str(value)+"'"+',' # print "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';" - cursor.execute("UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';") + cursor.execute( + "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';") else: - column_string='' - value_string='' - for key,value in line.iteritems(): - if key=='ID': + column_string = '' + value_string = '' + for key, value in line.iteritems(): + if key == 'ID': continue if key not in available_columns: continue - if not str(value).replace(' ','')=='': # ignore if nothing in csv field - value_string+="'"+value+"'"+',' - column_string+=key+',' + # ignore if nothing in csv field + if not str(value).replace(' ', '') == '': + value_string += "'"+value+"'"+',' + column_string += key+',' # print sampleID # print "INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");" - cursor.execute("INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");") + cursor.execute( + "INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");") connect.commit() - def update_data_source(self,sampleID,data_dict): + def update_data_source(self, sampleID, data_dict): print 'here' - data_dict['LastUpdated']=str(datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by']=getpass.getuser() + data_dict['LastUpdated'] = str( + datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict['LastUpdated_by'] = getpass.getuser() # need to do this since some older sqlite files contain a columnn called # DataProcessingResolutionHigh1.5sigma # and this does not go down well with the SQLite statement below - removeKey='' + removeKey = '' for key in data_dict: if '.5' in key: - removeKey=key + removeKey = key break if removeKey != '': del data_dict[removeKey] - connect=sqlite3.connect(self.data_source_file) + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - update_string='' + update_string = '' for key in data_dict: - value=data_dict[key] - if key=='ID' or key=='CrystalName': + value = data_dict[key] + if key == 'ID' or key == 'CrystalName': continue - if not str(value).replace(' ','')=='': # ignore empty fields - update_string+=str(key)+'='+"'"+str(value)+"'"+',' + if not str(value).replace(' ', '') == '': # ignore empty fields + update_string += str(key)+'='+"'"+str(value)+"'"+',' else: - update_string+=str(key)+' = null,' + update_string += str(key)+' = null,' if update_string != '': -# print "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"'" - cursor.execute("UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"'") + # print "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"'" + cursor.execute("UPDATE mainTable SET " + + update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"'") connect.commit() - def update_panddaTable(self,sampleID,site_index,data_dict): - data_dict['LastUpdated']=str(datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by']=getpass.getuser() - connect=sqlite3.connect(self.data_source_file) + def update_panddaTable(self, sampleID, site_index, data_dict): + data_dict['LastUpdated'] = str( + datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict['LastUpdated_by'] = getpass.getuser() + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - update_string='' + update_string = '' for key in data_dict: - value=data_dict[key] - if key=='ID' or key=='CrystalName' or key=='PANDDA_site_index': + value = data_dict[key] + if key == 'ID' or key == 'CrystalName' or key == 'PANDDA_site_index': continue - if not str(value).replace(' ','')=='': # ignore empty fields - update_string+=str(key)+'='+"'"+str(value)+"'"+',' + if not str(value).replace(' ', '') == '': # ignore empty fields + update_string += str(key)+'='+"'"+str(value)+"'"+',' else: - update_string+=str(key)+' = null,' + update_string += str(key)+' = null,' if update_string != '': - cursor.execute("UPDATE panddaTable SET "+update_string[:-1]+" WHERE CrystalName='{0!s}' and PANDDA_site_index='{1!s}'".format(sampleID, site_index)) + cursor.execute("UPDATE panddaTable SET " + + update_string[:-1]+" WHERE CrystalName='{0!s}' and PANDDA_site_index='{1!s}'".format(sampleID, site_index)) connect.commit() - def update_site_event_panddaTable(self,sampleID,site_index,event_index,data_dict): - data_dict['LastUpdated']=str(datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by']=getpass.getuser() - connect=sqlite3.connect(self.data_source_file) + def update_site_event_panddaTable(self, sampleID, site_index, event_index, data_dict): + data_dict['LastUpdated'] = str( + datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict['LastUpdated_by'] = getpass.getuser() + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - update_string='' + update_string = '' for key in data_dict: - value=data_dict[key] - if key=='ID' or key=='CrystalName' or key=='PANDDA_site_index' or key=='PANDDA_site_event_index': + value = data_dict[key] + if key == 'ID' or key == 'CrystalName' or key == 'PANDDA_site_index' or key == 'PANDDA_site_event_index': continue - if not str(value).replace(' ','')=='': # ignore empty fields - update_string+=str(key)+'='+"'"+str(value)+"'"+',' + if not str(value).replace(' ', '') == '': # ignore empty fields + update_string += str(key)+'='+"'"+str(value)+"'"+',' else: - update_string+=str(key)+' = null,' + update_string += str(key)+' = null,' if update_string != '': - cursor.execute("UPDATE panddaTable SET "+update_string[:-1]+" WHERE CrystalName='{0!s}' and PANDDA_site_index='{1!s}' and PANDDA_site_event_index='{2!s}'".format(sampleID, site_index, event_index)) + cursor.execute("UPDATE panddaTable SET " + + update_string[:-1]+" WHERE CrystalName='{0!s}' and PANDDA_site_index='{1!s}' and PANDDA_site_event_index='{2!s}'".format(sampleID, site_index, event_index)) connect.commit() - def update_depositTable(self,sampleID,structure_type,data_dict): - data_dict['LastUpdated']=str(datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by']=getpass.getuser() - connect=sqlite3.connect(self.data_source_file) + def update_depositTable(self, sampleID, structure_type, data_dict): + data_dict['LastUpdated'] = str( + datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict['LastUpdated_by'] = getpass.getuser() + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - update_string='' + update_string = '' for key in data_dict: - value=data_dict[key] - if key=='ID' or key=='CrystalName' or key=='StructureType': + value = data_dict[key] + if key == 'ID' or key == 'CrystalName' or key == 'StructureType': continue - if not str(value).replace(' ','')=='': # ignore empty fields -# update_string+=str(key)+'='+"'"+str(value)+"'"+',' -# update_string+=str(key)+'='+'"'+str(value)+'"'+',' - update_string+=str(key)+'='+'"'+str(value).replace('\r','').replace('\n','')+'"'+',' + if not str(value).replace(' ', '') == '': # ignore empty fields + # update_string+=str(key)+'='+"'"+str(value)+"'"+',' + # update_string+=str(key)+'='+'"'+str(value)+'"'+',' + update_string += str(key)+'='+'"' + \ + str(value).replace('\r', '').replace('\n', '')+'"'+',' else: - update_string+=str(key)+' = null,' + update_string += str(key)+' = null,' if update_string != '': -# print '-->',"UPDATE depositTable SET "+update_string[:-1]+" WHERE CrystalName='{0!s}' and StructureType='{1!s}'".format(sampleID, structure_type) -# cursor.execute("UPDATE depositTable SET "+update_string[:-1]+" WHERE CrystalName='{0!s}' and StructureType='{1!s}'".format(sampleID, structure_type)) - cursor.execute('UPDATE depositTable SET '+update_string[:-1]+' WHERE CrystalName="{0!s}" and StructureType="{1!s}"'.format(sampleID, structure_type)) + # print '-->',"UPDATE depositTable SET "+update_string[:-1]+" WHERE CrystalName='{0!s}' and StructureType='{1!s}'".format(sampleID, structure_type) + # cursor.execute("UPDATE depositTable SET "+update_string[:-1]+" WHERE CrystalName='{0!s}' and StructureType='{1!s}'".format(sampleID, structure_type)) + cursor.execute('UPDATE depositTable SET ' + + update_string[:-1]+' WHERE CrystalName="{0!s}" and StructureType="{1!s}"'.format(sampleID, structure_type)) connect.commit() - - def update_specified_table(self,sampleID,data_dict,table): - data_dict['LastUpdated']=str(datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by']=getpass.getuser() - connect=sqlite3.connect(self.data_source_file) + def update_specified_table(self, sampleID, data_dict, table): + data_dict['LastUpdated'] = str( + datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict['LastUpdated_by'] = getpass.getuser() + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - update_string='' + update_string = '' for key in data_dict: - value=data_dict[key] - if key=='ID' or key=='CrystalName': + value = data_dict[key] + if key == 'ID' or key == 'CrystalName': continue - if not str(value).replace(' ','')=='': # ignore empty fields - update_string+=str(key)+'='+"'"+str(value)+"'"+',' + if not str(value).replace(' ', '') == '': # ignore empty fields + update_string += str(key)+'='+"'"+str(value)+"'"+',' if update_string != '': - cursor.execute("UPDATE "+table+" SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"'") + cursor.execute("UPDATE "+table+" SET " + + update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"'") connect.commit() - def update_insert_data_source(self,sampleID,data_dict): - data_dict['LastUpdated']=str(datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by']=getpass.getuser() - connect=sqlite3.connect(self.data_source_file) + def update_insert_data_source(self, sampleID, data_dict): + data_dict['LastUpdated'] = str( + datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict['LastUpdated_by'] = getpass.getuser() + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute('Select CrystalName FROM mainTable') - available_columns=[] + available_columns = [] cursor.execute("SELECT * FROM mainTable") for column in cursor.description: # only update existing columns in data source available_columns.append(column[0]) if self.check_if_sample_exists_in_data_source(sampleID): for key in data_dict: - value=data_dict[key] - if key=='ID' or key=='CrystalName': + value = data_dict[key] + if key == 'ID' or key == 'CrystalName': continue - if not str(value).replace(' ','')=='': # ignore empty fields - update_string=str(key)+'='+"'"+str(value)+"'" - cursor.execute("UPDATE mainTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"';") + if not str(value).replace(' ', '') == '': # ignore empty fields + update_string = str(key)+'='+"'"+str(value)+"'" + cursor.execute("UPDATE mainTable SET "+update_string + + " WHERE CrystalName="+"'"+sampleID+"';") else: - column_string='CrystalName'+',' - value_string="'"+sampleID+"'"+',' + column_string = 'CrystalName'+',' + value_string = "'"+sampleID+"'"+',' for key in data_dict: - value=data_dict[key] - if key=='ID': + value = data_dict[key] + if key == 'ID': continue if key not in available_columns: continue - if not str(value).replace(' ','')=='': # ignore if nothing in csv field - value_string+="'"+str(value)+"'"+',' - column_string+=key+',' - cursor.execute("INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");") + if not str(value).replace(' ', '') == '': # ignore if nothing in csv field + value_string += "'"+str(value)+"'"+',' + column_string += key+',' + cursor.execute( + "INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");") connect.commit() - - - def update_insert_panddaTable(self,sampleID,data_dict): - data_dict['LastUpdated']=str(datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by']=getpass.getuser() - connect=sqlite3.connect(self.data_source_file) + def update_insert_panddaTable(self, sampleID, data_dict): + data_dict['LastUpdated'] = str( + datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict['LastUpdated_by'] = getpass.getuser() + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute('Select CrystalName,PANDDA_site_index FROM panddaTable') # available_columns=[] # cursor.execute("SELECT * FROM panddaTable") # for column in cursor.description: # only update existing columns in data source # available_columns.append(column[0]) - samples_sites_in_table=[] - tmp=cursor.fetchall() + samples_sites_in_table = [] + tmp = cursor.fetchall() for item in tmp: - line=[x.encode('UTF8') for x in list(item)] + line = [x.encode('UTF8') for x in list(item)] samples_sites_in_table.append(line) - found_sample_site=False + found_sample_site = False for entry in samples_sites_in_table: - if entry[0]==sampleID and entry[1]==data_dict['PANDDA_site_index']: - found_sample_site=True + if entry[0] == sampleID and entry[1] == data_dict['PANDDA_site_index']: + found_sample_site = True if found_sample_site: for key in data_dict: - value=data_dict[key] - if key=='ID' or key=='CrystalName' or key=='PANDDA_site_index': + value = data_dict[key] + if key == 'ID' or key == 'CrystalName' or key == 'PANDDA_site_index': continue - if not str(value).replace(' ','')=='': # ignore empty fields - update_string=str(key)+'='+"'"+str(value)+"'" + if not str(value).replace(' ', '') == '': # ignore empty fields + update_string = str(key)+'='+"'"+str(value)+"'" # print "UPDATE panddaTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and PANDDA_site_index is '"+data_dict['PANDDA_site_index']+"';" - cursor.execute("UPDATE panddaTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and PANDDA_site_index is '"+data_dict['PANDDA_site_index']+"';") + cursor.execute("UPDATE panddaTable SET "+update_string+" WHERE CrystalName=" + + "'"+sampleID+"' and PANDDA_site_index is '"+data_dict['PANDDA_site_index']+"';") else: - column_string='' - value_string='' + column_string = '' + value_string = '' for key in data_dict: - value=data_dict[key] - if key=='ID': + value = data_dict[key] + if key == 'ID': continue # if key not in available_columns: # continue - if not str(value).replace(' ','')=='': # ignore if nothing in csv field - value_string+="'"+str(value)+"'"+',' - column_string+=key+',' - print "INSERT INTO panddaTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");" - cursor.execute("INSERT INTO panddaTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");") + if not str(value).replace(' ', '') == '': # ignore if nothing in csv field + value_string += "'"+str(value)+"'"+',' + column_string += key+',' + print "INSERT INTO panddaTable (" + \ + column_string[:-1]+") VALUES ("+value_string[:-1]+");" + cursor.execute("INSERT INTO panddaTable (" + + column_string[:-1]+") VALUES ("+value_string[:-1]+");") connect.commit() - def update_insert_any_table(self,table,data_dict,condition_dict): - data_dict['LastUpdated'] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) + def update_insert_any_table(self, table, data_dict, condition_dict): + data_dict['LastUpdated'] = str( + datetime.now().strftime("%Y-%m-%d %H:%M")) data_dict['LastUpdated_by'] = getpass.getuser() connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() @@ -992,28 +1446,31 @@ def update_insert_any_table(self,table,data_dict,condition_dict): # columns columns = '' for c in condition_dict: - columns+=c+',' + columns += c+',' # condition condition_string = '' for key in condition_dict: condition = condition_dict[key] - condition_string += str(key) + '=' + "'" + str(condition) + "' and " + condition_string += str(key) + '=' + "'" + \ + str(condition) + "' and " - cursor.execute('Select %s FROM %s where %s' %(columns[:-1],table,condition_string[:-5])) + cursor.execute('Select %s FROM %s where %s' % + (columns[:-1], table, condition_string[:-5])) tmp = cursor.fetchall() if not tmp: data_dict.update(condition_dict) - value_string='' - column_string='' + value_string = '' + column_string = '' for key in data_dict: value = data_dict[key] value_string += "'" + str(value) + "'" + ',' column_string += key + ',' - cursor.execute("INSERT INTO "+table+" (" + column_string[:-1] + ") VALUES (" + value_string[:-1] + ");") + cursor.execute("INSERT INTO "+table+" (" + + column_string[:-1] + ") VALUES (" + value_string[:-1] + ");") else: - update_string='' + update_string = '' for key in data_dict: value = data_dict[key] update_string += str(key) + '=' + "'" + str(value) + "'," @@ -1023,156 +1480,163 @@ def update_insert_any_table(self,table,data_dict,condition_dict): " WHERE " + condition_string[:-5] + ";") connect.commit() - - def update_insert_site_event_panddaTable(self,sampleID,data_dict): - data_dict['LastUpdated']=str(datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by']=getpass.getuser() - connect=sqlite3.connect(self.data_source_file) + def update_insert_site_event_panddaTable(self, sampleID, data_dict): + data_dict['LastUpdated'] = str( + datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict['LastUpdated_by'] = getpass.getuser() + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute('Select CrystalName,PANDDA_site_index,PANDDA_site_event_index FROM panddaTable') + cursor.execute( + 'Select CrystalName,PANDDA_site_index,PANDDA_site_event_index FROM panddaTable') # available_columns=[] # cursor.execute("SELECT * FROM panddaTable") # for column in cursor.description: # only update existing columns in data source # available_columns.append(column[0]) - samples_sites_in_table=[] - tmp=cursor.fetchall() + samples_sites_in_table = [] + tmp = cursor.fetchall() for item in tmp: - line=[x.encode('UTF8') for x in list(item)] + line = [x.encode('UTF8') for x in list(item)] samples_sites_in_table.append(line) - found_sample_site=False + found_sample_site = False for entry in samples_sites_in_table: - if entry[0]==sampleID and entry[1]==data_dict['PANDDA_site_index'] and entry[2]==data_dict['PANDDA_site_event_index']: - found_sample_site=True + if entry[0] == sampleID and entry[1] == data_dict['PANDDA_site_index'] and entry[2] == data_dict['PANDDA_site_event_index']: + found_sample_site = True if found_sample_site: for key in data_dict: - value=data_dict[key] - if key=='ID' or key=='CrystalName' or key=='PANDDA_site_index' or key=='PANDDA_site_event_index': + value = data_dict[key] + if key == 'ID' or key == 'CrystalName' or key == 'PANDDA_site_index' or key == 'PANDDA_site_event_index': continue - if not str(value).replace(' ','')=='': # ignore empty fields - update_string=str(key)+'='+"'"+str(value)+"'" + if not str(value).replace(' ', '') == '': # ignore empty fields + update_string = str(key)+'='+"'"+str(value)+"'" # print "UPDATE panddaTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and PANDDA_site_index is '"+data_dict['PANDDA_site_index']+"';" - cursor.execute("UPDATE panddaTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and PANDDA_site_index is '"+data_dict['PANDDA_site_index']+"' and PANDDA_site_event_index is '"+data_dict['PANDDA_site_event_index']+"';") + cursor.execute("UPDATE panddaTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and PANDDA_site_index is '" + + data_dict['PANDDA_site_index']+"' and PANDDA_site_event_index is '"+data_dict['PANDDA_site_event_index']+"';") else: - column_string='' - value_string='' + column_string = '' + value_string = '' for key in data_dict: - value=data_dict[key] - if key=='ID': + value = data_dict[key] + if key == 'ID': continue # if key not in available_columns: # continue - if not str(value).replace(' ','')=='': # ignore if nothing in csv field - value_string+="'"+str(value)+"'"+',' - column_string+=key+',' - print "INSERT INTO panddaTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");" - cursor.execute("INSERT INTO panddaTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");") + if not str(value).replace(' ', '') == '': # ignore if nothing in csv field + value_string += "'"+str(value)+"'"+',' + column_string += key+',' + print "INSERT INTO panddaTable (" + \ + column_string[:-1]+") VALUES ("+value_string[:-1]+");" + cursor.execute("INSERT INTO panddaTable (" + + column_string[:-1]+") VALUES ("+value_string[:-1]+");") connect.commit() - - - def update_insert_depositTable(self,sampleID,data_dict): - data_dict['LastUpdated']=str(datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by']=getpass.getuser() - connect=sqlite3.connect(self.data_source_file) + def update_insert_depositTable(self, sampleID, data_dict): + data_dict['LastUpdated'] = str( + datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict['LastUpdated_by'] = getpass.getuser() + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - available_columns=[] + available_columns = [] cursor.execute("SELECT * FROM depositTable") for column in cursor.description: # only update existing columns in data source available_columns.append(column[0]) - cursor.execute('Select CrystalName FROM depositTable') - samples_in_table=[] - tmp=cursor.fetchall() + samples_in_table = [] + tmp = cursor.fetchall() for item in tmp: - line=[x.encode('UTF8') for x in list(item)] + line = [x.encode('UTF8') for x in list(item)] # print 'a',item # print 'b',str(item) # print 'c',line # print 'd',line[0] # print 'e',str(line[0]) - if str(item) not in samples_in_table: samples_in_table.append(str(line[0])) + if str(item) not in samples_in_table: + samples_in_table.append(str(line[0])) # samples_in_table.append(line) - - if sampleID in samples_in_table: for key in data_dict: - value=data_dict[key] - if key=='ID' or key=='CrystalName': + value = data_dict[key] + if key == 'ID' or key == 'CrystalName': continue - if not str(value).replace(' ','')=='': # ignore empty fields - update_string=str(key)+'='+"'"+str(value)+"'" - print "UPDATE depositTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"';" - cursor.execute("UPDATE depositTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"';") + if not str(value).replace(' ', '') == '': # ignore empty fields + update_string = str(key)+'='+"'"+str(value)+"'" + print "UPDATE depositTable SET "+update_string + \ + " WHERE CrystalName="+"'"+sampleID+"';" + cursor.execute( + "UPDATE depositTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"';") else: - column_string='CrystalName'+',' - value_string="'"+sampleID+"'"+',' + column_string = 'CrystalName'+',' + value_string = "'"+sampleID+"'"+',' for key in data_dict: - value=data_dict[key] - if key=='ID': + value = data_dict[key] + if key == 'ID': continue if key not in available_columns: continue - if not str(value).replace(' ','')=='': # ignore if nothing in csv field - value_string+="'"+str(value)+"'"+',' - column_string+=key+',' - print "INSERT INTO depositTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");" - cursor.execute("INSERT INTO depositTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");") + if not str(value).replace(' ', '') == '': # ignore if nothing in csv field + value_string += "'"+str(value)+"'"+',' + column_string += key+',' + print "INSERT INTO depositTable (" + \ + column_string[:-1]+") VALUES ("+value_string[:-1]+");" + cursor.execute("INSERT INTO depositTable (" + + column_string[:-1]+") VALUES ("+value_string[:-1]+");") connect.commit() - - - def update_insert_not_null_fields_only(self,sampleID,data_dict): - data_dict['LastUpdated']=str(datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by']=getpass.getuser() - connect=sqlite3.connect(self.data_source_file) + def update_insert_not_null_fields_only(self, sampleID, data_dict): + data_dict['LastUpdated'] = str( + datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict['LastUpdated_by'] = getpass.getuser() + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute('Select CrystalName FROM mainTable') - available_columns=[] + available_columns = [] cursor.execute("SELECT * FROM mainTable") for column in cursor.description: # only update existing columns in data source available_columns.append(column[0]) if self.check_if_sample_exists_in_data_source(sampleID): for key in data_dict: - value=data_dict[key] + value = data_dict[key] # print value - if key=='ID' or key=='CrystalName': + if key == 'ID' or key == 'CrystalName': continue - if not str(value).replace(' ','')=='': # ignore empty fields - update_string=str(key)+'='+"'"+str(value)+"'" + if not str(value).replace(' ', '') == '': # ignore empty fields + update_string = str(key)+'='+"'"+str(value)+"'" # cursor.execute("UPDATE mainTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and "+str(key)+" is null;") - cursor.execute("UPDATE mainTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and ("+str(key)+" is null or "+str(key)+"='');") + cursor.execute("UPDATE mainTable SET "+update_string+" WHERE CrystalName=" + + "'"+sampleID+"' and ("+str(key)+" is null or "+str(key)+"='');") else: - column_string='CrystalName'+',' - value_string="'"+sampleID+"'"+',' + column_string = 'CrystalName'+',' + value_string = "'"+sampleID+"'"+',' for key in data_dict: - value=data_dict[key] - if key=='ID': + value = data_dict[key] + if key == 'ID': continue if key not in available_columns: continue - if not str(value).replace(' ','')=='': # ignore if nothing in csv field - value_string+="'"+str(value)+"'"+',' - column_string+=key+',' - cursor.execute("INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");") + if not str(value).replace(' ', '') == '': # ignore if nothing in csv field + value_string += "'"+str(value)+"'"+',' + column_string += key+',' + cursor.execute( + "INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");") connect.commit() - def get_value_from_field(self,sampleID,column): - connect=sqlite3.connect(self.data_source_file) + def get_value_from_field(self, sampleID, column): + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("SELECT "+column+" FROM mainTable WHERE CrystalName='"+sampleID+"';") + cursor.execute("SELECT "+column + + " FROM mainTable WHERE CrystalName='"+sampleID+"';") return cursor.fetchone() - def export_to_csv_file(self,csv_file): - connect=sqlite3.connect(self.data_source_file) + def export_to_csv_file(self, csv_file): + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute("SELECT * FROM mainTable") - header=() + header = () for column in cursor.description: - header+=(column[0],) + header += (column[0],) rows = cursor.fetchall() csvWriter = csv.writer(open(csv_file, "w")) csvWriter.writerows([header]+rows) @@ -1190,18 +1654,15 @@ def export_to_csv_file(self,csv_file): # return ([header,data]) def load_samples_from_data_source(self): - header=[] - data=[] - connect=sqlite3.connect(self.data_source_file) + header = [] + data = [] + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute("SELECT * FROM mainTable") for column in cursor.description: header.append(column[0]) data = cursor.fetchall() - return header,data - - - + return header, data # def get_samples_for_coot(self,RefinementOutcome,pandda_site): @@ -1266,9 +1727,9 @@ def load_samples_from_data_source(self): # # return sample_list_for_coot - def get_pandda_info_for_coot(self,xtalID,pandda_site): - pandda_info_for_coot=[] - connect=sqlite3.connect(self.data_source_file) + def get_pandda_info_for_coot(self, xtalID, pandda_site): + pandda_info_for_coot = [] + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() sqlite = ( @@ -1280,52 +1741,50 @@ def get_pandda_info_for_coot(self,xtalID,pandda_site): " PANDDA_site_spider_plot " "from panddaTable " "where " - " CrystalName is '%s'" %xtalID+ + " CrystalName is '%s'" % xtalID + " and PANDDA_site_index is '{0!s}';".format(pandda_site) - ) + ) cursor.execute(sqlite) tmp = cursor.fetchall() for item in tmp: - tmpx=[] + tmpx = [] for i in list(item): if i is None: tmpx.append('None') else: tmpx.append(i) - line=[x.encode('UTF8') for x in tmpx] + line = [x.encode('UTF8') for x in tmpx] pandda_info_for_coot.append(line) return pandda_info_for_coot - - - def get_todo_list_for_coot(self,RefinementOutcome,pandda_site): - sample_list_for_coot=[] - connect=sqlite3.connect(self.data_source_file) + def get_todo_list_for_coot(self, RefinementOutcome, pandda_site): + sample_list_for_coot = [] + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - if RefinementOutcome=='0 - All Datasets': + if RefinementOutcome == '0 - All Datasets': outcome = " not null " else: outcome = " '{0!s}' ".format(RefinementOutcome) if int(pandda_site) > 0: -# sqlite = ( -# "select" -# " mainTable.CrystalName," -# " mainTable.CompoundCode," -# " mainTable.RefinementCIF," -# " mainTable.RefinementMTZfree," -# " mainTable.RefinementPathToRefinementFolder," -# " panddaTable.RefinementOutcome, " -# " panddaTable.PANDDA_site_confidence " -# "from mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " -# "where panddaTable.PANDDA_site_index is '%s'" %pandda_site+ -# " and panddaTable.PANDDA_site_ligand_placed is 'True'" -# " and panddaTable.RefinementOutcome is %s;" %outcome -# ) + # sqlite = ( + # "select" + # " mainTable.CrystalName," + # " mainTable.CompoundCode," + # " mainTable.RefinementCIF," + # " mainTable.RefinementMTZfree," + # " mainTable.RefinementPathToRefinementFolder," + # " panddaTable.RefinementOutcome, " + # " panddaTable.PANDDA_site_confidence " + # "from mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " + # "where panddaTable.PANDDA_site_index is '%s'" %pandda_site+ + # " and panddaTable.PANDDA_site_ligand_placed is 'True'" + # " and panddaTable.RefinementOutcome is %s;" %outcome + # ) sqlite = ( "select" " mainTable.CrystalName," @@ -1336,10 +1795,11 @@ def get_todo_list_for_coot(self,RefinementOutcome,pandda_site): " panddaTable.RefinementOutcome, " " panddaTable.PANDDA_site_confidence " "from mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " - "where panddaTable.PANDDA_site_index is '%s'" %pandda_site+ + "where panddaTable.PANDDA_site_index is '%s'" % pandda_site + " and panddaTable.PANDDA_site_ligand_placed is 'True'" - " and panddaTable.RefinementOutcome like "+outcome.split()[0]+"%';" - ) + " and panddaTable.RefinementOutcome like " + + outcome.split()[0]+"%';" + ) # sqlite = ( # "select" # " mainTable.CrystalName," @@ -1364,30 +1824,29 @@ def get_todo_list_for_coot(self,RefinementOutcome,pandda_site): " RefinementOutcome," " RefinementLigandConfidence " "from mainTable " - "where RefinementOutcome is %s and DimpleRfree is not Null;" %outcome - ) + "where RefinementOutcome is %s and DimpleRfree is not Null;" % outcome + ) cursor.execute(sqlite) tmp = cursor.fetchall() for item in tmp: - tmpx=[] + tmpx = [] for i in list(item): if i is None: tmpx.append('None') else: tmpx.append(i) - line=[x.encode('UTF8') for x in tmpx] + line = [x.encode('UTF8') for x in tmpx] sample_list_for_coot.append(line) return sample_list_for_coot - - def get_todoList_for_coot(self,RefinementOutcome): - sample_list_for_coot=[] - connect=sqlite3.connect(self.data_source_file) + def get_todoList_for_coot(self, RefinementOutcome): + sample_list_for_coot = [] + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - if RefinementOutcome=='0 - All Datasets': + if RefinementOutcome == '0 - All Datasets': outcome = " not null " else: outcome = " '{0!s}' ".format(RefinementOutcome) @@ -1402,56 +1861,55 @@ def get_todoList_for_coot(self,RefinementOutcome): " RefinementOutcome," " RefinementLigandConfidence " "from mainTable " - "where RefinementOutcome is %s and (DimpleRfree is not Null or RefinementRfree is not Null) order by CrystalName ASC;" %outcome - ) + "where RefinementOutcome is %s and (DimpleRfree is not Null or RefinementRfree is not Null) order by CrystalName ASC;" % outcome + ) cursor.execute(sqlite) tmp = cursor.fetchall() for item in tmp: - tmpx=[] + tmpx = [] for i in list(item): if i is None: tmpx.append('None') else: tmpx.append(i) - line=[x.encode('UTF8') for x in tmpx] + line = [x.encode('UTF8') for x in tmpx] sample_list_for_coot.append(line) - crystalDict={} + crystalDict = {} for entry in sample_list_for_coot: if entry[0] not in crystalDict: - sqlite = ( "select" - " PANDDA_site_event_map," - " PANDDA_site_x," - " PANDDA_site_y," - " PANDDA_site_z," - " PANDDA_site_spider_plot," - " PANDDA_site_index," - " PANDDA_site_event_index," - " PANDDA_site_confidence," - " PANDDA_site_name," - " PANDDA_site_InspectConfidence," - " PANDDA_site_interesting," - " PANDDA_site_event_comment " - "from panddaTable " - "where " - " CrystalName is '%s';" %entry[0] ) + sqlite = ("select" + " PANDDA_site_event_map," + " PANDDA_site_x," + " PANDDA_site_y," + " PANDDA_site_z," + " PANDDA_site_spider_plot," + " PANDDA_site_index," + " PANDDA_site_event_index," + " PANDDA_site_confidence," + " PANDDA_site_name," + " PANDDA_site_InspectConfidence," + " PANDDA_site_interesting," + " PANDDA_site_event_comment " + "from panddaTable " + "where " + " CrystalName is '%s';" % entry[0]) cursor.execute(sqlite) tmp = cursor.fetchall() if tmp: - crystalDict[entry[0]]=[] + crystalDict[entry[0]] = [] for item in tmp: - print [entry[0], str(item[0]),str(item[1]),str(item[2]),str(item[3]),str(item[4]),str(item[5]),str(item[6]),str(item[7]),str(item[8]),str(item[9]),str(item[10]),str(item[11]) ] - crystalDict[entry[0]].append( [ str(item[0]),str(item[1]),str(item[2]),str(item[3]),str(item[4]),str(item[5]),str(item[6]),str(item[7]),str(item[8]),str(item[9]),str(item[10]),str(item[11]) ]) - - return sample_list_for_coot,crystalDict - + print [entry[0], str(item[0]), str(item[1]), str(item[2]), str(item[3]), str(item[4]), str( + item[5]), str(item[6]), str(item[7]), str(item[8]), str(item[9]), str(item[10]), str(item[11])] + crystalDict[entry[0]].append([str(item[0]), str(item[1]), str(item[2]), str(item[3]), str(item[4]), str( + item[5]), str(item[6]), str(item[7]), str(item[8]), str(item[9]), str(item[10]), str(item[11])]) + return sample_list_for_coot, crystalDict - - def translate_xce_column_list_to_sqlite(self,column_list): - out_list=[] + def translate_xce_column_list_to_sqlite(self, column_list): + out_list = [] for item in column_list: if item.startswith('Exclude'): out_list.append(['Exclude']) @@ -1461,167 +1919,181 @@ def translate_xce_column_list_to_sqlite(self,column_list): # out_list.append([item,item]) # continue if item.startswith('Export'): -# out_list.append('Export') - out_list.append(['Export',item]) + # out_list.append('Export') + out_list.append(['Export', item]) continue if item.startswith('Show'): - out_list.append([item,item]) + out_list.append([item, item]) continue if item.startswith('Run\nDimple'): - out_list.append([item,item]) + out_list.append([item, item]) continue if item.startswith('Select'): - out_list.append([item,item]) + out_list.append([item, item]) continue if item.startswith('Run\nxia2'): - out_list.append([item,item]) + out_list.append([item, item]) continue if item.startswith('Dataset ID'): - out_list.append([item,item]) + out_list.append([item, item]) continue if item.startswith('Reference\nSpaceGroup'): - out_list.append([item,item]) + out_list.append([item, item]) continue if item.startswith('Difference\nUC Volume (%)'): - out_list.append([item,item]) + out_list.append([item, item]) continue if item.startswith('Reference File'): - out_list.append([item,item]) + out_list.append([item, item]) continue if item.startswith('PanDDA site details'): - out_list.append([item,item]) + out_list.append([item, item]) continue for entry in self.column_list: - if entry[1]==item: - out_list.append([item,entry[0]]) + if entry[1] == item: + out_list.append([item, entry[0]]) break return out_list def get_list_of_pandda_sites_for_coot(self): - site_list=[ ['0','any site'] ] + site_list = [['0', 'any site']] sqlite = ( 'select distinct' ' panddaTable.PANDDA_site_index,' ' panddaTable.PANDDA_site_name ' 'from panddaTable ' 'order by cast (panddaTable.PANDDA_site_index as integer) ASC;' - ) + ) - print 'data source',self.data_source_file - connect=sqlite3.connect(self.data_source_file) + print 'data source', self.data_source_file + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute(sqlite) - tmp=cursor.fetchall() + tmp = cursor.fetchall() for item in tmp: -# print item -# print str(item[0]) -# print str(item[1]) -# line=[x.encode('UTF8') for x in list(item)] - site_list.append([str(item[0]),str(item[1])]) + # print item + # print str(item[0]) + # print str(item[1]) + # line=[x.encode('UTF8') for x in list(item)] + site_list.append([str(item[0]), str(item[1])]) return site_list def export_csv_for_WONKA(self): - SQLite = ( "select" - " panddaTable.PANDDA_site_ligand_resname," - " panddaTable.PANDDA_site_ligand_sequence_number," - " panddaTable.PANDDA_site_ligand_chain," - " panddaTable.RefinementOutcome," - " mainTable.CompoundSMILES," - " mainTable.RefinementBoundConformation," - " panddaTable.PANDDA_site_initial_mtz," - " panddaTable.PANDDA_site_event_map," - " panddaTable.CrystalName," - " mainTable.CompoundCode " - "from" - " mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " - "where" - " (panddaTable.RefinementOutcome like '3%' or panddaTable.RefinementOutcome like '4%' or panddaTable.RefinementOutcome like '5%')" ) - connect=sqlite3.connect(self.data_source_file) + SQLite = ("select" + " panddaTable.PANDDA_site_ligand_resname," + " panddaTable.PANDDA_site_ligand_sequence_number," + " panddaTable.PANDDA_site_ligand_chain," + " panddaTable.RefinementOutcome," + " mainTable.CompoundSMILES," + " mainTable.RefinementBoundConformation," + " panddaTable.PANDDA_site_initial_mtz," + " panddaTable.PANDDA_site_event_map," + " panddaTable.CrystalName," + " mainTable.CompoundCode " + "from" + " mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " + "where" + " (panddaTable.RefinementOutcome like '3%' or panddaTable.RefinementOutcome like '4%' or panddaTable.RefinementOutcome like '5%')") + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute(SQLite) - header=() + header = () for column in cursor.description: - header+=(column[0],) + header += (column[0],) rows = cursor.fetchall() csvWriter = csv.writer(open('for_wonka.csv', "w")) csvWriter.writerows([header]+rows) - def create_missing_apo_records_in_depositTable(self,xce_logfile): - Logfile=XChemLog.updateLog(xce_logfile) - connect=sqlite3.connect(self.data_source_file) + def create_missing_apo_records_in_depositTable(self, xce_logfile): + Logfile = XChemLog.updateLog(xce_logfile) + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("select panddaTable.ApoStructures from panddaTable where panddaTable.ApoStructures is not Null") + cursor.execute( + "select panddaTable.ApoStructures from panddaTable where panddaTable.ApoStructures is not Null") tmp = cursor.fetchall() # print str(tmp) - apoStructureList=[] + apoStructureList = [] for item in tmp: for xtal in str(item[0]).split(';'): - if xtal not in apoStructureList: apoStructureList.append(xtal) + if xtal not in apoStructureList: + apoStructureList.append(xtal) if not apoStructureList: - Logfile.insert('no apo structures were assigned to your pandda models') + Logfile.insert( + 'no apo structures were assigned to your pandda models') else: - Logfile.insert('the following datasets were at some point used as apo structures for pandda.analyse: '+str(apoStructureList)) - apoInDB=[] - cursor.execute("select CrystalName from depositTable where StructureType is 'apo'") + Logfile.insert( + 'the following datasets were at some point used as apo structures for pandda.analyse: '+str(apoStructureList)) + apoInDB = [] + cursor.execute( + "select CrystalName from depositTable where StructureType is 'apo'") tmp = cursor.fetchall() for xtal in tmp: - Logfile.insert(str(xtal[0])+' exists as entry for apo structure in database') + Logfile.insert( + str(xtal[0])+' exists as entry for apo structure in database') apoInDB.append(str(xtal[0])) - newEntries='' + newEntries = '' for xtal in apoStructureList: if xtal not in apoInDB: Logfile.insert('no entry for '+xtal+' in depositTable') - newEntries+="('{0!s}','apo'),".format(xtal) + newEntries += "('{0!s}','apo'),".format(xtal) if newEntries != '': - sqlite='insert into depositTable (CrystalName,StructureType) values {0!s};'.format(newEntries[:-1]) - Logfile.insert('creating new entries with the following SQLite command:\n'+sqlite) + sqlite = 'insert into depositTable (CrystalName,StructureType) values {0!s};'.format( + newEntries[:-1]) + Logfile.insert( + 'creating new entries with the following SQLite command:\n'+sqlite) cursor.execute(sqlite) connect.commit() - def create_missing_apo_records_for_all_structures_in_depositTable(self,projectDir,xce_logfile): - Logfile=XChemLog.updateLog(xce_logfile) - connect=sqlite3.connect(self.data_source_file) + def create_missing_apo_records_for_all_structures_in_depositTable(self, projectDir, xce_logfile): + Logfile = XChemLog.updateLog(xce_logfile) + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("select CrystalName from depositTable where StructureType is 'apo'") + cursor.execute( + "select CrystalName from depositTable where StructureType is 'apo'") tmp = cursor.fetchall() # print str(tmp) - apoStructureList=[] + apoStructureList = [] for item in tmp: apoStructureList.append(str(item[0])) - counter=0 # there is a SQLite limit which does not allow to insert more than 500 records at once - newEntries='' - for files in glob.glob(os.path.join(projectDir,'*')): - xtal=files[files.rfind('/')+1:] + counter = 0 # there is a SQLite limit which does not allow to insert more than 500 records at once + newEntries = '' + for files in glob.glob(os.path.join(projectDir, '*')): + xtal = files[files.rfind('/')+1:] if xtal not in apoStructureList: - dimple_pdb=False - dimple_mtz=False - aimless_log=False - if os.path.isfile(os.path.join(files,'dimple.pdb')): - dimple_pdb=True - if os.path.isfile(os.path.join(files,'dimple.mtz')): - dimple_mtz=True - if os.path.isfile(os.path.join(files,xtal+'.log')) or os.path.isfile(os.path.join('aimless.log')): - aimless_log=True - - if dimple_mtz==False or dimple_pdb==False or aimless_log==False: - Logfile.insert('{0!s}: missing files -> dimple.pdb: {1!s}, dimple.mtz: {2!s}, {3!s}.log: {4!s}'.format(xtal, str(dimple_pdb), str(dimple_mtz), xtal, str(aimless_log))) + dimple_pdb = False + dimple_mtz = False + aimless_log = False + if os.path.isfile(os.path.join(files, 'dimple.pdb')): + dimple_pdb = True + if os.path.isfile(os.path.join(files, 'dimple.mtz')): + dimple_mtz = True + if os.path.isfile(os.path.join(files, xtal+'.log')) or os.path.isfile(os.path.join('aimless.log')): + aimless_log = True + + if dimple_mtz == False or dimple_pdb == False or aimless_log == False: + Logfile.insert('{0!s}: missing files -> dimple.pdb: {1!s}, dimple.mtz: {2!s}, {3!s}.log: {4!s}'.format( + xtal, str(dimple_pdb), str(dimple_mtz), xtal, str(aimless_log))) else: - newEntries+="('{0!s}','apo'),".format(xtal) - counter+=1 + newEntries += "('{0!s}','apo'),".format(xtal) + counter += 1 if counter == 450: # set to 450 to stay well below 500 records limit - sqlite='insert into depositTable (CrystalName,StructureType) values {0!s};'.format(newEntries[:-1]) - Logfile.insert('creating new entries with the following SQLite command:\n'+sqlite) + sqlite = 'insert into depositTable (CrystalName,StructureType) values {0!s};'.format( + newEntries[:-1]) + Logfile.insert( + 'creating new entries with the following SQLite command:\n'+sqlite) cursor.execute(sqlite) connect.commit() - counter=0 - newEntries='' + counter = 0 + newEntries = '' if newEntries != '': - sqlite='insert into depositTable (CrystalName,StructureType) values {0!s};'.format(newEntries[:-1]) - Logfile.insert('creating new entries with the following SQLite command:\n'+sqlite) + sqlite = 'insert into depositTable (CrystalName,StructureType) values {0!s};'.format( + newEntries[:-1]) + Logfile.insert( + 'creating new entries with the following SQLite command:\n'+sqlite) cursor.execute(sqlite) connect.commit() else: @@ -1650,71 +2122,85 @@ def create_missing_apo_records_for_all_structures_in_depositTable(self,projectDi # def get_deposit_dict_for_xtal(self,sampleID,structure_type): - def create_or_remove_missing_records_in_depositTable(self,xce_logfile,xtal,type,db_dict): - connect=sqlite3.connect(self.data_source_file) + def create_or_remove_missing_records_in_depositTable(self, xce_logfile, xtal, type, db_dict): + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - Logfile=XChemLog.updateLog(xce_logfile) + Logfile = XChemLog.updateLog(xce_logfile) oldRefiStage = '' if type == 'ligand_bound': - cursor.execute("select RefinementOutcome from mainTable where CrystalName is '{0!s}'".format(xtal)) + cursor.execute( + "select RefinementOutcome from mainTable where CrystalName is '{0!s}'".format(xtal)) tmp = cursor.fetchall() - oldRefiStage=str(tmp[0][0]) - Logfile.insert('setting RefinementOutcome field to "'+db_dict['RefinementOutcome']+'" for '+xtal) - self.update_insert_data_source(xtal,db_dict) + oldRefiStage = str(tmp[0][0]) + Logfile.insert('setting RefinementOutcome field to "' + + db_dict['RefinementOutcome']+'" for '+xtal) + self.update_insert_data_source(xtal, db_dict) elif type == 'ground_state': - cursor.execute("select DimplePANDDApath from depositTable where StructureType is '{0!s}' and DimplePANDDApath is '{1!s}'".format(type,db_dict['DimplePANDDApath'])) + cursor.execute("select DimplePANDDApath from depositTable where StructureType is '{0!s}' and DimplePANDDApath is '{1!s}'".format( + type, db_dict['DimplePANDDApath'])) tmp = cursor.fetchall() if not tmp: - Logfile.insert('entry for ground-state model in depositTable does not exist') + Logfile.insert( + 'entry for ground-state model in depositTable does not exist') else: - Logfile.warning('entry for ground-state model in depositTable does already exist') - Logfile.warning('updating PDB, MTZ and DimplePANDDApath for ground-state entry') - cursor.execute("update depositTable set PDB_file='%s', MTZ_file='%s', DimplePANDDApath='%s' where StructureType='ground_state'" %(db_dict['PDB_file'],db_dict['MTZ_file'],db_dict['DimplePANDDApath'])) + Logfile.warning( + 'entry for ground-state model in depositTable does already exist') + Logfile.warning( + 'updating PDB, MTZ and DimplePANDDApath for ground-state entry') + cursor.execute("update depositTable set PDB_file='%s', MTZ_file='%s', DimplePANDDApath='%s' where StructureType='ground_state'" % ( + db_dict['PDB_file'], db_dict['MTZ_file'], db_dict['DimplePANDDApath'])) connect.commit() return - cursor.execute("select CrystalName,StructureType from depositTable where CrystalName is '{0!s}' and StructureType is '{1!s}'".format(xtal, type)) + cursor.execute( + "select CrystalName,StructureType from depositTable where CrystalName is '{0!s}' and StructureType is '{1!s}'".format(xtal, type)) tmp = cursor.fetchall() if type == 'ligand_bound': if not tmp and int(db_dict['RefinementOutcome'].split()[0]) == 5: - sqlite="insert into depositTable (CrystalName,StructureType) values ('{0!s}','{1!s}');".format(xtal, type) - Logfile.insert('creating new entry for '+str(type)+' structure of '+xtal+' in depositTable') + sqlite = "insert into depositTable (CrystalName,StructureType) values ('{0!s}','{1!s}');".format( + xtal, type) + Logfile.insert('creating new entry for '+str(type) + + ' structure of '+xtal+' in depositTable') cursor.execute(sqlite) connect.commit() else: if int(db_dict['RefinementOutcome'].split()[0]) != 5: - sqlite="delete from depositTable where CrystalName is '{0!s}' and StructureType is '{1!s}'".format(xtal, type) + sqlite = "delete from depositTable where CrystalName is '{0!s}' and StructureType is '{1!s}'".format( + xtal, type) if oldRefiStage.startswith('5'): - Logfile.insert('removing entry for '+str(type)+' structure of '+xtal+' from depositTable') + Logfile.insert( + 'removing entry for '+str(type)+' structure of '+xtal+' from depositTable') cursor.execute(sqlite) connect.commit() elif type == 'ground_state': - sqlite = "insert into depositTable (CrystalName,StructureType,DimplePANDDApath,PDB_file,MTZ_file) values ('{0!s}','{1!s}','{2!s}','{3!s}','{4!s}');".format(xtal, type, db_dict['DimplePANDDApath'], db_dict['PDB_file'], db_dict['MTZ_file']) - Logfile.insert('creating new entry for ' + str(type) + ' structure of ' + xtal + ' in depositTable') + sqlite = "insert into depositTable (CrystalName,StructureType,DimplePANDDApath,PDB_file,MTZ_file) values ('{0!s}','{1!s}','{2!s}','{3!s}','{4!s}');".format( + xtal, type, db_dict['DimplePANDDApath'], db_dict['PDB_file'], db_dict['MTZ_file']) + Logfile.insert('creating new entry for ' + str(type) + + ' structure of ' + xtal + ' in depositTable') cursor.execute(sqlite) connect.commit() - def remove_selected_apo_structures_from_depositTable(self,xce_logfile,xtalList): - connect=sqlite3.connect(self.data_source_file) + def remove_selected_apo_structures_from_depositTable(self, xce_logfile, xtalList): + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - Logfile=XChemLog.updateLog(xce_logfile) + Logfile = XChemLog.updateLog(xce_logfile) - Logfile.insert('removing the following apo structures from depositTable') + Logfile.insert( + 'removing the following apo structures from depositTable') deleteStrg = "(" for xtal in xtalList: Logfile.insert(xtal) - deleteStrg+="Crystalname is '"+xtal+"' or " - deleteStrg=deleteStrg[:-4]+")" + deleteStrg += "Crystalname is '"+xtal+"' or " + deleteStrg = deleteStrg[:-4]+")" - sqlite="delete from depositTable where {0!s} and StructureType is 'apo'".format(deleteStrg) + sqlite = "delete from depositTable where {0!s} and StructureType is 'apo'".format( + deleteStrg) Logfile.insert('executing the following SQLite command:\n'+sqlite) cursor.execute(sqlite) connect.commit() - - # for item in tmp: # print item # for xtal in str(item[0]).split(';'): @@ -1741,54 +2227,61 @@ def remove_selected_apo_structures_from_depositTable(self,xce_logfile,xtalList): # connect.commit() # - def collected_xtals_during_visit(self,visitID): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + + def collected_xtals_during_visit(self, visitID): + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("select CrystalName from collectionTable where DataCollectionVisit = '{0!s}'".format(visitID)) - collectedXtals=[] + cursor.execute( + "select CrystalName from collectionTable where DataCollectionVisit = '{0!s}'".format(visitID)) + collectedXtals = [] samples = cursor.fetchall() for sample in samples: if str(sample[0]) not in collectedXtals: collectedXtals.append(str(sample[0])) return collectedXtals - def collected_xtals_during_visit_for_scoring(self,visit): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def collected_xtals_during_visit_for_scoring(self, visit): + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() xtalList = [] # if rescore == True: # cursor.execute("select CrystalName from mainTable where DataCollectionVisit = '%s'" %visit) # else: # cursor.execute("select CrystalName from mainTable where DataProcessingAutoAssigned = 'True' and DataCollectionVisit = '%s'" %visit) - cursor.execute("select distinct CrystalName from collectionTable where DataCollectionVisit = '%s'" %visit) + cursor.execute( + "select distinct CrystalName from collectionTable where DataCollectionVisit = '%s'" % visit) samples = cursor.fetchall() for sample in samples: if str(sample[0]) not in xtalList: xtalList.append(str(sample[0])) return xtalList - def autoprocessing_result_user_assigned(self,sample): + def autoprocessing_result_user_assigned(self, sample): userassigned = False - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("select DataProcessingAutoAssigned from mainTable where CrystalName = '%s'" %sample) + cursor.execute( + "select DataProcessingAutoAssigned from mainTable where CrystalName = '%s'" % sample) outcome = cursor.fetchall() try: if 'false' in str(outcome[0]).lower() or str(outcome[0]).encode('ascii', 'ignore') == '': userassigned = True # a bit counterintuitive, but here we ask about userassigned - # whereas DB records autoassigned + # whereas DB records autoassigned except IndexError: pass # this is the case when sample is encountered the first time - # and not yet in mainTable + # and not yet in mainTable return userassigned - - def all_results_of_xtals_collected_during_visit_as_dict(self,visitID): + def all_results_of_xtals_collected_during_visit_as_dict(self, visitID): # first get all collected xtals as list collectedXtals = self.collected_xtals_during_visit(visitID) xtalDict = {} - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() for xtal in sorted(collectedXtals): if xtal not in xtalDict: @@ -1810,8 +2303,9 @@ def all_results_of_xtals_collected_during_visit_as_dict(self,visitID): sq = cursor.fetchall() # print sq for s in sq: -# print s - t=[str(s[0]),str(s[1]),str(s[2]),str(s[3]),str(s[4]),str(s[5]),str(s[6]),str(s[7]),str(s[8]),str(s[9])] + # print s + t = [str(s[0]), str(s[1]), str(s[2]), str(s[3]), str(s[4]), str( + s[5]), str(s[6]), str(s[7]), str(s[8]), str(s[9])] inDict = False for entry in xtalDict[xtal]: if t[0] == entry[0] and t[1] == entry[1] and t[2] == entry[2]: @@ -1821,49 +2315,54 @@ def all_results_of_xtals_collected_during_visit_as_dict(self,visitID): xtalDict[xtal].append(t) return xtalDict - def all_autoprocessing_results_for_xtal_as_dict(self,xtal): + def all_autoprocessing_results_for_xtal_as_dict(self, xtal): dbList = [] - header=[] - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + header = [] + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("select * from collectionTable where CrystalName='{0!s}';".format(xtal)) + cursor.execute( + "select * from collectionTable where CrystalName='{0!s}';".format(xtal)) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() for result in data: db_dict = {} - for n,item in enumerate(result): - db_dict[header[n]]=str(item) + for n, item in enumerate(result): + db_dict[header[n]] = str(item) dbList.append(db_dict) return dbList - def get_db_list_for_sample_in_panddaTable(self,xtal): + def get_db_list_for_sample_in_panddaTable(self, xtal): dbList = [] - header=[] - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + header = [] + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("select * from panddaTable where CrystalName='{0!s}';".format(xtal)) + cursor.execute( + "select * from panddaTable where CrystalName='{0!s}';".format(xtal)) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() for result in data: db_dict = {} - for n,item in enumerate(result): - db_dict[header[n]]=str(item) + for n, item in enumerate(result): + db_dict[header[n]] = str(item) dbList.append(db_dict) return dbList - def get_db_dict_for_visit_run_autoproc(self,xtal,visit,run,autoproc): + def get_db_dict_for_visit_run_autoproc(self, xtal, visit, run, autoproc): db_dict = {} - header=[] - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + header = [] + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - sqlite = ( 'select * ' - 'from collectionTable ' - "where CrystalName ='%s' and" %xtal + - " DataCollectionVisit = '%s' and" %visit + - " DataCollectionRun = '%s' and" %run + - " DataProcessingProgram = '%s'" %autoproc ) + sqlite = ('select * ' + 'from collectionTable ' + "where CrystalName ='%s' and" % xtal + + " DataCollectionVisit = '%s' and" % visit + + " DataCollectionRun = '%s' and" % run + + " DataProcessingProgram = '%s'" % autoproc) cursor.execute(sqlite) for column in cursor.description: header.append(column[0]) @@ -1872,18 +2371,19 @@ def get_db_dict_for_visit_run_autoproc(self,xtal,visit,run,autoproc): db_dict[header[n]] = str(item) return db_dict - def get_db_dict_for_visit_run_autoproc_score(self,xtal,visit,run,autoproc,score): + def get_db_dict_for_visit_run_autoproc_score(self, xtal, visit, run, autoproc, score): db_dict = {} - header=[] - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + header = [] + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - sqlite = ( 'select * ' - 'from collectionTable ' - "where CrystalName ='%s' and" %xtal + - " DataCollectionVisit = '%s' and" %visit + - " DataCollectionRun = '%s' and" %run + - " DataProcessingProgram = '%s' and" %autoproc + - " DataProcessingScore = '%s'" %score ) + sqlite = ('select * ' + 'from collectionTable ' + "where CrystalName ='%s' and" % xtal + + " DataCollectionVisit = '%s' and" % visit + + " DataCollectionRun = '%s' and" % run + + " DataProcessingProgram = '%s' and" % autoproc + + " DataProcessingScore = '%s'" % score) cursor.execute(sqlite) for column in cursor.description: header.append(column[0]) @@ -1894,9 +2394,9 @@ def get_db_dict_for_visit_run_autoproc_score(self,xtal,visit,run,autoproc,score) db_dict[header[n]] = str(item) return db_dict - def xtals_collected_during_visit_as_dict(self,visitID): + def xtals_collected_during_visit_as_dict(self, visitID): # first get all collected xtals as list - if isinstance(visitID,list): # for Agamemnon data structure + if isinstance(visitID, list): # for Agamemnon data structure collectedXtals = [] for visit in visitID: x = self.collected_xtals_during_visit(visit) @@ -1905,54 +2405,59 @@ def xtals_collected_during_visit_as_dict(self,visitID): else: collectedXtals = self.collected_xtals_during_visit(visitID) xtalDict = {} - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() for xtal in sorted(collectedXtals): db_dict = self.get_db_dict_for_sample(xtal) xtalDict[xtal] = db_dict return xtalDict - - - def getCrystalImageDict(self,visit,xtalList): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def getCrystalImageDict(self, visit, xtalList): + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() imageDict = {} for xtal in xtalList: - sqlite = ( "select CrystalName," - " min(DataCollectionDate)," - " DataCollectionCrystalImage1," - " DataCollectionCrystalImage2," - " DataCollectionCrystalImage3," - " DataCollectionCrystalImage4 " - "from collectionTable " - "where DataCollectionVisit = '%s'" %visit+ - " and CrystalName = '%s'" % xtal ) + sqlite = ("select CrystalName," + " min(DataCollectionDate)," + " DataCollectionCrystalImage1," + " DataCollectionCrystalImage2," + " DataCollectionCrystalImage3," + " DataCollectionCrystalImage4 " + "from collectionTable " + "where DataCollectionVisit = '%s'" % visit + + " and CrystalName = '%s'" % xtal) cursor.execute(sqlite) img = cursor.fetchall() - imageDict[xtal]=[str(img[1]),str(img[2]),str(img[3]),str(img[4])] + imageDict[xtal] = [str(img[1]), str( + img[2]), str(img[3]), str(img[4])] return imageDict - def samples_for_html_summary(self,whichSamples): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def samples_for_html_summary(self, whichSamples): + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() if whichSamples.startswith('4'): - cursor.execute("select CrystalName from mainTable where RefinementOutcome like '4%' order by CrystalName ASC") + cursor.execute( + "select CrystalName from mainTable where RefinementOutcome like '4%' order by CrystalName ASC") elif whichSamples.startswith('5'): - cursor.execute("select CrystalName from mainTable where RefinementOutcome like '5%' order by CrystalName ASC") + cursor.execute( + "select CrystalName from mainTable where RefinementOutcome like '5%' order by CrystalName ASC") else: cursor.execute("select CrystalName from mainTable where RefinementOutcome like '4%' or " - "RefinementOutcome like '5%' or " - "RefinementOutcome like '6%' order by CrystalName ASC") - xtalList=[] + "RefinementOutcome like '5%' or " + "RefinementOutcome like '6%' order by CrystalName ASC") + xtalList = [] samples = cursor.fetchall() for sample in samples: if str(sample[0]) not in xtalList: xtalList.append(str(sample[0])) return xtalList - def get_event_map_for_ligand(self,xtal,ligChain,ligNumber,ligName): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def get_event_map_for_ligand(self, xtal, ligChain, ligNumber, ligName): + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() sql = ( @@ -1961,10 +2466,10 @@ def get_event_map_for_ligand(self,xtal,ligChain,ligNumber,ligName): 'from ' ' panddaTable ' 'where ' - " CrystalName = '%s' and " %xtal + - " PANDDA_site_ligand_chain='%s' and " %ligChain + - " PANDDA_site_ligand_sequence_number='%s' and " %ligNumber + - " PANDDA_site_ligand_resname='%s'" %ligName + " CrystalName = '%s' and " % xtal + + " PANDDA_site_ligand_chain='%s' and " % ligChain + + " PANDDA_site_ligand_sequence_number='%s' and " % ligNumber + + " PANDDA_site_ligand_resname='%s'" % ligName ) cursor.execute(sql) @@ -1976,8 +2481,9 @@ def get_event_map_for_ligand(self,xtal,ligChain,ligNumber,ligName): return eventMap - def get_ligand_confidence_for_ligand(self,xtal,ligChain,ligNumber,ligName): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def get_ligand_confidence_for_ligand(self, xtal, ligChain, ligNumber, ligName): + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() sql = ( @@ -1986,10 +2492,10 @@ def get_ligand_confidence_for_ligand(self,xtal,ligChain,ligNumber,ligName): 'from ' ' panddaTable ' 'where ' - " CrystalName = '%s' and " %xtal + - " PANDDA_site_ligand_chain='%s' and " %ligChain + - " PANDDA_site_ligand_sequence_number='%s' and " %ligNumber + - " PANDDA_site_ligand_resname='%s'" %ligName + " CrystalName = '%s' and " % xtal + + " PANDDA_site_ligand_chain='%s' and " % ligChain + + " PANDDA_site_ligand_sequence_number='%s' and " % ligNumber + + " PANDDA_site_ligand_resname='%s'" % ligName ) cursor.execute(sql) @@ -2002,7 +2508,8 @@ def get_ligand_confidence_for_ligand(self,xtal,ligChain,ligNumber,ligName): return ligConfidence def get_labels_from_db(self): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute('select Label from labelTable') labels = cursor.fetchall() @@ -2012,19 +2519,22 @@ def get_labels_from_db(self): return labelList def get_label_info_from_db(self): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute('select Label,Description from labelTable') labels = cursor.fetchall() labelList = [] for l in labels: - labelList.append([str(l[0]),str(l[1])]) + labelList.append([str(l[0]), str(l[1])]) return labelList - def get_label_of_sample(self,xtalID): - connect=sqlite3.connect(self.data_source_file) # creates sqlite file if non existent + def get_label_of_sample(self, xtalID): + # creates sqlite file if non existent + connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("select label from mainTable where CrystalName is '%s'" %xtalID) + cursor.execute( + "select label from mainTable where CrystalName is '%s'" % xtalID) label = None lab = cursor.fetchall() for l in lab: diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 9258a0fd..34fcb5e0 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -1,5 +1,13 @@ # last edited: 16/05/2017, 15:00 +from XChemUtils import parse +from XChemUtils import smilestools +from XChemUtils import mtztools +from XChemUtils import pdbtools +import XChemMain +import XChemToolTips +import XChemDB +import XChemLog import sys import fileinput import os @@ -10,21 +18,16 @@ from lxml import etree sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') -import XChemLog -import XChemDB -import XChemToolTips -import XChemMain -from XChemUtils import pdbtools -from XChemUtils import mtztools -from XChemUtils import smilestools -from XChemUtils import parse -def create_SF_mmcif(outDir,mtzList): + +def create_SF_mmcif(outDir, mtzList): print 'hallo' -def get_protein_sequence(database,xtalID): + +def get_protein_sequence(database, xtalID): print 'hallo' + def check_depositDict(depositDict): # check depositDict for entry in depositDict: @@ -35,18 +38,21 @@ def check_depositDict(depositDict): elif depositDict[entry] == '': print 'ERROR' + def update_title(depositDict): print 'hallo' + def create_data_template_text(): - data_template_text=data_template(depositDict,sequence) + data_template_text = data_template(depositDict, sequence) -def create_Model_mmcif(outDir,pdbList): + +def create_Model_mmcif(outDir, pdbList): print 'hallo' -#def update_file_locations_of_apo_structuresin_DB(database,projectDir,xce_logfile): +# def update_file_locations_of_apo_structuresin_DB(database,projectDir,xce_logfile): # Logfile=XChemLog.updateLog(xce_logfile) # Logfile.insert('updating file information for apo structures') # db=XChemDB.data_source(database) @@ -64,97 +70,52 @@ def create_Model_mmcif(outDir,pdbList): # db.update_depositTable(xtal,'apo',db_dict) - class templates: - def data_template_cif(self,depositDict): + def data_template_cif(self, depositDict): - taxonomy_dict=XChemMain.NCBI_taxonomy_ID() + taxonomy_dict = XChemMain.NCBI_taxonomy_ID() for key in taxonomy_dict: - if taxonomy_dict[key]==depositDict['Source_organism_scientific_name']: - pdbx_gene_src_ncbi_taxonomy_id=key - if taxonomy_dict[key]==depositDict['Expression_system_scientific_name']: - pdbx_host_org_ncbi_taxonomy_id=key + if taxonomy_dict[key] == depositDict['Source_organism_scientific_name']: + pdbx_gene_src_ncbi_taxonomy_id = key + if taxonomy_dict[key] == depositDict['Expression_system_scientific_name']: + pdbx_host_org_ncbi_taxonomy_id = key # structure_author_name='' # for name in depositDict['structure_author_name'].split(';'): # structure_author_name+='\n' %name - audit_author_name='' + audit_author_name = '' # one name must be within quotation, last name and first initial must be separated by comma and space for name in depositDict['structure_author_name'].split(';'): - if name.replace(' ','') == '': + if name.replace(' ', '') == '': continue if name[name.find(',')+1:name.find(',')+2] != ' ': - name=name.replace(',',', ') - audit_author_name+="'{0!s}'\n".format(name) + name = name.replace(',', ', ') + audit_author_name += "'{0!s}'\n".format(name) - primary_citation_author_name='' + primary_citation_author_name = '' # one name must be within quotation, last name and first initial must be separated by comma and space for name in depositDict['primary_citation_author_name'].split(';'): - if name.replace(' ','') == '': + if name.replace(' ', '') == '': continue if name[name.find(',')+1:name.find(',')+2] != ' ': - name=name.replace(',',', ') - primary_citation_author_name+="primary '{0!s}'\n".format(name) + name = name.replace(',', ', ') + primary_citation_author_name += "primary '{0!s}'\n".format(name) - molecule_one_letter_sequence=';' - counter=1 + molecule_one_letter_sequence = ';' + counter = 1 for aa in depositDict['molecule_one_letter_sequence']: if counter < 70: - molecule_one_letter_sequence+=aa + molecule_one_letter_sequence += aa if counter == 70: - molecule_one_letter_sequence+='\n'+aa + molecule_one_letter_sequence += '\n'+aa counter = 0 - counter+=1 + counter += 1 - if depositDict['molecule_name_two'].replace(' ','') == '' or depositDict['molecule_name_two'].replace(' ','').lower() == 'none': + if depositDict['molecule_name_two'].replace(' ', '') == '' or depositDict['molecule_name_two'].replace(' ', '').lower() == 'none': try: entity = ( - 'loop_\n' - '_entity.id\n' - '_entity.type\n' - '_entity.src_method\n' - '_entity.pdbx_description\n' - '_entity.pdbx_mutation\n' - '1 polymer man "%s" %s\n' % (depositDict['Source_organism_gene'], depositDict['fragment_name_one_specific_mutation']) + - '#\n' - 'loop_\n' - '_entity_poly.entity_id\n' - '_entity_poly.type\n' - '_entity_poly.pdbx_seq_one_letter_code\n' - '_entity_poly.pdbx_strand_id\n' - '_entity_poly.pdbx_seq_db_id\n' - '_entity_poly.pdbx_seq_db_name\n' - '1 "polypeptide(L)"\n' - + molecule_one_letter_sequence + '\n' - ';\n' - '%s %s UNP\n' %(depositDict['protein_chains'],depositDict['molecule_one_letter_sequence_uniprot_id'])+ - '#\n' - 'loop_\n' - '_entity_src_gen.entity_id\n' - '_entity_src_gen.gene_src_strain\n' - '_entity_src_gen.pdbx_gene_src_scientific_name\n' - '_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id\n' - '_entity_src_gen.pdbx_host_org_scientific_name\n' - '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n' - '1 ? "%s" %s "%s" %s\n' % (depositDict['Source_organism_scientific_name'], pdbx_gene_src_ncbi_taxonomy_id,depositDict['Expression_system_scientific_name'], pdbx_host_org_ncbi_taxonomy_id) + - '#\n' - ) - except UnboundLocalError: - print 'Error: Something went wrong! Please check if you have saved the .deposit file to the database: Menu Deposition -> Edit Information' - else: - molecule_two_letter_sequence=';' - counter=1 - for aa in depositDict['molecule_two_letter_sequence']: - if counter < 70: - molecule_two_letter_sequence+=aa - if counter == 70: - molecule_two_letter_sequence+='\n'+aa - counter = 0 - counter+=1 - - entity = ( 'loop_\n' '_entity.id\n' '_entity.type\n' @@ -162,7 +123,6 @@ def data_template_cif(self,depositDict): '_entity.pdbx_description\n' '_entity.pdbx_mutation\n' '1 polymer man "%s" %s\n' % (depositDict['Source_organism_gene'], depositDict['fragment_name_one_specific_mutation']) + - '2 polymer man "%s" %s\n' % (depositDict['Source_organism_gene_two'], depositDict['fragment_name_two_specific_mutation']) + '#\n' 'loop_\n' '_entity_poly.entity_id\n' @@ -174,12 +134,7 @@ def data_template_cif(self,depositDict): '1 "polypeptide(L)"\n' + molecule_one_letter_sequence + '\n' ';\n' - '%s %s UNP\n' %(depositDict['molecule_chain_one'],depositDict['molecule_one_letter_sequence_uniprot_id'])+ -# ';\n' - '2 "polypeptide(L)"\n' - + molecule_two_letter_sequence + '\n' - ';\n' - '%s %s UNP\n' %(depositDict['molecule_chain_two'],depositDict['molecule_two_letter_sequence_uniprot_id'])+ + '%s %s UNP\n' % (depositDict['protein_chains'], depositDict['molecule_one_letter_sequence_uniprot_id']) + '#\n' 'loop_\n' '_entity_src_gen.entity_id\n' @@ -188,42 +143,91 @@ def data_template_cif(self,depositDict): '_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id\n' '_entity_src_gen.pdbx_host_org_scientific_name\n' '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n' - '1 ? "%s" %s "%s" %s\n' % (depositDict['Source_organism_scientific_name'], pdbx_gene_src_ncbi_taxonomy_id,depositDict['Expression_system_scientific_name'], pdbx_host_org_ncbi_taxonomy_id) + - '2 ? "%s" %s "%s" %s\n' % (depositDict['Source_organism_scientific_name'], pdbx_gene_src_ncbi_taxonomy_id,depositDict['Expression_system_scientific_name'], pdbx_host_org_ncbi_taxonomy_id) + + '1 ? "%s" %s "%s" %s\n' % (depositDict['Source_organism_scientific_name'], pdbx_gene_src_ncbi_taxonomy_id, depositDict['Expression_system_scientific_name'], pdbx_host_org_ncbi_taxonomy_id) + '#\n' - ) + ) + except UnboundLocalError: + print 'Error: Something went wrong! Please check if you have saved the .deposit file to the database: Menu Deposition -> Edit Information' + else: + molecule_two_letter_sequence = ';' + counter = 1 + for aa in depositDict['molecule_two_letter_sequence']: + if counter < 70: + molecule_two_letter_sequence += aa + if counter == 70: + molecule_two_letter_sequence += '\n'+aa + counter = 0 + counter += 1 + entity = ( + 'loop_\n' + '_entity.id\n' + '_entity.type\n' + '_entity.src_method\n' + '_entity.pdbx_description\n' + '_entity.pdbx_mutation\n' + '1 polymer man "%s" %s\n' % (depositDict['Source_organism_gene'], depositDict['fragment_name_one_specific_mutation']) + + '2 polymer man "%s" %s\n' % (depositDict['Source_organism_gene_two'], depositDict['fragment_name_two_specific_mutation']) + + '#\n' + 'loop_\n' + '_entity_poly.entity_id\n' + '_entity_poly.type\n' + '_entity_poly.pdbx_seq_one_letter_code\n' + '_entity_poly.pdbx_strand_id\n' + '_entity_poly.pdbx_seq_db_id\n' + '_entity_poly.pdbx_seq_db_name\n' + '1 "polypeptide(L)"\n' + + molecule_one_letter_sequence + '\n' + ';\n' + '%s %s UNP\n' % (depositDict['molecule_chain_one'], depositDict['molecule_one_letter_sequence_uniprot_id']) + + # ';\n' + '2 "polypeptide(L)"\n' + + molecule_two_letter_sequence + '\n' + ';\n' + '%s %s UNP\n' % (depositDict['molecule_chain_two'], depositDict['molecule_two_letter_sequence_uniprot_id']) + + '#\n' + 'loop_\n' + '_entity_src_gen.entity_id\n' + '_entity_src_gen.gene_src_strain\n' + '_entity_src_gen.pdbx_gene_src_scientific_name\n' + '_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id\n' + '_entity_src_gen.pdbx_host_org_scientific_name\n' + '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n' + '1 ? "%s" %s "%s" %s\n' % (depositDict['Source_organism_scientific_name'], pdbx_gene_src_ncbi_taxonomy_id, depositDict['Expression_system_scientific_name'], pdbx_host_org_ncbi_taxonomy_id) + + '2 ? "%s" %s "%s" %s\n' % (depositDict['Source_organism_scientific_name'], pdbx_gene_src_ncbi_taxonomy_id, depositDict['Expression_system_scientific_name'], pdbx_host_org_ncbi_taxonomy_id) + + '#\n' + ) data_template_cif = ( 'data_UNNAMED\n' '#\n' '_pdbx_database_status.entry_id UNNAMED\n' - "_pdbx_database_status.dep_release_code_coordinates '%s'\n" %depositDict['Release_status_for_coordinates']+ - "_pdbx_database_status.dep_release_code_sequence '{0!s}'\n".format(depositDict['Release_status_for_sequence'])+ + "_pdbx_database_status.dep_release_code_coordinates '%s'\n" % depositDict['Release_status_for_coordinates'] + + "_pdbx_database_status.dep_release_code_sequence '{0!s}'\n".format(depositDict['Release_status_for_sequence']) + '#\n' '_pdbx_deposit_group.group_id UNNAMED\n' - '_pdbx_deposit_group.group_description "%s"\n' %depositDict['group_description']+ - '_pdbx_deposit_group.group_title "{0!s}"\n'.format(depositDict['group_title'])+ - '_pdbx_deposit_group.group_type "{0!s}"\n'.format(depositDict['group_type'])+ + '_pdbx_deposit_group.group_description "%s"\n' % depositDict['group_description'] + + '_pdbx_deposit_group.group_title "{0!s}"\n'.format(depositDict['group_title']) + + '_pdbx_deposit_group.group_type "{0!s}"\n'.format(depositDict['group_type']) + '#\n' '_exptl_crystal_grow.crystal_id 1\n' - "_exptl_crystal_grow.method '%s'\n" %depositDict['crystallization_method']+ - '_exptl_crystal_grow.pH {0!s}\n'.format(depositDict['crystallization_pH'])+ - '_exptl_crystal_grow.temp {0!s}\n'.format(depositDict['crystallization_temperature'])+ - '_exptl_crystal_grow.pdbx_details "{0!s}"\n'.format(depositDict['crystallization_details'])+ + "_exptl_crystal_grow.method '%s'\n" % depositDict['crystallization_method'] + + '_exptl_crystal_grow.pH {0!s}\n'.format(depositDict['crystallization_pH']) + + '_exptl_crystal_grow.temp {0!s}\n'.format(depositDict['crystallization_temperature']) + + '_exptl_crystal_grow.pdbx_details "{0!s}"\n'.format(depositDict['crystallization_details']) + '#\n' '_diffrn.id 1\n' - '_diffrn.ambient_temp %s\n' %depositDict['data_collection_temperature']+ + '_diffrn.ambient_temp %s\n' % depositDict['data_collection_temperature'] + '_diffrn.crystal_id 1\n' '#\n' '_diffrn_source.diffrn_id 1\n' - '_diffrn_source.source %s\n' %depositDict['radiation_source']+ - '_diffrn_source.type "{0!s}"\n'.format(depositDict['radiation_source_type'])+ - '_diffrn_source.pdbx_wavelength_list {0!s}\n'.format(depositDict['radiation_wavelengths'])+ + '_diffrn_source.source %s\n' % depositDict['radiation_source'] + + '_diffrn_source.type "{0!s}"\n'.format(depositDict['radiation_source_type']) + + '_diffrn_source.pdbx_wavelength_list {0!s}\n'.format(depositDict['radiation_wavelengths']) + '#\n' - '_diffrn_detector.detector %s\n' %depositDict['radiation_detector']+ - "_diffrn_detector.type '{0!s}'\n".format(depositDict['radiation_detector_type'])+ - '_diffrn_detector.pdbx_collection_date {0!s}\n'.format(depositDict['data_collection_date'])+ + '_diffrn_detector.detector %s\n' % depositDict['radiation_detector'] + + "_diffrn_detector.type '{0!s}'\n".format(depositDict['radiation_detector_type']) + + '_diffrn_detector.pdbx_collection_date {0!s}\n'.format(depositDict['data_collection_date']) + '_diffrn_detector.diffrn_id 1\n' '#\n' '_diffrn_radiation.diffrn_id 1\n' @@ -231,39 +235,39 @@ def data_template_cif(self,depositDict): "_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'\n" '#\n' '_diffrn_radiation_wavelength.id 1\n' - '_diffrn_radiation_wavelength.wavelength %s\n' %depositDict['radiation_wavelengths']+ + '_diffrn_radiation_wavelength.wavelength %s\n' % depositDict['radiation_wavelengths'] + '#\n' '#\n' + entity + -# 'loop_\n' -# '_entity.id\n' -# '_entity.type\n' -# '_entity.src_method\n' -# '_entity.pdbx_description\n' -# '_entity.pdbx_mutation\n' -# '1 polymer man "%s" %s\n' %(depositDict['Source_organism_gene'],depositDict['fragment_name_one_specific_mutation'])+ -# '#\n' -# 'loop_\n' -# '_entity_poly.entity_id\n' -# '_entity_poly.type\n' -# '_entity_poly.pdbx_seq_one_letter_code\n' -# '_entity_poly.pdbx_strand_id\n' -# '_entity_poly.pdbx_seq_db_id\n' -# '_entity_poly.pdbx_seq_db_name\n' -# '1 "polypeptide(L)"\n' -# +molecule_one_letter_sequence+'\n' -# ';\n' -# '%s %s UNP\n' %(depositDict['protein_chains'],depositDict['molecule_one_letter_sequence_uniprot_id'])+ -# '#\n' -# 'loop_\n' -# '_entity_src_gen.entity_id\n' -# '_entity_src_gen.gene_src_strain\n' -# '_entity_src_gen.pdbx_gene_src_scientific_name\n' -# '_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id\n' -# '_entity_src_gen.pdbx_host_org_scientific_name\n' -# '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n' -# '1 ? "%s" %s "%s" %s\n' %(depositDict['Source_organism_scientific_name'],pdbx_gene_src_ncbi_taxonomy_id,depositDict['Expression_system_scientific_name'],pdbx_host_org_ncbi_taxonomy_id)+ -# '#\n' + # 'loop_\n' + # '_entity.id\n' + # '_entity.type\n' + # '_entity.src_method\n' + # '_entity.pdbx_description\n' + # '_entity.pdbx_mutation\n' + # '1 polymer man "%s" %s\n' %(depositDict['Source_organism_gene'],depositDict['fragment_name_one_specific_mutation'])+ + # '#\n' + # 'loop_\n' + # '_entity_poly.entity_id\n' + # '_entity_poly.type\n' + # '_entity_poly.pdbx_seq_one_letter_code\n' + # '_entity_poly.pdbx_strand_id\n' + # '_entity_poly.pdbx_seq_db_id\n' + # '_entity_poly.pdbx_seq_db_name\n' + # '1 "polypeptide(L)"\n' + # +molecule_one_letter_sequence+'\n' + # ';\n' + # '%s %s UNP\n' %(depositDict['protein_chains'],depositDict['molecule_one_letter_sequence_uniprot_id'])+ + # '#\n' + # 'loop_\n' + # '_entity_src_gen.entity_id\n' + # '_entity_src_gen.gene_src_strain\n' + # '_entity_src_gen.pdbx_gene_src_scientific_name\n' + # '_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id\n' + # '_entity_src_gen.pdbx_host_org_scientific_name\n' + # '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n' + # '1 ? "%s" %s "%s" %s\n' %(depositDict['Source_organism_scientific_name'],pdbx_gene_src_ncbi_taxonomy_id,depositDict['Expression_system_scientific_name'],pdbx_host_org_ncbi_taxonomy_id)+ + # '#\n' 'loop_\n' '_pdbx_contact_author.id \n' "_pdbx_contact_author.address_1 \n" @@ -279,111 +283,114 @@ def data_template_cif(self,depositDict): '_pdbx_contact_author.role \n' '_pdbx_contact_author.organization_type \n' '_pdbx_contact_author.identifier_ORCID \n' - "1 '%s' '%s' '%s' '?' '%s' %s %s '%s' '%s' '%s' '%s' %s %s\n" %(depositDict['contact_author_PI_address'],depositDict['contact_author_PI_organization_name'],depositDict['contact_author_PI_city'],depositDict['contact_author_PI_Zip_Code'],depositDict['contact_author_PI_email'],depositDict['contact_author_PI_first_name'],depositDict['contact_author_PI_last_name'],depositDict['contact_author_PI_Country'],depositDict['contact_author_PI_phone_number'],depositDict['contact_author_PI_role'],depositDict['contact_author_PI_organization_type'],depositDict['contact_author_PI_ORCID'])+ - "2 '{0!s}' '{1!s}' '{2!s}' '?' '{3!s}' '{4!s}' {5!s} {6!s} '{7!s}' '{8!s}' '{9!s}' '{10!s}' {11!s}\n".format(depositDict['contact_author_address'], depositDict['contact_author_organization_name'], depositDict['contact_author_city'], depositDict['contact_author_Zip_Code'].replace(' ',''), depositDict['contact_author_email'], depositDict['contact_author_first_name'], depositDict['contact_author_last_name'], depositDict['contact_author_Country'], depositDict['contact_author_phone_number'], depositDict['contact_author_role'], depositDict['contact_author_organization_type'],depositDict['contact_author_ORCID'])+ + "1 '%s' '%s' '%s' '?' '%s' %s %s '%s' '%s' '%s' '%s' %s %s\n" % (depositDict['contact_author_PI_address'], depositDict['contact_author_PI_organization_name'], depositDict['contact_author_PI_city'], depositDict['contact_author_PI_Zip_Code'], depositDict['contact_author_PI_email'], depositDict['contact_author_PI_first_name'], depositDict['contact_author_PI_last_name'], depositDict['contact_author_PI_Country'], depositDict['contact_author_PI_phone_number'], depositDict['contact_author_PI_role'], depositDict['contact_author_PI_organization_type'], depositDict['contact_author_PI_ORCID']) + + "2 '{0!s}' '{1!s}' '{2!s}' '?' '{3!s}' '{4!s}' {5!s} {6!s} '{7!s}' '{8!s}' '{9!s}' '{10!s}' {11!s}\n".format(depositDict['contact_author_address'], depositDict['contact_author_organization_name'], depositDict['contact_author_city'], depositDict['contact_author_Zip_Code'].replace(' ', ''), depositDict['contact_author_email'], depositDict['contact_author_first_name'], depositDict['contact_author_last_name'], depositDict['contact_author_Country'], depositDict['contact_author_phone_number'], depositDict['contact_author_role'], depositDict['contact_author_organization_type'], depositDict['contact_author_ORCID']) + '#\n' 'loop_\n' '_audit_author.name\n' - +audit_author_name+ -# "'%s, %s.'\n" %(depositDict['contact_author_last_name'],depositDict['contact_author_first_name'][0])+ + + audit_author_name + + # "'%s, %s.'\n" %(depositDict['contact_author_last_name'],depositDict['contact_author_first_name'][0])+ '#\n' '_citation.id primary\n' - "_citation.title '%s'\n" %depositDict['group_title']+ + "_citation.title '%s'\n" % depositDict['group_title'] + "_citation.journal_abbrev 'To Be Published'\n" '#\n' 'loop_\n' '_citation_author.citation_id\n' '_citation_author.name\n' - +primary_citation_author_name+ -# "primary 'Krojer, T.'\n" -# "primary 'Von Delft, F.'\n" + + primary_citation_author_name + + # "primary 'Krojer, T.'\n" + # "primary 'Von Delft, F.'\n" '#\n' '_struct.entry_id UNNAMED\n' '_struct.title\n' - ';%s\n' %depositDict['title']+ + ';%s\n' % depositDict['title'] + ';\n' '#\n' '_struct_keywords.entry_id UNNAMED\n' - '_struct_keywords.text "%s"\n' %depositDict['structure_keywords']+ + '_struct_keywords.text "%s"\n' % depositDict['structure_keywords'] + '#\n' '_pdbx_struct_assembly_depositor_info.id 1\n' "_pdbx_struct_assembly_depositor_info.method_details PISA\n" - '_pdbx_struct_assembly_depositor_info.oligomeric_count %s\n' %depositDict['biological_assembly_chain_number']+ - '#\n' - ) + '_pdbx_struct_assembly_depositor_info.oligomeric_count %s\n' % depositDict['biological_assembly_chain_number'] + + '#\n' + ) return data_template_cif - class update_depositTable(QtCore.QThread): - def __init__(self,deposit_dict,database,xce_logfile): + def __init__(self, deposit_dict, database, xce_logfile): QtCore.QThread.__init__(self) - self.deposit_dict=deposit_dict - self.database=database - self.Logfile=XChemLog.updateLog(xce_logfile) - self.db=XChemDB.data_source(database) + self.deposit_dict = deposit_dict + self.database = database + self.Logfile = XChemLog.updateLog(xce_logfile) + self.db = XChemDB.data_source(database) def run(self): - self.Logfile.insert('all entries in the depositTable will be updated with the following values:') + self.Logfile.insert( + 'all entries in the depositTable will be updated with the following values:') for key in self.deposit_dict: self.Logfile.insert(key+': '+self.deposit_dict[key]) - dbEntries=self.db.execute_statement("select CrystalName,StructureType from depositTable;") + dbEntries = self.db.execute_statement( + "select CrystalName,StructureType from depositTable;") for item in dbEntries: - xtal=str(item[0]) - type=str(item[1]) - db_dict=self.deposit_dict # need to do this because individual fields might need updating for some xtals + xtal = str(item[0]) + type = str(item[1]) + # need to do this because individual fields might need updating for some xtals + db_dict = self.deposit_dict # try to get information about the diffraction experiment try: - diffractionExperiment=self.db.execute_statement("select DataCollectionBeamline,DataCollectionDate from mainTable where CrystalName is '{0!s}'".format(xtal)) - beamline=str(diffractionExperiment[0][0]) - date=str(diffractionExperiment[0][1]) - except (UnboundLocalError,IndexError): - self.Logfile.warning('%s: cannot find details about diffraction experiment in mainTable' %xtal) + diffractionExperiment = self.db.execute_statement( + "select DataCollectionBeamline,DataCollectionDate from mainTable where CrystalName is '{0!s}'".format(xtal)) + beamline = str(diffractionExperiment[0][0]) + date = str(diffractionExperiment[0][1]) + except (UnboundLocalError, IndexError): + self.Logfile.warning( + '%s: cannot find details about diffraction experiment in mainTable' % xtal) beamline = db_dict['radiation_source'] date = db_dict['data_collection_date'] - self.Logfile.warning('%s: using values provided in depositTable for beamline and data collection date' %xtal) + self.Logfile.warning( + '%s: using values provided in depositTable for beamline and data collection date' % xtal) if beamline.lower() != 'none': - db_dict=self.tweak_deposit_dict(xtal,db_dict) + db_dict = self.tweak_deposit_dict(xtal, db_dict) if date.lower() != 'none': - db_dict['data_collection_date']=date.split()[0] + db_dict['data_collection_date'] = date.split()[0] self.Logfile.insert('updating depositTable for '+xtal+' @ '+type) - self.db.update_depositTable(xtal,type,db_dict) + self.db.update_depositTable(xtal, type, db_dict) self.Logfile.insert('Note: use DBbrowser to edit individual entries') - def tweak_deposit_dict(self,xtal,db_dict): - dls_beamlines=['i02','i03','i04','i04-1','i23','i24'] - dls_beamline_dict = { 'i02': ['DIAMOND BEAMLINE I02', 'DECTRIS PILATUS 6M'], - 'i03': ['DIAMOND BEAMLINE I03', 'DECTRIS PILATUS 6M'], - 'i04': ['DIAMOND BEAMLINE I04', 'DECTRIS PILATUS 6M'], - 'i04-1': ['DIAMOND BEAMLINE I04-1', 'DECTRIS PILATUS 6M'], - 'i23': ['DIAMOND BEAMLINE I23', 'DECTRIS PILATUS 12M'], - 'i24': ['DIAMOND BEAMLINE I24', 'DECTRIS PILATUS 6M'] , } + def tweak_deposit_dict(self, xtal, db_dict): + dls_beamlines = ['i02', 'i03', 'i04', 'i04-1', 'i23', 'i24'] + dls_beamline_dict = {'i02': ['DIAMOND BEAMLINE I02', 'DECTRIS PILATUS 6M'], + 'i03': ['DIAMOND BEAMLINE I03', 'DECTRIS PILATUS 6M'], + 'i04': ['DIAMOND BEAMLINE I04', 'DECTRIS PILATUS 6M'], + 'i04-1': ['DIAMOND BEAMLINE I04-1', 'DECTRIS PILATUS 6M'], + 'i23': ['DIAMOND BEAMLINE I23', 'DECTRIS PILATUS 12M'], + 'i24': ['DIAMOND BEAMLINE I24', 'DECTRIS PILATUS 6M'], } if db_dict['radiation_source_type'] in dls_beamlines: - db_dict['radiation_source_type']= dls_beamline_dict[db_dict['radiation_source_type']][0] - db_dict['radiation_detector_type']= dls_beamline_dict[db_dict['radiation_source_type']][1] - db_dict['radiation_detector']= 'PIXEL' - db_dict['radiation_source']= 'SYNCHROTRON' + db_dict['radiation_source_type'] = dls_beamline_dict[db_dict['radiation_source_type']][0] + db_dict['radiation_detector_type'] = dls_beamline_dict[db_dict['radiation_source_type']][1] + db_dict['radiation_detector'] = 'PIXEL' + db_dict['radiation_source'] = 'SYNCHROTRON' return db_dict - - class prepare_mmcif_files_for_deposition(QtCore.QThread): - def __init__(self,database,xce_logfile,overwrite_existing_mmcif,projectDir,ground_state,ignore_event_map): + def __init__(self, database, xce_logfile, overwrite_existing_mmcif, projectDir, ground_state, ignore_event_map): QtCore.QThread.__init__(self) - self.database=database - self.xce_logfile=xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) - self.db=XChemDB.data_source(database) - self.overwrite_existing_mmcif=overwrite_existing_mmcif - self.projectDir=projectDir - self.data_template_dict={} + self.database = database + self.xce_logfile = xce_logfile + self.Logfile = XChemLog.updateLog(xce_logfile) + self.db = XChemDB.data_source(database) + self.overwrite_existing_mmcif = overwrite_existing_mmcif + self.projectDir = projectDir + self.data_template_dict = {} self.errorList = [] self.eventList = [] @@ -412,29 +419,35 @@ def __init__(self,database,xce_logfile,overwrite_existing_mmcif,projectDir,groun def run(self): - self.Logfile.insert('======= preparing mmcif files for wwPDB deposition =======') + self.Logfile.insert( + '======= preparing mmcif files for wwPDB deposition =======') self.Logfile.insert('checking DB for structures to deposit...') if self.ground_state: - toDeposit = self.db.execute_statement("select CrystalName from depositTable where DimplePANDDApath = '%s';" %self.panddaDir) + toDeposit = self.db.execute_statement( + "select CrystalName from depositTable where DimplePANDDApath = '%s';" % self.panddaDir) else: - toDeposit = self.db.execute_statement("select CrystalName from mainTable where RefinementOutcome like '5%';") - self.Logfile.insert('found ' + str(len(toDeposit)) + ' samples ready for deposition') + toDeposit = self.db.execute_statement( + "select CrystalName from mainTable where RefinementOutcome like '5%';") + self.Logfile.insert('found ' + str(len(toDeposit)) + + ' samples ready for deposition') - progress_step=1 + progress_step = 1 if len(toDeposit) != 0: - progress_step=100/float(len(toDeposit)) + progress_step = 100/float(len(toDeposit)) else: - progress_step=1 - progress=0 + progress_step = 1 + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) for item in sorted(toDeposit): - xtal=str(item[0]) + xtal = str(item[0]) if self.ground_state: - os.chdir(self.projectDir) # projectDir == referenceDir in this case + # projectDir == referenceDir in this case + os.chdir(self.projectDir) else: os.chdir(os.path.join(self.projectDir, xtal)) - self.Logfile.insert('%s: ----- preparing files for deposition -----' %xtal) + self.Logfile.insert( + '%s: ----- preparing files for deposition -----' % xtal) if self.ground_state: if not self.data_template_dict_exists(xtal): @@ -516,254 +529,294 @@ def run(self): self.make_table_one(xtal) - self.print_errorlist() - self.Logfile.insert('======= finished preparing mmcif files for wwPDB deposition =======') + self.Logfile.insert( + '======= finished preparing mmcif files for wwPDB deposition =======') def ground_state_mmcif_exists(self): mmcifStatus = False for dirs in glob.glob(os.path.join(self.panddaDir, 'processed_datasets', '*')): xtal = dirs[dirs.rfind('/') + 1:] if os.path.isfile(os.path.join(dirs, xtal + '_sf.mmcif')): - self.Logfile.insert('%s: found mmcif file for apo structure' %xtal) + self.Logfile.insert( + '%s: found mmcif file for apo structure' % xtal) mmcifStatus = True return mmcifStatus - def data_template_dict_exists(self,xtal): + def data_template_dict_exists(self, xtal): dictStatus = False self.data_template_dict = None - self.Logfile.insert('%s: reading information from depositTable for sample' % xtal) + self.Logfile.insert( + '%s: reading information from depositTable for sample' % xtal) self.data_template_dict = self.db.get_deposit_dict_for_sample(xtal) if self.data_template_dict == {}: - self.Logfile.error('%s: cannot find data_template dictionary in depositTable; moving to next dataset...' %xtal) + self.Logfile.error( + '%s: cannot find data_template dictionary in depositTable; moving to next dataset...' % xtal) self.add_to_errorList(xtal) else: - self.Logfile.insert('%s: found data_template dictionary in depositTable' % xtal) + self.Logfile.insert( + '%s: found data_template dictionary in depositTable' % xtal) dictStatus = True - return dictStatus + return dictStatus - def update_beamline_info_data_template_dict(self,xtal): - dls_beamlines=['i02','i03','i04','i04-1','i23','i24'] - dls_beamline_dict = { 'i02': ['DIAMOND BEAMLINE I02', 'DECTRIS PILATUS 6M'], - 'i03': ['DIAMOND BEAMLINE I03', 'DECTRIS PILATUS 6M'], - 'i04': ['DIAMOND BEAMLINE I04', 'DECTRIS PILATUS 6M'], - 'i04-1': ['DIAMOND BEAMLINE I04-1', 'DECTRIS PILATUS 6M'], - 'i23': ['DIAMOND BEAMLINE I23', 'DECTRIS PILATUS 12M'], - 'i24': ['DIAMOND BEAMLINE I24', 'DECTRIS PILATUS 6M'] , } + def update_beamline_info_data_template_dict(self, xtal): + dls_beamlines = ['i02', 'i03', 'i04', 'i04-1', 'i23', 'i24'] + dls_beamline_dict = {'i02': ['DIAMOND BEAMLINE I02', 'DECTRIS PILATUS 6M'], + 'i03': ['DIAMOND BEAMLINE I03', 'DECTRIS PILATUS 6M'], + 'i04': ['DIAMOND BEAMLINE I04', 'DECTRIS PILATUS 6M'], + 'i04-1': ['DIAMOND BEAMLINE I04-1', 'DECTRIS PILATUS 6M'], + 'i23': ['DIAMOND BEAMLINE I23', 'DECTRIS PILATUS 12M'], + 'i24': ['DIAMOND BEAMLINE I24', 'DECTRIS PILATUS 6M'], } if self.db_dict['DataCollectionBeamline'] in dls_beamlines: - self.data_template_dict['radiation_source_type']= dls_beamline_dict[self.db_dict['DataCollectionBeamline']][0] - self.data_template_dict['radiation_detector_type']= dls_beamline_dict[self.db_dict['DataCollectionBeamline']][1] - self.data_template_dict['radiation_detector']= 'PIXEL' - self.data_template_dict['radiation_source']= 'SYNCHROTRON' - self.Logfile.insert(('%s: setting data collection beamline to %s' %(xtal,self.data_template_dict['radiation_source_type']))) - - - def db_dict_exists(self,xtal): + self.data_template_dict['radiation_source_type'] = dls_beamline_dict[self.db_dict['DataCollectionBeamline']][0] + self.data_template_dict['radiation_detector_type'] = dls_beamline_dict[self.db_dict['DataCollectionBeamline']][1] + self.data_template_dict['radiation_detector'] = 'PIXEL' + self.data_template_dict['radiation_source'] = 'SYNCHROTRON' + self.Logfile.insert(('%s: setting data collection beamline to %s' % ( + xtal, self.data_template_dict['radiation_source_type']))) + + def db_dict_exists(self, xtal): dictStatus = False self.db_dict = None - self.Logfile.insert('%s: reading information from mainTable for sample' % xtal) + self.Logfile.insert( + '%s: reading information from mainTable for sample' % xtal) self.db_dict = self.db.get_db_dict_for_sample(xtal) if self.db_dict == {}: - self.Logfile.error('%s: cannot find db_dict dictionary in mainTable; moving to next dataset...' %xtal) + self.Logfile.error( + '%s: cannot find db_dict dictionary in mainTable; moving to next dataset...' % xtal) self.add_to_errorList(xtal) else: - self.Logfile.insert('%s: found db_dict dictionary in mainTable' % xtal) + self.Logfile.insert( + '%s: found db_dict dictionary in mainTable' % xtal) self.update_beamline_info_data_template_dict(xtal) dictStatus = True - return dictStatus + return dictStatus - def zenodo_dict_exists(self,xtal): + def zenodo_dict_exists(self, xtal): dictStatus = False self.zenodo_dict = None if self.ground_state: - self.zenodo_dict = self.db.get_zenodo_dict_for_pandda_analysis(self.panddaDir) + self.zenodo_dict = self.db.get_zenodo_dict_for_pandda_analysis( + self.panddaDir) else: - self.Logfile.insert('%s: reading information from zenodoTable for pandda run: %s' % (xtal, self.db_dict['DimplePANDDApath'])) - self.zenodo_dict = self.db.get_zenodo_dict_for_pandda_analysis(self.db_dict['DimplePANDDApath']) + self.Logfile.insert('%s: reading information from zenodoTable for pandda run: %s' % ( + xtal, self.db_dict['DimplePANDDApath'])) + self.zenodo_dict = self.db.get_zenodo_dict_for_pandda_analysis( + self.db_dict['DimplePANDDApath']) if self.zenodo_dict == {}: dictStatus = True self.zenodo_dict['ZenodoDOI'] = '' - self.Logfile.warning('%s: cannot find information about zenodo deposition in zenodoTable!!!' %xtal) + self.Logfile.warning( + '%s: cannot find information about zenodo deposition in zenodoTable!!!' % xtal) # self.Logfile.error('%s: cannot find information about zenodo deposition in zenodoTable; moving to next dataset...' %xtal) # self.add_to_errorList(xtal) else: - self.Logfile.insert('%s: found zenodo_dict dictionary in zenodoTable' % xtal) + self.Logfile.insert( + '%s: found zenodo_dict dictionary in zenodoTable' % xtal) dictStatus = True - return dictStatus + return dictStatus - - def mmcif_files_can_be_replaced(self,xtal): + def mmcif_files_can_be_replaced(self, xtal): status = True if self.overwrite_existing_mmcif: - self.Logfile.insert('%s: removing existing mmcif files as chosen by user' %xtal) - self.db.execute_statement("update depositTable set mmCIF_model_file='',mmCIF_SF_file='' where CrystalName is '{0!s}'".format(xtal)) + self.Logfile.insert( + '%s: removing existing mmcif files as chosen by user' % xtal) + self.db.execute_statement( + "update depositTable set mmCIF_model_file='',mmCIF_SF_file='' where CrystalName is '{0!s}'".format(xtal)) for mmcif in glob.glob('*.mmcif'): - self.Logfile.warning('%s: removing %s' %(xtal,mmcif)) + self.Logfile.warning('%s: removing %s' % (xtal, mmcif)) os.system('/bin/rm ' + mmcif) else: for mmcif in glob.glob('*.mmcif'): - self.Logfile.warning('%s: %s exists; skipping...' %(xtal,mmcif)) + self.Logfile.warning( + '%s: %s exists; skipping...' % (xtal, mmcif)) status = False return status - - - def refine_bound_exists(self,xtal): + def refine_bound_exists(self, xtal): self.pdb = None - self.Logfile.insert('%s: checking if refine.split.bound-state.pdb exists' %xtal) + self.Logfile.insert( + '%s: checking if refine.split.bound-state.pdb exists' % xtal) fileStatus = False if os.path.isfile('refine.split.bound-state.pdb'): - self.Logfile.insert('%s: found refine.split.bound-state.pdb' %xtal) + self.Logfile.insert( + '%s: found refine.split.bound-state.pdb' % xtal) self.pdb = pdbtools('refine.split.bound-state.pdb') fileStatus = True else: - self.Logfile.error('%s: cannot find refine.split.bound-state.pdb; moving to next dataset...' %xtal) + self.Logfile.error( + '%s: cannot find refine.split.bound-state.pdb; moving to next dataset...' % xtal) self.add_to_errorList(xtal) - return fileStatus + return fileStatus - def refine_mtz_exists(self,xtal): + def refine_mtz_exists(self, xtal): self.mtz = None - self.Logfile.insert('%s: checking if refine.mtz exists' %xtal) + self.Logfile.insert('%s: checking if refine.mtz exists' % xtal) fileStatus = False if os.path.isfile('refine.mtz'): - self.Logfile.insert('%s: found refine.mtz' %xtal) + self.Logfile.insert('%s: found refine.mtz' % xtal) self.mtz = mtztools('refine.mtz') fileStatus = True else: - self.Logfile.error('%s: cannot find refine.mtz; moving to next dataset...' %xtal) + self.Logfile.error( + '%s: cannot find refine.mtz; moving to next dataset...' % xtal) self.add_to_errorList(xtal) - return fileStatus + return fileStatus - def run_aimless_merge_only(self,xtal,unmerged,APpath): + def run_aimless_merge_only(self, xtal, unmerged, APpath): cmd = ( - 'aimless hklin %s hklout mergeonly.mtz << eof > %s\n' %(unmerged, unmerged.replace('.mtz','.log')) + + 'aimless hklin %s hklout mergeonly.mtz << eof > %s\n' % (unmerged, unmerged.replace('.mtz', '.log')) + ' onlymerge\n' 'eof' ) - self.Logfile.insert('%s: running AIMLESS in onlymerge mode...' %xtal) + self.Logfile.insert('%s: running AIMLESS in onlymerge mode...' % xtal) os.system(cmd) os.chdir(os.path.join(self.projectDir, xtal)) - os.system('/bin/rm %s.log' %xtal) - os.system('ln -s %s/%s %s.log' %(APpath,unmerged.replace('.mtz','.log'),xtal)) - self.Logfile.insert('%s: finished running AIMLESS' %xtal) + os.system('/bin/rm %s.log' % xtal) + os.system('ln -s %s/%s %s.log' % + (APpath, unmerged.replace('.mtz', '.log'), xtal)) + self.Logfile.insert('%s: finished running AIMLESS' % xtal) if os.path.isfile(xtal+'.log'): - self.Logfile.insert('%s: AIMLESS logfile successfully created' %xtal) + self.Logfile.insert( + '%s: AIMLESS logfile successfully created' % xtal) else: - self.Logfile.error('%s: cannot find AIMLESS logfile...' %xtal) + self.Logfile.error('%s: cannot find AIMLESS logfile...' % xtal) - def prepare_aimless_log(self,xtal): + def prepare_aimless_log(self, xtal): parse().make_pseudo_aimless_log_from_json(xtal + '.log') - def aimless_logfile_exists(self,xtal): - self.Logfile.insert('%s: checking if aimless logfile, i.e. %s.log, exists' %(xtal,xtal)) + def aimless_logfile_exists(self, xtal): + self.Logfile.insert( + '%s: checking if aimless logfile, i.e. %s.log, exists' % (xtal, xtal)) fileStatus = False - if os.path.isfile('%s.log' %xtal): - self.Logfile.insert('%s: found %s.log' %(xtal,xtal)) - for n,line in enumerate(open('%s.log' %xtal)): + if os.path.isfile('%s.log' % xtal): + self.Logfile.insert('%s: found %s.log' % (xtal, xtal)) + for n, line in enumerate(open('%s.log' % xtal)): if 'AIMLESS' in line: fileStatus = True break # if n < 10: # print line if not fileStatus: - if os.path.realpath('%s.log' %xtal).endswith('.table1'): - self.Logfile.warning('{0!s}: {1!s}.log seems to be a staraniso .table1 file'.format(xtal,xtal)) + if os.path.realpath('%s.log' % xtal).endswith('.table1'): + self.Logfile.warning( + '{0!s}: {1!s}.log seems to be a staraniso .table1 file'.format(xtal, xtal)) fileStatus = True if not fileStatus: - self.Logfile.warning('%s: this does not seem to be an AIMLESS logfile' %xtal) - Filepath = os.path.relpath(os.path.realpath('%s.log' %xtal)) + self.Logfile.warning( + '%s: this does not seem to be an AIMLESS logfile' % xtal) + Filepath = os.path.relpath(os.path.realpath('%s.log' % xtal)) APpath = Filepath[:Filepath.rfind('/')] - self.Logfile.insert('%s: relative path to logfile %s' %(xtal,APpath)) - self.Logfile.insert('%s: file path to logfile %s' %(xtal,Filepath)) + self.Logfile.insert( + '%s: relative path to logfile %s' % (xtal, APpath)) + self.Logfile.insert( + '%s: file path to logfile %s' % (xtal, Filepath)) if os.path.isdir(APpath): os.chdir(APpath) for unmerged in glob.glob('*_scaled_unmerged.mtz'): - self.Logfile.insert('%s: found %s in %s' %(xtal,unmerged,APpath)) - self.run_aimless_merge_only(xtal,unmerged,APpath) + self.Logfile.insert('%s: found %s in %s' % + (xtal, unmerged, APpath)) + self.run_aimless_merge_only(xtal, unmerged, APpath) fileStatus = True break else: - self.Logfile.error('%s: %s is not a directory' %(xtal,APpath)) + self.Logfile.error( + '%s: %s is not a directory' % (xtal, APpath)) self.add_to_errorList(xtal) if not fileStatus: - os.chdir(os.path.join(self.projectDir,xtal)) - self.Logfile.insert('%s: trying to prepare a pseudo-aimless file from json file...' %xtal) + os.chdir(os.path.join(self.projectDir, xtal)) + self.Logfile.insert( + '%s: trying to prepare a pseudo-aimless file from json file...' % xtal) self.prepare_aimless_log(xtal) if os.path.isfile('aimless_dials.log'): - self.Logfile.insert('%s: found aimless_dials.log' %xtal) + self.Logfile.insert( + '%s: found aimless_dials.log' % xtal) fileStatus = True if not fileStatus: - self.Logfile.error('%s: cannot find a suitable AIMLESS logfile' %xtal) + self.Logfile.error( + '%s: cannot find a suitable AIMLESS logfile' % xtal) self.add_to_errorList(xtal) # fileStatus = True else: - self.Logfile.error('%s: cannot find %s.log; moving to next dataset...' %(xtal,xtal)) + self.Logfile.error( + '%s: cannot find %s.log; moving to next dataset...' % (xtal, xtal)) self.add_to_errorList(xtal) return fileStatus - - def mtzFree_exists(self,xtal): - self.Logfile.insert('%s: checking if %s.free.mtz exists' %(xtal,xtal)) + def mtzFree_exists(self, xtal): + self.Logfile.insert( + '%s: checking if %s.free.mtz exists' % (xtal, xtal)) fileStatus = False - if os.path.isfile('%s.free.mtz' %xtal): - self.Logfile.insert('%s: found %s.free.mtz' %(xtal,xtal)) + if os.path.isfile('%s.free.mtz' % xtal): + self.Logfile.insert('%s: found %s.free.mtz' % (xtal, xtal)) fileStatus = True else: - self.Logfile.error('%s: cannot find %s.free.mtz; moving to next dataset...' %(xtal,xtal)) + self.Logfile.error( + '%s: cannot find %s.free.mtz; moving to next dataset...' % (xtal, xtal)) self.add_to_errorList(xtal) - return fileStatus - + return fileStatus - def ligand_in_pdb_file(self,xtal): - self.Logfile.insert('%s: checking if refine.split.bound-state.pdb contains ligands of type LIG' %xtal) + def ligand_in_pdb_file(self, xtal): + self.Logfile.insert( + '%s: checking if refine.split.bound-state.pdb contains ligands of type LIG' % xtal) ligandStatus = False - ligList = pdbtools('refine.split.bound-state.pdb').get_residues_with_resname('LIG') + ligList = pdbtools( + 'refine.split.bound-state.pdb').get_residues_with_resname('LIG') if ligList is []: - self.Logfile.error('%s: refine.split.bound-state.pdb does not contain any modelled ligands of type LIG' %xtal) + self.Logfile.error( + '%s: refine.split.bound-state.pdb does not contain any modelled ligands of type LIG' % xtal) self.add_to_errorList(xtal) else: - self.Logfile.insert(xtal + ': found ' + str(len(ligList)) + ' ligands of type LIG') + self.Logfile.insert(xtal + ': found ' + + str(len(ligList)) + ' ligands of type LIG') ligandStatus = True return ligandStatus - def eventMTZ_exists(self,xtal): - self.Logfile.insert('%s: checking if mtz of event maps exists' %xtal) + def eventMTZ_exists(self, xtal): + self.Logfile.insert('%s: checking if mtz of event maps exists' % xtal) eventMTZlist = [] eventMTZexists = False if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: - self.Logfile.warning('%s: found empty file named "no_pandda_analysis_performed" which suggests we will ignore event maps for this sample' %xtal) + self.Logfile.warning( + '%s: found empty file named "no_pandda_analysis_performed" which suggests we will ignore event maps for this sample' % xtal) eventMTZexists = True elif self.ignore_event_map: - self.Logfile.warning('%s: user selected to not include event map in SF mmcif file' %xtal) + self.Logfile.warning( + '%s: user selected to not include event map in SF mmcif file' % xtal) eventMTZexists = True else: for mtz in glob.glob('*event*.native*.mtz'): eventMTZlist.append(mtz[mtz.rfind('/')+1:]) if eventMTZlist is []: - self.Logfile.error('%s: MTZ files of event maps do not exists! Go to PANDDA tab and run "Event Map -> SF"' %xtal) + self.Logfile.error( + '%s: MTZ files of event maps do not exists! Go to PANDDA tab and run "Event Map -> SF"' % xtal) self.add_to_errorList(xtal) else: - self.Logfile.insert(xtal + ': found ' + str(len(eventMTZlist)) + ' MTZ files of event maps') + self.Logfile.insert( + xtal + ': found ' + str(len(eventMTZlist)) + ' MTZ files of event maps') eventMTZexists = True return eventMTZexists - - def find_matching_event_map(self,xtal): + def find_matching_event_map(self, xtal): self.eventList = [] - self.Logfile.insert('%s: trying to find fitting event maps for modelled ligands' %xtal) - ligList = self.pdb.save_residues_with_resname(os.path.join(self.projectDir,xtal), 'LIG') + self.Logfile.insert( + '%s: trying to find fitting event maps for modelled ligands' % xtal) + ligList = self.pdb.save_residues_with_resname( + os.path.join(self.projectDir, xtal), 'LIG') foundMatchingMap = None if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: - self.Logfile.warning('%s: found empty file named "no_pandda_analysis_performed" which suggests we will ignore event maps for this sample' %xtal) + self.Logfile.warning( + '%s: found empty file named "no_pandda_analysis_performed" which suggests we will ignore event maps for this sample' % xtal) foundMatchingMap = True ligList = [] - self.Logfile.insert('%s: looking for event maps for the following ligands -> %s' %(xtal,str(ligList))) + self.Logfile.insert( + '%s: looking for event maps for the following ligands -> %s' % (xtal, str(ligList))) for lig in sorted(ligList): - ligID = lig.replace('.pdb','') + ligID = lig.replace('.pdb', '') # if os.path.isfile('no_pandda_analysis_performed'): # self.Logfile.warning('%s: no pandda analysis performed; skipping this step...' %xtal) # foundMatchingMap = True @@ -772,7 +825,7 @@ def find_matching_event_map(self,xtal): # for newer BUSTER export # print '>>>> %s-event_*.native_%s.mtz' %(xtal,lig.replace('.pdb','')) - for mtz in glob.glob(('%s-event_*.native_%s.mtz' %(xtal,lig.replace('.pdb','')))): + for mtz in glob.glob(('%s-event_*.native_%s.mtz' % (xtal, lig.replace('.pdb', '')))): self.Logfile.insert(xtal + ': found ' + mtz) foundMatchingMap = True self.eventList.append(mtz) @@ -784,24 +837,26 @@ def find_matching_event_map(self,xtal): for mtz in sorted(glob.glob('*event*.native.mtz')): self.get_lig_cc(xtal, mtz, lig) cc = self.check_lig_cc(mtz.replace('.mtz', '_CC'+ligID+'.log')) - self.Logfile.insert('%s: %s -> CC = %s for %s' %(xtal,ligID,cc,mtz)) + self.Logfile.insert('%s: %s -> CC = %s for %s' % + (xtal, ligID, cc, mtz)) try: - ligCC.append([mtz,float(cc)]) + ligCC.append([mtz, float(cc)]) except ValueError: ligCC.append([mtz, 0.00]) - for mtz in sorted(glob.glob('*event*.native*P1.mtz')): self.get_lig_cc(xtal, mtz, lig) cc = self.check_lig_cc(mtz.replace('.mtz', '_CC'+ligID+'.log')) - self.Logfile.insert('%s: %s -> CC = %s for %s' %(xtal,ligID,cc,mtz)) + self.Logfile.insert('%s: %s -> CC = %s for %s' % + (xtal, ligID, cc, mtz)) try: - ligCC.append([mtz,float(cc)]) + ligCC.append([mtz, float(cc)]) except ValueError: ligCC.append([mtz, 0.00]) try: for cm in ligCC: - self.Logfile.insert('%s: cc = %s - %s' %(xtal,cm[1],cm[0])) + self.Logfile.insert('%s: cc = %s - %s' % + (xtal, cm[1], cm[0])) # highestCC = max(ligCC, key=lambda x: x[0])[1] highestCCeventmap = max(ligCC, key=lambda x: float(x[1]))[0] except ValueError: @@ -810,47 +865,52 @@ def find_matching_event_map(self,xtal): # if highestCC == 0.00 or ligCC is []: if highestCCeventmap is None or ligCC is []: - self.Logfile.error('%s: best CC of ligand %s for any event map is 0!' %(xtal,lig)) + self.Logfile.error( + '%s: best CC of ligand %s for any event map is 0!' % (xtal, lig)) self.add_to_errorList(xtal) foundMatchingMap = False else: - self.Logfile.insert('%s: selected event map for ligand %s is %s' %(xtal,lig,highestCCeventmap)) - if os.path.isfile(highestCCeventmap.replace('.mtz','_'+ligID+'.mtz')): - self.Logfile.warning('%s: symlink exists %s' %(xtal,highestCCeventmap.replace('.mtz','_'+ligID+'.mtz'))) + self.Logfile.insert('%s: selected event map for ligand %s is %s' % ( + xtal, lig, highestCCeventmap)) + if os.path.isfile(highestCCeventmap.replace('.mtz', '_'+ligID+'.mtz')): + self.Logfile.warning('%s: symlink exists %s' % ( + xtal, highestCCeventmap.replace('.mtz', '_'+ligID+'.mtz'))) else: - self.Logfile.insert('%s: making symlink %s' %(xtal,highestCCeventmap.replace('.mtz','_'+ligID+'.mtz'))) - os.system('ln -s %s %s' %(highestCCeventmap,highestCCeventmap.replace('.mtz','_'+ligID+'.mtz'))) + self.Logfile.insert('%s: making symlink %s' % ( + xtal, highestCCeventmap.replace('.mtz', '_'+ligID+'.mtz'))) + os.system('ln -s %s %s' % (highestCCeventmap, + highestCCeventmap.replace('.mtz', '_'+ligID+'.mtz'))) if highestCCeventmap not in self.eventList: self.eventList.append(highestCCeventmap) if foundMatchingMap is None: foundMatchingMap = True return foundMatchingMap - def get_lig_cc(self, xtal, mtz, lig): - ligID = lig.replace('.pdb','') - self.Logfile.insert('%s: calculating CC for %s in %s' %(xtal,lig,mtz)) + ligID = lig.replace('.pdb', '') + self.Logfile.insert('%s: calculating CC for %s in %s' % + (xtal, lig, mtz)) if os.path.isfile(mtz.replace('.mtz', '_CC'+ligID+'.log')): self.Logfile.warning('logfile of CC analysis exists; skipping...') return - cmd = ( 'module load phenix\n' - 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log')) ) + cmd = ('module load phenix\n' + 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log'))) os.system(cmd) - def check_lig_cc(self,log): + def check_lig_cc(self, log): cc = 'n/a' if os.path.isfile(log): for line in open(log): if line.startswith('local'): cc = line.split()[len(line.split()) - 1] else: - self.Logfile.error('logfile does not exist: %s' %log) + self.Logfile.error('logfile does not exist: %s' % log) return cc - - def add_to_errorList(self,xtal): - if xtal.replace(' ','') == '': - self.Logfile.warning('trying to add xtal to error list, but xtal string is empty') + def add_to_errorList(self, xtal): + if xtal.replace(' ', '') == '': + self.Logfile.warning( + 'trying to add xtal to error list, but xtal string is empty') else: if xtal not in self.errorList: self.errorList.append(xtal) @@ -865,20 +925,25 @@ def print_errorlist(self): for xtal in self.errorList: self.Logfile.error(xtal) - - def save_data_template_dict(self,xtal): + def save_data_template_dict(self, xtal): # check if file exists noError = True - self.Logfile.insert('%s: preparing data_template.cif file' %xtal) + self.Logfile.insert('%s: preparing data_template.cif file' % xtal) if self.overwrite_existing_mmcif: - self.data_template_dict['radiation_wavelengths'] = self.mtz.get_wavelength() + self.data_template_dict['radiation_wavelengths'] = self.mtz.get_wavelength( + ) if str(self.data_template_dict['radiation_wavelengths']).startswith('0.0'): - self.Logfile.error('%s: this does not seem to be the true experimental wavelength: %s' %(xtal,str(self.data_template_dict['radiation_wavelengths']))) - self.Logfile.insert('%s: trying to find it from %s.free.mtz...' %(xtal,xtal)) - if os.path.isfile('%s.free.mtz' %xtal): - self.data_template_dict['radiation_wavelengths'] = mtztools(xtal+'.free.mtz').get_wavelength() - self.Logfile.warning('%s: found the following wavelength -> %s' %(xtal,str(self.data_template_dict['radiation_wavelengths']))) - self.Logfile.insert('%s: experimental wavelength according to %s is %s' %(xtal,self.mtz,self.data_template_dict['radiation_wavelengths'])) + self.Logfile.error('%s: this does not seem to be the true experimental wavelength: %s' % ( + xtal, str(self.data_template_dict['radiation_wavelengths']))) + self.Logfile.insert( + '%s: trying to find it from %s.free.mtz...' % (xtal, xtal)) + if os.path.isfile('%s.free.mtz' % xtal): + self.data_template_dict['radiation_wavelengths'] = mtztools( + xtal+'.free.mtz').get_wavelength() + self.Logfile.warning('%s: found the following wavelength -> %s' % ( + xtal, str(self.data_template_dict['radiation_wavelengths']))) + self.Logfile.insert('%s: experimental wavelength according to %s is %s' % ( + xtal, self.mtz, self.data_template_dict['radiation_wavelengths'])) if self.ground_state: os.chdir(self.projectDir) # self.data_template_dict['radiation_wavelengths'] = '1.000' @@ -886,36 +951,36 @@ def save_data_template_dict(self,xtal): self.data_template_dict['group_title'] = 'PanDDA analysis group deposition of ground-state model' self.data_template_dict['group_description'] = self.data_template_dict['group_description'].replace('$ProteinName', self.data_template_dict[ - 'Source_organism_gene']) + 'Source_organism_gene']) self.data_template_dict['title'] = self.data_template_dict['structure_title_apo'].replace('$ProteinName', - self.data_template_dict[ - 'Source_organism_gene']) + self.data_template_dict[ + 'Source_organism_gene']) else: os.chdir(os.path.join(self.projectDir, xtal)) # edit wavelength # self.data_template_dict['radiation_wavelengths'] = self.mtz.get_wavelength() title = self.data_template_dict['structure_title'].replace('$ProteinName', self.data_template_dict[ - 'Source_organism_gene']).replace('$CompoundName', self.db_dict['CompoundCode']).replace('($SampleID)','('+xtal+')') + 'Source_organism_gene']).replace('$CompoundName', self.db_dict['CompoundCode']).replace('($SampleID)', '('+xtal+')') self.data_template_dict['group_type'] = 'changed state' - # edit title self.data_template_dict['group_title'] = self.data_template_dict['group_deposition_title'].replace('$ProteinName', - self.data_template_dict[ - 'Source_organism_gene']).replace( - '$CompoundName', self.db_dict['CompoundCode']) + self.data_template_dict[ + 'Source_organism_gene']).replace( + '$CompoundName', self.db_dict['CompoundCode']) # self.data_template_dict[ # 'group_title'] = 'PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)' self.data_template_dict['group_description'] = self.data_template_dict['group_description'].replace('$ProteinName', self.data_template_dict[ - 'Source_organism_gene']) + 'Source_organism_gene']) self.data_template_dict['title'] = self.data_template_dict['group_title'] + ' -- ' + title if ('$ProteinName' or '$CompoundName') in self.data_template_dict['title']: - self.Logfile.error('%s: data_template - title not correctly formatted') + self.Logfile.error( + '%s: data_template - title not correctly formatted') self.add_to_errorList(xtal) noError = False @@ -924,7 +989,8 @@ def save_data_template_dict(self,xtal): if mutations.lower().replace(' ', '').replace('none', '').replace('null', '') == '': self.data_template_dict['fragment_name_one_specific_mutation'] = '?' else: - self.data_template_dict['fragment_name_one_specific_mutation'] = '"' + mutations.replace(' ', '') + '"' + self.data_template_dict['fragment_name_one_specific_mutation'] = '"' + \ + mutations.replace(' ', '') + '"' # get protein chains self.data_template_dict['protein_chains'] = '' @@ -937,17 +1003,18 @@ def save_data_template_dict(self,xtal): # site_details = self.make_site_description(xtal) # data_template += site_details if self.ground_state: - f = open(os.path.join(self.projectDir, 'data_template.cif'), 'w') + f = open(os.path.join(self.projectDir, + 'data_template.cif'), 'w') else: - f = open(os.path.join(self.projectDir, xtal, 'data_template.cif'), 'w') + f = open(os.path.join(self.projectDir, + xtal, 'data_template.cif'), 'w') f.write(data_template) f.close() return noError - - def create_model_mmcif(self,xtal): + def create_model_mmcif(self, xtal): fileStatus = False if self.ground_state: os.chdir(os.path.join(self.projectDir)) @@ -956,38 +1023,47 @@ def create_model_mmcif(self,xtal): refSoft = self.pdb.get_refinement_program() if os.path.isdir('/dls'): -# if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): -# pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-v3.26/pdb-extract-v3.26-prod-src/setup.sh\n' -# pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-v3.26/pdb-extract-v3.26-prod-src/bin/pdb_extract' -# else: + # if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): + # pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-v3.26/pdb-extract-v3.26-prod-src/setup.sh\n' + # pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-v3.26/pdb-extract-v3.26-prod-src/bin/pdb_extract' + # else: pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n' pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-prod/bin/pdb_extract' else: - if os.path.isfile(os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/bin/pdb_extract')): - pdb_extract_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/setup.sh') + '\n' - pdb_extract_init += os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/bin/pdb_extract') + if os.path.isfile(os.path.join(os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/bin/pdb_extract')): + pdb_extract_init = 'source ' + \ + os.path.join(os.getenv('XChemExplorer_DIR'), + 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' + pdb_extract_init += os.path.join( + os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/bin/pdb_extract') else: pdb_extract_init = 'pdb_extract' if self.ground_state: - refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] - self.Logfile.insert('ground_state deposition reference dataset: {0!s}'.format(refXtal)) - aimless = os.path.join(self.logDir,refXtal,refXtal+'.log') + refXtal = self.ground_state_pdb.split( + '/')[len(self.ground_state_pdb.split('/')) - 2] + self.Logfile.insert( + 'ground_state deposition reference dataset: {0!s}'.format(refXtal)) + aimless = os.path.join(self.logDir, refXtal, refXtal+'.log') else: - aimless = '%s.log' %xtal + aimless = '%s.log' % xtal isAimlessFile = False - for n,line in enumerate(open(aimless)): + for n, line in enumerate(open(aimless)): if 'AIMLESS' in line: isAimlessFile = True break if not isAimlessFile: - self.Logfile.warning('processing log file does not seem to be an aimless file: {0!s}'.format(aimless)) - self.Logfile.insert('realpath of processing logfile: {0!s}'.format(os.path.realpath(aimless))) + self.Logfile.warning( + 'processing log file does not seem to be an aimless file: {0!s}'.format(aimless)) + self.Logfile.insert('realpath of processing logfile: {0!s}'.format( + os.path.realpath(aimless))) if os.path.realpath(aimless).endswith('.table1'): - self.Logfile.warning('{0!s}: {1!s}.log seems to be a staraniso .table1 file'.format(xtal,xtal)) + self.Logfile.warning( + '{0!s}: {1!s}.log seems to be a staraniso .table1 file'.format(xtal, xtal)) isAimlessFile = True - self.Logfile.warning('it does not seem to originate from staraniso either') + self.Logfile.warning( + 'it does not seem to originate from staraniso either') if not isAimlessFile: if os.path.isfile('aimless_dials.log'): aimless = 'aimless_dials.log' @@ -1005,8 +1081,8 @@ def create_model_mmcif(self,xtal): # aimless = 'aimless_dials.log' if self.ground_state: -# refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] -# aimless = os.path.join(self.logDir,refXtal,refXtal+'.log') + # refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] + # aimless = os.path.join(self.logDir,refXtal,refXtal+'.log') self.Logfile.insert('aimless.log file: ' + aimless) Cmd = (pdb_extract_init + ' -r {0!s}'.format(refSoft) + @@ -1017,48 +1093,51 @@ def create_model_mmcif(self,xtal): ' -iENT data_template.cif' ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) else: -# if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): -# self.Logfile.insert('%s: found MMCIF file; will use instead of PDB: %s' %(xtal,self.db_dict['RefinementMMCIFmodel_latest'])) -# Cmd = (pdb_extract_init + -# ' -r {0!s}'.format(refSoft) + -# ' -iCIF {0!s}'.format(self.db_dict['RefinementMMCIFmodel_latest']) + -# ' -e MR' -# ' -s AIMLESS' -# ' -iLOG {0!s}.log'.format(xtal) + -# ' -iENT data_template.cif' -# ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) -# else: + # if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): + # self.Logfile.insert('%s: found MMCIF file; will use instead of PDB: %s' %(xtal,self.db_dict['RefinementMMCIFmodel_latest'])) + # Cmd = (pdb_extract_init + + # ' -r {0!s}'.format(refSoft) + + # ' -iCIF {0!s}'.format(self.db_dict['RefinementMMCIFmodel_latest']) + + # ' -e MR' + # ' -s AIMLESS' + # ' -iLOG {0!s}.log'.format(xtal) + + # ' -iENT data_template.cif' + # ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) + # else: Cmd = (pdb_extract_init + - ' -r {0!s}'.format(refSoft) + - ' -iPDB {0!s}'.format('refine.split.bound-state.pdb') + - ' -e MR' - ' -s AIMLESS' - ' -iLOG {0!s}'.format(aimless) + - ' -iENT data_template.cif' - ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) + ' -r {0!s}'.format(refSoft) + + ' -iPDB {0!s}'.format('refine.split.bound-state.pdb') + + ' -e MR' + ' -s AIMLESS' + ' -iLOG {0!s}'.format(aimless) + + ' -iENT data_template.cif' + ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) self.Logfile.insert(xtal + ': running pdb_extract: ' + Cmd) os.system(Cmd) self.update_model_mmcif_header(xtal) - if os.path.isfile(xtal+'.mmcif') and os.path.getsize(xtal+'.mmcif') > 20000 : - self.Logfile.insert('%s: model mmcif file successfully created' %xtal) + if os.path.isfile(xtal+'.mmcif') and os.path.getsize(xtal+'.mmcif') > 20000: + self.Logfile.insert( + '%s: model mmcif file successfully created' % xtal) if self.ground_state: self.db.execute_statement( "update depositTable set mmCIF_model_file='{0!s}.mmcif' where CrystalName is '{1!s}' and DimplePANDDApath is '{2!s}'".format(xtal, - xtal,self.panddaDir)) + xtal, self.panddaDir)) else: - self.db.execute_statement("update depositTable set mmCIF_model_file='{0!s}.mmcif' where CrystalName is '{1!s}'".format(xtal,xtal)) + self.db.execute_statement( + "update depositTable set mmCIF_model_file='{0!s}.mmcif' where CrystalName is '{1!s}'".format(xtal, xtal)) fileStatus = True else: - self.Logfile.error('%s: model mmcif file was not created successfully') + self.Logfile.error( + '%s: model mmcif file was not created successfully') self.add_to_errorList(xtal) return fileStatus - def update_model_mmcif_header(self,xtal): - self.Logfile.insert('%s: updating header of model mmcif file' %xtal) + def update_model_mmcif_header(self, xtal): + self.Logfile.insert('%s: updating header of model mmcif file' % xtal) foundSoftwareBlock = False amendSoftwareBlock = False softwareEntry = [] @@ -1070,30 +1149,32 @@ def update_model_mmcif_header(self,xtal): if not line.startswith('_'): try: softwareEntry.append(int(line.split()[0])) - except (ValueError,IndexError): + except (ValueError, IndexError): pass if '#' in line: amendSoftwareBlock = True foundSoftwareBlock = False if '_refine.pdbx_ls_cross_valid_method' in line: - sys.stdout.write('_refine.pdbx_ls_cross_valid_method THROUGHOUT \n') + sys.stdout.write( + '_refine.pdbx_ls_cross_valid_method THROUGHOUT \n') elif '_refine.pdbx_starting_model' in line: sys.stdout.write('_refine.pdbx_starting_model {0!s} \n'.format( self.data_template_dict['pdbx_starting_model'])) elif '_refine.pdbx_method_to_determine_struct' in line: - sys.stdout.write("_refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS'\n") + sys.stdout.write( + "_refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS'\n") elif '_struct.title ---' in line: -# self.Logfile.warning('structure title was not created by pdb_extract; there might be an issue with REFMAC 5.8.0238') -# self.Logfile.insert('trying to get title from data_template.cif file') + # self.Logfile.warning('structure title was not created by pdb_extract; there might be an issue with REFMAC 5.8.0238') + # self.Logfile.insert('trying to get title from data_template.cif file') Title = '' foundTitle = False for li in open('data_template.cif'): if li.startswith('_struct.title'): foundTitle = True if foundTitle: - if li.replace(' ','').replace('\n','').replace('\r','') == ';': + if li.replace(' ', '').replace('\n', '').replace('\r', '') == ';': Title += li break Title += li @@ -1101,24 +1182,24 @@ def update_model_mmcif_header(self,xtal): elif amendSoftwareBlock: cifItem = ( "{0!s} {1!s} ? ? program ? ? 'data reduction' ? ?\n".format(str(max(softwareEntry) + 1), - self.data_template_dict[ - 'data_integration_software']) + + self.data_template_dict[ + 'data_integration_software']) + '{0!s} {1!s} ? ? program ? ? phasing ? ?\n'.format(str(max(softwareEntry) + 2), - self.data_template_dict[ - 'phasing_software']) -# '#\n' -# "loop_\n" -# "_pdbx_related_exp_data_set.ordinal\n" -# "_pdbx_related_exp_data_set.data_reference\n" -# "_pdbx_related_exp_data_set.metadata_reference\n" -# "_pdbx_related_exp_data_set.data_set_type\n" -# "_pdbx_related_exp_data_set.details\n" -# " 1 " -# " 'doi:%s' " %self.zenodo_dict['ZenodoDOI']+ -# " 'doi:%s' " %self.zenodo_dict['ZenodoDOI']+ -# " 'other data' " # 'other data' is only thing wwPDB accepts at the moment -# " 'Complete PanDDA analysis'\n" -# "\n" + self.data_template_dict[ + 'phasing_software']) + # '#\n' + # "loop_\n" + # "_pdbx_related_exp_data_set.ordinal\n" + # "_pdbx_related_exp_data_set.data_reference\n" + # "_pdbx_related_exp_data_set.metadata_reference\n" + # "_pdbx_related_exp_data_set.data_set_type\n" + # "_pdbx_related_exp_data_set.details\n" + # " 1 " + # " 'doi:%s' " %self.zenodo_dict['ZenodoDOI']+ + # " 'doi:%s' " %self.zenodo_dict['ZenodoDOI']+ + # " 'other data' " # 'other data' is only thing wwPDB accepts at the moment + # " 'Complete PanDDA analysis'\n" + # "\n" ) sys.stdout.write(cifItem) @@ -1128,15 +1209,13 @@ def update_model_mmcif_header(self,xtal): sys.stdout.write(line) - - # elif '_reflns.d_resolution_low' in line and len(line.split()) == 2: # sys.stdout.write('_reflns.d_resolution_low {0!s}\n'.format(min(low_reso_list))) # # elif '_refine.ls_d_res_low' in line and len(line.split()) == 2: # sys.stdout.write('_refine.ls_d_res_low {0!s}\n'.format(min(low_reso_list))) - def add_funding_information(self,xtal): + def add_funding_information(self, xtal): pdbx_funding_ordinal_one = self.data_template_dict['pdbx_funding_ordinal_one'] if pdbx_funding_ordinal_one.lower().replace(' ', '').replace('none', '').replace('null', '') == '': self.data_template_dict['pdbx_funding_ordinal_one'] = '' @@ -1145,7 +1224,8 @@ def add_funding_information(self,xtal): self.data_template_dict['pdbx_grant_country_one'] = '' funding_one = '' else: - funding_one = "%s '%s' '%s' '%s'\n" %(self.data_template_dict['pdbx_funding_ordinal_one'],self.data_template_dict['pdbx_funding_organization_one'],self.data_template_dict['pdbx_grant_number_one'],self.data_template_dict['pdbx_grant_country_one']) + funding_one = "%s '%s' '%s' '%s'\n" % (self.data_template_dict['pdbx_funding_ordinal_one'], self.data_template_dict[ + 'pdbx_funding_organization_one'], self.data_template_dict['pdbx_grant_number_one'], self.data_template_dict['pdbx_grant_country_one']) pdbx_funding_ordinal_two = self.data_template_dict['pdbx_funding_ordinal_two'] if pdbx_funding_ordinal_two.lower().replace(' ', '').replace('none', '').replace('null', '') == '': @@ -1155,7 +1235,8 @@ def add_funding_information(self,xtal): self.data_template_dict['pdbx_grant_country_two'] = '' funding_two = '' else: - funding_two = "%s '%s' '%s' '%s'\n" %(self.data_template_dict['pdbx_funding_ordinal_two'],self.data_template_dict['pdbx_funding_organization_two'],self.data_template_dict['pdbx_grant_number_two'],self.data_template_dict['pdbx_grant_country_two']) + funding_two = "%s '%s' '%s' '%s'\n" % (self.data_template_dict['pdbx_funding_ordinal_two'], self.data_template_dict[ + 'pdbx_funding_organization_two'], self.data_template_dict['pdbx_grant_number_two'], self.data_template_dict['pdbx_grant_country_two']) pdbx_funding_ordinal_three = self.data_template_dict['pdbx_funding_ordinal_three'] if pdbx_funding_ordinal_three.lower().replace(' ', '').replace('none', '').replace('null', '') == '': @@ -1165,7 +1246,8 @@ def add_funding_information(self,xtal): self.data_template_dict['pdbx_grant_country_three'] = '' funding_three = '' else: - funding_three = "%s '%s' '%s' '%s'\n" %(self.data_template_dict['pdbx_funding_ordinal_three'],self.data_template_dict['pdbx_funding_organization_three'],self.data_template_dict['pdbx_grant_number_three'],self.data_template_dict['pdbx_grant_country_three']) + funding_three = "%s '%s' '%s' '%s'\n" % (self.data_template_dict['pdbx_funding_ordinal_three'], self.data_template_dict[ + 'pdbx_funding_organization_three'], self.data_template_dict['pdbx_grant_number_three'], self.data_template_dict['pdbx_grant_country_three']) funding_info = ( '#\n' @@ -1182,41 +1264,44 @@ def add_funding_information(self,xtal): f.write(funding_info) f.close() - def add_ligand_cif_to_model_mmcif(self,xtal): + def add_ligand_cif_to_model_mmcif(self, xtal): filestatus = False - self.Logfile.insert('%s: looking for ligand restraints file...' %xtal) + self.Logfile.insert('%s: looking for ligand restraints file...' % xtal) os.chdir(os.path.join(self.projectDir, xtal)) if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): - self.Logfile.insert('%s: found %s; assuming that ligand cif dictionary is already included...' %(xtal,self.db_dict['RefinementMMCIFmodel_latest'])) + self.Logfile.insert('%s: found %s; assuming that ligand cif dictionary is already included...' % ( + xtal, self.db_dict['RefinementMMCIFmodel_latest'])) filestatus = True else: if os.path.isfile(self.db_dict['CompoundCode']+'.cif'): - self.Logfile.insert('%s: found ligand restraints file -> %s' %(xtal,self.db_dict['CompoundCode']+'.cif')) - self.Logfile.insert('%s: adding ligand restraints file to model mmcif' %xtal) + self.Logfile.insert('%s: found ligand restraints file -> %s' % + (xtal, self.db_dict['CompoundCode']+'.cif')) + self.Logfile.insert( + '%s: adding ligand restraints file to model mmcif' % xtal) cif = '' for line in open(self.db_dict['CompoundCode']+'.cif'): cif += line - f = open(xtal+'.mmcif','a') + f = open(xtal+'.mmcif', 'a') f.write(cif) f.close() filestatus = True else: - self.Logfile.warning('%s: could not find %s' %(xtal,self.db_dict['CompoundCode']+'.cif')) + self.Logfile.warning('%s: could not find %s' % ( + xtal, self.db_dict['CompoundCode']+'.cif')) return filestatus - - def make_table_one(self,xtal): + def make_table_one(self, xtal): os.chdir(os.path.join(self.projectDir, xtal)) if os.path.isfile(xtal + '.mmcif') and os.path.getsize(xtal + '.mmcif') > 20000: - self.Logfile.insert('making table_1 for %s.mmcif' %xtal) + self.Logfile.insert('making table_1 for %s.mmcif' % xtal) if os.path.isdir('/dls'): extract_table_init = 'source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n' extract_table_init += '/dls/science/groups/i04-1/software/pdb-extract-prod/bin/extract_table' else: extract_table_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' + 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' extract_table_init += os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/bin/extract_table') + 'pdb_extract/pdb-extract-prod/bin/extract_table') Cmd = extract_table_init + ' ' + xtal + '.mmcif' @@ -1224,14 +1309,15 @@ def make_table_one(self,xtal): os.system(Cmd) if os.path.isfile('cryst-table-1.out'): - os.system('/bin/mv cryst-table-1.out %s-table-1.txt' %xtal) - self.Logfile.insert('%s: table_1 successfully created; updating database...' %xtal) - self.db.execute_statement("update mainTable set table_one='{0!s}-table-1.txt' where CrystalName is '{1!s}'".format(xtal,xtal)) + os.system('/bin/mv cryst-table-1.out %s-table-1.txt' % xtal) + self.Logfile.insert( + '%s: table_1 successfully created; updating database...' % xtal) + self.db.execute_statement( + "update mainTable set table_one='{0!s}-table-1.txt' where CrystalName is '{1!s}'".format(xtal, xtal)) else: - self.Logfile.warning('%s: could not create table_1' %xtal) + self.Logfile.warning('%s: could not create table_1' % xtal) - - def create_sf_mmcif(self,xtal): + def create_sf_mmcif(self, xtal): fileStatus = False if self.ground_state: os.chdir(self.projectDir) @@ -1252,33 +1338,39 @@ def create_sf_mmcif(self,xtal): pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n' pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-prod/bin/sf_convert' else: - if os.path.isfile(os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/bin/sf_convert')): + if os.path.isfile(os.path.join(os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/bin/sf_convert')): pdb_extract_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' - pdb_extract_init += os.path.join(os.getenv('XChemExplorer_DIR'),'pdb_extract/pdb-extract-prod/bin/sf_convert') + pdb_extract_init += os.path.join( + os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/bin/sf_convert') else: pdb_extract_init = 'sf_convert' Cmd = (pdb_extract_init + - ' -o mmcif' - ' -sf %s' % mtzin + - ' -out {0!s}_sf.mmcif > {1!s}.sf_mmcif.log'.format(xtal, xtal)) + ' -o mmcif' + ' -sf %s' % mtzin + + ' -out {0!s}_sf.mmcif > {1!s}.sf_mmcif.log'.format(xtal, xtal)) self.Logfile.insert(xtal + ': running sf_convert: ' + Cmd) os.system(Cmd) - os.system('/bin/rm sf_format_guess.text mtzdmp.log SF_4_validate.cif sf_information.cif') + os.system( + '/bin/rm sf_format_guess.text mtzdmp.log SF_4_validate.cif sf_information.cif') self.update_sf_mmcif_file(xtal) - if os.path.isfile(xtal+'_sf.mmcif') and os.path.getsize(xtal+'_sf.mmcif') > 20000 : - self.Logfile.insert('%s: SF mmcif file successfully created' %xtal) + if os.path.isfile(xtal+'_sf.mmcif') and os.path.getsize(xtal+'_sf.mmcif') > 20000: + self.Logfile.insert( + '%s: SF mmcif file successfully created' % xtal) if self.ground_state: - self.db.execute_statement("update depositTable set mmCIF_SF_file='{0!s}_sf.mmcif' where CrystalName is '{1!s}' and DimplePANDDApath is '{2!s}'".format(xtal,xtal,self.panddaDir)) + self.db.execute_statement( + "update depositTable set mmCIF_SF_file='{0!s}_sf.mmcif' where CrystalName is '{1!s}' and DimplePANDDApath is '{2!s}'".format(xtal, xtal, self.panddaDir)) else: - self.db.execute_statement("update depositTable set mmCIF_SF_file='{0!s}_sf.mmcif' where CrystalName is '{1!s}'".format(xtal,xtal)) + self.db.execute_statement( + "update depositTable set mmCIF_SF_file='{0!s}_sf.mmcif' where CrystalName is '{1!s}'".format(xtal, xtal)) fileStatus = True else: - self.Logfile.error('%s: SF mmcif file was not created successfully') + self.Logfile.error( + '%s: SF mmcif file was not created successfully') self.add_to_errorList(xtal) return fileStatus @@ -1287,25 +1379,29 @@ def apo_mmcif_exists(self): fileStatus = False self.Logfile.insert('checking if mmcif files of apo structures exist') counter = 0 - for mmcif in glob.glob(os.path.join(self.panddaDir,'processed_datasets','*','*.mmcif')): + for mmcif in glob.glob(os.path.join(self.panddaDir, 'processed_datasets', '*', '*.mmcif')): if os.path.isfile(mmcif): counter += 1 if counter < 40: - self.Logfile.error('found only %s apo mmcif files' %str(counter)) - self.Logfile.warning('you may need to run "PanDDA tab"/"apo -> mmcif"') + self.Logfile.error('found only %s apo mmcif files' % str(counter)) + self.Logfile.warning( + 'you may need to run "PanDDA tab"/"apo -> mmcif"') else: - self.Logfile.insert('found %s apo mmcif files; seems OK!' %str(counter)) + self.Logfile.insert( + 'found %s apo mmcif files; seems OK!' % str(counter)) fileStatus = True return fileStatus - def add_apo_sf_mmcif_to_ground_state_mmcif(self): os.chdir(self.projectDir) - self.Logfile.insert('checking pandda directory for apo mmcif files: '+self.panddaDir) - f = open('ground_state_sf.mmcif','w') - - refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/'))-2] - xtalList = [refXtal] # make sure that mmcof belonging to ref PDB file is first + self.Logfile.insert( + 'checking pandda directory for apo mmcif files: '+self.panddaDir) + f = open('ground_state_sf.mmcif', 'w') + + refXtal = self.ground_state_pdb.split( + '/')[len(self.ground_state_pdb.split('/'))-2] + # make sure that mmcof belonging to ref PDB file is first + xtalList = [refXtal] for dirs in glob.glob(os.path.join(self.panddaDir, 'processed_datasets', '*')): xtal = dirs[dirs.rfind('/') + 1:] if xtal not in xtalList: @@ -1313,40 +1409,47 @@ def add_apo_sf_mmcif_to_ground_state_mmcif(self): counter = 1 for xtal in xtalList: - if not os.path.isdir(os.path.join(self.panddaDir, 'processed_datasets', xtal)): # this is needed in case single files are in processed_datasets + # this is needed in case single files are in processed_datasets + if not os.path.isdir(os.path.join(self.panddaDir, 'processed_datasets', xtal)): continue else: dirs = os.path.join(self.panddaDir, 'processed_datasets', xtal) - self.Logfile.insert('%s: reading saoked compound information from database' %xtal) + self.Logfile.insert( + '%s: reading saoked compound information from database' % xtal) xtalDict = self.db.get_db_dict_for_sample(xtal) - if xtalDict['CompoundSMILES'].lower().replace(' ','') == '': + if xtalDict['CompoundSMILES'].lower().replace(' ', '') == '': smiles = 'none' - elif 'none' in xtalDict['CompoundSMILES'].lower().replace(' ',''): + elif 'none' in xtalDict['CompoundSMILES'].lower().replace(' ', ''): smiles = 'none' - elif 'null' in xtalDict['CompoundSMILES'].lower().replace(' ',''): + elif 'null' in xtalDict['CompoundSMILES'].lower().replace(' ', ''): smiles = 'none' else: - smiles = xtalDict['CompoundSMILES'].replace(' ','') - self.Logfile.insert('%s: compound SMILES -> %s' %(xtal,smiles)) - if os.path.isfile(os.path.join(dirs,xtal+'_sf.mmcif')): - self.Logfile.insert('adding %s_sf.mmcif to ground-state_sf.mmcif' %xtal) - for line in open(os.path.join(dirs,xtal+'_sf.mmcif')): + smiles = xtalDict['CompoundSMILES'].replace(' ', '') + self.Logfile.insert('%s: compound SMILES -> %s' % (xtal, smiles)) + if os.path.isfile(os.path.join(dirs, xtal+'_sf.mmcif')): + self.Logfile.insert( + 'adding %s_sf.mmcif to ground-state_sf.mmcif' % xtal) + for line in open(os.path.join(dirs, xtal+'_sf.mmcif')): if line.startswith('_cell.angle_gamma'): newLine = line newLine += '#\n' newLine += '_diffrn.id 1\n' - newLine += '_diffrn.details "diffraction data from crystal %s; soaked compound: %s"\n' %(str(counter),smiles.replace('\n','').replace('\r','')) + newLine += '_diffrn.details "diffraction data from crystal %s; soaked compound: %s"\n' % ( + str(counter), smiles.replace('\n', '').replace('\r', '')) f.write(newLine) counter += 1 else: f.write(line) f.close() - self.Logfile.insert('added %s apo mmcif files to ground-state mmcif' %str(counter)) + self.Logfile.insert( + 'added %s apo mmcif files to ground-state mmcif' % str(counter)) return True def add_data_increment_to_apo_mmcif(self): - self.Logfile.insert('inrementing data_rxxxxsf in ground-state_sf.mmcif') - x = ['','A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'] + self.Logfile.insert( + 'inrementing data_rxxxxsf in ground-state_sf.mmcif') + x = ['', 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', + 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'] a = 0 b = 0 c = 0 @@ -1354,9 +1457,9 @@ def add_data_increment_to_apo_mmcif(self): foundFirstLine = False foundCulprit = False datasetCounter = 0 - if os.path.isfile(os.path.join(self.panddaDir,'ground_state_sf.mmcif')): - f = open('ground_state_sf_tmp.mmcif','w') - for n,line in enumerate(open(os.path.join(self.panddaDir,'ground_state_sf.mmcif'))): + if os.path.isfile(os.path.join(self.panddaDir, 'ground_state_sf.mmcif')): + f = open('ground_state_sf_tmp.mmcif', 'w') + for n, line in enumerate(open(os.path.join(self.panddaDir, 'ground_state_sf.mmcif'))): if line.startswith('data_rxxxxsf') and not foundFirstLine: foundFirstLine = True a += 1 @@ -1369,11 +1472,13 @@ def add_data_increment_to_apo_mmcif(self): a = 1 b = 1 c += 1 - newLine = line.replace('xsf','s%ssf' %str(x[a]+x[b]+x[c])) + newLine = line.replace('xsf', 's%ssf' % + str(x[a]+x[b]+x[c])) datasetCounter += 1 f.write(newLine) a += 1 - self.Logfile.insert('new dataset block: %s -> %s' %(str(datasetCounter),newLine.replace('\n','').replace('\r',''))) + self.Logfile.insert('new dataset block: %s -> %s' % ( + str(datasetCounter), newLine.replace('\n', '').replace('\r', ''))) # if datasetCounter % 50 == 0: # self.Logfile.insert('%s data_rxxxxsf records edited...' %str(datasetCounter)) else: @@ -1382,21 +1487,25 @@ def add_data_increment_to_apo_mmcif(self): os.chdir(self.panddaDir) os.system('/bin/mv ground_state_sf_tmp.mmcif ground_state_sf.mmcif') - if os.path.isfile('ground_state_sf.mmcif') and os.path.getsize('ground_state_sf.mmcif') > 20000 : - self.Logfile.insert('ground_state: SF mmcif file successfully created') - self.db.execute_statement("update depositTable set mmCIF_SF_file='ground_state_sf.mmcif' where CrystalName is 'ground_state' and DimplePANDDApath is '{0!s}'".format(self.panddaDir)) + if os.path.isfile('ground_state_sf.mmcif') and os.path.getsize('ground_state_sf.mmcif') > 20000: + self.Logfile.insert( + 'ground_state: SF mmcif file successfully created') + self.db.execute_statement( + "update depositTable set mmCIF_SF_file='ground_state_sf.mmcif' where CrystalName is 'ground_state' and DimplePANDDApath is '{0!s}'".format(self.panddaDir)) else: - self.Logfile.error('%s: SF mmcif file was not created successfully') + self.Logfile.error( + '%s: SF mmcif file was not created successfully') self.add_to_errorList(xtal) return True - - def event_maps_exist_in_sf_mmcif(self,xtal): + def event_maps_exist_in_sf_mmcif(self, xtal): fileOK = False - n_eventMTZ_found = -2 # set to -2 since first two data blocks are initial/final.mtz and data.mtz + # set to -2 since first two data blocks are initial/final.mtz and data.mtz + n_eventMTZ_found = -2 if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: - self.Logfile.warning('%s: no pandda analysis performed; skipping this step...' %xtal) + self.Logfile.warning( + '%s: no pandda analysis performed; skipping this step...' % xtal) fileOK = True else: for line in open(xtal + '_sf.mmcif'): @@ -1404,30 +1513,32 @@ def event_maps_exist_in_sf_mmcif(self,xtal): n_eventMTZ_found += 1 if n_eventMTZ_found == len(self.eventList): fileOK = True - self.Logfile.insert('%s: %s_sf.mmcif should contains %s of %s event maps' %(xtal,xtal,n_eventMTZ_found,len(self.eventList))) + self.Logfile.insert('%s: %s_sf.mmcif should contains %s of %s event maps' % ( + xtal, xtal, n_eventMTZ_found, len(self.eventList))) else: self.Logfile.error('%s: %s_sf.mmcif should contains only %s of %s event maps' % ( - xtal, xtal, n_eventMTZ_found, len(self.eventList))) + xtal, xtal, n_eventMTZ_found, len(self.eventList))) self.add_to_errorList(xtal) return fileOK - - def update_sf_mmcif_file(self,xtal): - self.Logfile.insert('%s: updating %s_sf.mmcif' %(xtal,xtal)) + def update_sf_mmcif_file(self, xtal): + self.Logfile.insert('%s: updating %s_sf.mmcif' % (xtal, xtal)) if self.ground_state: - bound = [ "data for PanDDA ground-state-mean-map" ] + bound = ["data for PanDDA ground-state-mean-map"] else: - bound = [ "data from final refinement with ligand, final.mtz", - "data from original reflections, data.mtz", - "data for ligand evidence map (PanDDA event map), event_map_$.mtz" ] + bound = ["data from final refinement with ligand, final.mtz", + "data from original reflections, data.mtz", + "data for ligand evidence map (PanDDA event map), event_map_$.mtz"] block = -1 - self.Logfile.insert('%s: reading wavelength from mtz file; lambda = %s' %(xtal,str(self.data_template_dict['radiation_wavelengths']))) + self.Logfile.insert('%s: reading wavelength from mtz file; lambda = %s' % ( + xtal, str(self.data_template_dict['radiation_wavelengths']))) if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: - self.Logfile.warning('%s: apparently not a pandda deposition; will skip this step...' %xtal) + self.Logfile.warning( + '%s: apparently not a pandda deposition; will skip this step...' % xtal) return None for i, line in enumerate(fileinput.input(xtal + '_sf.mmcif', inplace=1)): @@ -1443,110 +1554,123 @@ def update_sf_mmcif_file(self,xtal): sys.stdout.write(line) newLines = ('#\n' '_diffrn.id 1\n' - '_diffrn.details "%s"\n' % bound[n]).replace('$',str(block-1)) + '_diffrn.details "%s"\n' % bound[n]).replace('$', str(block-1)) sys.stdout.write(newLines) elif line.startswith('_diffrn_radiation_wavelength.wavelength'): - sys.stdout.write('_diffrn_radiation_wavelength.wavelength {0!s}\n'.format(str(self.data_template_dict['radiation_wavelengths']))) + sys.stdout.write('_diffrn_radiation_wavelength.wavelength {0!s}\n'.format( + str(self.data_template_dict['radiation_wavelengths']))) else: sys.stdout.write(line) - - - class prepare_for_group_deposition_upload(QtCore.QThread): - def __init__(self,database,xce_logfile,depositDir,projectDir,type): + def __init__(self, database, xce_logfile, depositDir, projectDir, type): QtCore.QThread.__init__(self) - self.database=database - self.Logfile=XChemLog.updateLog(xce_logfile) - self.db=XChemDB.data_source(database) - self.depositDir=depositDir - self.projectDir=projectDir - self.type=type - - + self.database = database + self.Logfile = XChemLog.updateLog(xce_logfile) + self.db = XChemDB.data_source(database) + self.depositDir = depositDir + self.projectDir = projectDir + self.type = type def run(self): - TextIndex='' + TextIndex = '' os.chdir(self.depositDir) # ligand bound structures if self.type == 'ligand_bound': - self.Logfile.insert('checking depositionTable for mmcif files of ligand-bound structures') - depositList = self.db.execute_statement("select CrystalName from mainTable where RefinementOutcome like '5%';") + self.Logfile.insert( + 'checking depositionTable for mmcif files of ligand-bound structures') + depositList = self.db.execute_statement( + "select CrystalName from mainTable where RefinementOutcome like '5%';") xtalString = '(' for item in depositList: - xtal=str(item[0]) - self.Logfile.insert('%s: adding mmcif files to final tar.bz2 file' %xtal) + xtal = str(item[0]) + self.Logfile.insert( + '%s: adding mmcif files to final tar.bz2 file' % xtal) xtalString += "CrystalName = '"+xtal+"' or " xtalString = xtalString[:-4] + ')' - toDeposit=self.db.execute_statement("select CrystalName,mmCIF_model_file,mmCIF_SF_file,DimplePANDDApath from depositTable where StructureType is 'ligand_bound' and %s;" %xtalString) + toDeposit = self.db.execute_statement( + "select CrystalName,mmCIF_model_file,mmCIF_SF_file,DimplePANDDApath from depositTable where StructureType is 'ligand_bound' and %s;" % xtalString) elif self.type == 'ground_state': - self.Logfile.insert('checking depositionTable for mmcif files of ground-state structures') - toDeposit = self.db.execute_statement("select CrystalName,mmCIF_model_file,mmCIF_SF_file,DimplePANDDApath from depositTable where StructureType is 'ground_state';") + self.Logfile.insert( + 'checking depositionTable for mmcif files of ground-state structures') + toDeposit = self.db.execute_statement( + "select CrystalName,mmCIF_model_file,mmCIF_SF_file,DimplePANDDApath from depositTable where StructureType is 'ground_state';") else: return - for n,item in enumerate(sorted(toDeposit)): - xtal=str(item[0]) + for n, item in enumerate(sorted(toDeposit)): + xtal = str(item[0]) if self.type == 'ligand_bound': - mmcif=os.path.join(self.projectDir,xtal,str(item[1])) - mmcif_sf=os.path.join(self.projectDir,xtal,str(item[2])) + mmcif = os.path.join(self.projectDir, xtal, str(item[1])) + mmcif_sf = os.path.join(self.projectDir, xtal, str(item[2])) elif self.type == 'ground_state': - mmcif=os.path.join(str(item[3]),str(item[1])) - mmcif_sf=os.path.join(str(item[3]),str(item[2])) + mmcif = os.path.join(str(item[3]), str(item[1])) + mmcif_sf = os.path.join(str(item[3]), str(item[2])) else: continue - self.Logfile.insert('%s: %s/ %s' %(xtal,mmcif,mmcif_sf)) + self.Logfile.insert('%s: %s/ %s' % (xtal, mmcif, mmcif_sf)) if os.path.isfile(mmcif) and os.path.isfile(mmcif_sf): - self.Logfile.insert('copying {0!s} to {1!s}'.format(mmcif, self.depositDir)) + self.Logfile.insert( + 'copying {0!s} to {1!s}'.format(mmcif, self.depositDir)) os.system('/bin/cp {0!s} .'.format(mmcif)) if self.type == 'ground_state': - os.system('/bin/mv ground_state.mmcif ground_state_{0!s}.mmcif'.format(str(n))) - mmcif = mmcif.replace('ground_state.mmcif','ground_state_{0!s}.mmcif'.format(str(n))) - self.Logfile.insert('copying {0!s} to {1!s}'.format(mmcif_sf, self.depositDir)) + os.system( + '/bin/mv ground_state.mmcif ground_state_{0!s}.mmcif'.format(str(n))) + mmcif = mmcif.replace( + 'ground_state.mmcif', 'ground_state_{0!s}.mmcif'.format(str(n))) + self.Logfile.insert('copying {0!s} to {1!s}'.format( + mmcif_sf, self.depositDir)) os.system('/bin/cp {0!s} .'.format(mmcif_sf)) if self.type == 'ground_state': - os.system('/bin/mv ground_state_sf.mmcif ground_state_{0!s}_sf.mmcif'.format(str(n))) - mmcif_sf = mmcif_sf.replace('ground_state_sf.mmcif', 'ground_state_{0!s}_sf.mmcif'.format(str(n))) + os.system( + '/bin/mv ground_state_sf.mmcif ground_state_{0!s}_sf.mmcif'.format(str(n))) + mmcif_sf = mmcif_sf.replace( + 'ground_state_sf.mmcif', 'ground_state_{0!s}_sf.mmcif'.format(str(n))) else: self.Logfile.error('cannot find mmcif file for '+xtal) - text = ( 'label: {0!s}-{1!s}\n'.format(xtal,self.type)+ - 'description: {0!s} structure of {1!s}\n'.format(self.type,xtal)+ - 'model: {0!s}\n'.format(mmcif[mmcif.rfind('/')+1:])+ - 'sf: {0!s}\n\n'.format(mmcif_sf[mmcif_sf.rfind('/')+1:]) ) - TextIndex+=text + text = ('label: {0!s}-{1!s}\n'.format(xtal, self.type) + + 'description: {0!s} structure of {1!s}\n'.format(self.type, xtal) + + 'model: {0!s}\n'.format(mmcif[mmcif.rfind('/')+1:]) + + 'sf: {0!s}\n\n'.format(mmcif_sf[mmcif_sf.rfind('/')+1:])) + TextIndex += text - f = open('index.txt','w') + f = open('index.txt', 'w') f.write(TextIndex) f.close() # checking of tar.bz2 files exisit fileList = [] - for i in sorted(glob.glob('%s_structures.tar.bz2.*' %self.type)): + for i in sorted(glob.glob('%s_structures.tar.bz2.*' % self.type)): fileList.append(int(i[i.rfind('.')+1:])) - if os.path.isfile('%s_structures.tar.bz2' %self.type): + if os.path.isfile('%s_structures.tar.bz2' % self.type): if fileList == []: - self.Logfile.warning('moving existing %s_structures.tar.bz2 to %s_structures.tar.bz2.1' %(self.type,self.type)) - os.system('/bin/mv %s_structures.tar.bz2 %s_structures.tar.bz2.1' %(self.type,self.type)) + self.Logfile.warning( + 'moving existing %s_structures.tar.bz2 to %s_structures.tar.bz2.1' % (self.type, self.type)) + os.system( + '/bin/mv %s_structures.tar.bz2 %s_structures.tar.bz2.1' % (self.type, self.type)) else: - self.Logfile.warning('moving existing %s_structures.tar.bz2 %s_structures.tar.bz2.%s' %(self.type,self.type,str(max(fileList)+1))) - os.system('/bin/mv %s_structures.tar.bz2 %s_structures.tar.bz2.%s' %(self.type,self.type,str(max(fileList)+1))) + self.Logfile.warning('moving existing %s_structures.tar.bz2 %s_structures.tar.bz2.%s' % ( + self.type, self.type, str(max(fileList)+1))) + os.system('/bin/mv %s_structures.tar.bz2 %s_structures.tar.bz2.%s' % + (self.type, self.type, str(max(fileList)+1))) self.Logfile.insert('preparing tar archive...') - os.system('tar -cvf {0!s}_structures.tar *mmcif index.txt'.format(self.type)) + os.system( + 'tar -cvf {0!s}_structures.tar *mmcif index.txt'.format(self.type)) self.Logfile.insert('bzipping archive...') os.system('bzip2 {0!s}_structures.tar'.format(self.type)) - self.Logfile.insert('removing all bound mmcif files and index.txt file from '+self.depositDir) + self.Logfile.insert( + 'removing all bound mmcif files and index.txt file from '+self.depositDir) os.system('/bin/rm -f *mmcif index.txt') self.Logfile.insert('done!') - # # apo structures # TextIndex='' # toDeposit=self.db.execute_statement("select CrystalName,mmCIF_model_file,mmCIF_SF_file from depositTable where StructureType is 'apo';") @@ -1582,79 +1706,83 @@ def run(self): # - class import_PDB_IDs(QtCore.QThread): - def __init__(self,pdbCodes,database,xce_logfile): + def __init__(self, pdbCodes, database, xce_logfile): QtCore.QThread.__init__(self) - self.pdbCodes=pdbCodes - self.database=database - self.Logfile=XChemLog.updateLog(xce_logfile) - self.db=XChemDB.data_source(database) + self.pdbCodes = pdbCodes + self.database = database + self.Logfile = XChemLog.updateLog(xce_logfile) + self.db = XChemDB.data_source(database) def run(self): for line in self.pdbCodes.split('\n'): if len(line.split('/')) == 2 and '-ligand_bound' in line: - xtal=line[:line.rfind('-ligand_bound')].replace(' ','') - pdbID=line.split('/')[1].replace(' ','') + xtal = line[:line.rfind('-ligand_bound')].replace(' ', '') + pdbID = line.split('/')[1].replace(' ', '') self.Logfile.insert('setting PDB ID for '+xtal+' to '+pdbID) - sqlite="UPDATE mainTable SET Deposition_PDB_ID='{0!s}',RefinementOutcome='6 - Deposited' where CrystalName is '{1!s}';".format(pdbID, xtal) + sqlite = "UPDATE mainTable SET Deposition_PDB_ID='{0!s}',RefinementOutcome='6 - Deposited' where CrystalName is '{1!s}';".format( + pdbID, xtal) self.db.execute_statement(sqlite) class compare_smiles_in_db_with_ligand_in_pdb(QtCore.QThread): - def __init__(self,projectDir,database,xce_logfile): + def __init__(self, projectDir, database, xce_logfile): QtCore.QThread.__init__(self) - self.projectDir=projectDir - self.database=database - self.Logfile=XChemLog.updateLog(xce_logfile) - self.db=XChemDB.data_source(database) - self.ErrorDict={} + self.projectDir = projectDir + self.database = database + self.Logfile = XChemLog.updateLog(xce_logfile) + self.db = XChemDB.data_source(database) + self.ErrorDict = {} - def update_ErrorDict(self,xtal,message): + def update_ErrorDict(self, xtal, message): if xtal not in self.ErrorDict: - self.ErrorDict[xtal]=[] + self.ErrorDict[xtal] = [] self.ErrorDict[xtal].append(message) def run(self): os.chdir(self.projectDir) - progress_step=1 + progress_step = 1 if len(glob.glob('*')) != 0: - progress_step=100/float(len(glob.glob('*'))) + progress_step = 100/float(len(glob.glob('*'))) else: - progress_step=1 - progress=0 + progress_step = 1 + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - for xtal in sorted(glob.glob('*')): - if os.path.isfile(os.path.join(xtal,'refine.pdb')): - smiles=self.db.execute_statement("select CompoundSmiles,CompoundCode from mainTable where CrystalName is '{0!s}'".format(xtal)) + if os.path.isfile(os.path.join(xtal, 'refine.pdb')): + smiles = self.db.execute_statement( + "select CompoundSmiles,CompoundCode from mainTable where CrystalName is '{0!s}'".format(xtal)) try: - LigandSmiles=str(smiles[0][0]) - LigandCode=str(smiles[0][1]) - elementDict_smiles=smilestools(LigandSmiles).ElementDict() + LigandSmiles = str(smiles[0][0]) + LigandCode = str(smiles[0][1]) + elementDict_smiles = smilestools( + LigandSmiles).ElementDict() except IndexError: - self.Logfile.error("{0!s}: something is seems to be wrong with the CompoundCode or SMILES string: {1!s}".format(xtal, str(smiles))) + self.Logfile.error( + "{0!s}: something is seems to be wrong with the CompoundCode or SMILES string: {1!s}".format(xtal, str(smiles))) continue - pdb=pdbtools(os.path.join(xtal,'refine.pdb')) - ligandList=pdb.ligand_details_as_list() + pdb = pdbtools(os.path.join(xtal, 'refine.pdb')) + ligandList = pdb.ligand_details_as_list() for ligand in ligandList: - resname = ligand[0] - chainID = ligand[1] - resseq = ligand[2] - altLoc = ligand[3] - elementDict_ligand=pdb.ElementDict(resname,chainID,resseq,altLoc) + resname = ligand[0] + chainID = ligand[1] + resseq = ligand[2] + altLoc = ligand[3] + elementDict_ligand = pdb.ElementDict( + resname, chainID, resseq, altLoc) for element in elementDict_ligand: if elementDict_ligand[element] != elementDict_smiles[element]: - self.Logfile.error('{0!s}: {1!s} {2!s} {3!s} {4!s} contains different number of atoms than smiles in DB: {5!s} -> {6!s}'.format(xtal, resname, chainID, resseq, altLoc, LigandSmiles, LigandCode)) - self.update_ErrorDict(xtal, '{0!s} {1!s} {2!s} {3!s} contains different number of atoms than smiles in DB'.format(resname, chainID, resseq, altLoc)) + self.Logfile.error('{0!s}: {1!s} {2!s} {3!s} {4!s} contains different number of atoms than smiles in DB: {5!s} -> {6!s}'.format( + xtal, resname, chainID, resseq, altLoc, LigandSmiles, LigandCode)) + self.update_ErrorDict(xtal, '{0!s} {1!s} {2!s} {3!s} contains different number of atoms than smiles in DB'.format( + resname, chainID, resseq, altLoc)) break - progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) diff --git a/lib/XChemDialogs.py b/lib/XChemDialogs.py index 921ee67f..7d333f6e 100755 --- a/lib/XChemDialogs.py +++ b/lib/XChemDialogs.py @@ -3,33 +3,35 @@ import XChemDB + class select_columns_to_show(QtGui.QDialog): - def __init__(self, data_source_file,parent = None): + def __init__(self, data_source_file, parent=None): super(select_columns_to_show, self).__init__(parent) - self.columns_in_data_source=XChemDB.data_source(data_source_file).return_column_list() + self.columns_in_data_source = XChemDB.data_source( + data_source_file).return_column_list() - self.column_dict={} + self.column_dict = {} layout = QtGui.QVBoxLayout(self) - number_of_entries=len(self.columns_in_data_source) - columns_shown_in_dialog_column=25 + number_of_entries = len(self.columns_in_data_source) + columns_shown_in_dialog_column = 25 grid = QtGui.QGridLayout() - x=0 - y=0 - columns_to_ignore=['Sample ID','ID'] + x = 0 + y = 0 + columns_to_ignore = ['Sample ID', 'ID'] for entries_added in range(number_of_entries): if not self.columns_in_data_source[entries_added][1] in columns_to_ignore: - data_source_column = QtGui.QCheckBox(self.columns_in_data_source[entries_added][1]) - self.column_dict[entries_added]=data_source_column + data_source_column = QtGui.QCheckBox( + self.columns_in_data_source[entries_added][1]) + self.column_dict[entries_added] = data_source_column # data_source_column.toggle() - grid.addWidget(data_source_column, y,x) - y+=1 - if y==columns_shown_in_dialog_column: - y=0 - x+=1 + grid.addWidget(data_source_column, y, x) + y += 1 + if y == columns_shown_in_dialog_column: + y = 0 + x += 1 layout.addLayout(grid) - # OK and Cancel buttons buttons = QtGui.QDialogButtonBox( QtGui.QDialogButtonBox.Ok | QtGui.QDialogButtonBox.Cancel, @@ -39,7 +41,7 @@ def __init__(self, data_source_file,parent = None): layout.addWidget(buttons) def data_source_column_active(self): - columns_to_show=['Sample ID'] + columns_to_show = ['Sample ID'] for key in self.column_dict: if self.column_dict[key].isChecked(): columns_to_show.append(self.columns_in_data_source[key][1]) @@ -47,8 +49,8 @@ def data_source_column_active(self): # static method to create the dialog and return (date, time, accepted) @staticmethod - def return_selected_columns(parent = None): + def return_selected_columns(parent=None): dialog = select_columns_to_show(parent) result = dialog.exec_() columns = dialog.data_source_column_active() - return (columns,result == QtGui.QDialog.Accepted) + return (columns, result == QtGui.QDialog.Accepted) diff --git a/lib/XChemLigand.py b/lib/XChemLigand.py index 45f1f38a..857cc0b9 100755 --- a/lib/XChemLigand.py +++ b/lib/XChemLigand.py @@ -2,10 +2,12 @@ from rdkit import Chem from rdkit.Chem import AllChem + def generate_steroisomers(input_smiles): """ Function to generate all stereoisomers from a SMILES String. Only works on latest version of RDKit. """ mol = Chem.MolFromSmiles(input_smiles) - out_mols = AllChem.EnumerateStereoisomers(mol,AllChem.StereoEnumerationOptions(onlyUnassigned=False,tryEmbedding=True)) - return [Chem.MolToSmiles(x,isomericSmiles=True) for x in out_mols] + out_mols = AllChem.EnumerateStereoisomers( + mol, AllChem.StereoEnumerationOptions(onlyUnassigned=False, tryEmbedding=True)) + return [Chem.MolToSmiles(x, isomericSmiles=True) for x in out_mols] diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 94ebc741..33af521e 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -1,22 +1,24 @@ # last edited: 09/02/2017, 15:00 from __future__ import print_function -import os,glob +import os +import glob import sys from datetime import datetime -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + class startLog: - def __init__(self,logfile): - self.logfile=logfile + def __init__(self, logfile): + self.logfile = logfile - def create_logfile(self,version): + def create_logfile(self, version): - pasteVersion=version - for i in range(0,20-len(version)): - pasteVersion+=' ' + pasteVersion = version + for i in range(0, 20-len(version)): + pasteVersion += ' ' message = ( '\n\n' @@ -24,7 +26,7 @@ def create_logfile(self,version): ' # #\n' ' # XCHEMEXPLORER - multi dataset analysis #\n' ' # #\n' - ' # Version: %s #\n' %pasteVersion+ + ' # Version: %s #\n' % pasteVersion + ' # #\n' ' # Date: 10/10/2022 #\n' ' # #\n' @@ -37,14 +39,16 @@ def create_logfile(self,version): if not os.path.isfile(self.logfile): os.system('touch '+self.logfile) - message+='creating new logfile for the current XChemExplorer ('+version+') session:\n'+self.logfile+'\n' + message += 'creating new logfile for the current XChemExplorer (' + \ + version+') session:\n'+self.logfile+'\n' else: - message+='writing into existing logfile for current XChemExplorer ('+version+') session:\n'+self.logfile+'\n' + message += 'writing into existing logfile for current XChemExplorer (' + \ + version+') session:\n'+self.logfile+'\n' updateLog(self.logfile).insert(message) - #print(message) + # print(message) -#class depositLog: +# class depositLog: # # def __init__(self,logfile): # self.logfile=logfile @@ -102,28 +106,32 @@ def create_logfile(self,version): # # updateLog(self.logfile).insert(message) + class updateLog: - def __init__(self,logfile): - self.logfile=open(logfile, "a") + def __init__(self, logfile): + self.logfile = open(logfile, "a") - def insert(self,message): - present_time=datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] - print( str(present_time)+' ==> XCE: '+message, file = self.logfile) + def insert(self, message): + present_time = datetime.strftime( + datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] + print(str(present_time)+' ==> XCE: '+message, file=self.logfile) print('==> XCE: '+message) - def warning(self,message): - present_time=datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] - print( str(present_time)+' ==> XCE: WARNING! '+message, file = self.logfile) + def warning(self, message): + present_time = datetime.strftime( + datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] + print(str(present_time)+' ==> XCE: WARNING! '+message, file=self.logfile) print('==> XCE: WARNING! '+message) - def error(self,message): - present_time=datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] - print( str(present_time)+' ==> XCE: ERROR!!! '+message, file = self.logfile) + def error(self, message): + present_time = datetime.strftime( + datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] + print(str(present_time)+' ==> XCE: ERROR!!! '+message, file=self.logfile) print('==> XCE: ERROR!!! '+message) - def hint(self,message): - present_time=datetime.strftime(datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] - print( str(present_time)+' ==> XCE: HINT -> '+message, file = self.logfile) + def hint(self, message): + present_time = datetime.strftime( + datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] + print(str(present_time)+' ==> XCE: HINT -> '+message, file=self.logfile) print('==> XCE: HINT -> '+message) - diff --git a/lib/XChemMain.py b/lib/XChemMain.py index 695c3beb..b79d693c 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -1,6 +1,9 @@ # last edited: 15/05/2017, 15:00 -import os,glob +import XChemLog +import XChemDB +import os +import glob import sys import subprocess import getpass @@ -8,35 +11,32 @@ from datetime import datetime from PyQt4 import QtGui, QtCore -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) - -import XChemDB -import XChemLog +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) def space_group_list(): - space_group_list = [ 'P1', - 'P2','P21','C121','P1211','P121','I2','I121', - 'P222','P2122','P2212','P2221', - 'P21212','P21221','P22121','P212121', - 'C222','C2221','F222', 'I222', 'I212121', - 'P4','P41','P42','P43','I4','I41', - 'P422','P4212','P4122','P41212','P4222', - 'P42212','P4322','P43212','I422','I4122' , - 'P3','P31','P32', - 'P312','P321','P3112','P3121','P3212','P3221', - 'P6','P61','P65','P62','P64','P63', - 'P622','P6122','P6522','P6222','P6422','P6322', - 'H3','H32', - 'P23','F23','I23','P213','I213', - 'P432','P4232','F432','F4132','I432','P4332','P4132','I4132' ] + space_group_list = ['P1', + 'P2', 'P21', 'C121', 'P1211', 'P121', 'I2', 'I121', + 'P222', 'P2122', 'P2212', 'P2221', + 'P21212', 'P21221', 'P22121', 'P212121', + 'C222', 'C2221', 'F222', 'I222', 'I212121', + 'P4', 'P41', 'P42', 'P43', 'I4', 'I41', + 'P422', 'P4212', 'P4122', 'P41212', 'P4222', + 'P42212', 'P4322', 'P43212', 'I422', 'I4122', + 'P3', 'P31', 'P32', + 'P312', 'P321', 'P3112', 'P3121', 'P3212', 'P3221', + 'P6', 'P61', 'P65', 'P62', 'P64', 'P63', + 'P622', 'P6122', 'P6522', 'P6222', 'P6422', 'P6322', + 'H3', 'H32', + 'P23', 'F23', 'I23', 'P213', 'I213', + 'P432', 'P4232', 'F432', 'F4132', 'I432', 'P4332', 'P4132', 'I4132'] return space_group_list -def get_target_and_visit_list(beamline_directory,agamemnon): -# target_list=['*'] # always give the option to read in all targets - target_list=['=== SELECT TARGET ===','=== project directory ==='] - visit_list=[] +def get_target_and_visit_list(beamline_directory, agamemnon): + # target_list=['*'] # always give the option to read in all targets + target_list = ['=== SELECT TARGET ===', '=== project directory ==='] + visit_list = [] # the beamline directory could be a the real directory or # a directory where the visits are linked into # if agamemnon: @@ -53,30 +53,30 @@ def get_target_and_visit_list(beamline_directory,agamemnon): # target_list.append(target[target.rfind('/') + 1:]) # else: if len(beamline_directory.split('/')) and \ - beamline_directory.split('/')[1]=='dls' and beamline_directory.split('/')[3]=='data' \ - and not 'labxchem' in beamline_directory: + beamline_directory.split('/')[1] == 'dls' and beamline_directory.split('/')[3] == 'data' \ + and not 'labxchem' in beamline_directory: visit_list.append(beamline_directory) else: visit_list.append(os.path.realpath(beamline_directory)) for visit in visit_list: - print '-->',os.path.join(visit,'processed','*') + print '-->', os.path.join(visit, 'processed', '*') if agamemnon: - for target in glob.glob(os.path.join(visit,'processed','auto','*')): + for target in glob.glob(os.path.join(visit, 'processed', 'auto', '*')): print target - if target[target.rfind('/')+1:] not in ['results','README-log','edna-latest.html']: + if target[target.rfind('/')+1:] not in ['results', 'README-log', 'edna-latest.html']: if target[target.rfind('/')+1:] not in target_list: target_list.append(target[target.rfind('/')+1:]) else: - for target in glob.glob(os.path.join(visit,'processed','*')): + for target in glob.glob(os.path.join(visit, 'processed', '*')): print target - if target[target.rfind('/')+1:] not in ['results','README-log','edna-latest.html']: + if target[target.rfind('/')+1:] not in ['results', 'README-log', 'edna-latest.html']: if target[target.rfind('/')+1:] not in target_list: target_list.append(target[target.rfind('/')+1:]) - return target_list,visit_list + return target_list, visit_list -#def get_target_and_visit_list_for_Pietro(beamline_directory): -## target_list=['*'] # always give the option to read in all targets +# def get_target_and_visit_list_for_Pietro(beamline_directory): +# target_list=['*'] # always give the option to read in all targets # target_list=['=== SELECT TARGET ==='] # always give the option to read in all targets # visit_list=[] # # the beamline directory could be a the real directory or @@ -93,36 +93,38 @@ def get_target_and_visit_list(beamline_directory,agamemnon): def get_dewar_configuration(beamline_directory): - dewar_sample_configuration_dict={} + dewar_sample_configuration_dict = {} # need to do it like this for now until we got a way to query ispyb - for xml in glob.glob(os.path.join(beamline_directory,'xml','exptTableParams-*.xml')): - prefix='' - container_reference='' - sample_location='' + for xml in glob.glob(os.path.join(beamline_directory, 'xml', 'exptTableParams-*.xml')): + prefix = '' + container_reference = '' + sample_location = '' for line in open(xml): if 'prefix' in line: - prefix=line[line.find('>')+1:line.rfind('<')] + prefix = line[line.find('>')+1:line.rfind('<')] if 'container_reference' in line: - container_reference=line[line.find('>')+1:line.rfind('<')] + container_reference = line[line.find('>')+1:line.rfind('<')] if 'sample_location' in line: - sample_location=line[line.find('>')+1:line.rfind('<')] - dewar_sample_configuration_dict[str(container_reference)+'-'+str(sample_location)]=prefix + sample_location = line[line.find('>')+1:line.rfind('<')] + dewar_sample_configuration_dict[str( + container_reference)+'-'+str(sample_location)] = prefix return dewar_sample_configuration_dict + def get_jobs_running_on_cluster(): - out_dict={} + out_dict = {} - dimple_jobs=[] - acedrg_jobs=[] - pandda_jobs=[] - refmac_jobs=[] - xia2_jobs=[] - others_jobs=[] + dimple_jobs = [] + acedrg_jobs = [] + pandda_jobs = [] + refmac_jobs = [] + xia2_jobs = [] + others_jobs = [] # note: each job_details list contains a list with # [job_ID, status, run_time] - out=subprocess.Popen(['qstat'],stdout=subprocess.PIPE) - for n,line in enumerate(iter(out.stdout.readline,'')): + out = subprocess.Popen(['qstat'], stdout=subprocess.PIPE) + for n, line in enumerate(iter(out.stdout.readline, '')): if len(line.split()) >= 7: if line.split()[3] == getpass.getuser(): @@ -132,174 +134,212 @@ def get_jobs_running_on_cluster(): ########################################################## # determine run time of each job in minutes - start_date='' - start_time='' - run_time_minutes='' - start_date=line.split()[5] + start_date = '' + start_time = '' + run_time_minutes = '' + start_date = line.split()[5] if len(start_date.split('/')) == 3: - month_start=start_date.split('/')[0] - day_start=start_date.split('/')[1] - year_start=start_date.split('/')[2] - - start_time=line.split()[6] + month_start = start_date.split('/')[0] + day_start = start_date.split('/')[1] + year_start = start_date.split('/')[2] + + start_time = line.split()[6] if len(start_time.split(':')) == 3: - hour_start=start_time.split(':')[0] - minute_start=start_time.split(':')[1] - second_start=start_time.split(':')[2] + hour_start = start_time.split(':')[0] + minute_start = start_time.split(':')[1] + second_start = start_time.split(':')[2] if start_time != '' and start_date != '': - start='{0!s}-{1!s}-{2!s} {3!s}:{4!s}:{5!s}'.format(year_start, month_start, day_start, hour_start, minute_start, second_start) - run_time=datetime.now()-datetime.strptime(start,"%Y-%m-%d %H:%M:%S") - run_time_seconds=int(run_time.total_seconds()) - run_time_minutes=int(run_time.total_seconds() / 60) - run_time_hours=int(run_time.total_seconds() / 3600) + start = '{0!s}-{1!s}-{2!s} {3!s}:{4!s}:{5!s}'.format( + year_start, month_start, day_start, hour_start, minute_start, second_start) + run_time = datetime.now()-datetime.strptime(start, "%Y-%m-%d %H:%M:%S") + run_time_seconds = int(run_time.total_seconds()) + run_time_minutes = int(run_time.total_seconds() / 60) + run_time_hours = int(run_time.total_seconds() / 3600) ########################################################## # determine run time of each job in minutes if 'dimple' in job_name: - dimple_jobs.append([job_id,job_status,run_time_minutes]) + dimple_jobs.append([job_id, job_status, run_time_minutes]) elif 'acedrg' in job_name: - acedrg_jobs.append([job_id,job_status,run_time_minutes]) + acedrg_jobs.append([job_id, job_status, run_time_minutes]) elif 'pandda' in job_name: - pandda_jobs.append([job_id,job_status,run_time_minutes]) + pandda_jobs.append([job_id, job_status, run_time_minutes]) elif 'refmac' in job_name: - refmac_jobs.append([job_id,job_status,run_time_minutes]) + refmac_jobs.append([job_id, job_status, run_time_minutes]) elif 'xia2' in job_name: - xia2_jobs.append([job_id,job_status,run_time_minutes]) + xia2_jobs.append([job_id, job_status, run_time_minutes]) else: - others_jobs.append([job_id,job_status,run_time_minutes]) + others_jobs.append([job_id, job_status, run_time_minutes]) - out_dict['dimple']=dimple_jobs - out_dict['acedrg']=acedrg_jobs - out_dict['pandda']=pandda_jobs - out_dict['refmac']=refmac_jobs - out_dict['xia2']=xia2_jobs - out_dict['others']=others_jobs + out_dict['dimple'] = dimple_jobs + out_dict['acedrg'] = acedrg_jobs + out_dict['pandda'] = pandda_jobs + out_dict['refmac'] = refmac_jobs + out_dict['xia2'] = xia2_jobs + out_dict['others'] = others_jobs return out_dict -def print_acedrg_status(xce_logfile,xtal_db_dict): - Logfile=XChemLog.updateLog(xce_logfile) + +def print_acedrg_status(xce_logfile, xtal_db_dict): + Logfile = XChemLog.updateLog(xce_logfile) Logfile.insert('compound restraints summary:') - pending=0 - started=0 - running=0 - missing_smiles=0 - failed=0 - success=0 - unknown=0 + pending = 0 + started = 0 + running = 0 + missing_smiles = 0 + failed = 0 + success = 0 + unknown = 0 for xtal in xtal_db_dict: - db_dict=xtal_db_dict[xtal] - status=db_dict['RefinementCIFStatus'] + db_dict = xtal_db_dict[xtal] + status = db_dict['RefinementCIFStatus'] if 'pending' in status: - pending+=1 + pending += 1 elif 'started' in status: - started+=1 + started += 1 elif 'running' in status: - running+=1 + running += 1 elif 'missing' in status: - missing_smiles+=1 + missing_smiles += 1 elif 'failed' in status: - failed +=1 + failed += 1 elif 'generated' in status: - success+=1 + success += 1 else: - unknown+=1 - Logfile.insert('restraint generation pending: ...... {0!s}'.format(str(pending))) - Logfile.insert('restraint generation started: ...... {0!s}'.format(str(started))) - Logfile.insert('restraint generation running: ...... {0!s}'.format(str(running))) - Logfile.insert('missing smiles string: ............. {0!s}'.format(str(missing_smiles))) - Logfile.insert('restraint generation failed: ....... {0!s}'.format(str(failed))) - Logfile.insert('restraints successfully created: ... {0!s}'.format(str(success))) - Logfile.insert('unknown status: .................... {0!s}'.format(str(unknown))) - -def print_cluster_status_message(program,cluster_dict,xce_logfile): - Logfile=XChemLog.updateLog(xce_logfile) + unknown += 1 + Logfile.insert( + 'restraint generation pending: ...... {0!s}'.format(str(pending))) + Logfile.insert( + 'restraint generation started: ...... {0!s}'.format(str(started))) + Logfile.insert( + 'restraint generation running: ...... {0!s}'.format(str(running))) + Logfile.insert( + 'missing smiles string: ............. {0!s}'.format(str(missing_smiles))) + Logfile.insert( + 'restraint generation failed: ....... {0!s}'.format(str(failed))) + Logfile.insert( + 'restraints successfully created: ... {0!s}'.format(str(success))) + Logfile.insert( + 'unknown status: .................... {0!s}'.format(str(unknown))) + + +def print_cluster_status_message(program, cluster_dict, xce_logfile): + Logfile = XChemLog.updateLog(xce_logfile) Logfile.insert('cluster status summary:') - Logfile.insert('{0!s} {1!s} jobs are running on the cluster'.format(len(cluster_dict[program]), program)) + Logfile.insert('{0!s} {1!s} jobs are running on the cluster'.format( + len(cluster_dict[program]), program)) if len(cluster_dict[program]) > 0: - cumulative_runtime=0 + cumulative_runtime = 0 job_ids = [] - for n,item in enumerate(cluster_dict[program]): + for n, item in enumerate(cluster_dict[program]): cumulative_runtime += item[2] if not item[0] in job_ids: job_ids.append(item[0]) - average_runtime=round(float(cumulative_runtime)/float(n+1),0) + average_runtime = round(float(cumulative_runtime)/float(n+1), 0) Logfile.insert('average run time '+str(average_runtime)+' minutes') if job_ids: - Logfile.insert('you can kill them by pasting the following line into a new terminal window:') - out='qdel ' + Logfile.insert( + 'you can kill them by pasting the following line into a new terminal window:') + out = 'qdel ' for job in job_ids: out += str(job)+' ' Logfile.insert(out) - def display_queue_status_in_terminal(in_dict): # latest_run=max(tmp,key=lambda x: x[1])[0] - max_dimple_runtime=max(in_dict['dimple'],key=lambda x:x[2])[2] + max_dimple_runtime = max(in_dict['dimple'], key=lambda x: x[2])[2] print '----------------------------------------------------------------------------' print '| Task | Nr. Jobs | Max. Runtime (minutes) |' print '----------------------------------------------------------------------------' - print '{0:24} {1:24} {2:24} {3:1}'.format('| DIMPLE', '| {0!s}'.format(len(in_dict['dimple'])),'| %s' &max_dimple_runtime,'|') + print '{0:24} {1:24} {2:24} {3:1}'.format('| DIMPLE', '| {0!s}'.format( + len(in_dict['dimple'])), '| %s' & max_dimple_runtime, '|') print '----------------------------------------------------------------------------' + def get_datasource_summary(db_file): - db=XChemDB.data_source(db_file) - - out_dict={} - - out_dict['nr_samples']=len(db.execute_statement("select CrystalName from mainTable where CrystalName is not NULL;")) - out_dict['nr_samples_failed_to_mount']=len(db.execute_statement("select HarvestStatus from mainTable where HarvestStatus is 'fail';")) - - out_dict['nr_smiles_for_samples']=len(db.execute_statement("select compoundSMILES from mainTable where compoundSMILES is not (NULL or '')")) - - out_dict['nr_data_collection_success']=len(db.execute_statement("select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'success';")) - out_dict['nr_data_collection_centring_fail']=len(db.execute_statement("select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - centring failed';")) - out_dict['nr_data_collection_no-diffraction']=len(db.execute_statement("select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - no diffraction';")) - out_dict['nr_data_collection_processing_fail']=len(db.execute_statement("select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - processing';")) - out_dict['nr_data_collection_loop-empty']=len(db.execute_statement("select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - loop empty';")) - out_dict['nr_data_collection_loop-broken']=len(db.execute_statement("select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - loop broken';")) - out_dict['nr_data_collection_low-resolution']=len(db.execute_statement("select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - low resolution';")) - out_dict['nr_data_collection_no-X-rays']=len(db.execute_statement("select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - no X-rays';")) - out_dict['nr_data_collection_unknown']=len(db.execute_statement("select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - unknown';")) - - out_dict['nr_data_collection_failed']= out_dict['nr_data_collection_centring_fail'] + \ - out_dict['nr_data_collection_no-diffraction'] + \ - out_dict['nr_data_collection_processing_fail'] + \ - out_dict['nr_data_collection_loop-empty'] + \ - out_dict['nr_data_collection_loop-broken'] + \ - out_dict['nr_data_collection_low-resolution'] + \ - out_dict['nr_data_collection_no-X-rays'] + \ - out_dict['nr_data_collection_unknown'] - - - out_dict['nr_data_collection_pending']=out_dict['nr_samples'] - out_dict['nr_data_collection_success'] - \ - out_dict['nr_data_collection_centring_fail'] - \ - out_dict['nr_data_collection_no-diffraction'] - \ - out_dict['nr_data_collection_processing_fail'] - \ - out_dict['nr_data_collection_loop-empty'] - \ - out_dict['nr_data_collection_loop-broken'] - \ - out_dict['nr_data_collection_low-resolution'] - \ - out_dict['nr_data_collection_no-X-rays'] - \ - out_dict['nr_data_collection_unknown'] - - out_dict['nr_initial_maps_available']=len(db.execute_statement("select DimplePathToMTZ from mainTable where DimplePathToMTZ is not '';")) - out_dict['nr_initial_maps_fail']=len(db.execute_statement("select DataProcessingDimpleSuccessful from mainTable where DataProcessingDimpleSuccessful = 'False';")) - out_dict['nr_initial_maps_pending']=out_dict['nr_data_collection_success']-out_dict['nr_initial_maps_available']-out_dict['nr_initial_maps_fail'] - - out_dict['nr_pandda_hits']=len(db.execute_statement("select DimplePANDDAhit from mainTable where DimplePANDDAhit = 'True';")) - out_dict['nr_pandda_reject']=len(db.execute_statement("select DimplePANDDAreject from mainTable where DimplePANDDAreject = 'True';")) - out_dict['nr_pandda_processed']=len(db.execute_statement("select DimplePANDDAwasRun from mainTable where DimplePANDDAwasRun = 'True';"))-out_dict['nr_pandda_hits']-out_dict['nr_pandda_reject'] - out_dict['nr_pandda_pending']=out_dict['nr_initial_maps_available']-out_dict['nr_pandda_hits']-out_dict['nr_pandda_reject']-out_dict['nr_pandda_processed'] - - out_dict['nr_cif_files']=len(db.execute_statement("select RefinementCIF from mainTable where RefinementCIF is not (Null or '');")) - - out_dict['nr_analysis-pending']=len(db.execute_statement("select RefinementOutcome from mainTable where RefinementOutcome is '1 - Analysis Pending';")) - out_dict['nr_pandda-models']=len(db.execute_statement("select RefinementOutcome from mainTable where RefinementOutcome is '2 - PANDDA model';")) - out_dict['nr_in-refinement']=len(db.execute_statement("select RefinementOutcome from mainTable where RefinementOutcome is '3 - In Refinement';")) - out_dict['nr_comp-chem-ready']=len(db.execute_statement("select RefinementOutcome from mainTable where RefinementOutcome is '4 - ComChem ready';")) - out_dict['nr_deposition-ready']=len(db.execute_statement("select RefinementOutcome from mainTable where RefinementOutcome is '5 - Deposition ready';")) + db = XChemDB.data_source(db_file) + + out_dict = {} + + out_dict['nr_samples'] = len(db.execute_statement( + "select CrystalName from mainTable where CrystalName is not NULL;")) + out_dict['nr_samples_failed_to_mount'] = len(db.execute_statement( + "select HarvestStatus from mainTable where HarvestStatus is 'fail';")) + + out_dict['nr_smiles_for_samples'] = len(db.execute_statement( + "select compoundSMILES from mainTable where compoundSMILES is not (NULL or '')")) + + out_dict['nr_data_collection_success'] = len(db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'success';")) + out_dict['nr_data_collection_centring_fail'] = len(db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - centring failed';")) + out_dict['nr_data_collection_no-diffraction'] = len(db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - no diffraction';")) + out_dict['nr_data_collection_processing_fail'] = len(db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - processing';")) + out_dict['nr_data_collection_loop-empty'] = len(db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - loop empty';")) + out_dict['nr_data_collection_loop-broken'] = len(db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - loop broken';")) + out_dict['nr_data_collection_low-resolution'] = len(db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - low resolution';")) + out_dict['nr_data_collection_no-X-rays'] = len(db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - no X-rays';")) + out_dict['nr_data_collection_unknown'] = len(db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - unknown';")) + + out_dict['nr_data_collection_failed'] = out_dict['nr_data_collection_centring_fail'] + \ + out_dict['nr_data_collection_no-diffraction'] + \ + out_dict['nr_data_collection_processing_fail'] + \ + out_dict['nr_data_collection_loop-empty'] + \ + out_dict['nr_data_collection_loop-broken'] + \ + out_dict['nr_data_collection_low-resolution'] + \ + out_dict['nr_data_collection_no-X-rays'] + \ + out_dict['nr_data_collection_unknown'] + + out_dict['nr_data_collection_pending'] = out_dict['nr_samples'] - out_dict['nr_data_collection_success'] - \ + out_dict['nr_data_collection_centring_fail'] - \ + out_dict['nr_data_collection_no-diffraction'] - \ + out_dict['nr_data_collection_processing_fail'] - \ + out_dict['nr_data_collection_loop-empty'] - \ + out_dict['nr_data_collection_loop-broken'] - \ + out_dict['nr_data_collection_low-resolution'] - \ + out_dict['nr_data_collection_no-X-rays'] - \ + out_dict['nr_data_collection_unknown'] + + out_dict['nr_initial_maps_available'] = len(db.execute_statement( + "select DimplePathToMTZ from mainTable where DimplePathToMTZ is not '';")) + out_dict['nr_initial_maps_fail'] = len(db.execute_statement( + "select DataProcessingDimpleSuccessful from mainTable where DataProcessingDimpleSuccessful = 'False';")) + out_dict['nr_initial_maps_pending'] = out_dict['nr_data_collection_success'] - \ + out_dict['nr_initial_maps_available']-out_dict['nr_initial_maps_fail'] + + out_dict['nr_pandda_hits'] = len(db.execute_statement( + "select DimplePANDDAhit from mainTable where DimplePANDDAhit = 'True';")) + out_dict['nr_pandda_reject'] = len(db.execute_statement( + "select DimplePANDDAreject from mainTable where DimplePANDDAreject = 'True';")) + out_dict['nr_pandda_processed'] = len(db.execute_statement( + "select DimplePANDDAwasRun from mainTable where DimplePANDDAwasRun = 'True';"))-out_dict['nr_pandda_hits']-out_dict['nr_pandda_reject'] + out_dict['nr_pandda_pending'] = out_dict['nr_initial_maps_available'] - \ + out_dict['nr_pandda_hits']-out_dict['nr_pandda_reject'] - \ + out_dict['nr_pandda_processed'] + + out_dict['nr_cif_files'] = len(db.execute_statement( + "select RefinementCIF from mainTable where RefinementCIF is not (Null or '');")) + + out_dict['nr_analysis-pending'] = len(db.execute_statement( + "select RefinementOutcome from mainTable where RefinementOutcome is '1 - Analysis Pending';")) + out_dict['nr_pandda-models'] = len(db.execute_statement( + "select RefinementOutcome from mainTable where RefinementOutcome is '2 - PANDDA model';")) + out_dict['nr_in-refinement'] = len(db.execute_statement( + "select RefinementOutcome from mainTable where RefinementOutcome is '3 - In Refinement';")) + out_dict['nr_comp-chem-ready'] = len(db.execute_statement( + "select RefinementOutcome from mainTable where RefinementOutcome is '4 - ComChem ready';")) + out_dict['nr_deposition-ready'] = len(db.execute_statement( + "select RefinementOutcome from mainTable where RefinementOutcome is '5 - Deposition ready';")) return out_dict @@ -308,43 +348,50 @@ def remove_all_refmac_jobs_from_cluster_and_reinstate_last_stable_state(): print 'hallo' -def change_links_to_selected_data_collection_outcome(sample,data_collection_dict,data_collection_column_three_dict,dataset_outcome_dict,initial_model_directory,data_source_file,xce_logfile): - Logfile=XChemLog.updateLog(xce_logfile) +def change_links_to_selected_data_collection_outcome(sample, data_collection_dict, data_collection_column_three_dict, dataset_outcome_dict, initial_model_directory, data_source_file, xce_logfile): + Logfile = XChemLog.updateLog(xce_logfile) # find out which row was selected in respective data collection table - selected_processing_result='n/a' - indexes=data_collection_column_three_dict[sample][0].selectionModel().selectedRows() + selected_processing_result = 'n/a' + indexes = data_collection_column_three_dict[sample][0].selectionModel( + ).selectedRows() if indexes: # i.e. logfile exists for index in sorted(indexes): - selected_processing_result=index.row() - - for n,entry in enumerate(data_collection_dict[sample]): - if entry[0]=='logfile': - if entry[7]==selected_processing_result: - visit=entry[1] - run=entry[2] - autoproc=entry[4] - db_dict=entry[6] - outcome=dataset_outcome_dict[sample] - path_to_logfile=db_dict['DataProcessingPathToLogfile'] - path_to_mtzfile=db_dict['DataProcessingPathToMTZfile'] - mtz_filename=db_dict['DataProcessingMTZfileName'] - log_filename=db_dict['DataProcessingLOGfileName'] + selected_processing_result = index.row() + + for n, entry in enumerate(data_collection_dict[sample]): + if entry[0] == 'logfile': + if entry[7] == selected_processing_result: + visit = entry[1] + run = entry[2] + autoproc = entry[4] + db_dict = entry[6] + outcome = dataset_outcome_dict[sample] + path_to_logfile = db_dict['DataProcessingPathToLogfile'] + path_to_mtzfile = db_dict['DataProcessingPathToMTZfile'] + mtz_filename = db_dict['DataProcessingMTZfileName'] + log_filename = db_dict['DataProcessingLOGfileName'] # relative_path_to_mtzfile='./'+path_to_mtzfile.replace(initial_model_directory,'') - relative_path_to_mtzfile='./'+path_to_mtzfile.replace(os.path.join(initial_model_directory,sample),'') + relative_path_to_mtzfile = './' + \ + path_to_mtzfile.replace(os.path.join( + initial_model_directory, sample), '') if relative_path_to_mtzfile.startswith('.//'): - relative_path_to_mtzfile=relative_path_to_mtzfile.replace('.//','./') - relative_path_to_logfile='./'+path_to_logfile.replace(os.path.join(initial_model_directory,sample),'') + relative_path_to_mtzfile = relative_path_to_mtzfile.replace( + './/', './') + relative_path_to_logfile = './' + \ + path_to_logfile.replace(os.path.join( + initial_model_directory, sample), '') if relative_path_to_logfile.startswith('.//'): - relative_path_to_logfile=relative_path_to_logfile.replace('.//','./') - + relative_path_to_logfile = relative_path_to_logfile.replace( + './/', './') # first check if folders and files exist # since user might do this before data are actually copied over - if os.path.isdir(os.path.join(initial_model_directory,sample,'autoprocessing',visit+'-'+run+autoproc)): - db_dict['DataProcessingAutoAssigned']='False' - Logfile.insert('changing directory to: '+os.path.join(initial_model_directory,sample)) - os.chdir(os.path.join(initial_model_directory,sample)) + if os.path.isdir(os.path.join(initial_model_directory, sample, 'autoprocessing', visit+'-'+run+autoproc)): + db_dict['DataProcessingAutoAssigned'] = 'False' + Logfile.insert('changing directory to: ' + + os.path.join(initial_model_directory, sample)) + os.chdir(os.path.join(initial_model_directory, sample)) # first remove old links os.system('/bin/rm '+sample+'.mtz 2> /dev/null') os.system('/bin/rm '+sample+'.log 2> /dev/null') @@ -353,20 +400,25 @@ def change_links_to_selected_data_collection_outcome(sample,data_collection_dict # os.symlink(os.path.join(path_to_logfile,log_filename),sample+'.log') # Logfile.insert('setting symlink: '+os.path.join(path_to_mtzfile,mtz_filename)+' -> '+sample+'.mtz') # os.symlink(os.path.join(path_to_mtzfile,mtz_filename),sample+'.mtz') - Logfile.insert('setting relative symlink: '+os.path.join(relative_path_to_logfile,log_filename)+' -> '+sample+'.log') - os.symlink(os.path.join(relative_path_to_logfile,log_filename),sample+'.log') - Logfile.insert('setting relative symlink: '+os.path.join(relative_path_to_mtzfile,mtz_filename)+' -> '+sample+'.mtz') - os.symlink(os.path.join(relative_path_to_mtzfile,mtz_filename),sample+'.mtz') + Logfile.insert('setting relative symlink: '+os.path.join( + relative_path_to_logfile, log_filename)+' -> '+sample+'.log') + os.symlink(os.path.join(relative_path_to_logfile, + log_filename), sample+'.log') + Logfile.insert('setting relative symlink: '+os.path.join( + relative_path_to_mtzfile, mtz_filename)+' -> '+sample+'.mtz') + os.symlink(os.path.join(relative_path_to_mtzfile, + mtz_filename), sample+'.mtz') # update data source - data_source=XChemDB.data_source(data_source_file) - data_source.update_insert_data_source(sample,db_dict) + data_source = XChemDB.data_source(data_source_file) + data_source.update_insert_data_source(sample, db_dict) else: - Logfile.insert('please copy data to PROJECT DIRECTORY first!') + Logfile.insert( + 'please copy data to PROJECT DIRECTORY first!') -#def find_diffraction_image_directory(diffraction_data_directory): +# def find_diffraction_image_directory(diffraction_data_directory): # data_dict={} # diffraction_image_extension = ['.img','.cbf','.mccd','.mar2560','.mar2300'] # os.chdir(diffraction_data_directory) @@ -385,84 +437,94 @@ def change_links_to_selected_data_collection_outcome(sample,data_collection_dict # return data_dict def get_nr_files_from_gda_log_folder(beamline): - n=len(glob.glob(os.path.join('/dls_sw',beamline,'logs','gda_server*'))) + n = len(glob.glob(os.path.join('/dls_sw', beamline, 'logs', 'gda_server*'))) return n + def get_dict_of_gda_barcodes(beamline): - out_dict={} - for files in glob.glob(os.path.join('/dls_sw',beamline,'logs','*')): - found_barcode_entry=False - gda_log= files[files.rfind('/')+1:] + out_dict = {} + for files in glob.glob(os.path.join('/dls_sw', beamline, 'logs', '*')): + found_barcode_entry = False + gda_log = files[files.rfind('/')+1:] if gda_log.startswith('gda_server.') and gda_log.endswith('.gz'): - with gzip.open(files,'r') as f: - print 'parsing',files + with gzip.open(files, 'r') as f: + print 'parsing', files # for line in fin: for line in f: if 'BART SampleChanger - getBarcode() returning' in line: - barcode=line.split()[len(line.split())-1] - found_barcode_entry=True + barcode = line.split()[len(line.split())-1] + found_barcode_entry = True if found_barcode_entry: if 'Snapshots will be saved' in line: - sampleID=line.split()[len(line.split())-1].split('/')[-1] - out_dict[sampleID]=barcode - found_barcode_entry=False + sampleID = line.split()[len( + line.split())-1].split('/')[-1] + out_dict[sampleID] = barcode + found_barcode_entry = False elif gda_log.startswith('gda_server.') and gda_log.endswith('.log'): for line in files: if 'BART SampleChanger - getBarcode() returning' in line: - barcode=line.split()[len(line.split())-1] - found_barcode_entry=True + barcode = line.split()[len(line.split())-1] + found_barcode_entry = True if found_barcode_entry: if 'Snapshots will be saved' in line: - sampleID=line.split()[len(line.split())-1].split('/')[-1] - out_dict[sampleID]=barcode - found_barcode_entry=False + sampleID = line.split()[len( + line.split())-1].split('/')[-1] + out_dict[sampleID] = barcode + found_barcode_entry = False return out_dict -def append_dict_of_gda_barcodes(out_dict,files,xce_logfile): -# out_dict={} -# for files in glob.glob(os.path.join('/dls_sw',beamline,'logs','*')): - Logfile=XChemLog.updateLog(xce_logfile) - found_barcode_entry=False - gda_log= files[files.rfind('/')+1:] + +def append_dict_of_gda_barcodes(out_dict, files, xce_logfile): + # out_dict={} + # for files in glob.glob(os.path.join('/dls_sw',beamline,'logs','*')): + Logfile = XChemLog.updateLog(xce_logfile) + found_barcode_entry = False + gda_log = files[files.rfind('/')+1:] if gda_log.startswith('gda_server.') or gda_log.startswith('gda-server.') and gda_log.endswith('.gz'): - with gzip.open(files,'r') as f: + with gzip.open(files, 'r') as f: for line in f: if 'BART SampleChanger - getBarcode() returning' in line: - barcode=line.split()[len(line.split())-1] - found_barcode_entry=True + barcode = line.split()[len(line.split())-1] + found_barcode_entry = True if found_barcode_entry: if 'Snapshots will be saved' in line: - sampleID=line.split()[len(line.split())-1].split('/')[-1] - out_dict[sampleID]=barcode - Logfile.insert('found: sample={0!s}, barcode={1!s}, file={2!s}'.format(sampleID, barcode, files)) - found_barcode_entry=False + sampleID = line.split()[len( + line.split())-1].split('/')[-1] + out_dict[sampleID] = barcode + Logfile.insert('found: sample={0!s}, barcode={1!s}, file={2!s}'.format( + sampleID, barcode, files)) + found_barcode_entry = False elif gda_log.startswith('gda_server') or gda_log.startswith('gda-server') and gda_log.endswith('txt'): for line in open(files): if 'BART SampleChanger - getBarcode() returning' in line: - barcode=line.split()[len(line.split())-1] - found_barcode_entry=True + barcode = line.split()[len(line.split())-1] + found_barcode_entry = True if found_barcode_entry: if 'Snapshots will be saved' in line: - sampleID=line.split()[len(line.split())-1].split('/')[-1] - out_dict[sampleID]=barcode - Logfile.insert('found: sample={0!s}, barcode={1!s}, file={2!s}'.format(sampleID, barcode, files)) - found_barcode_entry=False + sampleID = line.split()[len(line.split())-1].split('/')[-1] + out_dict[sampleID] = barcode + Logfile.insert('found: sample={0!s}, barcode={1!s}, file={2!s}'.format( + sampleID, barcode, files)) + found_barcode_entry = False return out_dict -def get_gda_barcodes(sampleList,gzipped_logs_parsed,gda_log_start_line,beamline,xce_logfile): - Logfile=XChemLog.updateLog(xce_logfile) - Logfile.insert('checking GDA logfile in {0!s}'.format(os.path.join('/dls_sw',beamline,'logs'))) + +def get_gda_barcodes(sampleList, gzipped_logs_parsed, gda_log_start_line, beamline, xce_logfile): + Logfile = XChemLog.updateLog(xce_logfile) + Logfile.insert('checking GDA logfile in {0!s}'.format( + os.path.join('/dls_sw', beamline, 'logs'))) pinDict = {} - found_barcode_entry=False - for gdaLogFile in glob.glob(os.path.join('/dls_sw',beamline,'logs','gda-server*log*')): + found_barcode_entry = False + for gdaLogFile in glob.glob(os.path.join('/dls_sw', beamline, 'logs', 'gda-server*log*')): if gdaLogFile.endswith('tmp'): Logfile.warning('ignoring temporary file ' + gdaLogFile) continue Logfile.insert('parsing {0!s}'.format(gdaLogFile)) if gzipped_logs_parsed and gdaLogFile.endswith('.gz'): - Logfile.insert('{0!s} was already parsed during this visit'.format(gdaLogFile)) + Logfile.insert( + '{0!s} was already parsed during this visit'.format(gdaLogFile)) continue if gdaLogFile.endswith('.gz'): try: @@ -473,75 +535,84 @@ def get_gda_barcodes(sampleList,gzipped_logs_parsed,gda_log_start_line,beamline, found_barcode_entry = True if found_barcode_entry: if 'Snapshots will be saved' in line: - sampleID = line.split()[len(line.split()) - 1].split('/')[-1] + sampleID = line.split()[len( + line.split()) - 1].split('/')[-1] if sampleID in sampleList: pinDict[sampleID] = barcode Logfile.insert( - 'found: sample={0!s}, barcode={1!s}, file={2!s}'.format(sampleID, barcode, gdaLogFile)) + 'found: sample={0!s}, barcode={1!s}, file={2!s}'.format(sampleID, barcode, gdaLogFile)) found_barcode_entry = False except IOError: - Logfile.warning('cannot open file %s' %gdaLogFile) + Logfile.warning('cannot open file %s' % gdaLogFile) else: try: - for n,line in enumerate(open(gdaLogFile).readlines()[gda_log_start_line:]): + for n, line in enumerate(open(gdaLogFile).readlines()[gda_log_start_line:]): if 'BART SampleChanger - getBarcode() returning' in line: barcode = line.split()[len(line.split()) - 1] found_barcode_entry = True if found_barcode_entry: if 'Snapshots will be saved' in line: - sampleID = line.split()[len(line.split()) - 1].split('/')[-1] + sampleID = line.split()[len( + line.split()) - 1].split('/')[-1] if sampleID in sampleList: pinDict[sampleID] = barcode Logfile.insert( - 'found: sample={0!s}, barcode={1!s}, file={2!s}'.format(sampleID, barcode, gdaLogFile)) + 'found: sample={0!s}, barcode={1!s}, file={2!s}'.format(sampleID, barcode, gdaLogFile)) found_barcode_entry = False except IOError: Logfile.error('IOError -> ' + gdaLogFile) try: - gda_log_start_line = gda_log_start_line + n -1 + gda_log_start_line = gda_log_start_line + n - 1 except UnboundLocalError: gda_log_start_line = gda_log_start_line - return pinDict,gda_log_start_line + return pinDict, gda_log_start_line -def linkAutoProcessingResult(xtal,dbDict,projectDir,xce_logfile): - Logfile=XChemLog.updateLog(xce_logfile) +def linkAutoProcessingResult(xtal, dbDict, projectDir, xce_logfile): + Logfile = XChemLog.updateLog(xce_logfile) - run = dbDict['DataCollectionRun'] - subDir = dbDict['DataCollectionSubdir'] + run = dbDict['DataCollectionRun'] + subDir = dbDict['DataCollectionSubdir'] if subDir != '': procCode = '_' + subDir else: procCode = '' - visit = dbDict['DataCollectionVisit'] + visit = dbDict['DataCollectionVisit'] autoproc = dbDict['DataProcessingProgram'] mtzFileAbs = dbDict['DataProcessingPathToMTZfile'] mtzfile = mtzFileAbs[mtzFileAbs.rfind('/')+1:] logFileAbs = dbDict['DataProcessingPathToLogfile'] logfile = logFileAbs[logFileAbs.rfind('/')+1:] - Logfile.insert('changing directory to ' + os.path.join(projectDir,xtal)) - os.chdir(os.path.join(projectDir,xtal)) + Logfile.insert('changing directory to ' + os.path.join(projectDir, xtal)) + os.chdir(os.path.join(projectDir, xtal)) # MTZ file - Logfile.warning('removing %s.mtz' %xtal) - os.system('/bin/rm %s.mtz' %xtal) - Logfile.insert(xtal+': looking for '+os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile)) + Logfile.warning('removing %s.mtz' % xtal) + os.system('/bin/rm %s.mtz' % xtal) + Logfile.insert(xtal+': looking for '+os.path.join('autoprocessing', + visit + '-' + run + autoproc + procCode, mtzfile)) if os.path.isfile(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile)): - os.symlink(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile), xtal + '.mtz') - Logfile.insert('linking MTZ file from different auto-processing pipeline:') - Logfile.insert('ln -s ' + os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile) + ' ' + xtal + '.mtz') + os.symlink(os.path.join('autoprocessing', visit + '-' + + run + autoproc + procCode, mtzfile), xtal + '.mtz') + Logfile.insert( + 'linking MTZ file from different auto-processing pipeline:') + Logfile.insert('ln -s ' + os.path.join('autoprocessing', visit + + '-' + run + autoproc + procCode, mtzfile) + ' ' + xtal + '.mtz') # LOG file - Logfile.warning('removing %s.log' %xtal) - os.system('/bin/rm %s.log' %xtal) - Logfile.insert(xtal+': looking for '+os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfile)) + Logfile.warning('removing %s.log' % xtal) + os.system('/bin/rm %s.log' % xtal) + Logfile.insert(xtal+': looking for '+os.path.join('autoprocessing', + visit + '-' + run + autoproc + procCode, logfile)) if os.path.isfile(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfile)): - os.symlink(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfile), xtal + '.log') - Logfile.insert('linking LOG file from different auto-processing pipeline:') - Logfile.insert('ln -s ' + os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfile) + ' ' + xtal + '.log') - + os.symlink(os.path.join('autoprocessing', visit + '-' + + run + autoproc + procCode, logfile), xtal + '.log') + Logfile.insert( + 'linking LOG file from different auto-processing pipeline:') + Logfile.insert('ln -s ' + os.path.join('autoprocessing', visit + + '-' + run + autoproc + procCode, logfile) + ' ' + xtal + '.log') def getProgressSteps(iterations): @@ -551,131 +622,136 @@ def getProgressSteps(iterations): progress_step = 100 / float(iterations) return progress_step + def getVisitAndBeamline(visitDirectory): visit = 'unknown' beamline = 'unknown' if 'attic' in visitDirectory: try: - visit=visitDirectory.split('/')[6] - beamline=visitDirectory.split('/')[3] + visit = visitDirectory.split('/')[6] + beamline = visitDirectory.split('/')[3] except IndexError: pass else: try: - visit=visitDirectory.split('/')[5] - beamline=visitDirectory.split('/')[2] + visit = visitDirectory.split('/')[5] + beamline = visitDirectory.split('/')[2] except IndexError: pass if not visitDirectory.startswith('/dls'): # this is all a bit of a fudge in case someone transfers a DLS visit directory back home # does most certainly not catch all possible scenarios if visitDirectory.split('/')[len(visitDirectory.split('/')) - 2] == 'processed': - visit = visitDirectory.split('/')[len(visitDirectory.split('/')) - 3] + visit = visitDirectory.split( + '/')[len(visitDirectory.split('/')) - 3] else: visit = visitDirectory.split('/')[len(visitDirectory.split('/'))-1] beamline = 'unknown' - return visit,beamline - - + return visit, beamline def crystal_growth_methods(): - methods = [ 'VAPOR DIFFUSION, SITTING DROP', - 'VAPOR DIFFUSION, HANGING DROP', - 'BATCH MODE', - 'LIPIDIC CUBIC PHASE', - 'MICROBATCH', - 'MICROFLUIDIC' ] + methods = ['VAPOR DIFFUSION, SITTING DROP', + 'VAPOR DIFFUSION, HANGING DROP', + 'BATCH MODE', + 'LIPIDIC CUBIC PHASE', + 'MICROBATCH', + 'MICROFLUIDIC'] return methods + def wwBeamlines(): - beamlines = [ 'DIAMOND BEAMLINE I02', - 'DIAMOND BEAMLINE I03', - 'DIAMOND BEAMLINE I04', - 'DIAMOND BEAMLINE I04-1', - 'DIAMOND BEAMLINE I23', - 'DIAMOND BEAMLINE I24' ] + beamlines = ['DIAMOND BEAMLINE I02', + 'DIAMOND BEAMLINE I03', + 'DIAMOND BEAMLINE I04', + 'DIAMOND BEAMLINE I04-1', + 'DIAMOND BEAMLINE I23', + 'DIAMOND BEAMLINE I24'] return beamlines + def radiationSource(): - source = [ 'SYNCHROTRON', - 'ROTATING ANODE', - 'SEALED TUBE' ] + source = ['SYNCHROTRON', + 'ROTATING ANODE', + 'SEALED TUBE'] return source + def detector(): - detectorPrinciple = [ 'PIXEL', - 'CCD', - 'IMAGE PLATE', - 'CMOS' ] + detectorPrinciple = ['PIXEL', + 'CCD', + 'IMAGE PLATE', + 'CMOS'] return detectorPrinciple + def detectorType(): - detector = [ 'DECTRIS PILATUS 2M', - 'DECTRIS PILATUS 2M-F', - 'DECTRIS PILATUS 6M', - 'DECTRIS PILATUS 6M-F', - 'DECTRIS PILATUS 12M', - 'DECTRIS PILATUS3 2M', - 'DECTRIS PILATUS3 6M', - 'DECTRIS EIGER X 9M', - 'DECTRIS EIGER X 16M', - 'ADSC QUANTUM 315', - 'ADSC QUANTUM 315r' ] + detector = ['DECTRIS PILATUS 2M', + 'DECTRIS PILATUS 2M-F', + 'DECTRIS PILATUS 6M', + 'DECTRIS PILATUS 6M-F', + 'DECTRIS PILATUS 12M', + 'DECTRIS PILATUS3 2M', + 'DECTRIS PILATUS3 6M', + 'DECTRIS EIGER X 9M', + 'DECTRIS EIGER X 16M', + 'ADSC QUANTUM 315', + 'ADSC QUANTUM 315r'] return detector + def NCBI_taxonomy_ID(): - taxonomy_dict = { '9606': 'Homo sapiens', - '10090': 'Mus musculus', - '7108': 'SPODOPTERA FRUGIPERDA', - '5693 ': 'Trypanosoma cruzi', - '1508227': 'BAT SARS-LIKE CORONAVIRUS', - '2697049': 'SARS-CoV-2', - '562': 'Escherichia coli', - '837': 'Porphyromonas gingivalis' - } + taxonomy_dict = {'9606': 'Homo sapiens', + '10090': 'Mus musculus', + '7108': 'SPODOPTERA FRUGIPERDA', + '5693 ': 'Trypanosoma cruzi', + '1508227': 'BAT SARS-LIKE CORONAVIRUS', + '2697049': 'SARS-CoV-2', + '562': 'Escherichia coli', + '837': 'Porphyromonas gingivalis' + } return taxonomy_dict def data_integration_software(): - software = [ 'XDS', - 'HKL', - 'DENZO', - 'DTREK', - 'MOSFLM' ] + software = ['XDS', + 'HKL', + 'DENZO', + 'DTREK', + 'MOSFLM'] return software def phasing_software(): - software = [ 'REFMAC', - 'PHENIX', - 'SOLVE', - 'PHASER', - 'CNS', - 'XPLOR', - 'MLPHARE', - 'SHELX', - 'SNB', - 'BnP', - 'BP3', - 'SHARP', - 'PHASES', - 'WARP' ] + software = ['REFMAC', + 'PHENIX', + 'SOLVE', + 'PHASER', + 'CNS', + 'XPLOR', + 'MLPHARE', + 'SHELX', + 'SNB', + 'BnP', + 'BP3', + 'SHARP', + 'PHASES', + 'WARP'] return software @@ -770,87 +846,89 @@ def pdbx_keywords(): return keywords + def pdbx_country(): countries = [ - 'United Kingdom', - 'United States', - 'Japan', - 'Albania', - 'Andorra', - 'Argentina', - 'Armenia', - 'Australia', - 'Austria', - 'Azerbaijan', - 'Bahamas', - 'Bangladesh', - 'Barbados', - 'Belarus', - 'Belgium', - 'Brazil', - 'Bulgaria', - 'Canada', - 'Chile', - 'China', - 'Croatia', - 'Cuba', - 'Cyprus', - 'Czech Republic', - 'Denmark', - 'Estonia', - 'Finland', - 'France', - 'Germany', - 'Greece', - 'Hungary', - 'Iceland', - 'India', - 'Indonesia', - 'Iran, Islamic Republic Of', - 'Iraq', - 'Ireland', - 'Israel', - 'Italy', - 'Jamaica', - 'Jordan', - 'Kazakhstan', - 'Kenya', - 'Kiribati', - 'Korea, Republic Of', - 'Latvia', - 'Lithuania', - 'Luxembourg', - 'Malta', - 'Mexico', - 'Netherlands', - 'New Zealand', - 'Norway', - 'Pakistan', - 'Paraguay', - 'Peru', - 'Philippines', - 'Poland', - 'Portugal', - 'Romania', - 'Russian Federation', - 'Serbia', - 'Singapore', - 'Slovakia', - 'Slovenia', - 'South Africa', - 'Spain', - 'Sweden', - 'Switzerland', - 'Taiwan', - 'Thailand', - 'Turkey', - 'Ukraine', - 'United Arab Emirates', - 'Uruguay' + 'United Kingdom', + 'United States', + 'Japan', + 'Albania', + 'Andorra', + 'Argentina', + 'Armenia', + 'Australia', + 'Austria', + 'Azerbaijan', + 'Bahamas', + 'Bangladesh', + 'Barbados', + 'Belarus', + 'Belgium', + 'Brazil', + 'Bulgaria', + 'Canada', + 'Chile', + 'China', + 'Croatia', + 'Cuba', + 'Cyprus', + 'Czech Republic', + 'Denmark', + 'Estonia', + 'Finland', + 'France', + 'Germany', + 'Greece', + 'Hungary', + 'Iceland', + 'India', + 'Indonesia', + 'Iran, Islamic Republic Of', + 'Iraq', + 'Ireland', + 'Israel', + 'Italy', + 'Jamaica', + 'Jordan', + 'Kazakhstan', + 'Kenya', + 'Kiribati', + 'Korea, Republic Of', + 'Latvia', + 'Lithuania', + 'Luxembourg', + 'Malta', + 'Mexico', + 'Netherlands', + 'New Zealand', + 'Norway', + 'Pakistan', + 'Paraguay', + 'Peru', + 'Philippines', + 'Poland', + 'Portugal', + 'Romania', + 'Russian Federation', + 'Serbia', + 'Singapore', + 'Slovakia', + 'Slovenia', + 'South Africa', + 'Spain', + 'Sweden', + 'Switzerland', + 'Taiwan', + 'Thailand', + 'Turkey', + 'Ukraine', + 'United Arab Emirates', + 'Uruguay' ] return countries + def html_header(): header = ( @@ -896,400 +974,402 @@ def html_header(): return header -def html_ngl(firstPDB,firstEvent,firstMap,firstDiffMap,ligID): + +def html_ngl(firstPDB, firstEvent, firstMap, firstDiffMap, ligID): ligChain = ligID.split('-')[1] ligResid = ligID.split('-')[2] ngl = ( "\n" - ' \n' - '\n' + ' \n' + '\n' ) return ngl + def html_download(protein_name): download = ( - '
\n' - '

%s - XChem results

\n' %protein_name + - " \n" - '
\n' - '

\n' - '

Click event map in table to view a different crystal / compound pair (press SHIFT and scroll mouse wheel to change contour level of event map)

\n' - ' \n' - '
\n' - '\n' + '
\n' + '

%s - XChem results

\n' % protein_name + + " \n" + ' \n' + '\n' ) return download + def html_guide(): guide = ( - " \n" - "
\n" - "

Ligand-bound models for Summary

Interpreting 'Ligand confidence'

\n" - '

4 - High Confidence: The expected ligand was easily interpretable from clear density, and subsequent refinement was well-behaved. This ligand can be trusted.\n' - '
3 - Clear density, unexpected ligand: Density very clearly showed a well-defined ligand, but that ligand was unexpected in that crystal/dataset. The observed ligand was modelled anyway, because its presence could be explained in some way.\n' - '
2 - Correct ligand, weak density: Though density was weak, it was possible to model the expected ligand, possibly including other circumstantial evidence (e.g. similar ligand in another model).\n' - '
1 - Low Confidence: The ligand model is to be treated with scepticism, because the evidence (density, identity, pose) were not convincing.\n' - "

Interpreting 'Model status':

\n" - '

6 - Deposited: The model has been deposited in the PDB.\n' - '
5 - Deposition ready: The model is fully error-free, in every residue, and is ready for deposition.\n' - '
4 - CompChem ready: The model is complete and correct in the region of the bound ligand. There may be remaining small errors elsewhere in the structure, but they are far away and unlikely to be relevant to any computational analysis or compound design.\n' - "

Interpreting 'Ligand validation' spider plots:

Each axis represents one of the values described below; small is better, and large values on any axis implies that further investigation is warranted.\n" - '

Quality (RSCC) reflects the fit of the atoms to the experimental density, and should typically be greater than 0.7.\n' - '
Accuracy (RSZD) measures the amount of difference density that is found around these atoms, and should be below 3.\n' - '
B-factor ratio measures the consistency of the model with surrounding protein, and is calculated from the B factors of respectively the changed atoms and all side-chain atoms within 4Å. Large values (>3) reflect poor evidence for the model, and intermediate values (1.5+) indicate errors in refinement or modelling; for weakly-binding ligands, systematically large ratios may be justifiable.\n' - '
RMSD compares the positions of all atoms built into event density, with their positions after final refinement, and should be below 1Å.\n' - '
Precision (RSZO/OCC) measures how clear the density is after refinement. (This is not a quality indicator, but is related to strength of binding but not in a straightforward way.)\n' - '

\n' - '

\n' - '\n' + " \n" + "
\n" + "

Ligand-bound models for Summary

Interpreting 'Ligand confidence'

\n" + '

4 - High Confidence: The expected ligand was easily interpretable from clear density, and subsequent refinement was well-behaved. This ligand can be trusted.\n' + '
3 - Clear density, unexpected ligand: Density very clearly showed a well-defined ligand, but that ligand was unexpected in that crystal/dataset. The observed ligand was modelled anyway, because its presence could be explained in some way.\n' + '
2 - Correct ligand, weak density: Though density was weak, it was possible to model the expected ligand, possibly including other circumstantial evidence (e.g. similar ligand in another model).\n' + '
1 - Low Confidence: The ligand model is to be treated with scepticism, because the evidence (density, identity, pose) were not convincing.\n' + "

Interpreting 'Model status':

\n" + '

6 - Deposited: The model has been deposited in the PDB.\n' + '
5 - Deposition ready: The model is fully error-free, in every residue, and is ready for deposition.\n' + '
4 - CompChem ready: The model is complete and correct in the region of the bound ligand. There may be remaining small errors elsewhere in the structure, but they are far away and unlikely to be relevant to any computational analysis or compound design.\n' + "

Interpreting 'Ligand validation' spider plots:

Each axis represents one of the values described below; small is better, and large values on any axis implies that further investigation is warranted.\n" + '

Quality (RSCC) reflects the fit of the atoms to the experimental density, and should typically be greater than 0.7.\n' + '
Accuracy (RSZD) measures the amount of difference density that is found around these atoms, and should be below 3.\n' + '
B-factor ratio measures the consistency of the model with surrounding protein, and is calculated from the B factors of respectively the changed atoms and all side-chain atoms within 4Å. Large values (>3) reflect poor evidence for the model, and intermediate values (1.5+) indicate errors in refinement or modelling; for weakly-binding ligands, systematically large ratios may be justifiable.\n' + '
RMSD compares the positions of all atoms built into event density, with their positions after final refinement, and should be below 1Å.\n' + '
Precision (RSZO/OCC) measures how clear the density is after refinement. (This is not a quality indicator, but is related to strength of binding but not in a straightforward way.)\n' + '

\n' + '

\n' + '\n' ) return guide + def html_table_header(): table = ( - "\n" - '\n' - '\n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' + "\n" + '\n' + '
Crystal IDPDB IDLigand IDLigand confidenceModel statusCompoundLigand ValidationEvent Map 3DResolSPG/ CellFiles
\n' + ' \n' + ' \n' + ' \n' + ' \n' + ' \n' + ' \n' + ' \n' + ' \n' + ' \n' + ' \n' + ' \n' + ' \n' + ' \n' + ' \n' + ' \n' + ' \n' ) - - return table -def html_table_row(xtalID,pdbID,ligID,compoundImage,residuePlot,pdb,event,thumbNail,resoHigh,spg,unitCell,FWT,DELFWT,ligConfidence,modelStatus): +def html_table_row(xtalID, pdbID, ligID, compoundImage, residuePlot, pdb, event, thumbNail, resoHigh, spg, unitCell, FWT, DELFWT, ligConfidence, modelStatus): ligChain = ligID.split('-')[1] ligResid = ligID.split('-')[2] @@ -1310,26 +1390,25 @@ def html_table_row(xtalID,pdbID,ligID,compoundImage,residuePlot,pdb,event,thumbN # '\n' # ) - row = ( ' \n' - ' \n' %xtalID + - ' \n' %(pdbID,pdbID) + - ' \n' %ligID + - ' \n' %ligConfidence + - ' \n' %modelStatus + - " \n" %compoundImage + - " \n" %residuePlot + - " \n" %(pdbID,pdb,event,FWT,DELFWT,ligChain,ligResid,thumbNail) + - ' \n' %resoHigh + - ' \n' %(spg,unitCell) + - " \n" %(pdb.replace('.pdb',''),ligID) + + ' \n' % xtalID + + ' \n' % (pdbID, pdbID) + + ' \n' % ligID + + ' \n' % ligConfidence + + ' \n' % modelStatus + + " \n" % compoundImage + + " \n" % residuePlot + + " \n" % (pdbID, pdb, event, FWT, DELFWT, ligChain, ligResid, thumbNail) + + ' \n' % resoHigh + + ' \n' % (spg, unitCell) + + " \n" % (pdb.replace('.pdb', ''), ligID) + ' \n' ) - return row + def html_footer(): footer = ( @@ -1341,7 +1420,8 @@ def html_footer(): return footer -def coot_prepare_input(x,y,z,ligID,sampleDir,eventMap): + +def coot_prepare_input(x, y, z, ligID, sampleDir, eventMap): os.chdir(sampleDir) cmd = ( @@ -1350,151 +1430,169 @@ def coot_prepare_input(x,y,z,ligID,sampleDir,eventMap): 'import coot\n' 'set_nomenclature_errors_on_read("ignore")\n' 'molecule = read_pdb("refine.split.bound-state.pdb")\n' - 'set_rotation_centre(%s, %s, %s)\n' %(x,y,z) + + 'set_rotation_centre(%s, %s, %s)\n' % (x, y, z) + 'set_zoom(30.)\n' 'set_view_quaternion(-0.180532, -0.678828, 0, 0.711759)\n' - 'coot.handle_read_ccp4_map(("%s"),0)\n' %eventMap + -# 'mtz = "final.mtz"\n' -# 'map21 = make_and_draw_map(mtz, "FWT", "PHWT", "", 0, 0)\n' -# 'map11 = make_and_draw_map(mtz, "DELFWT", "PHDELWT", "", 0, 1)\n' - 'coot.raster3d("%s.r3d")\n' %ligID + + 'coot.handle_read_ccp4_map(("%s"),0)\n' % eventMap + + # 'mtz = "final.mtz"\n' + # 'map21 = make_and_draw_map(mtz, "FWT", "PHWT", "", 0, 0)\n' + # 'map11 = make_and_draw_map(mtz, "DELFWT", "PHDELWT", "", 0, 1)\n' + 'coot.raster3d("%s.r3d")\n' % ligID + 'coot_real_exit(0)\n' ) f = open(ligID+'.py', 'w') f.write(cmd) f.close() -def coot_write_raster_file(ligID,sampleDir): + +def coot_write_raster_file(ligID, sampleDir): os.chdir(sampleDir) - os.system('coot --no-graphics --no-guano --script %s.py' %ligID) + os.system('coot --no-graphics --no-guano --script %s.py' % ligID) + -def render_scene(xtal,ligID,sampleDir): +def render_scene(xtal, ligID, sampleDir): os.chdir(sampleDir) - os.system('render < %s.r3d -png %s_%s.png' %(ligID,xtal,ligID)) + os.system('render < %s.r3d -png %s_%s.png' % (ligID, xtal, ligID)) -def make_thumbnail(xtal,ligID,sampleDir): + +def make_thumbnail(xtal, ligID, sampleDir): os.chdir(sampleDir) - os.system('convert -thumbnail 150x150 %s_%s.png %s_%s_thumb.png' %(xtal,ligID,xtal,ligID)) + os.system('convert -thumbnail 150x150 %s_%s.png %s_%s_thumb.png' % + (xtal, ligID, xtal, ligID)) + + +def backup_soakDB(database, xce_logfile): + Logfile = XChemLog.updateLog(xce_logfile) + Logfile.insert('backing up soakDB: ' + database + + str(datetime.now()).replace(' ', '_')) + os.system('/bin/cp %s %s' % (database, database+'.' + + str(datetime.now()).replace(' ', '_').replace(':', '-'))) -def backup_soakDB(database,xce_logfile): - Logfile=XChemLog.updateLog(xce_logfile) - Logfile.insert('backing up soakDB: ' + database+str(datetime.now()).replace(' ','_')) - os.system('/bin/cp %s %s' %(database,database+'.'+str(datetime.now()).replace(' ','_').replace(':','-'))) class find_diffraction_image_directory(QtCore.QThread): - def __init__(self,diffraction_data_directory): + def __init__(self, diffraction_data_directory): QtCore.QThread.__init__(self) - self.diffraction_data_directory=diffraction_data_directory - self.data_dict={} - self.diffraction_image_extension = ['.img','.cbf','.mccd','.mar2560','.mar2300'] + self.diffraction_data_directory = diffraction_data_directory + self.data_dict = {} + self.diffraction_image_extension = [ + '.img', '.cbf', '.mccd', '.mar2560', '.mar2300'] # self.datasetID_to_sampleID_conversion='*' def run(self): os.chdir(self.diffraction_data_directory) - if len(glob.glob(os.path.join(self.diffraction_data_directory,'*'))) != 0: - progress_step=100/float(len(glob.glob(os.path.join(self.diffraction_data_directory,'*')))) + if len(glob.glob(os.path.join(self.diffraction_data_directory, '*'))) != 0: + progress_step = 100 / \ + float(len(glob.glob(os.path.join(self.diffraction_data_directory, '*')))) else: - progress_step=100 - progress=0 + progress_step = 100 + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'searching diffraction data directory') + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'searching diffraction data directory') for xtal in glob.glob('*'): - self.data_dict[xtal]=[[],[]] - for root,dirs,files in os.walk(xtal): + self.data_dict[xtal] = [[], []] + for root, dirs, files in os.walk(xtal): if 'screening' in root: continue image_file_list = [] - for n,image_file in enumerate(glob.glob(os.path.join(root,'*'))): - file_extension=image_file[image_file.rfind('.'):] + for n, image_file in enumerate(glob.glob(os.path.join(root, '*'))): + file_extension = image_file[image_file.rfind('.'):] if file_extension in self.diffraction_image_extension: image_file_list.append(image_file) if n > 20 and file_extension in self.diffraction_image_extension: - if os.path.join(self.diffraction_data_directory,root) not in self.data_dict[xtal][0]: - self.data_dict[xtal][0].append(os.path.join(self.diffraction_data_directory,root)) + if os.path.join(self.diffraction_data_directory, root) not in self.data_dict[xtal][0]: + self.data_dict[xtal][0].append(os.path.join( + self.diffraction_data_directory, root)) # break if self.data_dict[xtal][0]: - found_new_file_root=False - run_list=[] - counter=0 - current_file_root='' + found_new_file_root = False + run_list = [] + counter = 0 + current_file_root = '' for image in image_file_list: - file_root=image[image.rfind('/')+1:image.rfind('_')] + file_root = image[image.rfind('/')+1:image.rfind('_')] if file_root not in run_list and not found_new_file_root: - counter=0 - found_new_file_root=True - current_file_root=file_root + counter = 0 + found_new_file_root = True + current_file_root = file_root if counter > 20 and file_root not in run_list: - print counter,file_root + print counter, file_root run_list.append(file_root) - found_new_file_root=False - counter=0 - if found_new_file_root and file_root==current_file_root: - counter+=1 + found_new_file_root = False + counter = 0 + if found_new_file_root and file_root == current_file_root: + counter += 1 if run_list: - self.data_dict[xtal][1]=run_list - + self.data_dict[xtal][1] = run_list - if self.data_dict[xtal]==[[],[]]: + if self.data_dict[xtal] == [[], []]: del self.data_dict[xtal] progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - self.emit(QtCore.SIGNAL('update_datasets_reprocess_table'), self.data_dict) + self.emit(QtCore.SIGNAL( + 'update_datasets_reprocess_table'), self.data_dict) + class find_diffraction_image_directory_fast(QtCore.QThread): - def __init__(self,diffraction_data_directory): + def __init__(self, diffraction_data_directory): QtCore.QThread.__init__(self) - self.diffraction_data_directory=diffraction_data_directory - self.data_dict={} - self.diffraction_image_extension = ['.img','.cbf','.mccd','.mar2560','.mar2300'] + self.diffraction_data_directory = diffraction_data_directory + self.data_dict = {} + self.diffraction_image_extension = [ + '.img', '.cbf', '.mccd', '.mar2560', '.mar2300'] # self.datasetID_to_sampleID_conversion='*' def run(self): - print('Running diffraction image search in ' + str(self.diffraction_data_directory)) + print('Running diffraction image search in ' + + str(self.diffraction_data_directory)) os.chdir(self.diffraction_data_directory) - if len(glob.glob(os.path.join(self.diffraction_data_directory,'*'))) != 0: - progress_step=100/float(len(glob.glob(os.path.join(self.diffraction_data_directory,'*')))) + if len(glob.glob(os.path.join(self.diffraction_data_directory, '*'))) != 0: + progress_step = 100 / \ + float(len(glob.glob(os.path.join(self.diffraction_data_directory, '*')))) else: - progress_step=100 - progress=0 + progress_step = 100 + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'searching diffraction data directory') + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'searching diffraction data directory') for xtal in glob.glob('*'): #print xtal if 'screening' in xtal: continue - self.data_dict[xtal]=[] - rootList=[] - imageCounter=0 + self.data_dict[xtal] = [] + rootList = [] + imageCounter = 0 # find image file extension; the assumption is that there is only one file type - imageExtension='cbf' - for files in sorted(glob.glob(os.path.join(xtal,'*'))): - fileName=os.path.join(self.diffraction_data_directory,files) - file_extension=fileName[fileName.rfind('.'):] + imageExtension = 'cbf' + for files in sorted(glob.glob(os.path.join(xtal, '*'))): + fileName = os.path.join(self.diffraction_data_directory, files) + file_extension = fileName[fileName.rfind('.'):] if file_extension in self.diffraction_image_extension: - imageExtension=file_extension + imageExtension = file_extension break - for files in sorted(glob.glob(os.path.join(xtal,'*'+imageExtension))): - fileName=files[files.rfind('/')+1:] - file_root=fileName[:fileName.rfind('_')] + for files in sorted(glob.glob(os.path.join(xtal, '*'+imageExtension))): + fileName = files[files.rfind('/')+1:] + file_root = fileName[:fileName.rfind('_')] if file_root not in rootList: rootList.append(file_root) - currentRoot=file_root - imageCounter=0 + currentRoot = file_root + imageCounter = 0 if imageCounter == 20: - self.data_dict[xtal].append([os.path.join(self.diffraction_data_directory,xtal),file_root]) + self.data_dict[xtal].append( + [os.path.join(self.diffraction_data_directory, xtal), file_root]) # self.data_dict[xtal][1].append(file_root) - imageCounter+=1 + imageCounter += 1 if not self.data_dict[xtal]: del self.data_dict[xtal] @@ -1502,5 +1600,5 @@ def run(self): progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - self.emit(QtCore.SIGNAL('update_datasets_reprocess_table'), self.data_dict) - + self.emit(QtCore.SIGNAL( + 'update_datasets_reprocess_table'), self.data_dict) diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 3b9fcf26..21dfb918 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -1,6 +1,9 @@ # last edited: 10/08/2017, 10:25 -import os, sys, glob, subprocess +import os +import sys +import glob +import subprocess from datetime import datetime from PyQt4 import QtGui, QtCore import math @@ -18,7 +21,7 @@ except ImportError: pass -#def get_names_of_current_clusters(xce_logfile,panddas_directory): +# def get_names_of_current_clusters(xce_logfile,panddas_directory): # Logfile=XChemLog.updateLog(xce_logfile) # Logfile.insert('parsing {0!s}/cluster_analysis'.format(panddas_directory)) # os.chdir('{0!s}/cluster_analysis'.format(panddas_directory)) @@ -37,10 +40,9 @@ # return cluster_dict - class export_and_refine_ligand_bound_models(QtCore.QThread): - def __init__(self,PanDDA_directory,datasource,project_directory,xce_logfile,which_models): + def __init__(self, PanDDA_directory, datasource, project_directory, xce_logfile, which_models): QtCore.QThread.__init__(self) self.PanDDA_directory = PanDDA_directory self.datasource = datasource @@ -48,8 +50,9 @@ def __init__(self,PanDDA_directory,datasource,project_directory,xce_logfile,whic self.Logfile = XChemLog.updateLog(xce_logfile) self.xce_logfile = xce_logfile self.project_directory = project_directory - self.which_models=which_models - self.external_software=XChemUtils.external_software(xce_logfile).check() + self.which_models = which_models + self.external_software = XChemUtils.external_software( + xce_logfile).check() # self.initial_model_directory=initial_model_directory # self.db.create_missing_columns() @@ -61,7 +64,8 @@ def __init__(self,PanDDA_directory,datasource,project_directory,xce_logfile,whic def run(self): - self.Logfile.warning(XChemToolTips.pandda_export_ligand_bound_models_only_disclaimer()) + self.Logfile.warning( + XChemToolTips.pandda_export_ligand_bound_models_only_disclaimer()) # find all folders with *-pandda-model.pdb modelsDict = self.find_modeled_structures_and_timestamps() @@ -72,8 +76,9 @@ def run(self): # find pandda_inspect_events.csv and read in as pandas dataframe inspect_csv = None - if os.path.isfile(os.path.join(self.PanDDA_directory,'analyses','pandda_inspect_events.csv')): - inspect_csv = pandas.read_csv(os.path.join(self.PanDDA_directory,'analyses','pandda_inspect_events.csv')) + if os.path.isfile(os.path.join(self.PanDDA_directory, 'analyses', 'pandda_inspect_events.csv')): + inspect_csv = pandas.read_csv(os.path.join( + self.PanDDA_directory, 'analyses', 'pandda_inspect_events.csv')) progress = 0 try: @@ -84,22 +89,27 @@ def run(self): for xtal in sorted(modelsDict): - os.chdir(os.path.join(self.PanDDA_directory,'processed_datasets',xtal)) - pandda_model = os.path.join('modelled_structures',xtal + '-pandda-model.pdb') + os.chdir(os.path.join(self.PanDDA_directory, + 'processed_datasets', xtal)) + pandda_model = os.path.join( + 'modelled_structures', xtal + '-pandda-model.pdb') pdb = gemmi.read_structure(pandda_model) # find out ligand event map relationship - ligandDict = XChemUtils.pdbtools_gemmi(pandda_model).center_of_mass_ligand_dict('LIG') + ligandDict = XChemUtils.pdbtools_gemmi( + pandda_model).center_of_mass_ligand_dict('LIG') if ligandDict == {}: - self.Logfile.error(xtal + ': cannot find ligand of type LIG; skipping...') + self.Logfile.error( + xtal + ': cannot find ligand of type LIG; skipping...') continue - self.show_ligands_in_model(xtal,ligandDict) - emapLigandDict = self.find_ligands_matching_event_map(inspect_csv,xtal,ligandDict) + self.show_ligands_in_model(xtal, ligandDict) + emapLigandDict = self.find_ligands_matching_event_map( + inspect_csv, xtal, ligandDict) self.Logfile.warning('emapLigandDict' + str(emapLigandDict)) # convert event map to SF - self.event_map_to_sf(pdb.resolution,emapLigandDict) + self.event_map_to_sf(pdb.resolution, emapLigandDict) # move existing event maps in project directory to old folder self.move_old_event_to_backup_folder(xtal) @@ -111,10 +121,10 @@ def run(self): self.copy_pandda_model_to_project_directory(xtal) # make map from MTZ and cut around ligand - self.make_and_cut_map(xtal,emapLigandDict) + self.make_and_cut_map(xtal, emapLigandDict) # update database - self.update_database(xtal,modelsDict) + self.update_database(xtal, modelsDict) # refine models self.refine_exported_model(xtal) @@ -122,443 +132,495 @@ def run(self): progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - def update_database(self,xtal,modelsDict): + def update_database(self, xtal, modelsDict): db_dict = {} timestamp_file = modelsDict[xtal] db_dict['DatePanDDAModelCreated'] = timestamp_file db_dict['RefinementOutcome'] = '3 - In Refinement' - self.Logfile.insert('updating database for '+xtal+' setting time model was created to '+db_dict['DatePanDDAModelCreated']) - self.db.update_data_source(xtal,db_dict) - - - - def make_and_cut_map(self,xtal,emapLigandDict): - self.Logfile.insert('changing directory to ' + os.path.join(self.project_directory,xtal)) - os.chdir(os.path.join(self.project_directory,xtal)) - XChemUtils.pdbtools_gemmi(xtal + '-pandda-model.pdb').save_ligands_to_pdb('LIG') + self.Logfile.insert('updating database for '+xtal + + ' setting time model was created to '+db_dict['DatePanDDAModelCreated']) + self.db.update_data_source(xtal, db_dict) + + def make_and_cut_map(self, xtal, emapLigandDict): + self.Logfile.insert('changing directory to ' + + os.path.join(self.project_directory, xtal)) + os.chdir(os.path.join(self.project_directory, xtal)) + XChemUtils.pdbtools_gemmi( + xtal + '-pandda-model.pdb').save_ligands_to_pdb('LIG') for ligID in emapLigandDict: m = emapLigandDict[ligID] - emtz = m.replace('.ccp4','_' + ligID + '.mtz') - emap = m.replace('.ccp4','_' + ligID + '.ccp4') - XChemUtils.maptools().calculate_map(emtz,'FWT','PHWT') - XChemUtils.maptools().cut_map_around_ligand(emap,ligID+'.pdb','7') - if os.path.isfile(emap.replace('.ccp4','_mapmask.ccp4')): - os.system('/bin/mv %s %s_%s_event.ccp4' %(emap.replace('.ccp4','_mapmask.ccp4'),xtal,ligID)) - os.system('ln -s %s_%s_event.ccp4 %s_%s_event_cut.ccp4' %(xtal,ligID,xtal,ligID)) - - - def copy_pandda_model_to_project_directory(self,xtal): - os.chdir(os.path.join(self.project_directory,xtal)) - model = os.path.join(self.PanDDA_directory,'processed_datasets',xtal,'modelled_structures',xtal+'-pandda-model.pdb') - self.Logfile.insert('copying %s to project directory' %model) - os.system('/bin/cp %s .' %model) - - def copy_event_mtz_to_project_directory(self,xtal): - self.Logfile.insert('changing directory to ' + os.path.join(self.PanDDA_directory,'processed_datasets',xtal)) - os.chdir(os.path.join(self.PanDDA_directory,'processed_datasets',xtal)) + emtz = m.replace('.ccp4', '_' + ligID + '.mtz') + emap = m.replace('.ccp4', '_' + ligID + '.ccp4') + XChemUtils.maptools().calculate_map(emtz, 'FWT', 'PHWT') + XChemUtils.maptools().cut_map_around_ligand(emap, ligID+'.pdb', '7') + if os.path.isfile(emap.replace('.ccp4', '_mapmask.ccp4')): + os.system('/bin/mv %s %s_%s_event.ccp4' % + (emap.replace('.ccp4', '_mapmask.ccp4'), xtal, ligID)) + os.system('ln -s %s_%s_event.ccp4 %s_%s_event_cut.ccp4' % + (xtal, ligID, xtal, ligID)) + + def copy_pandda_model_to_project_directory(self, xtal): + os.chdir(os.path.join(self.project_directory, xtal)) + model = os.path.join(self.PanDDA_directory, 'processed_datasets', + xtal, 'modelled_structures', xtal+'-pandda-model.pdb') + self.Logfile.insert('copying %s to project directory' % model) + os.system('/bin/cp %s .' % model) + + def copy_event_mtz_to_project_directory(self, xtal): + self.Logfile.insert('changing directory to ' + + os.path.join(self.PanDDA_directory, 'processed_datasets', xtal)) + os.chdir(os.path.join(self.PanDDA_directory, 'processed_datasets', xtal)) for emap in glob.glob('*-BDC_*.mtz'): - self.Logfile.insert('copying %s to %s...' %(emap,os.path.join(self.project_directory,xtal))) - os.system('/bin/cp %s %s' %(emap,os.path.join(self.project_directory,xtal))) - - - def move_old_event_to_backup_folder(self,xtal): - self.Logfile.insert('changing directory to ' + os.path.join(self.project_directory,xtal)) - os.chdir(os.path.join(self.project_directory,xtal)) + self.Logfile.insert('copying %s to %s...' % ( + emap, os.path.join(self.project_directory, xtal))) + os.system('/bin/cp %s %s' % + (emap, os.path.join(self.project_directory, xtal))) + + def move_old_event_to_backup_folder(self, xtal): + self.Logfile.insert('changing directory to ' + + os.path.join(self.project_directory, xtal)) + os.chdir(os.path.join(self.project_directory, xtal)) if not os.path.isdir('event_map_backup'): os.mkdir('event_map_backup') self.Logfile.insert('moving existing event maps to event_map_backup') for emap in glob.glob('*-BDC_*.ccp4'): - os.system('/bin/mv %s event_map_backup/%s' %(emap,emap+'.'+str(datetime.now()).replace(' ','_').replace(':','-'))) + os.system('/bin/mv %s event_map_backup/%s' % (emap, emap + + '.'+str(datetime.now()).replace(' ', '_').replace(':', '-'))) - def show_ligands_in_model(self,xtal,ligandDict): + def show_ligands_in_model(self, xtal, ligandDict): self.Logfile.insert(xtal + ': found the following ligands...') for lig in ligandDict: - self.Logfile.insert(lig + ' -> coordinates ' + str(ligandDict[lig])) - + self.Logfile.insert( + lig + ' -> coordinates ' + str(ligandDict[lig])) def find_modeled_structures_and_timestamps(self): - self.Logfile.insert('finding out modelled structures in ' + self.PanDDA_directory) - modelsDict={} - for model in sorted(glob.glob(os.path.join(self.PanDDA_directory,'processed_datasets','*','modelled_structures','*-pandda-model.pdb'))): - sample=model[model.rfind('/')+1:].replace('-pandda-model.pdb','') - timestamp=datetime.fromtimestamp(os.path.getmtime(model)).strftime('%Y-%m-%d %H:%M:%S') - self.Logfile.insert(sample+'-pandda-model.pdb was created on '+str(timestamp)) - modelsDict[sample]=timestamp + self.Logfile.insert( + 'finding out modelled structures in ' + self.PanDDA_directory) + modelsDict = {} + for model in sorted(glob.glob(os.path.join(self.PanDDA_directory, 'processed_datasets', '*', 'modelled_structures', '*-pandda-model.pdb'))): + sample = model[model.rfind( + '/')+1:].replace('-pandda-model.pdb', '') + timestamp = datetime.fromtimestamp( + os.path.getmtime(model)).strftime('%Y-%m-%d %H:%M:%S') + self.Logfile.insert( + sample+'-pandda-model.pdb was created on '+str(timestamp)) + modelsDict[sample] = timestamp return modelsDict - def find_new_models(self,modelsDict): + def find_new_models(self, modelsDict): samples_to_export = {} - self.Logfile.hint('XCE will never export/ refine models that are "5-deposition ready" or "6-deposited"') - self.Logfile.hint('Please change the RefinementOutcome flag in the Refinement table if you wish to re-export them') + self.Logfile.hint( + 'XCE will never export/ refine models that are "5-deposition ready" or "6-deposited"') + self.Logfile.hint( + 'Please change the RefinementOutcome flag in the Refinement table if you wish to re-export them') self.Logfile.insert('checking timestamps of models in database...') for xtal in modelsDict: timestamp_file = modelsDict[xtal] - db_query=self.db.execute_statement("select DatePanDDAModelCreated from mainTable where CrystalName is '"+xtal+"' and (RefinementOutcome like '3%' or RefinementOutcome like '4%')") + db_query = self.db.execute_statement("select DatePanDDAModelCreated from mainTable where CrystalName is '" + + xtal+"' and (RefinementOutcome like '3%' or RefinementOutcome like '4%')") try: - timestamp_db=str(db_query[0][0]) + timestamp_db = str(db_query[0][0]) except IndexError: - self.Logfile.warning('%s: database query gave no results for DatePanDDAModelCreated; skipping...' %xtal) - self.Logfile.warning('%s: this might be a brand new model; will continue with export!' %xtal) - samples_to_export[xtal]=timestamp_file - timestamp_db = "2100-01-01 00:00:00" # some time in the future... + self.Logfile.warning( + '%s: database query gave no results for DatePanDDAModelCreated; skipping...' % xtal) + self.Logfile.warning( + '%s: this might be a brand new model; will continue with export!' % xtal) + samples_to_export[xtal] = timestamp_file + # some time in the future... + timestamp_db = "2100-01-01 00:00:00" try: - difference=(datetime.strptime(timestamp_file,'%Y-%m-%d %H:%M:%S') - datetime.strptime(timestamp_db,'%Y-%m-%d %H:%M:%S') ) + difference = (datetime.strptime(timestamp_file, '%Y-%m-%d %H:%M:%S') - + datetime.strptime(timestamp_db, '%Y-%m-%d %H:%M:%S')) if difference.seconds != 0: - self.Logfile.insert('exporting '+xtal+' -> was already refined, but newer PanDDA model available') - samples_to_export[xtal]=timestamp_file + self.Logfile.insert( + 'exporting '+xtal+' -> was already refined, but newer PanDDA model available') + samples_to_export[xtal] = timestamp_file else: - self.Logfile.insert('%s: model has not changed since it was created on %s' %(xtal,timestamp_db)) + self.Logfile.insert( + '%s: model has not changed since it was created on %s' % (xtal, timestamp_db)) except (ValueError, IndexError), e: self.Logfile.error(str(e)) - return samples_to_export + return samples_to_export - def event_map_to_sf(self,resolution,emapLigandDict): + def event_map_to_sf(self, resolution, emapLigandDict): for lig in emapLigandDict: emap = emapLigandDict[lig] - emtz = emap.replace('.ccp4','.mtz') - emtz_ligand = emap.replace('.ccp4','_' + lig + '.mtz') - self.Logfile.insert('trying to convert %s to SF -> %s' %(emap,emtz_ligand)) + emtz = emap.replace('.ccp4', '.mtz') + emtz_ligand = emap.replace('.ccp4', '_' + lig + '.mtz') + self.Logfile.insert( + 'trying to convert %s to SF -> %s' % (emap, emtz_ligand)) self.Logfile.insert('>>> ' + emtz) XChemUtils.maptools_gemmi(emap).map_to_sf(resolution) if os.path.isfile(emtz): - os.system('/bin/mv %s %s' %(emtz,emtz_ligand)) - self.Logfile.insert('success; %s exists' %emtz_ligand) + os.system('/bin/mv %s %s' % (emtz, emtz_ligand)) + self.Logfile.insert('success; %s exists' % emtz_ligand) else: - self.Logfile.warning('something went wrong; %s could not be created...' %emtz_ligand) + self.Logfile.warning( + 'something went wrong; %s could not be created...' % emtz_ligand) - def find_ligands_matching_event_map(self,inspect_csv,xtal,ligandDict): + def find_ligands_matching_event_map(self, inspect_csv, xtal, ligandDict): emapLigandDict = {} for index, row in inspect_csv.iterrows(): if row['dtag'] == xtal: for emap in glob.glob('*-BDC_*.ccp4'): - self.Logfile.insert('checking if event and ligand are within 7A of each other') + self.Logfile.insert( + 'checking if event and ligand are within 7A of each other') x = float(row['x']) y = float(row['y']) z = float(row['z']) - matching_ligand = self.calculate_distance_to_ligands(ligandDict,x,y,z) + matching_ligand = self.calculate_distance_to_ligands( + ligandDict, x, y, z) if matching_ligand is not None: emapLigandDict[matching_ligand] = emap - self.Logfile.insert('found matching ligand (%s) for %s' %(matching_ligand,emap)) + self.Logfile.insert( + 'found matching ligand (%s) for %s' % (matching_ligand, emap)) break else: - self.Logfile.warning('current ligand not close to event...') + self.Logfile.warning( + 'current ligand not close to event...') if emapLigandDict == {}: - self.Logfile.error('could not find ligands within 7A of PanDDA events') + self.Logfile.error( + 'could not find ligands within 7A of PanDDA events') return emapLigandDict - def calculate_distance_to_ligands(self,ligandDict,x,y,z): + def calculate_distance_to_ligands(self, ligandDict, x, y, z): matching_ligand = None p_event = gemmi.Position(x, y, z) for ligand in ligandDict: c = ligandDict[ligand] p_ligand = gemmi.Position(c[0], c[1], c[2]) - self.Logfile.insert('coordinates ligand: ' + str(c[0])+' '+ str(c[1])+' '+str(c[2])) - self.Logfile.insert('coordinates event: ' + str(x)+' '+ str(y)+' '+str(z)) + self.Logfile.insert('coordinates ligand: ' + + str(c[0])+' ' + str(c[1])+' '+str(c[2])) + self.Logfile.insert('coordinates event: ' + + str(x)+' ' + str(y)+' '+str(z)) distance = p_event.dist(p_ligand) - self.Logfile.insert('distance between ligand and event: %s A' %str(distance)) + self.Logfile.insert( + 'distance between ligand and event: %s A' % str(distance)) if distance < 7: matching_ligand = ligand break return matching_ligand - - - - def refine_exported_model(self,xtal): - - RefmacParams={ 'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '', - 'WATER': '', - 'LIGOCC': '', - 'SANITY': '' } + def refine_exported_model(self, xtal): + + RefmacParams = {'HKLIN': '', 'HKLOUT': '', + 'XYZIN': '', 'XYZOUT': '', + 'LIBIN': '', 'LIBOUT': '', + 'TLSIN': '', 'TLSOUT': '', + 'TLSADD': '', + 'NCYCLES': '10', + 'MATRIX_WEIGHT': 'AUTO', + 'BREF': ' bref ISOT\n', + 'TLS': '', + 'NCS': '', + 'TWIN': '', + 'WATER': '', + 'LIGOCC': '', + 'SANITY': ''} if 'nocheck' in self.which_models: RefmacParams['SANITY'] = 'off' self.Logfile.insert('trying to refine ' + xtal + '...') - self.Logfile.insert('%s: getting compound code from database' %xtal) - query=self.db.execute_statement("select CompoundCode from mainTable where CrystalName='%s';" %xtal) - compoundID=str(query[0][0]) - self.Logfile.insert('%s: compounds code = %s' %(xtal,compoundID)) - if os.path.isfile(os.path.join(self.project_directory,xtal,xtal+'.free.mtz')): - if os.path.isfile(os.path.join(self.project_directory,xtal,xtal+'-pandda-model.pdb')): - self.Logfile.insert('running inital refinement on PANDDA model of '+xtal) - Serial=XChemRefine.GetSerial(self.project_directory,xtal) - if not os.path.isdir(os.path.join(self.project_directory,xtal,'cootOut')): - os.mkdir(os.path.join(self.project_directory,xtal,'cootOut')) + self.Logfile.insert('%s: getting compound code from database' % xtal) + query = self.db.execute_statement( + "select CompoundCode from mainTable where CrystalName='%s';" % xtal) + compoundID = str(query[0][0]) + self.Logfile.insert('%s: compounds code = %s' % (xtal, compoundID)) + if os.path.isfile(os.path.join(self.project_directory, xtal, xtal+'.free.mtz')): + if os.path.isfile(os.path.join(self.project_directory, xtal, xtal+'-pandda-model.pdb')): + self.Logfile.insert( + 'running inital refinement on PANDDA model of '+xtal) + Serial = XChemRefine.GetSerial(self.project_directory, xtal) + if not os.path.isdir(os.path.join(self.project_directory, xtal, 'cootOut')): + os.mkdir(os.path.join( + self.project_directory, xtal, 'cootOut')) # create folder for new refinement cycle - if os.path.isdir(os.path.join(self.project_directory,xtal,'cootOut','Refine_'+str(Serial))): - os.chdir(os.path.join(self.project_directory,xtal,'cootOut','Refine_'+str(Serial))) + if os.path.isdir(os.path.join(self.project_directory, xtal, 'cootOut', 'Refine_'+str(Serial))): + os.chdir(os.path.join(self.project_directory, + xtal, 'cootOut', 'Refine_'+str(Serial))) else: - os.mkdir(os.path.join(self.project_directory,xtal,'cootOut','Refine_'+str(Serial))) - os.chdir(os.path.join(self.project_directory,xtal,'cootOut','Refine_'+str(Serial))) - os.system('/bin/cp %s in.pdb' %os.path.join(self.project_directory,xtal,xtal+'-pandda-model.pdb')) - Refine=XChemRefine.Refine(self.project_directory,xtal,compoundID,self.datasource) - Refine.RunBuster(str(Serial),RefmacParams,self.external_software,self.xce_logfile,None) + os.mkdir(os.path.join(self.project_directory, + xtal, 'cootOut', 'Refine_'+str(Serial))) + os.chdir(os.path.join(self.project_directory, + xtal, 'cootOut', 'Refine_'+str(Serial))) + os.system('/bin/cp %s in.pdb' % + os.path.join(self.project_directory, xtal, xtal+'-pandda-model.pdb')) + Refine = XChemRefine.Refine( + self.project_directory, xtal, compoundID, self.datasource) + Refine.RunBuster(str(Serial), RefmacParams, + self.external_software, self.xce_logfile, None) else: - self.Logfile.error('%s: cannot find %s-pandda-model.pdb; cannot start refinement...' %(xtal,xtal)) + self.Logfile.error( + '%s: cannot find %s-pandda-model.pdb; cannot start refinement...' % (xtal, xtal)) else: self.Logfile.error('%s: cannot start refinement because %s.free.mtz is missing in %s' % ( - xtal, xtal, os.path.join(self.project_directory, xtal))) - - - - - - - - - - - - + xtal, xtal, os.path.join(self.project_directory, xtal))) class refine_bound_state_with_buster(QtCore.QThread): - def __init__(self,panddas_directory,datasource,initial_model_directory,xce_logfile,which_models): + def __init__(self, panddas_directory, datasource, initial_model_directory, xce_logfile, which_models): QtCore.QThread.__init__(self) - self.panddas_directory=panddas_directory - self.datasource=datasource - self.initial_model_directory=initial_model_directory - self.db=XChemDB.data_source(self.datasource) + self.panddas_directory = panddas_directory + self.datasource = datasource + self.initial_model_directory = initial_model_directory + self.db = XChemDB.data_source(self.datasource) self.db.create_missing_columns() - self.db_list=self.db.get_empty_db_dict() - self.external_software=XChemUtils.external_software(xce_logfile).check() - self.xce_logfile=xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) - self.which_models=which_models - self.already_exported_models=[] + self.db_list = self.db.get_empty_db_dict() + self.external_software = XChemUtils.external_software( + xce_logfile).check() + self.xce_logfile = xce_logfile + self.Logfile = XChemLog.updateLog(xce_logfile) + self.which_models = which_models + self.already_exported_models = [] def run(self): - samples_to_export=self.export_models() + samples_to_export = self.export_models() self.refine_exported_models(samples_to_export) - - def refine_exported_models(self,samples_to_export): + def refine_exported_models(self, samples_to_export): self.Logfile.insert('will try to refine the following crystals:') for xtal in sorted(samples_to_export): self.Logfile.insert(xtal) for xtal in sorted(samples_to_export): - self.Logfile.insert('%s: getting compound code from database' %xtal) - query=self.db.execute_statement("select CompoundCode from mainTable where CrystalName='%s';" %xtal) - compoundID=str(query[0][0]) - self.Logfile.insert('%s: compounds code = %s' %(xtal,compoundID)) + self.Logfile.insert( + '%s: getting compound code from database' % xtal) + query = self.db.execute_statement( + "select CompoundCode from mainTable where CrystalName='%s';" % xtal) + compoundID = str(query[0][0]) + self.Logfile.insert('%s: compounds code = %s' % (xtal, compoundID)) # compoundID=str(item[1]) - if os.path.isfile(os.path.join(self.initial_model_directory,xtal,xtal+'.free.mtz')): - if os.path.isfile(os.path.join(self.initial_model_directory,xtal,xtal+'-pandda-model.pdb')): - self.Logfile.insert('running inital refinement on PANDDA model of '+xtal) - Serial=XChemRefine.GetSerial(self.initial_model_directory,xtal) + if os.path.isfile(os.path.join(self.initial_model_directory, xtal, xtal+'.free.mtz')): + if os.path.isfile(os.path.join(self.initial_model_directory, xtal, xtal+'-pandda-model.pdb')): + self.Logfile.insert( + 'running inital refinement on PANDDA model of '+xtal) + Serial = XChemRefine.GetSerial( + self.initial_model_directory, xtal) ####################################################### - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'cootOut')): - os.mkdir(os.path.join(self.initial_model_directory,xtal,'cootOut')) + if not os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'cootOut')): + os.mkdir(os.path.join( + self.initial_model_directory, xtal, 'cootOut')) # create folder for new refinement cycle - if os.path.isdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))): - os.chdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))) + if os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'cootOut', 'Refine_'+str(Serial))): + os.chdir(os.path.join(self.initial_model_directory, + xtal, 'cootOut', 'Refine_'+str(Serial))) else: - os.mkdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))) - os.chdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))) - os.system('/bin/cp %s in.pdb' %os.path.join(self.initial_model_directory,xtal,xtal+'-pandda-model.pdb')) - Refine=XChemRefine.Refine(self.initial_model_directory,xtal,compoundID,self.datasource) - Refine.RunBuster(str(Serial),self.external_software,self.xce_logfile,None) + os.mkdir(os.path.join(self.initial_model_directory, + xtal, 'cootOut', 'Refine_'+str(Serial))) + os.chdir(os.path.join(self.initial_model_directory, + xtal, 'cootOut', 'Refine_'+str(Serial))) + os.system('/bin/cp %s in.pdb' % os.path.join( + self.initial_model_directory, xtal, xtal+'-pandda-model.pdb')) + Refine = XChemRefine.Refine( + self.initial_model_directory, xtal, compoundID, self.datasource) + Refine.RunBuster( + str(Serial), self.external_software, self.xce_logfile, None) else: - self.Logfile.error('%s: cannot find %s-pandda-model.pdb; cannot start refinement...' %(xtal,xtal)) + self.Logfile.error( + '%s: cannot find %s-pandda-model.pdb; cannot start refinement...' % (xtal, xtal)) elif xtal in samples_to_export and not os.path.isfile( os.path.join(self.initial_model_directory, xtal, xtal + '.free.mtz')): self.Logfile.error('%s: cannot start refinement because %s.free.mtz is missing in %s' % ( - xtal, xtal, os.path.join(self.initial_model_directory, xtal))) + xtal, xtal, os.path.join(self.initial_model_directory, xtal))) else: self.Logfile.insert('%s: nothing to refine' % (xtal)) - def export_models(self): - self.Logfile.insert('finding out which PanDDA models need to be exported') + self.Logfile.insert( + 'finding out which PanDDA models need to be exported') # first find which samples are in interesting datasets and have a model # and determine the timestamp - fileModelsDict={} - queryModels='' - for model in glob.glob(os.path.join(self.panddas_directory,'processed_datasets','*','modelled_structures','*-pandda-model.pdb')): - sample=model[model.rfind('/')+1:].replace('-pandda-model.pdb','') - timestamp=datetime.fromtimestamp(os.path.getmtime(model)).strftime('%Y-%m-%d %H:%M:%S') - self.Logfile.insert(sample+'-pandda-model.pdb was created on '+str(timestamp)) - queryModels+="'"+sample+"'," - fileModelsDict[sample]=timestamp + fileModelsDict = {} + queryModels = '' + for model in glob.glob(os.path.join(self.panddas_directory, 'processed_datasets', '*', 'modelled_structures', '*-pandda-model.pdb')): + sample = model[model.rfind( + '/')+1:].replace('-pandda-model.pdb', '') + timestamp = datetime.fromtimestamp( + os.path.getmtime(model)).strftime('%Y-%m-%d %H:%M:%S') + self.Logfile.insert( + sample+'-pandda-model.pdb was created on '+str(timestamp)) + queryModels += "'"+sample+"'," + fileModelsDict[sample] = timestamp # now get these models from the database and compare the datestamps # Note: only get the models that underwent some form of refinement, # because only if the model was updated in pandda.inspect will it be exported and refined - dbModelsDict={} + dbModelsDict = {} if queryModels != '': - dbEntries=self.db.execute_statement("select CrystalName,DatePanDDAModelCreated from mainTable where CrystalName in ("+queryModels[:-1]+") and (RefinementOutcome like '3%' or RefinementOutcome like '4%' or RefinementOutcome like '5%')") + dbEntries = self.db.execute_statement("select CrystalName,DatePanDDAModelCreated from mainTable where CrystalName in (" + + queryModels[:-1]+") and (RefinementOutcome like '3%' or RefinementOutcome like '4%' or RefinementOutcome like '5%')") for item in dbEntries: - xtal=str(item[0]) - timestamp=str(item[1]) - dbModelsDict[xtal]=timestamp - self.Logfile.insert('PanDDA model for '+xtal+' is in database and was created on '+str(timestamp)) + xtal = str(item[0]) + timestamp = str(item[1]) + dbModelsDict[xtal] = timestamp + self.Logfile.insert( + 'PanDDA model for '+xtal+' is in database and was created on '+str(timestamp)) # compare timestamps and only export the ones where the timestamp of the file is newer than the one in the DB - samples_to_export={} - self.Logfile.insert('checking which PanDDA models were newly created or updated') - if self.which_models=='all': - self.Logfile.insert('Note: you chose to export ALL available PanDDA!') + samples_to_export = {} + self.Logfile.insert( + 'checking which PanDDA models were newly created or updated') + if self.which_models == 'all': + self.Logfile.insert( + 'Note: you chose to export ALL available PanDDA!') for sample in fileModelsDict: - if self.which_models=='all': + if self.which_models == 'all': self.Logfile.insert('exporting '+sample) - samples_to_export[sample]=fileModelsDict[sample] + samples_to_export[sample] = fileModelsDict[sample] else: if sample in dbModelsDict: try: - difference=(datetime.strptime(fileModelsDict[sample],'%Y-%m-%d %H:%M:%S') - datetime.strptime(dbModelsDict[sample],'%Y-%m-%d %H:%M:%S') ) + difference = (datetime.strptime( + fileModelsDict[sample], '%Y-%m-%d %H:%M:%S') - datetime.strptime(dbModelsDict[sample], '%Y-%m-%d %H:%M:%S')) if difference.seconds != 0: - self.Logfile.insert('exporting '+sample+' -> was already refined, but newer PanDDA model available') - samples_to_export[sample]=fileModelsDict[sample] + self.Logfile.insert( + 'exporting '+sample+' -> was already refined, but newer PanDDA model available') + samples_to_export[sample] = fileModelsDict[sample] except ValueError: # this will be raised if timestamp is not properly formatted; # which will usually be the case when respective field in database is blank # these are hopefully legacy cases which are from before this extensive check was introduced (13/01/2017) - advice = ( 'The pandda model of '+xtal+' was changed, but it was already refined! ' - 'This is most likely because this was done with an older version of XCE. ' - 'If you really want to export and refine this model, you need to open the database ' - 'with DBbroweser (sqlitebrowser.org); then change the RefinementOutcome field ' - 'of the respective sample to "2 - PANDDA model", save the database and repeat the export prodedure.' ) + advice = ('The pandda model of '+xtal+' was changed, but it was already refined! ' + 'This is most likely because this was done with an older version of XCE. ' + 'If you really want to export and refine this model, you need to open the database ' + 'with DBbroweser (sqlitebrowser.org); then change the RefinementOutcome field ' + 'of the respective sample to "2 - PANDDA model", save the database and repeat the export prodedure.') self.Logfile.insert(advice) else: - self.Logfile.insert('exporting '+sample+' -> first time to be exported and refined') - samples_to_export[sample]=fileModelsDict[sample] + self.Logfile.insert( + 'exporting '+sample+' -> first time to be exported and refined') + samples_to_export[sample] = fileModelsDict[sample] # update the DB: # set timestamp to current timestamp of file and set RefinementOutcome to '2-pandda...' if samples_to_export != {}: - select_dir_string='' - select_dir_string_new_pannda=' ' + select_dir_string = '' + select_dir_string_new_pannda = ' ' for sample in samples_to_export: - self.Logfile.insert('changing directory to ' + os.path.join(self.initial_model_directory,sample)) - os.chdir(os.path.join(self.initial_model_directory,sample)) - self.Logfile.insert(sample + ': copying ' + os.path.join(self.panddas_directory,'processed_datasets',sample,'modelled_structures',sample+'-pandda-model.pdb')) - os.system('/bin/cp %s .' %os.path.join(self.panddas_directory,'processed_datasets',sample,'modelled_structures',sample+'-pandda-model.pdb')) - db_dict= {'RefinementOutcome': '2 - PANDDA model', 'DatePanDDAModelCreated': samples_to_export[sample]} + self.Logfile.insert( + 'changing directory to ' + os.path.join(self.initial_model_directory, sample)) + os.chdir(os.path.join(self.initial_model_directory, sample)) + self.Logfile.insert(sample + ': copying ' + os.path.join(self.panddas_directory, + 'processed_datasets', sample, 'modelled_structures', sample+'-pandda-model.pdb')) + os.system('/bin/cp %s .' % os.path.join(self.panddas_directory, + 'processed_datasets', sample, 'modelled_structures', sample+'-pandda-model.pdb')) + db_dict = {'RefinementOutcome': '2 - PANDDA model', + 'DatePanDDAModelCreated': samples_to_export[sample]} for old_event_map in glob.glob('*-BDC_*.ccp4'): if not os.path.isdir('old_event_maps'): os.mkdir('old_event_maps') - self.Logfile.warning(sample + ': moving ' + old_event_map + ' to old_event_maps folder') - os.system('/bin/mv %s old_event_maps' %old_event_map) - for event_map in glob.glob(os.path.join(self.panddas_directory,'processed_datasets',sample,'*-BDC_*.ccp4')): + self.Logfile.warning( + sample + ': moving ' + old_event_map + ' to old_event_maps folder') + os.system('/bin/mv %s old_event_maps' % old_event_map) + for event_map in glob.glob(os.path.join(self.panddas_directory, 'processed_datasets', sample, '*-BDC_*.ccp4')): self.Logfile.insert(sample + ': copying ' + event_map) - os.system('/bin/cp %s .' %event_map) - select_dir_string+="select_dir={0!s} ".format(sample) - select_dir_string_new_pannda+='{0!s} '.format(sample) - self.Logfile.insert('updating database for '+sample+' setting time model was created to '+db_dict['DatePanDDAModelCreated']+' and RefinementOutcome to '+db_dict['RefinementOutcome']) - self.db.update_data_source(sample,db_dict) - + os.system('/bin/cp %s .' % event_map) + select_dir_string += "select_dir={0!s} ".format(sample) + select_dir_string_new_pannda += '{0!s} '.format(sample) + self.Logfile.insert('updating database for '+sample+' setting time model was created to ' + + db_dict['DatePanDDAModelCreated']+' and RefinementOutcome to '+db_dict['RefinementOutcome']) + self.db.update_data_source(sample, db_dict) return samples_to_export - - - - - - - - - - - - - - class run_pandda_export(QtCore.QThread): - def __init__(self,panddas_directory,datasource,initial_model_directory,xce_logfile,update_datasource_only,which_models,pandda_params): + def __init__(self, panddas_directory, datasource, initial_model_directory, xce_logfile, update_datasource_only, which_models, pandda_params): QtCore.QThread.__init__(self) - self.panddas_directory=panddas_directory - self.datasource=datasource - self.initial_model_directory=initial_model_directory - self.db=XChemDB.data_source(self.datasource) + self.panddas_directory = panddas_directory + self.datasource = datasource + self.initial_model_directory = initial_model_directory + self.db = XChemDB.data_source(self.datasource) self.db.create_missing_columns() - self.db_list=self.db.get_empty_db_dict() - self.external_software=XChemUtils.external_software(xce_logfile).check() - self.xce_logfile=xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) - self.update_datasource_only=update_datasource_only - self.which_models=which_models - self.already_exported_models=[] + self.db_list = self.db.get_empty_db_dict() + self.external_software = XChemUtils.external_software( + xce_logfile).check() + self.xce_logfile = xce_logfile + self.Logfile = XChemLog.updateLog(xce_logfile) + self.update_datasource_only = update_datasource_only + self.which_models = which_models + self.already_exported_models = [] self.pandda_analyse_data_table = pandda_params['pandda_table'] - self.RefmacParams={ 'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '' } + self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', + 'XYZIN': '', 'XYZOUT': '', + 'LIBIN': '', 'LIBOUT': '', + 'TLSIN': '', 'TLSOUT': '', + 'TLSADD': '', + 'NCYCLES': '10', + 'MATRIX_WEIGHT': 'AUTO', + 'BREF': ' bref ISOT\n', + 'TLS': '', + 'NCS': '', + 'TWIN': ''} def run(self): # v1.3.8.2 - removed option to update database only -# if not self.update_datasource_only: - samples_to_export=self.export_models() + # if not self.update_datasource_only: + samples_to_export = self.export_models() self.import_samples_into_datasouce(samples_to_export) # if not self.update_datasource_only: self.refine_exported_models(samples_to_export) - - def refine_exported_models(self,samples_to_export): + def refine_exported_models(self, samples_to_export): self.Logfile.insert('will try to refine the following crystals:') - for xtal in samples_to_export: self.Logfile.insert(xtal) + for xtal in samples_to_export: + self.Logfile.insert(xtal) # sample_list=self.db.execute_statement("select CrystalName,CompoundCode from mainTable where RefinementOutcome='2 - PANDDA model';") # for item in sample_list: # xtal=str(item[0]) for xtal in sorted(samples_to_export): - self.Logfile.insert('%s: getting compound code from database' %xtal) - query=self.db.execute_statement("select CompoundCode from mainTable where CrystalName='%s';" %xtal) - compoundID=str(query[0][0]) - self.Logfile.insert('%s: compounds code = %s' %(xtal,compoundID)) + self.Logfile.insert( + '%s: getting compound code from database' % xtal) + query = self.db.execute_statement( + "select CompoundCode from mainTable where CrystalName='%s';" % xtal) + compoundID = str(query[0][0]) + self.Logfile.insert('%s: compounds code = %s' % (xtal, compoundID)) # compoundID=str(item[1]) - if os.path.isfile(os.path.join(self.initial_model_directory,xtal,xtal+'.free.mtz')): - if os.path.isfile(os.path.join(self.initial_model_directory,xtal,xtal+'-ensemble-model.pdb')): - self.Logfile.insert('running inital refinement on PANDDA model of '+xtal) - Serial=XChemRefine.GetSerial(self.initial_model_directory,xtal) + if os.path.isfile(os.path.join(self.initial_model_directory, xtal, xtal+'.free.mtz')): + if os.path.isfile(os.path.join(self.initial_model_directory, xtal, xtal+'-ensemble-model.pdb')): + self.Logfile.insert( + 'running inital refinement on PANDDA model of '+xtal) + Serial = XChemRefine.GetSerial( + self.initial_model_directory, xtal) ####################################################### - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'cootOut')): - os.mkdir(os.path.join(self.initial_model_directory,xtal,'cootOut')) + if not os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'cootOut')): + os.mkdir(os.path.join( + self.initial_model_directory, xtal, 'cootOut')) # create folder for new refinement cycle - if os.path.isdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))): - os.chdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))) + if os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'cootOut', 'Refine_'+str(Serial))): + os.chdir(os.path.join(self.initial_model_directory, + xtal, 'cootOut', 'Refine_'+str(Serial))) try: - os.system('/bin/rm *-ensemble-model.pdb *restraints*') + os.system( + '/bin/rm *-ensemble-model.pdb *restraints*') except: - self.Logfile.error("Restraint files didn't exist to remove. Will try to continue") + self.Logfile.error( + "Restraint files didn't exist to remove. Will try to continue") else: - os.mkdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))) - os.chdir(os.path.join(self.initial_model_directory,xtal,'cootOut','Refine_'+str(Serial))) - Refine=XChemRefine.panddaRefine(self.initial_model_directory,xtal,compoundID,self.datasource) - os.symlink(os.path.join(self.initial_model_directory,xtal,xtal+'-ensemble-model.pdb'),xtal+'-ensemble-model.pdb') - Refine.RunQuickRefine(Serial,self.RefmacParams,self.external_software,self.xce_logfile,'pandda_refmac',None) + os.mkdir(os.path.join(self.initial_model_directory, + xtal, 'cootOut', 'Refine_'+str(Serial))) + os.chdir(os.path.join(self.initial_model_directory, + xtal, 'cootOut', 'Refine_'+str(Serial))) + Refine = XChemRefine.panddaRefine( + self.initial_model_directory, xtal, compoundID, self.datasource) + os.symlink(os.path.join(self.initial_model_directory, xtal, + xtal+'-ensemble-model.pdb'), xtal+'-ensemble-model.pdb') + Refine.RunQuickRefine( + Serial, self.RefmacParams, self.external_software, self.xce_logfile, 'pandda_refmac', None) # elif xtal in os.path.join(self.panddas_directory,'processed_datasets',xtal,'modelled_structures', # '{}-pandda-model.pdb'.format(xtal)): @@ -567,141 +629,155 @@ def refine_exported_models(self,samples_to_export): # ' have a modelled structure, compare pandda.inspect and datasource,' # ' then tell XCHEMBB ') else: - self.Logfile.error('%s: cannot find %s-ensemble-model.pdb; cannot start refinement...' %(xtal,xtal)) - self.Logfile.error('Please check terminal window for any PanDDA related tracebacks') + self.Logfile.error( + '%s: cannot find %s-ensemble-model.pdb; cannot start refinement...' % (xtal, xtal)) + self.Logfile.error( + 'Please check terminal window for any PanDDA related tracebacks') elif xtal in samples_to_export and not os.path.isfile( os.path.join(self.initial_model_directory, xtal, xtal + '.free.mtz')): self.Logfile.error('%s: cannot start refinement because %s.free.mtz is missing in %s' % ( - xtal, xtal, os.path.join(self.initial_model_directory, xtal))) + xtal, xtal, os.path.join(self.initial_model_directory, xtal))) else: self.Logfile.insert('%s: nothing to refine' % (xtal)) - def import_samples_into_datasouce(self,samples_to_export): + def import_samples_into_datasouce(self, samples_to_export): # first make a note of all the datasets which were used in pandda directory - os.chdir(os.path.join(self.panddas_directory,'processed_datasets')) + os.chdir(os.path.join(self.panddas_directory, 'processed_datasets')) for xtal in glob.glob('*'): - self.db.execute_statement("update mainTable set DimplePANDDAwasRun = 'True',DimplePANDDAreject = 'False',DimplePANDDApath='{0!s}' where CrystalName is '{1!s}'".format(self.panddas_directory, xtal)) + self.db.execute_statement("update mainTable set DimplePANDDAwasRun = 'True',DimplePANDDAreject = 'False',DimplePANDDApath='{0!s}' where CrystalName is '{1!s}'".format( + self.panddas_directory, xtal)) # do the same as before, but look for rejected datasets try: - os.chdir(os.path.join(self.panddas_directory,'rejected_datasets')) + os.chdir(os.path.join(self.panddas_directory, 'rejected_datasets')) for xtal in glob.glob('*'): - self.db.execute_statement("update mainTable set DimplePANDDAwasRun = 'True',DimplePANDDAreject = 'True',DimplePANDDApath='{0!s}',DimplePANDDAhit = 'False' where CrystalName is '{1!s}'".format(self.panddas_directory, xtal)) + self.db.execute_statement("update mainTable set DimplePANDDAwasRun = 'True',DimplePANDDAreject = 'True',DimplePANDDApath='{0!s}',DimplePANDDAhit = 'False' where CrystalName is '{1!s}'".format( + self.panddas_directory, xtal)) except OSError: pass site_list = [] - pandda_hit_list=[] + pandda_hit_list = [] - with open(os.path.join(self.panddas_directory,'analyses','pandda_inspect_sites.csv'),'rb') as csv_import: + with open(os.path.join(self.panddas_directory, 'analyses', 'pandda_inspect_sites.csv'), 'rb') as csv_import: csv_dict = csv.DictReader(csv_import) self.Logfile.insert('reding pandda_inspect_sites.csv') - for i,line in enumerate(csv_dict): - self.Logfile.insert(str(line).replace('\n','').replace('\r','')) - site_index=line['site_idx'] - name=line['Name'].replace("'","") - comment=line['Comment'] - site_list.append([site_index,name,comment]) - self.Logfile.insert('add to site_list_:' + str([site_index,name,comment])) - - progress_step=1 - for i,line in enumerate(open(os.path.join(self.panddas_directory,'analyses','pandda_inspect_events.csv'))): - n_lines=i + for i, line in enumerate(csv_dict): + self.Logfile.insert(str(line).replace( + '\n', '').replace('\r', '')) + site_index = line['site_idx'] + name = line['Name'].replace("'", "") + comment = line['Comment'] + site_list.append([site_index, name, comment]) + self.Logfile.insert('add to site_list_:' + + str([site_index, name, comment])) + + progress_step = 1 + for i, line in enumerate(open(os.path.join(self.panddas_directory, 'analyses', 'pandda_inspect_events.csv'))): + n_lines = i if n_lines != 0: - progress_step=100/float(n_lines) + progress_step = 100/float(n_lines) else: - progress_step=0 - progress=0 + progress_step = 0 + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - self.Logfile.insert('reading '+os.path.join(self.panddas_directory,'analyses','pandda_inspect_events.csv')) - with open(os.path.join(self.panddas_directory,'analyses','pandda_inspect_events.csv'),'rb') as csv_import: + self.Logfile.insert('reading '+os.path.join(self.panddas_directory, + 'analyses', 'pandda_inspect_events.csv')) + with open(os.path.join(self.panddas_directory, 'analyses', 'pandda_inspect_events.csv'), 'rb') as csv_import: csv_dict = csv.DictReader(csv_import) - for i,line in enumerate(csv_dict): - db_dict={} - sampleID=line['dtag'] + for i, line in enumerate(csv_dict): + db_dict = {} + sampleID = line['dtag'] if sampleID not in samples_to_export: - self.Logfile.warning('%s: not to be exported; will not add to panddaTable...' %sampleID) + self.Logfile.warning( + '%s: not to be exported; will not add to panddaTable...' % sampleID) continue if sampleID not in pandda_hit_list: pandda_hit_list.append(sampleID) - site_index=str(line['site_idx']).replace('.0','') - event_index=str(line['event_idx']).replace('.0','') + site_index = str(line['site_idx']).replace('.0', '') + event_index = str(line['event_idx']).replace('.0', '') self.Logfile.insert(str(line)) - self.Logfile.insert('reading {0!s} -> site {1!s} -> event {2!s}'.format(sampleID, site_index, event_index)) + self.Logfile.insert( + 'reading {0!s} -> site {1!s} -> event {2!s}'.format(sampleID, site_index, event_index)) for entry in site_list: - if entry[0]==site_index: - site_name=entry[1] - site_comment=entry[2] + if entry[0] == site_index: + site_name = entry[1] + site_comment = entry[2] break # check if EVENT map exists in project directory - event_map='' - for file in glob.glob(os.path.join(self.initial_model_directory,sampleID,'*ccp4')): - filename=file[file.rfind('/')+1:] + event_map = '' + for file in glob.glob(os.path.join(self.initial_model_directory, sampleID, '*ccp4')): + filename = file[file.rfind('/')+1:] if filename.startswith(sampleID+'-event_'+event_index) and filename.endswith('map.native.ccp4'): - event_map=file - self.Logfile.insert('found respective event maps in {0!s}: {1!s}'.format(self.initial_model_directory, event_map)) + event_map = file + self.Logfile.insert('found respective event maps in {0!s}: {1!s}'.format( + self.initial_model_directory, event_map)) break # initial pandda model and mtz file - pandda_model='' - for file in glob.glob(os.path.join(self.initial_model_directory,sampleID,'*pdb')): - filename=file[file.rfind('/')+1:] + pandda_model = '' + for file in glob.glob(os.path.join(self.initial_model_directory, sampleID, '*pdb')): + filename = file[file.rfind('/')+1:] if filename.endswith('-ensemble-model.pdb'): - pandda_model=file + pandda_model = file if sampleID not in self.already_exported_models: self.already_exported_models.append(sampleID) break - inital_mtz='' - for file in glob.glob(os.path.join(self.initial_model_directory,sampleID,'*mtz')): - filename=file[file.rfind('/')+1:] + inital_mtz = '' + for file in glob.glob(os.path.join(self.initial_model_directory, sampleID, '*mtz')): + filename = file[file.rfind('/')+1:] if filename.endswith('pandda-input.mtz'): - inital_mtz=file + inital_mtz = file break - db_dict['CrystalName'] = sampleID - db_dict['PANDDApath'] = self.panddas_directory - db_dict['PANDDA_site_index'] = site_index - db_dict['PANDDA_site_name'] = site_name - db_dict['PANDDA_site_comment'] = site_comment - db_dict['PANDDA_site_event_index'] = event_index - db_dict['PANDDA_site_event_comment'] = line['Comment'].replace("'","") - db_dict['PANDDA_site_confidence'] = line['Ligand Confidence'] - db_dict['PANDDA_site_InspectConfidence'] = line['Ligand Confidence'] - db_dict['PANDDA_site_ligand_placed'] = line['Ligand Placed'] - db_dict['PANDDA_site_viewed'] = line['Viewed'] - db_dict['PANDDA_site_interesting'] = line['Interesting'] - db_dict['PANDDA_site_z_peak'] = line['z_peak'] - db_dict['PANDDA_site_x'] = line['x'] - db_dict['PANDDA_site_y'] = line['y'] - db_dict['PANDDA_site_z'] = line['z'] - db_dict['PANDDA_site_ligand_id'] = '' - db_dict['PANDDA_site_event_map'] = event_map - db_dict['PANDDA_site_initial_model'] = pandda_model - db_dict['PANDDA_site_initial_mtz'] = inital_mtz - db_dict['PANDDA_site_spider_plot'] = '' + db_dict['CrystalName'] = sampleID + db_dict['PANDDApath'] = self.panddas_directory + db_dict['PANDDA_site_index'] = site_index + db_dict['PANDDA_site_name'] = site_name + db_dict['PANDDA_site_comment'] = site_comment + db_dict['PANDDA_site_event_index'] = event_index + db_dict['PANDDA_site_event_comment'] = line['Comment'].replace( + "'", "") + db_dict['PANDDA_site_confidence'] = line['Ligand Confidence'] + db_dict['PANDDA_site_InspectConfidence'] = line['Ligand Confidence'] + db_dict['PANDDA_site_ligand_placed'] = line['Ligand Placed'] + db_dict['PANDDA_site_viewed'] = line['Viewed'] + db_dict['PANDDA_site_interesting'] = line['Interesting'] + db_dict['PANDDA_site_z_peak'] = line['z_peak'] + db_dict['PANDDA_site_x'] = line['x'] + db_dict['PANDDA_site_y'] = line['y'] + db_dict['PANDDA_site_z'] = line['z'] + db_dict['PANDDA_site_ligand_id'] = '' + db_dict['PANDDA_site_event_map'] = event_map + db_dict['PANDDA_site_initial_model'] = pandda_model + db_dict['PANDDA_site_initial_mtz'] = inital_mtz + db_dict['PANDDA_site_spider_plot'] = '' # find apo structures which were used # XXX missing XXX - self.db.update_insert_site_event_panddaTable(sampleID,db_dict) + self.db.update_insert_site_event_panddaTable(sampleID, db_dict) # this is necessary, otherwise RefinementOutcome will be reset for samples that are actually already in refinement - self.db.execute_statement("update panddaTable set RefinementOutcome = '2 - PANDDA model' where CrystalName is '{0!s}' and RefinementOutcome is null".format(sampleID)) - self.db.execute_statement("update mainTable set RefinementOutcome = '2 - PANDDA model' where CrystalName is '{0!s}' and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending')".format(sampleID)) - self.db.execute_statement("update mainTable set DimplePANDDAhit = 'True' where CrystalName is '{0!s}'".format(sampleID)) + self.db.execute_statement( + "update panddaTable set RefinementOutcome = '2 - PANDDA model' where CrystalName is '{0!s}' and RefinementOutcome is null".format(sampleID)) + self.db.execute_statement( + "update mainTable set RefinementOutcome = '2 - PANDDA model' where CrystalName is '{0!s}' and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending')".format(sampleID)) + self.db.execute_statement( + "update mainTable set DimplePANDDAhit = 'True' where CrystalName is '{0!s}'".format(sampleID)) progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) self.Logfile.insert('done reading pandda_inspect_sites.csv') # finally find all samples which do not have a pandda hit - os.chdir(os.path.join(self.panddas_directory,'processed_datasets')) + os.chdir(os.path.join(self.panddas_directory, 'processed_datasets')) self.Logfile.insert('check which datasets are not interesting') # DimplePANDDAhit # for xtal in glob.glob('*'): @@ -709,114 +785,125 @@ def import_samples_into_datasouce(self,samples_to_export): # self.Logfile.insert(xtal+': not in interesting_datasets; updating database...') # self.db.execute_statement("update mainTable set DimplePANDDAhit = 'False' where CrystalName is '{0!s}'".format(xtal)) - def export_models(self): - self.Logfile.insert('finding out which PanDDA models need to be exported') + self.Logfile.insert( + 'finding out which PanDDA models need to be exported') # first find which samples are in interesting datasets and have a model # and determine the timestamp - fileModelsDict={} - queryModels='' - for model in glob.glob(os.path.join(self.panddas_directory,'processed_datasets','*','modelled_structures','*-pandda-model.pdb')): - sample=model[model.rfind('/')+1:].replace('-pandda-model.pdb','') - timestamp=datetime.fromtimestamp(os.path.getmtime(model)).strftime('%Y-%m-%d %H:%M:%S') - self.Logfile.insert(sample+'-pandda-model.pdb was created on '+str(timestamp)) - queryModels+="'"+sample+"'," - fileModelsDict[sample]=timestamp + fileModelsDict = {} + queryModels = '' + for model in glob.glob(os.path.join(self.panddas_directory, 'processed_datasets', '*', 'modelled_structures', '*-pandda-model.pdb')): + sample = model[model.rfind( + '/')+1:].replace('-pandda-model.pdb', '') + timestamp = datetime.fromtimestamp( + os.path.getmtime(model)).strftime('%Y-%m-%d %H:%M:%S') + self.Logfile.insert( + sample+'-pandda-model.pdb was created on '+str(timestamp)) + queryModels += "'"+sample+"'," + fileModelsDict[sample] = timestamp # now get these models from the database and compare the datestamps # Note: only get the models that underwent some form of refinement, # because only if the model was updated in pandda.inspect will it be exported and refined - dbModelsDict={} + dbModelsDict = {} if queryModels != '': - dbEntries=self.db.execute_statement("select CrystalName,DatePanDDAModelCreated from mainTable where CrystalName in ("+queryModels[:-1]+") and (RefinementOutcome like '3%' or RefinementOutcome like '4%' or RefinementOutcome like '5%')") + dbEntries = self.db.execute_statement("select CrystalName,DatePanDDAModelCreated from mainTable where CrystalName in (" + + queryModels[:-1]+") and (RefinementOutcome like '3%' or RefinementOutcome like '4%' or RefinementOutcome like '5%')") for item in dbEntries: - xtal=str(item[0]) - timestamp=str(item[1]) - dbModelsDict[xtal]=timestamp - self.Logfile.insert('PanDDA model for '+xtal+' is in database and was created on '+str(timestamp)) + xtal = str(item[0]) + timestamp = str(item[1]) + dbModelsDict[xtal] = timestamp + self.Logfile.insert( + 'PanDDA model for '+xtal+' is in database and was created on '+str(timestamp)) # compare timestamps and only export the ones where the timestamp of the file is newer than the one in the DB - samples_to_export={} - self.Logfile.insert('checking which PanDDA models were newly created or updated') - if self.which_models=='all': - self.Logfile.insert('Note: you chose to export ALL available PanDDA!') + samples_to_export = {} + self.Logfile.insert( + 'checking which PanDDA models were newly created or updated') + if self.which_models == 'all': + self.Logfile.insert( + 'Note: you chose to export ALL available PanDDA!') for sample in fileModelsDict: - if self.which_models=='all': + if self.which_models == 'all': self.Logfile.insert('exporting '+sample) - samples_to_export[sample]=fileModelsDict[sample] + samples_to_export[sample] = fileModelsDict[sample] elif self.which_models == 'selected': for i in range(0, self.pandda_analyse_data_table.rowCount()): if str(self.pandda_analyse_data_table.item(i, 0).text()) == sample: if self.pandda_analyse_data_table.cellWidget(i, 1).isChecked(): - self.Logfile.insert('Dataset selected by user -> exporting '+sample) - samples_to_export[sample]=fileModelsDict[sample] + self.Logfile.insert( + 'Dataset selected by user -> exporting '+sample) + samples_to_export[sample] = fileModelsDict[sample] break else: if sample in dbModelsDict: try: - difference=(datetime.strptime(fileModelsDict[sample],'%Y-%m-%d %H:%M:%S') - datetime.strptime(dbModelsDict[sample],'%Y-%m-%d %H:%M:%S') ) + difference = (datetime.strptime( + fileModelsDict[sample], '%Y-%m-%d %H:%M:%S') - datetime.strptime(dbModelsDict[sample], '%Y-%m-%d %H:%M:%S')) if difference.seconds != 0: - self.Logfile.insert('exporting '+sample+' -> was already refined, but newer PanDDA model available') - samples_to_export[sample]=fileModelsDict[sample] + self.Logfile.insert( + 'exporting '+sample+' -> was already refined, but newer PanDDA model available') + samples_to_export[sample] = fileModelsDict[sample] except ValueError: # this will be raised if timestamp is not properly formatted; # which will usually be the case when respective field in database is blank # these are hopefully legacy cases which are from before this extensive check was introduced (13/01/2017) - advice = ( 'The pandda model of '+xtal+' was changed, but it was already refined! ' - 'This is most likely because this was done with an older version of XCE. ' - 'If you really want to export and refine this model, you need to open the database ' - 'with DBbroweser (sqlitebrowser.org); then change the RefinementOutcome field ' - 'of the respective sample to "2 - PANDDA model", save the database and repeat the export prodedure.' ) + advice = ('The pandda model of '+xtal+' was changed, but it was already refined! ' + 'This is most likely because this was done with an older version of XCE. ' + 'If you really want to export and refine this model, you need to open the database ' + 'with DBbroweser (sqlitebrowser.org); then change the RefinementOutcome field ' + 'of the respective sample to "2 - PANDDA model", save the database and repeat the export prodedure.') self.Logfile.insert(advice) else: - self.Logfile.insert('exporting '+sample+' -> first time to be exported and refined') - samples_to_export[sample]=fileModelsDict[sample] + self.Logfile.insert( + 'exporting '+sample+' -> first time to be exported and refined') + samples_to_export[sample] = fileModelsDict[sample] # update the DB: # set timestamp to current timestamp of file and set RefinementOutcome to '2-pandda...' if samples_to_export != {}: - select_dir_string='' - select_dir_string_new_pannda=' ' + select_dir_string = '' + select_dir_string_new_pannda = ' ' for sample in samples_to_export: - db_dict= {'RefinementOutcome': '2 - PANDDA model', 'DatePanDDAModelCreated': samples_to_export[sample]} - select_dir_string+="select_dir={0!s} ".format(sample) - select_dir_string_new_pannda+='{0!s} '.format(sample) - self.Logfile.insert('updating database for '+sample+' setting time model was created to '+db_dict['DatePanDDAModelCreated']+' and RefinementOutcome to '+db_dict['RefinementOutcome']) - self.db.update_data_source(sample,db_dict) - + db_dict = {'RefinementOutcome': '2 - PANDDA model', + 'DatePanDDAModelCreated': samples_to_export[sample]} + select_dir_string += "select_dir={0!s} ".format(sample) + select_dir_string_new_pannda += '{0!s} '.format(sample) + self.Logfile.insert('updating database for '+sample+' setting time model was created to ' + + db_dict['DatePanDDAModelCreated']+' and RefinementOutcome to '+db_dict['RefinementOutcome']) + self.db.update_data_source(sample, db_dict) - if os.path.isdir(os.path.join(self.panddas_directory,'rejected_datasets')): + if os.path.isdir(os.path.join(self.panddas_directory, 'rejected_datasets')): Cmds = ( 'pandda.export' - ' pandda_dir=%s' %self.panddas_directory+ - ' export_dir={0!s}'.format(self.initial_model_directory)+ - ' {0!s}'.format(select_dir_string)+ + ' pandda_dir=%s' % self.panddas_directory + + ' export_dir={0!s}'.format(self.initial_model_directory) + + ' {0!s}'.format(select_dir_string) + ' export_ligands=False' ' generate_occupancy_groupings=True\n' - ) + ) else: Cmds = ( 'module load ccp4/7.1.016\n' -# 'source /dls/science/groups/i04-1/software/pandda-update/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' -# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' + # 'source /dls/science/groups/i04-1/software/pandda-update/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' + # 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' 'pandda.export' - ' pandda_dir=%s' %self.panddas_directory+ - ' export_dir={0!s}'.format(self.initial_model_directory)+ - ' {0!s}'.format(select_dir_string_new_pannda)+ + ' pandda_dir=%s' % self.panddas_directory + + ' export_dir={0!s}'.format(self.initial_model_directory) + + ' {0!s}'.format(select_dir_string_new_pannda) + ' generate_restraints=True\n' - ) - - + ) - self.Logfile.insert('running pandda.export with the following settings:\n'+Cmds) + self.Logfile.insert( + 'running pandda.export with the following settings:\n'+Cmds) os.system(Cmds) return samples_to_export @@ -824,48 +911,50 @@ def export_models(self): class run_pandda_analyse(QtCore.QThread): - def __init__(self,pandda_params,xce_logfile,datasource): + def __init__(self, pandda_params, xce_logfile, datasource): QtCore.QThread.__init__(self) - self.data_directory=pandda_params['data_dir'] - self.panddas_directory=pandda_params['out_dir'] - self.submit_mode=pandda_params['submit_mode'] + self.data_directory = pandda_params['data_dir'] + self.panddas_directory = pandda_params['out_dir'] + self.submit_mode = pandda_params['submit_mode'] self.pandda_analyse_data_table = pandda_params['pandda_table'] - self.nproc=pandda_params['nproc'] - self.min_build_datasets=pandda_params['min_build_datasets'] - self.pdb_style=pandda_params['pdb_style'] - self.mtz_style=pandda_params['mtz_style'] - self.sort_event=pandda_params['sort_event'] - self.number_of_datasets=pandda_params['N_datasets'] - self.max_new_datasets=pandda_params['max_new_datasets'] - self.grid_spacing=pandda_params['grid_spacing'] - self.reference_dir=pandda_params['reference_dir'] - self.filter_pdb=os.path.join(self.reference_dir,pandda_params['filter_pdb']) + self.nproc = pandda_params['nproc'] + self.min_build_datasets = pandda_params['min_build_datasets'] + self.pdb_style = pandda_params['pdb_style'] + self.mtz_style = pandda_params['mtz_style'] + self.sort_event = pandda_params['sort_event'] + self.number_of_datasets = pandda_params['N_datasets'] + self.max_new_datasets = pandda_params['max_new_datasets'] + self.grid_spacing = pandda_params['grid_spacing'] + self.reference_dir = pandda_params['reference_dir'] + self.filter_pdb = os.path.join( + self.reference_dir, pandda_params['filter_pdb']) self.wilson_scaling = pandda_params['perform_diffraction_data_scaling'] - self.Logfile=XChemLog.updateLog(xce_logfile) - self.datasource=datasource - self.db=XChemDB.data_source(datasource) - self.appendix=pandda_params['appendix'] - self.write_mean_maps=pandda_params['write_mean_map'] + self.Logfile = XChemLog.updateLog(xce_logfile) + self.datasource = datasource + self.db = XChemDB.data_source(datasource) + self.appendix = pandda_params['appendix'] + self.write_mean_maps = pandda_params['write_mean_map'] self.calc_map_by = pandda_params['average_map'] - self.select_ground_state_model='' + self.select_ground_state_model = '' projectDir = self.data_directory.replace('/*', '') - self.make_ligand_links='$CCP4/bin/ccp4-python %s %s %s\n' %(os.path.join(os.getenv('XChemExplorer_DIR'), - 'helpers', - 'make_ligand_links_after_pandda.py') - ,projectDir,self.panddas_directory) + self.make_ligand_links = '$CCP4/bin/ccp4-python %s %s %s\n' % (os.path.join(os.getenv('XChemExplorer_DIR'), + 'helpers', + 'make_ligand_links_after_pandda.py'), projectDir, self.panddas_directory) self.use_remote = pandda_params['use_remote'] self.remote_string = pandda_params['remote_string'] if self.appendix != '': - self.panddas_directory=os.path.join(self.reference_dir,'pandda_'+self.appendix) + self.panddas_directory = os.path.join( + self.reference_dir, 'pandda_'+self.appendix) if os.path.isdir(self.panddas_directory): - os.system('/bin/rm -fr %s' %self.panddas_directory) + os.system('/bin/rm -fr %s' % self.panddas_directory) os.mkdir(self.panddas_directory) if self.data_directory.startswith('/dls'): self.select_ground_state_model = 'module load ccp4/7.1.018\n' - self.select_ground_state_model +='$CCP4/bin/ccp4-python %s %s\n' %(os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','select_ground_state_dataset.py'),self.panddas_directory) - self.make_ligand_links='' + self.select_ground_state_model += '$CCP4/bin/ccp4-python %s %s\n' % (os.path.join(os.getenv( + 'XChemExplorer_DIR'), 'helpers', 'select_ground_state_dataset.py'), self.panddas_directory) + self.make_ligand_links = '' def run(self): @@ -885,44 +974,51 @@ def run(self): # # 3) Repeat 2) until you don't add any "new" datasets. Then you can build the models as normal. - - number_of_cyles=int(self.number_of_datasets)/int(self.max_new_datasets) - if int(self.number_of_datasets) % int(self.max_new_datasets) != 0: # modulo gives remainder after integer division - number_of_cyles+=1 - self.Logfile.insert('will run %s rounds of pandda.analyse' %str(number_of_cyles)) - - if os.path.isfile(os.path.join(self.panddas_directory,'pandda.running')): - self.Logfile.insert('it looks as if a pandda.analyse job is currently running in: '+self.panddas_directory) - msg = ( 'there are three possibilities:\n' - '1.) choose another PANDDA directory\n' - '2.) - check if the job is really running either on the cluster (qstat) or on your local machine\n' - ' - if so, be patient and wait until the job has finished\n' - '3.) same as 2., but instead of waiting, kill the job and remove at least the pandda.running file\n' - ' (or all the contents in the directory if you want to start from scratch)\n' ) + number_of_cyles = int(self.number_of_datasets) / \ + int(self.max_new_datasets) + # modulo gives remainder after integer division + if int(self.number_of_datasets) % int(self.max_new_datasets) != 0: + number_of_cyles += 1 + self.Logfile.insert( + 'will run %s rounds of pandda.analyse' % str(number_of_cyles)) + + if os.path.isfile(os.path.join(self.panddas_directory, 'pandda.running')): + self.Logfile.insert( + 'it looks as if a pandda.analyse job is currently running in: '+self.panddas_directory) + msg = ('there are three possibilities:\n' + '1.) choose another PANDDA directory\n' + '2.) - check if the job is really running either on the cluster (qstat) or on your local machine\n' + ' - if so, be patient and wait until the job has finished\n' + '3.) same as 2., but instead of waiting, kill the job and remove at least the pandda.running file\n' + ' (or all the contents in the directory if you want to start from scratch)\n') self.Logfile.insert(msg) return None else: -# if os.getenv('SHELL') == '/bin/tcsh' or os.getenv('SHELL') == '/bin/csh': -# source_file=os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh\n') -# elif os.getenv('SHELL') == '/bin/bash' or self.use_remote: -# source_file='export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' -# source_file+='source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') -# else: -# source_file='' + # if os.getenv('SHELL') == '/bin/tcsh' or os.getenv('SHELL') == '/bin/csh': + # source_file=os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh\n') + # elif os.getenv('SHELL') == '/bin/bash' or self.use_remote: + # source_file='export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' + # source_file+='source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') + # else: + # source_file='' # v1.2.1 - pandda.setup files should be obsolete now that pandda is part of ccp4 # 08/10/2020 - pandda v0.2.12 installation at DLS is obsolete -# source_file='source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' + # source_file='source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' source_file = '' - source_file += 'export XChemExplorer_DIR="' + os.getenv('XChemExplorer_DIR') + '"\n' + source_file += 'export XChemExplorer_DIR="' + \ + os.getenv('XChemExplorer_DIR') + '"\n' if os.path.isfile(self.filter_pdb + '.pdb'): print('filter pdb located') - filter_pdb=' filter.pdb='+self.filter_pdb+'.pdb' - print('will use ' + filter_pdb + 'as a filter for pandda.analyse') + filter_pdb = ' filter.pdb='+self.filter_pdb+'.pdb' + print('will use ' + filter_pdb + + 'as a filter for pandda.analyse') else: if self.use_remote: - stat_command = self.remote_string.replace("qsub'", str('stat ' + self.filter_pdb + "'")) - output = subprocess.Popen(stat_command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + stat_command = self.remote_string.replace( + "qsub'", str('stat ' + self.filter_pdb + "'")) + output = subprocess.Popen( + stat_command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) out, err = output.communicate() if 'cannot stat' in out: filter_pdb = '' @@ -930,7 +1026,7 @@ def run(self): filter_pdb = ' filter.pdb=' + self.filter_pdb + '.pdb' else: - filter_pdb='' + filter_pdb = '' os.chdir(self.panddas_directory) @@ -953,32 +1049,38 @@ def run(self): dls + 'cd ' + self.panddas_directory + '\n' + '\n' - ) + ) ignore = [] char = [] zmap = [] for i in range(0, self.pandda_analyse_data_table.rowCount()): - ignore_all_checkbox = self.pandda_analyse_data_table.cellWidget(i, 7) - ignore_characterisation_checkbox = self.pandda_analyse_data_table.cellWidget(i, 8) - ignore_zmap_checkbox = self.pandda_analyse_data_table.cellWidget(i, 9) + ignore_all_checkbox = self.pandda_analyse_data_table.cellWidget( + i, 7) + ignore_characterisation_checkbox = self.pandda_analyse_data_table.cellWidget( + i, 8) + ignore_zmap_checkbox = self.pandda_analyse_data_table.cellWidget( + i, 9) if ignore_all_checkbox.isChecked(): - ignore.append(str(self.pandda_analyse_data_table.item(i, 0).text())) + ignore.append( + str(self.pandda_analyse_data_table.item(i, 0).text())) if ignore_characterisation_checkbox.isChecked(): - char.append(str(self.pandda_analyse_data_table.item(i, 0).text())) + char.append( + str(self.pandda_analyse_data_table.item(i, 0).text())) if ignore_zmap_checkbox.isChecked(): - zmap.append(str(self.pandda_analyse_data_table.item(i, 0).text())) + zmap.append( + str(self.pandda_analyse_data_table.item(i, 0).text())) def append_to_ignore_string(datasets_list, append_string): - if len(datasets_list)==0: + if len(datasets_list) == 0: append_string = '' for i in range(0, len(datasets_list)): if i < len(datasets_list)-1: append_string += str(datasets_list[i] + ',') else: - append_string += str(datasets_list[i] +'"') + append_string += str(datasets_list[i] + '"') print(append_string) return append_string @@ -993,27 +1095,27 @@ def append_to_ignore_string(datasets_list, append_string): for i in range(number_of_cyles): Cmds += ( - 'pandda.analyse '+ - ' data_dirs="'+self.data_directory.replace('/*','')+'/*"'+ + 'pandda.analyse ' + + ' data_dirs="'+self.data_directory.replace('/*', '')+'/*"' + ' out_dir="'+self.panddas_directory+'"' - ' min_build_datasets='+self.min_build_datasets+ - ' max_new_datasets='+self.max_new_datasets+ - ' grid_spacing='+self.grid_spacing+ - ' cpus='+self.nproc+ - ' events.order_by='+self.sort_event+ - filter_pdb+ - ' pdb_style='+self.pdb_style+ - ' mtz_style='+self.mtz_style+ - ' lig_style=/compound/*.cif'+ - ' apply_b_factor_scaling='+self.wilson_scaling+ + ' min_build_datasets='+self.min_build_datasets + + ' max_new_datasets='+self.max_new_datasets + + ' grid_spacing='+self.grid_spacing + + ' cpus='+self.nproc + + ' events.order_by='+self.sort_event + + filter_pdb + + ' pdb_style='+self.pdb_style + + ' mtz_style='+self.mtz_style + + ' lig_style=/compound/*.cif' + + ' apply_b_factor_scaling='+self.wilson_scaling + ' write_average_map='+self.write_mean_maps + ' average_map=' + self.calc_map_by + ' ' + - ignore_string +' '+ - char_string +' '+ - zmap_string +' '+ + ignore_string + ' ' + + char_string + ' ' + + zmap_string + ' ' + '\n' - ) + ) Cmds += self.select_ground_state_model Cmds += self.make_ligand_links @@ -1022,37 +1124,35 @@ def append_to_ignore_string(datasets_list, append_string): data_dir_string = self.data_directory.replace('/*', '') Cmds += str( - 'find ' + data_dir_string + - '/*/compound -name "*.cif" | while read line; do echo ${line//"' + - data_dir_string + '"/"' + self.panddas_directory + - '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' - 'done; done;') + 'find ' + data_dir_string + + '/*/compound -name "*.cif" | while read line; do echo ${line//"' + + data_dir_string + '"/"' + self.panddas_directory + + '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' + 'done; done;') Cmds += '\n' - - Cmds += str( - 'find ' + data_dir_string + - '/*/compound -name "*.pdb" | while read line; do echo ${line//"' + - data_dir_string + '"/"' + self.panddas_directory + - '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' - 'done; done;') - - self.Logfile.insert('running pandda.analyse with the following command:\n'+Cmds) - + 'find ' + data_dir_string + + '/*/compound -name "*.pdb" | while read line; do echo ${line//"' + + data_dir_string + '"/"' + self.panddas_directory + + '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' + 'done; done;') + self.Logfile.insert( + 'running pandda.analyse with the following command:\n'+Cmds) - f = open('pandda.sh','w') + f = open('pandda.sh', 'w') f.write(Cmds) f.close() # #>>> for testing # self.submit_mode='local machine' - self.Logfile.insert('trying to run pandda.analyse on ' + str(self.submit_mode)) + self.Logfile.insert( + 'trying to run pandda.analyse on ' + str(self.submit_mode)) - if self.submit_mode=='local machine': + if self.submit_mode == 'local machine': self.Logfile.insert('running PANDDA on local machine') os.system('chmod +x pandda.sh') os.system('./pandda.sh &') @@ -1064,48 +1164,51 @@ def append_to_ignore_string(datasets_list, append_string): '; ' + "qsub -P labxchem -q medium.q -N pandda 5 -l exclusive,m_mem_free=100G pandda.sh'")) os.system(submission_string) - self.Logfile.insert(str('running PANDDA remotely, using: ' + submission_string)) + self.Logfile.insert( + str('running PANDDA remotely, using: ' + submission_string)) else: self.Logfile.insert('running PANDDA on cluster, using qsub...') - os.system('qsub -P labxchem -q medium.q -N pandda -l exclusive,m_mem_free=100G pandda.sh') + os.system( + 'qsub -P labxchem -q medium.q -N pandda -l exclusive,m_mem_free=100G pandda.sh') self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) - class run_pandda_two_analyse(QtCore.QThread): - def __init__(self,pandda_params,xce_logfile,datasource): + def __init__(self, pandda_params, xce_logfile, datasource): QtCore.QThread.__init__(self) - self.data_directory=pandda_params['data_dir'] - self.panddas_directory=pandda_params['out_dir'] - self.submit_mode=pandda_params['submit_mode'] + self.data_directory = pandda_params['data_dir'] + self.panddas_directory = pandda_params['out_dir'] + self.submit_mode = pandda_params['submit_mode'] self.pandda_analyse_data_table = pandda_params['pandda_table'] - self.nproc=pandda_params['nproc'] - self.min_build_datasets=pandda_params['min_build_datasets'] - self.pdb_style=pandda_params['pdb_style'] - self.mtz_style=pandda_params['mtz_style'] - self.sort_event=pandda_params['sort_event'] - self.number_of_datasets=pandda_params['N_datasets'] - self.max_new_datasets=pandda_params['max_new_datasets'] - self.grid_spacing=pandda_params['grid_spacing'] + self.nproc = pandda_params['nproc'] + self.min_build_datasets = pandda_params['min_build_datasets'] + self.pdb_style = pandda_params['pdb_style'] + self.mtz_style = pandda_params['mtz_style'] + self.sort_event = pandda_params['sort_event'] + self.number_of_datasets = pandda_params['N_datasets'] + self.max_new_datasets = pandda_params['max_new_datasets'] + self.grid_spacing = pandda_params['grid_spacing'] self.keyword_arguments = pandda_params['keyword_arguments'] - self.reference_dir=pandda_params['reference_dir'] - self.filter_pdb=os.path.join(self.reference_dir,pandda_params['filter_pdb']) + self.reference_dir = pandda_params['reference_dir'] + self.filter_pdb = os.path.join( + self.reference_dir, pandda_params['filter_pdb']) self.wilson_scaling = pandda_params['perform_diffraction_data_scaling'] - self.Logfile=XChemLog.updateLog(xce_logfile) - self.datasource=datasource - self.db=XChemDB.data_source(datasource) - self.appendix=pandda_params['appendix'] - self.write_mean_maps=pandda_params['write_mean_map'] + self.Logfile = XChemLog.updateLog(xce_logfile) + self.datasource = datasource + self.db = XChemDB.data_source(datasource) + self.appendix = pandda_params['appendix'] + self.write_mean_maps = pandda_params['write_mean_map'] self.calc_map_by = pandda_params['average_map'] - self.select_ground_state_model='' + self.select_ground_state_model = '' def run(self): if not self.data_directory.startswith('/dls'): - self.Logfile.error('Sorry, you need to be at DLS for pandda2 to work!') + self.Logfile.error( + 'Sorry, you need to be at DLS for pandda2 to work!') return None os.chdir(self.panddas_directory) @@ -1128,142 +1231,156 @@ def run(self): 'unset __conda_setup\n' 'export PYTHONPATH=""\n' 'conda activate pandda2_ray\n' - 'python -u /dls/science/groups/i04-1/conor_dev/pandda_2_gemmi/pandda_gemmi/analyse.py' - ' --data_dirs={0!s}'.format(self.data_directory.replace('/*','')) + + 'python -u /dls/science/groups/i04-1/conor_dev/pandda_2_gemmi/pandda_gemmi/analyse.py' + ' --data_dirs={0!s}'.format(self.data_directory.replace('/*', '')) + ' --out_dir={0!s}'.format(self.panddas_directory) + ' --pdb_regex="{0!s}" '.format(self.pdb_style) + ' --mtz_regex="{0!s}" '.format(self.mtz_style) + ' --autobuild=True ' - ' --global_processing="serial" ' + ' --global_processing="serial" ' ' --local_cpus=6 ' - ' --local_processing="ray" ' + ' --local_processing="ray" ' ' --rank_method=autobuild ' - ' --comparison_strategy="hybrid" ' - ' --min_characterisation_datasets=25 ' + ' --comparison_strategy="hybrid" ' + ' --min_characterisation_datasets=25 ' ' {0!s} '.format(self.keyword_arguments) + ' --debug=True --memory_availability="low" | tee livelog_20220324_event_class_old_score\n' ) - self.Logfile.insert('running pandda.analyse with the following command:\n' + cmd) + self.Logfile.insert( + 'running pandda.analyse with the following command:\n' + cmd) - f = open('pandda2.sh','w') + f = open('pandda2.sh', 'w') f.write(cmd) f.close() self.Logfile.warning('ignoring selected submission option') self.Logfile.insert('running PANDDA on cluster, using qsub...') - os.system('qsub -pe smp 6 -l m_mem_free=30G -q medium.q -o log.out -e log.err pandda2.sh') + os.system( + 'qsub -pe smp 6 -l m_mem_free=30G -q medium.q -o log.out -e log.err pandda2.sh') self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) - - - - - - - class giant_cluster_datasets(QtCore.QThread): - def __init__(self,initial_model_directory,pandda_params,xce_logfile,datasource,): + def __init__(self, initial_model_directory, pandda_params, xce_logfile, datasource,): QtCore.QThread.__init__(self) - self.panddas_directory=pandda_params['out_dir'] - self.pdb_style=pandda_params['pdb_style'] - self.mtz_style=pandda_params['mtz_style'] - self.Logfile=XChemLog.updateLog(xce_logfile) - self.initial_model_directory=initial_model_directory - self.db=XChemDB.data_source(datasource) - + self.panddas_directory = pandda_params['out_dir'] + self.pdb_style = pandda_params['pdb_style'] + self.mtz_style = pandda_params['mtz_style'] + self.Logfile = XChemLog.updateLog(xce_logfile) + self.initial_model_directory = initial_model_directory + self.db = XChemDB.data_source(datasource) def run(self): self.emit(QtCore.SIGNAL('update_progress_bar'), 0) - if self.pdb_style.replace(' ','') == '': + if self.pdb_style.replace(' ', '') == '': self.Logfile.insert('PDB style is not set in pandda.analyse!') self.Logfile.insert('cannot start pandda.analyse') - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'PDB style is not set in pandda.analyse!') + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'PDB style is not set in pandda.analyse!') return None - if self.mtz_style.replace(' ','') == '': + if self.mtz_style.replace(' ', '') == '': self.Logfile.insert('MTZ style is not set in pandda.analyse!') self.Logfile.insert('cannot start pandda.analyse') - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'MTZ style is not set in pandda.analyse!') + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'MTZ style is not set in pandda.analyse!') return None # 1.) prepare output directory os.chdir(self.panddas_directory) if os.path.isdir('cluster_analysis'): - self.Logfile.insert('removing old cluster_analysis directory in {0!s}'.format(self.panddas_directory)) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'removing old cluster_analysis directory in {0!s}'.format(self.panddas_directory)) + self.Logfile.insert('removing old cluster_analysis directory in {0!s}'.format( + self.panddas_directory)) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'removing old cluster_analysis directory in {0!s}'.format(self.panddas_directory)) os.system('/bin/rm -fr cluster_analysis 2> /dev/null') - self.Logfile.insert('creating cluster_analysis directory in {0!s}'.format(self.panddas_directory)) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'creating cluster_analysis directory in {0!s}'.format(self.panddas_directory)) + self.Logfile.insert( + 'creating cluster_analysis directory in {0!s}'.format(self.panddas_directory)) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'creating cluster_analysis directory in {0!s}'.format(self.panddas_directory)) os.mkdir('cluster_analysis') self.emit(QtCore.SIGNAL('update_progress_bar'), 10) # 2.) go through project directory and make sure that all pdb files really exist # broken links derail the giant.cluster_mtzs_and_pdbs script - self.Logfile.insert('cleaning up broken links of {0!s} and {1!s} in {2!s}'.format(self.pdb_style, self.mtz_style, self.initial_model_directory)) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'cleaning up broken links of {0!s} and {1!s} in {2!s}'.format(self.pdb_style, self.mtz_style, self.initial_model_directory)) + self.Logfile.insert('cleaning up broken links of {0!s} and {1!s} in {2!s}'.format( + self.pdb_style, self.mtz_style, self.initial_model_directory)) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'cleaning up broken links of {0!s} and {1!s} in {2!s}'.format( + self.pdb_style, self.mtz_style, self.initial_model_directory)) os.chdir(self.initial_model_directory) for xtal in glob.glob('*'): - if not os.path.isfile(os.path.join(xtal,self.pdb_style)): - self.Logfile.insert('missing {0!s} and {1!s} for {2!s}'.format(self.pdb_style, self.mtz_style, xtal)) - os.system('/bin/rm {0!s}/{1!s} 2> /dev/null'.format(xtal, self.pdb_style)) - os.system('/bin/rm {0!s}/{1!s} 2> /dev/null'.format(xtal, self.mtz_style)) + if not os.path.isfile(os.path.join(xtal, self.pdb_style)): + self.Logfile.insert('missing {0!s} and {1!s} for {2!s}'.format( + self.pdb_style, self.mtz_style, xtal)) + os.system( + '/bin/rm {0!s}/{1!s} 2> /dev/null'.format(xtal, self.pdb_style)) + os.system( + '/bin/rm {0!s}/{1!s} 2> /dev/null'.format(xtal, self.mtz_style)) self.emit(QtCore.SIGNAL('update_progress_bar'), 20) # 3.) giant.cluster_mtzs_and_pdbs - self.Logfile.insert("running giant.cluster_mtzs_and_pdbs {0!s}/*/{1!s} pdb_regex='{2!s}/(.*)/{3!s}' out_dir='{4!s}/cluster_analysis'".format(self.initial_model_directory, self.pdb_style, self.initial_model_directory, self.pdb_style, self.panddas_directory)) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'running giant.cluster_mtzs_and_pdbs') + self.Logfile.insert("running giant.cluster_mtzs_and_pdbs {0!s}/*/{1!s} pdb_regex='{2!s}/(.*)/{3!s}' out_dir='{4!s}/cluster_analysis'".format( + self.initial_model_directory, self.pdb_style, self.initial_model_directory, self.pdb_style, self.panddas_directory)) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'running giant.cluster_mtzs_and_pdbs') if os.getenv('SHELL') == '/bin/tcsh' or os.getenv('SHELL') == '/bin/csh': - source_file=os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh') + source_file = os.path.join( + os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-csh') elif os.getenv('SHELL') == '/bin/bash': - source_file=os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh') + source_file = os.path.join( + os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-sh') else: - source_file='' + source_file = '' Cmds = ( - '#!'+os.getenv('SHELL')+'\n' - 'unset PYTHONPATH\n' - 'source '+source_file+'\n' - "giant.datasets.cluster %s/*/%s pdb_regex='%s/(.*)/%s' out_dir='%s/cluster_analysis'" %(self.initial_model_directory,self.pdb_style,self.initial_model_directory,self.pdb_style,self.panddas_directory) - ) + '#!'+os.getenv('SHELL')+'\n' + 'unset PYTHONPATH\n' + 'source '+source_file+'\n' + "giant.datasets.cluster %s/*/%s pdb_regex='%s/(.*)/%s' out_dir='%s/cluster_analysis'" % ( + self.initial_model_directory, self.pdb_style, self.initial_model_directory, self.pdb_style, self.panddas_directory) + ) # os.system("giant.cluster_mtzs_and_pdbs %s/*/%s pdb_regex='%s/(.*)/%s' out_dir='%s/cluster_analysis'" %(self.initial_model_directory,self.pdb_style,self.initial_model_directory,self.pdb_style,self.panddas_directory)) os.system(Cmds) self.emit(QtCore.SIGNAL('update_progress_bar'), 80) # 4.) analyse output - self.Logfile.insert('parsing {0!s}/cluster_analysis'.format(self.panddas_directory)) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'parsing {0!s}/cluster_analysis'.format(self.panddas_directory)) + self.Logfile.insert( + 'parsing {0!s}/cluster_analysis'.format(self.panddas_directory)) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'parsing {0!s}/cluster_analysis'.format(self.panddas_directory)) os.chdir('{0!s}/cluster_analysis'.format(self.panddas_directory)) - cluster_dict={} + cluster_dict = {} for out_dir in sorted(glob.glob('*')): if os.path.isdir(out_dir): - cluster_dict[out_dir]=[] - for folder in glob.glob(os.path.join(out_dir,'pdbs','*')): - xtal=folder[folder.rfind('/')+1:] + cluster_dict[out_dir] = [] + for folder in glob.glob(os.path.join(out_dir, 'pdbs', '*')): + xtal = folder[folder.rfind('/')+1:] cluster_dict[out_dir].append(xtal) self.emit(QtCore.SIGNAL('update_progress_bar'), 90) # 5.) update datasource - self.Logfile.insert('updating datasource with results from giant.cluster_mtzs_and_pdbs') + self.Logfile.insert( + 'updating datasource with results from giant.cluster_mtzs_and_pdbs') if cluster_dict != {}: for key in cluster_dict: for xtal in cluster_dict[key]: - db_dict= {'CrystalFormName': key} - self.db.update_data_source(xtal,db_dict) + db_dict = {'CrystalFormName': key} + self.db.update_data_source(xtal, db_dict) # 6.) finish self.emit(QtCore.SIGNAL('update_progress_bar'), 100) self.Logfile.insert('finished giant.cluster_mtzs_and_pdbs') self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) + class check_if_pandda_can_run: # reasons why pandda cannot be run @@ -1272,144 +1389,153 @@ class check_if_pandda_can_run: # - required input paramters are not complete # - map amplitude and phase labels don't exist - def __init__(self,pandda_params,xce_logfile,datasource): - self.data_directory=pandda_params['data_dir'] - self.panddas_directory=pandda_params['out_dir'] - self.min_build_datasets=pandda_params['min_build_datasets'] - self.pdb_style=pandda_params['pdb_style'] - self.mtz_style=pandda_params['mtz_style'] - self.input_dir_structure=pandda_params['pandda_dir_structure'] - self.problem_found=False - self.error_code=-1 - self.Logfile=XChemLog.updateLog(xce_logfile) - self.db=XChemDB.data_source(datasource) + def __init__(self, pandda_params, xce_logfile, datasource): + self.data_directory = pandda_params['data_dir'] + self.panddas_directory = pandda_params['out_dir'] + self.min_build_datasets = pandda_params['min_build_datasets'] + self.pdb_style = pandda_params['pdb_style'] + self.mtz_style = pandda_params['mtz_style'] + self.input_dir_structure = pandda_params['pandda_dir_structure'] + self.problem_found = False + self.error_code = -1 + self.Logfile = XChemLog.updateLog(xce_logfile) + self.db = XChemDB.data_source(datasource) def number_of_available_datasets(self): - counter=0 - for file in glob.glob(os.path.join(self.input_dir_structure,self.pdb_style)): + counter = 0 + for file in glob.glob(os.path.join(self.input_dir_structure, self.pdb_style)): if os.path.isfile(file): - counter+=1 - self.Logfile.insert('pandda.analyse: found {0!s} useable datasets'.format(counter)) + counter += 1 + self.Logfile.insert( + 'pandda.analyse: found {0!s} useable datasets'.format(counter)) return counter def get_first_dataset_in_project_directory(self): - first_dataset='' - for file in glob.glob(os.path.join(self.input_dir_structure,self.pdb_style)): + first_dataset = '' + for file in glob.glob(os.path.join(self.input_dir_structure, self.pdb_style)): if os.path.isfile(file): - first_dataset=file + first_dataset = file break return first_dataset - def compare_number_of_atoms_in_reference_vs_all_datasets(self,refData,dataset_list): - mismatched_datasets=[] - pdbtools=XChemUtils.pdbtools(refData) - refPDB=refData[refData.rfind('/')+1:] - refPDBlist=pdbtools.get_init_pdb_as_list() - n_atom_ref=len(refPDBlist) - for n_datasets,dataset in enumerate(dataset_list): - if os.path.isfile(os.path.join(self.data_directory.replace('*',''),dataset,self.pdb_style)): - n_atom=len(pdbtools.get_pdb_as_list(os.path.join(self.data_directory.replace('*',''),dataset,self.pdb_style))) + def compare_number_of_atoms_in_reference_vs_all_datasets(self, refData, dataset_list): + mismatched_datasets = [] + pdbtools = XChemUtils.pdbtools(refData) + refPDB = refData[refData.rfind('/')+1:] + refPDBlist = pdbtools.get_init_pdb_as_list() + n_atom_ref = len(refPDBlist) + for n_datasets, dataset in enumerate(dataset_list): + if os.path.isfile(os.path.join(self.data_directory.replace('*', ''), dataset, self.pdb_style)): + n_atom = len(pdbtools.get_pdb_as_list(os.path.join( + self.data_directory.replace('*', ''), dataset, self.pdb_style))) if n_atom_ref == n_atom: - self.Logfile.insert('{0!s}: atoms in PDB file ({1!s}): {2!s}; atoms in Reference file: {3!s} ===> OK'.format(dataset, self.pdb_style, str(n_atom), str(n_atom_ref))) + self.Logfile.insert('{0!s}: atoms in PDB file ({1!s}): {2!s}; atoms in Reference file: {3!s} ===> OK'.format( + dataset, self.pdb_style, str(n_atom), str(n_atom_ref))) if n_atom_ref != n_atom: - self.Logfile.insert('{0!s}: atoms in PDB file ({1!s}): {2!s}; atoms in Reference file: {3!s} ===> ERROR'.format(dataset, self.pdb_style, str(n_atom), str(n_atom_ref))) + self.Logfile.insert('{0!s}: atoms in PDB file ({1!s}): {2!s}; atoms in Reference file: {3!s} ===> ERROR'.format( + dataset, self.pdb_style, str(n_atom), str(n_atom_ref))) mismatched_datasets.append(dataset) - return n_datasets,mismatched_datasets - - def get_datasets_which_fit_to_reference_file(self,ref,reference_directory,cluster_dict,allowed_unitcell_difference_percent): - refStructure=XChemUtils.pdbtools(os.path.join(reference_directory,ref+'.pdb')) - symmRef=refStructure.get_spg_number_from_pdb() - ucVolRef=refStructure.calc_unitcell_volume_from_pdb() - cluster_dict[ref]=[] - cluster_dict[ref].append(os.path.join(reference_directory,ref+'.pdb')) - for dataset in glob.glob(os.path.join(self.data_directory,self.pdb_style)): - datasetStructure=XChemUtils.pdbtools(dataset) - symmDataset=datasetStructure.get_spg_number_from_pdb() - ucVolDataset=datasetStructure.calc_unitcell_volume_from_pdb() + return n_datasets, mismatched_datasets + + def get_datasets_which_fit_to_reference_file(self, ref, reference_directory, cluster_dict, allowed_unitcell_difference_percent): + refStructure = XChemUtils.pdbtools( + os.path.join(reference_directory, ref+'.pdb')) + symmRef = refStructure.get_spg_number_from_pdb() + ucVolRef = refStructure.calc_unitcell_volume_from_pdb() + cluster_dict[ref] = [] + cluster_dict[ref].append(os.path.join(reference_directory, ref+'.pdb')) + for dataset in glob.glob(os.path.join(self.data_directory, self.pdb_style)): + datasetStructure = XChemUtils.pdbtools(dataset) + symmDataset = datasetStructure.get_spg_number_from_pdb() + ucVolDataset = datasetStructure.calc_unitcell_volume_from_pdb() if symmDataset == symmRef: try: - difference=math.fabs(1-(float(ucVolRef)/float(ucVolDataset)))*100 + difference = math.fabs( + 1-(float(ucVolRef)/float(ucVolDataset)))*100 if difference < allowed_unitcell_difference_percent: - sampleID=dataset.replace('/'+self.pdb_style,'')[dataset.replace('/'+self.pdb_style,'').rfind('/')+1:] + sampleID = dataset.replace( + '/'+self.pdb_style, '')[dataset.replace('/'+self.pdb_style, '').rfind('/')+1:] cluster_dict[ref].append(sampleID) except ZeroDivisionError: continue return cluster_dict - def remove_dimple_files(self,dataset_list): - for n_datasets,dataset in enumerate(dataset_list): - db_dict={} - if os.path.isfile(os.path.join(self.data_directory.replace('*',''),dataset,self.pdb_style)): - os.system('/bin/rm '+os.path.join(self.data_directory.replace('*',''),dataset,self.pdb_style)) - self.Logfile.insert('{0!s}: removing {1!s}'.format(dataset, self.pdb_style)) - db_dict['DimplePathToPDB']='' - db_dict['DimpleRcryst']='' - db_dict['DimpleRfree']='' - db_dict['DimpleResolutionHigh']='' - db_dict['DimpleStatus']='pending' - if os.path.isfile(os.path.join(self.data_directory.replace('*',''),dataset,self.mtz_style)): - os.system('/bin/rm '+os.path.join(self.data_directory.replace('*',''),dataset,self.mtz_style)) - self.Logfile.insert('{0!s}: removing {1!s}'.format(dataset, self.mtz_style)) - db_dict['DimplePathToMTZ']='' + def remove_dimple_files(self, dataset_list): + for n_datasets, dataset in enumerate(dataset_list): + db_dict = {} + if os.path.isfile(os.path.join(self.data_directory.replace('*', ''), dataset, self.pdb_style)): + os.system( + '/bin/rm '+os.path.join(self.data_directory.replace('*', ''), dataset, self.pdb_style)) + self.Logfile.insert( + '{0!s}: removing {1!s}'.format(dataset, self.pdb_style)) + db_dict['DimplePathToPDB'] = '' + db_dict['DimpleRcryst'] = '' + db_dict['DimpleRfree'] = '' + db_dict['DimpleResolutionHigh'] = '' + db_dict['DimpleStatus'] = 'pending' + if os.path.isfile(os.path.join(self.data_directory.replace('*', ''), dataset, self.mtz_style)): + os.system( + '/bin/rm '+os.path.join(self.data_directory.replace('*', ''), dataset, self.mtz_style)) + self.Logfile.insert( + '{0!s}: removing {1!s}'.format(dataset, self.mtz_style)) + db_dict['DimplePathToMTZ'] = '' if db_dict != {}: - self.db.update_data_source(dataset,db_dict) - + self.db.update_data_source(dataset, db_dict) def analyse_pdb_style(self): - pdb_found=False - for file in glob.glob(os.path.join(self.data_directory,self.pdb_style)): + pdb_found = False + for file in glob.glob(os.path.join(self.data_directory, self.pdb_style)): if os.path.isfile(file): - pdb_found=True + pdb_found = True break if not pdb_found: - self.error_code=1 - message=self.warning_messages() + self.error_code = 1 + message = self.warning_messages() return message def analyse_mtz_style(self): - mtz_found=False - for file in glob.glob(os.path.join(self.data_directory,self.mtz_style)): + mtz_found = False + for file in glob.glob(os.path.join(self.data_directory, self.mtz_style)): if os.path.isfile(file): - mtz_found=True + mtz_found = True break if not mtz_found: - self.error_code=2 - message=self.warning_messages() + self.error_code = 2 + message = self.warning_messages() return message def analyse_min_build_dataset(self): - counter=0 - for file in glob.glob(os.path.join(self.data_directory,self.mtz_style)): + counter = 0 + for file in glob.glob(os.path.join(self.data_directory, self.mtz_style)): if os.path.isfile(file): - counter+=1 + counter += 1 if counter <= self.min_build_datasets: - self.error_code=3 - message=self.warning_messages() + self.error_code = 3 + message = self.warning_messages() return message - def warning_messages(self): - message='' - if self.error_code==1: - message='PDB file does not exist' - if self.error_code==2: - message='MTZ file does not exist' - if self.error_code==3: - message='Not enough datasets available' + message = '' + if self.error_code == 1: + message = 'PDB file does not exist' + if self.error_code == 2: + message = 'MTZ file does not exist' + if self.error_code == 3: + message = 'Not enough datasets available' return message class convert_all_event_maps_in_database(QtCore.QThread): - def __init__(self,initial_model_directory,xce_logfile,datasource): + def __init__(self, initial_model_directory, xce_logfile, datasource): QtCore.QThread.__init__(self) - self.xce_logfile=xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) - self.initial_model_directory=initial_model_directory - self.datasource=datasource - self.db=XChemDB.data_source(datasource) + self.xce_logfile = xce_logfile + self.Logfile = XChemLog.updateLog(xce_logfile) + self.initial_model_directory = initial_model_directory + self.datasource = datasource + self.db = XChemDB.data_source(datasource) def run(self): sqlite = ( @@ -1424,72 +1550,81 @@ def run(self): 'where PANDDA_site_event_map not like "event%"' ) - query=self.db.execute_statement(sqlite) + query = self.db.execute_statement(sqlite) - progress_step=1 + progress_step = 1 if len(query) != 0: - progress_step=100/float(len(query)) + progress_step = 100/float(len(query)) else: - progress_step=1 - progress=0 + progress_step = 1 + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) for item in query: - xtalID=str(item[0]) - event_map=str(item[1]) - resname=str(item[2]) - chainID=str(item[3]) - resseq=str(item[4]) - altLoc=str(item[5]) - - if os.path.isfile(os.path.join(self.initial_model_directory,xtalID,'refine.pdb')): - os.chdir(os.path.join(self.initial_model_directory,xtalID)) - self.Logfile.insert('extracting ligand ({0!s},{1!s},{2!s},{3!s}) from refine.pdb'.format(str(resname), str(chainID), str(resseq), str(altLoc))) - XChemUtils.pdbtools(os.path.join(self.initial_model_directory,xtalID,'refine.pdb')).save_specific_ligands_to_pdb(resname,chainID,resseq,altLoc) + xtalID = str(item[0]) + event_map = str(item[1]) + resname = str(item[2]) + chainID = str(item[3]) + resseq = str(item[4]) + altLoc = str(item[5]) + + if os.path.isfile(os.path.join(self.initial_model_directory, xtalID, 'refine.pdb')): + os.chdir(os.path.join(self.initial_model_directory, xtalID)) + self.Logfile.insert('extracting ligand ({0!s},{1!s},{2!s},{3!s}) from refine.pdb'.format( + str(resname), str(chainID), str(resseq), str(altLoc))) + XChemUtils.pdbtools(os.path.join(self.initial_model_directory, xtalID, 'refine.pdb') + ).save_specific_ligands_to_pdb(resname, chainID, resseq, altLoc) if os.path.isfile('ligand_{0!s}_{1!s}_{2!s}_{3!s}.pdb'.format(str(resname), str(chainID), str(resseq), str(altLoc))): - ligand_pdb='ligand_{0!s}_{1!s}_{2!s}_{3!s}.pdb'.format(str(resname), str(chainID), str(resseq), str(altLoc)) + ligand_pdb = 'ligand_{0!s}_{1!s}_{2!s}_{3!s}.pdb'.format( + str(resname), str(chainID), str(resseq), str(altLoc)) else: - self.Logfile.insert('could not extract ligand; trying next...') + self.Logfile.insert( + 'could not extract ligand; trying next...') continue else: - self.Logfile.insert('directory: '+os.path.join(self.initial_model_directory,xtalID)+' -> cannot find refine.pdb; trying next') + self.Logfile.insert('directory: '+os.path.join( + self.initial_model_directory, xtalID)+' -> cannot find refine.pdb; trying next') continue - if os.path.isfile(os.path.join(self.initial_model_directory,xtalID,'refine.mtz')): - resolution=XChemUtils.mtztools(os.path.join(self.initial_model_directory,xtalID,'refine.mtz')).get_high_resolution_from_mtz() + if os.path.isfile(os.path.join(self.initial_model_directory, xtalID, 'refine.mtz')): + resolution = XChemUtils.mtztools(os.path.join( + self.initial_model_directory, xtalID, 'refine.mtz')).get_high_resolution_from_mtz() else: - self.Logfile.insert('directory: '+os.path.join(self.initial_model_directory,xtalID)+' -> cannot find refine.mtz; trying next') + self.Logfile.insert('directory: '+os.path.join( + self.initial_model_directory, xtalID)+' -> cannot find refine.mtz; trying next') continue - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'eventMap -> SF for '+event_map) - convert_event_map_to_SF(self.initial_model_directory,xtalID,event_map,ligand_pdb,self.xce_logfile,self.datasource,resolution).run() + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'eventMap -> SF for '+event_map) + convert_event_map_to_SF(self.initial_model_directory, xtalID, event_map, + ligand_pdb, self.xce_logfile, self.datasource, resolution).run() progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - class convert_event_map_to_SF: - def __init__(self,project_directory,xtalID,event_map,ligand_pdb,xce_logfile,db_file,resolution): - self.Logfile=XChemLog.updateLog(xce_logfile) + def __init__(self, project_directory, xtalID, event_map, ligand_pdb, xce_logfile, db_file, resolution): + self.Logfile = XChemLog.updateLog(xce_logfile) - self.event_map=event_map + self.event_map = event_map if not os.path.isfile(self.event_map): self.Logfile.insert('cannot find Event map: '+self.event_map) - self.Logfile.insert('cannot convert event_map to structure factors!') + self.Logfile.insert( + 'cannot convert event_map to structure factors!') return None - self.project_directory=project_directory - self.xtalID=xtalID - self.event_map=event_map - self.ligand_pdb=ligand_pdb - self.event=event_map[event_map.rfind('/')+1:].replace('.map','').replace('.ccp4','') - self.db=XChemDB.data_source(db_file) - self.resolution=resolution + self.project_directory = project_directory + self.xtalID = xtalID + self.event_map = event_map + self.ligand_pdb = ligand_pdb + self.event = event_map[event_map.rfind( + '/')+1:].replace('.map', '').replace('.ccp4', '') + self.db = XChemDB.data_source(db_file) + self.resolution = resolution def run(self): - os.chdir(os.path.join(self.project_directory,self.xtalID)) - + os.chdir(os.path.join(self.project_directory, self.xtalID)) # remove exisiting mtz file if os.path.isfile(self.event+'.mtz'): @@ -1511,33 +1646,33 @@ def run(self): if not os.path.isfile('{0!s}.mtz'.format(self.event)): self.Logfile.insert('cannot find {0!s}.mtz'.format(self.event)) else: - self.Logfile.insert('conversion successful, {0!s}.mtz exists'.format(self.event)) + self.Logfile.insert( + 'conversion successful, {0!s}.mtz exists'.format(self.event)) # update datasource with event_map_mtz information self.update_database() - - - def calculate_electron_density_map(self,mtzin): - missing_columns=False - column_dict=XChemUtils.mtztools(mtzin).get_all_columns_as_dict() + def calculate_electron_density_map(self, mtzin): + missing_columns = False + column_dict = XChemUtils.mtztools(mtzin).get_all_columns_as_dict() if 'FWT' in column_dict['F'] and 'PHWT' in column_dict['PHS']: - labin=' labin F1=FWT PHI=PHWT\n' + labin = ' labin F1=FWT PHI=PHWT\n' elif '2FOFCWT' in column_dict['F'] and 'PH2FOFCWT' in column_dict['PHS']: - labin=' labin F1=2FOFCWT PHI=PH2FOFCWT\n' + labin = ' labin F1=2FOFCWT PHI=PH2FOFCWT\n' else: - missing_columns=True + missing_columns = True if not missing_columns: - os.chdir(os.path.join(self.project_directory,self.xtalID)) + os.chdir(os.path.join(self.project_directory, self.xtalID)) cmd = ( 'fft hklin '+mtzin+' mapout 2fofc.map << EOF\n' - +labin+ + + labin + 'EOF\n' - ) + ) self.Logfile.insert('calculating 2fofc map from '+mtzin) os.system(cmd) else: - self.Logfile.insert('cannot calculate 2fofc.map; missing map coefficients') + self.Logfile.insert( + 'cannot calculate 2fofc.map; missing map coefficients') def prepare_conversion_script(self): @@ -1547,34 +1682,34 @@ def prepare_conversion_script(self): # http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model if os.getcwd().startswith('/dls'): - phenix_module='module_load_phenix\n' + phenix_module = 'module_load_phenix\n' else: - phenix_module='' + phenix_module = '' cmd = ( '#!'+os.getenv('SHELL')+'\n' '\n' - +phenix_module+ + + phenix_module + '\n' - 'pdbset XYZIN %s XYZOUT mask_ligand.pdb << eof\n' %self.ligand_pdb+ - ' SPACEGROUP {0!s}\n'.format(self.space_group)+ - ' CELL {0!s}\n'.format((' '.join(self.unit_cell)))+ + 'pdbset XYZIN %s XYZOUT mask_ligand.pdb << eof\n' % self.ligand_pdb + + ' SPACEGROUP {0!s}\n'.format(self.space_group) + + ' CELL {0!s}\n'.format((' '.join(self.unit_cell))) + ' END\n' 'eof\n' '\n' 'ncsmask XYZIN mask_ligand.pdb MSKOUT mask_ligand.msk << eof\n' - ' GRID %s\n' %(' '.join(self.gridElectronDensityMap))+ + ' GRID %s\n' % (' '.join(self.gridElectronDensityMap)) + ' RADIUS 10\n' ' PEAK 1\n' 'eof\n' '\n' - 'mapmask MAPIN %s MAPOUT onecell_event_map.map << eof\n' %self.event_map+ + 'mapmask MAPIN %s MAPOUT onecell_event_map.map << eof\n' % self.event_map + ' XYZLIM CELL\n' 'eof\n' '\n' 'maprot MAPIN onecell_event_map.map MSKIN mask_ligand.msk WRKOUT masked_event_map.map << eof\n' ' MODE FROM\n' - ' SYMMETRY WORK %s\n' %self.space_group_numberElectronDensityMap+ + ' SYMMETRY WORK %s\n' % self.space_group_numberElectronDensityMap + ' AVERAGE\n' ' ROTATE EULER 0 0 0\n' ' TRANSLATE 0 0 0\n' @@ -1585,77 +1720,80 @@ def prepare_conversion_script(self): ' PAD 0.0\n' 'eof\n' '\n' - 'sfall HKLOUT %s.mtz MAPIN masked_event_map_fullcell.map << eof\n' %self.event+ + 'sfall HKLOUT %s.mtz MAPIN masked_event_map_fullcell.map << eof\n' % self.event + ' LABOUT FC=FC_event PHIC=PHIC_event\n' ' MODE SFCALC MAPIN\n' - ' RESOLUTION %s\n' %self.resolution+ + ' RESOLUTION %s\n' % self.resolution + ' END\n' ) - self.Logfile.insert('preparing script for conversion of Event map to SF') - f = open('eventMap2sf.sh','w') + self.Logfile.insert( + 'preparing script for conversion of Event map to SF') + f = open('eventMap2sf.sh', 'w') f.write(cmd) f.close() os.system('chmod +x eventMap2sf.sh') - def run_conversion_script(self): self.Logfile.insert('running conversion script...') os.system('./eventMap2sf.sh') def convert_map_to_p1(self): self.Logfile.insert('running mapmask -> converting map to p1...') - cmd = ( '#!'+os.getenv('SHELL')+'\n' - '\n' - 'mapmask mapin %s mapout %s_p1.map << eof\n' %(self.event_map,self.event) + - 'xyzlin cell\n' - 'symmetry p1\n' ) - self.Logfile.insert('mapmask command:\n%s' %cmd) + cmd = ('#!'+os.getenv('SHELL')+'\n' + '\n' + 'mapmask mapin %s mapout %s_p1.map << eof\n' % (self.event_map, self.event) + + 'xyzlin cell\n' + 'symmetry p1\n') + self.Logfile.insert('mapmask command:\n%s' % cmd) os.system(cmd) def run_phenix_map_to_structure_factors(self): if float(self.resolution) < 1.21: # program complains if resolution is 1.2 or higher - self.resolution='1.21' - self.Logfile.insert('running phenix.map_to_structure_factors {0!s}_p1.map d_min={1!s} output_file_name={2!s}_tmp.mtz'.format(self.event, self.resolution, self.event)) - os.system('phenix.map_to_structure_factors {0!s}_p1.map d_min={1!s} output_file_name={2!s}_tmp.mtz'.format(self.event, self.resolution, self.event)) + self.resolution = '1.21' + self.Logfile.insert('running phenix.map_to_structure_factors {0!s}_p1.map d_min={1!s} output_file_name={2!s}_tmp.mtz'.format( + self.event, self.resolution, self.event)) + os.system('phenix.map_to_structure_factors {0!s}_p1.map d_min={1!s} output_file_name={2!s}_tmp.mtz'.format( + self.event, self.resolution, self.event)) - def run_cinvfft(self,mtzin): + def run_cinvfft(self, mtzin): # mtzin is usually refine.mtz - self.Logfile.insert('running cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz -colout event'.format(self.event_map, mtzin, self.event)) - os.system('cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz -colout event'.format(self.event_map, mtzin, self.event)) - + self.Logfile.insert( + 'running cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz -colout event'.format(self.event_map, mtzin, self.event)) + os.system('cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz -colout event'.format( + self.event_map, mtzin, self.event)) def remove_and_rename_column_labels(self): - cmd = ( '#!'+os.getenv('SHELL')+'\n' - '\n' - 'cad hklin1 %s_tmp.mtz hklout %s.mtz << eof\n' %(self.event,self.event)+ - ' labin file_number 1 E1=F-obs E2=PHIF\n' - ' labout file_number 1 E1=F_ampl E2=PHIF\n' - 'eof\n' - '\n' ) + cmd = ('#!'+os.getenv('SHELL')+'\n' + '\n' + 'cad hklin1 %s_tmp.mtz hklout %s.mtz << eof\n' % (self.event, self.event) + + ' labin file_number 1 E1=F-obs E2=PHIF\n' + ' labout file_number 1 E1=F_ampl E2=PHIF\n' + 'eof\n' + '\n') self.Logfile.insert('running CAD: new column labels F_ampl,PHIF') os.system(cmd) def remove_and_rename_column_labels_after_cinvfft(self): - cmd = ( '#!'+os.getenv('SHELL')+'\n' - '\n' - 'cad hklin1 %s_tmp.mtz hklout %s.mtz << eof\n' %(self.event,self.event)+ - ' labin file_number 1 E1=event.F_phi.F E2=event.F_phi.phi\n' - ' labout file_number 1 E1=F_ampl E2=PHIF\n' - 'eof\n' - '\n' ) - self.Logfile.insert('running CAD: renaming event.F_phi.F -> F_ampl and event.F_phi.phi -> PHIF') + cmd = ('#!'+os.getenv('SHELL')+'\n' + '\n' + 'cad hklin1 %s_tmp.mtz hklout %s.mtz << eof\n' % (self.event, self.event) + + ' labin file_number 1 E1=event.F_phi.F E2=event.F_phi.phi\n' + ' labout file_number 1 E1=F_ampl E2=PHIF\n' + 'eof\n' + '\n') + self.Logfile.insert( + 'running CAD: renaming event.F_phi.F -> F_ampl and event.F_phi.phi -> PHIF') os.system(cmd) - - def update_database(self): - sqlite = ( "update panddaTable set " - " PANDDA_site_event_map_mtz = '%s' " %os.path.join(self.project_directory,self.xtalID,self.event+'.mtz')+ - " where PANDDA_site_event_map is '{0!s}' ".format(self.event_map) - ) + sqlite = ("update panddaTable set " + " PANDDA_site_event_map_mtz = '%s' " % os.path.join(self.project_directory, self.xtalID, self.event+'.mtz') + + " where PANDDA_site_event_map is '{0!s}' ".format( + self.event_map) + ) self.db.execute_statement(sqlite) self.Logfile.insert('updating data source: '+sqlite) @@ -1671,30 +1809,32 @@ def clean_output_directory(self): class run_pandda_inspect_at_home(QtCore.QThread): - def __init__(self,panddaDir,xce_logfile): + def __init__(self, panddaDir, xce_logfile): QtCore.QThread.__init__(self) - self.panddaDir=panddaDir - self.Logfile=XChemLog.updateLog(xce_logfile) + self.panddaDir = panddaDir + self.Logfile = XChemLog.updateLog(xce_logfile) def run(self): - os.chdir(os.path.join(self.panddaDir,'processed_datasets')) + os.chdir(os.path.join(self.panddaDir, 'processed_datasets')) - progress_step=1 + progress_step = 1 if len(glob.glob('*')) != 0: - progress_step=100/float(len(glob.glob('*'))) + progress_step = 100/float(len(glob.glob('*'))) else: - progress_step=1 - progress=0 + progress_step = 1 + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - self.Logfile.insert('parsing '+self.panddaDir) for xtal in sorted(glob.glob('*')): for files in glob.glob(xtal+'/ligand_files/*'): if os.path.islink(files): - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'replacing symlink for {0!s} with real file'.format(files)) - self.Logfile.insert('replacing symlink for {0!s} with real file'.format(files)) - os.system('cp --remove-destination {0!s} {1!s}/ligand_files'.format(os.path.realpath(files), xtal)) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'replacing symlink for {0!s} with real file'.format(files)) + self.Logfile.insert( + 'replacing symlink for {0!s} with real file'.format(files)) + os.system( + 'cp --remove-destination {0!s} {1!s}/ligand_files'.format(os.path.realpath(files), xtal)) progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) @@ -1703,10 +1843,10 @@ def run(self): class convert_apo_structures_to_mmcif(QtCore.QThread): - def __init__(self,panddaDir,xce_logfile): + def __init__(self, panddaDir, xce_logfile): QtCore.QThread.__init__(self) - self.panddaDir=panddaDir - self.Logfile=XChemLog.updateLog(xce_logfile) + self.panddaDir = panddaDir + self.Logfile = XChemLog.updateLog(xce_logfile) def sf_convert_environment(self): pdb_extract_init = '' @@ -1715,91 +1855,87 @@ def sf_convert_environment(self): pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-prod/bin/sf_convert' else: pdb_extract_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' + 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' pdb_extract_init += +os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/bin/sf_convert') + 'pdb_extract/pdb-extract-prod/bin/sf_convert') return pdb_extract_init - def run(self): - self.Logfile.insert('converting apo structures in pandda directory to mmcif files') + self.Logfile.insert( + 'converting apo structures in pandda directory to mmcif files') self.Logfile.insert('chanfing to '+self.panddaDir) - progress_step=1 + progress_step = 1 if len(glob.glob('*')) != 0: - progress_step=100/float(len(glob.glob(os.path.join(self.panddaDir,'processed_datasets','*')))) + progress_step = 100 / \ + float( + len(glob.glob(os.path.join(self.panddaDir, 'processed_datasets', '*')))) else: - progress_step=1 - progress=0 + progress_step = 1 + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) pdb_extract_init = self.sf_convert_environment() self.Logfile.insert('parsing '+self.panddaDir) - for dirs in glob.glob(os.path.join(self.panddaDir,'processed_datasets','*')): + for dirs in glob.glob(os.path.join(self.panddaDir, 'processed_datasets', '*')): xtal = dirs[dirs.rfind('/')+1:] - self.Logfile.insert('%s: converting %s to mmcif' %(xtal,xtal+'-pandda-input.mtz')) - if os.path.isfile(os.path.join(dirs,xtal+'-pandda-input.mtz')): - if os.path.isfile(os.path.join(dirs,xtal+'_sf.mmcif')): - self.Logfile.insert('%s: %s_sf.mmcif exists; skipping...' %(xtal,xtal)) + self.Logfile.insert('%s: converting %s to mmcif' % + (xtal, xtal+'-pandda-input.mtz')) + if os.path.isfile(os.path.join(dirs, xtal+'-pandda-input.mtz')): + if os.path.isfile(os.path.join(dirs, xtal+'_sf.mmcif')): + self.Logfile.insert( + '%s: %s_sf.mmcif exists; skipping...' % (xtal, xtal)) else: os.chdir(dirs) Cmd = (pdb_extract_init + - ' -o mmcif' - ' -sf %s' % xtal+'-pandda-input.mtz' + - ' -out {0!s}_sf.mmcif > {1!s}.sf_mmcif.log'.format(xtal, xtal)) + ' -o mmcif' + ' -sf %s' % xtal+'-pandda-input.mtz' + + ' -out {0!s}_sf.mmcif > {1!s}.sf_mmcif.log'.format(xtal, xtal)) self.Logfile.insert('running command: '+Cmd) os.system(Cmd) progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - - - - - - - - class check_number_of_modelled_ligands(QtCore.QThread): - def __init__(self,project_directory,xce_logfile,db_file): + def __init__(self, project_directory, xce_logfile, db_file): QtCore.QThread.__init__(self) - self.Logfile=XChemLog.updateLog(xce_logfile) - self.project_directory=project_directory - self.db=XChemDB.data_source(db_file) - self.errorDict={} + self.Logfile = XChemLog.updateLog(xce_logfile) + self.project_directory = project_directory + self.db = XChemDB.data_source(db_file) + self.errorDict = {} - def update_errorDict(self,xtal,message): + def update_errorDict(self, xtal, message): if xtal not in self.errorDict: - self.errorDict[xtal]=[] + self.errorDict[xtal] = [] self.errorDict[xtal].append(message) - def insert_new_row_in_panddaTable(self,xtal,ligand,site,dbDict): - resname= site[0] - chain= site[1] - seqnum= site[2] - altLoc= site[3] - x_site= site[5][0] - y_site= site[5][1] - z_site= site[5][2] + def insert_new_row_in_panddaTable(self, xtal, ligand, site, dbDict): + resname = site[0] + chain = site[1] + seqnum = site[2] + altLoc = site[3] + x_site = site[5][0] + y_site = site[5][1] + z_site = site[5][2] - resnameSimilarSite= ligand[0] - chainSimilarSite= ligand[1] - seqnumSimilarSite= ligand[2] + resnameSimilarSite = ligand[0] + chainSimilarSite = ligand[1] + seqnumSimilarSite = ligand[2] - siteList=[] + siteList = [] for entry in dbDict[xtal]: siteList.append(str(entry[0])) if entry[4] == resnameSimilarSite and entry[5] == chainSimilarSite and entry[6] == seqnumSimilarSite: - eventMap= str(entry[7]) - eventMap_mtz= str(entry[8]) - initialPDB= str(entry[9]) - initialMTZ= str(entry[10]) - event_id= str(entry[12]) - PanDDApath= str(entry[13]) - - db_dict={ + eventMap = str(entry[7]) + eventMap_mtz = str(entry[8]) + initialPDB = str(entry[9]) + initialMTZ = str(entry[10]) + event_id = str(entry[12]) + PanDDApath = str(entry[13]) + + db_dict = { 'PANDDA_site_index': str(int(max(siteList))+1), 'PANDDApath': PanDDApath, 'PANDDA_site_ligand_id': resname+'-'+chain+'-'+seqnum, @@ -1815,150 +1951,167 @@ def insert_new_row_in_panddaTable(self,xtal,ligand,site,dbDict): 'PANDDA_site_ligand_placed': 'True', 'PANDDA_site_x': x_site, 'PANDDA_site_y': y_site, - 'PANDDA_site_z': z_site } - + 'PANDDA_site_z': z_site} def run(self): self.Logfile.insert('reading modelled ligands from panddaTable') - dbDict={} - - sqlite = ( "select " - " CrystalName," - " PANDDA_site_index," - " PANDDA_site_x," - " PANDDA_site_y," - " PANDDA_site_z," - " PANDDA_site_ligand_resname," - " PANDDA_site_ligand_chain," - " PANDDA_site_ligand_sequence_number," - " PANDDA_site_event_map," - " PANDDA_site_event_map_mtz," - " PANDDA_site_initial_model," - " PANDDA_site_initial_mtz," - " RefinementOutcome," - " PANDDA_site_event_index," - " PANDDApath " - "from panddaTable " ) - - - dbEntries=self.db.execute_statement(sqlite) + dbDict = {} + + sqlite = ("select " + " CrystalName," + " PANDDA_site_index," + " PANDDA_site_x," + " PANDDA_site_y," + " PANDDA_site_z," + " PANDDA_site_ligand_resname," + " PANDDA_site_ligand_chain," + " PANDDA_site_ligand_sequence_number," + " PANDDA_site_event_map," + " PANDDA_site_event_map_mtz," + " PANDDA_site_initial_model," + " PANDDA_site_initial_mtz," + " RefinementOutcome," + " PANDDA_site_event_index," + " PANDDApath " + "from panddaTable ") + + dbEntries = self.db.execute_statement(sqlite) for item in dbEntries: - xtal= str(item[0]) - site= str(item[1]) - x= str(item[2]) - y= str(item[3]) - z= str(item[4]) - resname= str(item[5]) - chain= str(item[6]) - seqnum= str(item[7]) - eventMap= str(item[8]) - eventMap_mtz= str(item[9]) - initialPDB= str(item[10]) - initialMTZ= str(item[11]) - outcome= str(item[12]) - event= str(item[13]) - PanDDApath= str(item[14]) + xtal = str(item[0]) + site = str(item[1]) + x = str(item[2]) + y = str(item[3]) + z = str(item[4]) + resname = str(item[5]) + chain = str(item[6]) + seqnum = str(item[7]) + eventMap = str(item[8]) + eventMap_mtz = str(item[9]) + initialPDB = str(item[10]) + initialMTZ = str(item[11]) + outcome = str(item[12]) + event = str(item[13]) + PanDDApath = str(item[14]) if xtal not in dbDict: - dbDict[xtal]=[] - dbDict[xtal].append([site,x,y,z,resname,chain,seqnum,eventMap,eventMap_mtz,initialPDB,initialMTZ,outcome,event,PanDDApath]) - + dbDict[xtal] = [] + dbDict[xtal].append([site, x, y, z, resname, chain, seqnum, eventMap, + eventMap_mtz, initialPDB, initialMTZ, outcome, event, PanDDApath]) os.chdir(self.project_directory) - progress_step=1 + progress_step = 1 if len(glob.glob('*')) != 0: - progress_step=100/float(len(glob.glob('*'))) + progress_step = 100/float(len(glob.glob('*'))) else: - progress_step=1 - progress=0 + progress_step = 1 + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) for xtal in sorted(glob.glob('*')): - if os.path.isfile(os.path.join(xtal,'refine.pdb')): - ligands=XChemUtils.pdbtools(os.path.join(xtal,'refine.pdb')).ligand_details_as_list() - self.Logfile.insert('{0!s}: found file refine.pdb'.format(xtal)) + if os.path.isfile(os.path.join(xtal, 'refine.pdb')): + ligands = XChemUtils.pdbtools(os.path.join( + xtal, 'refine.pdb')).ligand_details_as_list() + self.Logfile.insert( + '{0!s}: found file refine.pdb'.format(xtal)) if ligands: - if os.path.isdir(os.path.join(xtal,'xceTmp')): - os.system('/bin/rm -fr {0!s}'.format(os.path.join(xtal,'xceTmp'))) - os.mkdir(os.path.join(xtal,'xceTmp')) + if os.path.isdir(os.path.join(xtal, 'xceTmp')): + os.system( + '/bin/rm -fr {0!s}'.format(os.path.join(xtal, 'xceTmp'))) + os.mkdir(os.path.join(xtal, 'xceTmp')) else: - self.Logfile.warning('{0!s}: cannot find ligand molecule in refine.pdb; skipping...'.format(xtal)) + self.Logfile.warning( + '{0!s}: cannot find ligand molecule in refine.pdb; skipping...'.format(xtal)) continue - made_sym_copies=False - ligands_not_in_panddaTable=[] - for n,item in enumerate(ligands): - resnameLIG= item[0] - chainLIG= item[1] - seqnumLIG= item[2] - altLocLIG= item[3] - occupancyLig= item[4] - if altLocLIG.replace(' ','') == '': - self.Logfile.insert(xtal+': found a ligand not modelled with pandda.inspect -> {0!s} {1!s} {2!s}'.format(resnameLIG, chainLIG, seqnumLIG)) - residue_xyz = XChemUtils.pdbtools(os.path.join(xtal,'refine.pdb')).get_center_of_gravity_of_residue_ish(item[1],item[2]) + made_sym_copies = False + ligands_not_in_panddaTable = [] + for n, item in enumerate(ligands): + resnameLIG = item[0] + chainLIG = item[1] + seqnumLIG = item[2] + altLocLIG = item[3] + occupancyLig = item[4] + if altLocLIG.replace(' ', '') == '': + self.Logfile.insert( + xtal+': found a ligand not modelled with pandda.inspect -> {0!s} {1!s} {2!s}'.format(resnameLIG, chainLIG, seqnumLIG)) + residue_xyz = XChemUtils.pdbtools(os.path.join( + xtal, 'refine.pdb')).get_center_of_gravity_of_residue_ish(item[1], item[2]) ligands[n].append(residue_xyz) - foundLigand=False + foundLigand = False if xtal in dbDict: for entry in dbDict[xtal]: - resnameTable=entry[4] - chainTable=entry[5] - seqnumTable=entry[6] - self.Logfile.insert('panddaTable: {0!s} {1!s} {2!s} {3!s}'.format(xtal, resnameTable, chainTable, seqnumTable)) + resnameTable = entry[4] + chainTable = entry[5] + seqnumTable = entry[6] + self.Logfile.insert('panddaTable: {0!s} {1!s} {2!s} {3!s}'.format( + xtal, resnameTable, chainTable, seqnumTable)) if resnameLIG == resnameTable and chainLIG == chainTable and seqnumLIG == seqnumTable: - self.Logfile.insert('{0!s}: found ligand in database -> {1!s} {2!s} {3!s}'.format(xtal, resnameTable, chainTable, seqnumTable)) - foundLigand=True + self.Logfile.insert('{0!s}: found ligand in database -> {1!s} {2!s} {3!s}'.format( + xtal, resnameTable, chainTable, seqnumTable)) + foundLigand = True if not foundLigand: - self.Logfile.error('{0!s}: did NOT find ligand in database -> {1!s} {2!s} {3!s}'.format(xtal, resnameLIG, chainLIG, seqnumLIG)) - ligands_not_in_panddaTable.append([resnameLIG,chainLIG,seqnumLIG,altLocLIG,occupancyLig,residue_xyz]) + self.Logfile.error('{0!s}: did NOT find ligand in database -> {1!s} {2!s} {3!s}'.format( + xtal, resnameLIG, chainLIG, seqnumLIG)) + ligands_not_in_panddaTable.append( + [resnameLIG, chainLIG, seqnumLIG, altLocLIG, occupancyLig, residue_xyz]) else: - self.Logfile.warning('ligand in PDB file, but dataset not listed in panddaTable: {0!s} -> {1!s} {2!s} {3!s}'.format(xtal, item[0], item[1], item[2])) + self.Logfile.warning( + 'ligand in PDB file, but dataset not listed in panddaTable: {0!s} -> {1!s} {2!s} {3!s}'.format(xtal, item[0], item[1], item[2])) for entry in ligands_not_in_panddaTable: - self.Logfile.error('{0!s}: refine.pdb contains a ligand that is not assigned in the panddaTable: {1!s} {2!s} {3!s} {4!s}'.format(xtal, entry[0], entry[1], entry[2], entry[3])) + self.Logfile.error('{0!s}: refine.pdb contains a ligand that is not assigned in the panddaTable: {1!s} {2!s} {3!s} {4!s}'.format( + xtal, entry[0], entry[1], entry[2], entry[3])) for site in ligands_not_in_panddaTable: - for files in glob.glob(os.path.join(self.project_directory,xtal,'xceTmp','ligand_*_*.pdb')): - mol_xyz = XChemUtils.pdbtools(files).get_center_of_gravity_of_molecule_ish() + for files in glob.glob(os.path.join(self.project_directory, xtal, 'xceTmp', 'ligand_*_*.pdb')): + mol_xyz = XChemUtils.pdbtools( + files).get_center_of_gravity_of_molecule_ish() # now need to check if there is a unassigned entry in panddaTable that is close for entry in dbDict[xtal]: - distance = XChemUtils.misc().calculate_distance_between_coordinates(mol_xyz[0], mol_xyz[1],mol_xyz[2],entry[1],entry[2], entry[3]) - self.Logfile.insert('{0!s}: {1!s} {2!s} {3!s} <---> {4!s} {5!s} {6!s}'.format(xtal, mol_xyz[0], mol_xyz[1], mol_xyz[2], entry[1], entry[2], entry[3])) - self.Logfile.insert('{0!s}: symm equivalent molecule: {1!s}'.format(xtal, files)) - self.Logfile.insert('{0!s}: distance: {1!s}'.format(xtal, str(distance))) + distance = XChemUtils.misc().calculate_distance_between_coordinates( + mol_xyz[0], mol_xyz[1], mol_xyz[2], entry[1], entry[2], entry[3]) + self.Logfile.insert('{0!s}: {1!s} {2!s} {3!s} <---> {4!s} {5!s} {6!s}'.format( + xtal, mol_xyz[0], mol_xyz[1], mol_xyz[2], entry[1], entry[2], entry[3])) + self.Logfile.insert( + '{0!s}: symm equivalent molecule: {1!s}'.format(xtal, files)) + self.Logfile.insert( + '{0!s}: distance: {1!s}'.format(xtal, str(distance))) progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) if self.errorDict != {}: - self.update_errorDict('General','The aforementioned PDB files were automatically changed by XCE!\nPlease check and refine them!!!') + self.update_errorDict( + 'General', 'The aforementioned PDB files were automatically changed by XCE!\nPlease check and refine them!!!') self.emit(QtCore.SIGNAL('show_error_dict'), self.errorDict) - class find_event_map_for_ligand(QtCore.QThread): - def __init__(self,project_directory,xce_logfile,external_software): + def __init__(self, project_directory, xce_logfile, external_software): QtCore.QThread.__init__(self) - self.Logfile=XChemLog.updateLog(xce_logfile) - self.project_directory=project_directory - self.external_software=external_software + self.Logfile = XChemLog.updateLog(xce_logfile) + self.project_directory = project_directory + self.external_software = external_software try: import gemmi self.Logfile.insert('found gemmi library in ccp4-python') except ImportError: self.external_software['gemmi'] = False - self.Logfile.warning('cannot import gemmi; will use phenix.map_to_structure_factors instead') + self.Logfile.warning( + 'cannot import gemmi; will use phenix.map_to_structure_factors instead') def run(self): - self.Logfile.insert('======== checking ligand CC in event maps ========') - for dirs in sorted(glob.glob(os.path.join(self.project_directory,'*'))): + self.Logfile.insert( + '======== checking ligand CC in event maps ========') + for dirs in sorted(glob.glob(os.path.join(self.project_directory, '*'))): xtal = dirs[dirs.rfind('/')+1:] - if os.path.isfile(os.path.join(dirs,'refine.pdb')) and \ - os.path.isfile(os.path.join(dirs,'refine.mtz')): - self.Logfile.insert('%s: found refine.pdb' %xtal) + if os.path.isfile(os.path.join(dirs, 'refine.pdb')) and \ + os.path.isfile(os.path.join(dirs, 'refine.mtz')): + self.Logfile.insert('%s: found refine.pdb' % xtal) os.chdir(dirs) try: p = gemmi.read_structure('refine.pdb') @@ -1966,76 +2119,87 @@ def run(self): self.Logfile.error('gemmi library not available') self.external_software['gemmi'] = False reso = XChemUtils.mtztools('refine.mtz').get_dmin() - ligList = XChemUtils.pdbtools('refine.pdb').save_residues_with_resname(dirs,'LIG') - self.Logfile.insert('%s: found %s ligands of type LIG in refine.pdb' %(xtal,str(len(ligList)))) + ligList = XChemUtils.pdbtools( + 'refine.pdb').save_residues_with_resname(dirs, 'LIG') + self.Logfile.insert( + '%s: found %s ligands of type LIG in refine.pdb' % (xtal, str(len(ligList)))) - for maps in glob.glob(os.path.join(dirs,'*event*.native.ccp4')): + for maps in glob.glob(os.path.join(dirs, '*event*.native.ccp4')): if self.external_software['gemmi']: - self.convert_map_to_sf_with_gemmi(maps,p) + self.convert_map_to_sf_with_gemmi(maps, p) else: self.expand_map_to_p1(maps) - self.convert_map_to_sf(maps.replace('.ccp4','.P1.ccp4'),reso) + self.convert_map_to_sf( + maps.replace('.ccp4', '.P1.ccp4'), reso) summary = '' for lig in sorted(ligList): if self.external_software['gemmi']: - for mtz in sorted(glob.glob(os.path.join(dirs,'*event*.native.mtz'))): - self.get_lig_cc(mtz,lig) - cc = self.check_lig_cc(mtz.replace('.mtz', '_CC.log')) - summary += '%s: %s LIG CC = %s (%s)\n' %(xtal,lig,cc,mtz[mtz.rfind('/')+1:]) + for mtz in sorted(glob.glob(os.path.join(dirs, '*event*.native.mtz'))): + self.get_lig_cc(mtz, lig) + cc = self.check_lig_cc( + mtz.replace('.mtz', '_CC.log')) + summary += '%s: %s LIG CC = %s (%s)\n' % ( + xtal, lig, cc, mtz[mtz.rfind('/')+1:]) else: - for mtz in sorted(glob.glob(os.path.join(dirs,'*event*.native*P1.mtz'))): - self.get_lig_cc(mtz,lig) - cc = self.check_lig_cc(mtz.replace('.mtz', '_CC.log')) - summary += '%s: %s LIG CC = %s (%s)\n' %(xtal,lig,cc,mtz[mtz.rfind('/')+1:]) - self.Logfile.insert('\nsummary of CC analysis:\n======================:\n'+summary) - - def expand_map_to_p1(self,emap): - self.Logfile.insert('expanding map to P1: %s' %emap) - if os.path.isfile(emap.replace('.ccp4','.P1.ccp4')): + for mtz in sorted(glob.glob(os.path.join(dirs, '*event*.native*P1.mtz'))): + self.get_lig_cc(mtz, lig) + cc = self.check_lig_cc( + mtz.replace('.mtz', '_CC.log')) + summary += '%s: %s LIG CC = %s (%s)\n' % ( + xtal, lig, cc, mtz[mtz.rfind('/')+1:]) + self.Logfile.insert( + '\nsummary of CC analysis:\n======================:\n'+summary) + + def expand_map_to_p1(self, emap): + self.Logfile.insert('expanding map to P1: %s' % emap) + if os.path.isfile(emap.replace('.ccp4', '.P1.ccp4')): self.Logfile.warning('P1 map exists; skipping...') return - cmd = ( 'mapmask MAPIN %s MAPOUT %s << eof\n' %(emap,emap.replace('.ccp4','.P1.ccp4'))+ - ' XYZLIM CELL\n' - ' PAD 0.0\n' - ' SYMMETRY 1\n' - 'eof\n' ) + cmd = ('mapmask MAPIN %s MAPOUT %s << eof\n' % (emap, emap.replace('.ccp4', '.P1.ccp4')) + + ' XYZLIM CELL\n' + ' PAD 0.0\n' + ' SYMMETRY 1\n' + 'eof\n') os.system(cmd) - def convert_map_to_sf(self,emap,reso): - self.Logfile.insert('converting ccp4 map to mtz with phenix.map_to_structure_factors: %s' %emap) - if os.path.isfile(emap.replace('.ccp4','.mtz')): + def convert_map_to_sf(self, emap, reso): + self.Logfile.insert( + 'converting ccp4 map to mtz with phenix.map_to_structure_factors: %s' % emap) + if os.path.isfile(emap.replace('.ccp4', '.mtz')): self.Logfile.warning('mtz file of event map exists; skipping...') return - cmd = ( 'module load phenix\n' - 'phenix.map_to_structure_factors %s d_min=%s\n' %(emap,reso)+ - '/bin/mv map_to_structure_factors.mtz %s' %emap.replace('.ccp4', '.mtz') ) + cmd = ('module load phenix\n' + 'phenix.map_to_structure_factors %s d_min=%s\n' % (emap, reso) + + '/bin/mv map_to_structure_factors.mtz %s' % emap.replace('.ccp4', '.mtz')) os.system(cmd) - def get_lig_cc(self,mtz,lig): - self.Logfile.insert('calculating CC for %s in %s' %(lig,mtz)) + def get_lig_cc(self, mtz, lig): + self.Logfile.insert('calculating CC for %s in %s' % (lig, mtz)) if os.path.isfile(mtz.replace('.mtz', '_CC.log')): self.Logfile.warning('logfile of CC analysis exists; skipping...') return - cmd = ( 'module load phenix\n' - 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC.log')) ) + cmd = ('module load phenix\n' + 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC.log'))) os.system(cmd) - def check_lig_cc(self,log): + def check_lig_cc(self, log): cc = 'n/a' if os.path.isfile(log): for line in open(log): if line.startswith('local'): cc = line.split()[len(line.split()) - 1] else: - self.Logfile.error('logfile does not exist: %s' %log) + self.Logfile.error('logfile does not exist: %s' % log) return cc - def convert_map_to_sf_with_gemmi(self,emap,p): - self.Logfile.insert('converting ccp4 map to mtz with gemmi map2sf: %s' %emap) - if os.path.isfile(emap.replace('.ccp4','.mtz')): + def convert_map_to_sf_with_gemmi(self, emap, p): + self.Logfile.insert( + 'converting ccp4 map to mtz with gemmi map2sf: %s' % emap) + if os.path.isfile(emap.replace('.ccp4', '.mtz')): self.Logfile.warning('mtz file of event map exists; skipping...') return - cmd = 'gemmi map2sf %s %s FWT PHWT --dmin=%s' %(emap,emap.replace('.ccp4','.mtz'),p.resolution) + cmd = 'gemmi map2sf %s %s FWT PHWT --dmin=%s' % ( + emap, emap.replace('.ccp4', '.mtz'), p.resolution) self.Logfile.insert('converting map with command:\n' + cmd) - os.system(cmd) \ No newline at end of file + os.system(cmd) diff --git a/lib/XChemPlots.py b/lib/XChemPlots.py index 6b8fca19..5f48f218 100755 --- a/lib/XChemPlots.py +++ b/lib/XChemPlots.py @@ -1,70 +1,70 @@ # last edited: 29/07/2016, 15:00 -import os,sys - -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) - +import numpy as np +from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas +import matplotlib.pyplot as plt import XChemMain +import os +import sys -import matplotlib.pyplot as plt -from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas -import numpy as np +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) class summary_plot(object): - def __init__(self,datasource,overview_axes): - self.datasource=datasource - self.overview_axes=overview_axes + def __init__(self, datasource, overview_axes): + self.datasource = datasource + self.overview_axes = overview_axes def update_overview(self): - db_dict=XChemMain.get_datasource_summary(self.datasource) - - category = ( 'Crystals mounted', - 'Data Collection', - 'Maps', - 'PANDDA', - 'Refinement', - 'Comp Chem' ) + db_dict = XChemMain.get_datasource_summary(self.datasource) + category = ('Crystals mounted', + 'Data Collection', + 'Maps', + 'PANDDA', + 'Refinement', + 'Comp Chem') N = len(category) - Success = np.array([ db_dict['nr_samples'], - db_dict['nr_data_collection_success'], - db_dict['nr_initial_maps_available'], - db_dict['nr_pandda_hits'], - 5, - 6 ]) - - Processed = np.array([ 0, - 0, - 0, - db_dict['nr_pandda_processed'], - 0, - 0 ]) - - Pending = np.array([ 0, - db_dict['nr_data_collection_pending'], - db_dict['nr_initial_maps_pending'], - db_dict['nr_pandda_pending'], - 2, - 1 ]) - - Failure = np.array([ db_dict['nr_samples_failed_to_mount'], - db_dict['nr_data_collection_failed'], - db_dict['nr_initial_maps_fail'], - db_dict['nr_pandda_reject'], - 2, - 3 ]) + Success = np.array([db_dict['nr_samples'], + db_dict['nr_data_collection_success'], + db_dict['nr_initial_maps_available'], + db_dict['nr_pandda_hits'], + 5, + 6]) + + Processed = np.array([0, + 0, + 0, + db_dict['nr_pandda_processed'], + 0, + 0]) + + Pending = np.array([0, + db_dict['nr_data_collection_pending'], + db_dict['nr_initial_maps_pending'], + db_dict['nr_pandda_pending'], + 2, + 1]) + + Failure = np.array([db_dict['nr_samples_failed_to_mount'], + db_dict['nr_data_collection_failed'], + db_dict['nr_initial_maps_fail'], + db_dict['nr_pandda_reject'], + 2, + 3]) ind = np.arange(N) # the x locations for the groups width = 0.35 # the width of the bars p0 = self.overview_axes.bar(ind, Success, width, color='g') - p1 = self.overview_axes.bar(ind, Processed, width, color='b', bottom=Success) - p2 = self.overview_axes.bar(ind, Pending, width, color='y', bottom=Success+Processed) - p3 = self.overview_axes.bar(ind, Failure, width, color='r', bottom=Pending+Success+Processed) - + p1 = self.overview_axes.bar( + ind, Processed, width, color='b', bottom=Success) + p2 = self.overview_axes.bar( + ind, Pending, width, color='y', bottom=Success+Processed) + p3 = self.overview_axes.bar( + ind, Failure, width, color='r', bottom=Pending+Success+Processed) # add some text for labels, title and axes ticks self.overview_axes.set_ylabel('N') @@ -72,4 +72,5 @@ def update_overview(self): self.overview_axes.set_xticks(ind + width) self.overview_axes.set_xticklabels(category) - self.overview_axes.legend((p0[0], p1[0], p2[0], p3[0]), ('Success', 'Processed', 'Pending', 'Failure')) + self.overview_axes.legend( + (p0[0], p1[0], p2[0], p3[0]), ('Success', 'Processed', 'Pending', 'Failure')) diff --git a/lib/XChemProcess.py b/lib/XChemProcess.py index 0b18b03a..1b6093f5 100755 --- a/lib/XChemProcess.py +++ b/lib/XChemProcess.py @@ -1,52 +1,58 @@ # last edited: 24/03/2017, 15:00 -import os, sys, glob +import XChemDB +import XChemLog +import os +import sys +import glob from PyQt4 import QtGui, QtCore -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) -import XChemLog -import XChemDB +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + class run_xia2(QtCore.QThread): - def __init__(self,initial_model_directory,run_dict,protocol,spg,ref,reso_limit,cc_half,xce_logfile,external_software,ccp4_scratch_directory,max_queue_jobs,database,overwrite): + def __init__(self, initial_model_directory, run_dict, protocol, spg, ref, reso_limit, cc_half, xce_logfile, external_software, ccp4_scratch_directory, max_queue_jobs, database, overwrite): QtCore.QThread.__init__(self) - self.initial_model_directory=initial_model_directory - self.run_dict=run_dict - self.protocol=protocol - self.spg=spg - self.ref=ref - self.reso_limit=reso_limit - self.cc_half=cc_half - self.xce_logfile=xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) - self.external_software=external_software - self.ccp4_scratch_directory=ccp4_scratch_directory - self.max_queue_jobs=max_queue_jobs - self.database=database - self.db=XChemDB.data_source(database) - self.overwrite=overwrite + self.initial_model_directory = initial_model_directory + self.run_dict = run_dict + self.protocol = protocol + self.spg = spg + self.ref = ref + self.reso_limit = reso_limit + self.cc_half = cc_half + self.xce_logfile = xce_logfile + self.Logfile = XChemLog.updateLog(xce_logfile) + self.external_software = external_software + self.ccp4_scratch_directory = ccp4_scratch_directory + self.max_queue_jobs = max_queue_jobs + self.database = database + self.db = XChemDB.data_source(database) + self.overwrite = overwrite def run(self): os.chdir(os.path.join(self.initial_model_directory)) # first create directories if they do not exist if not self.protocol: - self.Logfile.insert('please select data processing protocol first!') + self.Logfile.insert( + 'please select data processing protocol first!') return None - for i,xtal in enumerate(self.run_dict): + for i, xtal in enumerate(self.run_dict): - script='' + script = '' if self.external_software['qsub']: - script+='#PBS -joe -N XCE_reprocess\n' + script += '#PBS -joe -N XCE_reprocess\n' else: - script+='#!'+os.getenv('SHELL')+'\n' + script += '#!'+os.getenv('SHELL')+'\n' if 'bash' in os.getenv('SHELL'): - script += 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' + script += 'export XChemExplorer_DIR="' + \ + os.getenv('XChemExplorer_DIR')+'"\n' elif 'csh' in os.getenv('SHELL'): - script += 'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n' + script += 'setenv XChemExplorer_DIR ' + \ + os.getenv('XChemExplorer_DIR')+'\n' if os.getcwd().startswith('/dls'): script += 'module load ccp4/7.1.018\n' @@ -60,34 +66,35 @@ def run(self): # print 'hallo' if not self.spg: - spg_option='' + spg_option = '' else: - spg_option='space_group='+str(self.spg[0]) + spg_option = 'space_group='+str(self.spg[0]) if not self.ref: - ref_option='' + ref_option = '' else: - ref_option='reference_reflection_file='+str(self.ref[0]) + ref_option = 'reference_reflection_file='+str(self.ref[0]) if not self.reso_limit: - reso_limit_option='' + reso_limit_option = '' else: - reso_limit_option='misigma='+str(self.reso_limit[0]) + reso_limit_option = 'misigma='+str(self.reso_limit[0]) if not self.cc_half: - cc_half_option='' + cc_half_option = '' else: - cc_half_option='cc_half='+str(self.cc_half[0]) - + cc_half_option = 'cc_half='+str(self.cc_half[0]) # first link diffraction images into directory - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal)): - os.mkdir(os.path.join(self.initial_model_directory,xtal)) - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'diffraction_images')): - os.mkdir(os.path.join(self.initial_model_directory,xtal,'diffraction_images')) - - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'processed')): - os.mkdir(os.path.join(self.initial_model_directory,xtal,'processed')) + if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): + os.mkdir(os.path.join(self.initial_model_directory, xtal)) + if not os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'diffraction_images')): + os.mkdir(os.path.join(self.initial_model_directory, + xtal, 'diffraction_images')) + + if not os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'processed')): + os.mkdir(os.path.join( + self.initial_model_directory, xtal, 'processed')) # 2018-09-19 - disabled this for Joe's test # if os.path.isfile(os.path.join(self.initial_model_directory,xtal,'processed','run_in_progress')): # self.Logfile.insert('data processing is in progress; skipping...') @@ -97,81 +104,113 @@ def run(self): print 'hallo' else: if self.overwrite: - os.chdir(os.path.join(self.initial_model_directory,xtal,'diffraction_images')) - self.Logfile.insert('removing all links to diffraction images in '+os.path.join(self.initial_model_directory,xtal,'diffraction_images')) + os.chdir(os.path.join(self.initial_model_directory, + xtal, 'diffraction_images')) + self.Logfile.insert('removing all links to diffraction images in '+os.path.join( + self.initial_model_directory, xtal, 'diffraction_images')) os.system('/bin/rm -fr *') - os.chdir(os.path.join(self.initial_model_directory,xtal,'processed')) - self.Logfile.insert('removing all links to diffraction images in '+os.path.join(self.initial_model_directory,xtal,'processed')) + os.chdir(os.path.join( + self.initial_model_directory, xtal, 'processed')) + self.Logfile.insert('removing all links to diffraction images in '+os.path.join( + self.initial_model_directory, xtal, 'processed')) os.system('/bin/rm -fr *') - os.chdir(os.path.join(self.initial_model_directory,xtal,'processed')) + os.chdir(os.path.join( + self.initial_model_directory, xtal, 'processed')) # 2018-09-19 - disabled this for Joe's test # os.system('touch run_in_progress') - for n,entry in enumerate(sorted(self.run_dict[xtal])): - newRun=1 - for runDir in sorted(glob.glob(os.path.join(self.initial_model_directory,xtal,'diffraction_images','run_*'))): - newRun=int(runDir[runDir.rfind('_')+1:])+1 + for n, entry in enumerate(sorted(self.run_dict[xtal])): + newRun = 1 + for runDir in sorted(glob.glob(os.path.join(self.initial_model_directory, xtal, 'diffraction_images', 'run_*'))): + newRun = int(runDir[runDir.rfind('_')+1:])+1 - os.mkdir(os.path.join(self.initial_model_directory,xtal,'diffraction_images','run_'+str(newRun))) - image_dir=os.path.join(self.initial_model_directory,xtal,'diffraction_images','run_'+str(newRun)) - os.chdir(os.path.join(self.initial_model_directory,xtal,'diffraction_images','run_'+str(newRun))) - os.system('ln -s '+os.path.join(entry[0],entry[1])+'* .') + os.mkdir(os.path.join(self.initial_model_directory, + xtal, 'diffraction_images', 'run_'+str(newRun))) + image_dir = os.path.join( + self.initial_model_directory, xtal, 'diffraction_images', 'run_'+str(newRun)) + os.chdir(os.path.join(self.initial_model_directory, + xtal, 'diffraction_images', 'run_'+str(newRun))) + os.system('ln -s '+os.path.join(entry[0], entry[1])+'* .') - os.chdir(os.path.join(self.initial_model_directory,xtal,'processed')) - os.mkdir(os.path.join(self.initial_model_directory,xtal,'processed','run_'+str(newRun))) + os.chdir(os.path.join( + self.initial_model_directory, xtal, 'processed')) + os.mkdir(os.path.join(self.initial_model_directory, + xtal, 'processed', 'run_'+str(newRun))) for pipeline in self.protocol: - script+='cd '+os.path.join(self.initial_model_directory,xtal,'processed','run_'+str(newRun),pipeline)+'\n' - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'processed','run_'+str(newRun),pipeline)): - os.mkdir(os.path.join(self.initial_model_directory,xtal,'processed','run_'+str(newRun),pipeline)) + script += 'cd ' + \ + os.path.join(self.initial_model_directory, xtal, + 'processed', 'run_'+str(newRun), pipeline)+'\n' + if not os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'processed', 'run_'+str(newRun), pipeline)): + os.mkdir(os.path.join(self.initial_model_directory, + xtal, 'processed', 'run_'+str(newRun), pipeline)) - script+='$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_status_flag.py')+' {0!s} {1!s} {2!s} {3!s}\n'.format(self.database, xtal, 'DataProcessingStatus', 'running') + script += '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_status_flag.py') + \ + ' {0!s} {1!s} {2!s} {3!s}\n'.format( + self.database, xtal, 'DataProcessingStatus', 'running') # 2018-09-19 - changed this for Joe's test # script+='$CCP4/bin/xia2 pipeline='+pipeline+' '+ref_option+' '+spg_option+' '+reso_limit_option+' '+cc_half_option+' '+image_dir+'\n' - script+='xia2 pipeline='+pipeline+' '+ref_option+' '+spg_option+' '+reso_limit_option+' '+cc_half_option+' '+image_dir+'\n' + script += 'xia2 pipeline='+pipeline+' '+ref_option+' '+spg_option + \ + ' '+reso_limit_option+' '+cc_half_option+' '+image_dir+'\n' - script+='$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_status_flag.py')+' {0!s} {1!s} {2!s} {3!s}\n'.format(self.database, xtal, 'DataProcessingStatus', 'finished') - script+='cd '+os.path.join(self.initial_model_directory,xtal,'processed')+'\n' - script+='/bin/rm run_in_progress\n' + script += '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_status_flag.py') + \ + ' {0!s} {1!s} {2!s} {3!s}\n'.format( + self.database, xtal, 'DataProcessingStatus', 'finished') + script += 'cd ' + \ + os.path.join(self.initial_model_directory, + xtal, 'processed')+'\n' + script += '/bin/rm run_in_progress\n' os.chdir(self.ccp4_scratch_directory) - f = open('xce_xia2_{0!s}.sh'.format(str(i+1)),'w') + f = open('xce_xia2_{0!s}.sh'.format(str(i+1)), 'w') f.write(script) f.close() os.system('chmod +x xce_xia2_{0!s}.sh'.format(str(i+1))) - db_dict= {'DataProcessingStatus': 'started'} - self.Logfile.insert('{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) - self.db.update_data_source(xtal,db_dict) + db_dict = {'DataProcessingStatus': 'started'} + self.Logfile.insert( + '{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) + self.db.update_data_source(xtal, db_dict) # submit job - self.Logfile.insert('created input scripts for '+str(n+1)+' in '+self.ccp4_scratch_directory) + self.Logfile.insert('created input scripts for ' + + str(n+1)+' in '+self.ccp4_scratch_directory) os.chdir(self.ccp4_scratch_directory) if os.getcwd().startswith('/dls'): if self.external_software['qsub_array']: Cmds = ( - '#PBS -joe -N xce_xia2_master\n' - './xce_xia2_$SGE_TASK_ID.sh\n' - ) - f = open('xia2_master.sh','w') + '#PBS -joe -N xce_xia2_master\n' + './xce_xia2_$SGE_TASK_ID.sh\n' + ) + f = open('xia2_master.sh', 'w') f.write(Cmds) f.close() - self.Logfile.insert('submitting array job with maximal 100 jobs running on cluster') + self.Logfile.insert( + 'submitting array job with maximal 100 jobs running on cluster') self.Logfile.insert('using the following command:') - self.Logfile.insert('qsub -t 1:{0!s} -tc {1!s} xia2_master.sh'.format(str(i+1), self.max_queue_jobs)) - os.system('qsub -P labxchem -q medium.q -N xia2 -t 1:{0!s} -tc {1!s} xia2_master.sh'.format(str(i+1), self.max_queue_jobs)) + self.Logfile.insert( + 'qsub -t 1:{0!s} -tc {1!s} xia2_master.sh'.format(str(i+1), self.max_queue_jobs)) + os.system('qsub -P labxchem -q medium.q -N xia2 -t 1:{0!s} -tc {1!s} xia2_master.sh'.format( + str(i+1), self.max_queue_jobs)) else: - self.Logfile.insert("cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") + self.Logfile.insert( + "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") elif self.external_software['qsub']: - self.Logfile.insert('submitting {0!s} individual jobs to cluster'.format((str(i+1)))) - self.Logfile.insert('WARNING: this could potentially lead to a crash...') + self.Logfile.insert( + 'submitting {0!s} individual jobs to cluster'.format((str(i+1)))) + self.Logfile.insert( + 'WARNING: this could potentially lead to a crash...') for n in range(i+1): - self.Logfile.insert('qsub xce_xia2_{0!s}.sh'.format((str(n+1)))) - os.system('qsub -q medium.q -N xia2 xce_xia2_{0!s}.sh'.format((str(n+1)))) + self.Logfile.insert( + 'qsub xce_xia2_{0!s}.sh'.format((str(n+1)))) + os.system( + 'qsub -q medium.q -N xia2 xce_xia2_{0!s}.sh'.format((str(n+1)))) else: - self.Logfile.insert('running %s consecutive XIA2 jobs on your local machine') + self.Logfile.insert( + 'running %s consecutive XIA2 jobs on your local machine') for n in range(i+1): - self.Logfile.insert('starting xce_xia2_{0!s}.sh'.format((str(n+1)))) + self.Logfile.insert( + 'starting xce_xia2_{0!s}.sh'.format((str(n+1)))) os.system('./xce_xia2_{0!s}.sh'.format((str(n+1)))) @@ -189,8 +228,6 @@ def run(self): # os.system('touch dimple_run_in_progress') - - # header='#!'+os.getenv('SHELL')+'\n' # if external_software['qsub']: # if not external_software['qsub_array']: diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index a34a7785..fde183cf 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -1,74 +1,74 @@ # last edited: 08/08/2017, 15:00 +import pango +import gtk +from XChemUtils import mtztools_gemmi +from XChemUtils import pdbtools +import XChemLog +from datetime import datetime +import time +import fileinput +import getpass +import sys +import glob +import os import pygtk pygtk.require('2.0') -import gtk, pango -import os -import glob -import sys -import getpass -import fileinput -import time -from datetime import datetime -#sys.path.append(os.path.join(os.getenv('CCP4'),'lib/python2.7/site-packages')) +# sys.path.append(os.path.join(os.getenv('CCP4'),'lib/python2.7/site-packages')) #import coot -#sys.path.append('/usr/local/coot/SoakProc/lib') +# sys.path.append('/usr/local/coot/SoakProc/lib') #import coot_utils_XChem sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') -import XChemLog -from XChemUtils import pdbtools -from XChemUtils import mtztools_gemmi -def GetSerial(ProjectPath,xtalID): + +def GetSerial(ProjectPath, xtalID): # check if there were already previous refinements # if no: create a folder Refine_1 # if yes: create a folder Refine_ temp = [] found = 0 - if os.path.isdir(os.path.join(ProjectPath,xtalID)): - for item in glob.glob(os.path.join(ProjectPath,xtalID,'*')): - if item.startswith(os.path.join(ProjectPath,xtalID,'Refine_')): - if item.endswith('-report'): - continue - try: - temp.append(int(item[item.rfind('_')+1:])) - except ValueError: - continue - found = 1 + if os.path.isdir(os.path.join(ProjectPath, xtalID)): + for item in glob.glob(os.path.join(ProjectPath, xtalID, '*')): + if item.startswith(os.path.join(ProjectPath, xtalID, 'Refine_')): + if item.endswith('-report'): + continue + try: + temp.append(int(item[item.rfind('_')+1:])) + except ValueError: + continue + found = 1 if found: Serial = max(temp) + 1 else: - Serial=1 + Serial = 1 return Serial - class RefineParams(object): - def __init__(self,ProjectPath,xtalID,compoundID,datasource): + def __init__(self, ProjectPath, xtalID, compoundID, datasource): self.ProjectPath = ProjectPath self.xtalID = xtalID self.compoundID = compoundID self.prefix = 'refine' - self.datasource=datasource + self.datasource = datasource - - def RefmacRefinementParams(self,RefmacParams): - self.RefmacParams=RefmacParams + def RefmacRefinementParams(self, RefmacParams): + self.RefmacParams = RefmacParams self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) self.window.connect("delete_event", gtk.main_quit) self.window.set_border_width(10) self.window.set_title("Refmac Parameters") self.vbox = gtk.VBox() - self.hbox1=gtk.HBox() + self.hbox1 = gtk.HBox() self.hbox1.add(gtk.Label('Refine')) self.cb = gtk.combo_box_new_text() self.cb.connect("changed", self.ChooseBfacRefinement) - for item in ['isotropic','anisotropic']: + for item in ['isotropic', 'anisotropic']: self.cb.append_text(item) if 'ISOT' in self.RefmacParams['BREF']: self.cb.set_active(0) @@ -78,88 +78,95 @@ def RefmacRefinementParams(self,RefmacParams): self.hbox1.add(gtk.Label('temperature factors')) self.vbox.add(self.hbox1) - self.hbox2=gtk.HBox() + self.hbox2 = gtk.HBox() self.hbox2.add(gtk.Label('Number of Cycles: ')) - self.Ncycles=gtk.Entry() + self.Ncycles = gtk.Entry() self.Ncycles.add_events(gtk.gdk.KEY_RELEASE_MASK) self.Ncycles.connect("key-release-event", self.on_key_release_Ncycles) self.Ncycles.set_text(self.RefmacParams['NCYCLES']) self.hbox2.add(self.Ncycles) self.vbox.add(self.hbox2) - self.hbox3=gtk.HBox() + self.hbox3 = gtk.HBox() self.hbox3.add(gtk.Label('MATRIX WEIGHT: ')) - self.MATRIX_WEIGHT=gtk.Entry() + self.MATRIX_WEIGHT = gtk.Entry() self.MATRIX_WEIGHT.add_events(gtk.gdk.KEY_RELEASE_MASK) - self.MATRIX_WEIGHT.connect("key-release-event", self.on_key_release_MATRIX_WEIGHT) + self.MATRIX_WEIGHT.connect( + "key-release-event", self.on_key_release_MATRIX_WEIGHT) self.MATRIX_WEIGHT.set_text(self.RefmacParams['MATRIX_WEIGHT']) self.hbox3.add(self.MATRIX_WEIGHT) self.vbox.add(self.hbox3) - self.TLS = gtk.CheckButton('TLS (find TLS groups with phenix.find_tls_groups)') + self.TLS = gtk.CheckButton( + 'TLS (find TLS groups with phenix.find_tls_groups)') self.TLS.connect("toggled", self.TLSCallback) - if self.RefmacParams['TLS']=='refi tlsc 10\n': self.TLS.set_active(True) - self.vbox.pack_start(self.TLS,False) + if self.RefmacParams['TLS'] == 'refi tlsc 10\n': + self.TLS.set_active(True) + self.vbox.pack_start(self.TLS, False) self.NCS = gtk.CheckButton('NCS (if applicable') self.NCS.connect("toggled", self.NCSCallback) - if self.RefmacParams['NCS']=='NCSR LOCAL\n': self.NCS.set_active(True) - self.vbox.pack_start(self.NCS,False) + if self.RefmacParams['NCS'] == 'NCSR LOCAL\n': + self.NCS.set_active(True) + self.vbox.pack_start(self.NCS, False) self.TWIN = gtk.CheckButton('Twin?') self.TWIN.connect("toggled", self.TWINCallback) - if self.RefmacParams['TWIN']=='TWIN\n': self.TWIN.set_active(True) - self.vbox.pack_start(self.TWIN,False) + if self.RefmacParams['TWIN'] == 'TWIN\n': + self.TWIN.set_active(True) + self.vbox.pack_start(self.TWIN, False) self.WATER = gtk.CheckButton('Update waters (BUSTER)') self.WATER.connect("toggled", self.WATERCallback) - if self.RefmacParams['WATER']=='WATER\n': self.WATER.set_active(True) - self.vbox.pack_start(self.WATER,False) + if self.RefmacParams['WATER'] == 'WATER\n': + self.WATER.set_active(True) + self.vbox.pack_start(self.WATER, False) self.LIGOCC = gtk.CheckButton('Refine ligand occupancy (BUSTER)') self.LIGOCC.connect("toggled", self.LIGOCCCallback) - if self.RefmacParams['LIGOCC']=='LIGOCC\n': self.LIGOCC.set_active(True) - self.vbox.pack_start(self.LIGOCC,False) + if self.RefmacParams['LIGOCC'] == 'LIGOCC\n': + self.LIGOCC.set_active(True) + self.vbox.pack_start(self.LIGOCC, False) self.SANITY = gtk.CheckButton('Ignore sanity checks (BUSTER)') self.SANITY.connect("toggled", self.SANITYCallback) - if self.RefmacParams['SANITY']=='off\n': self.SANITY.set_active(True) - self.vbox.pack_start(self.SANITY,False) + if self.RefmacParams['SANITY'] == 'off\n': + self.SANITY.set_active(True) + self.vbox.pack_start(self.SANITY, False) self.OKbutton = gtk.Button(label="OK") - self.OKbutton.connect("clicked",self.OK) + self.OKbutton.connect("clicked", self.OK) self.vbox.add(self.OKbutton) self.window.add(self.vbox) self.window.show_all() return self.RefmacParams - def TLSCallback(self, widget): if widget.get_active(): - self.RefmacParams['TLS']='refi tlsc 10\n' - self.RefmacParams['TLSIN']='refmac.tls\n' - self.RefmacParams['TLSOUT']='out.tls\n' - self.RefmacParams['TLSADD']='TLSO ADDU\n' + self.RefmacParams['TLS'] = 'refi tlsc 10\n' + self.RefmacParams['TLSIN'] = 'refmac.tls\n' + self.RefmacParams['TLSOUT'] = 'out.tls\n' + self.RefmacParams['TLSADD'] = 'TLSO ADDU\n' else: - self.RefmacParams['TLS']='' - self.RefmacParams['TLSIN']='' - self.RefmacParams['TLSOUT']='' - self.RefmacParams['TLSADD']='' + self.RefmacParams['TLS'] = '' + self.RefmacParams['TLSIN'] = '' + self.RefmacParams['TLSOUT'] = '' + self.RefmacParams['TLSADD'] = '' return self.RefmacParams def NCSCallback(self, widget): if widget.get_active(): - self.RefmacParams['NCS']='NCSR LOCAL\n' + self.RefmacParams['NCS'] = 'NCSR LOCAL\n' else: - self.RefmacParams['NCS']='' + self.RefmacParams['NCS'] = '' return self.RefmacParams - def ChooseBfacRefinement(self,widget): - if widget.get_active_text()=='isotropic': - self.RefmacParams['BREF']=' bref ISOT\n' - if widget.get_active_text()=='anisotropic': - self.RefmacParams['BREF']=' bref ANIS\n' + def ChooseBfacRefinement(self, widget): + if widget.get_active_text() == 'isotropic': + self.RefmacParams['BREF'] = ' bref ISOT\n' + if widget.get_active_text() == 'anisotropic': + self.RefmacParams['BREF'] = ' bref ANIS\n' return self.RefmacParams def on_key_release_Ncycles(self, widget, event): @@ -173,119 +180,121 @@ def on_key_release_MATRIX_WEIGHT(self, widget, event): def TWINCallback(self, widget): if widget.get_active(): - self.RefmacParams['TWIN']='TWIN\n' + self.RefmacParams['TWIN'] = 'TWIN\n' else: - self.RefmacParams['TWIN']='' + self.RefmacParams['TWIN'] = '' return self.RefmacParams def WATERCallback(self, widget): if widget.get_active(): - self.RefmacParams['WATER']='WATER\n' + self.RefmacParams['WATER'] = 'WATER\n' else: - self.RefmacParams['WATER']='' + self.RefmacParams['WATER'] = '' return self.RefmacParams def LIGOCCCallback(self, widget): if widget.get_active(): - self.RefmacParams['LIGOCC']='LIGOCC\n' + self.RefmacParams['LIGOCC'] = 'LIGOCC\n' else: - self.RefmacParams['LIGOCC']='' + self.RefmacParams['LIGOCC'] = '' return self.RefmacParams def SANITYCallback(self, widget): if widget.get_active(): - self.RefmacParams['SANITY']='off\n' + self.RefmacParams['SANITY'] = 'off\n' else: - self.RefmacParams['SANITY']='' + self.RefmacParams['SANITY'] = '' return self.RefmacParams - def OK(self,widget): + def OK(self, widget): self.window.destroy() - - def ParamsFromPreviousCycle(self,Serial): - - RefmacParams={ 'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '', - 'WATER': '', - 'LIGOCC': '', - 'SANITY': '' } + def ParamsFromPreviousCycle(self, Serial): + + RefmacParams = {'HKLIN': '', 'HKLOUT': '', + 'XYZIN': '', 'XYZOUT': '', + 'LIBIN': '', 'LIBOUT': '', + 'TLSIN': '', 'TLSOUT': '', + 'TLSADD': '', + 'NCYCLES': '10', + 'MATRIX_WEIGHT': 'AUTO', + 'BREF': ' bref ISOT\n', + 'TLS': '', + 'NCS': '', + 'TWIN': '', + 'WATER': '', + 'LIGOCC': '', + 'SANITY': ''} if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): if line.startswith('refi tlsc'): - RefmacParams['TLS']=line + RefmacParams['TLS'] = line if line.startswith('TLSO'): - RefmacParams['TLSADD']=line + RefmacParams['TLSADD'] = line if line.startswith('NCSR LOCAL'): - RefmacParams['NCS']=line + RefmacParams['NCS'] = line if line.startswith(' bref '): - RefmacParams['BREF']=line + RefmacParams['BREF'] = line if line.startswith('ncyc'): RefmacParams['Ncycles'] = line.split()[1] if line.startswith('weight'): - RefmacParams['MATRIX_WEIGHT'] = line.split()[len(line.split())-1] + RefmacParams['MATRIX_WEIGHT'] = line.split()[ + len(line.split())-1] if line.startswith('TWIN'): - RefmacParams['TWIN']=line - elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'refmac.csh')): - for line in open(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'refmac.csh')): + RefmacParams['TWIN'] = line + elif os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'refmac.csh')): + for line in open(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'refmac.csh')): if line.startswith('refi tlsc'): - RefmacParams['TLS']=line + RefmacParams['TLS'] = line if line.startswith('TLSO'): - RefmacParams['TLSADD']=line + RefmacParams['TLSADD'] = line if line.startswith('NCSR LOCAL'): - RefmacParams['NCS']=line + RefmacParams['NCS'] = line if line.startswith(' bref '): - RefmacParams['BREF']=line + RefmacParams['BREF'] = line if line.startswith('ncyc'): RefmacParams['Ncycles'] = line.split()[1] if line.startswith('weight'): - RefmacParams['MATRIX_WEIGHT'] = line.split()[len(line.split())-1] + RefmacParams['MATRIX_WEIGHT'] = line.split()[ + len(line.split())-1] if line.startswith('TWIN'): - RefmacParams['TWIN']=line + RefmacParams['TWIN'] = line return RefmacParams def GetRefinementHistory(self): -# RefinementHistory='' + # RefinementHistory='' RefinementCycle = [] - RcrystList=[] - RfreeList=[] + RcrystList = [] + RfreeList = [] found = False - for item in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): - if item.startswith(os.path.join(self.ProjectPath,self.xtalID,'Refine_')): - print item[item.rfind('_')+1:] - RefinementCycle.append(int(item[item.rfind('_')+1:])) - found = True + for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): + if item.startswith(os.path.join(self.ProjectPath, self.xtalID, 'Refine_')): + print item[item.rfind('_')+1:] + RefinementCycle.append(int(item[item.rfind('_')+1:])) + found = True if found: for cycle in sorted(RefinementCycle): -# for cycle in RefinementCycle: -# Rcryst=0 -# Rfree=0 -# LigandCC=0 + # for cycle in RefinementCycle: + # Rcryst=0 + # Rfree=0 + # LigandCC=0 try: - found_Rcryst=False - found_Rfree=False - newestPDB = max(glob.iglob(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/refine_'+str(cycle)+'.pdb'), key=os.path.getctime) + found_Rcryst = False + found_Rfree = False + newestPDB = max(glob.iglob(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str( + cycle)+'/refine_'+str(cycle)+'.pdb'), key=os.path.getctime) for line in open(newestPDB): if line.startswith('REMARK 3 R VALUE (WORKING + TEST SET) :'): Rcryst = line.split()[9] RcrystList.append(float(Rcryst)) - found_Rcryst=True + found_Rcryst = True if line.startswith('REMARK 3 FREE R VALUE :'): Rfree = line.split()[6] RfreeList.append(float(Rfree)) - found_Rfree=True + found_Rfree = True if not found_Rcryst: RcrystList.append(0) if not found_Rfree: @@ -300,23 +309,20 @@ def GetRefinementHistory(self): # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' else: RefinementCycle = [0] - RcrystList=[0] - RfreeList=[0] - print RefinementCycle,RcrystList,RfreeList - return(sorted(RefinementCycle),RcrystList,RfreeList) - - - + RcrystList = [0] + RfreeList = [0] + print RefinementCycle, RcrystList, RfreeList + return(sorted(RefinementCycle), RcrystList, RfreeList) class Refine(object): - def __init__(self,ProjectPath,xtalID,compoundID,datasource): + def __init__(self, ProjectPath, xtalID, compoundID, datasource): self.ProjectPath = ProjectPath self.xtalID = xtalID self.compoundID = compoundID self.prefix = 'refine' - self.datasource=datasource + self.datasource = datasource self.error = False self.Logfile = None @@ -326,21 +332,20 @@ def GetSerial(self): # if yes: create a folder Refine_ temp = [] found = 0 - if os.path.isdir(os.path.join(self.ProjectPath,self.xtalID)): - for item in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): - if item.startswith(os.path.join(self.ProjectPath,self.xtalID,'Refine_')): - print int(item[item.rfind('_')+1:]) - temp.append(int(item[item.rfind('_')+1:])) - found = 1 + if os.path.isdir(os.path.join(self.ProjectPath, self.xtalID)): + for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): + if item.startswith(os.path.join(self.ProjectPath, self.xtalID, 'Refine_')): + print int(item[item.rfind('_')+1:]) + temp.append(int(item[item.rfind('_')+1:])) + found = 1 if found: Serial = max(temp) + 1 else: - Serial=1 + Serial = 1 return Serial - - def make_covalent_link(self,covLinkAtomSpec,Logfile): - residuesToModify = ['CYS','SER'] + def make_covalent_link(self, covLinkAtomSpec, Logfile): + residuesToModify = ['CYS', 'SER'] atom1 = covLinkAtomSpec[1][5] atom2 = covLinkAtomSpec[2][5] @@ -348,90 +353,106 @@ def make_covalent_link(self,covLinkAtomSpec,Logfile): residue_2 = covLinkAtomSpec[4] if residue_2 in residuesToModify: - bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' %(residue_1,self.compoundID,atom1,residue_2,atom2) + bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' % ( + residue_1, self.compoundID, atom1, residue_2, atom2) else: - bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' % (residue_2, self.compoundID, atom2, residue_1, atom1) + bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' % ( + residue_2, self.compoundID, atom2, residue_1, atom1) - os.chdir(os.path.join(self.ProjectPath,self.xtalID)) - f = open('covalent_bond.txt','w') + os.chdir(os.path.join(self.ProjectPath, self.xtalID)) + f = open('covalent_bond.txt', 'w') f.write(bond_text) f.close() # seems somewhat unncessary, but acedrg does not like some certain descriptions generated by phenix.elbow - os.system('acedrg -c %s.cif -o %s_acedrg' %(self.compoundID,self.compoundID)) + os.system('acedrg -c %s.cif -o %s_acedrg' % + (self.compoundID, self.compoundID)) - os.system('acedrg -L covalent_bond.txt -o %s' %self.compoundID) + os.system('acedrg -L covalent_bond.txt -o %s' % self.compoundID) - if os.path.isfile('%s_link.cif' %self.compoundID): - Logfile.insert('succefully created link file %s_link.cif' %self.compoundID) - os.system('/bin/rm %s.cif' %self.compoundID) - os.system('ln -s %s_link.cif %s.cif' %(self.compoundID,self.compoundID)) + if os.path.isfile('%s_link.cif' % self.compoundID): + Logfile.insert( + 'succefully created link file %s_link.cif' % self.compoundID) + os.system('/bin/rm %s.cif' % self.compoundID) + os.system('ln -s %s_link.cif %s.cif' % + (self.compoundID, self.compoundID)) else: - Logfile.error('could not create linkfile; please check logs in %s/%s' %(self.ProjectPath,self.xtalID)) + Logfile.error('could not create linkfile; please check logs in %s/%s' % + (self.ProjectPath, self.xtalID)) - def get_hklin_hklout(self,Serial): + def get_hklin_hklout(self, Serial): ####################################################### # HKLIN & HKLOUT hklin = None hklout = None - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz')): - hklin=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz') + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'.free.mtz')): + hklin = os.path.join( + self.ProjectPath, self.xtalID, self.xtalID+'.free.mtz') # elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): # RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') else: - self.Logfile.error('%s: cannot find HKLIN for refinement' %self.xtalID) + self.Logfile.error( + '%s: cannot find HKLIN for refinement' % self.xtalID) self.error = True - hklout=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz') + hklout = os.path.join(self.ProjectPath, self.xtalID, + 'Refine_'+Serial, 'refine_'+Serial+'.mtz') return hklin, hklout - def get_xyzin_xyzout(self,Serial): + def get_xyzin_xyzout(self, Serial): ####################################################### # XYZIN & XYZOUT xyzin = None xyzout = None - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb')): - xyzin = os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb') - xyzout = os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.pdb') - elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'in.pdb')): - xyzin = os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'in.pdb') + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'in.pdb')): + xyzin = os.path.join( + self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'in.pdb') + xyzout = os.path.join( + self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'refine_'+Serial+'.pdb') + elif os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'in.pdb')): + xyzin = os.path.join(self.ProjectPath, self.xtalID, + 'cootOut', 'Refine_'+str(Serial), 'in.pdb') else: - self.Logfile.error('%s: cannot find XYZIN for refinement' %self.xtalID) + self.Logfile.error( + '%s: cannot find XYZIN for refinement' % self.xtalID) self.error = True return xyzin, xyzout - def get_libin_libout(self,Serial): + def get_libin_libout(self, Serial): ####################################################### # LIBIN & LIBOUT libin = None libout = None - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif')): - libin = os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif') - libout = os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.cif') + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.compoundID+'.cif')): + libin = os.path.join( + self.ProjectPath, self.xtalID, self.compoundID+'.cif') + libout = os.path.join( + self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'refine_'+Serial+'.cif') else: - self.Logfile.error('%s: cannot find CIF file for refinement' %self.xtalID) + self.Logfile.error( + '%s: cannot find CIF file for refinement' % self.xtalID) self.error = True return libin, libout def write_refinement_in_progress(self): ####################################################### # we write 'REFINEMENT_IN_PROGRESS' immediately to avoid unncessary refiment - os.chdir(os.path.join(self.ProjectPath,self.xtalID)) + os.chdir(os.path.join(self.ProjectPath, self.xtalID)) os.system('touch REFINEMENT_IN_PROGRESS') def clean_up_before_refinement(self): ####################################################### # clean up! # and remove all files which will be re-created by current refinement cycle - os.chdir(os.path.join(self.ProjectPath,self.xtalID)) + os.chdir(os.path.join(self.ProjectPath, self.xtalID)) os.system('/bin/rm refine.pdb refine.mtz refine.split.bound-state.pdb validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log') - def get_shebang(self,program,qsub): + def get_shebang(self, program, qsub): cmd = '#!'+os.getenv('SHELL')+'\n' if qsub: - cmd += '#PBS -joe -N xce_%s\n' %program + cmd += '#PBS -joe -N xce_%s\n' % program return cmd - def load_modules(self,cmd): + def load_modules(self, cmd): ####################################################### # PHENIX stuff (if working at DLS) if os.getcwd().startswith('/dls'): @@ -439,49 +460,49 @@ def load_modules(self,cmd): cmd += 'module load buster\n' return cmd - def get_source_line(self,cmd): + def get_source_line(self, cmd): if 'bash' in os.getenv('SHELL'): - cmd += 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' + cmd += 'export XChemExplorer_DIR="' + \ + os.getenv('XChemExplorer_DIR')+'"\n' elif 'csh' in os.getenv('SHELL'): - cmd += 'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n' + cmd += 'setenv XChemExplorer_DIR ' + \ + os.getenv('XChemExplorer_DIR')+'\n' return cmd - def set_refinement_status(self,cmd): + def set_refinement_status(self, cmd): cmd += ('$CCP4/bin/ccp4-python ' ' $XChemExplorer_DIR/helpers/update_status_flag.py ' - + self.datasource + ' ' + self.xtalID + ' RefinementStatus running\n') + + self.datasource + ' ' + self.xtalID + ' RefinementStatus running\n') return cmd - def add_buster_command(self,cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water,refine_ligand_occupancy,ignore_sanity_check): + def add_buster_command(self, cmd, xyzin, hklin, libin, Serial, anisotropic_Bfactor, update_water, refine_ligand_occupancy, ignore_sanity_check): cmd += ( 'refine ' - ' -p %s' %xyzin + - ' -m %s' %hklin + - ' -l %s' %libin + + ' -p %s' % xyzin + + ' -m %s' % hklin + + ' -l %s' % libin + ' -autoncs' + anisotropic_Bfactor + update_water + refine_ligand_occupancy + ignore_sanity_check + - ' -d Refine_%s\n' %str(Serial) + ' -d Refine_%s\n' % str(Serial) ) return cmd - def run_giant_score_model(self,cmd,cycle): + def run_giant_score_model(self, cmd, cycle): old_ccp4 = '' if os.path.isfile('/dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh'): # giant.score_model does not work with ccp4 7.1-000 old_ccp4 = 'source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-model.pdb')): - cmd += ( 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+cycle+'\n' + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'-pandda-model.pdb')): + cmd += ('cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+cycle+'\n' + old_ccp4 + - 'giant.score_model ' - ' pdb1=../%s-pandda-model.pdb ' %self.xtalID + - ' mtz1=../dimple.mtz ' - ' pdb2=refine.pdb ' - ' mtz2=refine.mtz\n' ) + 'giant.score_model ' + ' pdb1=../%s-pandda-model.pdb ' % self.xtalID + + ' mtz1=../dimple.mtz ' + ' pdb2=refine.pdb ' + ' mtz2=refine.mtz\n') return cmd - - - def add_validation(self,cmd,cycle,program): + def add_validation(self, cmd, cycle, program): buster_report = '' if program == 'refmac': Serial = '_' + cycle @@ -492,28 +513,28 @@ def add_validation(self,cmd,cycle,program): buster_report += 'corr -p refine.pdb -m refine.mtz -F 2FOFCWT -P PH2FOFCWT\n' buster_report += 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' buster_report += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' - buster_report += 'buster-report -d Refine_%s\n' %cycle + buster_report += 'buster-report -d Refine_%s\n' % cycle cmd += ( '\n' + buster_report + 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' - 'ln -s ./Refine_%s/refine%s.pdb refine.pdb\n' %(cycle,Serial)+ - 'ln -s ./Refine_%s/refine%s.mtz refine.mtz\n' %(cycle,Serial)+ + 'ln -s ./Refine_%s/refine%s.pdb refine.pdb\n' % (cycle, Serial) + + 'ln -s ./Refine_%s/refine%s.mtz refine.mtz\n' % (cycle, Serial) + 'ln -s refine.pdb refine.split.bound-state.pdb\n' '\n' - 'phenix.molprobity refine%s.pdb refine%s.mtz\n' %(Serial,Serial)+ + 'phenix.molprobity refine%s.pdb refine%s.mtz\n' % (Serial, Serial) + '/bin/mv molprobity.out refine_molprobity.log\n' - 'mmtbx.validate_ligands refine%s.pdb refine%s.mtz LIG > validate_ligands.txt\n' %(Serial,Serial)+ + 'mmtbx.validate_ligands refine%s.pdb refine%s.mtz LIG > validate_ligands.txt\n' % (Serial, Serial) + '\n' -# 'ln -s Refine_%s/validate_ligands.txt .\n' %cycle+ -# 'ln -s Refine_%s/refine_molprobity.log .\n' %cycle+ + # 'ln -s Refine_%s/validate_ligands.txt .\n' %cycle+ + # 'ln -s Refine_%s/refine_molprobity.log .\n' %cycle+ 'mmtbx.validation_summary refine.pdb > validation_summary.txt\n' '\n' ) return cmd - def calculate_maps(self,cmd,program): + def calculate_maps(self, cmd, program): if program == 'refmac': FWT = 'FWT' PHWT = 'PHWT' @@ -528,31 +549,31 @@ def calculate_maps(self,cmd,program): 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' '\n' 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' - ' labin F1=%s PHI=%s\n' %(FWT,PHWT) + + ' labin F1=%s PHI=%s\n' % (FWT, PHWT) + ' grid samp 4.5\n' 'EOF\n' '\n' -# 'mapmask mapin 2fofc_asu.map xyzin refine.pdb mapout 2fofc.map << EOF\n' -# ' border 5\n' -# 'EOF\n' -# '\n' -# '/bin/rm 2fofc_asu.map\n' -# '\n' + # 'mapmask mapin 2fofc_asu.map xyzin refine.pdb mapout 2fofc.map << EOF\n' + # ' border 5\n' + # 'EOF\n' + # '\n' + # '/bin/rm 2fofc_asu.map\n' + # '\n' 'fft hklin refine.mtz mapout fofc.map << EOF\n' - ' labin F1=%s PHI=%s\n' %(DELFWT,PHDELWT) + + ' labin F1=%s PHI=%s\n' % (DELFWT, PHDELWT) + ' grid samp 4.5\n' 'EOF\n' '\n' -# 'mapmask mapin fofc_asu.map xyzin refine.pdb mapout fofc.map << EOF\n' -# ' border 5\n' -# 'EOF\n' -# '\n' -# '/bin/rm fofc_asu.map\n' + # 'mapmask mapin fofc_asu.map xyzin refine.pdb mapout fofc.map << EOF\n' + # ' border 5\n' + # 'EOF\n' + # '\n' + # '/bin/rm fofc_asu.map\n' '\n' ) return cmd - def run_edstats(self,cmd,resh,resl): + def run_edstats(self, cmd, resh, resl): cmd += ( '\n' 'edstats XYZIN refine.pdb MAPIN1 2fofc.map MAPIN2 fofc.map OUT refine.edstats << eof\n' @@ -563,8 +584,7 @@ def run_edstats(self,cmd,resh,resl): ) return cmd - - def update_database(self,cmd,Serial): + def update_database(self, cmd, Serial): date = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] user = getpass.getuser() ccp4_module = '' # need to source again, because giant.score_model still needs outdated version which does not have gemmi @@ -574,39 +594,43 @@ def update_database(self,cmd,Serial): + ccp4_module + '\n' '$CCP4/bin/ccp4-python ' - +os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+ - ' %s %s %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial),user,date) ) - cmd += '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' %(self.ProjectPath,self.xtalID) + + os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_data_source_after_refinement.py') + + ' %s %s %s %s %s %s\n' % (self.datasource, self.xtalID, self.ProjectPath, os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial), user, date)) + cmd += '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' % ( + self.ProjectPath, self.xtalID) return cmd - def write_refinement_script(self,cmd,program): - os.chdir(os.path.join(self.ProjectPath,self.xtalID)) - f = open(program + '.sh','w') + def write_refinement_script(self, cmd, program): + os.chdir(os.path.join(self.ProjectPath, self.xtalID)) + f = open(program + '.sh', 'w') f.write(cmd) f.close() - def run_script(self,program,external_software): - os.chdir(os.path.join(self.ProjectPath,self.xtalID)) + def run_script(self, program, external_software): + os.chdir(os.path.join(self.ProjectPath, self.xtalID)) if external_software['qsub'] and os.path.isdir('/dls'): - self.Logfile.insert('starting refinement with command: qsub -P labxchem -q medium.q %s.sh' %program) - os.system("qsub -P labxchem -q medium.q %s.sh" %program) + self.Logfile.insert( + 'starting refinement with command: qsub -P labxchem -q medium.q %s.sh' % program) + os.system("qsub -P labxchem -q medium.q %s.sh" % program) elif external_software['qsub'] and not os.path.isdir('/dls'): - self.Logfile.insert('starting refinement with command: qsub %s.sh' %program) - os.system("qsub %s.sh" %program) + self.Logfile.insert( + 'starting refinement with command: qsub %s.sh' % program) + os.system("qsub %s.sh" % program) elif external_software['qsub_remote'] != '': Logfile.insert('starting refinement on remote cluster') - remote_command=external_software['qsub_remote'].replace('qsub','cd %s; qsub' %os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) - self.Logfile.insert('starting refinement with command: %s' %remote_command) - os.system('%s -P labxchem refmac.csh' %remote_command) + remote_command = external_software['qsub_remote'].replace('qsub', 'cd %s; qsub' % os.path.join( + self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) + self.Logfile.insert( + 'starting refinement with command: %s' % remote_command) + os.system('%s -P labxchem refmac.csh' % remote_command) else: - self.Logfile.insert('starting refinement with command: ./%s.sh &' %program) - os.system('chmod +x %s.sh' %program) - os.system('./%s.sh &' %program) - + self.Logfile.insert( + 'starting refinement with command: ./%s.sh &' % program) + os.system('chmod +x %s.sh' % program) + os.system('./%s.sh &' % program) - - def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtomSpec): + def RunBuster(self, Serial, RefmacParams, external_software, xce_logfile, covLinkAtomSpec): if RefmacParams == None: anisotropic_Bfactor = ' -M ADP ' @@ -627,19 +651,19 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom else: ignore_sanity_check = '' - self.error = False if os.path.isfile(xce_logfile): - self.Logfile=XChemLog.updateLog(xce_logfile) - Serial=str(Serial) + self.Logfile = XChemLog.updateLog(xce_logfile) + Serial = str(Serial) if covLinkAtomSpec is not None: - self.make_covalent_link(covLinkAtomSpec,self.Logfile) + self.make_covalent_link(covLinkAtomSpec, self.Logfile) # first check if refinement is ongoing and exit if yes - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'REFINEMENT_IN_PROGRESS')): - self.Logfile.insert('cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' %self.xtalID) + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'REFINEMENT_IN_PROGRESS')): + self.Logfile.insert( + 'cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' % self.xtalID) return None hklin, hklout = self.get_hklin_hklout(Serial) @@ -661,7 +685,7 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom self.write_refinement_in_progress() - cmd = self.get_shebang('buster',external_software['qsub']) + cmd = self.get_shebang('buster', external_software['qsub']) cmd = self.load_modules(cmd) @@ -669,36 +693,41 @@ def RunBuster(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom cmd = self.set_refinement_status(cmd) - cmd = self.add_buster_command(cmd,xyzin,hklin,libin,Serial,anisotropic_Bfactor,update_water,refine_ligand_occupancy,ignore_sanity_check) + cmd = self.add_buster_command(cmd, xyzin, hklin, libin, Serial, anisotropic_Bfactor, + update_water, refine_ligand_occupancy, ignore_sanity_check) - cmd = self.add_validation(cmd,Serial,'buster') + cmd = self.add_validation(cmd, Serial, 'buster') - cmd = self.run_giant_score_model(cmd,Serial) + cmd = self.run_giant_score_model(cmd, Serial) - cmd = self.calculate_maps(cmd,'buster') + cmd = self.calculate_maps(cmd, 'buster') - cmd = self.run_edstats(cmd,resh,resl) + cmd = self.run_edstats(cmd, resh, resl) - cmd = self.update_database(cmd,Serial) + cmd = self.update_database(cmd, Serial) if self.error: - self.Logfile.error('%s: cannot start refinement; check error message above' %self.xtalID) + self.Logfile.error( + '%s: cannot start refinement; check error message above' % self.xtalID) else: - self.Logfile.insert('%s: writing buster.sh file in %s' %(self.xtalID,os.path.join(self.ProjectPath,self.xtalID))) - self.write_refinement_script(cmd,'buster') - self.Logfile.insert('%s: starting refinement...' %self.xtalID) - self.run_script('buster',external_software) + self.Logfile.insert('%s: writing buster.sh file in %s' % ( + self.xtalID, os.path.join(self.ProjectPath, self.xtalID))) + self.write_refinement_script(cmd, 'buster') + self.Logfile.insert('%s: starting refinement...' % self.xtalID) + self.run_script('buster', external_software) - def prepare_gelly_dat(self,ligand_info): + def prepare_gelly_dat(self, ligand_info): found_ligand = False gelly = 'NOTE BUSTER_SET Ligand = ' - for n,lig in enumerate(ligand_info): + for n, lig in enumerate(ligand_info): resseq = lig[1] chain = lig[2] if n == 0: - gelly += '{ %s|%s }' %(chain.replace(' ',''),resseq.replace(' ','')) + gelly += '{ %s|%s }' % (chain.replace(' ', ''), + resseq.replace(' ', '')) else: - gelly += ' + { %s|%s }' %(chain.replace(' ',''),resseq.replace(' ','')) + gelly += ' + { %s|%s }' % (chain.replace(' ', ''), + resseq.replace(' ', '')) found_ligand = True if '{' in gelly: gelly += '\n' @@ -707,83 +736,95 @@ def prepare_gelly_dat(self,ligand_info): 'NOTE BUSTER_CONSTANT OCC NotLigand \n' 'NOTE BUSTER_COMBINE OCC Ligand \n' 'NOTE BUSTER_COMBINE B Ligand \n' - ) - os.chdir(os.path.join(self.ProjectPath,self.xtalID)) - f = open('gelly.dat','w') + ) + os.chdir(os.path.join(self.ProjectPath, self.xtalID)) + f = open('gelly.dat', 'w') f.write(gelly) f.close() return found_ligand + def RunRefmac(self, Serial, RefmacParams, external_software, xce_logfile, covLinkAtomSpec): - def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtomSpec): - - if os.path.isfile(xce_logfile): Logfile=XChemLog.updateLog(xce_logfile) - Serial=str(Serial) + if os.path.isfile(xce_logfile): + Logfile = XChemLog.updateLog(xce_logfile) + Serial = str(Serial) if covLinkAtomSpec is not None: - self.make_covalent_link(covLinkAtomSpec,Logfile) + self.make_covalent_link(covLinkAtomSpec, Logfile) # first check if refinement is ongoing and exit if yes - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'REFINEMENT_IN_PROGRESS')): -# coot.info_dialog('*** REFINEMENT IN PROGRESS ***') - Logfile.insert('cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' %self.xtalID) + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'REFINEMENT_IN_PROGRESS')): + # coot.info_dialog('*** REFINEMENT IN PROGRESS ***') + Logfile.insert( + 'cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' % self.xtalID) return None ####################################################### # HKLIN & HKLOUT - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz')): - RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz \\\n') + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'.free.mtz')): + RefmacParams['HKLIN'] = 'HKLIN '+os.path.join( + self.ProjectPath, self.xtalID, self.xtalID+'.free.mtz \\\n') # elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): # RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') else: - Logfile.error('%s: cannot find HKLIN for refinement; aborting...' %self.xtalID) + Logfile.error( + '%s: cannot find HKLIN for refinement; aborting...' % self.xtalID) return None - RefmacParams['HKLOUT']='HKLOUT '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz \\\n') + RefmacParams['HKLOUT'] = 'HKLOUT '+os.path.join( + self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'refine_'+Serial+'.mtz \\\n') ####################################################### # XYZIN & XYZOUT - RefmacParams['XYZIN']='XYZIN '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb \\\n') - RefmacParams['XYZOUT']='XYZOUT '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.pdb \\\n') + RefmacParams['XYZIN'] = 'XYZIN ' + \ + os.path.join(self.ProjectPath, self.xtalID, + 'Refine_'+Serial, 'in.pdb \\\n') + RefmacParams['XYZOUT'] = 'XYZOUT '+os.path.join( + self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'refine_'+Serial+'.pdb \\\n') ####################################################### # LIBIN & LIBOUT - found_cif=False - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif')): - RefmacParams['LIBIN']='LIBIN '+self.ProjectPath+'/'+self.xtalID+'/'+self.compoundID+'.cif \\\n' - RefmacParams['LIBOUT']='LIBOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine_'+Serial+'.cif \\\n' + found_cif = False + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.compoundID+'.cif')): + RefmacParams['LIBIN'] = 'LIBIN '+self.ProjectPath + \ + '/'+self.xtalID+'/'+self.compoundID+'.cif \\\n' + RefmacParams['LIBOUT'] = 'LIBOUT '+self.ProjectPath+'/' + \ + self.xtalID+'/Refine_'+Serial+'/refine_'+Serial+'.cif \\\n' ####################################################### # TLSIN & TLSOUT - findTLS='\n' - TLSphenix='' + findTLS = '\n' + TLSphenix = '' if RefmacParams['TLS'].startswith('refi'): if external_software['phenix.find_tls_groups']: - findTLS=os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','phenix_find_TLS_groups.py')+' in.pdb\n' - RefmacParams['TLSIN']='TLSIN '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refmac.tls \\\n' - RefmacParams['TLSOUT']='TLSOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine.tls \\\n' - TLSphenix=' phenix.tls ' + findTLS = os.path.join(os.getenv( + 'XChemExplorer_DIR'), 'helpers', 'phenix_find_TLS_groups.py')+' in.pdb\n' + RefmacParams['TLSIN'] = 'TLSIN '+self.ProjectPath + \ + '/'+self.xtalID+'/Refine_'+Serial+'/refmac.tls \\\n' + RefmacParams['TLSOUT'] = 'TLSOUT '+self.ProjectPath + \ + '/'+self.xtalID+'/Refine_'+Serial+'/refine.tls \\\n' + TLSphenix = ' phenix.tls ' else: - RefmacParams['TLS']='\n' + RefmacParams['TLS'] = '\n' print '==> XCE: assembling refmac.csh' ####################################################### # we write 'REFINEMENT_IN_PROGRESS' immediately to avoid unncessary refiment - os.chdir(os.path.join(self.ProjectPath,self.xtalID)) + os.chdir(os.path.join(self.ProjectPath, self.xtalID)) os.system('touch REFINEMENT_IN_PROGRESS') ####################################################### # Database updates: # no DB will be specified when a reference model is built and refined - refinementStatus='' - updateDB='' + refinementStatus = '' + updateDB = '' date = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] user = getpass.getuser() if os.path.isfile(self.datasource): - refinementStatus='$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(self.datasource,self.xtalID,'RefinementStatus','running') - updateDB = ( '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+ - ' %s %s %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial),user,date) ) - + refinementStatus = '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' % ( + self.datasource, self.xtalID, 'RefinementStatus', 'running') + updateDB = ('$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_data_source_after_refinement.py') + + ' %s %s %s %s %s %s\n' % (self.datasource, self.xtalID, self.ProjectPath, os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial), user, date)) ####################################################### # clean up! @@ -791,77 +832,83 @@ def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom os.system('/bin/rm refine.pdb refine.mtz refine.split.bound-state.pdb validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log') if external_software['qsub']: - pbs_line='#PBS -joe -N XCE_refmac\n' + pbs_line = '#PBS -joe -N XCE_refmac\n' else: - pbs_line='\n' + pbs_line = '\n' ####################################################### # weight if str(RefmacParams['MATRIX_WEIGHT']).lower() == 'auto': - weight='weight AUTO\n' + weight = 'weight AUTO\n' else: - weight='weight matrix '+str(RefmacParams['MATRIX_WEIGHT'])+'\n' + weight = 'weight matrix '+str(RefmacParams['MATRIX_WEIGHT'])+'\n' ####################################################### # PHENIX stuff (if working at DLS) - module_load='' + module_load = '' if os.getcwd().startswith('/dls'): - module_load='module load phenix\n' + module_load = 'module load phenix\n' - source ='' + source = '' if 'bash' in os.getenv('SHELL'): source = ( - 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' + 'export XChemExplorer_DIR="' + + os.getenv('XChemExplorer_DIR')+'"\n' '\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-sh')+'\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' ) + 'source '+os.path.join(os.getenv('XChemExplorer_DIR'), + 'setup-scripts', 'xce.setup-sh')+'\n' + 'source '+os.path.join(os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-sh')+'\n') elif 'csh' in os.getenv('SHELL'): source = ( 'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n' '\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-csh')+'\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh')+'\n' ) - - - spider_plot='' - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-ensemble-model.pdb')): - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): - pdb_two=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-ensemble-model.pdb') - mtz_two=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz') - pdb_one=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+str(Serial),'refine_'+str(Serial)+'.pdb') - mtz_one=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+str(Serial),'refine_'+str(Serial)+'.mtz') + 'source '+os.path.join(os.getenv('XChemExplorer_DIR'), + 'setup-scripts', 'xce.setup-csh')+'\n' + 'source '+os.path.join(os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-csh')+'\n') + + spider_plot = '' + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'-ensemble-model.pdb')): + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'-pandda-input.mtz')): + pdb_two = os.path.join( + self.ProjectPath, self.xtalID, self.xtalID+'-ensemble-model.pdb') + mtz_two = os.path.join( + self.ProjectPath, self.xtalID, self.xtalID+'-pandda-input.mtz') + pdb_one = os.path.join( + self.ProjectPath, self.xtalID, 'Refine_'+str(Serial), 'refine_'+str(Serial)+'.pdb') + mtz_one = os.path.join( + self.ProjectPath, self.xtalID, 'Refine_'+str(Serial), 'refine_'+str(Serial)+'.mtz') spider_plot = ( - 'cd ' + self.ProjectPath + '/' + self.xtalID + '/Refine_' + Serial + '\n' - '\n' -# 'giant.merge_conformations ' -# ' major=../refine.split.ground-state.pdb' -# ' minor=../refine.split.bound-state.pdb' -# ' reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0\n' - 'giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' % (pdb_one, mtz_one, pdb_two, mtz_two) + 'cd ' + self.ProjectPath + '/' + self.xtalID + '/Refine_' + Serial + '\n' + '\n' + # 'giant.merge_conformations ' + # ' major=../refine.split.ground-state.pdb' + # ' minor=../refine.split.bound-state.pdb' + # ' reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0\n' + 'giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' % ( + pdb_one, mtz_one, pdb_two, mtz_two) ) - refmacCmds = ( '#!'+os.getenv('SHELL')+'\n' - +pbs_line+ + + pbs_line + '\n' + module_load + '\n' - +source+ + + source + 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'\n' '\n' - +refinementStatus+ + + refinementStatus + '\n' - +findTLS+ + + findTLS + 'refmac5 ' - +RefmacParams['HKLIN'] - +RefmacParams['HKLOUT'] - +RefmacParams['XYZIN'] - +RefmacParams['XYZOUT'] - +RefmacParams['LIBIN'] - +RefmacParams['LIBOUT'] - +RefmacParams['TLSIN'] - +RefmacParams['TLSOUT']+ + + RefmacParams['HKLIN'] + + RefmacParams['HKLOUT'] + + RefmacParams['XYZIN'] + + RefmacParams['XYZOUT'] + + RefmacParams['LIBIN'] + + RefmacParams['LIBOUT'] + + RefmacParams['TLSIN'] + + RefmacParams['TLSOUT'] + ' << EOF > refmac.log\n' 'make -\n' ' hydrogen ALL -\n' @@ -873,21 +920,21 @@ def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom ' sugar YES -\n' ' connectivity NO -\n' ' link NO\n' - +RefmacParams['NCS']+ + + RefmacParams['NCS'] + 'refi -\n' ' type REST -\n' ' resi MLKF -\n' ' meth CGMAT -\n' - +RefmacParams['BREF'] - +RefmacParams['TLS'] - +RefmacParams['TWIN']+ + + RefmacParams['BREF'] + + RefmacParams['TLS'] + + RefmacParams['TWIN'] + 'ncyc '+RefmacParams['NCYCLES']+'\n' 'scal -\n' ' type SIMP -\n' ' LSSC -\n' ' ANISO -\n' ' EXPE\n' - +weight+ + + weight + 'solvent YES\n' 'monitor MEDIUM -\n' ' torsion 10.0 -\n' @@ -901,23 +948,23 @@ def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom ' ncsr 10.0\n' 'labin FP=F SIGFP=SIGF FREE=FreeR_flag\n' 'labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM\n' - +RefmacParams['TLSADD']+'\n' + + RefmacParams['TLSADD']+'\n' 'DNAME '+self.xtalID+'\n' 'END\n' 'EOF\n' '\n' - 'phenix.molprobity refine_%s.pdb refine_%s.mtz\n' %(Serial,Serial)+ + 'phenix.molprobity refine_%s.pdb refine_%s.mtz\n' % (Serial, Serial) + '/bin/mv molprobity.out refine_molprobity.log\n' - 'mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n' %(Serial,Serial)+ + 'mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n' % (Serial, Serial) + 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' - '#ln -s %s/%s/Refine_%s/refine_%s.pdb refine.pdb\n' %(self.ProjectPath,self.xtalID,Serial,Serial)+ - '#ln -s %s/%s/Refine_%s/refine_%s.mtz refine.mtz\n' %(self.ProjectPath,self.xtalID,Serial,Serial)+ - 'ln -s ./Refine_%s/refine_%s.pdb refine.pdb\n' %(Serial,Serial)+ - 'ln -s ./Refine_%s/refine_%s.mtz refine.mtz\n' %(Serial,Serial)+ + '#ln -s %s/%s/Refine_%s/refine_%s.pdb refine.pdb\n' % (self.ProjectPath, self.xtalID, Serial, Serial) + + '#ln -s %s/%s/Refine_%s/refine_%s.mtz refine.mtz\n' % (self.ProjectPath, self.xtalID, Serial, Serial) + + 'ln -s ./Refine_%s/refine_%s.pdb refine.pdb\n' % (Serial, Serial) + + 'ln -s ./Refine_%s/refine_%s.mtz refine.mtz\n' % (Serial, Serial) + 'ln -s refine.pdb refine.split.bound-state.pdb\n' '\n' - 'ln -s Refine_%s/validate_ligands.txt .\n' %Serial+ - 'ln -s Refine_%s/refine_molprobity.log .\n' %Serial+ + 'ln -s Refine_%s/validate_ligands.txt .\n' % Serial + + 'ln -s Refine_%s/refine_molprobity.log .\n' % Serial + 'mmtbx.validation_summary refine.pdb > validation_summary.txt\n' '\n' 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' @@ -927,58 +974,67 @@ def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile,covLinkAtom 'fft hklin refine.mtz mapout fofc.map << EOF\n' 'labin F1=DELFWT PHI=PHDELWT\n' 'EOF\n' - '\n' - +updateDB+ '\n' - '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' %(self.ProjectPath,self.xtalID)+ + + updateDB + + '\n' + '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' % (self.ProjectPath, self.xtalID) + '\n' 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'\n' '\n' - +spider_plot+ + + spider_plot + '\n' - ) + ) - if os.path.isfile(xce_logfile): Logfile.insert('writing refinement shell script to'+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac.csh')) - cmd = open(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac.csh'),'w') + if os.path.isfile(xce_logfile): + Logfile.insert('writing refinement shell script to'+os.path.join( + self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'refmac.csh')) + cmd = open(os.path.join(self.ProjectPath, self.xtalID, + 'Refine_'+Serial, 'refmac.csh'), 'w') cmd.write(refmacCmds) cmd.close() - os.chdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) + os.chdir(os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial)) # os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) - if os.path.isfile(xce_logfile): Logfile.insert('changing directory to %s' %(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial))) + if os.path.isfile(xce_logfile): + Logfile.insert('changing directory to %s' % ( + os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial))) if external_software['qsub_remote'] != '': print os.getenv('LD_LIBRARY_PATH') - if os.path.isfile(xce_logfile): Logfile.insert('starting refinement on remote cluster') - remote_command=external_software['qsub_remote'].replace("qsub'",'cd %s; qsub' %os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) - os.system("%s -P labxchem -q medium.q refmac.csh'" %remote_command) - print '%s -P labxchem -q medium.q refmac.csh' %remote_command + if os.path.isfile(xce_logfile): + Logfile.insert('starting refinement on remote cluster') + remote_command = external_software['qsub_remote'].replace( + "qsub'", 'cd %s; qsub' % os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial)) + os.system("%s -P labxchem -q medium.q refmac.csh'" % + remote_command) + print '%s -P labxchem -q medium.q refmac.csh' % remote_command elif external_software['qsub'] and os.path.isdir('/dls'): - Logfile.insert('starting refinement on cluster with command "qsub -P labxchem -q medium.q refmac.csh"') + Logfile.insert( + 'starting refinement on cluster with command "qsub -P labxchem -q medium.q refmac.csh"') os.system("qsub -P labxchem -q medium.q refmac.csh") elif external_software['qsub'] and not os.path.isdir('/dls'): - Logfile.insert('starting refinement on cluster with command "qsub refmac.csh"') + Logfile.insert( + 'starting refinement on cluster with command "qsub refmac.csh"') os.system("qsub refmac.csh") else: os.system('chmod +x refmac.csh') - if os.path.isfile(xce_logfile): Logfile.insert('starting refinement on local machine') + if os.path.isfile(xce_logfile): + Logfile.insert('starting refinement on local machine') os.system('./refmac.csh &') - - - def RefinementParams(self,RefmacParams): - self.RefmacParams=RefmacParams + def RefinementParams(self, RefmacParams): + self.RefmacParams = RefmacParams self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) self.window.connect("delete_event", gtk.main_quit) self.window.set_border_width(10) self.window.set_title("Refmac Parameters") self.vbox = gtk.VBox() - self.hbox1=gtk.HBox() + self.hbox1 = gtk.HBox() self.hbox1.add(gtk.Label('Refine')) self.cb = gtk.combo_box_new_text() self.cb.connect("changed", self.ChooseBfacRefinement) - for item in ['isotropic','anisotropic']: + for item in ['isotropic', 'anisotropic']: self.cb.append_text(item) if 'ISOT' in self.RefmacParams['BREF']: self.cb.set_active(0) @@ -988,73 +1044,77 @@ def RefinementParams(self,RefmacParams): self.hbox1.add(gtk.Label('temperature factors')) self.vbox.add(self.hbox1) - self.hbox2=gtk.HBox() + self.hbox2 = gtk.HBox() self.hbox2.add(gtk.Label('Number of Cycles: ')) - self.Ncycles=gtk.Entry() + self.Ncycles = gtk.Entry() self.Ncycles.add_events(gtk.gdk.KEY_RELEASE_MASK) self.Ncycles.connect("key-release-event", self.on_key_release_Ncycles) self.Ncycles.set_text(self.RefmacParams['NCYCLES']) self.hbox2.add(self.Ncycles) self.vbox.add(self.hbox2) - self.hbox3=gtk.HBox() + self.hbox3 = gtk.HBox() self.hbox3.add(gtk.Label('MATRIX WEIGHT: ')) - self.MATRIX_WEIGHT=gtk.Entry() + self.MATRIX_WEIGHT = gtk.Entry() self.MATRIX_WEIGHT.add_events(gtk.gdk.KEY_RELEASE_MASK) - self.MATRIX_WEIGHT.connect("key-release-event", self.on_key_release_MATRIX_WEIGHT) + self.MATRIX_WEIGHT.connect( + "key-release-event", self.on_key_release_MATRIX_WEIGHT) self.MATRIX_WEIGHT.set_text(self.RefmacParams['MATRIX_WEIGHT']) self.hbox3.add(self.MATRIX_WEIGHT) self.vbox.add(self.hbox3) - self.TLS = gtk.CheckButton('TLS (find TLS groups with phenix.find_tls_groups)') + self.TLS = gtk.CheckButton( + 'TLS (find TLS groups with phenix.find_tls_groups)') self.TLS.connect("toggled", self.TLSCallback) - if self.RefmacParams['TLS']=='refi tlsc 10\n': self.TLS.set_active(True) - self.vbox.pack_start(self.TLS,False) + if self.RefmacParams['TLS'] == 'refi tlsc 10\n': + self.TLS.set_active(True) + self.vbox.pack_start(self.TLS, False) self.NCS = gtk.CheckButton('NCS (if applicable') self.NCS.connect("toggled", self.NCSCallback) - if self.RefmacParams['NCS']=='NCSR LOCAL\n': self.NCS.set_active(True) - self.vbox.pack_start(self.NCS,False) + if self.RefmacParams['NCS'] == 'NCSR LOCAL\n': + self.NCS.set_active(True) + self.vbox.pack_start(self.NCS, False) self.TWIN = gtk.CheckButton('Twin?') self.TWIN.connect("toggled", self.TWINCallback) - if self.RefmacParams['TWIN']=='TWIN\n': self.TWIN.set_active(True) - self.vbox.pack_start(self.TWIN,False) + if self.RefmacParams['TWIN'] == 'TWIN\n': + self.TWIN.set_active(True) + self.vbox.pack_start(self.TWIN, False) self.OKbutton = gtk.Button(label="OK") - self.OKbutton.connect("clicked",self.OK) + self.OKbutton.connect("clicked", self.OK) self.vbox.add(self.OKbutton) self.window.add(self.vbox) self.window.show_all() return self.RefmacParams - def TLSCallback(self, widget): if widget.get_active(): - self.RefmacParams['TLS']='refi tlsc 10\n' - self.RefmacParams['TLSIN']='refmac.tls\n' - self.RefmacParams['TLSOUT']='out.tls\n' - self.RefmacParams['TLSADD']='TLSO ADDU\n' + self.RefmacParams['TLS'] = 'refi tlsc 10\n' + self.RefmacParams['TLSIN'] = 'refmac.tls\n' + self.RefmacParams['TLSOUT'] = 'out.tls\n' + self.RefmacParams['TLSADD'] = 'TLSO ADDU\n' else: - self.RefmacParams['TLS']='' - self.RefmacParams['TLSIN']='' - self.RefmacParams['TLSOUT']='' - self.RefmacParams['TLSADD']='' + self.RefmacParams['TLS'] = '' + self.RefmacParams['TLSIN'] = '' + self.RefmacParams['TLSOUT'] = '' + self.RefmacParams['TLSADD'] = '' return self.RefmacParams def NCSCallback(self, widget): if widget.get_active(): - self.RefmacParams['NCS']='NCSR LOCAL\n' + self.RefmacParams['NCS'] = 'NCSR LOCAL\n' else: - self.RefmacParams['NCS']='' + self.RefmacParams['NCS'] = '' return self.RefmacParams - def ChooseBfacRefinement(self,widget): - if widget.get_active_text()=='isotropic': - self.RefmacParams['BREF']=' bref ISOT\n' - if widget.get_active_text()=='anisotropic': - self.RefmacParams['BREF']=' bref ANIS\n' + def ChooseBfacRefinement(self, widget): + if widget.get_active_text() == 'isotropic': + self.RefmacParams['BREF'] = ' bref ISOT\n' + if widget.get_active_text() == 'anisotropic': + self.RefmacParams['BREF'] = ' bref ANIS\n' return self.RefmacParams def on_key_release_Ncycles(self, widget, event): @@ -1068,98 +1128,100 @@ def on_key_release_MATRIX_WEIGHT(self, widget, event): def TWINCallback(self, widget): if widget.get_active(): - self.RefmacParams['TWIN']='TWIN\n' + self.RefmacParams['TWIN'] = 'TWIN\n' else: - self.RefmacParams['TWIN']='' + self.RefmacParams['TWIN'] = '' return self.RefmacParams - def OK(self,widget): + def OK(self, widget): self.window.destroy() - - def ParamsFromPreviousCycle(self,Serial): - - RefmacParams={ 'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '', - 'WATER': '', - 'LIGOCC': '', - 'SANITY': '' } + def ParamsFromPreviousCycle(self, Serial): + + RefmacParams = {'HKLIN': '', 'HKLOUT': '', + 'XYZIN': '', 'XYZOUT': '', + 'LIBIN': '', 'LIBOUT': '', + 'TLSIN': '', 'TLSOUT': '', + 'TLSADD': '', + 'NCYCLES': '10', + 'MATRIX_WEIGHT': 'AUTO', + 'BREF': ' bref ISOT\n', + 'TLS': '', + 'NCS': '', + 'TWIN': '', + 'WATER': '', + 'LIGOCC': '', + 'SANITY': ''} if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): if line.startswith('refi tlsc'): - RefmacParams['TLS']=line + RefmacParams['TLS'] = line if line.startswith('TLSO'): - RefmacParams['TLSADD']=line + RefmacParams['TLSADD'] = line if line.startswith('NCSR LOCAL'): - RefmacParams['NCS']=line + RefmacParams['NCS'] = line if line.startswith(' bref '): - RefmacParams['BREF']=line + RefmacParams['BREF'] = line if line.startswith('ncyc'): RefmacParams['Ncycles'] = line.split()[1] if line.startswith('weight'): - RefmacParams['MATRIX_WEIGHT'] = line.split()[len(line.split())-1] + RefmacParams['MATRIX_WEIGHT'] = line.split()[ + len(line.split())-1] if line.startswith('TWIN'): - RefmacParams['TWIN']=line - elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'multi-state-restraints.refmac.params')): - for line in open(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'multi-state-restraints.refmac.params')): + RefmacParams['TWIN'] = line + elif os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-restraints.refmac.params')): + for line in open(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-restraints.refmac.params')): if 'refi tlsc' in line: - RefmacParams['TLS']=line + RefmacParams['TLS'] = line if 'TLSO' in line: - RefmacParams['TLSADD']=line + RefmacParams['TLSADD'] = line if 'NCSR LOCAL' in line: - RefmacParams['NCS']=line + RefmacParams['NCS'] = line if 'bref' in line: - RefmacParams['BREF']=line + RefmacParams['BREF'] = line if 'ncyc' in line: RefmacParams['Ncycles'] = line.split()[1] if 'weight' in line: - RefmacParams['MATRIX_WEIGHT'] = line.split()[len(line.split())-1] + RefmacParams['MATRIX_WEIGHT'] = line.split()[ + len(line.split())-1] if 'TWIN' in line: - RefmacParams['TWIN']=line + RefmacParams['TWIN'] = line return RefmacParams def GetRefinementHistory(self): -# RefinementHistory='' + # RefinementHistory='' RefinementCycle = [] - RcrystList=[] - RfreeList=[] + RcrystList = [] + RfreeList = [] found = False - for item in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): - if item.startswith(os.path.join(self.ProjectPath,self.xtalID,'Refine_')): - print item[item.rfind('_')+1:] - RefinementCycle.append(int(item[item.rfind('_')+1:])) - found = True + for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): + if item.startswith(os.path.join(self.ProjectPath, self.xtalID, 'Refine_')): + print item[item.rfind('_')+1:] + RefinementCycle.append(int(item[item.rfind('_')+1:])) + found = True if found: for cycle in sorted(RefinementCycle): -# for cycle in RefinementCycle: -# Rcryst=0 -# Rfree=0 -# LigandCC=0 + # for cycle in RefinementCycle: + # Rcryst=0 + # Rfree=0 + # LigandCC=0 try: - found_Rcryst=False - found_Rfree=False - newestPDB = max(glob.iglob(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/refine_'+str(cycle)+'.pdb'), key=os.path.getctime) + found_Rcryst = False + found_Rfree = False + newestPDB = max(glob.iglob(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str( + cycle)+'/refine_'+str(cycle)+'.pdb'), key=os.path.getctime) for line in open(newestPDB): if line.startswith('REMARK 3 R VALUE (WORKING + TEST SET) :'): Rcryst = line.split()[9] RcrystList.append(float(Rcryst)) - found_Rcryst=True + found_Rcryst = True if line.startswith('REMARK 3 FREE R VALUE :'): Rfree = line.split()[6] RfreeList.append(float(Rfree)) - found_Rfree=True + found_Rfree = True if not found_Rcryst: RcrystList.append(0) if not found_Rfree: @@ -1174,26 +1236,23 @@ def GetRefinementHistory(self): # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' else: RefinementCycle = [0] - RcrystList=[0] - RfreeList=[0] - print RefinementCycle,RcrystList,RfreeList - return(sorted(RefinementCycle),RcrystList,RfreeList) - - + RcrystList = [0] + RfreeList = [0] + print RefinementCycle, RcrystList, RfreeList + return(sorted(RefinementCycle), RcrystList, RfreeList) class panddaRefine(object): - def __init__(self,ProjectPath,xtalID,compoundID,datasource): + def __init__(self, ProjectPath, xtalID, compoundID, datasource): self.ProjectPath = ProjectPath self.xtalID = xtalID self.compoundID = compoundID self.prefix = 'refine' - self.datasource=datasource + self.datasource = datasource - - def make_covalent_link(self,covLinkAtomSpec,Logfile): - residuesToModify = ['CYS','SER'] + def make_covalent_link(self, covLinkAtomSpec, Logfile): + residuesToModify = ['CYS', 'SER'] atom1 = covLinkAtomSpec[1][5] atom2 = covLinkAtomSpec[2][5] @@ -1201,107 +1260,125 @@ def make_covalent_link(self,covLinkAtomSpec,Logfile): residue_2 = covLinkAtomSpec[4] if residue_2 in residuesToModify: - bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' %(residue_1,self.compoundID,atom1,residue_2,atom2) + bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' % ( + residue_1, self.compoundID, atom1, residue_2, atom2) else: - bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' % (residue_2, self.compoundID, atom2, residue_1, atom1) + bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' % ( + residue_2, self.compoundID, atom2, residue_1, atom1) - os.chdir(os.path.join(self.ProjectPath,self.xtalID)) - f = open('covalent_bond.txt','w') + os.chdir(os.path.join(self.ProjectPath, self.xtalID)) + f = open('covalent_bond.txt', 'w') f.write(bond_text) f.close() # seems somewhat unncessary, but acedrg does not like some certain descriptions generated by phenix.elbow - os.system('acedrg -c %s.cif -o %s_acedrg' %(self.compoundID,self.compoundID)) + os.system('acedrg -c %s.cif -o %s_acedrg' % + (self.compoundID, self.compoundID)) - os.system('acedrg -L covalent_bond.txt -o %s' %self.compoundID) + os.system('acedrg -L covalent_bond.txt -o %s' % self.compoundID) - if os.path.isfile('%s_link.cif' %self.compoundID): - Logfile.insert('succefully created link file %s_link.cif' %self.compoundID) - os.system('/bin/rm %s.cif' %self.compoundID) - os.system('ln -s %s_link.cif %s.cif' %(self.compoundID,self.compoundID)) + if os.path.isfile('%s_link.cif' % self.compoundID): + Logfile.insert( + 'succefully created link file %s_link.cif' % self.compoundID) + os.system('/bin/rm %s.cif' % self.compoundID) + os.system('ln -s %s_link.cif %s.cif' % + (self.compoundID, self.compoundID)) else: - Logfile.error('could not create linkfile; please check logs in %s/%s' %(self.ProjectPath,self.xtalID)) - - + Logfile.error('could not create linkfile; please check logs in %s/%s' % + (self.ProjectPath, self.xtalID)) - - def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refinementProtocol,covLinkAtomSpec): - Logfile=XChemLog.updateLog(xce_logfile) + def RunQuickRefine(self, Serial, RefmacParams, external_software, xce_logfile, refinementProtocol, covLinkAtomSpec): + Logfile = XChemLog.updateLog(xce_logfile) Logfile.insert('preparing files for giant.quick_refine') # panddaSerial because giant.quick_refine writes Refine_0001 instead of Refine_1 - panddaSerial=(4-len(str(Serial)))*'0'+str(Serial) + panddaSerial = (4-len(str(Serial)))*'0'+str(Serial) make_all_links = True add_links_line = '' if covLinkAtomSpec is not None: - self.make_covalent_link(covLinkAtomSpec,Logfile) + self.make_covalent_link(covLinkAtomSpec, Logfile) # first check if refinement is ongoing and exit if yes - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'REFINEMENT_IN_PROGRESS')): -# coot.info_dialog('*** REFINEMENT IN PROGRESS ***') - Logfile.insert('cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' %self.xtalID) + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'REFINEMENT_IN_PROGRESS')): + # coot.info_dialog('*** REFINEMENT IN PROGRESS ***') + Logfile.insert( + 'cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' % self.xtalID) return None ####################################################### # HKLIN & HKLOUT - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz')): - RefmacParams['HKLIN']=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz') - elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): - RefmacParams['HKLIN']=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz') + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'.free.mtz')): + RefmacParams['HKLIN'] = os.path.join( + self.ProjectPath, self.xtalID, self.xtalID+'.free.mtz') + elif os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'-pandda-input.mtz')): + RefmacParams['HKLIN'] = os.path.join( + self.ProjectPath, self.xtalID, self.xtalID+'-pandda-input.mtz') else: - Logfile.error('%s: cannot find HKLIN for refinement; aborting...' %self.xtalID) + Logfile.error( + '%s: cannot find HKLIN for refinement; aborting...' % self.xtalID) return None ####################################################### # LIBIN & LIBOUT - found_cif=False - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif')): - found_cif=True - RefmacParams['LIBIN']=os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif') + found_cif = False + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.compoundID+'.cif')): + found_cif = True + RefmacParams['LIBIN'] = os.path.join( + self.ProjectPath, self.xtalID, self.compoundID+'.cif') if not found_cif: - # this should actually not be necessary, but the following scenario can happen: - # if a new data source is created from a file system, but smiles and compoundID where not updated; - # so the ligand may still be in the structure, but since the compoundID is unknown to the datasource, - # its restraints won't be read in and refmac will fail - for file in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): + # this should actually not be necessary, but the following scenario can happen: + # if a new data source is created from a file system, but smiles and compoundID where not updated; + # so the ligand may still be in the structure, but since the compoundID is unknown to the datasource, + # its restraints won't be read in and refmac will fail + for file in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): if file.endswith('.cif'): - RefmacParams['LIBIN']=file + RefmacParams['LIBIN'] = file break ####################################################### # giant_merge_conformations - Logfile.insert('trying to merge modified bound state with ground state') - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),self.xtalID+'-ensemble-model.pdb')): - Logfile.insert('seems to be an initial refinement after pandda.export, no need to merge the conformations') - os.chdir(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) - Logfile.insert('running giant.make_restraints %s:' %self.xtalID+'-ensemble-model.pdb') + Logfile.insert( + 'trying to merge modified bound state with ground state') + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), self.xtalID+'-ensemble-model.pdb')): + Logfile.insert( + 'seems to be an initial refinement after pandda.export, no need to merge the conformations') + os.chdir(os.path.join(self.ProjectPath, self.xtalID, + 'cootOut', 'Refine_'+str(Serial))) + Logfile.insert('running giant.make_restraints %s:' % + self.xtalID+'-ensemble-model.pdb') # os.system('giant.make_restraints %s' %self.xtalID+'-ensemble-model.pdb') cmd = ( - 'export XChemExplorer_DIR="%s"\n' %os.getenv('XChemExplorer_DIR')+ - 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') + - 'giant.make_restraints %s-ensemble-model.pdb' %self.xtalID + 'export XChemExplorer_DIR="%s"\n' % os.getenv('XChemExplorer_DIR') + + 'source %s\n' % os.path.join(os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-sh\n') + + 'giant.make_restraints %s-ensemble-model.pdb' % self.xtalID ) Logfile.insert(cmd+'\n') os.system(cmd) - elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'refine.split.ground-state.pdb')): - Logfile.insert('found model of ground state: '+os.path.join(self.ProjectPath,self.xtalID,'refine.split.ground-state.pdb')) - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'refine.modified.pdb')): + elif os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'refine.split.ground-state.pdb')): + Logfile.insert('found model of ground state: '+os.path.join( + self.ProjectPath, self.xtalID, 'refine.split.ground-state.pdb')) + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'refine.modified.pdb')): Logfile.insert('found model of modified bound state') - os.chdir(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) - ground_state=os.path.join(self.ProjectPath,self.xtalID,'refine.split.ground-state.pdb') - bound_state='refine.modified.pdb' - Logfile.insert('running giant.merge_conformations major=%s minor=%s' %(ground_state,bound_state)) + os.chdir(os.path.join(self.ProjectPath, self.xtalID, + 'cootOut', 'Refine_'+str(Serial))) + ground_state = os.path.join( + self.ProjectPath, self.xtalID, 'refine.split.ground-state.pdb') + bound_state = 'refine.modified.pdb' + Logfile.insert('running giant.merge_conformations major=%s minor=%s' % ( + ground_state, bound_state)) if os.getcwd().startswith('/dls'): cmd = ( - 'export XChemExplorer_DIR="%s"\n' %os.getenv('XChemExplorer_DIR')+ -# 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') + - 'module load ccp4/7.1.018\n' - 'giant.merge_conformations major=%s minor=%s reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0' %(ground_state,bound_state) + 'export XChemExplorer_DIR="%s"\n' % os.getenv('XChemExplorer_DIR') + + # 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') + + 'module load ccp4/7.1.018\n' + 'giant.merge_conformations major=%s minor=%s reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0' % ( + ground_state, bound_state) ) else: cmd = ( - 'giant.merge_conformations major=%s minor=%s reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0' %(ground_state,bound_state) + 'giant.merge_conformations major=%s minor=%s reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0' % ( + ground_state, bound_state) ) Logfile.insert(cmd+'\n') os.system(cmd) @@ -1314,53 +1391,62 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine if os.path.isfile('multi-state-model.pdb'): for line in open('multi-state-model.pdb'): if line.startswith('CRYST'): - Logfile.insert('adding LINK lines to multi-state-model.pdb') + Logfile.insert( + 'adding LINK lines to multi-state-model.pdb') out = link_line + line else: out += line Logfile.insert('writing updated multi-state-model.pdb') - f = open('multi-state-model.pdb','w') + f = open('multi-state-model.pdb', 'w') f.write(out) f.close() else: Logfile.error('cannot find multi-state-model.pdb') else: - Logfile.error('cannot find modified version of bound state in %s' %os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) + Logfile.error('cannot find modified version of bound state in %s' % os.path.join( + self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) return None else: - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'refine.modified.pdb')): - os.chdir(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) - Logfile.warning('%s: ground-state model does not exist, but refine.modified.pdb does exist' %self.xtalID) - Logfile.warning('This may be a case where there are no differences between bound and ground state') - Logfile.warning('creating symbolic link: ln -s refine.modified.pdb %s-ensemble-model.pdb' %self.xtalID) - os.system('ln -s refine.modified.pdb %s-ensemble-model.pdb' %self.xtalID) + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'refine.modified.pdb')): + os.chdir(os.path.join(self.ProjectPath, self.xtalID, + 'cootOut', 'Refine_'+str(Serial))) + Logfile.warning( + '%s: ground-state model does not exist, but refine.modified.pdb does exist' % self.xtalID) + Logfile.warning( + 'This may be a case where there are no differences between bound and ground state') + Logfile.warning( + 'creating symbolic link: ln -s refine.modified.pdb %s-ensemble-model.pdb' % self.xtalID) + os.system( + 'ln -s refine.modified.pdb %s-ensemble-model.pdb' % self.xtalID) # note: after first cycle of refinement, REFMAC will remove alternate conformer from the ligand # i.e. need to link refine.pdb to refine.split.bound-state.pdb make_all_links = False add_links_line = 'ln -s refine.pdb refine.split.bound-state.pdb' Logfile.insert('trying to continue with refinement') else: - Logfile.error('cannot find any suitable PDB file for refinement, aborting...') + Logfile.error( + 'cannot find any suitable PDB file for refinement, aborting...') return None - ####################################################### # checking if input PDB files are present Logfile.insert('checking if input PDB files for REFMAC are present') - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),self.xtalID+'-ensemble-model.pdb')): - RefmacParams['XYZIN']=os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),self.xtalID+'-ensemble-model.pdb') - elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'multi-state-model.pdb')): - RefmacParams['XYZIN']=os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'multi-state-model.pdb') + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), self.xtalID+'-ensemble-model.pdb')): + RefmacParams['XYZIN'] = os.path.join( + self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), self.xtalID+'-ensemble-model.pdb') + elif os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-model.pdb')): + RefmacParams['XYZIN'] = os.path.join( + self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-model.pdb') else: - Logfile.error('cannot find multi-state-model.pdb in %s; aborting...' %os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) + Logfile.error('cannot find multi-state-model.pdb in %s; aborting...' % + os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) return None - ####################################################### # checking if multi-state-restraints.refmac.params file is present - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'multi-state-restraints.refmac.params')): + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-restraints.refmac.params')): # add REFMAC keywords to multi-state-restraints.refmac.params - with open('multi-state-restraints.refmac.params','a') as refmacParams: + with open('multi-state-restraints.refmac.params', 'a') as refmacParams: refmacParams.write(RefmacParams['BREF']+'\n') refmacParams.write(RefmacParams['TLS']+'\n') refmacParams.write(RefmacParams['TWIN']+'\n') @@ -1368,15 +1454,20 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine if str(RefmacParams['MATRIX_WEIGHT']).lower() == 'auto': refmacParams.write('weight AUTO' + '\n') else: - refmacParams.write('weight matrix '+str(RefmacParams['MATRIX_WEIGHT'])+'\n') + refmacParams.write( + 'weight matrix '+str(RefmacParams['MATRIX_WEIGHT'])+'\n') refmacParams.write(RefmacParams['TLSADD']+'\n') else: - Logfile.warning('cannot find multi-state-restraints.refmac.params in %s!' %os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) + Logfile.warning('cannot find multi-state-restraints.refmac.params in %s!' % + os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) try: - os.chdir(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) - Logfile.insert('checking if %s-ensemble-model.pdb contains residue of type LIG, DRG, FRG, UNK or UNL' %self.xtalID) + os.chdir(os.path.join(self.ProjectPath, self.xtalID, + 'cootOut', 'Refine_'+str(Serial))) + Logfile.insert( + 'checking if %s-ensemble-model.pdb contains residue of type LIG, DRG, FRG, UNK or UNL' % self.xtalID) knowLigandIDs = ['LIG', 'DRG', 'FRG', 'UNK', 'UNL'] - ligandsInFile = pdbtools(self.xtalID+'-ensemble-model.pdb').find_ligands() + ligandsInFile = pdbtools( + self.xtalID+'-ensemble-model.pdb').find_ligands() found_lig = False for lig in ligandsInFile: if lig[0] in knowLigandIDs: @@ -1391,76 +1482,84 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine 'additional REFMAC keywords and otherwise try to continue with refinement') os.system('touch multi-state-restraints.refmac.params') else: - Logfile.error('%s-ensemble-model.pdb does not contain any modelled ligand; aborting refinement' %self.xtalID) + Logfile.error( + '%s-ensemble-model.pdb does not contain any modelled ligand; aborting refinement' % self.xtalID) return None except OSError: - Logfile.error('directory does not exisit: %s' %os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) + Logfile.error('directory does not exisit: %s' % os.path.join( + self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) Logfile.error('aborting refinement...') return None ####################################################### # we write 'REFINEMENT_IN_PROGRESS' immediately to avoid unncessary refinement - os.chdir(os.path.join(self.ProjectPath,self.xtalID)) + os.chdir(os.path.join(self.ProjectPath, self.xtalID)) os.system('touch REFINEMENT_IN_PROGRESS') ####################################################### # clean up! # and remove all files which will be re-created by current refinement cycle - os.chdir(os.path.join(self.ProjectPath,self.xtalID)) - files_to_remove = ( 'refine.pdb ' - 'refine.mtz ' - 'refine.split.bound-state.pdb ' - 'refine.split.ground-state.pdb ' - 'validation_summary.txt ' - 'validate_ligands.txt ' - '2fofc.map ' - 'fofc.map ' - 'refine_molprobity.log' ) - os.system('/bin/rm %s' %files_to_remove) + os.chdir(os.path.join(self.ProjectPath, self.xtalID)) + files_to_remove = ('refine.pdb ' + 'refine.mtz ' + 'refine.split.bound-state.pdb ' + 'refine.split.ground-state.pdb ' + 'validation_summary.txt ' + 'validate_ligands.txt ' + '2fofc.map ' + 'fofc.map ' + 'refine_molprobity.log') + os.system('/bin/rm %s' % files_to_remove) if external_software['qsub']: - pbs_line='#PBS -joe -N XCE_refmac\n' + pbs_line = '#PBS -joe -N XCE_refmac\n' else: - pbs_line='\n' + pbs_line = '\n' ####################################################### # PANDDA validation @ spider plot - spider_plot='' - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-ensemble-model.pdb')): - if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): - pdb_two=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-ensemble-model.pdb') - mtz_two=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz') - pdb_one=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+str(panddaSerial),'refine_'+str(Serial)+'.pdb') - mtz_one=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+str(panddaSerial),'refine_'+str(Serial)+'.mtz') - spider_plot+='giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' %(pdb_one,mtz_one,pdb_two,mtz_two) + spider_plot = '' + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'-ensemble-model.pdb')): + if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'-pandda-input.mtz')): + pdb_two = os.path.join( + self.ProjectPath, self.xtalID, self.xtalID+'-ensemble-model.pdb') + mtz_two = os.path.join( + self.ProjectPath, self.xtalID, self.xtalID+'-pandda-input.mtz') + pdb_one = os.path.join( + self.ProjectPath, self.xtalID, 'Refine_'+str(panddaSerial), 'refine_'+str(Serial)+'.pdb') + mtz_one = os.path.join( + self.ProjectPath, self.xtalID, 'Refine_'+str(panddaSerial), 'refine_'+str(Serial)+'.mtz') + spider_plot += 'giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' % ( + pdb_one, mtz_one, pdb_two, mtz_two) ####################################################### # CCP4 & PHENIX stuff (if working at DLS) - module_load='' + module_load = '' if os.getcwd().startswith('/dls'): module_load = 'module load ccp4/7.1.018\n' module_load += 'module load phenix\n' # 2017-07-20: for the time being this will explicitly source pandda since version 0.2 really only works at DLS # 2020-11-02: will start using default ccp4 installation at DLS otherwise gemmi does not work - source ='' + source = '' if 'bash' in os.getenv('SHELL'): source = ( - 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' + 'export XChemExplorer_DIR="' + + os.getenv('XChemExplorer_DIR')+'"\n' '\n' -# 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') + # 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') ) elif 'csh' in os.getenv('SHELL'): source = ( 'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n' '\n' -# 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh\n') + # 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh\n') ) - - if refinementProtocol=='pandda_refmac': - refinementProgram='refmac' - refinementParams=os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'multi-state-restraints.refmac.params') + if refinementProtocol == 'pandda_refmac': + refinementProgram = 'refmac' + refinementParams = os.path.join( + self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-restraints.refmac.params') mapCalculation = ( 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' 'labin F1=FWT PHI=PHWT\n' @@ -1468,14 +1567,15 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine '\n' 'fft hklin refine.mtz mapout fofc.map << EOF\n' 'labin F1=DELFWT PHI=PHDELWT\n' - 'EOF\n' ) - elif refinementProtocol=='pandda_phenix': + 'EOF\n') + elif refinementProtocol == 'pandda_phenix': if os.getcwd().startswith('/dls'): module_load = 'module load phenix/1.13\n' - refinementProgram='phenix' - refinementParams=os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'multi-state-restraints.phenix.params') + refinementProgram = 'phenix' + refinementParams = os.path.join( + self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-restraints.phenix.params') mapCalculation = ( 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' 'labin F1=2FOFCWT PHI=PH2FOFCWT\n' @@ -1483,14 +1583,15 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine '\n' 'fft hklin refine.mtz mapout fofc.map << EOF\n' 'labin F1=FOFCWT PHI=PHFOFCWT\n' - 'EOF\n' ) + 'EOF\n') if make_all_links: add_links_line = ( - 'ln -s Refine_%s/refine_%s.split.bound-state.pdb ./refine.split.bound-state.pdb\n' %(panddaSerial,Serial)+ - 'ln -s Refine_%s/refine_%s.split.ground-state.pdb ./refine.split.ground-state.pdb\n' %(panddaSerial,Serial) -# 'ln -s Refine_%s/refine_%s.output.bound-state.pdb ./refine.output.bound-state.pdb\n' %(panddaSerial,Serial)+ -# 'ln -s Refine_%s/refine_%s.output.ground-state.pdb ./refine.output.ground-state.pdb\n' %(panddaSerial,Serial) + 'ln -s Refine_%s/refine_%s.split.bound-state.pdb ./refine.split.bound-state.pdb\n' % (panddaSerial, Serial) + + 'ln -s Refine_%s/refine_%s.split.ground-state.pdb ./refine.split.ground-state.pdb\n' % ( + panddaSerial, Serial) + # 'ln -s Refine_%s/refine_%s.output.bound-state.pdb ./refine.output.bound-state.pdb\n' %(panddaSerial,Serial)+ + # 'ln -s Refine_%s/refine_%s.output.ground-state.pdb ./refine.output.ground-state.pdb\n' %(panddaSerial,Serial) ) date = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] @@ -1498,53 +1599,58 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine refmacCmds = ( '#!'+os.getenv('SHELL')+'\n' - +pbs_line+ + + pbs_line + '\n' + module_load + '\n' - +source+ + + source + 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' '\n' - '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(self.datasource,self.xtalID,'RefinementStatus','running') + + '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' % (self.datasource, self.xtalID, 'RefinementStatus', 'running') + '\n' 'giant.quick_refine' - ' input.pdb=%s' %RefmacParams['XYZIN']+ - ' mtz=%s' %RefmacParams['HKLIN']+ - ' cif=%s' %RefmacParams['LIBIN']+ - ' program=%s' %refinementProgram + - ' params=%s' %refinementParams+ + ' input.pdb=%s' % RefmacParams['XYZIN'] + + ' mtz=%s' % RefmacParams['HKLIN'] + + ' cif=%s' % RefmacParams['LIBIN'] + + ' program=%s' % refinementProgram + + ' params=%s' % refinementParams + " dir_prefix='Refine_'" - " out_prefix='refine_%s'" %str(Serial)+ + " out_prefix='refine_%s'" % str(Serial) + " split_conformations='False'" '\n' - 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'\n' + 'cd '+self.ProjectPath+'/'+self.xtalID + + '/Refine_'+str(panddaSerial)+'\n' - 'ln -s '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'/refine_'+str(Serial)+'_001.pdb ' - +self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'/refine_'+str(Serial)+'.pdb' +'\n' + 'ln -s '+self.ProjectPath+'/'+self.xtalID+'/Refine_' + + str(panddaSerial)+'/refine_'+str(Serial)+'_001.pdb ' + + self.ProjectPath+'/'+self.xtalID+'/Refine_' + + str(panddaSerial)+'/refine_'+str(Serial)+'.pdb' + '\n' - 'ln -s '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'/refine_'+str(Serial)+'_001.mtz ' - +self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(panddaSerial)+'/refine_'+str(Serial)+'.mtz' +'\n' + 'ln -s '+self.ProjectPath+'/'+self.xtalID+'/Refine_' + + str(panddaSerial)+'/refine_'+str(Serial)+'_001.mtz ' + + self.ProjectPath+'/'+self.xtalID+'/Refine_' + + str(panddaSerial)+'/refine_'+str(Serial)+'.mtz' + '\n' 'giant.split_conformations' - " input.pdb='refine_%s.pdb'" %str(Serial)+ + " input.pdb='refine_%s.pdb'" % str(Serial) + ' reset_occupancies=False' ' suffix_prefix=split' '\n' 'giant.split_conformations' - " input.pdb='refine_%s.pdb'" %str(Serial)+ + " input.pdb='refine_%s.pdb'" % str(Serial) + ' reset_occupancies=True' ' suffix_prefix=output ' '\n' - +spider_plot+ + + spider_plot + '\n' - 'phenix.molprobity refine_%s.pdb refine_%s.mtz\n' %(Serial,Serial)+ + 'phenix.molprobity refine_%s.pdb refine_%s.mtz\n' % (Serial, Serial) + '/bin/mv molprobity.out refine_molprobity.log\n' 'module load phenix\n' - 'mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n' %(Serial,Serial)+ + 'mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n' % (Serial, Serial) + 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' '\n' - 'ln -s Refine_%s/validate_ligands.txt .\n' %panddaSerial+ - 'ln -s Refine_%s/refine_molprobity.log .\n' %panddaSerial+ + 'ln -s Refine_%s/validate_ligands.txt .\n' % panddaSerial + + 'ln -s Refine_%s/refine_molprobity.log .\n' % panddaSerial + '\n' + add_links_line + '\n' @@ -1552,32 +1658,38 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine '\n' + mapCalculation + '\n' - '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+ - ' %s %s %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+str(panddaSerial)),user,date)+ + '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_data_source_after_refinement.py') + + ' %s %s %s %s %s %s\n' % (self.datasource, self.xtalID, self.ProjectPath, os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+str(panddaSerial)), user, date) + '\n' - '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' %(self.ProjectPath,self.xtalID)+ + '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' % (self.ProjectPath, self.xtalID) + '\n' - ) + ) - Logfile.insert('writing refinement shell script to'+os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'refmac.csh')) - cmd = open(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial),'refmac.csh'),'w') + Logfile.insert('writing refinement shell script to'+os.path.join( + self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'refmac.csh')) + cmd = open(os.path.join(self.ProjectPath, self.xtalID, + 'cootOut', 'Refine_'+str(Serial), 'refmac.csh'), 'w') cmd.write(refmacCmds) cmd.close() - os.chdir(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) + os.chdir(os.path.join(self.ProjectPath, self.xtalID, + 'cootOut', 'Refine_'+str(Serial))) # os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) - Logfile.insert('changing directory to %s' %(os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial)))) + Logfile.insert('changing directory to %s' % (os.path.join( + self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial)))) if external_software['qsub']: Logfile.insert('starting refinement on cluster') os.system('qsub -P labxchem refmac.csh') elif external_software['qsub_remote'] != '': Logfile.insert('starting refinement on remote cluster') - remote_command=external_software['qsub_remote'].replace('qsub','cd %s; qsub' %os.path.join(self.ProjectPath,self.xtalID,'cootOut','Refine_'+str(Serial))) - os.system('%s -P labxchem refmac.csh' %remote_command) - print '%s -P labxchem refmac.csh' %remote_command + remote_command = external_software['qsub_remote'].replace('qsub', 'cd %s; qsub' % os.path.join( + self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) + os.system('%s -P labxchem refmac.csh' % remote_command) + print '%s -P labxchem refmac.csh' % remote_command else: - Logfile.insert('changing permission of refmac.csh: chmod +x refmac.csh') + Logfile.insert( + 'changing permission of refmac.csh: chmod +x refmac.csh') os.system('chmod +x refmac.csh') Logfile.insert('starting refinement on local machine') os.system('./refmac.csh &') @@ -1587,22 +1699,19 @@ def RunQuickRefine(self,Serial,RefmacParams,external_software,xce_logfile,refine # else: # os.system('./refmac.csh &') - - - - def RefinementParams(self,RefmacParams): - self.RefmacParams=RefmacParams + def RefinementParams(self, RefmacParams): + self.RefmacParams = RefmacParams self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) self.window.connect("delete_event", gtk.main_quit) self.window.set_border_width(10) self.window.set_title("Refmac Parameters") self.vbox = gtk.VBox() - self.hbox1=gtk.HBox() + self.hbox1 = gtk.HBox() self.hbox1.add(gtk.Label('Refine')) self.cb = gtk.combo_box_new_text() self.cb.connect("changed", self.ChooseBfacRefinement) - for item in ['isotropic','anisotropic']: + for item in ['isotropic', 'anisotropic']: self.cb.append_text(item) if 'ISOT' in self.RefmacParams['BREF']: self.cb.set_active(0) @@ -1612,73 +1721,77 @@ def RefinementParams(self,RefmacParams): self.hbox1.add(gtk.Label('temperature factors')) self.vbox.add(self.hbox1) - self.hbox2=gtk.HBox() + self.hbox2 = gtk.HBox() self.hbox2.add(gtk.Label('Number of Cycles: ')) - self.Ncycles=gtk.Entry() + self.Ncycles = gtk.Entry() self.Ncycles.add_events(gtk.gdk.KEY_RELEASE_MASK) self.Ncycles.connect("key-release-event", self.on_key_release_Ncycles) self.Ncycles.set_text(self.RefmacParams['NCYCLES']) self.hbox2.add(self.Ncycles) self.vbox.add(self.hbox2) - self.hbox3=gtk.HBox() + self.hbox3 = gtk.HBox() self.hbox3.add(gtk.Label('MATRIX WEIGHT: ')) - self.MATRIX_WEIGHT=gtk.Entry() + self.MATRIX_WEIGHT = gtk.Entry() self.MATRIX_WEIGHT.add_events(gtk.gdk.KEY_RELEASE_MASK) - self.MATRIX_WEIGHT.connect("key-release-event", self.on_key_release_MATRIX_WEIGHT) + self.MATRIX_WEIGHT.connect( + "key-release-event", self.on_key_release_MATRIX_WEIGHT) self.MATRIX_WEIGHT.set_text(self.RefmacParams['MATRIX_WEIGHT']) self.hbox3.add(self.MATRIX_WEIGHT) self.vbox.add(self.hbox3) - self.TLS = gtk.CheckButton('TLS (find TLS groups with phenix.find_tls_groups)') + self.TLS = gtk.CheckButton( + 'TLS (find TLS groups with phenix.find_tls_groups)') self.TLS.connect("toggled", self.TLSCallback) - if self.RefmacParams['TLS']=='refi tlsc 10\n': self.TLS.set_active(True) - self.vbox.pack_start(self.TLS,False) + if self.RefmacParams['TLS'] == 'refi tlsc 10\n': + self.TLS.set_active(True) + self.vbox.pack_start(self.TLS, False) self.NCS = gtk.CheckButton('NCS (if applicable') self.NCS.connect("toggled", self.NCSCallback) - if self.RefmacParams['NCS']=='NCSR LOCAL\n': self.NCS.set_active(True) - self.vbox.pack_start(self.NCS,False) + if self.RefmacParams['NCS'] == 'NCSR LOCAL\n': + self.NCS.set_active(True) + self.vbox.pack_start(self.NCS, False) self.TWIN = gtk.CheckButton('Twin?') self.TWIN.connect("toggled", self.TWINCallback) - if self.RefmacParams['TWIN']=='TWIN\n': self.TWIN.set_active(True) - self.vbox.pack_start(self.TWIN,False) + if self.RefmacParams['TWIN'] == 'TWIN\n': + self.TWIN.set_active(True) + self.vbox.pack_start(self.TWIN, False) self.OKbutton = gtk.Button(label="OK") - self.OKbutton.connect("clicked",self.OK) + self.OKbutton.connect("clicked", self.OK) self.vbox.add(self.OKbutton) self.window.add(self.vbox) self.window.show_all() return self.RefmacParams - def TLSCallback(self, widget): if widget.get_active(): - self.RefmacParams['TLS']='refi tlsc 10\n' - self.RefmacParams['TLSIN']='refmac.tls\n' - self.RefmacParams['TLSOUT']='out.tls\n' - self.RefmacParams['TLSADD']='TLSO ADDU\n' + self.RefmacParams['TLS'] = 'refi tlsc 10\n' + self.RefmacParams['TLSIN'] = 'refmac.tls\n' + self.RefmacParams['TLSOUT'] = 'out.tls\n' + self.RefmacParams['TLSADD'] = 'TLSO ADDU\n' else: - self.RefmacParams['TLS']='' - self.RefmacParams['TLSIN']='' - self.RefmacParams['TLSOUT']='' - self.RefmacParams['TLSADD']='' + self.RefmacParams['TLS'] = '' + self.RefmacParams['TLSIN'] = '' + self.RefmacParams['TLSOUT'] = '' + self.RefmacParams['TLSADD'] = '' return self.RefmacParams def NCSCallback(self, widget): if widget.get_active(): - self.RefmacParams['NCS']='NCSR LOCAL\n' + self.RefmacParams['NCS'] = 'NCSR LOCAL\n' else: - self.RefmacParams['NCS']='' + self.RefmacParams['NCS'] = '' return self.RefmacParams - def ChooseBfacRefinement(self,widget): - if widget.get_active_text()=='isotropic': - self.RefmacParams['BREF']=' bref ISOT\n' - if widget.get_active_text()=='anisotropic': - self.RefmacParams['BREF']=' bref ANIS\n' + def ChooseBfacRefinement(self, widget): + if widget.get_active_text() == 'isotropic': + self.RefmacParams['BREF'] = ' bref ISOT\n' + if widget.get_active_text() == 'anisotropic': + self.RefmacParams['BREF'] = ' bref ANIS\n' return self.RefmacParams def on_key_release_Ncycles(self, widget, event): @@ -1692,79 +1805,80 @@ def on_key_release_MATRIX_WEIGHT(self, widget, event): def TWINCallback(self, widget): if widget.get_active(): - self.RefmacParams['TWIN']='TWIN\n' + self.RefmacParams['TWIN'] = 'TWIN\n' else: - self.RefmacParams['TWIN']='' + self.RefmacParams['TWIN'] = '' return self.RefmacParams - def OK(self,widget): + def OK(self, widget): self.window.destroy() + def ParamsFromPreviousCycle(self, Serial): - def ParamsFromPreviousCycle(self,Serial): - - RefmacParams={ 'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '' } + RefmacParams = {'HKLIN': '', 'HKLOUT': '', + 'XYZIN': '', 'XYZOUT': '', + 'LIBIN': '', 'LIBOUT': '', + 'TLSIN': '', 'TLSOUT': '', + 'TLSADD': '', + 'NCYCLES': '10', + 'MATRIX_WEIGHT': 'AUTO', + 'BREF': ' bref ISOT\n', + 'TLS': '', + 'NCS': '', + 'TWIN': ''} if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): if line.startswith('refi tlsc'): - RefmacParams['TLS']=line + RefmacParams['TLS'] = line if line.startswith('TLSO'): - RefmacParams['TLSADD']=line + RefmacParams['TLSADD'] = line if line.startswith('NCSR LOCAL'): - RefmacParams['NCS']=line + RefmacParams['NCS'] = line if line.startswith(' bref '): - RefmacParams['BREF']=line + RefmacParams['BREF'] = line if line.startswith('ncyc'): RefmacParams['Ncycles'] = line.split()[1] if line.startswith('weight'): - RefmacParams['MATRIX_WEIGHT'] = line.split()[len(line.split())-1] + RefmacParams['MATRIX_WEIGHT'] = line.split()[ + len(line.split())-1] if line.startswith('TWIN'): - RefmacParams['TWIN']=line + RefmacParams['TWIN'] = line return RefmacParams def GetRefinementHistory(self): -# RefinementHistory='' + # RefinementHistory='' RefinementCycle = [] - RcrystList=[] - RfreeList=[] + RcrystList = [] + RfreeList = [] found = False - for item in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): - if item.startswith(os.path.join(self.ProjectPath,self.xtalID,'Refine_')): - print item[item.rfind('_')+1:] - RefinementCycle.append(int(item[item.rfind('_')+1:])) - found = True + for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): + if item.startswith(os.path.join(self.ProjectPath, self.xtalID, 'Refine_')): + print item[item.rfind('_')+1:] + RefinementCycle.append(int(item[item.rfind('_')+1:])) + found = True if found: for cycle in sorted(RefinementCycle): -# for cycle in RefinementCycle: -# Rcryst=0 -# Rfree=0 -# LigandCC=0 + # for cycle in RefinementCycle: + # Rcryst=0 + # Rfree=0 + # LigandCC=0 try: - found_Rcryst=False - found_Rfree=False - newestPDB = max(glob.iglob(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/refine_'+str(cycle)+'.pdb'), key=os.path.getctime) + found_Rcryst = False + found_Rfree = False + newestPDB = max(glob.iglob(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str( + cycle)+'/refine_'+str(cycle)+'.pdb'), key=os.path.getctime) for line in open(newestPDB): if line.startswith('REMARK 3 R VALUE (WORKING + TEST SET) :'): Rcryst = line.split()[9] RcrystList.append(float(Rcryst)) - found_Rcryst=True + found_Rcryst = True if line.startswith('REMARK 3 FREE R VALUE :'): Rfree = line.split()[6] RfreeList.append(float(Rfree)) - found_Rfree=True + found_Rfree = True if not found_Rcryst: RcrystList.append(0) if not found_Rfree: @@ -1779,13 +1893,13 @@ def GetRefinementHistory(self): # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' else: RefinementCycle = [0] - RcrystList=[0] - RfreeList=[0] - print RefinementCycle,RcrystList,RfreeList - return(sorted(RefinementCycle),RcrystList,RfreeList) + RcrystList = [0] + RfreeList = [0] + print RefinementCycle, RcrystList, RfreeList + return(sorted(RefinementCycle), RcrystList, RfreeList) -#class RefineOld(object): +# class RefineOld(object): # # def __init__(self,ProjectPath,xtalID,compoundID,datasource): # self.ProjectPath = ProjectPath @@ -1853,7 +1967,7 @@ def GetRefinementHistory(self): # if file.endswith('.cif'): # if self.compoundID not in file: # additional_cif_file=file -## additional_cif=True <- should be true, but need to check this part of the code! 16/11/2016 +# additional_cif=True <- should be true, but need to check this part of the code! 16/11/2016 # additional_cif=False # if additional_cif: # Cmds = ( @@ -1900,16 +2014,16 @@ def GetRefinementHistory(self): # # ## ####################################################### -## # create folder for new refinement cycle -## os.mkdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) +# create folder for new refinement cycle +# os.mkdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) ## ## ####################################################### -## # write PDB file -## # now take protein pdb file and write it to newly create Refine_ folder -## # note: the user has to make sure that the ligand file was merged into main file -## for item in coot_utils_XChem.molecule_number_list(): -## if coot.molecule_name(item).endswith(self.prefix+'.pdb'): -## coot.write_pdb_file(item,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb')) +# write PDB file +# now take protein pdb file and write it to newly create Refine_ folder +# note: the user has to make sure that the ligand file was merged into main file +# for item in coot_utils_XChem.molecule_number_list(): +# if coot.molecule_name(item).endswith(self.prefix+'.pdb'): +# coot.write_pdb_file(item,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb')) # # ####################################################### # # PANDDAs stuff @@ -1923,7 +2037,7 @@ def GetRefinementHistory(self): # 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' # "giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'\n" ) ## os.system("giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'") -## os.system(cmd) +# os.system(cmd) # print "==> XCE: running giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'" # os.system("giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'") # # quick fix for the moment; need to talk to Nick since this should not be necessary @@ -1933,7 +2047,7 @@ def GetRefinementHistory(self): # if 'incomplete' in line: # line=line.replace('incomplete','complete') # print line, -## elif 'occupancy refine' in line: +# elif 'occupancy refine' in line: ## line=line.replace('occupancy refine','occupancy refine ncycle 10\noccupancy refine') ## print line, # else: @@ -2129,9 +2243,9 @@ def GetRefinementHistory(self): # os.system('chmod +x refmac.csh') # Logfile.insert('starting refinement on local machine') # os.system('./refmac.csh &') -## if '/work/' in os.getcwd(): +# if '/work/' in os.getcwd(): ## os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) -## else: +# else: ## os.system('./refmac.csh &') # # @@ -2282,7 +2396,7 @@ def GetRefinementHistory(self): # return RefmacParams # # def GetRefinementHistory(self): -## RefinementHistory='' +# RefinementHistory='' # RefinementCycle = [] # RcrystList=[] # RfreeList=[] @@ -2295,10 +2409,10 @@ def GetRefinementHistory(self): # found = True # if found: # for cycle in sorted(RefinementCycle): -## for cycle in RefinementCycle: -## Rcryst=0 -## Rfree=0 -## LigandCC=0 +# for cycle in RefinementCycle: +# Rcryst=0 +# Rfree=0 +# LigandCC=0 # try: # found_Rcryst=False # found_Rfree=False @@ -2316,14 +2430,14 @@ def GetRefinementHistory(self): # RcrystList.append(0) # if not found_Rfree: # RfreeList.append(0) -## if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): -## for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): +# if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): +# for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): ## if line.startswith('| LIG'): LigandCC = line.split()[6] -## RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' +# RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' # except ValueError: # RcrystList.append(0) # RfreeList.append(0) -## RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' +# RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' # else: # RefinementCycle = [0] # RcrystList=[0] @@ -2331,4 +2445,3 @@ def GetRefinementHistory(self): # print RefinementCycle,RcrystList,RfreeList # return(sorted(RefinementCycle),RcrystList,RfreeList) # - diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 30c3bd5b..7e6bb366 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -1,6 +1,20 @@ # last edited: 31/07/2017, 10:30 -import os, sys, glob +import iotbx.mtz +import XChemMain +import XChemLog +import XChemDB +from XChemUtils import misc +from XChemUtils import reference +from XChemUtils import helpers +from XChemUtils import pdbtools +from XChemUtils import mtztools +from XChemUtils import queue +from XChemUtils import parse +from XChemUtils import process +import os +import sys +import glob from datetime import datetime from PyQt4 import QtGui, QtCore @@ -20,19 +34,6 @@ from iotbx.reflection_file_reader import any_reflection_file sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') -from XChemUtils import process -from XChemUtils import parse -from XChemUtils import queue -from XChemUtils import mtztools -from XChemUtils import pdbtools -from XChemUtils import helpers -from XChemUtils import reference -from XChemUtils import misc -import XChemDB -import XChemLog -import XChemMain - -import iotbx.mtz class synchronise_db_and_filesystem(QtCore.QThread): @@ -43,40 +44,44 @@ class synchronise_db_and_filesystem(QtCore.QThread): - update data for existing samples ''' - def __init__(self,initial_model_directory,datasource,panddas_directory,xce_logfile,mode): + def __init__(self, initial_model_directory, datasource, panddas_directory, xce_logfile, mode): QtCore.QThread.__init__(self) - self.initial_model_directory=initial_model_directory - self.datasource=datasource - self.db=XChemDB.data_source(self.datasource) - self.all_samples_in_datasource=self.db.get_all_samples_in_data_source_as_list() - self.panddas_directory=panddas_directory + self.initial_model_directory = initial_model_directory + self.datasource = datasource + self.db = XChemDB.data_source(self.datasource) + self.all_samples_in_datasource = self.db.get_all_samples_in_data_source_as_list() + self.panddas_directory = panddas_directory self.xce_logfile = xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) - self.mode=mode + self.Logfile = XChemLog.updateLog(xce_logfile) + self.mode = mode def run(self): self.Logfile.insert('synchronising database and filesystem') - self.Logfile.insert('current project directory: '+self.initial_model_directory) + self.Logfile.insert('current project directory: ' + + self.initial_model_directory) - XChemMain.backup_soakDB(self.datasource,self.xce_logfile) + XChemMain.backup_soakDB(self.datasource, self.xce_logfile) # # get list of xtals # self.xtal_list = [] - progress_step=1 - progress=0 + progress_step = 1 + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) if self.mode != 'project_directory': # if only a single xtal is synched, then self.mode==xtalID self.Logfile.insert('synchronising '+self.mode+' only') self.xtal_list.append(self.mode) else: - if len(glob.glob(os.path.join(self.initial_model_directory,'*'))) != 0: - progress_step=100/float(len(glob.glob(os.path.join(self.initial_model_directory,'*')))) - self.Logfile.insert('found '+str(len(glob.glob(os.path.join(self.initial_model_directory,'*'))))+' samples in project directory') - for directory in sorted(glob.glob(os.path.join(self.initial_model_directory,'*'))): + if len(glob.glob(os.path.join(self.initial_model_directory, '*'))) != 0: + progress_step = 100 / \ + float( + len(glob.glob(os.path.join(self.initial_model_directory, '*')))) + self.Logfile.insert('found '+str(len(glob.glob(os.path.join( + self.initial_model_directory, '*'))))+' samples in project directory') + for directory in sorted(glob.glob(os.path.join(self.initial_model_directory, '*'))): try: os.chdir(directory) except OSError: @@ -85,7 +90,7 @@ def run(self): if os.listdir(directory) == []: self.Logfile.warning(directory + ' is empty; skipping...') continue - xtal=directory[directory.rfind('/')+1:] + xtal = directory[directory.rfind('/')+1:] self.xtal_list.append(xtal) # @@ -93,325 +98,363 @@ def run(self): # for xtal in self.xtal_list: - self.Logfile.insert('directory name: '+xtal+' = sampleID in database') - os.chdir(os.path.join(self.initial_model_directory,xtal)) + self.Logfile.insert('directory name: '+xtal + + ' = sampleID in database') + os.chdir(os.path.join(self.initial_model_directory, xtal)) if xtal not in self.all_samples_in_datasource: - self.Logfile.insert('sampleID not found in database: inserting '+xtal) - self.db.execute_statement("insert into mainTable (CrystalName) values ('{0!s}');".format(xtal)) + self.Logfile.insert( + 'sampleID not found in database: inserting '+xtal) + self.db.execute_statement( + "insert into mainTable (CrystalName) values ('{0!s}');".format(xtal)) self.all_samples_in_datasource.append(xtal) - db_dict=self.db.get_db_dict_for_sample(xtal) + db_dict = self.db.get_db_dict_for_sample(xtal) db_dict['ProjectDirectory'] = self.initial_model_directory - db_dict=self.sync_data_processing(xtal,db_dict) + db_dict = self.sync_data_processing(xtal, db_dict) - db_dict=self.sync_dimple_results(xtal,db_dict) + db_dict = self.sync_dimple_results(xtal, db_dict) - db_dict=self.sync_compound_information(db_dict) + db_dict = self.sync_compound_information(db_dict) - db_dict=self.sync_refinement_results(xtal,db_dict) + db_dict = self.sync_refinement_results(xtal, db_dict) if db_dict != {}: - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'updating datasource for '+xtal) - self.db.update_data_source(xtal,db_dict) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'updating datasource for '+xtal) + self.db.update_data_source(xtal, db_dict) progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) self.Logfile.insert('database mainTable update finished') self.Logfile.insert('updating panddaTable') - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'updating panddaTable') + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'updating panddaTable') # self.sync_pandda_table() self.sync_pandda_table_NEW() - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'database panddaTable update finished') + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'database panddaTable update finished') self.Logfile.insert('database panddaTable update finished') self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) - - def change_absolute_to_relative_links(self,target,filename): + def change_absolute_to_relative_links(self, target, filename): os.unlink(filename) - os.symlink(os.path.relpath(target),filename) - self.Logfile.insert('{0!s} -> {1!s}'.format(os.readlink(filename), target)) + os.symlink(os.path.relpath(target), filename) + self.Logfile.insert( + '{0!s} -> {1!s}'.format(os.readlink(filename), target)) - def find_file(self,filename,xtal): - found_file=False + def find_file(self, filename, xtal): + found_file = False for files in glob.glob('*'): if files == filename: # at this point, this could ba a file or a (broken) symbolic link try: - link=os.readlink(filename) + link = os.readlink(filename) if link.startswith('/'): - if os.path.isfile(link.replace(link[:link.find(xtal)],self.initial_model_directory+'/')): - target=link.replace(link[:link.find(xtal)],self.initial_model_directory+'/') - found_file=True - self.change_absolute_to_relative_links(target,filename) + if os.path.isfile(link.replace(link[:link.find(xtal)], self.initial_model_directory+'/')): + target = link.replace( + link[:link.find(xtal)], self.initial_model_directory+'/') + found_file = True + self.change_absolute_to_relative_links( + target, filename) elif os.path.isfile(files): # this will leave the absolute path - found_file=True + found_file = True else: - self.Logfile.insert('removing broken link: '+filename) - os.system('/bin/rm {0!s} 2> /dev/null'.format(filename)) + self.Logfile.insert( + 'removing broken link: '+filename) + os.system( + '/bin/rm {0!s} 2> /dev/null'.format(filename)) else: if not os.path.isfile(link): - self.Logfile.insert('removing broken link: '+filename) - os.system('/bin/rm {0!s} 2> /dev/null'.format(filename)) + self.Logfile.insert( + 'removing broken link: '+filename) + os.system( + '/bin/rm {0!s} 2> /dev/null'.format(filename)) else: - found_file=True + found_file = True except OSError: if os.path.isfile(filename): - found_file=True + found_file = True break return found_file - - - - def sync_data_processing(self,xtal,db_dict): + def sync_data_processing(self, xtal, db_dict): # AIMLESS logfile # in case the MTZ file which is used for refinement is different to the one used for refinement if os.path.isfile('refine.mtz'): if os.path.isfile(xtal+'.free.mtz'): - freeMTZ=mtztools(xtal+'.free.mtz') - nREFfree=freeMTZ.get_number_measured_reflections() + freeMTZ = mtztools(xtal+'.free.mtz') + nREFfree = freeMTZ.get_number_measured_reflections() if os.path.isfile(xtal+'.mtz'): - procMTZ=mtztools(xtal+'.mtz') - nREF=procMTZ.get_number_measured_reflections() - CC,errorMessage=freeMTZ.calculate_correlaton_between_intensities_in_mtzfiles(xtal+'.mtz') - self.Logfile.insert('%s: calculating CC between %s.free.mtz (%s refl) and %s.mtz (%s refl): %s' %(xtal,xtal,str(nREFfree),xtal,str(nREF),str(CC))) + procMTZ = mtztools(xtal+'.mtz') + nREF = procMTZ.get_number_measured_reflections() + CC, errorMessage = freeMTZ.calculate_correlaton_between_intensities_in_mtzfiles( + xtal+'.mtz') + self.Logfile.insert('%s: calculating CC between %s.free.mtz (%s refl) and %s.mtz (%s refl): %s' % ( + xtal, xtal, str(nREFfree), xtal, str(nREF), str(CC))) if errorMessage != '': - self.Logfile.insert('pointless failed with the following error: %s' %errorMessage) + self.Logfile.insert( + 'pointless failed with the following error: %s' % errorMessage) try: if float(CC) < 0.999: - self.Logfile.insert('correlation coefficient between the two files is below 0.999; will try to understand from dimple.log which one was used for initial map calculation') + self.Logfile.insert( + 'correlation coefficient between the two files is below 0.999; will try to understand from dimple.log which one was used for initial map calculation') if os.path.isfile('dimple/dimple_rerun_on_selected_file/dimple/dimple.log'): - foundLine=False - mtzin='' + foundLine = False + mtzin = '' for line in open('dimple/dimple_rerun_on_selected_file/dimple/dimple.log'): if foundLine: - mtzin=line.replace(' ','').replace('\n','').replace('\r','') - self.Logfile.insert('%s was used for inital map calculation' %mtzin) + mtzin = line.replace(' ', '').replace( + '\n', '').replace('\r', '') + self.Logfile.insert( + '%s was used for inital map calculation' % mtzin) break if line.startswith(' --no-cleanup'): - foundLine=True + foundLine = True if os.path.isfile(mtzin): - self.Logfile.insert('%s: mtzfile used for refinement is not the same as the one chosen from autoprocessing' %xtal) - self.Logfile.insert('%s: current mtzfile after autoprocessing: %s' %(xtal,os.path.realpath(xtal+'.mtz'))) - self.Logfile.insert('%s: removing links for %s.mtz/%s.log' %(xtal,xtal,xtal)) - os.system('/bin/rm %s.mtz 2> /dev/null' %xtal) - os.system('/bin/rm %s.log 2> /dev/null' %xtal) - self.Logfile.insert('linking %s to %s.mtz' %(os.path.relpath(mtzin),xtal)) - os.symlink(os.path.relpath(mtzin),xtal+'.mtz') - for logfile in glob.glob(os.path.join(mtzin[:mtzin.rfind('/')],'*log')): - self.Logfile.insert('linking %s to %s.log' %(os.path.relpath(logfile),xtal)) - os.symlink(os.path.relpath(logfile),xtal+'.log') + self.Logfile.insert( + '%s: mtzfile used for refinement is not the same as the one chosen from autoprocessing' % xtal) + self.Logfile.insert('%s: current mtzfile after autoprocessing: %s' % ( + xtal, os.path.realpath(xtal+'.mtz'))) + self.Logfile.insert( + '%s: removing links for %s.mtz/%s.log' % (xtal, xtal, xtal)) + os.system( + '/bin/rm %s.mtz 2> /dev/null' % xtal) + os.system( + '/bin/rm %s.log 2> /dev/null' % xtal) + self.Logfile.insert('linking %s to %s.mtz' % ( + os.path.relpath(mtzin), xtal)) + os.symlink(os.path.relpath( + mtzin), xtal+'.mtz') + for logfile in glob.glob(os.path.join(mtzin[:mtzin.rfind('/')], '*log')): + self.Logfile.insert('linking %s to %s.log' % ( + os.path.relpath(logfile), xtal)) + os.symlink(os.path.relpath( + logfile), xtal+'.log') break except ValueError: - self.Logfile.insert('something went wrong: calculated CC value does not seem to be a floating point number') + self.Logfile.insert( + 'something went wrong: calculated CC value does not seem to be a floating point number') - found_logfile=False + found_logfile = False if os.path.isfile(xtal+'.log'): - found_logfile=True + found_logfile = True # db_dict['DataProcessingPathToLogfile']=os.path.realpath(xtal+'.log').replace(os.getcwd()+'/','') - db_dict['DataProcessingPathToLogfile']=os.path.realpath(xtal+'.log') - db_dict['DataProcessingLOGfileName']=xtal+'.log' - if db_dict['DataCollectionOutcome']=='None' or db_dict['DataCollectionOutcome']=='': - db_dict['DataCollectionOutcome']='success' + db_dict['DataProcessingPathToLogfile'] = os.path.realpath( + xtal+'.log') + db_dict['DataProcessingLOGfileName'] = xtal+'.log' + if db_dict['DataCollectionOutcome'] == 'None' or db_dict['DataCollectionOutcome'] == '': + db_dict['DataCollectionOutcome'] = 'success' # aimless_results=parse().read_aimless_logfile(xtal+'.log') - aimless_results=parse().read_aimless_logfile(db_dict['DataProcessingPathToLogfile']) + aimless_results = parse().read_aimless_logfile( + db_dict['DataProcessingPathToLogfile']) db_dict.update(aimless_results) else: - db_dict['DataProcessingPathToLogfile']='' - db_dict['DataProcessingLOGfileName']='' + db_dict['DataProcessingPathToLogfile'] = '' + db_dict['DataProcessingLOGfileName'] = '' # MTZ file # found_mtzfile=self.find_file(xtal+'.mtz',xtal) # if found_mtzfile: if os.path.isfile(xtal+'.mtz'): - db_dict['DataProcessingPathToMTZfile']=os.path.realpath(xtal+'.mtz') + db_dict['DataProcessingPathToMTZfile'] = os.path.realpath( + xtal+'.mtz') # db_dict['DataProcessingPathToMTZfile']=os.path.realpath(xtal+'.mtz').replace(os.getcwd()+'/','') - db_dict['DataProcessingMTZfileName']=xtal+'.mtz' + db_dict['DataProcessingMTZfileName'] = xtal+'.mtz' if not found_logfile: - mtz_info=mtztools(xtal+'.mtz').get_information_for_datasource() + mtz_info = mtztools( + xtal+'.mtz').get_information_for_datasource() db_dict.update(mtz_info) - db_dict['DataCollectionOutcome']='success' + db_dict['DataCollectionOutcome'] = 'success' else: - db_dict['DataProcessingPathToMTZfile']='' - db_dict['DataProcessingMTZfileName']='' + db_dict['DataProcessingPathToMTZfile'] = '' + db_dict['DataProcessingMTZfileName'] = '' return db_dict - - def sync_dimple_results(self,xtal,db_dict): + def sync_dimple_results(self, xtal, db_dict): # DIMPLE pdb -# found_dimple_pdb=self.find_file('dimple.pdb',xtal) -# if found_dimple_pdb: + # found_dimple_pdb=self.find_file('dimple.pdb',xtal) + # if found_dimple_pdb: if os.path.isfile('dimple.pdb'): -# db_dict['DimplePathToPDB']=os.path.realpath('dimple.pdb').replace(os.getcwd()+'/','') - db_dict['DimplePathToPDB']=os.path.realpath('dimple.pdb') - pdb_info=parse().PDBheader('dimple.pdb') - db_dict['DimpleRcryst']=pdb_info['Rcryst'] - db_dict['DimpleRfree']=pdb_info['Rfree'] - db_dict['DimpleResolutionHigh']=pdb_info['ResolutionHigh'] - db_dict['DimpleStatus']='finished' + # db_dict['DimplePathToPDB']=os.path.realpath('dimple.pdb').replace(os.getcwd()+'/','') + db_dict['DimplePathToPDB'] = os.path.realpath('dimple.pdb') + pdb_info = parse().PDBheader('dimple.pdb') + db_dict['DimpleRcryst'] = pdb_info['Rcryst'] + db_dict['DimpleRfree'] = pdb_info['Rfree'] + db_dict['DimpleResolutionHigh'] = pdb_info['ResolutionHigh'] + db_dict['DimpleStatus'] = 'finished' else: - db_dict['DimplePathToPDB']='' - db_dict['DimpleRcryst']='' - db_dict['DimpleRfree']='' - db_dict['DimpleResolutionHigh']='' - db_dict['DimpleStatus']='pending' + db_dict['DimplePathToPDB'] = '' + db_dict['DimpleRcryst'] = '' + db_dict['DimpleRfree'] = '' + db_dict['DimpleResolutionHigh'] = '' + db_dict['DimpleStatus'] = 'pending' # DIMPLE mtz - dimple_path='' + dimple_path = '' # found_dimple_mtz=self.find_file('dimple.mtz',xtal) # if found_dimple_mtz: if os.path.isfile('dimple.mtz'): -# db_dict['DimplePathToMTZ']=os.path.realpath('dimple.mtz').replace(os.getcwd()+'/','') - db_dict['DimplePathToMTZ']=os.path.realpath('dimple.mtz') - dimple_mtz=db_dict['DimplePathToMTZ'] - dimple_path=dimple_mtz[:dimple_mtz.rfind('/')] + # db_dict['DimplePathToMTZ']=os.path.realpath('dimple.mtz').replace(os.getcwd()+'/','') + db_dict['DimplePathToMTZ'] = os.path.realpath('dimple.mtz') + dimple_mtz = db_dict['DimplePathToMTZ'] + dimple_path = dimple_mtz[:dimple_mtz.rfind('/')] else: - db_dict['DimplePathToMTZ']='' - db_dict['DimpleStatus']='pending' + db_dict['DimplePathToMTZ'] = '' + db_dict['DimpleStatus'] = 'pending' - if os.path.isfile(os.path.join(dimple_path,'dimple','dimple_rerun_on_selected_file','dimple_run_in_progress')): - db_dict['DimpleStatus']='running' + if os.path.isfile(os.path.join(dimple_path, 'dimple', 'dimple_rerun_on_selected_file', 'dimple_run_in_progress')): + db_dict['DimpleStatus'] = 'running' # MTZ free file # found_free_mtz=self.find_file(xtal+'.free.mtz',xtal) # if found_free_mtz: if os.path.isfile(xtal+'.free.mtz'): - db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz') + db_dict['RefinementMTZfree'] = os.path.realpath(xtal+'.free.mtz') # db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz').replace(os.getcwd()+'/','') else: - db_dict['RefinementMTZfree']='' - os.system('/bin/rm %s.free.mtz 2> /dev/null' %xtal) - if os.path.isfile(os.path.join(dimple_path,'prepared2.mtz')): - os.symlink(os.path.relpath(os.path.join(dimple_path,'prepared2.mtz')),xtal+'.free.mtz') + db_dict['RefinementMTZfree'] = '' + os.system('/bin/rm %s.free.mtz 2> /dev/null' % xtal) + if os.path.isfile(os.path.join(dimple_path, 'prepared2.mtz')): + os.symlink(os.path.relpath(os.path.join( + dimple_path, 'prepared2.mtz')), xtal+'.free.mtz') # db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz').replace(os.getcwd()+'/','') - db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz') + db_dict['RefinementMTZfree'] = os.path.realpath( + xtal+'.free.mtz') # db_dict['RefinementMTZfree']=xtal+'.free.mtz' - elif os.path.isfile(os.path.join(dimple_path,'prepared.mtz')): - os.symlink(os.path.relpath(os.path.join(dimple_path,'prepared.mtz')),xtal+'.free.mtz') - db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz') + elif os.path.isfile(os.path.join(dimple_path, 'prepared.mtz')): + os.symlink(os.path.relpath(os.path.join( + dimple_path, 'prepared.mtz')), xtal+'.free.mtz') + db_dict['RefinementMTZfree'] = os.path.realpath( + xtal+'.free.mtz') # db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz').replace(os.getcwd()+'/','') # db_dict['RefinementMTZfree']=xtal+'.free.mtz' - elif os.path.isfile(os.path.join(dimple_path,'free.mtz')): - os.symlink(os.path.relpath(os.path.join(dimple_path,'free.mtz')),xtal+'.free.mtz') - db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz') + elif os.path.isfile(os.path.join(dimple_path, 'free.mtz')): + os.symlink(os.path.relpath(os.path.join( + dimple_path, 'free.mtz')), xtal+'.free.mtz') + db_dict['RefinementMTZfree'] = os.path.realpath( + xtal+'.free.mtz') return db_dict - - def sync_compound_information(self,db_dict): + def sync_compound_information(self, db_dict): # only update database if SMILES or compoundID field is blank! - compoundID=db_dict['CompoundCode'] - if compoundID=='None' or compoundID=='': + compoundID = db_dict['CompoundCode'] + if compoundID == 'None' or compoundID == '': if os.path.isdir('compound'): for smiles in glob.glob('compound/*'): if smiles.endswith('smiles'): for line in open(smiles): if len(line.split()) >= 1: - db_dict['CompoundCode']=smiles[smiles.rfind('/')+1:smiles.rfind('.')] - compoundID=db_dict['CompoundCode'] + db_dict['CompoundCode'] = smiles[smiles.rfind( + '/')+1:smiles.rfind('.')] + compoundID = db_dict['CompoundCode'] break if os.path.isfile(compoundID+'.cif') and os.path.getsize(compoundID+'.cif') > 20: - db_dict['RefinementCIF']=os.path.realpath(compoundID+'.cif').replace(os.getcwd()+'/','') - db_dict['RefinementCIFStatus']='restraints generated' + db_dict['RefinementCIF'] = os.path.realpath( + compoundID+'.cif').replace(os.getcwd()+'/', '') + db_dict['RefinementCIFStatus'] = 'restraints generated' else: os.system('/bin/rm {0!s}.cif 2> /dev/null'.format(compoundID)) - os.system('/bin/rm compound/{0!s}.cif 2> /dev/null'.format(compoundID)) - db_dict['RefinementCIF']='' - db_dict['RefinementCIFStatus']='pending' - - smilesDB=db_dict['CompoundSMILES'] - smiles_found=True - if smilesDB=='None' or smilesDB=='': - smiles_found=False + os.system( + '/bin/rm compound/{0!s}.cif 2> /dev/null'.format(compoundID)) + db_dict['RefinementCIF'] = '' + db_dict['RefinementCIFStatus'] = 'pending' + + smilesDB = db_dict['CompoundSMILES'] + smiles_found = True + if smilesDB == 'None' or smilesDB == '': + smiles_found = False if os.path.isdir('compound'): for smiles in glob.glob('compound/*'): if smiles.endswith('smiles'): for line in open(smiles): if len(line.split()) >= 1: - db_dict['CompoundSMILES']=line.split()[0] - smilesDB=db_dict['CompoundSMILES'] - smiles_found=True + db_dict['CompoundSMILES'] = line.split()[0] + smilesDB = db_dict['CompoundSMILES'] + smiles_found = True break if not smiles_found: - db_dict['RefinementCIFStatus']='missing smiles' + db_dict['RefinementCIFStatus'] = 'missing smiles' - if not os.path.isfile(compoundID+'.pdb') or os.path.getsize(compoundID+'.pdb') < 20: + if not os.path.isfile(compoundID+'.pdb') or os.path.getsize(compoundID+'.pdb') < 20: os.system('/bin/rm {0!s}.pdb 2> /dev/null'.format(compoundID)) - os.system('/bin/rm compound/{0!s}.pdb 2> /dev/null'.format(compoundID)) + os.system( + '/bin/rm compound/{0!s}.pdb 2> /dev/null'.format(compoundID)) - if not os.path.isfile(compoundID+'.png') or os.path.getsize(compoundID+'.png') < 20: + if not os.path.isfile(compoundID+'.png') or os.path.getsize(compoundID+'.png') < 20: os.system('/bin/rm {0!s}.png 2> /dev/null'.format(compoundID)) - os.system('/bin/rm compound/{0!s}.png 2> /dev/null'.format(compoundID)) + os.system( + '/bin/rm compound/{0!s}.png 2> /dev/null'.format(compoundID)) return db_dict - - def sync_refinement_results(self,xtal,db_dict): + def sync_refinement_results(self, xtal, db_dict): # # REFINE pdb # -# found_refine_pdb=self.find_file('refine.pdb',xtal) -# if found_refine_pdb and not 'dimple' in os.path.realpath('refine.pdb'): + # found_refine_pdb=self.find_file('refine.pdb',xtal) + # if found_refine_pdb and not 'dimple' in os.path.realpath('refine.pdb'): -# if os.path.isfile('refine.pdb') and not 'dimple' in os.path.realpath('refine.pdb'): + # if os.path.isfile('refine.pdb') and not 'dimple' in os.path.realpath('refine.pdb'): if os.path.isfile('refine.pdb'): - db_dict['RefinementPDB_latest']=os.path.realpath('refine.pdb') + db_dict['RefinementPDB_latest'] = os.path.realpath('refine.pdb') # db_dict['RefinementPDB_latest']=os.path.realpath('refine.pdb').replace(os.getcwd()+'/','') - db_dict['RefinementStatus']='finished' - pdb_info=parse().dict_for_datasource_update('refine.pdb') + db_dict['RefinementStatus'] = 'finished' + pdb_info = parse().dict_for_datasource_update('refine.pdb') db_dict.update(pdb_info) - if db_dict['RefinementOutcome']=='None' or db_dict['RefinementOutcome']=='': - db_dict['RefinementOutcome']='3 - In Refinement' + if db_dict['RefinementOutcome'] == 'None' or db_dict['RefinementOutcome'] == '': + db_dict['RefinementOutcome'] = '3 - In Refinement' elif str(db_dict['RefinementOutcome']).startswith('1'): - db_dict['RefinementOutcome']='3 - In Refinement' + db_dict['RefinementOutcome'] = '3 - In Refinement' elif str(db_dict['RefinementOutcome']).startswith('2'): - db_dict['RefinementOutcome']='3 - In Refinement' + db_dict['RefinementOutcome'] = '3 - In Refinement' else: - db_dict['RefinementPDB_latest']='' - db_dict['RefinementStatus']='pending' - db_dict['RefinementOutcome']='1 - Analysis Pending' + db_dict['RefinementPDB_latest'] = '' + db_dict['RefinementStatus'] = 'pending' + db_dict['RefinementOutcome'] = '1 - Analysis Pending' os.system('/bin/rm refine.pdb 2> /dev/null') if os.path.isfile('REFINEMENT_IN_PROGRESS'): - db_dict['RefinementStatus']='running' + db_dict['RefinementStatus'] = 'running' # # REFINE bound pdb # if os.path.isfile('refine.split.bound-state.pdb'): - db_dict['RefinementBoundConformation']=os.path.realpath('refine.split.bound-state.pdb') + db_dict['RefinementBoundConformation'] = os.path.realpath( + 'refine.split.bound-state.pdb') # db_dict['RefinementBoundConformation']='refine.bound.pdb' else: -# if os.path.isfile('refine.pdb'): -# os.system("giant.strip_conformations pdb=refine.pdb suffix='.bound.pdb'") -# if os.path.isfile('refine.bound.pdb'): -# db_dict['RefinementBoundConformation']=os.path.realpath('refine.bound.pdb') -# else: -# db_dict['RefinementBoundConformation']='' -# else: -# db_dict['RefinementBoundConformation']='' - db_dict['RefinementBoundConformation']='' + # if os.path.isfile('refine.pdb'): + # os.system("giant.strip_conformations pdb=refine.pdb suffix='.bound.pdb'") + # if os.path.isfile('refine.bound.pdb'): + # db_dict['RefinementBoundConformation']=os.path.realpath('refine.bound.pdb') + # else: + # db_dict['RefinementBoundConformation']='' + # else: + # db_dict['RefinementBoundConformation']='' + db_dict['RefinementBoundConformation'] = '' # # REFINE mtz @@ -421,16 +464,15 @@ def sync_refinement_results(self,xtal,db_dict): # if found_refine_mtz and not 'dimple' in os.path.realpath('refine.mtz'): # if os.path.isfile('refine.mtz') and not 'dimple' in os.path.realpath('refine.mtz'): if os.path.isfile('refine.mtz'): - db_dict['RefinementMTZ_latest']=os.path.realpath('refine.mtz') + db_dict['RefinementMTZ_latest'] = os.path.realpath('refine.mtz') # db_dict['RefinementMTZ_latest']=os.path.realpath('refine.mtz').replace(os.getcwd()+'/','') else: - db_dict['RefinementMTZ_latest']='' + db_dict['RefinementMTZ_latest'] = '' os.system('/bin/rm refine.mtz 2> /dev/null') return db_dict - - def find_apo_structures_for_PanDDA(self,panddaPATH): + def find_apo_structures_for_PanDDA(self, panddaPATH): # first check if structure is already present in DB and if so if all the # information concur @@ -444,32 +486,32 @@ def find_apo_structures_for_PanDDA(self,panddaPATH): # newer pandda versions seem to have severl copies of pandda.log with names like # pandda-2016-09-01-2139.log - panddaLog=glob.glob(os.path.join(panddaPATH,'pandda*log')) + panddaLog = glob.glob(os.path.join(panddaPATH, 'pandda*log')) panddaLog.sort(key=os.path.getmtime) - panddaVersion='unknown' + panddaVersion = 'unknown' readindApoStructures = False apoStructures = [] apoStructureDict = {} - apoString='' + apoString = '' for files in panddaLog: for line in open(files): if line.startswith('- Pandda Version'): if len(line.split()) >= 4: - panddaVersion=line.split()[3] + panddaVersion = line.split()[3] if 'No Statistical Maps Found:' in line: - readindApoStructures=True + readindApoStructures = True if readindApoStructures: if 'Pickling Object: processed_datasets' in line: if line.split() >= 2: # e.g. line.split() -> ['Pickling', 'Object:', 'processed_datasets/NUDT22A-x0055/pickles/dataset.pickle'] - xtal=line.split()[2].split('/')[1] - if os.path.isfile(os.path.join(panddaPATH,'processed_datasets',xtal,xtal+'-pandda-input.pdb')): + xtal = line.split()[2].split('/')[1] + if os.path.isfile(os.path.join(panddaPATH, 'processed_datasets', xtal, xtal+'-pandda-input.pdb')): apoStructures.append(xtal) - apoString+=xtal+';' + apoString += xtal+';' if 'Pre-existing statistical maps (from previous runs) have been found and will be reused:' in line: - readindApoStructures=False - apoStructureDict[panddaPATH]=apoStructures + readindApoStructures = False + apoStructureDict[panddaPATH] = apoStructures return apoString[:-1] @@ -502,7 +544,7 @@ def find_apo_structures_for_PanDDA(self,panddaPATH): # # do not update pandda path since this one is updated during pandda export! # # instead try to get apo semi-colon separated list of apo structures that were used to # # calculate event maps; but only if field is blank! -## db_pandda_dict['PANDDApath']=self.panddas_directory +# db_pandda_dict['PANDDApath']=self.panddas_directory # if str(apoStructures)=='None' or apoStructures=='': # if panddaPATH != 'None' or panddaPATH != '': # self.Logfile.insert('trying to find which apo structures were used to calculate the event maps in '+panddaPATH) @@ -519,7 +561,7 @@ def find_apo_structures_for_PanDDA(self,panddaPATH): # if filename.startswith(xtal+'-event_'+event_index) and filename.endswith('map.native.ccp4'): # event_map=file # db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map) -## db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map).replace(os.getcwd()+'/','') +# db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map).replace(os.getcwd()+'/','') # found_event_map=True # break # if not found_event_map: @@ -580,7 +622,7 @@ def find_apo_structures_for_PanDDA(self,panddaPATH): # spider_plot=os.path.join(tmp[:tmp.rfind('/')],'residue_plots',residue_name+'-'+residue_chain+'-'+residue_number+'.png') # if os.path.isfile(spider_plot): # db_pandda_dict['PANDDA_site_spider_plot']=os.path.realpath(spider_plot) -## db_pandda_dict['PANDDA_site_spider_plot']=os.path.realpath(spider_plot).replace(os.getcwd()+'/','') +# db_pandda_dict['PANDDA_site_spider_plot']=os.path.realpath(spider_plot).replace(os.getcwd()+'/','') # if os.path.isfile(os.path.join(tmp[:tmp.rfind('/')],'residue_scores.csv')): # # with open(os.path.join(tmp[:tmp.rfind('/')],'residue_scores.csv'), 'rb') as csv_import: @@ -606,28 +648,29 @@ def find_apo_structures_for_PanDDA(self,panddaPATH): # self.emit(QtCore.SIGNAL('update_progress_bar'), progress) # - def sync_pandda_table_NEW(self): - progress_step=1 - progress=0 + progress_step = 1 + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) # also need to update PANDDA table... - pandda_models=self.db.execute_statement("select CrystalName,PANDDA_site_index,PANDDA_site_event_index,PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDApath,ApoStructures from panddaTable") + pandda_models = self.db.execute_statement( + "select CrystalName,PANDDA_site_index,PANDDA_site_event_index,PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDApath,ApoStructures from panddaTable") if len(pandda_models) > 0: - progress_step=100/float(len(pandda_models)) + progress_step = 100/float(len(pandda_models)) else: self.Logfile.warning('panddaTable seems to be empty!') if pandda_models: for entry in pandda_models: - db_pandda_dict={} - xtal=entry[0] - site_index=entry[1] - event_index=entry[2] - panddaPATH=entry[6] - apoStructures=entry[7] - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'checking {0!s} -> site {1!s} -> event {2!s} '.format(xtal, site_index, event_index)) + db_pandda_dict = {} + xtal = entry[0] + site_index = entry[1] + event_index = entry[2] + panddaPATH = entry[6] + apoStructures = entry[7] + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'checking {0!s} -> site {1!s} -> event {2!s} '.format(xtal, site_index, event_index)) self.emit(QtCore.SIGNAL('update_progress_bar'), progress) progress += progress_step @@ -642,43 +685,48 @@ def sync_pandda_table_NEW(self): # instead try to get apo semi-colon separated list of apo structures that were used to # calculate event maps; but only if field is blank! # db_pandda_dict['PANDDApath']=self.panddas_directory - if str(apoStructures)=='None' or apoStructures=='': + if str(apoStructures) == 'None' or apoStructures == '': if panddaPATH != 'None' or panddaPATH != '': - self.Logfile.insert('trying to find which apo structures were used to calculate the event maps in '+panddaPATH) - db_pandda_dict['ApoStructures']=self.find_apo_structures_for_PanDDA(panddaPATH) + self.Logfile.insert( + 'trying to find which apo structures were used to calculate the event maps in '+panddaPATH) + db_pandda_dict['ApoStructures'] = self.find_apo_structures_for_PanDDA( + panddaPATH) else: - self.Logfile.insert('pandda path for '+xtal+' is empty in database') + self.Logfile.insert( + 'pandda path for '+xtal+' is empty in database') # event map - found_event_map=False - db_pandda_dict['PANDDA_site_event_map']='' - for file in glob.glob(os.path.join(self.initial_model_directory,xtal,'*ccp4')): - filename=file[file.rfind('/')+1:] + found_event_map = False + db_pandda_dict['PANDDA_site_event_map'] = '' + for file in glob.glob(os.path.join(self.initial_model_directory, xtal, '*ccp4')): + filename = file[file.rfind('/')+1:] if filename.startswith(xtal+'-event_'+event_index) and filename.endswith('map.native.ccp4'): - event_map=file - db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map) + event_map = file + db_pandda_dict['PANDDA_site_event_map'] = os.path.realpath( + event_map) # db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map).replace(os.getcwd()+'/','') - found_event_map=True + found_event_map = True break if not found_event_map: - db_pandda_dict['PANDDA_site_event_map']='' + db_pandda_dict['PANDDA_site_event_map'] = '' - db_pandda_dict['PANDDA_site_initial_model']='' - for file in glob.glob(os.path.join(self.initial_model_directory,xtal,'*pdb')): - filename=file[file.rfind('/')+1:] + db_pandda_dict['PANDDA_site_initial_model'] = '' + for file in glob.glob(os.path.join(self.initial_model_directory, xtal, '*pdb')): + filename = file[file.rfind('/')+1:] if filename.endswith('-ensemble-model.pdb'): - db_pandda_dict['PANDDA_site_initial_model']=os.path.realpath(file).replace(os.getcwd()+'/','') + db_pandda_dict['PANDDA_site_initial_model'] = os.path.realpath( + file).replace(os.getcwd()+'/', '') break - db_pandda_dict['PANDDA_site_initial_mtz']='' - for file in glob.glob(os.path.join(self.initial_model_directory,xtal,'*mtz')): - filename=file[file.rfind('/')+1:] + db_pandda_dict['PANDDA_site_initial_mtz'] = '' + for file in glob.glob(os.path.join(self.initial_model_directory, xtal, '*mtz')): + filename = file[file.rfind('/')+1:] if filename.endswith('pandda-input.mtz'): - db_pandda_dict['PANDDA_site_initial_mtz']=os.path.realpath(file).replace(os.getcwd()+'/','') + db_pandda_dict['PANDDA_site_initial_mtz'] = os.path.realpath( + file).replace(os.getcwd()+'/', '') break - db_pandda_dict['PANDDA_site_ligand_resname'] = '' db_pandda_dict['PANDDA_site_ligand_chain'] = '' db_pandda_dict['PANDDA_site_ligand_sequence_number'] = '' @@ -695,57 +743,72 @@ def sync_pandda_table_NEW(self): db_pandda_dict['PANDDA_site_RSR'] = '' db_pandda_dict['PANDDA_site_RSZD'] = '' - if os.path.isfile(os.path.join(self.initial_model_directory,xtal,'refine.pdb')): - ligands_in_file=pdbtools(os.path.join(self.initial_model_directory,xtal,'refine.pdb')).find_xce_ligand_details() + if os.path.isfile(os.path.join(self.initial_model_directory, xtal, 'refine.pdb')): + ligands_in_file = pdbtools(os.path.join( + self.initial_model_directory, xtal, 'refine.pdb')).find_xce_ligand_details() if not ligands_in_file: - self.Logfile.warning('{0!s}: could not find any ligands in refine.pdb'.format(xtal)) + self.Logfile.warning( + '{0!s}: could not find any ligands in refine.pdb'.format(xtal)) continue else: - self.Logfile.insert('{0!s}: found the following ligands in refine.pdb: {1!s}'.format(xtal, str(ligands_in_file))) + self.Logfile.insert('{0!s}: found the following ligands in refine.pdb: {1!s}'.format( + xtal, str(ligands_in_file))) - distanceList=[] + distanceList = [] for ligand in ligands_in_file: - residue_name= ligand[0] - residue_chain= ligand[1] - residue_number= ligand[2] - residue_altLoc= ligand[3] - residue_xyz = pdbtools(os.path.join(self.initial_model_directory,xtal,'refine.pdb')).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) - distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1],residue_xyz[2],event_x, event_y,event_z) - distanceList.append([distance,residue_name,residue_chain,residue_number,residue_altLoc]) - self.Logfile.insert('{0!s}: calculating distance between event and ligand ({1!s} {2!s} {3!s}): {4!s}'.format(xtal, residue_name, residue_chain, residue_number, str(distance))) + residue_name = ligand[0] + residue_chain = ligand[1] + residue_number = ligand[2] + residue_altLoc = ligand[3] + residue_xyz = pdbtools(os.path.join(self.initial_model_directory, xtal, 'refine.pdb') + ).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) + distance = misc().calculate_distance_between_coordinates( + residue_xyz[0], residue_xyz[1], residue_xyz[2], event_x, event_y, event_z) + distanceList.append( + [distance, residue_name, residue_chain, residue_number, residue_altLoc]) + self.Logfile.insert('{0!s}: calculating distance between event and ligand ({1!s} {2!s} {3!s}): {4!s}'.format( + xtal, residue_name, residue_chain, residue_number, str(distance))) # now take the ligand that is closest to the event try: - smallestDistance = min(distanceList, key=lambda x: x[0]) + smallestDistance = min( + distanceList, key=lambda x: x[0]) except ValueError: - self.Logfile.error('could not determine smallest distance between current ligand pandda events') + self.Logfile.error( + 'could not determine smallest distance between current ligand pandda events') continue - distance = smallestDistance[0] - residue_name = smallestDistance[1] - residue_chain = smallestDistance[2] - residue_number = smallestDistance[3] - residue_altLoc = smallestDistance[4] - self.Logfile.insert('{0!s}: ligand with the shorted distance ({1!s}A) to the current event (id: {2!s}): {3!s} {4!s} {5!s} {6!s}'.format(xtal, str(distance), event_index, residue_name, residue_chain, residue_number, residue_altLoc)) + distance = smallestDistance[0] + residue_name = smallestDistance[1] + residue_chain = smallestDistance[2] + residue_number = smallestDistance[3] + residue_altLoc = smallestDistance[4] + self.Logfile.insert('{0!s}: ligand with the shorted distance ({1!s}A) to the current event (id: {2!s}): {3!s} {4!s} {5!s} {6!s}'.format( + xtal, str(distance), event_index, residue_name, residue_chain, residue_number, residue_altLoc)) db_pandda_dict['PANDDA_site_ligand_resname'] = residue_name db_pandda_dict['PANDDA_site_ligand_chain'] = residue_chain db_pandda_dict['PANDDA_site_ligand_sequence_number'] = residue_number db_pandda_dict['PANDDA_site_ligand_altLoc'] = residue_altLoc db_pandda_dict['PANDDA_site_ligand_placed'] = 'True' - db_pandda_dict['PANDDA_site_ligand_id']=residue_name+'-'+residue_chain+'-'+residue_number - - if xtal+'/Refine_' in os.path.realpath(os.path.join(self.initial_model_directory,xtal,'refine.pdb')): - tmp=os.path.realpath(os.path.join(self.initial_model_directory,xtal,'refine.pdb')) - spider_plot=os.path.join(tmp[:tmp.rfind('/')],'residue_plots',residue_chain+'-'+residue_number+'.png').replace(' ','') + db_pandda_dict['PANDDA_site_ligand_id'] = residue_name + \ + '-'+residue_chain+'-'+residue_number + + if xtal+'/Refine_' in os.path.realpath(os.path.join(self.initial_model_directory, xtal, 'refine.pdb')): + tmp = os.path.realpath(os.path.join( + self.initial_model_directory, xtal, 'refine.pdb')) + spider_plot = os.path.join(tmp[:tmp.rfind( + '/')], 'residue_plots', residue_chain+'-'+residue_number+'.png').replace(' ', '') if os.path.isfile(spider_plot): - db_pandda_dict['PANDDA_site_spider_plot']=os.path.realpath(spider_plot) - if os.path.isfile(os.path.join(tmp[:tmp.rfind('/')],'residue_scores.csv')): - with open(os.path.join(tmp[:tmp.rfind('/')],'residue_scores.csv'), 'rb') as csv_import: + db_pandda_dict['PANDDA_site_spider_plot'] = os.path.realpath( + spider_plot) + if os.path.isfile(os.path.join(tmp[:tmp.rfind('/')], 'residue_scores.csv')): + with open(os.path.join(tmp[:tmp.rfind('/')], 'residue_scores.csv'), 'rb') as csv_import: csv_dict = csv.DictReader(csv_import) for i, line in enumerate(csv_dict): residueNameChainNumber = line[''] if residueNameChainNumber == residue_chain+'-'+residue_number: db_pandda_dict['PANDDA_site_occupancy'] = line['Occupancy'] - db_pandda_dict['PANDDA_site_B_average'] = line['Average B-factor (Residue)'] + db_pandda_dict['PANDDA_site_B_average'] = line[ + 'Average B-factor (Residue)'] db_pandda_dict['PANDDA_site_B_ratio_residue_surroundings'] = line['Surroundings B-factor Ratio'] db_pandda_dict['PANDDA_site_rmsd'] = line['Model RMSD'] db_pandda_dict['PANDDA_site_RSCC'] = line['RSCC'] @@ -754,60 +817,64 @@ def sync_pandda_table_NEW(self): # break if db_pandda_dict != {}: -# self.db.update_panddaTable(xtal, site_index, db_pandda_dict) - self.db.update_site_event_panddaTable(xtal, site_index, event_index, db_pandda_dict) - self.Logfile.insert('updating panddaTable for xtal: {0!s}, site: {1!s}, event: {2!s}'.format(xtal, site_index,event_index)) - self.Logfile.insert('-> panddaDict: ' + str(db_pandda_dict)) + # self.db.update_panddaTable(xtal, site_index, db_pandda_dict) + self.db.update_site_event_panddaTable( + xtal, site_index, event_index, db_pandda_dict) + self.Logfile.insert('updating panddaTable for xtal: {0!s}, site: {1!s}, event: {2!s}'.format( + xtal, site_index, event_index)) + self.Logfile.insert( + '-> panddaDict: ' + str(db_pandda_dict)) # progress += progress_step # self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - - - class create_png_and_cif_of_compound(QtCore.QThread): - def __init__(self,external_software,initial_model_directory,compound_list,database_directory,data_source_file,todo,ccp4_scratch_directory,xce_logfile,max_queue_jobs,restraints_program): + def __init__(self, external_software, initial_model_directory, compound_list, database_directory, data_source_file, todo, ccp4_scratch_directory, xce_logfile, max_queue_jobs, restraints_program): QtCore.QThread.__init__(self) - self.external_software=external_software - self.initial_model_directory=initial_model_directory - self.compound_list=compound_list - self.database_directory=database_directory - self.data_source_file=data_source_file - self.todo=todo - self.ccp4_scratch_directory=ccp4_scratch_directory - self.xce_logfile=xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) - self.max_queue_jobs=max_queue_jobs - self.db=XChemDB.data_source(os.path.join(self.database_directory,self.data_source_file)) - self.restraints_program=restraints_program + self.external_software = external_software + self.initial_model_directory = initial_model_directory + self.compound_list = compound_list + self.database_directory = database_directory + self.data_source_file = data_source_file + self.todo = todo + self.ccp4_scratch_directory = ccp4_scratch_directory + self.xce_logfile = xce_logfile + self.Logfile = XChemLog.updateLog(xce_logfile) + self.max_queue_jobs = max_queue_jobs + self.db = XChemDB.data_source(os.path.join( + self.database_directory, self.data_source_file)) + self.restraints_program = restraints_program def run(self): # first remove all ACEDRG input scripts in ccp4_scratch directory - self.Logfile.insert('removing all xce_acedrg scripts from '+self.ccp4_scratch_directory) + self.Logfile.insert( + 'removing all xce_acedrg scripts from '+self.ccp4_scratch_directory) os.chdir(self.ccp4_scratch_directory) os.system('/bin/rm -f xce_acedrg*') - progress_step=100/float(len(self.compound_list)) - progress=0 - counter=1 + progress_step = 100/float(len(self.compound_list)) + progress = 0 + counter = 1 for item in self.compound_list: - sampleID=item[0] - compoundID=item[1] - sm=item[2] + sampleID = item[0] + compoundID = item[1] + sm = item[2] # if counterions are present, split and take the longest string in list smiles = max(sm.split('.'), key=len) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'creating ACEDRG shell script for '+sampleID) - if compoundID=='' or compoundID is None: - compoundID='compound' + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'creating ACEDRG shell script for '+sampleID) + if compoundID == '' or compoundID is None: + compoundID = 'compound' - if not os.path.isdir(os.path.join(self.initial_model_directory,sampleID)): - os.mkdir(os.path.join(self.initial_model_directory,sampleID)) + if not os.path.isdir(os.path.join(self.initial_model_directory, sampleID)): + os.mkdir(os.path.join(self.initial_model_directory, sampleID)) - if self.todo=='ALL' or self.todo=='SELECTED': + if self.todo == 'ALL' or self.todo == 'SELECTED': # remove symbolic links if present - if os.path.isfile(os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.pdb')): - os.system('/bin/rm '+os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.pdb')) + if os.path.isfile(os.path.join(self.initial_model_directory, sampleID, compoundID.replace(' ', '')+'.pdb')): + os.system('/bin/rm '+os.path.join(self.initial_model_directory, + sampleID, compoundID.replace(' ', '')+'.pdb')) # commented this out since people found the presence of the old.cif file interfering with pandda.inspect # if os.path.isfile(os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.cif')): # # copy existing CIF file to old.cif so that it can be used as input in @@ -815,112 +882,134 @@ def run(self): # os.chdir(os.path.join(self.initial_model_directory,sampleID)) # os.system('/bin/cp %s old.cif' %(compoundID.replace(' ','')+'.cif')) # os.system('/bin/rm '+os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.cif')) - if os.path.isfile(os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.png')): - os.system('/bin/rm '+os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.png')) - if os.path.isdir(os.path.join(self.initial_model_directory,sampleID,'compound')): - os.system('/bin/rm -fr '+os.path.join(self.initial_model_directory,sampleID,'compound')) - db_dict= {'RefinementCIFStatus': 'pending'} - self.Logfile.insert('{0!s}: removed compound directory and all its contents'.format(sampleID)) - self.Logfile.insert('{0!s}: setting RefinementCIFStatus flag to started'.format(sampleID)) - self.db.update_data_source(sampleID,db_dict) + if os.path.isfile(os.path.join(self.initial_model_directory, sampleID, compoundID.replace(' ', '')+'.png')): + os.system('/bin/rm '+os.path.join(self.initial_model_directory, + sampleID, compoundID.replace(' ', '')+'.png')) + if os.path.isdir(os.path.join(self.initial_model_directory, sampleID, 'compound')): + os.system( + '/bin/rm -fr '+os.path.join(self.initial_model_directory, sampleID, 'compound')) + db_dict = {'RefinementCIFStatus': 'pending'} + self.Logfile.insert( + '{0!s}: removed compound directory and all its contents'.format(sampleID)) + self.Logfile.insert( + '{0!s}: setting RefinementCIFStatus flag to started'.format(sampleID)) + self.db.update_data_source(sampleID, db_dict) # create 'compound' directory if not present - if not os.path.isdir(os.path.join(self.initial_model_directory,sampleID,'compound')): - os.mkdir(os.path.join(self.initial_model_directory,sampleID,'compound')) + if not os.path.isdir(os.path.join(self.initial_model_directory, sampleID, 'compound')): + os.mkdir(os.path.join( + self.initial_model_directory, sampleID, 'compound')) # create text file which contains the smiles string - if not os.path.isfile(os.path.join(self.initial_model_directory,sampleID,'compound',compoundID+'.smiles')): - os.chdir(os.path.join(self.initial_model_directory,sampleID,'compound')) - f=open(compoundID+'.smiles','w') + if not os.path.isfile(os.path.join(self.initial_model_directory, sampleID, 'compound', compoundID+'.smiles')): + os.chdir(os.path.join( + self.initial_model_directory, sampleID, 'compound')) + f = open(compoundID+'.smiles', 'w') f.write(smiles) f.close() - if not os.path.isfile(os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.cif')) \ - or self.todo=='SELECTED': - os.chdir(os.path.join(self.initial_model_directory,sampleID)) - os.system('/bin/rm -f %s*' %compoundID.replace(' ','')) - os.chdir(os.path.join(self.initial_model_directory,sampleID,'compound')) - - - helpers().make_png( self.initial_model_directory, - sampleID, - compoundID, - smiles, - self.external_software, - self.database_directory, - self.data_source_file, - self.ccp4_scratch_directory, - counter, - self.xce_logfile, - self.restraints_program ) + if not os.path.isfile(os.path.join(self.initial_model_directory, sampleID, compoundID.replace(' ', '')+'.cif')) \ + or self.todo == 'SELECTED': + os.chdir(os.path.join(self.initial_model_directory, sampleID)) + os.system('/bin/rm -f %s*' % compoundID.replace(' ', '')) + os.chdir(os.path.join( + self.initial_model_directory, sampleID, 'compound')) + + helpers().make_png(self.initial_model_directory, + sampleID, + compoundID, + smiles, + self.external_software, + self.database_directory, + self.data_source_file, + self.ccp4_scratch_directory, + counter, + self.xce_logfile, + self.restraints_program) counter += 1 - db_dict= {'RefinementCIFprogram': self.restraints_program, 'RefinementCIFStatus': 'started'} - self.Logfile.insert('{0!s}: setting RefinementCIFStatus flag to started'.format(sampleID)) - self.db.update_data_source(sampleID,db_dict) + db_dict = {'RefinementCIFprogram': self.restraints_program, + 'RefinementCIFStatus': 'started'} + self.Logfile.insert( + '{0!s}: setting RefinementCIFStatus flag to started'.format(sampleID)) + self.db.update_data_source(sampleID, db_dict) progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) # submit array job at Diamond - self.Logfile.insert('created input scripts for '+str(counter)+' ACEDRG jobs in '+self.ccp4_scratch_directory) + self.Logfile.insert('created input scripts for '+str(counter) + + ' ACEDRG jobs in '+self.ccp4_scratch_directory) os.chdir(self.ccp4_scratch_directory) - self.Logfile.insert('changing directory to '+self.ccp4_scratch_directory) + self.Logfile.insert('changing directory to ' + + self.ccp4_scratch_directory) if counter > 1: -# if os.getcwd().startswith('/dls'): + # if os.getcwd().startswith('/dls'): if os.path.isdir('/dls'): if self.external_software['qsub_array']: Cmds = ( - '#PBS -joe -N xce_%s_master\n' %self.restraints_program + - './xce_%s_$SGE_TASK_ID.sh\n' %self.restraints_program - ) - f = open('%s_master.sh' %self.restraints_program,'w') + '#PBS -joe -N xce_%s_master\n' % self.restraints_program + + './xce_%s_$SGE_TASK_ID.sh\n' % self.restraints_program + ) + f = open('%s_master.sh' % self.restraints_program, 'w') f.write(Cmds) f.close() - self.Logfile.insert('submitting array job with maximal 100 jobs running on cluster') + self.Logfile.insert( + 'submitting array job with maximal 100 jobs running on cluster') self.Logfile.insert('using the following command:') - self.Logfile.insert(' qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh'.format(str(counter), self.max_queue_jobs,self.restraints_program)) - os.system('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} -N {2!s} {3!s}_master.sh'.format(str(counter), self.max_queue_jobs,self.restraints_program,self.restraints_program)) + self.Logfile.insert(' qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh'.format( + str(counter), self.max_queue_jobs, self.restraints_program)) + os.system('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} -N {2!s} {3!s}_master.sh'.format( + str(counter), self.max_queue_jobs, self.restraints_program, self.restraints_program)) else: - self.Logfile.insert("cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") + self.Logfile.insert( + "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") elif self.external_software['qsub']: - self.Logfile.insert('submitting {0!s} individual jobs to cluster'.format((str(counter)))) - self.Logfile.insert('WARNING: this could potentially lead to a crash...') + self.Logfile.insert( + 'submitting {0!s} individual jobs to cluster'.format((str(counter)))) + self.Logfile.insert( + 'WARNING: this could potentially lead to a crash...') for i in range(counter): - self.Logfile.insert('qsub -q medium.q -N {0!s} xce_{1!s}_{2!s}.sh'.format(self.restraints_program,self.restraints_program,(str(i+1)))) - os.system('qsub -N {0!s} xce_{1!s}_{2!s}.sh'.format(self.restraints_program,self.restraints_program,(str(i+1)))) + self.Logfile.insert('qsub -q medium.q -N {0!s} xce_{1!s}_{2!s}.sh'.format( + self.restraints_program, self.restraints_program, (str(i+1)))) + os.system('qsub -N {0!s} xce_{1!s}_{2!s}.sh'.format( + self.restraints_program, self.restraints_program, (str(i+1)))) else: - self.Logfile.insert('running %s consecutive %s jobs on your local machine' %(str(counter),self.restraints_program)) + self.Logfile.insert('running %s consecutive %s jobs on your local machine' % ( + str(counter), self.restraints_program)) for i in range(counter): - self.Logfile.insert('starting xce_{0!s}_{1!s}.sh'.format(self.restraints_program,(str(i+1)))) - os.system('./xce_{0!s}_{1!s}.sh'.format(self.restraints_program,(str(i+1)))) + self.Logfile.insert('starting xce_{0!s}_{1!s}.sh'.format( + self.restraints_program, (str(i+1)))) + os.system( + './xce_{0!s}_{1!s}.sh'.format(self.restraints_program, (str(i+1)))) # self.emit(QtCore.SIGNAL("finished()")) self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) - class fit_ligands(QtCore.QThread): - def __init__(self,external_software,initial_model_directory,compound_list,database_directory,data_source_file,ccp4_scratch_directory,xce_logfile,max_queue_jobs): + def __init__(self, external_software, initial_model_directory, compound_list, database_directory, data_source_file, ccp4_scratch_directory, xce_logfile, max_queue_jobs): QtCore.QThread.__init__(self) - self.external_software=external_software + self.external_software = external_software self.queueing_system_available = external_software['qsub'] - self.initial_model_directory=initial_model_directory - self.compound_list=compound_list - self.database_directory=database_directory - self.data_source_file=data_source_file - self.ccp4_scratch_directory=ccp4_scratch_directory - self.xce_logfile=xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) - self.max_queue_jobs=max_queue_jobs - self.db=XChemDB.data_source(os.path.join(self.database_directory,self.data_source_file)) + self.initial_model_directory = initial_model_directory + self.compound_list = compound_list + self.database_directory = database_directory + self.data_source_file = data_source_file + self.ccp4_scratch_directory = ccp4_scratch_directory + self.xce_logfile = xce_logfile + self.Logfile = XChemLog.updateLog(xce_logfile) + self.max_queue_jobs = max_queue_jobs + self.db = XChemDB.data_source(os.path.join( + self.database_directory, self.data_source_file)) self.n = 1 - def prepareInput(self,cmd,ligList): + def prepareInput(self, cmd, ligList): for cif in ligList: - cmd += 'rhofit -m ../init.mtz -p ../init.pdb -l ../compound/%s.cif -scanchirals -d %s_rhofit\n' %(cif,cif) - cmd += 'phenix.ligandfit data=../init.mtz model=../init.pdb ligand=../compound/%s.cif clean_up=True\n' %cif - cmd += '/bin/mv LigandFit_run_1_ %s_phenix\n' %cif + cmd += 'rhofit -m ../init.mtz -p ../init.pdb -l ../compound/%s.cif -scanchirals -d %s_rhofit\n' % ( + cif, cif) + cmd += 'phenix.ligandfit data=../init.mtz model=../init.pdb ligand=../compound/%s.cif clean_up=True\n' % cif + cmd += '/bin/mv LigandFit_run_1_ %s_phenix\n' % cif cmd += '/bin/rm -fr PDS\n\n' return cmd # rhofit -m refine.mtz -p refine.pdb -l ../compound/NU074105a.cif -d NU074105a_rhofit @@ -928,7 +1017,7 @@ def prepareInput(self,cmd,ligList): # phenix.get_cc_mtz_pdb LigandFit_run_1_/ligand_fit_1_1.pdb refine.mtz > log # grep 'local CC:' log - def get_header(self,sampleID): + def get_header(self, sampleID): if self.queueing_system_available: top_line = '#PBS -joe -N XCE_dimple\n' else: @@ -940,44 +1029,47 @@ def get_header(self,sampleID): module += 'module load buster\n' cmd = ( - '{0!s}\n'.format(top_line)+ + '{0!s}\n'.format(top_line) + '\n' 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,sampleID,'autofit_ligand') + + 'cd %s\n' % os.path.join(self.initial_model_directory, sampleID, 'autofit_ligand') + '\n' + module ) return cmd - def get_footer(self,cmd,sampleID,compoundID): + def get_footer(self, cmd, sampleID, compoundID): cmd += ('$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/find_best_fitting_ligand.py {0!s} {1!s} {2!s}' .format(compoundID.replace(' ', ''), os.path.join(self.initial_model_directory, sampleID), - os.path.join(self.database_directory, self.data_source_file)) ) + os.path.join(self.database_directory, self.data_source_file))) return cmd def run(self): # first remove all ACEDRG input scripts in ccp4_scratch directory - self.Logfile.insert('removing all xce_fit_ligands scripts from '+self.ccp4_scratch_directory) + self.Logfile.insert( + 'removing all xce_fit_ligands scripts from '+self.ccp4_scratch_directory) os.chdir(self.ccp4_scratch_directory) os.system('/bin/rm -f xce_autofit_ligand*') - progress_step=100/float(len(self.compound_list)) - progress=0 - counter=1 + progress_step = 100/float(len(self.compound_list)) + progress = 0 + counter = 1 for item in self.compound_list: - sampleID=item[0] - compoundID=item[1] + sampleID = item[0] + compoundID = item[1] if os.path.isdir(os.path.join(self.initial_model_directory, sampleID, 'autofit_ligand')): - os.system('/bin/rm -fr ' + os.path.join(self.initial_model_directory, sampleID, 'autofit_ligand')) - os.mkdir(os.path.join(self.initial_model_directory, sampleID, 'autofit_ligand')) + os.system( + '/bin/rm -fr ' + os.path.join(self.initial_model_directory, sampleID, 'autofit_ligand')) + os.mkdir(os.path.join(self.initial_model_directory, + sampleID, 'autofit_ligand')) # find ligands to fit (there might be more than one in case of stereoisomers ligList = [] - for file in glob.glob(os.path.join(self.initial_model_directory, sampleID, 'compound',compoundID+'*.cif')): - cif = file[file.rfind('/')+1:].replace('.cif','') + for file in glob.glob(os.path.join(self.initial_model_directory, sampleID, 'compound', compoundID+'*.cif')): + cif = file[file.rfind('/')+1:].replace('.cif', '') if 'with_H' in cif: continue else: @@ -985,20 +1077,19 @@ def run(self): if ligList != []: cmd = self.get_header(sampleID) - cmd = self.prepareInput(cmd,ligList) + cmd = self.prepareInput(cmd, ligList) cmd = self.get_footer(cmd, sampleID, compoundID) self.write_script(cmd) self.run_script() self.n += 1 - progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) # self.emit(QtCore.SIGNAL("finished()")) self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) - def write_script(self,cmd): + def write_script(self, cmd): os.chdir(self.ccp4_scratch_directory) f = open('xce_autofit_ligand_{0!s}.sh'.format(str(self.n)), 'w') f.write(cmd) @@ -1007,128 +1098,129 @@ def write_script(self,cmd): def run_script(self): # submit job - self.Logfile.insert('created input scripts for ' + str(self.n) + ' in ' + self.ccp4_scratch_directory) + self.Logfile.insert('created input scripts for ' + + str(self.n) + ' in ' + self.ccp4_scratch_directory) os.chdir(self.ccp4_scratch_directory) if os.path.isdir('/dls'): if self.external_software['qsub_array']: Cmds = ( - '#PBS -joe -N xce_autofit_ligand_master\n' + - './xce_autofit_ligand_$SGE_TASK_ID.sh\n' + '#PBS -joe -N xce_autofit_ligand_master\n' + + './xce_autofit_ligand_$SGE_TASK_ID.sh\n' ) f = open('autofit_ligand_master.sh', 'w') f.write(Cmds) f.close() - self.Logfile.insert('submitting array job with maximal 100 jobs running on cluster') + self.Logfile.insert( + 'submitting array job with maximal 100 jobs running on cluster') self.Logfile.insert('using the following command:') self.Logfile.insert( 'qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} autofit_ligand_master.sh'.format(str(self.n), - self.max_queue_jobs)) + self.max_queue_jobs)) os.system( 'qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} autofit_ligand_master.sh'.format(str(self.n - 1), - self.max_queue_jobs)) + self.max_queue_jobs)) else: self.Logfile.insert( "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") elif self.external_software['qsub']: - self.Logfile.insert('submitting {0!s} individual jobs to cluster'.format((str(self.n)))) - self.Logfile.insert('WARNING: this could potentially lead to a crash...') + self.Logfile.insert( + 'submitting {0!s} individual jobs to cluster'.format((str(self.n)))) + self.Logfile.insert( + 'WARNING: this could potentially lead to a crash...') for i in range(1, self.n): - self.Logfile.insert('qsub -q medium.q xce_autofit_ligand_{0!s}.sh'.format(str(i))) - os.system('qsub -q medium.q xce_autofit_ligand_{0!s}.sh'.format(str(i))) + self.Logfile.insert( + 'qsub -q medium.q xce_autofit_ligand_{0!s}.sh'.format(str(i))) + os.system( + 'qsub -q medium.q xce_autofit_ligand_{0!s}.sh'.format(str(i))) else: self.Logfile.insert( 'running {0!s} consecutive autofit_ligand jobs on your local machine'.format(str(self.n - 1))) for i in range(1, self.n+1): - self.Logfile.insert('starting xce_autofit_ligand_{0!s}.sh'.format(str(i))) + self.Logfile.insert( + 'starting xce_autofit_ligand_{0!s}.sh'.format(str(i))) os.system('./xce_autofit_ligand_{0!s}.sh'.format(str(i))) - - - - - - - - - - - - class merge_cif_files(QtCore.QThread): - def __init__(self,initial_model_directory,xce_logfile,second_cif_file,compound_list,todo): + def __init__(self, initial_model_directory, xce_logfile, second_cif_file, compound_list, todo): QtCore.QThread.__init__(self) - self.initial_model_directory=initial_model_directory - self.xce_logfile=xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) + self.initial_model_directory = initial_model_directory + self.xce_logfile = xce_logfile + self.Logfile = XChemLog.updateLog(xce_logfile) self.second_cif_file = second_cif_file - self.compound_list=compound_list - self.todo=todo + self.compound_list = compound_list + self.todo = todo def run(self): - progress_step=100/float(len(self.compound_list)) - progress=0 - counter=1 + progress_step = 100/float(len(self.compound_list)) + progress = 0 + counter = 1 for item in self.compound_list: - sampleID=item[0] - compoundID=item[1] + sampleID = item[0] + compoundID = item[1] if os.path.isfile(os.path.join(self.initial_model_directory, sampleID, 'compound', compoundID + '.cif')): - self.Logfile.insert('%s: found %s.cif file in compound sub-directory' % (sampleID, compoundID)) + self.Logfile.insert( + '%s: found %s.cif file in compound sub-directory' % (sampleID, compoundID)) else: self.Logfile.error( '%s: %s.cif file does not exist in compound sub-directory; skipping...' % (sampleID, compoundID)) continue - os.chdir(os.path.join(self.initial_model_directory,sampleID)) - if os.path.isfile(os.path.join(self.initial_model_directory,sampleID,compoundID+'.cif')): - self.Logfile.warning('%s: removing symbolic link to (or file) %s.cif from sample directory' %(sampleID,compoundID)) - os.system('/bin/rm %s.cif 2> /dev/null' %compoundID) + os.chdir(os.path.join(self.initial_model_directory, sampleID)) + if os.path.isfile(os.path.join(self.initial_model_directory, sampleID, compoundID+'.cif')): + self.Logfile.warning( + '%s: removing symbolic link to (or file) %s.cif from sample directory' % (sampleID, compoundID)) + os.system('/bin/rm %s.cif 2> /dev/null' % compoundID) if self.todo == 'merge': - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), sampleID+' merging CIF files') + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + sampleID+' merging CIF files') - self.run_libcheck(sampleID,compoundID) + self.run_libcheck(sampleID, compoundID) elif self.todo == 'restore': - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), sampleID + ' restoring original CIF file') - self.Logfile.insert('%s: restoring symbolic link -> ln -s compound/%s.cif .' %(sampleID,compoundID)) - os.system('ln -s compound/%s.cif .' %compoundID) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + sampleID + ' restoring original CIF file') + self.Logfile.insert( + '%s: restoring symbolic link -> ln -s compound/%s.cif .' % (sampleID, compoundID)) + os.system('ln -s compound/%s.cif .' % compoundID) progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) self.emit(QtCore.SIGNAL("finished()")) - def run_libcheck(self,sampleID,compoundID): + def run_libcheck(self, sampleID, compoundID): cmd = ( - '#!/bin/bash\n' - '\n' - '$CCP4/bin/libcheck << eof \n' - '_Y\n' - '_FILE_L compound/%s.cif\n' %compoundID+ - '_FILE_L2 '+self.second_cif_file+'\n' - '_FILE_O '+compoundID+'.cif\n' - '_END\n' - 'eof\n' - ) - self.Logfile.insert('%s: running libcheck with the following input:\n%s' %(sampleID,cmd)) + '#!/bin/bash\n' + '\n' + '$CCP4/bin/libcheck << eof \n' + '_Y\n' + '_FILE_L compound/%s.cif\n' % compoundID + + '_FILE_L2 '+self.second_cif_file+'\n' + '_FILE_O '+compoundID+'.cif\n' + '_END\n' + 'eof\n' + ) + self.Logfile.insert( + '%s: running libcheck with the following input:\n%s' % (sampleID, cmd)) os.system(cmd) if os.path.isfile(compoundID+'.cif.lib'): - self.Logfile.insert('%s: merged CIF file successfully created' %sampleID) - os.system('/bin/mv %s %s' %(compoundID+'.cif.lib',compoundID+'.cif')) + self.Logfile.insert( + '%s: merged CIF file successfully created' % sampleID) + os.system('/bin/mv %s %s' % + (compoundID+'.cif.lib', compoundID+'.cif')) else: - self.Logfile.error('%s: could not create merged CIF file' %sampleID) - self.Logfile.warning('%s: will re-create symbolic links to original restraints file' %sampleID) - os.system('ln -s compound/%s.cif .' %compoundID) - - - - + self.Logfile.error( + '%s: could not create merged CIF file' % sampleID) + self.Logfile.warning( + '%s: will re-create symbolic links to original restraints file' % sampleID) + os.system('ln -s compound/%s.cif .' % compoundID) -#class run_dimple_on_all_autoprocessing_files(QtCore.QThread): +# class run_dimple_on_all_autoprocessing_files(QtCore.QThread): # def __init__(self,sample_list,initial_model_directory,external_software,ccp4_scratch_directory,database_directory, # data_source_file,max_queue_jobs,xce_logfile, remote_submission, remote_submission_string, # dimple_twin_mode,pipeline): @@ -1162,7 +1254,7 @@ def run_libcheck(self,sampleID,compoundID): # db=XChemDB.data_source(os.path.join(self.database_directory,self.data_source_file)) # database=os.path.join(self.database_directory,self.data_source_file) # -## print(self.sample_list) +# print(self.sample_list) # # for n,item in enumerate(self.sample_list): # @@ -1176,22 +1268,22 @@ def run_libcheck(self,sampleID,compoundID): # # check if reference mtzfile has an Rfree column; if not, then ignore # # DIMPLE assumes an Rfree column and barfs if it is not present # # note: ref_mtz looks like this: ref mtz -R reference.mtz -## if os.path.isfile(ref_mtz.split()[len(ref_mtz.split())-1]): -## mtz_column_dict=mtztools(ref_mtz.split()[len(ref_mtz.split())-1]).get_all_columns_as_dict() +# if os.path.isfile(ref_mtz.split()[len(ref_mtz.split())-1]): +# mtz_column_dict=mtztools(ref_mtz.split()[len(ref_mtz.split())-1]).get_all_columns_as_dict() # if os.path.isfile(ref_mtz): # if 'FreeR_flag' not in mtz.object(ref_mtz).column_labels(): -## mtz_column_dict=mtztools(ref_mtz).get_all_columns_as_dict() -## if 'FreeR_flag' not in mtz_column_dict['RFREE']: +# mtz_column_dict=mtztools(ref_mtz).get_all_columns_as_dict() +# if 'FreeR_flag' not in mtz_column_dict['RFREE']: # self.Logfile.insert('cannot find FreeR_flag in reference mtz file: {0!s} -> ignoring reference mtzfile!!!'.format(ref_mtz)) # ref_mtz = '' -## if mtz_column_dict['RFREE'] != []: +# if mtz_column_dict['RFREE'] != []: ## self.Logfile.insert('found Rfree set with other column name though: {0!s}'.format(str(mtz_column_dict['RFREE']))) ## self.Logfile.insert('try renaming Rfree column to FreeR_flag with CAD!') # ## uniqueify = '' -## if 'FreeR_flag' in mtz.object(mtzin).column_labels(): +# if 'FreeR_flag' in mtz.object(mtzin).column_labels(): ## uniqueify = 'uniqueify -f FreeR_flag ' + mtzin + ' ' + xtal + '-unique.mtz' + '\n' -## else: +# else: ## uniqueify = 'uniqueify ' + mtzin + ' ' + xtal + '-unique.mtz' + '\n' # # db_dict= {'DimpleReferencePDB': ref_pdb} @@ -1308,17 +1400,17 @@ def run_libcheck(self,sampleID,compoundID): # "dimple --no-cleanup %s.999A.mtz %s %s %s %s dimple\n" %(xtal,ref_pdb,ref_mtz,ref_cif,twin) + # '\n' # 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc,'dimple') + -## + uniqueify + -## '\n' -## 'cad hklin1 %s hklout %s < ignoring reference mtzfile!!!' %ref_mtz) -# ref_mtz = '' -# if mtz_column_dict['RFREE'] != []: -# self.Logfile.insert('found Rfree set with other column name though: %s' %str(mtz_column_dict['RFREE'])) -# self.Logfile.insert('try renaming Rfree column to FreeR_flag with CAD!') -# -# db_dict={} -# db_dict['DimpleReferencePDB']=ref_pdb -# self.db.update_data_source(xtal,db_dict) -# -# self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'creating input script for '+xtal+' in '+visit_run_autoproc) -# - - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal)): - os.mkdir(os.path.join(self.initial_model_directory,xtal)) - os.chdir(os.path.join(self.initial_model_directory,xtal)) - if os.path.isdir(os.path.join(self.initial_model_directory,xtal,'phenix.ligand_pipeline')): + # if os.path.isfile(ref_mtz): + # mtz_column_dict=mtztools(ref_mtz).get_all_columns_as_dict() + # if 'FreeR_flag' not in mtz_column_dict['RFREE']: + # self.Logfile.insert('cannot find FreeR_flag in reference mtz file: %s -> ignoring reference mtzfile!!!' %ref_mtz) + # ref_mtz = '' + # if mtz_column_dict['RFREE'] != []: + # self.Logfile.insert('found Rfree set with other column name though: %s' %str(mtz_column_dict['RFREE'])) + # self.Logfile.insert('try renaming Rfree column to FreeR_flag with CAD!') + # + # db_dict={} + # db_dict['DimpleReferencePDB']=ref_pdb + # self.db.update_data_source(xtal,db_dict) + # + # self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'creating input script for '+xtal+' in '+visit_run_autoproc) + # + + if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): + os.mkdir(os.path.join(self.initial_model_directory, xtal)) + os.chdir(os.path.join(self.initial_model_directory, xtal)) + if os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'phenix.ligand_pipeline')): os.system('/bin/rm -fr phenix.ligand_pipeline') - os.mkdir(os.path.join(self.initial_model_directory,xtal,'phenix.ligand_pipeline')) + os.mkdir(os.path.join(self.initial_model_directory, + xtal, 'phenix.ligand_pipeline')) os.system('touch phenix.ligand_pipeline_run_in_progress') if self.queueing_system_available: - top_line='#PBS -joe -N XCE_{0!s}\n'.format(self.pipeline) + top_line = '#PBS -joe -N XCE_{0!s}\n'.format(self.pipeline) else: - top_line='#!'+os.getenv('SHELL')+'\n' + top_line = '#!'+os.getenv('SHELL')+'\n' if 'csh' in os.getenv('SHELL'): - ccp4_scratch='setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' + ccp4_scratch = 'setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' elif 'bash' in os.getenv('SHELL'): - ccp4_scratch='export CCP4_SCR='+self.ccp4_scratch_directory+'\n' + ccp4_scratch = 'export CCP4_SCR='+self.ccp4_scratch_directory+'\n' else: - ccp4_scratch='' + ccp4_scratch = '' if os.path.isdir('/dls'): - ccp4_scratch+='module load phenix\n' - ccp4_scratch+='module load ccp4/7.1.018\n' + ccp4_scratch += 'module load phenix\n' + ccp4_scratch += 'module load ccp4/7.1.018\n' - mtz_column_list=mtztools(mtzin).get_all_columns_as_list() + mtz_column_list = mtztools(mtzin).get_all_columns_as_list() rfree = '' if 'FreeR_flag' in mtz_column_list: rfree = ' xray_data.r_free_flags.label="FreeR_flag"' Cmds = ( - '{0!s}\n'.format(top_line)+ - '\n' - 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' - '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'phenix.ligand_pipeline') + - '\n' - 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' - '\n' - +ccp4_scratch+ - '\n' - '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(os.path.join(self.database_directory,self.data_source_file),xtal,'DimpleStatus','running') + - '\n' - 'phenix.ligand_pipeline %s %s' %(ref_pdb,mtzin)+ - ' mr=False' - ' ligand_copies=0' - ' build=False' - ' prune=False' - ' remove_waters=False' - ' stop_if_r_free_greater_than=0.4' - ' update_waters=False' - + rfree + - ' build_hydrogens=False\n' - '\n' - 'fft hklin pipeline_1/refine_final.mtz mapout 2fofc.map << EOF\n' - ' labin F1=2FOFCWT_filled PHI=PH2FOFCWT\n' - 'EOF\n' - '\n' - 'fft hklin pipeline_1/refine_final.mtz mapout fofc.map << EOF\n' - ' labin F1=FOFCWT PHI=PHFOFCWT\n' - 'EOF\n' - '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,xtal) + - '\n' - '/bin/rm phenix.ligand_pipeline.pdb\n' - '/bin/rm phenix.ligand_pipeline.mtz\n' - '\n' - 'ln -s phenix.ligand_pipeline/pipeline_1/refine_final.pdb phenix.ligand_pipeline.pdb\n' - 'ln -s phenix.ligand_pipeline/pipeline_1/refine_final.mtz phenix.ligand_pipeline.mtz\n' - '\n' - '/bin/rm init.pdb\n' - '/bin/rm init.mtz\n' - '\n' - 'ln -s phenix.ligand_pipeline.pdb init.pdb\n' - 'ln -s phenix.ligand_pipeline.mtz init.mtz\n' - '\n' - '/bin/rm 2fofc.map\n' - '/bin/rm fofc.map\n' - '\n' - 'ln -s phenix.ligand_pipeline/2fofc.map .\n' - 'ln -s phenix.ligand_pipeline/fofc.map .\n' - '\n' - '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_for_new_dimple_pdb.py')+ - ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory,self.data_source_file), xtal, self.initial_model_directory)+ - '\n' - '/bin/rm phenix.ligand_pipeline_run_in_progress\n' - ) + '{0!s}\n'.format(top_line) + + '\n' + 'export XChemExplorer_DIR="' + + os.getenv('XChemExplorer_DIR')+'"\n' + '\n' + 'cd %s\n' % os.path.join(self.initial_model_directory, xtal, 'phenix.ligand_pipeline') + + '\n' + 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' + '\n' + + ccp4_scratch + + '\n' + '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' % (os.path.join(self.database_directory, self.data_source_file), xtal, 'DimpleStatus', 'running') + + '\n' + 'phenix.ligand_pipeline %s %s' % (ref_pdb, mtzin) + + ' mr=False' + ' ligand_copies=0' + ' build=False' + ' prune=False' + ' remove_waters=False' + ' stop_if_r_free_greater_than=0.4' + ' update_waters=False' + + rfree + + ' build_hydrogens=False\n' + '\n' + 'fft hklin pipeline_1/refine_final.mtz mapout 2fofc.map << EOF\n' + ' labin F1=2FOFCWT_filled PHI=PH2FOFCWT\n' + 'EOF\n' + '\n' + 'fft hklin pipeline_1/refine_final.mtz mapout fofc.map << EOF\n' + ' labin F1=FOFCWT PHI=PHFOFCWT\n' + 'EOF\n' + '\n' + 'cd %s\n' % os.path.join(self.initial_model_directory, xtal) + + '\n' + '/bin/rm phenix.ligand_pipeline.pdb\n' + '/bin/rm phenix.ligand_pipeline.mtz\n' + '\n' + 'ln -s phenix.ligand_pipeline/pipeline_1/refine_final.pdb phenix.ligand_pipeline.pdb\n' + 'ln -s phenix.ligand_pipeline/pipeline_1/refine_final.mtz phenix.ligand_pipeline.mtz\n' + '\n' + '/bin/rm init.pdb\n' + '/bin/rm init.mtz\n' + '\n' + 'ln -s phenix.ligand_pipeline.pdb init.pdb\n' + 'ln -s phenix.ligand_pipeline.mtz init.mtz\n' + '\n' + '/bin/rm 2fofc.map\n' + '/bin/rm fofc.map\n' + '\n' + 'ln -s phenix.ligand_pipeline/2fofc.map .\n' + 'ln -s phenix.ligand_pipeline/fofc.map .\n' + '\n' + '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_data_source_for_new_dimple_pdb.py') + + ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory, self.data_source_file), xtal, self.initial_model_directory) + + '\n' + '/bin/rm phenix.ligand_pipeline_run_in_progress\n' + ) os.chdir(self.ccp4_scratch_directory) - f = open('xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n)),'w') + f = open('xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n)), 'w') f.write(Cmds) f.close() - os.system('chmod +x xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n))) - self.n+=1 - db_dict= {'DimpleStatus': 'started'} - self.Logfile.insert('{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) - self.db.update_data_source(xtal,db_dict) + os.system( + 'chmod +x xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n))) + self.n += 1 + db_dict = {'DimpleStatus': 'started'} + self.Logfile.insert( + '{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) + self.db.update_data_source(xtal, db_dict) twin = '' return twin + def prepare_pipedream_shell_script(self, xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif): - def prepare_pipedream_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,ref_mtz,ref_cif): - - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal)): - os.mkdir(os.path.join(self.initial_model_directory,xtal)) - if os.path.isdir(os.path.join(self.initial_model_directory,xtal,'pipedream')): - os.chdir(os.path.join(self.initial_model_directory,xtal)) + if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): + os.mkdir(os.path.join(self.initial_model_directory, xtal)) + if os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'pipedream')): + os.chdir(os.path.join(self.initial_model_directory, xtal)) os.system('/bin/rm -fr pipedream') - os.mkdir(os.path.join(self.initial_model_directory,xtal,'pipedream')) + os.mkdir(os.path.join(self.initial_model_directory, xtal, 'pipedream')) os.system('touch pipedream_run_in_progress') if self.queueing_system_available: - top_line='#PBS -joe -N XCE_{0!s}\n'.format(self.pipeline) + top_line = '#PBS -joe -N XCE_{0!s}\n'.format(self.pipeline) else: - top_line='#!'+os.getenv('SHELL')+'\n' + top_line = '#!'+os.getenv('SHELL')+'\n' if 'csh' in os.getenv('SHELL'): - ccp4_scratch='setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' + ccp4_scratch = 'setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' elif 'bash' in os.getenv('SHELL'): - ccp4_scratch='export CCP4_SCR='+self.ccp4_scratch_directory+'\n' + ccp4_scratch = 'export CCP4_SCR='+self.ccp4_scratch_directory+'\n' else: - ccp4_scratch='' + ccp4_scratch = '' if os.path.isdir('/dls'): - ccp4_scratch+='module load buster\n' - ccp4_scratch+='module load ccp4/7.1.018\n' + ccp4_scratch += 'module load buster\n' + ccp4_scratch += 'module load ccp4/7.1.018\n' if os.path.isfile(ref_mtz): - hklref_line=' -hklref {0!s}'.format(ref_mtz) + hklref_line = ' -hklref {0!s}'.format(ref_mtz) else: - hklref_line=' -nofreeref' + hklref_line = ' -nofreeref' Cmds = ( - '{0!s}\n'.format(top_line)+ - '\n' - 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' - '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'pipedream') + - '\n' - 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' - '\n' - +ccp4_scratch+ - '\n' - '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(os.path.join(self.database_directory,self.data_source_file),xtal,'DimpleStatus','running') + - '\n' - 'pointless hklin {0!s} xyzin {1!s} hklout pointless.mtz > pointless.log\n'.format(mtzin,ref_pdb)+ - '\n' - 'pipedream ' - ' -d pipedreamDir' - ' -xyzin %s' %ref_pdb+ - hklref_line+ - ' -hklin pointless.mtz' - ' -keepwater\n' - '\n' - 'fft hklin pipedreamDir/refine/refine.mtz mapout 2fofc.map << EOF\n' - ' labin F1=2FOFCWT PHI=PH2FOFCWT\n' - 'EOF\n' - '\n' - 'fft hklin pipedreamDir/refine/refine.mtz mapout fofc.map << EOF\n' - ' labin F1=FOFCWT PHI=PHFOFCWT\n' - 'EOF\n' - '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,xtal) + - '\n' - '/bin/rm pipedream.pdb\n' - '/bin/rm pipedream.mtz\n' - '\n' - 'ln -s pipedream/pipedreamDir/refine/refine.pdb pipedream.pdb\n' - 'ln -s pipedream/pipedreamDir/refine/refine.mtz pipedream.mtz\n' - '\n' - '/bin/rm init.pdb\n' - '/bin/rm init.mtz\n' - '\n' - 'ln -s pipedream.pdb init.pdb\n' - 'ln -s pipedream.mtz init.mtz\n' - '\n' - '/bin/rm 2fofc.map\n' - '/bin/rm fofc.map\n' - '\n' - 'ln -s pipedream/2fofc.map .\n' - 'ln -s pipedream/fofc.map .\n' - '\n' - '$CCP4/libexec/python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_for_new_dimple_pdb.py')+ - ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory,self.data_source_file), xtal, self.initial_model_directory)+ - '\n' - '/bin/rm pipedream_run_in_progress\n' - ) + '{0!s}\n'.format(top_line) + + '\n' + 'export XChemExplorer_DIR="' + + os.getenv('XChemExplorer_DIR')+'"\n' + '\n' + 'cd %s\n' % os.path.join(self.initial_model_directory, xtal, 'pipedream') + + '\n' + 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' + '\n' + + ccp4_scratch + + '\n' + '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' % (os.path.join(self.database_directory, self.data_source_file), xtal, 'DimpleStatus', 'running') + + '\n' + 'pointless hklin {0!s} xyzin {1!s} hklout pointless.mtz > pointless.log\n'.format(mtzin, ref_pdb) + + '\n' + 'pipedream ' + ' -d pipedreamDir' + ' -xyzin %s' % ref_pdb + + hklref_line + + ' -hklin pointless.mtz' + ' -keepwater\n' + '\n' + 'fft hklin pipedreamDir/refine/refine.mtz mapout 2fofc.map << EOF\n' + ' labin F1=2FOFCWT PHI=PH2FOFCWT\n' + 'EOF\n' + '\n' + 'fft hklin pipedreamDir/refine/refine.mtz mapout fofc.map << EOF\n' + ' labin F1=FOFCWT PHI=PHFOFCWT\n' + 'EOF\n' + '\n' + 'cd %s\n' % os.path.join(self.initial_model_directory, xtal) + + '\n' + '/bin/rm pipedream.pdb\n' + '/bin/rm pipedream.mtz\n' + '\n' + 'ln -s pipedream/pipedreamDir/refine/refine.pdb pipedream.pdb\n' + 'ln -s pipedream/pipedreamDir/refine/refine.mtz pipedream.mtz\n' + '\n' + '/bin/rm init.pdb\n' + '/bin/rm init.mtz\n' + '\n' + 'ln -s pipedream.pdb init.pdb\n' + 'ln -s pipedream.mtz init.mtz\n' + '\n' + '/bin/rm 2fofc.map\n' + '/bin/rm fofc.map\n' + '\n' + 'ln -s pipedream/2fofc.map .\n' + 'ln -s pipedream/fofc.map .\n' + '\n' + '$CCP4/libexec/python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_data_source_for_new_dimple_pdb.py') + + ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory, self.data_source_file), xtal, self.initial_model_directory) + + '\n' + '/bin/rm pipedream_run_in_progress\n' + ) os.chdir(self.ccp4_scratch_directory) - f = open('xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n)),'w') + f = open('xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n)), 'w') f.write(Cmds) f.close() - os.system('chmod +x xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n))) - self.n+=1 - db_dict= {'DimpleStatus': 'started'} - self.Logfile.insert('{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) - self.db.update_data_source(xtal,db_dict) + os.system( + 'chmod +x xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n))) + self.n += 1 + db_dict = {'DimpleStatus': 'started'} + self.Logfile.insert( + '{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) + self.db.update_data_source(xtal, db_dict) twin = '' return twin +# pipedream -d pipedreamDir -xyzin $reference.pdb -hklref $referenceDataset.mtz -hklin $mtzFileUnique.mtz -rhofit $inhib.cif -target $reference.pdb -keepwater -nthreads 12 -postquick -allclusters |tee -a pipedream.log -#pipedream -d pipedreamDir -xyzin $reference.pdb -hklref $referenceDataset.mtz -hklin $mtzFileUnique.mtz -rhofit $inhib.cif -target $reference.pdb -keepwater -nthreads 12 -postquick -allclusters |tee -a pipedream.log - - - def prepare_dimple_shell_script(self,xtal,visit_run_autoproc,mtzin,ref_pdb,ref_mtz,ref_cif): + def prepare_dimple_shell_script(self, xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif): # check if reference mtzfile has an Rfree column; if not, then ignore # DIMPLE assumes an Rfree column and barfs if it is not present # note: ref_mtz looks like this: ref mtz -R reference.mtz if os.path.isfile(ref_mtz): - mtz_column_dict=mtztools(ref_mtz).get_all_columns_as_dict() + mtz_column_dict = mtztools(ref_mtz).get_all_columns_as_dict() if 'FreeR_flag' not in mtz_column_dict['RFREE']: - self.Logfile.insert('cannot find FreeR_flag in reference mtz file: {0!s} -> ignoring reference mtzfile!!!'.format(ref_mtz)) + self.Logfile.insert( + 'cannot find FreeR_flag in reference mtz file: {0!s} -> ignoring reference mtzfile!!!'.format(ref_mtz)) ref_mtz = '' if mtz_column_dict['RFREE']: - self.Logfile.insert('found Rfree set with other column name though: {0!s}'.format(str(mtz_column_dict['RFREE']))) - self.Logfile.insert('try renaming Rfree column to FreeR_flag with CAD!') + self.Logfile.insert('found Rfree set with other column name though: {0!s}'.format( + str(mtz_column_dict['RFREE']))) + self.Logfile.insert( + 'try renaming Rfree column to FreeR_flag with CAD!') - db_dict= {'DimpleReferencePDB': ref_pdb} - self.db.update_data_source(xtal,db_dict) + db_dict = {'DimpleReferencePDB': ref_pdb} + self.db.update_data_source(xtal, db_dict) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'creating input script for '+xtal+' in '+visit_run_autoproc) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'creating input script for '+xtal+' in '+visit_run_autoproc) - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal)): - os.mkdir(os.path.join(self.initial_model_directory,xtal)) - os.chdir(os.path.join(self.initial_model_directory,xtal)) + if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): + os.mkdir(os.path.join(self.initial_model_directory, xtal)) + os.chdir(os.path.join(self.initial_model_directory, xtal)) twin = '' twinRefmac = "" if self.dimple_twin_mode: twinRefmac = "--refmac-key 'TWIN'" twin = '_twin' - if os.path.isdir(os.path.join(self.initial_model_directory,xtal,'dimple_twin')): + if os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'dimple_twin')): os.system('/bin/rm -fr dimple_twin') - os.mkdir(os.path.join(self.initial_model_directory,xtal,'dimple_twin')) + os.mkdir(os.path.join( + self.initial_model_directory, xtal, 'dimple_twin')) os.system('touch dimple_twin_run_in_progress') else: - if os.path.isdir(os.path.join(self.initial_model_directory,xtal,'dimple')): + if os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'dimple')): os.system('/bin/rm -fr dimple') - os.mkdir(os.path.join(self.initial_model_directory,xtal,'dimple')) + os.mkdir(os.path.join(self.initial_model_directory, xtal, 'dimple')) os.system('touch dimple_run_in_progress') os.system('/bin/rm final.mtz 2> /dev/null') os.system('/bin/rm final.pdb 2> /dev/null') if self.queueing_system_available: - top_line='#PBS -joe -N XCE_dimple\n' + top_line = '#PBS -joe -N XCE_dimple\n' else: - top_line='#!'+os.getenv('SHELL')+'\n' + top_line = '#!'+os.getenv('SHELL')+'\n' if 'csh' in os.getenv('SHELL'): - ccp4_scratch='setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' + ccp4_scratch = 'setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' elif 'bash' in os.getenv('SHELL'): - ccp4_scratch='export CCP4_SCR='+self.ccp4_scratch_directory+'\n' + ccp4_scratch = 'export CCP4_SCR='+self.ccp4_scratch_directory+'\n' else: - ccp4_scratch='' + ccp4_scratch = '' if os.path.isdir('/dls'): - ccp4_scratch+='module load ccp4/7.1.018\n' + ccp4_scratch += 'module load ccp4/7.1.018\n' hkl = any_reflection_file(file_name=mtzin) miller_arrays = hkl.as_miller_arrays() mtzFile = miller_arrays[0] - if mtzFile.space_group_info().symbol_and_number() == 'R 3 :H (No. 146)': + if mtzFile.space_group_info().symbol_and_number() == 'R 3 :H (No. 146)': symNoAbsence = 'H3' elif mtzFile.space_group_info().symbol_and_number() == 'R 3 2 :H (No. 155)': symNoAbsence = 'H32' else: - symNoAbsence = str([x[0] for x in str(mtzFile.space_group_info().symbol_and_number().split('(')[0]).split()]).replace('[','').replace(']','').replace("'","").replace(',','').replace(' ','') + symNoAbsence = str([x[0] for x in str(mtzFile.space_group_info().symbol_and_number().split( + '(')[0]).split()]).replace('[', '').replace(']', '').replace("'", "").replace(',', '').replace(' ', '') Cmds = ( - '{0!s}\n'.format(top_line)+ - '\n' - 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' - '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple%s' %twin) + - '\n' - 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' - '\n' - +ccp4_scratch+ - '\n' - '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(os.path.join(self.database_directory,self.data_source_file),xtal,'DimpleStatus','running') + - '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple%s' %twin) + - '\n' - 'unique hklout unique.mtz << eof\n' - ' cell %s\n' %str([round(float(i),2) for i in mtzFile.unit_cell().parameters()]).replace('[','').replace(']','')+ - ' symmetry %s\n' %symNoAbsence+ - ' resolution %s\n' %str(round(float(mtzFile.d_min()),3))+ - 'eof\n' - '\n' -# 'freerflag hklin unique.mtz hklout free.mtz > freerflag.log\n' - '\n' - 'sftools << eof > sftools.log\n' - ' read unique.mtz\n' - ' calc col F = 10.0\n' - ' calc col SIGF = 1.0\n' - ' write sftools.mtz\n' - 'eof\n' - '\n' - 'cad hklin1 sftools.mtz hklin2 %s hklout %s.999A.mtz << eof\n' %(mtzin,xtal) + - ' monitor BRIEF\n' - ' labin file 1 E1=F E2=SIGF\n' - ' labout file 1 E1=F_unique E2=SIGF_unique\n' - ' labin file 2 ALL\n' - ' resolution file 1 999.0 %s\n' %str(round(float(mtzFile.d_min()),2))+ - 'eof\n' - '\n' - 'pointless hklin %s.999A.mtz hklout %s.999A.reind.mtz xyzin %s << eof > pointless.reind.log\n' %(xtal,xtal,ref_pdb) + - ' tolerance 5\n' - 'eof\n' - '\n' - "dimple --no-cleanup %s.999A.reind.mtz %s %s %s %s dimple%s\n" % (xtal, ref_pdb, ref_mtz, ref_cif, twinRefmac, twin) + - '\n' - 'fft hklin dimple%s/final.mtz mapout 2fofc%s.map << EOF\n' %(twin,twin) + - ' labin F1=FWT PHI=PHWT\n' - 'EOF\n' - '\n' - 'fft hklin dimple%s/final.mtz mapout fofc%s.map << EOF\n' %(twin,twin) + - ' labin F1=DELFWT PHI=PHDELWT\n' - 'EOF\n' - '\n' - 'cd %s\n' %os.path.join(self.initial_model_directory,xtal) + - '\n' - '/bin/rm dimple%s.pdb\n' %twin + - '/bin/rm dimple%s.mtz\n' %twin + - '\n' - 'ln -s dimple%s/dimple%s/final.pdb dimple%s.pdb\n' %(twin,twin,twin) + - 'ln -s dimple%s/dimple%s/final.mtz dimple%s.mtz\n' %(twin,twin,twin) + - '\n' - '/bin/rm init%s.pdb\n' %twin + - '/bin/rm init%s.mtz\n' %twin + - '\n' - 'ln -s dimple%s.pdb init%s.pdb\n' %(twin,twin) + - 'ln -s dimple%s.mtz init%s.mtz\n' %(twin,twin) + - '\n' - '/bin/rm 2fofc%s.map\n' %twin + - '/bin/rm fofc%s.map\n' %twin + - '\n' - 'ln -s dimple%s/2fofc%s.map .\n' %(twin,twin) + - 'ln -s dimple%s/fofc%s.map .\n' %(twin,twin) + - '\n' - '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_for_new_dimple%s_pdb.py' %twin)+ - ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory,self.data_source_file), xtal, self.initial_model_directory) + - '\n' - '/bin/rm dimple_run_in_progress\n' - '\n' - ) + '{0!s}\n'.format(top_line) + + '\n' + 'export XChemExplorer_DIR="' + + os.getenv('XChemExplorer_DIR')+'"\n' + '\n' + 'cd %s\n' % os.path.join(self.initial_model_directory, xtal, 'dimple%s' % twin) + + '\n' + 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' + '\n' + + ccp4_scratch + + '\n' + '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' % (os.path.join(self.database_directory, self.data_source_file), xtal, 'DimpleStatus', 'running') + + '\n' + 'cd %s\n' % os.path.join(self.initial_model_directory, xtal, 'dimple%s' % twin) + + '\n' + 'unique hklout unique.mtz << eof\n' + ' cell %s\n' % str([round(float(i), 2) for i in mtzFile.unit_cell().parameters()]).replace('[', '').replace(']', '') + + ' symmetry %s\n' % symNoAbsence + + ' resolution %s\n' % str(round(float(mtzFile.d_min()), 3)) + + 'eof\n' + '\n' + # 'freerflag hklin unique.mtz hklout free.mtz > freerflag.log\n' + '\n' + 'sftools << eof > sftools.log\n' + ' read unique.mtz\n' + ' calc col F = 10.0\n' + ' calc col SIGF = 1.0\n' + ' write sftools.mtz\n' + 'eof\n' + '\n' + 'cad hklin1 sftools.mtz hklin2 %s hklout %s.999A.mtz << eof\n' % (mtzin, xtal) + + ' monitor BRIEF\n' + ' labin file 1 E1=F E2=SIGF\n' + ' labout file 1 E1=F_unique E2=SIGF_unique\n' + ' labin file 2 ALL\n' + ' resolution file 1 999.0 %s\n' % str(round(float(mtzFile.d_min()), 2)) + + 'eof\n' + '\n' + 'pointless hklin %s.999A.mtz hklout %s.999A.reind.mtz xyzin %s << eof > pointless.reind.log\n' % (xtal, xtal, ref_pdb) + + ' tolerance 5\n' + 'eof\n' + '\n' + "dimple --no-cleanup %s.999A.reind.mtz %s %s %s %s dimple%s\n" % (xtal, ref_pdb, ref_mtz, ref_cif, twinRefmac, twin) + + '\n' + 'fft hklin dimple%s/final.mtz mapout 2fofc%s.map << EOF\n' % (twin, twin) + + ' labin F1=FWT PHI=PHWT\n' + 'EOF\n' + '\n' + 'fft hklin dimple%s/final.mtz mapout fofc%s.map << EOF\n' % (twin, twin) + + ' labin F1=DELFWT PHI=PHDELWT\n' + 'EOF\n' + '\n' + 'cd %s\n' % os.path.join(self.initial_model_directory, xtal) + + '\n' + '/bin/rm dimple%s.pdb\n' % twin + + '/bin/rm dimple%s.mtz\n' % twin + + '\n' + 'ln -s dimple%s/dimple%s/final.pdb dimple%s.pdb\n' % (twin, twin, twin) + + 'ln -s dimple%s/dimple%s/final.mtz dimple%s.mtz\n' % (twin, twin, twin) + + '\n' + '/bin/rm init%s.pdb\n' % twin + + '/bin/rm init%s.mtz\n' % twin + + '\n' + 'ln -s dimple%s.pdb init%s.pdb\n' % (twin, twin) + + 'ln -s dimple%s.mtz init%s.mtz\n' % (twin, twin) + + '\n' + '/bin/rm 2fofc%s.map\n' % twin + + '/bin/rm fofc%s.map\n' % twin + + '\n' + 'ln -s dimple%s/2fofc%s.map .\n' % (twin, twin) + + 'ln -s dimple%s/fofc%s.map .\n' % (twin, twin) + + '\n' + '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_data_source_for_new_dimple%s_pdb.py' % twin) + + ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory, self.data_source_file), xtal, self.initial_model_directory) + + '\n' + '/bin/rm dimple_run_in_progress\n' + '\n' + ) os.chdir(self.ccp4_scratch_directory) - f = open('xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline,twin, str(self.n)),'w') + f = open('xce_{0!s}{1!s}_{2!s}.sh'.format( + self.pipeline, twin, str(self.n)), 'w') f.write(Cmds) f.close() - os.system('chmod +x xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline, twin, str(self.n))) - self.n+=1 - db_dict= {'DimpleStatus': 'started'} - self.Logfile.insert('{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) - self.db.update_data_source(xtal,db_dict) + os.system( + 'chmod +x xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline, twin, str(self.n))) + self.n += 1 + db_dict = {'DimpleStatus': 'started'} + self.Logfile.insert( + '{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) + self.db.update_data_source(xtal, db_dict) return twin - def run_script(self,twin): + def run_script(self, twin): # submit job - self.Logfile.insert('created input scripts for '+str(self.n)+' in '+self.ccp4_scratch_directory) + self.Logfile.insert('created input scripts for ' + + str(self.n)+' in '+self.ccp4_scratch_directory) os.chdir(self.ccp4_scratch_directory) if os.path.isdir('/dls'): if self.external_software['qsub_array']: Cmds = ( - '#PBS -joe -N xce_{0!s}{1!s}_master\n'.format(self.pipeline,twin)+ - './xce_{0!s}{1!s}_$SGE_TASK_ID.sh\n'.format(self.pipeline,twin) - ) - f = open('{0!s}{1!s}_master.sh'.format(self.pipeline,twin),'w') + '#PBS -joe -N xce_{0!s}{1!s}_master\n'.format(self.pipeline, twin) + + './xce_{0!s}{1!s}_$SGE_TASK_ID.sh\n'.format( + self.pipeline, twin) + ) + f = open('{0!s}{1!s}_master.sh'.format( + self.pipeline, twin), 'w') f.write(Cmds) f.close() - self.Logfile.insert('submitting array job with maximal 100 jobs running on cluster') + self.Logfile.insert( + 'submitting array job with maximal 100 jobs running on cluster') self.Logfile.insert('using the following command:') - self.Logfile.insert('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh'.format(str(self.n), self.max_queue_jobs, self.pipeline)) - os.system('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}{3!s}_master.sh'.format(str(self.n-1), self.max_queue_jobs, self.pipeline,twin)) + self.Logfile.insert('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh'.format( + str(self.n), self.max_queue_jobs, self.pipeline)) + os.system('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}{3!s}_master.sh'.format( + str(self.n-1), self.max_queue_jobs, self.pipeline, twin)) else: - self.Logfile.insert("cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") + self.Logfile.insert( + "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") elif self.external_software['qsub']: - self.Logfile.insert('submitting {0!s} individual jobs to cluster'.format((str(self.n)))) - self.Logfile.insert('WARNING: this could potentially lead to a crash...') - for i in range(1,self.n): - self.Logfile.insert('qsub -q medium.q xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline,twin,str(i))) - os.system('qsub -q medium.q xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline,twin,str(i))) + self.Logfile.insert( + 'submitting {0!s} individual jobs to cluster'.format((str(self.n)))) + self.Logfile.insert( + 'WARNING: this could potentially lead to a crash...') + for i in range(1, self.n): + self.Logfile.insert( + 'qsub -q medium.q xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline, twin, str(i))) + os.system( + 'qsub -q medium.q xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline, twin, str(i))) else: - self.Logfile.insert('running {0!s} consecutive {1!s} jobs on your local machine'.format(str(self.n-1),self.pipeline)) - for i in range(1,self.n): - self.Logfile.insert('starting xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline,twin,str(i))) - os.system('./xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline,twin,str(i))) - + self.Logfile.insert('running {0!s} consecutive {1!s} jobs on your local machine'.format( + str(self.n-1), self.pipeline)) + for i in range(1, self.n): + self.Logfile.insert('starting xce_{0!s}{1!s}_{2!s}.sh'.format( + self.pipeline, twin, str(i))) + os.system( + './xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline, twin, str(i))) class remove_selected_dimple_files(QtCore.QThread): - def __init__(self,sample_list,initial_model_directory,xce_logfile,database_directory,data_source_file,pipeline): + def __init__(self, sample_list, initial_model_directory, xce_logfile, database_directory, data_source_file, pipeline): QtCore.QThread.__init__(self) - self.sample_list=sample_list - self.initial_model_directory=initial_model_directory - self.xce_logfile=xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) - self.db=XChemDB.data_source(os.path.join(database_directory,data_source_file)) + self.sample_list = sample_list + self.initial_model_directory = initial_model_directory + self.xce_logfile = xce_logfile + self.Logfile = XChemLog.updateLog(xce_logfile) + self.db = XChemDB.data_source(os.path.join( + database_directory, data_source_file)) self.pipeline = pipeline def run(self): - progress_step=1 + progress_step = 1 if len(self.sample_list) != 0: - progress_step=100/float(len(self.sample_list)) - progress=0 + progress_step = 100/float(len(self.sample_list)) + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - for n,xtal in enumerate(self.sample_list): - db_dict={} - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal)): - self.Logfile.insert('{0!s}: directory does not exist'.format(xtal)) + for n, xtal in enumerate(self.sample_list): + db_dict = {} + if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): + self.Logfile.insert( + '{0!s}: directory does not exist'.format(xtal)) continue - os.chdir(os.path.join(self.initial_model_directory,xtal)) + os.chdir(os.path.join(self.initial_model_directory, xtal)) - if self.pipeline=='dimple': + if self.pipeline == 'dimple': if os.path.isfile('init.pdb'): if 'dimple' in os.path.realpath('init.pdb'): - self.Logfile.warning('{0!s}: init.pdb & init.mtz is linked to dimple outcome'.format(xtal)) - self.Logfile.warning('{0!s}: removing init.pdb & init.mtz & (2)fofc maps'.format(xtal)) + self.Logfile.warning( + '{0!s}: init.pdb & init.mtz is linked to dimple outcome'.format(xtal)) + self.Logfile.warning( + '{0!s}: removing init.pdb & init.mtz & (2)fofc maps'.format(xtal)) db_dict = self.remove_init(db_dict) else: db_dict = self.remove_init(db_dict) - self.Logfile.warning('{0!s}: removing dimple folder & dimple.pdb/dimple.mtz'.format(xtal)) + self.Logfile.warning( + '{0!s}: removing dimple folder & dimple.pdb/dimple.mtz'.format(xtal)) os.system('/bin/rm dimple_run_in_progress 2> /dev/null') os.system('/bin/rm dimple.pdb 2> /dev/null') os.system('/bin/rm dimple.mtz 2> /dev/null') os.system('/bin/rm -fr dimple') - elif self.pipeline=='pipedream': + elif self.pipeline == 'pipedream': if os.path.isfile('init.pdb'): if 'dimple' in os.path.realpath('init.pdb'): - self.Logfile.warning('{0!s}: init.pdb & init.mtz is linked to pipedream outcome'.format(xtal)) - self.Logfile.warning('{0!s}: removing init.pdb & init.mtz & (2)fofc maps'.format(xtal)) + self.Logfile.warning( + '{0!s}: init.pdb & init.mtz is linked to pipedream outcome'.format(xtal)) + self.Logfile.warning( + '{0!s}: removing init.pdb & init.mtz & (2)fofc maps'.format(xtal)) db_dict = self.remove_init(db_dict) else: db_dict = self.remove_init(db_dict) - self.Logfile.warning('{0!s}: removing pipedream folder & pipedream.pdb/pipedream.mtz'.format(xtal)) + self.Logfile.warning( + '{0!s}: removing pipedream folder & pipedream.pdb/pipedream.mtz'.format(xtal)) os.system('/bin/rm pipedream_run_in_progress 2> /dev/null') os.system('/bin/rm pipedream.pdb 2> /dev/null') os.system('/bin/rm pipedream.mtz 2> /dev/null') os.system('/bin/rm -fr pipedream') - elif self.pipeline=='phenix.ligand_pipeline': + elif self.pipeline == 'phenix.ligand_pipeline': if os.path.isfile('init.pdb'): if 'dimple' in os.path.realpath('init.pdb'): - self.Logfile.warning('{0!s}: init.pdb & init.mtz is linked to phenix.ligand_pipeline outcome'.format(xtal)) - self.Logfile.warning('{0!s}: removing init.pdb & init.mtz & (2)fofc maps'.format(xtal)) + self.Logfile.warning( + '{0!s}: init.pdb & init.mtz is linked to phenix.ligand_pipeline outcome'.format(xtal)) + self.Logfile.warning( + '{0!s}: removing init.pdb & init.mtz & (2)fofc maps'.format(xtal)) db_dict = self.remove_init(db_dict) else: db_dict = self.remove_init(db_dict) - self.Logfile.warning('{0!s}: removing phenix.ligand_pipeline folder & phenix.ligand_pipeline.pdb/phenix.ligand_pipeline.mtz'.format(xtal)) - os.system('/bin/rm phenix.ligand_pipeline_run_in_progress 2> /dev/null') + self.Logfile.warning( + '{0!s}: removing phenix.ligand_pipeline folder & phenix.ligand_pipeline.pdb/phenix.ligand_pipeline.mtz'.format(xtal)) + os.system( + '/bin/rm phenix.ligand_pipeline_run_in_progress 2> /dev/null') os.system('/bin/rm phenix.ligand_pipeline.pdb 2> /dev/null') os.system('/bin/rm phenix.ligand_pipeline.mtz 2> /dev/null') os.system('/bin/rm -fr phenix.ligand_pipeline') if db_dict != {}: self.Logfile.insert('{0!s}: updating database'.format(xtal)) - self.db.update_data_source(xtal,db_dict) + self.db.update_data_source(xtal, db_dict) progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) - def remove_init(self,db_dict): + def remove_init(self, db_dict): os.system('/bin/rm init.pdb') os.system('/bin/rm init.mtz') os.system('/bin/rm 2fofc.map') os.system('/bin/rm fofc.map') - db_dict['DimpleResolutionHigh']='' - db_dict['DimpleRcryst']='' - db_dict['DimpleRfree']='' - db_dict['DimplePathToPDB']='' - db_dict['DimplePathToMTZ']='' - db_dict['DimpleReferencePDB']='' - db_dict['DimplePANDDAwasRun']='False' - db_dict['DimplePANDDAhit']='False' - db_dict['DimplePANDDAreject']='False' - db_dict['DimplePANDDApath']='' - db_dict['DimpleStatus']='pending' + db_dict['DimpleResolutionHigh'] = '' + db_dict['DimpleRcryst'] = '' + db_dict['DimpleRfree'] = '' + db_dict['DimplePathToPDB'] = '' + db_dict['DimplePathToMTZ'] = '' + db_dict['DimpleReferencePDB'] = '' + db_dict['DimplePANDDAwasRun'] = 'False' + db_dict['DimplePANDDAhit'] = 'False' + db_dict['DimplePANDDAreject'] = 'False' + db_dict['DimplePANDDApath'] = '' + db_dict['DimpleStatus'] = 'pending' return db_dict class set_results_from_selected_pipeline(QtCore.QThread): - def __init__(self,sample_list,initial_model_directory,xce_logfile,database_directory,data_source_file,pipeline): + def __init__(self, sample_list, initial_model_directory, xce_logfile, database_directory, data_source_file, pipeline): QtCore.QThread.__init__(self) - self.sample_list=sample_list - self.initial_model_directory=initial_model_directory - self.xce_logfile=xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) - self.db=XChemDB.data_source(os.path.join(database_directory,data_source_file)) + self.sample_list = sample_list + self.initial_model_directory = initial_model_directory + self.xce_logfile = xce_logfile + self.Logfile = XChemLog.updateLog(xce_logfile) + self.db = XChemDB.data_source(os.path.join( + database_directory, data_source_file)) self.pipeline = pipeline def run(self): - progress_step=1 + progress_step = 1 if len(self.sample_list) != 0: - progress_step=100/float(len(self.sample_list)) - progress=0 + progress_step = 100/float(len(self.sample_list)) + progress = 0 self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - for n,xtal in enumerate(self.sample_list): - db_dict={} - if not os.path.isdir(os.path.join(self.initial_model_directory,xtal)): - self.Logfile.insert('{0!s}: directory does not exist'.format(xtal)) + for n, xtal in enumerate(self.sample_list): + db_dict = {} + if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): + self.Logfile.insert( + '{0!s}: directory does not exist'.format(xtal)) continue - os.chdir(os.path.join(self.initial_model_directory,xtal)) + os.chdir(os.path.join(self.initial_model_directory, xtal)) if os.path.isfile('init.pdb'): - self.Logfile.warning('{0!s}: init.pdb & init.mtz exist'.format(xtal)) - self.Logfile.warning('{0!s}: removing init.pdb & init.mtz & (2)fofc maps'.format(xtal)) + self.Logfile.warning( + '{0!s}: init.pdb & init.mtz exist'.format(xtal)) + self.Logfile.warning( + '{0!s}: removing init.pdb & init.mtz & (2)fofc maps'.format(xtal)) os.system('/bin/rm init.pdb') os.system('/bin/rm init.mtz') os.system('/bin/rm 2fofc.map') os.system('/bin/rm fofc.map') - db_dict['DimpleResolutionHigh']='' - db_dict['DimpleRcryst']='' - db_dict['DimpleRfree']='' - db_dict['DimplePathToPDB']='' - db_dict['DimplePathToMTZ']='' - db_dict['DimpleReferencePDB']='' - db_dict['DimplePANDDAwasRun']='False' - db_dict['DimplePANDDAhit']='False' - db_dict['DimplePANDDAreject']='False' - db_dict['DimplePANDDApath']='' - db_dict['DimpleStatus']='pending' - - if self.pipeline=='dimple': + db_dict['DimpleResolutionHigh'] = '' + db_dict['DimpleRcryst'] = '' + db_dict['DimpleRfree'] = '' + db_dict['DimplePathToPDB'] = '' + db_dict['DimplePathToMTZ'] = '' + db_dict['DimpleReferencePDB'] = '' + db_dict['DimplePANDDAwasRun'] = 'False' + db_dict['DimplePANDDAhit'] = 'False' + db_dict['DimplePANDDAreject'] = 'False' + db_dict['DimplePANDDApath'] = '' + db_dict['DimpleStatus'] = 'pending' + + if self.pipeline == 'dimple': if os.path.isfile('dimple.pdb'): - self.Logfile.insert('%s: selecting output from dimple' %xtal) + self.Logfile.insert( + '%s: selecting output from dimple' % xtal) os.system('ln -s dimple.pdb init.pdb') - pdb_info=parse().PDBheader('dimple.pdb') - db_dict['DimpleRcryst']=pdb_info['Rcryst'] - db_dict['DimpleRfree']=pdb_info['Rfree'] - db_dict['DimpleResolutionHigh']=pdb_info['ResolutionHigh'] - db_dict['DimpleStatus']='finished' - db_dict['DimplePathToPDB']=os.path.realpath('dimple.pdb') + pdb_info = parse().PDBheader('dimple.pdb') + db_dict['DimpleRcryst'] = pdb_info['Rcryst'] + db_dict['DimpleRfree'] = pdb_info['Rfree'] + db_dict['DimpleResolutionHigh'] = pdb_info['ResolutionHigh'] + db_dict['DimpleStatus'] = 'finished' + db_dict['DimplePathToPDB'] = os.path.realpath('dimple.pdb') if os.path.isfile('dimple.mtz'): os.system('ln -s dimple.mtz init.mtz') - db_dict['DimplePathToMTZ']=os.path.realpath('dimple.mtz') + db_dict['DimplePathToMTZ'] = os.path.realpath('dimple.mtz') if os.path.isfile('dimple/2fofc.map'): os.system('ln -s dimple/2fofc.map .') if os.path.isfile('dimple/fofc.map'): os.system('ln -s dimple/fofc.map .') - elif self.pipeline=='pipedream': + elif self.pipeline == 'pipedream': if os.path.isfile('pipedream.pdb'): - self.Logfile.insert('%s: selecting output from pipedream' %xtal) + self.Logfile.insert( + '%s: selecting output from pipedream' % xtal) os.system('ln -s pipedream.pdb init.pdb') - pdb_info=parse().PDBheader('pipedream.pdb') - db_dict['DimpleRcryst']=pdb_info['Rcryst'] - db_dict['DimpleRfree']=pdb_info['Rfree'] - db_dict['DimpleResolutionHigh']=pdb_info['ResolutionHigh'] - db_dict['DimpleStatus']='finished' - db_dict['DimplePathToPDB']=os.path.realpath('pipedream.pdb') + pdb_info = parse().PDBheader('pipedream.pdb') + db_dict['DimpleRcryst'] = pdb_info['Rcryst'] + db_dict['DimpleRfree'] = pdb_info['Rfree'] + db_dict['DimpleResolutionHigh'] = pdb_info['ResolutionHigh'] + db_dict['DimpleStatus'] = 'finished' + db_dict['DimplePathToPDB'] = os.path.realpath( + 'pipedream.pdb') if os.path.isfile('pipedream.mtz'): os.system('ln -s pipedream.mtz init.mtz') - db_dict['DimplePathToMTZ']=os.path.realpath('pipedream.mtz') + db_dict['DimplePathToMTZ'] = os.path.realpath( + 'pipedream.mtz') if os.path.isfile('pipedream/2fofc.map'): os.system('ln -s pipedream/2fofc.map .') if os.path.isfile('pipedream/fofc.map'): os.system('ln -s pipedream/fofc.map .') - elif self.pipeline=='phenix.ligand_pipeline': + elif self.pipeline == 'phenix.ligand_pipeline': if os.path.isfile('phenix.ligand_pipeline.pdb'): - self.Logfile.insert('%s: selecting output from phenix.ligand_pipeline' %xtal) + self.Logfile.insert( + '%s: selecting output from phenix.ligand_pipeline' % xtal) os.system('ln -s phenix.ligand_pipeline.pdb init.pdb') - pdb_info=parse().PDBheader('phenix.ligand_pipeline.pdb') - db_dict['DimpleRcryst']=pdb_info['Rcryst'] - db_dict['DimpleRfree']=pdb_info['Rfree'] - db_dict['DimpleResolutionHigh']=pdb_info['ResolutionHigh'] - db_dict['DimpleStatus']='finished' - db_dict['DimplePathToPDB']=os.path.realpath('phenix.ligand_pipeline.pdb') + pdb_info = parse().PDBheader('phenix.ligand_pipeline.pdb') + db_dict['DimpleRcryst'] = pdb_info['Rcryst'] + db_dict['DimpleRfree'] = pdb_info['Rfree'] + db_dict['DimpleResolutionHigh'] = pdb_info['ResolutionHigh'] + db_dict['DimpleStatus'] = 'finished' + db_dict['DimplePathToPDB'] = os.path.realpath( + 'phenix.ligand_pipeline.pdb') if os.path.isfile('phenix.ligand_pipeline.mtz'): os.system('ln -s phenix.ligand_pipeline.mtz init.mtz') - db_dict['DimplePathToMTZ']=os.path.realpath('phenix.ligand_pipeline.mtz') + db_dict['DimplePathToMTZ'] = os.path.realpath( + 'phenix.ligand_pipeline.mtz') if os.path.isfile('phenix.ligand_pipeline/2fofc.map'): os.system('ln -s phenix.ligand_pipeline/2fofc.map .') if os.path.isfile('phenix.ligand_pipeline/fofc.map'): os.system('ln -s phenix.ligand_pipeline/fofc.map .') self.Logfile.insert('{0!s}: updating database'.format(xtal)) - self.db.update_data_source(xtal,db_dict) + self.db.update_data_source(xtal, db_dict) progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) @@ -2068,74 +2210,80 @@ def run(self): self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) - class start_COOT(QtCore.QThread): - def __init__(self,settings,interface): + def __init__(self, settings, interface): QtCore.QThread.__init__(self) - self.settings=settings - if interface=='test': - self.pylib='XChemCoot.py' - elif interface=='new': - self.pylib='XChemCootNew.py' - elif interface=='panddaV1': - self.pylib='XChemCootOld.py' - elif interface=='reference': - self.pylib='XChemCootReference.py' - elif interface=='buster': - self.pylib='XChemCootBuster.py' - elif interface=='dimple_twin': - self.pylib='XChemCootTwin.py' + self.settings = settings + if interface == 'test': + self.pylib = 'XChemCoot.py' + elif interface == 'new': + self.pylib = 'XChemCootNew.py' + elif interface == 'panddaV1': + self.pylib = 'XChemCootOld.py' + elif interface == 'reference': + self.pylib = 'XChemCootReference.py' + elif interface == 'buster': + self.pylib = 'XChemCootBuster.py' + elif interface == 'dimple_twin': + self.pylib = 'XChemCootTwin.py' def run(self): - cwd=os.getcwd() + cwd = os.getcwd() # coot at Diamond always or sometimes at least open in home directory, so then it won't find the .pkl file - pickle.dump(self.settings,open(os.path.join(os.getenv('HOME'),'.xce_settings.pkl'),'wb')) - os.system('cd {0!s}\ncoot --no-guano --no-state-script --script {1!s}'.format(os.getenv('HOME'), os.path.join(os.getenv('XChemExplorer_DIR'),'lib',self.pylib))) + pickle.dump(self.settings, open(os.path.join( + os.getenv('HOME'), '.xce_settings.pkl'), 'wb')) + os.system('cd {0!s}\ncoot --no-guano --no-state-script --script {1!s}'.format( + os.getenv('HOME'), os.path.join(os.getenv('XChemExplorer_DIR'), 'lib', self.pylib))) + class start_ICM(QtCore.QThread): - def __init__(self,html_export_directory): + def __init__(self, html_export_directory): QtCore.QThread.__init__(self) - self.html_export_directory=html_export_directory + self.html_export_directory = html_export_directory def run(self): - cwd=os.getcwd() + cwd = os.getcwd() if cwd.startswith('/dls'): -# if not os.path.isfile(os.path.join('/home',getpass.getuser(),'.flexlmrc')): -# os.system('touch '+os.path.join('/home',getpass.getuser(),'.flexlmrc')) -# f=open(os.path.join('/home',getpass.getuser(),'.flexlmrc'),'w') -# f.write('MOLSOFTD_LICENSE_FILE=@diamvicmpro.diamond.ac.uk') -# f.close() + # if not os.path.isfile(os.path.join('/home',getpass.getuser(),'.flexlmrc')): + # os.system('touch '+os.path.join('/home',getpass.getuser(),'.flexlmrc')) + # f=open(os.path.join('/home',getpass.getuser(),'.flexlmrc'),'w') + # f.write('MOLSOFTD_LICENSE_FILE=@diamvicmpro.diamond.ac.uk') + # f.close() os.system('nautilus {0!s} &'.format(self.html_export_directory)) os.system('/dls/science/groups/i04-1/software/icm-3.8-5/icm64 -g') + class start_pandda_inspect(QtCore.QThread): - def __init__(self,settings,xce_logfile): + def __init__(self, settings, xce_logfile): QtCore.QThread.__init__(self) # self.settings=settings - self.panddas_directory=settings['panddas_directory'] - self.xce_logfile=xce_logfile - self.Logfile=XChemLog.updateLog(xce_logfile) + self.panddas_directory = settings['panddas_directory'] + self.xce_logfile = xce_logfile + self.Logfile = XChemLog.updateLog(xce_logfile) def run(self): if os.getenv('SHELL') == '/bin/tcsh' or os.getenv('SHELL') == '/bin/csh': - source_file=os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh') + source_file = os.path.join( + os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-csh') elif os.getenv('SHELL') == '/bin/bash': - source_file=os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh') + source_file = os.path.join( + os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-sh') else: - source_file='' + source_file = '' Cmds = ( - '#!'+os.getenv('SHELL')+'\n' - 'unset PYTHONPATH\n' - 'source '+source_file+'\n' - 'cd '+self.panddas_directory+'\n' - 'pandda.inspect\n' - ) - - self.Logfile.insert('starting pandda.inspect with the following command:\n'+Cmds) + '#!'+os.getenv('SHELL')+'\n' + 'unset PYTHONPATH\n' + 'source '+source_file+'\n' + 'cd '+self.panddas_directory+'\n' + 'pandda.inspect\n' + ) + + self.Logfile.insert( + 'starting pandda.inspect with the following command:\n'+Cmds) os.system(Cmds) # Cmds = ( @@ -2149,21 +2297,16 @@ def run(self): # os.system('/bin/bash\n'+Cmds) - - - class start_dials_image_viewer(QtCore.QThread): - def __init__(self,diffraction_image): + def __init__(self, diffraction_image): QtCore.QThread.__init__(self) - self.diffraction_image=diffraction_image + self.diffraction_image = diffraction_image def run(self): os.system('dials.image_viewer '+self.diffraction_image) - - # # --- new module from hell ------------------------------------------------------------------------------------------- # @@ -2183,7 +2326,8 @@ def __init__(self, self.Logfile = XChemLog.updateLog(xce_logfile) self.db = XChemDB.data_source(database) - self.allSamples = self.db.collected_xtals_during_visit_for_scoring(visit) + self.allSamples = self.db.collected_xtals_during_visit_for_scoring( + visit) self.gdaLogInstructions = gdaLogInstructions self.gda_log_start_line = gdaLogInstructions[0] @@ -2191,56 +2335,63 @@ def __init__(self, def run(self): if self.gzipped_logs_parsed: - self.Logfile.insert("parsed gzipped gda logfiles before, won't do again...") - self.Logfile.insert("will start parsing of current gda logfile at line {0!s}".format(str(self.gda_log_start_line))) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'checking GDA logiles for pinID details') + self.Logfile.insert( + "parsed gzipped gda logfiles before, won't do again...") + self.Logfile.insert("will start parsing of current gda logfile at line {0!s}".format( + str(self.gda_log_start_line))) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'checking GDA logiles for pinID details') pinDict, self.gda_log_start_line = XChemMain.get_gda_barcodes(self.allSamples, - self.gzipped_logs_parsed, - self.gda_log_start_line, - self.beamline, - self.xce_logfile) + self.gzipped_logs_parsed, + self.gda_log_start_line, + self.beamline, + self.xce_logfile) self.update_database(pinDict) - self.gdaLogInstructions = [self.gda_log_start_line,True] + self.gdaLogInstructions = [self.gda_log_start_line, True] self.Logfile.insert('====== finished checking GDA logfiles ======') - self.emit(QtCore.SIGNAL('update_gdaLog_parsing_instructions_and_score'), self.gdaLogInstructions) + self.emit(QtCore.SIGNAL( + 'update_gdaLog_parsing_instructions_and_score'), self.gdaLogInstructions) self.emit(QtCore.SIGNAL("finished()")) - def update_database(self,pinDict): + def update_database(self, pinDict): self.Logfile.insert('updating database with pinDIs from GDA logfiles') progress = 0 progress_step = XChemMain.getProgressSteps(len(pinDict)) for sample in pinDict: - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'updating pinID in DB for ' + sample) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'updating pinID in DB for ' + sample) dbDict = {} dbDict['DataCollectionPinBarcode'] = pinDict[sample] # self.db.update_data_source(sample,dbDict) - self.db.update_specified_table(sample,dbDict,'collectionTable') + self.db.update_specified_table(sample, dbDict, 'collectionTable') progress += progress_step self.emit(QtCore.SIGNAL('update_progress_bar'), progress) class choose_autoprocessing_outcome(QtCore.QThread): def __init__(self, - database, - visit, - reference_file_list, - preferences, - projectDir, - rescore, - xce_logfile, - agamemnon): + database, + visit, + reference_file_list, + preferences, + projectDir, + rescore, + xce_logfile, + agamemnon): QtCore.QThread.__init__(self) self.visit = visit self.projectDir = projectDir self.reference_file_list = reference_file_list self.rescore = rescore self.selection_mechanism = preferences['dataset_selection_mechanism'] - self.acceptable_unitcell_volume_difference = preferences['allowed_unitcell_difference_percent'] - self.acceptable_low_resolution_limit_for_data = preferences['acceptable_low_resolution_limit_for_data'] + self.acceptable_unitcell_volume_difference = preferences[ + 'allowed_unitcell_difference_percent'] + self.acceptable_low_resolution_limit_for_data = preferences[ + 'acceptable_low_resolution_limit_for_data'] self.acceptable_low_resolution_Rmerge = preferences['acceptable_low_resolution_Rmerge'] self.agamemnon = agamemnon self.xce_logfile = xce_logfile @@ -2254,11 +2405,11 @@ def __init__(self, for e in x: self.allSamples.append(e) else: - self.allSamples = self.db.collected_xtals_during_visit_for_scoring(visit) + self.allSamples = self.db.collected_xtals_during_visit_for_scoring( + visit) # print 'here', self.allSamples # self.allSamples = self.db.collected_xtals_during_visit_for_scoring(visit,rescore) - def run(self): progress = 0 @@ -2266,24 +2417,32 @@ def run(self): for sample in sorted(self.allSamples): if self.db.autoprocessing_result_user_assigned(sample) and not self.rescore: - if os.path.isfile(os.path.join(self.projectDir,sample,sample+'.mtz')): - self.Logfile.warning('{0!s}: user has manually selected auto-processing result; will NOT auto-select!'.format(sample)) + if os.path.isfile(os.path.join(self.projectDir, sample, sample+'.mtz')): + self.Logfile.warning( + '{0!s}: user has manually selected auto-processing result; will NOT auto-select!'.format(sample)) continue else: - self.Logfile.warning('{0!s}: user has manually selected auto-processing result before, but {1!s}.mtz does not exist'.format(sample,sample)) - self.Logfile.insert('%s: selecting autoprocessing result' % sample) + self.Logfile.warning( + '{0!s}: user has manually selected auto-processing result before, but {1!s}.mtz does not exist'.format(sample, sample)) + self.Logfile.insert( + '%s: selecting autoprocessing result' % sample) elif self.rescore: - self.Logfile.warning('{0!s}: rescore selected -> might overwrite user selection!'.format(sample)) + self.Logfile.warning( + '{0!s}: rescore selected -> might overwrite user selection!'.format(sample)) else: - self.Logfile.insert('%s: selecting autoprocessing result' % sample) - dbList = self.db.all_autoprocessing_results_for_xtal_as_dict(sample) - self.Logfile.insert('%s: found %s different autoprocessing results' %(sample,str(len(dbList)))) + self.Logfile.insert( + '%s: selecting autoprocessing result' % sample) + dbList = self.db.all_autoprocessing_results_for_xtal_as_dict( + sample) + self.Logfile.insert( + '%s: found %s different autoprocessing results' % (sample, str(len(dbList)))) # 0.) first check for which results files actually exist # - dbList = self.checkExistingFiles(dbList,sample) + dbList = self.checkExistingFiles(dbList, sample) if not dbList: - self.Logfile.error(sample + ': cannot find any MTZ & LOG files; skipping...') + self.Logfile.error( + sample + ': cannot find any MTZ & LOG files; skipping...') continue # 1.) if posssible, only carry forward samples with similar UCvolume and same point group @@ -2302,31 +2461,39 @@ def run(self): dbDict = self.selectSpecificPipelineOnly(dbList) # 4.) Set new symbolic links in project directory - XChemMain.linkAutoProcessingResult(sample,dbDict,self.projectDir,self.xce_logfile) + XChemMain.linkAutoProcessingResult( + sample, dbDict, self.projectDir, self.xce_logfile) # 5.) Determine DataProcessing Outcome - dbDict['DataCollectionOutcome'] = self.determine_processing_outcome(dbDict) + dbDict['DataCollectionOutcome'] = self.determine_processing_outcome( + dbDict) # 6.) update database dbDict['DataProcessingAutoAssigned'] = 'True' - self.updateDB(sample,dbDict) + self.updateDB(sample, dbDict) progress += progress_step - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'scoring auto-processing results for '+sample) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'scoring auto-processing results for '+sample) self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - self.Logfile.insert('====== finished scoring data processing results ======') + self.Logfile.insert( + '====== finished scoring data processing results ======') self.emit(QtCore.SIGNAL('populate_datasets_summary_table_NEW')) self.emit(QtCore.SIGNAL("finished()")) - def report_forward_carried_pipelines(self,dbListOut,dbList): + def report_forward_carried_pipelines(self, dbListOut, dbList): if not dbListOut: dbListOut = dbList - self.Logfile.warning('none of the MTZ files fulfilled criteria; will carry forward all results:') + self.Logfile.warning( + 'none of the MTZ files fulfilled criteria; will carry forward all results:') else: - self.Logfile.insert('will carry forward the MTZ files from the following auto-processing pipelines:') - self.Logfile.insert('{0:30} {1:10} {2:10} {3:10}'.format('pipeline','Rmerge(Low)','PG','Score')) - self.Logfile.insert('----------------------------------------------------------------------') + self.Logfile.insert( + 'will carry forward the MTZ files from the following auto-processing pipelines:') + self.Logfile.insert('{0:30} {1:10} {2:10} {3:10}'.format( + 'pipeline', 'Rmerge(Low)', 'PG', 'Score')) + self.Logfile.insert( + '----------------------------------------------------------------------') for resultDict in dbListOut: self.Logfile.insert('{0:30} {1:10} {2:10} {3:10}'.format(resultDict['DataProcessingProgram'], resultDict['DataProcessingRmergeLow'], @@ -2334,29 +2501,31 @@ def report_forward_carried_pipelines(self,dbListOut,dbList): resultDict['DataProcessingScore'])) return dbListOut - def checkExistingFiles(self,dbList,xtal): + def checkExistingFiles(self, dbList, xtal): self.Logfile.insert('checking if MTZ & LOG files exisit') - os.chdir(os.path.join(self.projectDir,xtal)) - self.Logfile.insert(xtal + ': changing directory ' + os.path.join(self.projectDir,xtal)) + os.chdir(os.path.join(self.projectDir, xtal)) + self.Logfile.insert(xtal + ': changing directory ' + + os.path.join(self.projectDir, xtal)) dbListOut = [] for resultDict in dbList: try: - run = resultDict['DataCollectionRun'] - subDir = resultDict['DataCollectionSubdir'] + run = resultDict['DataCollectionRun'] + subDir = resultDict['DataCollectionSubdir'] if subDir != '': procCode = '_' + subDir else: procCode = '' - visit = resultDict['DataCollectionVisit'] + visit = resultDict['DataCollectionVisit'] autoproc = resultDict['DataProcessingProgram'] mtzFileAbs = resultDict['DataProcessingPathToMTZfile'] mtzfileName = mtzFileAbs[mtzFileAbs.rfind('/')+1:] logFileAbs = resultDict['DataProcessingPathToLogfile'] logfileName = logFileAbs[logFileAbs.rfind('/')+1:] - mtzfile = os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfileName) - logfile = os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfileName) - + mtzfile = os.path.join( + 'autoprocessing', visit + '-' + run + autoproc + procCode, mtzfileName) + logfile = os.path.join( + 'autoprocessing', visit + '-' + run + autoproc + procCode, logfileName) if os.path.isfile(mtzfile): self.Logfile.insert(xtal + ': found ' + mtzfile) @@ -2364,44 +2533,51 @@ def checkExistingFiles(self,dbList,xtal): self.Logfile.insert(xtal + ': found ' + logfile) dbListOut.append(resultDict) else: - self.Logfile.error(xtal + ': cannot find ' + logfile + ' ; skipping...') + self.Logfile.error( + xtal + ': cannot find ' + logfile + ' ; skipping...') else: - self.Logfile.error(xtal + ': cannot find ' + mtzfile + ' ; skipping...') + self.Logfile.error( + xtal + ': cannot find ' + mtzfile + ' ; skipping...') except ValueError: pass return dbListOut - - - def selectResultsSimilarToReference(self,dbList): - self.Logfile.insert('checking if MTZ files are similar to supplied reference files') + def selectResultsSimilarToReference(self, dbList): + self.Logfile.insert( + 'checking if MTZ files are similar to supplied reference files') dbListOut = [] for resultDict in dbList: try: - if isinstance(float(resultDict['DataProcessingUnitCellVolume']),float): - self.Logfile.insert('checking unit cell volume difference and point group:') + if isinstance(float(resultDict['DataProcessingUnitCellVolume']), float): + self.Logfile.insert( + 'checking unit cell volume difference and point group:') for reference_file in self.reference_file_list: - if not reference_file[4]==0: - self.Logfile.insert('unitcell volume reference:' + str(reference_file[4])) - self.Logfile.insert('unitcell volume dataset: ' + str(resultDict['DataProcessingUnitCellVolume'])) - unitcell_difference=round((math.fabs(reference_file[4]-float(resultDict['DataProcessingUnitCellVolume']))/reference_file[4])*100,1) + if not reference_file[4] == 0: + self.Logfile.insert( + 'unitcell volume reference:' + str(reference_file[4])) + self.Logfile.insert( + 'unitcell volume dataset: ' + str(resultDict['DataProcessingUnitCellVolume'])) + unitcell_difference = round((math.fabs( + reference_file[4]-float(resultDict['DataProcessingUnitCellVolume']))/reference_file[4])*100, 1) self.Logfile.insert(resultDict['DataProcessingProgram'] + ': ' + str(unitcell_difference) + '% difference -> pg(ref): ' + reference_file[5] + ' -> pg(mtz): ' + resultDict['DataProcessingPointGroup']) - if unitcell_difference < self.acceptable_unitcell_volume_difference and reference_file[5]==resultDict['DataProcessingPointGroup']: - self.Logfile.insert('=> passed -> mtz file has same point group as reference file and similar unit cell volume') + if unitcell_difference < self.acceptable_unitcell_volume_difference and reference_file[5] == resultDict['DataProcessingPointGroup']: + self.Logfile.insert( + '=> passed -> mtz file has same point group as reference file and similar unit cell volume') dbListOut.append(resultDict) else: - self.Logfile.warning('mtz file has different point group/ unit cell volume as reference file') + self.Logfile.warning( + 'mtz file has different point group/ unit cell volume as reference file') except ValueError: pass - dbListOut = self.report_forward_carried_pipelines(dbListOut,dbList) + dbListOut = self.report_forward_carried_pipelines(dbListOut, dbList) return dbListOut - - def selectResultsWithAcceptableLowResoRmerge(self,dbList): - self.Logfile.insert('checking if MTZ files have acceptable low resolution Rmerge values (currently set to %s)' %str(self.acceptable_low_resolution_Rmerge)) + def selectResultsWithAcceptableLowResoRmerge(self, dbList): + self.Logfile.insert('checking if MTZ files have acceptable low resolution Rmerge values (currently set to %s)' % str( + self.acceptable_low_resolution_Rmerge)) dbListOut = [] for resultDict in dbList: try: @@ -2416,11 +2592,10 @@ def selectResultsWithAcceptableLowResoRmerge(self,dbList): str(resultDict['DataProcessingRmergeLow'])) except ValueError: pass - dbListOut = self.report_forward_carried_pipelines(dbListOut,dbList) + dbListOut = self.report_forward_carried_pipelines(dbListOut, dbList) return dbListOut - - def selectHighestScore(self,dbList): + def selectHighestScore(self, dbList): tmp = [] for resultDict in dbList: try: @@ -2430,7 +2605,7 @@ def selectHighestScore(self,dbList): highestScoreDict = dbList[tmp.index(max(tmp))] return highestScoreDict - def selectHighestResolution(self,dbList): + def selectHighestResolution(self, dbList): tmp = [] for resultDict in dbList: try: @@ -2440,9 +2615,10 @@ def selectHighestResolution(self,dbList): highestResoDict = dbList[tmp.index(min(tmp))] return highestResoDict - def selectSpecificPipelineOnly(self,dbList): + def selectSpecificPipelineOnly(self, dbList): tmp = [] - self.Logfile.insert('selecting datasets by auto-processing pipeline: ' + self.selection_mechanism) + self.Logfile.insert( + 'selecting datasets by auto-processing pipeline: ' + self.selection_mechanism) for resultDict in dbList: if self.selection_mechanism == 'dials - only' and 'dials' in resultDict['DataProcessingProgram']: tmp.append(resultDict) @@ -2459,8 +2635,7 @@ def selectSpecificPipelineOnly(self,dbList): pipelineDict = self.selectHighestScore(tmp) return pipelineDict - - def determine_processing_outcome(self,db_dict): + def determine_processing_outcome(self, db_dict): outcome = 'Failed - unknown' try: if float(db_dict['DataProcessingResolutionHigh']) < self.acceptable_low_resolution_limit_for_data: @@ -2471,8 +2646,7 @@ def determine_processing_outcome(self,db_dict): pass return outcome - - def updateDB(self,sample, dbDict): + def updateDB(self, sample, dbDict): self.Logfile.insert('{0!s}: updating database'.format(sample)) self.db.update_insert_data_source(sample, dbDict) @@ -2495,6 +2669,7 @@ class read_write_autoprocessing_results_from_to_disc(QtCore.QThread): - at the moment one can only review/ rescore crystals collected during the selected visit - parsing of pinIDs in gda logfiles is still missing """ + def __init__(self, processedDir, database, @@ -2504,8 +2679,9 @@ def __init__(self, agamemnon): QtCore.QThread.__init__(self) # self.target = target - self.processedDir = processedDir - self.visit,self.beamline = XChemMain.getVisitAndBeamline(self.processedDir) + self.processedDir = processedDir + self.visit, self.beamline = XChemMain.getVisitAndBeamline( + self.processedDir) # print 'visit' self.projectDir = projectDir self.Logfile = XChemLog.updateLog(xce_logfile) @@ -2513,9 +2689,9 @@ def __init__(self, self.agamemnon = agamemnon # if self.agamemnon: ## print 'procDir',self.processedDir -## if len(procDir.split('/')) >= 8: -## if procDir.split('/')[7] == 'agamemnon' -## quit() +# if len(procDir.split('/')) >= 8: +# if procDir.split('/')[7] == 'agamemnon' +# quit() # self.visit = 'agamemnon' # this is for trouble-shooting only self.db = XChemDB.data_source(os.path.join(database)) @@ -2526,39 +2702,39 @@ def __init__(self, # break # quit() - self.toParse = [ - [ os.path.join('*'), - os.path.join('LogFiles', '*aimless.log'), - os.path.join('DataFiles', '*free.mtz')], - [ os.path.join('*'), - os.path.join('LogFiles', '*merging-statistics.json'), - os.path.join('DataFiles', '*free.mtz')], - [ os.path.join('multi-xia2', '*'), - os.path.join('LogFiles', '*aimless.log'), - os.path.join('DataFiles', '*free.mtz')], -# [ os.path.join('autoPROC', '*'), -# '*aimless.log', -# '*truncate-unique.mtz'], -# [ os.path.join('autoPROC', '*'), -# '*staraniso_alldata-unique.table1', -# '*staraniso_alldata-unique.mtz'], - [ os.path.join('autoPROC'), - '*aimless.log', - '*truncate-unique.mtz'], - [ os.path.join('autoPROC'), - '*summary.tar.gz', # staraniso_alldata-unique.table1 only available in tar archive - '*staraniso_alldata-unique.mtz'], - [ os.path.join('autoPROC-*'), - '*aimless.log', - '*truncate-unique.mtz'], - [ os.path.join('autoPROC-*'), - '*summary.tar.gz', - '*staraniso_alldata-unique.mtz'], -# [ os.path.join('*'), -# os.path.join('LogFiles', '*aimless.log'), -# os.path.join('DataFiles', '*free.mtz')] - ] + [os.path.join('*'), + os.path.join('LogFiles', '*aimless.log'), + os.path.join('DataFiles', '*free.mtz')], + [os.path.join('*'), + os.path.join('LogFiles', '*merging-statistics.json'), + os.path.join('DataFiles', '*free.mtz')], + [os.path.join('multi-xia2', '*'), + os.path.join('LogFiles', '*aimless.log'), + os.path.join('DataFiles', '*free.mtz')], + # [ os.path.join('autoPROC', '*'), + # '*aimless.log', + # '*truncate-unique.mtz'], + # [ os.path.join('autoPROC', '*'), + # '*staraniso_alldata-unique.table1', + # '*staraniso_alldata-unique.mtz'], + [os.path.join('autoPROC'), + '*aimless.log', + '*truncate-unique.mtz'], + [os.path.join('autoPROC'), + # staraniso_alldata-unique.table1 only available in tar archive + '*summary.tar.gz', + '*staraniso_alldata-unique.mtz'], + [os.path.join('autoPROC-*'), + '*aimless.log', + '*truncate-unique.mtz'], + [os.path.join('autoPROC-*'), + '*summary.tar.gz', + '*staraniso_alldata-unique.mtz'], + # [ os.path.join('*'), + # os.path.join('LogFiles', '*aimless.log'), + # os.path.join('DataFiles', '*free.mtz')] + ] # self.toParse = [ # [ os.path.join('*'), @@ -2629,78 +2805,87 @@ def __init__(self, # os.path.join('DataFiles', '*free.mtz')] # ] - def run(self): -# if self.agamemnon: -# self.parse_agamemnon_file_system() -# else: -# self.parse_file_system() + # if self.agamemnon: + # self.parse_agamemnon_file_system() + # else: + # self.parse_file_system() self.parse_file_system() - def getExistingSamples(self): - existingSamples={} + existingSamples = {} self.Logfile.insert('reading existing samples from collectionTable') - allEntries = self.db.execute_statement('select CrystalName,DataCollectionVisit,DataCollectionRun,DataProcessingProgram, DataCollectionSubdir from collectionTable where DataCollectionOutcome = "success"') + allEntries = self.db.execute_statement( + 'select CrystalName,DataCollectionVisit,DataCollectionRun,DataProcessingProgram, DataCollectionSubdir from collectionTable where DataCollectionOutcome = "success"') for item in allEntries: if str(item[0]) not in existingSamples: - existingSamples[str(item[0])]=[] - self.Logfile.insert('%s: adding %s' %(str(item[0]),str(item[1]))) + existingSamples[str(item[0])] = [] + self.Logfile.insert('%s: adding %s' % + (str(item[0]), str(item[1]))) # visit-runautoproc-subdir - existingSamples[str(item[0])].append(str(item[1])+ '-' + str(item[2])+str(item[3])+'-'+str(item[4])) + existingSamples[str(item[0])].append( + str(item[1]) + '-' + str(item[2])+str(item[3])+'-'+str(item[4])) return existingSamples - def createSampleDir(self,xtal): - if not os.path.isdir(os.path.join(self.projectDir,xtal)): - os.mkdir(os.path.join(self.projectDir,xtal)) + def createSampleDir(self, xtal): + if not os.path.isdir(os.path.join(self.projectDir, xtal)): + os.mkdir(os.path.join(self.projectDir, xtal)) - def createAutoprocessingDir(self,xtal,run,autoproc,proc_code): + def createAutoprocessingDir(self, xtal, run, autoproc, proc_code): # create all the directories if necessary - self.Logfile.insert('%s: checking if new directory needs to be created for %s' %(xtal,os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc + '_' + proc_code))) - if not os.path.isdir(os.path.join(self.projectDir,xtal,'autoprocessing')): - os.mkdir(os.path.join(self.projectDir,xtal,'autoprocessing')) + self.Logfile.insert('%s: checking if new directory needs to be created for %s' % (xtal, os.path.join( + self.projectDir, xtal, 'autoprocessing', self.visit + '-' + run + autoproc + '_' + proc_code))) + if not os.path.isdir(os.path.join(self.projectDir, xtal, 'autoprocessing')): + os.mkdir(os.path.join(self.projectDir, xtal, 'autoprocessing')) if not os.path.isdir( - os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code)): - self.Logfile.insert('%s: making directory %s' %(xtal,os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code))) - os.mkdir(os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code)) + os.path.join(self.projectDir, xtal, 'autoprocessing', self.visit + '-' + run + autoproc + '_' + proc_code)): + self.Logfile.insert('%s: making directory %s' % (xtal, os.path.join( + self.projectDir, xtal, 'autoprocessing', self.visit + '-' + run + autoproc + '_' + proc_code))) + os.mkdir(os.path.join(self.projectDir, xtal, 'autoprocessing', + self.visit + '-' + run + autoproc + '_' + proc_code)) else: - self.Logfile.warning('%s: directory exists; skipping...' %xtal) + self.Logfile.warning('%s: directory exists; skipping...' % xtal) - def cleanUpDir(self,xtal,run,autoproc,mtzfile,logfile,proc_code): - toKeep = ['staraniso_alldata-unique.mtz','staraniso_alldata-unique.table1', - 'staraniso_alldata.log',xtal+'.mtz',xtal+'.log'] - os.chdir(os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code)) + def cleanUpDir(self, xtal, run, autoproc, mtzfile, logfile, proc_code): + toKeep = ['staraniso_alldata-unique.mtz', 'staraniso_alldata-unique.table1', + 'staraniso_alldata.log', xtal+'.mtz', xtal+'.log'] + os.chdir(os.path.join(self.projectDir, xtal, 'autoprocessing', + self.visit + '-' + run + autoproc + '_' + proc_code)) for files in glob.glob('*'): if files not in toKeep: os.system('/bin/rm -f ' + files) - - def copyMTZandLOGfiles(self,xtal,run,autoproc,mtzfile,logfile,proc_code): + def copyMTZandLOGfiles(self, xtal, run, autoproc, mtzfile, logfile, proc_code): mtzNew = '' logNew = '' - os.chdir(os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code)) + os.chdir(os.path.join(self.projectDir, xtal, 'autoprocessing', + self.visit + '-' + run + autoproc + '_' + proc_code)) # MTZ file if not os.path.isfile(mtzfile[mtzfile.rfind('/') + 1:]): self.Logfile.insert('%s: copying %s' % (xtal, mtzfile)) os.system('/bin/cp ' + mtzfile + ' .') - for mmcif in glob.glob(os.path.join(mtzfile[:mtzfile.rfind('/')],'*')): + for mmcif in glob.glob(os.path.join(mtzfile[:mtzfile.rfind('/')], '*')): if mmcif.endswith('.mmcif'): - self.Logfile.insert('%s: copying %s' %(xtal,mmcif)) + self.Logfile.insert('%s: copying %s' % (xtal, mmcif)) os.system('/bin/cp ' + mmcif + ' .') elif mmcif.endswith('.mmcif.bz2'): - self.Logfile.insert('%s: copying and decompressing %s' %(xtal,mmcif)) + self.Logfile.insert( + '%s: copying and decompressing %s' % (xtal, mmcif)) os.system('/bin/cp ' + mmcif + ' .') os.system('bzip2 -d ./' + mmcif) if os.path.isfile(mtzfile[mtzfile.rfind('/')+1:]) and not os.path.isfile(xtal+'.mtz'): os.symlink(mtzfile[mtzfile.rfind('/')+1:], xtal + '.mtz') if os.path.isfile(mtzfile[mtzfile.rfind('/') + 1:]): - mtzNew=os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code, mtzfile[mtzfile.rfind('/')+1:]) + mtzNew = os.path.join(self.projectDir, xtal, 'autoprocessing', self.visit + + '-' + run + autoproc + '_' + proc_code, mtzfile[mtzfile.rfind('/')+1:]) # MTZ file unmerged - if os.path.isfile(mtzfile.replace('_free.mtz','_scaled_unmerged.mtz')): - self.Logfile.insert('%s: found unmerged mtz file' %xtal) + if os.path.isfile(mtzfile.replace('_free.mtz', '_scaled_unmerged.mtz')): + self.Logfile.insert('%s: found unmerged mtz file' % xtal) if not os.path.isfile(xtal+'_unmerged.mtz'): - self.Logfile.insert('%s: copying %s' %(xtal,mtzfile.replace('_free.mtz','_scaled_unmerged.mtz'))) - os.system('/bin/cp ' + mtzfile.replace('_free.mtz','_scaled_unmerged.mtz') + ' .') + self.Logfile.insert('%s: copying %s' % ( + xtal, mtzfile.replace('_free.mtz', '_scaled_unmerged.mtz'))) + os.system('/bin/cp ' + mtzfile.replace('_free.mtz', + '_scaled_unmerged.mtz') + ' .') # AIMLESS logfile if not os.path.isfile(logfile[logfile.rfind('/')+1:]): self.Logfile.insert('%s: copying %s' % (xtal, logfile)) @@ -2708,93 +2893,106 @@ def copyMTZandLOGfiles(self,xtal,run,autoproc,mtzfile,logfile,proc_code): if logfile.endswith('summary.tar.gz'): self.Logfile.insert('unpacking summary.tar.gz') os.system('tar -xzvf summary.tar.gz') - logfile = logfile.replace('summary.tar.gz','staraniso_alldata-unique.table1') - self.cleanUpDir(xtal,run,autoproc,mtzfile,logfile,proc_code) + logfile = logfile.replace( + 'summary.tar.gz', 'staraniso_alldata-unique.table1') + self.cleanUpDir(xtal, run, autoproc, + mtzfile, logfile, proc_code) if os.path.isfile(logfile[logfile.rfind('/')+1:]) and not os.path.isfile(xtal+'.log'): os.symlink(logfile[logfile.rfind('/')+1:], xtal + '.log') if os.path.isfile(logfile[logfile.rfind('/') + 1:]): - logNew=os.path.join(self.projectDir,xtal,'autoprocessing', self.visit + '-' + run + autoproc+ '_' + proc_code, logfile[logfile.rfind('/') + 1:]) + logNew = os.path.join(self.projectDir, xtal, 'autoprocessing', self.visit + + '-' + run + autoproc + '_' + proc_code, logfile[logfile.rfind('/') + 1:]) # September 2021: xia2 does not also output a xia2.mmcif and json merging statistics file, even if aimless was used # for scaling, however, the xia2.mmcif file is differently formatted than the one from dials # hence, if xtal.log file already exists, use this one if 'aimless' in os.readlink(xtal + '.log'): logNew = os.path.join(self.projectDir, xtal, 'autoprocessing', self.visit + '-' + run + autoproc + '_' + proc_code, xtal + '.log') - return mtzNew,logNew + return mtzNew, logNew - def makeJPGdir(self,xtal,run): - if not os.path.isdir(os.path.join(self.projectDir,xtal,'jpg')): + def makeJPGdir(self, xtal, run): + if not os.path.isdir(os.path.join(self.projectDir, xtal, 'jpg')): self.Logfile.insert('making jpg directory in '+xtal) - os.mkdir(os.path.join(self.projectDir,xtal,'jpg')) + os.mkdir(os.path.join(self.projectDir, xtal, 'jpg')) if not os.path.isdir( - os.path.join(self.projectDir,xtal,'jpg', self.visit + '-' + run)): - os.mkdir(os.path.join(self.projectDir,xtal,'jpg', self.visit + '-' + run)) - - def copyJPGs(self,xtal,run,auto): -# for img in glob.glob(os.path.join(self.processedDir.replace('processed','jpegs'),xtal,run+'*t.png')): -# for img in glob.glob(os.path.join(self.processedDir.replace('processed', 'jpegs'), run + '*t.png')): - self.Logfile.insert('%s: trying to copy crystal snapshots...' %xtal) + os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run)): + os.mkdir(os.path.join(self.projectDir, xtal, + 'jpg', self.visit + '-' + run)) + + def copyJPGs(self, xtal, run, auto): + # for img in glob.glob(os.path.join(self.processedDir.replace('processed','jpegs'),xtal,run+'*t.png')): + # for img in glob.glob(os.path.join(self.processedDir.replace('processed', 'jpegs'), run + '*t.png')): + self.Logfile.insert('%s: trying to copy crystal snapshots...' % xtal) found = False if self.agamemnon: proposal = self.visit.split('-')[0] - self.Logfile.insert('looking for images in '+os.path.join(self.processedDir.replace(proposal,self.visit),'jpegs',auto,self.target,xtal,run + '*.0.png')) - for img in glob.glob(os.path.join(self.processedDir.replace(proposal,self.visit),'jpegs',auto,self.target,xtal,run + '*.0.png')): - if not os.path.isfile(os.path.join(self.projectDir,xtal,'jpg', self.visit +'-'+ run,img[img.rfind('/')+1:])): + self.Logfile.insert('looking for images in '+os.path.join(self.processedDir.replace( + proposal, self.visit), 'jpegs', auto, self.target, xtal, run + '*.0.png')) + for img in glob.glob(os.path.join(self.processedDir.replace(proposal, self.visit), 'jpegs', auto, self.target, xtal, run + '*.0.png')): + if not os.path.isfile(os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run, img[img.rfind('/')+1:])): self.Logfile.insert('%s: copying %s' % (xtal, img)) - os.system('/bin/cp %s %s' %(img,os.path.join(self.projectDir,xtal,'jpg', self.visit + '-' + auto+'_'+ run))) + os.system('/bin/cp %s %s' % (img, os.path.join(self.projectDir, + xtal, 'jpg', self.visit + '-' + auto+'_' + run))) else: for img in glob.glob(os.path.join(self.processedDir.replace('processed', 'jpegs'), run + '*.0.png')): found = True - if not os.path.isfile(os.path.join(self.projectDir,xtal,'jpg', self.visit +'-'+ run,img[img.rfind('/')+1:])): + if not os.path.isfile(os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run, img[img.rfind('/')+1:])): self.Logfile.insert('%s: copying %s' % (xtal, img)) - os.system('/bin/cp %s %s' %(img,os.path.join(self.projectDir,xtal,'jpg', self.visit + '-' + run))) + os.system('/bin/cp %s %s' % (img, os.path.join(self.projectDir, + xtal, 'jpg', self.visit + '-' + run))) if not found: for img in glob.glob(os.path.join(self.processedDir.replace('processed', 'jpegs'), xtal, run + '*.0.png')): if not os.path.isfile(os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run, img[img.rfind('/') + 1:])): self.Logfile.insert('%s: copying %s' % (xtal, img)) - os.system('/bin/cp %s %s' % (img, os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run))) + os.system( + '/bin/cp %s %s' % (img, os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run))) - - - def findJPGs(self,xtal,run): - jpgDict={} + def findJPGs(self, xtal, run): + jpgDict = {} # for n,img in enumerate(glob.glob(os.path.join(self.projectDir,xtal,'jpg', self.visit +'-'+ run,'*t.png'))): - for n,img in enumerate(glob.glob(os.path.join(self.projectDir,xtal,'jpg', self.visit +'-'+ run,'*.0.png'))): - if n <= 3: jpgDict['DataCollectionCrystalImage'+str(n+1)]=img + for n, img in enumerate(glob.glob(os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run, '*.0.png'))): + if n <= 3: + jpgDict['DataCollectionCrystalImage'+str(n+1)] = img return jpgDict - - def readProcessingUpdateResults(self,xtal,folder,log,mtz,timestamp,current_run,autoproc,proc_code): + def readProcessingUpdateResults(self, xtal, folder, log, mtz, timestamp, current_run, autoproc, proc_code): db_dict = {} - self.Logfile.warning('%s: looking for %s' %(xtal,os.path.join(folder, mtz))) - for mtzfile in glob.glob(os.path.join(folder,mtz)): - self.Logfile.insert('%s: found %s' %(xtal,mtzfile)) - self.Logfile.warning('%s: looking for %s' %(xtal,os.path.join(folder, log))) + self.Logfile.warning('%s: looking for %s' % + (xtal, os.path.join(folder, mtz))) + for mtzfile in glob.glob(os.path.join(folder, mtz)): + self.Logfile.insert('%s: found %s' % (xtal, mtzfile)) + self.Logfile.warning('%s: looking for %s' % + (xtal, os.path.join(folder, log))) for logfile in glob.glob(os.path.join(folder, log)): self.Logfile.insert('%s: found %s' % (xtal, logfile)) - self.createAutoprocessingDir(xtal, current_run, autoproc,proc_code) - mtzNew,logNew = self.copyMTZandLOGfiles(xtal,current_run,autoproc,mtzfile,logfile,proc_code) + self.createAutoprocessingDir( + xtal, current_run, autoproc, proc_code) + mtzNew, logNew = self.copyMTZandLOGfiles( + xtal, current_run, autoproc, mtzfile, logfile, proc_code) if self.target == '=== project directory ===': target = 'unknown' else: target = self.target - db_dict = { 'DataCollectionDate': timestamp, - 'DataProcessingPathToLogfile': logNew, - 'DataProcessingPathToMTZfile': mtzNew, - 'DataProcessingDirectoryOriginal': folder, - 'DataCollectionOutcome': 'success', # success in collection Table only means that a logfile was found - 'ProteinName': target } + db_dict = {'DataCollectionDate': timestamp, + 'DataProcessingPathToLogfile': logNew, + 'DataProcessingPathToMTZfile': mtzNew, + 'DataProcessingDirectoryOriginal': folder, + # success in collection Table only means that a logfile was found + 'DataCollectionOutcome': 'success', + 'ProteinName': target} db_dict.update(parse().read_aimless_logfile(logNew)) - db_dict.update(self.findJPGs(xtal,current_run)) # image exist even if data processing failed + # image exist even if data processing failed + db_dict.update(self.findJPGs(xtal, current_run)) db_dict['DataCollectionBeamline'] = self.beamline - self.update_data_collection_table(xtal,current_run,autoproc,db_dict,proc_code) + self.update_data_collection_table( + xtal, current_run, autoproc, db_dict, proc_code) # return db_dict - def getAutoProc(self,folder_rel,staraniso): + def getAutoProc(self, folder_rel, staraniso): self.Logfile.insert('checking name of auto-processing pipeline...') folder = os.path.realpath(folder_rel) self.Logfile.insert('folder: ' + folder) - autoproc='unknown' + autoproc = 'unknown' if 'ap-run' in folder: autoproc = 'autoPROC' else: @@ -2808,24 +3006,27 @@ def getAutoProc(self,folder_rel,staraniso): elif 'dials' in f: autoproc = f break - self.Logfile.insert('name of auto-processing pipeline: %s' %autoproc) + self.Logfile.insert('name of auto-processing pipeline: %s' % autoproc) return autoproc - def update_data_collection_table(self,xtal,current_run,autoproc,db_dict,proc_code): - condition_dict = { 'CrystalName': xtal, - 'DataCollectionVisit': self.visit, - 'DataCollectionRun': current_run, - 'DataCollectionSubdir': proc_code, - 'DataProcessingProgram': autoproc } - self.db.update_insert_any_table('collectionTable', db_dict, condition_dict) - - def alreadyParsed(self,xtal,current_run,proc_code,autoproc): - parsed=False - self.Logfile.insert('checking if this processed directory was already parsed') + def update_data_collection_table(self, xtal, current_run, autoproc, db_dict, proc_code): + condition_dict = {'CrystalName': xtal, + 'DataCollectionVisit': self.visit, + 'DataCollectionRun': current_run, + 'DataCollectionSubdir': proc_code, + 'DataProcessingProgram': autoproc} + self.db.update_insert_any_table( + 'collectionTable', db_dict, condition_dict) + + def alreadyParsed(self, xtal, current_run, proc_code, autoproc): + parsed = False + self.Logfile.insert( + 'checking if this processed directory was already parsed') if xtal in self.exisitingSamples: self.Logfile.insert(xtal + ' exists in collectionTable') self.Logfile.insert('current identifier:') - self.Logfile.insert(self.visit + '-' + current_run + autoproc + '-' + proc_code) + self.Logfile.insert(self.visit + '-' + + current_run + autoproc + '-' + proc_code) self.Logfile.insert('indentifier in collectionTable') for x in self.exisitingSamples[xtal]: self.Logfile.insert(x) @@ -2834,13 +3035,13 @@ def alreadyParsed(self,xtal,current_run,proc_code,autoproc): self.Logfile.warning( '%s: results from %s already parsed; skipping...' % ( xtal, self.visit + '-' + current_run + autoproc)) - parsed=True + parsed = True return parsed - def empty_folder(self,xtal,folder): + def empty_folder(self, xtal, folder): empty = True stuff = [] - for x in glob.glob(os.path.join(folder,'*')): + for x in glob.glob(os.path.join(folder, '*')): stuff.append(x) if not stuff: self.Logfile.warning( @@ -2849,7 +3050,7 @@ def empty_folder(self,xtal,folder): empty = False return empty - def junk(self,folder): + def junk(self, folder): do_not_parse = False if not os.path.isdir(folder): do_not_parse = True @@ -2861,19 +3062,21 @@ def parse_file_system(self): if self.agamemnon: d = self.processedDir[:self.processedDir.rfind('/')] t = self.processedDir[self.processedDir.rfind('/')+1:] - autoDir = os.path.join(d,'auto',t) + autoDir = os.path.join(d, 'auto', t) else: autoDir = self.processedDir - self.Logfile.insert('checking for new data processing results in '+autoDir) + self.Logfile.insert( + 'checking for new data processing results in '+autoDir) progress = 0 - progress_step = XChemMain.getProgressSteps(len(glob.glob(os.path.join(autoDir,'*')))) + progress_step = XChemMain.getProgressSteps( + len(glob.glob(os.path.join(autoDir, '*')))) runList = [] # for auto in autoDir: - self.Logfile.insert('--> ' + os.path.join(autoDir,'*')) - for nx,collected_xtals in enumerate(sorted(glob.glob(os.path.join(autoDir,'*')))): - self.Logfile.insert('%s: %s' %(nx,collected_xtals)) + self.Logfile.insert('--> ' + os.path.join(autoDir, '*')) + for nx, collected_xtals in enumerate(sorted(glob.glob(os.path.join(autoDir, '*')))): + self.Logfile.insert('%s: %s' % (nx, collected_xtals)) self.visit = collected_xtals.split('/')[5] if 'tmp' in collected_xtals or 'results' in collected_xtals or 'scre' in collected_xtals: continue @@ -2894,65 +3097,77 @@ def parse_file_system(self): # tmp = xtal[:xtal.rfind('_')] # xtal = tmp[:tmp.rfind('_')] - self.Logfile.insert('%s: checking auto-processing results' %xtal) + self.Logfile.insert('%s: checking auto-processing results' % xtal) self.createSampleDir(xtal) if self.target == '=== project directory ===': - runDir = os.path.join(collected_xtals,'processed','*') + runDir = os.path.join(collected_xtals, 'processed', '*') # elif self.agamemnon: # tmpDir = collected_xtals[:collected_xtals.rfind('/')] # runDir = os.path.join(tmpDir,xtal+'_*_') else: - runDir = os.path.join(collected_xtals,'*') + runDir = os.path.join(collected_xtals, '*') self.Logfile.insert('current runDir: ' + runDir) for run in sorted(glob.glob(runDir)): - current_run=run[run.rfind('/')+1:] - for code in glob.glob(os.path.join(run,'*')): + current_run = run[run.rfind('/')+1:] + for code in glob.glob(os.path.join(run, '*')): if os.path.islink(code): continue # else: # proc_code = code[code.rfind('/')+1:] proc_code = code.split('/')[len(code.split('/'))-1] - self.Logfile.insert(xtal + ': processed directory -> ' + proc_code) + self.Logfile.insert( + xtal + ': processed directory -> ' + proc_code) if current_run+proc_code in runList: continue - self.Logfile.insert('%s -> run: %s -> current run: %s -> %s' %(xtal,run,current_run,proc_code)) - timestamp=datetime.fromtimestamp(os.path.getmtime(run)).strftime('%Y-%m-%d %H:%M:%S') + self.Logfile.insert( + '%s -> run: %s -> current run: %s -> %s' % (xtal, run, current_run, proc_code)) + timestamp = datetime.fromtimestamp( + os.path.getmtime(run)).strftime('%Y-%m-%d %H:%M:%S') # create directory for crystal aligment images in projectDir - self.makeJPGdir(xtal,current_run) - self.copyJPGs(xtal, current_run, 'non-auto') # 'non-auto' is irrelevant here + self.makeJPGdir(xtal, current_run) + # 'non-auto' is irrelevant here + self.copyJPGs(xtal, current_run, 'non-auto') for item in self.toParse: - procDir = os.path.join(code,item[0]) + procDir = os.path.join(code, item[0]) logfile = item[1] mtzfile = item[2] - self.Logfile.insert('%s: search template: procDir - logfile - mtzfile' %xtal) - self.Logfile.insert('%s: procDir = %s' %(xtal,procDir)) - self.Logfile.insert('%s: logfile = %s' %(xtal,logfile)) - self.Logfile.insert('%s: mtzfile = %s' %(xtal,mtzfile)) + self.Logfile.insert( + '%s: search template: procDir - logfile - mtzfile' % xtal) + self.Logfile.insert( + '%s: procDir = %s' % (xtal, procDir)) + self.Logfile.insert( + '%s: logfile = %s' % (xtal, logfile)) + self.Logfile.insert( + '%s: mtzfile = %s' % (xtal, mtzfile)) for folder in glob.glob(procDir): staraniso = '' - self.Logfile.insert('%s: searching %s' %(xtal,folder)) + self.Logfile.insert( + '%s: searching %s' % (xtal, folder)) if self.junk(folder): continue - if self.empty_folder(xtal,folder): + if self.empty_folder(xtal, folder): continue if 'staraniso' in logfile or 'summary.tar.gz' in logfile: staraniso = '_staraniso' - autoproc = self.getAutoProc(folder,staraniso) - if self.alreadyParsed(xtal,current_run,proc_code,autoproc): + autoproc = self.getAutoProc(folder, staraniso) + if self.alreadyParsed(xtal, current_run, proc_code, autoproc): continue - self.readProcessingUpdateResults(xtal,folder,logfile,mtzfile,timestamp,current_run,autoproc,proc_code) + self.readProcessingUpdateResults( + xtal, folder, logfile, mtzfile, timestamp, current_run, autoproc, proc_code) runList.append(current_run+proc_code) # quit() progress += progress_step - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'parsing auto-processing results for '+xtal) + self.emit(QtCore.SIGNAL('update_status_bar(QString)'), + 'parsing auto-processing results for '+xtal) self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - self.Logfile.insert('====== finished parsing beamline directory ======') + self.Logfile.insert( + '====== finished parsing beamline directory ======') self.emit(QtCore.SIGNAL('read_pinIDs_from_gda_logs')) self.emit(QtCore.SIGNAL("finished()")) @@ -3023,8 +3238,8 @@ def parse_file_system(self): # self.Logfile.insert('%s: logfile = %s' % (xtal, logfile)) # self.Logfile.insert('%s: mtzfile = %s' % (xtal, mtzfile)) # -## for folder in glob.glob(procDir): -## for mtz in glob.glob(os.path.join(procDir,mtzfile)): +# for folder in glob.glob(procDir): +# for mtz in glob.glob(os.path.join(procDir,mtzfile)): ## print mtz # # for folder in glob.glob(procDir): @@ -3054,4 +3269,3 @@ def parse_file_system(self): # self.Logfile.insert('====== finished parsing beamline directory ======') # self.emit(QtCore.SIGNAL('read_pinIDs_from_gda_logs')) # self.emit(QtCore.SIGNAL("finished()")) - diff --git a/lib/XChemToolTips.py b/lib/XChemToolTips.py index 7ca1eecb..d60e33b8 100755 --- a/lib/XChemToolTips.py +++ b/lib/XChemToolTips.py @@ -3,258 +3,292 @@ import os import getpass + def dataset_task_tip(): - tip = ( 'describes what you can do' ) + tip = ('describes what you can do') return tip + def dataset_task_run_button_tip(): - tip = ( 'Run dataset' ) + tip = ('Run dataset') return tip + def dataset_task_status_button_tip(): - tip = ( 'Status dataset' ) + tip = ('Status dataset') return tip + def map_cif_file_task_tip(): - tip = ( 'describes what you can do' ) + tip = ('describes what you can do') return tip + def map_cif_file_task_run_button_tip(): - tip = ( 'Run map_cif_file' ) + tip = ('Run map_cif_file') return tip + def map_cif_file_task_status_button_tip(): - tip = ( 'Status map_cif_file' ) + tip = ('Status map_cif_file') return tip + def panddas_file_task_tip(): - tip = ( 'describes what you can do' ) + tip = ('describes what you can do') return tip + def panddas_file_task_run_button_tip(): - tip = ( 'Run panddas_file' ) + tip = ('Run panddas_file') return tip + def panddas_file_task_status_button_tip(): - tip = ( 'Status panddas_file' ) + tip = ('Status panddas_file') return tip + def refine_file_task_tip(): - tip = ( 'describes what you can do' ) + tip = ('describes what you can do') return tip + def refine_file_task_run_button_tip(): - tip = ( 'Run refine_file' ) + tip = ('Run refine_file') return tip + def refine_file_task_status_button_tip(): - tip = ( 'Status refine_file' ) + tip = ('Status refine_file') return tip + def validation_file_task_tip(): - tip = ( 'describes what you can do' ) + tip = ('describes what you can do') return tip + def validation_file_task_run_button_tip(): - tip = ( 'Run validation_file' ) + tip = ('Run validation_file') return tip + def validation_file_task_status_button_tip(): - tip = ( 'Status validation_file' ) + tip = ('Status validation_file') return tip + def update_from_datasource_button_tip(): - tip = ( 'Status validation_file' ) + tip = ('Status validation_file') return tip - - def load_samples_from_datasource(): - tip = ( 'loads all information\n' - 'which is currently in the\n' - 'data source' ) + tip = ('loads all information\n' + 'which is currently in the\n' + 'data source') return tip + def save_samples_to_datasource(): - tip = ( 'saves all changes you made\n' - 'to any of the cells to the\n' - 'data source' ) + tip = ('saves all changes you made\n' + 'to any of the cells to the\n' + 'data source') return tip + def create_pdb_cif_png_files(): - tip = ( 'uses ACEDRG to create pdb,cif and png files for all compounds\n' - 'that have a smiles string assigned. The compounds ID\n' - 'serves as name if available.\n' - 'The files are written to initial_model//compound\n' - 'data source' ) + tip = ('uses ACEDRG to create pdb,cif and png files for all compounds\n' + 'that have a smiles string assigned. The compounds ID\n' + 'serves as name if available.\n' + 'The files are written to initial_model//compound\n' + 'data source') return tip + def check_status_create_pdb_cif_png_files(): - tip = ( 'the jobs are sent to a computer cluster if available\n' - 'gives you an overview about how it progresses') + tip = ('the jobs are sent to a computer cluster if available\n' + 'gives you an overview about how it progresses') return tip + def run_pandda_inspect_at_home(pandda_directory): -# instruction = ( '\n\n' -# 'Please follow the instructions below to run pandda.inspect at your home institution:\n\n' -# ' 1. Make sure that the pandda package is installed at your home institution.\n' -# ' For more details see: http://pandda.bitbucket.org\n\n' -# ' 2. At home: go to the folder where you want the files from pandda.analyse to be;\n' -# ' e.g. cd /home/tkrojer/fragment_screening\n\n' -# ' 3. At home: run the following command:\n' -# ' rsync -av %s@nx.diamond.ac.uk:%s .\n\n' %(getpass.getuser(),pandda_directory)+ -# ' 4. At home: go into the pandda directory\n' -# ' cd %s\n\n' %pandda_directory[pandda_directory.rfind('/')+1:]+ -# ' 5. At home: run pandda.inspect\n' -# ' pandda.inspect\n\n' -# ' 6. Once you finished inspecting your models, close pandda.inspect and copy the data back to DLS\n' -# ' with the following command:\n' -# ' rsync -av * %s@nx.diamond.ac.uk:%s\n\n' %(getpass.getuser(),pandda_directory)+ -# ' 7. At DLS: continue using XChemExplorer; go to the PANDDA tab and run:\n' -# ' "Export PANDDA models"\n' -# ' This will trigger the following steps:\n' -# ' - transform the pandda models back into the crystallographic unit cell\n' -# ' - copy the transformed models into the respective folder of the project directory\n' -# ' - launch an initial round of refinement with REFMAC\n' -# ' Note: All refinement jobs run on the cluster at DLS.\n' -# ' You can check the status of the jobs by typing:\n' -# ' module load global/cluster\n' -# ' qstat\n\n' -# ' 8. At DLS: go to the REFINEMENT tab and run "Open COOT" to review and further refine your models if necessary\n' ) - - instruction = ( '\n\n' - 'Be sure to have pandda installed at home, and go to a clean subdirectory.\n' - 'From that directory, do the steps below.\n' - 'This moves the relevant files to your site so you can do the model building locally, and then moves the files back to Diamond.\n' - '1. run: rsync -av %s@nx.diamond.ac.uk:%s .\n' %(getpass.getuser(),pandda_directory)+ - '2. run: "pandda.inspect", and build all relevant models, etc.\n' - '3. run: rsync -av * %s@nx.diamond.ac.uk:%s\n' %(getpass.getuser(),pandda_directory)+ - 'Now proceed within XChemExplorer as before.\n' ) + # instruction = ( '\n\n' + # 'Please follow the instructions below to run pandda.inspect at your home institution:\n\n' + # ' 1. Make sure that the pandda package is installed at your home institution.\n' + # ' For more details see: http://pandda.bitbucket.org\n\n' + # ' 2. At home: go to the folder where you want the files from pandda.analyse to be;\n' + # ' e.g. cd /home/tkrojer/fragment_screening\n\n' + # ' 3. At home: run the following command:\n' + # ' rsync -av %s@nx.diamond.ac.uk:%s .\n\n' %(getpass.getuser(),pandda_directory)+ + # ' 4. At home: go into the pandda directory\n' + # ' cd %s\n\n' %pandda_directory[pandda_directory.rfind('/')+1:]+ + # ' 5. At home: run pandda.inspect\n' + # ' pandda.inspect\n\n' + # ' 6. Once you finished inspecting your models, close pandda.inspect and copy the data back to DLS\n' + # ' with the following command:\n' + # ' rsync -av * %s@nx.diamond.ac.uk:%s\n\n' %(getpass.getuser(),pandda_directory)+ + # ' 7. At DLS: continue using XChemExplorer; go to the PANDDA tab and run:\n' + # ' "Export PANDDA models"\n' + # ' This will trigger the following steps:\n' + # ' - transform the pandda models back into the crystallographic unit cell\n' + # ' - copy the transformed models into the respective folder of the project directory\n' + # ' - launch an initial round of refinement with REFMAC\n' + # ' Note: All refinement jobs run on the cluster at DLS.\n' + # ' You can check the status of the jobs by typing:\n' + # ' module load global/cluster\n' + # ' qstat\n\n' + # ' 8. At DLS: go to the REFINEMENT tab and run "Open COOT" to review and further refine your models if necessary\n' ) + + instruction = ('\n\n' + 'Be sure to have pandda installed at home, and go to a clean subdirectory.\n' + 'From that directory, do the steps below.\n' + 'This moves the relevant files to your site so you can do the model building locally, and then moves the files back to Diamond.\n' + '1. run: rsync -av %s@nx.diamond.ac.uk:%s .\n' % (getpass.getuser(), pandda_directory) + + '2. run: "pandda.inspect", and build all relevant models, etc.\n' + '3. run: rsync -av * %s@nx.diamond.ac.uk:%s\n' % (getpass.getuser(), pandda_directory) + + 'Now proceed within XChemExplorer as before.\n') print instruction + def deposition_interface_note(): - note = ( '\n\n' - 'Note: you can use this mask to save identical information for ALL structures to be deposited.\n' - 'However, this may not be suitable in cases where the information is different for certain samples.\n' - 'In such cases, please use for example SQLiteBrowser to edit the relevant fields in the depositTable.' ) + note = ('\n\n' + 'Note: you can use this mask to save identical information for ALL structures to be deposited.\n' + 'However, this may not be suitable in cases where the information is different for certain samples.\n' + 'In such cases, please use for example SQLiteBrowser to edit the relevant fields in the depositTable.') return note + def html_summary_introduction(): - text = ( 'This section describes how to generate an HTML summary page of the current project. \n' - 'All you need to do is select the HTML output directory where the html and additional auxiliary files \n' - 'and will be written to. ' - 'Then press the "Export to HTML" button and \nall bound structures that are labeled as "4 - compchem ready"' - 'or higher will be included in the final document. \n' - 'Please checkout https://www.thesgc.org/fragment-screening to see what the final pages look like. ') + text = ('This section describes how to generate an HTML summary page of the current project. \n' + 'All you need to do is select the HTML output directory where the html and additional auxiliary files \n' + 'and will be written to. ' + 'Then press the "Export to HTML" button and \nall bound structures that are labeled as "4 - compchem ready"' + 'or higher will be included in the final document. \n' + 'Please checkout https://www.thesgc.org/fragment-screening to see what the final pages look like. ') return text + def html_export_directory_background(): - text = ( 'The HTML export directory will contain all files necessary to generate the summary file.\n' - 'It is also makes it easy to share the results with collaborators.') + text = ('The HTML export directory will contain all files necessary to generate the summary file.\n' + 'It is also makes it easy to share the results with collaborators.') return text + def html_export_step(): - text = ( 'This step will create an index.html file and it will copy pdb, mtz and cif files\n' - 'as well as PanDDA event maps into the html export directory.' ) + text = ('This step will create an index.html file and it will copy pdb, mtz and cif files\n' + 'as well as PanDDA event maps into the html export directory.') return text def icb_file_background(): - text = ( 'This step will use ICM-pro to create interactive structure thumbnails in the html file (http://www.molsoft.com/activeicmjs.html)') + text = ('This step will use ICM-pro to create interactive structure thumbnails in the html file (http://www.molsoft.com/activeicmjs.html)') return text - def prepare_ICB_files(): - instruction = ( '- Open file browser and navigate to HTML export directory.\n' - '- Open ICM (at DLS: select SERVER and enter diamvicmpro.diamond.ac.uk in case ICM asks).\n' - '- Drag-and-drop dsEvent_sqlite.icm file into ICM main window.\n' - '- In ICM workspace panel: right-click on dsEvent_sqlite.icm and select "RUN".') + instruction = ('- Open file browser and navigate to HTML export directory.\n' + '- Open ICM (at DLS: select SERVER and enter diamvicmpro.diamond.ac.uk in case ICM asks).\n' + '- Drag-and-drop dsEvent_sqlite.icm file into ICM main window.\n' + '- In ICM workspace panel: right-click on dsEvent_sqlite.icm and select "RUN".') return instruction + def zenodo_upload_start(html_export_directory): - instruction = ( 'This will copy all files required for ZENODO upload to\n' - '%s' %os.path.join(html_export_directory,'zenodo') ) + instruction = ('This will copy all files required for ZENODO upload to\n' + '%s' % os.path.join(html_export_directory, 'zenodo')) return instruction + def zenodo_upload_part_one(html_export_directory): - instruction = ( '- Register with ZENODO (www.zenodo.org)\n' - '- Select Upload -> New Upload\n' - '- upload all files from %s/zenodo, BUT NOT any of the .html files!!!' %html_export_directory ) + instruction = ('- Register with ZENODO (www.zenodo.org)\n' + '- Select Upload -> New Upload\n' + '- upload all files from %s/zenodo, BUT NOT any of the .html files!!!' % html_export_directory) return instruction + def zenodo_upload_part_two(): - instruction = ( 'You might have noticed that once you started uploading files, the address bar in your browser will change to something like this:') + instruction = ( + 'You might have noticed that once you started uploading files, the address bar in your browser will change to something like this:') return instruction + def zenodo_upload_part_three(): - instruction = ( 'Please enter the upload ID, i.e. the number at the end of the line, into the field below') + instruction = ( + 'Please enter the upload ID, i.e. the number at the end of the line, into the field below') return instruction + def zenodo_upload_part_four(html_export_directory): - instruction = ( 'Upload ALL html files in {0!s} to ZENODO and publish the page.'.format(os.path.join(html_export_directory,'zenodo'))) + instruction = ('Upload ALL html files in {0!s} to ZENODO and publish the page.'.format( + os.path.join(html_export_directory, 'zenodo'))) return instruction + def deposition_pandda_site_not_ready(xtal): - msg = ( 'Please make sure that all placed ligands in '+xtal+' are ready for deposition.\n' - 'Go to the Refinement tab -> Open COOT and either delete the ligand or set the site ' - ' to "5 - Deposition ready"' ) + msg = ('Please make sure that all placed ligands in '+xtal+' are ready for deposition.\n' + 'Go to the Refinement tab -> Open COOT and either delete the ligand or set the site ' + ' to "5 - Deposition ready"') return msg + def pandda_pre_run(reference_directory): - msg = ( 'The aim of the pre-run is NOT to identify bound ligands,\n' - 'but to create mean ground state maps.\n' - 'Hence, the pre-run will only comprise 100 datasets.\n' - 'After the pre-run is finished use the resulting ground state mean maps\n' - 'to build a suitable reference model for the subsequent PanDDA production run.\n' - 'The appendix will determine the name of the folder where the results from\n' - 'the pre-run will be stored. It is used by the COOT plugin to distinguish\n' - 'between different pre-runs.\n' - 'The result from the pre-run will be stored in:\n' - '%s/pannda_'https://openlabnotebooks.org/update-on-batch-deposition-of-xchem-structures'" ) return lnk + def deposition_bound_state_prerequisites(): msg = ( '1. Event map to MTZ conversion.\n' @@ -269,6 +303,7 @@ def deposition_bound_state_prerequisites(): ) return msg + def deposition_bound_state_preparation_step_one_text(): msg = ( '1. Press the button below to generate structure and structure factor mmcif files of all selected datasets.\n' @@ -276,6 +311,7 @@ def deposition_bound_state_preparation_step_one_text(): ) return msg + def deposition_bound_state_preparation_step_two_text(): msg = ( '2. Press the button below to copy all the mmcif files into the "group deposition directory" (see settings tab).\n' @@ -283,18 +319,21 @@ def deposition_bound_state_preparation_step_two_text(): ) return msg + def pdb_group_deposition_instruction_one(): msg = ( '3. Go to the group deposition website, create a session and upload the ligand-bound.tar.bz2 file from the group deposition directory.' ) return msg + def pdb_group_deposition_link(): lnk = ( "'https://deposit-group-1.rcsb.rutgers.edu/groupdeposit'" ) return lnk + def pdb_group_deposition_instruction_two(): msg = ( ' user: grouptester\n' @@ -302,6 +341,7 @@ def pdb_group_deposition_instruction_two(): ) return msg + def deposition_ground_state_prerequisites(): msg = ( '1. Convert all apo MTZ files to mmcif format.\n' @@ -319,14 +359,16 @@ def deposition_ground_state_preparation_step_one_text(): ) return msg + def deposition_ground_state_log_info(): msg = ( - ' IMPORTANT:\n' - ' Make sure that a file or symlink to an AIMLESS logile with the same name root as your ground-state PDB file\n' - ' is present in the same folder. This is currently not generated automatically! ' + ' IMPORTANT:\n' + ' Make sure that a file or symlink to an AIMLESS logile with the same name root as your ground-state PDB file\n' + ' is present in the same folder. This is currently not generated automatically! ' ) return msg + def deposition_ground_state_preparation_step_two_text(): msg = ( '2. Select ground-state MTZ file.\n' @@ -336,6 +378,7 @@ def deposition_ground_state_preparation_step_two_text(): ) return msg + def deposition_ground_state_preparation_step_three_text(): msg = ( '1. Please check the settings tab that you have selected the correct pandda directory.\n' @@ -344,29 +387,33 @@ def deposition_ground_state_preparation_step_three_text(): ) return msg + def deposition_ground_state_preparation_step_four_text(): msg = ( '2. Add the ground-state entry to the database.' ) return msg + def deposition_ground_state_preparation_step_five_text(): msg = ( - '3. Enter meta-data for ground-state model:\n' - ' - Open "Deposition -> Edit information"\n' - ' - Fill out form or load .deposit file\n' - ' - Press "Save to Database"\n' - ' - Press "OK"' + '3. Enter meta-data for ground-state model:\n' + ' - Open "Deposition -> Edit information"\n' + ' - Fill out form or load .deposit file\n' + ' - Press "Save to Database"\n' + ' - Press "OK"' ) return msg + def deposition_ground_state_preparation_step_six_text(): msg = ( - '4. Prepare the ground-state mmcif file.\n' - ' Note: the mmcif files are saved into the selected pandda directory' + '4. Prepare the ground-state mmcif file.\n' + ' Note: the mmcif files are saved into the selected pandda directory' ) return msg + def deposition_ground_state_preparation_step_seven_text(): msg = ( '5. Press the button below to copy the structire and structure factor mmcif files into the "group deposition directory" (see settings tab).\n' @@ -374,12 +421,14 @@ def deposition_ground_state_preparation_step_seven_text(): ) return msg + def deposition_ground_state_preparation_step_eight_text(): msg = ( '6. Go to the group deposition website, create a session and upload the ligand-bound.tar.bz2 file from the group deposition directory.' ) return msg + def after_deposition_step_one_text(): msg = ( 'After you have successfully submitted the ligand-bound structures via the PDB group deposition interface, you will immediately get\n' @@ -388,37 +437,40 @@ def after_deposition_step_one_text(): ) return msg + def deposition_bounnd_state_preparation_ignore_event_map(): msg = ( 'do NOT include PanDDA event maps (ONLY USE IN CASE IF DATA WERE NOT ANALYSED WITH PANDDA!)' ) return msg + def second_cif_file_info(cif_file): second_cif_file = str(cif_file) if os.path.isfile(second_cif_file): msg = ( 'You have selected the following restraints file\n' 'for merging into the the ligand CIF files:\n' - +second_cif_file+ + + second_cif_file + '\n' 'Press NO in case you do not want to continue\n' 'In case you want to use another file, open the preferences menu and set it there\n' 'Please check the XCE logfile in case of unexpected behaviour' ) - elif second_cif_file.replace(' ','') == '' or second_cif_file.lower() == 'none': + elif second_cif_file.replace(' ', '') == '' or second_cif_file.lower() == 'none': msg = ( 'No restraints file was selected!' ) else: msg = ( 'The selected restraints file does not exist:\n' - +second_cif_file+ + + second_cif_file + '\n' 'Open the preferences menu and set it there\n' ) return msg + def second_cif_file_not_exists(): msg = ( 'The CIF file for the non-standard ligand does not exist! ' @@ -427,6 +479,7 @@ def second_cif_file_not_exists(): ) return msg + def notification_about_changes_to_apo_deposition(): msg = ( 'The ground-state deposition procedure has changes in XCE v1.5.0!\n\n' @@ -443,6 +496,7 @@ def notification_about_changes_to_apo_deposition(): ) return msg + def pandda_export_ligand_bound_models_only_disclaimer(): msg = ( 'You have chosen to export and refine the ligand-bound model only. ' @@ -452,4 +506,4 @@ def pandda_export_ligand_bound_models_only_disclaimer(): 'ligands and conformational changes, but it may not be ideal for weakly bound fragments and corresponding ' 'conformational changes.' ) - return msg \ No newline at end of file + return msg diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 798d9f3c..80e03feb 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -1,3 +1,5 @@ +import XChemLog +import XChemDB import sys import os import glob @@ -27,8 +29,7 @@ from iotbx import mtz sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') -import XChemDB -import XChemLog + def open_decompress_file(filename, mode="rb"): """Open file for reading, decompressing silently if necessary.""" @@ -41,39 +42,39 @@ def open_decompress_file(filename, mode="rb"): return open(filename, mode=mode) + class process: - def __init__(self,dimple): - self.project_directory=dimple['project_directory'] - self.delete_old=dimple['delete_old'] - self.xtalID=dimple['xtalID'] - self.reference=dimple['reference'] - self.queueing_system_available=dimple['queueing_system_available'] - self.ccp4_scratch_directory=dimple['ccp4_scratch'] - self.fileroot_in=dimple['fileroot_in'] - self.mtz_free=self.fileroot_in+'.free.mtz' - self.mtz_in=self.fileroot_in+'.mtz' + def __init__(self, dimple): + self.project_directory = dimple['project_directory'] + self.delete_old = dimple['delete_old'] + self.xtalID = dimple['xtalID'] + self.reference = dimple['reference'] + self.queueing_system_available = dimple['queueing_system_available'] + self.ccp4_scratch_directory = dimple['ccp4_scratch'] + self.fileroot_in = dimple['fileroot_in'] + self.mtz_free = self.fileroot_in+'.free.mtz' + self.mtz_in = self.fileroot_in+'.mtz' # need to set $CCP4_SCR, because the default directory in /home/zqr16691/tmp fills up easily # and then dimple will not run # if not os.path.isdir(self.project_directory[:self.project_directory.find('processing')+11]+'/tmp'): # os.mkdir(self.project_directory[:self.project_directory.find('processing')+11]+'/tmp') # self.ccp4_scratch=self.project_directory[:self.project_directory.find('processing')+11]+'/tmp' - def get_Rfree(self): - Cmds='' - if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_free)): - if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.reference+'.mtz')): + Cmds = '' + if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_free)): + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.reference+'.mtz')): Cmds = ( -# '#!'+os.getenv('SHELL')+'\n' + # '#!'+os.getenv('SHELL')+'\n' '\n' - 'cd %s/%s/Dimple\n' %(self.project_directory,self.xtalID) + + 'cd %s/%s/Dimple\n' % (self.project_directory, self.xtalID) + '\n' - 'pointless hklin ../%s hklref %s.mtz hklout %s.reind.mtz << EOF > pointless.log\n' %(self.mtz_in,self.reference,self.xtalID)+ + 'pointless hklin ../%s hklref %s.mtz hklout %s.reind.mtz << EOF > pointless.log\n' % (self.mtz_in, self.reference, self.xtalID) + ' tolerance 5\n' 'EOF\n' '\n' - 'cad hklin1 %s.reind.mtz hklin2 %s.mtz hklout cad.mtz << EOF > cad.log\n' %(self.xtalID,self.reference) + + 'cad hklin1 %s.reind.mtz hklin2 %s.mtz hklout cad.mtz << EOF > cad.log\n' % (self.xtalID, self.reference) + ' labin file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n' ' labout file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n' ' labin file_number 2 E1=FreeR_flag\n' @@ -81,64 +82,67 @@ def get_Rfree(self): ' END\n' 'EOF\n' '\n' - 'freerflag hklin cad.mtz hklout ../%s << EOF > freerflag.log\n' %self.mtz_free + + 'freerflag hklin cad.mtz hklout ../%s << EOF > freerflag.log\n' % self.mtz_free + ' COMPLETE FREE=FreeR_flag\n' ' END\n' 'EOF\n' - '#uniqueify -f FreeR_flag cad.mtz ../%s\n' %self.mtz_free - ) + '#uniqueify -f FreeR_flag cad.mtz ../%s\n' % self.mtz_free + ) else: Cmds = ( -# '#!'+os.getenv('SHELL')+'\n' + # '#!'+os.getenv('SHELL')+'\n' '\n' - 'cd %s/%s/Dimple\n' %(self.project_directory,self.xtalID) + + 'cd %s/%s/Dimple\n' % (self.project_directory, self.xtalID) + '\n' - 'pointless hklin ../%s xyzin %s.pdb hklout %s.reind.mtz << EOF > pointless.log\n' %(self.mtz_in,self.reference,self.xtalID)+ + 'pointless hklin ../%s xyzin %s.pdb hklout %s.reind.mtz << EOF > pointless.log\n' % (self.mtz_in, self.reference, self.xtalID) + ' tolerance 5\n' 'EOF\n' '\n' - 'cad hklin1 %s.reind.mtz hklout cad.mtz << EOF > cad.log\n' %self.xtalID + + 'cad hklin1 %s.reind.mtz hklout cad.mtz << EOF > cad.log\n' % self.xtalID + ' labin file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n' ' labout file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n' ' END\n' 'EOF\n' '\n' - 'freerflag hklin cad.mtz hklout ../%s > freerflag.log\n' %self.mtz_free + + 'freerflag hklin cad.mtz hklout ../%s > freerflag.log\n' % self.mtz_free + '#uniqueify cad.mtz ../{0!s}\n'.format(self.mtz_free) - ) + ) # os.chdir(os.path.join(self.project_directory,self.xtalID)) # os.system(Cmds) -## os.symlink(os.path.join('Dimple',self.xtalID+'.free.mtz'),self.xtalID+'.free.mtz') +# os.symlink(os.path.join('Dimple',self.xtalID+'.free.mtz'),self.xtalID+'.free.mtz') return Cmds def dimple(self): os.chdir('{0!s}/{1!s}'.format(self.project_directory, self.xtalID)) - generate_Rfree_Cmds='' + generate_Rfree_Cmds = '' if os.path.isdir('{0!s}/{1!s}/Dimple'.format(self.project_directory, self.xtalID)): # this 'if not' step is usually not necessary; only if process was stopped in an odd way if not os.path.isfile(self.project_directory+'/'+self.xtalID+'/'+self.mtz_free): - generate_Rfree_Cmds=self.get_Rfree() + generate_Rfree_Cmds = self.get_Rfree() if self.delete_old: os.system('rm -fr Dimple') - os.mkdir('{0!s}/{1!s}/Dimple'.format(self.project_directory, self.xtalID)) + os.mkdir( + '{0!s}/{1!s}/Dimple'.format(self.project_directory, self.xtalID)) else: return None else: - os.mkdir('{0!s}/{1!s}/Dimple'.format(self.project_directory, self.xtalID)) - generate_Rfree_Cmds=self.get_Rfree() - os.chdir('{0!s}/{1!s}/Dimple'.format(self.project_directory, self.xtalID)) + os.mkdir( + '{0!s}/{1!s}/Dimple'.format(self.project_directory, self.xtalID)) + generate_Rfree_Cmds = self.get_Rfree() + os.chdir( + '{0!s}/{1!s}/Dimple'.format(self.project_directory, self.xtalID)) if self.queueing_system_available: - top_line='#PBS -joe -N XCE_dimple' + top_line = '#PBS -joe -N XCE_dimple' else: - top_line='#!'+os.getenv('SHELL') + top_line = '#!'+os.getenv('SHELL') if 'csh' in os.getenv('SHELL'): - ccp4_scratch='setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' + ccp4_scratch = 'setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' elif 'bash' in os.getenv('SHELL'): - ccp4_scratch='export CCP4_SCR='+self.ccp4_scratch_directory+'\n' + ccp4_scratch = 'export CCP4_SCR='+self.ccp4_scratch_directory+'\n' else: - ccp4_scratch='' + ccp4_scratch = '' ################################################################################ # in case additional ligands are present in the reference.pdb file, @@ -147,55 +151,53 @@ def dimple(self): # - .cif # this file contains restraints for all the ligands in the respective pdb file if os.path.isfile(self.reference+'.cif'): - ref_lib=' --libin '+self.reference+'.cif' + ref_lib = ' --libin '+self.reference+'.cif' else: - ref_lib='' + ref_lib = '' Cmds = ( - '{0!s}\n'.format(top_line)+ - generate_Rfree_Cmds+ - '\n' - 'cd %s/%s/Dimple\n' %(self.project_directory,self.xtalID) + - '\n' - +ccp4_scratch+ - '\n' - 'dimple %s ../%s %s.pdb dimple' %(ref_lib,self.mtz_free,self.reference) + - '\n' - 'cd %s/%s\n' %(self.project_directory,self.xtalID) + - '\n' - '/bin/rm refine.pdb\n' - '/bin/rm refine.mtz\n' - 'ln -s Dimple/dimple/final.pdb refine.pdb\n' - 'ln -s Dimple/dimple/final.mtz refine.mtz\n' - '\n' - 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' - ' labin F1=2FOFCWT PHI=PH2FOFCWT\n' - 'EOF\n' - '\n' - 'fft hklin refine.mtz mapout fofc.map << EOF\n' - ' labin F1=FOFCWT PHI=PHFOFCWT\n' - 'EOF\n' - '\n' - 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' - ' labin F1=FWT PHI=PHWT\n' - 'EOF\n' - '\n' - 'fft hklin refine.mtz mapout fofc.map << EOF\n' - ' labin F1=DELFWT PHI=PHDELWT\n' - 'EOF\n' - '\n' - '/bin/rm dimple_run_in_progress\n' - ) + '{0!s}\n'.format(top_line) + + generate_Rfree_Cmds + + '\n' + 'cd %s/%s/Dimple\n' % (self.project_directory, self.xtalID) + + '\n' + + ccp4_scratch + + '\n' + 'dimple %s ../%s %s.pdb dimple' % (ref_lib, self.mtz_free, self.reference) + + '\n' + 'cd %s/%s\n' % (self.project_directory, self.xtalID) + + '\n' + '/bin/rm refine.pdb\n' + '/bin/rm refine.mtz\n' + 'ln -s Dimple/dimple/final.pdb refine.pdb\n' + 'ln -s Dimple/dimple/final.mtz refine.mtz\n' + '\n' + 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' + ' labin F1=2FOFCWT PHI=PH2FOFCWT\n' + 'EOF\n' + '\n' + 'fft hklin refine.mtz mapout fofc.map << EOF\n' + ' labin F1=FOFCWT PHI=PHFOFCWT\n' + 'EOF\n' + '\n' + 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' + ' labin F1=FWT PHI=PHWT\n' + 'EOF\n' + '\n' + 'fft hklin refine.mtz mapout fofc.map << EOF\n' + ' labin F1=DELFWT PHI=PHDELWT\n' + 'EOF\n' + '\n' + '/bin/rm dimple_run_in_progress\n' + ) self.Run(Cmds) - - - def Run(self,Cmds): + def Run(self, Cmds): os.chdir(self.project_directory+'/'+self.xtalID) os.system('touch dimple_run_in_progress') os.chdir(self.project_directory+'/'+self.xtalID+'/Dimple') - f = open('xce_dimple.sh','w') + f = open('xce_dimple.sh', 'w') f.write(Cmds) f.close() if self.queueing_system_available: @@ -204,43 +206,47 @@ def Run(self,Cmds): os.system('chmod +x xce_dimple.sh') os.system('./xce_dimple.sh') -class helpers: +class helpers: def __init__(self): try: # this sys path append is only meaningful if non-CCP4 python is used to launch XCE -# sys.path.append(os.path.join(os.getenv('CCP4'),'lib','python2.7','site-packages')) + # sys.path.append(os.path.join(os.getenv('CCP4'),'lib','python2.7','site-packages')) from rdkit import Chem from rdkit.Chem import AllChem from rdkit.Chem import Draw - self.pil_rdkit_present=True + self.pil_rdkit_present = True except ImportError: - self.pil_rdkit_present=False + self.pil_rdkit_present = False pass def pil_rdkit_exist(self): return self.pil_rdkit_present - def make_png(self,initial_model_directory,sample,compoundID,smiles,external_software,database_directory,data_source_file,ccp4_scratch_directory,counter,xce_logfile,restraints_program): - Logfile=XChemLog.updateLog(xce_logfile) + def make_png(self, initial_model_directory, sample, compoundID, smiles, external_software, database_directory, data_source_file, ccp4_scratch_directory, counter, xce_logfile, restraints_program): + Logfile = XChemLog.updateLog(xce_logfile) # if not os.path.isfile(os.path.join(initial_model_directory,sample,'compound','ACEDRG_IN_PROGRESS')): os.system('touch RESTRAINTS_IN_PROGRESS') - header='#!'+os.getenv('SHELL')+'\n' + header = '#!'+os.getenv('SHELL')+'\n' if external_software['qsub']: if not external_software['qsub_array']: - header='#PBS -joe -N xce_acedrg\n' + header = '#PBS -joe -N xce_acedrg\n' # check for combisoaks/ cocktails # note: compoundIDs and smiles are semi-colon separated if len(compoundID.split(';')) > 1: - Logfile.insert('looks like you are working with cocktails; found the following IDs and smiles:') + Logfile.insert( + 'looks like you are working with cocktails; found the following IDs and smiles:') if len(compoundID.split(';')) != len(smiles.split(';')): - Logfile.error('Number of compoundIDs and SMILES does not match:') - Logfile.error('N(compoundID): {0!s} -> {1!s}'.format(len(compoundID.split(';')), compoundID.split(';'))) - Logfile.error('N(SMILES): {0!s} -> {1!s}'.format(len(smiles.split(';')), smiles.split(';'))) + Logfile.error( + 'Number of compoundIDs and SMILES does not match:') + Logfile.error('N(compoundID): {0!s} -> {1!s}'.format( + len(compoundID.split(';')), compoundID.split(';'))) + Logfile.error( + 'N(SMILES): {0!s} -> {1!s}'.format(len(smiles.split(';')), smiles.split(';'))) Logfile.error('aborting...') return else: @@ -250,40 +256,44 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft software += 'module load ccp4/7.1.018\n' elif restraints_program == 'phenix.elbow': if os.getcwd().startswith('/dls'): - software += 'module load ccp4/7.1.018\n' + software += 'module load ccp4/7.1.018\n' software += 'module load phenix\n' elif restraints_program == 'grade': if os.getcwd().startswith('/dls'): - software += 'module load ccp4/7.1.018\n' + software += 'module load ccp4/7.1.018\n' software += 'module load buster\n' software += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' software += "export BDG_TOOL_OBABEL='none'\n" for i in range(len(compoundID.split(';'))): - Logfile.insert('{0!s} - {1!s}'.format(compoundID.split(';')[i], smiles.split(';')[i])) + Logfile.insert( + '{0!s} - {1!s}'.format(compoundID.split(';')[i], smiles.split(';')[i])) cID = 'L' + (2 - len(str(i))) * '0' + str(i) - if restraints_program=='acedrg': - software += 'acedrg --res {0!s} -i "{1!s}" -o {2!s}\n'.format(cID, smiles.split(';')[i], compoundID.split(';')[i].replace(' ', '')) - elif restraints_program=='phenix.elbow': - software+='phenix.elbow --smiles="{0!s}" --id {1!s}} --output {2!s}\n'.format(smiles.split(';')[i], cID, compoundID.split(';')[i].replace(' ','')) - elif restraints_program=='grade': + if restraints_program == 'acedrg': + software += 'acedrg --res {0!s} -i "{1!s}" -o {2!s}\n'.format( + cID, smiles.split(';')[i], compoundID.split(';')[i].replace(' ', '')) + elif restraints_program == 'phenix.elbow': + software += 'phenix.elbow --smiles="{0!s}" --id {1!s}} --output {2!s}\n'.format( + smiles.split(';')[i], cID, compoundID.split(';')[i].replace(' ', '')) + elif restraints_program == 'grade': if external_software['mogul']: mogul = '' else: mogul = '-nomogul' - software+='grade -resname {0!s} {1!s} "{2!s}" -ocif {3!s}.cif -opdb {4!s}.pdb\n'.format( - cID, mogul, smiles.split(';')[i], compoundID.split(';')[i].replace(' ',''), compoundID.split(';')[i].replace(' ','')) + software += 'grade -resname {0!s} {1!s} "{2!s}" -ocif {3!s}.cif -opdb {4!s}.pdb\n'.format( + cID, mogul, smiles.split(';')[i], compoundID.split(';')[i].replace(' ', ''), compoundID.split(';')[i].replace(' ', '')) else: # check if CompoundSMILEScovalent field is not Null # CompoundSMILESproduct can be used to create only a CIF file for the product to make fitting easier # however, the complete smiles string will be used to make the png file productSmiles = None - db = XChemDB.data_source(os.path.join(database_directory,data_source_file)) - sql = "select CompoundSMILESproduct from mainTable where CrystalName = '%s'" %sample + db = XChemDB.data_source(os.path.join( + database_directory, data_source_file)) + sql = "select CompoundSMILESproduct from mainTable where CrystalName = '%s'" % sample query = db.execute_statement(sql) productSmiles = query[0][0] - if str(productSmiles).replace(' ','') == '': + if str(productSmiles).replace(' ', '') == '': productSmiles = smiles elif 'none' in str(productSmiles).lower(): productSmiles = smiles @@ -292,43 +302,46 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft else: productSmiles = str(productSmiles) - software='' - if restraints_program=='acedrg': + software = '' + if restraints_program == 'acedrg': if os.getcwd().startswith('/dls'): software += 'module load ccp4/7.1.018\n' - if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): - software+='acedrg --res LIG -c ../old.cif -o {0!s}\n'.format((compoundID.replace(' ',''))) + if os.path.isfile(os.path.join(initial_model_directory, sample, 'old.cif')): + software += 'acedrg --res LIG -c ../old.cif -o {0!s}\n'.format( + (compoundID.replace(' ', ''))) else: - software+='acedrg --res LIG -i "{0!s}" -o {1!s}\n'.format(productSmiles, compoundID.replace(' ','')) - elif restraints_program=='phenix.elbow': + software += 'acedrg --res LIG -i "{0!s}" -o {1!s}\n'.format( + productSmiles, compoundID.replace(' ', '')) + elif restraints_program == 'phenix.elbow': if os.getcwd().startswith('/dls'): - software += 'module load ccp4/7.1.018\n' + software += 'module load ccp4/7.1.018\n' software += 'module load phenix\n' - if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): - software+='phenix.elbow --file=../old.cif --id LIG --output {0!s}\n'.format((compoundID.replace(' ',''))) + if os.path.isfile(os.path.join(initial_model_directory, sample, 'old.cif')): + software += 'phenix.elbow --file=../old.cif --id LIG --output {0!s}\n'.format( + (compoundID.replace(' ', ''))) else: - software+='phenix.elbow --smiles="{0!s}" --id LIG --output {1!s}\n'\ - .format(productSmiles, compoundID.replace(' ','')) - elif restraints_program=='grade': + software += 'phenix.elbow --smiles="{0!s}" --id LIG --output {1!s}\n'\ + .format(productSmiles, compoundID.replace(' ', '')) + elif restraints_program == 'grade': if os.getcwd().startswith('/dls'): - software += 'module load ccp4/7.1.018\n' + software += 'module load ccp4/7.1.018\n' software += 'module load buster\n' software += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' - software+="export BDG_TOOL_OBABEL='none'\n" + software += "export BDG_TOOL_OBABEL='none'\n" if external_software['mogul']: mogul = '' else: mogul = '-nomogul' - if os.path.isfile(os.path.join(initial_model_directory,sample,'old.cif')): - software+='grade -resname LIG {0!s} -in ../old.cif -ocif {1!s}.cif -opdb {2!s}.pdb\n'\ - .format(mogul, compoundID.replace(' ',''), compoundID.replace(' ','')) + if os.path.isfile(os.path.join(initial_model_directory, sample, 'old.cif')): + software += 'grade -resname LIG {0!s} -in ../old.cif -ocif {1!s}.cif -opdb {2!s}.pdb\n'\ + .format(mogul, compoundID.replace(' ', ''), compoundID.replace(' ', '')) else: - software+='grade -resname LIG {0!s} "{1!s}" -ocif {2!s}.cif -opdb {3!s}.pdb\n'\ - .format(mogul, productSmiles, compoundID.replace(' ',''), compoundID.replace(' ','')) + software += 'grade -resname LIG {0!s} "{1!s}" -ocif {2!s}.cif -opdb {3!s}.pdb\n'\ + .format(mogul, productSmiles, compoundID.replace(' ', ''), compoundID.replace(' ', '')) # merge all compound CIFs into 1 file called merged.cif - software += '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/merge_ligand_cif_files.py {0!s}\n'.format(os.path.join(initial_model_directory, sample, 'compound')) - + software += '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/merge_ligand_cif_files.py {0!s}\n'.format( + os.path.join(initial_model_directory, sample, 'compound')) # Removal of the hydrogen atoms in PDB files is required for REFMAC 5 run. With hydrogens some ligands fail to # pass the external restraints in pandda.giant.make_restraints. @@ -346,7 +359,7 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft .format(os.path.join(database_directory, data_source_file), sample, 'RefinementCIFStatus', 'running') + '\n' '$CCP4/bin/ccp4-python {0!s} "{1!s}" {2!s} {3!s} {4!s}\n' - .format(os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers','create_png_of_compound.py'), + .format(os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'create_png_of_compound.py'), smiles, compoundID.replace(' ', ''), sample, initial_model_directory) + '\n' 'cd ' + os.path.join(initial_model_directory, sample, 'compound') + @@ -367,16 +380,17 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft '/bin/rm -f compound/RESTRAINTS_IN_PROGRESS\n' ) - os.chdir(ccp4_scratch_directory) - Logfile.insert('creating ACEDRG shell script for {0!s},{1!s} in {2!s}'.format(sample, compoundID, ccp4_scratch_directory)) + Logfile.insert('creating ACEDRG shell script for {0!s},{1!s} in {2!s}'.format( + sample, compoundID, ccp4_scratch_directory)) # print Cmds # print 'ccp4_scratch',ccp4_scratch_directory - f = open('xce_{0!s}_{1!s}.sh'.format(restraints_program,str(counter)),'w') + f = open('xce_{0!s}_{1!s}.sh'.format( + restraints_program, str(counter)), 'w') f.write(Cmds) f.close() - os.system('chmod +x xce_{0!s}_{1!s}.sh'.format(restraints_program,str(counter))) - + os.system( + 'chmod +x xce_{0!s}_{1!s}.sh'.format(restraints_program, str(counter))) # if queueing_system_available: @@ -400,175 +414,173 @@ def make_png(self,initial_model_directory,sample,compoundID,smiles,external_soft class parse: def __init__(self): - self.space_group_dict= { 'triclinic': ['P1'], -# 'monoclinic': ['P2','P21','C121','P1211','P121'], - 'monoclinic_P': ['P2','P21','P1211','P121'], - 'monoclinic_C': ['C2','C121'], - 'orthorhombic': ['P222','P2122','P2212','P2221', - 'P21212','P21221','P22121','P212121', - 'C222','C2221', - 'F222', 'I222', 'I212121'], - 'tetragonal': ['P4','P41','P42','P43','I4','I41', - 'P422','P4212','P4122','P41212','P4222', - 'P42212','P4322','P43212','I422','I4122' ], - 'hexagonal': ['P3','P31','P32', - 'P312','P321','P3112','P3121','P3212','P3221', - 'P6','P61','P65','P62','P64','P63', - 'P622','P6122','P6522','P6222','P6422','P6322' ], - 'rhombohedral': ['H3','H32'], - 'cubic': ['P23','F23','I23','P213','I213', - 'P432','P4232','F432','F4132','I432','P4332','P4132','I4132' ] } - - self.point_group_dict= { '1': ['P1'], - '2': ['P2','P21','C121','P1211','P121','C2'], - '222': ['P222','P2122','P2212','P2221', - 'P21212','P21221','P22121','P212121', - 'C222','C2221', - 'F222', 'I222', 'I212121'], - '4': ['P4','P41','P42','P43','I4','I41'], - '422': ['P422','P4212','P4122','P41212','P4222', - 'P42212','P4322','P43212','I422','I4122' ], - '3': ['P3','P31','P32','H3'], - '32': ['P312','P321','P3112','P3121','P3212','P3221','H32'], - '6': ['P6','P61','P65','P62','P64','P63'], - '622': ['P622','P6122','P6522','P6222','P6422','P6322' ], - '23': ['P23','F23','I23','P213','I213'], - '432': ['P432','P4232','F432','F4132','I432','P4332','P4132','I4132' ] } - - self.nr_asu_in_unitcell_for_point_group = { '1': 1, - '2': 2, - '222': 4, - '4': 4, - '422': 8, - '3': 3, - '32': 6, - '6': 6, - '622': 12, - '23': 12, - '432': 24 } - - self.aimless = { 'DataProcessingProgram': 'n/a', -# 'DataCollectionRun': 'n/a', - 'DataProcessingSpaceGroup': 'n/a', - 'DataProcessingUnitCell': 'n/a', - 'DataProcessingA': 'n/a', - 'DataProcessingB': 'n/a', - 'DataProcessingC': 'n/a', - 'DataProcessingAlpha': 'n/a', - 'DataProcessingBeta': 'n/a', - 'DataProcessingGamma': 'n/a', - 'DataProcessingResolutionLow': 'n/a', - 'DataProcessingResolutionLowInnerShell': 'n/a', - 'DataProcessingResolutionHigh': 'n/a', - 'DataProcessingResolutionHighOuterShell': 'n/a', - 'DataProcessingResolutionOverall': 'n/a', - 'DataProcessingRmergeOverall': 'n/a', - 'DataProcessingRmergeLow': 'n/a', - 'DataProcessingRmergeHigh': 'n/a', - 'DataProcessingIsigOverall': 'n/a', - 'DataProcessingIsigLow': 'n/a', - 'DataProcessingIsigHigh': 'n/a', - 'DataProcessingCompletenessOverall': 'n/a', - 'DataProcessingCompletenessLow': 'n/a', - 'DataProcessingCompletenessHigh': 'n/a', - 'DataProcessingMultiplicityOverall': 'n/a', - 'DataProcessingMultiplicityLow': 'n/a', - 'DataProcessingMultiplicityHigh': 'n/a', - 'DataProcessingCChalfOverall': 'n/a', - 'DataProcessingCChalfLow': 'n/a', - 'DataProcessingCChalfHigh': 'n/a', - 'DataProcessingResolutionHigh15sigma': 'n/a', - 'DataProcessingUniqueReflectionsLow': 'n/a', - 'DataProcessingUniqueReflectionsHigh': 'n/a', - 'DataProcessingUniqueReflectionsOverall': 'n/a', - 'DataProcessingLattice': 'n/a', - 'DataProcessingPointGroup': 'n/a', - 'DataProcessingUnitCellVolume': 0, - 'DataProcessingAlert': '#FF0000', - 'DataCollectionWavelength': 'n/a', - 'DataProcessingScore': 'n/a' } - - - - def GetAimlessLog(self,Logfile): - self.Logfile=Logfile - Aimless = { 'AutoProc': 'n/a', - 'Run': 'n/a', - 'SpaceGroup': 'n/a', - 'UnitCell': 'n/a', - 'ResolutionLow': 'n/a', - 'ResolutionLowInnerShell': 'n/a', - 'ResolutionHigh': 'n/a', - 'ResolutionHighOuterShell': 'n/a', - 'RmergeOverall': 'n/a', - 'RmergeLow': 'n/a', - 'RmergeHigh': 'n/a', - 'IsigOverall': 'n/a', - 'IsigLow': 'n/a', - 'IsigHigh': 'n/a', - 'CompletenessOverall': 'n/a', - 'CompletenessLow': 'n/a', - 'CompletenessHigh': 'n/a', - 'MultiplicityOverall': 'n/a', - 'MultiplicityLow': 'n/a', - 'MultiplicityHigh': 'n/a', - 'UniqueReflectionsOverall': 'n/a', - 'Lattice': 'n/a', - 'UnitCellVolume': 0, - 'Alert': '#FF0000' } - - spg='n/a' - a='n/a' - b='n/a' - c='n/a' - alpha='n/a' - beta='n/a' - gamma='n/a' + self.space_group_dict = {'triclinic': ['P1'], + # 'monoclinic': ['P2','P21','C121','P1211','P121'], + 'monoclinic_P': ['P2', 'P21', 'P1211', 'P121'], + 'monoclinic_C': ['C2', 'C121'], + 'orthorhombic': ['P222', 'P2122', 'P2212', 'P2221', + 'P21212', 'P21221', 'P22121', 'P212121', + 'C222', 'C2221', + 'F222', 'I222', 'I212121'], + 'tetragonal': ['P4', 'P41', 'P42', 'P43', 'I4', 'I41', + 'P422', 'P4212', 'P4122', 'P41212', 'P4222', + 'P42212', 'P4322', 'P43212', 'I422', 'I4122'], + 'hexagonal': ['P3', 'P31', 'P32', + 'P312', 'P321', 'P3112', 'P3121', 'P3212', 'P3221', + 'P6', 'P61', 'P65', 'P62', 'P64', 'P63', + 'P622', 'P6122', 'P6522', 'P6222', 'P6422', 'P6322'], + 'rhombohedral': ['H3', 'H32'], + 'cubic': ['P23', 'F23', 'I23', 'P213', 'I213', + 'P432', 'P4232', 'F432', 'F4132', 'I432', 'P4332', 'P4132', 'I4132']} + + self.point_group_dict = {'1': ['P1'], + '2': ['P2', 'P21', 'C121', 'P1211', 'P121', 'C2'], + '222': ['P222', 'P2122', 'P2212', 'P2221', + 'P21212', 'P21221', 'P22121', 'P212121', + 'C222', 'C2221', + 'F222', 'I222', 'I212121'], + '4': ['P4', 'P41', 'P42', 'P43', 'I4', 'I41'], + '422': ['P422', 'P4212', 'P4122', 'P41212', 'P4222', + 'P42212', 'P4322', 'P43212', 'I422', 'I4122'], + '3': ['P3', 'P31', 'P32', 'H3'], + '32': ['P312', 'P321', 'P3112', 'P3121', 'P3212', 'P3221', 'H32'], + '6': ['P6', 'P61', 'P65', 'P62', 'P64', 'P63'], + '622': ['P622', 'P6122', 'P6522', 'P6222', 'P6422', 'P6322'], + '23': ['P23', 'F23', 'I23', 'P213', 'I213'], + '432': ['P432', 'P4232', 'F432', 'F4132', 'I432', 'P4332', 'P4132', 'I4132']} + + self.nr_asu_in_unitcell_for_point_group = {'1': 1, + '2': 2, + '222': 4, + '4': 4, + '422': 8, + '3': 3, + '32': 6, + '6': 6, + '622': 12, + '23': 12, + '432': 24} + + self.aimless = {'DataProcessingProgram': 'n/a', + # 'DataCollectionRun': 'n/a', + 'DataProcessingSpaceGroup': 'n/a', + 'DataProcessingUnitCell': 'n/a', + 'DataProcessingA': 'n/a', + 'DataProcessingB': 'n/a', + 'DataProcessingC': 'n/a', + 'DataProcessingAlpha': 'n/a', + 'DataProcessingBeta': 'n/a', + 'DataProcessingGamma': 'n/a', + 'DataProcessingResolutionLow': 'n/a', + 'DataProcessingResolutionLowInnerShell': 'n/a', + 'DataProcessingResolutionHigh': 'n/a', + 'DataProcessingResolutionHighOuterShell': 'n/a', + 'DataProcessingResolutionOverall': 'n/a', + 'DataProcessingRmergeOverall': 'n/a', + 'DataProcessingRmergeLow': 'n/a', + 'DataProcessingRmergeHigh': 'n/a', + 'DataProcessingIsigOverall': 'n/a', + 'DataProcessingIsigLow': 'n/a', + 'DataProcessingIsigHigh': 'n/a', + 'DataProcessingCompletenessOverall': 'n/a', + 'DataProcessingCompletenessLow': 'n/a', + 'DataProcessingCompletenessHigh': 'n/a', + 'DataProcessingMultiplicityOverall': 'n/a', + 'DataProcessingMultiplicityLow': 'n/a', + 'DataProcessingMultiplicityHigh': 'n/a', + 'DataProcessingCChalfOverall': 'n/a', + 'DataProcessingCChalfLow': 'n/a', + 'DataProcessingCChalfHigh': 'n/a', + 'DataProcessingResolutionHigh15sigma': 'n/a', + 'DataProcessingUniqueReflectionsLow': 'n/a', + 'DataProcessingUniqueReflectionsHigh': 'n/a', + 'DataProcessingUniqueReflectionsOverall': 'n/a', + 'DataProcessingLattice': 'n/a', + 'DataProcessingPointGroup': 'n/a', + 'DataProcessingUnitCellVolume': 0, + 'DataProcessingAlert': '#FF0000', + 'DataCollectionWavelength': 'n/a', + 'DataProcessingScore': 'n/a'} + + def GetAimlessLog(self, Logfile): + self.Logfile = Logfile + Aimless = {'AutoProc': 'n/a', + 'Run': 'n/a', + 'SpaceGroup': 'n/a', + 'UnitCell': 'n/a', + 'ResolutionLow': 'n/a', + 'ResolutionLowInnerShell': 'n/a', + 'ResolutionHigh': 'n/a', + 'ResolutionHighOuterShell': 'n/a', + 'RmergeOverall': 'n/a', + 'RmergeLow': 'n/a', + 'RmergeHigh': 'n/a', + 'IsigOverall': 'n/a', + 'IsigLow': 'n/a', + 'IsigHigh': 'n/a', + 'CompletenessOverall': 'n/a', + 'CompletenessLow': 'n/a', + 'CompletenessHigh': 'n/a', + 'MultiplicityOverall': 'n/a', + 'MultiplicityLow': 'n/a', + 'MultiplicityHigh': 'n/a', + 'UniqueReflectionsOverall': 'n/a', + 'Lattice': 'n/a', + 'UnitCellVolume': 0, + 'Alert': '#FF0000'} + + spg = 'n/a' + a = 'n/a' + b = 'n/a' + c = 'n/a' + alpha = 'n/a' + beta = 'n/a' + gamma = 'n/a' if 'fast_dp' in self.Logfile: - Aimless['AutoProc']='fast_dp' + Aimless['AutoProc'] = 'fast_dp' if '3d-run' in self.Logfile: - Aimless['AutoProc']='xia2 3d' + Aimless['AutoProc'] = 'xia2 3d' if '3dii-run' in self.Logfile: - Aimless['AutoProc']='xia2 3dii' + Aimless['AutoProc'] = 'xia2 3dii' if 'dials-run' in self.Logfile: - Aimless['AutoProc']='dials' + Aimless['AutoProc'] = 'dials' if 'autoPROC' in self.Logfile: - Aimless['AutoProc']='autoPROC' + Aimless['AutoProc'] = 'autoPROC' # get run number from logfile # Note: only works if file is in original directory, but not once it lifes in 'inital_model' # print self.Logfile.split('/')[9].split('_')[1] # if len(self.Logfile.split('/'))>8 and len(self.Logfile.split('/')[9].split('_'))==1: try: - Aimless['Run']=self.Logfile.split('/')[9].split('_')[1] + Aimless['Run'] = self.Logfile.split('/')[9].split('_')[1] except IndexError: pass for line in open(self.Logfile): - if line.startswith('Low resolution limit') and len(line.split())==6: + if line.startswith('Low resolution limit') and len(line.split()) == 6: Aimless['ResolutionLow'] = line.split()[3] Aimless['ResolutionHighOuterShell'] = line.split()[5] - if line.startswith('High resolution limit') and len(line.split())==6: + if line.startswith('High resolution limit') and len(line.split()) == 6: Aimless['ResolutionHigh'] = line.split()[3] Aimless['ResolutionLowInnerShell'] = line.split()[4] - if line.startswith('Rmerge (all I+ and I-)') and len(line.split())==8: + if line.startswith('Rmerge (all I+ and I-)') and len(line.split()) == 8: Aimless['RmergeOverall'] = line.split()[5] Aimless['RmergeLow'] = line.split()[6] - Aimless['RmergeHigh'] = line.split()[7] - if line.startswith('Mean((I)/sd(I))') and len(line.split())==4: + Aimless['RmergeHigh'] = line.split()[7] + if line.startswith('Mean((I)/sd(I))') and len(line.split()) == 4: Aimless['IsigOverall'] = line.split()[1] Aimless['IsigHigh'] = line.split()[3] Aimless['IsigLow'] = line.split()[2] - if line.startswith('Completeness') and len(line.split())==4: + if line.startswith('Completeness') and len(line.split()) == 4: Aimless['CompletenessOverall'] = line.split()[1] Aimless['CompletenessHigh'] = line.split()[3] Aimless['CompletenessLow'] = line.split()[2] - if line.startswith('Multiplicity') and len(line.split())==4: + if line.startswith('Multiplicity') and len(line.split()) == 4: Aimless['MultiplicityOverall'] = line.split()[1] Aimless['MultiplicityHigh'] = line.split()[3] Aimless['MultiplicityLow'] = line.split()[3] - if line.startswith('Average unit cell:') and len(line.split())==9: + if line.startswith('Average unit cell:') and len(line.split()) == 9: tmp = [line.split()] a = int(float(tmp[0][3])) b = int(float(tmp[0][4])) @@ -576,19 +588,24 @@ def GetAimlessLog(self,Logfile): alpha = int(float(tmp[0][6])) beta = int(float(tmp[0][7])) gamma = int(float(tmp[0][8])) - if line.startswith('Total number unique') and len(line.split())==6: - Aimless['UniqueReflectionsOverall']=line.split()[3] + if line.startswith('Total number unique') and len(line.split()) == 6: + Aimless['UniqueReflectionsOverall'] = line.split()[3] if line.startswith('Space group:'): - Aimless['SpaceGroup']=line.replace('Space group: ','')[:-1] - Aimless['Lattice']=self.get_lattice_from_space_group(Aimless['SpaceGroup']) + Aimless['SpaceGroup'] = line.replace('Space group: ', '')[:-1] + Aimless['Lattice'] = self.get_lattice_from_space_group( + Aimless['SpaceGroup']) if a != 'n/a' and b != 'n/a' and c != 'n/a' and \ alpha != 'n/a' and beta != 'n/a' and gamma != 'n/a' and Aimless['Lattice'] != 'n/a': - Aimless['UnitCellVolume']=self.calc_unitcell_volume_from_logfile(float(a),float(b),float(c), - math.radians(float(alpha)), - math.radians(float(beta)), - math.radians(float(gamma)), - Aimless['Lattice']) - Aimless['UnitCell']=str(a)+' '+str(b)+' '+str(c)+' '+str(alpha)+' '+str(beta)+' '+str(gamma) + Aimless['UnitCellVolume'] = self.calc_unitcell_volume_from_logfile(float(a), float(b), float(c), + math.radians( + float(alpha)), + math.radians( + float(beta)), + math.radians( + float(gamma)), + Aimless['Lattice']) + Aimless['UnitCell'] = str( + a)+' '+str(b)+' '+str(c)+' '+str(alpha)+' '+str(beta)+' '+str(gamma) # Hex Color code: # red: #FF0000 @@ -596,7 +613,7 @@ def GetAimlessLog(self,Logfile): # green: #00FF00 # gray: #E0E0E0 - if Aimless['ResolutionHigh']=='n/a' or Aimless['RmergeLow'] =='n/a': + if Aimless['ResolutionHigh'] == 'n/a' or Aimless['RmergeLow'] == 'n/a': Aimless['Alert'] = '#FF0000' else: if float(Aimless['ResolutionHigh']) > 3.5 or float(Aimless['RmergeLow']) > 0.1: @@ -612,51 +629,49 @@ def GetAimlessLog(self,Logfile): def return_empty_aimless_dict_for_db(self): return self.aimless - def read_aimless_logfile(self,logfile): + def read_aimless_logfile(self, logfile): # essentially same as above, but compatible with datasource # will hopefully supersede function above - spg='n/a' - a='n/a' - b='n/a' - c='n/a' - alpha='n/a' - beta='n/a' - gamma='n/a' + spg = 'n/a' + a = 'n/a' + b = 'n/a' + c = 'n/a' + alpha = 'n/a' + beta = 'n/a' + gamma = 'n/a' if 'fast_dp' in logfile: - self.aimless['DataProcessingProgram']='fast_dp' + self.aimless['DataProcessingProgram'] = 'fast_dp' elif '3d-run' in logfile: - self.aimless['DataProcessingProgram']='xia2-3d' + self.aimless['DataProcessingProgram'] = 'xia2-3d' elif '3dii-run' in logfile: - self.aimless['DataProcessingProgram']='xia2-3dii' + self.aimless['DataProcessingProgram'] = 'xia2-3dii' elif 'xia2-3dii' in logfile: self.aimless['DataProcessingProgram'] = 'xia2-3dii' elif 'dials-run' in logfile: - self.aimless['DataProcessingProgram']='dials' + self.aimless['DataProcessingProgram'] = 'dials' elif 'dials' in logfile: - self.aimless['DataProcessingProgram']='dials' + self.aimless['DataProcessingProgram'] = 'dials' elif 'autoPROC' in logfile: - self.aimless['DataProcessingProgram']='autoPROC' + self.aimless['DataProcessingProgram'] = 'autoPROC' elif 'staraniso' in logfile: - self.aimless['DataProcessingProgram']='aP_staraniso' + self.aimless['DataProcessingProgram'] = 'aP_staraniso' # get run number from logfile # Note: only works if file is in original directory, but not once it moved to 'inital_model' folder# ## print self.Logfile.split('/')[9].split('_')[1] -## if len(self.Logfile.split('/'))>8 and len(self.Logfile.split('/')[9].split('_'))==1: +# if len(self.Logfile.split('/'))>8 and len(self.Logfile.split('/')[9].split('_'))==1: # try: # self.aimless['DataCollectionRun']=logfile.split('/')[9].split('_')[1] # except IndexError: # pass - if logfile.endswith('.log') or logfile.endswith('.table1'): self.aimless_logile(logfile) elif logfile.endswith('.json'): self.json_logfile(logfile) - # Hex Color code: # red: #FF0000 # orange: #FF9900 @@ -674,16 +689,19 @@ def read_aimless_logfile(self,logfile): gamma = self.aimless['DataProcessingGamma'] self.aimless['DataProcessingUnitCellVolume'] = str( self.calc_unitcell_volume_from_logfile(float(a), float(b), float(c), - math.radians(float(alpha)), - math.radians(float(beta)), - math.radians(float(gamma)), - self.aimless['DataProcessingLattice'])) + math.radians( + float(alpha)), + math.radians( + float(beta)), + math.radians( + float(gamma)), + self.aimless['DataProcessingLattice'])) try: high_symmetry_boost = self.nr_asu_in_unitcell_for_point_group[ - self.aimless['DataProcessingPointGroup']] + self.aimless['DataProcessingPointGroup']] self.aimless['DataProcessingScore'] = (float( - self.aimless['DataProcessingUniqueReflectionsOverall']) * float(self.aimless['DataProcessingCompletenessOverall']) * high_symmetry_boost * float(self.aimless['DataProcessingIsigOverall'])) / float( - self.aimless['DataProcessingUnitCellVolume']) + self.aimless['DataProcessingUniqueReflectionsOverall']) * float(self.aimless['DataProcessingCompletenessOverall']) * high_symmetry_boost * float(self.aimless['DataProcessingIsigOverall'])) / float( + self.aimless['DataProcessingUnitCellVolume']) # When P-6 was accidentally used self.aimless['DataProcessingPointGroup'] through a KeyError, so handling this except (ValueError, KeyError): self.aimless['DataProcessingScore'] = 0.0 @@ -692,8 +710,7 @@ def read_aimless_logfile(self,logfile): self.aimless['DataProcessingResolutionOverall'] = str( self.aimless['DataProcessingResolutionLow']) + ' - ' + str(self.aimless['DataProcessingResolutionHigh']) - - if self.aimless['DataProcessingResolutionHigh']=='n/a' or self.aimless['DataProcessingRmergeLow'] =='n/a': + if self.aimless['DataProcessingResolutionHigh'] == 'n/a' or self.aimless['DataProcessingRmergeLow'] == 'n/a': self.aimless['DataProcessingAlert'] = '#FF0000' else: if float(self.aimless['DataProcessingResolutionHigh']) > 3.5 or float(self.aimless['DataProcessingRmergeLow']) > 0.1: @@ -706,7 +723,7 @@ def read_aimless_logfile(self,logfile): return self.aimless - def aimless_logile(self,logfile): + def aimless_logile(self, logfile): resolution_at_15_sigma_line_overall_found = False resolution_at_20_sigma_line_overall_found = False resolution_at_sigma_line_overall_found = False @@ -718,10 +735,12 @@ def aimless_logile(self,logfile): self.aimless['DataCollectionWavelength'] = line.split()[1] if 'Low resolution limit' in line and len(line.split()) == 6: self.aimless['DataProcessingResolutionLow'] = line.split()[3] - self.aimless['DataProcessingResolutionHighOuterShell'] = line.split()[5] + self.aimless['DataProcessingResolutionHighOuterShell'] = line.split()[ + 5] if 'High resolution limit' in line and len(line.split()) == 6: self.aimless['DataProcessingResolutionHigh'] = line.split()[3] - self.aimless['DataProcessingResolutionLowInnerShell'] = line.split()[4] + self.aimless['DataProcessingResolutionLowInnerShell'] = line.split()[ + 4] if 'Rmerge (all I+ and I-)' in line and len(line.split()) == 8: self.aimless['DataProcessingRmergeOverall'] = line.split()[5] self.aimless['DataProcessingRmergeLow'] = line.split()[6] @@ -739,16 +758,22 @@ def aimless_logile(self,logfile): self.aimless['DataProcessingIsigHigh'] = line.split()[3] self.aimless['DataProcessingIsigLow'] = line.split()[2] if line.startswith('Completeness') and len(line.split()) == 4: - self.aimless['DataProcessingCompletenessOverall'] = line.split()[1] - self.aimless['DataProcessingCompletenessHigh'] = line.split()[3] + self.aimless['DataProcessingCompletenessOverall'] = line.split()[ + 1] + self.aimless['DataProcessingCompletenessHigh'] = line.split()[ + 3] self.aimless['DataProcessingCompletenessLow'] = line.split()[2] if 'Completeness (ellipsoidal)' in line and len(line.split()) == 5: - self.aimless['DataProcessingCompletenessOverall'] = line.split()[2] - self.aimless['DataProcessingCompletenessHigh'] = line.split()[4] + self.aimless['DataProcessingCompletenessOverall'] = line.split()[ + 2] + self.aimless['DataProcessingCompletenessHigh'] = line.split()[ + 4] self.aimless['DataProcessingCompletenessLow'] = line.split()[3] if 'Multiplicity' in line and len(line.split()) == 4: - self.aimless['DataProcessingMultiplicityOverall'] = line.split()[1] - self.aimless['DataProcessingMultiplicityHigh'] = line.split()[3] + self.aimless['DataProcessingMultiplicityOverall'] = line.split()[ + 1] + self.aimless['DataProcessingMultiplicityHigh'] = line.split()[ + 3] self.aimless['DataProcessingMultiplicityLow'] = line.split()[3] if line.startswith('Mn(I) half-set correlation CC(1/2)') and len(line.split()) == 7: self.aimless['DataProcessingCChalfOverall'] = line.split()[4] @@ -764,12 +789,14 @@ def aimless_logile(self,logfile): if resolution_at_15_sigma_line_overall_found: if 'from Mn(I/sd)' in line and len(line.split()) >= 7: if '1.5' in line.split()[3]: - self.aimless['DataProcessingResolutionHigh15sigma'] = line.split()[6][:-1] + self.aimless['DataProcessingResolutionHigh15sigma'] = line.split()[ + 6][:-1] resolution_at_15_sigma_line_overall_found = False if resolution_at_20_sigma_line_overall_found: if 'from Mn(I/sd)' in line and len(line.split()) >= 7: if '2.0' in line.split()[3]: - self.aimless['DataProcessingResolutionHigh20sigma'] = line.split()[6][:-1] + self.aimless['DataProcessingResolutionHigh20sigma'] = line.split()[ + 6][:-1] resolution_at_20_sigma_line_overall_found = False if (line.startswith('Average unit cell:') or line.startswith(' Unit cell parameters')) and len( line.split()) == 9: @@ -787,7 +814,8 @@ def aimless_logile(self,logfile): self.aimless['DataProcessingBeta'] = str(beta) self.aimless['DataProcessingGamma'] = str(gamma) if 'Total number unique' in line and len(line.split()) == 6: - self.aimless['DataProcessingUniqueReflectionsOverall'] = line.split()[3] + self.aimless['DataProcessingUniqueReflectionsOverall'] = line.split()[ + 3] if line.startswith('Space group:') or line.startswith(' Spacegroup name'): if 'Laue' in line: continue @@ -795,7 +823,8 @@ def aimless_logile(self,logfile): self.aimless['DataProcessingSpaceGroup'] = line.replace(' Spacegroup name', '')[:-1].replace(' ', '') else: - self.aimless['DataProcessingSpaceGroup'] = line.replace('Space group: ', '')[:-1] + self.aimless['DataProcessingSpaceGroup'] = line.replace('Space group: ', '')[ + :-1] self.aimless['DataProcessingLattice'] = self.get_lattice_from_space_group( self.aimless['DataProcessingSpaceGroup']) self.aimless['DataProcessingPointGroup'] = self.get_pointgroup_from_space_group( @@ -823,48 +852,72 @@ def aimless_logile(self,logfile): # self.aimless['DataProcessingResolutionOverall'] = str( # self.aimless['DataProcessingResolutionLow']) + ' - ' + str(self.aimless['DataProcessingResolutionHigh']) - def json_logfile(self,logfile): + def json_logfile(self, logfile): with open(logfile, 'r') as log: data = log.read() obj = json.loads(data) - self.aimless['DataProcessingResolutionLow'] = str(round(math.sqrt(1/float(obj['d_star_sq_max'][0])),2)) - self.aimless['DataProcessingResolutionLowInnerShell'] = str(round(math.sqrt(1/float(obj['d_star_sq_max'][1])),2)) - self.aimless['DataProcessingResolutionHigh'] = str(round(math.sqrt(1/float(obj['d_star_sq_min'][len(obj['d_star_sq_min'])-1])),2)) - self.aimless['DataProcessingResolutionHighOuterShell'] = str(round(math.sqrt(1/float(obj['d_star_sq_min'][len(obj['d_star_sq_min'])-2])),2)) - self.aimless['DataProcessingResolutionOverall'] = self.aimless['DataProcessingResolutionLow'] + '-' + self.aimless['DataProcessingResolutionHigh'] - self.aimless['DataProcessingRmergeOverall'] = str(round(obj['overall']['r_merge'],3)) - self.aimless['DataProcessingRmergeLow'] = str(round(obj['r_merge'][0],3)) - self.aimless['DataProcessingRmergeHigh'] = str(round(obj['r_merge'][len(obj['r_merge'])-1],3)) - self.aimless['DataProcessingIsigOverall'] = str(round(obj['overall']['i_over_sigma_mean'],1)) - self.aimless['DataProcessingIsigLow'] = str(round(obj['i_over_sigma_mean'][0],1)) - self.aimless['DataProcessingIsigHigh'] = str(round(obj['i_over_sigma_mean'][len(obj['i_over_sigma_mean'])-1],1)) - self.aimless['DataProcessingCompletenessOverall'] = str(round(obj['overall']['completeness'],1)) - self.aimless['DataProcessingCompletenessLow'] = str(round(obj['completeness'][0],1)) - self.aimless['DataProcessingCompletenessHigh'] = str(round(obj['completeness'][len(obj['completeness'])-1],1)) - self.aimless['DataProcessingMultiplicityOverall'] = str(round(obj['overall']['multiplicity'],1)) - self.aimless['DataProcessingMultiplicityLow'] = str(round(obj['multiplicity'][0],1)) - self.aimless['DataProcessingMultiplicityHigh'] = str(round(obj['multiplicity'][len(obj['multiplicity'])-1],1)) - self.aimless['DataProcessingCChalfOverall'] = str(round(obj['overall']['cc_one_half'],2)) - self.aimless['DataProcessingCChalfLow'] = str(round(obj['cc_one_half'][0],2)) - self.aimless['DataProcessingCChalfHigh'] = str(round(obj['cc_one_half'][len(obj['cc_one_half'])-1],2)) + self.aimless['DataProcessingResolutionLow'] = str( + round(math.sqrt(1/float(obj['d_star_sq_max'][0])), 2)) + self.aimless['DataProcessingResolutionLowInnerShell'] = str( + round(math.sqrt(1/float(obj['d_star_sq_max'][1])), 2)) + self.aimless['DataProcessingResolutionHigh'] = str( + round(math.sqrt(1/float(obj['d_star_sq_min'][len(obj['d_star_sq_min'])-1])), 2)) + self.aimless['DataProcessingResolutionHighOuterShell'] = str( + round(math.sqrt(1/float(obj['d_star_sq_min'][len(obj['d_star_sq_min'])-2])), 2)) + self.aimless['DataProcessingResolutionOverall'] = self.aimless['DataProcessingResolutionLow'] + \ + '-' + self.aimless['DataProcessingResolutionHigh'] + self.aimless['DataProcessingRmergeOverall'] = str( + round(obj['overall']['r_merge'], 3)) + self.aimless['DataProcessingRmergeLow'] = str( + round(obj['r_merge'][0], 3)) + self.aimless['DataProcessingRmergeHigh'] = str( + round(obj['r_merge'][len(obj['r_merge'])-1], 3)) + self.aimless['DataProcessingIsigOverall'] = str( + round(obj['overall']['i_over_sigma_mean'], 1)) + self.aimless['DataProcessingIsigLow'] = str( + round(obj['i_over_sigma_mean'][0], 1)) + self.aimless['DataProcessingIsigHigh'] = str( + round(obj['i_over_sigma_mean'][len(obj['i_over_sigma_mean'])-1], 1)) + self.aimless['DataProcessingCompletenessOverall'] = str( + round(obj['overall']['completeness'], 1)) + self.aimless['DataProcessingCompletenessLow'] = str( + round(obj['completeness'][0], 1)) + self.aimless['DataProcessingCompletenessHigh'] = str( + round(obj['completeness'][len(obj['completeness'])-1], 1)) + self.aimless['DataProcessingMultiplicityOverall'] = str( + round(obj['overall']['multiplicity'], 1)) + self.aimless['DataProcessingMultiplicityLow'] = str( + round(obj['multiplicity'][0], 1)) + self.aimless['DataProcessingMultiplicityHigh'] = str( + round(obj['multiplicity'][len(obj['multiplicity'])-1], 1)) + self.aimless['DataProcessingCChalfOverall'] = str( + round(obj['overall']['cc_one_half'], 2)) + self.aimless['DataProcessingCChalfLow'] = str( + round(obj['cc_one_half'][0], 2)) + self.aimless['DataProcessingCChalfHigh'] = str( + round(obj['cc_one_half'][len(obj['cc_one_half'])-1], 2)) # self.aimless['DataProcessingResolutionHigh15sigma'] = - self.aimless['DataProcessingUniqueReflectionsLow'] = str(obj['n_uniq'][0]) - self.aimless['DataProcessingUniqueReflectionsHigh'] = str(obj['n_uniq'][len(obj['n_uniq'])-1]) + self.aimless['DataProcessingUniqueReflectionsLow'] = str( + obj['n_uniq'][0]) + self.aimless['DataProcessingUniqueReflectionsHigh'] = str( + obj['n_uniq'][len(obj['n_uniq'])-1]) - self.aimless['DataProcessingUniqueReflectionsOverall'] = str(obj['overall']['n_obs']) + self.aimless['DataProcessingUniqueReflectionsOverall'] = str( + obj['overall']['n_obs']) # self.aimless['DataProcessingPointGroup'] = # self.aimless['DataProcessingUnitCellVolume'] = # self.aimless['DataProcessingAlert'] = # self.aimless['DataProcessingScore'] = json_name = logfile[logfile.rfind('/')+1:] - mmcif_file = logfile.replace('LogFiles','DataFiles').replace(json_name,'xia2.mmcif') + mmcif_file = logfile.replace( + 'LogFiles', 'DataFiles').replace(json_name, 'xia2.mmcif') if os.path.isfile(mmcif_file): self.read_mmcif(mmcif_file) elif os.path.isfile("%s.bz2" % mmcif_file): self.read_mmcif("%s.bz2" % mmcif_file) - def make_pseudo_aimless_log_from_json(self,logfile): + def make_pseudo_aimless_log_from_json(self, logfile): self.json_logfile(logfile) template = ( '==============================================================\n' @@ -873,29 +926,29 @@ def make_pseudo_aimless_log_from_json(self,logfile): 'Summary data for Project: nt11175v63 Crystal: xPHIPAx17245 Dataset: SAD\n' '\n' ' Overall InnerShell OuterShell\n' - 'Low resolution limit {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingResolutionLow'],self.aimless['DataProcessingResolutionLow'],self.aimless['DataProcessingResolutionHighOuterShell'])+ - 'High resolution limit {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingResolutionHigh'],self.aimless['DataProcessingResolutionLowInnerShell'],self.aimless['DataProcessingResolutionHigh'])+ + 'Low resolution limit {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingResolutionLow'], self.aimless['DataProcessingResolutionLow'], self.aimless['DataProcessingResolutionHighOuterShell']) + + 'High resolution limit {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingResolutionHigh'], self.aimless['DataProcessingResolutionLowInnerShell'], self.aimless['DataProcessingResolutionHigh']) + '\n' - 'Rmerge (within I+/I-) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingRmergeOverall'],self.aimless['DataProcessingRmergeLow'],self.aimless['DataProcessingRmergeHigh']) + - 'Rmerge (all I+ and I-) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingRmergeOverall'],self.aimless['DataProcessingRmergeLow'],self.aimless['DataProcessingRmergeHigh']) + + 'Rmerge (within I+/I-) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingRmergeOverall'], self.aimless['DataProcessingRmergeLow'], self.aimless['DataProcessingRmergeHigh']) + + 'Rmerge (all I+ and I-) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingRmergeOverall'], self.aimless['DataProcessingRmergeLow'], self.aimless['DataProcessingRmergeHigh']) + 'Rmeas (within I+/I-) - - - \n' 'Rmeas (all I+ & I-) - - - \n' 'Rpim (within I+/I-) - - - \n' 'Rpim (all I+ & I-) - - - \n' 'Rmerge in top intensity bin - - - \n' 'Total number of observations - - - \n' - 'Total number unique {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingUniqueReflectionsOverall'],self.aimless['DataProcessingUniqueReflectionsLow'],self.aimless['DataProcessingUniqueReflectionsHigh']) + - 'Mean((I)/sd(I)) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingIsigOverall'],self.aimless['DataProcessingIsigLow'],self.aimless['DataProcessingIsigHigh']) + - 'Mn(I) half-set correlation CC(1/2) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingCChalfOverall'],self.aimless['DataProcessingCChalfLow'],self.aimless['DataProcessingCChalfHigh']) + - 'Completeness {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingCompletenessOverall'],self.aimless['DataProcessingCompletenessLow'],self.aimless['DataProcessingCompletenessHigh']) + - 'Multiplicity {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingMultiplicityOverall'],self.aimless['DataProcessingMultiplicityLow'],self.aimless['DataProcessingMultiplicityHigh']) + 'Total number unique {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingUniqueReflectionsOverall'], self.aimless['DataProcessingUniqueReflectionsLow'], self.aimless['DataProcessingUniqueReflectionsHigh']) + + 'Mean((I)/sd(I)) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingIsigOverall'], self.aimless['DataProcessingIsigLow'], self.aimless['DataProcessingIsigHigh']) + + 'Mn(I) half-set correlation CC(1/2) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingCChalfOverall'], self.aimless['DataProcessingCChalfLow'], self.aimless['DataProcessingCChalfHigh']) + + 'Completeness {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingCompletenessOverall'], self.aimless['DataProcessingCompletenessLow'], self.aimless['DataProcessingCompletenessHigh']) + + 'Multiplicity {0!s} {1!s} {2!s}\n'.format( + self.aimless['DataProcessingMultiplicityOverall'], self.aimless['DataProcessingMultiplicityLow'], self.aimless['DataProcessingMultiplicityHigh']) ) - f = open('aimless_dials.log','w') + f = open('aimless_dials.log', 'w') f.write(template) f.close() - - def read_mmcif(self,mmcif): + def read_mmcif(self, mmcif): for line in open_decompress_file(mmcif): if line.startswith('_cell.angle_alpha '): self.aimless['DataProcessingAlpha'] = line.split()[1] @@ -912,7 +965,8 @@ def read_mmcif(self,mmcif): elif line.startswith('_diffrn_radiation_wavelength.wavelength'): self.aimless['DataCollectionWavelength'] = line.split()[1] elif line.startswith('_symmetry.space_group_name_H-M'): - self.aimless['DataProcessingSpaceGroup'] = line[line.find("'")+1:line.rfind("'")].replace(' ','') + self.aimless['DataProcessingSpaceGroup'] = line[line.find( + "'")+1:line.rfind("'")].replace(' ', '') if 'R32:H' in self.aimless['DataProcessingSpaceGroup']: self.aimless['DataProcessingSpaceGroup'] = 'H32' if 'R3:H' in self.aimless['DataProcessingSpaceGroup']: @@ -924,45 +978,43 @@ def read_mmcif(self,mmcif): if self.aimless['DataProcessingLattice'] == 'trigonal': self.aimless['DataProcessingLattice'] = 'hexagonal' self.aimless['DataProcessingUnitCell'] = self.aimless['DataProcessingA'] + ' ' + self.aimless[ - 'DataProcessingA'] + ' ' + self.aimless['DataProcessingA'] + ' ' + self.aimless[ - 'DataProcessingA'] + ' ' + self.aimless[ - 'DataProcessingA'] + ' ' + self.aimless['DataProcessingA'] + 'DataProcessingA'] + ' ' + self.aimless['DataProcessingA'] + ' ' + self.aimless[ + 'DataProcessingA'] + ' ' + self.aimless[ + 'DataProcessingA'] + ' ' + self.aimless['DataProcessingA'] - def get_lattice_from_space_group(self,logfile_spacegroup): - lattice_type='n/a' + def get_lattice_from_space_group(self, logfile_spacegroup): + lattice_type = 'n/a' for lattice in self.space_group_dict: for spacegroup in self.space_group_dict[lattice]: - if logfile_spacegroup.replace(' ','')==spacegroup: - lattice_type=lattice + if logfile_spacegroup.replace(' ', '') == spacegroup: + lattice_type = lattice break return lattice_type - def get_pointgroup_from_space_group(self,logfile_spacegroup): - pointgroup='n/a' + def get_pointgroup_from_space_group(self, logfile_spacegroup): + pointgroup = 'n/a' for pg in self.point_group_dict: for spacegroup in self.point_group_dict[pg]: - if logfile_spacegroup.replace(' ','')==spacegroup: - pointgroup=pg + if logfile_spacegroup.replace(' ', '') == spacegroup: + pointgroup = pg break return pointgroup - - - def calc_unitcell_volume_from_logfile(self,a,b,c,alpha,beta,gamma,lattice): -# print '>>>',a,b,c,alpha,beta,gamma,lattice - unitcell_volume=0 - if lattice=='triclinic': - unitcell_volume=a*b*c* \ - math.sqrt((1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2) \ - +2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma))) + def calc_unitcell_volume_from_logfile(self, a, b, c, alpha, beta, gamma, lattice): + # print '>>>',a,b,c,alpha,beta,gamma,lattice + unitcell_volume = 0 + if lattice == 'triclinic': + unitcell_volume = a*b*c * \ + math.sqrt((1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2) + + 2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma))) # print 'unit cell volume',unitcell_volume # if lattice=='monoclinic': if 'monoclinic' in lattice: - unitcell_volume=round(a*b*c*math.sin(beta),1) - if lattice=='orthorhombic' or lattice=='tetragonal' or lattice=='cubic': - unitcell_volume=round(a*b*c,1) - if lattice=='hexagonal' or lattice=='rhombohedral': - unitcell_volume=round(a*b*c*(math.sin(math.radians(60))),1) + unitcell_volume = round(a*b*c*math.sin(beta), 1) + if lattice == 'orthorhombic' or lattice == 'tetragonal' or lattice == 'cubic': + unitcell_volume = round(a*b*c, 1) + if lattice == 'hexagonal' or lattice == 'rhombohedral': + unitcell_volume = round(a*b*c*(math.sin(math.radians(60))), 1) return unitcell_volume # def get_all_values_as_dict(self): @@ -971,86 +1023,91 @@ def calc_unitcell_volume_from_logfile(self,a,b,c,alpha,beta,gamma,lattice): # 'unitcell_volume': 'n/a', # 'bravais_lattice': 'n/a' } - - - - - def PDBheader(self,pdbfile): - PDBinfo = { 'Rcryst': 'n/a', - 'RcrystTL': 'gray', - 'Rfree': 'n/a', - 'RfreeTL': 'gray', - 'SpaceGroup': 'n/a', - 'PointGroup': 'n/a', - 'UnitCell': 'n/a', - 'ResolutionHigh': 'n/a', - 'ResolutionColor': 'gray', - 'Lattice': 'n/a', - 'UnitCellVolume': 0, - 'Alert': '#E0E0E0', - 'rmsdBonds': 'n/a', - 'rmsdBondsTL': 'gray', - 'rmsdAngles': 'n/a', - 'rmsdAnglesTL': 'gray', - 'TwinFraction': 'n/a' } - - a='n/a' - b='n/a' - c='n/a' - alpha='n/a' - beta='n/a' - gamma='n/a' + def PDBheader(self, pdbfile): + PDBinfo = {'Rcryst': 'n/a', + 'RcrystTL': 'gray', + 'Rfree': 'n/a', + 'RfreeTL': 'gray', + 'SpaceGroup': 'n/a', + 'PointGroup': 'n/a', + 'UnitCell': 'n/a', + 'ResolutionHigh': 'n/a', + 'ResolutionColor': 'gray', + 'Lattice': 'n/a', + 'UnitCellVolume': 0, + 'Alert': '#E0E0E0', + 'rmsdBonds': 'n/a', + 'rmsdBondsTL': 'gray', + 'rmsdAngles': 'n/a', + 'rmsdAnglesTL': 'gray', + 'TwinFraction': 'n/a'} + + a = 'n/a' + b = 'n/a' + c = 'n/a' + alpha = 'n/a' + beta = 'n/a' + gamma = 'n/a' if os.path.isfile(pdbfile): for line in open(pdbfile): try: if line.startswith('REMARK 3 R VALUE (WORKING + TEST SET) :'): - PDBinfo['Rcryst']=line.split()[9] + PDBinfo['Rcryst'] = line.split()[9] if float(PDBinfo['Rcryst']) > 0.4: - PDBinfo['Alert']='#FF0000' + PDBinfo['Alert'] = '#FF0000' PDBinfo['RcrystTL'] = 'red' if 0.4 >= float(PDBinfo['Rcryst']) >= 0.3: - PDBinfo['Alert']='#FF9900' + PDBinfo['Alert'] = '#FF9900' PDBinfo['RcrystTL'] = 'orange' if float(PDBinfo['Rcryst']) < 0.3: - PDBinfo['Alert']='#00FF00' + PDBinfo['Alert'] = '#00FF00' PDBinfo['RcrystTL'] = 'green' if line.startswith('REMARK 3 FREE R VALUE :'): - PDBinfo['Rfree']=line.split()[6] + PDBinfo['Rfree'] = line.split()[6] if float(PDBinfo['Rfree']) > 0.4: - PDBinfo['Alert']='#FF0000' + PDBinfo['Alert'] = '#FF0000' PDBinfo['RfreeTL'] = 'red' if 0.4 >= float(PDBinfo['Rfree']) >= 0.3: - PDBinfo['Alert']='#FF9900' + PDBinfo['Alert'] = '#FF9900' PDBinfo['RfreeTL'] = 'orange' if float(PDBinfo['Rfree']) < 0.3: - PDBinfo['Alert']='#00FF00' + PDBinfo['Alert'] = '#00FF00' PDBinfo['RfreeTL'] = 'green' except ValueError: pass if line.startswith('REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) :'): - PDBinfo['ResolutionHigh']=line.split()[7] + PDBinfo['ResolutionHigh'] = line.split()[7] try: - if float(line.split()[7]) < 2.4: PDBinfo['ResolutionColor'] = 'green' - if 2.4 <= float(line.split()[7]) < 2.8: PDBinfo['ResolutionColor'] = 'orange' - if float(line.split()[7]) >= 2.8: PDBinfo['ResolutionColor'] = 'red' + if float(line.split()[7]) < 2.4: + PDBinfo['ResolutionColor'] = 'green' + if 2.4 <= float(line.split()[7]) < 2.8: + PDBinfo['ResolutionColor'] = 'orange' + if float(line.split()[7]) >= 2.8: + PDBinfo['ResolutionColor'] = 'red' except ValueError: pass if line.startswith('REMARK 3 BOND LENGTHS REFINED ATOMS (A):'): PDBinfo['rmsdBonds'] = line.split()[9] try: - if float(line.split()[9]) < 0.02: PDBinfo['rmsdBondsTL'] = 'green' - if 0.02 <= float(line.split()[9]) < 0.03: PDBinfo['rmsdBondsTL'] = 'orange' - if float(line.split()[9]) >= 0.03: PDBinfo['rmsdBondsTL'] = 'red' + if float(line.split()[9]) < 0.02: + PDBinfo['rmsdBondsTL'] = 'green' + if 0.02 <= float(line.split()[9]) < 0.03: + PDBinfo['rmsdBondsTL'] = 'orange' + if float(line.split()[9]) >= 0.03: + PDBinfo['rmsdBondsTL'] = 'red' except ValueError: pass if line.startswith('REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES):'): PDBinfo['rmsdAngles'] = line.split()[9] try: - if float(line.split()[9]) < 2.0: PDBinfo['rmsdAnglesTL'] = 'green' - if 2.0 <= float(line.split()[9]) < 3.0: PDBinfo['rmsdAnglesTL'] = 'orange' - if float(line.split()[9]) >= 3.0: PDBinfo['rmsdAnglesTL'] = 'red' + if float(line.split()[9]) < 2.0: + PDBinfo['rmsdAnglesTL'] = 'green' + if 2.0 <= float(line.split()[9]) < 3.0: + PDBinfo['rmsdAnglesTL'] = 'orange' + if float(line.split()[9]) >= 3.0: + PDBinfo['rmsdAnglesTL'] = 'red' except ValueError: pass @@ -1060,61 +1117,60 @@ def PDBheader(self,pdbfile): except IndexError: pass - if line.startswith('CRYST1'): - a=int(float(line.split()[1])) - b=int(float(line.split()[2])) - c=int(float(line.split()[3])) - alpha=int(float(line.split()[4])) - beta=int(float(line.split()[5])) - gamma=int(float(line.split()[6])) - - PDBinfo['UnitCell']=line.split()[1]+' '+line.split()[2]+' '+line.split()[3]+' '+ \ - line.split()[4]+' '+line.split()[5]+' '+line.split()[6] + a = int(float(line.split()[1])) + b = int(float(line.split()[2])) + c = int(float(line.split()[3])) + alpha = int(float(line.split()[4])) + beta = int(float(line.split()[5])) + gamma = int(float(line.split()[6])) + + PDBinfo['UnitCell'] = line.split()[1]+' '+line.split()[2]+' '+line.split()[3]+' ' + \ + line.split()[4]+' '+line.split()[5]+' '+line.split()[6] # PDBinfo['SpaceGroup']=line[55:len(line)-1].replace(' ','').rstrip('\r') - PDBinfo['SpaceGroup']=str(line[55:65]).rstrip() + PDBinfo['SpaceGroup'] = str(line[55:65]).rstrip() - PDBinfo['Lattice']=self.get_lattice_from_space_group(PDBinfo['SpaceGroup']) - PDBinfo['PointGroup']=self.get_pointgroup_from_space_group(PDBinfo['SpaceGroup']) + PDBinfo['Lattice'] = self.get_lattice_from_space_group( + PDBinfo['SpaceGroup']) + PDBinfo['PointGroup'] = self.get_pointgroup_from_space_group( + PDBinfo['SpaceGroup']) if a != 'n/a' and b != 'n/a' and c != 'n/a' and \ - alpha != 'n/a' and beta != 'n/a' and gamma != 'n/a' and PDBinfo['Lattice'] != 'n/a': - PDBinfo['UnitCellVolume']=self.calc_unitcell_volume_from_logfile(float(a),float(b),float(c), - math.radians(float(alpha)), - math.radians(float(beta)), - math.radians(float(gamma)), - PDBinfo['Lattice']) - - + alpha != 'n/a' and beta != 'n/a' and gamma != 'n/a' and PDBinfo['Lattice'] != 'n/a': + PDBinfo['UnitCellVolume'] = self.calc_unitcell_volume_from_logfile(float(a), float(b), float(c), + math.radians( + float(alpha)), + math.radians( + float(beta)), + math.radians( + float(gamma)), + PDBinfo['Lattice']) return PDBinfo - - def dict_for_datasource_update(self,pdbfile): + def dict_for_datasource_update(self, pdbfile): pdb = self.PDBheader(pdbfile) - db_dict= {'RefinementPDB_latest': os.path.realpath(pdbfile), 'RefinementRcryst': pdb['Rcryst'], - 'RefinementRcrystTraficLight': pdb['RcrystTL'], 'RefinementRfree': pdb['Rfree'], - 'RefinementRfreeTraficLight': pdb['RfreeTL'], 'RefinementRmsdBonds': pdb['rmsdBonds'], - 'RefinementRmsdBondsTL': pdb['rmsdBondsTL'], 'RefinementRmsdAngles': pdb['rmsdAngles'], - 'RefinementRmsdAnglesTL': pdb['rmsdAnglesTL'], 'RefinementSpaceGroup': pdb['SpaceGroup'], - 'RefinementResolution': pdb['ResolutionHigh'], 'RefinementResolutionTL': pdb['ResolutionColor']} + db_dict = {'RefinementPDB_latest': os.path.realpath(pdbfile), 'RefinementRcryst': pdb['Rcryst'], + 'RefinementRcrystTraficLight': pdb['RcrystTL'], 'RefinementRfree': pdb['Rfree'], + 'RefinementRfreeTraficLight': pdb['RfreeTL'], 'RefinementRmsdBonds': pdb['rmsdBonds'], + 'RefinementRmsdBondsTL': pdb['rmsdBondsTL'], 'RefinementRmsdAngles': pdb['rmsdAngles'], + 'RefinementRmsdAnglesTL': pdb['rmsdAnglesTL'], 'RefinementSpaceGroup': pdb['SpaceGroup'], + 'RefinementResolution': pdb['ResolutionHigh'], 'RefinementResolutionTL': pdb['ResolutionColor']} return db_dict - - - def update_datasource_with_PDBheader(self,xtal,datasource,pdbfile): + def update_datasource_with_PDBheader(self, xtal, datasource, pdbfile): pdb = self.PDBheader(pdbfile) - db_dict= {'RefinementPDB_latest': os.path.realpath(pdbfile), 'RefinementRcryst': pdb['Rcryst'], - 'RefinementRcrystTraficLight': pdb['RcrystTL'], 'RefinementRfree': pdb['Rfree'], - 'RefinementRfreeTraficLight': pdb['RfreeTL'], 'RefinementRmsdBonds': pdb['rmsdBonds'], - 'RefinementRmsdBondsTL': pdb['rmsdBondsTL'], 'RefinementRmsdAngles': pdb['rmsdAngles'], - 'RefinementRmsdAnglesTL': pdb['rmsdAnglesTL'], 'RefinementSpaceGroup': pdb['SpaceGroup'], - 'RefinementResolution': pdb['ResolutionHigh'], 'RefinementResolutionTL': pdb['ResolutionColor']} + db_dict = {'RefinementPDB_latest': os.path.realpath(pdbfile), 'RefinementRcryst': pdb['Rcryst'], + 'RefinementRcrystTraficLight': pdb['RcrystTL'], 'RefinementRfree': pdb['Rfree'], + 'RefinementRfreeTraficLight': pdb['RfreeTL'], 'RefinementRmsdBonds': pdb['rmsdBonds'], + 'RefinementRmsdBondsTL': pdb['rmsdBondsTL'], 'RefinementRmsdAngles': pdb['rmsdAngles'], + 'RefinementRmsdAnglesTL': pdb['rmsdAnglesTL'], 'RefinementSpaceGroup': pdb['SpaceGroup'], + 'RefinementResolution': pdb['ResolutionHigh'], 'RefinementResolutionTL': pdb['ResolutionColor']} print db_dict - db=XChemDB.data_source(datasource) - db.update_data_source(xtal,db_dict) + db = XChemDB.data_source(datasource) + db.update_data_source(xtal, db_dict) - def update_datasource_with_phenix_validation_summary(self,xtal,datasource,validation_summary): - db_dict={} + def update_datasource_with_phenix_validation_summary(self, xtal, datasource, validation_summary): + db_dict = {} if os.path.isfile(validation_summary): for line in open(validation_summary): if 'molprobity score' in line.lower(): @@ -1129,7 +1185,8 @@ def update_datasource_with_phenix_validation_summary(self,xtal,datasource,valida if 'ramachandran outliers' in line.lower(): if len(line.split()) >= 4: - db_dict['RefinementRamachandranOutliers'] = line.split()[3] + db_dict['RefinementRamachandranOutliers'] = line.split()[ + 3] if float(line.split()[3]) < 0.3: db_dict['RefinementRamachandranOutliersTL'] = 'green' if 0.3 <= float(line.split()[3]) < 1: @@ -1139,7 +1196,8 @@ def update_datasource_with_phenix_validation_summary(self,xtal,datasource,valida if 'favored' in line.lower(): if len(line.split()) >= 3: - db_dict['RefinementRamachandranFavored'] = line.split()[2] + db_dict['RefinementRamachandranFavored'] = line.split()[ + 2] if float(line.split()[2]) < 90: db_dict['RefinementRamachandranFavoredTL'] = 'red' if 90 <= float(line.split()[2]) < 98: @@ -1147,35 +1205,36 @@ def update_datasource_with_phenix_validation_summary(self,xtal,datasource,valida if float(line.split()[2]) >= 98: db_dict['RefinementRamachandranFavoredTL'] = 'green' else: - db_dict['RefinementMolProbityScore'] = '-' - db_dict['RefinementMolProbityScoreTL'] = 'gray' - db_dict['RefinementRamachandranOutliers'] = '-' + db_dict['RefinementMolProbityScore'] = '-' + db_dict['RefinementMolProbityScoreTL'] = 'gray' + db_dict['RefinementRamachandranOutliers'] = '-' db_dict['RefinementRamachandranOutliersTL'] = 'gray' - db_dict['RefinementRamachandranFavored'] = '-' - db_dict['RefinementRamachandranFavoredTL'] = 'gray' - db=XChemDB.data_source(datasource) - db.update_data_source(xtal,db_dict) + db_dict['RefinementRamachandranFavored'] = '-' + db_dict['RefinementRamachandranFavoredTL'] = 'gray' + db = XChemDB.data_source(datasource) + db.update_data_source(xtal, db_dict) + class mtztools: - def __init__(self,mtzfile): - self.mtzfile=mtzfile + def __init__(self, mtzfile): + self.mtzfile = mtzfile self.hkl = any_reflection_file(file_name=self.mtzfile) self.miller_arrays = self.hkl.as_miller_arrays() self.mtz = self.miller_arrays[0] self.iotbxMTZ = mtz.object(self.mtzfile) - self.space_group_dict= { 'triclinic': [1], -# 'monoclinic': [3,4,5], - 'monoclinic_P': [3,4], - 'monoclinic_C': [5], - 'orthorhombic': [16,17,18,19,20,21,22,23,24], - 'tetragonal': [75,76,77,78,79,80,89,90,91,92,93,94,95,96,97,98], - 'hexagonal': [143,144,145,149,150,151,152,153,154,168,169,170, - 171,172,173,177,178,179,180,181,182], - 'rhombohedral': [146,155], - 'cubic': [195,196,197,198,199, - 207,208,209,210,211,212,213,214] } + self.space_group_dict = {'triclinic': [1], + # 'monoclinic': [3,4,5], + 'monoclinic_P': [3, 4], + 'monoclinic_C': [5], + 'orthorhombic': [16, 17, 18, 19, 20, 21, 22, 23, 24], + 'tetragonal': [75, 76, 77, 78, 79, 80, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98], + 'hexagonal': [143, 144, 145, 149, 150, 151, 152, 153, 154, 168, 169, 170, + 171, 172, 173, 177, 178, 179, 180, 181, 182], + 'rhombohedral': [146, 155], + 'cubic': [195, 196, 197, 198, 199, + 207, 208, 209, 210, 211, 212, 213, 214]} self.translate_spg_to_number_dict = { 'p1': 1, 'p121': 3, 'p1211': 4, 'c2': 5, 'c121': 5, 'i2': 5, 'i121': 5, 'p222': 16, @@ -1193,69 +1252,68 @@ def __init__(self,mtzfile): 'p4132': 213, 'i4132': 214 } - - self.point_group_dict= { '1': [1], - '2': [3,4,5], - '222': [16,17,18,19,20,21,22,23,24], - '4': [75,76,77,78,79,80], - '422': [89,90,91,92,93,94,95,96,97,98], - '3': [143,144,145,146], - '32': [149,150,151,152,153,154,155], - '6': [168,169,170,171,172,173], - '622': [177,178,179,180,181,182], - '23': [195,196,197,198,199], - '432': [207,208,209,210,211,212,213,214] } - - self.nr_asu_in_unitcell_for_point_group = { '1': 1, - '2': 2, - '222': 4, - '4': 4, - '422': 8, - '3': 3, - '32': 6, - '6': 6, - '622': 12, - '23': 12, - '432': 24 } - - self.aimless = { 'DataProcessingProgram': 'n/a', -# 'DataCollectionRun': 'n/a', - 'DataProcessingSpaceGroup': 'n/a', - 'DataProcessingUnitCell': 'n/a', - 'DataProcessingA': 'n/a', - 'DataProcessingB': 'n/a', - 'DataProcessingC': 'n/a', - 'DataProcessingAlpha': 'n/a', - 'DataProcessingBeta': 'n/a', - 'DataProcessingGamma': 'n/a', - 'DataProcessingResolutionLow': 'n/a', - 'DataProcessingResolutionLowInnerShell': 'n/a', - 'DataProcessingResolutionHigh': 'n/a', - 'DataProcessingResolutionHighOuterShell': 'n/a', - 'DataProcessingResolutionOverall': 'n/a', - 'DataProcessingRmergeOverall': 'n/a', - 'DataProcessingRmergeLow': 'n/a', - 'DataProcessingRmergeHigh': 'n/a', - 'DataProcessingIsigOverall': 'n/a', - 'DataProcessingIsigLow': 'n/a', - 'DataProcessingIsigHigh': 'n/a', - 'DataProcessingCompletenessOverall': 'n/a', - 'DataProcessingCompletenessLow': 'n/a', - 'DataProcessingCompletenessHigh': 'n/a', - 'DataProcessingMultiplicityOverall': 'n/a', - 'DataProcessingMultiplicityLow': 'n/a', - 'DataProcessingMultiplicityHigh': 'n/a', - 'DataProcessingCChalfOverall': 'n/a', - 'DataProcessingCChalfLow': 'n/a', - 'DataProcessingCChalfHigh': 'n/a', - 'DataProcessingResolutionHigh15sigma': 'n/a', - 'DataProcessingUniqueReflectionsOverall': 'n/a', - 'DataProcessingLattice': 'n/a', - 'DataProcessingPointGroup': 'n/a', - 'DataProcessingUnitCellVolume': 0, - 'DataProcessingAlert': '#FF0000', - 'DataCollectionWavelength': 'n/a', - 'DataProcessingScore': 'n/a' } + self.point_group_dict = {'1': [1], + '2': [3, 4, 5], + '222': [16, 17, 18, 19, 20, 21, 22, 23, 24], + '4': [75, 76, 77, 78, 79, 80], + '422': [89, 90, 91, 92, 93, 94, 95, 96, 97, 98], + '3': [143, 144, 145, 146], + '32': [149, 150, 151, 152, 153, 154, 155], + '6': [168, 169, 170, 171, 172, 173], + '622': [177, 178, 179, 180, 181, 182], + '23': [195, 196, 197, 198, 199], + '432': [207, 208, 209, 210, 211, 212, 213, 214]} + + self.nr_asu_in_unitcell_for_point_group = {'1': 1, + '2': 2, + '222': 4, + '4': 4, + '422': 8, + '3': 3, + '32': 6, + '6': 6, + '622': 12, + '23': 12, + '432': 24} + + self.aimless = {'DataProcessingProgram': 'n/a', + # 'DataCollectionRun': 'n/a', + 'DataProcessingSpaceGroup': 'n/a', + 'DataProcessingUnitCell': 'n/a', + 'DataProcessingA': 'n/a', + 'DataProcessingB': 'n/a', + 'DataProcessingC': 'n/a', + 'DataProcessingAlpha': 'n/a', + 'DataProcessingBeta': 'n/a', + 'DataProcessingGamma': 'n/a', + 'DataProcessingResolutionLow': 'n/a', + 'DataProcessingResolutionLowInnerShell': 'n/a', + 'DataProcessingResolutionHigh': 'n/a', + 'DataProcessingResolutionHighOuterShell': 'n/a', + 'DataProcessingResolutionOverall': 'n/a', + 'DataProcessingRmergeOverall': 'n/a', + 'DataProcessingRmergeLow': 'n/a', + 'DataProcessingRmergeHigh': 'n/a', + 'DataProcessingIsigOverall': 'n/a', + 'DataProcessingIsigLow': 'n/a', + 'DataProcessingIsigHigh': 'n/a', + 'DataProcessingCompletenessOverall': 'n/a', + 'DataProcessingCompletenessLow': 'n/a', + 'DataProcessingCompletenessHigh': 'n/a', + 'DataProcessingMultiplicityOverall': 'n/a', + 'DataProcessingMultiplicityLow': 'n/a', + 'DataProcessingMultiplicityHigh': 'n/a', + 'DataProcessingCChalfOverall': 'n/a', + 'DataProcessingCChalfLow': 'n/a', + 'DataProcessingCChalfHigh': 'n/a', + 'DataProcessingResolutionHigh15sigma': 'n/a', + 'DataProcessingUniqueReflectionsOverall': 'n/a', + 'DataProcessingLattice': 'n/a', + 'DataProcessingPointGroup': 'n/a', + 'DataProcessingUnitCellVolume': 0, + 'DataProcessingAlert': '#FF0000', + 'DataCollectionWavelength': 'n/a', + 'DataProcessingScore': 'n/a'} def get_dmin(self): return str(round(float(self.mtz.d_min()), 2)) @@ -1265,252 +1323,263 @@ def get_wavelength(self): for crystal in self.iotbxMTZ.crystals(): for dataset in crystal.datasets(): if not dataset.wavelength() == 0.0: - wavelength = str(round(dataset.wavelength(),5)) + wavelength = str(round(dataset.wavelength(), 5)) break return wavelength def get_information_for_datasource(self): - db_dict={} - mtz_dict=self.get_all_values_as_dict() - pg=self.get_pointgroup_from_mtz() + db_dict = {} + mtz_dict = self.get_all_values_as_dict() + pg = self.get_pointgroup_from_mtz() if mtz_dict != {}: - db_dict['DataProcessingResolutionHigh']=mtz_dict['resolution_high'] - db_dict['DataProcessingUnitCell']=mtz_dict['unitcell'] - db_dict['DataProcessingSpaceGroup']=mtz_dict['spacegroup'] - db_dict['DataProcessingUnitCellVolume']=mtz_dict['unitcell_volume'] - db_dict['DataProcessingLattice']=mtz_dict['bravais_lattice'] + db_dict['DataProcessingResolutionHigh'] = mtz_dict['resolution_high'] + db_dict['DataProcessingUnitCell'] = mtz_dict['unitcell'] + db_dict['DataProcessingSpaceGroup'] = mtz_dict['spacegroup'] + db_dict['DataProcessingUnitCellVolume'] = mtz_dict['unitcell_volume'] + db_dict['DataProcessingLattice'] = mtz_dict['bravais_lattice'] if pg != '': - db_dict['DataProcessingPointGroup']=pg + db_dict['DataProcessingPointGroup'] = pg return db_dict - def get_bravais_lattice_from_spg_number(self,number): - lattice='' + def get_bravais_lattice_from_spg_number(self, number): + lattice = '' for bravaislattice in self.space_group_dict: for spg_number in self.space_group_dict[bravaislattice]: - if spg_number==number: - lattice=bravaislattice + if spg_number == number: + lattice = bravaislattice return lattice - def get_point_group_from_spg_number(self,number): - pointgroup='' + def get_point_group_from_spg_number(self, number): + pointgroup = '' for pg in self.point_group_dict: for spg_number in self.point_group_dict[pg]: - if spg_number==number: - pointgroup=pg + if spg_number == number: + pointgroup = pg return pointgroup - def get_unit_cell_from_mtz(self): - unitcell=[] - cell_line=100000 - a=0 - b=0 - c=0 - alpha=0 - beta=0 - gamma=0 - mtzdmp=subprocess.Popen(['mtzdmp',self.mtzfile],stdout=subprocess.PIPE) - for n,line in enumerate(iter(mtzdmp.stdout.readline,'')): + unitcell = [] + cell_line = 100000 + a = 0 + b = 0 + c = 0 + alpha = 0 + beta = 0 + gamma = 0 + mtzdmp = subprocess.Popen( + ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): if line.startswith(' * Cell Dimensions :'): - cell_line=n+2 - if n==cell_line and len(line.split())==6: - a=line.split()[0] - b=line.split()[1] - c=line.split()[2] - alpha=line.split()[3] - beta=line.split()[4] - gamma=line.split()[5] - return [a,b,c,alpha,beta,gamma] + cell_line = n+2 + if n == cell_line and len(line.split()) == 6: + a = line.split()[0] + b = line.split()[1] + c = line.split()[2] + alpha = line.split()[3] + beta = line.split()[4] + gamma = line.split()[5] + return [a, b, c, alpha, beta, gamma] def get_spg_number_from_mtz(self): - spg_number=0 - mtzdmp=subprocess.Popen(['mtzdmp',self.mtzfile],stdout=subprocess.PIPE) - for n,line in enumerate(iter(mtzdmp.stdout.readline,'')): + spg_number = 0 + mtzdmp = subprocess.Popen( + ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): if line.startswith(' * Space group ='): - spg_number=int(line[line.rfind(')')-3:line.rfind(')')]) + spg_number = int(line[line.rfind(')')-3:line.rfind(')')]) return spg_number def get_spg_from_mtz(self): - spg='' - mtzdmp=subprocess.Popen(['mtzdmp',self.mtzfile],stdout=subprocess.PIPE) - for n,line in enumerate(iter(mtzdmp.stdout.readline,'')): + spg = '' + mtzdmp = subprocess.Popen( + ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): if line.startswith(' * Space group ='): - spg=line[line.find("'")+1:line.rfind("'")] + spg = line[line.find("'")+1:line.rfind("'")] return spg def get_bravais_lattice_from_mtz(self): - bravais_lattice='' - spg_number=self.get_spg_number_from_mtz() - bravais_lattice=self.get_bravais_lattice_from_spg_number(spg_number) + bravais_lattice = '' + spg_number = self.get_spg_number_from_mtz() + bravais_lattice = self.get_bravais_lattice_from_spg_number(spg_number) return bravais_lattice def get_pointgroup_from_mtz(self): - pointgroup='' - spg_number=self.get_spg_number_from_mtz() - pointgroup=self.get_point_group_from_spg_number(spg_number) + pointgroup = '' + spg_number = self.get_spg_number_from_mtz() + pointgroup = self.get_point_group_from_spg_number(spg_number) return pointgroup def calc_unitcell_volume_from_mtz(self): - spg_number=self.get_spg_number_from_mtz() - lattice=self.get_bravais_lattice_from_spg_number(spg_number) - unitcell=self.get_unit_cell_from_mtz() - a=float(unitcell[0]) - b=float(unitcell[1]) - c=float(unitcell[2]) - alpha=math.radians(float(unitcell[3])) - beta= math.radians(float(unitcell[4])) - gamma=math.radians(float(unitcell[5])) - unitcell_volume=0 - if lattice=='triclinic': - unitcell_volume=a*b*c* \ - math.sqrt((1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2) \ - +2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma))) + spg_number = self.get_spg_number_from_mtz() + lattice = self.get_bravais_lattice_from_spg_number(spg_number) + unitcell = self.get_unit_cell_from_mtz() + a = float(unitcell[0]) + b = float(unitcell[1]) + c = float(unitcell[2]) + alpha = math.radians(float(unitcell[3])) + beta = math.radians(float(unitcell[4])) + gamma = math.radians(float(unitcell[5])) + unitcell_volume = 0 + if lattice == 'triclinic': + unitcell_volume = a*b*c * \ + math.sqrt((1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2) + + 2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma))) if 'monoclinic' in lattice: - unitcell_volume=round(a*b*c*math.sin(beta),1) - if lattice=='orthorhombic' or lattice=='tetragonal' or lattice=='cubic': - unitcell_volume=round(a*b*c,1) - if lattice=='hexagonal' or lattice=='rhombohedral': - unitcell_volume=round(a*b*c*(math.sin(math.radians(60))),1) + unitcell_volume = round(a*b*c*math.sin(beta), 1) + if lattice == 'orthorhombic' or lattice == 'tetragonal' or lattice == 'cubic': + unitcell_volume = round(a*b*c, 1) + if lattice == 'hexagonal' or lattice == 'rhombohedral': + unitcell_volume = round(a*b*c*(math.sin(math.radians(60))), 1) return unitcell_volume def get_high_resolution_from_mtz(self): - resolution_high='n/a' - resolution_line=1000000 - mtzdmp=subprocess.Popen(['mtzdmp',self.mtzfile],stdout=subprocess.PIPE) - for n,line in enumerate(iter(mtzdmp.stdout.readline,'')): + resolution_high = 'n/a' + resolution_line = 1000000 + mtzdmp = subprocess.Popen( + ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): if line.startswith(' * Resolution Range :'): - resolution_line=n+2 - if n==resolution_line and len(line.split())==8: - resolution_high=line.split()[5] + resolution_line = n+2 + if n == resolution_line and len(line.split()) == 8: + resolution_high = line.split()[5] return resolution_high def get_low_resolution_from_mtz(self): - resolution_low='n/a' - resolution_line=1000000 - mtzdmp=subprocess.Popen(['mtzdmp',self.mtzfile],stdout=subprocess.PIPE) - for n,line in enumerate(iter(mtzdmp.stdout.readline,'')): + resolution_low = 'n/a' + resolution_line = 1000000 + mtzdmp = subprocess.Popen( + ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): if line.startswith(' * Resolution Range :'): - resolution_line=n+2 - if n==resolution_line and len(line.split())==8: - resolution_low=line.split()[3] + resolution_line = n+2 + if n == resolution_line and len(line.split()) == 8: + resolution_low = line.split()[3] return resolution_low def get_number_measured_reflections(self): - missing_reflections='0' - all_reflections='0' - meassured_reflections='0' - resolution_line=1000000 - mtzdmp=subprocess.Popen(['mtzdmp',self.mtzfile],stdout=subprocess.PIPE) - foundTable=False - for n,line in enumerate(iter(mtzdmp.stdout.readline,'')): + missing_reflections = '0' + all_reflections = '0' + meassured_reflections = '0' + resolution_line = 1000000 + mtzdmp = subprocess.Popen( + ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) + foundTable = False + for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): if line.startswith(' Col Sort Min Max Num % Mean Mean Resolution Type Column'): - foundTable=True - if foundTable and len(line.split())==12: - if line.split()[11]=='F': - missing_reflections=line.split()[4] - foundTable=False + foundTable = True + if foundTable and len(line.split()) == 12: + if line.split()[11] == 'F': + missing_reflections = line.split()[4] + foundTable = False if line.startswith(' No. of reflections used in FILE STATISTICS'): - all_reflections=line.split()[7] + all_reflections = line.split()[7] break try: - meassured_reflections=int(all_reflections)-int(missing_reflections) + meassured_reflections = int( + all_reflections)-int(missing_reflections) except ValueError: pass return meassured_reflections - def calculate_correlaton_between_intensities_in_mtzfiles(self,mtzin): + def calculate_correlaton_between_intensities_in_mtzfiles(self, mtzin): CC = '0.0' - errorMessage='' + errorMessage = '' # cmd = ( 'pointless hklin %s hklref %s << eof\n' %(mtzin,self.mtzfile)+ # 'labref F=F\n' # 'labin F=F\n' # 'eof\n' ) - cmd = ( 'pointless hklin %s hklref %s << eof\n' %(mtzin,self.mtzfile)+ - 'labref I=IMEAN\n' - 'labin I=IMEAN\n' - 'eof\n' ) - - pointless=subprocess.Popen(cmd,shell=True,stdout=subprocess.PIPE) - foundLine=False - for line in iter(pointless.stdout.readline,''): + cmd = ('pointless hklin %s hklref %s << eof\n' % (mtzin, self.mtzfile) + + 'labref I=IMEAN\n' + 'labin I=IMEAN\n' + 'eof\n') + + pointless = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE) + foundLine = False + for line in iter(pointless.stdout.readline, ''): if foundLine: - CC=line.split()[3] + CC = line.split()[3] break if 'Alternative reindexing Lklhd CC' in line: - foundLine=True + foundLine = True if '**** Incompatible symmetries ****' in line: - errorMessage='**** Incompatible symmetries ****' + errorMessage = '**** Incompatible symmetries ****' break if 'Merged test dataset (HKLIN) has different Laue symmetry to reference set' in line: - errorMessage='%s has different Laue symmetry to %s' %(mtzin,self.mtzfile) + errorMessage = '%s has different Laue symmetry to %s' % ( + mtzin, self.mtzfile) break - return CC,errorMessage + return CC, errorMessage def get_all_values_as_dict(self): - mtz = { 'resolution_high': 'n/a', - 'unitcell': 'n/a', - 'spacegroup': 'n/a', - 'unitcell_volume': 'n/a', - 'bravais_lattice': 'n/a' } - a=0.0 - b=0.0 - c=0.0 - alpha_rad=0.0 - beta_rad=0.0 - gamma_rad=0.0 - resolution_line=1000000 - cell_line=1000000 - mtzdmp=subprocess.Popen(['mtzdmp',self.mtzfile],stdout=subprocess.PIPE) - for n,line in enumerate(iter(mtzdmp.stdout.readline,'')): + mtz = {'resolution_high': 'n/a', + 'unitcell': 'n/a', + 'spacegroup': 'n/a', + 'unitcell_volume': 'n/a', + 'bravais_lattice': 'n/a'} + a = 0.0 + b = 0.0 + c = 0.0 + alpha_rad = 0.0 + beta_rad = 0.0 + gamma_rad = 0.0 + resolution_line = 1000000 + cell_line = 1000000 + mtzdmp = subprocess.Popen( + ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): if line.startswith(' * Resolution Range :'): - resolution_line=n+2 - if n==resolution_line and len(line.split())==8: - mtz['resolution_high']=round(float(line.split()[5]),2) + resolution_line = n+2 + if n == resolution_line and len(line.split()) == 8: + mtz['resolution_high'] = round(float(line.split()[5]), 2) if line.startswith(' * Cell Dimensions :'): - cell_line=n+2 - if n==cell_line and len(line.split())==6: - a= round(float(line.split()[0]),1) - b= round(float(line.split()[1]),1) - c= round(float(line.split()[2]),1) - alpha= round(float(line.split()[3]),1) - beta= round(float(line.split()[4]),1) - gamma= round(float(line.split()[5]),1) - mtz['unitcell']=str(a)+' '+str(b)+' '+str(c)+' '+ \ - str(alpha)+' '+str(beta)+' '+str(gamma) - alpha_rad=math.radians(alpha) - beta_rad= math.radians(beta) - gamma_rad=math.radians(gamma) + cell_line = n+2 + if n == cell_line and len(line.split()) == 6: + a = round(float(line.split()[0]), 1) + b = round(float(line.split()[1]), 1) + c = round(float(line.split()[2]), 1) + alpha = round(float(line.split()[3]), 1) + beta = round(float(line.split()[4]), 1) + gamma = round(float(line.split()[5]), 1) + mtz['unitcell'] = str(a)+' '+str(b)+' '+str(c)+' ' + \ + str(alpha)+' '+str(beta)+' '+str(gamma) + alpha_rad = math.radians(alpha) + beta_rad = math.radians(beta) + gamma_rad = math.radians(gamma) if line.startswith(' * Space group ='): - spg_number=int(line[line.rfind(')')-3:line.rfind(')')]) - mtz['bravais_lattice']=self.get_bravais_lattice_from_spg_number(spg_number) - mtz['spacegroup']=line[line.find("'")+1:line.rfind("'")] - if mtz['bravais_lattice']=='triclinic': - mtz['unitcell_volume']=a*b*c* \ - math.sqrt((1-math.cos(alpha_rad)**2-math.cos(beta_rad)**2-math.cos(gamma_rad)**2) \ - +2*(math.cos(alpha_rad)*math.cos(beta_rad)*math.cos(gamma_rad))) + spg_number = int(line[line.rfind(')')-3:line.rfind(')')]) + mtz['bravais_lattice'] = self.get_bravais_lattice_from_spg_number( + spg_number) + mtz['spacegroup'] = line[line.find("'")+1:line.rfind("'")] + if mtz['bravais_lattice'] == 'triclinic': + mtz['unitcell_volume'] = a*b*c * \ + math.sqrt((1-math.cos(alpha_rad)**2-math.cos(beta_rad)**2-math.cos(gamma_rad)**2) + + 2*(math.cos(alpha_rad)*math.cos(beta_rad)*math.cos(gamma_rad))) # elif mtz['bravais_lattice']=='monoclinic': elif 'monoclinic' in mtz['bravais_lattice']: - mtz['unitcell_volume']=round(a*b*c*math.sin(beta_rad),1) - elif mtz['bravais_lattice']=='orthorhombic' or mtz['bravais_lattice']=='tetragonal' or mtz['bravais_lattice']=='cubic': - mtz['unitcell_volume']=round(a*b*c,1) - elif mtz['bravais_lattice']=='hexagonal' or mtz['bravais_lattice']=='rhombohedral': - mtz['unitcell_volume']=round(a*b*c*(math.sin(math.radians(60))),1) + mtz['unitcell_volume'] = round(a*b*c*math.sin(beta_rad), 1) + elif mtz['bravais_lattice'] == 'orthorhombic' or mtz['bravais_lattice'] == 'tetragonal' or mtz['bravais_lattice'] == 'cubic': + mtz['unitcell_volume'] = round(a*b*c, 1) + elif mtz['bravais_lattice'] == 'hexagonal' or mtz['bravais_lattice'] == 'rhombohedral': + mtz['unitcell_volume'] = round( + a*b*c*(math.sin(math.radians(60))), 1) return mtz def get_all_columns_as_dict(self): - column_dict = { 'F': [], - 'I': [], - 'SIG': [], - 'PHS': [], - 'FOM': [], - 'RFREE': [] } - startline=1000000 - mtzdmp=subprocess.Popen(['mtzdmp',self.mtzfile],stdout=subprocess.PIPE) - for n,line in enumerate(iter(mtzdmp.stdout.readline,'')): + column_dict = {'F': [], + 'I': [], + 'SIG': [], + 'PHS': [], + 'FOM': [], + 'RFREE': []} + startline = 1000000 + mtzdmp = subprocess.Popen( + ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): if line.startswith(' Col Sort Min Max Num'): - startline=n+2 + startline = n+2 if n >= startline and len(line.split()) > 10: if line.split()[10] == 'F': column_dict['F'].append(line.split()[11]) @@ -1531,224 +1600,249 @@ def get_all_columns_as_list(self): column_list = self.iotbxMTZ.column_labels() return column_list + class queue: def jobs_in_queue(self): - jobs=[] - qstat=subprocess.Popen(['qstat -r'],stdout=subprocess.PIPE) - counter=0 - for n,line in enumerate(iter(qstat.stdout.readline,'')): - jobID='' - job_name='' - user_name='' - if getpass.getuser() in line: - counter +=1 - jobID=line.split()[0] - user_name=line.split()[3] - if "Full jobname:" in line: - job_name=line.split()[2] - jobs.append([counter,jobID,True,job_name,user_name]) - return jobs + jobs = [] + qstat = subprocess.Popen(['qstat -r'], stdout=subprocess.PIPE) + counter = 0 + for n, line in enumerate(iter(qstat.stdout.readline, '')): + jobID = '' + job_name = '' + user_name = '' + if getpass.getuser() in line: + counter += 1 + jobID = line.split()[0] + user_name = line.split()[3] + if "Full jobname:" in line: + job_name = line.split()[2] + jobs.append([counter, jobID, True, job_name, user_name]) + return jobs def remove_all_jobs_from_queue(self): - jobs_in_queue=self.jobs_in_queue() - if jobs_in_queue: - for job in jobs_in_queue: - os.system('qdel '+job[0]) - + jobs_in_queue = self.jobs_in_queue() + if jobs_in_queue: + for job in jobs_in_queue: + os.system('qdel '+job[0]) class external_software: - def __init__(self,xce_logfile): + def __init__(self, xce_logfile): self.available_programs = {} - self.Logfile=XChemLog.updateLog(xce_logfile) + self.Logfile = XChemLog.updateLog(xce_logfile) def check(self): self.Logfile.insert('Searching for external software...') # default is False; user needs to explicitely set this - self.available_programs['qsub_remote']='' + self.available_programs['qsub_remote'] = '' FNULL = open(os.devnull, 'w') try: -# subprocess.call(['qstat'], stdout=FNULL, stderr=subprocess.STDOUT) - p = subprocess.Popen('qstat', shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, close_fds=True) - status='found' + # subprocess.call(['qstat'], stdout=FNULL, stderr=subprocess.STDOUT) + p = subprocess.Popen('qstat', shell=True, stdin=subprocess.PIPE, + stdout=subprocess.PIPE, stderr=subprocess.STDOUT, close_fds=True) + status = 'found' try: for line in p.stdout: if 'symbol lookup error:' in line or 'command not found' in line or 'error' in line: - self.available_programs['qsub']=False - self.available_programs['qsub_array']=False - status='not found' - array_status='not found' + self.available_programs['qsub'] = False + self.available_programs['qsub_array'] = False + status = 'not found' + array_status = 'not found' except IOError: - self.available_programs['qsub']=False - self.available_programs['qsub_array']=False - status='not found' - array_status='not found' + self.available_programs['qsub'] = False + self.available_programs['qsub_array'] = False + status = 'not found' + array_status = 'not found' if status == 'found': - self.available_programs['qsub']=True + self.available_programs['qsub'] = True # if os.getcwd().startswith('/dls'): if os.path.isdir('/dls'): - self.available_programs['qsub_array']=True - array_status='found' + self.available_programs['qsub_array'] = True + array_status = 'found' else: - self.available_programs['qsub_array']=False - array_status='not found' + self.available_programs['qsub_array'] = False + array_status = 'not found' except OSError: - self.available_programs['qsub']=False - self.available_programs['qsub_array']=False - status='not found' - array_status='not found' - self.Logfile.insert('{0:50} {1:10}'.format('checking for qsub:', status)) + self.available_programs['qsub'] = False + self.available_programs['qsub_array'] = False + status = 'not found' + array_status = 'not found' + self.Logfile.insert('{0:50} {1:10}'.format( + 'checking for qsub:', status)) # print '{0:50} {1:10}'.format('-checking for qsub:', status) # if os.getcwd().startswith('/dls'): if os.path.isdir('/dls'): - self.Logfile.insert('{0:50} {1:10}'.format('checking for array qsub:', array_status)) + self.Logfile.insert('{0:50} {1:10}'.format( + 'checking for array qsub:', array_status)) try: - subprocess.call(['refmac5','end'], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['refmac5']=True - status='found' + subprocess.call(['refmac5', 'end'], stdout=FNULL, + stderr=subprocess.STDOUT) + self.available_programs['refmac5'] = True + status = 'found' except OSError: - self.available_programs['refmac5']=False - status='not found' - self.Logfile.insert('{0:50} {1:10}'.format('checking for refmac5:', status)) + self.available_programs['refmac5'] = False + status = 'not found' + self.Logfile.insert('{0:50} {1:10}'.format( + 'checking for refmac5:', status)) try: - subprocess.call(['phenix.molprobity'], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['phenix.molprobity']=True - status='found' + subprocess.call(['phenix.molprobity'], + stdout=FNULL, stderr=subprocess.STDOUT) + self.available_programs['phenix.molprobity'] = True + status = 'found' except OSError: - self.available_programs['phenix.molprobity']=False - status='not found' - self.Logfile.insert('{0:50} {1:10}'.format('checking for phenix.molprobity:', status)) + self.available_programs['phenix.molprobity'] = False + status = 'not found' + self.Logfile.insert('{0:50} {1:10}'.format( + 'checking for phenix.molprobity:', status)) try: - subprocess.call(['phenix.find_tls_groups'], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['phenix.find_tls_groups']=True - status='found' + subprocess.call(['phenix.find_tls_groups'], + stdout=FNULL, stderr=subprocess.STDOUT) + self.available_programs['phenix.find_tls_groups'] = True + status = 'found' except OSError: - self.available_programs['phenix.find_tls_groups']=False - status='not found' - self.Logfile.insert('{0:50} {1:10}'.format('checking for phenix.find_tls_groups:', status)) + self.available_programs['phenix.find_tls_groups'] = False + status = 'not found' + self.Logfile.insert('{0:50} {1:10}'.format( + 'checking for phenix.find_tls_groups:', status)) try: - subprocess.call(['mmtbx.validate_ligands'], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['mmtbx.validate_ligands']=True - status='found' + subprocess.call(['mmtbx.validate_ligands'], + stdout=FNULL, stderr=subprocess.STDOUT) + self.available_programs['mmtbx.validate_ligands'] = True + status = 'found' except OSError: - self.available_programs['mmtbx.validate_ligands']=False - status='not found' - self.Logfile.insert('{0:50} {1:10}'.format('checking for mmtbx.validate_ligands:', status)) + self.available_programs['mmtbx.validate_ligands'] = False + status = 'not found' + self.Logfile.insert('{0:50} {1:10}'.format( + 'checking for mmtbx.validate_ligands:', status)) try: subprocess.call(['acedrg'], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['acedrg']=True + self.available_programs['acedrg'] = True shutil.rmtree('AcedrgOut_TMP') - status='found' + status = 'found' except OSError: - self.available_programs['acedrg']=False - status='not found' - self.Logfile.insert('{0:50} {1:10}'.format('checking for acedrg:', status)) + self.available_programs['acedrg'] = False + status = 'not found' + self.Logfile.insert('{0:50} {1:10}'.format( + 'checking for acedrg:', status)) try: - subprocess.call(['phenix.elbow'], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['phenix.elbow']=True - status='found' + subprocess.call(['phenix.elbow'], stdout=FNULL, + stderr=subprocess.STDOUT) + self.available_programs['phenix.elbow'] = True + status = 'found' except OSError: - self.available_programs['phenix.elbow']=False - status='not found' - self.Logfile.insert('{0:50} {1:10}'.format('checking for phenix.elbow:', status)) + self.available_programs['phenix.elbow'] = False + status = 'not found' + self.Logfile.insert('{0:50} {1:10}'.format( + 'checking for phenix.elbow:', status)) try: subprocess.call(['grade'], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['grade']=True - status='found' + self.available_programs['grade'] = True + status = 'found' except OSError: - self.available_programs['grade']=False - status='not found' - self.Logfile.insert('{0:50} {1:10}'.format('checking for grade:', status)) + self.available_programs['grade'] = False + status = 'not found' + self.Logfile.insert('{0:50} {1:10}'.format( + 'checking for grade:', status)) try: - subprocess.call(['giant.create_occupancy_params'], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['giant.create_occupancy_params']=True - status='found' + subprocess.call(['giant.create_occupancy_params'], + stdout=FNULL, stderr=subprocess.STDOUT) + self.available_programs['giant.create_occupancy_params'] = True + status = 'found' except OSError: - self.available_programs['giant.create_occupancy_params']=False - status='not found' - self.Logfile.insert('{0:50} {1:10}'.format('checking for giant.create_occupancy_params:', status)) + self.available_programs['giant.create_occupancy_params'] = False + status = 'not found' + self.Logfile.insert('{0:50} {1:10}'.format( + 'checking for giant.create_occupancy_params:', status)) self.Logfile.insert('checking if MOGUL is configured...') - self.available_programs['mogul']=False + self.available_programs['mogul'] = False if "BDG_TOOL_MOGUL" in os.environ: - self.Logfile.insert('BDG_TOOL_MOGUL is set to ' + os.environ['BDG_TOOL_MOGUL']) + self.Logfile.insert('BDG_TOOL_MOGUL is set to ' + + os.environ['BDG_TOOL_MOGUL']) if str(os.environ['BDG_TOOL_MOGUL']).lower() == 'none': - self.Logfile.warning('BDG_TOOL_MOGUL is not properly configured!') - self.Logfile.hint('try adding "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul" to your .bashrc file') + self.Logfile.warning( + 'BDG_TOOL_MOGUL is not properly configured!') + self.Logfile.hint( + 'try adding "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul" to your .bashrc file') else: if os.path.isfile(os.getenv('BDG_TOOL_MOGUL')): - self.available_programs['mogul']=True - status='found' + self.available_programs['mogul'] = True + status = 'found' else: - status='not found' - self.Logfile.hint('try adding "export PATH=/dls_sw/apps/ccdc/CSD_2020/bin:$PATH" to your .bashrc file') + status = 'not found' + self.Logfile.hint( + 'try adding "export PATH=/dls_sw/apps/ccdc/CSD_2020/bin:$PATH" to your .bashrc file') else: self.Logfile.warning('BDG_TOOL_MOGUL is not set!') - self.Logfile.hint('try adding "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul" to your .bashrc file') - status='not found' - self.Logfile.insert('{0:50} {1:10}'.format('checking for mogul:', status)) + self.Logfile.hint( + 'try adding "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul" to your .bashrc file') + status = 'not found' + self.Logfile.insert('{0:50} {1:10}'.format( + 'checking for mogul:', status)) try: subprocess.call(['gemmi'], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['gemmi']=True - status='found' + self.available_programs['gemmi'] = True + status = 'found' except OSError: - self.available_programs['gemmi']=False - status='not found' - self.Logfile.insert('{0:50} {1:10}'.format('checking for gemmi:', status)) + self.available_programs['gemmi'] = False + status = 'not found' + self.Logfile.insert('{0:50} {1:10}'.format( + 'checking for gemmi:', status)) return self.available_programs class ParseFiles: - def __init__(self,DataPath,xtalID): + def __init__(self, DataPath, xtalID): # probably need to read in compoundID, because for custom projects, need to take newest pdb file # that has not same root as compoundID self.DataPath = DataPath self.xtalID = xtalID if '' in DataPath: - self.newestPDB = max(glob.iglob(self.DataPath.replace('',xtalID)+'/*.pdb'), key=os.path.getctime) + self.newestPDB = max(glob.iglob(self.DataPath.replace( + '', xtalID)+'/*.pdb'), key=os.path.getctime) else: self.newestPDB = self.DataPath+'/'+self.xtalID+'/refine.pdb' def UpdateQualityIndicators(self): - QualityIndicators = { 'R': '-', - 'RRfree': '-', - 'RRfreeColor': 'gray', - 'Resolution': 'n/a', - 'ResolutionColor': 'gray', - 'MolprobityScore': 'n/a', - 'MolprobityScoreColor': 'gray', - 'RamachandranOutliers': 'n/a', - 'RamachandranOutliersColor': 'gray', - 'RamachandranFavored': 'n/a', - 'RamachandranFavoredColor': 'gray', - 'LigandCCcolor': 'gray', - 'LigandCC': 'n/a', - 'rmsdBonds': 'n/a', - 'rmsdBondsColor': 'gray', - 'rmsdAngles': 'n/a', - 'rmsdAnglesColor': 'gray', - 'MatrixWeight': 'n/a' } + QualityIndicators = {'R': '-', + 'RRfree': '-', + 'RRfreeColor': 'gray', + 'Resolution': 'n/a', + 'ResolutionColor': 'gray', + 'MolprobityScore': 'n/a', + 'MolprobityScoreColor': 'gray', + 'RamachandranOutliers': 'n/a', + 'RamachandranOutliersColor': 'gray', + 'RamachandranFavored': 'n/a', + 'RamachandranFavoredColor': 'gray', + 'LigandCCcolor': 'gray', + 'LigandCC': 'n/a', + 'rmsdBonds': 'n/a', + 'rmsdBondsColor': 'gray', + 'rmsdAngles': 'n/a', + 'rmsdAnglesColor': 'gray', + 'MatrixWeight': 'n/a'} # R, Rfree, Resolution found = 0 @@ -1758,116 +1852,141 @@ def UpdateQualityIndicators(self): QualityIndicators['R'] = line.split()[9] if line.startswith('REMARK 3 FREE R VALUE :'): QualityIndicators['RRfree'] = line.split()[6] - if float(line.split()[6]) < 0.3: QualityIndicators['RRfreeColor'] = 'green' - if float(line.split()[6]) >= 0.3 and float(line.split()[6]): QualityIndicators['RRfreeColor'] = 'orange' - if float(line.split()[6]) >= 0.4: QualityIndicators['RRfreeColor'] = 'red' + if float(line.split()[6]) < 0.3: + QualityIndicators['RRfreeColor'] = 'green' + if float(line.split()[6]) >= 0.3 and float(line.split()[6]): + QualityIndicators['RRfreeColor'] = 'orange' + if float(line.split()[6]) >= 0.4: + QualityIndicators['RRfreeColor'] = 'red' if line.startswith('REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) :'): QualityIndicators['Resolution'] = line.split()[7] - if float(line.split()[7]) < 2.4: QualityIndicators['ResolutionColor'] = 'green' - if 2.4 <= float(line.split()[7]) < 2.8: QualityIndicators['ResolutionColor'] = 'orange' - if float(line.split()[7]) >= 2.8: QualityIndicators['ResolutionColor'] = 'red' + if float(line.split()[7]) < 2.4: + QualityIndicators['ResolutionColor'] = 'green' + if 2.4 <= float(line.split()[7]) < 2.8: + QualityIndicators['ResolutionColor'] = 'orange' + if float(line.split()[7]) >= 2.8: + QualityIndicators['ResolutionColor'] = 'red' if line.startswith('REMARK 3 BOND LENGTHS REFINED ATOMS (A):'): QualityIndicators['rmsdBonds'] = line.split()[9] - if float(line.split()[9]) < 0.02: QualityIndicators['rmsdBondsColor'] = 'green' - if 0.02 <= float(line.split()[9]) < 0.03: QualityIndicators['rmsdBondsColor'] = 'orange' - if float(line.split()[9]) >= 0.03: QualityIndicators['rmsdBondsColor'] = 'red' + if float(line.split()[9]) < 0.02: + QualityIndicators['rmsdBondsColor'] = 'green' + if 0.02 <= float(line.split()[9]) < 0.03: + QualityIndicators['rmsdBondsColor'] = 'orange' + if float(line.split()[9]) >= 0.03: + QualityIndicators['rmsdBondsColor'] = 'red' if line.startswith('REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES):'): QualityIndicators['rmsdAngles'] = line.split()[9] - if float(line.split()[9]) < 2.0: QualityIndicators['rmsdAnglesColor'] = 'green' - if 2.0 <= float(line.split()[9]) < 3.0: QualityIndicators['rmsdAnglesColor'] = 'orange' - if float(line.split()[9]) >= 3.0: QualityIndicators['rmsdAnglesColor'] = 'red' - + if float(line.split()[9]) < 2.0: + QualityIndicators['rmsdAnglesColor'] = 'green' + if 2.0 <= float(line.split()[9]) < 3.0: + QualityIndicators['rmsdAnglesColor'] = 'orange' + if float(line.split()[9]) >= 3.0: + QualityIndicators['rmsdAnglesColor'] = 'red' # Molprobity if os.path.isfile(self.DataPath+'/'+self.xtalID+'/validation_summary.txt'): for line in open(self.DataPath+'/'+self.xtalID+'/validation_summary.txt'): -# if line.startswith(' Molprobity score ='): -# if line.lower().startswith(' molprobity score'): + # if line.startswith(' Molprobity score ='): + # if line.lower().startswith(' molprobity score'): if 'molprobity score' in line.lower(): if len(line.split()) >= 4: QualityIndicators['MolprobityScore'] = line.split()[3] try: - if float(line.split()[3]) < 2: QualityIndicators['MolprobityScoreColor'] = 'green' - if 2 <= float(line.split()[3]) < 3: QualityIndicators['MolprobityScoreColor'] = 'orange' - if float(line.split()[3]) >= 3: QualityIndicators['MolprobityScoreColor'] = 'red' + if float(line.split()[3]) < 2: + QualityIndicators['MolprobityScoreColor'] = 'green' + if 2 <= float(line.split()[3]) < 3: + QualityIndicators['MolprobityScoreColor'] = 'orange' + if float(line.split()[3]) >= 3: + QualityIndicators['MolprobityScoreColor'] = 'red' except ValueError: pass # if line.lower().startswith(' ramachandran outliers ='): if 'ramachandran outliers' in line.lower(): if len(line.split()) >= 4: - QualityIndicators['RamachandranOutliers'] = line.split()[3] + QualityIndicators['RamachandranOutliers'] = line.split()[ + 3] try: - if float(line.split()[3]) < 0.3: QualityIndicators['RamachandranOutliersColor'] = 'green' - if 0.3 <= float(line.split()[3]) < 1: QualityIndicators['RamachandranOutliersColor'] = 'orange' - if float(line.split()[3]) >= 1: QualityIndicators['RamachandranOutliersColor'] = 'red' + if float(line.split()[3]) < 0.3: + QualityIndicators['RamachandranOutliersColor'] = 'green' + if 0.3 <= float(line.split()[3]) < 1: + QualityIndicators['RamachandranOutliersColor'] = 'orange' + if float(line.split()[3]) >= 1: + QualityIndicators['RamachandranOutliersColor'] = 'red' except ValueError: pass # if line.startswith(' favored ='): if 'favored' in line.lower(): if len(line.split()) >= 3: - QualityIndicators['RamachandranFavored'] = line.split()[2] + QualityIndicators['RamachandranFavored'] = line.split()[ + 2] try: - if float(line.split()[2]) < 90: QualityIndicators['RamachandranFavoredColor'] = 'red' - if 90 <= float(line.split()[2]) < 98: QualityIndicators['RamachandranFavoredColor'] = 'orange' - if float(line.split()[2]) >= 98: QualityIndicators['RamachandranFavoredColor'] = 'green' + if float(line.split()[2]) < 90: + QualityIndicators['RamachandranFavoredColor'] = 'red' + if 90 <= float(line.split()[2]) < 98: + QualityIndicators['RamachandranFavoredColor'] = 'orange' + if float(line.split()[2]) >= 98: + QualityIndicators['RamachandranFavoredColor'] = 'green' except ValueError: pass # LigandCC if os.path.isfile(self.DataPath+'/'+self.xtalID+'/validate_ligands.txt'): for line in open(self.DataPath+'/'+self.xtalID+'/validate_ligands.txt'): -# if line.startswith('| LIG'): + # if line.startswith('| LIG'): if 'LIG' in line: QualityIndicators['LigandCC'] = line.split()[6] - if float(line.split()[6]) < 0.8: QualityIndicators['LigandCCcolor'] = 'red' - if 0.8 <= float(line.split()[6]) < 0.9: QualityIndicators['LigandCCcolor'] = 'orange' - if float(line.split()[6]) >= 0.9: QualityIndicators['LigandCCcolor'] = 'green' + if float(line.split()[6]) < 0.8: + QualityIndicators['LigandCCcolor'] = 'red' + if 0.8 <= float(line.split()[6]) < 0.9: + QualityIndicators['LigandCCcolor'] = 'orange' + if float(line.split()[6]) >= 0.9: + QualityIndicators['LigandCCcolor'] = 'green' # Matrix Weight temp = [] found = 0 - if os.path.isdir(os.path.join(self.DataPath,self.xtalID)): - for item in glob.glob(os.path.join(self.DataPath,self.xtalID,'*')): - if item.startswith(os.path.join(self.DataPath,self.xtalID,'Refine_')): - temp.append(int(item[item.rfind('_')+1:])) - found = 1 + if os.path.isdir(os.path.join(self.DataPath, self.xtalID)): + for item in glob.glob(os.path.join(self.DataPath, self.xtalID, '*')): + if item.startswith(os.path.join(self.DataPath, self.xtalID, 'Refine_')): + temp.append(int(item[item.rfind('_')+1:])) + found = 1 if found: Serial = max(temp) - if os.path.isfile(os.path.join(self.DataPath,self.xtalID,'Refine_'+str(Serial),'refmac.log') ): - for line in open(os.path.join(self.DataPath,self.xtalID,'Refine_'+str(Serial),'refmac.log')): - if line.startswith(' Weight matrix') and len(line.split())==3: - QualityIndicators['MatrixWeight']=line.split()[2] + if os.path.isfile(os.path.join(self.DataPath, self.xtalID, 'Refine_'+str(Serial), 'refmac.log')): + for line in open(os.path.join(self.DataPath, self.xtalID, 'Refine_'+str(Serial), 'refmac.log')): + if line.startswith(' Weight matrix') and len(line.split()) == 3: + QualityIndicators['MatrixWeight'] = line.split()[2] return QualityIndicators + class pdbtools(object): - def __init__(self,pdb): + def __init__(self, pdb): self.pdb = pdb self.pdb_inp = iotbx.pdb.input(file_name=self.pdb) self.hierarchy = self.pdb_inp.construct_hierarchy() - - self.AminoAcids = ['ALA','ARG','ASN','ASP','CYS','GLU','GLN','GLY','HIS', - 'ILE','LEU','LYS','MET','PHE','PRO','SER','THR','TRP','TYR','VAL','CSO','HYP'] - self.Solvents = ['DMS','EDO','GOL','HOH'] - self.Ions = ['NA','MG','CL','K','SO4','PO4','CA'] - self.AAdict = {'ALA':'A','ARG':'R','ASN':'N','ASP':'D','CYS':'C','GLU':'E','GLN':'Q', - 'GLY':'G','HIS':'H','ILE':'I','LEU':'L','LYS':'K','MET':'M','PHE':'F', - 'PRO':'P','SER':'S','THR':'T','TRP':'W','TYR':'Y','VAL':'V'} - self.xce_ligands = ['LIG','DRG','FRS'] - - self.space_group_dict= { 'triclinic': [1], -# 'monoclinic': [3,4,5], - 'monoclinic_P': [3,4], - 'monoclinic_C': [5], - 'orthorhombic': [16,17,18,19,20,21,22,23,24], - 'tetragonal': [75,76,77,78,79,80,89,90,91,92,93,94,95,96,97,98], - 'hexagonal': [143,144,145,149,150,151,152,153,154,168,169,170, - 171,172,173,177,178,179,180,181,182], - 'rhombohedral': [146,155], - 'cubic': [195,196,197,198,199, - 207,208,209,210,211,212,213,214] } + self.AminoAcids = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLU', 'GLN', 'GLY', 'HIS', + 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'CSO', 'HYP'] + self.Solvents = ['DMS', 'EDO', 'GOL', 'HOH'] + self.Ions = ['NA', 'MG', 'CL', 'K', 'SO4', 'PO4', 'CA'] + self.AAdict = {'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D', 'CYS': 'C', 'GLU': 'E', 'GLN': 'Q', + 'GLY': 'G', 'HIS': 'H', 'ILE': 'I', 'LEU': 'L', 'LYS': 'K', 'MET': 'M', 'PHE': 'F', + 'PRO': 'P', 'SER': 'S', 'THR': 'T', 'TRP': 'W', 'TYR': 'Y', 'VAL': 'V'} + self.xce_ligands = ['LIG', 'DRG', 'FRS'] + + self.space_group_dict = {'triclinic': [1], + # 'monoclinic': [3,4,5], + 'monoclinic_P': [3, 4], + 'monoclinic_C': [5], + 'orthorhombic': [16, 17, 18, 19, 20, 21, 22, 23, 24], + 'tetragonal': [75, 76, 77, 78, 79, 80, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98], + 'hexagonal': [143, 144, 145, 149, 150, 151, 152, 153, 154, 168, 169, 170, + 171, 172, 173, 177, 178, 179, 180, 181, 182], + 'rhombohedral': [146, 155], + 'cubic': [195, 196, 197, 198, 199, + 207, 208, 209, 210, 211, 212, 213, 214]} self.translate_spg_to_number_dict = { 'p1': 1, 'p121': 3, 'p1211': 4, 'c2': 5, 'c121': 5, 'i2': 5, 'i121': 5, 'p222': 16, @@ -1885,30 +2004,29 @@ def __init__(self,pdb): 'p4132': 213, 'i4132': 214 } - - self.point_group_dict= { '1': [1], - '2': [3,4,5], - '222': [16,17,18,19,20,21,22,23,24], - '4': [75,76,77,78,79,80], - '422': [89,90,91,92,93,94,95,96,97,98], - '3': [143,144,145,146], - '32': [149,150,151,152,153,154,155], - '6': [168,169,170,171,172,173], - '622': [177,178,179,180,181,182], - '23': [195,196,197,198,199], - '432': [207,208,209,210,211,212,213,214] } - - self.nr_asu_in_unitcell_for_point_group = { '1': 1, - '2': 2, - '222': 4, - '4': 4, - '422': 8, - '3': 3, - '32': 6, - '6': 6, - '622': 12, - '23': 12, - '432': 24 } + self.point_group_dict = {'1': [1], + '2': [3, 4, 5], + '222': [16, 17, 18, 19, 20, 21, 22, 23, 24], + '4': [75, 76, 77, 78, 79, 80], + '422': [89, 90, 91, 92, 93, 94, 95, 96, 97, 98], + '3': [143, 144, 145, 146], + '32': [149, 150, 151, 152, 153, 154, 155], + '6': [168, 169, 170, 171, 172, 173], + '622': [177, 178, 179, 180, 181, 182], + '23': [195, 196, 197, 198, 199], + '432': [207, 208, 209, 210, 211, 212, 213, 214]} + + self.nr_asu_in_unitcell_for_point_group = {'1': 1, + '2': 2, + '222': 4, + '4': 4, + '422': 8, + '3': 3, + '32': 6, + '6': 6, + '622': 12, + '23': 12, + '432': 24} def amino_acids(self): return self.AminoAcids @@ -1923,9 +2041,9 @@ def get_refinement_program(self): program = 'PHENIX' elif 'buster' in remark.lower(): program = 'BUSTER' - return program + return program - def get_residues_with_resname(self,resname): + def get_residues_with_resname(self, resname): ligands = [] for model in self.hierarchy.models(): for chain in model.chains(): @@ -1933,11 +2051,12 @@ def get_residues_with_resname(self,resname): for residue in conformer.residues(): if residue.resname == resname: if [residue.resname, residue.resseq, chain.id] not in ligands: - ligands.append([residue.resname, residue.resseq, chain.id]) + ligands.append( + [residue.resname, residue.resseq, chain.id]) return ligands # def get_centre_of_gravity_of_residue(self,resname_resseq_chain): - def get_centre_of_gravity_of_residue(self,resname_chain_resseq): + def get_centre_of_gravity_of_residue(self, resname_chain_resseq): resname_x = resname_chain_resseq.split('-')[0] chain_x = resname_chain_resseq.split('-')[1] resseq_x = resname_chain_resseq.split('-')[2] @@ -1948,7 +2067,7 @@ def get_centre_of_gravity_of_residue(self,resname_chain_resseq): for chain in model.chains(): for conformer in chain.conformers(): for residue in conformer.residues(): - if residue.resname.replace(' ','') == resname_x and residue.resseq.replace(' ','') == resseq_x and chain.id.replace(' ','') == chain_x: + if residue.resname.replace(' ', '') == resname_x and residue.resseq.replace(' ', '') == resseq_x and chain.id.replace(' ', '') == chain_x: for atom in residue.atoms(): x.append(atom.xyz[0]) y.append(atom.xyz[1]) @@ -1959,23 +2078,26 @@ def get_centre_of_gravity_of_residue(self,resname_chain_resseq): y = ((max(y) - min(y)) / 2) + min(y) z = ((max(z) - min(z)) / 2) + min(z) - return x,y,z + return x, y, z - def save_residues_with_resname(self,outDir,resname): + def save_residues_with_resname(self, outDir, resname): ligands = self.get_residues_with_resname(resname) ligList = [] for l in ligands: sel_cache = self.hierarchy.atom_selection_cache() - lig_sel = sel_cache.selection("(resname %s and resseq %s and chain %s)" % (l[0], l[1], l[2])) + lig_sel = sel_cache.selection( + "(resname %s and resseq %s and chain %s)" % (l[0], l[1], l[2])) hierarchy_lig = self.hierarchy.select(lig_sel) # ligName = (l[0] + '-' + l[1] + '-' + l[2] + '.pdb').replace(' ', '') - ligName = (l[0] + '-' + l[2] + '-' + l[1] + '.pdb').replace(' ', '') + ligName = (l[0] + '-' + l[2] + '-' + + l[1] + '.pdb').replace(' ', '') ligList.append(ligName) try: - f = open(os.path.join(outDir,ligName), "w") - f.write(hierarchy_lig.as_pdb_string(crystal_symmetry=self.pdb_inp.crystal_symmetry())) + f = open(os.path.join(outDir, ligName), "w") + f.write(hierarchy_lig.as_pdb_string( + crystal_symmetry=self.pdb_inp.crystal_symmetry())) f.close() except IOError: print('ERROR: {0!s} exists; skipping...') @@ -1983,235 +2105,234 @@ def save_residues_with_resname(self,outDir,resname): return ligList def GetRefinementProgram(self): - program='' + program = '' for line in open(self.pdb): if line.startswith('REMARK') and 'REFMAC' in line: - program='REFMAC' + program = 'REFMAC' break if line.startswith('REMARK') and 'PHENIX' in line: - program='PHENIX' + program = 'PHENIX' break if line.startswith('REMARK') and 'BUSTER' in line: - program='BUSTER' + program = 'BUSTER' break return program - def GetSequence(self): chain = [] - Sequence='' + Sequence = '' # need to count residue numbers in case of alternative conformations - ResiNum=[] + ResiNum = [] for line in open(self.pdb): if line.startswith('ATOM') and line[17:20] in self.AminoAcids: if line[21:22] not in chain: chain.append(line[21:22]) - Sequence=Sequence+'\n>chain{0!s}.\n'.format(line[21:22]) - ResiNum=[] - if line[13:15]=='CA' and line[22:27] not in ResiNum: - Sequence=Sequence+self.AAdict[line[17:20]] + Sequence = Sequence+'\n>chain{0!s}.\n'.format(line[21:22]) + ResiNum = [] + if line[13:15] == 'CA' and line[22:27] not in ResiNum: + Sequence = Sequence+self.AAdict[line[17:20]] ResiNum.append(line[22:27]) return Sequence - def GetProteinChains(self): chain = [] for line in open(self.pdb): if line.startswith('ATOM'): if line[17:20] in self.AminoAcids: - if line[21:22] not in chain: chain.append(line[21:22]) + if line[21:22] not in chain: + chain.append(line[21:22]) return chain - def GetSymm(self): unitcell = [] - a='' - b='' - c='' - alpha='' - beta='' - gamma='' - spg='' + a = '' + b = '' + c = '' + alpha = '' + beta = '' + gamma = '' + spg = '' for line in open(self.pdb): if line.startswith('CRYST1'): - a=line.split()[1] - b=line.split()[2] - c=line.split()[3] - alpha=line.split()[4] - beta=line.split()[5] - gamma=line.split()[6] + a = line.split()[1] + b = line.split()[2] + c = line.split()[3] + alpha = line.split()[4] + beta = line.split()[5] + gamma = line.split()[6] # spg=line[55:len(line)-1] - spg=line[55:65] - return [a,b,c,alpha,beta,gamma,spg] + spg = line[55:65] + return [a, b, c, alpha, beta, gamma, spg] def get_spg_from_pdb(self): - spg=self.GetSymm()[6] + spg = self.GetSymm()[6] return spg def get_spg_number_from_pdb(self): - spg=self.get_spg_from_pdb().replace(' ','').lower().replace('\n','').replace('\r','') - spg_number='0' + spg = self.get_spg_from_pdb().replace( + ' ', '').lower().replace('\n', '').replace('\r', '') + spg_number = '0' for key in self.translate_spg_to_number_dict: - if key==spg: - spg_number=str(self.translate_spg_to_number_dict[key]) + if key == spg: + spg_number = str(self.translate_spg_to_number_dict[key]) break return spg_number def get_bravais_lattice_from_pdb(self): - bravais_lattice='' - spg_number=self.get_spg_number_from_pdb() - bravais_lattice=self.get_bravais_lattice_from_spg_number(spg_number) + bravais_lattice = '' + spg_number = self.get_spg_number_from_pdb() + bravais_lattice = self.get_bravais_lattice_from_spg_number(spg_number) return bravais_lattice - def get_bravais_lattice_from_spg_number(self,number): - lattice='' + def get_bravais_lattice_from_spg_number(self, number): + lattice = '' for bravaislattice in self.space_group_dict: for spg_number in self.space_group_dict[bravaislattice]: - if str(spg_number)==str(number): - lattice=bravaislattice + if str(spg_number) == str(number): + lattice = bravaislattice return lattice def get_pointgroup_from_pdb(self): - pointgroup='' - spg_number=self.get_spg_number_from_pdb() - pointgroup=self.get_point_group_from_spg_number(spg_number) + pointgroup = '' + spg_number = self.get_spg_number_from_pdb() + pointgroup = self.get_point_group_from_spg_number(spg_number) return pointgroup def get_unit_cell_from_pdb(self): - symm=self.GetSymm() - unit_cell=symm[0:6] + symm = self.GetSymm() + unit_cell = symm[0:6] return unit_cell def calc_unitcell_volume_from_pdb(self): - spg_number=self.get_spg_number_from_pdb() - lattice=self.get_bravais_lattice_from_spg_number(spg_number) - unitcell=self.get_unit_cell_from_pdb() - a=float(unitcell[0]) - b=float(unitcell[1]) - c=float(unitcell[2]) - alpha=math.radians(float(unitcell[3])) - beta= math.radians(float(unitcell[4])) - gamma=math.radians(float(unitcell[5])) - unitcell_volume=0 - if lattice=='triclinic': - unitcell_volume=a*b*c* \ - math.sqrt((1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2) \ - +2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma))) + spg_number = self.get_spg_number_from_pdb() + lattice = self.get_bravais_lattice_from_spg_number(spg_number) + unitcell = self.get_unit_cell_from_pdb() + a = float(unitcell[0]) + b = float(unitcell[1]) + c = float(unitcell[2]) + alpha = math.radians(float(unitcell[3])) + beta = math.radians(float(unitcell[4])) + gamma = math.radians(float(unitcell[5])) + unitcell_volume = 0 + if lattice == 'triclinic': + unitcell_volume = a*b*c * \ + math.sqrt((1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2) + + 2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma))) # if lattice=='monoclinic': if 'monoclinic' in lattice: - unitcell_volume=round(a*b*c*math.sin(beta),1) - if lattice=='orthorhombic' or lattice=='tetragonal' or lattice=='cubic': - unitcell_volume=round(a*b*c,1) - if lattice=='hexagonal' or lattice=='rhombohedral': - unitcell_volume=round(a*b*c*(math.sin(math.radians(60))),1) + unitcell_volume = round(a*b*c*math.sin(beta), 1) + if lattice == 'orthorhombic' or lattice == 'tetragonal' or lattice == 'cubic': + unitcell_volume = round(a*b*c, 1) + if lattice == 'hexagonal' or lattice == 'rhombohedral': + unitcell_volume = round(a*b*c*(math.sin(math.radians(60))), 1) return unitcell_volume - - def MatthewsCoefficient(self,sequence): - chain=self.GetProteinChains() - symm=self.GetSymm() - nres=0 + def MatthewsCoefficient(self, sequence): + chain = self.GetProteinChains() + symm = self.GetSymm() + nres = 0 for char in sequence: - if char != ' ': nres+=1 + if char != ' ': + nres += 1 cmd = ( '#!/bin/csh -f\n' 'matthews_coef << eof\n' - ' cell %s\n' %(symm[0]+' '+symm[1]+' '+symm[2]+' '+symm[3]+' '+symm[4]+' '+symm[5])+ - ' symm {0!s}\n'.format(symm[6].replace(' ',''))+ - ' nres {0!s}\n'.format(nres)+ + ' cell %s\n' % (symm[0]+' '+symm[1]+' '+symm[2]+' '+symm[3]+' '+symm[4]+' '+symm[5]) + + ' symm {0!s}\n'.format(symm[6].replace(' ', '')) + + ' nres {0!s}\n'.format(nres) + ' auto\n' ' end\n' 'eof\n' - ) + ) Log = subprocess.check_output(cmd, shell=True) - MatthewsCoeff='n/a' - Solvent='n/a' - found=0 + MatthewsCoeff = 'n/a' + Solvent = 'n/a' + found = 0 for line in Log.split(os.linesep): if found: if int(line.split()[0]) == len(chain): - MatthewsCoeff=line.split()[1] - Solvent=line.split()[2] + MatthewsCoeff = line.split()[1] + Solvent = line.split()[2] break if line.startswith('_______________'): - found=1 - - return [MatthewsCoeff,Solvent] + found = 1 + return [MatthewsCoeff, Solvent] def find_ligands(self): Ligands = [] # need to count residue numbers in case of alternative conformations - ResiNum=[] + ResiNum = [] for line in open(self.pdb): if (line.startswith('ATOM') or line.startswith('HETATM')) \ - and line[17:20].replace(' ','') not in self.AminoAcids+self.Solvents+self.Ions: - if [line[17:20],line[21:22],line[23:26]] not in Ligands: - Ligands.append([line[17:20],line[21:22],line[23:26]]) + and line[17:20].replace(' ', '') not in self.AminoAcids+self.Solvents+self.Ions: + if [line[17:20], line[21:22], line[23:26]] not in Ligands: + Ligands.append([line[17:20], line[21:22], line[23:26]]) return Ligands def save_ligands_to_pdb(self): - Ligands=self.find_ligands() + Ligands = self.find_ligands() if not Ligands == []: - for n,item in enumerate(Ligands): - pdb='' + for n, item in enumerate(Ligands): + pdb = '' for line in open(self.pdb): if line.startswith('CRYST'): - pdb+=line - if (line.startswith('ATOM') or line.startswith('HETATM')) and line[17:20]==item[0] and line[21:22]==item[1] and line[23:26]==item[2]: - pdb=pdb+line - f=open('ligand_{0!s}.pdb'.format(n),'w') + pdb += line + if (line.startswith('ATOM') or line.startswith('HETATM')) and line[17:20] == item[0] and line[21:22] == item[1] and line[23:26] == item[2]: + pdb = pdb+line + f = open('ligand_{0!s}.pdb'.format(n), 'w') f.write(pdb) f.close() return Ligands - def save_ligands_to_pdb_to_directory(self,outDir): - Ligands=self.find_ligands() + def save_ligands_to_pdb_to_directory(self, outDir): + Ligands = self.find_ligands() if not Ligands == []: - for n,item in enumerate(Ligands): - pdb='' + for n, item in enumerate(Ligands): + pdb = '' for line in open(self.pdb): if line.startswith('CRYST'): - pdb+=line - if (line.startswith('ATOM') or line.startswith('HETATM')) and line[17:20]==item[0] and line[21:22]==item[1] and line[23:26]==item[2]: - pdb=pdb+line - f=open(os.path.join(outDir,'ligand_{0!s}.pdb'.format(n)),'w') + pdb += line + if (line.startswith('ATOM') or line.startswith('HETATM')) and line[17:20] == item[0] and line[21:22] == item[1] and line[23:26] == item[2]: + pdb = pdb+line + f = open(os.path.join( + outDir, 'ligand_{0!s}.pdb'.format(n)), 'w') f.write(pdb) f.close() return Ligands - - def save_all_ligands_to_pdb(self,outDir): - Ligands=self.find_ligands() + def save_all_ligands_to_pdb(self, outDir): + Ligands = self.find_ligands() if not Ligands == []: - pdb='' + pdb = '' for line in open(self.pdb): if line.startswith('CRYST'): - pdb+=line - for n,item in enumerate(Ligands): + pdb += line + for n, item in enumerate(Ligands): for line in open(self.pdb): - if (line.startswith('ATOM') or line.startswith('HETATM')) and line[17:20]==item[0] and line[21:22]==item[1] and line[23:26]==item[2]: - pdb+=line - f=open(os.path.join(outDir,'all_ligands.pdb'),'w') + if (line.startswith('ATOM') or line.startswith('HETATM')) and line[17:20] == item[0] and line[21:22] == item[1] and line[23:26] == item[2]: + pdb += line + f = open(os.path.join(outDir, 'all_ligands.pdb'), 'w') f.write(pdb) f.close() - def save_specific_ligands_to_pdb(self,resname,chainID,resseq,altLoc): - pdb='' - outDir=self.pdb[:self.pdb.rfind('/')] + def save_specific_ligands_to_pdb(self, resname, chainID, resseq, altLoc): + pdb = '' + outDir = self.pdb[:self.pdb.rfind('/')] for line in open(self.pdb): if line.startswith('ATOM') or line.startswith('HETATM'): - resname_line=str(line[17:20]).replace(' ','') - chainID_line=str(line[21:23]).replace(' ','') - resseq_line=str(line[23:26]).replace(' ','') - altLoc_line=str(line[16:17]).replace(' ','') - if resname_line==str(resname) and chainID_line==str(chainID) and resseq_line==str(resseq) and altLoc_line==str(altLoc): - pdb=pdb+line + resname_line = str(line[17:20]).replace(' ', '') + chainID_line = str(line[21:23]).replace(' ', '') + resseq_line = str(line[23:26]).replace(' ', '') + altLoc_line = str(line[16:17]).replace(' ', '') + if resname_line == str(resname) and chainID_line == str(chainID) and resseq_line == str(resseq) and altLoc_line == str(altLoc): + pdb = pdb+line if pdb != '': - f=open('{0!s}/ligand_{1!s}_{2!s}_{3!s}_{4!s}.pdb'.format(outDir, str(resname), str(chainID), str(resseq), str(altLoc)),'w') + f = open('{0!s}/ligand_{1!s}_{2!s}_{3!s}_{4!s}.pdb'.format(outDir, + str(resname), str(chainID), str(resseq), str(altLoc)), 'w') f.write(pdb) f.close() @@ -2219,175 +2340,183 @@ def find_xce_ligand_details(self): Ligands = [] for line in open(self.pdb): if line.startswith('ATOM') or line.startswith('HETATM'): - resname=str(line[17:20]).replace(' ','') + resname = str(line[17:20]).replace(' ', '') if resname in self.xce_ligands: - chainID=str(line[21:23]).replace(' ','') - resseq=str(line[23:26]).replace(' ','') - altLoc=str(line[16:17]).replace(' ','') - if [resname,chainID,resseq,altLoc] not in Ligands: - Ligands.append([resname,chainID,resseq,altLoc]) + chainID = str(line[21:23]).replace(' ', '') + resseq = str(line[23:26]).replace(' ', '') + altLoc = str(line[16:17]).replace(' ', '') + if [resname, chainID, resseq, altLoc] not in Ligands: + Ligands.append([resname, chainID, resseq, altLoc]) return Ligands def ligand_details_as_list(self): Ligands = [] for line in open(self.pdb): if line.startswith('ATOM') or line.startswith('HETATM'): - resname=str(line[17:20]).replace(' ','') + resname = str(line[17:20]).replace(' ', '') if resname in self.xce_ligands: - chainID=str(line[21:23]).replace(' ','') - resseq=str(line[23:26]).replace(' ','') - altLoc=str(line[16:17]).replace(' ','') - occupancy=str(line[56:60]).replace(' ','') - if [resname,chainID,resseq,altLoc,occupancy] not in Ligands: - Ligands.append([resname,chainID,resseq,altLoc,occupancy]) + chainID = str(line[21:23]).replace(' ', '') + resseq = str(line[23:26]).replace(' ', '') + altLoc = str(line[16:17]).replace(' ', '') + occupancy = str(line[56:60]).replace(' ', '') + if [resname, chainID, resseq, altLoc, occupancy] not in Ligands: + Ligands.append( + [resname, chainID, resseq, altLoc, occupancy]) return Ligands - def residue_details_as_list(self,pdbin): + def residue_details_as_list(self, pdbin): residueList = [] for line in open(pdbin): if line.startswith('ATOM') or line.startswith('HETATM'): - resname=str(line[17:20]).replace(' ','') - chainID=str(line[21:23]).replace(' ','') - resseq=str(line[23:26]).replace(' ','') - altLoc=str(line[16:17]).replace(' ','') - occupancy=str(line[56:60]).replace(' ','') - if [resname,chainID,resseq,altLoc,occupancy] not in residueList: - residueList.append([resname,chainID,resseq,altLoc,occupancy]) + resname = str(line[17:20]).replace(' ', '') + chainID = str(line[21:23]).replace(' ', '') + resseq = str(line[23:26]).replace(' ', '') + altLoc = str(line[16:17]).replace(' ', '') + occupancy = str(line[56:60]).replace(' ', '') + if [resname, chainID, resseq, altLoc, occupancy] not in residueList: + residueList.append( + [resname, chainID, resseq, altLoc, occupancy]) return residueList - def check_occupancies(self): - errorText='' - warningText='' + errorText = '' + warningText = '' residueDict = {} for line in open(self.pdb): if line.startswith('ATOM') or line.startswith('HETATM'): - atomname=str(line[12:16]).replace(' ','') - resname=str(line[17:20]).replace(' ','') - chainID=str(line[21:22]).replace(' ','') - resseq=str(line[22:26]).replace(' ','') - altLoc=str(line[16:17]).replace(' ','') - occupancy=str(line[56:60]).replace(' ','') + atomname = str(line[12:16]).replace(' ', '') + resname = str(line[17:20]).replace(' ', '') + chainID = str(line[21:22]).replace(' ', '') + resseq = str(line[22:26]).replace(' ', '') + altLoc = str(line[16:17]).replace(' ', '') + occupancy = str(line[56:60]).replace(' ', '') if resname+'-'+chainID+'-'+resseq not in residueDict: residueDict[resname+'-'+chainID+'-'+resseq] = [] if altLoc == '': - altLoc='0' - residueDict[resname+'-'+chainID+'-'+resseq].append([altLoc,occupancy,atomname,resname,chainID,resseq]) + altLoc = '0' + residueDict[resname+'-'+chainID+'-'+resseq].append( + [altLoc, occupancy, atomname, resname, chainID, resseq]) for item in residueDict: - altLocDict={} + altLocDict = {} for atom in residueDict[item]: - altLoc=atom[0] - occupancy=atom[1] - atomname=atom[2] - resname=atom[3] - chainID=atom[4] - resseq=atom[5] + altLoc = atom[0] + occupancy = atom[1] + atomname = atom[2] + resname = atom[3] + chainID = atom[4] + resseq = atom[5] if altLoc not in altLocDict: - altLocDict[altLoc]=[] - altLocDict[altLoc].append([occupancy,atomname,resname,chainID,resseq]) + altLocDict[altLoc] = [] + altLocDict[altLoc].append( + [occupancy, atomname, resname, chainID, resseq]) if float(occupancy) > 1: - errorText+='ERROR: %s %s %s (%s) %s: occupancy is %s\n' %(chainID,resname,resseq,altLoc,atomname,occupancy) - occupancySumList=[] + errorText += 'ERROR: %s %s %s (%s) %s: occupancy is %s\n' % ( + chainID, resname, resseq, altLoc, atomname, occupancy) + occupancySumList = [] for altLoc in altLocDict: - occupancySum=0.0 - nAtom=float(len(altLocDict[altLoc])) - for n,atom in enumerate(altLocDict[altLoc]): - occupancy=atom[0] - occupancySum+=float(occupancy) - atomname=atom[1] - resname=atom[2] - chainID=atom[3] - resseq=atom[4] - if n==0: - occStart=occupancy + occupancySum = 0.0 + nAtom = float(len(altLocDict[altLoc])) + for n, atom in enumerate(altLocDict[altLoc]): + occupancy = atom[0] + occupancySum += float(occupancy) + atomname = atom[1] + resname = atom[2] + chainID = atom[3] + resseq = atom[4] + if n == 0: + occStart = occupancy else: if occupancy != occStart: - warningText+='%s %s %s (%s) %s: occupancy differs for altLoc -> %s\n' %(chainID,resname,resseq,altLoc,atomname,occupancy) + warningText += '%s %s %s (%s) %s: occupancy differs for altLoc -> %s\n' % ( + chainID, resname, resseq, altLoc, atomname, occupancy) occupancySumList.append(occupancySum/nAtom) - occAdd=0.0 + occAdd = 0.0 for entry in occupancySumList: - occAdd+=entry + occAdd += entry if occAdd > 1: - errorText+='ERROR: '+item+' -> summarised occupanies of alternative conformations are > 1.0 ('+str(occupancySumList)+')\n' - - return errorText,warningText - - def get_xyz_coordinated_of_residue(self,chain,number): - X=0.0 - Y=0.0 - Z=0.0 + errorText += 'ERROR: '+item + \ + ' -> summarised occupanies of alternative conformations are > 1.0 ('+str( + occupancySumList)+')\n' + + return errorText, warningText + + def get_xyz_coordinated_of_residue(self, chain, number): + X = 0.0 + Y = 0.0 + Z = 0.0 # pdb definition see: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM for line in open(self.pdb): - if (line.startswith('ATOM') or line.startswith('HETATM')) and line[21:22]==chain and line[22:26].replace(' ','')==str(number): - X=float(line[30:38]) - Y=float(line[38:46]) - Z=float(line[46:54]) + if (line.startswith('ATOM') or line.startswith('HETATM')) and line[21:22] == chain and line[22:26].replace(' ', '') == str(number): + X = float(line[30:38]) + Y = float(line[38:46]) + Z = float(line[46:54]) break - return X,Y,Z - - def get_center_of_gravity_of_residue_ish(self,chain,number): - print '-> chain:',chain - print '-> number:',number - X=0.0 - Y=0.0 - Z=0.0 - x_list=[] - y_list=[] - z_list=[] + return X, Y, Z + + def get_center_of_gravity_of_residue_ish(self, chain, number): + print '-> chain:', chain + print '-> number:', number + X = 0.0 + Y = 0.0 + Z = 0.0 + x_list = [] + y_list = [] + z_list = [] # pdb definition see: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM for line in open(self.pdb): -# print line[21:22],line[22:26] - if (line.startswith('ATOM') or line.startswith('HETATM')) and line[21:22].replace(' ','')==chain.replace(' ','') and line[22:26].replace(' ','')==str(number).replace(' ',''): - X=float(line[30:38]) + # print line[21:22],line[22:26] + if (line.startswith('ATOM') or line.startswith('HETATM')) and line[21:22].replace(' ', '') == chain.replace(' ', '') and line[22:26].replace(' ', '') == str(number).replace(' ', ''): + X = float(line[30:38]) x_list.append(X) - Y=float(line[38:46]) + Y = float(line[38:46]) y_list.append(Y) - Z=float(line[46:54]) + Z = float(line[46:54]) z_list.append(Z) # 'ish' because it's not really the centre of gravity, but the the middle of the min/max of each x,y,z - X=((max(x_list)-min(x_list))/2)+min(x_list) - Y=((max(y_list)-min(y_list))/2)+min(y_list) - Z=((max(z_list)-min(z_list))/2)+min(z_list) - return X,Y,Z + X = ((max(x_list)-min(x_list))/2)+min(x_list) + Y = ((max(y_list)-min(y_list))/2)+min(y_list) + Z = ((max(z_list)-min(z_list))/2)+min(z_list) + return X, Y, Z def get_center_of_gravity_of_molecule_ish(self): - X=0.0 - Y=0.0 - Z=0.0 - x_list=[] - y_list=[] - z_list=[] + X = 0.0 + Y = 0.0 + Z = 0.0 + x_list = [] + y_list = [] + z_list = [] # pdb definition see: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM for line in open(self.pdb): if (line.startswith('ATOM') or line.startswith('HETATM')): - X=float(line[30:38]) + X = float(line[30:38]) x_list.append(X) - Y=float(line[38:46]) + Y = float(line[38:46]) y_list.append(Y) - Z=float(line[46:54]) + Z = float(line[46:54]) z_list.append(Z) # 'ish' because it's not really the centre of gravity, but the the middle of the min/max of each x,y,z - X=((max(x_list)-min(x_list))/2)+min(x_list) - Y=((max(y_list)-min(y_list))/2)+min(y_list) - Z=((max(z_list)-min(z_list))/2)+min(z_list) - return X,Y,Z + X = ((max(x_list)-min(x_list))/2)+min(x_list) + Y = ((max(y_list)-min(y_list))/2)+min(y_list) + Z = ((max(z_list)-min(z_list))/2)+min(z_list) + return X, Y, Z def get_init_pdb_as_list(self): return self.get_pdb_as_list(self.pdb) - def get_pdb_as_list(self,pdbin): - pdb_list=[] + def get_pdb_as_list(self, pdbin): + pdb_list = [] for line in open(pdbin): if line.startswith('ATOM') or line.startswith('HETATM'): - atom_line=str(line[12:16]).replace(' ','') - resname_line=str(line[17:20]).replace(' ','') - chainID_line=str(line[21:23]).replace(' ','') - resseq_line=str(line[23:26]).replace(' ','') - altLoc_line=str(line[16:17]).replace(' ','') - pdb_list.append([atom_line,altLoc_line,resname_line,chainID_line,resseq_line]) + atom_line = str(line[12:16]).replace(' ', '') + resname_line = str(line[17:20]).replace(' ', '') + chainID_line = str(line[21:23]).replace(' ', '') + resseq_line = str(line[23:26]).replace(' ', '') + altLoc_line = str(line[16:17]).replace(' ', '') + pdb_list.append( + [atom_line, altLoc_line, resname_line, chainID_line, resseq_line]) return pdb_list - def ElementDict(self,resname,chainID,resseq,altLoc): + def ElementDict(self, resname, chainID, resseq, altLoc): ElementDict = { 'C': 0, @@ -2398,271 +2527,271 @@ def ElementDict(self,resname,chainID,resseq,altLoc): 'BR': 0, 'CL': 0, 'I': 0, - 'F': 0 } + 'F': 0} for line in open(self.pdb): if line.startswith('ATOM') or line.startswith('HETATM'): - atom_line=str(line[12:16]).replace(' ','') - resname_line=str(line[17:20]).replace(' ','') - chainID_line=str(line[21:23]).replace(' ','') - resseq_line=str(line[23:26]).replace(' ','') - altLoc_line=str(line[16:17]).replace(' ','') - element_line= str(line[66:78]).replace(' ','') - if resname_line==resname and chainID_line==chainID and resseq_line==resseq and altLoc_line==altLoc: + atom_line = str(line[12:16]).replace(' ', '') + resname_line = str(line[17:20]).replace(' ', '') + chainID_line = str(line[21:23]).replace(' ', '') + resseq_line = str(line[23:26]).replace(' ', '') + altLoc_line = str(line[16:17]).replace(' ', '') + element_line = str(line[66:78]).replace(' ', '') + if resname_line == resname and chainID_line == chainID and resseq_line == resseq and altLoc_line == altLoc: if element_line.upper() in ElementDict: ElementDict[element_line.upper()] += 1 return ElementDict - - def update_residue(self,resname_old,chainID_old,resseq_old,altLoc_old,occupancy_old,resname_new,chainID_new,resseq_new,altLoc_new,occupancy_new): - outPDB='' + def update_residue(self, resname_old, chainID_old, resseq_old, altLoc_old, occupancy_old, resname_new, chainID_new, resseq_new, altLoc_new, occupancy_new): + outPDB = '' for line in open(self.pdb): if line.startswith('ATOM') or line.startswith('HETATM'): - atom_line= str(line[0:6]) - serial_line= str(line[6:11]) - atomName_line= str(line[11:16]) - altLoc_line= str(line[16:17]) - resname_line= str(line[17:20]) - chainID_line= str(line[20:23]) - resseq_line= str(line[23:26]) - insert_line= str(line[26:30]) - x_line= str(line[30:38]) - y_line= str(line[38:46]) - z_line= str(line[46:54]) - occupancy_line= str(line[54:60]) - Bfac_line= str(line[60:66]) - element_line= str(line[66:78]) - charge_line= str(line[78:80]) - if resname_line.replace(' ','')==resname_old and chainID_line.replace(' ','')==chainID_old and resseq_line.replace(' ','')==resseq_old and altLoc_line.replace(' ','')==altLoc_old: - - NewResname=resname_line.replace(resname_old,resname_new) - - NewChain = chainID_line.replace(chainID_old,chainID_new) + atom_line = str(line[0:6]) + serial_line = str(line[6:11]) + atomName_line = str(line[11:16]) + altLoc_line = str(line[16:17]) + resname_line = str(line[17:20]) + chainID_line = str(line[20:23]) + resseq_line = str(line[23:26]) + insert_line = str(line[26:30]) + x_line = str(line[30:38]) + y_line = str(line[38:46]) + z_line = str(line[46:54]) + occupancy_line = str(line[54:60]) + Bfac_line = str(line[60:66]) + element_line = str(line[66:78]) + charge_line = str(line[78:80]) + if resname_line.replace(' ', '') == resname_old and chainID_line.replace(' ', '') == chainID_old and resseq_line.replace(' ', '') == resseq_old and altLoc_line.replace(' ', '') == altLoc_old: + + NewResname = resname_line.replace(resname_old, resname_new) + + NewChain = chainID_line.replace(chainID_old, chainID_new) if len(resseq_old) < len(resseq_new): - NewResseq=resseq_line.replace(resseq_old,' '*(len(resseq_old)-len(resseq_new))+resseq_new) + NewResseq = resseq_line.replace( + resseq_old, ' '*(len(resseq_old)-len(resseq_new))+resseq_new) elif len(resseq_old) == len(resseq_new): - NewResseq=resseq_line.replace(resseq_old,resseq_new) + NewResseq = resseq_line.replace(resseq_old, resseq_new) else: - NewResseq=resseq_line[len(resseq_new)-len(resseq_old):].replace(resseq_old,resseq_new) + NewResseq = resseq_line[len( + resseq_new)-len(resseq_old):].replace(resseq_old, resseq_new) if altLoc_line == ' ': - NewAltloc=altLoc_line.replace(' ',altLoc_new) + NewAltloc = altLoc_line.replace(' ', altLoc_new) else: - NewAltloc=altLoc_line.replace(altLoc_old,altLoc_new) + NewAltloc = altLoc_line.replace(altLoc_old, altLoc_new) - NewOccupany=occupancy_line.replace(occupancy_old,occupancy_new) + NewOccupany = occupancy_line.replace( + occupancy_old, occupancy_new) - outPDB+=atom_line+serial_line+atomName_line+NewAltloc+NewResname+NewChain+NewResseq+insert_line+x_line+y_line+z_line+NewOccupany+Bfac_line+element_line+charge_line + outPDB += atom_line+serial_line+atomName_line+NewAltloc+NewResname+NewChain+NewResseq + \ + insert_line+x_line+y_line+z_line+NewOccupany+Bfac_line+element_line+charge_line else: - outPDB+=line + outPDB += line else: - outPDB+=line + outPDB += line - f=open(self.pdb,'w') + f = open(self.pdb, 'w') f.write(outPDB) f.close() - def merge_pdb_file(self,pdbin): - outPDB='' + def merge_pdb_file(self, pdbin): + outPDB = '' # only merge if residue with same resname, chain and resnumber not already in self.pdb!!! - residueListReference= self.residue_details_as_list(self.pdb) - residueListPDBin= self.residue_details_as_list(pdbin) - DuplicateResidue=False + residueListReference = self.residue_details_as_list(self.pdb) + residueListPDBin = self.residue_details_as_list(pdbin) + DuplicateResidue = False for entry in residueListPDBin: if entry in residueListReference: print 'residue already exisits in '+self.pdb+':' print str(entry) - DuplicateResidue=True + DuplicateResidue = True if not DuplicateResidue: for line in open(self.pdb): if not line.startswith('END'): - outPDB+=line + outPDB += line for line in open(pdbin): if not line.startswith('END'): - outPDB+=line + outPDB += line - outPDB+='END\n' + outPDB += 'END\n' - f=open(self.pdb,'w') + f = open(self.pdb, 'w') f.write(outPDB) f.close() else: print 'cannot merge pdb files!' - def get_symmetry_operators(self): symop = [] - spg_number=str(self.get_spg_number_from_pdb()) + spg_number = str(self.get_spg_number_from_pdb()) # print 'spg',spg_number - foundSPG=False - if os.path.isfile(os.path.join(os.getenv('CCP4'),'lib','data','symop.lib')): -# print 'a',os.path.join(os.getenv('CCP4'),'lib','data','symop.lib') - for line in open(os.path.join(os.getenv('CCP4'),'lib','data','symop.lib')): -# print line.split()[0] + foundSPG = False + if os.path.isfile(os.path.join(os.getenv('CCP4'), 'lib', 'data', 'symop.lib')): + # print 'a',os.path.join(os.getenv('CCP4'),'lib','data','symop.lib') + for line in open(os.path.join(os.getenv('CCP4'), 'lib', 'data', 'symop.lib')): + # print line.split()[0] if foundSPG: if line.startswith(' '): - tmp=line.replace('\n','') + tmp = line.replace('\n', '') symop.append(tmp.split(',')) else: break if line.split()[0] == spg_number: - foundSPG=True + foundSPG = True else: print "CCP4 environmental variable is not set" return symop - def save_sym_equivalents(self): - unit_cell=self.get_unit_cell_from_pdb() - spg=self.get_spg_from_pdb() - symop=self.get_symmetry_operators() - outDir=self.pdb[:self.pdb.rfind('/')] - root=self.pdb[self.pdb.rfind('/')+1:self.pdb.rfind('.')] - outPDB=os.path.join(outDir,root+'_sym.pdb') - pdbset = ( '#!'+os.getenv('SHELL')+'\n' - 'pdbset xyzin %s xyzout %s << eof\n' %(self.pdb,outPDB)+ - 'cell {0!s}\n'.format((str(','.join(unit_cell))))+ - 'spacegroup {0!s}\n'.format(spg) ) + unit_cell = self.get_unit_cell_from_pdb() + spg = self.get_spg_from_pdb() + symop = self.get_symmetry_operators() + outDir = self.pdb[:self.pdb.rfind('/')] + root = self.pdb[self.pdb.rfind('/')+1:self.pdb.rfind('.')] + outPDB = os.path.join(outDir, root+'_sym.pdb') + pdbset = ('#!'+os.getenv('SHELL')+'\n' + 'pdbset xyzin %s xyzout %s << eof\n' % (self.pdb, outPDB) + + 'cell {0!s}\n'.format((str(','.join(unit_cell)))) + + 'spacegroup {0!s}\n'.format(spg)) for op in symop: - pdbset+='SYMGEN '+','.join(op)+'\n' - pdbset+='eof\n' + pdbset += 'SYMGEN '+','.join(op)+'\n' + pdbset += 'eof\n' os.system(pdbset) - def save_sym_equivalents_of_ligands_in_pdb(self,pdbIN): - unit_cell=self.get_unit_cell_from_pdb() - spg=self.get_spg_from_pdb() - symop=self.get_symmetry_operators() - outDir=pdbIN[:pdbIN.rfind('/')] - root=pdbIN[pdbIN.rfind('/')+1:pdbIN.rfind('.')] - pdbset = ( '#!'+os.getenv('SHELL')+'\n' - 'pdbset xyzin %s xyzout %s/%s_0.pdb << eof\n' %(pdbIN,outDir,root)+ - 'cell {0!s}\n'.format((str(','.join(unit_cell))))+ - 'spacegroup {0!s}\n'.format(spg) ) + def save_sym_equivalents_of_ligands_in_pdb(self, pdbIN): + unit_cell = self.get_unit_cell_from_pdb() + spg = self.get_spg_from_pdb() + symop = self.get_symmetry_operators() + outDir = pdbIN[:pdbIN.rfind('/')] + root = pdbIN[pdbIN.rfind('/')+1:pdbIN.rfind('.')] + pdbset = ('#!'+os.getenv('SHELL')+'\n' + 'pdbset xyzin %s xyzout %s/%s_0.pdb << eof\n' % (pdbIN, outDir, root) + + 'cell {0!s}\n'.format((str(','.join(unit_cell)))) + + 'spacegroup {0!s}\n'.format(spg)) for op in symop: - pdbset+='SYMGEN '+','.join(op)+'\n' - pdbset+='eof\n' + pdbset += 'SYMGEN '+','.join(op)+'\n' + pdbset += 'eof\n' os.system(pdbset) - return os.path.join(outDir,root+'_0.pdb') + return os.path.join(outDir, root+'_0.pdb') - def save_sym_equivalents_of_ligands_in_pdb_as_one_file_per_ligand(self,pdbIN): - nres=0 + def save_sym_equivalents_of_ligands_in_pdb_as_one_file_per_ligand(self, pdbIN): + nres = 0 for line in open(pdbIN): if line.startswith('ATOM') or line.startswith('HETATM'): - nres+=1 - print 'NRES',nres - unit_cell=self.get_unit_cell_from_pdb() - spg=self.get_spg_from_pdb() - symop=self.get_symmetry_operators() - outDir=pdbIN[:pdbIN.rfind('/')] - root=pdbIN[pdbIN.rfind('/')+1:pdbIN.rfind('.')] - pdbset = ( '#!'+os.getenv('SHELL')+'\n' - 'pdbset xyzin %s xyzout %s/out.pdb << eof 2> /dev/null\n' %(pdbIN,outDir)+ - 'cell {0!s}\n'.format((str(','.join(unit_cell))))+ - 'spacegroup {0!s}\n'.format(spg) ) + nres += 1 + print 'NRES', nres + unit_cell = self.get_unit_cell_from_pdb() + spg = self.get_spg_from_pdb() + symop = self.get_symmetry_operators() + outDir = pdbIN[:pdbIN.rfind('/')] + root = pdbIN[pdbIN.rfind('/')+1:pdbIN.rfind('.')] + pdbset = ('#!'+os.getenv('SHELL')+'\n' + 'pdbset xyzin %s xyzout %s/out.pdb << eof 2> /dev/null\n' % (pdbIN, outDir) + + 'cell {0!s}\n'.format((str(','.join(unit_cell)))) + + 'spacegroup {0!s}\n'.format(spg)) for op in symop: - pdbset+='SYMGEN '+','.join(op)+'\n' - pdbset+='eof\n' + pdbset += 'SYMGEN '+','.join(op)+'\n' + pdbset += 'eof\n' os.system(pdbset) - pdbList=[] - counter=0 - out='' - Cryst='' - n=0 - for line in open(os.path.join(outDir,'out.pdb')): + pdbList = [] + counter = 0 + out = '' + Cryst = '' + n = 0 + for line in open(os.path.join(outDir, 'out.pdb')): if line.startswith('CRYST'): - Cryst=line + Cryst = line if line.startswith('ATOM') or line.startswith('HETATM'): if counter < nres-1: if counter == 0: - out=Cryst - out+=line - counter+=1 + out = Cryst + out += line + counter += 1 else: - out+=line - pdbList.append(os.path.join(outDir,root+'_'+str(n)+'.pdb')) - f=open(os.path.join(outDir,root+'_'+str(n)+'.pdb'),'w') + out += line + pdbList.append(os.path.join( + outDir, root+'_'+str(n)+'.pdb')) + f = open(os.path.join(outDir, root+'_'+str(n)+'.pdb'), 'w') f.write(out) f.close() - out='' - counter=0 - n+=1 + out = '' + counter = 0 + n += 1 return pdbList - def save_surounding_unit_cells(self,pdbIN): + def save_surounding_unit_cells(self, pdbIN): translations = [ - [ 0, 1, 0 ], - [ 0, 1, 1 ], - [ 0, 0, 1 ], - [ 0, -1, 1 ], - [ 0, -1, 0 ], - [ 0, -1, -1 ], - [ 0, 0, -1 ], - [ 0, 1, -1 ], - - [ 1, 0, 0 ], - [ 1, 1, 0 ], - [ 1, 1, 1 ], - [ 1, 0, 1 ], - [ 1, -1, 1 ], - [ 1, -1, 0 ], - [ 1, -1, -1 ], - [ 1, 0, -1 ], - [ 1, 1, -1 ], - - [ -1, 0, 0 ], - [ -1, 1, 0 ], - [ -1, 1, 1 ], - [ -1, 0, 1 ], - [ -1, -1, 1 ], - [ -1, -1, 0 ], - [ -1, -1, -1 ], - [ -1, 0, -1 ], - [ -1, 1, -1 ], - - ] - - unit_cell=self.get_unit_cell_from_pdb() - spg=self.get_spg_from_pdb() - outDir=pdbIN[:pdbIN.rfind('/')] - root=pdbIN[pdbIN.rfind('/')+1:pdbIN.rfind('.')] - - for n,shift in enumerate(translations): - pdbset = ( '#!'+os.getenv('SHELL')+'\n' - 'pdbset xyzin %s/%s.pdb xyzout %s/%s_%s.pdb << eof 2> /dev/null\n' %(outDir,root,outDir,root,str(n+1))+ - 'cell {0!s}\n'.format((str(','.join(unit_cell))))+ - 'spacegroup {0!s}\n'.format(spg)+ - 'shift fractional {0!s}\n'.format(str(shift).replace('[','').replace(']',''))+ - 'eof\n' ) - print 'pdinin',pdbIN - print 'outdir',outDir - print 'root',root + [0, 1, 0], + [0, 1, 1], + [0, 0, 1], + [0, -1, 1], + [0, -1, 0], + [0, -1, -1], + [0, 0, -1], + [0, 1, -1], + + [1, 0, 0], + [1, 1, 0], + [1, 1, 1], + [1, 0, 1], + [1, -1, 1], + [1, -1, 0], + [1, -1, -1], + [1, 0, -1], + [1, 1, -1], + + [-1, 0, 0], + [-1, 1, 0], + [-1, 1, 1], + [-1, 0, 1], + [-1, -1, 1], + [-1, -1, 0], + [-1, -1, -1], + [-1, 0, -1], + [-1, 1, -1], + + ] + + unit_cell = self.get_unit_cell_from_pdb() + spg = self.get_spg_from_pdb() + outDir = pdbIN[:pdbIN.rfind('/')] + root = pdbIN[pdbIN.rfind('/')+1:pdbIN.rfind('.')] + + for n, shift in enumerate(translations): + pdbset = ('#!'+os.getenv('SHELL')+'\n' + 'pdbset xyzin %s/%s.pdb xyzout %s/%s_%s.pdb << eof 2> /dev/null\n' % (outDir, root, outDir, root, str(n+1)) + + 'cell {0!s}\n'.format((str(','.join(unit_cell)))) + + 'spacegroup {0!s}\n'.format(spg) + + 'shift fractional {0!s}\n'.format(str(shift).replace('[', '').replace(']', '')) + + 'eof\n') + print 'pdinin', pdbIN + print 'outdir', outDir + print 'root', root print pdbset os.system(pdbset) - class logtools: - def __init__(self,logfile): - self.logfile=logfile + def __init__(self, logfile): + self.logfile = logfile def phenix_molprobity(self): - QualityIndicators = { 'MolprobityScore': 'n/a', - 'MolprobityScoreColor': 'gray', - 'RamachandranOutliers': 'n/a', - 'RamachandranOutliersColor': 'gray', - 'RamachandranFavored': 'n/a', - 'RamachandranFavoredColor': 'gray' } - + QualityIndicators = {'MolprobityScore': 'n/a', + 'MolprobityScoreColor': 'gray', + 'RamachandranOutliers': 'n/a', + 'RamachandranOutliersColor': 'gray', + 'RamachandranFavored': 'n/a', + 'RamachandranFavoredColor': 'gray'} # Molprobity = validation_summary.txt if os.path.isfile(self.logfile): @@ -2671,102 +2800,114 @@ def phenix_molprobity(self): if len(line.split()) >= 4: QualityIndicators['MolprobityScore'] = line.split()[3] try: - if float(line.split()[3]) < 2: QualityIndicators['MolprobityScoreColor'] = 'green' - if 2 <= float(line.split()[3]) < 3: QualityIndicators['MolprobityScoreColor'] = 'orange' - if float(line.split()[3]) >= 3: QualityIndicators['MolprobityScoreColor'] = 'red' + if float(line.split()[3]) < 2: + QualityIndicators['MolprobityScoreColor'] = 'green' + if 2 <= float(line.split()[3]) < 3: + QualityIndicators['MolprobityScoreColor'] = 'orange' + if float(line.split()[3]) >= 3: + QualityIndicators['MolprobityScoreColor'] = 'red' except ValueError: pass # if line.lower().startswith(' ramachandran outliers ='): if 'ramachandran outliers' in line.lower(): if len(line.split()) >= 4: - QualityIndicators['RamachandranOutliers'] = line.split()[3] + QualityIndicators['RamachandranOutliers'] = line.split()[ + 3] try: - if float(line.split()[3]) < 0.3: QualityIndicators['RamachandranOutliersColor'] = 'green' - if 0.3 <= float(line.split()[3]) < 1: QualityIndicators['RamachandranOutliersColor'] = 'orange' - if float(line.split()[3]) >= 1: QualityIndicators['RamachandranOutliersColor'] = 'red' + if float(line.split()[3]) < 0.3: + QualityIndicators['RamachandranOutliersColor'] = 'green' + if 0.3 <= float(line.split()[3]) < 1: + QualityIndicators['RamachandranOutliersColor'] = 'orange' + if float(line.split()[3]) >= 1: + QualityIndicators['RamachandranOutliersColor'] = 'red' except ValueError: pass # if line.startswith(' favored ='): if 'favored' in line.lower(): if len(line.split()) == 4: - QualityIndicators['RamachandranFavored'] = line.split()[2] + QualityIndicators['RamachandranFavored'] = line.split()[ + 2] try: - if float(line.split()[2]) < 90: QualityIndicators['RamachandranFavoredColor'] = 'red' - if 90 <= float(line.split()[2]) < 98: QualityIndicators['RamachandranFavoredColor'] = 'orange' - if float(line.split()[2]) >= 98: QualityIndicators['RamachandranFavoredColor'] = 'green' + if float(line.split()[2]) < 90: + QualityIndicators['RamachandranFavoredColor'] = 'red' + if 90 <= float(line.split()[2]) < 98: + QualityIndicators['RamachandranFavoredColor'] = 'orange' + if float(line.split()[2]) >= 98: + QualityIndicators['RamachandranFavoredColor'] = 'green' except ValueError: pass return QualityIndicators - def refmac_log(self): - QualityIndicators = { 'MatrixWeight': 'n/a' } + QualityIndicators = {'MatrixWeight': 'n/a'} # Matrix Weight if os.path.isfile(self.logfile): for line in open(self.logfile): - if line.startswith(' Weight matrix') and len(line.split())==3: - QualityIndicators['MatrixWeight']=line.split()[2] + if line.startswith(' Weight matrix') and len(line.split()) == 3: + QualityIndicators['MatrixWeight'] = line.split()[2] return QualityIndicators - class reference: - def __init__(self,sample_mtz,reference_file_list): - self.sample_mtz=sample_mtz - self.reference_file_list=reference_file_list + def __init__(self, sample_mtz, reference_file_list): + self.sample_mtz = sample_mtz + self.reference_file_list = reference_file_list # print reference_file_list - def find_suitable_reference(self,allowed_unitcell_difference_percent): - found_suitable_reference=False - unitcell_reference='n/a' - reference='' - spg_reference='n/a' - unitcell_difference='n/a' - resolution_high='n/a' - spg_autoproc='n/a' - unitcell_autoproc='n/a' + def find_suitable_reference(self, allowed_unitcell_difference_percent): + found_suitable_reference = False + unitcell_reference = 'n/a' + reference = '' + spg_reference = 'n/a' + unitcell_difference = 'n/a' + resolution_high = 'n/a' + spg_autoproc = 'n/a' + unitcell_autoproc = 'n/a' if os.path.isfile(self.sample_mtz): - mtz_autoproc=mtztools(self.sample_mtz).get_all_values_as_dict() - resolution_high=mtz_autoproc['resolution_high'] - spg_autoproc=mtz_autoproc['spacegroup'] - unitcell_autoproc=mtz_autoproc['unitcell'] - lattice_autoproc=mtz_autoproc['bravais_lattice'] - unitcell_volume_autoproc=mtz_autoproc['unitcell_volume'] + mtz_autoproc = mtztools(self.sample_mtz).get_all_values_as_dict() + resolution_high = mtz_autoproc['resolution_high'] + spg_autoproc = mtz_autoproc['spacegroup'] + unitcell_autoproc = mtz_autoproc['unitcell'] + lattice_autoproc = mtz_autoproc['bravais_lattice'] + unitcell_volume_autoproc = mtz_autoproc['unitcell_volume'] # check which reference file is most similar - for o,reference_file in enumerate(self.reference_file_list): -# print reference_file + for o, reference_file in enumerate(self.reference_file_list): + # print reference_file try: - if not reference_file[4]==0: - unitcell_difference=round((math.fabs(reference_file[4]-unitcell_volume_autoproc)/reference_file[4])*100,1) + if not reference_file[4] == 0: + unitcell_difference = round( + (math.fabs(reference_file[4]-unitcell_volume_autoproc)/reference_file[4])*100, 1) # reference file is accepted when different in unitcell volume < 5% # and both files have the same lattice type - if unitcell_difference < allowed_unitcell_difference_percent and lattice_autoproc==reference_file[3]: - spg_reference=reference_file[1] - unitcell_reference=reference_file[2] - reference=reference_file[0] - found_suitable_reference=True + if unitcell_difference < allowed_unitcell_difference_percent and lattice_autoproc == reference_file[3]: + spg_reference = reference_file[1] + unitcell_reference = reference_file[2] + reference = reference_file[0] + found_suitable_reference = True break except IndexError: pass - return (spg_reference,unitcell_reference,reference,found_suitable_reference, - resolution_high,spg_autoproc,unitcell_autoproc,unitcell_difference) + return (spg_reference, unitcell_reference, reference, found_suitable_reference, + resolution_high, spg_autoproc, unitcell_autoproc, unitcell_difference) class misc: - def calculate_distance_between_coordinates(self,x1,y1,z1,x2,y2,z2): -# print '==> XCE: calculating distance between two coordinates' - distance=0.0 - distance=math.sqrt(math.pow(float(x1)-float(x2),2)+math.pow(float(y1)-float(y2),2)+math.pow(float(z1)-float(z2),2)) + def calculate_distance_between_coordinates(self, x1, y1, z1, x2, y2, z2): + # print '==> XCE: calculating distance between two coordinates' + distance = 0.0 + distance = math.sqrt(math.pow(float( + x1)-float(x2), 2)+math.pow(float(y1)-float(y2), 2)+math.pow(float(z1)-float(z2), 2)) return distance + class smilestools(object): - def __init__(self,smiles): - self.smiles=smiles + def __init__(self, smiles): + self.smiles = smiles def ElementDict(self): ElementDict = { @@ -2778,7 +2919,7 @@ def ElementDict(self): 'BR': 0, 'CL': 0, 'I': 0, - 'F': 0 } + 'F': 0} m = Chem.MolFromSmiles(self.smiles) for atom in m.GetAtoms(): @@ -2787,18 +2928,19 @@ def ElementDict(self): return ElementDict + class maptools(object): - def calculate_map(self,mtz,F,PH): + def calculate_map(self, mtz, F, PH): cmd = ( - 'fft hklin %s mapout %s << EOF\n' %(mtz,mtz.replace('.mtz','.ccp4')) + - 'labin F1=%s PHI=%s\n' %(F,PH) + + 'fft hklin %s mapout %s << EOF\n' % (mtz, mtz.replace('.mtz', '.ccp4')) + + 'labin F1=%s PHI=%s\n' % (F, PH) + 'EOF\n' ) os.system(cmd) # print(cmd) - def cut_map_around_ligand(self,map,ligPDB,border): + def cut_map_around_ligand(self, map, ligPDB, border): if map.endswith('.map'): map_extension = '.map' elif map.endswith('.ccp4'): @@ -2807,11 +2949,11 @@ def cut_map_around_ligand(self,map,ligPDB,border): map_extension = '' cmd = ( - 'mapmask mapin %s mapout %s xyzin %s << eof\n' %(map,map.replace(map_extension,'_mapmask'+map_extension),ligPDB) + - ' border %s\n' %border + + 'mapmask mapin %s mapout %s xyzin %s << eof\n' % (map, map.replace(map_extension, '_mapmask'+map_extension), ligPDB) + + ' border %s\n' % border + ' end\n' 'eof' - ) + ) os.system(cmd) # print(cmd) @@ -2870,7 +3012,7 @@ def cut_map_around_ligand(self,map,ligPDB,border): class mtztools_gemmi: - def __init__(self,mtz): + def __init__(self, mtz): self.mtz = gemmi.read_mtz_file(mtz) def get_map_labels(self): @@ -2908,25 +3050,28 @@ def get_high_low_resolution_limits(self): class maptools_gemmi: - def __init__(self,emap): + def __init__(self, emap): self.emap = emap - self.emtz = emap.replace('.ccp4','.mtz').replace('.map','.mtz') + self.emtz = emap.replace('.ccp4', '.mtz').replace('.map', '.mtz') - def map_to_sf(self,resolution): + def map_to_sf(self, resolution): if os.path.isfile(self.emtz): print('mtz file of event map exists; skipping...') return - cmd = 'gemmi map2sf %s %s FWT PHWT --dmin=%s' %(self.emap,self.emtz,resolution) + cmd = 'gemmi map2sf %s %s FWT PHWT --dmin=%s' % ( + self.emap, self.emtz, resolution) print('converting map with command:\n' + cmd) os.system(cmd) if os.path.isfile(self.emtz): print('event map to SF conversion successful') mtz = gemmi.read_mtz_file(self.emtz) - mtz.history += ['date created: ' + time.ctime(os.path.getmtime(self.emap))] + mtz.history += ['date created: ' + + time.ctime(os.path.getmtime(self.emap))] mtz.history += ['folder: ' + os.getcwd()] mtz.history += ['file name: ' + self.emap] if 'BDC' in self.emap: - mtz.history += ['BDC value: ' + self.emap[self.emap.find('BDC')+4:self.emap.find('BDC')+4+self.emap[self.emap.find('BDC')+4:].find('_')]] + mtz.history += ['BDC value: ' + self.emap[self.emap.find('BDC')+4:self.emap.find( + 'BDC')+4+self.emap[self.emap.find('BDC')+4:].find('_')]] # mtz.write_to_file(self.emtz) else: print('failed to convert event map to SF') @@ -2934,28 +3079,30 @@ def map_to_sf(self,resolution): class pdbtools_gemmi: - def __init__(self,pdb): + def __init__(self, pdb): self.pdb = gemmi.read_structure(pdb) - def get_ligand_models_as_dict(self,ligandID): + def get_ligand_models_as_dict(self, ligandID): ligandDict = {} for model in self.pdb: for chain in model: for residue in chain: if residue.name == ligandID: if str(residue.name + '-' + chain.name + '-' + str(residue.seqid.num)) not in ligandDict: - ligandDict[str(residue.name + '-' + chain.name + '-' + str(residue.seqid.num))] = None + ligandDict[str( + residue.name + '-' + chain.name + '-' + str(residue.seqid.num))] = None m = gemmi.Model('1') m.add_chain(gemmi.Chain('X')) c = m['X'].get_polymer() c.add_residue(gemmi.Residue(), 0) c[0].name = residue.name - for n,atom in enumerate(residue): + for n, atom in enumerate(residue): c[0].add_atom(atom, n) - ligandDict[str(residue.name + '-' + chain.name + '-' + str(residue.seqid.num))] = m + ligandDict[str( + residue.name + '-' + chain.name + '-' + str(residue.seqid.num))] = m return ligandDict - def center_of_mass_ligand_dict(self,ligandID): + def center_of_mass_ligand_dict(self, ligandID): ligandDict = self.get_ligand_models_as_dict(ligandID) ligandPositionDict = {} for ligand in ligandDict: @@ -2963,10 +3110,9 @@ def center_of_mass_ligand_dict(self,ligandID): ligandPositionDict[ligand] = [pos.x, pos.y, pos.z] return ligandPositionDict - def save_ligands_to_pdb(self,ligandID): + def save_ligands_to_pdb(self, ligandID): ligandDict = self.get_ligand_models_as_dict(ligandID) for ligand in ligandDict: s = gemmi.Structure() s.add_model(ligandDict[ligand]) s.write_pdb(ligand + '.pdb') - diff --git a/lib/coot_utils_XChem.py b/lib/coot_utils_XChem.py index 71ef6a78..0475c257 100755 --- a/lib/coot_utils_XChem.py +++ b/lib/coot_utils_XChem.py @@ -1,4 +1,4 @@ -# coot-utils.py +# coot-utils.py # adapted from coot-utils.scm # # Copyright 2004, 2005, 2006, 2007 by Bernhard Lohkamp @@ -21,11 +21,13 @@ # You should have received a copy of the GNU General Public License # along with this program. If not, see . +import os +import string +import re +import coot import sys sys.path.append('/usr/local/coot/current/lib/python2.7/site-packages') -import coot -import re, string, os # 3D annotations - a bit of a hack currently global annotations @@ -47,7 +49,6 @@ user_defined_alert_smarts = [] - # not sure if the implementation of the macros will work # 'Macro' to tidy up a a setup of functions to be run with no backup @@ -73,11 +74,11 @@ def with_no_backups(imol, *funcs): # 'Macro' to tidy up a set of functions to be run with automatic # accepting of the refinement # returns the result of last function run... -# +# # funcs is a normal set of functions (not a thunk), here i.e. a list of # functions with function as a list with func name and args, # e.g.: [centre_of_mass, 0], [func_name, arg1, arg2,...],... -# +# def with_auto_accept(*funcs): replace_state = refinement_immediate_replacement_state() @@ -101,6 +102,8 @@ def with_auto_accept(*funcs): # [[func1, extra_arg1, ..., "aa_imol", "aa_chain_id",..., extra_arg2, extra arg3, ..], [func2,...]] # returns what? The value from the last function evaluated # + + def using_active_atom(*funcs): from types import ListType @@ -163,12 +166,14 @@ def arg_to_append(item): # refine_zone(imol, "A", 43, 45, "") # accept_regularizement() # + + class NoBackups: """'Macro' to tidy up a a setup of functions to be run with no backup for a particular molecule. use with 'with', e.g.: - + > with WithNoBackups(imol=0): refine_zone(imol, "A", 43, 45, "") accept_regularizement() @@ -176,28 +181,32 @@ class NoBackups: def __init__(self, imol): self.imol = imol + def __enter__(self): self.b_state = backup_state(self.imol) turn_off_backup(self.imol) + def __exit__(self, type, value, traceback): if (self.b_state == 1): turn_on_backup(self.imol) # Pythonic 'Macro' to tidy up a set of functions to be run with automatic # accepting of the refinement. -# +# # use with 'with', e.g.: -# +# # >with AutoAccept(): # refine_zone(0, "A", 43, 45, "") # + + class AutoAccept: """ Pythonic 'Macro' to tidy up a set of functions to be run with automatic accepting of the refinement. - + use with 'with', e.g.: - + > with AutoAccept(): refine_zone(0, "A", 43, 45, "") @@ -206,9 +215,11 @@ class AutoAccept: def __init__(self): self.replace_state = -1 pass + def __enter__(self): self.replace_state = refinement_immediate_replacement_state() set_refinement_immediate_replacement(1) + def __exit__(self, type, value, traceback): accept_regularizement() if (self.replace_state == 0): @@ -220,7 +231,7 @@ class UsingActiveAtom: Run functions on the active atom. use with 'with', e.g.: - + > with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: refine_zone(aa_imol, aa_chain_id, aa_res_no-2, aa_res_no+2, aa_ins_code) """ @@ -228,6 +239,7 @@ class UsingActiveAtom: def __init__(self): self.no_residue = False pass + def __enter__(self): self.active_atom = active_residue() if (not self.active_atom): @@ -235,13 +247,14 @@ def __enter__(self): self.no_residue = True #self.__exit__(None, "dummy", None) else: - imol = self.active_atom[0] - chain_id = self.active_atom[1] - res_no = self.active_atom[2] - ins_code = self.active_atom[3] + imol = self.active_atom[0] + chain_id = self.active_atom[1] + res_no = self.active_atom[2] + ins_code = self.active_atom[3] atom_name = self.active_atom[4] - alt_conf = self.active_atom[5] + alt_conf = self.active_atom[5] return [imol, chain_id, res_no, ins_code, atom_name, alt_conf] + def __exit__(self, type, value, traceback): if (self.no_residue): # internal calling of exit, ignore errors @@ -254,11 +267,12 @@ def __exit__(self, type, value, traceback): def molecule_has_hydrogens(imol): return (molecule_has_hydrogens_raw(imol) == 1) + def add_hydrogens_using_refmac(imol): out_file_name = os.path.join("coot-refmac", - molecule_name_stub(imol, 0) + '-needs-H.pdb') + molecule_name_stub(imol, 0) + '-needs-H.pdb') in_file_name = os.path.join("coot-refmac", - molecule_name_stub(imol, 0) + '-with-H.pdb') + molecule_name_stub(imol, 0) + '-with-H.pdb') make_directory_maybe('coot-refmac') write_pdb_file(imol, out_file_name) return add_hydrogens_using_refmac_inner(imol, in_file_name, out_file_name) @@ -266,9 +280,9 @@ def add_hydrogens_using_refmac(imol): def add_hydrogens_to_chain_using_refmac(imol, chain_id): out_file_name = os.path.join("coot-refmac", - molecule_name_stub(imol, 0) + '-chain-' + chain_id + '-needs-H.pdb') + molecule_name_stub(imol, 0) + '-chain-' + chain_id + '-needs-H.pdb') in_file_name = os.path.join("coot-refmac", - molecule_name_stub(imol, 0) + '-chain-' + chain_id + '-with-H.pdb') + molecule_name_stub(imol, 0) + '-chain-' + chain_id + '-with-H.pdb') make_directory_maybe('coot-refmac') write_chain_to_pdb_file(imol, chain_id, out_file_name) return add_hydrogens_using_refmac_inner(imol, in_file_name, out_file_name) @@ -277,16 +291,15 @@ def add_hydrogens_to_chain_using_refmac(imol, chain_id): def add_hydrogens_using_refmac_inner(imol, in_file_name, out_file_name): status = popen_command("refmac5", - ['XYZIN', out_file_name, 'XYZOUT', in_file_name], - ['MAKE HOUT YES'], - 'refmac-H-addition.log', 0) + ['XYZIN', out_file_name, 'XYZOUT', in_file_name], + ['MAKE HOUT YES'], + 'refmac-H-addition.log', 0) try: - if (status == 0): - # all good - return add_hydrogens_from_file(imol, in_file_name) + if (status == 0): + # all good + return add_hydrogens_from_file(imol, in_file_name) except: - return False - + return False # set this to a function accepting two argument (the molecule number @@ -308,6 +321,8 @@ def add_hydrogens_using_refmac_inner(imol, in_file_name, out_file_name): # return a boolean # + + def pre_release_qm(): return "-pre" in coot_version() @@ -320,10 +335,11 @@ def molecule_number_list(): ret = [] for mol_no in range(coot.graphics_n_molecules()): if (valid_map_molecule_qm(mol_no) or - valid_model_molecule_qm(mol_no)): + valid_model_molecule_qm(mol_no)): ret.append(mol_no) return ret + def model_molecule_number_list(): return filter(valid_model_molecule_qm, molecule_number_list()) @@ -333,6 +349,8 @@ def model_molecule_number_list(): # # Return True or False. # + + def directory_is_modifiable_qm(prefix_dir): from types import StringType ret = False @@ -363,9 +381,12 @@ def directory_is_modifiable_qm(prefix_dir): # # return False on no-such-file # + + def most_recently_created_file(glob_str, dir): - import glob, time + import glob + import time patt = os.path.join(dir, glob_str) files = glob.glob(patt) @@ -390,18 +411,21 @@ def residue_spec2atom_selection_string(centre_residue_spec): "/" + str(centre_residue_spec[1]) return ret + def residue_atom2atom_name(ra): if not isinstance(ra, list): return False else: return ra[0][0] + def residue_atom2alt_conf(ra): if not isinstance(ra, list): return False else: return ra[0][1] + def residue_spec2chain_id(rs): if not isinstance(rs, list): return False @@ -414,6 +438,7 @@ def residue_spec2chain_id(rs): else: return False + def residue_spec2res_no(rs): if not isinstance(rs, list): return False @@ -425,6 +450,7 @@ def residue_spec2res_no(rs): return rs[2] return False + def residue_spec2ins_code(rs): if not isinstance(rs, list): return False @@ -436,6 +462,7 @@ def residue_spec2ins_code(rs): return rs[3] return False + def atom_spec2imol(atom_spec): import types if not (isinstance(atom_spec, types.ListType)): @@ -447,6 +474,7 @@ def atom_spec2imol(atom_spec): return atom_spec[1] return False + def residue_spec2residue_name(imol, spec): return residue_name(imol, spec[1], @@ -454,27 +482,33 @@ def residue_spec2residue_name(imol, spec): spec[3]) # Return a list of molecules that are maps -# +# + + def map_molecule_list(): map_list = [] for i in range(graphics_n_molecules()): - if is_valid_map_molecule(i): - map_list.append(i) + if is_valid_map_molecule(i): + map_list.append(i) return map_list # Return a list of molecules that are (coordinate) models -# +# + + def model_molecule_list(): model_list = [] for i in range(graphics_n_molecules()): - if is_valid_model_molecule(i): - model_list.append(i) + if is_valid_model_molecule(i): + model_list.append(i) return model_list # Return True(False) if @var{imol} is (isn't) a shelx molecule. # + + def shelx_molecule_qm(imol): if (is_shelx_molecule(imol) == 1): return True @@ -485,63 +519,77 @@ def shelx_molecule_qm(imol): # # trackball @var{type} is a string: either 'flat' or 'spherical-surface' # + + def set_virtual_trackball_type(type): if (type == "flat"): vt_surface(1) elif (type == "spherical-surface"): vt_surface(0) else: - print "virtual trackball type",type,"not understood" + print "virtual trackball type", type, "not understood" # Is ls a list of strings? Return True or False # + + def list_of_strings_qm(ls): import types - not_str =0 + not_str = 0 if type(ls) is not ListType: - return False + return False else: - for item in ls: - if isinstance(item,types.StringTypes): pass - else: not_str += 1 - if not_str == 0: - return True - else: - return False + for item in ls: + if isinstance(item, types.StringTypes): + pass + else: + not_str += 1 + if not_str == 0: + return True + else: + return False # string concat with spaces, @var{ls} must be a list of strings. # + + def string_append_with_spaces(ls): import string if ls: - return string.join(ls) + return string.join(ls) else: - return [""] + return [""] # The screen centre. # # return the rotation centre as a 3 membered list of numbers # is python list [...] !!! # + + def rotation_centre(): - return [coot.rotation_centre_position(0), - coot.rotation_centre_position(1), - coot.rotation_centre_position(2)] + return [coot.rotation_centre_position(0), + coot.rotation_centre_position(1), + coot.rotation_centre_position(2)] # this is actually not essentail since python has these funtion(s) -def number_list(a,b): + + +def number_list(a, b): result = [] if a == b: - result.append(a) - return result - elif a > b : return result - else : - while a <=b : - result.append(a) - a = a + 1 + result.append(a) + return result + elif a > b: + return result + else: + while a <= b: + result.append(a) + a = a + 1 return result + def file_n_lines(file_name): if not os.path.isfile(file_name): return False @@ -552,6 +600,8 @@ def file_n_lines(file_name): return n_lines # backport, so that we can replace once move to Python 2.7 is done + + def check_output(*popenargs, **kwargs): r"""Run command with arguments and return its output as a byte string. @@ -576,6 +626,8 @@ def check_output(*popenargs, **kwargs): # returns false of there is a problem running cmd # + + def shell_command_to_string(cmd): import subprocess @@ -599,6 +651,8 @@ def shell_command_to_string(cmd): # adapted from find_exe # this finds absolute file names too # + + def command_in_path_qm(cmd, only_extension_here=None, add_extensions_here=None): @@ -615,13 +669,13 @@ def command_in_path_qm(cmd, only_extension_here=None, return False - def command_in_path_qm_old_version(cmd, only_extension="", add_extensions=None): # test for command (see goosh-command-with-file-input description) - # + # if add_extensions is None: add_extensions = [] - import os, string + import os + import string # we shall check for full path names first if (os.path.isfile(cmd)): @@ -669,16 +723,20 @@ def command_in_path_qm_old_version(cmd, only_extension="", add_extensions=None): # Where cmd is e.g. "refmac" # args is ["HKLIN","thing.mtz"] # data_list is ["HEAD","END"] -# log_file_name is "refmac.log" +# log_file_name is "refmac.log" # screen_flag True/False to display or not in shell window -# +# # Return the exist status e.g. 0 or 1. Or False if cmd not found. # # uses os.popen if python version < 2.4 otherwise subprocess -# +# + + def popen_command(cmd, args, data_list, log_file, screen_flag=False): - import sys, string, os + import sys + import string + import os major, minor, micro, releaselevel, serial = sys.version_info @@ -692,15 +750,17 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): if (cmd_execfile): # minor = 2 - if (major >= 2 and minor >=4): + if (major >= 2 and minor >= 4): # subprocess import subprocess log = open(log_file, 'w') cmd_args = [cmd_execfile] + args if (screen_flag): - process = subprocess.Popen(cmd_args, stdin=subprocess.PIPE, stdout=subprocess.PIPE) + process = subprocess.Popen( + cmd_args, stdin=subprocess.PIPE, stdout=subprocess.PIPE) else: - process = subprocess.Popen(cmd_args, stdin=subprocess.PIPE, stdout=log) + process = subprocess.Popen( + cmd_args, stdin=subprocess.PIPE, stdout=log) for data in data_list: process.stdin.write(data + "\n") @@ -722,13 +782,14 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): args_string = string.join(args) # write tmp input file - input = file (data_list_file,'w') + input = file(data_list_file, 'w') for data in data_list: input.write(data + '\n') input.close() # print "BL DEBUG:: popen command is", cmd_execfile + " " + args_string + " < " + data_list_file + " > " + log_file - status = os.popen(cmd_execfile + " " + args_string + " < " + data_list_file + " > " + log_file, 'r') + status = os.popen(cmd_execfile + " " + args_string + + " < " + data_list_file + " > " + log_file, 'r') cmd_finished = status.close() if (cmd_finished is not None): print "running command ", cmd, " failed!" @@ -748,6 +809,8 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): # Crude test to see of 2 floats are the same (more or less). # Used in a unit test after setting the atom position. # + + def close_float_qm(x1, x2): return (abs(x1 - x2) < 0.001) @@ -755,45 +818,56 @@ def close_float_qm(x1, x2): # "a.b.res" -> "a.b" # file_name_sans_extension # + + def strip_extension(s): import os head, tail = os.path.splitext(s) return head # What is the extension of file_name? -# +# # "a.pdb" -> "pdb" # "" -> "" # + + def file_name_extension(file_name): - import os, string + import os + import string root, ext = os.path.splitext(file_name) if ext: - ext = string.lstrip(ext,'.') - return ext + ext = string.lstrip(ext, '.') + return ext else: - return "" + return "" # e.g. "a.pdb" -> "a-tmp.pdb" # + + def add_tmp_extension_to(file_name): import types - if isinstance(file_name,types.StringTypes): - root, ext = os.path.splitext(file_name) - f = root + "-tmp" + ext - return f + if isinstance(file_name, types.StringTypes): + root, ext = os.path.splitext(file_name) + f = root + "-tmp" + ext + return f else: - return "tmp" + return "tmp" # Same function as strip_extension, different name, as per scsh, in fact. -# +# + + def file_name_sans_extension(s): return strip_extension(s) # /a/b.t -> b.t d/e.ext -> e.ext # file-name-sans-path + + def strip_path(s): import os head, tail = os.path.split(s) @@ -803,24 +877,29 @@ def strip_path(s): # return True or False # # for windows return True when drive letter, e.g. C, or even \\ (backslash): + + def slash_start_qm(s): import types import string if isinstance(s, types.StringTypes): - if len(s) > 0: - if (s.startswith("/") or s.startswith("\\")): - return True - else: - if (os.name == 'nt' and len(s) > 1): - # for windows check if the start is a drive letter - drive_letter_ls = [dl + ':' for dl in string.ascii_uppercase] - if (s[0:2] in drive_letter_ls): - return True + if len(s) > 0: + if (s.startswith("/") or s.startswith("\\")): + return True + else: + if (os.name == 'nt' and len(s) > 1): + # for windows check if the start is a drive letter + drive_letter_ls = [ + dl + ':' for dl in string.ascii_uppercase] + if (s[0:2] in drive_letter_ls): + return True return False # return a string that contains the date/time # e.g. "2006-01-02_2216.03" # + + def unique_date_time_str(): import time lt = time.strftime("%Y-%m-%d_%H%M", time.localtime()) @@ -829,13 +908,15 @@ def unique_date_time_str(): # return a list that has only every-nth members; # e.g. @code{every_nth ([0,1,2,3,4,5,6,7,8],2)} -> [0,2,4,6,8] # @code{every_nth ([0,1,2,3,4,5,6,7,8],3)} -> [0,3,6] -# +# # @var{n} must be positive # + + def every_nth(ls, n): - elements = range(0,len(ls),n) - a =[] + elements = range(0, len(ls), n) + a = [] for i in elements: a.append(ls[i]) return a @@ -844,20 +925,21 @@ def every_nth(ls, n): # # residue_atoms must be a list # -def get_atom_from_residue(atom_name, residue_atoms, alt_conf): + +def get_atom_from_residue(atom_name, residue_atoms, alt_conf): """Get atom_info fomr a residue. residue_atoms must be a list """ if ((isinstance(residue_atoms, list)) and - (residue_atoms != [])): + (residue_atoms != [])): for residue_atom in residue_atoms: if (residue_atom[0][0] == atom_name and - residue_atom[0][1] == alt_conf): + residue_atom[0][1] == alt_conf): return residue_atom # print "BL WARNING:: no atom name %s found in residue" %atom_name - return False # no residue name found fail save + return False # no residue name found fail save # return atom info or False (if atom not found). @@ -873,6 +955,8 @@ def get_atom(imol, chain_id, resno, ins_code, atom_name, alt_conf_internal=""): return ret # + + def residue_info_dialog_displayed_qm(): if (residue_info_dialog_is_displayed == 1): return True @@ -885,8 +969,11 @@ def residue_info_dialog_displayed_qm(): # @code{multi_read_pdb("a*.pdb",".")} # BL says: in windows dir needs the 'C:/' pattern, '/c/'won't work # + + def multi_read_pdb(glob_pattern, dir): - import glob, os + import glob + import os patt = os.path.normpath(dir+'/*.'+glob_pattern) all_files = glob.glob(patt) for file in all_files: @@ -895,8 +982,11 @@ def multi_read_pdb(glob_pattern, dir): # read_pdb_all reads all the "*.pdb" files in the current directory. # + + def read_pdb_all(): - import glob, os + import glob + import os recentre_status = recentre_on_read_pdb() set_recentre_on_read_pdb(0) patt = os.path.normpath(os.path.abspath(".")+'/*.pdb') @@ -907,48 +997,60 @@ def read_pdb_all(): set_recentre_on_read_pdb(recentre_status) # return False if dir_name is a file or we can't do the mkdir + + def coot_mkdir(dir_name): - import os - if (os.path.isfile(dir_name)): - return False - else: - if (os.path.isdir(dir_name)): - return True - else: - os.mkdir(dir_name) - return True + import os + if (os.path.isfile(dir_name)): + return False + else: + if (os.path.isdir(dir_name)): + return True + else: + os.mkdir(dir_name) + return True # return the view matrix (useful for molscript, perhaps). # BL says: like all matrices is a python list [...] # + + def view_matrix(): - return [get_view_matrix_element(row_number,column_number) for row_number in range(3) for column_number in range(3)] + return [get_view_matrix_element(row_number, column_number) for row_number in range(3) for column_number in range(3)] # return the transposed view matrix (useful for molscript, perhaps). # BL says: like all matrices is a python list [...] # + + def view_matrix_transp(): - return [get_view_matrix_element(column_number,row_number) for row_number in range(3) for column_number in range(3)] + return [get_view_matrix_element(column_number, row_number) for row_number in range(3) for column_number in range(3)] # return the view quaternion # + + def view_quaternion(): - ret = map(get_view_quaternion_internal,[0,1,2,3]) - return ret + ret = map(get_view_quaternion_internal, [0, 1, 2, 3]) + return ret # Return the view number # + + def add_view(position, quaternion, zoom, view_name): - args = position + quaternion - args.append(zoom) - args.append(view_name) - ret = add_view_raw(*args) - return ret + args = position + quaternion + args.append(zoom) + args.append(view_name) + ret = add_view_raw(*args) + return ret # Convert a view matrix to a view quaternion to set Coot view internals. # + + def matrix2quaternion(m00, m10, m20, m01, m11, m21, m02, m12, m22): import math @@ -992,13 +1094,15 @@ def convert_sign(x, y): # matrix2quaternion(0.0347695872187614, 0.773433089256287, 0.632923781871796, # 0.774806916713715, 0.379149734973907, -0.505885183811188, # -0.631241261959076, 0.507983148097992, -0.586078405380249) -# -> +# -> # [-0.55715757608, -0.694704711, -7.549694273e-4, 0.45492890477] or similar -# Set the view matrix using matrix->quaternion. +# Set the view matrix using matrix->quaternion. # # Useful for using a view matrix from another program, perhaps. # + + def set_view_matrix(m00, m10, m20, m01, m11, m21, m02, m12, m22): set_view_quaternion(matrix2quaternion(m00, m10, m20, @@ -1007,6 +1111,8 @@ def set_view_matrix(m00, m10, m20, m01, m11, m21, m02, m12, m22): # Miguel's molecular orientation axes # + + def miguels_axes(): set_axis_orientation_matrix(*view_matrix()) set_axis_orientation_matrix_usage(1) @@ -1015,90 +1121,103 @@ def miguels_axes(): # # Note: mol_cen could contain values less than -9999. # + + def molecule_centre(imol): - return [coot.molecule_centre_internal(imol,0), - coot.molecule_centre_internal(imol,1), - coot.molecule_centre_internal(imol,2)] + return [coot.molecule_centre_internal(imol, 0), + coot.molecule_centre_internal(imol, 1), + coot.molecule_centre_internal(imol, 2)] # Move the centre of molecule number imol to the current screen centre # + + def move_molecule_to_screen_centre(imol): - if valid_model_molecule_qm(imol): - rotate_centre = rotation_centre() - coot.translate_molecule_by(imol,(rotate_centre[0]-molecule_centre(imol)[0]), - (rotate_centre[1]-molecule_centre(imol)[1]), - (rotate_centre[2]-molecule_centre(imol)[2])) + if valid_model_molecule_qm(imol): + rotate_centre = rotation_centre() + coot.translate_molecule_by(imol, (rotate_centre[0]-molecule_centre(imol)[0]), + (rotate_centre[1]-molecule_centre(imol)[1]), + (rotate_centre[2]-molecule_centre(imol)[2])) + + # This is a short name for the above. # deftexi move_molecule_here move_molecule_here = move_molecule_to_screen_centre # Return a nine-membered list of numbers. # + + def identity_matrix(): - return [1,0,0,0,1,0,0,0,1] + return [1, 0, 0, 0, 1, 0, 0, 0, 1] # e.g. translation('x',2) # -> [2, 0, 0] # Return: False on error # -def translation(axis,length): + + +def translation(axis, length): import operator # BL says: we dont check if axis is string, yet at least not directly if (operator.isNumberType(length)): - if (axis=="x"): - return [length,0,0] - elif (axis=="y"): - return [0,length,0] - elif (axis=="z"): - return [0,0,length] - else: - print "symbol axis: ", axis, " incomprehensible" - return False - else: - print "incomprehensible length argument: ",length - return False + if (axis == "x"): + return [length, 0, 0] + elif (axis == "y"): + return [0, length, 0] + elif (axis == "z"): + return [0, 0, length] + else: + print "symbol axis: ", axis, " incomprehensible" + return False + else: + print "incomprehensible length argument: ", length + return False # Rotate degrees about screen axis, where axis is either 'x', 'y' or 'z'. -# -def rotate_about_screen_axis(axis,degrees): - import math, operator +# + + +def rotate_about_screen_axis(axis, degrees): + import math + import operator def deg_to_rad(degs): - return (degs * 3.1415926 /180.0) + return (degs * 3.1415926 / 180.0) def simple_rotation_x(alpha): cos_alpha = math.cos(alpha) sin_alpha = math.sin(alpha) - return [1,0,0,0,cos_alpha,-sin_alpha,0,sin_alpha,cos_alpha] + return [1, 0, 0, 0, cos_alpha, -sin_alpha, 0, sin_alpha, cos_alpha] def simple_rotation_y(alpha): cos_alpha = math.cos(alpha) sin_alpha = math.sin(alpha) - return [cos_alpha,0,sin_alpha,0,1,0,-sin_alpha,0,cos_alpha] + return [cos_alpha, 0, sin_alpha, 0, 1, 0, -sin_alpha, 0, cos_alpha] def simple_rotation_z(alpha): cos_alpha = math.cos(alpha) sin_alpha = math.sin(alpha) - return [cos_alpha,-sin_alpha,0,sin_alpha,cos_alpha,0,0,0,] + return [cos_alpha, -sin_alpha, 0, sin_alpha, cos_alpha, 0, 0, 0, ] # BL says: I dont know what the next 2 defines are for... # looks not used and/or useless to me # seems that only 2nd matrix is used and not view_matrix! - def vm():view_matrix() - def mult(mat1,mat2):mat2 + def vm(): view_matrix() + def mult(mat1, mat2): mat2 # end of uselessness... if (operator.isNumberType(degrees)): - if (axis=="x"): - mult(view_matrix(),simple_rotation_x(deg_to_rad(degrees))) - elif (axis=="y"): - mult(view_matrix(),simple_rotation_y(deg_to_rad(degrees))) - elif (axis=="z"): - mult(view_matrix(),simple_rotation_z(deg_to_rad(degrees))) - else: - print "symbol axis: ", axis, " incomprehensible" + if (axis == "x"): + mult(view_matrix(), simple_rotation_x(deg_to_rad(degrees))) + elif (axis == "y"): + mult(view_matrix(), simple_rotation_y(deg_to_rad(degrees))) + elif (axis == "z"): + mult(view_matrix(), simple_rotation_z(deg_to_rad(degrees))) + else: + print "symbol axis: ", axis, " incomprehensible" else: - print "incomprehensible length argument: ", degrees + print "incomprehensible length argument: ", degrees # Support for old toggle functions. (consider instead the raw @@ -1112,6 +1231,8 @@ def toggle_display_map(imol, idummy): # toggle the display of imol # + + def toggle_display_mol(imol): if (mol_is_displayed(imol) == 0): set_mol_displayed(imol, 1) @@ -1120,6 +1241,8 @@ def toggle_display_mol(imol): # toggle the active state (clickability) of imol # + + def toggle_active_mol(imol): if (mol_is_active(imol) == 0): set_mol_active(imol, 1) @@ -1129,23 +1252,29 @@ def toggle_active_mol(imol): # return a python (list) representation of molecule imol, or False if we can't # do it (imol is a map, say) # + + def python_representation(imol): if (not valid_model_molecule_qm(imol)): return False else: ls = [] + def r_info(imol, chain_id, n): res_name = resname_from_serial_number(imol, chain_id, n) - res_no = seqnum_from_serial_number(imol, chain_id, n) + res_no = seqnum_from_serial_number(imol, chain_id, n) ins_code = insertion_code_from_serial_number(imol, chain_id, n) return [res_no, ins_code, res_name, residue_info(imol, chain_id, res_no, ins_code)] - ls = [map(lambda chain_id: [chain_id, map(lambda serial_number: r_info(imol, chain_id, serial_number), range(chain_n_residues(chain_id, imol)))], chain_ids(imol))] + ls = [map(lambda chain_id: [chain_id, map(lambda serial_number: r_info( + imol, chain_id, serial_number), range(chain_n_residues(chain_id, imol)))], chain_ids(imol))] return ls # reorder chains # + + def reorder_chains(imol): # reorder elements of chain_list: e.g. @@ -1181,14 +1310,17 @@ def transform_coords_molecule(imol, rtop): # # or @code{transform_map(imol, trans, about_pt, radius)} for a simple translation # -# or @code{transform_map(imol, trans, radius)} when using the default +# or @code{transform_map(imol, trans, radius)} when using the default # rotation-centre as the about-pt # # returns new map mol number or None if no map could be transformed/created # + + def transform_map(*args): ret = None + def tf(imol, mat, trans, about_pt, radius, space_group, cell): return transform_map_raw(imol, mat[0], mat[1], mat[2], @@ -1202,30 +1334,30 @@ def tf(imol, mat, trans, about_pt, radius, space_group, cell): cell[3], cell[4], cell[5]) # main line - if (len(args)==7): - ret = tf(args[0], args[1], args[2], args[3], args[4], args[5], args[6]) + if (len(args) == 7): + ret = tf(args[0], args[1], args[2], args[3], args[4], args[5], args[6]) # imol_map mat trans about_pt radius: - elif (len(args)==5): + elif (len(args) == 5): imol = args[0] ret = tf(imol, args[1], args[2], args[3], args[4], space_group(imol), cell(imol)) # no matrix specified: - elif (len(args)==4): + elif (len(args) == 4): imol = args[0] ret = tf(imol, identity_matrix(), args[1], args[2], args[3], space_group(imol), cell(imol)) # no matrix or about point specified: - elif (len(args)==3): + elif (len(args) == 3): imol = args[0] ret = tf(args[0], identity_matrix(), args[1], rotation_centre(), args[2], space_group(imol), cell(imol)) else: - print "arguments to transform-map incomprehensible: args: ",args + print "arguments to transform-map incomprehensible: args: ", args return ret # return then NCS master of the first molecule that has ncs. -# +# # return "" on fail to find an ncs chain # def get_first_ncs_master_chain(): @@ -1239,12 +1371,14 @@ def get_first_ncs_master_chain(): # Define a map transformation function that obeys Lapthorn's Law of # NCS Handling Programs -# +# # typical usage: transform_map_using_lsq_matrix(1, "A", 10, 30, 0, "A", 10, 30, 2, rotation_centre(), 6) # -# Remember, that now the about-pt is the "to" point, i.e. the maps are brought from +# Remember, that now the about-pt is the "to" point, i.e. the maps are brought from # somewhere else and generated about the about-pt. # + + def transform_map_using_lsq_matrix(imol_bref, ref_chain, ref_resno_start, ref_resno_end, imol_mov, mov_chain, mov_resno_start, mov_resno_end, imol_map, about_pt, radius): @@ -1256,7 +1390,8 @@ def transform_map_using_lsq_matrix(imol_bref, ref_chain, ref_resno_start, ref_re cell_params = cell(imol_ref) if not (space_group and cell): - message = "Bad cell or symmetry for molecule" + str(cell) + str(space_group) + str(imol_ref) + message = "Bad cell or symmetry for molecule" + \ + str(cell) + str(space_group) + str(imol_ref) print "Bad cell or symmetry for molecule", message ret = -1 # invalid mol! or return message!? @@ -1270,60 +1405,74 @@ def transform_map_using_lsq_matrix(imol_bref, ref_chain, ref_resno_start, ref_re # # Scale_factor > 1 makes brighter... # + + def brighten_map(imol, scale_factor): from types import ListType if valid_map_molecule_qm(imol): - current_colour = map_colour_components(imol) - if type(current_colour) is ListType: - new_v = [] - for i in range(len(current_colour)): - new_v.append(current_colour[i] * float(scale_factor)) - if new_v[i] < 0.05: - new_v[i] = 0.05 - elif new_v[i] > 1.0: - new_v[i] = 1.0 - else: - pass - set_map_colour(imol, *new_v) - else: - print "bad non-list current-colour ", current_colour - graphics_draw() + current_colour = map_colour_components(imol) + if type(current_colour) is ListType: + new_v = [] + for i in range(len(current_colour)): + new_v.append(current_colour[i] * float(scale_factor)) + if new_v[i] < 0.05: + new_v[i] = 0.05 + elif new_v[i] > 1.0: + new_v[i] = 1.0 + else: + pass + set_map_colour(imol, *new_v) + else: + print "bad non-list current-colour ", current_colour + graphics_draw() # Make all maps brighter # + + def brighten_maps(): map(lambda imap: brighten_map(imap, 1.25), map_molecule_list()) # Make all maps darker # + + def darken_maps(): map(lambda imap: brighten_map(imap, 0.8), map_molecule_list()) # return a list of chain ids for given molecule number @var{imol}. # return empty list on error # + + def chain_ids(imol): chain_id_is = [] number_of_chains = n_chains(imol) for chain_no in range(number_of_chains): - chain_id_is.append(chain_id(imol,chain_no)) + chain_id_is.append(chain_id(imol, chain_no)) return chain_id_is # convert from interface name to schemisch name to be equivalent to Paul's naming # # return True or False # -def is_solvent_chain_qm(imol,chain_id): - if (is_solvent_chain_p(imol,chain_id)==1): return True - else: return False + + +def is_solvent_chain_qm(imol, chain_id): + if (is_solvent_chain_p(imol, chain_id) == 1): + return True + else: + return False # convert from interface name to schemisch name to be equivalent to Paul's naming # # return True or False # + + def is_protein_chain_qm(imol, chain_id): return is_protein_chain_p(imol, chain_id) == 1 @@ -1331,27 +1480,39 @@ def is_protein_chain_qm(imol, chain_id): # # return True or False # + + def is_nucleotide_chain_qm(imol, chain_id): return is_nucleotide_chain_p(imol, chain_id) == 1 # python (schemeyish) interface to eponymous scripting interface function!? # return True or False # + + def valid_model_molecule_qm(imol): - if (coot.is_valid_model_molecule(imol)==1): return True - else: return False + if (coot.is_valid_model_molecule(imol) == 1): + return True + else: + return False # python (schemeyish) interface to eponymous scripting interface function. # return True or False # + + def valid_map_molecule_qm(imol): - if (coot.is_valid_map_molecule(imol)==1): return True - else: return False + if (coot.is_valid_map_molecule(imol) == 1): + return True + else: + return False # convenience function (slightly less typing). # # Return True or False # + + def valid_refinement_map_qm(): return valid_map_molecule_qm(imol_refinement_map()) @@ -1359,6 +1520,8 @@ def valid_refinement_map_qm(): # # Return True or False # + + def shelx_molecule_qm(imol): return is_shelx_molecule(imol) == 1 @@ -1367,6 +1530,8 @@ def shelx_molecule_qm(imol): # # Return True or False. # + + def is_difference_map_qm(imol_map): if (not valid_map_molecule_qm(imol_map)): return False @@ -1378,12 +1543,16 @@ def is_difference_map_qm(imol_map): # # Return True or False # -def residue_exists_qm(imol,chain_id,resno,ins_code): - return does_residue_exist_p(imol,chain_id,resno,ins_code) == 1 + + +def residue_exists_qm(imol, chain_id, resno, ins_code): + return does_residue_exist_p(imol, chain_id, resno, ins_code) == 1 # Does the residue contain hetatoms? # Return True or False. # + + def residue_has_hetatms_qm(imol, chain_id, res_no, ins_code): return residue_has_hetatms(imol, chain_id, res_no, ins_code) == 1 @@ -1391,26 +1560,31 @@ def residue_has_hetatms_qm(imol, chain_id, res_no, ins_code): # # on failure return False. # + + def centre_of_mass(imol): centre = eval(centre_of_mass_string(imol)) if (centre == 0): - print "molecule number",imol,"is not valid" - return False + print "molecule number", imol, "is not valid" + return False else: - print "Centre of mass for molecule {0!s} is {1!s}".format(imol, centre) - # for use somewhere let's return the centre - return centre + print "Centre of mass for molecule {0!s} is {1!s}".format(imol, centre) + # for use somewhere let's return the centre + return centre # Return as a list the occupancy, temperature_factor, x y z coordinates # of the given atom. # (the x,y,z are in Cartesian Angstroms). -# +# # on error (e.g. atom not found) return False -# +# + + def atom_specs(imol, chain_id, resno, ins_code, atom_name, alt_conf): return atom_info_string(imol, chain_id, resno, ins_code, atom_name, alt_conf) + def atom_spec2residue_spec(atom_spec): return atom_spec[2:][0:3] @@ -1419,6 +1593,8 @@ def atom_spec2residue_spec(atom_spec): # # Basically uses the first not difference map we find! # + + def guess_refinement_map(): map_list = map_molecule_list() @@ -1448,11 +1624,14 @@ def guess_refinement_map(): # The refinement map must be set!! At the end show the new weight in # the status bar. Seems to take about 5 rounds. (bails out after 20) # + + def auto_weight_for_refinement(): global target_auto_weighting_value # return a pair of the imol and a list of residue specs. # or False if that is not possible + def sphere_residues(radius): active_atom = active_residue() if not active_atom: # check for list? @@ -1461,7 +1640,8 @@ def sphere_residues(radius): else: centred_residue = active_atom[1:4] imol = active_atom[0] - other_residues = residues_near_residue(imol, centred_residue, radius) + other_residues = residues_near_residue( + imol, centred_residue, radius) all_residues = [centred_residue] if (isinstance(other_residues, list)): all_residues += other_residues @@ -1475,7 +1655,7 @@ def refinement_func(): if sr: ret = with_auto_accept([refine_residues, sr[0], sr[1]]) return ret - #return with_auto_accept([refine_residues, sr[0], sr[1]]) + # return with_auto_accept([refine_residues, sr[0], sr[1]]) else: return False @@ -1526,12 +1706,14 @@ def weight_scale_from_refinement_results(rr): else: # more refinement required - # squared causes ringing, + # squared causes ringing, # as does 1.5. # Simple is overdamped. current_weight = matrix_state() - new_weight = (target_auto_weighting_value * current_weight) / av_rms_d - print "INFO:: setting refinement weight to {0!s} from * {1!s} / {2!s}".format(new_weight, current_weight, av_rms_d) + new_weight = (target_auto_weighting_value * + current_weight) / av_rms_d + print "INFO:: setting refinement weight to {0!s} from * {1!s} / {2!s}".format( + new_weight, current_weight, av_rms_d) if (new_weight < 2): # weight refinement not converging print "BL INFO:: not convering, weight to set was", new_weight @@ -1545,13 +1727,17 @@ def weight_scale_from_refinement_results(rr): # # This is not really a util, perhaps it should be somewhere else? # + + def print_sequence(imol): for chain in chain_ids(imol): - print_sequence_chain(imol,chain) + print_sequence_chain(imol, chain) # simple utility function to return the contents of a file as a string. # + + def pir_file_name2pir_sequence(pir_file_name): import os if (not os.path.isfile(pir_file_name)): @@ -1567,6 +1753,8 @@ def pir_file_name2pir_sequence(pir_file_name): # Associate the contents of a PIR file with a molecule. # + + def associate_pir_file(imol, chain_id, pir_file_name): seq_text = pir_file_name2pir_sequence(pir_file_name) if seq_text: @@ -1576,6 +1764,8 @@ def associate_pir_file(imol, chain_id, pir_file_name): # Associate the contents of a fasta file with a molecule. # + + def associate_fasta_file(imol, chain_id, pir_file_name): seq_text = pir_file_name2pir_sequence(pir_file_name) if seq_text: @@ -1586,15 +1776,18 @@ def associate_fasta_file(imol, chain_id, pir_file_name): # comma key hook def graphics_comma_key_pressed_hook(): - pass + pass # dot key hook + + def graphics_dot_key_pressed_hook(): - pass + pass # a list of [code, key, name, thunk] # e.g. [103, "g", "Goto Blob", blob_under_pointer_to_screen_centre()] + global key_bindings # we shall see if it exists, if not initialize it try: @@ -1602,12 +1795,13 @@ def graphics_dot_key_pressed_hook(): except: key_bindings = [] + def decode_key(key_val_name): try: import gtk key_value = int(gtk.gdk.keyval_from_name(key_val_name)) # on some windows: special characters seem to have high value, - # so need to convert these properly too + # so need to convert these properly too if (not key_value or key_value >= 100000): # new python needs a long there!? I hope it wont harm old!? new_val = long(ord(key_val_name)) @@ -1621,16 +1815,19 @@ def decode_key(key_val_name): # with a given name, key (e.g. "x" or "S") and the function to run # (a thunk) when that key is pressed. # + + def add_key_binding(name, key, thunk): from types import IntType, StringType global key_bindings, std_key_bindings std_keys = [] if (use_gui_qm): std_keys = [elem[1] for elem in std_key_bindings] - keys = [elem[1] for elem in key_bindings] - codes = [elem[0] for elem in key_bindings] + keys = [elem[1] for elem in key_bindings] + codes = [elem[0] for elem in key_bindings] if (key in std_keys): - print "INFO:: you shall not overwrite a standard key binding ({0!s})".format(key) + print "INFO:: you shall not overwrite a standard key binding ({0!s})".format( + key) else: if (type(key) is IntType): if (key in keys): @@ -1654,7 +1851,7 @@ def add_key_binding(name, key, thunk): # general key press hook, not for public use!! # -def graphics_general_key_press_hook(key, control_flag = 0): +def graphics_general_key_press_hook(key, control_flag=0): global key_bindings # print "graphics_general_key_press_hook(): Key %s was pressed" %key if control_flag: @@ -1665,27 +1862,27 @@ def graphics_general_key_press_hook(key, control_flag = 0): funcs = [elem[3] for elem in key_bindings if not "Control_" in elem[1]] if (key in codes): index = codes.index(key) - func = funcs[index] + func = funcs[index] # print "BL DEBUG:: index and executing:", index, func apply(func) else: if coot_has_guile() and is_windows(): - run_scheme_command("(graphics-general-key-press-hook " + \ - str(key) + \ + run_scheme_command("(graphics-general-key-press-hook " + + str(key) + ")") print "Key {0!s} not found in (python) key bindings".format(key) # Function requested by Mark White. -# -# read XtalView (and maybe other) .vu files and convert them into generic -# objects. -# +# +# read XtalView (and maybe other) .vu files and convert them into generic +# objects. +# # Pass the filename and an object name e.g. # read_vu_file("axes.vu", "axes") -# +# # Returns: nothing interesting. -# +# def read_vu_file(filename, obj_name): from types import StringType @@ -1736,9 +1933,10 @@ def residues_matching_criteria(imol, residue_test_func): alt_conf_residue_list = [] for chain_id in chain_list: - for serial_number in range(chain_n_residues(chain_id,imol)): + for serial_number in range(chain_n_residues(chain_id, imol)): res_no = seqnum_from_serial_number(imol, chain_id, serial_number) - ins_code = insertion_code_from_serial_number(imol, chain_id, serial_number) + ins_code = insertion_code_from_serial_number( + imol, chain_id, serial_number) r = residue_test_func(chain_id, res_no, ins_code, serial_number) if r: seq_residue_list.append([chain_id, res_no, ins_code]) @@ -1749,12 +1947,16 @@ def residues_matching_criteria(imol, residue_test_func): # Return residue specs for all residues in imol (each spec is preceeded by True) # + + def all_residues(imol): return residues_matching_criteria(imol, lambda chain_id, resno, ins_code, serial: True) # Return a list of all residues that have alt confs: where a residue # is specified thusly: [[chain_id, resno, ins_code], [...] ] -# +# + + def residues_with_alt_confs(imol): # return False if there are no atoms with alt-confs, else return @@ -1773,7 +1975,9 @@ def alt_func1(chain_id, res_no, ins_code, res_serial_no): # Return a list of all the altconfs in the residue. # Typically this will return [""] or ["A", "B"] -# +# + + def residue_alt_confs(imol, chain_id, res_no, ins_code): atom_ls = residue_info(imol, chain_id, res_no, ins_code) @@ -1789,7 +1993,7 @@ def residue_alt_confs(imol, chain_id, res_no, ins_code): # Return a list of all atoms that have zero occupancy: where an atom # is specified thusly: [[chain_id, resno, ins_code, name, altconf], [...] ] -# +# def atoms_with_zero_occ(imol): r = [] @@ -1797,28 +2001,30 @@ def atoms_with_zero_occ(imol): n_residues = chain_n_residues(chain_id, imol) for serial_number in range(n_residues): - res_name = resname_from_serial_number(imol, chain_id, serial_number) + res_name = resname_from_serial_number( + imol, chain_id, serial_number) res_no = seqnum_from_serial_number(imol, chain_id, serial_number) - ins_code = insertion_code_from_serial_number(imol, chain_id, serial_number) + ins_code = insertion_code_from_serial_number( + imol, chain_id, serial_number) res_info = residue_info(imol, chain_id, res_no, ins_code) for atom_info in res_info: - occ = atom_info[1][0] - name = atom_info[0][0] + occ = atom_info[1][0] + name = atom_info[0][0] alt_conf = atom_info[0][1] if (occ < 0.01): - text = str(imol) + " " + chain_id + " " + \ - str(res_no) + " " + name + text = str(imol) + " " + chain_id + " " + \ + str(res_no) + " " + name if (alt_conf): text += " " text += alt_conf - r.append([text, imol, chain_id, res_no, ins_code, name, alt_conf]) + r.append([text, imol, chain_id, res_no, + ins_code, name, alt_conf]) return r # simple extraction function def res_spec2chain_id(res_spec): - """simple extraction function""" if not res_spec: @@ -1830,8 +2036,9 @@ def res_spec2chain_id(res_spec): return False # simple extraction function -def res_spec2res_no(res_spec): + +def res_spec2res_no(res_spec): """simple extraction function""" if not res_spec: @@ -1843,8 +2050,9 @@ def res_spec2res_no(res_spec): return False # simple extraction function -def res_spec2ins_code(res_spec): + +def res_spec2ins_code(res_spec): """simple extraction function""" if not res_spec: @@ -1857,11 +2065,11 @@ def res_spec2ins_code(res_spec): # Return False if no atom can be found given the spec else return a list -# consisting of the atom name and alt-conf specifier. -# +# consisting of the atom name and alt-conf specifier. +# # Choose an atom that is called " CA ". Failing that choose the # first atom. -# +# def residue_spec2atom_for_centre(imol, chain_id, res_no, ins_code): from types import ListType @@ -1877,7 +2085,7 @@ def residue_spec2atom_for_centre(imol, chain_id, res_no, ins_code): if (atom == " CA "): centre_atom_name_alt_conf = [atom, alt_conf_str] break - if (not centre_atom_name_alt_conf) and (len(atom_ls)>0): + if (not centre_atom_name_alt_conf) and (len(atom_ls) > 0): # take the first atom centre_atom_name_alt_conf = atom_ls[0][0][0:2] @@ -1895,12 +2103,12 @@ def update_go_to_atom_from_current_atom(): active_atom = active_residue() if active_atom: - imol = active_atom[0] - chain_id = active_atom[1] - resno = active_atom[2] - ins_code = active_atom[3] - atom_name = active_atom[4] - alt_conf = active_atom[5] + imol = active_atom[0] + chain_id = active_atom[1] + resno = active_atom[2] + ins_code = active_atom[3] + atom_name = active_atom[4] + alt_conf = active_atom[5] go_to_atom_imol_current = go_to_atom_molecule_number() set_go_to_atom_molecule(imol) # if imol != goto_atom_imol_current @@ -1910,40 +2118,44 @@ def update_go_to_atom_from_current_atom(): def flip_active_ligand(): active_atom = active_residue() - imol = active_atom[0] - chain_id = active_atom[1] - resno = active_atom[2] - ins_code = active_atom[3] + imol = active_atom[0] + chain_id = active_atom[1] + resno = active_atom[2] + ins_code = active_atom[3] atom_name = active_atom[4] - alt_conf = active_atom[5] + alt_conf = active_atom[5] flip_ligand(imol, chain_id, resno) # Typically one might want to use this on a water, but it deletes the # nearest CA currently... Needs a re-think. Should active-atom just # return the nearest atom and not be clever about returning a CA. -# +# + + def delete_atom_by_active_residue(): - active_atom = active_residue() - if active_atom: - delete_atom(active_atom) + active_atom = active_residue() + if active_atom: + delete_atom(active_atom) # general mutate -# +# # typically: -# +# # overlay PTY onto given TYR # # delete speced TYR -# +# # merge molecules PTY molecule int molecule number imol -# +# # change resno of PTY to that of the speced TYR -# +# # change chain id of PTY to that of speced TYR # # change chain ids with residue range for the PTY -# +# + + def mutate_by_overlap(imol, chain_id_in, resno, tlc): # get_monomer_and_dictionary, now we check to see if we have a @@ -1988,7 +2200,8 @@ def mutate_it(): if merge_status == 1: new_chain_id = new_chain_id_info[1] change_residue_number(imol, new_chain_id, 1, "", resno, "") - change_chain_id(imol, new_chain_id, chain_id_in, 1, resno, resno) + change_chain_id(imol, new_chain_id, + chain_id_in, 1, resno, resno) replacement_state = refinement_immediate_replacement_state() imol_map = imol_refinement_map() @@ -2000,14 +2213,15 @@ def mutate_it(): phos_dir = { 'PTR': [" CZ ", " OH "], 'SEP': [" CB ", " OG "], - 'TPO': [" CB ", " OG1"] } + 'TPO': [" CB ", " OG1"]} if tlc in phos_dir.keys(): dir_atoms = phos_dir[tlc] else: dir_atoms = False refine_zone(imol, chain_id_in, resno, resno, "") if dir_atoms: - spin_search(imol_map, imol, chain_id_in, resno, "", dir_atoms, spin_atoms) + spin_search(imol_map, imol, chain_id_in, + resno, "", dir_atoms, spin_atoms) refine_zone(imol, chain_id_in, resno, resno, "") accept_regularizement() set_refinement_immediate_replacement(replacement_state) @@ -2045,77 +2259,88 @@ def mutate_it(): # A bit of fun # + + def phosphorylate_active_residue(): - active_atom = active_residue() - imol = active_atom[0] - chain_id = active_atom[1] - resno = active_atom[2] - inscode = active_atom[3] - res_name = residue_name(imol, chain_id, resno, inscode) - - if res_name == 'TYR': - mutate_by_overlap(imol, chain_id, resno, "PTR") - elif res_name == 'SER': - mutate_by_overlap(imol, chain_id, resno, "SEP") - elif res_name == 'THR': - mutate_by_overlap(imol, chain_id, resno, "TPO") - else: - s = "Can't Phosphorylate residue of type " + res_name - info_dialog(s) + active_atom = active_residue() + imol = active_atom[0] + chain_id = active_atom[1] + resno = active_atom[2] + inscode = active_atom[3] + res_name = residue_name(imol, chain_id, resno, inscode) + + if res_name == 'TYR': + mutate_by_overlap(imol, chain_id, resno, "PTR") + elif res_name == 'SER': + mutate_by_overlap(imol, chain_id, resno, "SEP") + elif res_name == 'THR': + mutate_by_overlap(imol, chain_id, resno, "TPO") + else: + s = "Can't Phosphorylate residue of type " + res_name + info_dialog(s) # A function for Overlaying ligands. The transformation is applied # to all the atoms of the molecule that contains the moving ligand. # + + def overlay_my_ligands(imol_mov, chain_id_mov, resno_mov, imol_ref, chain_id_ref, resno_ref): imol_frag = new_molecule_by_atom_selection(imol_mov, - "//" + chain_id_mov + \ + "//" + chain_id_mov + "/" + str(resno_mov)) rtop_i = overlap_ligands(imol_frag, imol_ref, chain_id_ref, resno_ref) set_mol_displayed(imol_frag, 0) transform_coords_molecule(imol_mov, rtop_i[0]) + def label_all_CAs(imol): for chain_id in chain_ids(imol): if not (is_solvent_chain_qm(imol, chain_id)): n_residues = chain_n_residues(chain_id, imol) for serial_number in number_list(0, n_residues): - res_name = resname_from_serial_number(imol, chain_id, serial_number) - res_no = seqnum_from_serial_number(imol, chain_id, serial_number) - ins_code = insertion_code_from_serial_number(imol, chain_id, serial_number) + res_name = resname_from_serial_number( + imol, chain_id, serial_number) + res_no = seqnum_from_serial_number( + imol, chain_id, serial_number) + ins_code = insertion_code_from_serial_number( + imol, chain_id, serial_number) add_atom_label(imol, chain_id, res_no, " CA ") graphics_draw() def label_all_atoms_in_residue(imol, chain_id, resno, inscode): - import types + import types - atom_list = residue_info(imol, chain_id, resno, inscode) - if type(atom_list) is ListType: - for atom_info in atom_list: - add_atom_label(imol,chain_id, resno, atom_info[0][0]) - graphics_draw() + atom_list = residue_info(imol, chain_id, resno, inscode) + if type(atom_list) is ListType: + for atom_info in atom_list: + add_atom_label(imol, chain_id, resno, atom_info[0][0]) + graphics_draw() -def label_all_active_residue_atoms(): - active_atom = active_residue() - imol = active_atom[0] - chain_id = active_atom[1] - resno = active_atom[2] - inscode = active_atom[3] +def label_all_active_residue_atoms(): - atom_list = residue_info(imol, chain_id, resno, inscode) - if type(atom_list) is ListType: - for atom_info in atom_list: - add_atom_label(imol,chain_id, resno, atom_info[0][0]) - graphics_draw() + active_atom = active_residue() + imol = active_atom[0] + chain_id = active_atom[1] + resno = active_atom[2] + inscode = active_atom[3] + + atom_list = residue_info(imol, chain_id, resno, inscode) + if type(atom_list) is ListType: + for atom_info in atom_list: + add_atom_label(imol, chain_id, resno, atom_info[0][0]) + graphics_draw() # Resets alt confs and occupancies of atoms in residue that have # orphan alt-loc attributes # + + def sanitise_alt_confs(atom_info, atom_ls): # return a matching atom (name match) if it exists. Else return False @@ -2147,19 +2372,21 @@ def name_match_qm(atom_1, atom_ls): atom_name = compound_name[0] alt_conf = compound_name[1] if (alt_conf != ""): - matchers = name_match_qm (atom, atom_ls) + matchers = name_match_qm(atom, atom_ls) if (len(matchers) == 1): atom_attribute_settings.append([imol, chain_id, resno, inscode, atom_name, - alt_conf, "alt-conf", ""]) + alt_conf, "alt-conf", ""]) else: atom_attribute_settings.append([imol, chain_id, resno, inscode, atom_name, - alt_conf, "occ", ((shelx_molecule_qm(imol) and 11.0) or (1.0))]) + alt_conf, "occ", ((shelx_molecule_qm(imol) and 11.0) or (1.0))]) if (atom_attribute_settings != []): set_atom_attributes(atom_attribute_settings) if (residue_info_dialog_displayed_qm()): residue_info_dialog(imol, chain_id, resno, inscode) # + + def sanitise_alt_confs_in_residue(imol, chain_id, resno, inscode): atom_info = [imol, chain_id, resno, inscode, "dummy", "dummy"] @@ -2169,38 +2396,44 @@ def sanitise_alt_confs_in_residue(imol, chain_id, resno, inscode): # Resets alt confs and occupancies of atoms in residue that have # orphan alt-loc attributes. Use the active-residue. # + + def sanitise_alt_confs_active_residue(): active_atom = active_residue() if active_atom: - imol = active_atom[0] + imol = active_atom[0] chain_id = active_atom[2] - resno = active_atom[2] - inscode = active_atom[2] + resno = active_atom[2] + inscode = active_atom[2] atom_ls = residue_info(imol, chain_id, resno, inscode) if atom_ls: sanitise_alt_confs(active_atom, atom_ls) + def print_molecule_names(): - map(lambda molecule_number: printf( " {0!s} {1!s}\n".format(molecule_number, molecule_name(molecule_number))), + map(lambda molecule_number: printf(" {0!s} {1!s}\n".format(molecule_number, molecule_name(molecule_number))), molecule_number_list()) # save the dialog positions to the coot_dialog_positions.py file in ./coot-preferences # + + def save_dialog_positions_to_init_file(): import os # return False on failure to find .coot.py (or .coot-preferences) + def dump_positions_to_file(positions, preferences=False): home = 'HOME' port = False if (os.name == 'nt'): home = 'COOT_HOME' if preferences: - init_dir = os.path.join(os.getenv(home), - ".coot-preferences") + init_dir = os.path.join(os.getenv(home), + ".coot-preferences") init_file = os.path.join(init_dir, "saved_dialog_positions.py") if (not os.path.isdir(init_dir)): @@ -2217,9 +2450,12 @@ def dump_positions_to_file(positions, preferences=False): if port: - port.write("# ----------------------------------------------------------") - port.write("# the following were written by extraction from a state file") - port.write("# ----------------------------------------------------------") + port.write( + "# ----------------------------------------------------------") + port.write( + "# the following were written by extraction from a state file") + port.write( + "# ----------------------------------------------------------") for position in positions: port.write(position) port.write("# -------------------------") @@ -2231,14 +2467,15 @@ def dump_positions_to_file(positions, preferences=False): state_file = "0-coot.state.py" save_state() if (not os.path.isfile(state_file)): - print "Ooops {0!s} does not exist (either guile enabled or problem writing the file".format(state_file) + print "Ooops {0!s} does not exist (either guile enabled or problem writing the file".format( + state_file) else: port = open("0-coot.state.py", 'r') try: lines = port.readlines() except: lines = [] - positions =[] + positions = [] for line in lines: if ("_dialog_position" in line): print " Adding dialog position: ", line @@ -2259,10 +2496,12 @@ def dump_positions_to_file(positions, preferences=False): # False - default # True - overwrite file # + + def save_string_to_file(string, filename, overwrite=False): #home = 'HOME' - #if (os.name == 'nt'): + # if (os.name == 'nt'): # home = 'COOT_HOME' init_file = filename if (os.path.isfile(init_file)): @@ -2292,7 +2531,7 @@ def save_string_to_file(string, filename, overwrite=False): def remove_line_containing_from_file(remove_str_ls, filename): #home = 'HOME' - #if (os.name == 'nt'): + # if (os.name == 'nt'): # home = 'COOT_HOME' #init_file = os.path.join(os.getenv(home), ".coot.py") init_file = filename @@ -2302,10 +2541,11 @@ def remove_line_containing_from_file(remove_str_ls, filename): lines = port.readlines() port.close() else: - print "BL INFO:: no {0!s} file, so cannot remove line".format(init_file) + print "BL INFO:: no {0!s} file, so cannot remove line".format( + init_file) lines = [] if (lines): - patt = string.join(remove_str_ls,'|') + patt = string.join(remove_str_ls, '|') re_patt = re.compile(patt) tmp_ls = [] for line in lines: @@ -2318,10 +2558,12 @@ def remove_line_containing_from_file(remove_str_ls, filename): # multiple maps of varying colour from a given map. # -def multi_chicken(imol, n_colours = False): + + +def multi_chicken(imol, n_colours=False): def rotate_colour_map(col, degrees): - ret = [degrees/360 , col[1], col[2] - degrees/360] + ret = [degrees/360, col[1], col[2] - degrees/360] # ??? not sure about 1st element, think mistake in Paul's scheme script return ret @@ -2344,7 +2586,8 @@ def rotate_colour_map(col, degrees): frac = icol / float(n_col) # need a float!! contour_level_sigma = start + (stop - start) * frac set_last_map_contour_level(sigma * contour_level_sigma) - set_last_map_colour(*rotate_colour_map(initial_colour, colour_range * frac)) + set_last_map_colour( + *rotate_colour_map(initial_colour, colour_range * frac)) else: print "BL INFO:: {0!s} is not valid map".format(imol) @@ -2356,11 +2599,14 @@ def BALL_AND_STICK(): return 2 # hilight-colour is specified in degrees (round the colour wheel - # starting at yellow (e.g. 230 is purple)) # + + def hilight_binding_site(imol, centre_residue_spec, hilight_colour, radius): if (valid_model_molecule_qm(imol)): - other_residues = residues_near_residue(imol, centre_residue_spec, radius) + other_residues = residues_near_residue( + imol, centre_residue_spec, radius) atom_sel_str = residue_spec2atom_selection_string(centre_residue_spec) imol_new = new_molecule_by_atom_selection(imol, atom_sel_str) @@ -2389,6 +2635,7 @@ def hilight_binding_site(imol, centre_residue_spec, hilight_colour, radius): draw_hydrogens_flag), other_residues) + highlight_binding_site = hilight_binding_site # typo? @@ -2405,8 +2652,8 @@ def hilight_binding_site(imol, centre_residue_spec, hilight_colour, radius): # # To paraphrase: # The distance of the plane of the base to the following phosphate -# is highly correlated to the pucker of the ribose. -# +# is highly correlated to the pucker of the ribose. +# # An analysis of the structures in RNADB2005 shows that a critical # distance of 3.3A provides a partition function to separate C2' from # C3' endo puckering. Not all ribose follow this rule. There may be @@ -2429,7 +2676,8 @@ def add_questionable(r): residue_list.append(r) def get_ribose_residue_atom_name(imol, residue_spec, pucker_atom): - r_info = residue_info(imol, residue_spec[0], residue_spec[1], residue_spec[2]) + r_info = residue_info( + imol, residue_spec[0], residue_spec[1], residue_spec[2]) t_pucker_atom = pucker_atom[0:3] + "*" if (pucker_atom in map(lambda at: at[0][0], r_info)): return pucker_atom @@ -2443,9 +2691,12 @@ def get_ribose_residue_atom_name(imol, residue_spec, pucker_atom): for serial_number in range(n_residues): - res_name = resname_from_serial_number(imol, chain_id, serial_number) - res_no = seqnum_from_serial_number (imol, chain_id, serial_number) - ins_code = insertion_code_from_serial_number(imol, chain_id, serial_number) + res_name = resname_from_serial_number( + imol, chain_id, serial_number) + res_no = seqnum_from_serial_number( + imol, chain_id, serial_number) + ins_code = insertion_code_from_serial_number( + imol, chain_id, serial_number) if (not res_name == "HOH"): @@ -2456,11 +2707,11 @@ def get_ribose_residue_atom_name(imol, residue_spec, pucker_atom): if (len(pi) == 4): pucker_atom = pi[1] if ((abs(pi[0]) > crit_d) and - (pucker_atom == " C2'")): + (pucker_atom == " C2'")): add_questionable([pucker_atom, residue_spec, "Inconsistent phosphate distance for C2' pucker"]) if ((abs(pi[0]) < crit_d) and - (pucker_atom == " C3'")): + (pucker_atom == " C3'")): add_questionable([pucker_atom, residue_spec, "Inconsistent phosphate distance for C3' pucker"]) if not ((pucker_atom == " C2'") or @@ -2475,13 +2726,14 @@ def get_ribose_residue_atom_name(imol, residue_spec, pucker_atom): for residue in residue_list: residue_spec = residue[1] pucker_atom = residue[0] - at_name = get_ribose_residue_atom_name(imol, residue_spec, pucker_atom) - ls = [residue_spec[0] + " " + str(residue_spec[1]) + residue_spec[2] + \ + at_name = get_ribose_residue_atom_name( + imol, residue_spec, pucker_atom) + ls = [residue_spec[0] + " " + str(residue_spec[1]) + residue_spec[2] + ": " + residue[2], - ["set_go_to_atom_molecule("+ str(imol) +")", - "set_go_to_atom_chain_residue_atom_name(" +\ - "\"" + str(residue_spec[0]) + "\", " +\ - str(residue_spec[1]) + ", " +\ + ["set_go_to_atom_molecule(" + str(imol) + ")", + "set_go_to_atom_chain_residue_atom_name(" + + "\"" + str(residue_spec[0]) + "\", " + + str(residue_spec[1]) + ", " + "\"" + str(at_name) + "\")"] ] buttons.append(ls) @@ -2492,6 +2744,8 @@ def get_ribose_residue_atom_name(imol, residue_spec, pucker_atom): # Run libcheck to convert from SMILES string # + + def new_molecule_by_smiles_string(tlc_text, smiles_text): import shutil if len(smiles_text) > 0: @@ -2513,7 +2767,7 @@ def new_molecule_by_smiles_string(tlc_text, smiles_text): pdb_file_name = "libcheck_" + three_letter_code + ".pdb" cif_file_name = "libcheck_" + three_letter_code + ".cif" - smiles_input = file(smiles_file,'w') + smiles_input = file(smiles_file, 'w') smiles_input.write(smiles_text) smiles_input.close() # now let's run libcheck (based on libcheck.py) @@ -2522,7 +2776,8 @@ def new_molecule_by_smiles_string(tlc_text, smiles_text): if (not libcheck_exe_file): print " BL WARNING:: libcheck not found!" else: - status = popen_command(libcheck_exe_file, [], libcheck_data_lines, log_file_name, True) + status = popen_command(libcheck_exe_file, [], + libcheck_data_lines, log_file_name, True) # the output of libcheck goes to libcheck.lib, we want it in # (i.e. overwrite the minimal description in cif_file_name if (status == 0): @@ -2530,7 +2785,8 @@ def new_molecule_by_smiles_string(tlc_text, smiles_text): # copy rather than rename file to avoid accession issues shutil.copy("libcheck.lib", cif_file_name) sc = rotation_centre() - imol = handle_read_draw_molecule_with_recentre(pdb_file_name, 0) + imol = handle_read_draw_molecule_with_recentre( + pdb_file_name, 0) if (is_valid_model_molecule(imol)): mc = molecule_centre(imol) sc_mc = [sc[i]-mc[i] for i in range(len(mc))] @@ -2557,18 +2813,20 @@ def prodrg_ify(imol, chain_id, res_no, ins_code): if res_name: make_directory_maybe(prodrg_dir) - prodrg_xyzin = os.path.join(prodrg_dir, "prodrg-in.pdb") + prodrg_xyzin = os.path.join(prodrg_dir, "prodrg-in.pdb") prodrg_xyzout = os.path.join(prodrg_dir, "prodrg-" + res_name + ".pdb") - prodrg_cif = os.path.join(prodrg_dir, "prodrg-" + res_name + ".cif") - prodrg_log = os.path.join(prodrg_dir, "prodrg.log") + prodrg_cif = os.path.join(prodrg_dir, "prodrg-" + res_name + ".cif") + prodrg_log = os.path.join(prodrg_dir, "prodrg.log") delete_residue_hydrogens(new_mol, chain_id, res_no, ins_code, "") - delete_residue_hydrogens(imol, chain_id, res_no, ins_code, "") # otherwise they fly + delete_residue_hydrogens( + imol, chain_id, res_no, ins_code, "") # otherwise they fly write_pdb_file(new_mol, prodrg_xyzin) close_molecule(new_mol) prodrg_exe = find_exe("cprodrg", "CCP4_BIN", "PATH") if not prodrg_exe: - info_dialog("Cannot find cprodrg, so no prodrg-ifying of ligand possible") + info_dialog( + "Cannot find cprodrg, so no prodrg-ifying of ligand possible") else: print "BL DEBUG:: now run prodrg with", prodrg_exe, \ "XYZIN", prodrg_xyzin,\ @@ -2583,17 +2841,19 @@ def prodrg_ify(imol, chain_id, res_no, ins_code): True) if status == 0: read_cif_dictionary(prodrg_cif) - imol_new = handle_read_draw_molecule_with_recentre(prodrg_xyzout, 0) + imol_new = handle_read_draw_molecule_with_recentre( + prodrg_xyzout, 0) rn = residue_name(imol, chain_id, res_no, ins_code) with_auto_accept([regularize_zone, imol_new, "", 1, 1, ""]) overlap_ligands(imol_new, imol, chain_id, res_no) - match_ligand_torsions(imol_new, imol, chain_id, res_no) # broken? + match_ligand_torsions( + imol_new, imol, chain_id, res_no) # broken? overlap_ligands(imol_new, imol, chain_id, res_no) set_residue_name(imol_new, "", 1, "", rn) change_chain_id(imol_new, "", chain_id, 1, 1, 1) renumber_residue_range(imol_new, chain_id, 1, 1, res_no - 1) set_mol_displayed(imol_new, 0) - set_mol_active (imol_new, 0) + set_mol_active(imol_new, 0) #set_mol_displayed(imol, 0) #set_mol_active (imol, 0) @@ -2601,7 +2861,7 @@ def prodrg_ify(imol, chain_id, res_no, ins_code): # function because that does not copy across the hydrogen # atoms - and we want those, probably - #replace_fragment(imol, imol_new, + # replace_fragment(imol, imol_new, # "//" + chain_id + "/" + str(res_no)) imol_replacing = add_ligand_delete_residue_copy_molecule( @@ -2610,7 +2870,7 @@ def prodrg_ify(imol, chain_id, res_no, ins_code): new_col = col + 5 set_molecule_bonds_colour_map_rotation(imol_replacing, new_col) set_mol_displayed(imol_replacing, 0) - set_mol_active (imol_replacing, 0) + set_mol_active(imol_replacing, 0) graphics_draw() @@ -2625,9 +2885,11 @@ def add_annotation_here(text): place_text(*(ann + [0])) graphics_draw() + def add_annotation_at_click(text): global pass_text pass_text = text + def add_here(*args): global annotations global pass_text @@ -2642,15 +2904,17 @@ def add_here(*args): graphics_draw() user_defined_click(1, add_here) + def save_annotations(file_name): global annotations - #if (os.path.isfile(file_name)): - # remove existing file + # if (os.path.isfile(file_name)): + # remove existing file # print "BL INFO:: overwrite old annotation file", file_name # os.remove(file_name) save_string_to_file(str(annotations), file_name, True) + def load_annotations(file_name): if (os.path.isfile(file_name)): from types import ListType @@ -2679,10 +2943,12 @@ def load_annotations(file_name): # release info adding in "pre-release" if this binary is a # pre-release. # args ends up as something like: -# ["xxx/phone_home.py", "pre-release" +# ["xxx/phone_home.py", "pre-release" # "binary", "Linux-1386-fedora-10-python-gtk2" # "command-line", "/home/xx/coot/bin/coot"] # + + def make_latest_version_url(): build_type = coot_sys_build_type() # FIXME this is only for biop files !!! @@ -2693,15 +2959,14 @@ def make_latest_version_url(): host = "http://www.ysbl.york.ac.uk/~lohkamp/software/binaries/" pre_dir = "nightlies/pre-release" if pre_release_qm() else "stable" url = host + \ - pre_dir + \ - "/" + \ - "type-binary-" + \ - build_type + \ - "-latest.txt" + pre_dir + \ + "/" + \ + "type-binary-" + \ + build_type + \ + "-latest.txt" return url - # Get the binary (i.e. the action that happens when the download # button is pressed). This is run in a thread, so it cant do # any graphics stuff (except for updating the progress bar when @@ -2714,7 +2979,7 @@ def make_latest_version_url(): # def run_download_binary_curl(revision, version_string, pending_install_in_place_func, - set_file_name_func=False, # combine with progress_bar?! + set_file_name_func=False, # combine with progress_bar?! progress_bar=False, use_curl=False): @@ -2727,16 +2992,19 @@ def match_md5sums(tar_file_name, target_md5sum_file_name): else: if not os.path.isfile(target_md5sum_file_name): #print "OOps! %s does not exist" %target_md5sum_file_name - print "OOps! {0!s} does not exist".format(target_md5sum_file_name) + print "OOps! {0!s} does not exist".format( + target_md5sum_file_name) return False else: - target_md5_string = get_target_md5_string(target_md5sum_file_name) + target_md5_string = get_target_md5_string( + target_md5sum_file_name) # remove the md5sum file (not needed any more) os.remove(target_md5sum_file_name) md5_string = get_md5sum_string(tar_file_name) if not target_md5_string: # need to test if string? #print "OOps %s is not a string" %target_md5_string - print "OOps {0!s} is not a string".format(target_md5_string) + print "OOps {0!s} is not a string".format( + target_md5_string) return False else: if not md5_string: # as above @@ -2747,7 +3015,8 @@ def match_md5sums(tar_file_name, target_md5sum_file_name): if not (target_md5_string == md5_string): #print "Oops: md5sums do not match %s %s. Doing nothing" \ # %(target_md5_string, md5_string) - print "Oops: md5sums do not match {0!s} {1!s}. Doing nothing".format(target_md5_string, md5_string) + print "Oops: md5sums do not match {0!s} {1!s}. Doing nothing".format( + target_md5_string, md5_string) return False else: return True @@ -2755,7 +3024,7 @@ def match_md5sums(tar_file_name, target_md5sum_file_name): # return success status as a boolean # use_tar, use 'tar' function or pythonic tarfile function # - def install_coot_tar_file(tar_file_name, use_tar = False): + def install_coot_tar_file(tar_file_name, use_tar=False): prefix_dir = os.getenv("COOT_PREFIX") prefix_dir = os.path.normpath(prefix_dir) # FIXME do we need this? if not prefix_dir: @@ -2795,10 +3064,10 @@ def install_coot_tar_file(tar_file_name, use_tar = False): os.rename(a_tar_file_name, tar_file_name) os.chdir(current_dir) - return True # ? - + return True # ? # return as a string, or False + def get_target_md5_string(file_name): if not os.path.isfile(file_name): return False @@ -2820,7 +3089,6 @@ def get_md5sum_string(file_name): fin.close() return md5sum - # main line # #print "::::: run_download_binary_curl.... with revision %s with version_string %s" \ @@ -2865,7 +3133,7 @@ def get_md5sum_string(file_name): url = "http://" + host_dir + release_dir + tar_file_name md5_url = url + ".md5sum" - md5_tar_file_name = tar_file_name +".md5sum" + md5_tar_file_name = tar_file_name + ".md5sum" #print "md5sum url for curl:", md5_url #print "url for curl:", url @@ -2889,16 +3157,19 @@ def get_md5sum_string(file_name): # this is for pythonic urllib # we have graphics here, grrrr, shouldnt import urllib + def progress_function(count, blockSize, totalSize): global pending_install_in_place percent = int(count*blockSize*100/totalSize) dots = int(percent / 2.5) * "=" if percent < 100: dots += ">" - sys.stdout.write("\rProgress {0:d}%".format(percent) + " |{0:<40!s}|".format(dots)) + sys.stdout.write("\rProgress {0:d}%".format( + percent) + " |{0:<40!s}|".format(dots)) sys.stdout.flush() if progress_bar: - progress_bar.set_text("Downloading {0!s} %".format(percent)) + progress_bar.set_text( + "Downloading {0!s} %".format(percent)) progress_bar.set_fraction(percent/100.) if (pending_install_in_place == "cancelled"): # Brute force exit of thread! @@ -2907,14 +3178,16 @@ def progress_function(count, blockSize, totalSize): sys.exit() try: - md5_url_local_file_name, md5_url_info = urllib.urlretrieve(md5_url, md5_tar_file_name) + md5_url_local_file_name, md5_url_info = urllib.urlretrieve( + md5_url, md5_tar_file_name) except: print "BL ERROR:: could not download", md5_url return False try: print "\n" print "Downloading: {0!s}".format(tar_file_name) - url_local_file_name, url_info = urllib.urlretrieve(url, tar_file_name, progress_function) + url_local_file_name, url_info = urllib.urlretrieve( + url, tar_file_name, progress_function) pending_install_in_place = "full" print "\nDone" except: @@ -2943,6 +3216,8 @@ def progress_function(count, blockSize, totalSize): # # (used in downloading new version) # + + def get_revision_from_string(stri): # e.g. str is "coot-0.6-pre-1-revision-2060" (with a newline at the # end too). We want to return 2060 (a number) from here (or False). @@ -2958,13 +3233,15 @@ def get_revision_from_string(stri): # for true pythonic url retrievel # returns url as string or False if error # + + def get_url_as_string(my_url): import urllib try: s = urllib.urlopen(my_url).read() except: - s = False # not sure if that's the right way + s = False # not sure if that's the right way return s @@ -2982,6 +3259,8 @@ def coot_split_version_string(stri): return ls2 # convert file to string + + def file2string(file_name): if not os.path.isfile(file_name): return False @@ -3001,6 +3280,8 @@ def file2string(file_name): # matching. The protein sequence has to have at least 95% sequence # identity with the target sequence in "default.seq" # + + def load_default_sequence(): default_seq = "default.seq" @@ -3013,7 +3294,7 @@ def load_default_sequence(): # is for command line update # FIXME -# update self +# update self # # keep a copy of the old directories around in a directory named # after expiration time. @@ -3026,12 +3307,13 @@ def update_self(use_curl=False): url = make_latest_version_url() if use_curl: - #x=get_url_as_string(url) # dummy to fool the firewall FIXME + # x=get_url_as_string(url) # dummy to fool the firewall FIXME coot_url = coot_get_url_as_string(url) else: coot_url = get_url_as_string(url) if not coot_url: - print "BL INFO:: could not get string from URL {0!s}, so no update".format(url) + print "BL INFO:: could not get string from URL {0!s}, so no update".format( + url) else: version_string = coot_split_version_string(coot_url) revision = get_revision_from_string(version_string) @@ -3048,6 +3330,7 @@ def pending_install_in_place_func(val): global continue_status continue_status = True + def threaded_func(): ret = run_download_binary_curl(revision, version_string, pending_install_in_place_func, @@ -3069,7 +3352,7 @@ def threaded_func(): if operator.isNumberType(v2): f = v2 / v1 #sys.stdout.write("\rProgress %3.2f%%" %(f*100)) - #sys.stdout.flush() + # sys.stdout.flush() print "{0:3.2f}%".format((f*100)) if f > 0.999: continue_status = False @@ -3085,14 +3368,15 @@ def use_curl_status(): global use_curl return use_curl + def set_use_curl(status): global use_curl use_curl = status -# Invert the chiral centre of the atom we are centred on. +# Invert the chiral centre of the atom we are centred on. # If not centred on a chiral atom, then give a dialog. -# +# # The restraints for this monomer type are copied and renamed # (changing comp-id, 3-letter-code and name too). The monomer is # regularized. Chiral Hydrogen (if needed) is enabled now in the @@ -3105,6 +3389,7 @@ def chiral_centre_inverter(): info_dialog("BL waiting for PE to put in C++ code.\n") return False + def residue_is_close_to_screen_centre_qm(imol, chain_id, res_no, ins_code): def square(x): return x * x rc = residue_centre(imol, chain_id, res_no, ins_code) @@ -3116,11 +3401,12 @@ def square(x): return x * x return dist_sum_sq < 25. # return a string "DB00xxxx.mol" or some such - this is the file name -# of the mdl mol file from drugbank. Or False/undefined on fail. +# of the mdl mol file from drugbank. Or False/undefined on fail. # Test result with string?. -# -def get_drug_via_wikipedia(drug_name_in): +# + +def get_drug_via_wikipedia(drug_name_in): import urllib2 from xml.etree import ElementTree @@ -3133,31 +3419,30 @@ def parse_wiki_drug_xml(tree, key, redirect=False): drug_bank_id = False query_ele = tree.find("query") rev_iter = query_ele.getiterator("rev") - if len(rev_iter) > 0: - rev_text = rev_iter[0].text - # seems to be in some strange format!? - decode_text = rev_text.encode('ascii', 'ignore') - for line in decode_text.split("\n"): - # if key in line: # too simple, we need a regular expresssion search - if key_re.search(line): - if (redirect == False): - drug_bank_id = line.split(" ")[-1] - if not drug_bank_id: - # we can get an empty string - drug_bank_id = False - else: - # a REDIRECT was found - drug_bank_id = line[line.find("[[")+2:line.find("]]")] - else: - print 'Oops! len rev_text is 0' + if len(rev_iter) > 0: + rev_text = rev_iter[0].text + # seems to be in some strange format!? + decode_text = rev_text.encode('ascii', 'ignore') + for line in decode_text.split("\n"): + # if key in line: # too simple, we need a regular expresssion search + if key_re.search(line): + if (redirect == False): + drug_bank_id = line.split(" ")[-1] + if not drug_bank_id: + # we can get an empty string + drug_bank_id = False + else: + # a REDIRECT was found + drug_bank_id = line[line.find("[[")+2:line.find("]]")] + else: + print 'Oops! len rev_text is 0' return drug_bank_id - file_name = False if isinstance(drug_name_in, str): if len(drug_name_in) > 0: - drug_name = drug_name_in.lower() + drug_name = drug_name_in.lower() url = "http://en.wikipedia.org/w/api.php?format=xml&action=query&titles=" + \ drug_name + \ "&prop=revisions&rvprop=content" @@ -3222,8 +3507,8 @@ def get_SMILES_for_comp_id_from_pdbe(comp_id): # give a dialog, saying that the file will not be # overwritten msg = cif_file_name + \ - " exists but is empty." + \ - "\nNot overwriting." + " exists but is empty." + \ + "\nNot overwriting." info_dialog(msg) return False # use network then @@ -3254,8 +3539,9 @@ def get_SMILES_for_comp_id_from_pdbe(comp_id): # Add file with filename to preferences directory # -def file_to_preferences(filename): + +def file_to_preferences(filename): """Copy the file filename from python pkgdatadir directory to prefereneces directory. """ @@ -3301,6 +3587,7 @@ def file_to_preferences(filename): # PE comment - not sure why needed. #find_aligned_residue_type = find_terminal_residue_type + def using_gui(): # we shall see if coot_main_menubar is defined in guile or python ret = False @@ -3321,12 +3608,16 @@ def using_gui(): # for easier switching on of GL lighting on surfaces: # + + def GL_light_on(): set_do_GL_lighting(1) do_GL_lighting_state() # and to turn it off # + + def GL_light_off(): set_do_GL_lighting(0) do_GL_lighting_state() @@ -3340,35 +3631,43 @@ def set_b_factor_molecule(imol, bval): for chain_id in chain_ids(imol): start_res = seqnum_from_serial_number(imol, chain_id, 0) - end_res = seqnum_from_serial_number(imol, chain_id, chain_n_residues(chain_id, imol) - 1) + end_res = seqnum_from_serial_number( + imol, chain_id, chain_n_residues(chain_id, imol) - 1) set_b_factor_residue_range(imol, chain_id, start_res, end_res, bval) # reset B-factor for molecule imol to default value # + + def reset_b_factor_molecule(imol): for chain_id in chain_ids(imol): start_res = seqnum_from_serial_number(imol, chain_id, 0) - end_res = seqnum_from_serial_number(imol, chain_id, chain_n_residues(chain_id, imol) - 1) - set_b_factor_residue_range(imol, chain_id, start_res, end_res, default_new_atoms_b_factor()) + end_res = seqnum_from_serial_number( + imol, chain_id, chain_n_residues(chain_id, imol) - 1) + set_b_factor_residue_range( + imol, chain_id, start_res, end_res, default_new_atoms_b_factor()) # reset B-factor for active residue to default value # + + def reset_b_factor_active_residue(): active_atom = active_residue() if not active_atom: - print "No active atom" + print "No active atom" else: - imol = active_atom[0] - chain_id = active_atom[1] - res_no = active_atom[2] - ins_code = active_atom[3] - atom_name = active_atom[4] - alt_conf = active_atom[5] + imol = active_atom[0] + chain_id = active_atom[1] + res_no = active_atom[2] + ins_code = active_atom[3] + atom_name = active_atom[4] + alt_conf = active_atom[5] - set_b_factor_residue_range(imol, chain_id, res_no, res_no, default_new_atoms_b_factor()) + set_b_factor_residue_range( + imol, chain_id, res_no, res_no, default_new_atoms_b_factor()) # BL module to find exe files @@ -3389,12 +3688,13 @@ def reset_b_factor_active_residue(): # # on OS where "which" is available we use this first, rather than # searching in PATH etc. -# +# # returns full path of exe when successful, False otherwise # def find_exe(program_name, *args, **kwargs): - import os, string + import os + import string global search_disk search_disk = None @@ -3439,7 +3739,6 @@ def find_exe(program_name, *args, **kwargs): # list of extensions (no dot) only extensions = map(lambda ext: ext[1:], tmp_ext) - if "only_extension" in kwargs: if kwargs["only_extension"]: extensions = kwargs["only_extension"] @@ -3451,7 +3750,7 @@ def find_exe(program_name, *args, **kwargs): program_names = [program_name_noext] if extensions: program_names = map(lambda ext: program_name_noext + "." + ext, - extensions) + extensions) # usually we want to have the one with extension, if there is one program_names += [program_name_noext] @@ -3477,7 +3776,8 @@ def find_exe(program_name, *args, **kwargs): return program_exe except: if info: - print "BL WARNING:: {0!s} not defined!".format(search_path) + print "BL WARNING:: {0!s} not defined!".format( + search_path) # BL says: before we search everywhere we might want to ask # the user if he actually wishes to do so! @@ -3502,36 +3802,44 @@ def find_exe(program_name, *args, **kwargs): print "BL INFO:: we don't search the whole disk for", program_name_noext if info: - print "BL WARNING:: We cannot find {0!s} anywhere! Program {1!s} won't run!".format(program_name_noext, program_name_noext) + print "BL WARNING:: We cannot find {0!s} anywhere! Program {1!s} won't run!".format( + program_name_noext, program_name_noext) return False # for running online docs + + def open_url(url): import webbrowser try: - webbrowser.open(url,1,1) + webbrowser.open(url, 1, 1) except: - print "BL WARNING:: Cannot open the URL {0!s} in webbrowser {1!s}!".format(url, webbrowser.get()) + print "BL WARNING:: Cannot open the URL {0!s} in webbrowser {1!s}!".format( + url, webbrowser.get()) # to reload modules def reload_module(name): - import os - path = os.getenv('COOT_PYTHON_DIR') - file = os.path.join(path, name) - execfile(file) + import os + path = os.getenv('COOT_PYTHON_DIR') + file = os.path.join(path, name) + execfile(file) # to make print a function: + + def printf(*args): for arg in args: print arg, # to print elements of a list: + + def printl(ls): map(printf, ls) -# Where cmd is e.g. "bltwish" +# Where cmd is e.g. "bltwish" # args is list, e.g. [loggraph, "refmac.log"] # # in python < 2.4 (and if no logfile) @@ -3543,30 +3851,35 @@ def printl(ls): # Returns the process and the open log file object # # uses os.spawn if python version < 2.4 otherwise subprocess -# +# + + def run_concurrently(cmd, args=None, data_list=None, logfile=None, screen_flag=False): if args is None: args = [] - import sys, string, os + import sys + import string + import os major, minor, micro, releaselevel, serial = sys.version_info cmd_execfile = "" if not(command_in_path_qm(cmd)): - print "command ", cmd, " not found in $PATH!" - print "BL INFO:: Maybe we'll find it somewhere else later..." + print "command ", cmd, " not found in $PATH!" + print "BL INFO:: Maybe we'll find it somewhere else later..." else: - cmd_execfile = find_exe(cmd,"CCP4_BIN","PATH") + cmd_execfile = find_exe(cmd, "CCP4_BIN", "PATH") if (cmd_execfile): - if (major >= 2 and minor >=4): + if (major >= 2 and minor >= 4): # subprocess import subprocess cmd_args = [cmd_execfile] + args log = logfile if (logfile): log = open(logfile, 'w') - process = subprocess.Popen(cmd_args, stdin=subprocess.PIPE, stdout=log) + process = subprocess.Popen( + cmd_args, stdin=subprocess.PIPE, stdout=log) if (data_list): for data in data_list: @@ -3584,28 +3897,33 @@ def run_concurrently(cmd, args=None, data_list=None, logfile=None, screen_flag=F pid = os.spawnv(os.P_NOWAIT, cmd_execfile, [cmd_execfile] + args) return pid else: - print "WARNING:: could not find {0!s}, so not running this program".format(cmd) + print "WARNING:: could not find {0!s}, so not running this program".format( + cmd) return False # python command to see if we have pygtk available # return True if availabel otherwise False # + + def coot_has_pygtk(): - import sys - if ('pygtk' in sys.modules.keys()): - return True - else: - return False + import sys + if ('pygtk' in sys.modules.keys()): + return True + else: + return False # python command to see if we have pygobject available # return True if availabel otherwise False # + + def coot_has_gobject(): - import sys - if ('gobject' in sys.modules.keys()): - return True - else: - return False + import sys + if ('gobject' in sys.modules.keys()): + return True + else: + return False # function to kill a process, given the process pid @@ -3621,10 +3939,11 @@ def kill_process(pid): try: # for now use subprocess.call, maybe can use Popen.kill?! major, minor, micro, releaselevel, serial = sys.version_info - if (major >= 2 and minor >=4): + if (major >= 2 and minor >= 4): # new style import subprocess - ret = subprocess.call("taskkill /F /PID {0:d}".format(pid), shell=True) + ret = subprocess.call( + "taskkill /F /PID {0:d}".format(pid), shell=True) else: ret = os.system("taskkill /F /PID {0:d}".format(pid)) if (ret == 0): @@ -3651,6 +3970,7 @@ def stereo_mono_toggle(): else: mono_mode() + def side_by_side_stereo_mono_toggle(): display_state = stereo_mode_state() if (display_state == 0): @@ -3658,6 +3978,7 @@ def side_by_side_stereo_mono_toggle(): else: mono_mode() + def zalman_stereo_mono_toggle(): display_state = stereo_mode_state() if (display_state == 0): @@ -3665,10 +3986,12 @@ def zalman_stereo_mono_toggle(): else: mono_mode() + def switch_stereo_sides(): factor = -1. * hardware_stereo_angle_factor_state() set_hardware_stereo_angle_factor(factor) + def toggle_full_screen(widget=None): """ Toggle between full screen and window mode @@ -3686,6 +4009,7 @@ def toggle_full_screen(widget=None): # no alternative for now (could just go by state and change back and forth) print "BL WARNING:: no widget" + def split_active_water(): with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: split_water(aa_imol, aa_chain_id, aa_res_no, aa_ins_code) @@ -3693,6 +4017,8 @@ def split_active_water(): # helper function to test for a number # returns True if number, otherwise False # + + def isNumber(num): """ helper function to test for a number @@ -3725,7 +4051,7 @@ def merge_solvent_chains(imol): renumber_residue_range(imol, chain_id, 1, n_residues, last_prev_water) new_start = last_prev_water + 1 - new_end = last_prev_water + n_residues + new_end = last_prev_water + n_residues change_chain_id(imol, chain_id, master_chain, 1, new_start, new_end) last_prev_water = new_end @@ -3768,7 +4094,7 @@ def set_alt_conf_occ(imol, chain_id, res_no, ins_code, alt_conf_list): change_list = [] for i in range(len(atom_ls)): alt_conf_str = atom_ls[i][0][1] - atom_name = atom_ls[i][0][0] + atom_name = atom_ls[i][0][0] for (alt_conf_name, alt_conf_occ) in alt_conf_list: if (alt_conf_str == alt_conf_name): change_list.append([imol, chain_id, res_no, ins_code, atom_name, @@ -3784,6 +4110,8 @@ def is_windows(): # find all windows drives # + + def get_windows_drives(): from ctypes import windll drives = [] @@ -3801,7 +4129,6 @@ def get_windows_drives(): # solvent chains, renumber waters, etc. # def clean_pdb(imol): - """clean up pdb file (imol) a wrapper for fix_nomenclature errors, sort chains, residues, merge solvent chains, renumber waters, etc.""" @@ -3812,12 +4139,13 @@ def clean_pdb(imol): sort_chains(imol) sort_residues(imol) + # acronym merge_water_chains = merge_solvent_chains # the python run_thread function if no graphics #global use_gui_qm -#if not use_gui_qm: +# if not use_gui_qm: # import threading # # this has locked, so that no one else can use it # global python_thread_return diff --git a/web/XChemWeb.py b/web/XChemWeb.py index a0950646..872dcebe 100755 --- a/web/XChemWeb.py +++ b/web/XChemWeb.py @@ -1,29 +1,30 @@ # last edited: 05/07/2017, 15:00 -import os,sys +import XChemUtils +from XChemUtils import mtztools +from XChemUtils import pdbtools +import XChemMain +import XChemDB +import XChemLog +import os +import sys import glob sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') -import XChemLog -import XChemDB -import XChemMain -from XChemUtils import pdbtools -from XChemUtils import mtztools -import XChemUtils class export_to_html: - def __init__(self,htmlDir,projectDir,database,xce_logfile): + def __init__(self, htmlDir, projectDir, database, xce_logfile): self.htmlDir = htmlDir self.projectDir = projectDir - self.Logfile=XChemLog.updateLog(xce_logfile) - self.db=XChemDB.data_source(database) + self.Logfile = XChemLog.updateLog(xce_logfile) + self.db = XChemDB.data_source(database) self.db_dict = None self.pdb = None self.protein_name = None - def prepare(self,whichSamples): + def prepare(self, whichSamples): self.Logfile.insert('======== preparing HTML summary ========') self.makeFolders() self.copy_jscss() @@ -36,24 +37,29 @@ def prepare(self,whichSamples): self.Logfile.warning('could not determine protein name') try: self.protein_name = xtal.split('-')[0] - self.Logfile.warning('xtal name = %s => setting protein name to %s' %(xtal,self.protein_name)) + self.Logfile.warning( + 'xtal name = %s => setting protein name to %s' % (xtal, self.protein_name)) except IndexError: - self.Logfile.warning('could not determine protein name from cystal name; setting to None') + self.Logfile.warning( + 'could not determine protein name from cystal name; setting to None') self.protein_name = '' else: self.protein_name = self.db_dict['ProteinName'] - self.Logfile.insert('protein name is: ' + self.protein_name) + self.Logfile.insert( + 'protein name is: ' + self.protein_name) self.copy_pdb(xtal) self.copy_mtz(xtal) # self.copy_electron_density(xtal) self.copy_ligand_files(xtal) - os.chdir(os.path.join(self.projectDir,xtal)) - ligandDict = XChemUtils.pdbtools_gemmi('refine.pdb').center_of_mass_ligand_dict('LIG') - self.Logfile.insert(xtal + ': saving ligand(s) of type LIG in refine.pdb as PDB files...') + os.chdir(os.path.join(self.projectDir, xtal)) + ligandDict = XChemUtils.pdbtools_gemmi( + 'refine.pdb').center_of_mass_ligand_dict('LIG') + self.Logfile.insert( + xtal + ': saving ligand(s) of type LIG in refine.pdb as PDB files...') XChemUtils.pdbtools_gemmi('refine.pdb').save_ligands_to_pdb('LIG') for ligand in ligandDict: self.Logfile.insert(xtal + ': current ligand -> ' + ligand) - os.chdir(os.path.join(self.projectDir,xtal)) + os.chdir(os.path.join(self.projectDir, xtal)) # for ligand in self.ligands_in_pdbFile(xtal): ligName = ligand.split('-')[0] ligChain = ligand.split('-')[1] @@ -76,10 +82,12 @@ def prepare(self,whichSamples): x = ligandDict[ligand][0] y = ligandDict[ligand][1] z = ligandDict[ligand][2] - self.copy_spider_plot(xtal,ligand) + self.copy_spider_plot(xtal, ligand) pdbID = self.db_dict['Deposition_PDB_ID'] - compoundImage = xtal + '_' + self.db_dict['CompoundCode'] + '.png' - compoundCIF = xtal + '_' + self.db_dict['CompoundCode'] + '.cif' + compoundImage = xtal + '_' + \ + self.db_dict['CompoundCode'] + '.png' + compoundCIF = xtal + '_' + \ + self.db_dict['CompoundCode'] + '.cif' residuePlot = xtal + '_' + ligand + '.png' pdb = xtal + '.pdb' event = xtal + '_' + ligand + '_event.ccp4' @@ -89,138 +97,158 @@ def prepare(self,whichSamples): unitCell = self.db_dict['DataProcessingUnitCell'] t = '' for ax in unitCell.split(): - t += str(round(float(ax),1)) + ' ' + t += str(round(float(ax), 1)) + ' ' unitCell = t[:-1] - os.chdir(os.path.join(self.projectDir,xtal)) + os.chdir(os.path.join(self.projectDir, xtal)) # FWT = xtal + '-' + ligand + '_2fofc.ccp4' # self.cut_and_copy_map(xtal, ligand + '.pdb', '2fofc.map', FWT,'FWT','PHWT') # DELFWT = xtal + '-' + ligand + '_fofc.ccp4' # self.cut_and_copy_map(xtal, ligand + '.pdb', 'fofc.map', DELFWT,'DELFWT','PHDELWT') if os.path.isfile('refine.mtz'): - self.Logfile.insert('%s: found refine.mtz' %xtal) - FWTmap, DELFWTmap = self.prepare_e_density_maps(xtal,ligand) - self.copy_electron_density(xtal,ligand,eventMap) - ligConfidence = self.db.get_ligand_confidence_for_ligand(xtal, ligChain, ligNumber, ligName) + self.Logfile.insert('%s: found refine.mtz' % xtal) + FWTmap, DELFWTmap = self.prepare_e_density_maps( + xtal, ligand) + self.copy_electron_density(xtal, ligand, eventMap) + ligConfidence = self.db.get_ligand_confidence_for_ligand( + xtal, ligChain, ligNumber, ligName) if ligConfidence.startswith('0'): - self.Logfile.warning('%s: ligand confidence of %s-%s-%s is %s; ignoring...' %(xtal,ligChain,ligNumber,ligName,ligConfidence)) - self.Logfile.warning('%s: this seems unlikely because this structure is apparently ready for deposition' %xtal) - self.Logfile.warning('%s: will set it to "not assigned" for now, but please update in soakDB' %xtal) + self.Logfile.warning('%s: ligand confidence of %s-%s-%s is %s; ignoring...' % ( + xtal, ligChain, ligNumber, ligName, ligConfidence)) + self.Logfile.warning( + '%s: this seems unlikely because this structure is apparently ready for deposition' % xtal) + self.Logfile.warning( + '%s: will set it to "not assigned" for now, but please update in soakDB' % xtal) ligConfidence = 'not assigned' modelStatus = self.db_dict['RefinementOutcome'] if firstFile: - html += XChemMain.html_ngl(pdb,eventMap.replace(self.projectDir,''),FWTmap,DELFWTmap,ligand) + html += XChemMain.html_ngl(pdb, eventMap.replace( + self.projectDir, ''), FWTmap, DELFWTmap, ligand) html += XChemMain.html_download(self.protein_name) html += XChemMain.html_guide() html += XChemMain.html_table_header() firstFile = False - html += XChemMain.html_table_row(xtal,pdbID,ligand,compoundImage,residuePlot,pdb,event, - thumbNail,resoHigh,spg,unitCell,FWTmap,DELFWTmap,ligConfidence,modelStatus) - self.make_thumbnail(xtal,x,y,z,ligand,eventMap) - self.prepare_for_download(xtal, pdb, event, compoundCIF, ligand) + html += XChemMain.html_table_row(xtal, pdbID, ligand, compoundImage, residuePlot, pdb, event, + thumbNail, resoHigh, spg, unitCell, FWTmap, DELFWTmap, ligConfidence, modelStatus) + self.make_thumbnail(xtal, x, y, z, ligand, eventMap) + self.prepare_for_download( + xtal, pdb, event, compoundCIF, ligand) self.prepare_zip_archives() # html = XChemMain.html_download_all_section(html,self.protein_name) self.write_html_file(html) - self.Logfile.insert('======== finished preparing HTML summary ========') - + self.Logfile.insert( + '======== finished preparing HTML summary ========') - def prepare_e_density_maps(self,xtal,ligand): - FWT, PHWT, DELFWT, PHDELWT = XChemUtils.mtztools_gemmi('refine.mtz').get_map_labels() + def prepare_e_density_maps(self, xtal, ligand): + FWT, PHWT, DELFWT, PHDELWT = XChemUtils.mtztools_gemmi( + 'refine.mtz').get_map_labels() self.Logfile.insert(xtal + ': calculating 2fofc map...') - XChemUtils.maptools().calculate_map('refine.mtz',FWT,PHWT) + XChemUtils.maptools().calculate_map('refine.mtz', FWT, PHWT) if os.path.isfile('refine.ccp4'): self.Logfile.insert(xtal + ': 2fofc map successfully calculated') else: self.Logfile.error(xtal + ': 2fofc map could not be calculated') self.Logfile.insert(xtal + ': cutting 2fofc map 7A around ' + ligand) - XChemUtils.maptools().cut_map_around_ligand('refine.ccp4',ligand+'.pdb','7') + XChemUtils.maptools().cut_map_around_ligand('refine.ccp4', ligand+'.pdb', '7') if os.path.isfile('refine_mapmask.ccp4'): - self.Logfile.insert(xtal + ': 2fofc map around ' + ligand + ' successfully created') + self.Logfile.insert(xtal + ': 2fofc map around ' + + ligand + ' successfully created') else: - self.Logfile.error(xtal + ': 2fofc map around ' + ligand + ' could not be created') - os.system('/bin/mv %s %s_%s_2fofc.ccp4' %('refine_mapmask.ccp4',xtal,ligand)) + self.Logfile.error(xtal + ': 2fofc map around ' + + ligand + ' could not be created') + os.system('/bin/mv %s %s_%s_2fofc.ccp4' % + ('refine_mapmask.ccp4', xtal, ligand)) FWTmap = xtal + '_' + ligand + '_2fofc.ccp4' - self.Logfile.insert(xtal + ': current 2fofc map -> ' + xtal + '_' + ligand + '_2fofc.ccp4') - XChemUtils.maptools().calculate_map('refine.mtz',DELFWT,PHDELWT) - XChemUtils.maptools().cut_map_around_ligand('refine.ccp4',ligand+'.pdb','7') - os.system('/bin/mv %s %s_%s_fofc.ccp4' %('refine_mapmask.ccp4',xtal,ligand)) + self.Logfile.insert(xtal + ': current 2fofc map -> ' + + xtal + '_' + ligand + '_2fofc.ccp4') + XChemUtils.maptools().calculate_map('refine.mtz', DELFWT, PHDELWT) + XChemUtils.maptools().cut_map_around_ligand('refine.ccp4', ligand+'.pdb', '7') + os.system('/bin/mv %s %s_%s_fofc.ccp4' % + ('refine_mapmask.ccp4', xtal, ligand)) DELFWTmap = xtal + '_' + ligand + '_fofc.ccp4' return FWTmap, DELFWTmap - def prepare_zip_archives(self): - os.chdir(os.path.join(self.htmlDir,'files')) - self.Logfile.insert('%s: preparing ZIP archive of all PDB files' %self.protein_name) - os.system('zip %s_allPDBs.zip *.pdb' %self.protein_name) - self.Logfile.insert('%s: preparing ZIP archive of all PanDDA event maps' %self.protein_name) - os.system('zip %s_allEVENTmaps.zip *event.ccp4' %self.protein_name) - self.Logfile.insert('%s: preparing ZIP archive of all CIF files' %self.protein_name) - os.system('zip %s_allCIFs.zip *.cif' %self.protein_name) - self.Logfile.insert('%s: preparing ZIP archive of all MTZ files' %self.protein_name) - os.system('zip %s_allMTZs.zip *.mtz' %self.protein_name) - - - def prepare_for_download(self,xtal,pdb,event,compoundCIF,ligID): - os.chdir(os.path.join(self.htmlDir,'tmp')) - self.Logfile.insert('%s: preparing files for download' %xtal) + os.chdir(os.path.join(self.htmlDir, 'files')) + self.Logfile.insert( + '%s: preparing ZIP archive of all PDB files' % self.protein_name) + os.system('zip %s_allPDBs.zip *.pdb' % self.protein_name) + self.Logfile.insert( + '%s: preparing ZIP archive of all PanDDA event maps' % self.protein_name) + os.system('zip %s_allEVENTmaps.zip *event.ccp4' % self.protein_name) + self.Logfile.insert( + '%s: preparing ZIP archive of all CIF files' % self.protein_name) + os.system('zip %s_allCIFs.zip *.cif' % self.protein_name) + self.Logfile.insert( + '%s: preparing ZIP archive of all MTZ files' % self.protein_name) + os.system('zip %s_allMTZs.zip *.mtz' % self.protein_name) + + def prepare_for_download(self, xtal, pdb, event, compoundCIF, ligID): + os.chdir(os.path.join(self.htmlDir, 'tmp')) + self.Logfile.insert('%s: preparing files for download' % xtal) zip_in = '' - if os.path.isfile('../files/%s' %pdb): - os.system('/bin/cp ../files/%s .' %pdb) + if os.path.isfile('../files/%s' % pdb): + os.system('/bin/cp ../files/%s .' % pdb) zip_in += pdb + ' ' else: - self.Logfile.error('%s: cannot find %s' %(xtal,pdb)) + self.Logfile.error('%s: cannot find %s' % (xtal, pdb)) - if os.path.isfile('../files/%s' %event): - os.system('/bin/cp ../files/%s .' %event) + if os.path.isfile('../files/%s' % event): + os.system('/bin/cp ../files/%s .' % event) zip_in += event + ' ' else: - self.Logfile.error('%s: cannot find %s' %(xtal,event)) + self.Logfile.error('%s: cannot find %s' % (xtal, event)) - if os.path.isfile('../files/%s' %compoundCIF): - os.system('/bin/cp ../files/%s .' %compoundCIF) + if os.path.isfile('../files/%s' % compoundCIF): + os.system('/bin/cp ../files/%s .' % compoundCIF) zip_in += compoundCIF + ' ' else: - self.Logfile.error('%s: cannot find %s' %(xtal,compoundCIF)) + self.Logfile.error('%s: cannot find %s' % (xtal, compoundCIF)) if zip_in != '': - self.Logfile.insert('%s: preparing zip file -> zip %s_%s.zip %s' %(xtal,xtal,ligID,zip_in)) - os.system('zip %s_%s.zip %s' %(xtal,ligID,zip_in)) - os.system('/bin/mv %s_%s.zip ../download' %(xtal,ligID)) + self.Logfile.insert( + '%s: preparing zip file -> zip %s_%s.zip %s' % (xtal, xtal, ligID, zip_in)) + os.system('zip %s_%s.zip %s' % (xtal, ligID, zip_in)) + os.system('/bin/mv %s_%s.zip ../download' % (xtal, ligID)) os.system('/bin/rm -f *') else: - self.Logfile.error('%s: cannot find any input files for creating of zip archive of %s_%s' %(xtal,xtal,ligID)) - - + self.Logfile.error( + '%s: cannot find any input files for creating of zip archive of %s_%s' % (xtal, xtal, ligID)) def copy_jscss(self): os.chdir(self.htmlDir) self.Logfile.insert('copying css and js files to ' + self.htmlDir) - os.system('/bin/cp -r %s/web/jscss/css .' %os.getenv('XChemExplorer_DIR')) - os.system('/bin/cp -r %s/web/jscss/js .' %os.getenv('XChemExplorer_DIR')) - - - def make_thumbnail(self,xtal,x,y,z,ligID,eventMap): - self.Logfile.insert('%s: making thumbnail of for %s and %s' %(xtal,ligID,eventMap)) - sampleDir = os.path.join(self.projectDir,xtal) + os.system('/bin/cp -r %s/web/jscss/css .' % + os.getenv('XChemExplorer_DIR')) + os.system('/bin/cp -r %s/web/jscss/js .' % + os.getenv('XChemExplorer_DIR')) + + def make_thumbnail(self, xtal, x, y, z, ligID, eventMap): + self.Logfile.insert( + '%s: making thumbnail of for %s and %s' % (xtal, ligID, eventMap)) + sampleDir = os.path.join(self.projectDir, xtal) os.chdir(sampleDir) - if not os.path.isfile('%s_%s_thumb.png' %(xtal,ligID)): - self.Logfile.insert('%s: preparing thumbnail image of %s' %(xtal,ligID)) + if not os.path.isfile('%s_%s_thumb.png' % (xtal, ligID)): + self.Logfile.insert( + '%s: preparing thumbnail image of %s' % (xtal, ligID)) XChemMain.coot_prepare_input(x, y, z, ligID, sampleDir, eventMap) - XChemMain.coot_write_raster_file(ligID,sampleDir) - XChemMain.render_scene(xtal,ligID,sampleDir) + XChemMain.coot_write_raster_file(ligID, sampleDir) + XChemMain.render_scene(xtal, ligID, sampleDir) XChemMain.make_thumbnail(xtal, ligID, sampleDir) - if os.path.isfile('%s_%s_thumb.png' %(xtal,ligID)): - self.Logfile.insert('%s: managed to prepare %s_%s_thumb.png' %(xtal,xtal,ligID)) - self.copy_thumbnail(xtal,sampleDir,ligID) + if os.path.isfile('%s_%s_thumb.png' % (xtal, ligID)): + self.Logfile.insert( + '%s: managed to prepare %s_%s_thumb.png' % (xtal, xtal, ligID)) + self.copy_thumbnail(xtal, sampleDir, ligID) else: - self.Logfile.error('%s: could not generate %s_%s_thumb.png' %(xtal,xtal,ligID)) + self.Logfile.error( + '%s: could not generate %s_%s_thumb.png' % (xtal, xtal, ligID)) - def copy_thumbnail(self,xtal,sampleDir,ligID): + def copy_thumbnail(self, xtal, sampleDir, ligID): os.chdir(os.path.join(self.htmlDir, 'png')) - self.Logfile.insert('%s: copying %s_%s_thumb.png to html png' %(xtal,xtal,ligID)) - os.system('/bin/cp %s/%s_%s_thumb.png .' %(sampleDir,xtal,ligID)) - + self.Logfile.insert( + '%s: copying %s_%s_thumb.png to html png' % (xtal, xtal, ligID)) + os.system('/bin/cp %s/%s_%s_thumb.png .' % (sampleDir, xtal, ligID)) def makeFolders(self): self.Logfile.insert('preparing folders in html directory') @@ -236,84 +264,108 @@ def makeFolders(self): if not os.path.isdir('download'): os.mkdir('download') - def copy_pdb(self,xtal): + def copy_pdb(self, xtal): os.chdir(os.path.join(self.htmlDir, 'files')) self.pdb = None - if os.path.isfile(os.path.join(self.projectDir,xtal,'refine.split.bound-state.pdb')): - self.pdb = pdbtools(os.path.join(self.projectDir,xtal,'refine.split.bound-state.pdb')) - self.Logfile.insert('%s: copying refine.split.bound-state.pdb to html directory' %xtal) - os.system('/bin/cp %s/refine.split.bound-state.pdb %s.pdb' %(os.path.join(self.projectDir,xtal),xtal)) + if os.path.isfile(os.path.join(self.projectDir, xtal, 'refine.split.bound-state.pdb')): + self.pdb = pdbtools(os.path.join( + self.projectDir, xtal, 'refine.split.bound-state.pdb')) + self.Logfile.insert( + '%s: copying refine.split.bound-state.pdb to html directory' % xtal) + os.system('/bin/cp %s/refine.split.bound-state.pdb %s.pdb' % + (os.path.join(self.projectDir, xtal), xtal)) else: - self.Logfile.error('%s: cannot find refine.split.bound-state.pdb' %xtal) + self.Logfile.error( + '%s: cannot find refine.split.bound-state.pdb' % xtal) - def copy_mtz(self,xtal): + def copy_mtz(self, xtal): os.chdir(os.path.join(self.htmlDir, 'files')) - if os.path.isfile(os.path.join(self.projectDir,xtal,xtal+'.free.mtz')): - self.Logfile.insert('%s: copying %s.free.mtz to html directory' %(xtal,xtal)) - os.system('/bin/cp %s/%s.free.mtz .' %(os.path.join(self.projectDir,xtal),xtal)) + if os.path.isfile(os.path.join(self.projectDir, xtal, xtal+'.free.mtz')): + self.Logfile.insert( + '%s: copying %s.free.mtz to html directory' % (xtal, xtal)) + os.system('/bin/cp %s/%s.free.mtz .' % + (os.path.join(self.projectDir, xtal), xtal)) else: - self.Logfile.error('%s: cannot find %s.free.mtz' %(xtal,xtal)) + self.Logfile.error('%s: cannot find %s.free.mtz' % (xtal, xtal)) - def copy_electron_density(self,xtal,ligand,eventMap): + def copy_electron_density(self, xtal, ligand, eventMap): os.chdir(os.path.join(self.htmlDir, 'files')) emap = xtal+'_'+ligand+'_2fofc.ccp4' - if os.path.isfile(os.path.join(self.projectDir,xtal,emap)): - self.Logfile.insert('%s: copying %s to html directory' %(xtal,emap)) - os.system('/bin/cp %s/%s %s' %(os.path.join(self.projectDir,xtal),emap,emap)) + if os.path.isfile(os.path.join(self.projectDir, xtal, emap)): + self.Logfile.insert( + '%s: copying %s to html directory' % (xtal, emap)) + os.system('/bin/cp %s/%s %s' % + (os.path.join(self.projectDir, xtal), emap, emap)) else: - self.Logfile.error('%s: cannot find %s' %(xtal,emap)) + self.Logfile.error('%s: cannot find %s' % (xtal, emap)) emap = xtal+'_'+ligand+'_fofc.ccp4' - if os.path.isfile(os.path.join(self.projectDir,xtal,emap)): - self.Logfile.insert('%s: copying %s to html directory' %(xtal,emap)) - os.system('/bin/cp %s/%s %s' %(os.path.join(self.projectDir,xtal),emap,emap)) + if os.path.isfile(os.path.join(self.projectDir, xtal, emap)): + self.Logfile.insert( + '%s: copying %s to html directory' % (xtal, emap)) + os.system('/bin/cp %s/%s %s' % + (os.path.join(self.projectDir, xtal), emap, emap)) else: - self.Logfile.error('%s: cannot find %s' %(xtal,emap)) - - self.Logfile.insert('%s: looking for %s' %(xtal,os.path.join(self.projectDir,xtal,eventMap))) - if os.path.isfile(os.path.join(self.projectDir,xtal,eventMap)): - self.Logfile.insert('%s: copying %s to html directory' %(xtal,eventMap)) - os.system('/bin/cp %s/%s %s' %(os.path.join(self.projectDir,xtal),eventMap,eventMap)) + self.Logfile.error('%s: cannot find %s' % (xtal, emap)) + + self.Logfile.insert('%s: looking for %s' % ( + xtal, os.path.join(self.projectDir, xtal, eventMap))) + if os.path.isfile(os.path.join(self.projectDir, xtal, eventMap)): + self.Logfile.insert( + '%s: copying %s to html directory' % (xtal, eventMap)) + os.system('/bin/cp %s/%s %s' % + (os.path.join(self.projectDir, xtal), eventMap, eventMap)) else: - self.Logfile.error('%s: cannot find %s' %(xtal,eventMap)) + self.Logfile.error('%s: cannot find %s' % (xtal, eventMap)) - def copy_ligand_files(self,xtal): - os.chdir(os.path.join(self.htmlDir,'files')) + def copy_ligand_files(self, xtal): + os.chdir(os.path.join(self.htmlDir, 'files')) - if os.path.isfile(os.path.join(self.projectDir,xtal,self.db_dict['CompoundCode']+'.cif')): - self.Logfile.insert('%s: copying compound cif file' %xtal) - os.system('/bin/cp %s %s_%s' %(os.path.join(self.projectDir,xtal,self.db_dict['CompoundCode']+'.cif'),xtal,self.db_dict['CompoundCode']+'.cif')) + if os.path.isfile(os.path.join(self.projectDir, xtal, self.db_dict['CompoundCode']+'.cif')): + self.Logfile.insert('%s: copying compound cif file' % xtal) + os.system('/bin/cp %s %s_%s' % (os.path.join(self.projectDir, xtal, + self.db_dict['CompoundCode']+'.cif'), xtal, self.db_dict['CompoundCode']+'.cif')) else: - self.Logfile.error('%s: cannot find compound cif file -> %s' %(xtal,self.db_dict['CompoundCode']+'.cif')) + self.Logfile.error('%s: cannot find compound cif file -> %s' % + (xtal, self.db_dict['CompoundCode']+'.cif')) - os.chdir(os.path.join(self.htmlDir,'png')) + os.chdir(os.path.join(self.htmlDir, 'png')) - if os.path.isfile(os.path.join(self.projectDir,xtal,self.db_dict['CompoundCode']+'.png')): - self.Logfile.insert('%s: copying compound png file' %xtal) - os.system('/bin/cp %s %s_%s' %(os.path.join(self.projectDir,xtal,self.db_dict['CompoundCode']+'.png'),xtal,self.db_dict['CompoundCode']+'.png')) + if os.path.isfile(os.path.join(self.projectDir, xtal, self.db_dict['CompoundCode']+'.png')): + self.Logfile.insert('%s: copying compound png file' % xtal) + os.system('/bin/cp %s %s_%s' % (os.path.join(self.projectDir, xtal, + self.db_dict['CompoundCode']+'.png'), xtal, self.db_dict['CompoundCode']+'.png')) else: - self.Logfile.error('%s: cannot find compound png file -> %s' %(xtal,self.db_dict['CompoundCode']+'.png')) + self.Logfile.error('%s: cannot find compound png file -> %s' % + (xtal, self.db_dict['CompoundCode']+'.png')) - def copy_spider_plot(self,xtal,ligID): + def copy_spider_plot(self, xtal, ligID): os.chdir(os.path.join(self.htmlDir, 'png')) - refPDB = os.path.join(self.projectDir,xtal,'refine.pdb') - self.Logfile.insert('%s: looking for spider plots...' %xtal) + refPDB = os.path.join(self.projectDir, xtal, 'refine.pdb') + self.Logfile.insert('%s: looking for spider plots...' % xtal) if os.path.isfile(refPDB): - refPDBreal = os.path.realpath(refPDB)[:os.path.realpath(refPDB).rfind('/')] - plot = os.path.join(refPDBreal,'residue_plots',ligID.replace('LIG-','')+'.png') + refPDBreal = os.path.realpath( + refPDB)[:os.path.realpath(refPDB).rfind('/')] + plot = os.path.join(refPDBreal, 'residue_plots', + ligID.replace('LIG-', '')+'.png') self.Logfile.insert(xtal + ': looking for ' + plot) if os.path.isfile(plot): self.Logfile.insert('%s: found %s' % (xtal, plot)) - self.Logfile.insert('%s: copying spider plot for %s' % (xtal, ligID.replace('LIG-', '') + '.png')) + self.Logfile.insert('%s: copying spider plot for %s' % ( + xtal, ligID.replace('LIG-', '') + '.png')) os.system('/bin/cp %s %s_%s.png' % (plot, xtal, ligID)) else: - self.Logfile.error('%s: cannot find spider plot for %s' %(xtal,ligID.replace('LIG-','')+'.png')) - self.Logfile.warning('%s: using %s instead' %(xtal,'NO_SPIDER_PLOT_AVAILABLE.png')) - os.system('/bin/cp %s %s_%s.png' % (os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png'), xtal, ligID)) + self.Logfile.error('%s: cannot find spider plot for %s' % ( + xtal, ligID.replace('LIG-', '')+'.png')) + self.Logfile.warning('%s: using %s instead' % ( + xtal, 'NO_SPIDER_PLOT_AVAILABLE.png')) + os.system('/bin/cp %s %s_%s.png' % (os.path.join(os.getenv( + 'XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png'), xtal, ligID)) # else: - self.Logfile.error('%s: cannot find refine.pdb, i.e. cannot start looking for spider plots...' %xtal) + self.Logfile.error( + '%s: cannot find refine.pdb, i.e. cannot start looking for spider plots...' % xtal) # def ligands_in_pdbFile(self,xtal): @@ -390,7 +442,7 @@ def copy_spider_plot(self,xtal,ligID): # if os.path.isfile(mapout): # self.Logfile.warning('%s: removing map -> %s' %(xtal,mapout)) # os.system('/bin/rm '+mapout) -## else: +# else: # # if mapin.endswith('.map') or mapin.endswith('.ccp4'): # cmd = ( @@ -417,7 +469,6 @@ def copy_spider_plot(self,xtal,ligID): # self.Logfile.error(xtal+': creation of event map failed') - # def cut_eventMAP(self,xtal,ligID,eventMAP): # os.chdir(os.path.join(self.projectDir, xtal)) # self.Logfile.insert('%s: cutting event map around ligand %s' %(xtal,ligID)) @@ -440,12 +491,12 @@ def copy_spider_plot(self,xtal,ligID): # ligID = lig.replace('.pdb','') # ccLog = mtz.replace('.mtz', '_CC'+ligID+'.log') # self.Logfile.insert('%s: calculating CC for %s in %s' %(xtal,lig,mtz)) -## if os.path.isfile(mtz.replace('.mtz', '_CC'+ligID+'.log')): +# if os.path.isfile(mtz.replace('.mtz', '_CC'+ligID+'.log')): # if os.path.isfile(ccLog) and os.path.getsize(ccLog) != 0: # self.Logfile.warning('logfile of CC analysis exists; skipping...') # return -## cmd = ( 'module load phenix\n' -## 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log')) ) +# cmd = ( 'module load phenix\n' +# 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log')) ) # os.system('/bin/rm %s' %mtz.replace('.mtz', '_CC'+ligID+'.log') ) # cmd = ( 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log')) ) # os.system(cmd) @@ -460,13 +511,12 @@ def copy_spider_plot(self,xtal,ligID): # self.Logfile.error('logfile does not exist: %s' %log) # return cc - def write_html_file(self,html): + def write_html_file(self, html): os.chdir(self.htmlDir) self.Logfile.insert('writing index.html') html += XChemMain.html_footer() if os.path.isfile('index.html'): os.system('/bin/rm -f index.html') - f = open('index.html','w') + f = open('index.html', 'w') f.write(html) f.close() - diff --git a/web/process_sqlite.py b/web/process_sqlite.py index b81a854d..6c1511cf 100755 --- a/web/process_sqlite.py +++ b/web/process_sqlite.py @@ -3,9 +3,11 @@ #!/usr/local/anaconda/sgc_default/envs/sgc_default/bin/python # Author: Brian Marsden -# +# # handover date: 16/12/2016 +from rdkit.Chem import Draw +from rdkit import Chem import shutil import os import sys @@ -15,159 +17,184 @@ import zipfile import glob -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'),'lib')) +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) -from rdkit import Chem -from rdkit.Chem import Draw targetID = '' panddadir = '' -def writeTableRow (row,htmlfile): - "Write a row of data to the HTML file" - htmlfile.write("") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") + +def writeTableRow(row, htmlfile): + "Write a row of data to the HTML file" + htmlfile.write("") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") # htmlfile.write("\n") - htmlfile.write("\n") + htmlfile.write("\n") # htmlfile.write("\n") # htmlfile.write("\n" %row['Deposition_PDB_ID']) - htmlfile.write('\n'.format(row['Deposition_PDB_ID'], row['Deposition_PDB_ID'])) - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - return + htmlfile.write('\n'.format( + row['Deposition_PDB_ID'], row['Deposition_PDB_ID'])) + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + return -def writeICBPage (row,panddadir): - "Write HTML file for ICB visualisation" - icbhtmlfile=open(panddadir+"/icbs/"+row['ModelName']+".html", "w") - icbhtmlfile.write("\n") - icbhtmlfile.write("\n") - icbhtmlfile.write('\n') - icbhtmlfile.write('\n') - icbhtmlfile.write('\n') - icbhtmlfile.write(''+row['ModelName']+'\n') - icbhtmlfile.write("\n") - icbhtmlfile.write("\n") - icbhtmlfile.write("

"+row['CrystalName']+" "+row['CompoundCode']+" event

\n") - icbhtmlfile.write('

Please wait whilst the interactive viewer is loaded!

\n') - icbhtmlfile.write('
\n') - icbhtmlfile.write('\n') + +def writeICBPage(row, panddadir): + "Write HTML file for ICB visualisation" + icbhtmlfile = open(panddadir+"/icbs/"+row['ModelName']+".html", "w") + icbhtmlfile.write("\n") + icbhtmlfile.write("\n") + icbhtmlfile.write( + '\n') + icbhtmlfile.write( + '\n') + icbhtmlfile.write( + '\n') + icbhtmlfile.write(''+row['ModelName']+'\n') + icbhtmlfile.write("\n") + icbhtmlfile.write("\n") + icbhtmlfile.write("

"+row['CrystalName'] + + " "+row['CompoundCode']+" event

\n") + icbhtmlfile.write( + '

Please wait whilst the interactive viewer is loaded!

\n') + icbhtmlfile.write( + '
\n') + icbhtmlfile.write('\n') # icbhtmlfile.write('\n') - icbhtmlfile.write('
\n') - icbhtmlfile.write('
\n') - icbhtmlfile.write("
Crystal IDPDB IDLigand IDLigand confidenceModel statusCompoundLigand ValidationEvent Map 3DResolSPG/ CellFiles
%s%s%s%s%s
%s%s
%s		Save%s%s%s%s%s
%s%s
%s		Save
"+row['ModelName']+""+row['CompoundSMILES']+""+row['PANDDA_site_name']+""+row['LigandConfidence']+""+row['ModelStatus']+"
"+row['ModelName']+""+row['CompoundSMILES']+""+row['PANDDA_site_name']+""+row['LigandConfidence']+""+row['ModelStatus']+"
"+row['PANDDA_site_comment']+""+row['PANDDA_site_comment']+"TBDhttp://www.rcsb.org/pdb/explore/explore.do?structureId=%s{1!s}"+row['DataProcessingResolutionHigh']+""+row['DataProcessingSpaceGroup']+""+row['DataProcessingUnitCell']+"SaveSaveSave
{1!s}"+row['DataProcessingResolutionHigh']+""+row['DataProcessingSpaceGroup']+""+row['DataProcessingUnitCell']+"SaveSaveSave
\n") - icbhtmlfile.write("\n") - icbhtmlfile.write("\n") - icbhtmlfile.write("\n") - icbhtmlfile.write("
Protein: "+row['CrystalName']+"
Compound ID: "+row['CompoundCode']+"
Compound SMILES: "+row['CompoundSMILES']+"
\n") - icbhtmlfile.write("
\n") - icbhtmlfile.write('\n') - icbhtmlfile.write("\n") - icbhtmlfile.write("\n") - icbhtmlfile.close() - return + icbhtmlfile.write(' act.searchBarVisible = false;\n') + icbhtmlfile.write(' act.sequenceViewVisibleAuto = false;\n') + icbhtmlfile.write(' act.tableViewVisibleAuto = false;\n') + icbhtmlfile.write( + ' document.getElementById("wait").style.visibility = "hidden";\n') + icbhtmlfile.write('}\n') + icbhtmlfile.write('\n') + icbhtmlfile.write("\n") + icbhtmlfile.write("\n") + icbhtmlfile.close() + return + -def main (argv): - sqlitefile = '' - # Process command line options - try: - opts, args = getopt.getopt(argv,'t:s:d:',['targetID=','sqlitefile=','panddadir=']) - except getopt.GetoptError as err: - print err - print 'process.py -t -s -d ' - sys.exit(2) - if len(opts)<3: - print 'Missing arguments:' - print 'process.py -t -s -d ' - sys.exit(2) - for opt, arg in opts: - if opt == '-h': - print 'process.py -t -s ' - sys.exit() - elif opt in ("-t", "--targetID"): - targetID = arg - elif opt in ("-s", "--sqlitefile"): - sqlitefile = arg - elif opt in ("-d", "--panddadir"): - panddadir = arg +def main(argv): + sqlitefile = '' + # Process command line options + try: + opts, args = getopt.getopt( + argv, 't:s:d:', ['targetID=', 'sqlitefile=', 'panddadir=']) + except getopt.GetoptError as err: + print err + print 'process.py -t -s -d ' + sys.exit(2) + if len(opts) < 3: + print 'Missing arguments:' + print 'process.py -t -s -d ' + sys.exit(2) + for opt, arg in opts: + if opt == '-h': + print 'process.py -t -s ' + sys.exit() + elif opt in ("-t", "--targetID"): + targetID = arg + elif opt in ("-s", "--sqlitefile"): + sqlitefile = arg + elif opt in ("-d", "--panddadir"): + panddadir = arg - # Create directory structure - if not os.path.exists(panddadir+"/compoundImages"): - os.makedirs(panddadir+"/compoundImages") - if not os.path.exists(panddadir+"/icbs"): - os.makedirs(panddadir+"/icbs") - if not os.path.exists(panddadir+"/pdbs"): - os.makedirs(panddadir+"/pdbs") - if not os.path.exists(panddadir+"/maps"): - os.makedirs(panddadir+"/maps") - if not os.path.exists(panddadir+"/residueplots"): - os.makedirs(panddadir+"/residueplots") - if not os.path.exists(panddadir+"/mapImages"): - os.makedirs(panddadir+"/mapImages") + # Create directory structure + if not os.path.exists(panddadir+"/compoundImages"): + os.makedirs(panddadir+"/compoundImages") + if not os.path.exists(panddadir+"/icbs"): + os.makedirs(panddadir+"/icbs") + if not os.path.exists(panddadir+"/pdbs"): + os.makedirs(panddadir+"/pdbs") + if not os.path.exists(panddadir+"/maps"): + os.makedirs(panddadir+"/maps") + if not os.path.exists(panddadir+"/residueplots"): + os.makedirs(panddadir+"/residueplots") + if not os.path.exists(panddadir+"/mapImages"): + os.makedirs(panddadir+"/mapImages") - # Create HTML file and write header - htmlfile = open(panddadir+"/index.html", "w") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write('\n') - htmlfile.write('\n') - htmlfile.write('\n') - htmlfile.write(''+targetID+' Fragment Hits\n') - htmlfile.write('\n') - htmlfile.write('\n') - htmlfile.write('\n') - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("

Ligand-bound models for "+targetID+"

") - htmlfile.write("""

Interpreting 'Ligand confidence'

+ # Create HTML file and write header + htmlfile = open(panddadir+"/index.html", "w") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write( + '\n') + htmlfile.write( + '\n') + htmlfile.write( + '\n') + htmlfile.write(''+targetID+' Fragment Hits\n') + htmlfile.write( + '\n') + htmlfile.write( + '\n') + htmlfile.write('\n') + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("

Ligand-bound models for "+targetID+"

") + htmlfile.write("""

Interpreting 'Ligand confidence'

4 - High Confidence: The expected ligand was easily interpretable from clear density, and subsequent refinement was well-behaved. This ligand can be trusted.
3 - Clear density, unexpected ligand: Density very clearly showed a well-defined ligand, but that ligand was unexpected in that crystal/dataset. The observed ligand was modelled anyway, because its presence could be explained in some way.
2 - Correct ligand, weak density: Though density was weak, it was possible to model the expected ligand, possibly including other circumstantial evidence (e.g. similar ligand in another model). @@ -183,59 +210,61 @@ def main (argv):
RMSD compares the positions of all atoms built into event density, with their positions after final refinement, and should be below 1Å.
Precision (RSZO/OCC) measures how clear the density is after refinement. (This is not a quality indicator, but is related to strength of binding but not in a straightforward way.)

\n""") - htmlfile.write("

Download data

\n") - htmlfile.write("") - htmlfile.write('\n') - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.write("\n") + htmlfile.write("

Download data

\n") + htmlfile.write("") + htmlfile.write('
Model NameCompound SMILESCompound StructureSite NameLigand ConfidenceModel StatusLigand ValidationEvent Map 3DCommentPDB IdentifierResolSpacegroupCellPDBMTZEvent Map
Model NameCompound SMILESCompound StructureSite NameLigand ConfidenceModel StatusLigand ValidationEvent Map 3DCommentPDB IdentifierResolSpacegroupCellPDBMTZEvent Map
\n') + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") - # Now walk through the input data - with open('foricm.csv', 'wb') as f: - with sqlite3.connect(sqlitefile) as c: - c.row_factory=sqlite3.Row - cur=c.cursor() + # Now walk through the input data + with open('foricm.csv', 'wb') as f: + with sqlite3.connect(sqlitefile) as c: + c.row_factory = sqlite3.Row + cur = c.cursor() # sql = ( "select p.ID,p.CrystalName,p.PANDDA_site_event_index,p.CrystalName || '_event'|| p.PANDDA_site_event_index " # " as ModelName,m.CompoundCode,m.CompoundSMILES,p.PANDDA_site_name,p.PANDDA_site_confidence " @@ -249,113 +278,124 @@ def main (argv): # " order by p.CrystalName,ModelStatus desc,PANDDA_site_event_index" # ) - # query below is without the LigandConfidence being constrained; this is because some older DBs don't have a starting digit - # here we constrain RefinementOutcome of site + # query below is without the LigandConfidence being constrained; this is because some older DBs don't have a starting digit + # here we constrain RefinementOutcome of site # cur.execute("select p.ID,p.CrystalName,p.PANDDA_site_event_index,p.CrystalName || '_event'|| p.PANDDA_site_event_index as ModelName,m.CompoundCode,m.CompoundSMILES,m.Deposition_PDB_ID,p.PANDDA_site_name,p.PANDDA_site_confidence as LigandConfidence,p.RefinementOutcome as ModelStatus,p.PANDDA_site_comment,p.PANDDA_site_x,p.PANDDA_site_y,p.PANDDA_site_z, p.PANDDA_site_spider_plot,m.DataProcessingResolutionHigh,m.DataProcessingSpaceGroup,m.DataProcessingUnitCell,m.RefinementBoundConformation,m.RefinementMTZ_latest,p.PANDDA_site_event_map from panddaTable as p, mainTable as m where p.CrystalName=m.CrystalName and p.PANDDA_site_ligand_placed='True' and (p.RefinementOutcome like '4%' or p.RefinementOutcome like '5%' or p.RefinementOutcome like '6%') order by p.CrystalName,ModelStatus desc,PANDDA_site_event_index") + sql = ( + "select p.ID,p.CrystalName,p.PANDDA_site_event_index,p.CrystalName || '_event'|| p.PANDDA_site_event_index " + " as ModelName,m.CompoundCode,m.CompoundSMILES,m.Deposition_PDB_ID,p.PANDDA_site_name," + " p.PANDDA_site_confidence as LigandConfidence," + " p.RefinementOutcome as ModelStatus," + " p.PANDDA_site_comment,p.PANDDA_site_x,p.PANDDA_site_y,p.PANDDA_site_z, p.PANDDA_site_spider_plot," + " m.DataProcessingResolutionHigh,m.DataProcessingSpaceGroup,m.DataProcessingUnitCell," + " m.RefinementBoundConformation,m.RefinementMTZ_latest," + " p.PANDDA_site_event_map from panddaTable as p, " + " mainTable as m where p.CrystalName=m.CrystalName and p.PANDDA_site_ligand_placed='True' " + " and (p.RefinementOutcome like '4%' or p.RefinementOutcome like '5%' or p.RefinementOutcome like '6%') " + " and (LigandConfidence like '1%' or LigandConfidence like '2%' or LigandConfidence like '3%' or LigandConfidence like '4%')" + " order by p.CrystalName,ModelStatus desc,PANDDA_site_event_index" + ) - sql = ( - "select p.ID,p.CrystalName,p.PANDDA_site_event_index,p.CrystalName || '_event'|| p.PANDDA_site_event_index " - " as ModelName,m.CompoundCode,m.CompoundSMILES,m.Deposition_PDB_ID,p.PANDDA_site_name," - " p.PANDDA_site_confidence as LigandConfidence," - " p.RefinementOutcome as ModelStatus," - " p.PANDDA_site_comment,p.PANDDA_site_x,p.PANDDA_site_y,p.PANDDA_site_z, p.PANDDA_site_spider_plot," - " m.DataProcessingResolutionHigh,m.DataProcessingSpaceGroup,m.DataProcessingUnitCell," - " m.RefinementBoundConformation,m.RefinementMTZ_latest," - " p.PANDDA_site_event_map from panddaTable as p, " - " mainTable as m where p.CrystalName=m.CrystalName and p.PANDDA_site_ligand_placed='True' " - " and (p.RefinementOutcome like '4%' or p.RefinementOutcome like '5%' or p.RefinementOutcome like '6%') " - " and (LigandConfidence like '1%' or LigandConfidence like '2%' or LigandConfidence like '3%' or LigandConfidence like '4%')" - " order by p.CrystalName,ModelStatus desc,PANDDA_site_event_index" - ) - - sql = ( - "select p.ID,p.CrystalName,p.PANDDA_site_event_index,p.CrystalName || '_event'|| p.PANDDA_site_event_index " - " as ModelName,m.CompoundCode,m.CompoundSMILES,m.Deposition_PDB_ID,p.PANDDA_site_name," - " p.PANDDA_site_confidence as LigandConfidence," - " p.RefinementOutcome as ModelStatus," - " p.PANDDA_site_comment,p.PANDDA_site_x,p.PANDDA_site_y,p.PANDDA_site_z, p.PANDDA_site_spider_plot," - " m.DataProcessingResolutionHigh,m.DataProcessingSpaceGroup,m.DataProcessingUnitCell," - " m.RefinementBoundConformation,m.RefinementMTZ_latest," - " p.PANDDA_site_event_map from panddaTable as p, " - " mainTable as m where p.CrystalName=m.CrystalName and p.PANDDA_site_ligand_placed='True' " - " and (m.RefinementOutcome like '4%' or m.RefinementOutcome like '5%' or m.RefinementOutcome like '6%') " - " and (LigandConfidence like '1%' or LigandConfidence like '2%' or LigandConfidence like '3%' or LigandConfidence like '4%')" - " order by p.CrystalName,ModelStatus desc,PANDDA_site_event_index" - ) + sql = ( + "select p.ID,p.CrystalName,p.PANDDA_site_event_index,p.CrystalName || '_event'|| p.PANDDA_site_event_index " + " as ModelName,m.CompoundCode,m.CompoundSMILES,m.Deposition_PDB_ID,p.PANDDA_site_name," + " p.PANDDA_site_confidence as LigandConfidence," + " p.RefinementOutcome as ModelStatus," + " p.PANDDA_site_comment,p.PANDDA_site_x,p.PANDDA_site_y,p.PANDDA_site_z, p.PANDDA_site_spider_plot," + " m.DataProcessingResolutionHigh,m.DataProcessingSpaceGroup,m.DataProcessingUnitCell," + " m.RefinementBoundConformation,m.RefinementMTZ_latest," + " p.PANDDA_site_event_map from panddaTable as p, " + " mainTable as m where p.CrystalName=m.CrystalName and p.PANDDA_site_ligand_placed='True' " + " and (m.RefinementOutcome like '4%' or m.RefinementOutcome like '5%' or m.RefinementOutcome like '6%') " + " and (LigandConfidence like '1%' or LigandConfidence like '2%' or LigandConfidence like '3%' or LigandConfidence like '4%')" + " order by p.CrystalName,ModelStatus desc,PANDDA_site_event_index" + ) - cur.execute(sql) + cur.execute(sql) - rows=cur.fetchall() - if not rows: - print '==> WARNING: none of your samples seems to be at least CompChem ready (4)' - return None - writer = csv.DictWriter(f, fieldnames=rows[1].keys()) - writer.writeheader() - for row in rows: - # Make compound structure - print row['ModelName'],row['PANDDA_site_spider_plot'] - compound=Chem.MolFromSmiles(row['CompoundSMILES'].encode("ascii")) - Draw.MolToFile(compound,panddadir+'/compoundImages/'+row['CompoundCode']+'.png',(150,150)) - # Write out table information for event - eventID=row['ModelName']+"_"+row['CompoundCode'] - actID=(row['ModelName']+row['CompoundCode']).replace(targetID+'-','') - writeTableRow(row,htmlfile) - writeICBPage(row,panddadir) - try: - shutil.copy(row['RefinementBoundConformation'],panddadir+"/pdbs/"+row['ModelName']+".pdb") - shutil.copy(row['RefinementMTZ_latest'],panddadir+"/maps/"+row['ModelName']+".mtz") - shutil.copy(row['PANDDA_site_event_map'],panddadir+"/maps/"+row['ModelName']+".ccp4") - if row['PANDDA_site_spider_plot'] is not None: - shutil.copy(row['PANDDA_site_spider_plot'],panddadir+"/residueplots/"+row['ModelName']+".png") - except (IOError,TypeError): - print '*** WARNING: cannot find PDB and/or MTZ of '+row['ModelName']+' ***' - print 'PDB bound :', row['RefinementBoundConformation'] - print 'MTZ :', row['RefinementMTZ_latest'] - print 'event map :', row['PANDDA_site_event_map'] - print 'spider plot:', row['PANDDA_site_spider_plot'] - pass + rows = cur.fetchall() + if not rows: + print '==> WARNING: none of your samples seems to be at least CompChem ready (4)' + return None + writer = csv.DictWriter(f, fieldnames=rows[1].keys()) + writer.writeheader() + for row in rows: + # Make compound structure + print row['ModelName'], row['PANDDA_site_spider_plot'] + compound = Chem.MolFromSmiles( + row['CompoundSMILES'].encode("ascii")) + Draw.MolToFile(compound, panddadir+'/compoundImages/' + + row['CompoundCode']+'.png', (150, 150)) + # Write out table information for event + eventID = row['ModelName']+"_"+row['CompoundCode'] + actID = (row['ModelName']+row['CompoundCode'] + ).replace(targetID+'-', '') + writeTableRow(row, htmlfile) + writeICBPage(row, panddadir) + try: + shutil.copy(row['RefinementBoundConformation'], + panddadir+"/pdbs/"+row['ModelName']+".pdb") + shutil.copy(row['RefinementMTZ_latest'], + panddadir+"/maps/"+row['ModelName']+".mtz") + shutil.copy(row['PANDDA_site_event_map'], + panddadir+"/maps/"+row['ModelName']+".ccp4") + if row['PANDDA_site_spider_plot'] is not None: + shutil.copy(row['PANDDA_site_spider_plot'], + panddadir+"/residueplots/"+row['ModelName']+".png") + except (IOError, TypeError): + print '*** WARNING: cannot find PDB and/or MTZ of ' + \ + row['ModelName']+' ***' + print 'PDB bound :', row['RefinementBoundConformation'] + print 'MTZ :', row['RefinementMTZ_latest'] + print 'event map :', row['PANDDA_site_event_map'] + print 'spider plot:', row['PANDDA_site_spider_plot'] + pass # shutil.copy(row['RefinementPDB_latest'],panddadir+"/pdbs/"+row['ModelName']+".pdb") # if row['PANDDA_site_spider_plot'] is not None: # shutil.copy(row['PANDDA_site_spider_plot'],panddadir+"/residueplots/"+row['ModelName']+".png") - # Write row to CSV for ICM - writer.writerow(dict(row)) - - # Conclude HTML - htmlfile.write("\n") - htmlfile.write("
Model NameCompound SMILESCompound StructureSite NameLigand ConfidenceModel StatusLigand ValidationEvent Map 3DCommentPDB IdentifierResolSpacegroupCellPDBMTZEvent Map
Model NameCompound SMILESCompound StructureSite NameLigand ConfidenceModel StatusLigand ValidationEvent Map 3DCommentPDB IdentifierResolSpacegroupCellPDBMTZEvent Map
\n") - htmlfile.write("\n") - htmlfile.write("\n") - htmlfile.close() + # Write row to CSV for ICM + writer.writerow(dict(row)) + + # Conclude HTML + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.write("\n") + htmlfile.close() + + # Copy JS & CSS files + if not os.path.exists(panddadir+"/js"): + os.makedirs(panddadir+"/js") + if not os.path.exists(panddadir+"/css"): + os.makedirs(panddadir+"/css") + shutil.copy(os.path.join(os.getenv('XChemExplorer_DIR'), + "web/jscss/css/jquery.dataTables.min.css"), panddadir+"/css/jquery.dataTables.min.css") + shutil.copy(os.path.join(os.getenv('XChemExplorer_DIR'), + "web/jscss/js/jquery-1.12.3.min.js"), panddadir+"/js/jquery-1.12.3.min.js") + shutil.copy(os.path.join(os.getenv('XChemExplorer_DIR'), + "web/jscss/js/jquery.dataTables.min.js"), panddadir+"/js/jquery.dataTables.min.js") - # Copy JS & CSS files - if not os.path.exists(panddadir+"/js"): - os.makedirs(panddadir+"/js") - if not os.path.exists(panddadir+"/css"): - os.makedirs(panddadir+"/css") - shutil.copy(os.path.join(os.getenv('XChemExplorer_DIR'),"web/jscss/css/jquery.dataTables.min.css"),panddadir+"/css/jquery.dataTables.min.css") - shutil.copy(os.path.join(os.getenv('XChemExplorer_DIR'),"web/jscss/js/jquery-1.12.3.min.js"),panddadir+"/js/jquery-1.12.3.min.js") - shutil.copy(os.path.join(os.getenv('XChemExplorer_DIR'),"web/jscss/js/jquery.dataTables.min.js"),panddadir+"/js/jquery.dataTables.min.js") + # Create zip files + print "Creating zipfile of PDBs..." + os.chdir(panddadir+"/pdbs") + zf = zipfile.ZipFile("allPDBs.zip", "w") + for pdb in glob.glob("*.pdb"): + zf.write(pdb) + zf.close() - # Create zip files - print "Creating zipfile of PDBs..." - os.chdir(panddadir+"/pdbs") - zf=zipfile.ZipFile("allPDBs.zip","w") - for pdb in glob.glob("*.pdb"): - zf.write(pdb) - zf.close() + print "Creatig zipfile of event maps..." + os.chdir("../maps") + zf = zipfile.ZipFile("allEventMaps.zip", "w") + for pdb in glob.glob("*.mtz"): + zf.write(pdb) + zf.close() - print "Creatig zipfile of event maps..." - os.chdir("../maps") - zf=zipfile.ZipFile("allEventMaps.zip","w") - for pdb in glob.glob("*.mtz"): - zf.write(pdb) - zf.close() + # change folder permissions + os.system('chmod -R 775 {0!s}'.format(panddadir)) - # change folder permissions - os.system('chmod -R 775 {0!s}'.format(panddadir)) + return - return if __name__ == "__main__": - main(sys.argv[1:]) + main(sys.argv[1:]) From fc491a4453df21b25c9ef08150b40617bcea62d1 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 12:28:52 +0000 Subject: [PATCH 115/358] Add github workflow to check linting --- .github/workflows/code.yaml | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 .github/workflows/code.yaml diff --git a/.github/workflows/code.yaml b/.github/workflows/code.yaml new file mode 100644 index 00000000..44063c50 --- /dev/null +++ b/.github/workflows/code.yaml @@ -0,0 +1,29 @@ +name: Code CI + +on: + push: + branches: + - master + tags: + - "*" + pull_request: + +jobs: + lint: + runs-on: "ubuntu-latest" + steps: + - name: Checkout Source + uses: actions/checkout@v3 + with: + fetch-depth: 0 + + - name: Setup Python + uses: actions/setup-python@v4 + with: + python-version: "2.7" + + - name: Install linter + run: pip install flake8 + + - name: Lint project + run: flake8 . From e0be65e97d863ff400218db5f37418a14e638f16 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 12:49:50 +0000 Subject: [PATCH 116/358] Use defaultInterpreterPath --- .vscode/settings.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index acc2526f..ad201de9 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,3 +1,3 @@ { - "python.pythonPath": "/ccp4-7.1/bin/ccp4-python" + "python.defaultInterpreterPath": "/ccp4-7.1/bin/ccp4-python" } \ No newline at end of file From fbda573606f1e8efa06ca5c3d7bad5a79df461e9 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 12:51:29 +0000 Subject: [PATCH 117/358] Enable VSCode linting with flake8 --- .vscode/settings.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.vscode/settings.json b/.vscode/settings.json index ad201de9..30ad8f25 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,3 +1,4 @@ { - "python.defaultInterpreterPath": "/ccp4-7.1/bin/ccp4-python" + "python.defaultInterpreterPath": "/ccp4-7.1/bin/ccp4-python", + "python.linting.flake8Enabled": true } \ No newline at end of file From 95cfd2b2d12a94decef26282a2f3a2021f9593ac Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 13:30:58 +0000 Subject: [PATCH 118/358] Update syntax with python 2to3 --- XChemExplorer.py | 76 +- gui_scripts/layout.py | 6 +- gui_scripts/pandda_tab.py | 2 +- helpers/assign_stereochemistry.py | 172 +- ...ange_residues_in_ground_and_bound-state.py | 8 +- helpers/find_best_fitting_ligand.py | 214 +- helpers/phenix_find_TLS_groups.py | 2 +- helpers/prepare_for_zenodo_upload.py | 24 +- helpers/reset_interesting_datasets.py | 12 +- helpers/reset_occupancy_protein_to_one.py | 4 +- .../reset_to_last_successful_refinement.py | 12 +- helpers/select_ground_state_dataset.py | 20 +- .../update_data_source_after_refinement.py | 10 +- .../update_data_source_for_new_dimple_pdb.py | 2 +- ...ate_data_source_for_new_dimple_twin_pdb.py | 2 +- helpers/update_pandda_status_flag.py | 4 +- lib/PuckDB.py | 10 +- lib/XChemCoot.py | 100 +- lib/XChemCootBuster.py | 94 +- lib/XChemCootNew.py | 98 +- lib/XChemCootOld.py | 2420 ++++++++--------- lib/XChemCootReference.py | 34 +- lib/XChemCootTwin.py | 94 +- lib/XChemDB.py | 38 +- lib/XChemDeposit.py | 12 +- lib/XChemLog.py | 2 +- lib/XChemMain.py | 32 +- lib/XChemPANDDA.py | 6 +- lib/XChemProcess.py | 2 +- lib/XChemRefine.py | 28 +- lib/XChemThread.py | 2 +- lib/XChemToolTips.py | 2 +- lib/XChemUtils.py | 26 +- lib/coot_utils_XChem.py | 285 +- web/process_sqlite.py | 32 +- 35 files changed, 1943 insertions(+), 1944 deletions(-) diff --git a/XChemExplorer.py b/XChemExplorer.py index 40ce78ec..1553a233 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -177,7 +177,7 @@ def select_diffraction_data_directory(self): def search_for_datasets(self): self.update_log.insert( 'search diffraction data directory for datasets...') - print('will search ' + str(self.diffraction_data_directory)) + print(('will search ' + str(self.diffraction_data_directory))) self.work_thread = XChemMain.find_diffraction_image_directory_fast( self.diffraction_data_directory) self.explorer_active = 1 @@ -222,7 +222,7 @@ def translate_datasetID_to_sampleID(self): trans_dict[dataset] = new_sample_id if len(trans_dict) >= 1: allRows = self.datasets_reprocess_table.rowCount() - for row in xrange(0, allRows): + for row in range(0, allRows): dataset_id = str( self.datasets_reprocess_table.item(row, 0).text()) sample_id = str( @@ -243,7 +243,7 @@ def select_sample_for_xia2(self): for index in sorted(indexes): xtal = str(self.datasets_reprocess_table.item( index.row(), 1).text()) - print(xtal, self.diffraction_data_table_dict[xtal][0]) + print((xtal, self.diffraction_data_table_dict[xtal][0])) self.update_log.insert( '{0!s} marked for reprocessing'.format(index.row())) self.diffraction_data_table_dict[xtal][0].setChecked(True) @@ -481,7 +481,7 @@ def set_new_reference_if_applicable(self): pg_ref = '' ucVol_ref = 0.0 for reference in self.reference_file_list: - print(reference[0], reference_root) + print((reference[0], reference_root)) if reference[0] == reference_root: pg_ref = reference[5] ucVol_ref = reference[4] @@ -507,7 +507,7 @@ def set_new_reference_if_applicable(self): continue if pg_xtal == pg_ref and difference < self.allowed_unitcell_difference_percent: - print(xtal, pg_xtal, ucVol_xtal) + print((xtal, pg_xtal, ucVol_xtal)) index = reference_file_selection_combobox.findText( reference_root, QtCore.Qt.MatchFixedString) reference_file_selection_combobox.setCurrentIndex(index) @@ -807,7 +807,7 @@ def settings_button_clicked(self): self.pandda_output_data_dir_entry.setText(self.panddas_directory) self.ground_state_pandda_directory_label.setText( self.panddas_directory) - print('PANDDA', self.panddas_directory) + print(('PANDDA', self.panddas_directory)) self.settings['panddas_directory'] = self.panddas_directory self.layout_funcs.pandda_html(self) @@ -1050,7 +1050,7 @@ def dimple_change_twin_mode(self): def run_qsub_remotely(self): self.remote_qsub_submission = str(self.remote_qsub_command.text()) - print(str(self.remote_qsub_submission)) + print((str(self.remote_qsub_submission))) if self.remote_qsub_checkbox.isChecked(): self.update_log.insert( 'submitting jobs to remote machine with: %s' % self.remote_qsub_submission) @@ -2664,7 +2664,7 @@ def update_deposit_input(self): self.deposit_dict['pdbx_grant_country_three'], QtCore.Qt.MatchFixedString) self.pdbx_grant_country_three.setCurrentIndex(index) - except ValueError, e: + except ValueError as e: # self.update_status_bar('Sorry, this is not a XChemExplorer deposit file!') self.update_log.error( 'file is not a valid .deposit file: ' + str(e)) @@ -3058,7 +3058,7 @@ def update_header_and_data_from_datasource(self): db_dict[str(self.header[n])] = str(entry) self.xtal_db_dict[str(line[sampleID_column])] = db_dict - print('==> XCE: found ' + str(len(self.xtal_db_dict)) + ' samples') + print(('==> XCE: found ' + str(len(self.xtal_db_dict)) + ' samples')) def datasource_menu_save_samples(self): print('hallo') @@ -3122,7 +3122,7 @@ def undo_flag_sample_for_recollection(self): def show_html_summary_in_firefox(self, xtal): html_summary = self.albula_button_dict[xtal][2] - print('html_summary', html_summary) + print(('html_summary', html_summary)) new = 2 webbrowser.open(html_summary, new=new) @@ -3133,7 +3133,7 @@ def update_pandda_crystal_from_combobox(self): if os.path.isfile(os.path.join(self.database_directory, self.data_source_file)): self.load_crystal_form_from_datasource() if self.xtalform_dict != {}: - print(self.xtalform_dict) + print((self.xtalform_dict)) for key in self.xtalform_dict: self.pandda_analyse_crystal_from_selection_combobox.addItem( key) @@ -3209,10 +3209,10 @@ def open_config_file(self): command = str( 'self.settings["' + key_list[current_key] + '"]= self.' + current_key) exec(command) - print('==> XCE: found ' + key_list[current_key]) + print(('==> XCE: found ' + key_list[current_key])) except: - print('==> XCE: WARNING: Failed to find settings for: ' + key_list[current_key] + ' Error type: ' - + str(sys.exc_info()[0])) + print(('==> XCE: WARNING: Failed to find settings for: ' + key_list[current_key] + ' Error type: ' + + str(sys.exc_info()[0]))) exec(str(current_key + " = ''")) continue @@ -3287,7 +3287,7 @@ def open_config_file(self): 'Sorry, this is not a XChemExplorer config file!') except: - print("Unexpected error:", sys.exc_info()[0]) + print(("Unexpected error:", sys.exc_info()[0])) raise def save_config_file(self): @@ -3401,18 +3401,18 @@ def run_dimple_on_selected_autoprocessing_file(self, instruction): reference_file_mtz, reference_file_cif]) else: - print( - 'WARNING: ' + xtal + ' has not been submitted to dimple because no files were found: ') + print(( + 'WARNING: ' + xtal + ' has not been submitted to dimple because no files were found: ')) if not os.path.isfile(os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'], db_dict['DataProcessingMTZfileName'])): - print(' ' + str(os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'], - db_dict['DataProcessingMTZfileName'])) + ' is missing') + print((' ' + str(os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'], + db_dict['DataProcessingMTZfileName'])) + ' is missing')) if not os.path.isfile(os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'])): - print(' ' + str(os.path.join( - db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'])) + ' is missing') + print((' ' + str(os.path.join( + db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'])) + ' is missing')) if not os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'])): - print( - ' ' + str(os.path.join(db_dict['DataProcessingPathToMTZfile']) + ' is missing')) + print(( + ' ' + str(os.path.join(db_dict['DataProcessingPathToMTZfile']) + ' is missing'))) if job_list: self.update_log.insert( @@ -3535,7 +3535,7 @@ def run_xia2_on_selected_datasets(self, overwrite): run_dict = {} allRows = self.datasets_reprocess_table.rowCount() - for row in xrange(0, allRows): + for row in range(0, allRows): dataset_id = str(self.datasets_reprocess_table.item(row, 0).text()) sample_id = str(self.datasets_reprocess_table.item(row, 1).text()) if self.diffraction_data_table_dict[dataset_id][0].isChecked(): @@ -3574,7 +3574,7 @@ def run_xia2_on_selected_datasets(self, overwrite): def update_reprocessing_table(self): allRows = self.datasets_reprocess_table.rowCount() - for row in xrange(0, allRows): + for row in range(0, allRows): sample_id = str(self.datasets_reprocess_table.item(row, 1).text()) if sample_id in self.xtal_db_dict: db_dict = self.xtal_db_dict[sample_id] @@ -3881,8 +3881,8 @@ def button_clicked(self): if self.main_tab_widget.currentIndex() == task_index: if self.explorer_active == 0 and self.data_source_set == True: if action == 'Run': - print('==> XCE: Remote submission status = ' + - str(self.using_remote_qsub_submission)) + print(('==> XCE: Remote submission status = ' + + str(self.using_remote_qsub_submission))) # print(instruction) self.prepare_and_run_task(instruction) elif action == 'Status': @@ -5384,7 +5384,7 @@ def show_data_collection_details(self, state): def get_sample_list_from_table(self, table): sampleList = [] allRows = table.rowCount() - for row in xrange(0, allRows): + for row in range(0, allRows): sample_id = str(table.item(row, 0).text()) sampleList.append(sample_id) return sorted(sampleList) @@ -5392,7 +5392,7 @@ def get_sample_list_from_table(self, table): def get_row_of_sample_in_table(self, table, xtal): allRows = table.rowCount() sampleRow = allRows - for n, row in enumerate(xrange(0, allRows)): + for n, row in enumerate(range(0, allRows)): sample_id = str(table.item(row, 0).text()) if sample_id == xtal: sampleRow = n @@ -5485,9 +5485,9 @@ def update_row_in_table(self, sample, row, db_dict, table, columns_to_show): cell_text.setTextAlignment( QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) table.setItem(row, column, cell_text) - print('row: {0!s} column: {1!s} value: {2!s} header: {3!s}'.format( - row, column, cell_text, header[0])) - print('column_name {0!s}'.format(column_name)) + print(('row: {0!s} column: {1!s} value: {2!s} header: {3!s}'.format( + row, column, cell_text, header[0]))) + print(('column_name {0!s}'.format(column_name))) def populate_datasets_summary_table_NEW(self): self.status_bar.showMessage( @@ -5605,10 +5605,10 @@ def select_different_autoprocessing_result(self): score = self.data_collection_table.item(selected_row, 12).text() for q in range(13): try: - print('--> {0!s}: {1!s}'.format(q, - self.data_collection_table.item(selected_row, q).text())) + print(('--> {0!s}: {1!s}'.format(q, + self.data_collection_table.item(selected_row, q).text()))) except AttributeError: - print('--> {0!s}: None'.format(q)) + print(('--> {0!s}: None'.format(q))) # get db_dict from collectionTable for visit, run, autoproc # dbDict = self.db.get_db_dict_for_visit_run_autoproc(xtal,visit,run,autoproc) dbDict = self.db.get_db_dict_for_visit_run_autoproc_score( @@ -5651,7 +5651,7 @@ def user_update_selected_autoproc_datasets_summary_table(self): 'herere' + str(self.data_collection_column_three_dict)) dbTmp = self.xtal_db_dict[key] stage = dbTmp['RefinementOutcome'].split()[0] - print('===>', key, stage) + print(('===>', key, stage)) if int(stage) > 2: msgBox = QtGui.QMessageBox() msgBox.setText( @@ -5668,10 +5668,10 @@ def user_update_selected_autoproc_datasets_summary_table(self): 'will not change data processing selection') # restore previous selection for n, entry in enumerate(self.data_collection_dict[key]): - print('==>', n) + print(('==>', n)) if entry[0] == 'logfile': if entry[8]: - print('===> found:', n) + print(('===> found:', n)) self.data_collection_column_three_dict[key][0].selectRow( n) break diff --git a/gui_scripts/layout.py b/gui_scripts/layout.py index 05c825f1..8f91b0ec 100755 --- a/gui_scripts/layout.py +++ b/gui_scripts/layout.py @@ -392,7 +392,7 @@ def pandda_html(self, xce_object): # function for datasource, run and status button setup def setup_push_button(self, xce_object, button_dict): # use iterkeys to determine order of key by letter - for name in sorted(button_dict.iterkeys()): + for name in sorted(button_dict.keys()): # add current item to menu bar button = eval( 'QtGui.QPushButton("' + str(button_dict[name][0]) + '")') @@ -447,7 +447,7 @@ def bottom_box_setup(self, xce_object, label, dropdown_options, dropdown_tooltip # function to add items to top menu bar def setup_menubar(self, xce_object, menu_bar, menu_items_dict): # use iterkeys to determine order of key by letter - for config in sorted(menu_items_dict.iterkeys()): + for config in sorted(menu_items_dict.keys()): # add current item to menu bar menu = eval( 'menu_bar.addMenu("' + str(menu_items_dict[config][0]) + '")') @@ -465,7 +465,7 @@ def setup_menubar(self, xce_object, menu_bar, menu_items_dict): action.triggered.connect(menu_item[2]) menu.addAction(action) except: - print(menu_item[2]) + print((menu_item[2])) raise return menu_bar diff --git a/gui_scripts/pandda_tab.py b/gui_scripts/pandda_tab.py index 43874381..e98f80e8 100755 --- a/gui_scripts/pandda_tab.py +++ b/gui_scripts/pandda_tab.py @@ -115,7 +115,7 @@ def setup(self, xce_object): xce_object.pandda_analyse_input_params_vbox.addLayout( pandda_mtz_style_hbox) - print(xce_object.initial_model_directory) + print((xce_object.initial_model_directory)) data_dir_string = xce_object.initial_model_directory.replace('/*', '') def copy_ligands(obj): diff --git a/helpers/assign_stereochemistry.py b/helpers/assign_stereochemistry.py index a439533d..0f0dc3ae 100755 --- a/helpers/assign_stereochemistry.py +++ b/helpers/assign_stereochemistry.py @@ -1,86 +1,86 @@ -import XChemDB -import os -import sys -import glob -from rdkit import Chem -#from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions - -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) - - -def enumerateStereoChem(compoundID, sampleDir, db, xtal): - # first need to recreate the original CIF file with phenix.elbow because we cannot be sure - # which program was used to create the initial restrains - # this is because funny things happen to aromatic rings in case the file was made with GRADE - os.chdir(os.path.join(sampleDir, 'compound')) - sql = "select CompoundSMILES from mainTable where CrystalName = '%s'" % xtal - print 'sqlite query:', sql - query = db.execute_statement(sql) - originalSMILES = query[0][0] - print originalSMILES - cmd = 'phenix.elbow --smiles="%s" --id=LIG --output=tmp' % (originalSMILES) - print 'current working directory:', os.getcwd() - print 'runnning:', cmd - os.system(cmd) - - stereosmiles = None - pdb = None - if os.path.isfile(os.path.join(sampleDir, 'compound', 'tmp.pdb')): - pdb = os.path.join(sampleDir, 'compound', 'tmp.pdb') - else: - print 'cannot find tmp.pdb' - pass - if pdb: - mol = Chem.MolFromPDBFile(pdb) - Chem.AssignStereochemistry( - mol, cleanIt=True, force=True, flagPossibleStereoCenters=True) - if Chem.FindMolChiralCenters(mol, includeUnassigned=True) == []: - print 'no chiral centres found' - db_dict = {} - db_dict['CompoundStereo'] = 'FALSE' - updateDB(db, db_dict, xtal) - else: - stereosmiles = Chem.MolToSmiles(mol, isomericSmiles=True) - generateRestraints(compoundID, sampleDir, db, stereosmiles, xtal) - - -def generateRestraints(compoundID, sampleDir, db, stereosmiles, xtal): - cmd = 'phenix.elbow --smiles="%s" --chiral=enumerate --id=LIG --output=%s' % ( - stereosmiles, compoundID) - os.system(cmd) - checkFiles(compoundID, sampleDir, db, stereosmiles, xtal) - - -def checkFiles(compoundID, sampleDir, db, stereosmiles, xtal): - foundCIF = False - allCIF = '' - for cif in glob.glob(os.path.join(compoundID + '_*.cif')): - foundCIF = True - allCIF += cif+';' - print '---', cif, '===', allCIF - if foundCIF: - db_dict = {} - db_dict['CompoundStereo'] = 'TRUE' - db_dict['CompoundStereoSMILES'] = stereosmiles - db_dict['CompoundStereoCIFprogram'] = 'phenix.elbow' - db_dict['CompoundStereoCIFs'] = allCIF[:-1] - print '>>>', db_dict - updateDB(db, db_dict, xtal) - - -def updateDB(db, db_dict, xtal): - # update stereo field - # update restraintsprogram field - # update stereosmiles - db.update_data_source(xtal, db_dict) - - -if __name__ == '__main__': - compoundID = sys.argv[1] - sampleDir = sys.argv[2] - xtal = sampleDir[sampleDir.rfind('/')+1:] - print 'sampleID:', xtal - database = sys.argv[3] - print 'database:', database - db = XChemDB.data_source(database) - enumerateStereoChem(compoundID, sampleDir, db, xtal) +import XChemDB +import os +import sys +import glob +from rdkit import Chem +#from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions + +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + + +def enumerateStereoChem(compoundID, sampleDir, db, xtal): + # first need to recreate the original CIF file with phenix.elbow because we cannot be sure + # which program was used to create the initial restrains + # this is because funny things happen to aromatic rings in case the file was made with GRADE + os.chdir(os.path.join(sampleDir, 'compound')) + sql = "select CompoundSMILES from mainTable where CrystalName = '%s'" % xtal + print('sqlite query:', sql) + query = db.execute_statement(sql) + originalSMILES = query[0][0] + print(originalSMILES) + cmd = 'phenix.elbow --smiles="%s" --id=LIG --output=tmp' % (originalSMILES) + print('current working directory:', os.getcwd()) + print('runnning:', cmd) + os.system(cmd) + + stereosmiles = None + pdb = None + if os.path.isfile(os.path.join(sampleDir, 'compound', 'tmp.pdb')): + pdb = os.path.join(sampleDir, 'compound', 'tmp.pdb') + else: + print('cannot find tmp.pdb') + pass + if pdb: + mol = Chem.MolFromPDBFile(pdb) + Chem.AssignStereochemistry( + mol, cleanIt=True, force=True, flagPossibleStereoCenters=True) + if Chem.FindMolChiralCenters(mol, includeUnassigned=True) == []: + print('no chiral centres found') + db_dict = {} + db_dict['CompoundStereo'] = 'FALSE' + updateDB(db, db_dict, xtal) + else: + stereosmiles = Chem.MolToSmiles(mol, isomericSmiles=True) + generateRestraints(compoundID, sampleDir, db, stereosmiles, xtal) + + +def generateRestraints(compoundID, sampleDir, db, stereosmiles, xtal): + cmd = 'phenix.elbow --smiles="%s" --chiral=enumerate --id=LIG --output=%s' % ( + stereosmiles, compoundID) + os.system(cmd) + checkFiles(compoundID, sampleDir, db, stereosmiles, xtal) + + +def checkFiles(compoundID, sampleDir, db, stereosmiles, xtal): + foundCIF = False + allCIF = '' + for cif in glob.glob(os.path.join(compoundID + '_*.cif')): + foundCIF = True + allCIF += cif+';' + print('---', cif, '===', allCIF) + if foundCIF: + db_dict = {} + db_dict['CompoundStereo'] = 'TRUE' + db_dict['CompoundStereoSMILES'] = stereosmiles + db_dict['CompoundStereoCIFprogram'] = 'phenix.elbow' + db_dict['CompoundStereoCIFs'] = allCIF[:-1] + print('>>>', db_dict) + updateDB(db, db_dict, xtal) + + +def updateDB(db, db_dict, xtal): + # update stereo field + # update restraintsprogram field + # update stereosmiles + db.update_data_source(xtal, db_dict) + + +if __name__ == '__main__': + compoundID = sys.argv[1] + sampleDir = sys.argv[2] + xtal = sampleDir[sampleDir.rfind('/')+1:] + print('sampleID:', xtal) + database = sys.argv[3] + print('database:', database) + db = XChemDB.data_source(database) + enumerateStereoChem(compoundID, sampleDir, db, xtal) diff --git a/helpers/change_residues_in_ground_and_bound-state.py b/helpers/change_residues_in_ground_and_bound-state.py index dfd298b3..833672ec 100755 --- a/helpers/change_residues_in_ground_and_bound-state.py +++ b/helpers/change_residues_in_ground_and_bound-state.py @@ -13,7 +13,7 @@ def replace_residues(): if os.path.isfile(mol): if not os.path.isfile(mol+'_original'): os.system('/bin/cp %s %s' % (mol, mol+'_original')) - print '%s: found %s' % (xtal, mol) + print('%s: found %s' % (xtal, mol)) os.system('phenix.superpose_pdbs %s %s' % (mol, newModel)) out = '' changeResi = None @@ -25,13 +25,13 @@ def replace_residues(): resi = chainID + resseq if changeResi != None: if resi == changeResi: - print 'here', changeResi + print('here', changeResi) continue else: changeResi = None if resi in residues_to_change: changeResi = resi - print 'changeResi', changeResi + print('changeResi', changeResi) for line in open(newModelName+'_fitted.pdb'): if line.startswith('ATOM') or line.startswith('HETATM'): chainIDFitted = str( @@ -46,7 +46,7 @@ def replace_residues(): out += line else: out += line - print 'saving file', mol, '...' + print('saving file', mol, '...') newFile = open(mol, 'w') newFile.write(out) newFile.close() diff --git a/helpers/find_best_fitting_ligand.py b/helpers/find_best_fitting_ligand.py index 55afc17a..5e358f46 100755 --- a/helpers/find_best_fitting_ligand.py +++ b/helpers/find_best_fitting_ligand.py @@ -1,107 +1,107 @@ -import XChemDB -import sys -import os -import glob - -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) - - -def parse_autofit_folder(sampleDir, compoundID): - filenames = ['best.pdb', 'ligand_fit_1.pdb'] - pdbList = [] - for files in glob.glob(os.path.join(sampleDir, 'autofit_ligand', compoundID+'_*', '*')): - pdb = files[files.rfind('/')+1:] - if pdb in filenames: - pdbList.append(files) - return pdbList - - -def find_input_mtz(sampleDir): - possibleMTZ = ['refine.mtz', 'init.mtz', 'dimple.mtz', ] - mtzin = None - for mtz in possibleMTZ: - if os.path.isfile(os.path.join(sampleDir, mtz)): - mtzin = os.path.join(sampleDir, mtz) - break - return mtzin - - -def calculate_cc(sampleDir, compoundID, db): - xtal = sampleDir[sampleDir.rfind('/') + 1:] - pdbList = parse_autofit_folder(sampleDir, compoundID) - mtzin = find_input_mtz(sampleDir) - for pdb in pdbList: - autofitDir = pdb[:pdb.rfind('/')] - os.chdir(autofitDir) - os.system( - 'phenix.get_cc_mtz_pdb %s %s > phenix.get_cc_mtz_pdb.log' % (pdb, mtzin)) - new_file_links(pdbList) - bestRun, bestCC = parse_cc_log(sampleDir, compoundID) - changeLinks(sampleDir, pdbList, bestRun, compoundID) - fitting_program = None - if 'phenix' in bestRun: - fitting_program = 'phenix.ligandfit' - elif 'rhofit' in bestRun: - fitting_program = 'rhofit' - db_dict = {} - db_dict['CompoundAutofitprogram'] = fitting_program - db_dict['CompoundAutofitCC'] = str(bestCC) - updateDB(db, db_dict, xtal) - - -def new_file_links(pdbList): - for pdb in pdbList: - autofitDir = pdb[:pdb.rfind('/')] - autofitRun = pdb.split('/')[len(pdb.split('/')) - 2] - pdbFile = pdb[pdb.rfind('/')+1:] - os.chdir(autofitDir) - if not os.path.isfile(autofitRun+'.pdb'): - os.system('ln -s %s %s.pdb' % (pdbFile, autofitRun)) - - -def changeLinks(sampleDir, pdbList, bestRun, compoundID): - os.chdir(sampleDir) - for pdb in pdbList: - autofitDir = pdb.split('/')[len(pdb.split('/')) - 2] - if autofitDir == bestRun: - if os.path.isfile(pdb.replace(sampleDir, '.')): - os.system('/bin/rm %s.pdb' % compoundID) - os.system('ln -s %s %s.pdb' % - (pdb.replace(sampleDir, '.'), compoundID)) - - -def parse_cc_log(sampleDir, compoundID): - ccDict = {} - ccList = [] - for ccLog in glob.glob(os.path.join(sampleDir, 'autofit_ligand', compoundID+'_*', 'phenix.get_cc_mtz_pdb.log')): - autofitDir = ccLog.split('/')[len(ccLog.split('/'))-2] - for line in open(ccLog): - if line.startswith('local CC:') and len(line.split()) > 2: - cc = line.split()[2] - ccList.append(float(cc)) - ccDict[autofitDir] = cc - break - bestRun = None - try: - bestCC = max(ccList) - for ccRun in ccDict: - print ccRun, ccDict[ccRun], bestCC - if str(ccDict[ccRun]) == str(bestCC): - bestRun = ccRun - break - except ValueError: - pass - return bestRun, bestCC - - -def updateDB(db, db_dict, xtal): - db.update_data_source(xtal, db_dict) - - -if __name__ == '__main__': - compoundID = sys.argv[1] - sampleDir = sys.argv[2] - database = sys.argv[3] - db = XChemDB.data_source(database) - - calculate_cc(sampleDir, compoundID, db) +import XChemDB +import sys +import os +import glob + +sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + + +def parse_autofit_folder(sampleDir, compoundID): + filenames = ['best.pdb', 'ligand_fit_1.pdb'] + pdbList = [] + for files in glob.glob(os.path.join(sampleDir, 'autofit_ligand', compoundID+'_*', '*')): + pdb = files[files.rfind('/')+1:] + if pdb in filenames: + pdbList.append(files) + return pdbList + + +def find_input_mtz(sampleDir): + possibleMTZ = ['refine.mtz', 'init.mtz', 'dimple.mtz', ] + mtzin = None + for mtz in possibleMTZ: + if os.path.isfile(os.path.join(sampleDir, mtz)): + mtzin = os.path.join(sampleDir, mtz) + break + return mtzin + + +def calculate_cc(sampleDir, compoundID, db): + xtal = sampleDir[sampleDir.rfind('/') + 1:] + pdbList = parse_autofit_folder(sampleDir, compoundID) + mtzin = find_input_mtz(sampleDir) + for pdb in pdbList: + autofitDir = pdb[:pdb.rfind('/')] + os.chdir(autofitDir) + os.system( + 'phenix.get_cc_mtz_pdb %s %s > phenix.get_cc_mtz_pdb.log' % (pdb, mtzin)) + new_file_links(pdbList) + bestRun, bestCC = parse_cc_log(sampleDir, compoundID) + changeLinks(sampleDir, pdbList, bestRun, compoundID) + fitting_program = None + if 'phenix' in bestRun: + fitting_program = 'phenix.ligandfit' + elif 'rhofit' in bestRun: + fitting_program = 'rhofit' + db_dict = {} + db_dict['CompoundAutofitprogram'] = fitting_program + db_dict['CompoundAutofitCC'] = str(bestCC) + updateDB(db, db_dict, xtal) + + +def new_file_links(pdbList): + for pdb in pdbList: + autofitDir = pdb[:pdb.rfind('/')] + autofitRun = pdb.split('/')[len(pdb.split('/')) - 2] + pdbFile = pdb[pdb.rfind('/')+1:] + os.chdir(autofitDir) + if not os.path.isfile(autofitRun+'.pdb'): + os.system('ln -s %s %s.pdb' % (pdbFile, autofitRun)) + + +def changeLinks(sampleDir, pdbList, bestRun, compoundID): + os.chdir(sampleDir) + for pdb in pdbList: + autofitDir = pdb.split('/')[len(pdb.split('/')) - 2] + if autofitDir == bestRun: + if os.path.isfile(pdb.replace(sampleDir, '.')): + os.system('/bin/rm %s.pdb' % compoundID) + os.system('ln -s %s %s.pdb' % + (pdb.replace(sampleDir, '.'), compoundID)) + + +def parse_cc_log(sampleDir, compoundID): + ccDict = {} + ccList = [] + for ccLog in glob.glob(os.path.join(sampleDir, 'autofit_ligand', compoundID+'_*', 'phenix.get_cc_mtz_pdb.log')): + autofitDir = ccLog.split('/')[len(ccLog.split('/'))-2] + for line in open(ccLog): + if line.startswith('local CC:') and len(line.split()) > 2: + cc = line.split()[2] + ccList.append(float(cc)) + ccDict[autofitDir] = cc + break + bestRun = None + try: + bestCC = max(ccList) + for ccRun in ccDict: + print(ccRun, ccDict[ccRun], bestCC) + if str(ccDict[ccRun]) == str(bestCC): + bestRun = ccRun + break + except ValueError: + pass + return bestRun, bestCC + + +def updateDB(db, db_dict, xtal): + db.update_data_source(xtal, db_dict) + + +if __name__ == '__main__': + compoundID = sys.argv[1] + sampleDir = sys.argv[2] + database = sys.argv[3] + db = XChemDB.data_source(database) + + calculate_cc(sampleDir, compoundID, db) diff --git a/helpers/phenix_find_TLS_groups.py b/helpers/phenix_find_TLS_groups.py index b85db6b4..ac7d6087 100755 --- a/helpers/phenix_find_TLS_groups.py +++ b/helpers/phenix_find_TLS_groups.py @@ -4,7 +4,7 @@ def FindTLSgroups(pdbFile): - print '\n==> XCE @ helpers: running phenix.find_tls_groups on new pdb file' + print('\n==> XCE @ helpers: running phenix.find_tls_groups on new pdb file') os.system( 'phenix.find_tls_groups {0!s} > phenix.find_tls_groups.out'.format(pdbFile)) GroupNames = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', diff --git a/helpers/prepare_for_zenodo_upload.py b/helpers/prepare_for_zenodo_upload.py index 61376a62..5f425bce 100755 --- a/helpers/prepare_for_zenodo_upload.py +++ b/helpers/prepare_for_zenodo_upload.py @@ -11,28 +11,28 @@ def copy_files(htmlDir): os.mkdir('zenodo') os.chdir(os.path.join(htmlDir, 'zenodo')) - print 'copying compoundImages' + print('copying compoundImages') os.system('/bin/cp ../compoundImages/* .') - print 'copying pdbs' + print('copying pdbs') os.system('/bin/cp ../pdbs/* .') - print 'copying maps' + print('copying maps') os.system('/bin/cp ../maps/* .') - print 'copying residueplots' + print('copying residueplots') os.system('/bin/cp ../residueplots/* .') - print 'copying mapImages' + print('copying mapImages') os.system('/bin/cp ../mapImages/* .') - print 'copying icbs' + print('copying icbs') os.system('/bin/cp ../icbs/* .') - print 'copying css' + print('copying css') os.system('/bin/cp ../css/* .') - print 'copying js' + print('copying js') os.system('/bin/cp ../js/* .') @@ -67,7 +67,7 @@ def edit_index_html(htmlDir, uploadID): 'js/', 'https://zenodo.org/record/'+uploadID+'/files/') out += line - print 'writing index.html to', os.path.join(htmlDir, 'zenodo') + print('writing index.html to', os.path.join(htmlDir, 'zenodo')) f = open('0_index.html', 'w') f.write(out) f.close() @@ -92,7 +92,7 @@ def edit_icb_html_files(htmlDir, uploadID): line = line.replace( ' act.projectFile = "', ' act.projectFile = "https://zenodo.org/record/'+uploadID+'/files/') out += line - print 'updating', file + print('updating', file) f = open(file, 'w') f.write(out) f.close() @@ -100,7 +100,7 @@ def edit_icb_html_files(htmlDir, uploadID): if __name__ == '__main__': - print len(sys.argv) + print(len(sys.argv)) if len(sys.argv) == 2: htmlDir = sys.argv[1] @@ -115,4 +115,4 @@ def edit_icb_html_files(htmlDir, uploadID): edit_icb_html_files(htmlDir, uploadID) else: - print 'wrong input!' + print('wrong input!') diff --git a/helpers/reset_interesting_datasets.py b/helpers/reset_interesting_datasets.py index f9589354..1d1043ef 100755 --- a/helpers/reset_interesting_datasets.py +++ b/helpers/reset_interesting_datasets.py @@ -13,9 +13,9 @@ def relink_interesting_datasets(panddaDir): dirList.append(dirs) for dirs in dirList: - print '/bin/rm -fr {0!s}'.format(dirs) + print('/bin/rm -fr {0!s}'.format(dirs)) os.system('/bin/rm -fr {0!s}'.format(dirs)) - print 'ln -s ../processed_datasets/{0!s} .'.format(dirs) + print('ln -s ../processed_datasets/{0!s} .'.format(dirs)) os.system('ln -s ../processed_datasets/{0!s} .'.format(dirs)) @@ -27,12 +27,12 @@ def check_interesting_datasets(panddaDir): # print xtal # print os.path.join(panddaDir,'interesting_datasets',xtal,'modelled_structures',xtal+'-pandda-model.pdb') if os.path.isfile(os.path.join(panddaDir, 'interesting_datasets', xtal, 'modelled_structures', xtal+'-pandda-model.pdb')): - print 'mv --backup=numbered {0!s} {1!s}'.format(os.path.join( - panddaDir, 'interesting_datasets', xtal, 'modelled_structures'), os.path.join(panddaDir, 'processed_datasets', xtal)) + print('mv --backup=numbered {0!s} {1!s}'.format(os.path.join( + panddaDir, 'interesting_datasets', xtal, 'modelled_structures'), os.path.join(panddaDir, 'processed_datasets', xtal))) os.system('mv --backup=numbered {0!s} {1!s}'.format(os.path.join(panddaDir, 'interesting_datasets', xtal, 'modelled_structures'), os.path.join(panddaDir, 'processed_datasets', xtal))) - print 'cp {0!s} {1!s}'.format(os.path.join( - panddaDir, 'interesting_datasets', xtal, '*params'), os.path.join(panddaDir, 'processed_datasets', xtal)) + print('cp {0!s} {1!s}'.format(os.path.join( + panddaDir, 'interesting_datasets', xtal, '*params'), os.path.join(panddaDir, 'processed_datasets', xtal))) os.system('cp {0!s} {1!s}'.format(os.path.join(panddaDir, 'interesting_datasets', xtal, '*params'), os.path.join(panddaDir, 'processed_datasets', xtal))) diff --git a/helpers/reset_occupancy_protein_to_one.py b/helpers/reset_occupancy_protein_to_one.py index 01f42e10..7c20c482 100644 --- a/helpers/reset_occupancy_protein_to_one.py +++ b/helpers/reset_occupancy_protein_to_one.py @@ -11,7 +11,7 @@ def reset_residues(projectDir): if os.path.isfile(mol): if not os.path.isfile(mol+'_original'): os.system('/bin/cp %s %s' % (mol, mol+'_original')) - print '%s: found %s' % (xtal, mol) + print('%s: found %s' % (xtal, mol)) out = '' changeResi = None for line in open(mol): @@ -26,7 +26,7 @@ def reset_residues(projectDir): out += line[:56] + '1.00' + line[60:] else: out += line - print 'saving file', mol, '...' + print('saving file', mol, '...') newFile = open(mol, 'w') newFile.write(out) newFile.close() diff --git a/helpers/reset_to_last_successful_refinement.py b/helpers/reset_to_last_successful_refinement.py index 57c7a6ae..1ce5118c 100644 --- a/helpers/reset_to_last_successful_refinement.py +++ b/helpers/reset_to_last_successful_refinement.py @@ -22,30 +22,30 @@ def find_refine_pdb(xtal, dirList): for d in sorted_list: serial = int(d[0].split('_')[1]) if os.path.isfile(os.path.join(d[0], 'refine.pdb')): - print xtal + ': found refine.pdb in ' + d[0] + print(xtal + ': found refine.pdb in ' + d[0]) pdbLink = os.path.join(d[0], 'refine.pdb') mtzLink = os.path.join(d[0], 'refine.mtz') foundRefinePDB = True break elif os.path.isfile(os.path.join(d[0], 'refine_%s.pdb' % str(serial))): - print xtal + ': found refine_%s.pdb in %s' % (str(serial), d[0]) + print(xtal + ': found refine_%s.pdb in %s' % (str(serial), d[0])) foundRefinePDB = True pdbLink = os.path.join(d[0], 'refine_%s.pdb' % str(serial)) mtzLink = os.path.join(d[0], 'refine_%s.mtz' % str(serial)) break if not foundRefinePDB: - print xtal + ': ERROR -> cannot find refine.pdb' + print(xtal + ': ERROR -> cannot find refine.pdb') else: - print os.getcwd(), pdbLink, mtzLink + print(os.getcwd(), pdbLink, mtzLink) reset_links(xtal, pdbLink, mtzLink) def find_pandda_refine_pdb(xtal, dirList): - print 'hallp' + print('hallp') def reset_links(xtal, pdbLink, mtzLink): - print xtal + ': resetting links...' + print(xtal + ': resetting links...') os.system('/bin/rm refine.pdb') os.system('/bin/rm refine.mtz') os.system('/bin/rm refine.split.bound-state.pdb') diff --git a/helpers/select_ground_state_dataset.py b/helpers/select_ground_state_dataset.py index afc1d0c3..0e1e7c35 100755 --- a/helpers/select_ground_state_dataset.py +++ b/helpers/select_ground_state_dataset.py @@ -31,7 +31,7 @@ def find_highest_resolution_datasets(panddaDir): for item in tmpLine.split(','): if item != '': datasetList.append(item) - print datasetList + print(datasetList) return datasetList @@ -45,7 +45,7 @@ def get_datasets_without_event_map(panddaDir, datasetList): break if noEvent: datasetListwithoutEvent.append(dataset) - print datasetListwithoutEvent + print(datasetListwithoutEvent) return datasetListwithoutEvent @@ -58,7 +58,7 @@ def select_dataset_with_lowest_Rfree(panddaDir, datasetListwithoutEvent): panddaDir, 'processed_datasets', dataset, dataset+'-pandda-input.pdb')) Rfree = stats['Rfree'] try: - print dataset, Rfree, stats['ResolutionHigh'] + print(dataset, Rfree, stats['ResolutionHigh']) datasetList.append([dataset, float(Rfree)]) except ValueError: pass @@ -70,8 +70,8 @@ def select_dataset_with_lowest_Rfree(panddaDir, datasetListwithoutEvent): def link_pdb_mtz_files(panddaDir, lowestRfree): targetDir = '/'.join(panddaDir.split('/')[:len(panddaDir.split('/'))-1]) panddaFolder = panddaDir.split('/')[len(panddaDir.split('/'))-1] - print targetDir - print panddaFolder + print(targetDir) + print(panddaFolder) os.chdir(targetDir) if os.path.isfile(os.path.join(panddaDir, 'processed_datasets', lowestRfree, lowestRfree+'-pandda-input.pdb')): os.system('/bin/rm %s-ground-state.pdb 2> /dev/null' % lowestRfree) @@ -99,21 +99,21 @@ def link_pdb_mtz_files(panddaDir, lowestRfree): def convert_mean_map_to_mtz(emap, mtz): - print 'converting ground-state-mean-map to MTZ' + print('converting ground-state-mean-map to MTZ') cmd = ('mapmask MAPIN %s MAPOUT %s << eof\n' % (emap, emap.replace('.ccp4', '.P1.ccp4')) + ' XYZLIM CELL\n' ' PAD 0.0\n' ' SYMMETRY 1\n' 'eof\n') - print cmd + print(cmd) os.system(cmd) - print '--->', mtz + print('--->', mtz) reso = mtztools(mtz).get_dmin() - print '-> resolution:', reso + print('-> resolution:', reso) cmd = ('module load phenix\n' 'phenix.map_to_structure_factors %s d_min=%s\n' % (emap.replace('.ccp4', '.P1.ccp4'), reso) + '/bin/mv map_to_structure_factors.mtz %s' % emap.replace('.ccp4', '.mtz')) - print cmd + print(cmd) os.system(cmd) diff --git a/helpers/update_data_source_after_refinement.py b/helpers/update_data_source_after_refinement.py index 1715e59f..ca9218d6 100755 --- a/helpers/update_data_source_after_refinement.py +++ b/helpers/update_data_source_after_refinement.py @@ -43,7 +43,7 @@ def parse_pdb(inital_model_directory, xtal, db_dict): db_dict['RefinementBoundConformation'] = os.path.realpath( os.path.join(inital_model_directory, xtal, 'refine.pdb')) - print db_dict + print(db_dict) return db_dict @@ -147,7 +147,7 @@ def parse_ligand_validation(inital_model_directory, refinement_directory, xtal): site_index = str(coord[3]) distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1], residue_xyz[2], event_x, event_y, event_z) - print 'distance', distance + print('distance', distance) # if coordinate of ligand and event are closer than 7A, then we assume they belong together if distance < 7: db_pandda_dict['PANDDA_site_ligand_id'] = residue @@ -167,7 +167,7 @@ def parse_ligand_validation(inital_model_directory, refinement_directory, xtal): db_pandda_dict['PANDDA_site_spider_plot'] = '' if db_pandda_dict != {}: - print '==> XCE: updating pandda Table of data source' + print('==> XCE: updating pandda Table of data source') db.update_panddaTable( xtal, site_index, db_pandda_dict) @@ -206,13 +206,13 @@ def update_ligand_information_in_panddaTable(inital_model_directory, xtal): db_pandda_dict['PANDDA_site_ligand_altLoc'] = residue_altLoc db_pandda_dict['PANDDA_site_ligand_placed'] = 'True' if db_pandda_dict != {}: - print '==> XCE: updating pandda Table of data source' + print('==> XCE: updating pandda Table of data source') db.update_panddaTable(xtal, site_index, db_pandda_dict) def update_data_source(db_dict): if db_dict != {}: - print '==> xce: updating mainTable of data source' + print('==> xce: updating mainTable of data source') db.update_data_source(xtal, db_dict) # update refinement outcome if necessary sqlite = ( diff --git a/helpers/update_data_source_for_new_dimple_pdb.py b/helpers/update_data_source_for_new_dimple_pdb.py index 890396cd..73415541 100755 --- a/helpers/update_data_source_for_new_dimple_pdb.py +++ b/helpers/update_data_source_for_new_dimple_pdb.py @@ -99,7 +99,7 @@ # os.symlink('dimple.mtz','refine.mtz') # finally, update data source - print '==> xce: updating data source after DIMPLE run' + print('==> xce: updating data source after DIMPLE run') db.update_data_source(xtal, db_dict) else: diff --git a/helpers/update_data_source_for_new_dimple_twin_pdb.py b/helpers/update_data_source_for_new_dimple_twin_pdb.py index d9e2f9f7..8129344e 100755 --- a/helpers/update_data_source_for_new_dimple_twin_pdb.py +++ b/helpers/update_data_source_for_new_dimple_twin_pdb.py @@ -100,7 +100,7 @@ # os.symlink('dimple.mtz','refine.mtz') # finally, update data source - print '==> xce: updating data source after DIMPLE run' + print('==> xce: updating data source after DIMPLE run') db.update_data_source(xtal, db_dict) else: diff --git a/helpers/update_pandda_status_flag.py b/helpers/update_pandda_status_flag.py index 82a742a2..4f5606af 100755 --- a/helpers/update_pandda_status_flag.py +++ b/helpers/update_pandda_status_flag.py @@ -9,8 +9,8 @@ def update_data_source(db_file, crystalString, status): db = XChemDB.data_source(db_file) - print "update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format( - status, "'"+crystalString.replace(",", "','")+"'") + print("update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format( + status, "'"+crystalString.replace(",", "','")+"'")) db.execute_statement("update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format( status, "'"+crystalString.replace(",", "','")+"'")) diff --git a/lib/PuckDB.py b/lib/PuckDB.py index a6c25b2d..622f08f3 100755 --- a/lib/PuckDB.py +++ b/lib/PuckDB.py @@ -12,16 +12,16 @@ def __init__(self, data_base): self.data_base = data_base def get_all_pucks_from_DB(self): - print 'hello' + print('hello') def insert_mounted_crystals(self): - print 'hello' + print('hello') def kill_mounted_cryatsl(self): - print 'hello' + print('hello') def change_puck_location(self): - print 'hello' + print('hello') def execute_sqlite(self): - print 'hello' + print('hello') diff --git a/lib/XChemCoot.py b/lib/XChemCoot.py index 4bba48df..63dea5da 100755 --- a/lib/XChemCoot.py +++ b/lib/XChemCoot.py @@ -48,7 +48,7 @@ def __init__(self): self.data_source = self.settings['data_source'] self.db = XChemDB.data_source(self.data_source) - print self.settings + print(self.settings) # checking for external software packages self.external_software = XChemUtils.external_software( @@ -832,7 +832,7 @@ def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 for i, entry in enumerate(self.ligand_confidence_category): - print '--->', entry, self.ligand_confidence + print('--->', entry, self.ligand_confidence) try: if entry.split()[0] == self.ligand_confidence.split()[0]: current_stage = i @@ -869,8 +869,8 @@ def ChangeSite(self, widget, data=None): def ChooseSite(self, widget): tmp = str(widget.get_active_text()) - print self.siteDict - print self.site_index + print(self.siteDict) + print(self.site_index) self.site_index = tmp.split()[1] self.event_index = tmp.split()[4] for n, item in enumerate(self.siteDict[self.xtalID]): @@ -895,18 +895,18 @@ def RefreshSiteData(self): for w in self.label_button_list: w.set_active(False) - print 'pandda index', self.pandda_index + print('pandda index', self.pandda_index) self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] - print 'new spider plot:', self.spider_plot + print('new spider plot:', self.spider_plot) self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] - print 'new event map:', self.event_map + print('new event map:', self.event_map) self.ligand_confidence = str( self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) - print 'new site coordinates:', site_x, site_y, site_z + print('new site coordinates:', site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) # self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) @@ -916,7 +916,7 @@ def RefreshSiteData(self): self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, self.event_index) - print '>>>>> spider plot data', self.spider_plot_data + print('>>>>> spider plot data', self.spider_plot_data) self.ligandIDValue.set_label( self.spider_plot_data['PANDDA_site_ligand_id']) try: @@ -994,7 +994,7 @@ def RefreshSiteData(self): def experiment_stage_button_clicked(self, widget, data=None): if data == '4 - CompChem ready' and self.refinementProtocol.startswith('pandda'): - print "==> XCE: removing refine.pdb and linking refine_.split.bound-state.pdb to refine.pdb" + print("==> XCE: removing refine.pdb and linking refine_.split.bound-state.pdb to refine.pdb") os.chdir(os.path.join(self.project_directory, self.xtalID)) if os.path.realpath('refine.pdb').replace('.pdb', '.split.bound-state.pdb'): newPDB = os.path.realpath('refine.pdb').replace( @@ -1005,28 +1005,28 @@ def experiment_stage_button_clicked(self, widget, data=None): self.refinementProtocolcheckbox.set_active(False) self.refinementProtocol = 'refmac' else: - print '==> XCE ERROR: cannot find refine.output.bound-state.pdb' + print('==> XCE ERROR: cannot find refine.output.bound-state.pdb') pass self.db_dict_mainTable['RefinementOutcome'] = data - print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( - data) + ' in mainTable of datasource' + print('==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( + data) + ' in mainTable of datasource') # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, self.xtalID, 'ligand_bound', self.db_dict_mainTable) def ligand_confidence_button_clicked(self, widget, data=None): - print 'PANDDA_index', self.pandda_index + print('PANDDA_index', self.pandda_index) if self.pandda_index == -1: self.db_dict_mainTable['RefinementLigandConfidence'] = data - print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( - data) + ' in mainTable of datasource' + print('==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( + data) + ' in mainTable of datasource') self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.Todo[self.index][6] = data else: self.db_dict_panddaTable['PANDDA_site_confidence'] = data - print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( + print('==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( - data) + ' in panddaTable of datasource' + data) + ' in panddaTable of datasource') self.db.update_site_event_panddaTable(self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable) self.siteDict[self.xtalID][self.pandda_index][7] = data @@ -1083,21 +1083,21 @@ def RefreshData(self): if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): - print '==> XCE: updating quality indicators in data source for ' + self.xtalID + print('==> XCE: updating quality indicators in data source for ' + self.xtalID) XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, os.path.join(self.project_directory, self.xtalID, self.pdb_style)) XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, '') # '' because file does not exist elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.pdb')): - print '==> XCE: updating quality indicators in data source for ' + self.xtalID + print('==> XCE: updating quality indicators in data source for ' + self.xtalID) XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, os.path.join(self.project_directory, self.xtalID, 'init.pdb')) XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, '') # '' because file does not exist elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): - print '==> XCE: updating quality indicators in data source for ' + self.xtalID + print('==> XCE: updating quality indicators in data source for ' + self.xtalID) XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')) @@ -1114,7 +1114,7 @@ def RefreshData(self): if self.Serial > 1: self.RefmacParams = self.Refine.ParamsFromPreviousCycle( self.Serial - 1) - print '==> REFMAC params:', self.RefmacParams + print('==> REFMAC params:', self.RefmacParams) # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) # else: @@ -1149,12 +1149,12 @@ def RefreshData(self): os.chdir(os.path.join(self.project_directory, self.xtalID)) if self.refinementProtocol.startswith('pandda'): - print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, + print('=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, self.pdb_style.replace('.pdb', - '') + '.split.ground-state.pdb') + '') + '.split.ground-state.pdb')) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): - print '=> XCE: found ground-state model' + print('=> XCE: found ground-state model') os.chdir(os.path.join(self.project_directory, self.xtalID)) coot.set_colour_map_rotation_on_read_pdb(0) try: @@ -1169,13 +1169,13 @@ def RefreshData(self): coot.set_colour_by_molecule(imol) coot.set_mol_active(imol, 0) else: - print '=> XCE - ERROR: cannot find ground-state model' - print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, + print('=> XCE - ERROR: cannot find ground-state model') + print('=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, self.pdb_style.replace('.pdb', - '') + '.split.bound-state.pdb') + '') + '.split.bound-state.pdb')) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb')): - print '=> XCE: found bound-state model' + print('=> XCE: found bound-state model') os.chdir(os.path.join(self.project_directory, self.xtalID)) coot.set_colour_map_rotation_on_read_pdb(0) color_wheel_rotation = 21 / float(imol + 2) @@ -1186,8 +1186,8 @@ def RefreshData(self): 0) self.mol_dict['protein'] = imol else: - print '=> XCE - ERROR: cannot find bound-state model' - print '=> XCE: moving to next crystal...' + print('=> XCE - ERROR: cannot find bound-state model') + print('=> XCE: moving to next crystal...') self.go_to_next_xtal() else: if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): @@ -1361,7 +1361,7 @@ def REFINE(self, widget): os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) except OSError: - print '==> XCE: WARNING -> folder exists; will overwrite contents!' + print('==> XCE: WARNING -> folder exists; will overwrite contents!') ####################################################### # write PDB file @@ -1429,7 +1429,7 @@ def REFINE(self, widget): self.cb.set_active(self.index) def RefinementParams(self, widget): - print '\n==> XCE: changing refinement parameters' + print('\n==> XCE: changing refinement parameters') self.RefmacParams = XChemRefine.RefineParams(self.project_directory, self.xtalID, self.compoundID, self.data_source).RefmacRefinementParams(self.RefmacParams) @@ -1461,9 +1461,9 @@ def get_samples_to_look_at(self, widget): self.cb_site.set_sensitive(True) self.PREVbuttonSite.set_sensitive(True) self.NEXTbuttonSite.set_sensitive(True) - print '===========>', self.cb_select_samples.get_active_text() + print('===========>', self.cb_select_samples.get_active_text()) if int(self.cb_select_samples.get_active_text().split()[0]) > 3: - print '==> XCE: sorry cannot change refinement protocol since you are at a stage when we refine the ligand bound state only' + print('==> XCE: sorry cannot change refinement protocol since you are at a stage when we refine the ligand bound state only') self.refinementProtocol = 'refmac' self.refinementProtocolcheckbox.set_active(False) @@ -1479,38 +1479,38 @@ def update_plot(self, refinement_cycle, Rfree, Rcryst): return fig def place_ligand_here(self, widget): - print '===> XCE: moving ligand to pointer' + print('===> XCE: moving ligand to pointer') # coot.move_molecule_here() - print 'LIGAND: ', self.mol_dict['ligand'] + print('LIGAND: ', self.mol_dict['ligand']) coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) def merge_ligand_into_protein(self, widget): - print '===> XCE: merge ligand into protein structure' + print('===> XCE: merge ligand into protein structure') # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) coot.merge_molecules_py( [self.mol_dict['ligand']], self.mol_dict['protein']) - print '===> XCE: deleting ligand molecule' + print('===> XCE: deleting ligand molecule') coot.close_molecule(self.mol_dict['ligand']) def show_molprobity_to_do(self, widget): - print self.panddaSerial + print(self.panddaSerial) AdjPanddaSerial = (4 - len(str(self.Serial))) * \ '0' + str(int(self.panddaSerial) - 1) - print os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), - 'molprobity_coot.py') + print(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), + 'molprobity_coot.py')) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')): - print '==> XCE: running MolProbity Summary for', self.xtalID + print('==> XCE: running MolProbity Summary for', self.xtalID) coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')) elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), 'molprobity_coot.py')): - print '==> XCE: running MolProbity Summary for', self.xtalID + print('==> XCE: running MolProbity Summary for', self.xtalID) coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), 'molprobity_coot.py')) else: - print '==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py') + print('==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, + 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')) def refinementProtocolCallback(self, widget): if widget.get_active(): @@ -1525,7 +1525,7 @@ def refinementProtocolCallback(self, widget): self.refinementProtocol = 'refmac' self.PREVbuttonSite.set_sensitive(False) self.NEXTbuttonSite.set_sensitive(False) - print self.refinementProtocol + print(self.refinementProtocol) def refinementProgramCallback(self, widget): if widget.get_active(): @@ -1542,10 +1542,10 @@ def refinementProgramCallback(self, widget): else: self.refinementProtocol = 'refmac' if int(self.refinement_outcome.split()[0]) > 3: - print '==> XCE: sorry cannot change refinement protocol since you are at a stage when we refine the ligand bound state only' + print('==> XCE: sorry cannot change refinement protocol since you are at a stage when we refine the ligand bound state only') self.refinementProtocol = 'refmac' self.refinementProtocolcheckbox.set_active(False) - print self.refinementProtocol + print(self.refinementProtocol) def show_ground_state_mean_map(self, widget): if widget.get_label().startswith('Show'): @@ -1613,7 +1613,7 @@ def reset_occupancy(self): resetDict[chain] = residRange for chain in resetDict: for resid_range in resetDict[chain]: - print 'setting occupancy to 1: ->', chain, resid_range[0], resid_range[1] + print('setting occupancy to 1: ->', chain, resid_range[0], resid_range[1]) coot.fill_occupancy_residue_range( imol, chain, resid_range[0], resid_range[1]) diff --git a/lib/XChemCootBuster.py b/lib/XChemCootBuster.py index 0dccc0c4..dedd65a7 100755 --- a/lib/XChemCootBuster.py +++ b/lib/XChemCootBuster.py @@ -51,7 +51,7 @@ def __init__(self): self.data_source = self.settings['data_source'] self.db = XChemDB.data_source(self.data_source) - print self.settings + print(self.settings) # checking for external software packages self.external_software = XChemUtils.external_software( @@ -830,11 +830,11 @@ def select_cpd(self, widget): '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') else: molNameCIF = molName - print cpd, '-', imol, '-', coot.molecule_name(imol) + print(cpd, '-', imol, '-', coot.molecule_name(imol)) if molName == cpd: coot.set_mol_displayed(imol, 1) - print 'reading', os.path.join( - self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif') + print('reading', os.path.join( + self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) coot.read_cif_dictionary(os.path.join( self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) else: @@ -868,7 +868,7 @@ def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 for i, entry in enumerate(self.ligand_confidence_category): - print '--->', entry, self.ligand_confidence + print('--->', entry, self.ligand_confidence) try: if entry.split()[0] == self.ligand_confidence.split()[0]: current_stage = i @@ -905,8 +905,8 @@ def ChangeSite(self, widget, data=None): def ChooseSite(self, widget): tmp = str(widget.get_active_text()) - print self.siteDict - print self.site_index + print(self.siteDict) + print(self.site_index) self.site_index = tmp.split()[1] self.event_index = tmp.split()[4] for n, item in enumerate(self.siteDict[self.xtalID]): @@ -931,18 +931,18 @@ def RefreshSiteData(self): # for w in self.label_button_list: # w.set_active(False) - print 'pandda index', self.pandda_index + print('pandda index', self.pandda_index) self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] - print 'new spider plot:', self.spider_plot + print('new spider plot:', self.spider_plot) self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] - print 'new event map:', self.event_map + print('new event map:', self.event_map) self.ligand_confidence = str( self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) - print 'new site coordinates:', site_x, site_y, site_z + print('new site coordinates:', site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) # self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) @@ -952,7 +952,7 @@ def RefreshSiteData(self): self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, self.event_index) - print '>>>>> spider plot data', self.spider_plot_data + print('>>>>> spider plot data', self.spider_plot_data) self.ligandIDValue.set_label( self.spider_plot_data['PANDDA_site_ligand_id']) try: @@ -1043,7 +1043,7 @@ def experiment_stage_button_clicked(self, widget, data=None): self.xce_logfile, self.xtalID, 'ligand_bound', self.db_dict_mainTable) def ligand_confidence_button_clicked(self, widget, data=None): - print 'PANDDA_index', self.pandda_index + print('PANDDA_index', self.pandda_index) if self.pandda_index == -1: self.db_dict_mainTable['RefinementLigandConfidence'] = data self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( @@ -1117,21 +1117,21 @@ def RefreshData(self): if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): - print '==> XCE: updating quality indicators in data source for ' + self.xtalID + print('==> XCE: updating quality indicators in data source for ' + self.xtalID) XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, os.path.join(self.project_directory, self.xtalID, self.pdb_style)) XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, '') # '' because file does not exist elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.pdb')): - print '==> XCE: updating quality indicators in data source for ' + self.xtalID + print('==> XCE: updating quality indicators in data source for ' + self.xtalID) XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, os.path.join(self.project_directory, self.xtalID, 'init.pdb')) XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, '') # '' because file does not exist elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): - print '==> XCE: updating quality indicators in data source for ' + self.xtalID + print('==> XCE: updating quality indicators in data source for ' + self.xtalID) XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')) @@ -1148,7 +1148,7 @@ def RefreshData(self): if self.Serial > 1: self.RefmacParams = self.Refine.ParamsFromPreviousCycle( self.Serial - 1) - print '==> REFMAC params:', self.RefmacParams + print('==> REFMAC params:', self.RefmacParams) # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) # else: @@ -1160,11 +1160,11 @@ def RefreshData(self): ######################################################################################### # ligand files # first remove old samples if present - print '>>>', self.mol_dict['ligand_stereo'] + print('>>>', self.mol_dict['ligand_stereo']) for n, item in enumerate(self.mol_dict['ligand_stereo']): - print '__', item + print('__', item) self.select_cpd_cb.remove_text(0) - print 'done' + print('done') ######################################################################################### # remove potential generic line which indicates a possible covalent link @@ -1221,7 +1221,7 @@ def RefreshData(self): self.select_cpd_cb.set_sensitive(True) self.select_cpd_cb.set_active(0) else: - print 'no compound found in sample directory' + print('no compound found in sample directory') # self.select_cpd_cb.append_text('') self.select_cpd_cb.set_sensitive(False) @@ -1539,10 +1539,10 @@ def start_refinement(self): self.cb.set_active(self.index) def RefinementParams(self, widget): - print '\n==> XCE: changing refinement parameters' + print('\n==> XCE: changing refinement parameters') self.RefmacParams = XChemRefine.RefineParams(self.project_directory, self.xtalID, self.compoundID, self.data_source).RefmacRefinementParams(self.RefmacParams) - print self.RefmacParams + print(self.RefmacParams) def covalentLinkDef(self, widget): coot.user_defined_click_py(2, self.show_potential_link) @@ -1552,7 +1552,7 @@ def show_potential_link(self, *clicks): # it's a prerequisite that the ligand is merged into the protein imol_protein = None for imol in coot_utils_XChem.molecule_number_list(): - print '>', coot.molecule_name(imol) + print('>', coot.molecule_name(imol)) if coot.molecule_name(imol).endswith(self.pdb_style) or \ coot.molecule_name(imol).endswith('init.pdb') or \ coot.molecule_name(imol).endswith('dimple.pdb') or \ @@ -1560,15 +1560,15 @@ def show_potential_link(self, *clicks): imol_protein = imol break - print 'please click on the two atoms you want to link' + print('please click on the two atoms you want to link') if (len(clicks) == 2): click_1 = clicks[0] click_2 = clicks[1] imol_1 = click_1[1] imol_2 = click_2[1] - print 'imolp', imol, 'imo11', imol_1, 'imol2', imol_2 + print('imolp', imol, 'imo11', imol_1, 'imol2', imol_2) if imol_1 == imol_2 and imol_1 == imol_protein: - print 'click_1', click_1 + print('click_1', click_1) self.covLinkAtomSpec = None xyz_1 = atom_info_string( click_1[1], click_1[2], click_1[3], click_1[4], click_1[5], click_1[6]) @@ -1585,7 +1585,7 @@ def show_potential_link(self, *clicks): self.covLinkAtomSpec = [imol_protein, click_1, click_2, residue_1, residue_2] else: - print 'error: both atoms must belong to the same object; did you merge the ligand with your protein?' + print('error: both atoms must belong to the same object; did you merge the ligand with your protein?') def covalentLinkCreate(self, widget): if self.covLinkAtomSpec is not None: @@ -1598,7 +1598,7 @@ def covalentLinkCreate(self, widget): generic_object_clear(self.covLinkObject) self.start_refinement() else: - print 'error: no covalent link defined' + print('error: no covalent link defined') def set_selection_mode(self, widget): self.selection_mode = widget.get_active_text() @@ -1649,9 +1649,9 @@ def place_ligand_here(self, widget): molName = coot.molecule_name(imol)[coot.molecule_name( imol).rfind('/')+1:].replace('.pdb', '') if molName == cpd: - print '===> XCE: moving ligand to pointer' + print('===> XCE: moving ligand to pointer') coot_utils_XChem.move_molecule_here(imol) - print 'LIGAND: ', molName + print('LIGAND: ', molName) # print '===> XCE: moving ligand to pointer' # # coot.move_molecule_here() # print 'LIGAND: ', self.mol_dict['ligand'] @@ -1665,7 +1665,7 @@ def merge_ligand_into_protein(self, widget): molName = coot.molecule_name(imol)[coot.molecule_name( imol).rfind('/')+1:].replace('.pdb', '') if molName == cpd: - print '===> XCE: merge ligand into protein structure -->', cpd + print('===> XCE: merge ligand into protein structure -->', cpd) coot.merge_molecules_py([imol], self.mol_dict['protein']) if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( @@ -1673,24 +1673,24 @@ def merge_ligand_into_protein(self, widget): if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')): os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) - print 'XCE: changing directory', os.path.join( - self.project_directory, self.xtalID) + print('XCE: changing directory', os.path.join( + self.project_directory, self.xtalID)) os.chdir(os.path.join(self.project_directory, self.xtalID)) - print 'XCE: changing symlink ln -s %s %s.cif' % ( - os.path.join('compound', molName + '.cif'), self.compoundID) + print('XCE: changing symlink ln -s %s %s.cif' % ( + os.path.join('compound', molName + '.cif'), self.compoundID)) os.system( 'ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')) - print 'XCE: changing directory', os.path.join( - self.project_directory, self.xtalID) + print('XCE: changing directory', os.path.join( + self.project_directory, self.xtalID)) os.chdir(os.path.join(self.project_directory, self.xtalID)) - print 'XCE: changing symlink ln -s %s %s.pdb' % ( - os.path.join('compound', molName + '.pdb'), self.compoundID) + print('XCE: changing symlink ln -s %s %s.pdb' % ( + os.path.join('compound', molName + '.pdb'), self.compoundID)) os.system('ln -s %s %s.pdb' % (os.path.join('compound', molName + '.pdb'), self.compoundID)) - print '===> XCE: deleting ligand molecule', molName + print('===> XCE: deleting ligand molecule', molName) coot.close_molecule(imol) self.select_cpd_cb.set_sensitive(False) @@ -1702,15 +1702,15 @@ def merge_ligand_into_protein(self, widget): # coot.close_molecule(self.mol_dict['ligand']) def show_molprobity_to_do(self, widget): - print self.panddaSerial + print(self.panddaSerial) AdjPanddaSerial = (4 - len(str(self.Serial))) * \ '0' + str(int(self.panddaSerial) - 1) - print '==> XCE COOT: trying to find ' + os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py') + print('==> XCE COOT: trying to find ' + os.path.join(self.project_directory, self.xtalID, + 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py')) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py')): - print '==> XCE: running MolProbity Summary for', self.xtalID + print('==> XCE: running MolProbity Summary for', self.xtalID) coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py')) # elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), @@ -1719,8 +1719,8 @@ def show_molprobity_to_do(self, widget): # coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), # 'molprobity_coot.py')) else: - print '==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py') + print('==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, + 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')) # def refinementProtocolCallback(self, widget): # if widget.get_active(): diff --git a/lib/XChemCootNew.py b/lib/XChemCootNew.py index 6bae8402..c3acad77 100755 --- a/lib/XChemCootNew.py +++ b/lib/XChemCootNew.py @@ -51,7 +51,7 @@ def __init__(self): self.data_source = self.settings['data_source'] self.db = XChemDB.data_source(self.data_source) - print self.settings + print(self.settings) # checking for external software packages self.external_software = XChemUtils.external_software( @@ -831,11 +831,11 @@ def select_cpd(self, widget): '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') else: molNameCIF = molName - print cpd, '-', imol, '-', coot.molecule_name(imol) + print(cpd, '-', imol, '-', coot.molecule_name(imol)) if molName == cpd: coot.set_mol_displayed(imol, 1) - print 'reading', os.path.join( - self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif') + print('reading', os.path.join( + self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) coot.read_cif_dictionary(os.path.join( self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) else: @@ -869,7 +869,7 @@ def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 for i, entry in enumerate(self.ligand_confidence_category): - print '--->', entry, self.ligand_confidence + print('--->', entry, self.ligand_confidence) try: if entry.split()[0] == self.ligand_confidence.split()[0]: current_stage = i @@ -906,8 +906,8 @@ def ChangeSite(self, widget, data=None): def ChooseSite(self, widget): tmp = str(widget.get_active_text()) - print self.siteDict - print self.site_index + print(self.siteDict) + print(self.site_index) self.site_index = tmp.split()[1] self.event_index = tmp.split()[4] for n, item in enumerate(self.siteDict[self.xtalID]): @@ -932,18 +932,18 @@ def RefreshSiteData(self): # for w in self.label_button_list: # w.set_active(False) - print 'pandda index', self.pandda_index + print('pandda index', self.pandda_index) self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] - print 'new spider plot:', self.spider_plot + print('new spider plot:', self.spider_plot) self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] - print 'new event map:', self.event_map + print('new event map:', self.event_map) self.ligand_confidence = str( self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) - print 'new site coordinates:', site_x, site_y, site_z + print('new site coordinates:', site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) # self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) @@ -953,7 +953,7 @@ def RefreshSiteData(self): self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, self.event_index) - print '>>>>> spider plot data', self.spider_plot_data + print('>>>>> spider plot data', self.spider_plot_data) self.ligandIDValue.set_label( self.spider_plot_data['PANDDA_site_ligand_id']) try: @@ -1043,7 +1043,7 @@ def experiment_stage_button_clicked(self, widget, data=None): self.xce_logfile, self.xtalID, 'ligand_bound', self.db_dict_mainTable) def ligand_confidence_button_clicked(self, widget, data=None): - print 'PANDDA_index', self.pandda_index + print('PANDDA_index', self.pandda_index) if self.pandda_index == -1: self.db_dict_mainTable['RefinementLigandConfidence'] = data self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( @@ -1116,21 +1116,21 @@ def RefreshData(self): if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): - print '==> XCE: updating quality indicators in data source for ' + self.xtalID + print('==> XCE: updating quality indicators in data source for ' + self.xtalID) XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, os.path.join(self.project_directory, self.xtalID, self.pdb_style)) XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, '') # '' because file does not exist elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.pdb')): - print '==> XCE: updating quality indicators in data source for ' + self.xtalID + print('==> XCE: updating quality indicators in data source for ' + self.xtalID) XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, os.path.join(self.project_directory, self.xtalID, 'init.pdb')) XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, '') # '' because file does not exist elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): - print '==> XCE: updating quality indicators in data source for ' + self.xtalID + print('==> XCE: updating quality indicators in data source for ' + self.xtalID) XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')) @@ -1147,7 +1147,7 @@ def RefreshData(self): if self.Serial > 1: self.RefmacParams = self.Refine.ParamsFromPreviousCycle( self.Serial - 1) - print '==> REFMAC params:', self.RefmacParams + print('==> REFMAC params:', self.RefmacParams) # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) # else: @@ -1159,11 +1159,11 @@ def RefreshData(self): ######################################################################################### # ligand files # first remove old samples if present - print '>>>', self.mol_dict['ligand_stereo'] + print('>>>', self.mol_dict['ligand_stereo']) for n, item in enumerate(self.mol_dict['ligand_stereo']): - print '__', item + print('__', item) self.select_cpd_cb.remove_text(0) - print 'done' + print('done') ######################################################################################### # remove potential generic line which indicates a possible covalent link @@ -1220,7 +1220,7 @@ def RefreshData(self): self.select_cpd_cb.set_sensitive(True) self.select_cpd_cb.set_active(0) else: - print 'no compound found in sample directory' + print('no compound found in sample directory') # self.select_cpd_cb.append_text('') self.select_cpd_cb.set_sensitive(False) @@ -1537,7 +1537,7 @@ def start_refinement(self): self.cb.set_active(self.index) def RefinementParams(self, widget): - print '\n==> XCE: changing refinement parameters' + print('\n==> XCE: changing refinement parameters') self.RefmacParams = XChemRefine.RefineParams(self.project_directory, self.xtalID, self.compoundID, self.data_source).RefmacRefinementParams(self.RefmacParams) @@ -1549,7 +1549,7 @@ def show_potential_link(self, *clicks): # it's a prerequisite that the ligand is merged into the protein imol_protein = None for imol in coot_utils_XChem.molecule_number_list(): - print '>', coot.molecule_name(imol) + print('>', coot.molecule_name(imol)) if coot.molecule_name(imol).endswith(self.pdb_style) or \ coot.molecule_name(imol).endswith('init.pdb') or \ coot.molecule_name(imol).endswith('dimple.pdb') or \ @@ -1557,15 +1557,15 @@ def show_potential_link(self, *clicks): imol_protein = imol break - print 'please click on the two atoms you want to link' + print('please click on the two atoms you want to link') if (len(clicks) == 2): click_1 = clicks[0] click_2 = clicks[1] imol_1 = click_1[1] imol_2 = click_2[1] - print 'imolp', imol, 'imo11', imol_1, 'imol2', imol_2 + print('imolp', imol, 'imo11', imol_1, 'imol2', imol_2) if imol_1 == imol_2 and imol_1 == imol_protein: - print 'click_1', click_1 + print('click_1', click_1) self.covLinkAtomSpec = None xyz_1 = atom_info_string( click_1[1], click_1[2], click_1[3], click_1[4], click_1[5], click_1[6]) @@ -1582,7 +1582,7 @@ def show_potential_link(self, *clicks): self.covLinkAtomSpec = [imol_protein, click_1, click_2, residue_1, residue_2] else: - print 'error: both atoms must belong to the same object; did you merge the ligand with your protein?' + print('error: both atoms must belong to the same object; did you merge the ligand with your protein?') def covalentLinkCreate(self, widget): if self.covLinkAtomSpec is not None: @@ -1595,7 +1595,7 @@ def covalentLinkCreate(self, widget): generic_object_clear(self.covLinkObject) self.start_refinement() else: - print 'error: no covalent link defined' + print('error: no covalent link defined') def set_selection_mode(self, widget): self.selection_mode = widget.get_active_text() @@ -1646,9 +1646,9 @@ def place_ligand_here(self, widget): molName = coot.molecule_name(imol)[coot.molecule_name( imol).rfind('/')+1:].replace('.pdb', '') if molName == cpd: - print '===> XCE: moving ligand to pointer' + print('===> XCE: moving ligand to pointer') coot_utils_XChem.move_molecule_here(imol) - print 'LIGAND: ', molName + print('LIGAND: ', molName) # print '===> XCE: moving ligand to pointer' # # coot.move_molecule_here() # print 'LIGAND: ', self.mol_dict['ligand'] @@ -1662,7 +1662,7 @@ def merge_ligand_into_protein(self, widget): molName = coot.molecule_name(imol)[coot.molecule_name( imol).rfind('/')+1:].replace('.pdb', '') if molName == cpd: - print '===> XCE: merge ligand into protein structure -->', cpd + print('===> XCE: merge ligand into protein structure -->', cpd) coot.merge_molecules_py([imol], self.mol_dict['protein']) if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( @@ -1670,24 +1670,24 @@ def merge_ligand_into_protein(self, widget): if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')): os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) - print 'XCE: changing directory', os.path.join( - self.project_directory, self.xtalID) + print('XCE: changing directory', os.path.join( + self.project_directory, self.xtalID)) os.chdir(os.path.join(self.project_directory, self.xtalID)) - print 'XCE: changing symlink ln -s %s %s.cif' % ( - os.path.join('compound', molName + '.cif'), self.compoundID) + print('XCE: changing symlink ln -s %s %s.cif' % ( + os.path.join('compound', molName + '.cif'), self.compoundID)) os.system( 'ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')) - print 'XCE: changing directory', os.path.join( - self.project_directory, self.xtalID) + print('XCE: changing directory', os.path.join( + self.project_directory, self.xtalID)) os.chdir(os.path.join(self.project_directory, self.xtalID)) - print 'XCE: changing symlink ln -s %s %s.pdb' % ( - os.path.join('compound', molName + '.pdb'), self.compoundID) + print('XCE: changing symlink ln -s %s %s.pdb' % ( + os.path.join('compound', molName + '.pdb'), self.compoundID)) os.system('ln -s %s %s.pdb' % (os.path.join('compound', molName + '.pdb'), self.compoundID)) - print '===> XCE: deleting ligand molecule', molName + print('===> XCE: deleting ligand molecule', molName) coot.close_molecule(imol) self.select_cpd_cb.set_sensitive(False) @@ -1699,24 +1699,24 @@ def merge_ligand_into_protein(self, widget): # coot.close_molecule(self.mol_dict['ligand']) def show_molprobity_to_do(self, widget): - print self.panddaSerial + print(self.panddaSerial) AdjPanddaSerial = (4 - len(str(self.Serial))) * \ '0' + str(int(self.panddaSerial) - 1) - print os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), - 'molprobity_coot.py') + print(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), + 'molprobity_coot.py')) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')): - print '==> XCE: running MolProbity Summary for', self.xtalID + print('==> XCE: running MolProbity Summary for', self.xtalID) coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')) elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), 'molprobity_coot.py')): - print '==> XCE: running MolProbity Summary for', self.xtalID + print('==> XCE: running MolProbity Summary for', self.xtalID) coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), 'molprobity_coot.py')) else: - print '==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py') + print('==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, + 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')) def refinementProtocolCallback(self, widget): if widget.get_active(): @@ -1731,7 +1731,7 @@ def refinementProtocolCallback(self, widget): self.refinementProtocol = 'refmac' self.PREVbuttonSite.set_sensitive(False) self.NEXTbuttonSite.set_sensitive(False) - print self.refinementProtocol + print(self.refinementProtocol) def refinementProgramCallback(self, widget): if widget.get_active(): @@ -1747,7 +1747,7 @@ def refinementProgramCallback(self, widget): self.refinementProtocol = 'pandda_refmac' else: self.refinementProtocol = 'refmac' - print self.refinementProtocol + print(self.refinementProtocol) def show_ground_state_mean_map(self, widget): if widget.get_label().startswith('Show'): diff --git a/lib/XChemCootOld.py b/lib/XChemCootOld.py index 224b826a..b4198760 100755 --- a/lib/XChemCootOld.py +++ b/lib/XChemCootOld.py @@ -1,1210 +1,1210 @@ -# last edited: 21/07/2017 - 15:00 - -import pango -import gtk -import pygtk -import coot_utils_XChem -import coot -import XChemUtils -import XChemRefine -import XChemDB -import gobject -import sys -import os -import pickle - -from matplotlib.figure import Figure -#from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas - -# XCE libraries -sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') - -# libraries from COOT - -# had to adapt the original coot_utils.py file -# otherwise unable to import the original file without complaints about missing modules etc. -# modified file is now in $XChemExplorer_DIR/lib - - -class GUI(object): - - """ - main class which opens the actual GUI - """ - - def __init__(self): - - ########################################################################################### - # read in settings file from XChemExplorer to set the relevant paths - print 'current dir', os.getcwd() - self.settings = pickle.load(open(".xce_settings.pkl", "rb")) - remote_qsub_submission = self.settings['remote_qsub'] - print 'setting', self.settings -# self.refine_model_directory=self.settings['refine_model_directory'] - self.database_directory = self.settings['database_directory'] - self.xce_logfile = self.settings['xce_logfile'] - self.data_source = self.settings['data_source'] - self.db = XChemDB.data_source(self.data_source) - - # checking for external software packages - self.external_software = XChemUtils.external_software( - self.xce_logfile).check() - self.external_software['qsub_remote'] = remote_qsub_submission - - self.selection_criteria = ['0 - All Datasets', - '1 - Analysis Pending', - '2 - PANDDA model', - '3 - In Refinement', - '4 - CompChem ready', - '5 - Deposition ready', - '6 - Deposited'] - - self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], - ['In Refinement', - '3 - In Refinement', 65000, 0, 0], - ['Comp Chem Ready!', - '4 - CompChem ready', 65000, 0, 0], - ['Ready for Deposition!', - '5 - Deposition ready', 65000, 0, 0], - ['In PDB', '6 - Deposited', 65000, 0, 0]] - - self.ligand_confidence_category = ['0 - no ligand present', - '1 - Low Confidence', - '2 - Correct ligand, weak density', - '3 - Clear density, unexpected ligand', - '4 - High Confidence'] - - self.ligand_site_information = self.db.get_list_of_pandda_sites_for_coot() - - # this decides which samples will be looked at - self.selection_mode = '' -# self.selected_site='' - self.pandda_index = -1 # refers to the number of sites - self.site_index = '0' - self.event_index = '0' - - # the Folder is kind of a legacy thing because my inital idea was to have separate folders - # for Data Processing and Refinement - self.project_directory = self.settings['initial_model_directory'] - self.Serial = 0 - self.Refine = None - self.index = -1 - self.Todo = [] - self.siteDict = {} - - self.xtalID = '' - self.compoundID = '' - self.spider_plot = '' - self.ligand_confidence = '' - self.refinement_folder = '' -# self.datasetOutcome='' - - self.pdb_style = 'refine.pdb' - self.mtz_style = 'refine.mtz' - - # stores imol of currently loaded molecules and maps - self.mol_dict = {'protein': -1, - 'ligand': -1, - '2fofc': -1, - 'fofc': -1, - 'event': -1} - - # two dictionaries which are flushed when a new crystal is loaded - # and which contain information to update the data source if necessary - self.db_dict_mainTable = {} - self.db_dict_panddaTable = {} - - ########################################################################################### - # some COOT settings - coot.set_map_radius(15) - coot.set_colour_map_rotation_for_map(0) - coot.set_colour_map_rotation_on_read_pdb_flag(0) - - self.QualityIndicators = {'RefinementRcryst': '-', - 'RefinementRfree': '-', - 'RefinementRfreeTraficLight': 'gray', - 'RefinementResolution': '-', - 'RefinementResolutionTL': 'gray', - 'RefinementMolProbityScore': '-', - 'RefinementMolProbityScoreTL': 'gray', - 'RefinementRamachandranOutliers': '-', - 'RefinementRamachandranOutliersTL': 'gray', - 'RefinementRamachandranFavored': '-', - 'RefinementRamachandranFavoredTL': 'gray', - 'RefinementRmsdBonds': '-', - 'RefinementRmsdBondsTL': 'gray', - 'RefinementRmsdAngles': '-', - 'RefinementRmsdAnglesTL': 'gray', - 'RefinementMatrixWeight': '-'} - - self.spider_plot_data = {'PANDDA_site_ligand_id': '-', - 'PANDDA_site_occupancy': '-', - 'PANDDA_site_B_average': '-', - 'PANDDA_site_B_ratio_residue_surroundings': '-', - 'PANDDA_site_RSCC': '-', - 'PANDDA_site_rmsd': '-', - 'PANDDA_site_RSR': '-', - 'PANDDA_site_RSZD': '-'} - - # default refmac parameters - self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': ''} - - def StartGUI(self): - - self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) - self.window.connect("delete_event", gtk.main_quit) - self.window.set_border_width(10) - self.window.set_default_size(400, 800) - self.window.set_title("XChemExplorer") - self.vbox = gtk.VBox() # this is the main container - - ################################################################################# - # --- Sample Selection --- -# self.vbox.add(gtk.Label('Select Samples')) - - frame = gtk.Frame(label='Select Samples') - self.hbox_select_samples = gtk.HBox() -# vbox=gtk.VBox() - - self.cb_select_samples = gtk.combo_box_new_text() - self.cb_select_samples.connect("changed", self.set_selection_mode) - for citeria in self.selection_criteria: - self.cb_select_samples.append_text(citeria) - self.hbox_select_samples.add(self.cb_select_samples) - -# self.cb_select_sites = gtk.combo_box_new_text() -# self.cb_select_sites.connect("changed", self.set_site) -# for site in self.ligand_site_information: -# self.cb_select_sites.append_text(str(site[0])+' - '+str(site[1])) -# self.hbox_select_samples.add(self.cb_select_sites) - - self.select_samples_button = gtk.Button(label="GO") - self.select_samples_button.connect( - "clicked", self.get_samples_to_look_at) - self.hbox_select_samples.add(self.select_samples_button) - frame.add(self.hbox_select_samples) - self.vbox.pack_start(frame) - - ################################################################################# - # --- status window --- - frame = gtk.Frame() - self.status_label = gtk.Label() - frame.add(self.status_label) - self.vbox.pack_start(frame) - - # SPACER - self.vbox.add(gtk.Label(' ')) - - ################################################################################# - # --- Refinement Statistics --- - # next comes a section which displays some global quality indicators - # a combination of labels and textview widgets, arranged in a table - - RRfreeLabel_frame = gtk.Frame() - self.RRfreeLabel = gtk.Label('R/Rfree') - RRfreeLabel_frame.add(self.RRfreeLabel) - self.RRfreeValue = gtk.Label( - self.QualityIndicators['RefinementRcryst']+'/'+self.QualityIndicators['RefinementRfree']) - RRfreeBox_frame = gtk.Frame() - self.RRfreeBox = gtk.EventBox() - self.RRfreeBox.add(self.RRfreeValue) - RRfreeBox_frame.add(self.RRfreeBox) - - ResolutionLabel_frame = gtk.Frame() - self.ResolutionLabel = gtk.Label('Resolution') - ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label( - self.QualityIndicators['RefinementResolution']) - ResolutionBox_frame = gtk.Frame() - self.ResolutionBox = gtk.EventBox() - self.ResolutionBox.add(self.ResolutionValue) - ResolutionBox_frame.add(self.ResolutionBox) - - MolprobityScoreLabel_frame = gtk.Frame() - self.MolprobityScoreLabel = gtk.Label('MolprobityScore') - MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) - self.MolprobityScoreValue = gtk.Label( - self.QualityIndicators['RefinementMolProbityScore']) - MolprobityScoreBox_frame = gtk.Frame() - self.MolprobityScoreBox = gtk.EventBox() - self.MolprobityScoreBox.add(self.MolprobityScoreValue) - MolprobityScoreBox_frame.add(self.MolprobityScoreBox) - - RamachandranOutliersLabel_frame = gtk.Frame() - self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') - RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) - self.RamachandranOutliersValue = gtk.Label( - self.QualityIndicators['RefinementRamachandranOutliers']) - RamachandranOutliersBox_frame = gtk.Frame() - self.RamachandranOutliersBox = gtk.EventBox() - self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) - RamachandranOutliersBox_frame.add(self.RamachandranOutliersBox) - - RamachandranFavoredLabel_frame = gtk.Frame() - self.RamachandranFavoredLabel = gtk.Label('Rama Favored') - RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) - self.RamachandranFavoredValue = gtk.Label( - self.QualityIndicators['RefinementRamachandranFavored']) - RamachandranFavoredBox_frame = gtk.Frame() - self.RamachandranFavoredBox = gtk.EventBox() - self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) - RamachandranFavoredBox_frame.add(self.RamachandranFavoredBox) - - rmsdBondsLabel_frame = gtk.Frame() - self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') - rmsdBondsLabel_frame.add(self.rmsdBondsLabel) - self.rmsdBondsValue = gtk.Label( - self.QualityIndicators['RefinementRmsdBonds']) - rmsdBondsBox_frame = gtk.Frame() - self.rmsdBondsBox = gtk.EventBox() - self.rmsdBondsBox.add(self.rmsdBondsValue) - rmsdBondsBox_frame.add(self.rmsdBondsBox) - - rmsdAnglesLabel_frame = gtk.Frame() - self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') - rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) - self.rmsdAnglesValue = gtk.Label( - self.QualityIndicators['RefinementRmsdAngles']) - rmsdAnglesBox_frame = gtk.Frame() - self.rmsdAnglesBox = gtk.EventBox() - self.rmsdAnglesBox.add(self.rmsdAnglesValue) - rmsdAnglesBox_frame.add(self.rmsdAnglesBox) - - MatrixWeightLabel_frame = gtk.Frame() - self.MatrixWeightLabel = gtk.Label('Matrix Weight') - MatrixWeightLabel_frame.add(self.MatrixWeightLabel) - self.MatrixWeightValue = gtk.Label( - self.QualityIndicators['RefinementMatrixWeight']) - MatrixWeightBox_frame = gtk.Frame() - self.MatrixWeightBox = gtk.EventBox() - self.MatrixWeightBox.add(self.MatrixWeightValue) - MatrixWeightBox_frame.add(self.MatrixWeightBox) - - ligandIDLabel_frame = gtk.Frame() - self.ligandIDLabel = gtk.Label('Ligand ID') - ligandIDLabel_frame.add(self.ligandIDLabel) - self.ligandIDValue = gtk.Label( - self.spider_plot_data['PANDDA_site_ligand_id']) - ligandIDBox_frame = gtk.Frame() - self.ligandIDBox = gtk.EventBox() - self.ligandIDBox.add(self.ligandIDValue) - ligandIDBox_frame.add(self.ligandIDBox) - - ligand_occupancyLabel_frame = gtk.Frame() - self.ligand_occupancyLabel = gtk.Label('occupancy') - ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) - self.ligand_occupancyValue = gtk.Label( - self.spider_plot_data['PANDDA_site_occupancy']) - ligand_occupancyBox_frame = gtk.Frame() - self.ligand_occupancyBox = gtk.EventBox() - self.ligand_occupancyBox.add(self.ligand_occupancyValue) - ligand_occupancyBox_frame.add(self.ligand_occupancyBox) - - ligand_BaverageLabel_frame = gtk.Frame() - self.ligand_BaverageLabel = gtk.Label('B average') - ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) - self.ligand_BaverageValue = gtk.Label( - self.spider_plot_data['PANDDA_site_B_average']) - ligand_BaverageBox_frame = gtk.Frame() - self.ligand_BaverageBox = gtk.EventBox() - self.ligand_BaverageBox.add(self.ligand_BaverageValue) - ligand_BaverageBox_frame.add(self.ligand_BaverageBox) - - ligand_BratioSurroundingsLabel_frame = gtk.Frame() - self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') - ligand_BratioSurroundingsLabel_frame.add( - self.ligand_BratioSurroundingsLabel) - self.ligand_BratioSurroundingsValue = gtk.Label( - self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) - ligand_BratioSurroundingsBox_frame = gtk.Frame() - self.ligand_BratioSurroundingsBox = gtk.EventBox() - self.ligand_BratioSurroundingsBox.add( - self.ligand_BratioSurroundingsValue) - ligand_BratioSurroundingsBox_frame.add( - self.ligand_BratioSurroundingsBox) - - ligand_RSCCLabel_frame = gtk.Frame() - self.ligand_RSCCLabel = gtk.Label('RSCC') - ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) - self.ligand_RSCCValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSCC']) - ligand_RSCCBox_frame = gtk.Frame() - self.ligand_RSCCBox = gtk.EventBox() - self.ligand_RSCCBox.add(self.ligand_RSCCValue) - ligand_RSCCBox_frame.add(self.ligand_RSCCBox) - - ligand_rmsdLabel_frame = gtk.Frame() - self.ligand_rmsdLabel = gtk.Label('rmsd') - ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) - self.ligand_rmsdValue = gtk.Label( - self.spider_plot_data['PANDDA_site_rmsd']) - ligand_rmsdBox_frame = gtk.Frame() - self.ligand_rmsdBox = gtk.EventBox() - self.ligand_rmsdBox.add(self.ligand_rmsdValue) - ligand_rmsdBox_frame.add(self.ligand_rmsdBox) - - ligand_RSRLabel_frame = gtk.Frame() - self.ligand_RSRLabel = gtk.Label('RSR') - ligand_RSRLabel_frame.add(self.ligand_RSRLabel) - self.ligand_RSRValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSR']) - ligand_RSRBox_frame = gtk.Frame() - self.ligand_RSRBox = gtk.EventBox() - self.ligand_RSRBox.add(self.ligand_RSRValue) - ligand_RSRBox_frame.add(self.ligand_RSRBox) - - ligand_RSZDLabel_frame = gtk.Frame() - self.ligand_RSZDLabel = gtk.Label('RSZD') - ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) - self.ligand_RSZDValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSZD']) - ligand_RSZDBox_frame = gtk.Frame() - self.ligand_RSZDBox = gtk.EventBox() - self.ligand_RSZDBox.add(self.ligand_RSZDValue) - ligand_RSZDBox_frame.add(self.ligand_RSZDBox) - - outer_frame = gtk.Frame() - hbox = gtk.HBox() - - frame = gtk.Frame() - self.table_left = gtk.Table(8, 2, False) - self.table_left.attach(RRfreeLabel_frame, 0, 1, 0, 1) - self.table_left.attach(ResolutionLabel_frame, 0, 1, 1, 2) - self.table_left.attach(MolprobityScoreLabel_frame, 0, 1, 2, 3) - self.table_left.attach(RamachandranOutliersLabel_frame, 0, 1, 3, 4) - self.table_left.attach(RamachandranFavoredLabel_frame, 0, 1, 4, 5) - self.table_left.attach(rmsdBondsLabel_frame, 0, 1, 5, 6) - self.table_left.attach(rmsdAnglesLabel_frame, 0, 1, 6, 7) - self.table_left.attach(MatrixWeightLabel_frame, 0, 1, 7, 8) - self.table_left.attach(RRfreeBox_frame, 1, 2, 0, 1) - self.table_left.attach(ResolutionBox_frame, 1, 2, 1, 2) - self.table_left.attach(MolprobityScoreBox_frame, 1, 2, 2, 3) - self.table_left.attach(RamachandranOutliersBox_frame, 1, 2, 3, 4) - self.table_left.attach(RamachandranFavoredBox_frame, 1, 2, 4, 5) - self.table_left.attach(rmsdBondsBox_frame, 1, 2, 5, 6) - self.table_left.attach(rmsdAnglesBox_frame, 1, 2, 6, 7) - self.table_left.attach(MatrixWeightBox_frame, 1, 2, 7, 8) - frame.add(self.table_left) - hbox.add(frame) - - frame = gtk.Frame() - self.table_right = gtk.Table(8, 2, False) - self.table_right.attach(ligandIDLabel_frame, - 0, 1, 0, 1) - self.table_right.attach( - ligand_occupancyLabel_frame, 0, 1, 1, 2) - self.table_right.attach( - ligand_BaverageLabel_frame, 0, 1, 2, 3) - self.table_right.attach( - ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) - self.table_right.attach( - ligand_RSCCLabel_frame, 0, 1, 4, 5) - self.table_right.attach( - ligand_rmsdLabel_frame, 0, 1, 5, 6) - self.table_right.attach( - ligand_RSRLabel_frame, 0, 1, 6, 7) - self.table_right.attach( - ligand_RSZDLabel_frame, 0, 1, 7, 8) - self.table_right.attach(ligandIDBox_frame, - 1, 2, 0, 1) - self.table_right.attach( - ligand_occupancyBox_frame, 1, 2, 1, 2) - self.table_right.attach( - ligand_BaverageBox_frame, 1, 2, 2, 3) - self.table_right.attach( - ligand_BratioSurroundingsBox_frame, 1, 2, 3, 4) - self.table_right.attach( - ligand_RSCCBox_frame, 1, 2, 4, 5) - self.table_right.attach( - ligand_rmsdBox_frame, 1, 2, 5, 6) - self.table_right.attach(ligand_RSRBox_frame, - 1, 2, 6, 7) - self.table_right.attach( - ligand_RSZDBox_frame, 1, 2, 7, 8) - frame.add(self.table_right) - hbox.add(frame) - - outer_frame.add(hbox) - self.vbox.add(outer_frame) - - button = gtk.Button(label="Show MolProbity to-do list") - button.connect("clicked", self.show_molprobity_to_do) - self.vbox.add(button) - self.vbox.pack_start(frame) - - # SPACER - self.vbox.add(gtk.Label(' ')) - - ################################################################################# - # --- hbox for compound picture & spider_plot (formerly: refinement history) --- - frame = gtk.Frame() - self.hbox_for_info_graphics = gtk.HBox() - - # --- compound picture --- - compound_frame = gtk.Frame() - pic = gtk.gdk.pixbuf_new_from_file(os.path.join( - os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) - self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) - self.image = gtk.Image() - self.image.set_from_pixbuf(self.pic) - compound_frame.add(self.image) - self.hbox_for_info_graphics.add(compound_frame) - - # --- Refinement History --- -# self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) -# self.canvas.set_size_request(190, 190) -# self.hbox_for_info_graphics.add(self.canvas) - - # --- Spider Plot --- - spider_plot_frame = gtk.Frame() - spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join( - os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) - self.spider_plot_image = gtk.Image() - self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) - spider_plot_frame.add(self.spider_plot_image) - self.hbox_for_info_graphics.add(spider_plot_frame) - - frame.add(self.hbox_for_info_graphics) - self.vbox.add(frame) - - ################################################################################# - # --- pandda.inspect user comments --- - outer_frame = gtk.Frame(label='pandda.inspect comments') - vbox = gtk.VBox() - ligand_site_name_label_frame = gtk.Frame() - ligand_site_name_label = gtk.Label('Site Name') - ligand_site_name_label_frame.add(ligand_site_name_label) - ligand_inspect_confidence_label_frame = gtk.Frame() - ligand_inspect_confidence_label = gtk.Label('Confidence') - ligand_inspect_confidence_label_frame.add( - ligand_inspect_confidence_label) - ligand_inspect_interesting_label_frame = gtk.Frame() - ligand_inspect_interesting_label = gtk.Label('Interesting') - ligand_inspect_interesting_label_frame.add( - ligand_inspect_interesting_label) - ligand_inspect_comment_label_frame = gtk.Frame() - ligand_inspect_comment_label = gtk.Label('Comment') - ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) - ligand_site_name_value_frame = gtk.Frame() - self.ligand_site_name_value = gtk.Label('-') - ligand_site_name_value_frame.add(self.ligand_site_name_value) - ligand_inspect_confidence_value_frame = gtk.Frame() - self.ligand_inspect_confidence_value = gtk.Label('-') - ligand_inspect_confidence_value_frame.add( - self.ligand_inspect_confidence_value) - ligand_inspect_interesting_value_frame = gtk.Frame() - self.ligand_inspect_interesting_value = gtk.Label('-') - ligand_inspect_interesting_value_frame.add( - self.ligand_inspect_interesting_value) - ligand_inspect_comment_value_frame = gtk.Frame() - self.ligand_inspect_comment_value = gtk.Label('-') - ligand_inspect_comment_value_frame.add( - self.ligand_inspect_comment_value) - - frame_pandda_inspect_comments_table = gtk.Frame() - pandda_inspect_comments_table = gtk.Table(2, 6, False) - pandda_inspect_comments_table.attach( - ligand_site_name_label_frame, 0, 1, 0, 1) - pandda_inspect_comments_table.attach( - ligand_site_name_value_frame, 1, 2, 0, 1) - pandda_inspect_comments_table.attach( - ligand_inspect_confidence_label_frame, 2, 3, 0, 1) - pandda_inspect_comments_table.attach( - ligand_inspect_confidence_value_frame, 3, 4, 0, 1) - pandda_inspect_comments_table.attach( - ligand_inspect_interesting_label_frame, 4, 5, 0, 1) - pandda_inspect_comments_table.attach( - ligand_inspect_interesting_value_frame, 5, 6, 0, 1) - pandda_inspect_comments_table.attach( - ligand_inspect_comment_label_frame, 0, 1, 1, 2) - pandda_inspect_comments_table.attach( - ligand_inspect_comment_value_frame, 1, 6, 1, 2) - - frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) - vbox.add(frame_pandda_inspect_comments_table) - outer_frame.add(vbox) - self.vbox.pack_start(outer_frame) - -# # SPACER - self.vbox.add(gtk.Label(' ')) - - ################################################################################# - outer_frame = gtk.Frame(label='Sample Navigator') - hboxSample = gtk.HBox() - - # --- crystal navigator combobox --- - frame = gtk.Frame() - self.vbox_sample_navigator = gtk.VBox() - self.cb = gtk.combo_box_new_text() - self.cb.connect("changed", self.ChooseXtal) - self.vbox_sample_navigator.add(self.cb) - # --- crystal navigator backward/forward button --- - self.PREVbutton = gtk.Button(label="<<<") - self.NEXTbutton = gtk.Button(label=">>>") - self.PREVbutton.connect("clicked", self.ChangeXtal, -1) - self.NEXTbutton.connect("clicked", self.ChangeXtal, +1) - hbox = gtk.HBox() - hbox.pack_start(self.PREVbutton) - hbox.pack_start(self.NEXTbutton) - self.vbox_sample_navigator.add(hbox) - frame.add(self.vbox_sample_navigator) - hboxSample.add(frame) - - # --- site navigator combobox --- - frame = gtk.Frame() - self.vbox_site_navigator = gtk.VBox() - self.cb_site = gtk.combo_box_new_text() - self.cb_site.connect("changed", self.ChooseSite) - self.vbox_site_navigator.add(self.cb_site) - # --- site navigator backward/forward button --- - self.PREVbuttonSite = gtk.Button(label="<<<") - self.NEXTbuttonSite = gtk.Button(label=">>>") - self.PREVbuttonSite.connect("clicked", self.ChangeSite, -1) - self.NEXTbuttonSite.connect("clicked", self.ChangeSite, +1) - hbox = gtk.HBox() - hbox.pack_start(self.PREVbuttonSite) - hbox.pack_start(self.NEXTbuttonSite) - self.vbox_site_navigator.add(hbox) - frame.add(self.vbox_site_navigator) - hboxSample.add(frame) - - outer_frame.add(hboxSample) - self.vbox.add(outer_frame) - - # SPACER - self.vbox.add(gtk.Label(' ')) - - ################################################################################# - # --- current refinement stage --- - outer_frame = gtk.Frame() - hbox = gtk.HBox() - - frame = gtk.Frame(label='Analysis Status') - vbox = gtk.VBox() - self.experiment_stage_button_list = [] - for n, button in enumerate(self.experiment_stage): - if n == 0: - new_button = gtk.RadioButton(None, button[0]) - else: - new_button = gtk.RadioButton(new_button, button[0]) - new_button.connect( - "toggled", self.experiment_stage_button_clicked, button[1]) - vbox.add(new_button) - self.experiment_stage_button_list.append(new_button) - frame.add(vbox) - hbox.pack_start(frame) - - # --- ligand confidence --- - frame = gtk.Frame(label='Ligand Confidence') - vbox = gtk.VBox() - self.ligand_confidence_button_list = [] - for n, criteria in enumerate(self.ligand_confidence_category): - if n == 0: - new_button = gtk.RadioButton(None, criteria) - else: - new_button = gtk.RadioButton(new_button, criteria) - new_button.connect( - "toggled", self.ligand_confidence_button_clicked, criteria) - vbox.add(new_button) - self.ligand_confidence_button_list.append(new_button) - frame.add(vbox) - hbox.pack_start(frame) - - outer_frame.add(hbox) - self.vbox.pack_start(outer_frame) - - # SPACER - self.vbox.add(gtk.Label(' ')) - - # --- ligand modeling --- - frame = gtk.Frame(label='Ligand Modeling') - self.hbox_for_modeling = gtk.HBox() - self.merge_ligand_button = gtk.Button(label="Merge Ligand") - self.place_ligand_here_button = gtk.Button(label="Place Ligand here") - self.hbox_for_modeling.add(self.place_ligand_here_button) - self.place_ligand_here_button.connect( - "clicked", self.place_ligand_here) - self.hbox_for_modeling.add(self.merge_ligand_button) - self.merge_ligand_button.connect( - "clicked", self.merge_ligand_into_protein) - frame.add(self.hbox_for_modeling) - self.vbox.pack_start(frame) - - -# # --- ligand confidence --- -# self.cb_ligand_confidence = gtk.combo_box_new_text() -# self.cb_ligand_confidence.connect("changed", self.set_ligand_confidence) -# for citeria in self.ligand_confidence: -# self.cb_ligand_confidence.append_text(citeria) -# self.vbox.add(self.cb_ligand_confidence) - - # --- refinement & options --- - self.hbox_for_refinement = gtk.HBox() - self.REFINEbutton = gtk.Button(label="Refine") - self.RefinementParamsButton = gtk.Button(label="refinement parameters") - self.REFINEbutton.connect("clicked", self.REFINE) - self.hbox_for_refinement.add(self.REFINEbutton) - self.RefinementParamsButton.connect("clicked", self.RefinementParams) - self.hbox_for_refinement.add(self.RefinementParamsButton) - self.vbox.add(self.hbox_for_refinement) - -# self.VALIDATEbutton = gtk.Button(label="validate structure") -# self.DEPOSITbutton = gtk.Button(label="prepare for deposition") - - # --- CANCEL button --- - self.CANCELbutton = gtk.Button(label="CANCEL") - self.CANCELbutton.connect("clicked", self.CANCEL) - self.vbox.add(self.CANCELbutton) - - self.window.add(self.vbox) - self.window.show_all() - - def CANCEL(self, widget): - self.window.destroy() - - def ChangeXtal(self, widget, data=None): - self.index = self.index + data - if self.index < 0: - self.index = 0 - if self.index >= len(self.Todo): - # self.index = len(self.Todo) - self.index = 0 - self.cb.set_active(self.index) - - def ChooseXtal(self, widget): - self.xtalID = str(widget.get_active_text()) - for n, item in enumerate(self.Todo): - if str(item[0]) == self.xtalID: - self.index = n - self.merge_ligand_button.set_sensitive(True) - self.place_ligand_here_button.set_sensitive(True) - - self.ligand_site_name_value.set_label('-') - self.ligand_inspect_confidence_value.set_label('-') - self.ligand_inspect_interesting_value.set_label('-') - self.ligand_inspect_comment_value.set_label('-') - - self.refresh_site_combobox() - self.db_dict_mainTable = {} - self.db_dict_panddaTable = {} - if str(self.Todo[self.index][0]) is not None: - self.compoundID = str(self.Todo[self.index][1]) - self.refinement_folder = str(self.Todo[self.index][4]) - self.refinement_outcome = str(self.Todo[self.index][5]) - self.update_RefinementOutcome_radiobutton() - if self.xtalID not in self.siteDict: # i.e. we are not working with a PanDDA model - self.ligand_confidence = str(self.Todo[self.index][6]) - self.update_LigandConfidence_radiobutton() - - self.RefreshData() - - def update_RefinementOutcome_radiobutton(self): - # updating dataset outcome radiobuttons - current_stage = 0 - for i, entry in enumerate(self.experiment_stage): - if entry[1].split()[0] == self.refinement_outcome.split()[0]: - current_stage = i - break - for i, button in enumerate(self.experiment_stage_button_list): - if i == current_stage: - button.set_active(True) - break - - def update_LigandConfidence_radiobutton(self): - # updating ligand confidence radiobuttons - current_stage = 0 - for i, entry in enumerate(self.ligand_confidence_category): - print '--->', entry, self.ligand_confidence - try: - if entry.split()[0] == self.ligand_confidence.split()[0]: - current_stage = i - break - except IndexError: - pass - for i, button in enumerate(self.ligand_confidence_button_list): - if i == current_stage: - button.set_active(True) - break - - def refresh_site_combobox(self): - # reset self.pandda_index - self.pandda_index = -1 - # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites - for n in range(-1, 100): - self.cb_site.remove_text(0) - self.site_index = '0' - self.event_index = '0' - # only repopulate if site exists - if self.xtalID in self.siteDict: - for item in sorted(self.siteDict[self.xtalID]): - self.cb_site.append_text( - 'site: %s - event: %s' % (item[5], item[6])) - - def ChangeSite(self, widget, data=None): - if self.xtalID in self.siteDict: - self.pandda_index = self.pandda_index + data - if self.pandda_index < 0: - self.pandda_index = 0 - if self.pandda_index >= len(self.siteDict[self.xtalID]): - self.pandda_index = 0 - self.cb_site.set_active(self.pandda_index) - - def ChooseSite(self, widget): - tmp = str(widget.get_active_text()) - self.site_index = tmp.split()[1] - self.event_index = tmp.split()[4] - for n, item in enumerate(self.siteDict[self.xtalID]): - if item[5] == self.site_index and item[6] == self.event_index: - self.pandda_index = n - self.RefreshSiteData() - - def RefreshSiteData(self): - - if self.pandda_index == -1: - self.merge_ligand_button.set_sensitive(True) - self.place_ligand_here_button.set_sensitive(True) - else: - self.merge_ligand_button.set_sensitive(False) - self.place_ligand_here_button.set_sensitive(False) - # and remove ligand molecule so that there is no temptation to merge it - if len(coot_utils_XChem.molecule_number_list()) > 0: - for imol in coot_utils_XChem.molecule_number_list(): - if self.compoundID+'.pdb' in coot.molecule_name(imol): - coot.close_molecule(imol) - - print 'pandda index', self.pandda_index - self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] - print 'new spider plot:', self.spider_plot - self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] - print 'new event map:', self.event_map - self.ligand_confidence = str( - self.siteDict[self.xtalID][self.pandda_index][7]) - self.update_LigandConfidence_radiobutton() - site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) - site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) - site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) - print 'new site coordinates:', site_x, site_y, site_z - coot.set_rotation_centre(site_x, site_y, site_z) - - self.ligand_site_name_value.set_label( - str(self.siteDict[self.xtalID][self.pandda_index][8])) - self.ligand_inspect_confidence_value.set_label( - str(self.siteDict[self.xtalID][self.pandda_index][9])) - self.ligand_inspect_interesting_value.set_label( - str(self.siteDict[self.xtalID][self.pandda_index][10])) - self.ligand_inspect_comment_value.set_label( - str(self.siteDict[self.xtalID][self.pandda_index][11])) - - self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event( - self.xtalID, self.site_index, self.event_index) - print '>>>>> spider plot data', self.spider_plot_data - self.ligandIDValue.set_label( - self.spider_plot_data['PANDDA_site_ligand_id']) - try: - self.ligand_occupancyValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) - except ValueError: - self.ligand_occupancyValue.set_label('-') - - try: - self.ligand_BaverageValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) - except ValueError: - self.ligand_BaverageValue.set_label('-') - - try: - self.ligand_BratioSurroundingsValue.set_label(str(round( - float(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']), 2))) - except ValueError: - self.ligand_BratioSurroundingsValue.set_label('-') - - try: - self.ligand_RSCCValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) - except ValueError: - self.ligand_RSCCValue.set_label('-') - - try: - self.ligand_rmsdValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) - except ValueError: - self.ligand_rmsdValue.set_label('-') - - try: - self.ligand_RSRValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) - except ValueError: - self.ligand_RSRValue.set_label('-') - - try: - self.ligand_RSZDValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) - except ValueError: - self.ligand_RSZDValue.set_label('-') - - ######################################################################################### - # delete old Event MAPs - if len(coot_utils_XChem.molecule_number_list()) > 0: - for imol in coot_utils_XChem.molecule_number_list(): - if 'map.native.ccp4' in coot.molecule_name(imol): - coot.close_molecule(imol) - - ######################################################################################### - # Spider plot - # Note: refinement history was shown instead previously - if os.path.isfile(self.spider_plot): - spider_plot_pic = gtk.gdk.pixbuf_new_from_file(self.spider_plot) - else: - spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join( - os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = spider_plot_pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) - self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) - - ######################################################################################### - # check for PANDDAs EVENT maps - if os.path.isfile(self.event_map): - coot.handle_read_ccp4_map((self.event_map), 0) - for imol in coot_utils_XChem.molecule_number_list(): - if self.event_map in coot.molecule_name(imol): - coot.set_contour_level_in_sigma(imol, 2) -# coot.set_contour_level_absolute(imol,0.5) -# coot.set_last_map_colour(0.4,0,0.4) - coot.set_last_map_colour(0.74, 0.44, 0.02) - - def experiment_stage_button_clicked(self, widget, data=None): - self.db_dict_mainTable['RefinementOutcome'] = data - print '==> XCE: setting Refinement Outcome for ' + \ - self.xtalID+' to '+str(data)+' in mainTable of datasource' - self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - - def ligand_confidence_button_clicked(self, widget, data=None): - print 'PANDDA_index', self.pandda_index - if self.pandda_index == -1: - self.db_dict_mainTable['RefinementLigandConfidence'] = data - print '==> XCE: setting Ligand Confidence for ' + \ - self.xtalID+' to '+str(data)+' in mainTable of datasource' - self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - self.Todo[self.index][6] = data - else: - self.db_dict_panddaTable['PANDDA_site_confidence'] = data - print '==> XCE: setting Ligand Confidence for '+self.xtalID + \ - ' (site='+str(self.site_index)+', event='+str(self.event_index) + \ - ') to '+str(data)+' in panddaTable of datasource' - self.db.update_site_event_panddaTable( - self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable) - self.siteDict[self.xtalID][self.pandda_index][7] = data - - def RefreshData(self): - # reset spider plot image - spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join( - os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = spider_plot_pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) - self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) - - # initialize Refinement library - self.Refine = XChemRefine.RefineOld( - self.project_directory, self.xtalID, self.compoundID, self.data_source) - self.Serial = self.Refine.GetSerial() - if self.Serial == 1: - # i.e. no refinement has been done; data is probably straight out of dimple - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): - print '==> XCE: updating quality indicators in data source for '+self.xtalID - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, self.pdb_style)) - XChemUtils.parse().update_datasource_with_phenix_validation_summary( - self.xtalID, self.data_source, '') # '' because file does not exist - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): - print '==> XCE: updating quality indicators in data source for '+self.xtalID - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')) - XChemUtils.parse().update_datasource_with_phenix_validation_summary( - self.xtalID, self.data_source, '') # '' because file does not exist - - # all this information is now updated in the datasource after each refinement cycle - self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) - - ######################################################################################### - # history - # if the structure was previously refined, try to read the parameters -# self.hbox_for_info_graphics.remove(self.canvas) - if self.Serial > 1: - self.RefmacParams = self.Refine.ParamsFromPreviousCycle( - self.Serial-1) -# refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() -# self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) -# else: -# self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea -# self.canvas.set_size_request(190, 190) -# self.hbox_for_info_graphics.add(self.canvas) -# self.canvas.show() - - ######################################################################################### - # update pdb & maps - - ######################################################################################### - # delete old PDB and MAP files - # - get a list of all molecules which are currently opened in COOT - # - remove all molecules/ maps before loading a new set - if len(coot_utils_XChem.molecule_number_list()) > 0: - for item in coot_utils_XChem.molecule_number_list(): - coot.close_molecule(item) - - ######################################################################################### - # read new PDB files - # read protein molecule after ligand so that this one is the active molecule - coot.set_nomenclature_errors_on_read("ignore") - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID+'.pdb')): - imol = coot.handle_read_draw_molecule_with_recentre(os.path.join( - self.project_directory, self.xtalID, self.compoundID+'.pdb'), 0) - self.mol_dict['ligand'] = imol - coot.read_cif_dictionary(os.path.join( - self.project_directory, self.xtalID, self.compoundID+'.cif')) - if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): - os.chdir(os.path.join(self.project_directory, self.xtalID)) - # we want to be able to check dimple results immediately, but don't want to interfere with refinement -# if not os.path.isfile('REFINEMENT_IN_PROGRESS'): -# if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-ensemble-model.pdb')): -# os.symlink(self.xtalID+'-ensemble-model.pdb',self.pdb_style) -# elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.pdb')): -# os.symlink('dimple.pdb',self.pdb_style) -# else: -# self.go_to_next_xtal() - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): - os.chdir(os.path.join(self.project_directory, self.xtalID)) - imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): - os.chdir(os.path.join(self.project_directory, self.xtalID)) - imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, 'dimple.pdb'), 0) - else: - self.go_to_next_xtal() - self.mol_dict['protein'] = imol - for item in coot_utils_XChem.molecule_number_list(): - if coot.molecule_name(item).endswith(self.pdb_style): - # master switch to show symmetry molecules - coot.set_show_symmetry_master(1) - coot.set_show_symmetry_molecule(item, 1) # show symm for model - - ######################################################################################### - # read fofo maps - # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map - # read 2fofc map last so that one can change its contour level - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): - coot.set_default_initial_contour_level_for_difference_map(3) - coot.handle_read_ccp4_map(os.path.join( - self.project_directory, self.xtalID, 'fofc.map'), 1) - coot.set_default_initial_contour_level_for_map(1) - coot.handle_read_ccp4_map(os.path.join( - self.project_directory, self.xtalID, '2fofc.map'), 0) - coot.set_last_map_colour(0, 0, 1) - else: - # try to open mtz file with same name as pdb file - coot.set_default_initial_contour_level_for_map(1) -# if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): -# os.chdir(os.path.join(self.project_directory,self.xtalID)) -# if not os.path.isfile('REFINEMENT_IN_PROGRESS'): -# if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-pandda-input.mtz')): -# os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) -# elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): -# os.symlink('dimple.mtz',self.mtz_style) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, self.mtz_style)) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, 'dimple.mtz')) - - ######################################################################################### - # update Quality Indicator table - try: - self.RRfreeValue.set_label(str(round(float(self.QualityIndicators['RefinementRcryst']), 3)) + ' / '+str( - round(float(self.QualityIndicators['RefinementRfree']), 3))) - except ValueError: - self.RRfreeValue.set_label('-') - - try: - self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRfreeTraficLight'])) - except ValueError: - pass - self.ResolutionValue.set_label( - self.QualityIndicators['RefinementResolution']) - try: - self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementResolutionTL'])) - except ValueError: - pass - self.MolprobityScoreValue.set_label( - self.QualityIndicators['RefinementMolProbityScore']) - try: - self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementMolProbityScoreTL'])) - except ValueError: - pass - self.RamachandranOutliersValue.set_label( - self.QualityIndicators['RefinementRamachandranOutliers']) - try: - self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRamachandranOutliersTL'])) - except ValueError: - pass - self.RamachandranFavoredValue.set_label( - self.QualityIndicators['RefinementRamachandranFavored']) - try: - self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRamachandranFavoredTL'])) - except ValueError: - pass - self.rmsdBondsValue.set_label( - self.QualityIndicators['RefinementRmsdBonds']) - try: - self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRmsdBondsTL'])) - except ValueError: - pass - self.rmsdAnglesValue.set_label( - self.QualityIndicators['RefinementRmsdAngles']) - try: - self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRmsdAnglesTL'])) - except ValueError: - pass - self.MatrixWeightValue.set_label( - self.QualityIndicators['RefinementMatrixWeight']) - - try: - pic = gtk.gdk.pixbuf_new_from_file(os.path.join( - self.project_directory, self.xtalID, self.compoundID+'.png')) - except gobject.GError: - pic = gtk.gdk.pixbuf_new_from_file(os.path.join( - os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) - self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) - self.image.set_from_pixbuf(self.pic) - - def go_to_next_xtal(self): - self.index += 1 - if self.index >= len(self.Todo): - self.index = len(self.Todo) - self.cb.set_active(self.index) - - def REFINE(self, widget): - - ####################################################### - # create folder for new refinement cycle - os.mkdir(os.path.join(self.project_directory, - self.xtalID, 'Refine_'+str(self.Serial))) - - ####################################################### - # write PDB file - # now take protein pdb file and write it to newly create Refine_ folder - # note: the user has to make sure that the ligand file was merged into main file - for item in coot_utils_XChem.molecule_number_list(): - if coot.molecule_name(item).endswith(self.pdb_style): - coot.write_pdb_file(item, os.path.join( - self.project_directory, self.xtalID, 'Refine_'+str(self.Serial), 'in.pdb')) - break - elif coot.molecule_name(item).endswith('dimple.pdb'): - coot.write_pdb_file(item, os.path.join( - self.project_directory, self.xtalID, 'Refine_'+str(self.Serial), 'in.pdb')) - break - - ####################################################### - # run REFMAC - self.Refine.RunRefmac(self.Serial, self.RefmacParams, - self.external_software, self.xce_logfile) - - self.index += 1 - if self.index >= len(self.Todo): - # self.index = len(self.Todo) - self.index = 0 - self.cb.set_active(self.index) - - def RefinementParams(self, widget): - print '\n==> XCE: changing refinement parameters' - self.RefmacParams = self.Refine.RefinementParams(self.RefmacParams) - - def set_selection_mode(self, widget): - self.selection_mode = widget.get_active_text() - - def get_samples_to_look_at(self, widget): - if self.selection_mode == '': - self.status_label.set_text('select model stage') - return - self.status_label.set_text('checking datasource for samples... ') - # first remove old samples if present - if len(self.Todo) != 0: - for n, item in enumerate(self.Todo): - self.cb.remove_text(0) - self.Todo = [] - self.siteDict = {} - self.Todo, self.siteDict = self.db.get_todoList_for_coot( - self.selection_mode) - self.status_label.set_text('found %s samples' % len(self.Todo)) - # refresh sample CB - for item in sorted(self.Todo): - self.cb.append_text('%s' % item[0]) - if self.siteDict == {}: - self.cb_site.set_sensitive(False) - self.PREVbuttonSite.set_sensitive(False) - self.NEXTbuttonSite.set_sensitive(False) - else: - self.cb_site.set_sensitive(True) - self.PREVbuttonSite.set_sensitive(True) - self.NEXTbuttonSite.set_sensitive(True) - - def update_plot(self, refinement_cycle, Rfree, Rcryst): - fig = Figure(figsize=(2, 2), dpi=50) - Plot = fig.add_subplot(111) - Plot.set_ylim([0, max(Rcryst+Rfree)]) - Plot.set_xlabel('Refinement Cycle', fontsize=12) - Plot.plot(refinement_cycle, Rfree, label='Rfree', linewidth=2) - Plot.plot(refinement_cycle, Rcryst, label='Rcryst', linewidth=2) - Plot.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, - ncol=2, mode="expand", borderaxespad=0., fontsize=12) - return fig - - def place_ligand_here(self, widget): - print '===> XCE: moving ligand to pointer' -# coot.move_molecule_here() - print 'LIGAND: ', self.mol_dict['ligand'] - coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) - - def merge_ligand_into_protein(self, widget): - print '===> XCE: merge ligand into protein structure' - # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) - coot.merge_molecules_py( - [self.mol_dict['ligand']], self.mol_dict['protein']) - print '===> XCE: deleting ligand molecule' - coot.close_molecule(self.mol_dict['ligand']) - - def show_molprobity_to_do(self, widget): - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')): - print '==> XCE: running MolProbity Summary for', self.xtalID - coot.run_script(os.path.join(self.project_directory, self.xtalID, - 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')) - else: - print '==> XCE: cannot find ' + \ - os.path.join(self.project_directory, self.xtalID, - 'Refine_'+str(self.Serial-1), 'molprobity_coot.py') - -# def fit_ligand(self,widget): -# print 'fit' - - -if __name__ == '__main__': - GUI().StartGUI() +# last edited: 21/07/2017 - 15:00 + +import pango +import gtk +import pygtk +import coot_utils_XChem +import coot +import XChemUtils +import XChemRefine +import XChemDB +import gobject +import sys +import os +import pickle + +from matplotlib.figure import Figure +#from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas + +# XCE libraries +sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') + +# libraries from COOT + +# had to adapt the original coot_utils.py file +# otherwise unable to import the original file without complaints about missing modules etc. +# modified file is now in $XChemExplorer_DIR/lib + + +class GUI(object): + + """ + main class which opens the actual GUI + """ + + def __init__(self): + + ########################################################################################### + # read in settings file from XChemExplorer to set the relevant paths + print('current dir', os.getcwd()) + self.settings = pickle.load(open(".xce_settings.pkl", "rb")) + remote_qsub_submission = self.settings['remote_qsub'] + print('setting', self.settings) +# self.refine_model_directory=self.settings['refine_model_directory'] + self.database_directory = self.settings['database_directory'] + self.xce_logfile = self.settings['xce_logfile'] + self.data_source = self.settings['data_source'] + self.db = XChemDB.data_source(self.data_source) + + # checking for external software packages + self.external_software = XChemUtils.external_software( + self.xce_logfile).check() + self.external_software['qsub_remote'] = remote_qsub_submission + + self.selection_criteria = ['0 - All Datasets', + '1 - Analysis Pending', + '2 - PANDDA model', + '3 - In Refinement', + '4 - CompChem ready', + '5 - Deposition ready', + '6 - Deposited'] + + self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], + ['In Refinement', + '3 - In Refinement', 65000, 0, 0], + ['Comp Chem Ready!', + '4 - CompChem ready', 65000, 0, 0], + ['Ready for Deposition!', + '5 - Deposition ready', 65000, 0, 0], + ['In PDB', '6 - Deposited', 65000, 0, 0]] + + self.ligand_confidence_category = ['0 - no ligand present', + '1 - Low Confidence', + '2 - Correct ligand, weak density', + '3 - Clear density, unexpected ligand', + '4 - High Confidence'] + + self.ligand_site_information = self.db.get_list_of_pandda_sites_for_coot() + + # this decides which samples will be looked at + self.selection_mode = '' +# self.selected_site='' + self.pandda_index = -1 # refers to the number of sites + self.site_index = '0' + self.event_index = '0' + + # the Folder is kind of a legacy thing because my inital idea was to have separate folders + # for Data Processing and Refinement + self.project_directory = self.settings['initial_model_directory'] + self.Serial = 0 + self.Refine = None + self.index = -1 + self.Todo = [] + self.siteDict = {} + + self.xtalID = '' + self.compoundID = '' + self.spider_plot = '' + self.ligand_confidence = '' + self.refinement_folder = '' +# self.datasetOutcome='' + + self.pdb_style = 'refine.pdb' + self.mtz_style = 'refine.mtz' + + # stores imol of currently loaded molecules and maps + self.mol_dict = {'protein': -1, + 'ligand': -1, + '2fofc': -1, + 'fofc': -1, + 'event': -1} + + # two dictionaries which are flushed when a new crystal is loaded + # and which contain information to update the data source if necessary + self.db_dict_mainTable = {} + self.db_dict_panddaTable = {} + + ########################################################################################### + # some COOT settings + coot.set_map_radius(15) + coot.set_colour_map_rotation_for_map(0) + coot.set_colour_map_rotation_on_read_pdb_flag(0) + + self.QualityIndicators = {'RefinementRcryst': '-', + 'RefinementRfree': '-', + 'RefinementRfreeTraficLight': 'gray', + 'RefinementResolution': '-', + 'RefinementResolutionTL': 'gray', + 'RefinementMolProbityScore': '-', + 'RefinementMolProbityScoreTL': 'gray', + 'RefinementRamachandranOutliers': '-', + 'RefinementRamachandranOutliersTL': 'gray', + 'RefinementRamachandranFavored': '-', + 'RefinementRamachandranFavoredTL': 'gray', + 'RefinementRmsdBonds': '-', + 'RefinementRmsdBondsTL': 'gray', + 'RefinementRmsdAngles': '-', + 'RefinementRmsdAnglesTL': 'gray', + 'RefinementMatrixWeight': '-'} + + self.spider_plot_data = {'PANDDA_site_ligand_id': '-', + 'PANDDA_site_occupancy': '-', + 'PANDDA_site_B_average': '-', + 'PANDDA_site_B_ratio_residue_surroundings': '-', + 'PANDDA_site_RSCC': '-', + 'PANDDA_site_rmsd': '-', + 'PANDDA_site_RSR': '-', + 'PANDDA_site_RSZD': '-'} + + # default refmac parameters + self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', + 'XYZIN': '', 'XYZOUT': '', + 'LIBIN': '', 'LIBOUT': '', + 'TLSIN': '', 'TLSOUT': '', + 'TLSADD': '', + 'NCYCLES': '10', + 'MATRIX_WEIGHT': 'AUTO', + 'BREF': ' bref ISOT\n', + 'TLS': '', + 'NCS': '', + 'TWIN': ''} + + def StartGUI(self): + + self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) + self.window.connect("delete_event", gtk.main_quit) + self.window.set_border_width(10) + self.window.set_default_size(400, 800) + self.window.set_title("XChemExplorer") + self.vbox = gtk.VBox() # this is the main container + + ################################################################################# + # --- Sample Selection --- +# self.vbox.add(gtk.Label('Select Samples')) + + frame = gtk.Frame(label='Select Samples') + self.hbox_select_samples = gtk.HBox() +# vbox=gtk.VBox() + + self.cb_select_samples = gtk.combo_box_new_text() + self.cb_select_samples.connect("changed", self.set_selection_mode) + for citeria in self.selection_criteria: + self.cb_select_samples.append_text(citeria) + self.hbox_select_samples.add(self.cb_select_samples) + +# self.cb_select_sites = gtk.combo_box_new_text() +# self.cb_select_sites.connect("changed", self.set_site) +# for site in self.ligand_site_information: +# self.cb_select_sites.append_text(str(site[0])+' - '+str(site[1])) +# self.hbox_select_samples.add(self.cb_select_sites) + + self.select_samples_button = gtk.Button(label="GO") + self.select_samples_button.connect( + "clicked", self.get_samples_to_look_at) + self.hbox_select_samples.add(self.select_samples_button) + frame.add(self.hbox_select_samples) + self.vbox.pack_start(frame) + + ################################################################################# + # --- status window --- + frame = gtk.Frame() + self.status_label = gtk.Label() + frame.add(self.status_label) + self.vbox.pack_start(frame) + + # SPACER + self.vbox.add(gtk.Label(' ')) + + ################################################################################# + # --- Refinement Statistics --- + # next comes a section which displays some global quality indicators + # a combination of labels and textview widgets, arranged in a table + + RRfreeLabel_frame = gtk.Frame() + self.RRfreeLabel = gtk.Label('R/Rfree') + RRfreeLabel_frame.add(self.RRfreeLabel) + self.RRfreeValue = gtk.Label( + self.QualityIndicators['RefinementRcryst']+'/'+self.QualityIndicators['RefinementRfree']) + RRfreeBox_frame = gtk.Frame() + self.RRfreeBox = gtk.EventBox() + self.RRfreeBox.add(self.RRfreeValue) + RRfreeBox_frame.add(self.RRfreeBox) + + ResolutionLabel_frame = gtk.Frame() + self.ResolutionLabel = gtk.Label('Resolution') + ResolutionLabel_frame.add(self.ResolutionLabel) + self.ResolutionValue = gtk.Label( + self.QualityIndicators['RefinementResolution']) + ResolutionBox_frame = gtk.Frame() + self.ResolutionBox = gtk.EventBox() + self.ResolutionBox.add(self.ResolutionValue) + ResolutionBox_frame.add(self.ResolutionBox) + + MolprobityScoreLabel_frame = gtk.Frame() + self.MolprobityScoreLabel = gtk.Label('MolprobityScore') + MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) + self.MolprobityScoreValue = gtk.Label( + self.QualityIndicators['RefinementMolProbityScore']) + MolprobityScoreBox_frame = gtk.Frame() + self.MolprobityScoreBox = gtk.EventBox() + self.MolprobityScoreBox.add(self.MolprobityScoreValue) + MolprobityScoreBox_frame.add(self.MolprobityScoreBox) + + RamachandranOutliersLabel_frame = gtk.Frame() + self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') + RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) + self.RamachandranOutliersValue = gtk.Label( + self.QualityIndicators['RefinementRamachandranOutliers']) + RamachandranOutliersBox_frame = gtk.Frame() + self.RamachandranOutliersBox = gtk.EventBox() + self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) + RamachandranOutliersBox_frame.add(self.RamachandranOutliersBox) + + RamachandranFavoredLabel_frame = gtk.Frame() + self.RamachandranFavoredLabel = gtk.Label('Rama Favored') + RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) + self.RamachandranFavoredValue = gtk.Label( + self.QualityIndicators['RefinementRamachandranFavored']) + RamachandranFavoredBox_frame = gtk.Frame() + self.RamachandranFavoredBox = gtk.EventBox() + self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) + RamachandranFavoredBox_frame.add(self.RamachandranFavoredBox) + + rmsdBondsLabel_frame = gtk.Frame() + self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') + rmsdBondsLabel_frame.add(self.rmsdBondsLabel) + self.rmsdBondsValue = gtk.Label( + self.QualityIndicators['RefinementRmsdBonds']) + rmsdBondsBox_frame = gtk.Frame() + self.rmsdBondsBox = gtk.EventBox() + self.rmsdBondsBox.add(self.rmsdBondsValue) + rmsdBondsBox_frame.add(self.rmsdBondsBox) + + rmsdAnglesLabel_frame = gtk.Frame() + self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') + rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) + self.rmsdAnglesValue = gtk.Label( + self.QualityIndicators['RefinementRmsdAngles']) + rmsdAnglesBox_frame = gtk.Frame() + self.rmsdAnglesBox = gtk.EventBox() + self.rmsdAnglesBox.add(self.rmsdAnglesValue) + rmsdAnglesBox_frame.add(self.rmsdAnglesBox) + + MatrixWeightLabel_frame = gtk.Frame() + self.MatrixWeightLabel = gtk.Label('Matrix Weight') + MatrixWeightLabel_frame.add(self.MatrixWeightLabel) + self.MatrixWeightValue = gtk.Label( + self.QualityIndicators['RefinementMatrixWeight']) + MatrixWeightBox_frame = gtk.Frame() + self.MatrixWeightBox = gtk.EventBox() + self.MatrixWeightBox.add(self.MatrixWeightValue) + MatrixWeightBox_frame.add(self.MatrixWeightBox) + + ligandIDLabel_frame = gtk.Frame() + self.ligandIDLabel = gtk.Label('Ligand ID') + ligandIDLabel_frame.add(self.ligandIDLabel) + self.ligandIDValue = gtk.Label( + self.spider_plot_data['PANDDA_site_ligand_id']) + ligandIDBox_frame = gtk.Frame() + self.ligandIDBox = gtk.EventBox() + self.ligandIDBox.add(self.ligandIDValue) + ligandIDBox_frame.add(self.ligandIDBox) + + ligand_occupancyLabel_frame = gtk.Frame() + self.ligand_occupancyLabel = gtk.Label('occupancy') + ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) + self.ligand_occupancyValue = gtk.Label( + self.spider_plot_data['PANDDA_site_occupancy']) + ligand_occupancyBox_frame = gtk.Frame() + self.ligand_occupancyBox = gtk.EventBox() + self.ligand_occupancyBox.add(self.ligand_occupancyValue) + ligand_occupancyBox_frame.add(self.ligand_occupancyBox) + + ligand_BaverageLabel_frame = gtk.Frame() + self.ligand_BaverageLabel = gtk.Label('B average') + ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) + self.ligand_BaverageValue = gtk.Label( + self.spider_plot_data['PANDDA_site_B_average']) + ligand_BaverageBox_frame = gtk.Frame() + self.ligand_BaverageBox = gtk.EventBox() + self.ligand_BaverageBox.add(self.ligand_BaverageValue) + ligand_BaverageBox_frame.add(self.ligand_BaverageBox) + + ligand_BratioSurroundingsLabel_frame = gtk.Frame() + self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') + ligand_BratioSurroundingsLabel_frame.add( + self.ligand_BratioSurroundingsLabel) + self.ligand_BratioSurroundingsValue = gtk.Label( + self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) + ligand_BratioSurroundingsBox_frame = gtk.Frame() + self.ligand_BratioSurroundingsBox = gtk.EventBox() + self.ligand_BratioSurroundingsBox.add( + self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add( + self.ligand_BratioSurroundingsBox) + + ligand_RSCCLabel_frame = gtk.Frame() + self.ligand_RSCCLabel = gtk.Label('RSCC') + ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) + self.ligand_RSCCValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSCC']) + ligand_RSCCBox_frame = gtk.Frame() + self.ligand_RSCCBox = gtk.EventBox() + self.ligand_RSCCBox.add(self.ligand_RSCCValue) + ligand_RSCCBox_frame.add(self.ligand_RSCCBox) + + ligand_rmsdLabel_frame = gtk.Frame() + self.ligand_rmsdLabel = gtk.Label('rmsd') + ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) + self.ligand_rmsdValue = gtk.Label( + self.spider_plot_data['PANDDA_site_rmsd']) + ligand_rmsdBox_frame = gtk.Frame() + self.ligand_rmsdBox = gtk.EventBox() + self.ligand_rmsdBox.add(self.ligand_rmsdValue) + ligand_rmsdBox_frame.add(self.ligand_rmsdBox) + + ligand_RSRLabel_frame = gtk.Frame() + self.ligand_RSRLabel = gtk.Label('RSR') + ligand_RSRLabel_frame.add(self.ligand_RSRLabel) + self.ligand_RSRValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSR']) + ligand_RSRBox_frame = gtk.Frame() + self.ligand_RSRBox = gtk.EventBox() + self.ligand_RSRBox.add(self.ligand_RSRValue) + ligand_RSRBox_frame.add(self.ligand_RSRBox) + + ligand_RSZDLabel_frame = gtk.Frame() + self.ligand_RSZDLabel = gtk.Label('RSZD') + ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) + self.ligand_RSZDValue = gtk.Label( + self.spider_plot_data['PANDDA_site_RSZD']) + ligand_RSZDBox_frame = gtk.Frame() + self.ligand_RSZDBox = gtk.EventBox() + self.ligand_RSZDBox.add(self.ligand_RSZDValue) + ligand_RSZDBox_frame.add(self.ligand_RSZDBox) + + outer_frame = gtk.Frame() + hbox = gtk.HBox() + + frame = gtk.Frame() + self.table_left = gtk.Table(8, 2, False) + self.table_left.attach(RRfreeLabel_frame, 0, 1, 0, 1) + self.table_left.attach(ResolutionLabel_frame, 0, 1, 1, 2) + self.table_left.attach(MolprobityScoreLabel_frame, 0, 1, 2, 3) + self.table_left.attach(RamachandranOutliersLabel_frame, 0, 1, 3, 4) + self.table_left.attach(RamachandranFavoredLabel_frame, 0, 1, 4, 5) + self.table_left.attach(rmsdBondsLabel_frame, 0, 1, 5, 6) + self.table_left.attach(rmsdAnglesLabel_frame, 0, 1, 6, 7) + self.table_left.attach(MatrixWeightLabel_frame, 0, 1, 7, 8) + self.table_left.attach(RRfreeBox_frame, 1, 2, 0, 1) + self.table_left.attach(ResolutionBox_frame, 1, 2, 1, 2) + self.table_left.attach(MolprobityScoreBox_frame, 1, 2, 2, 3) + self.table_left.attach(RamachandranOutliersBox_frame, 1, 2, 3, 4) + self.table_left.attach(RamachandranFavoredBox_frame, 1, 2, 4, 5) + self.table_left.attach(rmsdBondsBox_frame, 1, 2, 5, 6) + self.table_left.attach(rmsdAnglesBox_frame, 1, 2, 6, 7) + self.table_left.attach(MatrixWeightBox_frame, 1, 2, 7, 8) + frame.add(self.table_left) + hbox.add(frame) + + frame = gtk.Frame() + self.table_right = gtk.Table(8, 2, False) + self.table_right.attach(ligandIDLabel_frame, + 0, 1, 0, 1) + self.table_right.attach( + ligand_occupancyLabel_frame, 0, 1, 1, 2) + self.table_right.attach( + ligand_BaverageLabel_frame, 0, 1, 2, 3) + self.table_right.attach( + ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach( + ligand_RSCCLabel_frame, 0, 1, 4, 5) + self.table_right.attach( + ligand_rmsdLabel_frame, 0, 1, 5, 6) + self.table_right.attach( + ligand_RSRLabel_frame, 0, 1, 6, 7) + self.table_right.attach( + ligand_RSZDLabel_frame, 0, 1, 7, 8) + self.table_right.attach(ligandIDBox_frame, + 1, 2, 0, 1) + self.table_right.attach( + ligand_occupancyBox_frame, 1, 2, 1, 2) + self.table_right.attach( + ligand_BaverageBox_frame, 1, 2, 2, 3) + self.table_right.attach( + ligand_BratioSurroundingsBox_frame, 1, 2, 3, 4) + self.table_right.attach( + ligand_RSCCBox_frame, 1, 2, 4, 5) + self.table_right.attach( + ligand_rmsdBox_frame, 1, 2, 5, 6) + self.table_right.attach(ligand_RSRBox_frame, + 1, 2, 6, 7) + self.table_right.attach( + ligand_RSZDBox_frame, 1, 2, 7, 8) + frame.add(self.table_right) + hbox.add(frame) + + outer_frame.add(hbox) + self.vbox.add(outer_frame) + + button = gtk.Button(label="Show MolProbity to-do list") + button.connect("clicked", self.show_molprobity_to_do) + self.vbox.add(button) + self.vbox.pack_start(frame) + + # SPACER + self.vbox.add(gtk.Label(' ')) + + ################################################################################# + # --- hbox for compound picture & spider_plot (formerly: refinement history) --- + frame = gtk.Frame() + self.hbox_for_info_graphics = gtk.HBox() + + # --- compound picture --- + compound_frame = gtk.Frame() + pic = gtk.gdk.pixbuf_new_from_file(os.path.join( + os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.image = gtk.Image() + self.image.set_from_pixbuf(self.pic) + compound_frame.add(self.image) + self.hbox_for_info_graphics.add(compound_frame) + + # --- Refinement History --- +# self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) +# self.canvas.set_size_request(190, 190) +# self.hbox_for_info_graphics.add(self.canvas) + + # --- Spider Plot --- + spider_plot_frame = gtk.Frame() + spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join( + os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + self.spider_plot_pic = pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_image = gtk.Image() + self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) + spider_plot_frame.add(self.spider_plot_image) + self.hbox_for_info_graphics.add(spider_plot_frame) + + frame.add(self.hbox_for_info_graphics) + self.vbox.add(frame) + + ################################################################################# + # --- pandda.inspect user comments --- + outer_frame = gtk.Frame(label='pandda.inspect comments') + vbox = gtk.VBox() + ligand_site_name_label_frame = gtk.Frame() + ligand_site_name_label = gtk.Label('Site Name') + ligand_site_name_label_frame.add(ligand_site_name_label) + ligand_inspect_confidence_label_frame = gtk.Frame() + ligand_inspect_confidence_label = gtk.Label('Confidence') + ligand_inspect_confidence_label_frame.add( + ligand_inspect_confidence_label) + ligand_inspect_interesting_label_frame = gtk.Frame() + ligand_inspect_interesting_label = gtk.Label('Interesting') + ligand_inspect_interesting_label_frame.add( + ligand_inspect_interesting_label) + ligand_inspect_comment_label_frame = gtk.Frame() + ligand_inspect_comment_label = gtk.Label('Comment') + ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) + ligand_site_name_value_frame = gtk.Frame() + self.ligand_site_name_value = gtk.Label('-') + ligand_site_name_value_frame.add(self.ligand_site_name_value) + ligand_inspect_confidence_value_frame = gtk.Frame() + self.ligand_inspect_confidence_value = gtk.Label('-') + ligand_inspect_confidence_value_frame.add( + self.ligand_inspect_confidence_value) + ligand_inspect_interesting_value_frame = gtk.Frame() + self.ligand_inspect_interesting_value = gtk.Label('-') + ligand_inspect_interesting_value_frame.add( + self.ligand_inspect_interesting_value) + ligand_inspect_comment_value_frame = gtk.Frame() + self.ligand_inspect_comment_value = gtk.Label('-') + ligand_inspect_comment_value_frame.add( + self.ligand_inspect_comment_value) + + frame_pandda_inspect_comments_table = gtk.Frame() + pandda_inspect_comments_table = gtk.Table(2, 6, False) + pandda_inspect_comments_table.attach( + ligand_site_name_label_frame, 0, 1, 0, 1) + pandda_inspect_comments_table.attach( + ligand_site_name_value_frame, 1, 2, 0, 1) + pandda_inspect_comments_table.attach( + ligand_inspect_confidence_label_frame, 2, 3, 0, 1) + pandda_inspect_comments_table.attach( + ligand_inspect_confidence_value_frame, 3, 4, 0, 1) + pandda_inspect_comments_table.attach( + ligand_inspect_interesting_label_frame, 4, 5, 0, 1) + pandda_inspect_comments_table.attach( + ligand_inspect_interesting_value_frame, 5, 6, 0, 1) + pandda_inspect_comments_table.attach( + ligand_inspect_comment_label_frame, 0, 1, 1, 2) + pandda_inspect_comments_table.attach( + ligand_inspect_comment_value_frame, 1, 6, 1, 2) + + frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) + vbox.add(frame_pandda_inspect_comments_table) + outer_frame.add(vbox) + self.vbox.pack_start(outer_frame) + +# # SPACER + self.vbox.add(gtk.Label(' ')) + + ################################################################################# + outer_frame = gtk.Frame(label='Sample Navigator') + hboxSample = gtk.HBox() + + # --- crystal navigator combobox --- + frame = gtk.Frame() + self.vbox_sample_navigator = gtk.VBox() + self.cb = gtk.combo_box_new_text() + self.cb.connect("changed", self.ChooseXtal) + self.vbox_sample_navigator.add(self.cb) + # --- crystal navigator backward/forward button --- + self.PREVbutton = gtk.Button(label="<<<") + self.NEXTbutton = gtk.Button(label=">>>") + self.PREVbutton.connect("clicked", self.ChangeXtal, -1) + self.NEXTbutton.connect("clicked", self.ChangeXtal, +1) + hbox = gtk.HBox() + hbox.pack_start(self.PREVbutton) + hbox.pack_start(self.NEXTbutton) + self.vbox_sample_navigator.add(hbox) + frame.add(self.vbox_sample_navigator) + hboxSample.add(frame) + + # --- site navigator combobox --- + frame = gtk.Frame() + self.vbox_site_navigator = gtk.VBox() + self.cb_site = gtk.combo_box_new_text() + self.cb_site.connect("changed", self.ChooseSite) + self.vbox_site_navigator.add(self.cb_site) + # --- site navigator backward/forward button --- + self.PREVbuttonSite = gtk.Button(label="<<<") + self.NEXTbuttonSite = gtk.Button(label=">>>") + self.PREVbuttonSite.connect("clicked", self.ChangeSite, -1) + self.NEXTbuttonSite.connect("clicked", self.ChangeSite, +1) + hbox = gtk.HBox() + hbox.pack_start(self.PREVbuttonSite) + hbox.pack_start(self.NEXTbuttonSite) + self.vbox_site_navigator.add(hbox) + frame.add(self.vbox_site_navigator) + hboxSample.add(frame) + + outer_frame.add(hboxSample) + self.vbox.add(outer_frame) + + # SPACER + self.vbox.add(gtk.Label(' ')) + + ################################################################################# + # --- current refinement stage --- + outer_frame = gtk.Frame() + hbox = gtk.HBox() + + frame = gtk.Frame(label='Analysis Status') + vbox = gtk.VBox() + self.experiment_stage_button_list = [] + for n, button in enumerate(self.experiment_stage): + if n == 0: + new_button = gtk.RadioButton(None, button[0]) + else: + new_button = gtk.RadioButton(new_button, button[0]) + new_button.connect( + "toggled", self.experiment_stage_button_clicked, button[1]) + vbox.add(new_button) + self.experiment_stage_button_list.append(new_button) + frame.add(vbox) + hbox.pack_start(frame) + + # --- ligand confidence --- + frame = gtk.Frame(label='Ligand Confidence') + vbox = gtk.VBox() + self.ligand_confidence_button_list = [] + for n, criteria in enumerate(self.ligand_confidence_category): + if n == 0: + new_button = gtk.RadioButton(None, criteria) + else: + new_button = gtk.RadioButton(new_button, criteria) + new_button.connect( + "toggled", self.ligand_confidence_button_clicked, criteria) + vbox.add(new_button) + self.ligand_confidence_button_list.append(new_button) + frame.add(vbox) + hbox.pack_start(frame) + + outer_frame.add(hbox) + self.vbox.pack_start(outer_frame) + + # SPACER + self.vbox.add(gtk.Label(' ')) + + # --- ligand modeling --- + frame = gtk.Frame(label='Ligand Modeling') + self.hbox_for_modeling = gtk.HBox() + self.merge_ligand_button = gtk.Button(label="Merge Ligand") + self.place_ligand_here_button = gtk.Button(label="Place Ligand here") + self.hbox_for_modeling.add(self.place_ligand_here_button) + self.place_ligand_here_button.connect( + "clicked", self.place_ligand_here) + self.hbox_for_modeling.add(self.merge_ligand_button) + self.merge_ligand_button.connect( + "clicked", self.merge_ligand_into_protein) + frame.add(self.hbox_for_modeling) + self.vbox.pack_start(frame) + + +# # --- ligand confidence --- +# self.cb_ligand_confidence = gtk.combo_box_new_text() +# self.cb_ligand_confidence.connect("changed", self.set_ligand_confidence) +# for citeria in self.ligand_confidence: +# self.cb_ligand_confidence.append_text(citeria) +# self.vbox.add(self.cb_ligand_confidence) + + # --- refinement & options --- + self.hbox_for_refinement = gtk.HBox() + self.REFINEbutton = gtk.Button(label="Refine") + self.RefinementParamsButton = gtk.Button(label="refinement parameters") + self.REFINEbutton.connect("clicked", self.REFINE) + self.hbox_for_refinement.add(self.REFINEbutton) + self.RefinementParamsButton.connect("clicked", self.RefinementParams) + self.hbox_for_refinement.add(self.RefinementParamsButton) + self.vbox.add(self.hbox_for_refinement) + +# self.VALIDATEbutton = gtk.Button(label="validate structure") +# self.DEPOSITbutton = gtk.Button(label="prepare for deposition") + + # --- CANCEL button --- + self.CANCELbutton = gtk.Button(label="CANCEL") + self.CANCELbutton.connect("clicked", self.CANCEL) + self.vbox.add(self.CANCELbutton) + + self.window.add(self.vbox) + self.window.show_all() + + def CANCEL(self, widget): + self.window.destroy() + + def ChangeXtal(self, widget, data=None): + self.index = self.index + data + if self.index < 0: + self.index = 0 + if self.index >= len(self.Todo): + # self.index = len(self.Todo) + self.index = 0 + self.cb.set_active(self.index) + + def ChooseXtal(self, widget): + self.xtalID = str(widget.get_active_text()) + for n, item in enumerate(self.Todo): + if str(item[0]) == self.xtalID: + self.index = n + self.merge_ligand_button.set_sensitive(True) + self.place_ligand_here_button.set_sensitive(True) + + self.ligand_site_name_value.set_label('-') + self.ligand_inspect_confidence_value.set_label('-') + self.ligand_inspect_interesting_value.set_label('-') + self.ligand_inspect_comment_value.set_label('-') + + self.refresh_site_combobox() + self.db_dict_mainTable = {} + self.db_dict_panddaTable = {} + if str(self.Todo[self.index][0]) is not None: + self.compoundID = str(self.Todo[self.index][1]) + self.refinement_folder = str(self.Todo[self.index][4]) + self.refinement_outcome = str(self.Todo[self.index][5]) + self.update_RefinementOutcome_radiobutton() + if self.xtalID not in self.siteDict: # i.e. we are not working with a PanDDA model + self.ligand_confidence = str(self.Todo[self.index][6]) + self.update_LigandConfidence_radiobutton() + + self.RefreshData() + + def update_RefinementOutcome_radiobutton(self): + # updating dataset outcome radiobuttons + current_stage = 0 + for i, entry in enumerate(self.experiment_stage): + if entry[1].split()[0] == self.refinement_outcome.split()[0]: + current_stage = i + break + for i, button in enumerate(self.experiment_stage_button_list): + if i == current_stage: + button.set_active(True) + break + + def update_LigandConfidence_radiobutton(self): + # updating ligand confidence radiobuttons + current_stage = 0 + for i, entry in enumerate(self.ligand_confidence_category): + print('--->', entry, self.ligand_confidence) + try: + if entry.split()[0] == self.ligand_confidence.split()[0]: + current_stage = i + break + except IndexError: + pass + for i, button in enumerate(self.ligand_confidence_button_list): + if i == current_stage: + button.set_active(True) + break + + def refresh_site_combobox(self): + # reset self.pandda_index + self.pandda_index = -1 + # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites + for n in range(-1, 100): + self.cb_site.remove_text(0) + self.site_index = '0' + self.event_index = '0' + # only repopulate if site exists + if self.xtalID in self.siteDict: + for item in sorted(self.siteDict[self.xtalID]): + self.cb_site.append_text( + 'site: %s - event: %s' % (item[5], item[6])) + + def ChangeSite(self, widget, data=None): + if self.xtalID in self.siteDict: + self.pandda_index = self.pandda_index + data + if self.pandda_index < 0: + self.pandda_index = 0 + if self.pandda_index >= len(self.siteDict[self.xtalID]): + self.pandda_index = 0 + self.cb_site.set_active(self.pandda_index) + + def ChooseSite(self, widget): + tmp = str(widget.get_active_text()) + self.site_index = tmp.split()[1] + self.event_index = tmp.split()[4] + for n, item in enumerate(self.siteDict[self.xtalID]): + if item[5] == self.site_index and item[6] == self.event_index: + self.pandda_index = n + self.RefreshSiteData() + + def RefreshSiteData(self): + + if self.pandda_index == -1: + self.merge_ligand_button.set_sensitive(True) + self.place_ligand_here_button.set_sensitive(True) + else: + self.merge_ligand_button.set_sensitive(False) + self.place_ligand_here_button.set_sensitive(False) + # and remove ligand molecule so that there is no temptation to merge it + if len(coot_utils_XChem.molecule_number_list()) > 0: + for imol in coot_utils_XChem.molecule_number_list(): + if self.compoundID+'.pdb' in coot.molecule_name(imol): + coot.close_molecule(imol) + + print('pandda index', self.pandda_index) + self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] + print('new spider plot:', self.spider_plot) + self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] + print('new event map:', self.event_map) + self.ligand_confidence = str( + self.siteDict[self.xtalID][self.pandda_index][7]) + self.update_LigandConfidence_radiobutton() + site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) + site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) + site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) + print('new site coordinates:', site_x, site_y, site_z) + coot.set_rotation_centre(site_x, site_y, site_z) + + self.ligand_site_name_value.set_label( + str(self.siteDict[self.xtalID][self.pandda_index][8])) + self.ligand_inspect_confidence_value.set_label( + str(self.siteDict[self.xtalID][self.pandda_index][9])) + self.ligand_inspect_interesting_value.set_label( + str(self.siteDict[self.xtalID][self.pandda_index][10])) + self.ligand_inspect_comment_value.set_label( + str(self.siteDict[self.xtalID][self.pandda_index][11])) + + self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event( + self.xtalID, self.site_index, self.event_index) + print('>>>>> spider plot data', self.spider_plot_data) + self.ligandIDValue.set_label( + self.spider_plot_data['PANDDA_site_ligand_id']) + try: + self.ligand_occupancyValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) + except ValueError: + self.ligand_occupancyValue.set_label('-') + + try: + self.ligand_BaverageValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) + except ValueError: + self.ligand_BaverageValue.set_label('-') + + try: + self.ligand_BratioSurroundingsValue.set_label(str(round( + float(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']), 2))) + except ValueError: + self.ligand_BratioSurroundingsValue.set_label('-') + + try: + self.ligand_RSCCValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) + except ValueError: + self.ligand_RSCCValue.set_label('-') + + try: + self.ligand_rmsdValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) + except ValueError: + self.ligand_rmsdValue.set_label('-') + + try: + self.ligand_RSRValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) + except ValueError: + self.ligand_RSRValue.set_label('-') + + try: + self.ligand_RSZDValue.set_label( + str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) + except ValueError: + self.ligand_RSZDValue.set_label('-') + + ######################################################################################### + # delete old Event MAPs + if len(coot_utils_XChem.molecule_number_list()) > 0: + for imol in coot_utils_XChem.molecule_number_list(): + if 'map.native.ccp4' in coot.molecule_name(imol): + coot.close_molecule(imol) + + ######################################################################################### + # Spider plot + # Note: refinement history was shown instead previously + if os.path.isfile(self.spider_plot): + spider_plot_pic = gtk.gdk.pixbuf_new_from_file(self.spider_plot) + else: + spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join( + os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + self.spider_plot_pic = spider_plot_pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) + + ######################################################################################### + # check for PANDDAs EVENT maps + if os.path.isfile(self.event_map): + coot.handle_read_ccp4_map((self.event_map), 0) + for imol in coot_utils_XChem.molecule_number_list(): + if self.event_map in coot.molecule_name(imol): + coot.set_contour_level_in_sigma(imol, 2) +# coot.set_contour_level_absolute(imol,0.5) +# coot.set_last_map_colour(0.4,0,0.4) + coot.set_last_map_colour(0.74, 0.44, 0.02) + + def experiment_stage_button_clicked(self, widget, data=None): + self.db_dict_mainTable['RefinementOutcome'] = data + print('==> XCE: setting Refinement Outcome for ' + \ + self.xtalID+' to '+str(data)+' in mainTable of datasource') + self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + + def ligand_confidence_button_clicked(self, widget, data=None): + print('PANDDA_index', self.pandda_index) + if self.pandda_index == -1: + self.db_dict_mainTable['RefinementLigandConfidence'] = data + print('==> XCE: setting Ligand Confidence for ' + \ + self.xtalID+' to '+str(data)+' in mainTable of datasource') + self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + self.Todo[self.index][6] = data + else: + self.db_dict_panddaTable['PANDDA_site_confidence'] = data + print('==> XCE: setting Ligand Confidence for '+self.xtalID + \ + ' (site='+str(self.site_index)+', event='+str(self.event_index) + \ + ') to '+str(data)+' in panddaTable of datasource') + self.db.update_site_event_panddaTable( + self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable) + self.siteDict[self.xtalID][self.pandda_index][7] = data + + def RefreshData(self): + # reset spider plot image + spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join( + os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + self.spider_plot_pic = spider_plot_pic.scale_simple( + 190, 190, gtk.gdk.INTERP_BILINEAR) + self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) + + # initialize Refinement library + self.Refine = XChemRefine.RefineOld( + self.project_directory, self.xtalID, self.compoundID, self.data_source) + self.Serial = self.Refine.GetSerial() + if self.Serial == 1: + # i.e. no refinement has been done; data is probably straight out of dimple + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + print('==> XCE: updating quality indicators in data source for '+self.xtalID) + XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, + os.path.join(self.project_directory, self.xtalID, self.pdb_style)) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, '') # '' because file does not exist + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): + print('==> XCE: updating quality indicators in data source for '+self.xtalID) + XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, + os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, '') # '' because file does not exist + + # all this information is now updated in the datasource after each refinement cycle + self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) + + ######################################################################################### + # history + # if the structure was previously refined, try to read the parameters +# self.hbox_for_info_graphics.remove(self.canvas) + if self.Serial > 1: + self.RefmacParams = self.Refine.ParamsFromPreviousCycle( + self.Serial-1) +# refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() +# self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) +# else: +# self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea +# self.canvas.set_size_request(190, 190) +# self.hbox_for_info_graphics.add(self.canvas) +# self.canvas.show() + + ######################################################################################### + # update pdb & maps + + ######################################################################################### + # delete old PDB and MAP files + # - get a list of all molecules which are currently opened in COOT + # - remove all molecules/ maps before loading a new set + if len(coot_utils_XChem.molecule_number_list()) > 0: + for item in coot_utils_XChem.molecule_number_list(): + coot.close_molecule(item) + + ######################################################################################### + # read new PDB files + # read protein molecule after ligand so that this one is the active molecule + coot.set_nomenclature_errors_on_read("ignore") + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID+'.pdb')): + imol = coot.handle_read_draw_molecule_with_recentre(os.path.join( + self.project_directory, self.xtalID, self.compoundID+'.pdb'), 0) + self.mol_dict['ligand'] = imol + coot.read_cif_dictionary(os.path.join( + self.project_directory, self.xtalID, self.compoundID+'.cif')) + if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + # we want to be able to check dimple results immediately, but don't want to interfere with refinement +# if not os.path.isfile('REFINEMENT_IN_PROGRESS'): +# if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-ensemble-model.pdb')): +# os.symlink(self.xtalID+'-ensemble-model.pdb',self.pdb_style) +# elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.pdb')): +# os.symlink('dimple.pdb',self.pdb_style) +# else: +# self.go_to_next_xtal() + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): + os.chdir(os.path.join(self.project_directory, self.xtalID)) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join(self.project_directory, self.xtalID, 'dimple.pdb'), 0) + else: + self.go_to_next_xtal() + self.mol_dict['protein'] = imol + for item in coot_utils_XChem.molecule_number_list(): + if coot.molecule_name(item).endswith(self.pdb_style): + # master switch to show symmetry molecules + coot.set_show_symmetry_master(1) + coot.set_show_symmetry_molecule(item, 1) # show symm for model + + ######################################################################################### + # read fofo maps + # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map + # read 2fofc map last so that one can change its contour level + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): + coot.set_default_initial_contour_level_for_difference_map(3) + coot.handle_read_ccp4_map(os.path.join( + self.project_directory, self.xtalID, 'fofc.map'), 1) + coot.set_default_initial_contour_level_for_map(1) + coot.handle_read_ccp4_map(os.path.join( + self.project_directory, self.xtalID, '2fofc.map'), 0) + coot.set_last_map_colour(0, 0, 1) + else: + # try to open mtz file with same name as pdb file + coot.set_default_initial_contour_level_for_map(1) +# if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): +# os.chdir(os.path.join(self.project_directory,self.xtalID)) +# if not os.path.isfile('REFINEMENT_IN_PROGRESS'): +# if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-pandda-input.mtz')): +# os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) +# elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): +# os.symlink('dimple.mtz',self.mtz_style) + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, self.mtz_style)) + elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')): + coot.auto_read_make_and_draw_maps(os.path.join( + self.project_directory, self.xtalID, 'dimple.mtz')) + + ######################################################################################### + # update Quality Indicator table + try: + self.RRfreeValue.set_label(str(round(float(self.QualityIndicators['RefinementRcryst']), 3)) + ' / '+str( + round(float(self.QualityIndicators['RefinementRfree']), 3))) + except ValueError: + self.RRfreeValue.set_label('-') + + try: + self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRfreeTraficLight'])) + except ValueError: + pass + self.ResolutionValue.set_label( + self.QualityIndicators['RefinementResolution']) + try: + self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementResolutionTL'])) + except ValueError: + pass + self.MolprobityScoreValue.set_label( + self.QualityIndicators['RefinementMolProbityScore']) + try: + self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementMolProbityScoreTL'])) + except ValueError: + pass + self.RamachandranOutliersValue.set_label( + self.QualityIndicators['RefinementRamachandranOutliers']) + try: + self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRamachandranOutliersTL'])) + except ValueError: + pass + self.RamachandranFavoredValue.set_label( + self.QualityIndicators['RefinementRamachandranFavored']) + try: + self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRamachandranFavoredTL'])) + except ValueError: + pass + self.rmsdBondsValue.set_label( + self.QualityIndicators['RefinementRmsdBonds']) + try: + self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRmsdBondsTL'])) + except ValueError: + pass + self.rmsdAnglesValue.set_label( + self.QualityIndicators['RefinementRmsdAngles']) + try: + self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( + self.QualityIndicators['RefinementRmsdAnglesTL'])) + except ValueError: + pass + self.MatrixWeightValue.set_label( + self.QualityIndicators['RefinementMatrixWeight']) + + try: + pic = gtk.gdk.pixbuf_new_from_file(os.path.join( + self.project_directory, self.xtalID, self.compoundID+'.png')) + except gobject.GError: + pic = gtk.gdk.pixbuf_new_from_file(os.path.join( + os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) + self.image.set_from_pixbuf(self.pic) + + def go_to_next_xtal(self): + self.index += 1 + if self.index >= len(self.Todo): + self.index = len(self.Todo) + self.cb.set_active(self.index) + + def REFINE(self, widget): + + ####################################################### + # create folder for new refinement cycle + os.mkdir(os.path.join(self.project_directory, + self.xtalID, 'Refine_'+str(self.Serial))) + + ####################################################### + # write PDB file + # now take protein pdb file and write it to newly create Refine_ folder + # note: the user has to make sure that the ligand file was merged into main file + for item in coot_utils_XChem.molecule_number_list(): + if coot.molecule_name(item).endswith(self.pdb_style): + coot.write_pdb_file(item, os.path.join( + self.project_directory, self.xtalID, 'Refine_'+str(self.Serial), 'in.pdb')) + break + elif coot.molecule_name(item).endswith('dimple.pdb'): + coot.write_pdb_file(item, os.path.join( + self.project_directory, self.xtalID, 'Refine_'+str(self.Serial), 'in.pdb')) + break + + ####################################################### + # run REFMAC + self.Refine.RunRefmac(self.Serial, self.RefmacParams, + self.external_software, self.xce_logfile) + + self.index += 1 + if self.index >= len(self.Todo): + # self.index = len(self.Todo) + self.index = 0 + self.cb.set_active(self.index) + + def RefinementParams(self, widget): + print('\n==> XCE: changing refinement parameters') + self.RefmacParams = self.Refine.RefinementParams(self.RefmacParams) + + def set_selection_mode(self, widget): + self.selection_mode = widget.get_active_text() + + def get_samples_to_look_at(self, widget): + if self.selection_mode == '': + self.status_label.set_text('select model stage') + return + self.status_label.set_text('checking datasource for samples... ') + # first remove old samples if present + if len(self.Todo) != 0: + for n, item in enumerate(self.Todo): + self.cb.remove_text(0) + self.Todo = [] + self.siteDict = {} + self.Todo, self.siteDict = self.db.get_todoList_for_coot( + self.selection_mode) + self.status_label.set_text('found %s samples' % len(self.Todo)) + # refresh sample CB + for item in sorted(self.Todo): + self.cb.append_text('%s' % item[0]) + if self.siteDict == {}: + self.cb_site.set_sensitive(False) + self.PREVbuttonSite.set_sensitive(False) + self.NEXTbuttonSite.set_sensitive(False) + else: + self.cb_site.set_sensitive(True) + self.PREVbuttonSite.set_sensitive(True) + self.NEXTbuttonSite.set_sensitive(True) + + def update_plot(self, refinement_cycle, Rfree, Rcryst): + fig = Figure(figsize=(2, 2), dpi=50) + Plot = fig.add_subplot(111) + Plot.set_ylim([0, max(Rcryst+Rfree)]) + Plot.set_xlabel('Refinement Cycle', fontsize=12) + Plot.plot(refinement_cycle, Rfree, label='Rfree', linewidth=2) + Plot.plot(refinement_cycle, Rcryst, label='Rcryst', linewidth=2) + Plot.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, + ncol=2, mode="expand", borderaxespad=0., fontsize=12) + return fig + + def place_ligand_here(self, widget): + print('===> XCE: moving ligand to pointer') +# coot.move_molecule_here() + print('LIGAND: ', self.mol_dict['ligand']) + coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) + + def merge_ligand_into_protein(self, widget): + print('===> XCE: merge ligand into protein structure') + # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) + coot.merge_molecules_py( + [self.mol_dict['ligand']], self.mol_dict['protein']) + print('===> XCE: deleting ligand molecule') + coot.close_molecule(self.mol_dict['ligand']) + + def show_molprobity_to_do(self, widget): + if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')): + print('==> XCE: running MolProbity Summary for', self.xtalID) + coot.run_script(os.path.join(self.project_directory, self.xtalID, + 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')) + else: + print('==> XCE: cannot find ' + \ + os.path.join(self.project_directory, self.xtalID, + 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')) + +# def fit_ligand(self,widget): +# print 'fit' + + +if __name__ == '__main__': + GUI().StartGUI() diff --git a/lib/XChemCootReference.py b/lib/XChemCootReference.py index 0881566e..c291fbeb 100755 --- a/lib/XChemCootReference.py +++ b/lib/XChemCootReference.py @@ -383,7 +383,7 @@ def RefreshData(self): self.Refine = XChemRefine.Refine( self.reference_directory, self.refinementDir, 'dummy_compound_ID', 'dummy_database') self.Serial = self.Refine.GetSerial() - print '====> Serial', self.Serial + print('====> Serial', self.Serial) ######################################################################################### # history @@ -404,7 +404,7 @@ def RefreshData(self): ######################################################################################### # update Quality Indicator table - print self.QualityIndicators + print(self.QualityIndicators) try: self.RRfreeValue.set_label(str(round(float( self.QualityIndicators['Rcryst']), 3)) + ' / '+str(round(float(self.QualityIndicators['Rfree']), 3))) @@ -497,8 +497,8 @@ def REFINE(self, widget): snooze = 0 while os.path.exists(os.path.join(self.reference_directory, self.refinementDir, 'REFINEMENT_IN_PROGRESS')): time.sleep(10) - print '==> XCE: waiting for refinement to finish; elapsed time = ' + \ - str(snooze) + 's' + print('==> XCE: waiting for refinement to finish; elapsed time = ' + \ + str(snooze) + 's') snooze += 10 self.update_pdb_mtz_files('') @@ -524,7 +524,7 @@ def REFINE(self, widget): # self.update_pdb_mtz_files('') def RefinementParams(self, widget): - print '\n==> XCE: changing refinement parameters' + print('\n==> XCE: changing refinement parameters') self.RefmacParams = self.Refine.RefinementParams(self.RefmacParams) def set_selection_mode(self, widget): @@ -554,12 +554,12 @@ def update_pdb_mtz_files(self, pdbRoot): # first we check if there is a refinement folder and the respective refine.pdb # from previous refinement cycles Root = self.cb_select_pdb.get_active_text() - print 'ROOT', Root - print 'REFI_DIR', os.path.join( - self.reference_directory, self.refinementDir, 'refine.pdb') + print('ROOT', Root) + print('REFI_DIR', os.path.join( + self.reference_directory, self.refinementDir, 'refine.pdb')) if os.path.isfile(os.path.join(self.reference_directory, self.refinementDir, 'refine.pdb')): os.chdir(self.reference_directory) - print 'CURRENT DIR', os.getcwd() + print('CURRENT DIR', os.getcwd()) os.system('/bin/rm %s 2> /dev/null' % Root) os.symlink(os.path.realpath(os.path.join( self.refinementDir, 'refine.pdb')), '%s' % Root) @@ -583,8 +583,8 @@ def update_pdb_mtz_files(self, pdbRoot): self.mol_dict['protein'] = imol if self.mtzFree == '': - print 'FREE', os.path.join( - self.reference_directory, pdbRoot.replace('.pdb', '')+'.free.mtz') + print('FREE', os.path.join( + self.reference_directory, pdbRoot.replace('.pdb', '')+'.free.mtz')) if os.path.isfile(os.path.join(self.reference_directory, pdbRoot.replace('.pdb', '')+'.free.mtz')): self.mtzFree = os.path.join( self.reference_directory, pdbRoot.replace('.pdb', '')+'.free.mtz') @@ -617,13 +617,13 @@ def update_pdb_mtz_files(self, pdbRoot): groundStateMap = os.path.join( self.reference_directory, Root+'-mean-map.native.ccp4').replace('.pdb', '') - print '===>', groundStateMap + print('===>', groundStateMap) if os.path.isfile(groundStateMap): imol = coot.handle_read_ccp4_map(groundStateMap, 0) coot.set_contour_level_in_sigma(imol, 1) coot.set_last_map_colour(0.6, 0.6, 0) else: - print '==> XCE: ERROR - cannot find ground state mean map!' + print('==> XCE: ERROR - cannot find ground state mean map!') self.RefreshData() @@ -696,9 +696,9 @@ def show_molprobity_to_do(self, widget): coot.run_script(os.path.join(self.reference_directory, self.refinementDir, 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')) else: - print '==> XCE: cannot find ' + \ + print('==> XCE: cannot find ' + \ os.path.join(self.reference_directory, self.xtalID, - 'Refine_'+str(self.Serial-1), 'molprobity_coot.py') + 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')) def update_plot(self, refinement_cycle, Rfree, Rcryst): fig = Figure(figsize=(2, 2), dpi=50) @@ -720,7 +720,7 @@ def get_ground_state_maps_by_resolution(self): # try: # resolution=float(line.split()[5]) resolution = line.split()[5] - print resolution + print(resolution) found = True foundLine = n # except ValueError: @@ -737,7 +737,7 @@ def get_ground_state_maps_by_resolution(self): def get_highest_reso_ground_state_map(self): mapList = self.get_ground_state_maps_by_resolution() - print mapList + print(mapList) self.ground_state_map_List = [] self.ground_state_map_List.append(min(mapList, key=lambda x: x[0])) return self.ground_state_map_List diff --git a/lib/XChemCootTwin.py b/lib/XChemCootTwin.py index 405be291..f8117e06 100755 --- a/lib/XChemCootTwin.py +++ b/lib/XChemCootTwin.py @@ -48,7 +48,7 @@ def __init__(self): self.data_source = self.settings['data_source'] self.db = XChemDB.data_source(self.data_source) - print self.settings + print(self.settings) # checking for external software packages self.external_software = XChemUtils.external_software( @@ -824,11 +824,11 @@ def select_cpd(self, widget): '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') else: molNameCIF = molName - print cpd, '-', imol, '-', coot.molecule_name(imol) + print(cpd, '-', imol, '-', coot.molecule_name(imol)) if molName == cpd: coot.set_mol_displayed(imol, 1) - print 'reading', os.path.join( - self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif') + print('reading', os.path.join( + self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) coot.read_cif_dictionary(os.path.join( self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) else: @@ -862,7 +862,7 @@ def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 for i, entry in enumerate(self.ligand_confidence_category): - print '--->', entry, self.ligand_confidence + print('--->', entry, self.ligand_confidence) try: if entry.split()[0] == self.ligand_confidence.split()[0]: current_stage = i @@ -899,8 +899,8 @@ def ChangeSite(self, widget, data=None): def ChooseSite(self, widget): tmp = str(widget.get_active_text()) - print self.siteDict - print self.site_index + print(self.siteDict) + print(self.site_index) self.site_index = tmp.split()[1] self.event_index = tmp.split()[4] for n, item in enumerate(self.siteDict[self.xtalID]): @@ -925,18 +925,18 @@ def RefreshSiteData(self): # for w in self.label_button_list: # w.set_active(False) - print 'pandda index', self.pandda_index + print('pandda index', self.pandda_index) self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] - print 'new spider plot:', self.spider_plot + print('new spider plot:', self.spider_plot) self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] - print 'new event map:', self.event_map + print('new event map:', self.event_map) self.ligand_confidence = str( self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) - print 'new site coordinates:', site_x, site_y, site_z + print('new site coordinates:', site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) # self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) @@ -946,7 +946,7 @@ def RefreshSiteData(self): self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, self.event_index) - print '>>>>> spider plot data', self.spider_plot_data + print('>>>>> spider plot data', self.spider_plot_data) self.ligandIDValue.set_label( self.spider_plot_data['PANDDA_site_ligand_id']) try: @@ -1033,7 +1033,7 @@ def experiment_stage_button_clicked(self, widget, data=None): self.xce_logfile, self.xtalID, 'ligand_bound', self.db_dict_mainTable) def ligand_confidence_button_clicked(self, widget, data=None): - print 'PANDDA_index', self.pandda_index + print('PANDDA_index', self.pandda_index) if self.pandda_index == -1: self.db_dict_mainTable['RefinementLigandConfidence'] = data self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( @@ -1107,21 +1107,21 @@ def RefreshData(self): if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): - print '==> XCE: updating quality indicators in data source for ' + self.xtalID + print('==> XCE: updating quality indicators in data source for ' + self.xtalID) XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, os.path.join(self.project_directory, self.xtalID, self.pdb_style)) XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, '') # '' because file does not exist elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init_twin.pdb')): - print '==> XCE: updating quality indicators in data source for ' + self.xtalID + print('==> XCE: updating quality indicators in data source for ' + self.xtalID) XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, os.path.join(self.project_directory, self.xtalID, 'init_twin.pdb')) XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, '') # '' because file does not exist elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple_twin.pdb')): - print '==> XCE: updating quality indicators in data source for ' + self.xtalID + print('==> XCE: updating quality indicators in data source for ' + self.xtalID) XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, os.path.join(self.project_directory, self.xtalID, 'dimple_twin.pdb')) @@ -1138,7 +1138,7 @@ def RefreshData(self): if self.Serial > 1: self.RefmacParams = self.Refine.ParamsFromPreviousCycle( self.Serial - 1) - print '==> REFMAC params:', self.RefmacParams + print('==> REFMAC params:', self.RefmacParams) # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) # else: @@ -1150,11 +1150,11 @@ def RefreshData(self): ######################################################################################### # ligand files # first remove old samples if present - print '>>>', self.mol_dict['ligand_stereo'] + print('>>>', self.mol_dict['ligand_stereo']) for n, item in enumerate(self.mol_dict['ligand_stereo']): - print '__', item + print('__', item) self.select_cpd_cb.remove_text(0) - print 'done' + print('done') ######################################################################################### # remove potential generic line which indicates a possible covalent link @@ -1211,7 +1211,7 @@ def RefreshData(self): self.select_cpd_cb.set_sensitive(True) self.select_cpd_cb.set_active(0) else: - print 'no compound found in sample directory' + print('no compound found in sample directory') # self.select_cpd_cb.append_text('') self.select_cpd_cb.set_sensitive(False) @@ -1524,7 +1524,7 @@ def start_refinement(self): self.cb.set_active(self.index) def RefinementParams(self, widget): - print '\n==> XCE: changing refinement parameters' + print('\n==> XCE: changing refinement parameters') self.RefmacParams = XChemRefine.RefineParams(self.project_directory, self.xtalID, self.compoundID, self.data_source).RefmacRefinementParams(self.RefmacParams) @@ -1536,7 +1536,7 @@ def show_potential_link(self, *clicks): # it's a prerequisite that the ligand is merged into the protein imol_protein = None for imol in coot_utils_XChem.molecule_number_list(): - print '>', coot.molecule_name(imol) + print('>', coot.molecule_name(imol)) if coot.molecule_name(imol).endswith(self.pdb_style) or \ coot.molecule_name(imol).endswith('init_twin.pdb') or \ coot.molecule_name(imol).endswith('dimple_twin.pdb') or \ @@ -1544,15 +1544,15 @@ def show_potential_link(self, *clicks): imol_protein = imol break - print 'please click on the two atoms you want to link' + print('please click on the two atoms you want to link') if (len(clicks) == 2): click_1 = clicks[0] click_2 = clicks[1] imol_1 = click_1[1] imol_2 = click_2[1] - print 'imolp', imol, 'imo11', imol_1, 'imol2', imol_2 + print('imolp', imol, 'imo11', imol_1, 'imol2', imol_2) if imol_1 == imol_2 and imol_1 == imol_protein: - print 'click_1', click_1 + print('click_1', click_1) self.covLinkAtomSpec = None xyz_1 = atom_info_string( click_1[1], click_1[2], click_1[3], click_1[4], click_1[5], click_1[6]) @@ -1569,7 +1569,7 @@ def show_potential_link(self, *clicks): self.covLinkAtomSpec = [imol_protein, click_1, click_2, residue_1, residue_2] else: - print 'error: both atoms must belong to the same object; did you merge the ligand with your protein?' + print('error: both atoms must belong to the same object; did you merge the ligand with your protein?') def covalentLinkCreate(self, widget): if self.covLinkAtomSpec is not None: @@ -1582,7 +1582,7 @@ def covalentLinkCreate(self, widget): generic_object_clear(self.covLinkObject) self.start_refinement() else: - print 'error: no covalent link defined' + print('error: no covalent link defined') def set_selection_mode(self, widget): self.selection_mode = widget.get_active_text() @@ -1633,9 +1633,9 @@ def place_ligand_here(self, widget): molName = coot.molecule_name(imol)[coot.molecule_name( imol).rfind('/')+1:].replace('.pdb', '') if molName == cpd: - print '===> XCE: moving ligand to pointer' + print('===> XCE: moving ligand to pointer') coot_utils_XChem.move_molecule_here(imol) - print 'LIGAND: ', molName + print('LIGAND: ', molName) # print '===> XCE: moving ligand to pointer' # # coot.move_molecule_here() # print 'LIGAND: ', self.mol_dict['ligand'] @@ -1649,7 +1649,7 @@ def merge_ligand_into_protein(self, widget): molName = coot.molecule_name(imol)[coot.molecule_name( imol).rfind('/')+1:].replace('.pdb', '') if molName == cpd: - print '===> XCE: merge ligand into protein structure -->', cpd + print('===> XCE: merge ligand into protein structure -->', cpd) coot.merge_molecules_py([imol], self.mol_dict['protein']) if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( @@ -1657,24 +1657,24 @@ def merge_ligand_into_protein(self, widget): if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')): os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')) - print 'XCE: changing directory', os.path.join( - self.project_directory, self.xtalID) + print('XCE: changing directory', os.path.join( + self.project_directory, self.xtalID)) os.chdir(os.path.join(self.project_directory, self.xtalID)) - print 'XCE: changing symlink ln -s %s %s.cif' % ( - os.path.join('compound', molName + '.cif'), self.compoundID) + print('XCE: changing symlink ln -s %s %s.cif' % ( + os.path.join('compound', molName + '.cif'), self.compoundID)) os.system( 'ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): os.system('/bin/rm %s' % os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')) - print 'XCE: changing directory', os.path.join( - self.project_directory, self.xtalID) + print('XCE: changing directory', os.path.join( + self.project_directory, self.xtalID)) os.chdir(os.path.join(self.project_directory, self.xtalID)) - print 'XCE: changing symlink ln -s %s %s.pdb' % ( - os.path.join('compound', molName + '.pdb'), self.compoundID) + print('XCE: changing symlink ln -s %s %s.pdb' % ( + os.path.join('compound', molName + '.pdb'), self.compoundID)) os.system('ln -s %s %s.pdb' % (os.path.join('compound', molName + '.pdb'), self.compoundID)) - print '===> XCE: deleting ligand molecule', molName + print('===> XCE: deleting ligand molecule', molName) coot.close_molecule(imol) self.select_cpd_cb.set_sensitive(False) @@ -1686,24 +1686,24 @@ def merge_ligand_into_protein(self, widget): # coot.close_molecule(self.mol_dict['ligand']) def show_molprobity_to_do(self, widget): - print self.panddaSerial + print(self.panddaSerial) AdjPanddaSerial = (4 - len(str(self.Serial))) * \ '0' + str(int(self.panddaSerial) - 1) - print os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), - 'molprobity_coot.py') + print(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), + 'molprobity_coot.py')) if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')): - print '==> XCE: running MolProbity Summary for', self.xtalID + print('==> XCE: running MolProbity Summary for', self.xtalID) coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')) elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), 'molprobity_coot.py')): - print '==> XCE: running MolProbity Summary for', self.xtalID + print('==> XCE: running MolProbity Summary for', self.xtalID) coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), 'molprobity_coot.py')) else: - print '==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py') + print('==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, + 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')) # def refinementProtocolCallback(self, widget): # if widget.get_active(): diff --git a/lib/XChemDB.py b/lib/XChemDB.py index f2926d27..635ccc6a 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -1086,12 +1086,12 @@ def get_db_dict_for_sample(self, sampleID): cursor = connect.cursor() cursor.execute( "select * from mainTable where CrystalName='{0!s}';".format(sampleID)) - print( - "SQLITE: select * from mainTable where CrystalName='{0!s}';".format(sampleID)) + print(( + "SQLITE: select * from mainTable where CrystalName='{0!s}';".format(sampleID))) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() - print("DATA: {0!s}".format(data)) + print(("DATA: {0!s}".format(data))) for n, item in enumerate(data[0]): db_dict[header[n]] = str(item) return db_dict @@ -1197,7 +1197,7 @@ def import_csv_file(self, csv_file): continue if self.check_if_sample_exists_in_data_source(sampleID): update_string = '' - for key, value in line.iteritems(): + for key, value in line.items(): if key == 'ID' or key == 'CrystalName': continue if key not in available_columns: @@ -1217,7 +1217,7 @@ def import_csv_file(self, csv_file): else: column_string = '' value_string = '' - for key, value in line.iteritems(): + for key, value in line.items(): if key == 'ID': continue if key not in available_columns: @@ -1234,7 +1234,7 @@ def import_csv_file(self, csv_file): connect.commit() def update_data_source(self, sampleID, data_dict): - print 'here' + print('here') data_dict['LastUpdated'] = str( datetime.now().strftime("%Y-%m-%d %H:%M")) data_dict['LastUpdated_by'] = getpass.getuser() @@ -1430,8 +1430,8 @@ def update_insert_panddaTable(self, sampleID, data_dict): if not str(value).replace(' ', '') == '': # ignore if nothing in csv field value_string += "'"+str(value)+"'"+',' column_string += key+',' - print "INSERT INTO panddaTable (" + \ - column_string[:-1]+") VALUES ("+value_string[:-1]+");" + print("INSERT INTO panddaTable (" + \ + column_string[:-1]+") VALUES ("+value_string[:-1]+");") cursor.execute("INSERT INTO panddaTable (" + column_string[:-1]+") VALUES ("+value_string[:-1]+");") connect.commit() @@ -1525,8 +1525,8 @@ def update_insert_site_event_panddaTable(self, sampleID, data_dict): if not str(value).replace(' ', '') == '': # ignore if nothing in csv field value_string += "'"+str(value)+"'"+',' column_string += key+',' - print "INSERT INTO panddaTable (" + \ - column_string[:-1]+") VALUES ("+value_string[:-1]+");" + print("INSERT INTO panddaTable (" + \ + column_string[:-1]+") VALUES ("+value_string[:-1]+");") cursor.execute("INSERT INTO panddaTable (" + column_string[:-1]+") VALUES ("+value_string[:-1]+");") connect.commit() @@ -1563,8 +1563,8 @@ def update_insert_depositTable(self, sampleID, data_dict): continue if not str(value).replace(' ', '') == '': # ignore empty fields update_string = str(key)+'='+"'"+str(value)+"'" - print "UPDATE depositTable SET "+update_string + \ - " WHERE CrystalName="+"'"+sampleID+"';" + print("UPDATE depositTable SET "+update_string + \ + " WHERE CrystalName="+"'"+sampleID+"';") cursor.execute( "UPDATE depositTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"';") else: @@ -1579,8 +1579,8 @@ def update_insert_depositTable(self, sampleID, data_dict): if not str(value).replace(' ', '') == '': # ignore if nothing in csv field value_string += "'"+str(value)+"'"+',' column_string += key+',' - print "INSERT INTO depositTable (" + \ - column_string[:-1]+") VALUES ("+value_string[:-1]+");" + print("INSERT INTO depositTable (" + \ + column_string[:-1]+") VALUES ("+value_string[:-1]+");") cursor.execute("INSERT INTO depositTable (" + column_string[:-1]+") VALUES ("+value_string[:-1]+");") connect.commit() @@ -1901,8 +1901,8 @@ def get_todoList_for_coot(self, RefinementOutcome): if tmp: crystalDict[entry[0]] = [] for item in tmp: - print [entry[0], str(item[0]), str(item[1]), str(item[2]), str(item[3]), str(item[4]), str( - item[5]), str(item[6]), str(item[7]), str(item[8]), str(item[9]), str(item[10]), str(item[11])] + print([entry[0], str(item[0]), str(item[1]), str(item[2]), str(item[3]), str(item[4]), str( + item[5]), str(item[6]), str(item[7]), str(item[8]), str(item[9]), str(item[10]), str(item[11])]) crystalDict[entry[0]].append([str(item[0]), str(item[1]), str(item[2]), str(item[3]), str(item[4]), str( item[5]), str(item[6]), str(item[7]), str(item[8]), str(item[9]), str(item[10]), str(item[11])]) @@ -1965,7 +1965,7 @@ def get_list_of_pandda_sites_for_coot(self): 'order by cast (panddaTable.PANDDA_site_index as integer) ASC;' ) - print 'data source', self.data_source_file + print('data source', self.data_source_file) connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute(sqlite) @@ -2388,8 +2388,8 @@ def get_db_dict_for_visit_run_autoproc_score(self, xtal, visit, run, autoproc, s for column in cursor.description: header.append(column[0]) data = cursor.fetchall() - print('SQLITE: {0!s}'.format(sqlite)) - print('DATA: {0!s}'.format(data)) + print(('SQLITE: {0!s}'.format(sqlite))) + print(('DATA: {0!s}'.format(data))) for n, item in enumerate(data[0]): db_dict[header[n]] = str(item) return db_dict diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index 34fcb5e0..e101e5d8 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -21,11 +21,11 @@ def create_SF_mmcif(outDir, mtzList): - print 'hallo' + print('hallo') def get_protein_sequence(database, xtalID): - print 'hallo' + print('hallo') def check_depositDict(depositDict): @@ -36,12 +36,12 @@ def check_depositDict(depositDict): elif 'State_or_Province' in depositDict[entry]: continue elif depositDict[entry] == '': - print 'ERROR' + print('ERROR') def update_title(depositDict): - print 'hallo' + print('hallo') def create_data_template_text(): @@ -50,7 +50,7 @@ def create_data_template_text(): def create_Model_mmcif(outDir, pdbList): - print 'hallo' + print('hallo') # def update_file_locations_of_apo_structuresin_DB(database,projectDir,xce_logfile): # Logfile=XChemLog.updateLog(xce_logfile) @@ -147,7 +147,7 @@ def data_template_cif(self, depositDict): '#\n' ) except UnboundLocalError: - print 'Error: Something went wrong! Please check if you have saved the .deposit file to the database: Menu Deposition -> Edit Information' + print('Error: Something went wrong! Please check if you have saved the .deposit file to the database: Menu Deposition -> Edit Information') else: molecule_two_letter_sequence = ';' counter = 1 diff --git a/lib/XChemLog.py b/lib/XChemLog.py index 33af521e..f576ae69 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -1,6 +1,6 @@ # last edited: 09/02/2017, 15:00 -from __future__ import print_function + import os import glob import sys diff --git a/lib/XChemMain.py b/lib/XChemMain.py index b79d693c..dfd6ca55 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -60,16 +60,16 @@ def get_target_and_visit_list(beamline_directory, agamemnon): visit_list.append(os.path.realpath(beamline_directory)) for visit in visit_list: - print '-->', os.path.join(visit, 'processed', '*') + print('-->', os.path.join(visit, 'processed', '*')) if agamemnon: for target in glob.glob(os.path.join(visit, 'processed', 'auto', '*')): - print target + print(target) if target[target.rfind('/')+1:] not in ['results', 'README-log', 'edna-latest.html']: if target[target.rfind('/')+1:] not in target_list: target_list.append(target[target.rfind('/')+1:]) else: for target in glob.glob(os.path.join(visit, 'processed', '*')): - print target + print(target) if target[target.rfind('/')+1:] not in ['results', 'README-log', 'edna-latest.html']: if target[target.rfind('/')+1:] not in target_list: target_list.append(target[target.rfind('/')+1:]) @@ -251,12 +251,12 @@ def print_cluster_status_message(program, cluster_dict, xce_logfile): def display_queue_status_in_terminal(in_dict): # latest_run=max(tmp,key=lambda x: x[1])[0] max_dimple_runtime = max(in_dict['dimple'], key=lambda x: x[2])[2] - print '----------------------------------------------------------------------------' - print '| Task | Nr. Jobs | Max. Runtime (minutes) |' - print '----------------------------------------------------------------------------' - print '{0:24} {1:24} {2:24} {3:1}'.format('| DIMPLE', '| {0!s}'.format( - len(in_dict['dimple'])), '| %s' & max_dimple_runtime, '|') - print '----------------------------------------------------------------------------' + print('----------------------------------------------------------------------------') + print('| Task | Nr. Jobs | Max. Runtime (minutes) |') + print('----------------------------------------------------------------------------') + print('{0:24} {1:24} {2:24} {3:1}'.format('| DIMPLE', '| {0!s}'.format( + len(in_dict['dimple'])), '| %s' & max_dimple_runtime, '|')) + print('----------------------------------------------------------------------------') def get_datasource_summary(db_file): @@ -345,7 +345,7 @@ def get_datasource_summary(db_file): def remove_all_refmac_jobs_from_cluster_and_reinstate_last_stable_state(): - print 'hallo' + print('hallo') def change_links_to_selected_data_collection_outcome(sample, data_collection_dict, data_collection_column_three_dict, dataset_outcome_dict, initial_model_directory, data_source_file, xce_logfile): @@ -448,7 +448,7 @@ def get_dict_of_gda_barcodes(beamline): gda_log = files[files.rfind('/')+1:] if gda_log.startswith('gda_server.') and gda_log.endswith('.gz'): with gzip.open(files, 'r') as f: - print 'parsing', files + print('parsing', files) # for line in fin: for line in f: if 'BART SampleChanger - getBarcode() returning' in line: @@ -1149,12 +1149,12 @@ def html_ngl(firstPDB, firstEvent, firstMap, firstDiffMap, ligID): " stage.mouseControls.add('scroll', function () {\n" ' if (fwtMap) {\n' ' var level2fofc = fwtMap.getParameters().isolevel.toFixed(1);\n' - " isolevel2fofcText.innerText = '2fofc level: ' + level2fofc + '\u03C3';\n" + " isolevel2fofcText.innerText = '2fofc level: ' + level2fofc + '\\u03C3';\n" ' }\n' ' \n' ' if (surfFofc) {\n' ' var levelFofc = surfFofc.getParameters().isolevel.toFixed(1);\n' - " isolevelFofcText.innerText = 'fofc level: ' + levelFofc + '\u03C3';\n" + " isolevelFofcText.innerText = 'fofc level: ' + levelFofc + '\\u03C3';\n" ' }\n' ' });\n' ' \n' @@ -1518,7 +1518,7 @@ def run(self): found_new_file_root = True current_file_root = file_root if counter > 20 and file_root not in run_list: - print counter, file_root + print(counter, file_root) run_list.append(file_root) found_new_file_root = False counter = 0 @@ -1548,8 +1548,8 @@ def __init__(self, diffraction_data_directory): # self.datasetID_to_sampleID_conversion='*' def run(self): - print('Running diffraction image search in ' + - str(self.diffraction_data_directory)) + print(('Running diffraction image search in ' + + str(self.diffraction_data_directory))) os.chdir(self.diffraction_data_directory) if len(glob.glob(os.path.join(self.diffraction_data_directory, '*'))) != 0: progress_step = 100 / \ diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 21dfb918..72d4749f 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -238,7 +238,7 @@ def find_new_models(self, modelsDict): else: self.Logfile.insert( '%s: model has not changed since it was created on %s' % (xtal, timestamp_db)) - except (ValueError, IndexError), e: + except (ValueError, IndexError) as e: self.Logfile.error(str(e)) return samples_to_export @@ -1011,8 +1011,8 @@ def run(self): if os.path.isfile(self.filter_pdb + '.pdb'): print('filter pdb located') filter_pdb = ' filter.pdb='+self.filter_pdb+'.pdb' - print('will use ' + filter_pdb + - 'as a filter for pandda.analyse') + print(('will use ' + filter_pdb + + 'as a filter for pandda.analyse')) else: if self.use_remote: stat_command = self.remote_string.replace( diff --git a/lib/XChemProcess.py b/lib/XChemProcess.py index 1b6093f5..c4f00518 100755 --- a/lib/XChemProcess.py +++ b/lib/XChemProcess.py @@ -101,7 +101,7 @@ def run(self): # continue f = True if f: - print 'hallo' + print('hallo') else: if self.overwrite: os.chdir(os.path.join(self.initial_model_directory, diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index fde183cf..d516e3d3 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -170,7 +170,7 @@ def ChooseBfacRefinement(self, widget): return self.RefmacParams def on_key_release_Ncycles(self, widget, event): - print widget.get_text() + print(widget.get_text()) self.RefmacParams['NCYCLES'] = widget.get_text() return self.RefmacParams @@ -272,7 +272,7 @@ def GetRefinementHistory(self): found = False for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): if item.startswith(os.path.join(self.ProjectPath, self.xtalID, 'Refine_')): - print item[item.rfind('_')+1:] + print(item[item.rfind('_')+1:]) RefinementCycle.append(int(item[item.rfind('_')+1:])) found = True if found: @@ -311,7 +311,7 @@ def GetRefinementHistory(self): RefinementCycle = [0] RcrystList = [0] RfreeList = [0] - print RefinementCycle, RcrystList, RfreeList + print(RefinementCycle, RcrystList, RfreeList) return(sorted(RefinementCycle), RcrystList, RfreeList) @@ -335,7 +335,7 @@ def GetSerial(self): if os.path.isdir(os.path.join(self.ProjectPath, self.xtalID)): for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): if item.startswith(os.path.join(self.ProjectPath, self.xtalID, 'Refine_')): - print int(item[item.rfind('_')+1:]) + print(int(item[item.rfind('_')+1:])) temp.append(int(item[item.rfind('_')+1:])) found = 1 if found: @@ -806,7 +806,7 @@ def RunRefmac(self, Serial, RefmacParams, external_software, xce_logfile, covLin else: RefmacParams['TLS'] = '\n' - print '==> XCE: assembling refmac.csh' + print('==> XCE: assembling refmac.csh') ####################################################### # we write 'REFINEMENT_IN_PROGRESS' immediately to avoid unncessary refiment @@ -999,14 +999,14 @@ def RunRefmac(self, Serial, RefmacParams, external_software, xce_logfile, covLin Logfile.insert('changing directory to %s' % ( os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial))) if external_software['qsub_remote'] != '': - print os.getenv('LD_LIBRARY_PATH') + print(os.getenv('LD_LIBRARY_PATH')) if os.path.isfile(xce_logfile): Logfile.insert('starting refinement on remote cluster') remote_command = external_software['qsub_remote'].replace( "qsub'", 'cd %s; qsub' % os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial)) os.system("%s -P labxchem -q medium.q refmac.csh'" % remote_command) - print '%s -P labxchem -q medium.q refmac.csh' % remote_command + print('%s -P labxchem -q medium.q refmac.csh' % remote_command) elif external_software['qsub'] and os.path.isdir('/dls'): Logfile.insert( @@ -1118,7 +1118,7 @@ def ChooseBfacRefinement(self, widget): return self.RefmacParams def on_key_release_Ncycles(self, widget, event): - print widget.get_text() + print(widget.get_text()) self.RefmacParams['NCYCLES'] = widget.get_text() return self.RefmacParams @@ -1199,7 +1199,7 @@ def GetRefinementHistory(self): found = False for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): if item.startswith(os.path.join(self.ProjectPath, self.xtalID, 'Refine_')): - print item[item.rfind('_')+1:] + print(item[item.rfind('_')+1:]) RefinementCycle.append(int(item[item.rfind('_')+1:])) found = True if found: @@ -1238,7 +1238,7 @@ def GetRefinementHistory(self): RefinementCycle = [0] RcrystList = [0] RfreeList = [0] - print RefinementCycle, RcrystList, RfreeList + print(RefinementCycle, RcrystList, RfreeList) return(sorted(RefinementCycle), RcrystList, RfreeList) @@ -1686,7 +1686,7 @@ def RunQuickRefine(self, Serial, RefmacParams, external_software, xce_logfile, r remote_command = external_software['qsub_remote'].replace('qsub', 'cd %s; qsub' % os.path.join( self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) os.system('%s -P labxchem refmac.csh' % remote_command) - print '%s -P labxchem refmac.csh' % remote_command + print('%s -P labxchem refmac.csh' % remote_command) else: Logfile.insert( 'changing permission of refmac.csh: chmod +x refmac.csh') @@ -1795,7 +1795,7 @@ def ChooseBfacRefinement(self, widget): return self.RefmacParams def on_key_release_Ncycles(self, widget, event): - print widget.get_text() + print(widget.get_text()) self.RefmacParams['NCYCLES'] = widget.get_text() return self.RefmacParams @@ -1856,7 +1856,7 @@ def GetRefinementHistory(self): found = False for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): if item.startswith(os.path.join(self.ProjectPath, self.xtalID, 'Refine_')): - print item[item.rfind('_')+1:] + print(item[item.rfind('_')+1:]) RefinementCycle.append(int(item[item.rfind('_')+1:])) found = True if found: @@ -1895,7 +1895,7 @@ def GetRefinementHistory(self): RefinementCycle = [0] RcrystList = [0] RfreeList = [0] - print RefinementCycle, RcrystList, RfreeList + print(RefinementCycle, RcrystList, RfreeList) return(sorted(RefinementCycle), RcrystList, RfreeList) diff --git a/lib/XChemThread.py b/lib/XChemThread.py index 7e6bb366..c7ac90f5 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -20,7 +20,7 @@ import time import pickle -import cPickle +import pickle import base64 import math import subprocess diff --git a/lib/XChemToolTips.py b/lib/XChemToolTips.py index d60e33b8..ed388045 100755 --- a/lib/XChemToolTips.py +++ b/lib/XChemToolTips.py @@ -150,7 +150,7 @@ def run_pandda_inspect_at_home(pandda_directory): '3. run: rsync -av * %s@nx.diamond.ac.uk:%s\n' % (getpass.getuser(), pandda_directory) + 'Now proceed within XChemExplorer as before.\n') - print instruction + print(instruction) def deposition_interface_note(): diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 80e03feb..31f72516 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -1165,7 +1165,7 @@ def update_datasource_with_PDBheader(self, xtal, datasource, pdbfile): 'RefinementRmsdBondsTL': pdb['rmsdBondsTL'], 'RefinementRmsdAngles': pdb['rmsdAngles'], 'RefinementRmsdAnglesTL': pdb['rmsdAnglesTL'], 'RefinementSpaceGroup': pdb['SpaceGroup'], 'RefinementResolution': pdb['ResolutionHigh'], 'RefinementResolutionTL': pdb['ResolutionColor']} - print db_dict + print(db_dict) db = XChemDB.data_source(datasource) db.update_data_source(xtal, db_dict) @@ -2454,8 +2454,8 @@ def get_xyz_coordinated_of_residue(self, chain, number): return X, Y, Z def get_center_of_gravity_of_residue_ish(self, chain, number): - print '-> chain:', chain - print '-> number:', number + print('-> chain:', chain) + print('-> number:', number) X = 0.0 Y = 0.0 Z = 0.0 @@ -2605,8 +2605,8 @@ def merge_pdb_file(self, pdbin): DuplicateResidue = False for entry in residueListPDBin: if entry in residueListReference: - print 'residue already exisits in '+self.pdb+':' - print str(entry) + print('residue already exisits in '+self.pdb+':') + print(str(entry)) DuplicateResidue = True if not DuplicateResidue: @@ -2624,7 +2624,7 @@ def merge_pdb_file(self, pdbin): f.write(outPDB) f.close() else: - print 'cannot merge pdb files!' + print('cannot merge pdb files!') def get_symmetry_operators(self): symop = [] @@ -2644,7 +2644,7 @@ def get_symmetry_operators(self): if line.split()[0] == spg_number: foundSPG = True else: - print "CCP4 environmental variable is not set" + print("CCP4 environmental variable is not set") return symop @@ -2685,7 +2685,7 @@ def save_sym_equivalents_of_ligands_in_pdb_as_one_file_per_ligand(self, pdbIN): for line in open(pdbIN): if line.startswith('ATOM') or line.startswith('HETATM'): nres += 1 - print 'NRES', nres + print('NRES', nres) unit_cell = self.get_unit_cell_from_pdb() spg = self.get_spg_from_pdb() symop = self.get_symmetry_operators() @@ -2773,10 +2773,10 @@ def save_surounding_unit_cells(self, pdbIN): 'spacegroup {0!s}\n'.format(spg) + 'shift fractional {0!s}\n'.format(str(shift).replace('[', '').replace(']', '')) + 'eof\n') - print 'pdinin', pdbIN - print 'outdir', outDir - print 'root', root - print pdbset + print('pdinin', pdbIN) + print('outdir', outDir) + print('root', root) + print(pdbset) os.system(pdbset) @@ -3060,7 +3060,7 @@ def map_to_sf(self, resolution): return cmd = 'gemmi map2sf %s %s FWT PHWT --dmin=%s' % ( self.emap, self.emtz, resolution) - print('converting map with command:\n' + cmd) + print(('converting map with command:\n' + cmd)) os.system(cmd) if os.path.isfile(self.emtz): print('event map to SF conversion successful') diff --git a/lib/coot_utils_XChem.py b/lib/coot_utils_XChem.py index 0475c257..753dc5ee 100755 --- a/lib/coot_utils_XChem.py +++ b/lib/coot_utils_XChem.py @@ -26,6 +26,7 @@ import re import coot import sys +import numbers sys.path.append('/usr/local/coot/current/lib/python2.7/site-packages') @@ -126,7 +127,7 @@ def arg_to_append(item): arg_ls.append(arg_to_append(ele)) return arg_ls else: - if aa_dict.has_key(item): + if item in aa_dict: return aa_dict[item] else: return item @@ -341,7 +342,7 @@ def molecule_number_list(): def model_molecule_number_list(): - return filter(valid_model_molecule_qm, molecule_number_list()) + return list(filter(valid_model_molecule_qm, molecule_number_list())) # Test for prefix-dir (1) being a string (2) existing (3) being a # directory (4-6) modifiable by user (ie. u+rwx). prefix_dir must be a @@ -465,7 +466,7 @@ def residue_spec2ins_code(rs): def atom_spec2imol(atom_spec): import types - if not (isinstance(atom_spec, types.ListType)): + if not (isinstance(atom_spec, list)): return False else: if (len(atom_spec) == 6): @@ -527,7 +528,7 @@ def set_virtual_trackball_type(type): elif (type == "spherical-surface"): vt_surface(0) else: - print "virtual trackball type", type, "not understood" + print("virtual trackball type", type, "not understood") # Is ls a list of strings? Return True or False # @@ -540,7 +541,7 @@ def list_of_strings_qm(ls): return False else: for item in ls: - if isinstance(item, types.StringTypes): + if isinstance(item, (str,)): pass else: not_str += 1 @@ -692,7 +693,7 @@ def command_in_path_qm_old_version(cmd, only_extension="", add_extensions=None): else: tmp_ext = os.environ["PATHEXT"].split(os.pathsep) # list of extensions (no dot) only - extensions = map(lambda ext: ext[1:], tmp_ext) + extensions = [ext[1:] for ext in tmp_ext] if only_extension: extensions = [only_extension] @@ -701,8 +702,7 @@ def command_in_path_qm_old_version(cmd, only_extension="", add_extensions=None): program_names = [cmd_noext] if extensions: - program_names += map(lambda ext: cmd_noext + "." + ext, - extensions) + program_names += [cmd_noext + "." + ext for ext in extensions] try: primary_path = os.environ["PATH"] @@ -714,7 +714,7 @@ def command_in_path_qm_old_version(cmd, only_extension="", add_extensions=None): return True return False except: - print "BL WARNING:: couldnt open $PATH" # this shouldnt happen + print("BL WARNING:: couldnt open $PATH") # this shouldnt happen return False @@ -744,8 +744,8 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): cmd_execfile = cmd else: if not(command_in_path_qm(cmd)): - print "command ", cmd, " not found in $PATH!" - print "BL INFO:: Maybe we'll find it somewhere else later..." + print("command ", cmd, " not found in $PATH!") + print("BL INFO:: Maybe we'll find it somewhere else later...") cmd_execfile = find_exe(cmd, "CCP4_BIN", "PATH") if (cmd_execfile): @@ -767,7 +767,7 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): process.stdin.close() if (screen_flag): for line in process.stdout: - print "#", line.rstrip(" \n") # remove trailing whitespace + print("#", line.rstrip(" \n")) # remove trailing whitespace log.write(line) process.wait() log.close() @@ -792,7 +792,7 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): " < " + data_list_file + " > " + log_file, 'r') cmd_finished = status.close() if (cmd_finished is not None): - print "running command ", cmd, " failed!" + print("running command ", cmd, " failed!") return 1 else: # print "cmd ", cmd ," seems to have run ok!" @@ -800,7 +800,7 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): return 0 os.remove(data_list_file) else: - print "WARNING:: could not find {0!s}, so not running".format(cmd) + print("WARNING:: could not find {0!s}, so not running".format(cmd)) return False # example usage: @@ -850,7 +850,7 @@ def file_name_extension(file_name): def add_tmp_extension_to(file_name): import types - if isinstance(file_name, types.StringTypes): + if isinstance(file_name, (str,)): root, ext = os.path.splitext(file_name) f = root + "-tmp" + ext return f @@ -882,7 +882,7 @@ def strip_path(s): def slash_start_qm(s): import types import string - if isinstance(s, types.StringTypes): + if isinstance(s, (str,)): if len(s) > 0: if (s.startswith("/") or s.startswith("\\")): return True @@ -915,7 +915,7 @@ def unique_date_time_str(): def every_nth(ls, n): - elements = range(0, len(ls), n) + elements = list(range(0, len(ls), n)) a = [] for i in elements: a.append(ls[i]) @@ -977,7 +977,7 @@ def multi_read_pdb(glob_pattern, dir): patt = os.path.normpath(dir+'/*.'+glob_pattern) all_files = glob.glob(patt) for file in all_files: - print "BL INFO:: reading ", file + print("BL INFO:: reading ", file) read_pdb(file) # read_pdb_all reads all the "*.pdb" files in the current directory. @@ -992,7 +992,7 @@ def read_pdb_all(): patt = os.path.normpath(os.path.abspath(".")+'/*.pdb') all_files = glob.glob(patt) for file in all_files: - print "BL INFO:: reading ", file + print("BL INFO:: reading ", file) read_pdb(file) set_recentre_on_read_pdb(recentre_status) @@ -1032,7 +1032,7 @@ def view_matrix_transp(): def view_quaternion(): - ret = map(get_view_quaternion_internal, [0, 1, 2, 3]) + ret = list(map(get_view_quaternion_internal, [0, 1, 2, 3])) return ret # Return the view number @@ -1084,7 +1084,7 @@ def convert_sign(x, y): v1 = v pr.append(math.sqrt(v1) / 2) - ls = map(convert_sign, pr[1:], [m21 - m12, m02 - m20, m10 - m01]) + ls = list(map(convert_sign, pr[1:], [m21 - m12, m02 - m20, m10 - m01])) ls.append(pr[0]) @@ -1160,7 +1160,7 @@ def identity_matrix(): def translation(axis, length): import operator # BL says: we dont check if axis is string, yet at least not directly - if (operator.isNumberType(length)): + if (isinstance(length, numbers.Number)): if (axis == "x"): return [length, 0, 0] elif (axis == "y"): @@ -1168,10 +1168,10 @@ def translation(axis, length): elif (axis == "z"): return [0, 0, length] else: - print "symbol axis: ", axis, " incomprehensible" + print("symbol axis: ", axis, " incomprehensible") return False else: - print "incomprehensible length argument: ", length + print("incomprehensible length argument: ", length) return False # Rotate degrees about screen axis, where axis is either 'x', 'y' or 'z'. @@ -1207,7 +1207,7 @@ def vm(): view_matrix() def mult(mat1, mat2): mat2 # end of uselessness... - if (operator.isNumberType(degrees)): + if (isinstance(degrees, numbers.Number)): if (axis == "x"): mult(view_matrix(), simple_rotation_x(deg_to_rad(degrees))) elif (axis == "y"): @@ -1215,9 +1215,9 @@ def mult(mat1, mat2): mat2 elif (axis == "z"): mult(view_matrix(), simple_rotation_z(deg_to_rad(degrees))) else: - print "symbol axis: ", axis, " incomprehensible" + print("symbol axis: ", axis, " incomprehensible") else: - print "incomprehensible length argument: ", degrees + print("incomprehensible length argument: ", degrees) # Support for old toggle functions. (consider instead the raw @@ -1267,8 +1267,8 @@ def r_info(imol, chain_id, n): ins_code = insertion_code_from_serial_number(imol, chain_id, n) return [res_no, ins_code, res_name, residue_info(imol, chain_id, res_no, ins_code)] - ls = [map(lambda chain_id: [chain_id, map(lambda serial_number: r_info( - imol, chain_id, serial_number), range(chain_n_residues(chain_id, imol)))], chain_ids(imol))] + ls = [[[chain_id, [r_info( + imol, chain_id, serial_number) for serial_number in range(chain_n_residues(chain_id, imol))]] for chain_id in chain_ids(imol)]] return ls # reorder chains @@ -1282,7 +1282,7 @@ def reorder_chains(imol): # chain_list: [["C", [xx]], ["A", [xx]], ["B", [xx]]] # def reorder_chains_in_model(chain_list): - map(lambda model: model.sort(), chain_list) + list(map(lambda model: model.sort(), chain_list)) p_rep = python_representation(imol) if (type(p_rep) is ListType): @@ -1352,7 +1352,7 @@ def tf(imol, mat, trans, about_pt, radius, space_group, cell): ret = tf(args[0], identity_matrix(), args[1], rotation_centre(), args[2], space_group(imol), cell(imol)) else: - print "arguments to transform-map incomprehensible: args: ", args + print("arguments to transform-map incomprehensible: args: ", args) return ret @@ -1392,7 +1392,7 @@ def transform_map_using_lsq_matrix(imol_bref, ref_chain, ref_resno_start, ref_re if not (space_group and cell): message = "Bad cell or symmetry for molecule" + \ str(cell) + str(space_group) + str(imol_ref) - print "Bad cell or symmetry for molecule", message + print("Bad cell or symmetry for molecule", message) ret = -1 # invalid mol! or return message!? else: @@ -1425,7 +1425,7 @@ def brighten_map(imol, scale_factor): pass set_map_colour(imol, *new_v) else: - print "bad non-list current-colour ", current_colour + print("bad non-list current-colour ", current_colour) graphics_draw() # Make all maps brighter @@ -1433,14 +1433,14 @@ def brighten_map(imol, scale_factor): def brighten_maps(): - map(lambda imap: brighten_map(imap, 1.25), map_molecule_list()) + list(map(lambda imap: brighten_map(imap, 1.25), map_molecule_list())) # Make all maps darker # def darken_maps(): - map(lambda imap: brighten_map(imap, 0.8), map_molecule_list()) + list(map(lambda imap: brighten_map(imap, 0.8), map_molecule_list())) # return a list of chain ids for given molecule number @var{imol}. # return empty list on error @@ -1565,10 +1565,10 @@ def residue_has_hetatms_qm(imol, chain_id, res_no, ins_code): def centre_of_mass(imol): centre = eval(centre_of_mass_string(imol)) if (centre == 0): - print "molecule number", imol, "is not valid" + print("molecule number", imol, "is not valid") return False else: - print "Centre of mass for molecule {0!s} is {1!s}".format(imol, centre) + print("Centre of mass for molecule {0!s} is {1!s}".format(imol, centre)) # for use somewhere let's return the centre return centre @@ -1604,7 +1604,7 @@ def guess_refinement_map(): for map_mol in map_list: if map_is_difference_map(map_mol) == 0: return map_mol - print "BL WARNING:: we couldnt find a non difference map for fitting!" + print("BL WARNING:: we couldnt find a non difference map for fitting!") return -1 @@ -1635,7 +1635,7 @@ def auto_weight_for_refinement(): def sphere_residues(radius): active_atom = active_residue() if not active_atom: # check for list? - print "No active atom" + print("No active atom") return False else: centred_residue = active_atom[1:4] @@ -1692,11 +1692,11 @@ def weight_scale_from_refinement_results(rr): n_trials = 0 while results: av_rms_d = weight_scale_from_refinement_results(results) - print "av_rms_d:", av_rms_d + print("av_rms_d:", av_rms_d) if not av_rms_d: # check for number? return False if n_trials > 20: - print "BL INFO:: refinement did not converge, bailing out" + print("BL INFO:: refinement did not converge, bailing out") return False if ((target_auto_weighting_value * 1.1) > av_rms_d > (target_auto_weighting_value * 0.9)): # done @@ -1712,11 +1712,11 @@ def weight_scale_from_refinement_results(rr): current_weight = matrix_state() new_weight = (target_auto_weighting_value * current_weight) / av_rms_d - print "INFO:: setting refinement weight to {0!s} from * {1!s} / {2!s}".format( - new_weight, current_weight, av_rms_d) + print("INFO:: setting refinement weight to {0!s} from * {1!s} / {2!s}".format( + new_weight, current_weight, av_rms_d)) if (new_weight < 2): # weight refinement not converging - print "BL INFO:: not convering, weight to set was", new_weight + print("BL INFO:: not convering, weight to set was", new_weight) set_matrix(new_weight) results = refinement_func() n_trials += 1 @@ -1760,7 +1760,7 @@ def associate_pir_file(imol, chain_id, pir_file_name): if seq_text: assign_pir_sequence(imol, chain_id, seq_text) else: - print "WARNING:: associate-pir-file: bad text for", pir_file_name + print("WARNING:: associate-pir-file: bad text for", pir_file_name) # Associate the contents of a fasta file with a molecule. # @@ -1771,7 +1771,7 @@ def associate_fasta_file(imol, chain_id, pir_file_name): if seq_text: assign_fasta_sequence(imol, chain_id, seq_text) else: - print "WARNING:: associate-fasta-file: bad text for", pir_file_name + print("WARNING:: associate-fasta-file: bad text for", pir_file_name) # comma key hook @@ -1804,7 +1804,7 @@ def decode_key(key_val_name): # so need to convert these properly too if (not key_value or key_value >= 100000): # new python needs a long there!? I hope it wont harm old!? - new_val = long(ord(key_val_name)) + new_val = int(ord(key_val_name)) key_value = int(gtk.gdk.unicode_to_keyval(new_val)) return key_value except: @@ -1826,27 +1826,27 @@ def add_key_binding(name, key, thunk): keys = [elem[1] for elem in key_bindings] codes = [elem[0] for elem in key_bindings] if (key in std_keys): - print "INFO:: you shall not overwrite a standard key binding ({0!s})".format( - key) + print("INFO:: you shall not overwrite a standard key binding ({0!s})".format( + key)) else: if (type(key) is IntType): if (key in keys): - print "INFO:: you are overwriting existing key", key + print("INFO:: you are overwriting existing key", key) key_bindings.pop(keys.index(key)) key_bindings.append([key, key, name, thunk]) elif (type(key) is StringType): code = decode_key(key) if (code in codes): - print "INFO:: you are overwriting existing key (from code)", key + print("INFO:: you are overwriting existing key (from code)", key) key_bindings.pop(codes.index(code)) if "Control_" in key: code = decode_key(key[-1]) if (("Control_" in key) or not (code == -1)): key_bindings.append([code, key, name, thunk]) else: - print "INFO:: key {0!s} not found in code table".format(key) + print("INFO:: key {0!s} not found in code table".format(key)) else: - print "BL WARNING:: invalid key", key + print("BL WARNING:: invalid key", key) # general key press hook, not for public use!! @@ -1870,7 +1870,7 @@ def graphics_general_key_press_hook(key, control_flag=0): run_scheme_command("(graphics-general-key-press-hook " + str(key) + ")") - print "Key {0!s} not found in (python) key bindings".format(key) + print("Key {0!s} not found in (python) key bindings".format(key)) # Function requested by Mark White. @@ -1909,9 +1909,9 @@ def colour_from_number(obj): if len(current_line) == 7: colour = colour_from_number(current_line[-1]) try: - coords = map(float, current_line[0:-1]) + coords = list(map(float, current_line[0:-1])) except: - print "BL WARNING:: cannot make float from cordinates", current_line[0:-1] + print("BL WARNING:: cannot make float from cordinates", current_line[0:-1]) return to_generic_object_add_line(n, colour, 2, *coords) @@ -2179,7 +2179,7 @@ def get_monomer_and_dictionary(tlc): if ((not have_tlc_molecule) or (not have_dict_for_tlc)): return get_monomer(tlc) else: - print "we have dict and model for tlc already" + print("we have dict and model for tlc already") return have_tlc_molecule # @@ -2195,7 +2195,7 @@ def mutate_it(): match_ligand_torsions(imol_ligand, imol, chain_id_in, resno) delete_residue(imol, chain_id_in, resno, "") new_chain_id_info = merge_molecules([imol_ligand], imol) - print "INFO:: new_chain_id_info: ", new_chain_id_info + print("INFO:: new_chain_id_info: ", new_chain_id_info) merge_status = new_chain_id_info[0] if merge_status == 1: new_chain_id = new_chain_id_info[1] @@ -2214,7 +2214,7 @@ def mutate_it(): 'PTR': [" CZ ", " OH "], 'SEP': [" CB ", " OG "], 'TPO': [" CB ", " OG1"]} - if tlc in phos_dir.keys(): + if tlc in list(phos_dir.keys()): dir_atoms = phos_dir[tlc] else: dir_atoms = False @@ -2231,7 +2231,7 @@ def mutate_it(): else: # guess merge failed!?! - print "BL WARNING:: merge failed!?" + print("BL WARNING:: merge failed!?") # main line # @@ -2242,16 +2242,16 @@ def mutate_it(): if (imol_map == -1): map_mols = map_molecule_list() if not map_mols: - print "BL WARNING:: no valid maps around! Cannot mutate." + print("BL WARNING:: no valid maps around! Cannot mutate.") else: # BL says:: I dunno how to wait for the input from map selection since there is no return # waiting for mouse/keyboard input may be an option but no curses on windows, maybe # fix later, for now we use the first map # show_select_map_dialog() if len(map_mols) > 1: - print "BL INFO:: we use the first map! If you wanna use another one, please select from Model/Fit/Refine" + print("BL INFO:: we use the first map! If you wanna use another one, please select from Model/Fit/Refine") else: - print "BL INFO:: no refinement map set, will set first one for you!" + print("BL INFO:: no refinement map set, will set first one for you!") set_imol_refinement_map(map_mols[0]) mutate_it() else: @@ -2414,8 +2414,8 @@ def sanitise_alt_confs_active_residue(): def print_molecule_names(): - map(lambda molecule_number: printf(" {0!s} {1!s}\n".format(molecule_number, molecule_name(molecule_number))), - molecule_number_list()) + list(map(lambda molecule_number: printf(" {0!s} {1!s}\n".format(molecule_number, molecule_name(molecule_number))), + molecule_number_list())) # save the dialog positions to the coot_dialog_positions.py file in ./coot-preferences # @@ -2439,14 +2439,14 @@ def dump_positions_to_file(positions, preferences=False): if (not os.path.isdir(init_dir)): return False port = open(init_file, 'w') - print "BL INFO:: writing dialog positions to .coot-preferences/saved_dialog_positions.py" + print("BL INFO:: writing dialog positions to .coot-preferences/saved_dialog_positions.py") else: init_file = os.path.join(os.getenv(home), ".coot.py") if (not os.path.isfile(init_file)): return False port = open(init_file, 'a') - print "BL INFO:: writing dialog positions to .coot.py" + print("BL INFO:: writing dialog positions to .coot.py") if port: @@ -2461,14 +2461,14 @@ def dump_positions_to_file(positions, preferences=False): port.write("# -------------------------") port.close() else: - print "BL ERROR:: no valid port to write to!" + print("BL ERROR:: no valid port to write to!") # main line state_file = "0-coot.state.py" save_state() if (not os.path.isfile(state_file)): - print "Ooops {0!s} does not exist (either guile enabled or problem writing the file".format( - state_file) + print("Ooops {0!s} does not exist (either guile enabled or problem writing the file".format( + state_file)) else: port = open("0-coot.state.py", 'r') try: @@ -2478,10 +2478,10 @@ def dump_positions_to_file(positions, preferences=False): positions = [] for line in lines: if ("_dialog_position" in line): - print " Adding dialog position: ", line + print(" Adding dialog position: ", line) positions.append(line) elif ("set_go_to_atom_window_position" in line): - print " Adding dialog position: ", line + print(" Adding dialog position: ", line) positions.append(line) port.close() @@ -2541,8 +2541,8 @@ def remove_line_containing_from_file(remove_str_ls, filename): lines = port.readlines() port.close() else: - print "BL INFO:: no {0!s} file, so cannot remove line".format( - init_file) + print("BL INFO:: no {0!s} file, so cannot remove line".format( + init_file)) lines = [] if (lines): patt = string.join(remove_str_ls, '|') @@ -2579,7 +2579,7 @@ def rotate_colour_map(col, degrees): n_col = n_colours sigma = map_sigma(imol) - print "range n_col returns: ", range(n_col) + print("range n_col returns: ", list(range(n_col))) for icol in range(n_col): new_map = copy_molecule(imol) @@ -2589,7 +2589,7 @@ def rotate_colour_map(col, degrees): set_last_map_colour( *rotate_colour_map(initial_colour, colour_range * frac)) else: - print "BL INFO:: {0!s} is not valid map".format(imol) + print("BL INFO:: {0!s} is not valid map".format(imol)) # simple enumeration @@ -2625,7 +2625,7 @@ def hilight_binding_site(imol, centre_residue_spec, hilight_colour, radius): bb_type, 6, draw_hydrogens_flag) - map(lambda spec: additional_representation_by_attributes(imol, + list(map(lambda spec: additional_representation_by_attributes(imol, spec[0], spec[1], spec[1], @@ -2633,7 +2633,7 @@ def hilight_binding_site(imol, centre_residue_spec, hilight_colour, radius): BALL_AND_STICK(), bb_type, 6, draw_hydrogens_flag), - other_residues) + other_residues)) highlight_binding_site = hilight_binding_site # typo? @@ -2679,7 +2679,7 @@ def get_ribose_residue_atom_name(imol, residue_spec, pucker_atom): r_info = residue_info( imol, residue_spec[0], residue_spec[1], residue_spec[2]) t_pucker_atom = pucker_atom[0:3] + "*" - if (pucker_atom in map(lambda at: at[0][0], r_info)): + if (pucker_atom in [at[0][0] for at in r_info]): return pucker_atom else: return t_pucker_atom @@ -2774,7 +2774,7 @@ def new_molecule_by_smiles_string(tlc_text, smiles_text): libcheck_exe_file = find_exe(libcheck_exe, "CCP4_BIN", "PATH") if (not libcheck_exe_file): - print " BL WARNING:: libcheck not found!" + print(" BL WARNING:: libcheck not found!") else: status = popen_command(libcheck_exe_file, [], libcheck_data_lines, log_file_name, True) @@ -2793,7 +2793,7 @@ def new_molecule_by_smiles_string(tlc_text, smiles_text): translate_molecule_by(imol, *sc_mc) read_cif_dictionary(cif_file_name) else: - print "OOPs.. libcheck returned exit status", status + print("OOPs.. libcheck returned exit status", status) # Generate restraints from the residue at the centre of the screen @@ -2828,10 +2828,10 @@ def prodrg_ify(imol, chain_id, res_no, ins_code): info_dialog( "Cannot find cprodrg, so no prodrg-ifying of ligand possible") else: - print "BL DEBUG:: now run prodrg with", prodrg_exe, \ + print("BL DEBUG:: now run prodrg with", prodrg_exe, \ "XYZIN", prodrg_xyzin,\ "XYZOUT", prodrg_xyzout,\ - "LIBOUT", prodrg_cif + "LIBOUT", prodrg_cif) status = popen_command(prodrg_exe, ["XYZIN", prodrg_xyzin, "XYZOUT", prodrg_xyzout, @@ -2992,8 +2992,8 @@ def match_md5sums(tar_file_name, target_md5sum_file_name): else: if not os.path.isfile(target_md5sum_file_name): #print "OOps! %s does not exist" %target_md5sum_file_name - print "OOps! {0!s} does not exist".format( - target_md5sum_file_name) + print("OOps! {0!s} does not exist".format( + target_md5sum_file_name)) return False else: target_md5_string = get_target_md5_string( @@ -3003,20 +3003,20 @@ def match_md5sums(tar_file_name, target_md5sum_file_name): md5_string = get_md5sum_string(tar_file_name) if not target_md5_string: # need to test if string? #print "OOps %s is not a string" %target_md5_string - print "OOps {0!s} is not a string".format( - target_md5_string) + print("OOps {0!s} is not a string".format( + target_md5_string)) return False else: if not md5_string: # as above #print "OOps %s is not a string" %md5_string - print "OOps {0!s} is not a string".format(md5_string) + print("OOps {0!s} is not a string".format(md5_string)) return False else: if not (target_md5_string == md5_string): #print "Oops: md5sums do not match %s %s. Doing nothing" \ # %(target_md5_string, md5_string) - print "Oops: md5sums do not match {0!s} {1!s}. Doing nothing".format( - target_md5_string, md5_string) + print("Oops: md5sums do not match {0!s} {1!s}. Doing nothing".format( + target_md5_string, md5_string)) return False else: return True @@ -3045,7 +3045,7 @@ def install_coot_tar_file(tar_file_name, use_tar=False): # with working dir !? current_dir = os.getcwd() os.chdir(pending_dir) - print "now current dir is", os.getcwd() + print("now current dir is", os.getcwd()) if use_tar: # non-pythonic popen_command("tar", ["xzf", a_tar_file_name], [], @@ -3096,7 +3096,7 @@ def get_md5sum_string(file_name): prefix = os.getenv("COOT_PREFIX") prefix = os.path.normpath(prefix) # FIXME do we need this? if not prefix: # do we need to check if prefix is string? - print "OOps! Can't find COOT_PREFIX" + print("OOps! Can't find COOT_PREFIX") return False else: pre_release_flag = "-pre" in coot_version() @@ -3141,7 +3141,7 @@ def get_md5sum_string(file_name): if set_file_name_func: set_file_name_func(tar_file_name) - print "INFO:: getting URL:", url + print("INFO:: getting URL:", url) if (use_curl): # this is for curl @@ -3156,7 +3156,7 @@ def get_md5sum_string(file_name): else: # this is for pythonic urllib # we have graphics here, grrrr, shouldnt - import urllib + import urllib.request, urllib.parse, urllib.error def progress_function(count, blockSize, totalSize): global pending_install_in_place @@ -3178,21 +3178,21 @@ def progress_function(count, blockSize, totalSize): sys.exit() try: - md5_url_local_file_name, md5_url_info = urllib.urlretrieve( + md5_url_local_file_name, md5_url_info = urllib.request.urlretrieve( md5_url, md5_tar_file_name) except: - print "BL ERROR:: could not download", md5_url + print("BL ERROR:: could not download", md5_url) return False try: - print "\n" - print "Downloading: {0!s}".format(tar_file_name) - url_local_file_name, url_info = urllib.urlretrieve( + print("\n") + print("Downloading: {0!s}".format(tar_file_name)) + url_local_file_name, url_info = urllib.request.urlretrieve( url, tar_file_name, progress_function) pending_install_in_place = "full" - print "\nDone" + print("\nDone") except: if not (pending_install_in_place == "cancelled"): - print "BL ERROR:: could not download", url + print("BL ERROR:: could not download", url) return False if not os.path.isfile(tar_file_name): @@ -3237,9 +3237,9 @@ def get_revision_from_string(stri): def get_url_as_string(my_url): - import urllib + import urllib.request, urllib.parse, urllib.error try: - s = urllib.urlopen(my_url).read() + s = urllib.request.urlopen(my_url).read() except: s = False # not sure if that's the right way return s @@ -3312,8 +3312,8 @@ def update_self(use_curl=False): else: coot_url = get_url_as_string(url) if not coot_url: - print "BL INFO:: could not get string from URL {0!s}, so no update".format( - url) + print("BL INFO:: could not get string from URL {0!s}, so no update".format( + url)) else: version_string = coot_split_version_string(coot_url) revision = get_revision_from_string(version_string) @@ -3348,12 +3348,12 @@ def threaded_func(): if curl_info: v1 = curl_info['content-length-download'] v2 = curl_info['size-download'] - if operator.isNumberType(v1): - if operator.isNumberType(v2): + if isinstance(v1, numbers.Number): + if isinstance(v2, numbers.Number): f = v2 / v1 #sys.stdout.write("\rProgress %3.2f%%" %(f*100)) # sys.stdout.flush() - print "{0:3.2f}%".format((f*100)) + print("{0:3.2f}%".format((f*100))) if f > 0.999: continue_status = False elif count >= 1500: # about 50 min @@ -3393,7 +3393,7 @@ def chiral_centre_inverter(): def residue_is_close_to_screen_centre_qm(imol, chain_id, res_no, ins_code): def square(x): return x * x rc = residue_centre(imol, chain_id, res_no, ins_code) - if not isinstance(rc, types.ListType): + if not isinstance(rc, list): return False else: sc = rotation_centre() @@ -3408,7 +3408,7 @@ def square(x): return x * x def get_drug_via_wikipedia(drug_name_in): - import urllib2 + import urllib.request, urllib.error, urllib.parse from xml.etree import ElementTree def get_redirected_drug_name(xml): @@ -3435,7 +3435,7 @@ def parse_wiki_drug_xml(tree, key, redirect=False): # a REDIRECT was found drug_bank_id = line[line.find("[[")+2:line.find("]]")] else: - print 'Oops! len rev_text is 0' + print('Oops! len rev_text is 0') return drug_bank_id @@ -3448,18 +3448,18 @@ def parse_wiki_drug_xml(tree, key, redirect=False): "&prop=revisions&rvprop=content" # we want to parse the Etree rather than xml as this is an addurlinfo thingy - xml = urllib2.urlopen(url) + xml = urllib.request.urlopen(url) xml_tree = ElementTree.parse(xml) mol_name = parse_wiki_drug_xml(xml_tree, "DrugBank *= ") if not isinstance(mol_name, str): - print "BL WARNING:: mol_name not a string (DrugBank entry from wikipedia)", mol_name + print("BL WARNING:: mol_name not a string (DrugBank entry from wikipedia)", mol_name) # try pubchem as fallback mol_name = parse_wiki_drug_xml(xml_tree, "PubChem *= ") if not isinstance(mol_name, str): - print "BL WARNING:: mol_name not a string (pubchem entry either)", mol_name + print("BL WARNING:: mol_name not a string (pubchem entry either)", mol_name) # so was there a redirect? # if so, get the name and call get_drug_via_wikipedia with it redirected_drug_name = get_redirected_drug_name(xml_tree) @@ -3512,7 +3512,7 @@ def get_SMILES_for_comp_id_from_pdbe(comp_id): info_dialog(msg) return False # use network then - print "BL INFO:: getting url:", url + print("BL INFO:: getting url:", url) state = coot_get_url(url, cif_file_name) if (state != 0): msg = "Problem downloading\n" + \ @@ -3578,7 +3578,7 @@ def file_to_preferences(filename): else: shutil.copyfile(ref_py, pref_file) if os.path.isfile(pref_file): - execfile(pref_file, globals()) + exec(compile(open(pref_file, "rb").read(), pref_file, 'exec'), globals()) # add terminal residue is the normal thing we do with an aligned # sequence, but also we can try ton find the residue type of a @@ -3594,7 +3594,7 @@ def using_gui(): if coot_has_guile(): ret = run_scheme_command("(defined? 'coot-main-menubar)") if not ret: - ret = globals().has_key("coot_python") # coot_main_menubar is not a global var + ret = "coot_python" in globals() # coot_main_menubar is not a global var return ret ############################################################################################ @@ -3657,7 +3657,7 @@ def reset_b_factor_active_residue(): active_atom = active_residue() if not active_atom: - print "No active atom" + print("No active atom") else: imol = active_atom[0] chain_id = active_atom[1] @@ -3709,8 +3709,8 @@ def find_exe(program_name, *args, **kwargs): # unix! May use subprocess at some point... # if the program is not found with which we use the usual way... if (os.name == 'posix'): - import commands - program_exe = commands.getoutput('which ' + program_name) + import subprocess + program_exe = subprocess.getoutput('which ' + program_name) if (os.path.isfile(program_exe)): return program_exe @@ -3737,7 +3737,7 @@ def find_exe(program_name, *args, **kwargs): else: tmp_ext = os.environ["PATHEXT"].split(os.pathsep) # list of extensions (no dot) only - extensions = map(lambda ext: ext[1:], tmp_ext) + extensions = [ext[1:] for ext in tmp_ext] if "only_extension" in kwargs: if kwargs["only_extension"]: @@ -3749,8 +3749,7 @@ def find_exe(program_name, *args, **kwargs): program_names = [program_name_noext] if extensions: - program_names = map(lambda ext: program_name_noext + "." + ext, - extensions) + program_names = [program_name_noext + "." + ext for ext in extensions] # usually we want to have the one with extension, if there is one program_names += [program_name_noext] @@ -3763,7 +3762,7 @@ def find_exe(program_name, *args, **kwargs): program_exe = os.path.join(search_path, file_name) if (os.path.isfile(program_exe)): if info: - print "BL INFO:: We found ", program_exe + print("BL INFO:: We found ", program_exe) return program_exe else: try: @@ -3772,12 +3771,12 @@ def find_exe(program_name, *args, **kwargs): program_exe = os.path.join(path, file_name) if (os.path.isfile(program_exe)): if info: - print "BL INFO:: We found ", program_exe + print("BL INFO:: We found ", program_exe) return program_exe except: if info: - print "BL WARNING:: {0!s} not defined!".format( - search_path) + print("BL WARNING:: {0!s} not defined!".format( + search_path)) # BL says: before we search everywhere we might want to ask # the user if he actually wishes to do so! @@ -3799,11 +3798,11 @@ def find_exe(program_name, *args, **kwargs): return program_exe else: if info: - print "BL INFO:: we don't search the whole disk for", program_name_noext + print("BL INFO:: we don't search the whole disk for", program_name_noext) if info: - print "BL WARNING:: We cannot find {0!s} anywhere! Program {1!s} won't run!".format( - program_name_noext, program_name_noext) + print("BL WARNING:: We cannot find {0!s} anywhere! Program {1!s} won't run!".format( + program_name_noext, program_name_noext)) return False # for running online docs @@ -3815,8 +3814,8 @@ def open_url(url): try: webbrowser.open(url, 1, 1) except: - print "BL WARNING:: Cannot open the URL {0!s} in webbrowser {1!s}!".format( - url, webbrowser.get()) + print("BL WARNING:: Cannot open the URL {0!s} in webbrowser {1!s}!".format( + url, webbrowser.get())) # to reload modules @@ -3824,20 +3823,20 @@ def reload_module(name): import os path = os.getenv('COOT_PYTHON_DIR') file = os.path.join(path, name) - execfile(file) + exec(compile(open(file, "rb").read(), file, 'exec')) # to make print a function: def printf(*args): for arg in args: - print arg, + print(arg, end=' ') # to print elements of a list: def printl(ls): - map(printf, ls) + list(map(printf, ls)) # Where cmd is e.g. "bltwish" # args is list, e.g. [loggraph, "refmac.log"] @@ -3865,8 +3864,8 @@ def run_concurrently(cmd, args=None, data_list=None, logfile=None, screen_flag=F cmd_execfile = "" if not(command_in_path_qm(cmd)): - print "command ", cmd, " not found in $PATH!" - print "BL INFO:: Maybe we'll find it somewhere else later..." + print("command ", cmd, " not found in $PATH!") + print("BL INFO:: Maybe we'll find it somewhere else later...") else: cmd_execfile = find_exe(cmd, "CCP4_BIN", "PATH") @@ -3897,8 +3896,8 @@ def run_concurrently(cmd, args=None, data_list=None, logfile=None, screen_flag=F pid = os.spawnv(os.P_NOWAIT, cmd_execfile, [cmd_execfile] + args) return pid else: - print "WARNING:: could not find {0!s}, so not running this program".format( - cmd) + print("WARNING:: could not find {0!s}, so not running this program".format( + cmd)) return False # python command to see if we have pygtk available @@ -3908,7 +3907,7 @@ def run_concurrently(cmd, args=None, data_list=None, logfile=None, screen_flag=F def coot_has_pygtk(): import sys - if ('pygtk' in sys.modules.keys()): + if ('pygtk' in list(sys.modules.keys())): return True else: return False @@ -3920,7 +3919,7 @@ def coot_has_pygtk(): def coot_has_gobject(): import sys - if ('gobject' in sys.modules.keys()): + if ('gobject' in list(sys.modules.keys())): return True else: return False @@ -4007,7 +4006,7 @@ def toggle_full_screen(widget=None): full_screen(0) else: # no alternative for now (could just go by state and change back and forth) - print "BL WARNING:: no widget" + print("BL WARNING:: no widget") def split_active_water(): @@ -4101,7 +4100,7 @@ def set_alt_conf_occ(imol, chain_id, res_no, ins_code, alt_conf_list): alt_conf_str, "occ", alt_conf_occ]) set_atom_attributes(change_list) else: - print "BL INFO:: no alt confs in residue", imol, chain_id, res_no, ins_code + print("BL INFO:: no alt confs in residue", imol, chain_id, res_no, ins_code) # simplyfy check for windows diff --git a/web/process_sqlite.py b/web/process_sqlite.py index 6c1511cf..c58599d5 100755 --- a/web/process_sqlite.py +++ b/web/process_sqlite.py @@ -117,16 +117,16 @@ def main(argv): opts, args = getopt.getopt( argv, 't:s:d:', ['targetID=', 'sqlitefile=', 'panddadir=']) except getopt.GetoptError as err: - print err - print 'process.py -t -s -d ' + print(err) + print('process.py -t -s -d ') sys.exit(2) if len(opts) < 3: - print 'Missing arguments:' - print 'process.py -t -s -d ' + print('Missing arguments:') + print('process.py -t -s -d ') sys.exit(2) for opt, arg in opts: if opt == '-h': - print 'process.py -t -s ' + print('process.py -t -s ') sys.exit() elif opt in ("-t", "--targetID"): targetID = arg @@ -316,13 +316,13 @@ def main(argv): rows = cur.fetchall() if not rows: - print '==> WARNING: none of your samples seems to be at least CompChem ready (4)' + print('==> WARNING: none of your samples seems to be at least CompChem ready (4)') return None - writer = csv.DictWriter(f, fieldnames=rows[1].keys()) + writer = csv.DictWriter(f, fieldnames=list(rows[1].keys())) writer.writeheader() for row in rows: # Make compound structure - print row['ModelName'], row['PANDDA_site_spider_plot'] + print(row['ModelName'], row['PANDDA_site_spider_plot']) compound = Chem.MolFromSmiles( row['CompoundSMILES'].encode("ascii")) Draw.MolToFile(compound, panddadir+'/compoundImages/' + @@ -344,12 +344,12 @@ def main(argv): shutil.copy(row['PANDDA_site_spider_plot'], panddadir+"/residueplots/"+row['ModelName']+".png") except (IOError, TypeError): - print '*** WARNING: cannot find PDB and/or MTZ of ' + \ - row['ModelName']+' ***' - print 'PDB bound :', row['RefinementBoundConformation'] - print 'MTZ :', row['RefinementMTZ_latest'] - print 'event map :', row['PANDDA_site_event_map'] - print 'spider plot:', row['PANDDA_site_spider_plot'] + print('*** WARNING: cannot find PDB and/or MTZ of ' + \ + row['ModelName']+' ***') + print('PDB bound :', row['RefinementBoundConformation']) + print('MTZ :', row['RefinementMTZ_latest']) + print('event map :', row['PANDDA_site_event_map']) + print('spider plot:', row['PANDDA_site_spider_plot']) pass # shutil.copy(row['RefinementPDB_latest'],panddadir+"/pdbs/"+row['ModelName']+".pdb") # if row['PANDDA_site_spider_plot'] is not None: @@ -377,14 +377,14 @@ def main(argv): "web/jscss/js/jquery.dataTables.min.js"), panddadir+"/js/jquery.dataTables.min.js") # Create zip files - print "Creating zipfile of PDBs..." + print("Creating zipfile of PDBs...") os.chdir(panddadir+"/pdbs") zf = zipfile.ZipFile("allPDBs.zip", "w") for pdb in glob.glob("*.pdb"): zf.write(pdb) zf.close() - print "Creatig zipfile of event maps..." + print("Creatig zipfile of event maps...") os.chdir("../maps") zf = zipfile.ZipFile("allEventMaps.zip", "w") for pdb in glob.glob("*.mtz"): From c5bd5716a31c09ddfb89d53e687c0a5a5a940338 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 13:31:16 +0000 Subject: [PATCH 119/358] Reformat with black --- XChemExplorer.py | 6820 ++++++++++------- gui_scripts/datasets_tab.py | 212 +- gui_scripts/deposition_tab.py | 390 +- gui_scripts/layout.py | 470 +- gui_scripts/maps_tab.py | 55 +- gui_scripts/overview_tab.py | 11 +- gui_scripts/pandda_tab.py | 283 +- gui_scripts/refinement_tab.py | 10 +- gui_scripts/settings_preferences.py | 1084 +-- gui_scripts/settings_tab.py | 202 +- gui_scripts/stylesheet.py | 14 +- helpers/assign_stereochemistry.py | 56 +- ...ange_residues_in_ground_and_bound-state.py | 49 +- helpers/create_png_of_compound.py | 9 +- helpers/find_best_fitting_ligand.py | 66 +- helpers/make_ligand_links_after_pandda.py | 14 +- helpers/merge_ligand_cif_files.py | 8 +- helpers/phenix_find_TLS_groups.py | 76 +- helpers/prepare_for_zenodo_upload.py | 125 +- helpers/reset_interesting_datasets.py | 78 +- helpers/reset_occupancy_protein_to_one.py | 34 +- .../reset_to_last_successful_refinement.py | 48 +- helpers/resort_ligand_atoms.py | 76 +- helpers/select_ground_state_dataset.py | 189 +- .../update_data_source_after_refinement.py | 355 +- .../update_data_source_for_new_cif_files.py | 51 +- .../update_data_source_for_new_dimple_pdb.py | 201 +- ...ate_data_source_for_new_dimple_twin_pdb.py | 225 +- helpers/update_pandda_status_flag.py | 19 +- helpers/update_status_flag.py | 5 +- lib/PuckDB.py | 13 +- lib/XChemCoot.py | 1504 ++-- lib/XChemCootBuster.py | 1815 +++-- lib/XChemCootNew.py | 1817 +++-- lib/XChemCootOld.py | 1074 +-- lib/XChemCootReference.py | 862 ++- lib/XChemCootTwin.py | 1803 +++-- lib/XChemDB.py | 3273 ++++---- lib/XChemDeposit.py | 2035 +++-- lib/XChemDialogs.py | 16 +- lib/XChemLigand.py | 3 +- lib/XChemLog.py | 86 +- lib/XChemMain.py | 2180 +++--- lib/XChemPANDDA.py | 2843 ++++--- lib/XChemPlots.py | 91 +- lib/XChemProcess.py | 365 +- lib/XChemRefine.py | 2610 ++++--- lib/XChemThread.py | 4064 ++++++---- lib/XChemToolTips.py | 358 +- lib/XChemUtils.py | 4375 ++++++----- lib/coot_utils_XChem.py | 1589 ++-- web/XChemWeb.py | 829 +- web/process_sqlite.py | 368 +- 53 files changed, 26824 insertions(+), 18384 deletions(-) diff --git a/XChemExplorer.py b/XChemExplorer.py index 1553a233..879d121c 100755 --- a/XChemExplorer.py +++ b/XChemExplorer.py @@ -15,7 +15,7 @@ ######################################################################################################################## # solve gtk startup error -#import gtk +# import gtk # gtk.set_interactive(False) @@ -48,9 +48,9 @@ from datetime import datetime from PyQt4 import QtGui, QtCore, QtWebKit -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'web')) -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "web")) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) class XChemExplorer(QtGui.QApplication): @@ -94,8 +94,10 @@ def start_GUI(self): self.backup_soakDB() def backup_soakDB(self): - XChemMain.backup_soakDB(os.path.join( - self.database_directory, self.data_source_file), self.xce_logfile) + XChemMain.backup_soakDB( + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile, + ) def checkLabXChemDir(self): dirCheck = QtGui.QMessageBox() @@ -103,9 +105,10 @@ def checkLabXChemDir(self): vbox = QtGui.QVBoxLayout() try: warning = ( - 'Are you sure you want to launch XCE here:\n\n' - + self.labxchem_directory_current+'\n\n' - 'If this is not where you should be running XCE, please close!\n' + "Are you sure you want to launch XCE here:\n\n" + + self.labxchem_directory_current + + "\n\n" + "If this is not where you should be running XCE, please close!\n" ) except AttributeError: return @@ -117,32 +120,40 @@ def checkLabXChemDir(self): def datasource_menu_reload_samples(self): self.update_log.insert( - 'reading samples from data source: ' + os.path.join(self.database_directory, self.data_source_file)) + "reading samples from data source: " + + os.path.join(self.database_directory, self.data_source_file) + ) self.update_status_bar( - 'reading samples from data source: ' + os.path.join(self.database_directory, self.data_source_file)) + "reading samples from data source: " + + os.path.join(self.database_directory, self.data_source_file) + ) self.update_header_and_data_from_datasource() self.update_all_tables() self.overview_datasource_table.resizeColumnsToContents() # function to create new datasource def create_new_data_source(self): - file_name = str(QtGui.QFileDialog.getSaveFileName( - self.window, 'Save file', self.database_directory)) + file_name = str( + QtGui.QFileDialog.getSaveFileName( + self.window, "Save file", self.database_directory + ) + ) # make sure that the file always has .sqlite extension - if file_name.rfind('.') != -1: - file_name = file_name[:file_name.rfind('.')] + '.sqlite' + if file_name.rfind(".") != -1: + file_name = file_name[: file_name.rfind(".")] + ".sqlite" else: - file_name = file_name + '.sqlite' + file_name = file_name + ".sqlite" self.db = XChemDB.data_source(file_name) - print('==> XCE: creating new data source') + print("==> XCE: creating new data source") self.db.create_empty_data_source_file() self.db.create_missing_columns() - self.database_directory = file_name[:file_name.rfind('/')] - self.data_source_file = file_name[file_name.rfind('/') + 1:] - self.data_source_file_label.setText(os.path.join( - self.database_directory, self.data_source_file)) - self.settings['database_directory'] = self.database_directory - self.settings['data_source'] = self.data_source_file + self.database_directory = file_name[: file_name.rfind("/")] + self.data_source_file = file_name[file_name.rfind("/") + 1 :] + self.data_source_file_label.setText( + os.path.join(self.database_directory, self.data_source_file) + ) + self.settings["database_directory"] = self.database_directory + self.settings["data_source"] = self.data_source_file self.data_source_set = True self.datasource_menu_reload_samples() @@ -154,12 +165,13 @@ def create_new_data_source(self): def continously_check_for_new_data_collection(self, state): self.timer_to_check_for_new_data_collection.timeout.connect( - lambda: self.check_for_new_autoprocessing_or_rescore(False)) + lambda: self.check_for_new_autoprocessing_or_rescore(False) + ) if state == QtCore.Qt.Checked: - print('==> XCE: checking automatically every 120s for new data collection') + print("==> XCE: checking automatically every 120s for new data collection") self.timer_to_check_for_new_data_collection.start(120000) else: - print('==> XCE: stopped checking for new data collections') + print("==> XCE: stopped checking for new data collections") self.timer_to_check_for_new_data_collection.stop() def target_selection_combobox_activated(self, text): @@ -167,115 +179,134 @@ def target_selection_combobox_activated(self, text): def select_diffraction_data_directory(self): self.diffraction_data_directory = str( - QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) - self.diffraction_data_dir_label.setText( - self.diffraction_data_directory) - self.settings['diffraction_data_directory'] = self.diffraction_data_directory + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory") + ) + self.diffraction_data_dir_label.setText(self.diffraction_data_directory) + self.settings["diffraction_data_directory"] = self.diffraction_data_directory self.update_log.insert( - 'setting diffraction data directory to ' + self.diffraction_data_directory) + "setting diffraction data directory to " + self.diffraction_data_directory + ) def search_for_datasets(self): - self.update_log.insert( - 'search diffraction data directory for datasets...') - print(('will search ' + str(self.diffraction_data_directory))) + self.update_log.insert("search diffraction data directory for datasets...") + print(("will search " + str(self.diffraction_data_directory))) self.work_thread = XChemMain.find_diffraction_image_directory_fast( - self.diffraction_data_directory) + self.diffraction_data_directory + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL("update_datasets_reprocess_table"), - self.update_datasets_reprocess_table) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_datasets_reprocess_table"), + self.update_datasets_reprocess_table, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() - #self.work_thread = self.update_datasets_reprocess_table(self.diffraction_data_directory) + # self.work_thread = self.update_datasets_reprocess_table(self.diffraction_data_directory) def translate_datasetID_to_sampleID(self): translate = QtGui.QMessageBox() translateLayout = translate.layout() - self.translate_datasetID_to_sampleID_file = '-' + self.translate_datasetID_to_sampleID_file = "-" vbox = QtGui.QVBoxLayout() - button = QtGui.QPushButton('Open CSV') - button.clicked.connect( - self.open_csv_file_translate_datasetID_to_sampleID) + button = QtGui.QPushButton("Open CSV") + button.clicked.connect(self.open_csv_file_translate_datasetID_to_sampleID) vbox.addWidget(button) self.translate_datasetID_to_sampleID_csv_label = QtGui.QLabel( - self.translate_datasetID_to_sampleID_file) + self.translate_datasetID_to_sampleID_file + ) vbox.addWidget(self.translate_datasetID_to_sampleID_csv_label) translateLayout.addLayout(vbox, 0, 0) - translate.addButton(QtGui.QPushButton('OK'), QtGui.QMessageBox.YesRole) - translate.addButton(QtGui.QPushButton('Cancel'), - QtGui.QMessageBox.RejectRole) + translate.addButton(QtGui.QPushButton("OK"), QtGui.QMessageBox.YesRole) + translate.addButton(QtGui.QPushButton("Cancel"), QtGui.QMessageBox.RejectRole) reply = translate.exec_() if reply == 0: if os.path.isfile(self.translate_datasetID_to_sampleID_file): trans_dict = {} for line in open(self.translate_datasetID_to_sampleID_file): - if len(line.split(',')) == 2: - dataset = line.split(',')[0] - new_sample_id = line.split(',')[1] + if len(line.split(",")) == 2: + dataset = line.split(",")[0] + new_sample_id = line.split(",")[1] trans_dict[dataset] = new_sample_id if len(trans_dict) >= 1: allRows = self.datasets_reprocess_table.rowCount() for row in range(0, allRows): dataset_id = str( - self.datasets_reprocess_table.item(row, 0).text()) + self.datasets_reprocess_table.item(row, 0).text() + ) sample_id = str( - self.datasets_reprocess_table.item(row, 1).text()) + self.datasets_reprocess_table.item(row, 1).text() + ) if dataset_id in trans_dict: cell_text = QtGui.QTableWidgetItem() cell_text.setText(trans_dict[dataset_id]) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.datasets_reprocess_table.setItem( - row, 1, cell_text) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) + self.datasets_reprocess_table.setItem(row, 1, cell_text) self.update_log.insert( - 'dataset: {0!s} -> changing sampleID to: {1!s}'.format(dataset_id, - trans_dict[dataset_id])) + "dataset: {0!s} -> changing sampleID to: {1!s}".format( + dataset_id, trans_dict[dataset_id] + ) + ) def select_sample_for_xia2(self): indexes = self.datasets_reprocess_table.selectionModel().selectedRows() for index in sorted(indexes): - xtal = str(self.datasets_reprocess_table.item( - index.row(), 1).text()) + xtal = str(self.datasets_reprocess_table.item(index.row(), 1).text()) print((xtal, self.diffraction_data_table_dict[xtal][0])) - self.update_log.insert( - '{0!s} marked for reprocessing'.format(index.row())) + self.update_log.insert("{0!s} marked for reprocessing".format(index.row())) self.diffraction_data_table_dict[xtal][0].setChecked(True) def select_reprocess_reference_mtz(self): self.update_log.insert( - 'trying to set new reference mtz file for reprocessing with xia2') - file_name = str(QtGui.QFileDialog.getOpenFileName( - self.window, 'Select file', self.database_directory)) + "trying to set new reference mtz file for reprocessing with xia2" + ) + file_name = str( + QtGui.QFileDialog.getOpenFileName( + self.window, "Select file", self.database_directory + ) + ) if os.path.isfile(file_name): - if file_name.endswith('.mtz'): + if file_name.endswith(".mtz"): self.diffraction_data_reference_mtz = file_name self.update_log.insert( - 'new reference file for data processing with xia2: ' + self.diffraction_data_reference_mtz) + "new reference file for data processing with xia2: " + + self.diffraction_data_reference_mtz + ) self.reprocess_reference_mtz_file_label.setText( - self.diffraction_data_reference_mtz) + self.diffraction_data_reference_mtz + ) else: self.update_log.insert( - 'this does not seem to be a mtz file: ' + file_name) + "this does not seem to be a mtz file: " + file_name + ) def check_for_new_autoprocessing_or_rescore(self, rescore_only): - self.update_log.insert('checking for new data collection') + self.update_log.insert("checking for new data collection") start_thread = False if rescore_only: # first pop up a warning message as this will overwrite all user selections msgBox = QtGui.QMessageBox() msgBox.setText( - "*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?") - msgBox.addButton(QtGui.QPushButton('Yes'), - QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton( - 'No'), QtGui.QMessageBox.RejectRole) + "*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?" + ) + msgBox.addButton(QtGui.QPushButton("Yes"), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.RejectRole) reply = msgBox.exec_() if reply == 0: start_thread = True @@ -285,50 +316,63 @@ def check_for_new_autoprocessing_or_rescore(self, rescore_only): start_thread = True if start_thread: - if self.target == '=== SELECT TARGET ===': + if self.target == "=== SELECT TARGET ===": msgBox = QtGui.QMessageBox() - warning = ('*** WARNING ***\n' - 'Please select a target or\n' - 'select "=== project directory ===" if you want to read reprocessed results\n' - 'In case target list is empty, make sure that you have selected the actual\n' - 'data collection visit (e.g. /dls/i04-1/data/2018/lb18145-70)') + warning = ( + "*** WARNING ***\n" + "Please select a target or\n" + 'select "=== project directory ===" if you want to read reprocessed results\n' + "In case target list is empty, make sure that you have selected the actual\n" + "data collection visit (e.g. /dls/i04-1/data/2018/lb18145-70)" + ) msgBox.setText(warning) start_thread = False -# msgBox.setText(warning) -# msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) -# msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) -# reply = msgBox.exec_(); -# if reply == 0: -# start_thread = True -# else: -# start_thread = False -# else: -# start_thread = True + # msgBox.setText(warning) + # msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) + # msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) + # reply = msgBox.exec_(); + # if reply == 0: + # start_thread = True + # else: + # start_thread = False + # else: + # start_thread = True if start_thread: - self.work_thread = XChemThread.read_autoprocessing_results_from_disc(self.visit_list, - self.target, - self.reference_file_list, - self.database_directory, - self.data_collection_dict, - self.preferences, - self.datasets_summary_file, - self.initial_model_directory, - rescore_only, - self.acceptable_low_resolution_limit_for_data, - os.path.join(self.database_directory, - self.data_source_file), - self.xce_logfile) + self.work_thread = XChemThread.read_autoprocessing_results_from_disc( + self.visit_list, + self.target, + self.reference_file_list, + self.database_directory, + self.data_collection_dict, + self.preferences, + self.datasets_summary_file, + self.initial_model_directory, + rescore_only, + self.acceptable_low_resolution_limit_for_data, + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("create_widgets_for_autoprocessing_results_only"), - self.create_widgets_for_autoprocessing_results_only) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("create_widgets_for_autoprocessing_results_only"), + self.create_widgets_for_autoprocessing_results_only, + ) self.work_thread.start() ################################################################################################################# @@ -343,68 +387,91 @@ def update_gdaLog_parsing_instructions_and_score(self, gdaLogInstructions): self.select_best_autoprocessing_result() def read_pinIDs_from_gda_logs(self): - self.update_log.insert('reading pinIDs from gda logfiles...') - visit, beamline = XChemMain.getVisitAndBeamline( - self.beamline_directory) - self.work_thread = XChemThread.read_pinIDs_from_gda_logs(beamline, - visit, - os.path.join( - self.database_directory, - self.data_source_file), - self.gdaLogInstructions, - self.xce_logfile) + self.update_log.insert("reading pinIDs from gda logfiles...") + visit, beamline = XChemMain.getVisitAndBeamline(self.beamline_directory) + self.work_thread = XChemThread.read_pinIDs_from_gda_logs( + beamline, + visit, + os.path.join(self.database_directory, self.data_source_file), + self.gdaLogInstructions, + self.xce_logfile, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("update_gdaLog_parsing_instructions_and_score"), - self.update_gdaLog_parsing_instructions_and_score) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_gdaLog_parsing_instructions_and_score"), + self.update_gdaLog_parsing_instructions_and_score, + ) self.work_thread.start() def check_for_new_autoprocessing_results(self): - self.update_log.insert('checking for new data collection') - if self.target == '=== SELECT TARGET ===': + self.update_log.insert("checking for new data collection") + if self.target == "=== SELECT TARGET ===": self.update_log.error( - 'NO TARGET SELECTED, PLEASE SELECT A TARGET AND TRY AGAIN!') + "NO TARGET SELECTED, PLEASE SELECT A TARGET AND TRY AGAIN!" + ) start_thread = False - elif self.target == '=== project directory ===': + elif self.target == "=== project directory ===": processedDir = self.initial_model_directory start_thread = True -# elif self.read_agamemnon.isChecked(): -# tmp = '/'.join(self.beamline_directory.split('/')[:6]) -# processedDir = tmp[:tmp.rfind('-')] -## processedDir = os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*/processed/agamemnon/'+self.target) -## processedDir = os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*/processed/*/'+self.target) -# start_thread = True + # elif self.read_agamemnon.isChecked(): + # tmp = '/'.join(self.beamline_directory.split('/')[:6]) + # processedDir = tmp[:tmp.rfind('-')] + ## processedDir = os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*/processed/agamemnon/'+self.target) + ## processedDir = os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*/processed/*/'+self.target) + # start_thread = True else: processedDir = os.path.join( - self.beamline_directory, 'processed', self.target) + self.beamline_directory, "processed", self.target + ) start_thread = True if start_thread: # processedDir=os.path.join(self.beamline_directory,'processed',self.target) - self.work_thread = XChemThread.read_write_autoprocessing_results_from_to_disc(processedDir, - os.path.join( - self.database_directory, - self.data_source_file), - self.initial_model_directory, - self.xce_logfile, - self.target, - self.read_agamemnon.isChecked()) + self.work_thread = ( + XChemThread.read_write_autoprocessing_results_from_to_disc( + processedDir, + os.path.join(self.database_directory, self.data_source_file), + self.initial_model_directory, + self.xce_logfile, + self.target, + self.read_agamemnon.isChecked(), + ) + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("read_pinIDs_from_gda_logs"), - self.read_pinIDs_from_gda_logs) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("read_pinIDs_from_gda_logs"), + self.read_pinIDs_from_gda_logs, + ) self.work_thread.start() def select_best_autoprocessing_result(self): @@ -412,11 +479,10 @@ def select_best_autoprocessing_result(self): # first pop up a warning message as this will overwrite all user selections msgBox = QtGui.QMessageBox() msgBox.setText( - "*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?") - msgBox.addButton(QtGui.QPushButton('Yes'), - QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton( - 'No'), QtGui.QMessageBox.RejectRole) + "*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?" + ) + msgBox.addButton(QtGui.QPushButton("Yes"), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.RejectRole) reply = msgBox.exec_() if reply != 0: start_thread = False @@ -426,43 +492,62 @@ def select_best_autoprocessing_result(self): start_thread = True if start_thread: - self.update_log.insert('selecting best autoprocessing result') + self.update_log.insert("selecting best autoprocessing result") self.update_log.insert( - 'samples where user made manual changes will be ignored!') + "samples where user made manual changes will be ignored!" + ) - if self.target == '=== project directory ===': + if self.target == "=== project directory ===": processedDir = self.initial_model_directory else: processedDir = os.path.join( - self.beamline_directory, 'processed', self.target) + self.beamline_directory, "processed", self.target + ) visit, beamline = XChemMain.getVisitAndBeamline(processedDir) if self.read_agamemnon.isChecked(): visit = [] for v in glob.glob( - os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*')): - visit.append(v[v.rfind('/') + 1:]) - - self.work_thread = XChemThread.choose_autoprocessing_outcome(os.path.join(self.database_directory, - self.data_source_file), - visit, - self.reference_file_list, - self.preferences, - self.initial_model_directory, - self.rescore, - self.xce_logfile, - self.read_agamemnon.isChecked()) + os.path.join( + self.beamline_directory[ + : self.beamline_directory.rfind("-") + 1 + ] + + "*" + ) + ): + visit.append(v[v.rfind("/") + 1 :]) + + self.work_thread = XChemThread.choose_autoprocessing_outcome( + os.path.join(self.database_directory, self.data_source_file), + visit, + self.reference_file_list, + self.preferences, + self.initial_model_directory, + self.rescore, + self.xce_logfile, + self.read_agamemnon.isChecked(), + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("populate_datasets_summary_table_NEW"), - self.populate_datasets_summary_table_NEW) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("populate_datasets_summary_table_NEW"), + self.populate_datasets_summary_table_NEW, + ) self.work_thread.start() # < end @@ -475,10 +560,9 @@ def select_best_autoprocessing_result(self): #################################################################################################################### def set_new_reference_if_applicable(self): - print('hallo') - reference_root = str( - self.reference_file_selection_combobox.currentText()) - pg_ref = '' + print("hallo") + reference_root = str(self.reference_file_selection_combobox.currentText()) + pg_ref = "" ucVol_ref = 0.0 for reference in self.reference_file_list: print((reference[0], reference_root)) @@ -488,36 +572,44 @@ def set_new_reference_if_applicable(self): break if ucVol_ref == 0.0: self.update_log.insert( - 'cannot set reference file since unit cell volume of reference pdb is 0!') + "cannot set reference file since unit cell volume of reference pdb is 0!" + ) return for xtal in self.initial_model_dimple_dict: reference_file_selection_combobox = self.initial_model_dimple_dict[xtal][1] self.populate_reference_combobox(reference_file_selection_combobox) db_dict = self.xtal_db_dict[xtal] - pg_xtal = db_dict['DataProcessingPointGroup'] - ucVol_xtal = db_dict['DataProcessingUnitCellVolume'] + pg_xtal = db_dict["DataProcessingPointGroup"] + ucVol_xtal = db_dict["DataProcessingUnitCellVolume"] try: - difference = math.fabs( - 1 - (float(ucVol_xtal) / float(ucVol_ref))) * 100 + difference = math.fabs(1 - (float(ucVol_xtal) / float(ucVol_ref))) * 100 except ValueError: self.update_log.insert( - xtal + ' -> cannot calculate unit cell volume difference') + xtal + " -> cannot calculate unit cell volume difference" + ) continue - if pg_xtal == pg_ref and difference < self.allowed_unitcell_difference_percent: + if ( + pg_xtal == pg_ref + and difference < self.allowed_unitcell_difference_percent + ): print((xtal, pg_xtal, ucVol_xtal)) index = reference_file_selection_combobox.findText( - reference_root, QtCore.Qt.MatchFixedString) + reference_root, QtCore.Qt.MatchFixedString + ) reference_file_selection_combobox.setCurrentIndex(index) self.update_log.insert( - xtal + ' -> setting ' + reference_root + ' as input PDB file for DIMPLE') + xtal + + " -> setting " + + reference_root + + " as input PDB file for DIMPLE" + ) def refresh_reference_file_list(self): - self.reference_file_list = self.get_reference_file_list(' ') - self.populate_reference_combobox( - self.reference_file_selection_combobox) + self.reference_file_list = self.get_reference_file_list(" ") + self.populate_reference_combobox(self.reference_file_selection_combobox) def on_context_menu_initial_model(self, point): # show context menu @@ -529,45 +621,50 @@ def on_context_menu_initial_model(self, point): # # #################################################################################################################### def select_pandda_input_template(self): - mtzin = '' - filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select Example PDB or MTZ File', - self.initial_model_directory, '*.pdb;;*.mtz') + mtzin = "" + filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter( + self.window, + "Select Example PDB or MTZ File", + self.initial_model_directory, + "*.pdb;;*.mtz", + ) filepath = str(tuple(filepath_temp)[0]) - pdbin = filepath.split('/')[-1] - if filepath.endswith('.pdb'): - pdbin = filepath.split('/')[-1] - mtzin_temp = pdbin.replace('.pdb', '.mtz') + pdbin = filepath.split("/")[-1] + if filepath.endswith(".pdb"): + pdbin = filepath.split("/")[-1] + mtzin_temp = pdbin.replace(".pdb", ".mtz") if os.path.isfile(filepath.replace(pdbin, mtzin_temp)): mtzin = mtzin_temp else: - mtzin = '' - if filepath.endswith('.mtz'): - mtzin = filepath.split('/')[-1] - pdbin_temp = pdbin.replace('.mtz', '.pdb') + mtzin = "" + if filepath.endswith(".mtz"): + mtzin = filepath.split("/")[-1] + pdbin_temp = pdbin.replace(".mtz", ".pdb") if os.path.isfile(filepath.replace(mtzin, pdbin_temp)): pdbin = pdbin_temp else: - pdbin = '' + pdbin = "" try: self.pandda_input_data_dir_entry.setText( - '/'+os.path.join(*filepath.split('/')[0:len(filepath.split('/'))-2])) + "/" + + os.path.join(*filepath.split("/")[0 : len(filepath.split("/")) - 2]) + ) except TypeError: - self.update_log.error('directory selection invalid') -# if len(filepath.split('/')) - len(self.initial_model_directory.split('/')) == 2: -# self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*')) -# elif len(filepath.split('/')) - len(self.initial_model_directory.split('/')) > 2: -# subdir = os.path.join( -# *filepath.split('/')[len(self.initial_model_directory.split('/')) + 1:len(filepath.split('/')) - 1]) -# self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*', subdir)) -# else: -# pass + self.update_log.error("directory selection invalid") + # if len(filepath.split('/')) - len(self.initial_model_directory.split('/')) == 2: + # self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*')) + # elif len(filepath.split('/')) - len(self.initial_model_directory.split('/')) > 2: + # subdir = os.path.join( + # *filepath.split('/')[len(self.initial_model_directory.split('/')) + 1:len(filepath.split('/')) - 1]) + # self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*', subdir)) + # else: + # pass self.pandda_pdb_style_entry.setText(pdbin) self.pandda_mtz_style_entry.setText(mtzin) def change_pandda_spg_label(self): - combo_text = str( - self.pandda_reference_file_selection_combobox.currentText()) + combo_text = str(self.pandda_reference_file_selection_combobox.currentText()) for file in self.reference_file_list: if file[0] == combo_text: self.pandda_reference_file_spg_label.setText(file[1]) @@ -583,129 +680,175 @@ def on_context_menu_pandda(self, point): # # #################################################################################################################### def export_to_html(self): - XChemWeb.export_to_html(self.html_export_directory, - self.initial_model_directory, - os.path.join(self.database_directory, - self.data_source_file), - self.xce_logfile).prepare('0') + XChemWeb.export_to_html( + self.html_export_directory, + self.initial_model_directory, + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile, + ).prepare("0") def export_to_html_CompChem(self): - XChemWeb.export_to_html(self.html_export_directory, - self.initial_model_directory, - os.path.join(self.database_directory, - self.data_source_file), - self.xce_logfile).prepare('4') + XChemWeb.export_to_html( + self.html_export_directory, + self.initial_model_directory, + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile, + ).prepare("4") def export_to_html_deposition_ready(self): - XChemWeb.export_to_html(self.html_export_directory, - self.initial_model_directory, - os.path.join(self.database_directory, - self.data_source_file), - self.xce_logfile).prepare('5') - -# self.update_log.insert('exporting contents of SQLite database into ' + self.html_export_directory) -# os.system( -# 'ccp4-python ' + os.getenv('XChemExplorer_DIR') + '/web/process_sqlite.py -t Summary -s ' + os.path.join( -# self.database_directory, self.data_source_file) + ' -d ' + self.html_export_directory) -# XChemWeb.create_ICM_input_file(self.html_export_directory, -# os.path.join(self.database_directory, self.data_source_file)) -# self.update_log.insert('open ICMpro:') -# self.update_log.insert('/dls/science/groups/i04-1/software/icm-3.8-5/icm64 -g') -# self.update_log.insert('open file browser and navigate to ' + self.html_export_directory) -# self.update_log.insert('drag and drop dsEvent_sqlite.icm into the main window') -# self.update_log.insert('the script will appear in the Workspace Panel') -# self.update_log.insert('right click on the script and select RUN') -# self.update_log.insert('be patient, this may take a while, depending on the number of events') -# self.status_bar.showMessage('please check terminal window for further information') - -# def select_ground_state_pdb(self): -# p = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', os.getcwd(),'*.pdb') -# pdb = str(tuple(p)[0]) -# self.ground_state_pdb_button_label.setText(pdb) + XChemWeb.export_to_html( + self.html_export_directory, + self.initial_model_directory, + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile, + ).prepare("5") + + # self.update_log.insert('exporting contents of SQLite database into ' + self.html_export_directory) + # os.system( + # 'ccp4-python ' + os.getenv('XChemExplorer_DIR') + '/web/process_sqlite.py -t Summary -s ' + os.path.join( + # self.database_directory, self.data_source_file) + ' -d ' + self.html_export_directory) + # XChemWeb.create_ICM_input_file(self.html_export_directory, + # os.path.join(self.database_directory, self.data_source_file)) + # self.update_log.insert('open ICMpro:') + # self.update_log.insert('/dls/science/groups/i04-1/software/icm-3.8-5/icm64 -g') + # self.update_log.insert('open file browser and navigate to ' + self.html_export_directory) + # self.update_log.insert('drag and drop dsEvent_sqlite.icm into the main window') + # self.update_log.insert('the script will appear in the Workspace Panel') + # self.update_log.insert('right click on the script and select RUN') + # self.update_log.insert('be patient, this may take a while, depending on the number of events') + # self.status_bar.showMessage('please check terminal window for further information') + + # def select_ground_state_pdb(self): + # p = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', os.getcwd(),'*.pdb') + # pdb = str(tuple(p)[0]) + # self.ground_state_pdb_button_label.setText(pdb) def select_ground_state_mtz(self): m = QtGui.QFileDialog.getOpenFileNameAndFilter( - self.window, 'Select File', os.getcwd(), '*.mtz') + self.window, "Select File", os.getcwd(), "*.mtz" + ) mtz = str(tuple(m)[0]) self.ground_state_mtz_button_label.setText(mtz) def add_ground_state_db(self): pdb, mtz = self.auto_select_ground_state_reference_PDB() if pdb != None: - db_dict = {'DimplePANDDApath': self.panddas_directory, - 'PDB_file': pdb, - 'MTZ_file': mtz} - self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, 'ground_state', 'ground_state', - db_dict) + db_dict = { + "DimplePANDDApath": self.panddas_directory, + "PDB_file": pdb, + "MTZ_file": mtz, + } + self.db.create_or_remove_missing_records_in_depositTable( + self.xce_logfile, "ground_state", "ground_state", db_dict + ) else: self.update_log.error( - 'could not find a suitable reference file; see messages above!') + "could not find a suitable reference file; see messages above!" + ) def auto_select_ground_state_reference_PDB(self): pdb = None mtz = None xtalList = [] - for dirs in glob.glob(os.path.join(self.panddas_directory, 'processed_datasets', '*')): - xtal = dirs[dirs.rfind('/')+1:] - if os.path.isfile(os.path.join(dirs, xtal+'-pandda-input.pdb')): - pdbHeader = parse().PDBheader(os.path.join(dirs, xtal+'-pandda-input.pdb')) + for dirs in glob.glob( + os.path.join(self.panddas_directory, "processed_datasets", "*") + ): + xtal = dirs[dirs.rfind("/") + 1 :] + if os.path.isfile(os.path.join(dirs, xtal + "-pandda-input.pdb")): + pdbHeader = parse().PDBheader( + os.path.join(dirs, xtal + "-pandda-input.pdb") + ) try: xtalList.append( - [xtal, float(pdbHeader['Rfree']), float(pdbHeader['ResolutionHigh'])]) + [ + xtal, + float(pdbHeader["Rfree"]), + float(pdbHeader["ResolutionHigh"]), + ] + ) except ValueError: self.update_log.error( - '%s: cannot read Rfree or Resolution from PDB header; skipping...') + "%s: cannot read Rfree or Resolution from PDB header; skipping..." + ) pass - self.update_log.insert('found %s PDB files in %s' % ( - str(len(xtalList)), os.path.join(self.panddas_directory, 'processed_datasets'))) + self.update_log.insert( + "found %s PDB files in %s" + % ( + str(len(xtalList)), + os.path.join(self.panddas_directory, "processed_datasets"), + ) + ) if len(xtalList) >= 10: self.update_log.insert( - 'sorting PDBs by Rfree and selecting the 10 with lowest value') + "sorting PDBs by Rfree and selecting the 10 with lowest value" + ) rfree = sorted(xtalList, key=lambda x: x[1])[:10] - self.update_log.insert('top 10 PDB files with lowest Rfree:') + self.update_log.insert("top 10 PDB files with lowest Rfree:") for item in rfree: - self.update_log.insert('%s: Rfree = %s | Resolution = %s' % ( - item[0], str(round(item[1], 3)), str(round(item[2], 2)))) - self.update_log.insert('selecting PDB with highest resolution') + self.update_log.insert( + "%s: Rfree = %s | Resolution = %s" + % (item[0], str(round(item[1], 3)), str(round(item[2], 2))) + ) + self.update_log.insert("selecting PDB with highest resolution") reso = sorted(rfree, key=lambda x: x[2])[:1] - self.update_log.insert('selected the following PDB file: %s: Rfree = %s | Resolution = %s' % ( - reso[0][0], str(round(reso[0][1], 3)), str(round(reso[0][2], 2)))) - pdb = os.path.join(self.panddas_directory, 'processed_datasets', - reso[0][0], reso[0][0]+'-pandda-input.pdb') - mtz = os.path.join(self.panddas_directory, 'processed_datasets', - reso[0][0], reso[0][0]+'-pandda-input.mtz') + self.update_log.insert( + "selected the following PDB file: %s: Rfree = %s | Resolution = %s" + % (reso[0][0], str(round(reso[0][1], 3)), str(round(reso[0][2], 2))) + ) + pdb = os.path.join( + self.panddas_directory, + "processed_datasets", + reso[0][0], + reso[0][0] + "-pandda-input.pdb", + ) + mtz = os.path.join( + self.panddas_directory, + "processed_datasets", + reso[0][0], + reso[0][0] + "-pandda-input.mtz", + ) else: - self.update_log.error('found less than 10 valid PDB files in %s' % os.path.join( - self.panddas_directory, 'processed_datasets')) + self.update_log.error( + "found less than 10 valid PDB files in %s" + % os.path.join(self.panddas_directory, "processed_datasets") + ) return pdb, mtz def prepare_ground_state_mmcif(self): - self.update_log.insert( - 'preparing mmcif file for apo structure deposition') - self.prepare_models_for_deposition_ligand_bound('ground_state') + self.update_log.insert("preparing mmcif file for apo structure deposition") + self.prepare_models_for_deposition_ligand_bound("ground_state") def open_icm(self): - self.update_log.insert('starting ICM...') + self.update_log.insert("starting ICM...") self.work_thread = XChemThread.start_ICM(self.html_export_directory) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def prepare_files_for_zenodo_upload(self): - self.update_log.insert('preparing files for ZENODO upload...') - os.system('ccp4-python ' + os.getenv( - 'XChemExplorer_DIR') + '/helpers/prepare_for_zenodo_upload.py ' + self.html_export_directory) + self.update_log.insert("preparing files for ZENODO upload...") + os.system( + "ccp4-python " + + os.getenv("XChemExplorer_DIR") + + "/helpers/prepare_for_zenodo_upload.py " + + self.html_export_directory + ) def update_html_for_zenodo_upload(self): try: uploadID = int(self.zenodo_upload_id_entry.text()) - self.update_log.insert('updating html files for ZENODO upload,...') - self.update_log.insert('ZENODO upload = ' + str(uploadID)) - os.system('ccp4-python ' + os.getenv( - 'XChemExplorer_DIR') + '/helpers/prepare_for_zenodo_upload.py {0!s} {1!s}'.format( - self.html_export_directory, uploadID)) + self.update_log.insert("updating html files for ZENODO upload,...") + self.update_log.insert("ZENODO upload = " + str(uploadID)) + os.system( + "ccp4-python " + + os.getenv("XChemExplorer_DIR") + + "/helpers/prepare_for_zenodo_upload.py {0!s} {1!s}".format( + self.html_export_directory, uploadID + ) + ) except ValueError: - self.update_log.insert('zenodo upload ID must be an integer!') + self.update_log.insert("zenodo upload ID must be an integer!") #################################################################################################################### # # @@ -713,118 +856,133 @@ def update_html_for_zenodo_upload(self): # # #################################################################################################################### def settings_button_clicked(self): - if self.sender().text() == 'Select Project Directory': + if self.sender().text() == "Select Project Directory": self.initial_model_directory = str( - QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) - self.initial_model_directory_label.setText( - self.initial_model_directory) - self.pandda_input_data_dir_entry.setText( - self.initial_model_directory) - self.settings['initial_model_directory'] = self.initial_model_directory - if self.sender().text() == 'Select Reference Structure Directory': + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory") + ) + self.initial_model_directory_label.setText(self.initial_model_directory) + self.pandda_input_data_dir_entry.setText(self.initial_model_directory) + self.settings["initial_model_directory"] = self.initial_model_directory + if self.sender().text() == "Select Reference Structure Directory": reference_directory_temp = str( - QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory") + ) if reference_directory_temp != self.reference_directory: self.reference_directory = reference_directory_temp - self.update_reference_files(' ') + self.update_reference_files(" ") self.reference_directory_label.setText(self.reference_directory) - self.settings['reference_directory'] = self.reference_directory - if self.sender().text() == 'Select Data Source File': - filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', - self.database_directory, '*.sqlite') + self.settings["reference_directory"] = self.reference_directory + if self.sender().text() == "Select Data Source File": + filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter( + self.window, "Select File", self.database_directory, "*.sqlite" + ) filepath = str(tuple(filepath_temp)[0]) - self.data_source_file = filepath.split('/')[-1] - self.database_directory = filepath[:filepath.rfind('/')] - self.settings['database_directory'] = self.database_directory - self.settings['data_source'] = os.path.join( - self.database_directory, self.data_source_file) + self.data_source_file = filepath.split("/")[-1] + self.database_directory = filepath[: filepath.rfind("/")] + self.settings["database_directory"] = self.database_directory + self.settings["data_source"] = os.path.join( + self.database_directory, self.data_source_file + ) write_enabled = self.check_write_permissions_of_data_source() if not write_enabled: self.data_source_set = False else: self.data_source_set = True - self.data_source_file_label.setText(os.path.join( - self.database_directory, self.data_source_file)) - self.db = XChemDB.data_source(os.path.join( - self.database_directory, self.data_source_file)) + self.data_source_file_label.setText( + os.path.join(self.database_directory, self.data_source_file) + ) + self.db = XChemDB.data_source( + os.path.join(self.database_directory, self.data_source_file) + ) self.db.create_missing_columns() self.datasource_menu_reload_samples() - if self.sender().text() == 'Select Data Collection Directory': - dir_name = str(QtGui.QFileDialog.getExistingDirectory( - self.window, "Select Directory")) + if self.sender().text() == "Select Data Collection Directory": + dir_name = str( + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory") + ) if dir_name != self.beamline_directory: self.beamline_directory = dir_name self.target_list, self.visit_list = XChemMain.get_target_and_visit_list( - self.beamline_directory, self.read_agamemnon.isChecked()) - self.populate_target_selection_combobox( - self.target_selection_combobox) + self.beamline_directory, self.read_agamemnon.isChecked() + ) + self.populate_target_selection_combobox(self.target_selection_combobox) self.beamline_directory_label.setText(self.beamline_directory) - self.settings['beamline_directory'] = self.beamline_directory - - if self.sender().text() == 'Select Existing\nCollection Summary File': - if self.datasets_summary_file != '': - filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', - self.datasets_summary_file[ - :self.datasets_summary_file.rfind( - '/')], '*.pkl') + self.settings["beamline_directory"] = self.beamline_directory + + if self.sender().text() == "Select Existing\nCollection Summary File": + if self.datasets_summary_file != "": + filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter( + self.window, + "Select File", + self.datasets_summary_file[: self.datasets_summary_file.rfind("/")], + "*.pkl", + ) else: - filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', os.getcwd(), - '*.pkl') + filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter( + self.window, "Select File", os.getcwd(), "*.pkl" + ) filepath = str(tuple(filepath_temp)[0]) self.datasets_summary_file = filepath - self.datasets_summary_file_label.setText( - self.datasets_summary_file) - self.settings['datasets_summary'] = self.datasets_summary_file - - if self.sender().text() == 'Assign New\nCollection Summary File': - if self.datasets_summary_file != '': - file_name = str(QtGui.QFileDialog.getSaveFileName(self.window, 'New file', - self.datasets_summary_file[ - :self.datasets_summary_file.rfind('/')])) + self.datasets_summary_file_label.setText(self.datasets_summary_file) + self.settings["datasets_summary"] = self.datasets_summary_file + + if self.sender().text() == "Assign New\nCollection Summary File": + if self.datasets_summary_file != "": + file_name = str( + QtGui.QFileDialog.getSaveFileName( + self.window, + "New file", + self.datasets_summary_file[ + : self.datasets_summary_file.rfind("/") + ], + ) + ) else: - file_name = str(QtGui.QFileDialog.getSaveFileName( - self.window, 'New file', self.current_directory)) + file_name = str( + QtGui.QFileDialog.getSaveFileName( + self.window, "New file", self.current_directory + ) + ) # make sure that the file always has .pkl extension - if str(file_name).rfind('.') != -1: - file_name = file_name[:file_name.rfind('.')] + '.pkl' + if str(file_name).rfind(".") != -1: + file_name = file_name[: file_name.rfind(".")] + ".pkl" else: - file_name = file_name + '.pkl' + file_name = file_name + ".pkl" self.datasets_summary_file = file_name - self.datasets_summary_file_label.setText( - self.datasets_summary_file) - self.settings['datasets_summary'] = self.datasets_summary_file + self.datasets_summary_file_label.setText(self.datasets_summary_file) + self.settings["datasets_summary"] = self.datasets_summary_file - if self.sender().text() == 'Select CCP4_SCR Directory': + if self.sender().text() == "Select CCP4_SCR Directory": self.ccp4_scratch_directory = str( - QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) - self.ccp4_scratch_directory_label.setText( - self.ccp4_scratch_directory) - self.settings['ccp4_scratch'] = self.ccp4_scratch_directory - if self.sender().text() == 'Select PanDDA Directory': + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory") + ) + self.ccp4_scratch_directory_label.setText(self.ccp4_scratch_directory) + self.settings["ccp4_scratch"] = self.ccp4_scratch_directory + if self.sender().text() == "Select PanDDA Directory": self.panddas_directory = str( - QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory") + ) self.panddas_directory_label.setText(self.panddas_directory) self.pandda_output_data_dir_entry.setText(self.panddas_directory) - self.ground_state_pandda_directory_label.setText( - self.panddas_directory) - print(('PANDDA', self.panddas_directory)) - self.settings['panddas_directory'] = self.panddas_directory + self.ground_state_pandda_directory_label.setText(self.panddas_directory) + print(("PANDDA", self.panddas_directory)) + self.settings["panddas_directory"] = self.panddas_directory self.layout_funcs.pandda_html(self) - if self.sender().text() == 'Select HTML Export Directory': + if self.sender().text() == "Select HTML Export Directory": self.html_export_directory = str( - QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) - self.html_export_directory_label.setText( - self.html_export_directory) - self.settings['html_export_directory'] = self.html_export_directory + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory") + ) + self.html_export_directory_label.setText(self.html_export_directory) + self.settings["html_export_directory"] = self.html_export_directory - if self.sender().text() == 'Select Group deposition Directory': + if self.sender().text() == "Select Group deposition Directory": self.group_deposit_directory = str( - QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory")) - self.group_deposition_directory_label.setText( - self.group_deposit_directory) - self.settings['group_deposit_directory'] = self.group_deposit_directory + QtGui.QFileDialog.getExistingDirectory(self.window, "Select Directory") + ) + self.group_deposition_directory_label.setText(self.group_deposit_directory) + self.settings["group_deposit_directory"] = self.group_deposit_directory # self.datasource_menu_reload_samples() @@ -834,14 +992,15 @@ def select_sample_for_dimple(self): indexes = self.maps_table.selectionModel().selectedRows() for index in sorted(indexes): xtal = str(self.maps_table.item(index.row(), 0).text()) - self.update_log.insert( - '{0!s} is marked for DIMPLE'.format(index.row())) + self.update_log.insert("{0!s} is marked for DIMPLE".format(index.row())) self.initial_model_dimple_dict[xtal][0].setChecked(True) def update_summary_plot(self): if self.data_source_set: - XChemPlots.summary_plot(os.path.join(self.database_directory, self.data_source_file), - self.overview_axes).update_overview() + XChemPlots.summary_plot( + os.path.join(self.database_directory, self.data_source_file), + self.overview_axes, + ).update_overview() self.overview_canvas.draw() def show_preferences(self): @@ -850,7 +1009,7 @@ def show_preferences(self): vbox = QtGui.QVBoxLayout() settings_hbox_filename_root = QtGui.QHBoxLayout() - filename_root_label = QtGui.QLabel('filename root:') + filename_root_label = QtGui.QLabel("filename root:") settings_hbox_filename_root.addWidget(filename_root_label) filename_root_input = QtGui.QLineEdit() filename_root_input.setFixedWidth(400) @@ -861,96 +1020,112 @@ def show_preferences(self): settings_hbox_adjust_allowed_unit_cell_difference = QtGui.QHBoxLayout() adjust_allowed_unit_cell_difference_label = QtGui.QLabel( - 'Max. Allowed Unit Cell Difference between Reference and Target (%):') + "Max. Allowed Unit Cell Difference between Reference and Target (%):" + ) settings_hbox_adjust_allowed_unit_cell_difference.addWidget( - adjust_allowed_unit_cell_difference_label) + adjust_allowed_unit_cell_difference_label + ) adjust_allowed_unit_cell_difference = QtGui.QLineEdit() adjust_allowed_unit_cell_difference.setFixedWidth(200) adjust_allowed_unit_cell_difference.setText( - str(self.allowed_unitcell_difference_percent)) + str(self.allowed_unitcell_difference_percent) + ) adjust_allowed_unit_cell_difference.textChanged[str].connect( - self.change_allowed_unitcell_difference_percent) + self.change_allowed_unitcell_difference_percent + ) settings_hbox_adjust_allowed_unit_cell_difference.addWidget( - adjust_allowed_unit_cell_difference) + adjust_allowed_unit_cell_difference + ) vbox.addLayout(settings_hbox_adjust_allowed_unit_cell_difference) settings_hbox_acceptable_low_resolution_limit = QtGui.QHBoxLayout() adjust_acceptable_low_resolution_limit_label = QtGui.QLabel( - 'Acceptable low resolution limit for datasets (in Angstrom):') + "Acceptable low resolution limit for datasets (in Angstrom):" + ) settings_hbox_acceptable_low_resolution_limit.addWidget( - adjust_acceptable_low_resolution_limit_label) + adjust_acceptable_low_resolution_limit_label + ) adjust_acceptable_low_resolution_limit = QtGui.QLineEdit() adjust_acceptable_low_resolution_limit.setFixedWidth(200) adjust_acceptable_low_resolution_limit.setText( - str(self.acceptable_low_resolution_limit_for_data)) + str(self.acceptable_low_resolution_limit_for_data) + ) adjust_acceptable_low_resolution_limit.textChanged[str].connect( - self.change_acceptable_low_resolution_limit) + self.change_acceptable_low_resolution_limit + ) settings_hbox_acceptable_low_resolution_limit.addWidget( - adjust_acceptable_low_resolution_limit) + adjust_acceptable_low_resolution_limit + ) vbox.addLayout(settings_hbox_acceptable_low_resolution_limit) vbox_data = QtGui.QVBoxLayout() vbox_data.addWidget( - QtGui.QLabel('Select amount of processed data you wish to copy to initial_model directory:')) + QtGui.QLabel( + "Select amount of processed data you wish to copy to initial_model directory:" + ) + ) self.preferences_data_to_copy_combobox = QtGui.QComboBox() for item in self.preferences_data_to_copy: self.preferences_data_to_copy_combobox.addItem(item[0]) self.preferences_data_to_copy_combobox.currentIndexChanged.connect( - self.preferences_data_to_copy_combobox_changed) + self.preferences_data_to_copy_combobox_changed + ) vbox_data.addWidget(self.preferences_data_to_copy_combobox) vbox.addLayout(vbox_data) vbox_select = QtGui.QVBoxLayout() - vbox_select.addWidget(QtGui.QLabel('Dataset Selection Mechanism:')) + vbox_select.addWidget(QtGui.QLabel("Dataset Selection Mechanism:")) self.preferences_selection_mechanism_combobox = QtGui.QComboBox() for item in self.preferences_selection_mechanism: self.preferences_selection_mechanism_combobox.addItem(item) self.preferences_selection_mechanism_combobox.currentIndexChanged.connect( - self.preferences_selection_mechanism_combobox_changed) + self.preferences_selection_mechanism_combobox_changed + ) index = self.preferences_selection_mechanism_combobox.findText( - self.preferences['dataset_selection_mechanism'], QtCore.Qt.MatchFixedString) + self.preferences["dataset_selection_mechanism"], QtCore.Qt.MatchFixedString + ) self.preferences_selection_mechanism_combobox.setCurrentIndex(index) vbox_select.addWidget(self.preferences_selection_mechanism_combobox) vbox.addLayout(vbox_select) -# vbox_inital_refinement = QtGui.QVBoxLayout() -# vbox_inital_refinement.addWidget(QtGui.QLabel('Initial Refinement Pipeline:')) -# self.preferences_initial_refinement_combobox = QtGui.QComboBox() -# for item in self.preferences_initial_refinement_pipeline: -# self.preferences_initial_refinement_combobox.addItem(item) -# self.preferences_initial_refinement_combobox.currentIndexChanged.connect( -# self.preferences_initial_refinement_combobox_changed) -# index = self.preferences_initial_refinement_combobox.findText(self.preferences['initial_refinement_pipeline'], QtCore.Qt.MatchFixedString) -# self.preferences_initial_refinement_combobox.setCurrentIndex(index) -# vbox_inital_refinement.addWidget(self.preferences_initial_refinement_combobox) -# vbox.addLayout(vbox_inital_refinement) + # vbox_inital_refinement = QtGui.QVBoxLayout() + # vbox_inital_refinement.addWidget(QtGui.QLabel('Initial Refinement Pipeline:')) + # self.preferences_initial_refinement_combobox = QtGui.QComboBox() + # for item in self.preferences_initial_refinement_pipeline: + # self.preferences_initial_refinement_combobox.addItem(item) + # self.preferences_initial_refinement_combobox.currentIndexChanged.connect( + # self.preferences_initial_refinement_combobox_changed) + # index = self.preferences_initial_refinement_combobox.findText(self.preferences['initial_refinement_pipeline'], QtCore.Qt.MatchFixedString) + # self.preferences_initial_refinement_combobox.setCurrentIndex(index) + # vbox_inital_refinement.addWidget(self.preferences_initial_refinement_combobox) + # vbox.addLayout(vbox_inital_refinement) vbox_restraints = QtGui.QVBoxLayout() - vbox_restraints.addWidget(QtGui.QLabel( - 'Restraints generation program:')) + vbox_restraints.addWidget(QtGui.QLabel("Restraints generation program:")) self.preferences_restraints_generation_combobox = QtGui.QComboBox() program_list = [] - if self.external_software['acedrg']: - program_list.append('acedrg') - self.restraints_program = 'acedrg' - if self.external_software['phenix.elbow']: - program_list.append('phenix.elbow') - if self.external_software['grade']: - program_list.append('grade') + if self.external_software["acedrg"]: + program_list.append("acedrg") + self.restraints_program = "acedrg" + if self.external_software["phenix.elbow"]: + program_list.append("phenix.elbow") + if self.external_software["grade"]: + program_list.append("grade") for item in program_list: self.preferences_restraints_generation_combobox.addItem(item) self.preferences_restraints_generation_combobox.currentIndexChanged.connect( - self.preferences_restraints_generation_combobox_changed) - index = self.preferences_restraints_generation_combobox.findText(self.restraints_program, - QtCore.Qt.MatchFixedString) + self.preferences_restraints_generation_combobox_changed + ) + index = self.preferences_restraints_generation_combobox.findText( + self.restraints_program, QtCore.Qt.MatchFixedString + ) self.preferences_restraints_generation_combobox.setCurrentIndex(index) - vbox_restraints.addWidget( - self.preferences_restraints_generation_combobox) + vbox_restraints.addWidget(self.preferences_restraints_generation_combobox) vbox.addLayout(vbox_restraints) hbox = QtGui.QHBoxLayout() - hbox.addWidget(QtGui.QLabel('XCE logfile:')) + hbox.addWidget(QtGui.QLabel("XCE logfile:")) self.xce_logfile_label = QtGui.QLabel(self.xce_logfile) hbox.addWidget(self.xce_logfile_label) button = QtGui.QPushButton("Change") @@ -960,31 +1135,32 @@ def show_preferences(self): settings_hbox_max_queue_jobs = QtGui.QHBoxLayout() adjust_max_queue_jobs_label = QtGui.QLabel( - 'Max. number of jobs running at once on DLS cluster:') + "Max. number of jobs running at once on DLS cluster:" + ) settings_hbox_max_queue_jobs.addWidget(adjust_max_queue_jobs_label) adjust_max_queue_jobs = QtGui.QLineEdit() adjust_max_queue_jobs.setFixedWidth(200) adjust_max_queue_jobs.setText(str(self.max_queue_jobs)) - adjust_max_queue_jobs.textChanged[str].connect( - self.change_max_queue_jobs) + adjust_max_queue_jobs.textChanged[str].connect(self.change_max_queue_jobs) settings_hbox_max_queue_jobs.addWidget(adjust_max_queue_jobs) vbox.addLayout(settings_hbox_max_queue_jobs) settings_hbox_remote_qsub = QtGui.QHBoxLayout() - remote_qsub_label = QtGui.QLabel('remote qsub:') + remote_qsub_label = QtGui.QLabel("remote qsub:") settings_hbox_remote_qsub.addWidget(remote_qsub_label) - self.remote_qsub_checkbox = QtGui.QCheckBox('use') + self.remote_qsub_checkbox = QtGui.QCheckBox("use") self.remote_qsub_checkbox.toggled.connect(self.run_qsub_remotely) settings_hbox_dimple_twin_mode = QtGui.QHBoxLayout() self.dimple_twin_mode_label_checkbox = QtGui.QCheckBox( - 'run DIMPLE in TWIN mode') - if self.preferences['dimple_twin_mode']: + "run DIMPLE in TWIN mode" + ) + if self.preferences["dimple_twin_mode"]: self.dimple_twin_mode_label_checkbox.setChecked(True) self.dimple_twin_mode_label_checkbox.toggled.connect( - self.dimple_change_twin_mode) - settings_hbox_dimple_twin_mode.addWidget( - self.dimple_twin_mode_label_checkbox) + self.dimple_change_twin_mode + ) + settings_hbox_dimple_twin_mode.addWidget(self.dimple_twin_mode_label_checkbox) vbox.addLayout(settings_hbox_dimple_twin_mode) if self.using_remote_qsub_submission: @@ -997,8 +1173,7 @@ def show_preferences(self): vbox.addLayout(settings_hbox_remote_qsub) hbox = QtGui.QHBoxLayout() - hbox.addWidget(QtGui.QLabel( - 'Additional CIF file for non-standard ligand:')) + hbox.addWidget(QtGui.QLabel("Additional CIF file for non-standard ligand:")) self.second_cif_file_label = QtGui.QLabel(self.second_cif_file) hbox.addWidget(self.second_cif_file_label) button = QtGui.QPushButton("Select") @@ -1006,61 +1181,62 @@ def show_preferences(self): hbox.addWidget(button) vbox.addLayout(hbox) - -# settings_hbox_max_queue_jobs.addWidget(adjust_max_queue_jobs_label) -# adjust_max_queue_jobs = QtGui.QLineEdit() -# adjust_max_queue_jobs.setFixedWidth(200) -# adjust_max_queue_jobs.setText(str(self.max_queue_jobs)) -# adjust_max_queue_jobs.textChanged[str].connect(self.change_max_queue_jobs) -# settings_hbox_max_queue_jobs.addWidget(adjust_max_queue_jobs) -# vbox.addLayout(settings_hbox_max_queue_jobs) -# -# apply_button = QtGui.QPushButton('Apply') -# apply_button.clicked.connect(self.run_qsub_remotely) -# settings_hbox_remote_qsub.addWidget(apply_button) + # settings_hbox_max_queue_jobs.addWidget(adjust_max_queue_jobs_label) + # adjust_max_queue_jobs = QtGui.QLineEdit() + # adjust_max_queue_jobs.setFixedWidth(200) + # adjust_max_queue_jobs.setText(str(self.max_queue_jobs)) + # adjust_max_queue_jobs.textChanged[str].connect(self.change_max_queue_jobs) + # settings_hbox_max_queue_jobs.addWidget(adjust_max_queue_jobs) + # vbox.addLayout(settings_hbox_max_queue_jobs) + # + # apply_button = QtGui.QPushButton('Apply') + # apply_button.clicked.connect(self.run_qsub_remotely) + # settings_hbox_remote_qsub.addWidget(apply_button) preferencesLayout.addLayout(vbox, 0, 0) preferences.exec_() -# def set_second_cif_file(self): -# mb = QtGui.QMessageBox() -# mbLayout = mb.layout() -# vbox = QtGui.QVBoxLayout() -# vbox.addWidget(QtGui.QLabel('CIF file to be merged into ligand CIF files:')) -# self.second_cif_file_label = QtGui.QLabel(self.second_cif_file) -# vbox.addWidget(self.second_cif_file_label) -# button = QtGui.QPushButton("Select") -# button.clicked.connect(self.set_second_cif_file) -# vbox.addWidget(button) -# mbLayout.addLayout(vbox, 0, 0) -# mb.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) -# mb.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) -# reply = mb.exec_(); + # def set_second_cif_file(self): + # mb = QtGui.QMessageBox() + # mbLayout = mb.layout() + # vbox = QtGui.QVBoxLayout() + # vbox.addWidget(QtGui.QLabel('CIF file to be merged into ligand CIF files:')) + # self.second_cif_file_label = QtGui.QLabel(self.second_cif_file) + # vbox.addWidget(self.second_cif_file_label) + # button = QtGui.QPushButton("Select") + # button.clicked.connect(self.set_second_cif_file) + # vbox.addWidget(button) + # mbLayout.addLayout(vbox, 0, 0) + # mb.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) + # mb.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) + # reply = mb.exec_(); def dimple_change_twin_mode(self): - if self.preferences['dimple_twin_mode']: + if self.preferences["dimple_twin_mode"]: self.update_log.insert( - 'changing preferences: turning off DIMPLE in TWIN mode') - self.preferences['dimple_twin_mode'] = False + "changing preferences: turning off DIMPLE in TWIN mode" + ) + self.preferences["dimple_twin_mode"] = False else: - self.update_log.insert( - 'changing preferences: changing DIMPLE to TWIN mode') - self.preferences['dimple_twin_mode'] = True + self.update_log.insert("changing preferences: changing DIMPLE to TWIN mode") + self.preferences["dimple_twin_mode"] = True def run_qsub_remotely(self): self.remote_qsub_submission = str(self.remote_qsub_command.text()) print((str(self.remote_qsub_submission))) if self.remote_qsub_checkbox.isChecked(): self.update_log.insert( - 'submitting jobs to remote machine with: %s' % self.remote_qsub_submission) - self.external_software['qsub_remote'] = self.remote_qsub_submission + "submitting jobs to remote machine with: %s" + % self.remote_qsub_submission + ) + self.external_software["qsub_remote"] = self.remote_qsub_submission self.using_remote_qsub_submission = True - self.settings['remote_qsub'] = self.remote_qsub_submission + self.settings["remote_qsub"] = self.remote_qsub_submission else: - self.update_log.insert('switching off remote job submission') - self.external_software['qsub_remote'] = '' - self.settings['remote_qsub'] = '' + self.update_log.insert("switching off remote job submission") + self.external_software["qsub_remote"] = "" + self.settings["remote_qsub"] = "" self.using_remote_qsub_submission = False def enter_pdb_codes(self): @@ -1074,9 +1250,9 @@ def enter_pdb_codes(self): grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Text from PDB email'), 0, 0) + grid.addWidget(QtGui.QLabel("Text from PDB email"), 0, 0) self.pdb_code_entry = QtGui.QTextEdit() - self.pdb_code_entry.setText('') + self.pdb_code_entry.setText("") self.pdb_code_entry.setFixedWidth(500) grid.addWidget(self.pdb_code_entry, 1, 0, 20, 1) @@ -1084,7 +1260,7 @@ def enter_pdb_codes(self): vbox.addWidget(frame) hbox = QtGui.QHBoxLayout() - button = QtGui.QPushButton('Update Database') + button = QtGui.QPushButton("Update Database") button.clicked.connect(self.update_database_with_pdb_codes) hbox.addWidget(button) @@ -1099,7 +1275,7 @@ def add_label_information(self): try: labelInfo = self.db.get_label_info_from_db() except AttributeError: - self.update_log.warning('please specify DB file first') + self.update_log.warning("please specify DB file first") return None vbox = QtGui.QVBoxLayout() @@ -1108,8 +1284,8 @@ def add_label_information(self): frame.setFrameShape(QtGui.QFrame.StyledPanel) grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('label'), 0, 0) - grid.addWidget(QtGui.QLabel('description'), 0, 1) + grid.addWidget(QtGui.QLabel("label"), 0, 0) + grid.addWidget(QtGui.QLabel("description"), 0, 1) self.remote_qsub_command = QtGui.QLineEdit() self.remote_qsub_command.setFixedWidth(550) @@ -1125,8 +1301,8 @@ def add_label_information(self): labelEdit.setText(labelInfo[i][0]) descriptionEdit.setText(labelInfo[i][1]) except IndexError: - labelEdit.setText('') - descriptionEdit.setText('') + labelEdit.setText("") + descriptionEdit.setText("") labelEdit.setFixedWidth(100) descriptionEdit.setFixedWidth(500) self.labelList.append([labelEdit, descriptionEdit]) @@ -1134,7 +1310,7 @@ def add_label_information(self): vbox.addWidget(frame) hbox = QtGui.QHBoxLayout() - button = QtGui.QPushButton('Update Database') + button = QtGui.QPushButton("Update Database") button.clicked.connect(self.update_database_with_labelInfo) hbox.addWidget(button) @@ -1143,55 +1319,55 @@ def add_label_information(self): label_entry.exec_() def create_missing_apo_records_in_depositTable(self): - self.db.create_missing_apo_records_for_all_structures_in_depositTable(self.initial_model_directory, - self.xce_logfile) + self.db.create_missing_apo_records_for_all_structures_in_depositTable( + self.initial_model_directory, self.xce_logfile + ) -# def update_file_information_of_apo_records(self): -# XChemDeposit.update_file_locations_of_apo_structuresin_DB( -# os.path.join(self.database_directory, self.data_source_file), self.initial_model_directory, -# self.xce_logfile) + # def update_file_information_of_apo_records(self): + # XChemDeposit.update_file_locations_of_apo_structuresin_DB( + # os.path.join(self.database_directory, self.data_source_file), self.initial_model_directory, + # self.xce_logfile) def prepare_models_for_deposition_ligand_bound(self, structureType): start_thread = True - self.update_log.insert( - 'preparing mmcif files for PDB group deposition...') + self.update_log.insert("preparing mmcif files for PDB group deposition...") ignore_event_map = False - if structureType == 'ground_state': + if structureType == "ground_state": try: - self.update_log.insert('ground-state deposition') - data_template_dict = self.db.get_deposit_dict_for_sample( - 'ground_state') - pdb = data_template_dict['PDB_file'] - self.update_log.insert('looking for ground-state PDB: ' + pdb) + self.update_log.insert("ground-state deposition") + data_template_dict = self.db.get_deposit_dict_for_sample("ground_state") + pdb = data_template_dict["PDB_file"] + self.update_log.insert("looking for ground-state PDB: " + pdb) if not os.path.isfile(pdb): self.update_log.error( - 'ground-state PDB does not exist; stopping...') + "ground-state PDB does not exist; stopping..." + ) start_thread = False - mtz = data_template_dict['MTZ_file'] - self.update_log.insert('looking for ground-state MTZ: ' + mtz) + mtz = data_template_dict["MTZ_file"] + self.update_log.insert("looking for ground-state MTZ: " + mtz) if not os.path.isfile(mtz): self.update_log.error( - 'ground-state MTZ does not exist; stopping...') + "ground-state MTZ does not exist; stopping..." + ) start_thread = False - ground_state = [pdb, - mtz, - self.panddas_directory] + ground_state = [pdb, mtz, self.panddas_directory] except KeyError: self.update_log.error( - 'seems like there is no entry for ground-state in database') + "seems like there is no entry for ground-state in database" + ) start_thread = False else: ground_state = [] if self.deposition_bounnd_state_preparation_ignore_event_map.isChecked(): ignore_event_map = True -# structureType = "ligand_bound" + # structureType = "ligand_bound" if start_thread: if ground_state != []: - self.update_log.insert('apo PDB: ' + ground_state[0]) - self.update_log.insert('apo MTZ: ' + ground_state[1]) - self.update_log.insert('pandda directory: ' + ground_state[2]) + self.update_log.insert("apo PDB: " + ground_state[0]) + self.update_log.insert("apo MTZ: " + ground_state[1]) + self.update_log.insert("pandda directory: " + ground_state[2]) overwrite_existing_mmcif = True self.work_thread = XChemDeposit.prepare_mmcif_files_for_deposition( os.path.join(self.database_directory, self.data_source_file), @@ -1199,14 +1375,22 @@ def prepare_models_for_deposition_ligand_bound(self, structureType): overwrite_existing_mmcif, self.initial_model_directory, ground_state, - ignore_event_map) + ignore_event_map, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def prepare_models_for_deposition_apo(self): @@ -1219,14 +1403,22 @@ def prepare_models_for_deposition_apo(self): self.xce_logfile, overwrite_existing_mmcif, self.initial_model_directory, - structureType) + structureType, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def prepare_for_group_deposition_upload_ligand_bound(self): @@ -1234,14 +1426,24 @@ def prepare_for_group_deposition_upload_ligand_bound(self): self.work_thread = XChemDeposit.prepare_for_group_deposition_upload( os.path.join(self.database_directory, self.data_source_file), self.xce_logfile, - self.group_deposit_directory, self.initial_model_directory, 'ligand_bound') + self.group_deposit_directory, + self.initial_model_directory, + "ligand_bound", + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def prepare_for_group_deposition_upload_ground_state(self): @@ -1249,31 +1451,50 @@ def prepare_for_group_deposition_upload_ground_state(self): self.work_thread = XChemDeposit.prepare_for_group_deposition_upload( os.path.join(self.database_directory, self.data_source_file), self.xce_logfile, - self.group_deposit_directory, self.initial_model_directory, 'ground_state') + self.group_deposit_directory, + self.initial_model_directory, + "ground_state", + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def check_smiles_in_db_and_pdb(self): - self.work_thread = XChemDeposit.compare_smiles_in_db_with_ligand_in_pdb(self.initial_model_directory, - os.path.join(self.database_directory, - self.data_source_file), - self.xce_logfile) + self.work_thread = XChemDeposit.compare_smiles_in_db_with_ligand_in_pdb( + self.initial_model_directory, + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL( - "show_error_dict"), self.show_error_dict) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, QtCore.SIGNAL("show_error_dict"), self.show_error_dict + ) self.work_thread.start() def deposition_data(self): @@ -1284,15 +1505,17 @@ def deposition_data(self): vbox = QtGui.QVBoxLayout() deposit_tab_widget = QtGui.QTabWidget() - deposit_tab_list = ['Contact', - 'General', - 'Authors', - 'Citation', - 'Molecule', - 'Misc', - 'Methods', - 'Software', - 'Funding'] + deposit_tab_list = [ + "Contact", + "General", + "Authors", + "Citation", + "Molecule", + "Misc", + "Methods", + "Software", + "Funding", + ] deposit_tab_dict = {} for page in deposit_tab_list: @@ -1309,102 +1532,104 @@ def deposition_data(self): frame.setFrameShape(QtGui.QFrame.StyledPanel) grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Principal Investigator'), 0, 0) + grid.addWidget(QtGui.QLabel("Principal Investigator"), 0, 0) - grid.addWidget(QtGui.QLabel('Salutation'), 1, 0) + grid.addWidget(QtGui.QLabel("Salutation"), 1, 0) self.contact_author_PI_salutation = QtGui.QLineEdit() - self.contact_author_PI_salutation.setText('Dr.') + self.contact_author_PI_salutation.setText("Dr.") self.contact_author_PI_salutation.setFixedWidth(200) grid.addWidget(self.contact_author_PI_salutation, 1, 1) - grid.addWidget(QtGui.QLabel('First name'), 2, 0) + grid.addWidget(QtGui.QLabel("First name"), 2, 0) self.contact_author_PI_first_name = QtGui.QLineEdit() - self.contact_author_PI_first_name.setText('') + self.contact_author_PI_first_name.setText("") self.contact_author_PI_first_name.setFixedWidth(200) grid.addWidget(self.contact_author_PI_first_name, 2, 1) - grid.addWidget(QtGui.QLabel('Last name'), 3, 0) + grid.addWidget(QtGui.QLabel("Last name"), 3, 0) self.contact_author_PI_last_name = QtGui.QLineEdit() - self.contact_author_PI_last_name.setText('') + self.contact_author_PI_last_name.setText("") self.contact_author_PI_last_name.setFixedWidth(200) grid.addWidget(self.contact_author_PI_last_name, 3, 1) - grid.addWidget(QtGui.QLabel('Middle name'), 4, 0) + grid.addWidget(QtGui.QLabel("Middle name"), 4, 0) self.contact_author_PI_middle_name = QtGui.QLineEdit() - self.contact_author_PI_middle_name.setText('') + self.contact_author_PI_middle_name.setText("") self.contact_author_PI_middle_name.setFixedWidth(200) self.contact_author_PI_middle_name.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.contact_author_PI_middle_name, 4, 1) - grid.addWidget(QtGui.QLabel('PI role'), 5, 0) + grid.addWidget(QtGui.QLabel("PI role"), 5, 0) self.contact_author_PI_role = QtGui.QComboBox() -# PIroles = ['group leader', 'principal investigator/group leader', 'investigator'] - PIroles = ['principal investigator/group leader'] + # PIroles = ['group leader', 'principal investigator/group leader', 'investigator'] + PIroles = ["principal investigator/group leader"] for item in PIroles: self.contact_author_PI_role.addItem(item) grid.addWidget(self.contact_author_PI_role, 5, 1) - grid.addWidget(QtGui.QLabel('Organization type'), 6, 0) + grid.addWidget(QtGui.QLabel("Organization type"), 6, 0) self.contact_author_PI_organization_type = QtGui.QComboBox() - Organizations = ['academic', 'commercial', 'government'] + Organizations = ["academic", "commercial", "government"] for item in Organizations: self.contact_author_PI_organization_type.addItem(item) grid.addWidget(self.contact_author_PI_organization_type, 6, 1) - grid.addWidget(QtGui.QLabel('Organization Name'), 7, 0) + grid.addWidget(QtGui.QLabel("Organization Name"), 7, 0) self.contact_author_PI_organization_name = QtGui.QLineEdit() - self.contact_author_PI_organization_name.setText('') + self.contact_author_PI_organization_name.setText("") self.contact_author_PI_organization_name.setFixedWidth(200) grid.addWidget(self.contact_author_PI_organization_name, 7, 1) - grid.addWidget(QtGui.QLabel('Email'), 8, 0) + grid.addWidget(QtGui.QLabel("Email"), 8, 0) self.contact_author_PI_email = QtGui.QLineEdit() - self.contact_author_PI_email.setText('') + self.contact_author_PI_email.setText("") self.contact_author_PI_email.setFixedWidth(200) grid.addWidget(self.contact_author_PI_email, 8, 1) - grid.addWidget(QtGui.QLabel('Street'), 9, 0) + grid.addWidget(QtGui.QLabel("Street"), 9, 0) self.contact_author_PI_address = QtGui.QLineEdit() - self.contact_author_PI_address.setText('') + self.contact_author_PI_address.setText("") self.contact_author_PI_address.setFixedWidth(200) grid.addWidget(self.contact_author_PI_address, 9, 1) - grid.addWidget(QtGui.QLabel('City'), 10, 0) + grid.addWidget(QtGui.QLabel("City"), 10, 0) self.contact_author_PI_city = QtGui.QLineEdit() - self.contact_author_PI_city.setText('') + self.contact_author_PI_city.setText("") self.contact_author_PI_city.setFixedWidth(200) grid.addWidget(self.contact_author_PI_city, 10, 1) - grid.addWidget(QtGui.QLabel('State'), 11, 0) + grid.addWidget(QtGui.QLabel("State"), 11, 0) self.contact_author_PI_State_or_Province = QtGui.QLineEdit() - self.contact_author_PI_State_or_Province.setText('') + self.contact_author_PI_State_or_Province.setText("") self.contact_author_PI_State_or_Province.setFixedWidth(200) self.contact_author_PI_State_or_Province.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.contact_author_PI_State_or_Province, 11, 1) - grid.addWidget(QtGui.QLabel('ZIP code'), 12, 0) + grid.addWidget(QtGui.QLabel("ZIP code"), 12, 0) self.contact_author_PI_Zip_Code = QtGui.QLineEdit() - self.contact_author_PI_Zip_Code.setText('') + self.contact_author_PI_Zip_Code.setText("") self.contact_author_PI_Zip_Code.setFixedWidth(200) grid.addWidget(self.contact_author_PI_Zip_Code, 12, 1) - grid.addWidget(QtGui.QLabel('Country'), 13, 0) + grid.addWidget(QtGui.QLabel("Country"), 13, 0) self.contact_author_PI_Country = QtGui.QLineEdit() - self.contact_author_PI_Country.setText('') + self.contact_author_PI_Country.setText("") self.contact_author_PI_Country.setFixedWidth(200) grid.addWidget(self.contact_author_PI_Country, 13, 1) - grid.addWidget(QtGui.QLabel('Phone'), 14, 0) + grid.addWidget(QtGui.QLabel("Phone"), 14, 0) self.contact_author_PI_phone_number = QtGui.QLineEdit() - self.contact_author_PI_phone_number.setText('') + self.contact_author_PI_phone_number.setText("") self.contact_author_PI_phone_number.setFixedWidth(200) grid.addWidget(self.contact_author_PI_phone_number, 14, 1) - grid.addWidget(QtGui.QLabel('ORCID'), 15, 0) + grid.addWidget(QtGui.QLabel("ORCID"), 15, 0) self.contact_author_PI_ORCID = QtGui.QLineEdit() - self.contact_author_PI_ORCID.setText('') + self.contact_author_PI_ORCID.setText("") self.contact_author_PI_ORCID.setFixedWidth(200) grid.addWidget(self.contact_author_PI_ORCID, 15, 1) @@ -1414,102 +1639,104 @@ def deposition_data(self): frame = QtGui.QFrame() frame.setFrameShape(QtGui.QFrame.StyledPanel) grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Responsible Scientist'), 0, 0) + grid.addWidget(QtGui.QLabel("Responsible Scientist"), 0, 0) - grid.addWidget(QtGui.QLabel('Salutation'), 1, 0) + grid.addWidget(QtGui.QLabel("Salutation"), 1, 0) self.contact_author_salutation = QtGui.QLineEdit() - self.contact_author_salutation.setText('Dr.') + self.contact_author_salutation.setText("Dr.") self.contact_author_salutation.setFixedWidth(200) grid.addWidget(self.contact_author_salutation, 1, 1) - grid.addWidget(QtGui.QLabel('First name'), 2, 0) + grid.addWidget(QtGui.QLabel("First name"), 2, 0) self.contact_author_first_name = QtGui.QLineEdit() - self.contact_author_first_name.setText('') + self.contact_author_first_name.setText("") self.contact_author_first_name.setFixedWidth(200) grid.addWidget(self.contact_author_first_name, 2, 1) - grid.addWidget(QtGui.QLabel('Last name'), 3, 0) + grid.addWidget(QtGui.QLabel("Last name"), 3, 0) self.contact_author_last_name = QtGui.QLineEdit() - self.contact_author_last_name.setText('') + self.contact_author_last_name.setText("") self.contact_author_last_name.setFixedWidth(200) grid.addWidget(self.contact_author_last_name, 3, 1) - grid.addWidget(QtGui.QLabel('Middle name'), 4, 0) + grid.addWidget(QtGui.QLabel("Middle name"), 4, 0) self.contact_author_middle_name = QtGui.QLineEdit() - self.contact_author_middle_name.setText('') + self.contact_author_middle_name.setText("") self.contact_author_middle_name.setFixedWidth(200) self.contact_author_middle_name.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.contact_author_middle_name, 4, 1) - grid.addWidget(QtGui.QLabel('Role'), 5, 0) + grid.addWidget(QtGui.QLabel("Role"), 5, 0) self.contact_author_role = QtGui.QComboBox() - ScientistRoles = ['responsible scientist', 'investigator'] + ScientistRoles = ["responsible scientist", "investigator"] for item in ScientistRoles: self.contact_author_role.addItem(item) grid.addWidget(self.contact_author_role, 5, 1) - grid.addWidget(QtGui.QLabel('Organization type'), 6, 0) + grid.addWidget(QtGui.QLabel("Organization type"), 6, 0) self.contact_author_organization_type = QtGui.QComboBox() for item in Organizations: self.contact_author_organization_type.addItem(item) grid.addWidget(self.contact_author_organization_type, 6, 1) - grid.addWidget(QtGui.QLabel('Organization Name'), 7, 0) + grid.addWidget(QtGui.QLabel("Organization Name"), 7, 0) self.contact_author_organization_name = QtGui.QLineEdit() - self.contact_author_organization_name.setText('') + self.contact_author_organization_name.setText("") self.contact_author_organization_name.setFixedWidth(200) grid.addWidget(self.contact_author_organization_name, 7, 1) - grid.addWidget(QtGui.QLabel('Email'), 8, 0) + grid.addWidget(QtGui.QLabel("Email"), 8, 0) self.contact_author_email = QtGui.QLineEdit() - self.contact_author_email.setText('') + self.contact_author_email.setText("") self.contact_author_email.setFixedWidth(200) grid.addWidget(self.contact_author_email, 8, 1) - grid.addWidget(QtGui.QLabel('Street'), 9, 0) + grid.addWidget(QtGui.QLabel("Street"), 9, 0) self.contact_author_address = QtGui.QLineEdit() - self.contact_author_address.setText('') + self.contact_author_address.setText("") self.contact_author_address.setFixedWidth(200) grid.addWidget(self.contact_author_address, 9, 1) - grid.addWidget(QtGui.QLabel('City'), 10, 0) + grid.addWidget(QtGui.QLabel("City"), 10, 0) self.contact_author_city = QtGui.QLineEdit() - self.contact_author_city.setText('') + self.contact_author_city.setText("") self.contact_author_city.setFixedWidth(200) grid.addWidget(self.contact_author_city, 10, 1) - grid.addWidget(QtGui.QLabel('State'), 11, 0) + grid.addWidget(QtGui.QLabel("State"), 11, 0) self.contact_author_State_or_Province = QtGui.QLineEdit() - self.contact_author_State_or_Province.setText('') + self.contact_author_State_or_Province.setText("") self.contact_author_State_or_Province.setFixedWidth(200) self.contact_author_State_or_Province.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.contact_author_State_or_Province, 11, 1) - grid.addWidget(QtGui.QLabel('ZIP code'), 12, 0) + grid.addWidget(QtGui.QLabel("ZIP code"), 12, 0) self.contact_author_Zip_Code = QtGui.QLineEdit() - self.contact_author_Zip_Code.setText('') + self.contact_author_Zip_Code.setText("") self.contact_author_Zip_Code.setFixedWidth(200) grid.addWidget(self.contact_author_Zip_Code, 12, 1) - grid.addWidget(QtGui.QLabel('Country'), 13, 0) + grid.addWidget(QtGui.QLabel("Country"), 13, 0) self.contact_author_Country = QtGui.QLineEdit() - self.contact_author_Country.setText('') + self.contact_author_Country.setText("") self.contact_author_Country.setFixedWidth(200) grid.addWidget(self.contact_author_Country, 13, 1) - grid.addWidget(QtGui.QLabel('Phone'), 14, 0) + grid.addWidget(QtGui.QLabel("Phone"), 14, 0) self.contact_author_phone_number = QtGui.QLineEdit() - self.contact_author_phone_number.setText('') + self.contact_author_phone_number.setText("") self.contact_author_phone_number.setFixedWidth(200) grid.addWidget(self.contact_author_phone_number, 14, 1) - grid.addWidget(QtGui.QLabel('ORCID'), 15, 0) + grid.addWidget(QtGui.QLabel("ORCID"), 15, 0) self.contact_author_ORCID = QtGui.QLineEdit() - self.contact_author_ORCID.setText('') + self.contact_author_ORCID.setText("") self.contact_author_ORCID.setFixedWidth(200) grid.addWidget(self.contact_author_ORCID, 15, 1) @@ -1520,7 +1747,7 @@ def deposition_data(self): vb.addWidget(QtGui.QLabel(XChemToolTips.deposition_interface_note())) vb.addStretch(1) - deposit_tab_dict['Contact'][1].addLayout(vb) + deposit_tab_dict["Contact"][1].addLayout(vb) # release status vb = QtGui.QVBoxLayout() @@ -1529,21 +1756,25 @@ def deposition_data(self): frame.setFrameShape(QtGui.QFrame.StyledPanel) grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Release status'), 0, 0) + grid.addWidget(QtGui.QLabel("Release status"), 0, 0) - grid.addWidget(QtGui.QLabel('Release Status for sequence'), 4, 0) + grid.addWidget(QtGui.QLabel("Release Status for sequence"), 4, 0) self.Release_status_for_sequence = QtGui.QComboBox() - codeStatus = ['RELEASE NOW', 'HOLD FOR RELEASE'] + codeStatus = ["RELEASE NOW", "HOLD FOR RELEASE"] for item in codeStatus: self.Release_status_for_sequence.addItem(item) grid.addWidget(self.Release_status_for_sequence, 4, 1) - grid.addWidget(QtGui.QLabel( - 'Release Status for coordinates/ SF'), 8, 0) + grid.addWidget(QtGui.QLabel("Release Status for coordinates/ SF"), 8, 0) self.Release_status_for_coordinates = QtGui.QComboBox() - coordStatus = ['RELEASE NOW', 'HOLD FOR PUBLICATION', 'HOLD FOR 4 WEEKS', 'HOLD FOR 6 MONTHS', - 'HOLD FOR 1 YEAR'] + coordStatus = [ + "RELEASE NOW", + "HOLD FOR PUBLICATION", + "HOLD FOR 4 WEEKS", + "HOLD FOR 6 MONTHS", + "HOLD FOR 1 YEAR", + ] for item in coordStatus: self.Release_status_for_coordinates.addItem(item) grid.addWidget(self.Release_status_for_coordinates, 8, 1) @@ -1555,39 +1786,41 @@ def deposition_data(self): frame.setFrameShape(QtGui.QFrame.StyledPanel) grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Title & Details'), 0, 0) - note = ( - 'Note: supported wildcards: $ProteinName,$CompoundName; e.g. "Crystal Structure of human JMJD2D in complex with N2317a"') + grid.addWidget(QtGui.QLabel("Title & Details"), 0, 0) + note = 'Note: supported wildcards: $ProteinName,$CompoundName; e.g. "Crystal Structure of human JMJD2D in complex with N2317a"' grid.addWidget(QtGui.QLabel(note), 1, 0) - grid.addWidget(QtGui.QLabel('Group deposition title'), 2, 0) + grid.addWidget(QtGui.QLabel("Group deposition title"), 2, 0) self.group_deposition_title = QtGui.QLineEdit() - self.group_deposition_title.setText('PanDDA analysis group deposition') + self.group_deposition_title.setText("PanDDA analysis group deposition") self.group_deposition_title.setFixedWidth(600) # self.group_deposition_title.setStyleSheet("background-color: rgb(192, 192, 192);") grid.addWidget(self.group_deposition_title, 2, 1) - grid.addWidget(QtGui.QLabel('Description'), 3, 0) + grid.addWidget(QtGui.QLabel("Description"), 3, 0) self.group_description = QtGui.QLineEdit() self.group_description.setText( - 'XDomainX of XOrganismX $ProteinName screened against the XXX Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1') + "XDomainX of XOrganismX $ProteinName screened against the XXX Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1" + ) self.group_description.setFixedWidth(600) grid.addWidget(self.group_description, 3, 1) - grid.addWidget(QtGui.QLabel('Structure Title (ligand bound)'), 4, 0) + grid.addWidget(QtGui.QLabel("Structure Title (ligand bound)"), 4, 0) self.structure_title = QtGui.QLineEdit() self.structure_title.setText( - 'Crystal Structure of $ProteinName in complex with $CompoundName') + "Crystal Structure of $ProteinName in complex with $CompoundName" + ) self.structure_title.setFixedWidth(600) grid.addWidget(self.structure_title, 4, 1) - note = ('\n\nApo Structure:\nonly use if you want to deposit PanDDA models!') + note = "\n\nApo Structure:\nonly use if you want to deposit PanDDA models!" grid.addWidget(QtGui.QLabel(note), 6, 0) - grid.addWidget(QtGui.QLabel('Structure Title (apo)'), 7, 0) + grid.addWidget(QtGui.QLabel("Structure Title (apo)"), 7, 0) self.structure_title_apo = QtGui.QLineEdit() self.structure_title_apo.setText( - 'PanDDA analysis group deposition of ground-state model of $ProteinName') + "PanDDA analysis group deposition of ground-state model of $ProteinName" + ) self.structure_title_apo.setFixedWidth(600) grid.addWidget(self.structure_title_apo, 7, 1) @@ -1596,7 +1829,7 @@ def deposition_data(self): vb.addStretch(1) - deposit_tab_dict['General'][1].addLayout(vb) + deposit_tab_dict["General"][1].addLayout(vb) # authors vb = QtGui.QVBoxLayout() @@ -1605,15 +1838,14 @@ def deposition_data(self): frame.setFrameShape(QtGui.QFrame.StyledPanel) grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel( - 'Deposition authors (e.g. Surname, F.M.)'), 0, 0) + grid.addWidget(QtGui.QLabel("Deposition authors (e.g. Surname, F.M.)"), 0, 0) self.structure_author_name_List = [] for column in range(0, 2): for row in range(1, 15): structure_author_name = QtGui.QLineEdit() - structure_author_name.setText('') + structure_author_name.setText("") structure_author_name.setFixedWidth(300) grid.addWidget(structure_author_name, row, column) self.structure_author_name_List.append(structure_author_name) @@ -1623,7 +1855,7 @@ def deposition_data(self): vb.addStretch(1) - deposit_tab_dict['Authors'][1].addLayout(vb) + deposit_tab_dict["Authors"][1].addLayout(vb) # primary citation vb = QtGui.QVBoxLayout() @@ -1632,58 +1864,63 @@ def deposition_data(self): frame.setFrameShape(QtGui.QFrame.StyledPanel) grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Primary Citation'), 0, 0) + grid.addWidget(QtGui.QLabel("Primary Citation"), 0, 0) - grid.addWidget(QtGui.QLabel('ID'), 1, 0) + grid.addWidget(QtGui.QLabel("ID"), 1, 0) self.primary_citation_id = QtGui.QLineEdit() - self.primary_citation_id.setText('primary') + self.primary_citation_id.setText("primary") self.primary_citation_id.setFixedWidth(500) grid.addWidget(self.primary_citation_id, 1, 1) - grid.addWidget(QtGui.QLabel('Journal'), 2, 0) + grid.addWidget(QtGui.QLabel("Journal"), 2, 0) self.primary_citation_journal_abbrev = QtGui.QLineEdit() - self.primary_citation_journal_abbrev.setText('To be published') + self.primary_citation_journal_abbrev.setText("To be published") self.primary_citation_journal_abbrev.setFixedWidth(500) grid.addWidget(self.primary_citation_journal_abbrev, 2, 1) - grid.addWidget(QtGui.QLabel('Title'), 3, 0) + grid.addWidget(QtGui.QLabel("Title"), 3, 0) self.primary_citation_title = QtGui.QLineEdit() - self.primary_citation_title.setText('') + self.primary_citation_title.setText("") self.primary_citation_title.setFixedWidth(500) self.primary_citation_title.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.primary_citation_title, 3, 1) - grid.addWidget(QtGui.QLabel('Year'), 4, 0) + grid.addWidget(QtGui.QLabel("Year"), 4, 0) self.primary_citation_year = QtGui.QLineEdit() - self.primary_citation_year.setText('') + self.primary_citation_year.setText("") self.primary_citation_year.setFixedWidth(500) self.primary_citation_year.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.primary_citation_year, 4, 1) - grid.addWidget(QtGui.QLabel('Volume'), 5, 0) + grid.addWidget(QtGui.QLabel("Volume"), 5, 0) self.primary_citation_journal_volume = QtGui.QLineEdit() - self.primary_citation_journal_volume.setText('') + self.primary_citation_journal_volume.setText("") self.primary_citation_journal_volume.setFixedWidth(500) self.primary_citation_journal_volume.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.primary_citation_journal_volume, 5, 1) - grid.addWidget(QtGui.QLabel('Page, first'), 6, 0) + grid.addWidget(QtGui.QLabel("Page, first"), 6, 0) self.primary_citation_page_first = QtGui.QLineEdit() - self.primary_citation_page_first.setText('') + self.primary_citation_page_first.setText("") self.primary_citation_page_first.setFixedWidth(500) self.primary_citation_page_first.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.primary_citation_page_first, 6, 1) - grid.addWidget(QtGui.QLabel('Page, last'), 7, 0) + grid.addWidget(QtGui.QLabel("Page, last"), 7, 0) self.primary_citation_page_last = QtGui.QLineEdit() - self.primary_citation_page_last.setText('') + self.primary_citation_page_last.setText("") self.primary_citation_page_last.setFixedWidth(500) self.primary_citation_page_last.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.primary_citation_page_last, 7, 1) frame.setLayout(grid) @@ -1695,9 +1932,13 @@ def deposition_data(self): grid = QtGui.QGridLayout() self.set_primary_citation_authors = QtGui.QCheckBox( - 'same as deposition authors') - self.layout_funcs.add_checkbox(self, self.set_primary_citation_authors, - 'xce_object.set_primary_citation_as_structure_authors') + "same as deposition authors" + ) + self.layout_funcs.add_checkbox( + self, + self.set_primary_citation_authors, + "xce_object.set_primary_citation_as_structure_authors", + ) grid.addWidget(self.set_primary_citation_authors, 0, 0) self.primary_citation_author_name_List = [] @@ -1705,18 +1946,19 @@ def deposition_data(self): for column in range(0, 2): for row in range(1, 15): primary_citation_author_name = QtGui.QLineEdit() - primary_citation_author_name.setText('') + primary_citation_author_name.setText("") primary_citation_author_name.setFixedWidth(300) grid.addWidget(primary_citation_author_name, row, column) self.primary_citation_author_name_List.append( - primary_citation_author_name) + primary_citation_author_name + ) frame.setLayout(grid) vb.addWidget(frame) vb.addStretch(1) - deposit_tab_dict['Citation'][1].addLayout(vb) + deposit_tab_dict["Citation"][1].addLayout(vb) # molecule info vb = QtGui.QVBoxLayout() @@ -1726,47 +1968,47 @@ def deposition_data(self): grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Entity 1'), 1, 0) + grid.addWidget(QtGui.QLabel("Entity 1"), 1, 0) - grid.addWidget(QtGui.QLabel('Molecule Name'), 2, 0) + grid.addWidget(QtGui.QLabel("Molecule Name"), 2, 0) self.molecule_name = QtGui.QLineEdit() - self.molecule_name.setText('') + self.molecule_name.setText("") self.molecule_name.setFixedWidth(300) -# self.molecule_name.setStyleSheet("background-color: rgb(192, 192, 192);") + # self.molecule_name.setStyleSheet("background-color: rgb(192, 192, 192);") grid.addWidget(self.molecule_name, 2, 1) - grid.addWidget(QtGui.QLabel('(e.g. RNA Hammerhead Ribozyme)'), 2, 2) + grid.addWidget(QtGui.QLabel("(e.g. RNA Hammerhead Ribozyme)"), 2, 2) - grid.addWidget(QtGui.QLabel('Fragment Name'), 3, 0) + grid.addWidget(QtGui.QLabel("Fragment Name"), 3, 0) self.fragment_name_one = QtGui.QLineEdit() - self.fragment_name_one.setText('') + self.fragment_name_one.setText("") self.fragment_name_one.setFixedWidth(300) - self.fragment_name_one.setStyleSheet( - "background-color: rgb(192, 192, 192);") + self.fragment_name_one.setStyleSheet("background-color: rgb(192, 192, 192);") grid.addWidget(self.fragment_name_one, 3, 1) - grid.addWidget(QtGui.QLabel( - '(e.g. ligand binding domain, hairpin)'), 3, 2) + grid.addWidget(QtGui.QLabel("(e.g. ligand binding domain, hairpin)"), 3, 2) - grid.addWidget(QtGui.QLabel('Specific Mutation'), 4, 0) + grid.addWidget(QtGui.QLabel("Specific Mutation"), 4, 0) self.fragment_name_one_specific_mutation = QtGui.QLineEdit() - self.fragment_name_one_specific_mutation.setText('') + self.fragment_name_one_specific_mutation.setText("") self.fragment_name_one_specific_mutation.setFixedWidth(300) self.fragment_name_one_specific_mutation.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.fragment_name_one_specific_mutation, 4, 1) - grid.addWidget(QtGui.QLabel('(e.g. C280S)'), 4, 2) + grid.addWidget(QtGui.QLabel("(e.g. C280S)"), 4, 2) - grid.addWidget(QtGui.QLabel('Enzyme Comission Number'), 5, 0) + grid.addWidget(QtGui.QLabel("Enzyme Comission Number"), 5, 0) self.fragment_name_one_enzyme_comission_number = QtGui.QLineEdit() - self.fragment_name_one_enzyme_comission_number.setText('') + self.fragment_name_one_enzyme_comission_number.setText("") self.fragment_name_one_enzyme_comission_number.setFixedWidth(300) self.fragment_name_one_enzyme_comission_number.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.fragment_name_one_enzyme_comission_number, 5, 1) - grid.addWidget(QtGui.QLabel('(if known: e.g. 2.7.7.7)'), 5, 2) + grid.addWidget(QtGui.QLabel("(if known: e.g. 2.7.7.7)"), 5, 2) - grid.addWidget(QtGui.QLabel('Genetically Manipulated Source'), 6, 0) + grid.addWidget(QtGui.QLabel("Genetically Manipulated Source"), 6, 0) - grid.addWidget(QtGui.QLabel('Source organism scientific name'), 7, 0) + grid.addWidget(QtGui.QLabel("Source organism scientific name"), 7, 0) self.Source_organism_scientific_name = QtGui.QComboBox() taxonomy_dict = XChemMain.NCBI_taxonomy_ID() @@ -1774,72 +2016,76 @@ def deposition_data(self): self.Source_organism_scientific_name.addItem(taxonomy_dict[item]) grid.addWidget(self.Source_organism_scientific_name, 7, 1) - grid.addWidget(QtGui.QLabel('Source organism gene'), 8, 0) + grid.addWidget(QtGui.QLabel("Source organism gene"), 8, 0) self.Source_organism_gene = QtGui.QLineEdit() - self.Source_organism_gene.setText('') + self.Source_organism_gene.setText("") self.Source_organism_gene.setFixedWidth(300) grid.addWidget(self.Source_organism_gene, 8, 1) - grid.addWidget(QtGui.QLabel('(e.g. RPOD, ALKA...)'), 8, 2) + grid.addWidget(QtGui.QLabel("(e.g. RPOD, ALKA...)"), 8, 2) - grid.addWidget(QtGui.QLabel('Source organism strain'), 9, 0) + grid.addWidget(QtGui.QLabel("Source organism strain"), 9, 0) self.Source_organism_strain = QtGui.QLineEdit() - self.Source_organism_strain.setText('') + self.Source_organism_strain.setText("") self.Source_organism_strain.setFixedWidth(300) self.Source_organism_strain.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.Source_organism_strain, 9, 1) - grid.addWidget(QtGui.QLabel('(e.g. BH10 ISOLATE, K-12...)'), 9, 2) + grid.addWidget(QtGui.QLabel("(e.g. BH10 ISOLATE, K-12...)"), 9, 2) - grid.addWidget(QtGui.QLabel( - 'Expression system scientific name'), 10, 0) + grid.addWidget(QtGui.QLabel("Expression system scientific name"), 10, 0) self.Expression_system_scientific_name = QtGui.QComboBox() for item in taxonomy_dict: self.Expression_system_scientific_name.addItem(taxonomy_dict[item]) grid.addWidget(self.Expression_system_scientific_name, 10, 1) - grid.addWidget(QtGui.QLabel('Expression system strain'), 11, 0) + grid.addWidget(QtGui.QLabel("Expression system strain"), 11, 0) self.Expression_system_strain = QtGui.QLineEdit() - self.Expression_system_strain.setText('') + self.Expression_system_strain.setText("") self.Expression_system_strain.setFixedWidth(300) self.Expression_system_strain.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.Expression_system_strain, 11, 1) - grid.addWidget(QtGui.QLabel('(e.g. BL21(DE3))'), 11, 2) + grid.addWidget(QtGui.QLabel("(e.g. BL21(DE3))"), 11, 2) - grid.addWidget(QtGui.QLabel('Expression system vector type'), 12, 0) + grid.addWidget(QtGui.QLabel("Expression system vector type"), 12, 0) self.Expression_system_vector_type = QtGui.QLineEdit() - self.Expression_system_vector_type.setText('') + self.Expression_system_vector_type.setText("") self.Expression_system_vector_type.setFixedWidth(300) self.Expression_system_vector_type.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.Expression_system_vector_type, 12, 1) - grid.addWidget(QtGui.QLabel('(e.g. plasmid)'), 12, 2) + grid.addWidget(QtGui.QLabel("(e.g. plasmid)"), 12, 2) - grid.addWidget(QtGui.QLabel('Expression_system_plasmid_name'), 13, 0) + grid.addWidget(QtGui.QLabel("Expression_system_plasmid_name"), 13, 0) self.Expression_system_plasmid_name = QtGui.QLineEdit() - self.Expression_system_plasmid_name.setText('') + self.Expression_system_plasmid_name.setText("") self.Expression_system_plasmid_name.setFixedWidth(300) self.Expression_system_plasmid_name.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.Expression_system_plasmid_name, 13, 1) - grid.addWidget(QtGui.QLabel('(e.g. pET26)'), 13, 2) + grid.addWidget(QtGui.QLabel("(e.g. pET26)"), 13, 2) - grid.addWidget(QtGui.QLabel('Manipulated_source_details'), 14, 0) + grid.addWidget(QtGui.QLabel("Manipulated_source_details"), 14, 0) self.Manipulated_source_details = QtGui.QLineEdit() - self.Manipulated_source_details.setText('') + self.Manipulated_source_details.setText("") self.Manipulated_source_details.setFixedWidth(300) self.Manipulated_source_details.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.Manipulated_source_details, 14, 1) - grid.addWidget(QtGui.QLabel('(any other relevant information)'), 14, 2) + grid.addWidget(QtGui.QLabel("(any other relevant information)"), 14, 2) - grid.addWidget(QtGui.QLabel('Chains'), 15, 0) + grid.addWidget(QtGui.QLabel("Chains"), 15, 0) self.molecule_chain_one = QtGui.QLineEdit() - self.molecule_chain_one.setText('') + self.molecule_chain_one.setText("") self.molecule_chain_one.setFixedWidth(300) grid.addWidget(self.molecule_chain_one, 15, 1) - grid.addWidget(QtGui.QLabel('(e.g. A or A,B)'), 15, 2) + grid.addWidget(QtGui.QLabel("(e.g. A or A,B)"), 15, 2) frame.setLayout(grid) vb.addWidget(frame) @@ -1851,123 +2097,130 @@ def deposition_data(self): grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel( - 'Entity 2 (IMPORTANT: only fill in if you are working with a protein-protein complex!)'), 1, 0) + grid.addWidget( + QtGui.QLabel( + "Entity 2 (IMPORTANT: only fill in if you are working with a protein-protein complex!)" + ), + 1, + 0, + ) - grid.addWidget(QtGui.QLabel('Molecule Name'), 2, 0) + grid.addWidget(QtGui.QLabel("Molecule Name"), 2, 0) self.molecule_name_two = QtGui.QLineEdit() - self.molecule_name_two.setText('') + self.molecule_name_two.setText("") self.molecule_name_two.setFixedWidth(300) -# self.molecule_name_two.setStyleSheet("background-color: rgb(192, 192, 192);") + # self.molecule_name_two.setStyleSheet("background-color: rgb(192, 192, 192);") grid.addWidget(self.molecule_name_two, 2, 1) - grid.addWidget(QtGui.QLabel('(e.g. RNA Hammerhead Ribozyme)'), 2, 2) + grid.addWidget(QtGui.QLabel("(e.g. RNA Hammerhead Ribozyme)"), 2, 2) - grid.addWidget(QtGui.QLabel('Fragment Name'), 3, 0) + grid.addWidget(QtGui.QLabel("Fragment Name"), 3, 0) self.fragment_name_two = QtGui.QLineEdit() - self.fragment_name_two.setText('') + self.fragment_name_two.setText("") self.fragment_name_two.setFixedWidth(300) - self.fragment_name_two.setStyleSheet( - "background-color: rgb(192, 192, 192);") + self.fragment_name_two.setStyleSheet("background-color: rgb(192, 192, 192);") grid.addWidget(self.fragment_name_two, 3, 1) - grid.addWidget(QtGui.QLabel( - '(e.g. ligand binding domain, hairpin)'), 3, 2) + grid.addWidget(QtGui.QLabel("(e.g. ligand binding domain, hairpin)"), 3, 2) - grid.addWidget(QtGui.QLabel('Specific Mutation'), 4, 0) + grid.addWidget(QtGui.QLabel("Specific Mutation"), 4, 0) self.fragment_name_two_specific_mutation = QtGui.QLineEdit() - self.fragment_name_two_specific_mutation.setText('') + self.fragment_name_two_specific_mutation.setText("") self.fragment_name_two_specific_mutation.setFixedWidth(300) self.fragment_name_two_specific_mutation.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.fragment_name_two_specific_mutation, 4, 1) - grid.addWidget(QtGui.QLabel('(e.g. C280S)'), 4, 2) + grid.addWidget(QtGui.QLabel("(e.g. C280S)"), 4, 2) - grid.addWidget(QtGui.QLabel('Enzyme Comission Number'), 5, 0) + grid.addWidget(QtGui.QLabel("Enzyme Comission Number"), 5, 0) self.fragment_name_two_enzyme_comission_number = QtGui.QLineEdit() - self.fragment_name_two_enzyme_comission_number.setText('') + self.fragment_name_two_enzyme_comission_number.setText("") self.fragment_name_two_enzyme_comission_number.setFixedWidth(300) self.fragment_name_two_enzyme_comission_number.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.fragment_name_two_enzyme_comission_number, 5, 1) - grid.addWidget(QtGui.QLabel('(if known: e.g. 2.7.7.7)'), 5, 2) + grid.addWidget(QtGui.QLabel("(if known: e.g. 2.7.7.7)"), 5, 2) - grid.addWidget(QtGui.QLabel('Genetically Manipulated Source'), 6, 0) + grid.addWidget(QtGui.QLabel("Genetically Manipulated Source"), 6, 0) - grid.addWidget(QtGui.QLabel('Source organism scientific name'), 7, 0) + grid.addWidget(QtGui.QLabel("Source organism scientific name"), 7, 0) self.Source_organism_scientific_name_two = QtGui.QComboBox() taxonomy_dict = XChemMain.NCBI_taxonomy_ID() for item in taxonomy_dict: - self.Source_organism_scientific_name_two.addItem( - taxonomy_dict[item]) + self.Source_organism_scientific_name_two.addItem(taxonomy_dict[item]) grid.addWidget(self.Source_organism_scientific_name_two, 7, 1) - grid.addWidget(QtGui.QLabel('Source organism gene'), 8, 0) + grid.addWidget(QtGui.QLabel("Source organism gene"), 8, 0) self.Source_organism_gene_two = QtGui.QLineEdit() - self.Source_organism_gene_two.setText('') + self.Source_organism_gene_two.setText("") self.Source_organism_gene_two.setFixedWidth(300) grid.addWidget(self.Source_organism_gene_two, 8, 1) - grid.addWidget(QtGui.QLabel('(e.g. RPOD, ALKA...)'), 8, 2) + grid.addWidget(QtGui.QLabel("(e.g. RPOD, ALKA...)"), 8, 2) - grid.addWidget(QtGui.QLabel('Source organism strain'), 9, 0) + grid.addWidget(QtGui.QLabel("Source organism strain"), 9, 0) self.Source_organism_strain_two = QtGui.QLineEdit() - self.Source_organism_strain_two.setText('') + self.Source_organism_strain_two.setText("") self.Source_organism_strain_two.setFixedWidth(300) self.Source_organism_strain_two.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.Source_organism_strain_two, 9, 1) - grid.addWidget(QtGui.QLabel('(e.g. BH10 ISOLATE, K-12...)'), 9, 2) + grid.addWidget(QtGui.QLabel("(e.g. BH10 ISOLATE, K-12...)"), 9, 2) - grid.addWidget(QtGui.QLabel( - 'Expression system scientific name'), 10, 0) + grid.addWidget(QtGui.QLabel("Expression system scientific name"), 10, 0) self.Expression_system_scientific_name_two = QtGui.QComboBox() for item in taxonomy_dict: - self.Expression_system_scientific_name_two.addItem( - taxonomy_dict[item]) + self.Expression_system_scientific_name_two.addItem(taxonomy_dict[item]) grid.addWidget(self.Expression_system_scientific_name_two, 10, 1) - grid.addWidget(QtGui.QLabel('Expression system strain'), 11, 0) + grid.addWidget(QtGui.QLabel("Expression system strain"), 11, 0) self.Expression_system_strain_two = QtGui.QLineEdit() - self.Expression_system_strain_two.setText('') + self.Expression_system_strain_two.setText("") self.Expression_system_strain_two.setFixedWidth(300) self.Expression_system_strain_two.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.Expression_system_strain_two, 11, 1) - grid.addWidget(QtGui.QLabel('(e.g. BL21(DE3))'), 11, 2) + grid.addWidget(QtGui.QLabel("(e.g. BL21(DE3))"), 11, 2) - grid.addWidget(QtGui.QLabel('Expression system vector type'), 12, 0) + grid.addWidget(QtGui.QLabel("Expression system vector type"), 12, 0) self.Expression_system_vector_type_two = QtGui.QLineEdit() - self.Expression_system_vector_type_two.setText('') + self.Expression_system_vector_type_two.setText("") self.Expression_system_vector_type_two.setFixedWidth(300) self.Expression_system_vector_type_two.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.Expression_system_vector_type_two, 12, 1) - grid.addWidget(QtGui.QLabel('(e.g. plasmid)'), 12, 2) + grid.addWidget(QtGui.QLabel("(e.g. plasmid)"), 12, 2) - grid.addWidget(QtGui.QLabel('Expression_system_plasmid_name'), 13, 0) + grid.addWidget(QtGui.QLabel("Expression_system_plasmid_name"), 13, 0) self.Expression_system_plasmid_name_two = QtGui.QLineEdit() - self.Expression_system_plasmid_name_two.setText('') + self.Expression_system_plasmid_name_two.setText("") self.Expression_system_plasmid_name_two.setFixedWidth(300) self.Expression_system_plasmid_name_two.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.Expression_system_plasmid_name_two, 13, 1) - grid.addWidget(QtGui.QLabel('(e.g. pET26)'), 13, 2) + grid.addWidget(QtGui.QLabel("(e.g. pET26)"), 13, 2) - grid.addWidget(QtGui.QLabel('Manipulated_source_details'), 14, 0) + grid.addWidget(QtGui.QLabel("Manipulated_source_details"), 14, 0) self.Manipulated_source_details_two = QtGui.QLineEdit() - self.Manipulated_source_details_two.setText('') + self.Manipulated_source_details_two.setText("") self.Manipulated_source_details_two.setFixedWidth(300) self.Manipulated_source_details_two.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) grid.addWidget(self.Manipulated_source_details_two, 14, 1) - grid.addWidget(QtGui.QLabel('(any other relevant information)'), 14, 2) + grid.addWidget(QtGui.QLabel("(any other relevant information)"), 14, 2) - grid.addWidget(QtGui.QLabel('Chains'), 15, 0) + grid.addWidget(QtGui.QLabel("Chains"), 15, 0) self.molecule_chain_two = QtGui.QLineEdit() - self.molecule_chain_two.setText('') + self.molecule_chain_two.setText("") self.molecule_chain_two.setFixedWidth(300) grid.addWidget(self.molecule_chain_two, 15, 1) - grid.addWidget(QtGui.QLabel('(e.g. A or A,B)'), 15, 2) + grid.addWidget(QtGui.QLabel("(e.g. A or A,B)"), 15, 2) frame.setLayout(grid) @@ -1977,7 +2230,7 @@ def deposition_data(self): vb.addStretch(1) - deposit_tab_dict['Molecule'][1].addLayout(vb) + deposit_tab_dict["Molecule"][1].addLayout(vb) # misc vb = QtGui.QVBoxLayout() @@ -1987,99 +2240,100 @@ def deposition_data(self): grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Keywords'), 1, 0) + grid.addWidget(QtGui.QLabel("Keywords"), 1, 0) self.structure_keywords = QtGui.QLineEdit() self.structure_keywords.setText( - 'SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer') + "SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer" + ) self.structure_keywords.setFixedWidth(300) grid.addWidget(self.structure_keywords, 1, 1) - grid.addWidget(QtGui.QLabel( - '(e.g. beta barrel, protein-DNA complex)'), 1, 2) + grid.addWidget(QtGui.QLabel("(e.g. beta barrel, protein-DNA complex)"), 1, 2) - grid.addWidget(QtGui.QLabel('Type'), 2, 0) + grid.addWidget(QtGui.QLabel("Type"), 2, 0) self.structure_keywords_type = QtGui.QComboBox() self.structure_keywords_type.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) for item in XChemMain.pdbx_keywords(): self.structure_keywords_type.addItem(item) grid.addWidget(self.structure_keywords_type, 2, 1) -# self.structure_keywords = QtGui.QLineEdit() -# self.structure_keywords.setText('SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer') -# self.structure_keywords.setFixedWidth(300) -# grid.addWidget(self.structure_keywords, 1, 1) -# grid.addWidget(QtGui.QLabel('(e.g. beta barrel, protein-DNA complex)'), 1, 2) + # self.structure_keywords = QtGui.QLineEdit() + # self.structure_keywords.setText('SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer') + # self.structure_keywords.setFixedWidth(300) + # grid.addWidget(self.structure_keywords, 1, 1) + # grid.addWidget(QtGui.QLabel('(e.g. beta barrel, protein-DNA complex)'), 1, 2) - grid.addWidget(QtGui.QLabel('Biological Assembly'), 3, 0) + grid.addWidget(QtGui.QLabel("Biological Assembly"), 3, 0) self.biological_assembly_chain_number = QtGui.QLineEdit() - self.biological_assembly_chain_number.setText('') + self.biological_assembly_chain_number.setText("") self.biological_assembly_chain_number.setFixedWidth(300) grid.addWidget(self.biological_assembly_chain_number, 3, 1) - grid.addWidget(QtGui.QLabel( - '(e.g. 1 for monomer, 2 for dimer ..)'), 3, 2) + grid.addWidget(QtGui.QLabel("(e.g. 1 for monomer, 2 for dimer ..)"), 3, 2) - grid.addWidget(QtGui.QLabel('Sequence UNIPROT ID'), 4, 0) + grid.addWidget(QtGui.QLabel("Sequence UNIPROT ID"), 4, 0) self.molecule_one_letter_sequence_uniprot_id = QtGui.QLineEdit() - self.molecule_one_letter_sequence_uniprot_id.setText('') + self.molecule_one_letter_sequence_uniprot_id.setText("") self.molecule_one_letter_sequence_uniprot_id.setFixedWidth(300) grid.addWidget(self.molecule_one_letter_sequence_uniprot_id, 4, 1) - grid.addWidget(QtGui.QLabel('(e.g. Q6B0I6)'), 4, 2) + grid.addWidget(QtGui.QLabel("(e.g. Q6B0I6)"), 4, 2) - grid.addWidget(QtGui.QLabel('Sequence'), 5, 0) + grid.addWidget(QtGui.QLabel("Sequence"), 5, 0) self.molecule_one_letter_sequence = QtGui.QTextEdit() self.molecule_one_letter_sequence.setStyleSheet( - "background-color: rgb(255, 255, 255);") -# self.molecule_one_letter_sequence.setStyleSheet("background-color: rgb(192, 192, 192);") - self.molecule_one_letter_sequence.setText('') + "background-color: rgb(255, 255, 255);" + ) + # self.molecule_one_letter_sequence.setStyleSheet("background-color: rgb(192, 192, 192);") + self.molecule_one_letter_sequence.setText("") self.molecule_one_letter_sequence.setFixedWidth(300) grid.addWidget(self.molecule_one_letter_sequence, 5, 1, 8, 2) -# grid.addWidget(QtGui.QLabel('Sequence information for entity 2'), 10, 0) -# grid.addWidget(QtGui.QLabel('(Important: only for protein-protein complex'), 10, 1) + # grid.addWidget(QtGui.QLabel('Sequence information for entity 2'), 10, 0) + # grid.addWidget(QtGui.QLabel('(Important: only for protein-protein complex'), 10, 1) - grid.addWidget(QtGui.QLabel( - 'Sequence UNIPROT ID (Entity 2) - optional'), 13, 0) + grid.addWidget(QtGui.QLabel("Sequence UNIPROT ID (Entity 2) - optional"), 13, 0) self.molecule_one_letter_sequence_uniprot_id_two = QtGui.QLineEdit() - self.molecule_one_letter_sequence_uniprot_id_two.setText('') + self.molecule_one_letter_sequence_uniprot_id_two.setText("") self.molecule_one_letter_sequence_uniprot_id_two.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) self.molecule_one_letter_sequence_uniprot_id_two.setFixedWidth(300) grid.addWidget(self.molecule_one_letter_sequence_uniprot_id_two, 13, 1) - grid.addWidget(QtGui.QLabel('(e.g. Q6B0I6)'), 13, 2) + grid.addWidget(QtGui.QLabel("(e.g. Q6B0I6)"), 13, 2) - grid.addWidget(QtGui.QLabel('Sequence (Entity 2) - optional'), 14, 0) + grid.addWidget(QtGui.QLabel("Sequence (Entity 2) - optional"), 14, 0) self.molecule_one_letter_sequence_two = QtGui.QTextEdit() - self.molecule_one_letter_sequence_two.setText('') + self.molecule_one_letter_sequence_two.setText("") self.molecule_one_letter_sequence_two.setFixedWidth(300) grid.addWidget(self.molecule_one_letter_sequence_two, 14, 1, 19, 2) - grid.addWidget(QtGui.QLabel('Structural Genomic (optional)'), 21, 0) + grid.addWidget(QtGui.QLabel("Structural Genomic (optional)"), 21, 0) - grid.addWidget(QtGui.QLabel('Project Name'), 22, 0) + grid.addWidget(QtGui.QLabel("Project Name"), 22, 0) self.SG_project_name = QtGui.QLineEdit() - self.SG_project_name.setText('') - self.SG_project_name.setStyleSheet( - "background-color: rgb(192, 192, 192);") + self.SG_project_name.setText("") + self.SG_project_name.setStyleSheet("background-color: rgb(192, 192, 192);") self.SG_project_name.setFixedWidth(300) grid.addWidget(self.SG_project_name, 22, 1) - grid.addWidget(QtGui.QLabel( - '(e.g. SGC, Structural Genomics Consortium)'), 22, 2) + grid.addWidget( + QtGui.QLabel("(e.g. SGC, Structural Genomics Consortium)"), 22, 2 + ) - grid.addWidget(QtGui.QLabel('Full Name'), 23, 0) + grid.addWidget(QtGui.QLabel("Full Name"), 23, 0) self.full_name_of_SG_center = QtGui.QLineEdit() - self.full_name_of_SG_center.setText('') + self.full_name_of_SG_center.setText("") self.full_name_of_SG_center.setStyleSheet( - "background-color: rgb(192, 192, 192);") + "background-color: rgb(192, 192, 192);" + ) self.full_name_of_SG_center.setFixedWidth(300) grid.addWidget(self.full_name_of_SG_center, 23, 1) - grid.addWidget(QtGui.QLabel( - '(e.g. Structural Genomics Consortium)'), 23, 2) + grid.addWidget(QtGui.QLabel("(e.g. Structural Genomics Consortium)"), 23, 2) frame.setLayout(grid) vb.addWidget(frame) vb.addStretch(1) - deposit_tab_dict['Misc'][1].addLayout(vb) + deposit_tab_dict["Misc"][1].addLayout(vb) # methods vb = QtGui.QVBoxLayout() @@ -2089,105 +2343,106 @@ def deposition_data(self): grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Crystallization'), 1, 0) + grid.addWidget(QtGui.QLabel("Crystallization"), 1, 0) - grid.addWidget(QtGui.QLabel('Method'), 2, 0) + grid.addWidget(QtGui.QLabel("Method"), 2, 0) self.crystallization_method = QtGui.QComboBox() for item in XChemMain.crystal_growth_methods(): self.crystallization_method.addItem(item) grid.addWidget(self.crystallization_method, 2, 1) - grid.addWidget(QtGui.QLabel('pH'), 3, 0) + grid.addWidget(QtGui.QLabel("pH"), 3, 0) self.crystallization_pH = QtGui.QLineEdit() - self.crystallization_pH.setText('') + self.crystallization_pH.setText("") self.crystallization_pH.setFixedWidth(300) grid.addWidget(self.crystallization_pH, 3, 1) - grid.addWidget(QtGui.QLabel('(e.g. 7.5 ...)'), 3, 2) + grid.addWidget(QtGui.QLabel("(e.g. 7.5 ...)"), 3, 2) - grid.addWidget(QtGui.QLabel('Temperature'), 4, 0) + grid.addWidget(QtGui.QLabel("Temperature"), 4, 0) self.crystallization_temperature = QtGui.QLineEdit() - self.crystallization_temperature.setText('') + self.crystallization_temperature.setText("") self.crystallization_temperature.setFixedWidth(300) grid.addWidget(self.crystallization_temperature, 4, 1) - grid.addWidget(QtGui.QLabel('(e.g. 298) (in Kelvin)'), 4, 2) + grid.addWidget(QtGui.QLabel("(e.g. 298) (in Kelvin)"), 4, 2) - grid.addWidget(QtGui.QLabel('Condition'), 5, 0) + grid.addWidget(QtGui.QLabel("Condition"), 5, 0) self.crystallization_details = QtGui.QLineEdit() - self.crystallization_details.setText('') + self.crystallization_details.setText("") self.crystallization_details.setFixedWidth(300) grid.addWidget(self.crystallization_details, 5, 1) - grid.addWidget(QtGui.QLabel('(e.g. PEG 4000, NaCl etc.)'), 5, 2) + grid.addWidget(QtGui.QLabel("(e.g. PEG 4000, NaCl etc.)"), 5, 2) - grid.addWidget(QtGui.QLabel('Diffraction Experiment'), 6, 0) - note = ('Note: this information will only be used if it is\n' - 'not already available in the mainTable!\n' - 'Ignore if data were collected at DLS') + grid.addWidget(QtGui.QLabel("Diffraction Experiment"), 6, 0) + note = ( + "Note: this information will only be used if it is\n" + "not already available in the mainTable!\n" + "Ignore if data were collected at DLS" + ) grid.addWidget(QtGui.QLabel(note), 7, 0) - grid.addWidget(QtGui.QLabel('Source'), 8, 0) + grid.addWidget(QtGui.QLabel("Source"), 8, 0) self.radiation_source = QtGui.QComboBox() for item in XChemMain.radiationSource(): self.radiation_source.addItem(item) grid.addWidget(self.radiation_source, 8, 1) - grid.addWidget(QtGui.QLabel('Source Type'), 9, 0) + grid.addWidget(QtGui.QLabel("Source Type"), 9, 0) self.radiation_source_type = QtGui.QComboBox() for item in XChemMain.wwBeamlines(): self.radiation_source_type.addItem(item) grid.addWidget(self.radiation_source_type, 9, 1) - grid.addWidget(QtGui.QLabel('Wavelength'), 10, 0) + grid.addWidget(QtGui.QLabel("Wavelength"), 10, 0) self.radiation_wavelengths = QtGui.QLineEdit() - self.radiation_wavelengths.setText('') + self.radiation_wavelengths.setText("") self.radiation_wavelengths.setFixedWidth(300) grid.addWidget(self.radiation_wavelengths, 10, 1) - grid.addWidget(QtGui.QLabel('(e.g. 1.502)'), 10, 2) + grid.addWidget(QtGui.QLabel("(e.g. 1.502)"), 10, 2) - grid.addWidget(QtGui.QLabel('Detector'), 11, 0) + grid.addWidget(QtGui.QLabel("Detector"), 11, 0) self.radiation_detector = QtGui.QComboBox() for item in XChemMain.detector(): self.radiation_detector.addItem(item) grid.addWidget(self.radiation_detector, 11, 1) - grid.addWidget(QtGui.QLabel('Detector Type'), 12, 0) + grid.addWidget(QtGui.QLabel("Detector Type"), 12, 0) self.radiation_detector_type = QtGui.QComboBox() for item in XChemMain.detectorType(): self.radiation_detector_type.addItem(item) grid.addWidget(self.radiation_detector_type, 12, 1) - grid.addWidget(QtGui.QLabel('Date'), 13, 0) + grid.addWidget(QtGui.QLabel("Date"), 13, 0) self.data_collection_date = QtGui.QLineEdit() - self.data_collection_date.setText('') + self.data_collection_date.setText("") self.data_collection_date.setFixedWidth(300) grid.addWidget(self.data_collection_date, 13, 1) - grid.addWidget(QtGui.QLabel('(e.g. 2004-01-07)'), 13, 2) + grid.addWidget(QtGui.QLabel("(e.g. 2004-01-07)"), 13, 2) - grid.addWidget(QtGui.QLabel('Temperature'), 14, 0) + grid.addWidget(QtGui.QLabel("Temperature"), 14, 0) self.data_collection_temperature = QtGui.QLineEdit() - self.data_collection_temperature.setText('') + self.data_collection_temperature.setText("") self.data_collection_temperature.setFixedWidth(300) grid.addWidget(self.data_collection_temperature, 14, 1) - grid.addWidget(QtGui.QLabel('(e.g. 100) (in Kelvin)'), 14, 2) + grid.addWidget(QtGui.QLabel("(e.g. 100) (in Kelvin)"), 14, 2) - grid.addWidget(QtGui.QLabel('Protocol'), 15, 0) + grid.addWidget(QtGui.QLabel("Protocol"), 15, 0) self.data_collection_protocol = QtGui.QLineEdit() - self.data_collection_protocol.setText('SINGLE WAVELENGTH') + self.data_collection_protocol.setText("SINGLE WAVELENGTH") self.data_collection_protocol.setFixedWidth(300) grid.addWidget(self.data_collection_protocol, 15, 1) - grid.addWidget(QtGui.QLabel( - '(e.g. SINGLE WAVELENGTH, MAD, ...)'), 15, 2) + grid.addWidget(QtGui.QLabel("(e.g. SINGLE WAVELENGTH, MAD, ...)"), 15, 2) frame.setLayout(grid) vb.addWidget(frame) vb.addStretch(1) - deposit_tab_dict['Methods'][1].addLayout(vb) + deposit_tab_dict["Methods"][1].addLayout(vb) # software vb = QtGui.QVBoxLayout() @@ -2197,20 +2452,20 @@ def deposition_data(self): grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('PDB starting model'), 1, 0) + grid.addWidget(QtGui.QLabel("PDB starting model"), 1, 0) self.pdbx_starting_model = QtGui.QLineEdit() - self.pdbx_starting_model.setText('') + self.pdbx_starting_model.setText("") self.pdbx_starting_model.setFixedWidth(300) grid.addWidget(self.pdbx_starting_model, 1, 1) - grid.addWidget(QtGui.QLabel('(e.g. 7.5 ...)'), 1, 2) + grid.addWidget(QtGui.QLabel("(e.g. 7.5 ...)"), 1, 2) - grid.addWidget(QtGui.QLabel('Data reduction'), 2, 0) + grid.addWidget(QtGui.QLabel("Data reduction"), 2, 0) self.data_integration_software = QtGui.QComboBox() for item in XChemMain.data_integration_software(): self.data_integration_software.addItem(item) grid.addWidget(self.data_integration_software, 2, 1) - grid.addWidget(QtGui.QLabel('Phasing'), 3, 0) + grid.addWidget(QtGui.QLabel("Phasing"), 3, 0) self.phasing_software = QtGui.QComboBox() for item in XChemMain.phasing_software(): self.phasing_software.addItem(item) @@ -2220,7 +2475,7 @@ def deposition_data(self): vb.addWidget(frame) vb.addStretch(1) - deposit_tab_dict['Software'][1].addLayout(vb) + deposit_tab_dict["Software"][1].addLayout(vb) # Funding @@ -2231,19 +2486,19 @@ def deposition_data(self): grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Funding Organization'), 1, 0) + grid.addWidget(QtGui.QLabel("Funding Organization"), 1, 0) self.pdbx_funding_organization_one = QtGui.QLineEdit() - self.pdbx_funding_organization_one.setText('') + self.pdbx_funding_organization_one.setText("") self.pdbx_funding_organization_one.setFixedWidth(700) grid.addWidget(self.pdbx_funding_organization_one, 1, 1) - grid.addWidget(QtGui.QLabel('Grant Number'), 2, 0) + grid.addWidget(QtGui.QLabel("Grant Number"), 2, 0) self.pdbx_grant_number_one = QtGui.QLineEdit() - self.pdbx_grant_number_one.setText('') + self.pdbx_grant_number_one.setText("") self.pdbx_grant_number_one.setFixedWidth(700) grid.addWidget(self.pdbx_grant_number_one, 2, 1) - grid.addWidget(QtGui.QLabel('Country'), 3, 0) + grid.addWidget(QtGui.QLabel("Country"), 3, 0) self.pdbx_grant_country_one = QtGui.QComboBox() for item in XChemMain.pdbx_country(): self.pdbx_grant_country_one.addItem(item) @@ -2257,19 +2512,19 @@ def deposition_data(self): grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Funding Organization'), 1, 0) + grid.addWidget(QtGui.QLabel("Funding Organization"), 1, 0) self.pdbx_funding_organization_two = QtGui.QLineEdit() - self.pdbx_funding_organization_two.setText('') + self.pdbx_funding_organization_two.setText("") self.pdbx_funding_organization_two.setFixedWidth(700) grid.addWidget(self.pdbx_funding_organization_two, 1, 1) - grid.addWidget(QtGui.QLabel('Grant Number'), 2, 0) + grid.addWidget(QtGui.QLabel("Grant Number"), 2, 0) self.pdbx_grant_number_two = QtGui.QLineEdit() - self.pdbx_grant_number_two.setText('') + self.pdbx_grant_number_two.setText("") self.pdbx_grant_number_two.setFixedWidth(700) grid.addWidget(self.pdbx_grant_number_two, 2, 1) - grid.addWidget(QtGui.QLabel('Country'), 3, 0) + grid.addWidget(QtGui.QLabel("Country"), 3, 0) self.pdbx_grant_country_two = QtGui.QComboBox() for item in XChemMain.pdbx_country(): self.pdbx_grant_country_two.addItem(item) @@ -2283,19 +2538,19 @@ def deposition_data(self): grid = QtGui.QGridLayout() - grid.addWidget(QtGui.QLabel('Funding Organization'), 1, 0) + grid.addWidget(QtGui.QLabel("Funding Organization"), 1, 0) self.pdbx_funding_organization_three = QtGui.QLineEdit() - self.pdbx_funding_organization_three.setText('') + self.pdbx_funding_organization_three.setText("") self.pdbx_funding_organization_three.setFixedWidth(700) grid.addWidget(self.pdbx_funding_organization_three, 1, 1) - grid.addWidget(QtGui.QLabel('Grant Number'), 2, 0) + grid.addWidget(QtGui.QLabel("Grant Number"), 2, 0) self.pdbx_grant_number_three = QtGui.QLineEdit() - self.pdbx_grant_number_three.setText('') + self.pdbx_grant_number_three.setText("") self.pdbx_grant_number_three.setFixedWidth(700) grid.addWidget(self.pdbx_grant_number_three, 2, 1) - grid.addWidget(QtGui.QLabel('Country'), 3, 0) + grid.addWidget(QtGui.QLabel("Country"), 3, 0) self.pdbx_grant_country_three = QtGui.QComboBox() for item in XChemMain.pdbx_country(): self.pdbx_grant_country_three.addItem(item) @@ -2306,22 +2561,22 @@ def deposition_data(self): vb.addStretch(1) - deposit_tab_dict['Funding'][1].addLayout(vb) + deposit_tab_dict["Funding"][1].addLayout(vb) vbox.addWidget(deposit_tab_widget) hbox = QtGui.QHBoxLayout() - button = QtGui.QPushButton('Load\nFile') + button = QtGui.QPushButton("Load\nFile") button.clicked.connect(self.load_deposit_config_file) hbox.addWidget(button) - button = QtGui.QPushButton('Save\nFile') + button = QtGui.QPushButton("Save\nFile") button.clicked.connect(self.save_deposit_config_file) hbox.addWidget(button) - button = QtGui.QPushButton('Load from\nDatabase') + button = QtGui.QPushButton("Load from\nDatabase") button.clicked.connect(self.load_deposit_from_database) button.setEnabled(False) hbox.addWidget(button) - button = QtGui.QPushButton('Save to\nDatabase') + button = QtGui.QPushButton("Save to\nDatabase") button.clicked.connect(self.save_deposit_to_database) hbox.addWidget(button) @@ -2332,624 +2587,772 @@ def deposition_data(self): def save_deposit_config_file(self): self.update_deposit_dict() - file_name = str(QtGui.QFileDialog.getSaveFileName( - self.window, 'Save file', self.current_directory)) + file_name = str( + QtGui.QFileDialog.getSaveFileName( + self.window, "Save file", self.current_directory + ) + ) # make sure that the file always has .deposit extension - if str(file_name).rfind('.') != -1: - file_name = file_name[:file_name.rfind('.')] + '.deposit' + if str(file_name).rfind(".") != -1: + file_name = file_name[: file_name.rfind(".")] + ".deposit" else: - file_name = file_name + '.deposit' - pickle.dump(self.deposit_dict, open(file_name, 'wb')) + file_name = file_name + ".deposit" + pickle.dump(self.deposit_dict, open(file_name, "wb")) def update_database_with_pdb_codes(self): - self.work_thread = XChemDeposit.import_PDB_IDs(str(self.pdb_code_entry.toPlainText()), - os.path.join( - self.database_directory, self.data_source_file), - self.xce_logfile) + self.work_thread = XChemDeposit.import_PDB_IDs( + str(self.pdb_code_entry.toPlainText()), + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def update_database_with_labelInfo(self): for n, l in enumerate(self.labelList): label = str(l[0].text()) description = str(l[1].text()) -# print "update labelTable set Label='%s',Description='%s' where ID=%s" %(label,description,str(n+1)) - self.db.execute_statement("update labelTable set Label='%s',Description='%s' where ID=%s" % ( - label, description, str(n+1))) -# print label,description + # print "update labelTable set Label='%s',Description='%s' where ID=%s" %(label,description,str(n+1)) + self.db.execute_statement( + "update labelTable set Label='%s',Description='%s' where ID=%s" + % (label, description, str(n + 1)) + ) + + # print label,description def load_deposit_config_file(self): - file_name_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Open file', self.current_directory, - '*.deposit') + file_name_temp = QtGui.QFileDialog.getOpenFileNameAndFilter( + self.window, "Open file", self.current_directory, "*.deposit" + ) file_name = tuple(file_name_temp)[0] self.deposit_dict = pickle.load(open(file_name, "rb")) -# print self.deposit_dict + # print self.deposit_dict for key in self.get_deposit_dict_template(): if key not in self.deposit_dict: - self.update_log.warning( - 'field not in .deposit file: ' + str(key)) - self.deposit_dict[key] = '' + self.update_log.warning("field not in .deposit file: " + str(key)) + self.deposit_dict[key] = "" self.update_deposit_input() def load_deposit_from_database(self): - print('hallo') + print("hallo") def save_deposit_to_database(self): self.update_deposit_dict() msgBox = QtGui.QMessageBox() msgBox.setText( - "*** WARNING ***\nAre you sure you want to update the database?\nThis will overwrite previous entries!") - msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) + "*** WARNING ***\nAre you sure you want to update the database?\nThis will overwrite previous entries!" + ) + msgBox.addButton(QtGui.QPushButton("Yes"), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.RejectRole) reply = msgBox.exec_() if reply == 0: - self.work_thread = XChemDeposit.update_depositTable(self.deposit_dict, - os.path.join(self.database_directory, - self.data_source_file), - self.xce_logfile) + self.work_thread = XChemDeposit.update_depositTable( + self.deposit_dict, + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def update_deposit_input(self): try: self.contact_author_PI_salutation.setText( - self.deposit_dict['contact_author_PI_salutation']) + self.deposit_dict["contact_author_PI_salutation"] + ) self.contact_author_PI_first_name.setText( - self.deposit_dict['contact_author_PI_first_name']) + self.deposit_dict["contact_author_PI_first_name"] + ) self.contact_author_PI_last_name.setText( - self.deposit_dict['contact_author_PI_last_name']) + self.deposit_dict["contact_author_PI_last_name"] + ) self.contact_author_PI_middle_name.setText( - self.deposit_dict['contact_author_PI_middle_name']) - index = self.contact_author_PI_role.findText(self.deposit_dict['contact_author_PI_role'], - QtCore.Qt.MatchFixedString) + self.deposit_dict["contact_author_PI_middle_name"] + ) + index = self.contact_author_PI_role.findText( + self.deposit_dict["contact_author_PI_role"], QtCore.Qt.MatchFixedString + ) self.contact_author_PI_role.setCurrentIndex(index) index = self.contact_author_PI_organization_type.findText( - self.deposit_dict['contact_author_PI_organization_type'], QtCore.Qt.MatchFixedString) + self.deposit_dict["contact_author_PI_organization_type"], + QtCore.Qt.MatchFixedString, + ) self.contact_author_PI_organization_type.setCurrentIndex(index) self.contact_author_PI_organization_name.setText( - self.deposit_dict['contact_author_PI_organization_name']) + self.deposit_dict["contact_author_PI_organization_name"] + ) self.contact_author_PI_email.setText( - self.deposit_dict['contact_author_PI_email']) + self.deposit_dict["contact_author_PI_email"] + ) self.contact_author_PI_address.setText( - self.deposit_dict['contact_author_PI_address']) + self.deposit_dict["contact_author_PI_address"] + ) self.contact_author_PI_city.setText( - self.deposit_dict['contact_author_PI_city']) + self.deposit_dict["contact_author_PI_city"] + ) self.contact_author_PI_State_or_Province.setText( - self.deposit_dict['contact_author_PI_State_or_Province']) + self.deposit_dict["contact_author_PI_State_or_Province"] + ) self.contact_author_PI_Zip_Code.setText( - self.deposit_dict['contact_author_PI_Zip_Code']) + self.deposit_dict["contact_author_PI_Zip_Code"] + ) self.contact_author_PI_Country.setText( - self.deposit_dict['contact_author_PI_Country']) + self.deposit_dict["contact_author_PI_Country"] + ) self.contact_author_PI_phone_number.setText( - self.deposit_dict['contact_author_PI_phone_number']) + self.deposit_dict["contact_author_PI_phone_number"] + ) self.contact_author_PI_ORCID.setText( - self.deposit_dict['contact_author_PI_ORCID']) + self.deposit_dict["contact_author_PI_ORCID"] + ) self.contact_author_salutation.setText( - self.deposit_dict['contact_author_salutation']) + self.deposit_dict["contact_author_salutation"] + ) self.contact_author_first_name.setText( - self.deposit_dict['contact_author_first_name']) + self.deposit_dict["contact_author_first_name"] + ) self.contact_author_last_name.setText( - self.deposit_dict['contact_author_last_name']) + self.deposit_dict["contact_author_last_name"] + ) self.contact_author_middle_name.setText( - self.deposit_dict['contact_author_middle_name']) - index = self.contact_author_role.findText(self.deposit_dict['contact_author_role'], - QtCore.Qt.MatchFixedString) + self.deposit_dict["contact_author_middle_name"] + ) + index = self.contact_author_role.findText( + self.deposit_dict["contact_author_role"], QtCore.Qt.MatchFixedString + ) self.contact_author_role.setCurrentIndex(index) index = self.contact_author_organization_type.findText( - self.deposit_dict['contact_author_organization_type'], QtCore.Qt.MatchFixedString) + self.deposit_dict["contact_author_organization_type"], + QtCore.Qt.MatchFixedString, + ) self.contact_author_organization_type.setCurrentIndex(index) self.contact_author_organization_name.setText( - self.deposit_dict['contact_author_organization_name']) - self.contact_author_email.setText( - self.deposit_dict['contact_author_email']) + self.deposit_dict["contact_author_organization_name"] + ) + self.contact_author_email.setText(self.deposit_dict["contact_author_email"]) self.contact_author_address.setText( - self.deposit_dict['contact_author_address']) - self.contact_author_city.setText( - self.deposit_dict['contact_author_city']) + self.deposit_dict["contact_author_address"] + ) + self.contact_author_city.setText(self.deposit_dict["contact_author_city"]) self.contact_author_State_or_Province.setText( - self.deposit_dict['contact_author_State_or_Province']) + self.deposit_dict["contact_author_State_or_Province"] + ) self.contact_author_Zip_Code.setText( - self.deposit_dict['contact_author_Zip_Code']) + self.deposit_dict["contact_author_Zip_Code"] + ) self.contact_author_Country.setText( - self.deposit_dict['contact_author_Country']) + self.deposit_dict["contact_author_Country"] + ) self.contact_author_phone_number.setText( - self.deposit_dict['contact_author_phone_number']) - self.contact_author_ORCID.setText( - self.deposit_dict['contact_author_ORCID']) - index = self.Release_status_for_coordinates.findText(self.deposit_dict['Release_status_for_coordinates'], - QtCore.Qt.MatchFixedString) + self.deposit_dict["contact_author_phone_number"] + ) + self.contact_author_ORCID.setText(self.deposit_dict["contact_author_ORCID"]) + index = self.Release_status_for_coordinates.findText( + self.deposit_dict["Release_status_for_coordinates"], + QtCore.Qt.MatchFixedString, + ) self.Release_status_for_coordinates.setCurrentIndex(index) - index = self.Release_status_for_sequence.findText(self.deposit_dict['Release_status_for_sequence'], - QtCore.Qt.MatchFixedString) + index = self.Release_status_for_sequence.findText( + self.deposit_dict["Release_status_for_sequence"], + QtCore.Qt.MatchFixedString, + ) self.Release_status_for_sequence.setCurrentIndex(index) self.group_deposition_title.setText( - self.deposit_dict['group_deposition_title']) - self.group_description.setText( - self.deposit_dict['group_description']) + self.deposit_dict["group_deposition_title"] + ) + self.group_description.setText(self.deposit_dict["group_description"]) - self.structure_title.setText(self.deposit_dict['structure_title']) - self.structure_title_apo.setText( - self.deposit_dict['structure_title_apo']) + self.structure_title.setText(self.deposit_dict["structure_title"]) + self.structure_title_apo.setText(self.deposit_dict["structure_title_apo"]) - for n, name in enumerate(self.deposit_dict['structure_author_name'].split(';')): + for n, name in enumerate( + self.deposit_dict["structure_author_name"].split(";") + ): self.structure_author_name_List[n].setText(name) - self.primary_citation_id.setText( - self.deposit_dict['primary_citation_id']) + self.primary_citation_id.setText(self.deposit_dict["primary_citation_id"]) self.primary_citation_journal_abbrev.setText( - self.deposit_dict['primary_citation_journal_abbrev']) + self.deposit_dict["primary_citation_journal_abbrev"] + ) self.primary_citation_title.setText( - self.deposit_dict['primary_citation_title']) + self.deposit_dict["primary_citation_title"] + ) self.primary_citation_year.setText( - self.deposit_dict['primary_citation_year']) + self.deposit_dict["primary_citation_year"] + ) self.primary_citation_journal_volume.setText( - self.deposit_dict['primary_citation_journal_volume']) + self.deposit_dict["primary_citation_journal_volume"] + ) self.primary_citation_page_first.setText( - self.deposit_dict['primary_citation_page_first']) + self.deposit_dict["primary_citation_page_first"] + ) self.primary_citation_page_last.setText( - self.deposit_dict['primary_citation_page_last']) + self.deposit_dict["primary_citation_page_last"] + ) - for n, name in enumerate(self.deposit_dict['primary_citation_author_name'].split(';')): + for n, name in enumerate( + self.deposit_dict["primary_citation_author_name"].split(";") + ): self.primary_citation_author_name_List[n].setText(name) # entity 1 - self.molecule_name.setText(self.deposit_dict['molecule_name']) + self.molecule_name.setText(self.deposit_dict["molecule_name"]) self.fragment_name_one_specific_mutation.setText( - self.deposit_dict['fragment_name_one_specific_mutation']) - index = self.Source_organism_scientific_name.findText(self.deposit_dict['Source_organism_scientific_name'], - QtCore.Qt.MatchFixedString) + self.deposit_dict["fragment_name_one_specific_mutation"] + ) + index = self.Source_organism_scientific_name.findText( + self.deposit_dict["Source_organism_scientific_name"], + QtCore.Qt.MatchFixedString, + ) self.Source_organism_scientific_name.setCurrentIndex(index) - self.Source_organism_gene.setText( - self.deposit_dict['Source_organism_gene']) + self.Source_organism_gene.setText(self.deposit_dict["Source_organism_gene"]) self.Source_organism_strain.setText( - self.deposit_dict['Source_organism_strain']) + self.deposit_dict["Source_organism_strain"] + ) index = self.Expression_system_scientific_name.findText( - self.deposit_dict['Expression_system_scientific_name'], QtCore.Qt.MatchFixedString) + self.deposit_dict["Expression_system_scientific_name"], + QtCore.Qt.MatchFixedString, + ) self.Expression_system_scientific_name.setCurrentIndex(index) self.Expression_system_strain.setText( - self.deposit_dict['Expression_system_strain']) + self.deposit_dict["Expression_system_strain"] + ) self.Expression_system_vector_type.setText( - self.deposit_dict['Expression_system_vector_type']) + self.deposit_dict["Expression_system_vector_type"] + ) self.Expression_system_plasmid_name.setText( - self.deposit_dict['Expression_system_plasmid_name']) + self.deposit_dict["Expression_system_plasmid_name"] + ) self.Manipulated_source_details.setText( - self.deposit_dict['Manipulated_source_details']) + self.deposit_dict["Manipulated_source_details"] + ) -# try: - self.molecule_chain_one.setText( - self.deposit_dict['molecule_chain_one']) + # try: + self.molecule_chain_one.setText(self.deposit_dict["molecule_chain_one"]) # entity 2 - self.molecule_name_two.setText( - self.deposit_dict['molecule_name_two']) + self.molecule_name_two.setText(self.deposit_dict["molecule_name_two"]) self.fragment_name_two_specific_mutation.setText( - self.deposit_dict['fragment_name_two_specific_mutation']) - index = self.Source_organism_scientific_name_two.findText(self.deposit_dict['Source_organism_scientific_name_two'], - QtCore.Qt.MatchFixedString) + self.deposit_dict["fragment_name_two_specific_mutation"] + ) + index = self.Source_organism_scientific_name_two.findText( + self.deposit_dict["Source_organism_scientific_name_two"], + QtCore.Qt.MatchFixedString, + ) self.Source_organism_scientific_name_two.setCurrentIndex(index) self.Source_organism_gene_two.setText( - self.deposit_dict['Source_organism_gene_two']) + self.deposit_dict["Source_organism_gene_two"] + ) self.Source_organism_strain_two.setText( - self.deposit_dict['Source_organism_strain_two']) + self.deposit_dict["Source_organism_strain_two"] + ) index = self.Expression_system_scientific_name_two.findText( - self.deposit_dict['Expression_system_scientific_name_two'], QtCore.Qt.MatchFixedString) + self.deposit_dict["Expression_system_scientific_name_two"], + QtCore.Qt.MatchFixedString, + ) self.Expression_system_scientific_name_two.setCurrentIndex(index) self.Expression_system_strain_two.setText( - self.deposit_dict['Expression_system_strain_two']) + self.deposit_dict["Expression_system_strain_two"] + ) self.Expression_system_vector_type_two.setText( - self.deposit_dict['Expression_system_vector_type_two']) + self.deposit_dict["Expression_system_vector_type_two"] + ) self.Expression_system_plasmid_name_two.setText( - self.deposit_dict['Expression_system_plasmid_name_two']) + self.deposit_dict["Expression_system_plasmid_name_two"] + ) self.Manipulated_source_details_two.setText( - self.deposit_dict['Manipulated_source_details_two']) - self.molecule_chain_two.setText( - self.deposit_dict['molecule_chain_two']) + self.deposit_dict["Manipulated_source_details_two"] + ) + self.molecule_chain_two.setText(self.deposit_dict["molecule_chain_two"]) self.molecule_one_letter_sequence_uniprot_id_two.setText( - self.deposit_dict['molecule_two_letter_sequence_uniprot_id']) + self.deposit_dict["molecule_two_letter_sequence_uniprot_id"] + ) self.molecule_one_letter_sequence_two.setText( - self.deposit_dict['molecule_two_letter_sequence']) -# except KeyError: -# self.molecule_chain_one.setText('') -# ### entity 2 -# self.molecule_name_two.setText('') -# self.fragment_name_two_specific_mutation.setText('') -# self.Source_organism_scientific_name_two.setCurrentIndex(0) -# self.Source_organism_gene_two.setText('') -# self.Source_organism_strain_two.setText('') -# self.Expression_system_scientific_name_two.setCurrentIndex(0) -# self.Expression_system_strain_two.setText('') -# self.Expression_system_vector_type_two.setText('') -# self.Expression_system_plasmid_name_two.setText('') -# self.Manipulated_source_details_two.setText('') -# self.molecule_chain_two.setText('') -# self.molecule_one_letter_sequence_uniprot_id_two.setText('') -# self.molecule_one_letter_sequence_two.setText('') + self.deposit_dict["molecule_two_letter_sequence"] + ) + # except KeyError: + # self.molecule_chain_one.setText('') + # ### entity 2 + # self.molecule_name_two.setText('') + # self.fragment_name_two_specific_mutation.setText('') + # self.Source_organism_scientific_name_two.setCurrentIndex(0) + # self.Source_organism_gene_two.setText('') + # self.Source_organism_strain_two.setText('') + # self.Expression_system_scientific_name_two.setCurrentIndex(0) + # self.Expression_system_strain_two.setText('') + # self.Expression_system_vector_type_two.setText('') + # self.Expression_system_plasmid_name_two.setText('') + # self.Manipulated_source_details_two.setText('') + # self.molecule_chain_two.setText('') + # self.molecule_one_letter_sequence_uniprot_id_two.setText('') + # self.molecule_one_letter_sequence_two.setText('') ### - self.structure_keywords.setText( - self.deposit_dict['structure_keywords']) + self.structure_keywords.setText(self.deposit_dict["structure_keywords"]) self.biological_assembly_chain_number.setText( - self.deposit_dict['biological_assembly_chain_number']) + self.deposit_dict["biological_assembly_chain_number"] + ) self.molecule_one_letter_sequence_uniprot_id.setText( - self.deposit_dict['molecule_one_letter_sequence_uniprot_id']) + self.deposit_dict["molecule_one_letter_sequence_uniprot_id"] + ) self.molecule_one_letter_sequence.setText( - self.deposit_dict['molecule_one_letter_sequence']) - self.SG_project_name.setText(self.deposit_dict['SG_project_name']) + self.deposit_dict["molecule_one_letter_sequence"] + ) + self.SG_project_name.setText(self.deposit_dict["SG_project_name"]) self.full_name_of_SG_center.setText( - self.deposit_dict['full_name_of_SG_center']) + self.deposit_dict["full_name_of_SG_center"] + ) - index = self.crystallization_method.findText(self.deposit_dict['crystallization_method'], - QtCore.Qt.MatchFixedString) + index = self.crystallization_method.findText( + self.deposit_dict["crystallization_method"], QtCore.Qt.MatchFixedString + ) self.crystallization_method.setCurrentIndex(index) - self.crystallization_pH.setText( - self.deposit_dict['crystallization_pH']) + self.crystallization_pH.setText(self.deposit_dict["crystallization_pH"]) self.crystallization_temperature.setText( - self.deposit_dict['crystallization_temperature']) + self.deposit_dict["crystallization_temperature"] + ) self.crystallization_details.setText( - self.deposit_dict['crystallization_details']) + self.deposit_dict["crystallization_details"] + ) index = self.radiation_source.findText( - self.deposit_dict['radiation_source'], QtCore.Qt.MatchFixedString) + self.deposit_dict["radiation_source"], QtCore.Qt.MatchFixedString + ) self.radiation_source.setCurrentIndex(index) - index = self.radiation_source_type.findText(self.deposit_dict['radiation_source_type'], - QtCore.Qt.MatchFixedString) + index = self.radiation_source_type.findText( + self.deposit_dict["radiation_source_type"], QtCore.Qt.MatchFixedString + ) self.radiation_source_type.setCurrentIndex(index) self.radiation_wavelengths.setText( - self.deposit_dict['radiation_wavelengths']) - index = self.radiation_detector.findText(self.deposit_dict['radiation_detector'], - QtCore.Qt.MatchFixedString) + self.deposit_dict["radiation_wavelengths"] + ) + index = self.radiation_detector.findText( + self.deposit_dict["radiation_detector"], QtCore.Qt.MatchFixedString + ) self.radiation_detector.setCurrentIndex(index) - index = self.radiation_detector_type.findText(self.deposit_dict['radiation_detector_type'], - QtCore.Qt.MatchFixedString) + index = self.radiation_detector_type.findText( + self.deposit_dict["radiation_detector_type"], QtCore.Qt.MatchFixedString + ) self.radiation_detector_type.setCurrentIndex(index) - self.data_collection_date.setText( - self.deposit_dict['data_collection_date']) + self.data_collection_date.setText(self.deposit_dict["data_collection_date"]) self.data_collection_temperature.setText( - self.deposit_dict['data_collection_temperature']) + self.deposit_dict["data_collection_temperature"] + ) self.data_collection_protocol.setText( - self.deposit_dict['data_collection_protocol']) + self.deposit_dict["data_collection_protocol"] + ) - self.pdbx_starting_model.setText( - self.deposit_dict['pdbx_starting_model']) - index = self.data_integration_software.findText(self.deposit_dict['data_integration_software'], - QtCore.Qt.MatchFixedString) + self.pdbx_starting_model.setText(self.deposit_dict["pdbx_starting_model"]) + index = self.data_integration_software.findText( + self.deposit_dict["data_integration_software"], + QtCore.Qt.MatchFixedString, + ) self.data_integration_software.setCurrentIndex(index) index = self.phasing_software.findText( - self.deposit_dict['phasing_software'], QtCore.Qt.MatchFixedString) + self.deposit_dict["phasing_software"], QtCore.Qt.MatchFixedString + ) self.phasing_software.setCurrentIndex(index) self.pdbx_funding_organization_one.setText( - self.deposit_dict['pdbx_funding_organization_one']) + self.deposit_dict["pdbx_funding_organization_one"] + ) self.pdbx_grant_number_one.setText( - self.deposit_dict['pdbx_grant_number_one']) + self.deposit_dict["pdbx_grant_number_one"] + ) index = self.pdbx_grant_country_one.findText( - self.deposit_dict['pdbx_grant_country_one'], QtCore.Qt.MatchFixedString) + self.deposit_dict["pdbx_grant_country_one"], QtCore.Qt.MatchFixedString + ) self.pdbx_grant_country_one.setCurrentIndex(index) self.pdbx_funding_organization_two.setText( - self.deposit_dict['pdbx_funding_organization_two']) + self.deposit_dict["pdbx_funding_organization_two"] + ) self.pdbx_grant_number_two.setText( - self.deposit_dict['pdbx_grant_number_two']) + self.deposit_dict["pdbx_grant_number_two"] + ) index = self.pdbx_grant_country_two.findText( - self.deposit_dict['pdbx_grant_country_two'], QtCore.Qt.MatchFixedString) + self.deposit_dict["pdbx_grant_country_two"], QtCore.Qt.MatchFixedString + ) self.pdbx_grant_country_two.setCurrentIndex(index) self.pdbx_funding_organization_three.setText( - self.deposit_dict['pdbx_funding_organization_three']) + self.deposit_dict["pdbx_funding_organization_three"] + ) self.pdbx_grant_number_three.setText( - self.deposit_dict['pdbx_grant_number_three']) + self.deposit_dict["pdbx_grant_number_three"] + ) index = self.pdbx_grant_country_three.findText( - self.deposit_dict['pdbx_grant_country_three'], QtCore.Qt.MatchFixedString) + self.deposit_dict["pdbx_grant_country_three"], + QtCore.Qt.MatchFixedString, + ) self.pdbx_grant_country_three.setCurrentIndex(index) except ValueError as e: # self.update_status_bar('Sorry, this is not a XChemExplorer deposit file!') - self.update_log.error( - 'file is not a valid .deposit file: ' + str(e)) + self.update_log.error("file is not a valid .deposit file: " + str(e)) def update_deposit_dict(self): - pdbx_funding_ordinal_one = '' - pdbx_funding_organization_one = '' - pdbx_grant_number_one = '' - pdbx_grant_country_one = '' - if str(self.pdbx_funding_organization_one.text()).replace(' ', '') != '': - pdbx_funding_ordinal_one = '1' + pdbx_funding_ordinal_one = "" + pdbx_funding_organization_one = "" + pdbx_grant_number_one = "" + pdbx_grant_country_one = "" + if str(self.pdbx_funding_organization_one.text()).replace(" ", "") != "": + pdbx_funding_ordinal_one = "1" pdbx_funding_organization_one = str( - self.pdbx_funding_organization_one.text()) + self.pdbx_funding_organization_one.text() + ) pdbx_grant_number_one = str(self.pdbx_grant_number_one.text()) - pdbx_grant_country_one = str( - self.pdbx_grant_country_one.currentText()) - - pdbx_funding_ordinal_two = '' - pdbx_funding_organization_two = '' - pdbx_grant_number_two = '' - pdbx_grant_country_two = '' - if str(self.pdbx_funding_organization_two.text()).replace(' ', '') != '': - pdbx_funding_ordinal_two = '2' + pdbx_grant_country_one = str(self.pdbx_grant_country_one.currentText()) + + pdbx_funding_ordinal_two = "" + pdbx_funding_organization_two = "" + pdbx_grant_number_two = "" + pdbx_grant_country_two = "" + if str(self.pdbx_funding_organization_two.text()).replace(" ", "") != "": + pdbx_funding_ordinal_two = "2" pdbx_funding_organization_two = str( - self.pdbx_funding_organization_two.text()) + self.pdbx_funding_organization_two.text() + ) pdbx_grant_number_two = str(self.pdbx_grant_number_two.text()) - pdbx_grant_country_two = str( - self.pdbx_grant_country_two.currentText()) - - pdbx_funding_ordinal_three = '' - pdbx_funding_organization_three = '' - pdbx_grant_number_three = '' - pdbx_grant_country_three = '' - if str(self.pdbx_funding_organization_three.text()).replace(' ', '') != '': - pdbx_funding_ordinal_three = '3' + pdbx_grant_country_two = str(self.pdbx_grant_country_two.currentText()) + + pdbx_funding_ordinal_three = "" + pdbx_funding_organization_three = "" + pdbx_grant_number_three = "" + pdbx_grant_country_three = "" + if str(self.pdbx_funding_organization_three.text()).replace(" ", "") != "": + pdbx_funding_ordinal_three = "3" pdbx_funding_organization_three = str( - self.pdbx_funding_organization_three.text()) + self.pdbx_funding_organization_three.text() + ) pdbx_grant_number_three = str(self.pdbx_grant_number_three.text()) - pdbx_grant_country_three = str( - self.pdbx_grant_country_three.currentText()) + pdbx_grant_country_three = str(self.pdbx_grant_country_three.currentText()) self.deposit_dict = { - 'contact_author_PI_salutation': str(self.contact_author_PI_salutation.text()), - 'contact_author_PI_first_name': str(self.contact_author_PI_first_name.text()), - 'contact_author_PI_last_name': str(self.contact_author_PI_last_name.text()), - 'contact_author_PI_middle_name': str(self.contact_author_PI_middle_name.text()), - 'contact_author_PI_role': str(self.contact_author_PI_role.currentText()), - 'contact_author_PI_organization_type': str(self.contact_author_PI_organization_type.currentText()), - 'contact_author_PI_organization_name': str(self.contact_author_PI_organization_name.text()), - 'contact_author_PI_email': str(self.contact_author_PI_email.text()), - 'contact_author_PI_address': str(self.contact_author_PI_address.text()), - 'contact_author_PI_city': str(self.contact_author_PI_city.text()), - 'contact_author_PI_State_or_Province': str(self.contact_author_PI_State_or_Province.text()), - 'contact_author_PI_Zip_Code': str(self.contact_author_PI_Zip_Code.text()), - 'contact_author_PI_Country': str(self.contact_author_PI_Country.text()), - 'contact_author_PI_phone_number': str(self.contact_author_PI_phone_number.text()), - 'contact_author_PI_ORCID': str(self.contact_author_PI_ORCID.text()), - - 'contact_author_salutation': str(self.contact_author_salutation.text()), - 'contact_author_first_name': str(self.contact_author_first_name.text()), - 'contact_author_last_name': str(self.contact_author_last_name.text()), - 'contact_author_middle_name': str(self.contact_author_middle_name.text()), - 'contact_author_role': str(self.contact_author_role.currentText()), - 'contact_author_organization_type': str(self.contact_author_organization_type.currentText()), - 'contact_author_organization_name': str(self.contact_author_organization_name.text()), - 'contact_author_email': str(self.contact_author_email.text()), - 'contact_author_address': str(self.contact_author_address.text()), - 'contact_author_city': str(self.contact_author_city.text()), - 'contact_author_State_or_Province': str(self.contact_author_State_or_Province.text()), - 'contact_author_Zip_Code': str(self.contact_author_Zip_Code.text()), - 'contact_author_Country': str(self.contact_author_Country.text()), - 'contact_author_phone_number': str(self.contact_author_phone_number.text()), - 'contact_author_ORCID': str(self.contact_author_ORCID.text()), - - 'Release_status_for_coordinates': str(self.Release_status_for_coordinates.currentText()), - 'Release_status_for_sequence': str(self.Release_status_for_sequence.currentText()), - - 'group_deposition_title': str(self.group_deposition_title.text()), - 'group_description': str(self.group_description.text()), - - 'structure_title': str(self.structure_title.text()), - 'structure_title_apo': str(self.structure_title_apo.text()), - - 'primary_citation_id': str(self.primary_citation_id.text()), - 'primary_citation_journal_abbrev': str(self.primary_citation_journal_abbrev.text()), - 'primary_citation_title': str(self.primary_citation_title.text()), - 'primary_citation_year': str(self.primary_citation_year.text()), - 'primary_citation_journal_volume': str(self.primary_citation_journal_volume.text()), - 'primary_citation_page_first': str(self.primary_citation_page_first.text()), - 'primary_citation_page_last': str(self.primary_citation_page_last.text()), + "contact_author_PI_salutation": str( + self.contact_author_PI_salutation.text() + ), + "contact_author_PI_first_name": str( + self.contact_author_PI_first_name.text() + ), + "contact_author_PI_last_name": str(self.contact_author_PI_last_name.text()), + "contact_author_PI_middle_name": str( + self.contact_author_PI_middle_name.text() + ), + "contact_author_PI_role": str(self.contact_author_PI_role.currentText()), + "contact_author_PI_organization_type": str( + self.contact_author_PI_organization_type.currentText() + ), + "contact_author_PI_organization_name": str( + self.contact_author_PI_organization_name.text() + ), + "contact_author_PI_email": str(self.contact_author_PI_email.text()), + "contact_author_PI_address": str(self.contact_author_PI_address.text()), + "contact_author_PI_city": str(self.contact_author_PI_city.text()), + "contact_author_PI_State_or_Province": str( + self.contact_author_PI_State_or_Province.text() + ), + "contact_author_PI_Zip_Code": str(self.contact_author_PI_Zip_Code.text()), + "contact_author_PI_Country": str(self.contact_author_PI_Country.text()), + "contact_author_PI_phone_number": str( + self.contact_author_PI_phone_number.text() + ), + "contact_author_PI_ORCID": str(self.contact_author_PI_ORCID.text()), + "contact_author_salutation": str(self.contact_author_salutation.text()), + "contact_author_first_name": str(self.contact_author_first_name.text()), + "contact_author_last_name": str(self.contact_author_last_name.text()), + "contact_author_middle_name": str(self.contact_author_middle_name.text()), + "contact_author_role": str(self.contact_author_role.currentText()), + "contact_author_organization_type": str( + self.contact_author_organization_type.currentText() + ), + "contact_author_organization_name": str( + self.contact_author_organization_name.text() + ), + "contact_author_email": str(self.contact_author_email.text()), + "contact_author_address": str(self.contact_author_address.text()), + "contact_author_city": str(self.contact_author_city.text()), + "contact_author_State_or_Province": str( + self.contact_author_State_or_Province.text() + ), + "contact_author_Zip_Code": str(self.contact_author_Zip_Code.text()), + "contact_author_Country": str(self.contact_author_Country.text()), + "contact_author_phone_number": str(self.contact_author_phone_number.text()), + "contact_author_ORCID": str(self.contact_author_ORCID.text()), + "Release_status_for_coordinates": str( + self.Release_status_for_coordinates.currentText() + ), + "Release_status_for_sequence": str( + self.Release_status_for_sequence.currentText() + ), + "group_deposition_title": str(self.group_deposition_title.text()), + "group_description": str(self.group_description.text()), + "structure_title": str(self.structure_title.text()), + "structure_title_apo": str(self.structure_title_apo.text()), + "primary_citation_id": str(self.primary_citation_id.text()), + "primary_citation_journal_abbrev": str( + self.primary_citation_journal_abbrev.text() + ), + "primary_citation_title": str(self.primary_citation_title.text()), + "primary_citation_year": str(self.primary_citation_year.text()), + "primary_citation_journal_volume": str( + self.primary_citation_journal_volume.text() + ), + "primary_citation_page_first": str(self.primary_citation_page_first.text()), + "primary_citation_page_last": str(self.primary_citation_page_last.text()), # entity 1 - 'molecule_name': str(self.molecule_name.text()), - 'Source_organism_scientific_name': str(self.Source_organism_scientific_name.currentText()), - 'Source_organism_gene': str(self.Source_organism_gene.text()), - 'Source_organism_strain': str(self.Source_organism_strain.text()), - 'Expression_system_scientific_name': str(self.Expression_system_scientific_name.currentText()), - 'Expression_system_strain': str(self.Expression_system_strain.text()), - 'Expression_system_plasmid_name': str(self.Expression_system_plasmid_name.text()), - 'Expression_system_vector_type': str(self.Expression_system_vector_type.text()), - 'Manipulated_source_details': str(self.Manipulated_source_details.text()), - 'fragment_name_one_specific_mutation': str(self.fragment_name_one_specific_mutation.text()), - 'molecule_chain_one': str(self.molecule_chain_one.text()), - + "molecule_name": str(self.molecule_name.text()), + "Source_organism_scientific_name": str( + self.Source_organism_scientific_name.currentText() + ), + "Source_organism_gene": str(self.Source_organism_gene.text()), + "Source_organism_strain": str(self.Source_organism_strain.text()), + "Expression_system_scientific_name": str( + self.Expression_system_scientific_name.currentText() + ), + "Expression_system_strain": str(self.Expression_system_strain.text()), + "Expression_system_plasmid_name": str( + self.Expression_system_plasmid_name.text() + ), + "Expression_system_vector_type": str( + self.Expression_system_vector_type.text() + ), + "Manipulated_source_details": str(self.Manipulated_source_details.text()), + "fragment_name_one_specific_mutation": str( + self.fragment_name_one_specific_mutation.text() + ), + "molecule_chain_one": str(self.molecule_chain_one.text()), # entity 2 - 'molecule_name_two': str(self.molecule_name_two.text()), - 'Source_organism_scientific_name_two': str(self.Source_organism_scientific_name_two.currentText()), - 'Source_organism_gene_two': str(self.Source_organism_gene_two.text()), - 'Source_organism_strain_two': str(self.Source_organism_strain_two.text()), - 'Expression_system_scientific_name_two': str(self.Expression_system_scientific_name_two.currentText()), - 'Expression_system_strain_two': str(self.Expression_system_strain_two.text()), - 'Expression_system_plasmid_name_two': str(self.Expression_system_plasmid_name_two.text()), - 'Expression_system_vector_type_two': str(self.Expression_system_vector_type_two.text()), - 'Manipulated_source_details_two': str(self.Manipulated_source_details_two.text()), - 'fragment_name_two_specific_mutation': str(self.fragment_name_two_specific_mutation.text()), - 'molecule_chain_two': str(self.molecule_chain_two.text()), - - 'structure_keywords': str(self.structure_keywords.text()), - 'biological_assembly_chain_number': str(self.biological_assembly_chain_number.text()), - 'molecule_one_letter_sequence_uniprot_id': str(self.molecule_one_letter_sequence_uniprot_id.text()), - 'molecule_two_letter_sequence_uniprot_id': str(self.molecule_one_letter_sequence_uniprot_id_two.text()), - 'SG_project_name': str(self.SG_project_name.text()), - 'full_name_of_SG_center': str(self.full_name_of_SG_center.text()), - 'molecule_one_letter_sequence': str(self.molecule_one_letter_sequence.toPlainText()).replace(' ', - '').replace( - '\n', '').replace('\r', ''), - 'molecule_two_letter_sequence': str(self.molecule_one_letter_sequence_two.toPlainText()).replace(' ', - '').replace( - '\n', '').replace('\r', ''), - - 'crystallization_method': str(self.crystallization_method.currentText()), - 'crystallization_pH': str(self.crystallization_pH.text()), - 'crystallization_temperature': str(self.crystallization_temperature.text()), - 'crystallization_details': str(self.crystallization_details.text()), - - 'radiation_source': str(self.radiation_source.currentText()), - 'radiation_source_type': str(self.radiation_source_type.currentText()), - 'radiation_wavelengths': str(self.radiation_wavelengths.text()), - 'radiation_detector': str(self.radiation_detector.currentText()), - 'radiation_detector_type': str(self.radiation_detector_type.currentText()), - 'data_collection_date': str(self.data_collection_date.text()), - 'data_collection_temperature': str(self.data_collection_temperature.text()), - 'data_collection_protocol': str(self.data_collection_protocol.text()), - 'pdbx_starting_model': str(self.pdbx_starting_model.text()), - 'data_integration_software': str(self.data_integration_software.currentText()), - 'phasing_software': str(self.phasing_software.currentText()), - - 'pdbx_funding_ordinal_one': pdbx_funding_ordinal_one, - 'pdbx_funding_organization_one': pdbx_funding_organization_one, - 'pdbx_grant_number_one': pdbx_grant_number_one, - 'pdbx_grant_country_one': pdbx_grant_country_one, - 'pdbx_funding_ordinal_two': pdbx_funding_ordinal_two, - 'pdbx_funding_organization_two': pdbx_funding_organization_two, - 'pdbx_grant_number_two': pdbx_grant_number_two, - 'pdbx_grant_country_two': pdbx_grant_country_two, - 'pdbx_funding_ordinal_three': pdbx_funding_ordinal_three, - 'pdbx_funding_organization_three': pdbx_funding_organization_three, - 'pdbx_grant_number_three': pdbx_grant_number_three, - 'pdbx_grant_country_three': pdbx_grant_country_three - + "molecule_name_two": str(self.molecule_name_two.text()), + "Source_organism_scientific_name_two": str( + self.Source_organism_scientific_name_two.currentText() + ), + "Source_organism_gene_two": str(self.Source_organism_gene_two.text()), + "Source_organism_strain_two": str(self.Source_organism_strain_two.text()), + "Expression_system_scientific_name_two": str( + self.Expression_system_scientific_name_two.currentText() + ), + "Expression_system_strain_two": str( + self.Expression_system_strain_two.text() + ), + "Expression_system_plasmid_name_two": str( + self.Expression_system_plasmid_name_two.text() + ), + "Expression_system_vector_type_two": str( + self.Expression_system_vector_type_two.text() + ), + "Manipulated_source_details_two": str( + self.Manipulated_source_details_two.text() + ), + "fragment_name_two_specific_mutation": str( + self.fragment_name_two_specific_mutation.text() + ), + "molecule_chain_two": str(self.molecule_chain_two.text()), + "structure_keywords": str(self.structure_keywords.text()), + "biological_assembly_chain_number": str( + self.biological_assembly_chain_number.text() + ), + "molecule_one_letter_sequence_uniprot_id": str( + self.molecule_one_letter_sequence_uniprot_id.text() + ), + "molecule_two_letter_sequence_uniprot_id": str( + self.molecule_one_letter_sequence_uniprot_id_two.text() + ), + "SG_project_name": str(self.SG_project_name.text()), + "full_name_of_SG_center": str(self.full_name_of_SG_center.text()), + "molecule_one_letter_sequence": str( + self.molecule_one_letter_sequence.toPlainText() + ) + .replace(" ", "") + .replace("\n", "") + .replace("\r", ""), + "molecule_two_letter_sequence": str( + self.molecule_one_letter_sequence_two.toPlainText() + ) + .replace(" ", "") + .replace("\n", "") + .replace("\r", ""), + "crystallization_method": str(self.crystallization_method.currentText()), + "crystallization_pH": str(self.crystallization_pH.text()), + "crystallization_temperature": str(self.crystallization_temperature.text()), + "crystallization_details": str(self.crystallization_details.text()), + "radiation_source": str(self.radiation_source.currentText()), + "radiation_source_type": str(self.radiation_source_type.currentText()), + "radiation_wavelengths": str(self.radiation_wavelengths.text()), + "radiation_detector": str(self.radiation_detector.currentText()), + "radiation_detector_type": str(self.radiation_detector_type.currentText()), + "data_collection_date": str(self.data_collection_date.text()), + "data_collection_temperature": str(self.data_collection_temperature.text()), + "data_collection_protocol": str(self.data_collection_protocol.text()), + "pdbx_starting_model": str(self.pdbx_starting_model.text()), + "data_integration_software": str( + self.data_integration_software.currentText() + ), + "phasing_software": str(self.phasing_software.currentText()), + "pdbx_funding_ordinal_one": pdbx_funding_ordinal_one, + "pdbx_funding_organization_one": pdbx_funding_organization_one, + "pdbx_grant_number_one": pdbx_grant_number_one, + "pdbx_grant_country_one": pdbx_grant_country_one, + "pdbx_funding_ordinal_two": pdbx_funding_ordinal_two, + "pdbx_funding_organization_two": pdbx_funding_organization_two, + "pdbx_grant_number_two": pdbx_grant_number_two, + "pdbx_grant_country_two": pdbx_grant_country_two, + "pdbx_funding_ordinal_three": pdbx_funding_ordinal_three, + "pdbx_funding_organization_three": pdbx_funding_organization_three, + "pdbx_grant_number_three": pdbx_grant_number_three, + "pdbx_grant_country_three": pdbx_grant_country_three, } - structure_author_name = '' + structure_author_name = "" for widget in self.structure_author_name_List: - structure_author_name += str(widget.text()) + ';' - self.deposit_dict['structure_author_name'] = structure_author_name[:-1] + structure_author_name += str(widget.text()) + ";" + self.deposit_dict["structure_author_name"] = structure_author_name[:-1] - primary_citation_author_name = '' + primary_citation_author_name = "" for widget in self.primary_citation_author_name_List: - primary_citation_author_name += str(widget.text()) + ';' - self.deposit_dict['primary_citation_author_name'] = primary_citation_author_name[:-1] + primary_citation_author_name += str(widget.text()) + ";" + self.deposit_dict[ + "primary_citation_author_name" + ] = primary_citation_author_name[:-1] def get_deposit_dict_template(self): deposit_dict_template = { - 'contact_author_PI_salutation': None, - 'contact_author_PI_first_name': None, - 'contact_author_PI_last_name': None, - 'contact_author_PI_middle_name': None, - 'contact_author_PI_role': None, - 'contact_author_PI_organization_type': None, - 'contact_author_PI_organization_name': None, - 'contact_author_PI_email': None, - 'contact_author_PI_address': None, - 'contact_author_PI_city': None, - 'contact_author_PI_State_or_Province': None, - 'contact_author_PI_Zip_Code': None, - 'contact_author_PI_Country': None, - 'contact_author_PI_phone_number': None, - 'contact_author_PI_ORCID': None, - - 'contact_author_salutation': None, - 'contact_author_first_name': None, - 'contact_author_last_name': None, - 'contact_author_middle_name': None, - 'contact_author_role': None, - 'contact_author_organization_type': None, - 'contact_author_organization_name': None, - 'contact_author_email': None, - 'contact_author_address': None, - 'contact_author_city': None, - 'contact_author_State_or_Province': None, - 'contact_author_Zip_Code': None, - 'contact_author_Country': None, - 'contact_author_phone_number': None, - 'contact_author_ORCID': None, - - 'Release_status_for_coordinates': None, - 'Release_status_for_sequence': None, - - 'group_deposition_title': None, - 'group_description': None, - - 'structure_title': None, - 'structure_title_apo': None, - - 'primary_citation_id': None, - 'primary_citation_journal_abbrev': None, - 'primary_citation_title': None, - 'primary_citation_year': None, - 'primary_citation_journal_volume': None, - 'primary_citation_page_first': None, - 'primary_citation_page_last': None, + "contact_author_PI_salutation": None, + "contact_author_PI_first_name": None, + "contact_author_PI_last_name": None, + "contact_author_PI_middle_name": None, + "contact_author_PI_role": None, + "contact_author_PI_organization_type": None, + "contact_author_PI_organization_name": None, + "contact_author_PI_email": None, + "contact_author_PI_address": None, + "contact_author_PI_city": None, + "contact_author_PI_State_or_Province": None, + "contact_author_PI_Zip_Code": None, + "contact_author_PI_Country": None, + "contact_author_PI_phone_number": None, + "contact_author_PI_ORCID": None, + "contact_author_salutation": None, + "contact_author_first_name": None, + "contact_author_last_name": None, + "contact_author_middle_name": None, + "contact_author_role": None, + "contact_author_organization_type": None, + "contact_author_organization_name": None, + "contact_author_email": None, + "contact_author_address": None, + "contact_author_city": None, + "contact_author_State_or_Province": None, + "contact_author_Zip_Code": None, + "contact_author_Country": None, + "contact_author_phone_number": None, + "contact_author_ORCID": None, + "Release_status_for_coordinates": None, + "Release_status_for_sequence": None, + "group_deposition_title": None, + "group_description": None, + "structure_title": None, + "structure_title_apo": None, + "primary_citation_id": None, + "primary_citation_journal_abbrev": None, + "primary_citation_title": None, + "primary_citation_year": None, + "primary_citation_journal_volume": None, + "primary_citation_page_first": None, + "primary_citation_page_last": None, # entity 1 - 'molecule_name': None, - 'Source_organism_scientific_name': None, - 'Source_organism_gene': None, - 'Source_organism_strain': None, - 'Expression_system_scientific_name': None, - 'Expression_system_strain': None, - 'Expression_system_plasmid_name': None, - 'Expression_system_vector_type': None, - 'Manipulated_source_details': None, - 'fragment_name_one_specific_mutation': None, - 'molecule_chain_one': None, - + "molecule_name": None, + "Source_organism_scientific_name": None, + "Source_organism_gene": None, + "Source_organism_strain": None, + "Expression_system_scientific_name": None, + "Expression_system_strain": None, + "Expression_system_plasmid_name": None, + "Expression_system_vector_type": None, + "Manipulated_source_details": None, + "fragment_name_one_specific_mutation": None, + "molecule_chain_one": None, # entity 2 - 'molecule_name_two': None, - 'Source_organism_scientific_name_two': None, - 'Source_organism_gene_two': None, - 'Source_organism_strain_two': None, - 'Expression_system_scientific_name_two': None, - 'Expression_system_strain_two': None, - 'Expression_system_plasmid_name_two': None, - 'Expression_system_vector_type_two': None, - 'Manipulated_source_details_two': None, - 'fragment_name_two_specific_mutation': None, - 'molecule_chain_two': None, - - 'structure_keywords': None, - 'biological_assembly_chain_number': None, - 'molecule_one_letter_sequence_uniprot_id': None, - 'molecule_two_letter_sequence_uniprot_id': None, - 'SG_project_name': None, - 'full_name_of_SG_center': None, - 'molecule_one_letter_sequence': None, - 'molecule_two_letter_sequence': None, - - 'crystallization_method': None, - 'crystallization_pH': None, - 'crystallization_temperature': None, - 'crystallization_details': None, - - 'radiation_source': None, - 'radiation_source_type': None, - 'radiation_wavelengths': None, - 'radiation_detector': None, - 'radiation_detector_type': None, - 'data_collection_date': None, - 'data_collection_temperature': None, - 'data_collection_protocol': None, - 'pdbx_starting_model': None, - 'data_integration_software': None, - 'phasing_software': None, - 'structure_author_name': None, - 'primary_citation_author_name': None, - - 'pdbx_funding_organization_one': '', - 'pdbx_grant_number_one': '', - 'pdbx_grant_country_one': '', - 'pdbx_funding_organization_two': '', - 'pdbx_grant_number_two': '', - 'pdbx_grant_country_two': '', - 'pdbx_funding_organization_three': '', - 'pdbx_grant_number_three': '', - 'pdbx_grant_country_three': '' - + "molecule_name_two": None, + "Source_organism_scientific_name_two": None, + "Source_organism_gene_two": None, + "Source_organism_strain_two": None, + "Expression_system_scientific_name_two": None, + "Expression_system_strain_two": None, + "Expression_system_plasmid_name_two": None, + "Expression_system_vector_type_two": None, + "Manipulated_source_details_two": None, + "fragment_name_two_specific_mutation": None, + "molecule_chain_two": None, + "structure_keywords": None, + "biological_assembly_chain_number": None, + "molecule_one_letter_sequence_uniprot_id": None, + "molecule_two_letter_sequence_uniprot_id": None, + "SG_project_name": None, + "full_name_of_SG_center": None, + "molecule_one_letter_sequence": None, + "molecule_two_letter_sequence": None, + "crystallization_method": None, + "crystallization_pH": None, + "crystallization_temperature": None, + "crystallization_details": None, + "radiation_source": None, + "radiation_source_type": None, + "radiation_wavelengths": None, + "radiation_detector": None, + "radiation_detector_type": None, + "data_collection_date": None, + "data_collection_temperature": None, + "data_collection_protocol": None, + "pdbx_starting_model": None, + "data_integration_software": None, + "phasing_software": None, + "structure_author_name": None, + "primary_citation_author_name": None, + "pdbx_funding_organization_one": "", + "pdbx_grant_number_one": "", + "pdbx_grant_country_one": "", + "pdbx_funding_organization_two": "", + "pdbx_grant_number_two": "", + "pdbx_grant_country_two": "", + "pdbx_funding_organization_three": "", + "pdbx_grant_number_three": "", + "pdbx_grant_country_three": "", } return deposit_dict_template @@ -2957,32 +3360,39 @@ def get_deposit_dict_template(self): def set_primary_citation_as_structure_authors(self, state): if state == QtCore.Qt.Checked: for n, entry in enumerate(self.structure_author_name_List): - self.primary_citation_author_name_List[n].setText( - str(entry.text())) + self.primary_citation_author_name_List[n].setText(str(entry.text())) else: for n, entry in enumerate(self.primary_citation_author_name_List): - entry.setText('') + entry.setText("") def set_xce_logfile(self): - file_name = str(QtGui.QFileDialog.getSaveFileName( - self.window, 'Save file', self.current_directory)) + file_name = str( + QtGui.QFileDialog.getSaveFileName( + self.window, "Save file", self.current_directory + ) + ) self.xce_logfile = str(file_name) self.xce_logfile_label.setText(str(self.xce_logfile)) - if self.xce_logfile == '' or self.xce_logfile[self.xce_logfile.rfind('/') + 1:] == '': - print('==> XCE: invalid file format') + if ( + self.xce_logfile == "" + or self.xce_logfile[self.xce_logfile.rfind("/") + 1 :] == "" + ): + print("==> XCE: invalid file format") else: - XChemLog.startLog(self.xce_logfile).create_logfile( - self.xce_version) + XChemLog.startLog(self.xce_logfile).create_logfile(self.xce_version) self.update_log = XChemLog.updateLog(self.xce_logfile) def set_second_cif_file(self): - filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select CIF File', - self.initial_model_directory, '*.cif') + filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter( + self.window, "Select CIF File", self.initial_model_directory, "*.cif" + ) filepath = str(tuple(filepath_temp)[0]) self.second_cif_file = str(filepath) self.second_cif_file_label.setText(str(self.second_cif_file)) self.update_log.insert( - 'user selected %s as CIF file for merging into ligand CIF files' % self.second_cif_file) + "user selected %s as CIF file for merging into ligand CIF files" + % self.second_cif_file + ) def select_datasource_columns_to_display(self): columns_to_show = QtGui.QMessageBox() @@ -2991,8 +3401,8 @@ def select_datasource_columns_to_display(self): try: columns_in_data_source = self.db.return_column_list() except AttributeError: - print('==> XCE: please select a datasource file') - self.status_bar.showMessage('please select a datasource file') + print("==> XCE: please select a datasource file") + self.status_bar.showMessage("please select a datasource file") return column_dict = {} @@ -3006,9 +3416,13 @@ def select_datasource_columns_to_display(self): for entries_added in range(number_of_entries): if not columns_in_data_source[entries_added][1] in columns_to_ignore: data_source_column = QtGui.QCheckBox( - columns_in_data_source[entries_added][1]) + columns_in_data_source[entries_added][1] + ) column_dict[entries_added] = data_source_column - if columns_in_data_source[entries_added][1] in self.overview_datasource_table_columns: + if ( + columns_in_data_source[entries_added][1] + in self.overview_datasource_table_columns + ): data_source_column.setChecked(True) grid.addWidget(data_source_column, y, x) y += 1 @@ -3018,13 +3432,13 @@ def select_datasource_columns_to_display(self): vbox.addLayout(grid) columns_to_showLayout.addLayout(vbox, 0, 0) - columns_to_show.addButton(QtGui.QPushButton( - 'OK'), QtGui.QMessageBox.YesRole) - columns_to_show.addButton(QtGui.QPushButton( - 'Cancel'), QtGui.QMessageBox.RejectRole) + columns_to_show.addButton(QtGui.QPushButton("OK"), QtGui.QMessageBox.YesRole) + columns_to_show.addButton( + QtGui.QPushButton("Cancel"), QtGui.QMessageBox.RejectRole + ) reply = columns_to_show.exec_() if reply == 0: - columns_to_show_list = ['Sample ID'] + columns_to_show_list = ["Sample ID"] for key in column_dict: if column_dict[key].isChecked(): columns_to_show_list.append(columns_in_data_source[key][1]) @@ -3033,71 +3447,90 @@ def select_datasource_columns_to_display(self): def update_header_and_data_from_datasource(self): self.update_log.insert( - 'getting information for all samples from data source...') - self.db = XChemDB.data_source(os.path.join( - self.database_directory, self.data_source_file)) - self.update_log.insert('creating missing columns in data source') + "getting information for all samples from data source..." + ) + self.db = XChemDB.data_source( + os.path.join(self.database_directory, self.data_source_file) + ) + self.update_log.insert("creating missing columns in data source") self.db.create_missing_columns() - self.update_log.insert('load header and data from data source') + self.update_log.insert("load header and data from data source") self.header, self.data = self.db.load_samples_from_data_source() - self.update_log.insert('get all samples in data source') + self.update_log.insert("get all samples in data source") all_samples_in_db = self.db.execute_statement( - "select CrystalName from mainTable where CrystalName is not '';") + "select CrystalName from mainTable where CrystalName is not '';" + ) self.xtal_db_dict = {} sampleID_column = 0 for n, entry in enumerate(self.header): - if entry == 'CrystalName': + if entry == "CrystalName": sampleID_column = n break for line in self.data: - if str(line[sampleID_column]) != '': + if str(line[sampleID_column]) != "": db_dict = {} for n, entry in enumerate(line): if n != sampleID_column: db_dict[str(self.header[n])] = str(entry) self.xtal_db_dict[str(line[sampleID_column])] = db_dict - print(('==> XCE: found ' + str(len(self.xtal_db_dict)) + ' samples')) + print(("==> XCE: found " + str(len(self.xtal_db_dict)) + " samples")) def datasource_menu_save_samples(self): - print('hallo') + print("hallo") def datasource_menu_export_csv_file(self): - file_name = str(QtGui.QFileDialog.getSaveFileName( - self.window, 'Save file', self.database_directory)) - if file_name.rfind('.') != -1: - file_name = file_name[:file_name.rfind('.')] + '.csv' + file_name = str( + QtGui.QFileDialog.getSaveFileName( + self.window, "Save file", self.database_directory + ) + ) + if file_name.rfind(".") != -1: + file_name = file_name[: file_name.rfind(".")] + ".csv" else: - file_name = file_name + '.csv' + file_name = file_name + ".csv" self.db.export_to_csv_file(file_name) def datasource_menu_import_csv_file(self): if self.data_source_set: file_name = QtGui.QFileDialog.getOpenFileName( - self.window, 'Open file', self.database_directory) + self.window, "Open file", self.database_directory + ) self.db.import_csv_file(file_name) else: - self.update_status_bar('Please load a data source file first') + self.update_status_bar("Please load a data source file first") def datasource_menu_update_datasource(self): - self.work_thread = XChemThread.synchronise_db_and_filesystem(self.initial_model_directory, - os.path.join(self.database_directory, - self.data_source_file), - self.panddas_directory, self.xce_logfile, - 'project_directory') - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), - self.datasource_menu_reload_samples) + self.work_thread = XChemThread.synchronise_db_and_filesystem( + self.initial_model_directory, + os.path.join(self.database_directory, self.data_source_file), + self.panddas_directory, + self.xce_logfile, + "project_directory", + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("datasource_menu_reload_samples"), + self.datasource_menu_reload_samples, + ) self.work_thread.start() def export_data_for_WONKA(self): - self.update_log.insert('exporting CSV file for input into WONKA') + self.update_log.insert("exporting CSV file for input into WONKA") self.db.export_csv_for_WONKA() def on_context_menu(self, point): @@ -3110,33 +3543,34 @@ def on_context_menu(self, point): def on_context_menu_reprocess_data(self, point): # show context menu self.popMenu_for_datasets_reprocess_table.exec_( - self.sender().mapToGlobal(point)) + self.sender().mapToGlobal(point) + ) def flag_sample_for_recollection(self): self.dewar_configuration_dict[self.dewar_label_active].setStyleSheet( - "background-color: yellow") + "background-color: yellow" + ) def undo_flag_sample_for_recollection(self): self.dewar_configuration_dict[self.dewar_label_active].setStyleSheet( - "background-color: gray") + "background-color: gray" + ) def show_html_summary_in_firefox(self, xtal): html_summary = self.albula_button_dict[xtal][2] - print(('html_summary', html_summary)) + print(("html_summary", html_summary)) new = 2 webbrowser.open(html_summary, new=new) def update_pandda_crystal_from_combobox(self): self.pandda_analyse_crystal_from_selection_combobox.clear() - self.pandda_analyse_crystal_from_selection_combobox.addItem( - 'use all datasets') + self.pandda_analyse_crystal_from_selection_combobox.addItem("use all datasets") if os.path.isfile(os.path.join(self.database_directory, self.data_source_file)): self.load_crystal_form_from_datasource() if self.xtalform_dict != {}: print((self.xtalform_dict)) for key in self.xtalform_dict: - self.pandda_analyse_crystal_from_selection_combobox.addItem( - key) + self.pandda_analyse_crystal_from_selection_combobox.addItem(key) def populate_reference_combobox(self, combobox): combobox.clear() @@ -3154,186 +3588,216 @@ def populate_target_selection_combobox(self, combobox): combobox.addItem(target) def combo_selected(self, text): - self.map_url = str(self.panddas_directory + - '/analyses/html_summaries/pandda_map_' + text + '.html') + self.map_url = str( + self.panddas_directory + + "/analyses/html_summaries/pandda_map_" + + text + + ".html" + ) self.pandda_maps_html.load(QtCore.QUrl(self.map_url)) self.pandda_maps_html.show() def add_map_html(self): self.map_list = glob.glob( - str(self.panddas_directory + '/analyses/html_summaries/pandda_map_*.html')) + str(self.panddas_directory + "/analyses/html_summaries/pandda_map_*.html") + ) self.list_options = [] for i in range(0, len(self.map_list)): string = self.map_list[i] - string = string.replace('/analyses/html_summaries/pandda_map_', '') - string = string.replace('.html', '') - string = string.replace(self.panddas_directory, '') + string = string.replace("/analyses/html_summaries/pandda_map_", "") + string = string.replace(".html", "") + string = string.replace(self.panddas_directory, "") self.list_options.append(string) self.pandda_map_list.clear() for i in range(0, len(self.list_options)): self.pandda_map_list.addItem(self.list_options[i]) - self.connect(self.pandda_map_list, QtCore.SIGNAL( - 'activated(QString)'), self.combo_selected) + self.connect( + self.pandda_map_list, + QtCore.SIGNAL("activated(QString)"), + self.combo_selected, + ) def open_config_file(self): - file_name_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Open file', self.current_directory, - '*.conf') + file_name_temp = QtGui.QFileDialog.getOpenFileNameAndFilter( + self.window, "Open file", self.current_directory, "*.conf" + ) file_name = tuple(file_name_temp)[0] try: - pickled_settings = pickle.load(open(file_name, 'rb')) + pickled_settings = pickle.load(open(file_name, "rb")) except: - print('==> XCE: failed to open config file...') + print("==> XCE: failed to open config file...") key_list = { # 'beamline_directory': 'beamline_directory', - 'initial_model_directory': 'initial_model_directory', - 'panddas_directory': 'panddas_directory', - 'html_export_directory': 'html_export_directory', - 'group_deposit_directory': 'group_deposit_directory', - 'database_directory': 'database_directory', - 'datasets_summary_file': 'datasets_summary', + "initial_model_directory": "initial_model_directory", + "panddas_directory": "panddas_directory", + "html_export_directory": "html_export_directory", + "group_deposit_directory": "group_deposit_directory", + "database_directory": "database_directory", + "datasets_summary_file": "datasets_summary", # "'data_source_file': 'data_source', - 'ccp4_scratch_directory': 'ccp4_scratch', - 'allowed_unitcell_difference_percent': 'unitcell_difference', - 'acceptable_low_resolution_limit_for_data': 'too_low_resolution_data', + "ccp4_scratch_directory": "ccp4_scratch", + "allowed_unitcell_difference_percent": "unitcell_difference", + "acceptable_low_resolution_limit_for_data": "too_low_resolution_data", # 'reference_directory_temp': 'reference_directory' } -# self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*')) + # self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*')) for current_key in key_list: try: command = str( - 'self.' + current_key + " = pickled_settings['" + key_list[current_key] + "']") + "self." + + current_key + + " = pickled_settings['" + + key_list[current_key] + + "']" + ) exec(command) command = str( - 'self.settings["' + key_list[current_key] + '"]= self.' + current_key) + 'self.settings["' + + key_list[current_key] + + '"]= self.' + + current_key + ) exec(command) - print(('==> XCE: found ' + key_list[current_key])) + print(("==> XCE: found " + key_list[current_key])) except: - print(('==> XCE: WARNING: Failed to find settings for: ' + key_list[current_key] + ' Error type: ' - + str(sys.exc_info()[0]))) + print( + ( + "==> XCE: WARNING: Failed to find settings for: " + + key_list[current_key] + + " Error type: " + + str(sys.exc_info()[0]) + ) + ) exec(str(current_key + " = ''")) continue try: pickled_settings = pickle.load(open(file_name, "rb")) - if pickled_settings['beamline_directory'] != self.beamline_directory: - self.beamline_directory = pickled_settings['beamline_directory'] + if pickled_settings["beamline_directory"] != self.beamline_directory: + self.beamline_directory = pickled_settings["beamline_directory"] self.target_list, self.visit_list = XChemMain.get_target_and_visit_list( - self.beamline_directory, self.read_agamemnon.isChecked()) - self.settings['beamline_directory'] = self.beamline_directory - self.populate_target_selection_combobox( - self.target_selection_combobox) + self.beamline_directory, self.read_agamemnon.isChecked() + ) + self.settings["beamline_directory"] = self.beamline_directory + self.populate_target_selection_combobox(self.target_selection_combobox) self.layout_funcs.pandda_html(self) self.show_pandda_html_summary() - self.html_export_directory_label.setText( - self.html_export_directory) + self.html_export_directory_label.setText(self.html_export_directory) - self.group_deposition_directory_label.setText( - self.group_deposit_directory) + self.group_deposition_directory_label.setText(self.group_deposit_directory) - self.datasets_summary_file_label.setText( - self.datasets_summary_file) + self.datasets_summary_file_label.setText(self.datasets_summary_file) - self.data_source_file = pickled_settings['data_source'] - if self.data_source_file != '': - self.settings['data_source'] = os.path.join( - self.database_directory, self.data_source_file) + self.data_source_file = pickled_settings["data_source"] + if self.data_source_file != "": + self.settings["data_source"] = os.path.join( + self.database_directory, self.data_source_file + ) # this is probably not necessary - if os.path.isfile(self.settings['data_source']): + if os.path.isfile(self.settings["data_source"]): write_enabled = self.check_write_permissions_of_data_source() if not write_enabled: - self.data_source_file_label.setText('') + self.data_source_file_label.setText("") self.data_source_set = False else: self.data_source_file_label.setText( - os.path.join(self.database_directory, self.data_source_file)) + os.path.join(self.database_directory, self.data_source_file) + ) self.data_source_set = True - self.db = XChemDB.data_source(os.path.join( - self.database_directory, self.data_source_file)) + self.db = XChemDB.data_source( + os.path.join(self.database_directory, self.data_source_file) + ) self.datasource_menu_reload_samples() - reference_directory_temp = pickled_settings['reference_directory'] + reference_directory_temp = pickled_settings["reference_directory"] if reference_directory_temp != self.reference_directory: self.reference_directory = reference_directory_temp - self.settings['reference_directory'] = self.reference_directory - self.update_reference_files(' ') + self.settings["reference_directory"] = self.reference_directory + self.update_reference_files(" ") for xtal in self.initial_model_dimple_dict: - reference_file_selection_combobox = self.initial_model_dimple_dict[xtal][1] - self.populate_reference_combobox( - reference_file_selection_combobox) + reference_file_selection_combobox = self.initial_model_dimple_dict[ + xtal + ][1] + self.populate_reference_combobox(reference_file_selection_combobox) - self.initial_model_directory_label.setText( - self.initial_model_directory) + self.initial_model_directory_label.setText(self.initial_model_directory) self.panddas_directory_label.setText(self.panddas_directory) self.pandda_output_data_dir_entry.setText(self.panddas_directory) self.reference_directory_label.setText(self.reference_directory) self.beamline_directory_label.setText(self.beamline_directory) - self.ccp4_scratch_directory_label.setText( - self.ccp4_scratch_directory) - self.reference_file_list = self.get_reference_file_list(' ') + self.ccp4_scratch_directory_label.setText(self.ccp4_scratch_directory) + self.reference_file_list = self.get_reference_file_list(" ") self.pandda_input_data_dir_entry.setText( - os.path.join(self.initial_model_directory, '*')) + os.path.join(self.initial_model_directory, "*") + ) self.update_all_tables() except KeyError: - self.update_status_bar( - 'Sorry, this is not a XChemExplorer config file!') - self.update_log.insert( - 'Sorry, this is not a XChemExplorer config file!') + self.update_status_bar("Sorry, this is not a XChemExplorer config file!") + self.update_log.insert("Sorry, this is not a XChemExplorer config file!") except: print(("Unexpected error:", sys.exc_info()[0])) raise def save_config_file(self): - file_name = str(QtGui.QFileDialog.getSaveFileName( - self.window, 'Save file', self.current_directory)) + file_name = str( + QtGui.QFileDialog.getSaveFileName( + self.window, "Save file", self.current_directory + ) + ) # make sure that the file always has .conf extension - if str(file_name).rfind('.') != -1: - file_name = file_name[:file_name.rfind('.')] + '.conf' + if str(file_name).rfind(".") != -1: + file_name = file_name[: file_name.rfind(".")] + ".conf" else: - file_name = file_name + '.conf' - pickle.dump(self.settings, open(file_name, 'wb')) + file_name = file_name + ".conf" + pickle.dump(self.settings, open(file_name, "wb")) def update_reference_files(self, reference_root): self.reference_file_list = self.get_reference_file_list(reference_root) - self.populate_reference_combobox( - self.reference_file_selection_combobox) - self.populate_reference_combobox( - self.pandda_reference_file_selection_combobox) + self.populate_reference_combobox(self.reference_file_selection_combobox) + self.populate_reference_combobox(self.pandda_reference_file_selection_combobox) def check_status_rerun_dimple_on_all_autoprocessing_files(self): - print('hallo') + print("hallo") def rerun_dimple_on_all_autoprocessing_files(self): job_list = [] - self.update_log.insert( - 'preparing to run DIMPLE on all autoprocessing files') + self.update_log.insert("preparing to run DIMPLE on all autoprocessing files") for xtal in self.data_collection_dict: for entry in self.data_collection_dict[xtal]: - if entry[0] == 'logfile': + if entry[0] == "logfile": db_dict = entry[6] try: - if os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'], - db_dict['DataProcessingMTZfileName'])) or \ - os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'])): + if os.path.isfile( + os.path.join( + db_dict["DataProcessingPathToMTZfile"], + db_dict["DataProcessingMTZfileName"], + ) + ) or os.path.isfile( + os.path.join(db_dict["DataProcessingPathToMTZfile"]) + ): job_list = self.get_job_list_for_dimple_rerun( - xtal, job_list, db_dict, entry) + xtal, job_list, db_dict, entry + ) except KeyError: try: - if os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'])): + if os.path.isfile( + os.path.join(db_dict["DataProcessingPathToMTZfile"]) + ): job_list = self.get_job_list_for_dimple_rerun( - xtal, job_list, db_dict, entry) + xtal, job_list, db_dict, entry + ) except KeyError: continue if job_list: - self.update_log.insert( - 'trying to run DIMPLE on ALL auto-processing files') + self.update_log.insert("trying to run DIMPLE on ALL auto-processing files") self.check_before_running_dimple(job_list) def run_dimple_on_selected_autoprocessing_file(self, instruction): @@ -3346,86 +3810,189 @@ def run_dimple_on_selected_autoprocessing_file(self, instruction): # the if statement below is so convoluted, so that it is compatible with older data source files - if os.path.isfile( - os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'], - db_dict['DataProcessingMTZfileName'])) or \ - os.path.isfile( - os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'])) or \ - os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'], - db_dict['DataProcessingMTZfileName'])) or \ - os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'])): + if ( + os.path.isfile( + os.path.join( + db_dict["ProjectDirectory"], + xtal, + db_dict["DataProcessingPathToMTZfile"], + db_dict["DataProcessingMTZfileName"], + ) + ) + or os.path.isfile( + os.path.join( + db_dict["ProjectDirectory"], + xtal, + db_dict["DataProcessingPathToMTZfile"], + ) + ) + or os.path.isfile( + os.path.join( + db_dict["DataProcessingPathToMTZfile"], + db_dict["DataProcessingMTZfileName"], + ) + ) + or os.path.isfile( + os.path.join(db_dict["DataProcessingPathToMTZfile"]) + ) + ): if os.path.isfile( - os.path.join(db_dict['DataProcessingPathToMTZfile'], db_dict['DataProcessingMTZfileName'])): - mtzin = os.path.join(db_dict['DataProcessingPathToMTZfile'], - db_dict['DataProcessingMTZfileName']) - elif os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'])): + os.path.join( + db_dict["DataProcessingPathToMTZfile"], + db_dict["DataProcessingMTZfileName"], + ) + ): mtzin = os.path.join( - db_dict['DataProcessingPathToMTZfile']) + db_dict["DataProcessingPathToMTZfile"], + db_dict["DataProcessingMTZfileName"], + ) elif os.path.isfile( - os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'], - db_dict['DataProcessingMTZfileName'])): - mtzin = os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'], - db_dict['DataProcessingMTZfileName']) + os.path.join(db_dict["DataProcessingPathToMTZfile"]) + ): + mtzin = os.path.join(db_dict["DataProcessingPathToMTZfile"]) elif os.path.isfile( - os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'])): + os.path.join( + db_dict["ProjectDirectory"], + xtal, + db_dict["DataProcessingPathToMTZfile"], + db_dict["DataProcessingMTZfileName"], + ) + ): mtzin = os.path.join( - db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile']) + db_dict["ProjectDirectory"], + xtal, + db_dict["DataProcessingPathToMTZfile"], + db_dict["DataProcessingMTZfileName"], + ) + elif os.path.isfile( + os.path.join( + db_dict["ProjectDirectory"], + xtal, + db_dict["DataProcessingPathToMTZfile"], + ) + ): + mtzin = os.path.join( + db_dict["ProjectDirectory"], + xtal, + db_dict["DataProcessingPathToMTZfile"], + ) reference_file = str( - self.initial_model_dimple_dict[xtal][1].currentText()) + self.initial_model_dimple_dict[xtal][1].currentText() + ) reference_file_pdb = os.path.join( - self.reference_directory, reference_file + '.pdb') + self.reference_directory, reference_file + ".pdb" + ) if not os.path.isfile(reference_file_pdb): continue - if os.path.isfile(os.path.join(self.reference_directory, reference_file + '.mtz')): - reference_file_mtz = ' -R ' + \ - os.path.join(self.reference_directory, - reference_file + '.mtz') + if os.path.isfile( + os.path.join(self.reference_directory, reference_file + ".mtz") + ): + reference_file_mtz = " -R " + os.path.join( + self.reference_directory, reference_file + ".mtz" + ) else: - reference_file_mtz = '' + reference_file_mtz = "" - if os.path.isfile(os.path.join(self.reference_directory, reference_file + '.cif')): - reference_file_cif = ' --libin ' + os.path.join(self.reference_directory, - reference_file + '.cif') + if os.path.isfile( + os.path.join(self.reference_directory, reference_file + ".cif") + ): + reference_file_cif = " --libin " + os.path.join( + self.reference_directory, reference_file + ".cif" + ) else: - reference_file_cif = '' - - job_list.append([xtal, - 'dimple_rerun_on_selected_file', - mtzin, - reference_file_pdb, - reference_file_mtz, - reference_file_cif]) + reference_file_cif = "" + + job_list.append( + [ + xtal, + "dimple_rerun_on_selected_file", + mtzin, + reference_file_pdb, + reference_file_mtz, + reference_file_cif, + ] + ) else: - print(( - 'WARNING: ' + xtal + ' has not been submitted to dimple because no files were found: ')) - if not os.path.isfile(os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'], - db_dict['DataProcessingMTZfileName'])): - print((' ' + str(os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'], - db_dict['DataProcessingMTZfileName'])) + ' is missing')) - if not os.path.isfile(os.path.join(db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'])): - print((' ' + str(os.path.join( - db_dict['ProjectDirectory'], xtal, db_dict['DataProcessingPathToMTZfile'])) + ' is missing')) - if not os.path.isfile(os.path.join(db_dict['DataProcessingPathToMTZfile'])): - print(( - ' ' + str(os.path.join(db_dict['DataProcessingPathToMTZfile']) + ' is missing'))) + print( + ( + "WARNING: " + + xtal + + " has not been submitted to dimple because no files were found: " + ) + ) + if not os.path.isfile( + os.path.join( + db_dict["ProjectDirectory"], + xtal, + db_dict["DataProcessingPathToMTZfile"], + db_dict["DataProcessingMTZfileName"], + ) + ): + print( + ( + " " + + str( + os.path.join( + db_dict["ProjectDirectory"], + xtal, + db_dict["DataProcessingPathToMTZfile"], + db_dict["DataProcessingMTZfileName"], + ) + ) + + " is missing" + ) + ) + if not os.path.isfile( + os.path.join( + db_dict["ProjectDirectory"], + xtal, + db_dict["DataProcessingPathToMTZfile"], + ) + ): + print( + ( + " " + + str( + os.path.join( + db_dict["ProjectDirectory"], + xtal, + db_dict["DataProcessingPathToMTZfile"], + ) + ) + + " is missing" + ) + ) + if not os.path.isfile( + os.path.join(db_dict["DataProcessingPathToMTZfile"]) + ): + print( + ( + " " + + str( + os.path.join(db_dict["DataProcessingPathToMTZfile"]) + + " is missing" + ) + ) + ) if job_list: self.update_log.insert( - 'trying to run DIMPLE on SELECTED auto-processing files') + "trying to run DIMPLE on SELECTED auto-processing files" + ) self.check_before_running_dimple(job_list, instruction) def remove_selected_dimple_files(self, instruction): - if 'dimple' in instruction.lower(): - pipeline = 'dimple' - elif 'pipedream' in instruction.lower(): - pipeline = 'pipedream' - elif 'phenix' in instruction.lower(): - pipeline = 'phenix.ligand_pipeline' + if "dimple" in instruction.lower(): + pipeline = "dimple" + elif "pipedream" in instruction.lower(): + pipeline = "pipedream" + elif "phenix" in instruction.lower(): + pipeline = "phenix.ligand_pipeline" job_list = [] for xtal in sorted(self.initial_model_dimple_dict): @@ -3434,71 +4001,99 @@ def remove_selected_dimple_files(self, instruction): if job_list: msgBox = QtGui.QMessageBox() - msgBox.setText("Do you really want to delete {0!s} {1!s} files?".format( - len(job_list), self.preferences['initial_refinement_pipeline'])) - msgBox.addButton(QtGui.QPushButton( - 'Go'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('Cancel'), - QtGui.QMessageBox.RejectRole) + msgBox.setText( + "Do you really want to delete {0!s} {1!s} files?".format( + len(job_list), self.preferences["initial_refinement_pipeline"] + ) + ) + msgBox.addButton(QtGui.QPushButton("Go"), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton("Cancel"), QtGui.QMessageBox.RejectRole) reply = msgBox.exec_() if reply == 0: self.status_bar.showMessage( - 'preparing to remove {0!s} files'.format(pipeline)) + "preparing to remove {0!s} files".format(pipeline) + ) self.update_log.insert( - 'preparing to remove {0!s} files'.format(pipeline)) - self.work_thread = XChemThread.remove_selected_dimple_files(job_list, - self.initial_model_directory, - self.xce_logfile, - self.database_directory, - self.data_source_file, - pipeline) + "preparing to remove {0!s} files".format(pipeline) + ) + self.work_thread = XChemThread.remove_selected_dimple_files( + job_list, + self.initial_model_directory, + self.xce_logfile, + self.database_directory, + self.data_source_file, + pipeline, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), - self.datasource_menu_reload_samples) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("datasource_menu_reload_samples"), + self.datasource_menu_reload_samples, + ) self.work_thread.start() def set_results_from_selected_pipeline(self, instruction): - if 'dimple' in instruction.lower(): - pipeline = 'dimple' - elif 'pipedream' in instruction.lower(): - pipeline = 'pipedream' - elif 'phenix' in instruction.lower(): - pipeline = 'phenix.ligand_pipeline' + if "dimple" in instruction.lower(): + pipeline = "dimple" + elif "pipedream" in instruction.lower(): + pipeline = "pipedream" + elif "phenix" in instruction.lower(): + pipeline = "phenix.ligand_pipeline" - self.update_log.warning( - 'selecting initial refinement results from '+pipeline) + self.update_log.warning("selecting initial refinement results from " + pipeline) job_list = [] for xtal in sorted(self.initial_model_dimple_dict): if self.initial_model_dimple_dict[xtal][0].isChecked(): job_list.append(xtal) - self.work_thread = XChemThread.set_results_from_selected_pipeline(job_list, - self.initial_model_directory, - self.xce_logfile, - self.database_directory, - self.data_source_file, - pipeline) + self.work_thread = XChemThread.set_results_from_selected_pipeline( + job_list, + self.initial_model_directory, + self.xce_logfile, + self.database_directory, + self.data_source_file, + pipeline, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), - self.datasource_menu_reload_samples) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("datasource_menu_reload_samples"), + self.datasource_menu_reload_samples, + ) self.work_thread.start() def run_xia2_on_selected_datasets(self, overwrite): @@ -3506,15 +4101,15 @@ def run_xia2_on_selected_datasets(self, overwrite): # check which programs should be run protocol = [] if self.xia2_3d_checkbox.isChecked(): - protocol.append('3d') + protocol.append("3d") if self.xia2_3dii_checkbox.isChecked(): - protocol.append('3dii') + protocol.append("3dii") if self.xia2_dials_checkbox.isChecked(): - protocol.append('dials') + protocol.append("dials") # space group spg = [] - if str(self.reprocess_space_group_comboxbox.currentText()) != 'ignore': + if str(self.reprocess_space_group_comboxbox.currentText()) != "ignore": spg.append(str(self.reprocess_space_group_comboxbox.currentText())) # reference file @@ -3524,13 +4119,12 @@ def run_xia2_on_selected_datasets(self, overwrite): # resolution limit reso_limit = [] - if str(self.reprocess_isigma_combobox.currentText()) != 'default': - reso_limit.append( - str(self.reprocess_isigma_combobox.currentText())) + if str(self.reprocess_isigma_combobox.currentText()) != "default": + reso_limit.append(str(self.reprocess_isigma_combobox.currentText())) # cc 1/2 cc_half = [] - if str(self.reprocess_cc_half_combobox.currentText()) != 'default': + if str(self.reprocess_cc_half_combobox.currentText()) != "default": cc_half.append(str(self.reprocess_cc_half_combobox.currentText())) run_dict = {} @@ -3542,35 +4136,46 @@ def run_xia2_on_selected_datasets(self, overwrite): run_dict[sample_id] = self.diffraction_data_dict[dataset_id] if protocol != [] and run_dict != {}: - self.work_thread = XChemProcess.run_xia2(self.initial_model_directory, - run_dict, - protocol, - spg, - ref, - reso_limit, - cc_half, - self.xce_logfile, - self.external_software, - self.ccp4_scratch_directory, - self.max_queue_jobs, - os.path.join( - self.database_directory, self.data_source_file), - overwrite) + self.work_thread = XChemProcess.run_xia2( + self.initial_model_directory, + run_dict, + protocol, + spg, + ref, + reso_limit, + cc_half, + self.xce_logfile, + self.external_software, + self.ccp4_scratch_directory, + self.max_queue_jobs, + os.path.join(self.database_directory, self.data_source_file), + overwrite, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() else: self.update_log.insert( - 'please select datasets and/ or data processing protocol') + "please select datasets and/ or data processing protocol" + ) self.update_status_bar( - 'please select datasets and/ or data processing protocol') + "please select datasets and/ or data processing protocol" + ) def update_reprocessing_table(self): allRows = self.datasets_reprocess_table.rowCount() @@ -3579,29 +4184,42 @@ def update_reprocessing_table(self): if sample_id in self.xtal_db_dict: db_dict = self.xtal_db_dict[sample_id] cell_text = QtGui.QTableWidgetItem() - cell_text.setText(db_dict['DataProcessingStatus']) + cell_text.setText(db_dict["DataProcessingStatus"]) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - if db_dict['DataProcessingStatus'] == 'running': + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) + if db_dict["DataProcessingStatus"] == "running": cell_text.setBackground(QtGui.QColor(100, 230, 150)) - elif db_dict['DataProcessingStatus'] == 'pending': + elif db_dict["DataProcessingStatus"] == "pending": cell_text.setBackground(QtGui.QColor(20, 100, 230)) - elif db_dict['DataProcessingStatus'] == 'started': + elif db_dict["DataProcessingStatus"] == "started": cell_text.setBackground(QtGui.QColor(230, 240, 110)) - elif db_dict['DataProcessingStatus'] == 'finished': + elif db_dict["DataProcessingStatus"] == "finished": cell_text.setBackground(QtGui.QColor(255, 255, 255)) self.datasets_reprocess_table.setItem(row, 7, cell_text) def get_job_list_for_dimple_rerun(self, xtal, job_list, db_dict, entry): - self.status_bar.showMessage('checking: ' + str( - os.path.join(db_dict['DataProcessingPathToMTZfile'], db_dict['DataProcessingMTZfileName']))) + self.status_bar.showMessage( + "checking: " + + str( + os.path.join( + db_dict["DataProcessingPathToMTZfile"], + db_dict["DataProcessingMTZfileName"], + ) + ) + ) suitable_reference = [] for reference in self.reference_file_list: # first we need one in the same pointgroup - if reference[5] == db_dict['DataProcessingPointGroup']: + if reference[5] == db_dict["DataProcessingPointGroup"]: try: difference = math.fabs( - 1 - (float(db_dict['DataProcessingUnitCellVolume']) / float(reference[4]))) + 1 + - ( + float(db_dict["DataProcessingUnitCellVolume"]) + / float(reference[4]) + ) + ) suitable_reference.append([reference[0], difference]) except ValueError: continue @@ -3612,35 +4230,46 @@ def get_job_list_for_dimple_rerun(self, xtal, job_list, db_dict, entry): autoproc = entry[4] reference_file_pdb = os.path.join( - self.reference_directory, reference_file + '.pdb') + self.reference_directory, reference_file + ".pdb" + ) - if os.path.isfile(os.path.join(self.reference_directory, reference_file + '.mtz')): - reference_file_mtz = ' -R ' + \ - os.path.join(self.reference_directory, - reference_file + '.mtz') + if os.path.isfile( + os.path.join(self.reference_directory, reference_file + ".mtz") + ): + reference_file_mtz = " -R " + os.path.join( + self.reference_directory, reference_file + ".mtz" + ) else: - reference_file_mtz = '' - - if os.path.isfile(os.path.join(self.reference_directory, reference_file + '.cif')): - reference_file_cif = ' --libin ' + \ - os.path.join(self.reference_directory, - reference_file + '.cif') + reference_file_mtz = "" + + if os.path.isfile( + os.path.join(self.reference_directory, reference_file + ".cif") + ): + reference_file_cif = " --libin " + os.path.join( + self.reference_directory, reference_file + ".cif" + ) else: - reference_file_cif = '' + reference_file_cif = "" - if os.path.isfile(os.path.join(self.initial_model_directory, xtal, xtal + '.mtz')): - mtzin = os.path.join( - self.initial_model_directory, xtal, xtal + '.mtz') + if os.path.isfile( + os.path.join(self.initial_model_directory, xtal, xtal + ".mtz") + ): + mtzin = os.path.join(self.initial_model_directory, xtal, xtal + ".mtz") self.update_log.insert( - 'adding ' + xtal + visit + '-' + run + autoproc + ' to list') - job_list.append([xtal, - visit + '-' + run + autoproc, - mtzin, - reference_file_pdb, - reference_file_mtz, - reference_file_cif]) - self.status_bar.showMessage('idle') + "adding " + xtal + visit + "-" + run + autoproc + " to list" + ) + job_list.append( + [ + xtal, + visit + "-" + run + autoproc, + mtzin, + reference_file_pdb, + reference_file_mtz, + reference_file_cif, + ] + ) + self.status_bar.showMessage("idle") return job_list def check_before_running_dimple(self, job_list, instruction): @@ -3648,80 +4277,104 @@ def check_before_running_dimple(self, job_list, instruction): msgBox = QtGui.QMessageBox() msgBox.setText( "Do you really want to run {0!s} {1!s} jobs?\nNote: we will not run more than {2!s} at once on the cluster!".format( - len(job_list), self.preferences['initial_refinement_pipeline'], self.preferences['max_queue_jobs'])) - msgBox.addButton(QtGui.QPushButton('Go'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('Cancel'), - QtGui.QMessageBox.RejectRole) + len(job_list), + self.preferences["initial_refinement_pipeline"], + self.preferences["max_queue_jobs"], + ) + ) + msgBox.addButton(QtGui.QPushButton("Go"), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton("Cancel"), QtGui.QMessageBox.RejectRole) reply = msgBox.exec_() if reply == 0: - if 'dimple' in instruction.lower(): - pipeline = 'dimple' - elif 'pipedream' in instruction.lower(): - pipeline = 'pipedream' - elif 'phenix' in instruction.lower(): - pipeline = 'phenix.ligand_pipeline' + if "dimple" in instruction.lower(): + pipeline = "dimple" + elif "pipedream" in instruction.lower(): + pipeline = "pipedream" + elif "phenix" in instruction.lower(): + pipeline = "phenix.ligand_pipeline" self.status_bar.showMessage( - 'preparing {0!s} DIMPLE jobs'.format(len(job_list))) + "preparing {0!s} DIMPLE jobs".format(len(job_list)) + ) self.update_log.insert( - 'preparing to run {0!s} DIMPLE jobs'.format(len(job_list))) - if self.external_software['qsub_array']: + "preparing to run {0!s} DIMPLE jobs".format(len(job_list)) + ) + if self.external_software["qsub_array"]: self.update_log.insert( - 'we will be running an ARRAY job on the DLS computer cluster') + "we will be running an ARRAY job on the DLS computer cluster" + ) self.update_log.insert( - 'please note that the maximum number of jobs that will be running at once is {0!s}'.format( - self.max_queue_jobs)) + "please note that the maximum number of jobs that will be running at once is {0!s}".format( + self.max_queue_jobs + ) + ) self.update_log.insert( - 'you can change this in the PREFERENCES menu, but be warned that to high a number might break the cluster!') - self.update_log.insert('preparing input files for DIMPLE...') - self.work_thread = XChemThread.run_dimple_on_all_autoprocessing_files_new(job_list, - self.initial_model_directory, - self.external_software, - self.ccp4_scratch_directory, - self.database_directory, - self.data_source_file, - self.max_queue_jobs, - self.xce_logfile, - self.using_remote_qsub_submission, - self.remote_qsub_submission, - self.preferences['dimple_twin_mode'], - pipeline) + "you can change this in the PREFERENCES menu, but be warned that to high a number might break the cluster!" + ) + self.update_log.insert("preparing input files for DIMPLE...") + self.work_thread = XChemThread.run_dimple_on_all_autoprocessing_files_new( + job_list, + self.initial_model_directory, + self.external_software, + self.ccp4_scratch_directory, + self.database_directory, + self.data_source_file, + self.max_queue_jobs, + self.xce_logfile, + self.using_remote_qsub_submission, + self.remote_qsub_submission, + self.preferences["dimple_twin_mode"], + pipeline, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), - self.datasource_menu_reload_samples) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("datasource_menu_reload_samples"), + self.datasource_menu_reload_samples, + ) self.work_thread.start() def open_csv_file_translate_datasetID_to_sampleID(self): - file_name_temp = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Open file', self.current_directory, - '*.csv') + file_name_temp = QtGui.QFileDialog.getOpenFileNameAndFilter( + self.window, "Open file", self.current_directory, "*.csv" + ) file_name = tuple(file_name_temp)[0] self.translate_datasetID_to_sampleID_csv_label.setText(file_name) self.translate_datasetID_to_sampleID_file = file_name def update_datasets_reprocess_table(self, data_dict): - self.update_log.insert('updating reprocess datasets table') - print('updating reprocess datasets table') + self.update_log.insert("updating reprocess datasets table") + print("updating reprocess datasets table") self.diffraction_data_table_dict = {} self.diffraction_data_dict = data_dict - self.diffraction_data_search_info = 'found ' + \ - str(len(self.diffraction_data_dict)) + ' datasets' - self.diffraction_data_search_label.setText( - self.diffraction_data_search_info) + self.diffraction_data_search_info = ( + "found " + str(len(self.diffraction_data_dict)) + " datasets" + ) + self.diffraction_data_search_label.setText(self.diffraction_data_search_info) self.update_log.insert(self.diffraction_data_search_info) self.datasource_menu_reload_samples() # update table column_name = self.db.translate_xce_column_list_to_sqlite( - self.datasets_reprocess_columns) + self.datasets_reprocess_columns + ) # set rows to 0 self.datasets_reprocess_table.setRowCount(0) for entry in sorted(self.diffraction_data_dict): @@ -3733,138 +4386,152 @@ def update_datasets_reprocess_table(self, data_dict): row = self.datasets_reprocess_table.rowCount() self.datasets_reprocess_table.insertRow(row) for column, header in enumerate(column_name): - if header[0] == 'Dataset ID' or header[0] == 'Sample ID': + if header[0] == "Dataset ID" or header[0] == "Sample ID": cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(entry)) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.datasets_reprocess_table.setItem( - row, column, cell_text) - elif header[0] == 'Run\nxia2': + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) + self.datasets_reprocess_table.setItem(row, column, cell_text) + elif header[0] == "Run\nxia2": run_xia2 = QtGui.QCheckBox() run_xia2.toggle() - self.datasets_reprocess_table.setCellWidget( - row, column, run_xia2) + self.datasets_reprocess_table.setCellWidget(row, column, run_xia2) run_xia2.setChecked(False) self.diffraction_data_table_dict[entry] = [run_xia2] else: cell_text = QtGui.QTableWidgetItem() if db_dict != {}: - if header[0] == 'DataProcessing\nStatus': - if str(db_dict[header[1]]) == 'running': - cell_text.setBackground( - QtGui.QColor(100, 230, 150)) - elif str(db_dict[header[1]]) == 'pending': - cell_text.setBackground( - QtGui.QColor(20, 100, 230)) - elif str(db_dict[header[1]]) == 'started': - cell_text.setBackground( - QtGui.QColor(230, 240, 110)) - elif str(db_dict[header[1]]) == 'finished': - cell_text.setBackground( - QtGui.QColor(255, 255, 255)) + if header[0] == "DataProcessing\nStatus": + if str(db_dict[header[1]]) == "running": + cell_text.setBackground(QtGui.QColor(100, 230, 150)) + elif str(db_dict[header[1]]) == "pending": + cell_text.setBackground(QtGui.QColor(20, 100, 230)) + elif str(db_dict[header[1]]) == "started": + cell_text.setBackground(QtGui.QColor(230, 240, 110)) + elif str(db_dict[header[1]]) == "finished": + cell_text.setBackground(QtGui.QColor(255, 255, 255)) cell_text.setText(str(db_dict[header[1]])) else: - cell_text.setText('') + cell_text.setText("") cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.datasets_reprocess_table.setItem( - row, column, cell_text) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) + self.datasets_reprocess_table.setItem(row, column, cell_text) def update_all_tables(self): - self.update_log.insert('checking for new reference files') - self.update_status_bar('checking for new reference files') - self.reference_file_list = self.get_reference_file_list(' ') - self.update_log.insert('updating Overview table') - self.update_status_bar('updating Overview table') + self.update_log.insert("checking for new reference files") + self.update_status_bar("checking for new reference files") + self.reference_file_list = self.get_reference_file_list(" ") + self.update_log.insert("updating Overview table") + self.update_status_bar("updating Overview table") self.populate_and_update_datasource_table() - self.update_log.insert('updating Maps table') - self.update_status_bar('updating Maps table') + self.update_log.insert("updating Maps table") + self.update_status_bar("updating Maps table") self.create_maps_table() - self.update_log.insert('updating PANDDA table') - self.update_status_bar('updating PANDDA table') + self.update_log.insert("updating PANDDA table") + self.update_status_bar("updating PANDDA table") self.populate_pandda_analyse_input_table() - self.update_log.insert('updating REFINEMENT table') - self.update_status_bar('updating REFINEMENT table') + self.update_log.insert("updating REFINEMENT table") + self.update_status_bar("updating REFINEMENT table") self.populate_and_update_refinement_table() - self.update_log.insert('updating REPROCESSING table') - self.update_status_bar('updating REPROCESSING table') + self.update_log.insert("updating REPROCESSING table") + self.update_status_bar("updating REPROCESSING table") self.update_reprocessing_table() - self.update_status_bar('idle') + self.update_status_bar("idle") self.update_summary_plot() def change_allowed_unitcell_difference_percent(self, text): try: self.allowed_unitcell_difference_percent = int(text) - self.settings['unitcell_difference'] = self.allowed_unitcell_difference_percent + self.settings[ + "unitcell_difference" + ] = self.allowed_unitcell_difference_percent self.update_log.insert( - 'changing max allowed unit cell difference between reference and xtal to {0!s} percent'.format( - self.allowed_unitcell_difference_percent)) + "changing max allowed unit cell difference between reference and xtal to {0!s} percent".format( + self.allowed_unitcell_difference_percent + ) + ) except ValueError: - if str(text).find('.') != -1: + if str(text).find(".") != -1: self.allowed_unitcell_difference_percent = int( - str(text)[:str(text).find('.')]) - self.settings['unitcell_difference'] = self.allowed_unitcell_difference_percent + str(text)[: str(text).find(".")] + ) + self.settings[ + "unitcell_difference" + ] = self.allowed_unitcell_difference_percent self.update_log.insert( - 'changing max allowed unit cell difference between reference and xtal to {0!s} percent'.format( - self.allowed_unitcell_difference_percent)) + "changing max allowed unit cell difference between reference and xtal to {0!s} percent".format( + self.allowed_unitcell_difference_percent + ) + ) else: pass def change_max_queue_jobs(self, text): try: self.max_queue_jobs = int(text) - self.settings['max_queue_jobs'] = self.max_queue_jobs - self.update_log.insert('changing max number of jobs running simultaneously on DLS cluster to {0!s}'.format( - self.max_queue_jobs)) + self.settings["max_queue_jobs"] = self.max_queue_jobs + self.update_log.insert( + "changing max number of jobs running simultaneously on DLS cluster to {0!s}".format( + self.max_queue_jobs + ) + ) except ValueError: - if str(text).find('.') != -1: - self.max_queue_jobs = int(str(text)[:str(text).find('.')]) - self.settings['max_queue_jobs'] = self.max_queue_jobs + if str(text).find(".") != -1: + self.max_queue_jobs = int(str(text)[: str(text).find(".")]) + self.settings["max_queue_jobs"] = self.max_queue_jobs self.update_log.insert( - 'changing max number of jobs running simultaneously on DLS cluster to {0!s}'.format( - self.max_queue_jobs)) + "changing max number of jobs running simultaneously on DLS cluster to {0!s}".format( + self.max_queue_jobs + ) + ) else: pass def change_acceptable_low_resolution_limit(self, text): try: self.acceptable_low_resolution_limit_for_data = float(text) - self.settings['too_low_resolution_data'] = self.acceptable_low_resolution_limit_for_data + self.settings[ + "too_low_resolution_data" + ] = self.acceptable_low_resolution_limit_for_data except ValueError: pass def change_filename_root(self, text): self.filename_root = str(text) - self.settings['filename_root'] = self.filename_root + self.settings["filename_root"] = self.filename_root def button_clicked(self): if not self.data_source_set: - print('sender text bit') + print("sender text bit") if self.sender().text() == "Create New Data\nSource (SQLite)": - file_name = str(QtGui.QFileDialog.getSaveFileName( - self.window, 'Save file', self.database_directory)) + file_name = str( + QtGui.QFileDialog.getSaveFileName( + self.window, "Save file", self.database_directory + ) + ) # make sure that the file always has .sqlite extension - if file_name.rfind('.') != -1: - file_name = file_name[:file_name.rfind('.')] + '.sqlite' + if file_name.rfind(".") != -1: + file_name = file_name[: file_name.rfind(".")] + ".sqlite" else: - file_name = file_name + '.sqlite' + file_name = file_name + ".sqlite" self.db = XChemDB.data_source(file_name) - print('==> XCE: creating new data source') + print("==> XCE: creating new data source") self.db.create_empty_data_source_file() self.db.create_missing_columns() - if self.data_source_file == '': - self.database_directory = file_name[:file_name.rfind('/')] - self.data_source_file = file_name[file_name.rfind( - '/') + 1:] - self.data_source_file_label.setText(os.path.join( - self.database_directory, self.data_source_file)) - self.settings['database_directory'] = self.database_directory - self.settings['data_source'] = self.data_source_file + if self.data_source_file == "": + self.database_directory = file_name[: file_name.rfind("/")] + self.data_source_file = file_name[file_name.rfind("/") + 1 :] + self.data_source_file_label.setText( + os.path.join(self.database_directory, self.data_source_file) + ) + self.settings["database_directory"] = self.database_directory + self.settings["data_source"] = self.data_source_file self.data_source_set = True else: self.no_data_source_selected() - print('No datasource selected') + print("No datasource selected") pass # first find out which of the 'Run' or 'Status' buttons is sending @@ -3874,34 +4541,44 @@ def button_clicked(self): # get index of item in self.workflow; Note this index should be the same as the index # of the self.main_tab_widget which belongs to this task task_index = self.workflow.index(item) - instruction = str( - self.workflow_widget_dict[item][0].currentText()) + instruction = str(self.workflow_widget_dict[item][0].currentText()) print(instruction) action = str(self.sender().text()) if self.main_tab_widget.currentIndex() == task_index: if self.explorer_active == 0 and self.data_source_set == True: - if action == 'Run': - print(('==> XCE: Remote submission status = ' + - str(self.using_remote_qsub_submission))) + if action == "Run": + print( + ( + "==> XCE: Remote submission status = " + + str(self.using_remote_qsub_submission) + ) + ) # print(instruction) self.prepare_and_run_task(instruction) - elif action == 'Status': - self.get_status_of_workflow_milestone( - instruction) - if os.path.exists(str(self.panddas_directory + '/pandda.done')): - self.pandda_status = 'Finished!' - self.pandda_status_label.setStyleSheet( - 'color: green') - if os.path.exists(str(self.panddas_directory + '/pandda.running')): - self.pandda_status = 'Running...' + elif action == "Status": + self.get_status_of_workflow_milestone(instruction) + if os.path.exists( + str(self.panddas_directory + "/pandda.done") + ): + self.pandda_status = "Finished!" self.pandda_status_label.setStyleSheet( - 'color: orange') - if os.path.exists(str(self.panddas_directory + '/pandda.errored')): - self.pandda_status = 'Error encountered... please check the log files for pandda!' + "color: green" + ) + if os.path.exists( + str(self.panddas_directory + "/pandda.running") + ): + self.pandda_status = "Running..." self.pandda_status_label.setStyleSheet( - 'color: red') + "color: orange" + ) + if os.path.exists( + str(self.panddas_directory + "/pandda.errored") + ): + self.pandda_status = "Error encountered... please check the log files for pandda!" + self.pandda_status_label.setStyleSheet("color: red") self.pandda_status_label.setText( - str('STATUS: ' + self.pandda_status)) + str("STATUS: " + self.pandda_status) + ) else: self.need_to_switch_main_tab(task_index) @@ -3911,214 +4588,228 @@ def get_status_of_workflow_milestone(self, instruction): cluster_dict = XChemMain.get_jobs_running_on_cluster() - self.update_log.insert('getting status updates...') + self.update_log.insert("getting status updates...") self.status_bar.showMessage( - 'please check terminal window for further information') + "please check terminal window for further information" + ) self.update_log.insert( - '{0!s} samples are currently in database'.format(str(len(self.xtal_db_dict)))) + "{0!s} samples are currently in database".format( + str(len(self.xtal_db_dict)) + ) + ) - if 'DIMPLE' in instruction: + if "DIMPLE" in instruction: XChemMain.print_cluster_status_message( - 'dimple', cluster_dict, self.xce_logfile) + "dimple", cluster_dict, self.xce_logfile + ) - elif 'Create CIF/PDB/PNG file' in instruction: + elif "Create CIF/PDB/PNG file" in instruction: XChemMain.print_acedrg_status(self.xce_logfile, self.xtal_db_dict) XChemMain.print_cluster_status_message( - 'acedrg', cluster_dict, self.xce_logfile) + "acedrg", cluster_dict, self.xce_logfile + ) - elif instruction.startswith('Run xia2 on selected datasets'): + elif instruction.startswith("Run xia2 on selected datasets"): XChemMain.print_cluster_status_message( - 'xia2', cluster_dict, self.xce_logfile) + "xia2", cluster_dict, self.xce_logfile + ) - elif 'pandda' in instruction.lower(): + elif "pandda" in instruction.lower(): XChemMain.print_cluster_status_message( - 'pandda', cluster_dict, self.xce_logfile) + "pandda", cluster_dict, self.xce_logfile + ) - elif 'coot' in instruction.lower(): + elif "coot" in instruction.lower(): XChemMain.print_cluster_status_message( - 'refmac', cluster_dict, self.xce_logfile) + "refmac", cluster_dict, self.xce_logfile + ) def prepare_and_run_task(self, instruction): - if instruction == 'Get New Results from Autoprocessing': + if instruction == "Get New Results from Autoprocessing": self.rescore = False self.check_for_new_autoprocessing_results() - elif instruction == 'Rescore Datasets': + elif instruction == "Rescore Datasets": self.rescore = True self.select_best_autoprocessing_result() -# if instruction == 'Get New Results from Autoprocessing': -# self.check_for_new_autoprocessing_or_rescore(False) -# self.update_header_and_data_from_datasource() -# self.update_all_tables() -# -# elif instruction == 'Rescore Datasets': -# self.check_for_new_autoprocessing_or_rescore(True) + # if instruction == 'Get New Results from Autoprocessing': + # self.check_for_new_autoprocessing_or_rescore(False) + # self.update_header_and_data_from_datasource() + # self.update_all_tables() + # + # elif instruction == 'Rescore Datasets': + # self.check_for_new_autoprocessing_or_rescore(True) -# elif instruction == "Read PKL file": -# summary = pickle.load(open(self.datasets_summary_file, "rb")) -# self.create_widgets_for_autoprocessing_results_only(summary) + # elif instruction == "Read PKL file": + # summary = pickle.load(open(self.datasets_summary_file, "rb")) + # self.create_widgets_for_autoprocessing_results_only(summary) - elif instruction == 'Run xia2 on selected datasets': + elif instruction == "Run xia2 on selected datasets": self.run_xia2_on_selected_datasets(False) - elif instruction == 'Run xia2 on selected datasets - overwrite': + elif instruction == "Run xia2 on selected datasets - overwrite": self.run_xia2_on_selected_datasets(True) -# elif instruction == 'Run DIMPLE on All Autoprocessing MTZ files': -# self.rerun_dimple_on_all_autoprocessing_files() + # elif instruction == 'Run DIMPLE on All Autoprocessing MTZ files': + # self.rerun_dimple_on_all_autoprocessing_files() -# elif instruction == 'Run initial refinement on selected MTZ files': -# self.run_dimple_on_selected_autoprocessing_file() + # elif instruction == 'Run initial refinement on selected MTZ files': + # self.run_dimple_on_selected_autoprocessing_file() - elif instruction == 'Run DIMPLE on selected MTZ files': + elif instruction == "Run DIMPLE on selected MTZ files": self.run_dimple_on_selected_autoprocessing_file(instruction) - elif instruction == 'Run PIPEDREAM on selected MTZ files': + elif instruction == "Run PIPEDREAM on selected MTZ files": self.run_dimple_on_selected_autoprocessing_file(instruction) - elif instruction == 'Run PHENIX.LIGAND_PIPELINE on selected MTZ files': + elif instruction == "Run PHENIX.LIGAND_PIPELINE on selected MTZ files": self.run_dimple_on_selected_autoprocessing_file(instruction) + # elif instruction == 'Remove selected initial refinement files': + # self.remove_selected_dimple_files() -# elif instruction == 'Remove selected initial refinement files': -# self.remove_selected_dimple_files() - - elif instruction == 'Remove selected DIMPLE files': + elif instruction == "Remove selected DIMPLE files": self.remove_selected_dimple_files(instruction) - elif instruction == 'Remove selected PIPEDREAM files': + elif instruction == "Remove selected PIPEDREAM files": self.remove_selected_dimple_files(instruction) - elif instruction == 'Remove selected PHENIX.LIGAND_PIPELINE files': + elif instruction == "Remove selected PHENIX.LIGAND_PIPELINE files": self.remove_selected_dimple_files(instruction) -# elif instruction == 'Set only results from selected pipeline': -# self.set_results_from_selected_pipeline() + # elif instruction == 'Set only results from selected pipeline': + # self.set_results_from_selected_pipeline() - elif instruction == 'Set DIMPLE output': + elif instruction == "Set DIMPLE output": self.set_results_from_selected_pipeline(instruction) - elif instruction == 'Set PIPEDREAM output': + elif instruction == "Set PIPEDREAM output": self.set_results_from_selected_pipeline(instruction) - elif instruction == 'Set PHENIX.LIGAND_PIPELINE output': + elif instruction == "Set PHENIX.LIGAND_PIPELINE output": self.set_results_from_selected_pipeline(instruction) + # elif instruction == 'Create CIF/PDB/PNG file of ALL compounds': + # self.create_cif_pdb_png_files('ALL') -# elif instruction == 'Create CIF/PDB/PNG file of ALL compounds': -# self.create_cif_pdb_png_files('ALL') + # elif instruction == 'Create CIF/PDB/PNG file of NEW compounds': + # self.create_cif_pdb_png_files('NEW') -# elif instruction == 'Create CIF/PDB/PNG file of NEW compounds': -# self.create_cif_pdb_png_files('NEW') + elif instruction == "Create CIF/PDB/PNG file of SELECTED compounds": + self.create_cif_pdb_png_files("SELECTED") - elif instruction == 'Create CIF/PDB/PNG file of SELECTED compounds': - self.create_cif_pdb_png_files('SELECTED') + elif instruction == "Merge ligand CIF file with selected compounds": + self.merge_cif_files("merge") - elif instruction == 'Merge ligand CIF file with selected compounds': - self.merge_cif_files('merge') + elif instruction == "Restore original CIF file of selected compounds": + self.merge_cif_files("restore") - elif instruction == 'Restore original CIF file of selected compounds': - self.merge_cif_files('restore') - - elif instruction == 'Fit ligands into maps after initial refinement': + elif instruction == "Fit ligands into maps after initial refinement": self.fit_ligands_into_dimple_maps() - elif instruction == 'pandda.analyse': - self.run_pandda_analyse('production_run') + elif instruction == "pandda.analyse": + self.run_pandda_analyse("production_run") - elif instruction == 'pandda.analyse (PanDDA2)': - self.run_pandda_analyse('production_run_pandda_two') + elif instruction == "pandda.analyse (PanDDA2)": + self.run_pandda_analyse("production_run_pandda_two") - elif instruction == 'pre-run for ground state model': - self.run_pandda_analyse('pre_run') + elif instruction == "pre-run for ground state model": + self.run_pandda_analyse("pre_run") - elif instruction == 'pandda.inspect': + elif instruction == "pandda.inspect": self.run_pandda_inspect() - elif instruction == 'run pandda.inspect at home': + elif instruction == "run pandda.inspect at home": self.run_pandda_inspect_at_home() - elif instruction == 'Export NEW PANDDA models': + elif instruction == "Export NEW PANDDA models": update_datasource_only = False - which_models = 'new' + which_models = "new" self.run_pandda_export(update_datasource_only, which_models) - elif instruction == 'Export ALL PANDDA models': + elif instruction == "Export ALL PANDDA models": update_datasource_only = False - which_models = 'all' + which_models = "all" self.run_pandda_export(update_datasource_only, which_models) - elif instruction == 'Export SELECTED PANDDA models': + elif instruction == "Export SELECTED PANDDA models": update_datasource_only = False - which_models = 'selected' + which_models = "selected" self.run_pandda_export(update_datasource_only, which_models) - elif instruction == 'refine ALL bound-state models with BUSTER': - self.run_refine_bound_state_with_buster('all') + elif instruction == "refine ALL bound-state models with BUSTER": + self.run_refine_bound_state_with_buster("all") - elif instruction == 'refine NEW bound-state models with BUSTER': - self.run_refine_bound_state_with_buster('new') + elif instruction == "refine NEW bound-state models with BUSTER": + self.run_refine_bound_state_with_buster("new") - elif instruction == 'refine ALL bound-state models with BUSTER (no sanity check)': - self.run_refine_bound_state_with_buster('allnocheck') + elif ( + instruction == "refine ALL bound-state models with BUSTER (no sanity check)" + ): + self.run_refine_bound_state_with_buster("allnocheck") - elif instruction == 'refine NEW bound-state models with BUSTER (no sanity check)': - self.run_refine_bound_state_with_buster('newnocheck') + elif ( + instruction == "refine NEW bound-state models with BUSTER (no sanity check)" + ): + self.run_refine_bound_state_with_buster("newnocheck") -# elif instruction == 'refine NEW bound-state models with BUSTER - NEW': -# self.run_refine_bound_state_with_buster_new('new') + # elif instruction == 'refine NEW bound-state models with BUSTER - NEW': + # self.run_refine_bound_state_with_buster_new('new') - elif instruction == 'cluster datasets': + elif instruction == "cluster datasets": self.cluster_datasets_for_pandda() - elif instruction == 'Update datasource with results from pandda.inspect': + elif instruction == "Update datasource with results from pandda.inspect": update_datasource_only = True - which_models = 'all' + which_models = "all" self.run_pandda_export(update_datasource_only, which_models) - elif instruction == 'Show HTML summary': + elif instruction == "Show HTML summary": self.show_pandda_html_summary() - elif instruction == 'Event Map -> SF': + elif instruction == "Event Map -> SF": self.convert_event_maps_to_SF() - elif instruction == 'apo -> mmcif': + elif instruction == "apo -> mmcif": self.convert_apo_to_mmcif() - elif instruction == 'check modelled ligands': + elif instruction == "check modelled ligands": self.compare_modelled_ligands_and_panddaTable() - elif instruction.startswith("Open COOT") or instruction == 'Build ground state model': + elif ( + instruction.startswith("Open COOT") + or instruction == "Build ground state model" + ): if not self.coot_running: - self.update_log.insert('starting coot...') + self.update_log.insert("starting coot...") if instruction == "Open COOT": - interface = 'new' + interface = "new" elif instruction == "Open COOT - REFMAC refinement -": - interface = 'new' + interface = "new" elif instruction == "Open COOT - test -": - interface = 'test' + interface = "test" elif instruction == "Open COOT for old PanDDA": - interface = 'panddaV1' - elif instruction == 'Build ground state model': - interface = 'reference' - elif instruction == 'Open COOT - BUSTER refinement -': - interface = 'buster' - elif instruction == 'Open COOT - dimple_twin -': - interface = 'dimple_twin' + interface = "panddaV1" + elif instruction == "Build ground state model": + interface = "reference" + elif instruction == "Open COOT - BUSTER refinement -": + interface = "buster" + elif instruction == "Open COOT - dimple_twin -": + interface = "dimple_twin" else: - interface = 'old' -# print self.settings - self.work_thread = XChemThread.start_COOT( - self.settings, interface) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + interface = "old" + # print self.settings + self.work_thread = XChemThread.start_COOT(self.settings, interface) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() - elif instruction == 'Update Deposition Table': + elif instruction == "Update Deposition Table": self.update_deposition_table() def check_status_create_png_of_soaked_compound(self): @@ -4126,37 +4817,48 @@ def check_status_create_png_of_soaked_compound(self): running = 0 timestamp_list = [] cif_file_generated = 0 - for folder in glob.glob(os.path.join(self.initial_model_directory, '*', 'compound')): + for folder in glob.glob( + os.path.join(self.initial_model_directory, "*", "compound") + ): number_of_samples += 1 - if os.path.isfile(os.path.join(folder, 'RESTRAINTS_IN_PROGRESS')): + if os.path.isfile(os.path.join(folder, "RESTRAINTS_IN_PROGRESS")): running += 1 timestamp = datetime.fromtimestamp( - os.path.getmtime(os.path.join(folder, 'RESTRAINTS_IN_PROGRESS'))).strftime('%Y-%m-%d %H:%M:%S') + os.path.getmtime(os.path.join(folder, "RESTRAINTS_IN_PROGRESS")) + ).strftime("%Y-%m-%d %H:%M:%S") timestamp_list.append(timestamp) - for cif_file in glob.glob(os.path.join(folder, '*.cif')): + for cif_file in glob.glob(os.path.join(folder, "*.cif")): if os.path.isfile(cif_file): cif_file_generated += 1 if timestamp_list: last_timestamp = max(timestamp_list) else: - last_timestamp = 'n/a' - message = 'Datasets: ' + str(number_of_samples) + ', jobs running: ' + str(running) + ', jobs finished: ' + str( - cif_file_generated) + ', last job submmitted: ' + str(last_timestamp) + last_timestamp = "n/a" + message = ( + "Datasets: " + + str(number_of_samples) + + ", jobs running: " + + str(running) + + ", jobs finished: " + + str(cif_file_generated) + + ", last job submmitted: " + + str(last_timestamp) + ) self.status_bar.showMessage(message) if start_thread: - if self.target == '=== SELECT TARGET ===': + if self.target == "=== SELECT TARGET ===": msgBox = QtGui.QMessageBox() - warning = ('*** WARNING ***\n' - 'You did not select a target!\n' - 'In this case we will only parse the project directory!\n' - 'Please note that this option is usually only useful in case you reprocessed your data.\n' - 'Do you want to continue?') + warning = ( + "*** WARNING ***\n" + "You did not select a target!\n" + "In this case we will only parse the project directory!\n" + "Please note that this option is usually only useful in case you reprocessed your data.\n" + "Do you want to continue?" + ) msgBox.setText(warning) - msgBox.addButton(QtGui.QPushButton('Yes'), - QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton( - 'No'), QtGui.QMessageBox.RejectRole) + msgBox.addButton(QtGui.QPushButton("Yes"), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.RejectRole) reply = msgBox.exec_() if reply == 0: start_thread = True @@ -4166,462 +4868,618 @@ def check_status_create_png_of_soaked_compound(self): start_thread = True if start_thread: - self.work_thread = XChemThread.read_autoprocessing_results_from_disc(self.visit_list, - self.target, - self.reference_file_list, - self.database_directory, - self.data_collection_dict, - self.preferences, - self.datasets_summary_file, - self.initial_model_directory, - rescore_only, - self.acceptable_low_resolution_limit_for_data, - os.path.join(self.database_directory, - self.data_source_file), - self.xce_logfile) + self.work_thread = XChemThread.read_autoprocessing_results_from_disc( + self.visit_list, + self.target, + self.reference_file_list, + self.database_directory, + self.data_collection_dict, + self.preferences, + self.datasets_summary_file, + self.initial_model_directory, + rescore_only, + self.acceptable_low_resolution_limit_for_data, + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("create_widgets_for_autoprocessing_results_only"), - self.create_widgets_for_autoprocessing_results_only) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("create_widgets_for_autoprocessing_results_only"), + self.create_widgets_for_autoprocessing_results_only, + ) self.work_thread.start() def save_files_to_initial_model_folder(self): - self.work_thread = XChemThread.save_autoprocessing_results_to_disc(self.dataset_outcome_dict, - self.data_collection_table_dict, - self.data_collection_column_three_dict, - self.data_collection_dict, - self.database_directory, - self.data_source_file, - self.initial_model_directory, - self.preferences, - self.datasets_summary_file) + self.work_thread = XChemThread.save_autoprocessing_results_to_disc( + self.dataset_outcome_dict, + self.data_collection_table_dict, + self.data_collection_column_three_dict, + self.data_collection_dict, + self.database_directory, + self.data_source_file, + self.initial_model_directory, + self.preferences, + self.datasets_summary_file, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def run_pandda_analyse(self, run): pandda_params = { - 'data_dir': str(self.pandda_input_data_dir_entry.text()), - 'out_dir': str(self.pandda_output_data_dir_entry.text()), - 'submit_mode': str(self.pandda_submission_mode_selection_combobox.currentText()), - 'nproc': str(self.pandda_nproc_entry.text()), - 'min_build_datasets': str(self.pandda_min_build_dataset_entry.text()), - 'pdb_style': str(self.pandda_pdb_style_entry.text()), - 'mtz_style': str(self.pandda_mtz_style_entry.text()), - 'sort_event': str(self.pandda_sort_event_combobox.currentText()), - 'average_map': str(self.pandda_calc_map_combobox.currentText()), - 'max_new_datasets': str(self.pandda_max_new_datasets_entry.text()), - 'grid_spacing': str(self.pandda_grid_spacing_entry.text()), - 'keyword_arguments': str(self.pandda_keyword_arguments_entry.text()), - 'pandda_dir_structure': str(self.pandda_input_data_dir_entry.text()), - 'perform_diffraction_data_scaling': str(self.wilson_checkbox.isChecked()), - 'filter_pdb': str(self.pandda_reference_file_selection_combobox.currentText()), - 'reference_dir': self.reference_directory, - 'appendix': '', - 'N_datasets': len(glob.glob(os.path.join(self.initial_model_directory, '*', 'dimple.pdb'))), - 'write_mean_map': 'interesting', - 'pandda_table': self.pandda_analyse_data_table, - 'use_remote': self.using_remote_qsub_submission, - 'remote_string': self.remote_qsub_submission + "data_dir": str(self.pandda_input_data_dir_entry.text()), + "out_dir": str(self.pandda_output_data_dir_entry.text()), + "submit_mode": str( + self.pandda_submission_mode_selection_combobox.currentText() + ), + "nproc": str(self.pandda_nproc_entry.text()), + "min_build_datasets": str(self.pandda_min_build_dataset_entry.text()), + "pdb_style": str(self.pandda_pdb_style_entry.text()), + "mtz_style": str(self.pandda_mtz_style_entry.text()), + "sort_event": str(self.pandda_sort_event_combobox.currentText()), + "average_map": str(self.pandda_calc_map_combobox.currentText()), + "max_new_datasets": str(self.pandda_max_new_datasets_entry.text()), + "grid_spacing": str(self.pandda_grid_spacing_entry.text()), + "keyword_arguments": str(self.pandda_keyword_arguments_entry.text()), + "pandda_dir_structure": str(self.pandda_input_data_dir_entry.text()), + "perform_diffraction_data_scaling": str(self.wilson_checkbox.isChecked()), + "filter_pdb": str( + self.pandda_reference_file_selection_combobox.currentText() + ), + "reference_dir": self.reference_directory, + "appendix": "", + "N_datasets": len( + glob.glob(os.path.join(self.initial_model_directory, "*", "dimple.pdb")) + ), + "write_mean_map": "interesting", + "pandda_table": self.pandda_analyse_data_table, + "use_remote": self.using_remote_qsub_submission, + "remote_string": self.remote_qsub_submission, } - if run == 'pre_run': + if run == "pre_run": msgBox = QtGui.QMessageBox() msgBoxLayout = msgBox.layout() vbox = QtGui.QVBoxLayout() - vbox.addWidget(QtGui.QLabel( - XChemToolTips.pandda_pre_run(self.reference_directory))) + vbox.addWidget( + QtGui.QLabel(XChemToolTips.pandda_pre_run(self.reference_directory)) + ) hbox = QtGui.QHBoxLayout() - hbox.addWidget(QtGui.QLabel('appendix:')) + hbox.addWidget(QtGui.QLabel("appendix:")) appendix = QtGui.QLineEdit() - appendix.setText('pre') + appendix.setText("pre") appendix.setFixedWidth(200) hbox.addWidget(appendix) vbox.addLayout(hbox) msgBoxLayout.addLayout(vbox, 0, 0) - msgBox.addButton(QtGui.QPushButton( - 'Go'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('Cancel'), - QtGui.QMessageBox.RejectRole) + msgBox.addButton(QtGui.QPushButton("Go"), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton("Cancel"), QtGui.QMessageBox.RejectRole) reply = msgBox.exec_() if reply == 0: - pandda_params['appendix'] = str(appendix.text()) - pandda_params['max_new_datasets'] = '100' - pandda_params['N_datasets'] = 100 - pandda_params['write_mean_map'] = 'all' + pandda_params["appendix"] = str(appendix.text()) + pandda_params["max_new_datasets"] = "100" + pandda_params["N_datasets"] = 100 + pandda_params["write_mean_map"] = "all" else: return None - self.update_log.insert('preparing pandda.analyse input script') - if run == 'production_run_pandda_two': - self.work_thread = XChemPANDDA.run_pandda_two_analyse(pandda_params, self.xce_logfile, - os.path.join(self.database_directory, self.data_source_file)) + self.update_log.insert("preparing pandda.analyse input script") + if run == "production_run_pandda_two": + self.work_thread = XChemPANDDA.run_pandda_two_analyse( + pandda_params, + self.xce_logfile, + os.path.join(self.database_directory, self.data_source_file), + ) else: - self.work_thread = XChemPANDDA.run_pandda_analyse(pandda_params, self.xce_logfile, - os.path.join(self.database_directory, self.data_source_file)) + self.work_thread = XChemPANDDA.run_pandda_analyse( + pandda_params, + self.xce_logfile, + os.path.join(self.database_directory, self.data_source_file), + ) # self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), - # self.datasource_menu_reload_samples) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + # self.datasource_menu_reload_samples) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def cluster_datasets_for_pandda(self): pandda_params = { - 'out_dir': str(self.pandda_output_data_dir_entry.text()), - 'pdb_style': str(self.pandda_pdb_style_entry.text()), - 'mtz_style': str(self.pandda_mtz_style_entry.text()) + "out_dir": str(self.pandda_output_data_dir_entry.text()), + "pdb_style": str(self.pandda_pdb_style_entry.text()), + "mtz_style": str(self.pandda_mtz_style_entry.text()), } - self.update_log.insert('starting giant.cluster_mtzs_and_pdbs') - self.work_thread = XChemPANDDA.giant_cluster_datasets(self.initial_model_directory, pandda_params, - self.xce_logfile, os.path.join(self.database_directory, - self.data_source_file), - run_pandda_analyse) + self.update_log.insert("starting giant.cluster_mtzs_and_pdbs") + self.work_thread = XChemPANDDA.giant_cluster_datasets( + self.initial_model_directory, + pandda_params, + self.xce_logfile, + os.path.join(self.database_directory, self.data_source_file), + run_pandda_analyse, + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), - self.datasource_menu_reload_samples) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("datasource_menu_reload_samples"), + self.datasource_menu_reload_samples, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def run_pandda_inspect(self): - self.settings['panddas_directory'] = str( - self.pandda_output_data_dir_entry.text()) - print('==> XCE: starting pandda.inspect') + self.settings["panddas_directory"] = str( + self.pandda_output_data_dir_entry.text() + ) + print("==> XCE: starting pandda.inspect") self.work_thread = XChemThread.start_pandda_inspect( - self.settings, self.xce_logfile) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.settings, self.xce_logfile + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def run_pandda_inspect_at_home(self): self.work_thread = XChemPANDDA.run_pandda_inspect_at_home( - self.panddas_directory, self.xce_logfile) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.panddas_directory, self.xce_logfile + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) def convert_event_maps_to_SF(self): - self.update_log.insert('converting all event maps in {0!s} to mtz files'.format( - self.initial_model_directory)) -# self.work_thread = XChemPANDDA.convert_all_event_maps_in_database(self.initial_model_directory, -# self.xce_logfile, -# os.path.join(self.database_directory, -# self.data_source_file)) - self.work_thread = XChemPANDDA.find_event_map_for_ligand(self.initial_model_directory, - self.xce_logfile, self.external_software) + self.update_log.insert( + "converting all event maps in {0!s} to mtz files".format( + self.initial_model_directory + ) + ) + # self.work_thread = XChemPANDDA.convert_all_event_maps_in_database(self.initial_model_directory, + # self.xce_logfile, + # os.path.join(self.database_directory, + # self.data_source_file)) + self.work_thread = XChemPANDDA.find_event_map_for_ligand( + self.initial_model_directory, self.xce_logfile, self.external_software + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def convert_apo_to_mmcif(self): - self.work_thread = XChemPANDDA.convert_apo_structures_to_mmcif(self.panddas_directory, - self.xce_logfile) + self.work_thread = XChemPANDDA.convert_apo_structures_to_mmcif( + self.panddas_directory, self.xce_logfile + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def compare_modelled_ligands_and_panddaTable(self): self.update_log.insert( - 'checking agreement of ligands in refine.pdb and entries in panddaTable') - self.work_thread = XChemPANDDA.check_number_of_modelled_ligands(self.initial_model_directory, - self.xce_logfile, - os.path.join(self.database_directory, - self.data_source_file)) + "checking agreement of ligands in refine.pdb and entries in panddaTable" + ) + self.work_thread = XChemPANDDA.check_number_of_modelled_ligands( + self.initial_model_directory, + self.xce_logfile, + os.path.join(self.database_directory, self.data_source_file), + ) self.explorer_active = 1 - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL( - "show_error_dict"), self.show_error_dict) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, QtCore.SIGNAL("show_error_dict"), self.show_error_dict + ) self.work_thread.start() def run_pandda_export(self, update_datasource_only, which_models): pandda_params = { - 'data_dir': str(self.pandda_input_data_dir_entry.text()), - 'out_dir': str(self.pandda_output_data_dir_entry.text()), - 'submit_mode': str(self.pandda_submission_mode_selection_combobox.currentText()), - 'nproc': str(self.pandda_nproc_entry.text()), - 'min_build_datasets': str(self.pandda_min_build_dataset_entry.text()), - 'pdb_style': str(self.pandda_pdb_style_entry.text()), - 'mtz_style': str(self.pandda_mtz_style_entry.text()), - 'sort_event': str(self.pandda_sort_event_combobox.currentText()), - 'average_map': str(self.pandda_calc_map_combobox.currentText()), - 'max_new_datasets': str(self.pandda_max_new_datasets_entry.text()), - 'grid_spacing': str(self.pandda_grid_spacing_entry.text()), - 'pandda_dir_structure': str(self.pandda_input_data_dir_entry.text()), - 'perform_diffraction_data_scaling': str(self.wilson_checkbox.isChecked()), - 'filter_pdb': str(self.pandda_reference_file_selection_combobox.currentText()), - 'reference_dir': self.reference_directory, - 'appendix': '', - 'N_datasets': len(glob.glob(os.path.join(self.initial_model_directory, '*', 'dimple.pdb'))), - 'write_mean_map': 'interesting', - 'pandda_table': self.pandda_analyse_data_table, - 'use_remote': self.using_remote_qsub_submission, - 'remote_string': self.remote_qsub_submission + "data_dir": str(self.pandda_input_data_dir_entry.text()), + "out_dir": str(self.pandda_output_data_dir_entry.text()), + "submit_mode": str( + self.pandda_submission_mode_selection_combobox.currentText() + ), + "nproc": str(self.pandda_nproc_entry.text()), + "min_build_datasets": str(self.pandda_min_build_dataset_entry.text()), + "pdb_style": str(self.pandda_pdb_style_entry.text()), + "mtz_style": str(self.pandda_mtz_style_entry.text()), + "sort_event": str(self.pandda_sort_event_combobox.currentText()), + "average_map": str(self.pandda_calc_map_combobox.currentText()), + "max_new_datasets": str(self.pandda_max_new_datasets_entry.text()), + "grid_spacing": str(self.pandda_grid_spacing_entry.text()), + "pandda_dir_structure": str(self.pandda_input_data_dir_entry.text()), + "perform_diffraction_data_scaling": str(self.wilson_checkbox.isChecked()), + "filter_pdb": str( + self.pandda_reference_file_selection_combobox.currentText() + ), + "reference_dir": self.reference_directory, + "appendix": "", + "N_datasets": len( + glob.glob(os.path.join(self.initial_model_directory, "*", "dimple.pdb")) + ), + "write_mean_map": "interesting", + "pandda_table": self.pandda_analyse_data_table, + "use_remote": self.using_remote_qsub_submission, + "remote_string": self.remote_qsub_submission, } - self.settings['panddas_directory'] = str( - self.pandda_output_data_dir_entry.text()) + self.settings["panddas_directory"] = str( + self.pandda_output_data_dir_entry.text() + ) if update_datasource_only: self.update_log.insert( - 'updating data source with results from pandda.inspect') + "updating data source with results from pandda.inspect" + ) else: self.update_log.insert( - 'exporting PANDDA models, updating data source and launching inital refinement for new models') + "exporting PANDDA models, updating data source and launching inital refinement for new models" + ) start_thread = False - if which_models == 'all': + if which_models == "all": self.update_log.insert( - 'exporting ALL models! *** WARNING *** This may overwrite previous refinements!!!') + "exporting ALL models! *** WARNING *** This may overwrite previous refinements!!!" + ) msgBox = QtGui.QMessageBox() msgBox.setText( - "*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?") - msgBox.addButton(QtGui.QPushButton('Yes'), - QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton( - 'No'), QtGui.QMessageBox.RejectRole) + "*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?" + ) + msgBox.addButton(QtGui.QPushButton("Yes"), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.RejectRole) reply = msgBox.exec_() if reply == 0: if update_datasource_only: - self.update_log.insert( - 'will update panddaTable in database only') + self.update_log.insert("will update panddaTable in database only") else: - self.update_log.insert('will export ALL models!') + self.update_log.insert("will export ALL models!") start_thread = True else: start_thread = False else: - self.update_log.insert('exporting new models only') + self.update_log.insert("exporting new models only") start_thread = True if start_thread: - self.work_thread = XChemPANDDA.run_pandda_export(self.panddas_directory, - os.path.join(self.database_directory, - self.data_source_file), - self.initial_model_directory, self.xce_logfile, - update_datasource_only, which_models, pandda_params) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.work_thread = XChemPANDDA.run_pandda_export( + self.panddas_directory, + os.path.join(self.database_directory, self.data_source_file), + self.initial_model_directory, + self.xce_logfile, + update_datasource_only, + which_models, + pandda_params, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() -# def run_refine_bound_state_with_buster(self,which_models): -# start_thread = True -# if start_thread: -# self.work_thread = XChemPANDDA.refine_bound_state_with_buster(self.panddas_directory, -# os.path.join(self.database_directory, -# self.data_source_file), -# self.initial_model_directory, self.xce_logfile, -# which_models) -# self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) -# self.work_thread.start() + # def run_refine_bound_state_with_buster(self,which_models): + # start_thread = True + # if start_thread: + # self.work_thread = XChemPANDDA.refine_bound_state_with_buster(self.panddas_directory, + # os.path.join(self.database_directory, + # self.data_source_file), + # self.initial_model_directory, self.xce_logfile, + # which_models) + # self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) + # self.work_thread.start() def run_refine_bound_state_with_buster(self, which_models): start_thread = True if start_thread: - self.work_thread = XChemPANDDA.export_and_refine_ligand_bound_models(self.panddas_directory, - os.path.join(self.database_directory, - self.data_source_file), - self.initial_model_directory, self.xce_logfile, - which_models) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) + self.work_thread = XChemPANDDA.export_and_refine_ligand_bound_models( + self.panddas_directory, + os.path.join(self.database_directory, self.data_source_file), + self.initial_model_directory, + self.xce_logfile, + which_models, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) self.work_thread.start() def show_pandda_html_summary(self): - self.pandda_initial_html.load( - QtCore.QUrl(self.pandda_initial_html_file)) + self.pandda_initial_html.load(QtCore.QUrl(self.pandda_initial_html_file)) self.pandda_initial_html.show() - self.pandda_analyse_html.load( - QtCore.QUrl(self.pandda_analyse_html_file)) + self.pandda_analyse_html.load(QtCore.QUrl(self.pandda_analyse_html_file)) self.pandda_analyse_html.show() self.add_map_html() - self.pandda_inspect_html.load( - QtCore.QUrl(self.pandda_inspect_html_file)) + self.pandda_inspect_html.load(QtCore.QUrl(self.pandda_inspect_html_file)) self.pandda_inspect_html.show() def create_cif_pdb_png_files(self, todo): tmp = self.db.execute_statement( - "select CrystalName,CompoundCode,CompoundSmiles from mainTable where CrystalName is not '' and CompoundSmiles is not '' and CompoundSmiles is not NULL;") + "select CrystalName,CompoundCode,CompoundSmiles from mainTable where CrystalName is not '' and CompoundSmiles is not '' and CompoundSmiles is not NULL;" + ) compound_list = [] for item in tmp: - if str(item[1]) == '' or str(item[1]) == 'NULL': - compoundID = 'compound' + if str(item[1]) == "" or str(item[1]) == "NULL": + compoundID = "compound" else: compoundID = str(item[1]) - if todo == 'ALL': + if todo == "ALL": compound_list.append([str(item[0]), compoundID, str(item[2])]) - elif todo == 'NEW': - if not os.path.isfile(os.path.join(self.initial_model_directory, str(item[0]), compoundID + '.cif')): - compound_list.append( - [str(item[0]), compoundID, str(item[2])]) - elif todo == 'SELECTED': + elif todo == "NEW": + if not os.path.isfile( + os.path.join( + self.initial_model_directory, str(item[0]), compoundID + ".cif" + ) + ): + compound_list.append([str(item[0]), compoundID, str(item[2])]) + elif todo == "SELECTED": if str(item[0]) in self.initial_model_dimple_dict: if self.initial_model_dimple_dict[str(item[0])][0].isChecked(): - compound_list.append( - [str(item[0]), compoundID, str(item[2])]) + compound_list.append([str(item[0]), compoundID, str(item[2])]) if compound_list: self.update_log.insert( - 'trying to create cif and pdb files for ' + str(len(compound_list)) + ' compounds using ACEDRG...') - if self.external_software['qsub']: + "trying to create cif and pdb files for " + + str(len(compound_list)) + + " compounds using ACEDRG..." + ) + if self.external_software["qsub"]: + self.update_log.insert( + "will try sending " + + str(len(compound_list)) + + " jobs to your computer cluster!" + ) + elif self.external_software["qsub_array"]: self.update_log.insert( - 'will try sending ' + str(len(compound_list)) + ' jobs to your computer cluster!') - elif self.external_software['qsub_array']: - self.update_log.insert('will try sending ' + str( - len(compound_list)) + ' jobs as part of an ARRAY job to your computer cluster!') + "will try sending " + + str(len(compound_list)) + + " jobs as part of an ARRAY job to your computer cluster!" + ) else: - self.update_log.insert('apparently no cluster available, so will run ' + str( - len(compound_list)) + ' sequential jobs on one core of your local machine.') - self.update_log.insert('this could take a while...') + self.update_log.insert( + "apparently no cluster available, so will run " + + str(len(compound_list)) + + " sequential jobs on one core of your local machine." + ) + self.update_log.insert("this could take a while...") self.explorer_active = 1 - self.work_thread = XChemThread.create_png_and_cif_of_compound(self.external_software, - self.initial_model_directory, - compound_list, - self.database_directory, - self.data_source_file, - todo, - self.ccp4_scratch_directory, - self.xce_logfile, - self.max_queue_jobs, - self.restraints_program) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), - self.datasource_menu_reload_samples) + self.work_thread = XChemThread.create_png_and_cif_of_compound( + self.external_software, + self.initial_model_directory, + compound_list, + self.database_directory, + self.data_source_file, + todo, + self.ccp4_scratch_directory, + self.xce_logfile, + self.max_queue_jobs, + self.restraints_program, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("datasource_menu_reload_samples"), + self.datasource_menu_reload_samples, + ) self.work_thread.start() def fit_ligands_into_dimple_maps(self): tmp = self.db.execute_statement( - "select CrystalName,CompoundCode,CompoundSmiles from mainTable where CrystalName is not '' and CompoundSmiles is not '' and CompoundSmiles is not NULL;") + "select CrystalName,CompoundCode,CompoundSmiles from mainTable where CrystalName is not '' and CompoundSmiles is not '' and CompoundSmiles is not NULL;" + ) compound_list = [] for item in tmp: - if str(item[1]) == '' or str(item[1]) == 'NULL': - compoundID = 'compound' + if str(item[1]) == "" or str(item[1]) == "NULL": + compoundID = "compound" else: compoundID = str(item[1]) if str(item[0]) in self.initial_model_dimple_dict: if self.initial_model_dimple_dict[str(item[0])][0].isChecked(): - compound_list.append( - [str(item[0]), compoundID, str(item[2])]) + compound_list.append([str(item[0]), compoundID, str(item[2])]) if compound_list: self.update_log.insert( - 'trying to auto-fitting into inital maps for ' + str(len(compound_list)) + ' compounds...') - if self.external_software['qsub']: + "trying to auto-fitting into inital maps for " + + str(len(compound_list)) + + " compounds..." + ) + if self.external_software["qsub"]: self.update_log.insert( - 'will try sending ' + str(len(compound_list)) + ' jobs to your computer cluster!') - elif self.external_software['qsub_array']: - self.update_log.insert('will try sending ' + str( - len(compound_list)) + ' jobs as part of an ARRAY job to your computer cluster!') + "will try sending " + + str(len(compound_list)) + + " jobs to your computer cluster!" + ) + elif self.external_software["qsub_array"]: + self.update_log.insert( + "will try sending " + + str(len(compound_list)) + + " jobs as part of an ARRAY job to your computer cluster!" + ) else: - self.update_log.insert('apparently no cluster available, so will run ' + str( - len(compound_list)) + ' sequential jobs on one core of your local machine.') - self.update_log.insert('this could take a while...') + self.update_log.insert( + "apparently no cluster available, so will run " + + str(len(compound_list)) + + " sequential jobs on one core of your local machine." + ) + self.update_log.insert("this could take a while...") self.explorer_active = 1 - self.work_thread = XChemThread.fit_ligands(self.external_software, - self.initial_model_directory, - compound_list, - self.database_directory, - self.data_source_file, - self.ccp4_scratch_directory, - self.xce_logfile, - self.max_queue_jobs) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), - self.datasource_menu_reload_samples) + self.work_thread = XChemThread.fit_ligands( + self.external_software, + self.initial_model_directory, + compound_list, + self.database_directory, + self.data_source_file, + self.ccp4_scratch_directory, + self.xce_logfile, + self.max_queue_jobs, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("datasource_menu_reload_samples"), + self.datasource_menu_reload_samples, + ) self.work_thread.start() def merge_cif_files(self, todo): start_thread = False - if todo == 'merge': + if todo == "merge": self.update_log.insert( - 'trying to merge %s with ligand restraint files in project directory' % self.second_cif_file) - elif todo == 'restore': - self.update_log.insert('restoring original CIF files') + "trying to merge %s with ligand restraint files in project directory" + % self.second_cif_file + ) + elif todo == "restore": + self.update_log.insert("restoring original CIF files") start_thread = True - if todo == 'merge': + if todo == "merge": if os.path.isfile(str(self.second_cif_file)): self.update_log.insert( - 'checking compound code of second CIF file (%s)' % self.second_cif_file) - self.update_log.insert('Note: LIG and DRG are not allowed!') + "checking compound code of second CIF file (%s)" + % self.second_cif_file + ) + self.update_log.insert("Note: LIG and DRG are not allowed!") import iotbx.cif - cif_model = iotbx.cif.reader( - file_path=self.second_cif_file).model() + + cif_model = iotbx.cif.reader(file_path=self.second_cif_file).model() cif_block = cif_model["comp_list"] ligID = cif_block["_chem_comp.id"] self.update_log.insert( - 'found the following compound codes in the supplied CIF file: %s' % str(list(ligID))) - if 'LIG' in list(ligID) or 'DRG' in list(ligID): + "found the following compound codes in the supplied CIF file: %s" + % str(list(ligID)) + ) + if "LIG" in list(ligID) or "DRG" in list(ligID): self.update_log.error( - 'please change compound code to something other than LIG or DRG') + "please change compound code to something other than LIG or DRG" + ) start_thread = False else: start_thread = True else: - self.update_log.error( - XChemToolTips.second_cif_file_not_exists()) + self.update_log.error(XChemToolTips.second_cif_file_not_exists()) start_thread = False if start_thread: msgBox = QtGui.QMessageBox() - msgBox.setText(XChemToolTips.second_cif_file_info( - self.second_cif_file)) - msgBox.addButton(QtGui.QPushButton( - 'OK'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('Cancel'), - QtGui.QMessageBox.RejectRole) + msgBox.setText(XChemToolTips.second_cif_file_info(self.second_cif_file)) + msgBox.addButton(QtGui.QPushButton("OK"), QtGui.QMessageBox.YesRole) + msgBox.addButton( + QtGui.QPushButton("Cancel"), QtGui.QMessageBox.RejectRole + ) reply = msgBox.exec_() if reply == 0: start_thread = True @@ -4629,63 +5487,88 @@ def merge_cif_files(self, todo): start_thread = False else: self.status_bar.showMessage( - 'Error. Please check terminal window for further information') + "Error. Please check terminal window for further information" + ) tmp = self.db.execute_statement( - "select CrystalName,CompoundCode from mainTable where CrystalName is not '' and CompoundSmiles is not '' and CompoundSmiles is not NULL;") + "select CrystalName,CompoundCode from mainTable where CrystalName is not '' and CompoundSmiles is not '' and CompoundSmiles is not NULL;" + ) compound_list = [] for item in tmp: xtal = str(item[0]) compoundID = str(item[1]) - if compoundID == '' or compoundID == 'NULL': + if compoundID == "" or compoundID == "NULL": self.update_log.warning( - '%s: no compound ID in database; skipping...' % xtal) + "%s: no compound ID in database; skipping..." % xtal + ) else: if str(item[0]) in self.initial_model_dimple_dict: if self.initial_model_dimple_dict[str(item[0])][0].isChecked(): self.update_log.warning( - '%s: %s is flagged for merging' % (xtal, compoundID)) + "%s: %s is flagged for merging" % (xtal, compoundID) + ) compound_list.append([xtal, compoundID]) if compound_list == []: self.update_log.error( - 'Either no compound ID information in database or no sample selected!') + "Either no compound ID information in database or no sample selected!" + ) start_thread = False if start_thread: self.explorer_active = 1 - self.work_thread = XChemThread.merge_cif_files(self.initial_model_directory, - self.xce_logfile, - self.second_cif_file, - compound_list, - todo) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_progress_bar"), self.update_progress_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "update_status_bar(QString)"), self.update_status_bar) - self.connect(self.work_thread, QtCore.SIGNAL( - "finished()"), self.thread_finished) - self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), - self.datasource_menu_reload_samples) + self.work_thread = XChemThread.merge_cif_files( + self.initial_model_directory, + self.xce_logfile, + self.second_cif_file, + compound_list, + todo, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_progress_bar"), + self.update_progress_bar, + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("update_status_bar(QString)"), + self.update_status_bar, + ) + self.connect( + self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished + ) + self.connect( + self.work_thread, + QtCore.SIGNAL("datasource_menu_reload_samples"), + self.datasource_menu_reload_samples, + ) self.work_thread.start() def update_deposition_table(self): # check if PanDDA models are ready for deposition depositChecks = XChemDeposit.update_deposition_table( - os.path.join(self.database_directory, self.data_source_file)) + os.path.join(self.database_directory, self.data_source_file) + ) toDeposit, mismatch = depositChecks.PanDDA_models_to_deposit() if mismatch != {}: self.update_log.insert( - 'The following samples contain ligand that are not ready for deposition:') + "The following samples contain ligand that are not ready for deposition:" + ) for entry in mismatch: self.update_log.insert( - entry[0] + ' -> site: ' + entry[1] + ' @ ' + entry[2] + ' => ' + entry[4]) - self.update_log.insert( - 'You need to change this before you can continue!') + entry[0] + + " -> site: " + + entry[1] + + " @ " + + entry[2] + + " => " + + entry[4] + ) + self.update_log.insert("You need to change this before you can continue!") return None for xtal in toDeposit: @@ -4694,39 +5577,48 @@ def update_deposition_table(self): def show_html_summary_and_diffraction_image(self): for key in self.albula_button_dict: if self.albula_button_dict[key][0] == self.sender(): - print('==> XCE: showing html summary in firefox') + print("==> XCE: showing html summary in firefox") self.show_html_summary_in_firefox(key) def need_to_switch_main_tab(self, task_index): msgBox = QtGui.QMessageBox() - msgBox.setText( - "Need to switch main tab before you can launch this job") - msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) + msgBox.setText("Need to switch main tab before you can launch this job") + msgBox.addButton(QtGui.QPushButton("Yes"), QtGui.QMessageBox.YesRole) + msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.RejectRole) reply = msgBox.exec_() if reply == 0: self.main_tab_widget.setCurrentIndex(task_index) def check_write_permissions_of_data_source(self): write_enabled = True - if not os.access(os.path.join(self.database_directory, self.data_source_file), os.W_OK): - QtGui.QMessageBox.warning(self.window, "Data Source Problem", - '\nData Source is Read-Only\n', - QtGui.QMessageBox.Cancel, QtGui.QMessageBox.NoButton, - QtGui.QMessageBox.NoButton) + if not os.access( + os.path.join(self.database_directory, self.data_source_file), os.W_OK + ): + QtGui.QMessageBox.warning( + self.window, + "Data Source Problem", + "\nData Source is Read-Only\n", + QtGui.QMessageBox.Cancel, + QtGui.QMessageBox.NoButton, + QtGui.QMessageBox.NoButton, + ) write_enabled = False return write_enabled def no_data_source_selected(self): - QtGui.QMessageBox.warning(self.window, "Data Source Problem", - ('Please set or create a data source file\n') + - ('Options:\n') + - ('1. Use an existing file:\n') + - ('- Settings -> Select Data Source File\n') + - ('2. Create a new file\n') + - ('- Data Source -> Create New Data\nSource (SQLite)'), - QtGui.QMessageBox.Cancel, QtGui.QMessageBox.NoButton, - QtGui.QMessageBox.NoButton) + QtGui.QMessageBox.warning( + self.window, + "Data Source Problem", + ("Please set or create a data source file\n") + + ("Options:\n") + + ("1. Use an existing file:\n") + + ("- Settings -> Select Data Source File\n") + + ("2. Create a new file\n") + + ("- Data Source -> Create New Data\nSource (SQLite)"), + QtGui.QMessageBox.Cancel, + QtGui.QMessageBox.NoButton, + QtGui.QMessageBox.NoButton, + ) def update_progress_bar(self, progress): self.progress_bar.setValue(progress) @@ -4737,41 +5629,46 @@ def update_status_bar(self, message): def thread_finished(self): self.explorer_active = 0 self.update_progress_bar(0) - self.update_status_bar('idle') + self.update_status_bar("idle") def show_error_dict(self, errorDict): - text = '' + text = "" for key in errorDict: - text += '{0!s}:\n'.format(key) + text += "{0!s}:\n".format(key) for entry in errorDict[key]: - text += ' - ' + entry + '\n' + text += " - " + entry + "\n" msgBox = QtGui.QMessageBox() msgBox.setText(text) msgBox.exec_() def create_widgets_for_autoprocessing_results_only(self, data_dict): self.status_bar.showMessage( - 'Building details table for data processing results') + "Building details table for data processing results" + ) self.data_collection_dict = data_dict - column_name = ['Program', - 'Resolution\nOverall', - 'Resolution\n[Mn = 2.0]', - 'DataProcessing\nSpaceGroup', - 'Mn\nHigh', - 'Rmerge\nLow', - 'Completeness\nOverall', - 'DataProcessing\nUnitCell', - 'DataProcessing\nRfree', - 'DataProcessing\nScore'] + column_name = [ + "Program", + "Resolution\nOverall", + "Resolution\n[Mn = 2.0]", + "DataProcessing\nSpaceGroup", + "Mn\nHigh", + "Rmerge\nLow", + "Completeness\nOverall", + "DataProcessing\nUnitCell", + "DataProcessing\nRfree", + "DataProcessing\nScore", + ] # need to do this because db_dict keys are SQLite column names diffraction_data_column_name = XChemDB.data_source( - os.path.join(self.database_directory, self.data_source_file)).translate_xce_column_list_to_sqlite( - column_name) + os.path.join(self.database_directory, self.data_source_file) + ).translate_xce_column_list_to_sqlite(column_name) for xtal in sorted(self.data_collection_dict): - if os.path.isfile(os.path.join(self.initial_model_directory, xtal, xtal + '.mtz')): + if os.path.isfile( + os.path.join(self.initial_model_directory, xtal, xtal + ".mtz") + ): mtz_already_in_inital_model_directory = True # column 2: data collection date @@ -4779,9 +5676,10 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): # first find latest run tmp = [] for entry in self.data_collection_dict[xtal]: - if entry[0] == 'image': - tmp.append([entry[3], datetime.strptime( - entry[3], '%Y-%m-%d %H:%M:%S')]) + if entry[0] == "image": + tmp.append( + [entry[3], datetime.strptime(entry[3], "%Y-%m-%d %H:%M:%S")] + ) latest_run = max(tmp, key=lambda x: x[1])[0] # first check if it does already exist @@ -4791,14 +5689,19 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): data_collection_table = QtGui.QTableWidget() selection_changed_by_user = False self.data_collection_column_three_dict[xtal] = [ - data_collection_table, selection_changed_by_user] + data_collection_table, + selection_changed_by_user, + ] xtal_in_table = True else: data_collection_table = self.data_collection_column_three_dict[xtal][0] - selection_changed_by_user = self.data_collection_column_three_dict[xtal][1] + selection_changed_by_user = self.data_collection_column_three_dict[ + xtal + ][1] data_collection_table.setVerticalScrollBarPolicy( - QtCore.Qt.ScrollBarAlwaysOff) + QtCore.Qt.ScrollBarAlwaysOff + ) data_collection_table.setColumnCount(len(column_name)) font = QtGui.QFont() font.setPointSize(8) @@ -4806,7 +5709,8 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): data_collection_table.setHorizontalHeaderLabels(column_name) data_collection_table.horizontalHeader().setFont(font) data_collection_table.setSelectionBehavior( - QtGui.QAbstractItemView.SelectRows) + QtGui.QAbstractItemView.SelectRows + ) ############################################################################# # crystal images @@ -4820,7 +5724,7 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): # a) get only image entries from self.data_collection_dict tmp = [] for entry in self.data_collection_dict[xtal]: - if entry[0] == 'image': + if entry[0] == "image": tmp.append(entry) # b) sort by the previously assigned run number @@ -4837,7 +5741,8 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): # then use image not available from $XChemExplorer_DIR/image/IMAGE_NOT_AVAILABLE.png # not sure how to do this at the moment; it will probably trigger an error that I can catch self.data_collection_image_dict[xtal].append( - [entry[6], entry[1], entry[2], entry[3], entry[5]]) + [entry[6], entry[1], entry[2], entry[3], entry[5]] + ) ############################################################################# # initialize dataset_outcome_dict for xtal @@ -4855,25 +5760,31 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): # reminder: ['logfile',visit,run,timestamp,autoproc,file_name,aimless_results,,False] logfile_list = [] for entry in self.data_collection_dict[xtal]: - if entry[0] == 'logfile': + if entry[0] == "logfile": logfile_list.append(entry) # sort by aimless_index and so make sure for entry in sorted(logfile_list, key=lambda x: x[7]): entry_already_in_table = False # that aimless_index == row for logfile in self.data_collection_table_dict[xtal]: - if entry[1] == logfile[1] and entry[2] == logfile[2] and entry[3] == logfile[3] and entry[4] == \ - logfile[4]: + if ( + entry[1] == logfile[1] + and entry[2] == logfile[2] + and entry[3] == logfile[3] + and entry[4] == logfile[4] + ): entry_already_in_table = True # might have to update Rfree column for column, header in enumerate(diffraction_data_column_name): - if header == 'DataProcessing\nRfree': + if header == "DataProcessing\nRfree": # entry[7]==aimless_index, i.e. row number cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(db_dict[header[1]])) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) data_collection_table.setItem( - entry[7], column, cell_text) + entry[7], column, cell_text + ) break break if not entry_already_in_table: @@ -4885,26 +5796,28 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): cell_text.setText(str(db_dict[header[1]])) except KeyError: # this may happen if not score exists - cell_text.setText('0') + cell_text.setText("0") cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - data_collection_table.setItem( - row_position, column, cell_text) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) + data_collection_table.setItem(row_position, column, cell_text) data_collection_table.setRowHeight(row_position, 20) row_position += 1 self.data_collection_table_dict[xtal].append( - ['logfile', entry[1], entry[2], entry[3], entry[4]]) # 'logfile' is just added to have + ["logfile", entry[1], entry[2], entry[3], entry[4]] + ) # 'logfile' is just added to have # same index numbers between lists data_collection_table.cellClicked.connect( - self.user_update_selected_autoproc_datasets_summary_table) + self.user_update_selected_autoproc_datasets_summary_table + ) # select best resolution file + set data collection outcome # the assumption is that index in data_collection_dict and row number are identical # the assumption for data collection outcome is that as long as a logfile is found, it's a success logfile_found = False for entry in self.data_collection_dict[xtal]: - if entry[0] == 'logfile': + if entry[0] == "logfile": index = entry[7] best_file = entry[8] logfile_found = True @@ -4917,15 +5830,23 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): def find_suitable_reference_file(self, db_dict): reference_file = [] - dummy = ['...', '', '', '', 0, '0'] + dummy = ["...", "", "", "", 0, "0"] reference_file.append([dummy, 999]) suitable_reference = [] for reference in self.reference_file_list: # first we need one in the same pointgroup - if reference[5] == db_dict['DataProcessingPointGroup']: + if reference[5] == db_dict["DataProcessingPointGroup"]: try: - difference = math.fabs( - 1 - (float(db_dict['DataProcessingUnitCellVolume']) / float(reference[4]))) * 100 + difference = ( + math.fabs( + 1 + - ( + float(db_dict["DataProcessingUnitCellVolume"]) + / float(reference[4]) + ) + ) + * 100 + ) reference_file.append([reference, difference]) except ValueError: continue @@ -4933,15 +5854,15 @@ def find_suitable_reference_file(self, db_dict): def create_maps_table(self): column_name = self.db.translate_xce_column_list_to_sqlite( - self.maps_table_columns) + self.maps_table_columns + ) for xtal in sorted(self.xtal_db_dict): new_xtal = False db_dict = self.xtal_db_dict[xtal] - if str(db_dict['DataCollectionOutcome']).lower().startswith('success'): + if str(db_dict["DataCollectionOutcome"]).lower().startswith("success"): reference_file = self.find_suitable_reference_file(db_dict) - smallest_uc_difference = min( - reference_file, key=lambda x: x[1]) + smallest_uc_difference = min(reference_file, key=lambda x: x[1]) row = self.maps_table.rowCount() if xtal not in self.initial_model_dimple_dict: self.maps_table.insertRow(row) @@ -4953,197 +5874,224 @@ def create_maps_table(self): current_row = table_row break for column, header in enumerate(column_name): - if header[0] == 'Sample ID': + if header[0] == "Sample ID": cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(xtal)) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) self.maps_table.setItem(current_row, column, cell_text) - elif header[0] == 'Select': + elif header[0] == "Select": if new_xtal: run_dimple = QtGui.QCheckBox() run_dimple.toggle() self.maps_table.setCellWidget( - current_row, column, run_dimple) + current_row, column, run_dimple + ) run_dimple.setChecked(False) - elif header[0] == 'Reference\nSpaceGroup': + elif header[0] == "Reference\nSpaceGroup": cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(smallest_uc_difference[0][1])) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) self.maps_table.setItem(current_row, column, cell_text) - elif header[0] == 'Difference\nUC Volume (%)': + elif header[0] == "Difference\nUC Volume (%)": cell_text = QtGui.QTableWidgetItem() - smallest_uc_difference = min( - reference_file, key=lambda x: x[1]) + smallest_uc_difference = min(reference_file, key=lambda x: x[1]) cell_text.setText( - str(round(float(smallest_uc_difference[1]), 1))) + str(round(float(smallest_uc_difference[1]), 1)) + ) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) self.maps_table.setItem(current_row, column, cell_text) - elif header[0] == 'Reference File': + elif header[0] == "Reference File": if new_xtal: reference_file_selection_combobox = QtGui.QComboBox() self.populate_reference_combobox( - reference_file_selection_combobox) - if float(smallest_uc_difference[1]) < self.allowed_unitcell_difference_percent: - index = reference_file_selection_combobox.findText(str(smallest_uc_difference[0][0]), - QtCore.Qt.MatchFixedString) - reference_file_selection_combobox.setCurrentIndex( - index) + reference_file_selection_combobox + ) + if ( + float(smallest_uc_difference[1]) + < self.allowed_unitcell_difference_percent + ): + index = reference_file_selection_combobox.findText( + str(smallest_uc_difference[0][0]), + QtCore.Qt.MatchFixedString, + ) + reference_file_selection_combobox.setCurrentIndex(index) else: - reference_file_selection_combobox.setCurrentIndex( - 0) - self.maps_table.setCellWidget(current_row, column, - reference_file_selection_combobox) + reference_file_selection_combobox.setCurrentIndex(0) + self.maps_table.setCellWidget( + current_row, column, reference_file_selection_combobox + ) else: - reference_file_selection_combobox = self.initial_model_dimple_dict[ - xtal][1] + reference_file_selection_combobox = ( + self.initial_model_dimple_dict[xtal][1] + ) self.populate_reference_combobox( - reference_file_selection_combobox) - if float(smallest_uc_difference[1]) < self.allowed_unitcell_difference_percent: - index = reference_file_selection_combobox.findText(str(smallest_uc_difference[0][0]), - QtCore.Qt.MatchFixedString) - reference_file_selection_combobox.setCurrentIndex( - index) + reference_file_selection_combobox + ) + if ( + float(smallest_uc_difference[1]) + < self.allowed_unitcell_difference_percent + ): + index = reference_file_selection_combobox.findText( + str(smallest_uc_difference[0][0]), + QtCore.Qt.MatchFixedString, + ) + reference_file_selection_combobox.setCurrentIndex(index) else: - reference_file_selection_combobox.setCurrentIndex( - 0) + reference_file_selection_combobox.setCurrentIndex(0) else: cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(db_dict[header[1]])) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - if header[0] == 'Dimple\nStatus': - if str(db_dict[header[1]]) == 'running': - cell_text.setBackground( - QtGui.QColor(100, 230, 150)) - elif str(db_dict[header[1]]) == 'pending': - cell_text.setBackground( - QtGui.QColor(20, 100, 230)) - elif str(db_dict[header[1]]) == 'started': - cell_text.setBackground( - QtGui.QColor(230, 240, 110)) - elif str(db_dict[header[1]]) == 'finished': - cell_text.setBackground( - QtGui.QColor(255, 255, 255)) - if header[0] == 'Compound\nStatus': - if str(db_dict[header[1]]) == 'running': - cell_text.setBackground( - QtGui.QColor(100, 230, 150)) - elif str(db_dict[header[1]]) == 'pending': - cell_text.setBackground( - QtGui.QColor(20, 100, 230)) - elif str(db_dict[header[1]]) == 'started': - cell_text.setBackground( - QtGui.QColor(230, 240, 110)) - elif str(db_dict[header[1]]) == 'restraints generated': - cell_text.setBackground( - QtGui.QColor(255, 255, 255)) - elif str(db_dict[header[1]]) == 'restraints failed': - cell_text.setBackground( - QtGui.QColor(255, 0, 0)) - elif str(db_dict[header[1]]) == 'missing smiles': - cell_text.setBackground( - QtGui.QColor(240, 150, 20)) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) + if header[0] == "Dimple\nStatus": + if str(db_dict[header[1]]) == "running": + cell_text.setBackground(QtGui.QColor(100, 230, 150)) + elif str(db_dict[header[1]]) == "pending": + cell_text.setBackground(QtGui.QColor(20, 100, 230)) + elif str(db_dict[header[1]]) == "started": + cell_text.setBackground(QtGui.QColor(230, 240, 110)) + elif str(db_dict[header[1]]) == "finished": + cell_text.setBackground(QtGui.QColor(255, 255, 255)) + if header[0] == "Compound\nStatus": + if str(db_dict[header[1]]) == "running": + cell_text.setBackground(QtGui.QColor(100, 230, 150)) + elif str(db_dict[header[1]]) == "pending": + cell_text.setBackground(QtGui.QColor(20, 100, 230)) + elif str(db_dict[header[1]]) == "started": + cell_text.setBackground(QtGui.QColor(230, 240, 110)) + elif str(db_dict[header[1]]) == "restraints generated": + cell_text.setBackground(QtGui.QColor(255, 255, 255)) + elif str(db_dict[header[1]]) == "restraints failed": + cell_text.setBackground(QtGui.QColor(255, 0, 0)) + elif str(db_dict[header[1]]) == "missing smiles": + cell_text.setBackground(QtGui.QColor(240, 150, 20)) self.maps_table.setItem(current_row, column, cell_text) if new_xtal: self.initial_model_dimple_dict[xtal] = [ - run_dimple, reference_file_selection_combobox] + run_dimple, + reference_file_selection_combobox, + ] def preferences_data_to_copy_combobox_changed(self, i): text = str(self.preferences_data_to_copy_combobox.currentText()) for item in self.preferences_data_to_copy: if item[0] == text: - self.preferences['processed_data_to_copy'] = item[1] + self.preferences["processed_data_to_copy"] = item[1] break def preferences_selection_mechanism_combobox_changed(self, i): text = str(self.preferences_selection_mechanism_combobox.currentText()) - self.preferences['dataset_selection_mechanism'] = text - self.update_log.insert( - 'setting datasets selection mechanism to ' + text) + self.preferences["dataset_selection_mechanism"] = text + self.update_log.insert("setting datasets selection mechanism to " + text) def preferences_initial_refinement_combobox_changed(self, i): text = str(self.preferences_initial_refinement_combobox.currentText()) - self.preferences['initial_refinement_pipeline'] = text - self.update_log.insert( - 'setting initial refinement pipeline to ' + text) + self.preferences["initial_refinement_pipeline"] = text + self.update_log.insert("setting initial refinement pipeline to " + text) def preferences_restraints_generation_combobox_changed(self): text = str(self.preferences_restraints_generation_combobox.currentText()) self.restraints_program = text self.update_log.insert( - 'will use {0!s} for generation of ligand coordinates and restraints'.format(text)) + "will use {0!s} for generation of ligand coordinates and restraints".format( + text + ) + ) def refinement_outcome_combobox_changed(self): for xtal in self.refinement_table_dict: if self.sender() == self.refinement_table_dict[xtal]: # db_dict = {'RefinementOutcome': str(self.sender().currentText())} db_dict = {} - db_dict['RefinementOutcome'] = str(self.sender().currentText()) - db_dict['RefinementOutcomePerson'] = getpass.getuser() - db_dict['RefinementOutcomeDate'] = datetime.strftime( - datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] - self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, xtal, 'ligand_bound', - db_dict) + db_dict["RefinementOutcome"] = str(self.sender().currentText()) + db_dict["RefinementOutcomePerson"] = getpass.getuser() + db_dict["RefinementOutcomeDate"] = datetime.strftime( + datetime.now(), "%Y-%m-%d_%H-%M-%S.%f" + )[:-4] + self.db.create_or_remove_missing_records_in_depositTable( + self.xce_logfile, xtal, "ligand_bound", db_dict + ) def get_reference_file_list(self, reference_root): # check available reference files reference_file_list = [] - dummy = ['...', '', '', '', 0, '0'] + dummy = ["...", "", "", "", 0, "0"] reference_file_list.append(dummy) - if os.path.isfile(os.path.join(self.reference_directory, reference_root + '.pdb')): - pdb_reference = parse().PDBheader(os.path.join( - self.reference_directory, reference_root + '.pdb')) - spg_reference = pdb_reference['SpaceGroup'] - unitcell_reference = pdb_reference['UnitCell'] - lattice_reference = pdb_reference['Lattice'] - unitcell_volume_reference = pdb_reference['UnitCellVolume'] - pointgroup_reference = pdb_reference['PointGroup'] - reference_file_list.append([reference_root, - spg_reference, - unitcell_reference, - lattice_reference, - unitcell_volume_reference, - pointgroup_reference]) + if os.path.isfile( + os.path.join(self.reference_directory, reference_root + ".pdb") + ): + pdb_reference = parse().PDBheader( + os.path.join(self.reference_directory, reference_root + ".pdb") + ) + spg_reference = pdb_reference["SpaceGroup"] + unitcell_reference = pdb_reference["UnitCell"] + lattice_reference = pdb_reference["Lattice"] + unitcell_volume_reference = pdb_reference["UnitCellVolume"] + pointgroup_reference = pdb_reference["PointGroup"] + reference_file_list.append( + [ + reference_root, + spg_reference, + unitcell_reference, + lattice_reference, + unitcell_volume_reference, + pointgroup_reference, + ] + ) else: - for files in glob.glob(self.reference_directory + '/*'): - if files.endswith('.pdb'): - reference_root = files[files.rfind( - '/') + 1:files.rfind('.')] + for files in glob.glob(self.reference_directory + "/*"): + if files.endswith(".pdb"): + reference_root = files[files.rfind("/") + 1 : files.rfind(".")] - if os.path.isfile(os.path.join(self.reference_directory, reference_root + '.pdb')): + if os.path.isfile( + os.path.join(self.reference_directory, reference_root + ".pdb") + ): # reference_file = reference_root + '.pdb' pdb_reference = parse().PDBheader( - os.path.join(self.reference_directory, reference_root + '.pdb')) - spg_reference = pdb_reference['SpaceGroup'] - unitcell_reference = pdb_reference['UnitCell'] - lattice_reference = pdb_reference['Lattice'] - unitcell_volume_reference = pdb_reference['UnitCellVolume'] - pointgroup_reference = pdb_reference['PointGroup'] - reference_file_list.append([reference_root, - spg_reference, - unitcell_reference, - lattice_reference, - unitcell_volume_reference, - pointgroup_reference]) + os.path.join( + self.reference_directory, reference_root + ".pdb" + ) + ) + spg_reference = pdb_reference["SpaceGroup"] + unitcell_reference = pdb_reference["UnitCell"] + lattice_reference = pdb_reference["Lattice"] + unitcell_volume_reference = pdb_reference["UnitCellVolume"] + pointgroup_reference = pdb_reference["PointGroup"] + reference_file_list.append( + [ + reference_root, + spg_reference, + unitcell_reference, + lattice_reference, + unitcell_volume_reference, + pointgroup_reference, + ] + ) for n, file in enumerate(reference_file_list): - self.update_log.insert( - 'reference file {0!s}: {1!s}'.format(n, file)) + self.update_log.insert("reference file {0!s}: {1!s}".format(n, file)) return reference_file_list def dataset_outcome_combobox_change_outcome(self, text): outcome = str(text) - xtal = '' + xtal = "" for key in self.dataset_outcome_combobox_dict: if self.dataset_outcome_combobox_dict[key] == self.sender(): xtal = key self.update_log.insert( - 'user changed data collection outcome of {0!s} to {1!s}'.format(xtal, outcome)) + "user changed data collection outcome of {0!s} to {1!s}".format( + xtal, outcome + ) + ) break self.dataset_outcome_dict[xtal] = outcome - if xtal != '': + if xtal != "": # # need to also update if not yet done # user_already_changed_selection = False # for n, entry in enumerate(self.data_collection_dict[xtal]): @@ -5158,8 +6106,9 @@ def dataset_outcome_combobox_change_outcome(self, text): # self.data_collection_dict[xtal].append(['user_changed_selection']) # # finally need to update outcome field in data source accordingly self.update_log.insert( - 'updating dataset outcome in datasource for {0!s}'.format(xtal)) - update_dict = {'DataCollectionOutcome': outcome} + "updating dataset outcome in datasource for {0!s}".format(xtal) + ) + update_dict = {"DataCollectionOutcome": outcome} self.db.update_insert_data_source(xtal, update_dict) def set_run_dimple_flag(self, state): @@ -5179,8 +6128,9 @@ def show_data_collection_details(self, state): tmp = [] allRows = self.datasets_summary_table.rowCount() for table_row in range(allRows): - tmp.append([self.datasets_summary_table.item( - table_row, 0).text(), table_row]) + tmp.append( + [self.datasets_summary_table.item(table_row, 0).text(), table_row] + ) for key in self.datasets_summary_dict: if self.datasets_summary_dict[key][3] == self.sender(): @@ -5188,191 +6138,193 @@ def show_data_collection_details(self, state): for item in tmp: if item[0] == key: self.datasets_summary_table.selectRow(item[1]) - self.data_collection_details_currently_on_display = self.data_collection_column_three_dict[ - key][0] + self.data_collection_details_currently_on_display = ( + self.data_collection_column_three_dict[key][0] + ) self.datasets_summarys_vbox_for_details.addWidget( - self.data_collection_details_currently_on_display) + self.data_collection_details_currently_on_display + ) self.data_collection_details_currently_on_display.show() else: # un-check all other ones self.datasets_summary_dict[key][3].setChecked(False) -# def populate_datasets_summary_table(self): -# self.status_bar.showMessage( -# 'Building summary table for data processing results; be patient this may take a while') -# row = self.datasets_summary_table.rowCount() -# column_name = self.db.translate_xce_column_list_to_sqlite(self.datasets_summary_table_columns) -# -# pinList = self.db.execute_statement( -# "Select CrystalName,PinBarcode,DataCollectionPinBarcode from mainTable where CrystalName is not ''") -# pinDict = {} -# for item in pinList: -# pinDict[str(item[0])] = [str(item[1]), str(item[2])] -# -# for xtal in sorted(self.data_collection_dict): -# new_xtal = False -# if xtal not in self.datasets_summary_dict: -# row = self.datasets_summary_table.rowCount() -# self.datasets_summary_table.insertRow(row) -# self.datasets_summary_dict[xtal] = [] -# new_xtal = True -# -# # check for dataset outcome -# outcome = '' -# logfile_found = False -# too_low_resolution = True -# db_dict = {} -# for entry in self.data_collection_dict[xtal]: -# if entry[0] == 'logfile': -# logfile_found = True -# if entry[8]: # if this was auto-selected best resolution file -# db_dict = entry[6] -# try: -# if float(db_dict['DataProcessingResolutionHigh']) <= float( -# self.acceptable_low_resolution_limit_for_data): -# too_low_resolution = False -# except ValueError: -# pass -# -# try: -# outcome = str(self.db.get_value_from_field(xtal, 'DataCollectionOutcome')[0]) -# except TypeError: -# outcome = 'Failed - unknown' -# self.update_log.insert('cannot find DataCollectionOutcome for {0!s}'.format(xtal)) -# self.dataset_outcome_dict[xtal] = outcome -# -# # find latest run for crystal and diffraction images -# tmp = [] -# for entry in self.data_collection_dict[xtal]: -# if entry[0] == 'image': -# tmp.append([entry, datetime.strptime(entry[3], '%Y-%m-%d %H:%M:%S')]) -# latest_run = max(tmp, key=lambda x: x[1])[0] -# -# new_run_for_exisiting_crystal_or_new_sample = True -# if new_xtal: -# self.datasets_summary_dict[xtal] = [outcome, db_dict, latest_run] -# else: -# # check if newer run appeared -# old_run_timestamp = self.datasets_summary_dict[xtal][2][3] -# new_run_timestamp = latest_run[3] -# if old_run_timestamp == new_run_timestamp: -# new_run_for_exisiting_crystal_or_new_sample = False -# else: -# checkbox_for_details = self.datasets_summary_dict[xtal][3] -# self.datasets_summary_dict[xtal] = [outcome, db_dict, latest_run, checkbox_for_details] -# -# if new_xtal: -# current_row = row -# else: -# allRows = self.datasets_summary_table.rowCount() -# for table_row in range(allRows): -# if self.datasets_summary_table.item(table_row, 0).text() == xtal: -# current_row = table_row -# break -# -# image_number = 0 -# for column, header in enumerate(column_name): -# if header[0] == 'Sample ID': -# cell_text = QtGui.QTableWidgetItem() -# cell_text.setText(str(xtal)) -# cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) -# self.datasets_summary_table.setItem(current_row, column, cell_text) -# elif header[0] == 'DataCollection\nOutcome': -# if new_xtal: -# dataset_outcome_combobox = QtGui.QComboBox() -# for outcomeItem in self.dataset_outcome: -# dataset_outcome_combobox.addItem(outcomeItem) -# self.datasets_summary_table.setCellWidget(current_row, column, dataset_outcome_combobox) -# dataset_outcome_combobox.activated[str].connect(self.dataset_outcome_combobox_change_outcome) -# self.dataset_outcome_combobox_dict[xtal] = dataset_outcome_combobox -# index = self.dataset_outcome_combobox_dict[xtal].findText(str(outcome), QtCore.Qt.MatchFixedString) -# self.dataset_outcome_combobox_dict[xtal].setCurrentIndex(index) -# continue -# -# elif header[0].startswith('img'): -# if new_run_for_exisiting_crystal_or_new_sample: -# img = latest_run[4] -# pixmap = QtGui.QPixmap() -# # can do this (img[image_number][1]) because made sure in the threading module -# # that there are always exactly 5 images in there -# pixmap.loadFromData(base64.b64decode(img[image_number][1])) -# image = QtGui.QLabel() -# image.resize(128, 80) -# image.setPixmap(pixmap.scaled(image.size(), QtCore.Qt.KeepAspectRatio)) -# self.datasets_summary_table.setCellWidget(current_row, column, image) -# image_number += 1 -# -# elif header[0].startswith('Show Diffraction\nImage'): -# if new_run_for_exisiting_crystal_or_new_sample: -# diffraction_image = latest_run[5] -# diffraction_image_name = diffraction_image[diffraction_image.rfind('/') + 1:] -# try: # need to try because older pkl file may not have this item in list -# html_summary = latest_run[7] -# except IndexError: -# html_summary = '' -# if new_xtal: -# start_albula_button = QtGui.QPushButton('Show: \n' + diffraction_image_name) -# start_albula_button.clicked.connect(self.show_html_summary_and_diffraction_image) -# self.albula_button_dict[xtal] = [start_albula_button, diffraction_image, html_summary] -# self.datasets_summary_table.setCellWidget(current_row, column, start_albula_button) -# else: -# self.albula_button_dict[xtal][1] = diffraction_image -# elif header[0].startswith('Show\nDetails'): -# if new_xtal: -# show_data_collection_details_checkbox = QtGui.QCheckBox() -# show_data_collection_details_checkbox.toggle() -# show_data_collection_details_checkbox.setChecked(False) -# show_data_collection_details_checkbox.stateChanged.connect(self.show_data_collection_details) -# self.datasets_summary_table.setCellWidget(current_row, column, -# show_data_collection_details_checkbox) -# self.datasets_summary_dict[xtal].append(show_data_collection_details_checkbox) -# elif header[0].startswith('SoakDB\nBarcode') or header[0].startswith('GDA\nBarcode'): -# if new_xtal: -# cell_text = QtGui.QTableWidgetItem() -# if xtal in pinDict: -# if header[0].startswith('SoakDB\nBarcode'): -# cell_text.setText(str(pinDict[xtal][0])) -# elif header[0].startswith('GDA\nBarcode'): -# cell_text.setText(str(pinDict[xtal][1])) -# if pinDict[xtal][0] == 'NULL' or pinDict[xtal][1] == 'NULL': -# cell_text.setBackground(QtGui.QColor(255, 215, 0)) -# elif pinDict[xtal][0] != pinDict[xtal][1]: -# cell_text.setBackground(QtGui.QColor(255, 0, 0)) -# else: -# cell_text.setText('') -# cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) -# self.datasets_summary_table.setItem(current_row, column, cell_text) -# else: -# cell_text = QtGui.QTableWidgetItem() -# # in case data collection failed for whatever reason -# if logfile_found: -# try: -# cell_text.setText(str(db_dict[header[1]])) -# except KeyError: # older pkl files may not have all the columns -# cell_text.setText('n/a') -# else: -# if header[0].startswith('Resolution\n[Mn = 1.5]'): -# cell_text.setText('999') -# elif header[0].startswith('DataProcessing\nRfree'): -# cell_text.setText('999') -# elif header[0].startswith('Rmerge\nLow'): -# cell_text.setText('999') -# else: -# cell_text.setText('') -# cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) -# self.datasets_summary_table.setItem(current_row, column, cell_text) -# -# row += 1 -# -# self.datasets_summary_table.resizeRowsToContents() -# self.datasets_summary_table.resizeColumnsToContents() -# -# self.status_bar.showMessage('updating Overview table') -# -# self.status_bar.showMessage('idle') -# -# self.save_files_to_initial_model_folder() -# + # def populate_datasets_summary_table(self): + # self.status_bar.showMessage( + # 'Building summary table for data processing results; be patient this may take a while') + # row = self.datasets_summary_table.rowCount() + # column_name = self.db.translate_xce_column_list_to_sqlite(self.datasets_summary_table_columns) + # + # pinList = self.db.execute_statement( + # "Select CrystalName,PinBarcode,DataCollectionPinBarcode from mainTable where CrystalName is not ''") + # pinDict = {} + # for item in pinList: + # pinDict[str(item[0])] = [str(item[1]), str(item[2])] + # + # for xtal in sorted(self.data_collection_dict): + # new_xtal = False + # if xtal not in self.datasets_summary_dict: + # row = self.datasets_summary_table.rowCount() + # self.datasets_summary_table.insertRow(row) + # self.datasets_summary_dict[xtal] = [] + # new_xtal = True + # + # # check for dataset outcome + # outcome = '' + # logfile_found = False + # too_low_resolution = True + # db_dict = {} + # for entry in self.data_collection_dict[xtal]: + # if entry[0] == 'logfile': + # logfile_found = True + # if entry[8]: # if this was auto-selected best resolution file + # db_dict = entry[6] + # try: + # if float(db_dict['DataProcessingResolutionHigh']) <= float( + # self.acceptable_low_resolution_limit_for_data): + # too_low_resolution = False + # except ValueError: + # pass + # + # try: + # outcome = str(self.db.get_value_from_field(xtal, 'DataCollectionOutcome')[0]) + # except TypeError: + # outcome = 'Failed - unknown' + # self.update_log.insert('cannot find DataCollectionOutcome for {0!s}'.format(xtal)) + # self.dataset_outcome_dict[xtal] = outcome + # + # # find latest run for crystal and diffraction images + # tmp = [] + # for entry in self.data_collection_dict[xtal]: + # if entry[0] == 'image': + # tmp.append([entry, datetime.strptime(entry[3], '%Y-%m-%d %H:%M:%S')]) + # latest_run = max(tmp, key=lambda x: x[1])[0] + # + # new_run_for_exisiting_crystal_or_new_sample = True + # if new_xtal: + # self.datasets_summary_dict[xtal] = [outcome, db_dict, latest_run] + # else: + # # check if newer run appeared + # old_run_timestamp = self.datasets_summary_dict[xtal][2][3] + # new_run_timestamp = latest_run[3] + # if old_run_timestamp == new_run_timestamp: + # new_run_for_exisiting_crystal_or_new_sample = False + # else: + # checkbox_for_details = self.datasets_summary_dict[xtal][3] + # self.datasets_summary_dict[xtal] = [outcome, db_dict, latest_run, checkbox_for_details] + # + # if new_xtal: + # current_row = row + # else: + # allRows = self.datasets_summary_table.rowCount() + # for table_row in range(allRows): + # if self.datasets_summary_table.item(table_row, 0).text() == xtal: + # current_row = table_row + # break + # + # image_number = 0 + # for column, header in enumerate(column_name): + # if header[0] == 'Sample ID': + # cell_text = QtGui.QTableWidgetItem() + # cell_text.setText(str(xtal)) + # cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + # self.datasets_summary_table.setItem(current_row, column, cell_text) + # elif header[0] == 'DataCollection\nOutcome': + # if new_xtal: + # dataset_outcome_combobox = QtGui.QComboBox() + # for outcomeItem in self.dataset_outcome: + # dataset_outcome_combobox.addItem(outcomeItem) + # self.datasets_summary_table.setCellWidget(current_row, column, dataset_outcome_combobox) + # dataset_outcome_combobox.activated[str].connect(self.dataset_outcome_combobox_change_outcome) + # self.dataset_outcome_combobox_dict[xtal] = dataset_outcome_combobox + # index = self.dataset_outcome_combobox_dict[xtal].findText(str(outcome), QtCore.Qt.MatchFixedString) + # self.dataset_outcome_combobox_dict[xtal].setCurrentIndex(index) + # continue + # + # elif header[0].startswith('img'): + # if new_run_for_exisiting_crystal_or_new_sample: + # img = latest_run[4] + # pixmap = QtGui.QPixmap() + # # can do this (img[image_number][1]) because made sure in the threading module + # # that there are always exactly 5 images in there + # pixmap.loadFromData(base64.b64decode(img[image_number][1])) + # image = QtGui.QLabel() + # image.resize(128, 80) + # image.setPixmap(pixmap.scaled(image.size(), QtCore.Qt.KeepAspectRatio)) + # self.datasets_summary_table.setCellWidget(current_row, column, image) + # image_number += 1 + # + # elif header[0].startswith('Show Diffraction\nImage'): + # if new_run_for_exisiting_crystal_or_new_sample: + # diffraction_image = latest_run[5] + # diffraction_image_name = diffraction_image[diffraction_image.rfind('/') + 1:] + # try: # need to try because older pkl file may not have this item in list + # html_summary = latest_run[7] + # except IndexError: + # html_summary = '' + # if new_xtal: + # start_albula_button = QtGui.QPushButton('Show: \n' + diffraction_image_name) + # start_albula_button.clicked.connect(self.show_html_summary_and_diffraction_image) + # self.albula_button_dict[xtal] = [start_albula_button, diffraction_image, html_summary] + # self.datasets_summary_table.setCellWidget(current_row, column, start_albula_button) + # else: + # self.albula_button_dict[xtal][1] = diffraction_image + # elif header[0].startswith('Show\nDetails'): + # if new_xtal: + # show_data_collection_details_checkbox = QtGui.QCheckBox() + # show_data_collection_details_checkbox.toggle() + # show_data_collection_details_checkbox.setChecked(False) + # show_data_collection_details_checkbox.stateChanged.connect(self.show_data_collection_details) + # self.datasets_summary_table.setCellWidget(current_row, column, + # show_data_collection_details_checkbox) + # self.datasets_summary_dict[xtal].append(show_data_collection_details_checkbox) + # elif header[0].startswith('SoakDB\nBarcode') or header[0].startswith('GDA\nBarcode'): + # if new_xtal: + # cell_text = QtGui.QTableWidgetItem() + # if xtal in pinDict: + # if header[0].startswith('SoakDB\nBarcode'): + # cell_text.setText(str(pinDict[xtal][0])) + # elif header[0].startswith('GDA\nBarcode'): + # cell_text.setText(str(pinDict[xtal][1])) + # if pinDict[xtal][0] == 'NULL' or pinDict[xtal][1] == 'NULL': + # cell_text.setBackground(QtGui.QColor(255, 215, 0)) + # elif pinDict[xtal][0] != pinDict[xtal][1]: + # cell_text.setBackground(QtGui.QColor(255, 0, 0)) + # else: + # cell_text.setText('') + # cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + # self.datasets_summary_table.setItem(current_row, column, cell_text) + # else: + # cell_text = QtGui.QTableWidgetItem() + # # in case data collection failed for whatever reason + # if logfile_found: + # try: + # cell_text.setText(str(db_dict[header[1]])) + # except KeyError: # older pkl files may not have all the columns + # cell_text.setText('n/a') + # else: + # if header[0].startswith('Resolution\n[Mn = 1.5]'): + # cell_text.setText('999') + # elif header[0].startswith('DataProcessing\nRfree'): + # cell_text.setText('999') + # elif header[0].startswith('Rmerge\nLow'): + # cell_text.setText('999') + # else: + # cell_text.setText('') + # cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + # self.datasets_summary_table.setItem(current_row, column, cell_text) + # + # row += 1 + # + # self.datasets_summary_table.resizeRowsToContents() + # self.datasets_summary_table.resizeColumnsToContents() + # + # self.status_bar.showMessage('updating Overview table') + # + # self.status_bar.showMessage('idle') + # + # self.save_files_to_initial_model_folder() + # ################################################################################################################ # @@ -5401,44 +6353,50 @@ def get_row_of_sample_in_table(self, table, xtal): def update_row_in_table(self, sample, row, db_dict, table, columns_to_show): xtal = str(sample) - column_name = self.db.translate_xce_column_list_to_sqlite( - columns_to_show) + column_name = self.db.translate_xce_column_list_to_sqlite(columns_to_show) for column, header in enumerate(column_name): - if header[0] == 'Sample ID': + if header[0] == "Sample ID": cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(xtal)) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) table.setItem(row, column, cell_text) - elif header[0] == 'DataCollection\nOutcome': + elif header[0] == "DataCollection\nOutcome": if xtal not in self.dataset_outcome_combobox_dict: dataset_outcome_combobox = QtGui.QComboBox() for outcomeItem in self.dataset_outcome: dataset_outcome_combobox.addItem(outcomeItem) dataset_outcome_combobox.activated[str].connect( - self.dataset_outcome_combobox_change_outcome) + self.dataset_outcome_combobox_change_outcome + ) self.dataset_outcome_combobox_dict[xtal] = dataset_outcome_combobox table.setCellWidget(row, column, dataset_outcome_combobox) index = self.dataset_outcome_combobox_dict[xtal].findText( - str(db_dict['DataCollectionOutcome']), QtCore.Qt.MatchFixedString) + str(db_dict["DataCollectionOutcome"]), QtCore.Qt.MatchFixedString + ) self.dataset_outcome_combobox_dict[xtal].setCurrentIndex(index) - elif header[0].startswith('img'): + elif header[0].startswith("img"): if os.path.isfile(db_dict[header[1]]): pixmap = QtGui.QPixmap(db_dict[header[1]]) else: pixmap = QtGui.QPixmap( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'IMAGE_NOT_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "IMAGE_NOT_AVAILABLE.png", + ) + ) image = QtGui.QLabel() image.resize(128, 80) - image.setPixmap(pixmap.scaled( - image.size(), QtCore.Qt.KeepAspectRatio)) + image.setPixmap(pixmap.scaled(image.size(), QtCore.Qt.KeepAspectRatio)) table.setCellWidget(row, column, image) - elif header[0] == 'Select': + elif header[0] == "Select": checkbox = QtGui.QCheckBox() checkbox.toggle() if table == self.deposition_table_apo: @@ -5451,28 +6409,28 @@ def update_row_in_table(self, sample, row, db_dict, table, columns_to_show): checkbox.setChecked(False) # elif header[0].startswith('SoakDB\nBarcode') or header[0].startswith('GDA\nBarcode'): - # if new_xtal: - # cell_text = QtGui.QTableWidgetItem() - # if xtal in pinDict: - # if header[0].startswith('SoakDB\nBarcode'): - # cell_text.setText(str(pinDict[xtal][0])) - # elif header[0].startswith('GDA\nBarcode'): - # cell_text.setText(str(pinDict[xtal][1])) - # if pinDict[xtal][0] == 'NULL' or pinDict[xtal][1] == 'NULL': - # cell_text.setBackground(QtGui.QColor(255, 215, 0)) - # elif pinDict[xtal][0] != pinDict[xtal][1]: - # cell_text.setBackground(QtGui.QColor(255, 0, 0)) - # else: - # cell_text.setText('') - # cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - # self.datasets_summary_table.setItem(current_row, column, cell_text) + # if new_xtal: + # cell_text = QtGui.QTableWidgetItem() + # if xtal in pinDict: + # if header[0].startswith('SoakDB\nBarcode'): + # cell_text.setText(str(pinDict[xtal][0])) + # elif header[0].startswith('GDA\nBarcode'): + # cell_text.setText(str(pinDict[xtal][1])) + # if pinDict[xtal][0] == 'NULL' or pinDict[xtal][1] == 'NULL': + # cell_text.setBackground(QtGui.QColor(255, 215, 0)) + # elif pinDict[xtal][0] != pinDict[xtal][1]: + # cell_text.setBackground(QtGui.QColor(255, 0, 0)) + # else: + # cell_text.setText('') + # cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + # self.datasets_summary_table.setItem(current_row, column, cell_text) else: cell_text = QtGui.QTableWidgetItem() # in case data collection failed for whatever reason try: cell_text.setText(str(db_dict[header[1]])) except KeyError: # older pkl files may not have all the columns - cell_text.setText('n/a') + cell_text.setText("n/a") # else: # if header[0].startswith('Resolution\n[Mn = 1.5]'): # cell_text.setText('999') @@ -5483,49 +6441,63 @@ def update_row_in_table(self, sample, row, db_dict, table, columns_to_show): # else: # cell_text.setText('') cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) table.setItem(row, column, cell_text) - print(('row: {0!s} column: {1!s} value: {2!s} header: {3!s}'.format( - row, column, cell_text, header[0]))) - print(('column_name {0!s}'.format(column_name))) + print( + ( + "row: {0!s} column: {1!s} value: {2!s} header: {3!s}".format( + row, column, cell_text, header[0] + ) + ) + ) + print(("column_name {0!s}".format(column_name))) def populate_datasets_summary_table_NEW(self): self.status_bar.showMessage( - 'Building summary table for data processing results; be patient this may take a while') + "Building summary table for data processing results; be patient this may take a while" + ) # get information about all samples collected during the current visit - visit, beamline = XChemMain.getVisitAndBeamline( - self.beamline_directory) + visit, beamline = XChemMain.getVisitAndBeamline(self.beamline_directory) if self.read_agamemnon.isChecked(): visit = [] - for v in glob.glob(os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*')): - visit.append(v[v.rfind('/')+1:]) + for v in glob.glob( + os.path.join( + self.beamline_directory[: self.beamline_directory.rfind("-") + 1] + + "*" + ) + ): + visit.append(v[v.rfind("/") + 1 :]) self.update_log.insert( - 'reading information about collected crystals from database...') - collectedXtalsDict = self.db.xtals_collected_during_visit_as_dict( - visit) + "reading information about collected crystals from database..." + ) + collectedXtalsDict = self.db.xtals_collected_during_visit_as_dict(visit) # instead of using dictionaries, query table of which crystals are in table - samples_in_table = self.get_sample_list_from_table( - self.datasets_summary_table) + samples_in_table = self.get_sample_list_from_table(self.datasets_summary_table) for xtal in sorted(collectedXtalsDict): if xtal not in samples_in_table: row = self.datasets_summary_table.rowCount() self.datasets_summary_table.insertRow(row) else: - row = self.get_row_of_sample_in_table( - self.datasets_summary_table, xtal) + row = self.get_row_of_sample_in_table(self.datasets_summary_table, xtal) db_dict = collectedXtalsDict[xtal] - self.update_row_in_table(xtal, row, db_dict, self.datasets_summary_table, - self.datasets_summary_table_columns) + self.update_row_in_table( + xtal, + row, + db_dict, + self.datasets_summary_table, + self.datasets_summary_table_columns, + ) self.datasets_summary_table.resizeRowsToContents() self.datasets_summary_table.resizeColumnsToContents() - self.status_bar.showMessage('updating Overview table') + self.status_bar.showMessage("updating Overview table") - self.status_bar.showMessage('idle') + self.status_bar.showMessage("idle") def get_selected_row(self, table): indexes = table.selectionModel().selectedRows() @@ -5546,20 +6518,35 @@ def show_results_from_all_pipelines(self): self.msgBox = QtGui.QMessageBox() # will reference it before it exists for db_dict in dbList: - if str(db_dict['DataProcessingSpaceGroup']).lower() == 'null' or str(db_dict['DataProcessingSpaceGroup']).lower() == 'none': + if ( + str(db_dict["DataProcessingSpaceGroup"]).lower() == "null" + or str(db_dict["DataProcessingSpaceGroup"]).lower() == "none" + ): continue row = self.data_collection_table.rowCount() self.data_collection_table.insertRow(row) self.update_row_in_table( - xtal, row, db_dict, self.data_collection_table, self.data_collection_table_columns) - if selectedResultDict['DataCollectionVisit'] == db_dict['DataCollectionVisit'] \ - and selectedResultDict['DataCollectionRun'] == db_dict['DataCollectionRun'] \ - and selectedResultDict['DataProcessingProgram'] == db_dict['DataProcessingProgram'] \ - and selectedResultDict['DataProcessingScore'] == db_dict['DataProcessingScore']: + xtal, + row, + db_dict, + self.data_collection_table, + self.data_collection_table_columns, + ) + if ( + selectedResultDict["DataCollectionVisit"] + == db_dict["DataCollectionVisit"] + and selectedResultDict["DataCollectionRun"] + == db_dict["DataCollectionRun"] + and selectedResultDict["DataProcessingProgram"] + == db_dict["DataProcessingProgram"] + and selectedResultDict["DataProcessingScore"] + == db_dict["DataProcessingScore"] + ): self.current_row = row self.data_collection_table.selectRow(row) self.data_collection_table.cellClicked.connect( - self.select_different_autoprocessing_result) + self.select_different_autoprocessing_result + ) self.data_collection_table_popup() def make_data_collection_table(self): @@ -5567,17 +6554,21 @@ def make_data_collection_table(self): # more elegant would be to delete or reset an existing widget... self.data_collection_table = QtGui.QTableWidget() self.data_collection_table.setVerticalScrollBarPolicy( - QtCore.Qt.ScrollBarAlwaysOff) + QtCore.Qt.ScrollBarAlwaysOff + ) self.data_collection_table.setColumnCount( - len(self.data_collection_table_columns)) + len(self.data_collection_table_columns) + ) font = QtGui.QFont() font.setPointSize(8) self.data_collection_table.setFont(font) self.data_collection_table.setHorizontalHeaderLabels( - self.data_collection_table_columns) + self.data_collection_table_columns + ) self.data_collection_table.horizontalHeader().setFont(font) self.data_collection_table.setSelectionBehavior( - QtGui.QAbstractItemView.SelectRows) + QtGui.QAbstractItemView.SelectRows + ) def data_collection_table_popup(self): # self.msgBox = QtGui.QMessageBox() @@ -5588,10 +6579,9 @@ def data_collection_table_popup(self): vbox = QtGui.QVBoxLayout() vbox.addWidget(self.data_collection_table) qWid.setLayout(vbox) -# msgBoxLayout.addLayout(vbox, 0, 0) + # msgBoxLayout.addLayout(vbox, 0, 0) msgBoxLayout.addWidget(qWid) - self.msgBox.addButton(QtGui.QPushButton( - 'Cancel'), QtGui.QMessageBox.RejectRole) + self.msgBox.addButton(QtGui.QPushButton("Cancel"), QtGui.QMessageBox.RejectRole) self.msgBox.resize(1000, 200) self.msgBox.exec_() @@ -5605,31 +6595,46 @@ def select_different_autoprocessing_result(self): score = self.data_collection_table.item(selected_row, 12).text() for q in range(13): try: - print(('--> {0!s}: {1!s}'.format(q, - self.data_collection_table.item(selected_row, q).text()))) + print( + ( + "--> {0!s}: {1!s}".format( + q, + self.data_collection_table.item(selected_row, q).text(), + ) + ) + ) except AttributeError: - print(('--> {0!s}: None'.format(q))) + print(("--> {0!s}: None".format(q))) # get db_dict from collectionTable for visit, run, autoproc -# dbDict = self.db.get_db_dict_for_visit_run_autoproc(xtal,visit,run,autoproc) + # dbDict = self.db.get_db_dict_for_visit_run_autoproc(xtal,visit,run,autoproc) dbDict = self.db.get_db_dict_for_visit_run_autoproc_score( - xtal, visit, run, autoproc, score) - dbDict['DataProcessingAutoAssigned'] = 'False' - self.update_log.insert('%s: changing selected autoprocessing result to %s %s %s' % ( - xtal, visit, run, autoproc)) + xtal, visit, run, autoproc, score + ) + dbDict["DataProcessingAutoAssigned"] = "False" + self.update_log.insert( + "%s: changing selected autoprocessing result to %s %s %s" + % (xtal, visit, run, autoproc) + ) # xtal is QString -> str(xtal) XChemMain.linkAutoProcessingResult( - str(xtal), dbDict, self.initial_model_directory, self.xce_logfile) - self.update_log.insert('%s: updating row in Datasets table' % xtal) + str(xtal), dbDict, self.initial_model_directory, self.xce_logfile + ) + self.update_log.insert("%s: updating row in Datasets table" % xtal) self.db.update_data_source(str(xtal), dbDict) self.update_log.insert( - '%s: getting updated information from DB mainTable' % xtal) + "%s: getting updated information from DB mainTable" % xtal + ) dbDict = self.db.get_db_dict_for_sample(xtal) - row = self.get_row_of_sample_in_table( - self.datasets_summary_table, xtal) - self.update_row_in_table(xtal, row, dbDict, self.datasets_summary_table, - self.datasets_summary_table_columns) + row = self.get_row_of_sample_in_table(self.datasets_summary_table, xtal) + self.update_row_in_table( + xtal, + row, + dbDict, + self.datasets_summary_table, + self.datasets_summary_table_columns, + ) else: - print('nothing to change') + print("nothing to change") self.msgBox.done(1) # < end @@ -5646,34 +6651,38 @@ def update_outcome_datasets_summary_table(self, sample, outcome): def user_update_selected_autoproc_datasets_summary_table(self): for key in self.data_collection_column_three_dict: if self.data_collection_column_three_dict[key][0] == self.sender(): - self.update_log.insert('here: ' + self.sender()) + self.update_log.insert("here: " + self.sender()) self.update_log.insert( - 'herere' + str(self.data_collection_column_three_dict)) + "herere" + str(self.data_collection_column_three_dict) + ) dbTmp = self.xtal_db_dict[key] - stage = dbTmp['RefinementOutcome'].split()[0] - print(('===>', key, stage)) + stage = dbTmp["RefinementOutcome"].split()[0] + print(("===>", key, stage)) if int(stage) > 2: msgBox = QtGui.QMessageBox() msgBox.setText( "*** WARNING ***\n%s is currently %s\nIt will disappear from the Refinement table,\n" - "when you refresh it next time.\nDo you want to continue?" % ( - key, dbTmp['RefinementOutcome'])) - msgBox.addButton(QtGui.QPushButton( - 'No'), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton('Yes'), - QtGui.QMessageBox.RejectRole) + "when you refresh it next time.\nDo you want to continue?" + % (key, dbTmp["RefinementOutcome"]) + ) + msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.YesRole) + msgBox.addButton( + QtGui.QPushButton("Yes"), QtGui.QMessageBox.RejectRole + ) reply = msgBox.exec_() if reply == 0: self.update_log.insert( - 'will not change data processing selection') + "will not change data processing selection" + ) # restore previous selection for n, entry in enumerate(self.data_collection_dict[key]): - print(('==>', n)) - if entry[0] == 'logfile': + print(("==>", n)) + if entry[0] == "logfile": if entry[8]: - print(('===> found:', n)) - self.data_collection_column_three_dict[key][0].selectRow( - n) + print(("===> found:", n)) + self.data_collection_column_three_dict[key][ + 0 + ].selectRow(n) break indexes = self.sender().selectionModel().selectedRows() @@ -5681,26 +6690,29 @@ def user_update_selected_autoproc_datasets_summary_table(self): for index in sorted(indexes): selected_processing_result = index.row() # the user changed the selection, i.e. no automated selection will update it - self.update_log.insert('user changed selection') + self.update_log.insert("user changed selection") self.data_collection_column_three_dict[key][1] = True # need to also update if not yet done user_already_changed_selection = False for n, entry in enumerate(self.data_collection_dict[key]): - if entry[0] == 'user_changed_selection': + if entry[0] == "user_changed_selection": user_already_changed_selection = True - if entry[0] == 'logfile': + if entry[0] == "logfile": db_dict = entry[6] - db_dict['DataProcessingAutoAssigned'] = 'False' + db_dict["DataProcessingAutoAssigned"] = "False" if entry[7] == selected_processing_result: db_dict_current = entry[6] - program = db_dict['DataProcessingProgram'] - visit = db_dict['DataCollectionVisit'] - run = db_dict['DataCollectionRun'] + program = db_dict["DataProcessingProgram"] + visit = db_dict["DataCollectionVisit"] + run = db_dict["DataCollectionRun"] self.update_log.insert( - 'user changed data processing files for {0!s} to visit={1!s}, ' - 'run={2!s}, program={3!s}'.format(key, visit, run, program)) + "user changed data processing files for {0!s} to visit={1!s}, " + "run={2!s}, program={3!s}".format( + key, visit, run, program + ) + ) # update datasource - self.update_log.insert('updating datasource...') + self.update_log.insert("updating datasource...") self.update_data_source(key, db_dict) entry[8] = True else: @@ -5709,41 +6721,45 @@ def user_update_selected_autoproc_datasets_summary_table(self): entry[6] = db_dict self.data_collection_dict[key][n] = entry if not user_already_changed_selection: - self.data_collection_dict[key].append( - ['user_changed_selection']) - XChemMain.change_links_to_selected_data_collection_outcome(key, self.data_collection_dict, - self.data_collection_column_three_dict, - self.dataset_outcome_dict, - self.initial_model_directory, - os.path.join(self.database_directory, - self.data_source_file), - self.xce_logfile) + self.data_collection_dict[key].append(["user_changed_selection"]) + XChemMain.change_links_to_selected_data_collection_outcome( + key, + self.data_collection_dict, + self.data_collection_column_three_dict, + self.dataset_outcome_dict, + self.initial_model_directory, + os.path.join(self.database_directory, self.data_source_file), + self.xce_logfile, + ) # update 'Datasets' table column_name = XChemDB.data_source( - os.path.join(self.database_directory, self.data_source_file)).translate_xce_column_list_to_sqlite( - self.datasets_summary_table_columns) + os.path.join(self.database_directory, self.data_source_file) + ).translate_xce_column_list_to_sqlite( + self.datasets_summary_table_columns + ) rows_in_table = self.datasets_summary_table.rowCount() for row in range(rows_in_table): if self.datasets_summary_table.item(row, 0).text() == key: for column, header in enumerate(column_name): - if header[0] == 'Sample ID': + if header[0] == "Sample ID": continue - elif header[0] == 'DataCollection\nOutcome': + elif header[0] == "DataCollection\nOutcome": continue - elif header[0].startswith('img'): + elif header[0].startswith("img"): continue - elif header[0].startswith('Show'): + elif header[0].startswith("Show"): continue else: cell_text = QtGui.QTableWidgetItem() try: - cell_text.setText( - str(db_dict_current[header[1]])) + cell_text.setText(str(db_dict_current[header[1]])) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) self.datasets_summary_table.setItem( - row, column, cell_text) + row, column, cell_text + ) except KeyError: pass @@ -5757,17 +6773,19 @@ def update_selected_autoproc_datasets_summary_table(self): selected_processing_result = index.row() for n, entry in enumerate(self.data_collection_dict[sample]): - if entry[0] == 'logfile': + if entry[0] == "logfile": if entry[7] == selected_processing_result: db_dict = entry[6] - program = db_dict['DataProcessingProgram'] - visit = db_dict['DataCollectionVisit'] - run = db_dict['DataCollectionRun'] + program = db_dict["DataProcessingProgram"] + visit = db_dict["DataCollectionVisit"] + run = db_dict["DataCollectionRun"] self.update_log.insert( - 'user changed data processing files for {0!s} to visit={1!s}, run={2!s}, program={3!s}'.format( - sample, visit, run, program)) + "user changed data processing files for {0!s} to visit={1!s}, run={2!s}, program={3!s}".format( + sample, visit, run, program + ) + ) # update datasource - self.update_log.insert('updating datasource...') + self.update_log.insert("updating datasource...") self.update_data_source(sample, db_dict) entry[8] = True else: @@ -5776,47 +6794,53 @@ def update_selected_autoproc_datasets_summary_table(self): # update 'Datasets' table column_name = XChemDB.data_source( - os.path.join(self.database_directory, self.data_source_file)).translate_xce_column_list_to_sqlite( - self.datasets_summary_table_columns) + os.path.join(self.database_directory, self.data_source_file) + ).translate_xce_column_list_to_sqlite(self.datasets_summary_table_columns) rows_in_table = self.datasets_summary_table.rowCount() for row in range(rows_in_table): if self.datasets_summary_table.item(row, 0).text() == sample: for column, header in enumerate(column_name): - if header[0] == 'Sample ID': + if header[0] == "Sample ID": continue - elif header[0] == 'DataCollection\nOutcome': + elif header[0] == "DataCollection\nOutcome": continue - elif header[0].startswith('img'): + elif header[0].startswith("img"): continue - elif header[0].startswith('Show'): + elif header[0].startswith("Show"): continue else: cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(db_dict[header[1]])) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.datasets_summary_table.setItem( - row, column, cell_text) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) + self.datasets_summary_table.setItem(row, column, cell_text) def populate_and_update_datasource_table(self): self.overview_datasource_table.setColumnCount( - len(self.overview_datasource_table_columns)) + len(self.overview_datasource_table_columns) + ) # first get a list of all the samples that are already in the table and which will be updated samples_in_table = [] current_row = self.overview_datasource_table.rowCount() for row in range(current_row): - sampleID = str(self.overview_datasource_table.item( - row, 0).text()) # this must be the case + sampleID = str( + self.overview_datasource_table.item(row, 0).text() + ) # this must be the case samples_in_table.append(sampleID) columns_to_show = self.get_columns_to_show( - self.overview_datasource_table_columns) + self.overview_datasource_table_columns + ) n_rows = self.get_rows_with_sample_id_not_null_from_datasource() - sample_id_column = self.get_columns_to_show(['Sample ID']) + sample_id_column = self.get_columns_to_show(["Sample ID"]) for row in self.data: - if str(row[sample_id_column[0]]).lower() == 'none' or str(row[sample_id_column[0]]).replace(' ', '') == '': + if ( + str(row[sample_id_column[0]]).lower() == "none" + or str(row[sample_id_column[0]]).replace(" ", "") == "" + ): # do not show rows where sampleID is null continue else: @@ -5826,26 +6850,31 @@ def populate_and_update_datasource_table(self): self.overview_datasource_table.insertRow(x) else: # find row of this sample in data_source_table - for present_rows in range(self.overview_datasource_table.rowCount()): + for present_rows in range( + self.overview_datasource_table.rowCount() + ): if str(row[sample_id_column[0]]) == str( - self.overview_datasource_table.item(present_rows, 0).text()): + self.overview_datasource_table.item(present_rows, 0).text() + ): x = present_rows break for y, item in enumerate(columns_to_show): cell_text = QtGui.QTableWidgetItem() if row[item] is None: - cell_text.setText('') + cell_text.setText("") else: cell_text.setText(str(row[item])) # assumption is that column 0 is always sampleID - if self.overview_datasource_table_columns[y] == 'Sample ID': + if self.overview_datasource_table_columns[y] == "Sample ID": # and this field cannot be changed cell_text.setFlags(QtCore.Qt.ItemIsEnabled) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) self.overview_datasource_table.setItem(x, y, cell_text) self.overview_datasource_table.setHorizontalHeaderLabels( - self.overview_datasource_table_columns) + self.overview_datasource_table_columns + ) def kill_other_pandda_options(self): for i in range(0, self.pandda_analyse_data_table.rowCount()): @@ -5864,12 +6893,13 @@ def kill_other_pandda_options(self): def populate_pandda_analyse_input_table(self): column_name = self.db.translate_xce_column_list_to_sqlite( - self.pandda_table_columns) + self.pandda_table_columns + ) print(column_name) for xtal in sorted(self.xtal_db_dict): new_xtal = False db_dict = self.xtal_db_dict[xtal] - if os.path.isfile(db_dict['DimplePathToPDB']): + if os.path.isfile(db_dict["DimplePathToPDB"]): row = self.pandda_analyse_data_table.rowCount() if xtal not in self.pandda_analyse_input_table_dict: self.pandda_analyse_data_table.insertRow(row) @@ -5877,91 +6907,102 @@ def populate_pandda_analyse_input_table(self): new_xtal = True else: for table_row in range(row): - if self.pandda_analyse_data_table.item(table_row, 0).text() == xtal: + if ( + self.pandda_analyse_data_table.item(table_row, 0).text() + == xtal + ): current_row = table_row break for column, header in enumerate(column_name): - if header[0] == 'Exclude': + if header[0] == "Exclude": deselect_button = QtGui.QCheckBox() deselect_button.stateChanged.connect( - self.kill_other_pandda_options) + self.kill_other_pandda_options + ) self.pandda_analyse_data_table.setCellWidget( - current_row, column, deselect_button) + current_row, column, deselect_button + ) - elif header[0] == 'Ignore': + elif header[0] == "Ignore": deselect_button = QtGui.QCheckBox() deselect_button.stateChanged.connect( - self.kill_other_pandda_options) + self.kill_other_pandda_options + ) self.pandda_analyse_data_table.setCellWidget( - current_row, column, deselect_button) + current_row, column, deselect_button + ) - elif header[0] == 'Export': + elif header[0] == "Export": deselect_button = QtGui.QCheckBox() deselect_button.stateChanged.connect( - self.kill_other_pandda_options) + self.kill_other_pandda_options + ) self.pandda_analyse_data_table.setCellWidget( - current_row, column, deselect_button) + current_row, column, deselect_button + ) - elif header[0] == 'Sample ID': + elif header[0] == "Sample ID": cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(xtal)) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) self.pandda_analyse_data_table.setItem( - current_row, column, cell_text) + current_row, column, cell_text + ) else: cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(db_dict[header[1]])) - if header[0] == 'PanDDA\nStatus': - if str(db_dict[header[1]]) == 'running': - cell_text.setBackground( - QtGui.QColor(100, 230, 150)) - elif str(db_dict[header[1]]) == 'pending': - cell_text.setBackground( - QtGui.QColor(20, 100, 230)) - elif str(db_dict[header[1]]) == 'started': - cell_text.setBackground( - QtGui.QColor(230, 240, 110)) - elif str(db_dict[header[1]]) == 'finished': - cell_text.setBackground( - QtGui.QColor(255, 255, 255)) - elif 'problem' in str(db_dict[header[1]]): - cell_text.setBackground( - QtGui.QColor(255, 0, 0)) + if header[0] == "PanDDA\nStatus": + if str(db_dict[header[1]]) == "running": + cell_text.setBackground(QtGui.QColor(100, 230, 150)) + elif str(db_dict[header[1]]) == "pending": + cell_text.setBackground(QtGui.QColor(20, 100, 230)) + elif str(db_dict[header[1]]) == "started": + cell_text.setBackground(QtGui.QColor(230, 240, 110)) + elif str(db_dict[header[1]]) == "finished": + cell_text.setBackground(QtGui.QColor(255, 255, 255)) + elif "problem" in str(db_dict[header[1]]): + cell_text.setBackground(QtGui.QColor(255, 0, 0)) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) self.pandda_analyse_data_table.setItem( - current_row, column, cell_text) + current_row, column, cell_text + ) if new_xtal: self.pandda_analyse_input_table_dict[xtal] = [] def select_sample_for_pandda(self, option): indexes = self.pandda_analyse_data_table.selectionModel().selectedRows() - if option == 'deselect': + if option == "deselect": for index in sorted(indexes): - self.pandda_analyse_data_table.cellWidget( - index.row(), 6).setChecked(False) - self.pandda_analyse_data_table.cellWidget( - index.row(), 7).setChecked(False) - self.pandda_analyse_data_table.cellWidget( - index.row(), 8).setChecked(False) + self.pandda_analyse_data_table.cellWidget(index.row(), 6).setChecked( + False + ) + self.pandda_analyse_data_table.cellWidget(index.row(), 7).setChecked( + False + ) + self.pandda_analyse_data_table.cellWidget(index.row(), 8).setChecked( + False + ) else: for index in sorted(indexes): - self.pandda_analyse_data_table.cellWidget( - index.row(), 6).setChecked(False) - self.pandda_analyse_data_table.cellWidget( - index.row(), 7).setChecked(False) - self.pandda_analyse_data_table.cellWidget( - index.row(), 8).setChecked(False) - if option == 'ignore': - checkbox = self.pandda_analyse_data_table.cellWidget( - index.row(), 6) - if option == 'char': - checkbox = self.pandda_analyse_data_table.cellWidget( - index.row(), 7) - if option == 'zmap': - checkbox = self.pandda_analyse_data_table.cellWidget( - index.row(), 8) + self.pandda_analyse_data_table.cellWidget(index.row(), 6).setChecked( + False + ) + self.pandda_analyse_data_table.cellWidget(index.row(), 7).setChecked( + False + ) + self.pandda_analyse_data_table.cellWidget(index.row(), 8).setChecked( + False + ) + if option == "ignore": + checkbox = self.pandda_analyse_data_table.cellWidget(index.row(), 6) + if option == "char": + checkbox = self.pandda_analyse_data_table.cellWidget(index.row(), 7) + if option == "zmap": + checkbox = self.pandda_analyse_data_table.cellWidget(index.row(), 8) checkbox.setChecked(True) self.kill_other_pandda_options() @@ -5978,13 +7019,14 @@ def populate_and_update_refinement_table(self): # panddaDict[str(item[0])].append([str(item[1]), str(item[2]), str(item[3])]) column_name = self.db.translate_xce_column_list_to_sqlite( - self.refinement_table_columns) + self.refinement_table_columns + ) for xtal in sorted(self.xtal_db_dict): new_xtal = False db_dict = self.xtal_db_dict[xtal] try: - stage = int(str(db_dict['RefinementOutcome']).split()[0]) - refinementStage = db_dict['RefinementOutcome'] + stage = int(str(db_dict["RefinementOutcome"]).split()[0]) + refinementStage = db_dict["RefinementOutcome"] except ValueError: stage = 0 except IndexError: @@ -6002,89 +7044,92 @@ def populate_and_update_refinement_table(self): current_row = table_row break for column, header in enumerate(column_name): - if header[0] == 'Sample ID': + if header[0] == "Sample ID": cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(xtal)) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.refinement_table.setItem( - current_row, column, cell_text) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) + self.refinement_table.setItem(current_row, column, cell_text) - elif header[0] == 'Refinement\nOutcome': + elif header[0] == "Refinement\nOutcome": if new_xtal: refinement_outcome_combobox = QtGui.QComboBox() self.populate_refinement_outcome_combobox( - refinement_outcome_combobox) + refinement_outcome_combobox + ) self.refinement_table.setCellWidget( - current_row, column, refinement_outcome_combobox) + current_row, column, refinement_outcome_combobox + ) else: - refinement_outcome_combobox = self.refinement_table_dict[xtal] + refinement_outcome_combobox = self.refinement_table_dict[ + xtal + ] index = refinement_outcome_combobox.findText( - refinementStage, QtCore.Qt.MatchFixedString) + refinementStage, QtCore.Qt.MatchFixedString + ) refinement_outcome_combobox.setCurrentIndex(index) refinement_outcome_combobox.currentIndexChanged.connect( - self.refinement_outcome_combobox_changed) + self.refinement_outcome_combobox_changed + ) - elif header[0] == 'buster-reports': + elif header[0] == "buster-reports": # "'NAME'".format(db_dict['RefinementBusterReportHTML']) - # db_dict['RefinementBusterReportHTML'] = 'www.google.com' - buster_report = db_dict['RefinementBusterReportHTML'] - ref_name = buster_report.split( - '/')[len(buster_report.split('/'))-2] + # db_dict['RefinementBusterReportHTML'] = 'www.google.com' + buster_report = db_dict["RefinementBusterReportHTML"] + ref_name = buster_report.split("/")[ + len(buster_report.split("/")) - 2 + ] buster_report_link = QtGui.QLabel( - "{1!s}".format(buster_report, ref_name)) + '{1!s}'.format(buster_report, ref_name) + ) buster_report_link.setOpenExternalLinks(True) -# buster_report_link.setTextInteractionFlags(QtCore.Qt.TextBrowserInteraction) -# buster_report_link.setTextFormat(QtCore.Qt.RichText) -# self.refinement_table.setItem(current_row, column, buster_report_link) + # buster_report_link.setTextInteractionFlags(QtCore.Qt.TextBrowserInteraction) + # buster_report_link.setTextFormat(QtCore.Qt.RichText) + # self.refinement_table.setItem(current_row, column, buster_report_link) self.refinement_table.setCellWidget( - current_row, column, buster_report_link) - - -# elif header[0] == 'PanDDA site details': -# try: -# panddaDict[xtal].insert(0, ['Index', 'Name', 'Status']) -# outerFrame = QtGui.QFrame() -# outerFrame.setFrameShape(QtGui.QFrame.Box) -# grid = QtGui.QGridLayout() -# for y, entry in enumerate(panddaDict[xtal]): -# for x, info in enumerate(entry): -# frame = QtGui.QFrame() -# frame.setFrameShape(QtGui.QFrame.Box) -# vbox = QtGui.QVBoxLayout() -# vbox.addWidget(QtGui.QLabel(str(entry[x]))) -# frame.setLayout(vbox) -# grid.addWidget(frame, y, x) -# outerFrame.setLayout(grid) -# self.refinement_table.setCellWidget(current_row, column, outerFrame) -# except KeyError: -# cell_text = QtGui.QTableWidgetItem() -# cell_text.setText('*** N/A ***') -# cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) -# self.refinement_table.setItem(current_row, column, cell_text) + current_row, column, buster_report_link + ) + + # elif header[0] == 'PanDDA site details': + # try: + # panddaDict[xtal].insert(0, ['Index', 'Name', 'Status']) + # outerFrame = QtGui.QFrame() + # outerFrame.setFrameShape(QtGui.QFrame.Box) + # grid = QtGui.QGridLayout() + # for y, entry in enumerate(panddaDict[xtal]): + # for x, info in enumerate(entry): + # frame = QtGui.QFrame() + # frame.setFrameShape(QtGui.QFrame.Box) + # vbox = QtGui.QVBoxLayout() + # vbox.addWidget(QtGui.QLabel(str(entry[x]))) + # frame.setLayout(vbox) + # grid.addWidget(frame, y, x) + # outerFrame.setLayout(grid) + # self.refinement_table.setCellWidget(current_row, column, outerFrame) + # except KeyError: + # cell_text = QtGui.QTableWidgetItem() + # cell_text.setText('*** N/A ***') + # cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) + # self.refinement_table.setItem(current_row, column, cell_text) else: cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(db_dict[header[1]])) - if header[0] == 'Refinement\nStatus': - if str(db_dict[header[1]]) == 'running': - cell_text.setBackground( - QtGui.QColor(100, 230, 150)) - elif str(db_dict[header[1]]) == 'pending': - cell_text.setBackground( - QtGui.QColor(20, 100, 230)) - elif str(db_dict[header[1]]) == 'started': - cell_text.setBackground( - QtGui.QColor(230, 240, 110)) - elif str(db_dict[header[1]]) == 'finished': - cell_text.setBackground( - QtGui.QColor(255, 255, 255)) - elif 'problem' in str(db_dict[header[1]]): - cell_text.setBackground( - QtGui.QColor(255, 0, 0)) + if header[0] == "Refinement\nStatus": + if str(db_dict[header[1]]) == "running": + cell_text.setBackground(QtGui.QColor(100, 230, 150)) + elif str(db_dict[header[1]]) == "pending": + cell_text.setBackground(QtGui.QColor(20, 100, 230)) + elif str(db_dict[header[1]]) == "started": + cell_text.setBackground(QtGui.QColor(230, 240, 110)) + elif str(db_dict[header[1]]) == "finished": + cell_text.setBackground(QtGui.QColor(255, 255, 255)) + elif "problem" in str(db_dict[header[1]]): + cell_text.setBackground(QtGui.QColor(255, 0, 0)) cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - self.refinement_table.setItem( - current_row, column, cell_text) + QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter + ) + self.refinement_table.setItem(current_row, column, cell_text) if new_xtal: self.refinement_table_dict[xtal] = refinement_outcome_combobox @@ -6098,7 +7143,7 @@ def get_columns_to_show(self, column_list): columns_to_show = [] for column in column_list: # first find out what the column name in the header is: - column_name = '' + column_name = "" for name in self.all_columns_in_data_source: if column == name[1]: column_name = name[0] @@ -6109,25 +7154,30 @@ def get_columns_to_show(self, column_list): return columns_to_show def get_rows_with_sample_id_not_null_from_datasource(self): - sample_id_column = self.get_columns_to_show(['Sample ID']) + sample_id_column = self.get_columns_to_show(["Sample ID"]) n_rows = 0 for row in self.data: - if not str(row[sample_id_column[0]]).lower() != 'none' or not str(row[sample_id_column[0]]).replace(' ', '') == '': + if ( + not str(row[sample_id_column[0]]).lower() != "none" + or not str(row[sample_id_column[0]]).replace(" ", "") == "" + ): n_rows += 1 return n_rows def update_data_source(self, sample, db_dict): - data_source = XChemDB.data_source(os.path.join( - self.database_directory, self.data_source_file)) + data_source = XChemDB.data_source( + os.path.join(self.database_directory, self.data_source_file) + ) def quit_xce(self): # save pkl file if self.data_collection_dict != {}: if os.path.isfile(self.datasets_summary_file): - self.update_log.insert('saving results to PKL file') - pickle.dump(self.data_collection_dict, open( - self.datasets_summary_file, 'wb')) - self.update_log.insert('quitting XCE... bye,bye!') + self.update_log.insert("saving results to PKL file") + pickle.dump( + self.data_collection_dict, open(self.datasets_summary_file, "wb") + ) + self.update_log.insert("quitting XCE... bye,bye!") QtGui.qApp.quit() diff --git a/gui_scripts/datasets_tab.py b/gui_scripts/datasets_tab.py index 0fa11007..1817cd2a 100755 --- a/gui_scripts/datasets_tab.py +++ b/gui_scripts/datasets_tab.py @@ -4,11 +4,11 @@ import os from PyQt4 import QtGui, QtCore, QtWebKit -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) -class DatasetsTab(): +class DatasetsTab: def __init__(self): self.layout_funcs = layout.LayoutFuncs() @@ -19,13 +19,16 @@ def setup(self, xce_object): # # ################################################################################################################ # define subtab list, widget and dict - datasets_tab_list = ['Summary', 'Reprocess'] + datasets_tab_list = ["Summary", "Reprocess"] xce_object.datasets_tab_widget = QtGui.QTabWidget() xce_object.datasets_tab_dict = {} # make subtabs self.layout_funcs.make_tab_dict( - datasets_tab_list, xce_object.datasets_tab_widget, xce_object.datasets_tab_dict) + datasets_tab_list, + xce_object.datasets_tab_widget, + xce_object.datasets_tab_dict, + ) # main body - things that are always displayed # add a container to hold everythting and add to main tab layout @@ -36,34 +39,42 @@ def setup(self, xce_object): # checkbox for autocollect xce_object.check_for_new_data_collection = QtGui.QCheckBox( - 'Check for new data collection every two minutes') + "Check for new data collection every two minutes" + ) xce_object.check_for_new_data_collection = QtGui.QCheckBox( - 'Check for new data collection every two minutes') - self.layout_funcs.add_checkbox(xce_object, xce_object.check_for_new_data_collection, - 'xce_object.continously_check_for_new_data_collection') + "Check for new data collection every two minutes" + ) + self.layout_funcs.add_checkbox( + xce_object, + xce_object.check_for_new_data_collection, + "xce_object.continously_check_for_new_data_collection", + ) # select target dropdown - select_target_label = QtGui.QLabel('Select Target: ') - select_target_label.setAlignment( - QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter) + select_target_label = QtGui.QLabel("Select Target: ") + select_target_label.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignVCenter) xce_object.target_selection_combobox = QtGui.QComboBox() xce_object.populate_target_selection_combobox( - xce_object.target_selection_combobox) + xce_object.target_selection_combobox + ) xce_object.target_selection_combobox.activated[str].connect( - xce_object.target_selection_combobox_activated) - xce_object.target = str( - xce_object.target_selection_combobox.currentText()) + xce_object.target_selection_combobox_activated + ) + xce_object.target = str(xce_object.target_selection_combobox.currentText()) # array defining order of xce_objects to add - xce_object.autocheck_hbox_widgets = [xce_object.check_for_new_data_collection, select_target_label, - xce_object.target_selection_combobox] + xce_object.autocheck_hbox_widgets = [ + xce_object.check_for_new_data_collection, + select_target_label, + xce_object.target_selection_combobox, + ] - self.layout_funcs.add_to_box(xce_object.autocheck_hbox, - xce_object.autocheck_hbox_widgets) # add xce_objects in order + self.layout_funcs.add_to_box( + xce_object.autocheck_hbox, xce_object.autocheck_hbox_widgets + ) # add xce_objects in order # add target dropdown to top bar - xce_object.datasets_data_collection_vbox.addLayout( - xce_object.autocheck_hbox) + xce_object.datasets_data_collection_vbox.addLayout(xce_object.autocheck_hbox) # summary sub-tab # table @@ -72,39 +83,47 @@ def setup(self, xce_object): xce_object.datasets_summary_table.resizeRowsToContents() xce_object.datasets_summary_table.resizeColumnsToContents() xce_object.datasets_summary_table.setSelectionBehavior( - QtGui.QAbstractItemView.SelectRows) + QtGui.QAbstractItemView.SelectRows + ) xce_object.datasets_summary_table.cellClicked.connect( - xce_object.show_results_from_all_pipelines) + xce_object.show_results_from_all_pipelines + ) self.layout_funcs.table_setup( - xce_object.datasets_summary_table, xce_object.datasets_summary_table_columns) + xce_object.datasets_summary_table, xce_object.datasets_summary_table_columns + ) # setup layout to hold table xce_object.datasets_summarys_vbox_for_table = QtGui.QVBoxLayout() xce_object.datasets_summarys_vbox_for_table.addWidget( - xce_object.datasets_summary_table) # add table to layout - xce_object.datasets_summarys_vbox_for_details = QtGui.QVBoxLayout() # vbox for details + xce_object.datasets_summary_table + ) # add table to layout + xce_object.datasets_summarys_vbox_for_details = ( + QtGui.QVBoxLayout() + ) # vbox for details # switch for displaying/updating table xce_object.data_collection_details_currently_on_display = None xce_object.datasets_data_collection_vbox.addWidget( - xce_object.datasets_tab_widget) # add subtab to main tab + xce_object.datasets_tab_widget + ) # add subtab to main tab # reprocessing sub-tab # top options # data collection label - dc_label = QtGui.QLabel('Data collection directory: ') + dc_label = QtGui.QLabel("Data collection directory: ") # align left and centre of container dc_label.setAlignment(QtCore.Qt.AlignLeft | QtCore.Qt.AlignVCenter) xce_object.diffraction_data_dir_label = QtGui.QLabel( - xce_object.diffraction_data_directory) # add directory as text + xce_object.diffraction_data_directory + ) # add directory as text xce_object.diffraction_data_dir_label.setAlignment( - QtCore.Qt.AlignLeft | QtCore.Qt.AlignVCenter) # align as above + QtCore.Qt.AlignLeft | QtCore.Qt.AlignVCenter + ) # align as above # select label select_button = QtGui.QPushButton("Select") # attach file open dialogue - select_button.clicked.connect( - xce_object.select_diffraction_data_directory) + select_button.clicked.connect(xce_object.select_diffraction_data_directory) # search button search_button = QtGui.QPushButton("Search Datasets") @@ -113,28 +132,34 @@ def setup(self, xce_object): # search info xce_object.diffraction_data_search_label = QtGui.QLabel( - xce_object.diffraction_data_search_info) + xce_object.diffraction_data_search_info + ) # translate label - translate_label = QtGui.QLabel( - 'Translate: datasetID -> sampleID') + translate_label = QtGui.QLabel("Translate: datasetID -> sampleID") # align in centre of container translate_label.setAlignment(QtCore.Qt.AlignCenter) # CSV button - csv_button = QtGui.QPushButton('Open CSV') + csv_button = QtGui.QPushButton("Open CSV") csv_button.setStyleSheet("QPushButton { padding: 1px; margin: 1px }") # open the relevant csv file csv_button.clicked.connect(xce_object.translate_datasetID_to_sampleID) # create hbox to hold everything and add widgets to it xce_object.hbox_select = QtGui.QHBoxLayout() # top options box - xce_object.hbox_select_widgets = [dc_label, xce_object.diffraction_data_dir_label, select_button, search_button, - xce_object.diffraction_data_search_label, - translate_label, - csv_button] # array defining order of xce_objects to be added + xce_object.hbox_select_widgets = [ + dc_label, + xce_object.diffraction_data_dir_label, + select_button, + search_button, + xce_object.diffraction_data_search_label, + translate_label, + csv_button, + ] # array defining order of xce_objects to be added self.layout_funcs.add_to_box( - xce_object.hbox_select, xce_object.hbox_select_widgets) # add xce_objects in order + xce_object.hbox_select, xce_object.hbox_select_widgets + ) # add xce_objects in order # frame to hold everything frame_select = QtGui.QFrame() @@ -143,57 +168,67 @@ def setup(self, xce_object): # table - main body xce_object.datasets_reprocess_table = QtGui.QTableWidget() - self.layout_funcs.table_setup(xce_object.datasets_reprocess_table, - xce_object.datasets_reprocess_columns) # setup + self.layout_funcs.table_setup( + xce_object.datasets_reprocess_table, xce_object.datasets_reprocess_columns + ) # setup # create context menu - no idea where this lives... xce_object.popMenu_for_datasets_reprocess_table = QtGui.QMenu() run_xia2_on_selected = QtGui.QAction( - "mark selected for reprocessing", xce_object.window) - run_xia2_on_selected.triggered.connect( - xce_object.select_sample_for_xia2) - xce_object.popMenu_for_datasets_reprocess_table.addAction( - run_xia2_on_selected) + "mark selected for reprocessing", xce_object.window + ) + run_xia2_on_selected.triggered.connect(xce_object.select_sample_for_xia2) + xce_object.popMenu_for_datasets_reprocess_table.addAction(run_xia2_on_selected) xce_object.datasets_reprocess_table.setContextMenuPolicy( - QtCore.Qt.CustomContextMenu) + QtCore.Qt.CustomContextMenu + ) xce_object.datasets_reprocess_table.customContextMenuRequested.connect( - xce_object.on_context_menu_reprocess_data) + xce_object.on_context_menu_reprocess_data + ) # options at bottom of tab # data processing label - label = QtGui.QLabel('Data processing protocol: ') + label = QtGui.QLabel("Data processing protocol: ") label.setAlignment(QtCore.Qt.AlignLeft | QtCore.Qt.AlignVCenter) # option checkboxes - xce_object.xia2_3d_checkbox = QtGui.QCheckBox('xia2 3d') - xce_object.xia2_3dii_checkbox = QtGui.QCheckBox('xia2 3dii') - xce_object.xia2_dials_checkbox = QtGui.QCheckBox('Dials') + xce_object.xia2_3d_checkbox = QtGui.QCheckBox("xia2 3d") + xce_object.xia2_3dii_checkbox = QtGui.QCheckBox("xia2 3dii") + xce_object.xia2_dials_checkbox = QtGui.QCheckBox("Dials") # spacegroup label - sg_label = QtGui.QLabel('Space Group:') + sg_label = QtGui.QLabel("Space Group:") # spacegroup dropdown menu xce_object.reprocess_space_group_comboxbox = QtGui.QComboBox() - xce_object.reprocess_space_group_comboxbox.addItem('ignore') + xce_object.reprocess_space_group_comboxbox.addItem("ignore") for sg in XChemMain.space_group_list(): xce_object.reprocess_space_group_comboxbox.addItem(sg) # mtz label - mtz_label = QtGui.QLabel('Reference MTZ:') + mtz_label = QtGui.QLabel("Reference MTZ:") # file label xce_object.reprocess_reference_mtz_file_label = QtGui.QLabel( - xce_object.diffraction_data_reference_mtz) + xce_object.diffraction_data_reference_mtz + ) # select button select_button = QtGui.QPushButton("Select") - select_button.clicked.connect( - xce_object.select_reprocess_reference_mtz) + select_button.clicked.connect(xce_object.select_reprocess_reference_mtz) # define order of widgets to be added to options hbox - hbox_options_widgets = [label, xce_object.xia2_3d_checkbox, xce_object.xia2_3dii_checkbox, - xce_object.xia2_dials_checkbox, sg_label, xce_object.reprocess_space_group_comboxbox, - mtz_label, xce_object.reprocess_reference_mtz_file_label, select_button] + hbox_options_widgets = [ + label, + xce_object.xia2_3d_checkbox, + xce_object.xia2_3dii_checkbox, + xce_object.xia2_dials_checkbox, + sg_label, + xce_object.reprocess_space_group_comboxbox, + mtz_label, + xce_object.reprocess_reference_mtz_file_label, + select_button, + ] # create hbox, add everything to it and then put it in a frame hbox_options = QtGui.QHBoxLayout() @@ -204,17 +239,19 @@ def setup(self, xce_object): # following are contained in vboxes # res limit isig label - label = QtGui.QLabel('Res.\nLimit:\nMn') + label = QtGui.QLabel("Res.\nLimit:\nMn") label.setAlignment(QtCore.Qt.AlignCenter) # res limit isig dropdown menu xce_object.reprocess_isigma_combobox = QtGui.QComboBox() - misigma = ['default', '4', '3', '2.5', '2', '1.5', '1', '0.5'] + misigma = ["default", "4", "3", "2.5", "2", "1.5", "1", "0.5"] self.layout_funcs.populate_combobox( - misigma, xce_object.reprocess_isigma_combobox) + misigma, xce_object.reprocess_isigma_combobox + ) xce_object.reprocess_isigma_combobox.setCurrentIndex(0) xce_object.reprocess_isigma_combobox.setStyleSheet( - " QComboBox { padding: 1px; margin: 1px }") + " QComboBox { padding: 1px; margin: 1px }" + ) # create vertical box to add labels and dropdowns to, create box and put in frame vbox_isigma = QtGui.QVBoxLayout() @@ -224,23 +261,34 @@ def setup(self, xce_object): frame_isigma.setLayout(vbox_isigma) # res limit cc half label - res_cc_label = QtGui.QLabel('Res.\nLimit:\nCC 1/2') + res_cc_label = QtGui.QLabel("Res.\nLimit:\nCC 1/2") res_cc_label.setAlignment(QtCore.Qt.AlignCenter) # res limit cc half dropdown xce_object.reprocess_cc_half_combobox = QtGui.QComboBox() - cc_half = ['default', '0.9', '0.8', '0.7', - '0.6', '0.5', '0.4', '0.3', '0.2', '0.1'] + cc_half = [ + "default", + "0.9", + "0.8", + "0.7", + "0.6", + "0.5", + "0.4", + "0.3", + "0.2", + "0.1", + ] self.layout_funcs.populate_combobox( - cc_half, xce_object.reprocess_cc_half_combobox) + cc_half, xce_object.reprocess_cc_half_combobox + ) xce_object.reprocess_cc_half_combobox.setCurrentIndex(0) xce_object.reprocess_cc_half_combobox.setStyleSheet( - " QComboBox { padding: 1px; margin: 1px }") + " QComboBox { padding: 1px; margin: 1px }" + ) # create a vbox for label and dropdown, and add items to it vbox_cc_half = QtGui.QVBoxLayout() - vbox_cc_half_widgets = [res_cc_label, - xce_object.reprocess_cc_half_combobox] + vbox_cc_half_widgets = [res_cc_label, xce_object.reprocess_cc_half_combobox] self.layout_funcs.add_to_box(vbox_cc_half, vbox_cc_half_widgets) # create frame to hold everything and add vbox @@ -249,10 +297,8 @@ def setup(self, xce_object): # create a hbox to hold the bottom frames and add everything data_protocol_hbox = QtGui.QHBoxLayout() - data_protocol_hbox_widgets = [ - frame_options, frame_isigma, frame_cc_half] - self.layout_funcs.add_to_box( - data_protocol_hbox, data_protocol_hbox_widgets) + data_protocol_hbox_widgets = [frame_options, frame_isigma, frame_cc_half] + self.layout_funcs.add_to_box(data_protocol_hbox, data_protocol_hbox_widgets) # create frame to hold everything (horizontal) bottom_options_frame = QtGui.QFrame() @@ -262,6 +308,10 @@ def setup(self, xce_object): # box to hold reprocessing subtab content xce_object.reprocess_vbox = QtGui.QVBoxLayout() xce_object.reprocess_hbox_widgets = [ - frame_select, xce_object.datasets_reprocess_table, bottom_options_frame] + frame_select, + xce_object.datasets_reprocess_table, + bottom_options_frame, + ] self.layout_funcs.add_to_box( - xce_object.reprocess_vbox, xce_object.reprocess_hbox_widgets) + xce_object.reprocess_vbox, xce_object.reprocess_hbox_widgets + ) diff --git a/gui_scripts/deposition_tab.py b/gui_scripts/deposition_tab.py index b65f1890..423cfe49 100755 --- a/gui_scripts/deposition_tab.py +++ b/gui_scripts/deposition_tab.py @@ -4,11 +4,11 @@ import os from PyQt4 import QtGui, QtCore, QtWebKit -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) -class DepositionTab(): +class DepositionTab: def __init__(self): self.layout_funcs = layout.LayoutFuncs() @@ -28,13 +28,16 @@ def setup(self, xce_object): # deposition page heading deposition_page_heading = self.layout_funcs.add_depo_heading( - 'Group deposition of bound-state structures & ground-state model') + "Group deposition of bound-state structures & ground-state model" + ) deposition_page_heading.setStyleSheet("font: bold 40pt Arial") deposition_page_introduction = QtGui.QLabel( - XChemToolTips.deposition_introduction()) + XChemToolTips.deposition_introduction() + ) deposition_page_introduction_link = QtGui.QLabel( - XChemToolTips.deposition_introduction_link()) + XChemToolTips.deposition_introduction_link() + ) deposition_page_introduction_link.setOpenExternalLinks(True) # @@ -42,238 +45,281 @@ def setup(self, xce_object): # deposition_bound_state_heading = self.layout_funcs.add_depo_heading( - 'Group deposition of bound-state structures') + "Group deposition of bound-state structures" + ) deposition_bound_state_heading.setStyleSheet("font: bold 20pt Arial") deposition_bound_state_prerequisites = self.layout_funcs.add_depo_heading( - 'Prerequisites') + "Prerequisites" + ) deposition_bound_state_prerequisites.setStyleSheet( - "font: italic bold 17pt Arial") + "font: italic bold 17pt Arial" + ) deposition_bound_state_prerequisites_text = self.layout_funcs.add_depo_text( - XChemToolTips.deposition_bound_state_prerequisites()) + XChemToolTips.deposition_bound_state_prerequisites() + ) deposition_bound_state_preparation = self.layout_funcs.add_depo_heading( - 'Procedure') + "Procedure" + ) deposition_bound_state_preparation.setStyleSheet( - "font: italic bold 17pt Arial ") - - deposition_bound_state_preparation_step_one_text = self.layout_funcs.add_depo_text( - XChemToolTips.deposition_bound_state_preparation_step_one_text()) - - xce_object.deposition_bounnd_state_preparation_ignore_event_map = QtGui.QCheckBox( - XChemToolTips.deposition_bounnd_state_preparation_ignore_event_map()) - - prepare_mmcif_button = QtGui.QPushButton('prepare mmcif') + "font: italic bold 17pt Arial " + ) + + deposition_bound_state_preparation_step_one_text = ( + self.layout_funcs.add_depo_text( + XChemToolTips.deposition_bound_state_preparation_step_one_text() + ) + ) + + xce_object.deposition_bounnd_state_preparation_ignore_event_map = ( + QtGui.QCheckBox( + XChemToolTips.deposition_bounnd_state_preparation_ignore_event_map() + ) + ) + + prepare_mmcif_button = QtGui.QPushButton("prepare mmcif") prepare_mmcif_button.clicked.connect( - xce_object.prepare_models_for_deposition_ligand_bound) + xce_object.prepare_models_for_deposition_ligand_bound + ) prepare_mmcif_button.setMaximumWidth(200) - deposition_bound_state_preparation_step_two_text = self.layout_funcs.add_depo_text( - XChemToolTips.deposition_bound_state_preparation_step_two_text()) + deposition_bound_state_preparation_step_two_text = ( + self.layout_funcs.add_depo_text( + XChemToolTips.deposition_bound_state_preparation_step_two_text() + ) + ) - copy_mmcif_button = QtGui.QPushButton('copy mmcif') + copy_mmcif_button = QtGui.QPushButton("copy mmcif") copy_mmcif_button.clicked.connect( - xce_object.prepare_for_group_deposition_upload_ligand_bound) + xce_object.prepare_for_group_deposition_upload_ligand_bound + ) copy_mmcif_button.setMaximumWidth(200) pdb_group_deposition_instruction_one = self.layout_funcs.add_depo_text( - XChemToolTips.pdb_group_deposition_instruction_one()) + XChemToolTips.pdb_group_deposition_instruction_one() + ) pdb_group_deposition_link = QtGui.QLabel( - XChemToolTips.pdb_group_deposition_link()) + XChemToolTips.pdb_group_deposition_link() + ) pdb_group_deposition_link.setOpenExternalLinks(True) pdb_group_deposition_link_two = QtGui.QLabel( - XChemToolTips.pdb_group_deposition_link()) + XChemToolTips.pdb_group_deposition_link() + ) pdb_group_deposition_link_two.setOpenExternalLinks(True) pdb_group_deposition_instruction_two = self.layout_funcs.add_depo_text( - XChemToolTips.pdb_group_deposition_instruction_two()) + XChemToolTips.pdb_group_deposition_instruction_two() + ) pdb_group_deposition_instruction_two_two = self.layout_funcs.add_depo_text( - XChemToolTips.pdb_group_deposition_instruction_two()) + XChemToolTips.pdb_group_deposition_instruction_two() + ) # # ground-state depostion # deposition_ground_state_heading = self.layout_funcs.add_depo_heading( - 'Group deposition of ground-state model') + "Group deposition of ground-state model" + ) deposition_ground_state_heading.setStyleSheet("font: bold 20pt Arial") - deposition_ground_state_preparation_step_one_text = self.layout_funcs.add_depo_text( - XChemToolTips.notification_about_changes_to_apo_deposition()) + deposition_ground_state_preparation_step_one_text = ( + self.layout_funcs.add_depo_text( + XChemToolTips.notification_about_changes_to_apo_deposition() + ) + ) deposition_ground_state_prerequisites = self.layout_funcs.add_depo_heading( - 'Prerequisites') + "Prerequisites" + ) deposition_ground_state_prerequisites.setStyleSheet( - "font: italic bold 17pt Arial") + "font: italic bold 17pt Arial" + ) deposition_ground_state_prerequisites_text = self.layout_funcs.add_depo_text( - XChemToolTips.deposition_ground_state_prerequisites()) + XChemToolTips.deposition_ground_state_prerequisites() + ) deposition_ground_state_preparation = self.layout_funcs.add_depo_heading( - 'Procedure') + "Procedure" + ) deposition_ground_state_preparation.setStyleSheet( - "font: italic bold 17pt Arial ") - -# deposition_ground_state_preparation_step_one_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_one_text()) - -# ground_state_pdb_button = QtGui.QPushButton('Select PDB file') -# ground_state_pdb_button.clicked.connect(xce_object.select_ground_state_pdb) -# ground_state_pdb_button.setMaximumWidth(200) -# xce_object.ground_state_pdb_button_label = QtGui.QLabel('') -# xce_object.ground_state_pdb_button_label.setStyleSheet('color: blue') -# -# deposition_ground_state_log_info = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_log_info()) -# -# deposition_ground_state_preparation_step_two_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_two_text()) -# -# ground_state_mtz_button = QtGui.QPushButton('Select MTZ file') -# ground_state_mtz_button.clicked.connect(xce_object.select_ground_state_mtz) -# ground_state_mtz_button.setMaximumWidth(200) -# xce_object.ground_state_mtz_button_label = QtGui.QLabel('') -# xce_object.ground_state_mtz_button_label.setStyleSheet('color: blue') - - deposition_ground_state_preparation_step_three_text = self.layout_funcs.add_depo_text( - XChemToolTips.deposition_ground_state_preparation_step_three_text()) - xce_object.ground_state_pandda_directory_label = QtGui.QLabel( - xce_object.panddas_directory) - xce_object.ground_state_pandda_directory_label.setStyleSheet( - 'color: blue') + "font: italic bold 17pt Arial " + ) - deposition_ground_state_preparation_step_four_text = self.layout_funcs.add_depo_text( - XChemToolTips.deposition_ground_state_preparation_step_four_text()) + # deposition_ground_state_preparation_step_one_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_one_text()) - add_ground_state_db_button = QtGui.QPushButton('Add to database') - add_ground_state_db_button.clicked.connect( - xce_object.add_ground_state_db) + # ground_state_pdb_button = QtGui.QPushButton('Select PDB file') + # ground_state_pdb_button.clicked.connect(xce_object.select_ground_state_pdb) + # ground_state_pdb_button.setMaximumWidth(200) + # xce_object.ground_state_pdb_button_label = QtGui.QLabel('') + # xce_object.ground_state_pdb_button_label.setStyleSheet('color: blue') + # + # deposition_ground_state_log_info = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_log_info()) + # + # deposition_ground_state_preparation_step_two_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_two_text()) + # + # ground_state_mtz_button = QtGui.QPushButton('Select MTZ file') + # ground_state_mtz_button.clicked.connect(xce_object.select_ground_state_mtz) + # ground_state_mtz_button.setMaximumWidth(200) + # xce_object.ground_state_mtz_button_label = QtGui.QLabel('') + # xce_object.ground_state_mtz_button_label.setStyleSheet('color: blue') + + deposition_ground_state_preparation_step_three_text = ( + self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_preparation_step_three_text() + ) + ) + xce_object.ground_state_pandda_directory_label = QtGui.QLabel( + xce_object.panddas_directory + ) + xce_object.ground_state_pandda_directory_label.setStyleSheet("color: blue") + + deposition_ground_state_preparation_step_four_text = ( + self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_preparation_step_four_text() + ) + ) + + add_ground_state_db_button = QtGui.QPushButton("Add to database") + add_ground_state_db_button.clicked.connect(xce_object.add_ground_state_db) add_ground_state_db_button.setMaximumWidth(200) - deposition_ground_state_preparation_step_five_text = self.layout_funcs.add_depo_text( - XChemToolTips.deposition_ground_state_preparation_step_five_text()) + deposition_ground_state_preparation_step_five_text = ( + self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_preparation_step_five_text() + ) + ) - deposition_ground_state_preparation_step_six_text = self.layout_funcs.add_depo_text( - XChemToolTips.deposition_ground_state_preparation_step_six_text()) + deposition_ground_state_preparation_step_six_text = ( + self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_preparation_step_six_text() + ) + ) - prepare_ground_state_mmcif_button = QtGui.QPushButton('Prepare mmcif') + prepare_ground_state_mmcif_button = QtGui.QPushButton("Prepare mmcif") prepare_ground_state_mmcif_button.clicked.connect( - xce_object.prepare_ground_state_mmcif) + xce_object.prepare_ground_state_mmcif + ) prepare_ground_state_mmcif_button.setMaximumWidth(200) - deposition_ground_state_preparation_step_seven_text = self.layout_funcs.add_depo_text( - XChemToolTips.deposition_ground_state_preparation_step_seven_text()) + deposition_ground_state_preparation_step_seven_text = ( + self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_preparation_step_seven_text() + ) + ) - copy_apo_mmcif_button = QtGui.QPushButton('copy mmcif') + copy_apo_mmcif_button = QtGui.QPushButton("copy mmcif") copy_apo_mmcif_button.clicked.connect( - xce_object.prepare_for_group_deposition_upload_ground_state) + xce_object.prepare_for_group_deposition_upload_ground_state + ) copy_apo_mmcif_button.setMaximumWidth(200) - deposition_ground_state_preparation_step_eight_text = self.layout_funcs.add_depo_text( - XChemToolTips.deposition_ground_state_preparation_step_eight_text()) + deposition_ground_state_preparation_step_eight_text = ( + self.layout_funcs.add_depo_text( + XChemToolTips.deposition_ground_state_preparation_step_eight_text() + ) + ) # # after ligand_bound depostion # after_deposition_heading = self.layout_funcs.add_depo_heading( - 'After deposition of ligand-bound structures') + "After deposition of ligand-bound structures" + ) after_deposition_heading.setStyleSheet("font: bold 20pt Arial") - after_deposition_preparation = self.layout_funcs.add_depo_heading( - 'Procedure') - after_deposition_preparation.setStyleSheet( - "font: italic bold 17pt Arial ") + after_deposition_preparation = self.layout_funcs.add_depo_heading("Procedure") + after_deposition_preparation.setStyleSheet("font: italic bold 17pt Arial ") after_deposition_preparation_text = self.layout_funcs.add_depo_text( - XChemToolTips.after_deposition_step_one_text()) - - -############################################### - -# deposition_html_heading = self.layout_funcs.add_depo_heading('HTML export') -# deposition_html_heading.setStyleSheet("font: 20pt Arial Bold") -# -# introduction_text = self.layout_funcs.add_depo_text(XChemToolTips.html_summary_introduction()) -# -# html_export_button = QtGui.QPushButton('Export to HTML') -# html_export_button.clicked.connect(xce_object.export_to_html) -# html_export_button.setMaximumWidth(200) - - deposition_widget_list = [deposition_page_heading, - QtGui.QLabel(' \n '), - deposition_page_introduction, deposition_page_introduction_link, - QtGui.QLabel(' \n '), - - deposition_bound_state_heading, QtGui.QLabel( - ' \n '), - deposition_bound_state_prerequisites, - deposition_bound_state_prerequisites_text, QtGui.QLabel( - ' \n '), - deposition_bound_state_preparation, - deposition_bound_state_preparation_step_one_text, - xce_object.deposition_bounnd_state_preparation_ignore_event_map, - prepare_mmcif_button, - deposition_bound_state_preparation_step_two_text, - copy_mmcif_button, - pdb_group_deposition_instruction_one, - pdb_group_deposition_link, - pdb_group_deposition_instruction_two_two, - - QtGui.QLabel(' \n\n\n '), - - after_deposition_heading, QtGui.QLabel( - ' \n '), - after_deposition_preparation, - after_deposition_preparation_text, - - QtGui.QLabel(' \n\n\n '), - - deposition_ground_state_heading, QtGui.QLabel( - ' \n '), - deposition_ground_state_preparation_step_one_text, QtGui.QLabel( - ' \n '), - deposition_ground_state_prerequisites, - deposition_ground_state_prerequisites_text, QtGui.QLabel( - ' \n '), - deposition_ground_state_preparation, - # ground_state_pdb_button, xce_object.ground_state_pdb_button_label, - # deposition_ground_state_log_info, - # deposition_ground_state_preparation_step_two_text, - # ground_state_mtz_button,xce_object.ground_state_mtz_button_label, - deposition_ground_state_preparation_step_three_text, - xce_object.ground_state_pandda_directory_label, - deposition_ground_state_preparation_step_four_text, - add_ground_state_db_button, - deposition_ground_state_preparation_step_five_text, - deposition_ground_state_preparation_step_six_text, - prepare_ground_state_mmcif_button, - deposition_ground_state_preparation_step_seven_text, - copy_apo_mmcif_button, - deposition_ground_state_preparation_step_eight_text, - pdb_group_deposition_link_two, - pdb_group_deposition_instruction_two, - - QtGui.QLabel(' \n\n\n ') - - # after_deposition_heading, QtGui.QLabel(' \n '), - # after_deposition_preparation, - # after_deposition_preparation_text - - ] - -# QtGui.QLabel(' \n\n\n '), -# -# deposition_html_heading, QtGui.QLabel(' \n '), -# introduction_text, -# html_export_button, QtGui.QLabel(' \n\n '), -# s QtGui.QLabel(' \n ')] -# -# deposition_widget_list2 = [update_html_button, QtGui.QLabel(' '), -# upload_html_heading, upload_html_text, QtGui.QLabel(' ')] + XChemToolTips.after_deposition_step_one_text() + ) + + ############################################### + + # deposition_html_heading = self.layout_funcs.add_depo_heading('HTML export') + # deposition_html_heading.setStyleSheet("font: 20pt Arial Bold") + # + # introduction_text = self.layout_funcs.add_depo_text(XChemToolTips.html_summary_introduction()) + # + # html_export_button = QtGui.QPushButton('Export to HTML') + # html_export_button.clicked.connect(xce_object.export_to_html) + # html_export_button.setMaximumWidth(200) + + deposition_widget_list = [ + deposition_page_heading, + QtGui.QLabel(" \n "), + deposition_page_introduction, + deposition_page_introduction_link, + QtGui.QLabel(" \n "), + deposition_bound_state_heading, + QtGui.QLabel(" \n "), + deposition_bound_state_prerequisites, + deposition_bound_state_prerequisites_text, + QtGui.QLabel(" \n "), + deposition_bound_state_preparation, + deposition_bound_state_preparation_step_one_text, + xce_object.deposition_bounnd_state_preparation_ignore_event_map, + prepare_mmcif_button, + deposition_bound_state_preparation_step_two_text, + copy_mmcif_button, + pdb_group_deposition_instruction_one, + pdb_group_deposition_link, + pdb_group_deposition_instruction_two_two, + QtGui.QLabel(" \n\n\n "), + after_deposition_heading, + QtGui.QLabel(" \n "), + after_deposition_preparation, + after_deposition_preparation_text, + QtGui.QLabel(" \n\n\n "), + deposition_ground_state_heading, + QtGui.QLabel(" \n "), + deposition_ground_state_preparation_step_one_text, + QtGui.QLabel(" \n "), + deposition_ground_state_prerequisites, + deposition_ground_state_prerequisites_text, + QtGui.QLabel(" \n "), + deposition_ground_state_preparation, + # ground_state_pdb_button, xce_object.ground_state_pdb_button_label, + # deposition_ground_state_log_info, + # deposition_ground_state_preparation_step_two_text, + # ground_state_mtz_button,xce_object.ground_state_mtz_button_label, + deposition_ground_state_preparation_step_three_text, + xce_object.ground_state_pandda_directory_label, + deposition_ground_state_preparation_step_four_text, + add_ground_state_db_button, + deposition_ground_state_preparation_step_five_text, + deposition_ground_state_preparation_step_six_text, + prepare_ground_state_mmcif_button, + deposition_ground_state_preparation_step_seven_text, + copy_apo_mmcif_button, + deposition_ground_state_preparation_step_eight_text, + pdb_group_deposition_link_two, + pdb_group_deposition_instruction_two, + QtGui.QLabel(" \n\n\n ") + # after_deposition_heading, QtGui.QLabel(' \n '), + # after_deposition_preparation, + # after_deposition_preparation_text + ] + + # QtGui.QLabel(' \n\n\n '), + # + # deposition_html_heading, QtGui.QLabel(' \n '), + # introduction_text, + # html_export_button, QtGui.QLabel(' \n\n '), + # s QtGui.QLabel(' \n ')] + # + # deposition_widget_list2 = [update_html_button, QtGui.QLabel(' '), + # upload_html_heading, upload_html_text, QtGui.QLabel(' ')] self.layout_funcs.add_to_box(scrollLayout, deposition_widget_list) -# scrollLayout.addLayout(hbox_zenodo_upload_id) -# self.layout_funcs.add_to_box(scrollLayout, deposition_widget_list2) + # scrollLayout.addLayout(hbox_zenodo_upload_id) + # self.layout_funcs.add_to_box(scrollLayout, deposition_widget_list2) # container settings scrollLayout.addStretch(1) diff --git a/gui_scripts/layout.py b/gui_scripts/layout.py index 8f91b0ec..a98d140c 100755 --- a/gui_scripts/layout.py +++ b/gui_scripts/layout.py @@ -17,12 +17,12 @@ from PyQt4 import QtGui, QtCore, QtWebKit from functools import partial -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'web')) -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "web")) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) -class LayoutObjects(): +class LayoutObjects: def __init__(self, xce_object): self.layout_funcs = LayoutFuncs() @@ -42,7 +42,8 @@ def initialise_menu_bar(self, xce_object): # create menu from menu dictionary menu_bar = self.layout_funcs.setup_menubar( - xce_object, menu_bar, xce_object.menu_dict) + xce_object, menu_bar, xce_object.menu_dict + ) # END OF MENU BAR - CODE BELOW: stuff removed from apo structure stuff that appears might have a funky # consequence - work out later. @@ -56,15 +57,15 @@ def initialise_menu_bar(self, xce_object): # function containing setup for bottom boxes def initialise_bottom_boxes(self, xce_object): - icons_directory = os.path.join( - (os.getenv('XChemExplorer_DIR')), 'icons') + icons_directory = os.path.join((os.getenv("XChemExplorer_DIR")), "icons") # import all buttons setup().bottom_box_buttons(xce_object) # setup datasource button - update_from_datasource_button = self.layout_funcs.setup_push_button(xce_object, - xce_object.datasource_button_dict) + update_from_datasource_button = self.layout_funcs.setup_push_button( + xce_object, xce_object.datasource_button_dict + ) ################################################################################################################ # # @@ -73,35 +74,47 @@ def initialise_bottom_boxes(self, xce_object): ################################################################################################################ # setup the run button with push button function - xce_object.dataset_task_run_button = self.layout_funcs.setup_push_button(xce_object, - xce_object.dataset_task_run_button_dict) + xce_object.dataset_task_run_button = self.layout_funcs.setup_push_button( + xce_object, xce_object.dataset_task_run_button_dict + ) # setup the task button with push button function - xce_object.dataset_task_status_button = self.layout_funcs.setup_push_button(xce_object, - xce_object.dataset_task_status_button_dict) + xce_object.dataset_task_status_button = self.layout_funcs.setup_push_button( + xce_object, xce_object.dataset_task_status_button_dict + ) # array of both button xce_objects to apply to bottom box layout - dataset_buttons = [xce_object.dataset_task_run_button, - xce_object.dataset_task_status_button] + dataset_buttons = [ + xce_object.dataset_task_run_button, + xce_object.dataset_task_status_button, + ] # label for the bottom box layout - dataset_label = str(" Datasets") + dataset_label = str( + " Datasets" + ) # return the frame and combobox from the bottom box setup function - frame_dataset_task, xce_object.dataset_tasks_combobox = self.layout_funcs.bottom_box_setup(xce_object, - dataset_label, - xce_object.dataset_tasks, - 'XChemToolTips.' - 'dataset_task_tip()', - dataset_buttons, - 'background: ' - 'rgb(240, 255, 140);') + ( + frame_dataset_task, + xce_object.dataset_tasks_combobox, + ) = self.layout_funcs.bottom_box_setup( + xce_object, + dataset_label, + xce_object.dataset_tasks, + "XChemToolTips." "dataset_task_tip()", + dataset_buttons, + "background: " "rgb(240, 255, 140);", + ) # define the combobox and buttons in dictionary key to determine behaviour - xce_object.workflow_widget_dict['Datasets'] = [xce_object.dataset_tasks_combobox, - xce_object.dataset_task_run_button, - xce_object.dataset_task_status_button] + xce_object.workflow_widget_dict["Datasets"] = [ + xce_object.dataset_tasks_combobox, + xce_object.dataset_task_run_button, + xce_object.dataset_task_status_button, + ] ################################################################################################################ # # @@ -111,38 +124,49 @@ def initialise_bottom_boxes(self, xce_object): # settings for the run button # setup the run button with push button function - xce_object.map_cif_file_task_run_button = \ - self.layout_funcs.setup_push_button(xce_object, - xce_object.map_cif_file_task_run_button_dict) + xce_object.map_cif_file_task_run_button = self.layout_funcs.setup_push_button( + xce_object, xce_object.map_cif_file_task_run_button_dict + ) # setup the task button with push button function - xce_object.map_cif_file_task_status_button = \ - self.layout_funcs.setup_push_button(xce_object, - xce_object.map_cif_file_task_status_button_dict) + xce_object.map_cif_file_task_status_button = ( + self.layout_funcs.setup_push_button( + xce_object, xce_object.map_cif_file_task_status_button_dict + ) + ) # array of both button xce_objects to apply to bottom box layout map_cif_file_buttons = [ - xce_object.map_cif_file_task_run_button, xce_object.map_cif_file_task_status_button] + xce_object.map_cif_file_task_run_button, + xce_object.map_cif_file_task_status_button, + ] # label for the bottom box layout map_cif_file_label = str( - " Maps & Restraints") + " Maps & Restraints" + ) # return the frame and combobox from the bottom box setup function - frame_map_cif_file_task, xce_object.map_cif_file_tasks_combobox = \ - self.layout_funcs.bottom_box_setup(xce_object, - map_cif_file_label, - xce_object.map_cif_file_tasks, - 'XChemToolTips.map_cif_file_' - 'task_tip()', - map_cif_file_buttons, - 'background: rgb(140, 255, ' - '150); ') + ( + frame_map_cif_file_task, + xce_object.map_cif_file_tasks_combobox, + ) = self.layout_funcs.bottom_box_setup( + xce_object, + map_cif_file_label, + xce_object.map_cif_file_tasks, + "XChemToolTips.map_cif_file_" "task_tip()", + map_cif_file_buttons, + "background: rgb(140, 255, " "150); ", + ) # define the combobox and buttons in dictionary key to determine behaviour - xce_object.workflow_widget_dict['Maps'] = [xce_object.map_cif_file_tasks_combobox, - xce_object.map_cif_file_task_run_button, - xce_object.map_cif_file_task_status_button] + xce_object.workflow_widget_dict["Maps"] = [ + xce_object.map_cif_file_tasks_combobox, + xce_object.map_cif_file_task_run_button, + xce_object.map_cif_file_task_status_button, + ] ################################################################################################################ # # @@ -152,38 +176,49 @@ def initialise_bottom_boxes(self, xce_object): # settings for the run button # setup the run button with push button function - xce_object.panddas_file_task_run_button = \ - self.layout_funcs.setup_push_button(xce_object, - xce_object.panddas_file_task_run_button_dict) + xce_object.panddas_file_task_run_button = self.layout_funcs.setup_push_button( + xce_object, xce_object.panddas_file_task_run_button_dict + ) # setup the task button with push button function - xce_object.panddas_file_task_status_button = \ - self.layout_funcs.setup_push_button(xce_object, - xce_object.panddas_file_task_status_button_dict) + xce_object.panddas_file_task_status_button = ( + self.layout_funcs.setup_push_button( + xce_object, xce_object.panddas_file_task_status_button_dict + ) + ) # array of both button xce_objects to apply to bottom box layout panddas_file_buttons = [ - xce_object.panddas_file_task_run_button, xce_object.panddas_file_task_status_button] + xce_object.panddas_file_task_run_button, + xce_object.panddas_file_task_status_button, + ] # label for the bottom box layout - panddas_file_label = str(" Hit Identification") + panddas_file_label = str( + " Hit Identification" + ) # return the frame and combobox from the bottom box setup function - frame_panddas_file_task, xce_object.panddas_file_tasks_combobox = \ - self.layout_funcs.bottom_box_setup(xce_object, - panddas_file_label, - xce_object.panddas_file_tasks, - 'XChemToolTips.panddas_file_' - 'task_tip()', - panddas_file_buttons, - 'background: rgb(140,200,255)' - '; ') + ( + frame_panddas_file_task, + xce_object.panddas_file_tasks_combobox, + ) = self.layout_funcs.bottom_box_setup( + xce_object, + panddas_file_label, + xce_object.panddas_file_tasks, + "XChemToolTips.panddas_file_" "task_tip()", + panddas_file_buttons, + "background: rgb(140,200,255)" "; ", + ) # define the combobox and buttons in dictionary key to determine behaviour - xce_object.workflow_widget_dict['PANDDAs'] = [xce_object.panddas_file_tasks_combobox, - xce_object.panddas_file_task_run_button, - xce_object.panddas_file_task_status_button] + xce_object.workflow_widget_dict["PANDDAs"] = [ + xce_object.panddas_file_tasks_combobox, + xce_object.panddas_file_task_run_button, + xce_object.panddas_file_task_status_button, + ] ################################################################################################################ # # @@ -193,49 +228,68 @@ def initialise_bottom_boxes(self, xce_object): # settings for the run button # setup the run button with push button function - xce_object.refine_file_task_run_button = \ - self.layout_funcs.setup_push_button( - xce_object, xce_object.refine_file_task_run_button_dict) + xce_object.refine_file_task_run_button = self.layout_funcs.setup_push_button( + xce_object, xce_object.refine_file_task_run_button_dict + ) # setup the task button with push button function - xce_object.refine_file_task_status_button = \ - self.layout_funcs.setup_push_button( - xce_object, xce_object.refine_file_task_status_button_dict) + xce_object.refine_file_task_status_button = self.layout_funcs.setup_push_button( + xce_object, xce_object.refine_file_task_status_button_dict + ) # array of both button xce_objects to apply to bottom box layout refine_file_buttons = [ - xce_object.refine_file_task_run_button, xce_object.refine_file_task_status_button] + xce_object.refine_file_task_run_button, + xce_object.refine_file_task_status_button, + ] # label for the bottom box layout refine_file_label = str( - " Refinement") + " Refinement" + ) # return the frame and combobox from the bottom box setup function - frame_refine_file_task, xce_object.refine_file_tasks_combobox = \ - self.layout_funcs.bottom_box_setup(xce_object, - refine_file_label, - xce_object.refine_file_tasks, - 'XChemToolTips.refine_file_task' - '_tip()', - refine_file_buttons, - 'background: rgb(245, 190, 255)' - ';') + ( + frame_refine_file_task, + xce_object.refine_file_tasks_combobox, + ) = self.layout_funcs.bottom_box_setup( + xce_object, + refine_file_label, + xce_object.refine_file_tasks, + "XChemToolTips.refine_file_task" "_tip()", + refine_file_buttons, + "background: rgb(245, 190, 255)" ";", + ) # define the combobox and buttons in dictionary key to determine behaviour - xce_object.workflow_widget_dict['Refinement'] = [xce_object.refine_file_tasks_combobox, - xce_object.refine_file_task_run_button, - xce_object.refine_file_task_status_button] - - return update_from_datasource_button, frame_dataset_task, frame_map_cif_file_task, frame_panddas_file_task, \ - frame_refine_file_task + xce_object.workflow_widget_dict["Refinement"] = [ + xce_object.refine_file_tasks_combobox, + xce_object.refine_file_task_run_button, + xce_object.refine_file_task_status_button, + ] + + return ( + update_from_datasource_button, + frame_dataset_task, + frame_map_cif_file_task, + frame_panddas_file_task, + frame_refine_file_task, + ) def main_layout(self, xce_object): # initialise menu bar menu_bar = self.initialise_menu_bar(xce_object) # initialise bottom boxes - update_from_datasource_button, frame_dataset_task, frame_map_cif_file_task, frame_panddas_file_task, \ - frame_refine_file_task = self.initialise_bottom_boxes(xce_object) + ( + update_from_datasource_button, + frame_dataset_task, + frame_map_cif_file_task, + frame_panddas_file_task, + frame_refine_file_task, + ) = self.initialise_bottom_boxes(xce_object) # Tab layout & content # -------------------- @@ -290,7 +344,8 @@ def main_layout(self, xce_object): menu_bar.setMaximumWidth(xce_object.screen.width()) vbox_main.addWidget(menu_bar) xce_object.main_tab_widget.setMaximumSize( - xce_object.screen.width(), xce_object.screen.height() - 245) + xce_object.screen.width(), xce_object.screen.height() - 245 + ) vbox_main.addWidget(xce_object.main_tab_widget) hboxTaskFrames = QtGui.QHBoxLayout() @@ -307,10 +362,10 @@ def main_layout(self, xce_object): xce_object.window.setLayout(vbox_main) - xce_object.status_bar.showMessage('Ready') + xce_object.status_bar.showMessage("Ready") xce_object.window.show() - if xce_object.data_source_file != '': + if xce_object.data_source_file != "": write_enabled = xce_object.check_write_permissions_of_data_source() if not write_enabled: xce_object.data_source_set = False @@ -323,22 +378,26 @@ def workflow(self, xce_object): ################################################################################################################ # workflow task container - order of tabs as they appear for the main window - xce_object.workflow = ['Overview', # 0 - 'Datasets', # 1 - 'Maps', # 2 - 'PANDDAs', # 3 - 'Refinement', # 4 - 'Deposition', # 6 - 'Settings'] # 5 + xce_object.workflow = [ + "Overview", # 0 + "Datasets", # 1 + "Maps", # 2 + "PANDDAs", # 3 + "Refinement", # 4 + "Deposition", # 6 + "Settings", + ] # 5 # dictionary with keys corresponding to each stage in the workflow - xce_object.workflow_dict = {xce_object.workflow[0]: 'Overview', - xce_object.workflow[1]: 'Datasets', - xce_object.workflow[2]: 'Maps', - xce_object.workflow[3]: 'PANDDAs', - xce_object.workflow[4]: 'Refinement', - xce_object.workflow[6]: 'Settings', - xce_object.workflow[5]: 'Deposition'} + xce_object.workflow_dict = { + xce_object.workflow[0]: "Overview", + xce_object.workflow[1]: "Datasets", + xce_object.workflow[2]: "Maps", + xce_object.workflow[3]: "PANDDAs", + xce_object.workflow[4]: "Refinement", + xce_object.workflow[6]: "Settings", + xce_object.workflow[5]: "Deposition", + } xce_object.workflow_widget_dict = {} @@ -346,10 +405,11 @@ def workflow(self, xce_object): xce_object.main_tab_widget = QtGui.QTabWidget() xce_object.tab_dict = {} self.layout_funcs.make_tab_dict( - xce_object.workflow, xce_object.main_tab_widget, xce_object.tab_dict) + xce_object.workflow, xce_object.main_tab_widget, xce_object.tab_dict + ) -class LayoutFuncs(): +class LayoutFuncs: def __init__(self): pass @@ -363,7 +423,7 @@ def make_tab_dict(self, tab_list, tab_widget, tab_dict): def add_checkbox(self, xce_object, checkbox, function, checkopt=False): checkbox.toggle() checkbox.setChecked(checkopt) - eval(str('checkbox.stateChanged.connect(' + function + ')')) + eval(str("checkbox.stateChanged.connect(" + function + ")")) def table_setup(self, table, table_columns, sortingopt=True): table.setColumnCount(len(table_columns)) @@ -373,62 +433,81 @@ def table_setup(self, table, table_columns, sortingopt=True): table.resizeColumnsToContents() def pandda_html(self, xce_object): - if os.path.exists(str(xce_object.panddas_directory + '/interesting_datasets')): + if os.path.exists(str(xce_object.panddas_directory + "/interesting_datasets")): print( - 'WARNING: USING RESULTS FROM OLD PANDDA ANALYSE! THIS IS NOT FULLY SUPPORTED IN XCE2') + "WARNING: USING RESULTS FROM OLD PANDDA ANALYSE! THIS IS NOT FULLY SUPPORTED IN XCE2" + ) print( - 'PLEASE CHANGE YOUR PANDDA DIRECTORY TO A NEW RUN, OR USE THE OLD VERSION OF XCE!') + "PLEASE CHANGE YOUR PANDDA DIRECTORY TO A NEW RUN, OR USE THE OLD VERSION OF XCE!" + ) xce_object.pandda_initial_html_file = str( - xce_object.panddas_directory + '/results_summareis/pandda_initial.html') + xce_object.panddas_directory + "/results_summareis/pandda_initial.html" + ) xce_object.pandda_analyse_html_file = str( - xce_object.panddas_directory + '/results_summaries/pandda_analyse.html') + xce_object.panddas_directory + "/results_summaries/pandda_analyse.html" + ) xce_object.pandda_initial_html_file = str( - xce_object.panddas_directory + '/analyses/html_summaries/' + 'pandda_initial.html') + xce_object.panddas_directory + + "/analyses/html_summaries/" + + "pandda_initial.html" + ) xce_object.pandda_analyse_html_file = str( - xce_object.panddas_directory + '/analyses/html_summaries/' + 'pandda_analyse.html') + xce_object.panddas_directory + + "/analyses/html_summaries/" + + "pandda_analyse.html" + ) xce_object.pandda_inspect_html_file = str( - xce_object.panddas_directory + '/analyses/html_summaries/' + 'pandda_inspect.html') + xce_object.panddas_directory + + "/analyses/html_summaries/" + + "pandda_inspect.html" + ) # function for datasource, run and status button setup def setup_push_button(self, xce_object, button_dict): # use iterkeys to determine order of key by letter for name in sorted(button_dict.keys()): # add current item to menu bar - button = eval( - 'QtGui.QPushButton("' + str(button_dict[name][0]) + '")') + button = eval('QtGui.QPushButton("' + str(button_dict[name][0]) + '")') # for each configuration item for button_config in button_dict[name][1]: - eval(str('button.setToolTip(' + str(button_config[0]) + ')')) - eval( - str('button.setStyleSheet("' + str(button_config[1] + '")'))) + eval(str("button.setToolTip(" + str(button_config[0]) + ")")) + eval(str('button.setStyleSheet("' + str(button_config[1] + '")'))) if len(button_config[2]) > 1: - eval(str('button.setFont(' + str(button_config[2]) + ')')) - eval( - str('button.clicked.connect(' + str(button_config[3]) + ')')) + eval(str("button.setFont(" + str(button_config[2]) + ")")) + eval(str("button.clicked.connect(" + str(button_config[3]) + ")")) return button # function to setup one of the bottom boxes - def bottom_box_setup(self, xce_object, label, dropdown_options, dropdown_tooltip, buttons, colour): + def bottom_box_setup( + self, xce_object, label, dropdown_options, dropdown_tooltip, buttons, colour + ): frame = QtGui.QFrame() frame.setFrameShape(QtGui.QFrame.StyledPanel) - frame.setStyleSheet("QFrame { " - "border-radius: 1px; padding: 0px; margin: 0px; background-color: rgb(255, 255, 255); }") + frame.setStyleSheet( + "QFrame { " + "border-radius: 1px; padding: 0px; margin: 0px; background-color: rgb(255, 255, 255); }" + ) vbox = QtGui.QVBoxLayout() label = QtGui.QLabel(label) label.setAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignVCenter) # label.setFont(xce_object.headlineLabelfont) - label.setStyleSheet(str(" QLabel { border: 1px solid rgb(184, 192, 210); border-radius: 1px;" + str(colour) + - "padding: 3px; margin: 0px; font: bold 14pt}")) + label.setStyleSheet( + str( + " QLabel { border: 1px solid rgb(184, 192, 210); border-radius: 1px;" + + str(colour) + + "padding: 3px; margin: 0px; font: bold 14pt}" + ) + ) vbox.addWidget(label) hboxAction = QtGui.QHBoxLayout() combobox = QtGui.QComboBox() for task in dropdown_options: combobox.addItem(task) - eval('combobox.setToolTip(' + str(dropdown_tooltip) + ')') + eval("combobox.setToolTip(" + str(dropdown_tooltip) + ")") combobox.setStyleSheet(" QComboBox { padding: 1px; margin: 1px }") hboxAction.addWidget(combobox) @@ -449,17 +528,16 @@ def setup_menubar(self, xce_object, menu_bar, menu_items_dict): # use iterkeys to determine order of key by letter for config in sorted(menu_items_dict.keys()): # add current item to menu bar - menu = eval( - 'menu_bar.addMenu("' + str(menu_items_dict[config][0]) + '")') + menu = eval('menu_bar.addMenu("' + str(menu_items_dict[config][0]) + '")') # for each configuration item for menu_item in menu_items_dict[config][1]: # add the drop down option action = eval( - str('QtGui.QAction("' + str(menu_item[0]) + '", xce_object.window)')) + str('QtGui.QAction("' + str(menu_item[0]) + '", xce_object.window)') + ) # add a shortcut if defined if len(menu_item[1]) > 1: - eval( - str('action.setShortcut("' + str(menu_item[1]) + '")')) + eval(str('action.setShortcut("' + str(menu_item[1]) + '")')) # connect the relevant function and add as an action try: action.triggered.connect(menu_item[2]) @@ -490,7 +568,9 @@ def add_depo_text(self, text): return out_text - def settings_section_setup(self, vbox, label_text, directory, button_text, button_function): + def settings_section_setup( + self, vbox, label_text, directory, button_text, button_function + ): vbox.addWidget(QtGui.QLabel(label_text)) hbox = QtGui.QHBoxLayout() @@ -502,49 +582,83 @@ def settings_section_setup(self, vbox, label_text, directory, button_text, butto hbox.addWidget(button) vbox.addLayout(hbox) - vbox.addWidget(QtGui.QLabel(' ')) - vbox.addWidget(QtGui.QLabel(' ')) + vbox.addWidget(QtGui.QLabel(" ")) + vbox.addWidget(QtGui.QLabel(" ")) return directory_label def add_widgets_layouts(self, xce_object): tab_add_widget = [ - [xce_object.tab_dict[xce_object.workflow_dict['Overview']] - [1], xce_object.overview_tab_widget], - [xce_object.overview_tab_dict['Data Source'] - [1], xce_object.overview_datasource_table], - [xce_object.overview_tab_dict['Summary'] - [1], xce_object.overview_canvas], - [xce_object.pandda_tab_dict['Dataset Summary'] - [1], xce_object.pandda_initial_html], - [xce_object.pandda_tab_dict['Processing Output'] - [1], xce_object.pandda_analyse_html], - [xce_object.pandda_tab_dict['pandda.inspect'][1], xce_object.pandda_inspect_html]] + [ + xce_object.tab_dict[xce_object.workflow_dict["Overview"]][1], + xce_object.overview_tab_widget, + ], + [ + xce_object.overview_tab_dict["Data Source"][1], + xce_object.overview_datasource_table, + ], + [xce_object.overview_tab_dict["Summary"][1], xce_object.overview_canvas], + [ + xce_object.pandda_tab_dict["Dataset Summary"][1], + xce_object.pandda_initial_html, + ], + [ + xce_object.pandda_tab_dict["Processing Output"][1], + xce_object.pandda_analyse_html, + ], + [ + xce_object.pandda_tab_dict["pandda.inspect"][1], + xce_object.pandda_inspect_html, + ], + ] tab_add_layout = [ - [xce_object.tab_dict[xce_object.workflow_dict['Datasets']] - [1], xce_object.datasets_data_collection_vbox], - [xce_object.datasets_tab_dict['Summary'][1], - xce_object.datasets_summarys_vbox_for_table], - [xce_object.datasets_tab_dict['Summary'][1], - xce_object.datasets_summarys_vbox_for_details], - [xce_object.datasets_tab_dict['Reprocess'] - [1], xce_object.reprocess_vbox], - [xce_object.tab_dict[xce_object.workflow_dict['Maps']] - [1], xce_object.maps_checkbutton_hbox], - [xce_object.tab_dict[xce_object.workflow_dict['Maps']] - [1], xce_object.initial_model_vbox_for_table], - [xce_object.pandda_tab_dict['Statistical Map Summaries'] - [1], xce_object.pandda_map_layout], - [xce_object.pandda_tab_dict['pandda.analyse'] - [1], xce_object.pandda_analyse_hbox], - [xce_object.tab_dict[xce_object.workflow_dict['PANDDAs']] - [1], xce_object.panddas_results_vbox], - [xce_object.tab_dict[xce_object.workflow_dict['Refinement']] - [1], xce_object.summary_vbox_for_table], - [xce_object.tab_dict[xce_object.workflow_dict['Deposition']] - [1], xce_object.deposition_vbox], - [xce_object.tab_dict[xce_object.workflow_dict['Settings']][1], xce_object.settings_vbox]] + [ + xce_object.tab_dict[xce_object.workflow_dict["Datasets"]][1], + xce_object.datasets_data_collection_vbox, + ], + [ + xce_object.datasets_tab_dict["Summary"][1], + xce_object.datasets_summarys_vbox_for_table, + ], + [ + xce_object.datasets_tab_dict["Summary"][1], + xce_object.datasets_summarys_vbox_for_details, + ], + [xce_object.datasets_tab_dict["Reprocess"][1], xce_object.reprocess_vbox], + [ + xce_object.tab_dict[xce_object.workflow_dict["Maps"]][1], + xce_object.maps_checkbutton_hbox, + ], + [ + xce_object.tab_dict[xce_object.workflow_dict["Maps"]][1], + xce_object.initial_model_vbox_for_table, + ], + [ + xce_object.pandda_tab_dict["Statistical Map Summaries"][1], + xce_object.pandda_map_layout, + ], + [ + xce_object.pandda_tab_dict["pandda.analyse"][1], + xce_object.pandda_analyse_hbox, + ], + [ + xce_object.tab_dict[xce_object.workflow_dict["PANDDAs"]][1], + xce_object.panddas_results_vbox, + ], + [ + xce_object.tab_dict[xce_object.workflow_dict["Refinement"]][1], + xce_object.summary_vbox_for_table, + ], + [ + xce_object.tab_dict[xce_object.workflow_dict["Deposition"]][1], + xce_object.deposition_vbox, + ], + [ + xce_object.tab_dict[xce_object.workflow_dict["Settings"]][1], + xce_object.settings_vbox, + ], + ] for item in tab_add_widget: item[0].addWidget(item[1]) diff --git a/gui_scripts/maps_tab.py b/gui_scripts/maps_tab.py index 89507e18..98e8f32f 100755 --- a/gui_scripts/maps_tab.py +++ b/gui_scripts/maps_tab.py @@ -3,10 +3,10 @@ import os from PyQt4 import QtGui, QtCore, QtWebKit -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) -class MapsTab(): +class MapsTab: def __init__(self): self.layout_funcs = layout.LayoutFuncs() @@ -18,53 +18,66 @@ def setup(self, xce_object): ################################################################################################################ # select box for dimple xce_object.select_sample_for_dimple_box = QtGui.QCheckBox( - '(de-)select all samples for DIMPLE') - self.layout_funcs.add_checkbox(xce_object, xce_object.select_sample_for_dimple_box, - 'xce_object.set_run_dimple_flag') + "(de-)select all samples for DIMPLE" + ) + self.layout_funcs.add_checkbox( + xce_object, + xce_object.select_sample_for_dimple_box, + "xce_object.set_run_dimple_flag", + ) # set new reference button set_new_reference_button = QtGui.QPushButton( - "Set New Reference (if applicable)") + "Set New Reference (if applicable)" + ) set_new_reference_button.clicked.connect( - xce_object.set_new_reference_if_applicable) + xce_object.set_new_reference_if_applicable + ) # refresh button refresh_reference_file_list_button = QtGui.QPushButton( - "Refresh reference file list") + "Refresh reference file list" + ) refresh_reference_file_list_button.clicked.connect( - xce_object.refresh_reference_file_list) + xce_object.refresh_reference_file_list + ) # list and populate reference files - xce_object.reference_file_list = xce_object.get_reference_file_list( - ' ') + xce_object.reference_file_list = xce_object.get_reference_file_list(" ") xce_object.reference_file_selection_combobox = QtGui.QComboBox() xce_object.populate_reference_combobox( - xce_object.reference_file_selection_combobox) + xce_object.reference_file_selection_combobox + ) # setup hbox to hold everything and add widgets xce_object.maps_checkbutton_hbox = QtGui.QHBoxLayout() - maps_checkbutton_widgets = [xce_object.select_sample_for_dimple_box, set_new_reference_button, - refresh_reference_file_list_button, xce_object.reference_file_selection_combobox] + maps_checkbutton_widgets = [ + xce_object.select_sample_for_dimple_box, + set_new_reference_button, + refresh_reference_file_list_button, + xce_object.reference_file_selection_combobox, + ] self.layout_funcs.add_to_box( - xce_object.maps_checkbutton_hbox, maps_checkbutton_widgets) + xce_object.maps_checkbutton_hbox, maps_checkbutton_widgets + ) # table setup xce_object.maps_table = QtGui.QTableWidget() self.layout_funcs.table_setup( - xce_object.maps_table, xce_object.maps_table_columns) + xce_object.maps_table, xce_object.maps_table_columns + ) # box for table, add to box, add to tab xce_object.initial_model_vbox_for_table = QtGui.QVBoxLayout() - xce_object.initial_model_vbox_for_table.addWidget( - xce_object.maps_table) + xce_object.initial_model_vbox_for_table.addWidget(xce_object.maps_table) # create context menu... no idea where this lives again. xce_object.popMenu_for_maps_table = QtGui.QMenu() - run_dimple = QtGui.QAction( - "mark selected for dimple run", xce_object.window) + run_dimple = QtGui.QAction("mark selected for dimple run", xce_object.window) run_dimple.triggered.connect(xce_object.select_sample_for_dimple) xce_object.popMenu_for_maps_table.addAction(run_dimple) xce_object.maps_table.setContextMenuPolicy(QtCore.Qt.CustomContextMenu) xce_object.maps_table.customContextMenuRequested.connect( - xce_object.on_context_menu_initial_model) + xce_object.on_context_menu_initial_model + ) diff --git a/gui_scripts/overview_tab.py b/gui_scripts/overview_tab.py index 7631e1e9..bf6fe00c 100755 --- a/gui_scripts/overview_tab.py +++ b/gui_scripts/overview_tab.py @@ -5,10 +5,10 @@ import os from PyQt4 import QtGui, QtCore, QtWebKit -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) -class OverviewTab(): +class OverviewTab: def __init__(self): self.layout_funcs = layout.LayoutFuncs() @@ -19,13 +19,16 @@ def setup(self, xce_object): # # ################################################################################################################ # define subtab list, widget and dict - overview_tab_list = ['Data Source', 'Summary'] + overview_tab_list = ["Data Source", "Summary"] xce_object.overview_tab_widget = QtGui.QTabWidget() xce_object.overview_tab_dict = {} # make subtabs self.layout_funcs.make_tab_dict( - overview_tab_list, xce_object.overview_tab_widget, xce_object.overview_tab_dict) + overview_tab_list, + xce_object.overview_tab_widget, + xce_object.overview_tab_dict, + ) # initiate the table in overview/datasource xce_object.overview_datasource_table = QtGui.QTableWidget() diff --git a/gui_scripts/pandda_tab.py b/gui_scripts/pandda_tab.py index e98f80e8..5ddaba1e 100755 --- a/gui_scripts/pandda_tab.py +++ b/gui_scripts/pandda_tab.py @@ -5,11 +5,11 @@ import multiprocessing from PyQt4 import QtGui, QtCore, QtWebKit -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) -class PanddaTab(): +class PanddaTab: def __init__(self): self.layout_funcs = layout.LayoutFuncs() @@ -20,17 +20,20 @@ def setup(self, xce_object): # # ################################################################################################################ # list of subtabs in PanDDA tab - pandda_tab_list = ['pandda.analyse', - 'Dataset Summary', - 'Processing Output', - 'pandda.inspect', - 'Statistical Map Summaries'] + pandda_tab_list = [ + "pandda.analyse", + "Dataset Summary", + "Processing Output", + "pandda.inspect", + "Statistical Map Summaries", + ] # setup tab widget, set up tab dict, and make tab dict xce_object.pandda_tab_widget = QtGui.QTabWidget() xce_object.pandda_tab_dict = {} self.layout_funcs.make_tab_dict( - pandda_tab_list, xce_object.pandda_tab_widget, xce_object.pandda_tab_dict) + pandda_tab_list, xce_object.pandda_tab_widget, xce_object.pandda_tab_dict + ) # pandda analyse subtab # setup a grid to hold everything @@ -41,21 +44,27 @@ def setup(self, xce_object): # table - left xce_object.pandda_analyse_data_table = QtGui.QTableWidget() self.layout_funcs.table_setup( - xce_object.pandda_analyse_data_table, xce_object.pandda_table_columns) + xce_object.pandda_analyse_data_table, xce_object.pandda_table_columns + ) # add table to grid frame_pandda = QtGui.QFrame() grid_pandda.addWidget(xce_object.pandda_analyse_data_table, 0, 0) # status of pandda job - under table - xce_object.pandda_status = 'UNKNOWN' + xce_object.pandda_status = "UNKNOWN" xce_object.pandda_status_label = QtGui.QLabel() # status options [filename, test to output, colour of text] - pandda_status_options = [['/pandda.done', 'Finished!', 'color: green'], - ['/pandda.running', 'Running...', 'color: orange'], - ['/pandda.errored', 'Error encountered... please check the log files for pandda!', - 'color: red']] + pandda_status_options = [ + ["/pandda.done", "Finished!", "color: green"], + ["/pandda.running", "Running...", "color: orange"], + [ + "/pandda.errored", + "Error encountered... please check the log files for pandda!", + "color: red", + ], + ] # enumerate text options and set text under table for option in pandda_status_options: @@ -64,9 +73,11 @@ def setup(self, xce_object): xce_object.pandda_status_label.setStyleSheet(option[2]) xce_object.pandda_status_label.setText( - str('STATUS: ' + xce_object.pandda_status)) + str("STATUS: " + xce_object.pandda_status) + ) xce_object.pandda_status_label.setFont( - QtGui.QFont("Arial", 25, QtGui.QFont.Bold)) + QtGui.QFont("Arial", 25, QtGui.QFont.Bold) + ) grid_pandda.addWidget(xce_object.pandda_status_label, 3, 0) header_font = QtGui.QFont() @@ -79,126 +90,135 @@ def setup(self, xce_object): # data directory section pandda_input_dir_hbox = QtGui.QHBoxLayout() - label = QtGui.QLabel('Input data directory:') + label = QtGui.QLabel("Input data directory:") label.setFont(header_font) xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_input_data_dir_entry = QtGui.QLineEdit() xce_object.pandda_input_data_dir_entry.setText( - os.path.join(xce_object.initial_model_directory, '*')) + os.path.join(xce_object.initial_model_directory, "*") + ) pandda_input_dir_hbox.addWidget(xce_object.pandda_input_data_dir_entry) xce_object.select_pandda_input_dir_button = QtGui.QPushButton( - "Select Input Template") + "Select Input Template" + ) xce_object.select_pandda_input_dir_button.clicked.connect( - xce_object.select_pandda_input_template) - pandda_input_dir_hbox.addWidget( - xce_object.select_pandda_input_dir_button) - xce_object.pandda_analyse_input_params_vbox.addLayout( - pandda_input_dir_hbox) + xce_object.select_pandda_input_template + ) + pandda_input_dir_hbox.addWidget(xce_object.select_pandda_input_dir_button) + xce_object.pandda_analyse_input_params_vbox.addLayout(pandda_input_dir_hbox) # pdb style section pandda_pdb_style_hbox = QtGui.QHBoxLayout() - label = QtGui.QLabel('pdb style') + label = QtGui.QLabel("pdb style") pandda_pdb_style_hbox.addWidget(label) xce_object.pandda_pdb_style_entry = QtGui.QLineEdit() - xce_object.pandda_pdb_style_entry.setText('dimple.pdb') + xce_object.pandda_pdb_style_entry.setText("dimple.pdb") pandda_pdb_style_hbox.addWidget(xce_object.pandda_pdb_style_entry) - xce_object.pandda_analyse_input_params_vbox.addLayout( - pandda_pdb_style_hbox) + xce_object.pandda_analyse_input_params_vbox.addLayout(pandda_pdb_style_hbox) # mtz style section pandda_mtz_style_hbox = QtGui.QHBoxLayout() - label = QtGui.QLabel('mtz style') + label = QtGui.QLabel("mtz style") pandda_mtz_style_hbox.addWidget(label) xce_object.pandda_mtz_style_entry = QtGui.QLineEdit() - xce_object.pandda_mtz_style_entry.setText('dimple.mtz') + xce_object.pandda_mtz_style_entry.setText("dimple.mtz") pandda_mtz_style_hbox.addWidget(xce_object.pandda_mtz_style_entry) - xce_object.pandda_analyse_input_params_vbox.addLayout( - pandda_mtz_style_hbox) + xce_object.pandda_analyse_input_params_vbox.addLayout(pandda_mtz_style_hbox) print((xce_object.initial_model_directory)) - data_dir_string = xce_object.initial_model_directory.replace('/*', '') + data_dir_string = xce_object.initial_model_directory.replace("/*", "") def copy_ligands(obj): - os.system(str( - 'find ' + data_dir_string + - '/*/compound -name "*.cif" | while read line; do echo ${line//"' + - data_dir_string + '"/"' + xce_object.panddas_directory + - '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' - 'done; done;')) - - os.system(str( - 'find ' + data_dir_string + - '/*/compound -name "*.pdb" | while read line; do echo ${line//"' + - data_dir_string + '"/"' + xce_object.panddas_directory + - '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' - 'done; done;')) - - print('==> XCE: Copied ligand restraints over') + os.system( + str( + "find " + + data_dir_string + + '/*/compound -name "*.cif" | while read line; do echo ${line//"' + + data_dir_string + + '"/"' + + xce_object.panddas_directory + + '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' + "done; done;" + ) + ) + + os.system( + str( + "find " + + data_dir_string + + '/*/compound -name "*.pdb" | while read line; do echo ${line//"' + + data_dir_string + + '"/"' + + xce_object.panddas_directory + + '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' + "done; done;" + ) + ) + + print("==> XCE: Copied ligand restraints over") # output directory section pandda_output_dir_hbox = QtGui.QHBoxLayout() - label = QtGui.QLabel('Output directory:') + label = QtGui.QLabel("Output directory:") label.setFont(header_font) xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_output_data_dir_entry = QtGui.QLineEdit() - xce_object.pandda_output_data_dir_entry.setText( - xce_object.panddas_directory) - pandda_output_dir_hbox.addWidget( - xce_object.pandda_output_data_dir_entry) + xce_object.pandda_output_data_dir_entry.setText(xce_object.panddas_directory) + pandda_output_dir_hbox.addWidget(xce_object.pandda_output_data_dir_entry) xce_object.select_pandda_output_dir_button = QtGui.QPushButton( - "Select PanDDA Directory") + "Select PanDDA Directory" + ) xce_object.select_pandda_output_dir_button.clicked.connect( - xce_object.settings_button_clicked) - pandda_output_dir_hbox.addWidget( - xce_object.select_pandda_output_dir_button) - xce_object.pandda_analyse_input_params_vbox.addLayout( - pandda_output_dir_hbox) + xce_object.settings_button_clicked + ) + pandda_output_dir_hbox.addWidget(xce_object.select_pandda_output_dir_button) + xce_object.pandda_analyse_input_params_vbox.addLayout(pandda_output_dir_hbox) pandda_add_ligands_button = QtGui.QPushButton( - 'Copy Ligand restraints for PanDDA') - pandda_add_ligands_button.clicked.connect( - lambda: copy_ligands(xce_object)) - xce_object.pandda_analyse_input_params_vbox.addWidget( - pandda_add_ligands_button) + "Copy Ligand restraints for PanDDA" + ) + pandda_add_ligands_button.clicked.connect(lambda: copy_ligands(xce_object)) + xce_object.pandda_analyse_input_params_vbox.addWidget(pandda_add_ligands_button) # spacer to separate out sections - spacer = QtGui.QLabel(' ') + spacer = QtGui.QLabel(" ") xce_object.pandda_analyse_input_params_vbox.addWidget(spacer) - label = QtGui.QLabel('Submission parameters') + label = QtGui.QLabel("Submission parameters") label.setFont(header_font) xce_object.pandda_analyse_input_params_vbox.addWidget(label) # qstat or local machine - label = QtGui.QLabel('Submit via:') + label = QtGui.QLabel("Submit via:") xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_submission_mode_selection_combobox = QtGui.QComboBox() - if xce_object.external_software['qsub']: - xce_object.pandda_submission_mode_selection_combobox.addItem( - 'qsub') - xce_object.pandda_submission_mode_selection_combobox.addItem( - 'local machine') + if xce_object.external_software["qsub"]: + xce_object.pandda_submission_mode_selection_combobox.addItem("qsub") + xce_object.pandda_submission_mode_selection_combobox.addItem("local machine") xce_object.pandda_analyse_input_params_vbox.addWidget( - xce_object.pandda_submission_mode_selection_combobox) + xce_object.pandda_submission_mode_selection_combobox + ) # number of processors section - label = QtGui.QLabel('Number of processors:') + label = QtGui.QLabel("Number of processors:") xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_nproc = multiprocessing.cpu_count() - 1 xce_object.pandda_nproc_entry = QtGui.QLineEdit() xce_object.pandda_nproc_entry.setText( - str(xce_object.pandda_nproc).replace(' ', '')) + str(xce_object.pandda_nproc).replace(" ", "") + ) xce_object.pandda_analyse_input_params_vbox.addWidget( - xce_object.pandda_nproc_entry) + xce_object.pandda_nproc_entry + ) xce_object.pandda_analyse_input_params_vbox.addWidget(spacer) params_hbox = QtGui.QHBoxLayout() - label = QtGui.QLabel('PanDDA parameters') + label = QtGui.QLabel("PanDDA parameters") label.setFont(header_font) params_hbox.addWidget(label) - url_html = "For docs: click here" + url_html = 'For docs: click here' label = QtGui.QLabel() label.setText(url_html) label.setOpenExternalLinks(True) @@ -208,80 +228,93 @@ def copy_ligands(obj): xce_object.pandda_analyse_input_params_vbox.addLayout(params_hbox) # checkbox for wilson scaling - xce_object.wilson_checkbox = QtGui.QCheckBox('Wilson B-factor Scaling') + xce_object.wilson_checkbox = QtGui.QCheckBox("Wilson B-factor Scaling") self.layout_funcs.add_checkbox( - xce_object, xce_object.wilson_checkbox, 'xce_object.set_run_dimple_flag') + xce_object, xce_object.wilson_checkbox, "xce_object.set_run_dimple_flag" + ) xce_object.pandda_analyse_input_params_vbox.addWidget( - xce_object.wilson_checkbox) + xce_object.wilson_checkbox + ) # crystal form option - label = QtGui.QLabel('Use space group of reference file as filter:') + label = QtGui.QLabel("Use space group of reference file as filter:") xce_object.pandda_analyse_input_params_vbox.addWidget(label) # reference file combobox, label with spg display hbox = QtGui.QHBoxLayout() # xce_object.reference_file_list = xce_object.get_reference_file_list('') xce_object.pandda_reference_file_selection_combobox = QtGui.QComboBox() xce_object.populate_reference_combobox( - xce_object.pandda_reference_file_selection_combobox) + xce_object.pandda_reference_file_selection_combobox + ) xce_object.pandda_reference_file_selection_combobox.activated[str].connect( - xce_object.change_pandda_spg_label) + xce_object.change_pandda_spg_label + ) hbox.addWidget(xce_object.pandda_reference_file_selection_combobox) xce_object.pandda_reference_file_spg_label = QtGui.QLabel() hbox.addWidget(xce_object.pandda_reference_file_spg_label) xce_object.pandda_analyse_input_params_vbox.addLayout(hbox) # how to order events - label = QtGui.QLabel('Order events by:') + label = QtGui.QLabel("Order events by:") xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_sort_event_combobox = QtGui.QComboBox() - pandda_events = ['cluster_size', 'z_peak'] + pandda_events = ["cluster_size", "z_peak"] self.layout_funcs.populate_combobox( - pandda_events, xce_object.pandda_sort_event_combobox) + pandda_events, xce_object.pandda_sort_event_combobox + ) xce_object.pandda_analyse_input_params_vbox.addWidget( - xce_object.pandda_sort_event_combobox) + xce_object.pandda_sort_event_combobox + ) # how calculate mean map - label = QtGui.QLabel('Calculate average map by:') + label = QtGui.QLabel("Calculate average map by:") xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_calc_map_combobox = QtGui.QComboBox() - average_map = ['mean_map', 'median_map'] + average_map = ["mean_map", "median_map"] self.layout_funcs.populate_combobox( - average_map, xce_object.pandda_calc_map_combobox) + average_map, xce_object.pandda_calc_map_combobox + ) xce_object.pandda_analyse_input_params_vbox.addWidget( - xce_object.pandda_calc_map_combobox) + xce_object.pandda_calc_map_combobox + ) # minimum number of datasets - label = QtGui.QLabel('min_build_datasets') + label = QtGui.QLabel("min_build_datasets") xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_min_build_dataset_entry = QtGui.QLineEdit() - xce_object.pandda_min_build_dataset_entry.setText('40') + xce_object.pandda_min_build_dataset_entry.setText("40") xce_object.pandda_analyse_input_params_vbox.addWidget( - xce_object.pandda_min_build_dataset_entry) + xce_object.pandda_min_build_dataset_entry + ) # maximum number of datasets - label = QtGui.QLabel('max_new_datasets') + label = QtGui.QLabel("max_new_datasets") xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_max_new_datasets_entry = QtGui.QLineEdit() - xce_object.pandda_max_new_datasets_entry.setText('300') + xce_object.pandda_max_new_datasets_entry.setText("300") xce_object.pandda_analyse_input_params_vbox.addWidget( - xce_object.pandda_max_new_datasets_entry) + xce_object.pandda_max_new_datasets_entry + ) # grid spacing label = QtGui.QLabel( - 'grid_spacing (default=0.5)\nNote: higher values speed up calculations, but maps might be less pretty)') + "grid_spacing (default=0.5)\nNote: higher values speed up calculations, but maps might be less pretty)" + ) xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_grid_spacing_entry = QtGui.QLineEdit() - xce_object.pandda_grid_spacing_entry.setText('0.5') + xce_object.pandda_grid_spacing_entry.setText("0.5") xce_object.pandda_analyse_input_params_vbox.addWidget( - xce_object.pandda_grid_spacing_entry) + xce_object.pandda_grid_spacing_entry + ) # keyword arguments (pandda2) - label = QtGui.QLabel('keyword arguments (pandda2 only)') + label = QtGui.QLabel("keyword arguments (pandda2 only)") xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_keyword_arguments_entry = QtGui.QLineEdit() - xce_object.pandda_keyword_arguments_entry.setText('') + xce_object.pandda_keyword_arguments_entry.setText("") xce_object.pandda_analyse_input_params_vbox.addWidget( - xce_object.pandda_keyword_arguments_entry) + xce_object.pandda_keyword_arguments_entry + ) frame_right.setLayout(xce_object.pandda_analyse_input_params_vbox) @@ -295,9 +328,12 @@ def copy_ligands(obj): # statistical map summaries vbox, add to vbox and add to layout xce_object.pandda_map_layout = QtGui.QVBoxLayout() pandda_map_layout_widgets = [ - xce_object.pandda_map_list, xce_object.pandda_maps_html] + xce_object.pandda_map_list, + xce_object.pandda_maps_html, + ] self.layout_funcs.add_to_box( - xce_object.pandda_map_layout, pandda_map_layout_widgets) + xce_object.pandda_map_layout, pandda_map_layout_widgets + ) xce_object.pandda_maps_html.show() xce_object.pandda_analyse_hbox = QtGui.QHBoxLayout() @@ -309,43 +345,54 @@ def copy_ligands(obj): xce_object.popMenu_for_pandda_table = QtGui.QMenu() ignore = QtGui.QAction("ignore selected", xce_object.window) exclude_characterisation = QtGui.QAction( - "exclude selected from characterisation", xce_object.window) + "exclude selected from characterisation", xce_object.window + ) exclude_zmap = QtGui.QAction( - "exclude selected from z-map analysis", xce_object.window) + "exclude selected from z-map analysis", xce_object.window + ) deselect = QtGui.QAction("deselect highlighted", xce_object.window) ignore.triggered.connect( - lambda: xce_object.select_sample_for_pandda(option='ignore')) + lambda: xce_object.select_sample_for_pandda(option="ignore") + ) exclude_characterisation.triggered.connect( - lambda: xce_object.select_sample_for_pandda(option='char')) + lambda: xce_object.select_sample_for_pandda(option="char") + ) exclude_zmap.triggered.connect( - lambda: xce_object.select_sample_for_pandda(option='zmap')) + lambda: xce_object.select_sample_for_pandda(option="zmap") + ) deselect.triggered.connect( - lambda: xce_object.select_sample_for_pandda(option='deselect')) + lambda: xce_object.select_sample_for_pandda(option="deselect") + ) xce_object.popMenu_for_pandda_table.addAction(ignore) xce_object.popMenu_for_pandda_table.addAction(exclude_characterisation) xce_object.popMenu_for_pandda_table.addAction(exclude_zmap) xce_object.popMenu_for_pandda_table.addAction(deselect) xce_object.pandda_analyse_data_table.setContextMenuPolicy( - QtCore.Qt.CustomContextMenu) + QtCore.Qt.CustomContextMenu + ) xce_object.pandda_analyse_data_table.customContextMenuRequested.connect( - xce_object.on_context_menu_pandda) + xce_object.on_context_menu_pandda + ) # next three blocks display html documents created by pandda.analyse self.layout_funcs.pandda_html(xce_object) xce_object.pandda_initial_html = QtWebKit.QWebView() xce_object.pandda_initial_html.load( - QtCore.QUrl(xce_object.pandda_initial_html_file)) + QtCore.QUrl(xce_object.pandda_initial_html_file) + ) xce_object.pandda_initial_html.show() xce_object.pandda_analyse_html = QtWebKit.QWebView() xce_object.pandda_analyse_html.load( - QtCore.QUrl(xce_object.pandda_analyse_html_file)) + QtCore.QUrl(xce_object.pandda_analyse_html_file) + ) xce_object.pandda_analyse_html.show() xce_object.pandda_inspect_html = QtWebKit.QWebView() xce_object.pandda_analyse_html.load( - QtCore.QUrl(xce_object.pandda_inspect_html_file)) + QtCore.QUrl(xce_object.pandda_inspect_html_file) + ) xce_object.pandda_analyse_html.show() xce_object.panddas_results_vbox = QtGui.QVBoxLayout() diff --git a/gui_scripts/refinement_tab.py b/gui_scripts/refinement_tab.py index dd8c7578..6af3c3b0 100755 --- a/gui_scripts/refinement_tab.py +++ b/gui_scripts/refinement_tab.py @@ -3,10 +3,10 @@ import os from PyQt4 import QtGui, QtCore, QtWebKit -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) -class RefinementTab(): +class RefinementTab: def __init__(self): self.layout_funcs = layout.LayoutFuncs() @@ -21,6 +21,6 @@ def setup(self, xce_object): # table xce_object.refinement_table = QtGui.QTableWidget() self.layout_funcs.table_setup( - xce_object.refinement_table, xce_object.refinement_table_columns) - xce_object.summary_vbox_for_table.addWidget( - xce_object.refinement_table) + xce_object.refinement_table, xce_object.refinement_table_columns + ) + xce_object.summary_vbox_for_table.addWidget(xce_object.refinement_table) diff --git a/gui_scripts/settings_preferences.py b/gui_scripts/settings_preferences.py index 72cc11fe..7d9646fc 100755 --- a/gui_scripts/settings_preferences.py +++ b/gui_scripts/settings_preferences.py @@ -10,34 +10,33 @@ from functools import partial import webbrowser -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'web')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "web")) -class setup(): +class setup: def __init__(self): pass def openFile(self, file): - if sys.platform == 'linux2': + if sys.platform == "linux2": subprocess.call(["xdg-open", file]) else: os.startfile(file) def set_xce_logfile(self, xce_object): - XChemLog.startLog(xce_object.xce_logfile).create_logfile( - xce_object.xce_version) + XChemLog.startLog(xce_object.xce_logfile).create_logfile(xce_object.xce_version) xce_object.update_log = XChemLog.updateLog(xce_object.xce_logfile) def settings(self, xce_object): # set XCE version - xce_object.xce_version = 'v1.9.4' + xce_object.xce_version = "v1.9.4" # general settings xce_object.allowed_unitcell_difference_percent = 12 xce_object.acceptable_low_resolution_limit_for_data = 3.5 - xce_object.filename_root = '${samplename}' + xce_object.filename_root = "${samplename}" xce_object.data_source_set = False xce_object.max_queue_jobs = 100 @@ -45,67 +44,110 @@ def settings(self, xce_object): # set current directory and direct log to it xce_object.current_directory = os.getcwd() - xce_object.xce_logfile = os.path.join( - xce_object.current_directory, 'xce.log') + xce_object.xce_logfile = os.path.join(xce_object.current_directory, "xce.log") # if in the correct place, set the various directories - if xce_object.current_directory.startswith('/dls/labxchem'): + if xce_object.current_directory.startswith("/dls/labxchem"): # if 'labxchem' in xce_object.current_directory: - if len(xce_object.current_directory.split('/')) >= 9 and xce_object.current_directory.split('/')[6] == 'processing' and xce_object.current_directory.split('/')[8] == 'processing': - xce_object.labxchem_directory = '/' + os.path.join( - *xce_object.current_directory.split('/')[1:8]) # need splat operator: * - xce_object.labxchem_directory_current = '/' + os.path.join( - *xce_object.current_directory.split('/')[1:9]) # labxchem_directory_current is where they actually have write permission + if ( + len(xce_object.current_directory.split("/")) >= 9 + and xce_object.current_directory.split("/")[6] == "processing" + and xce_object.current_directory.split("/")[8] == "processing" + ): + xce_object.labxchem_directory = "/" + os.path.join( + *xce_object.current_directory.split("/")[1:8] + ) # need splat operator: * + xce_object.labxchem_directory_current = "/" + os.path.join( + *xce_object.current_directory.split("/")[1:9] + ) # labxchem_directory_current is where they actually have write permission else: - xce_object.labxchem_directory = '/' + os.path.join( - *xce_object.current_directory.split('/')[1:6]) # need splat operator: * - xce_object.labxchem_directory_current = '/' + os.path.join( - *xce_object.current_directory.split('/')[1:7]) # need splat operator: * -# xce_object.labxchem_directory = '/' + os.path.join( -# *xce_object.current_directory.split('/')[1:6]) # need splat operator: * + xce_object.labxchem_directory = "/" + os.path.join( + *xce_object.current_directory.split("/")[1:6] + ) # need splat operator: * + xce_object.labxchem_directory_current = "/" + os.path.join( + *xce_object.current_directory.split("/")[1:7] + ) # need splat operator: * + # xce_object.labxchem_directory = '/' + os.path.join( + # *xce_object.current_directory.split('/')[1:6]) # need splat operator: * xce_object.beamline_directory = os.path.join( - xce_object.labxchem_directory, 'processing', 'beamline') - if os.path.isdir(os.path.join(xce_object.labxchem_directory, 'processing', 'analysis', 'model_building')): - xce_object.initial_model_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'analysis', - 'model_building') + xce_object.labxchem_directory, "processing", "beamline" + ) + if os.path.isdir( + os.path.join( + xce_object.labxchem_directory, + "processing", + "analysis", + "model_building", + ) + ): + xce_object.initial_model_directory = os.path.join( + xce_object.labxchem_directory, + "processing", + "analysis", + "model_building", + ) else: - xce_object.initial_model_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'analysis', - 'initial_model') + xce_object.initial_model_directory = os.path.join( + xce_object.labxchem_directory, + "processing", + "analysis", + "initial_model", + ) xce_object.reference_directory = os.path.join( - xce_object.labxchem_directory, 'processing', 'reference') + xce_object.labxchem_directory, "processing", "reference" + ) xce_object.database_directory = os.path.join( - xce_object.labxchem_directory, 'processing', 'database') - xce_object.panddas_directory = os.path.join(xce_object.labxchem_directory, 'processing', 'analysis', - 'panddas') + xce_object.labxchem_directory, "processing", "database" + ) + xce_object.panddas_directory = os.path.join( + xce_object.labxchem_directory, "processing", "analysis", "panddas" + ) xce_object.datasets_summary_file = None -# xce_object.datasets_summary_file = os.path.join(xce_object.database_directory, -# str(os.getcwd().split('/')[5]) + '_summary.pkl') - xce_object.data_source_file = '' + # xce_object.datasets_summary_file = os.path.join(xce_object.database_directory, + # str(os.getcwd().split('/')[5]) + '_summary.pkl') + xce_object.data_source_file = "" xce_object.html_export_directory = os.path.join( - xce_object.labxchem_directory, 'processing', 'html') - xce_object.group_deposit_directory = os.path.join(xce_object.labxchem_directory, 'processing', - 'group_deposition') + xce_object.labxchem_directory, "processing", "html" + ) + xce_object.group_deposit_directory = os.path.join( + xce_object.labxchem_directory, "processing", "group_deposition" + ) if os.path.isfile( - os.path.join(xce_object.labxchem_directory, 'processing', 'database', 'soakDBDataFile.sqlite')): - xce_object.data_source_file = 'soakDBDataFile.sqlite' + os.path.join( + xce_object.labxchem_directory, + "processing", + "database", + "soakDBDataFile.sqlite", + ) + ): + xce_object.data_source_file = "soakDBDataFile.sqlite" xce_object.database_directory = os.path.join( - xce_object.labxchem_directory, 'processing', 'database') + xce_object.labxchem_directory, "processing", "database" + ) xce_object.data_source_set = True xce_object.db = XChemDB.data_source( - os.path.join(xce_object.database_directory, xce_object.data_source_file)) + os.path.join( + xce_object.database_directory, xce_object.data_source_file + ) + ) xce_object.db.create_missing_columns() xce_object.ccp4_scratch_directory = os.path.join( - xce_object.labxchem_directory, 'processing', 'tmp') - - directory_list = [xce_object.beamline_directory, os.path.join(xce_object.labxchem_directory, - 'processing', 'analysis'), - xce_object.initial_model_directory, xce_object.panddas_directory, - xce_object.reference_directory, - xce_object.database_directory, xce_object.ccp4_scratch_directory, - xce_object.html_export_directory, - xce_object.group_deposit_directory] + xce_object.labxchem_directory, "processing", "tmp" + ) + + directory_list = [ + xce_object.beamline_directory, + os.path.join(xce_object.labxchem_directory, "processing", "analysis"), + xce_object.initial_model_directory, + xce_object.panddas_directory, + xce_object.reference_directory, + xce_object.database_directory, + xce_object.ccp4_scratch_directory, + xce_object.html_export_directory, + xce_object.group_deposit_directory, + ] for directory in directory_list: if not os.path.isdir(directory): @@ -118,10 +160,10 @@ def settings(self, xce_object): xce_object.initial_model_directory = xce_object.current_directory xce_object.reference_directory = xce_object.current_directory xce_object.database_directory = xce_object.current_directory - xce_object.data_source_file = '' - xce_object.ccp4_scratch_directory = os.getenv('CCP4_SCR') + xce_object.data_source_file = "" + xce_object.ccp4_scratch_directory = os.getenv("CCP4_SCR") xce_object.panddas_directory = xce_object.current_directory - xce_object.datasets_summary_file = '' + xce_object.datasets_summary_file = "" xce_object.group_deposit_directory = xce_object.current_directory # deposition @@ -132,7 +174,7 @@ def settings(self, xce_object): xce_object.data_collection_list = [] xce_object.visit_list = [] - xce_object.target = '' + xce_object.target = "" xce_object.dataset_outcome_combobox_dict = {} xce_object.data_collection_dict = {} xce_object.xtal_db_dict = {} @@ -142,10 +184,9 @@ def settings(self, xce_object): # contains toggle button if dimple should be run xce_object.initial_model_dimple_dict = {} xce_object.reference_file_list = [] - xce_object.all_columns_in_data_source = XChemDB.data_source(os.path.join - (xce_object.database_directory, - xce_object.data_source_file)) \ - .return_column_list() + xce_object.all_columns_in_data_source = XChemDB.data_source( + os.path.join(xce_object.database_directory, xce_object.data_source_file) + ).return_column_list() # using dials.image_viewer instead of albula, but keep name for dictionary xce_object.albula_button_dict = {} xce_object.xtalform_dict = {} @@ -161,8 +202,10 @@ def settings(self, xce_object): xce_object.timer_to_check_for_new_data_collection = QtCore.QTimer() xce_object.agamemnon = False - xce_object.target_list, xce_object.visit_list = XChemMain.get_target_and_visit_list( - xce_object.beamline_directory, False) + ( + xce_object.target_list, + xce_object.visit_list, + ) = XChemMain.get_target_and_visit_list(xce_object.beamline_directory, False) xce_object.diffraction_data_dict = {} @@ -179,24 +222,28 @@ def settings(self, xce_object): # can be any widget to be displayed in data collection summary tab xce_object.data_collection_details_currently_on_display = None - xce_object.dataset_outcome = ["success", - "Failed - centring failed", - "Failed - no diffraction", - "Failed - processing", - "Failed - loop empty", - "Failed - loop broken", - "Failed - low resolution", - "Failed - no X-rays", - "Failed - unknown"] - - xce_object.refinement_stage = ['0 - All Datasets', - '1 - Analysis Pending', - '2 - PANDDA model', - '3 - In Refinement', - '4 - CompChem ready', - '5 - Deposition ready', - '6 - Deposited', - '7 - Analysed & Rejected'] + xce_object.dataset_outcome = [ + "success", + "Failed - centring failed", + "Failed - no diffraction", + "Failed - processing", + "Failed - loop empty", + "Failed - loop broken", + "Failed - low resolution", + "Failed - no X-rays", + "Failed - unknown", + ] + + xce_object.refinement_stage = [ + "0 - All Datasets", + "1 - Analysis Pending", + "2 - PANDDA model", + "3 - In Refinement", + "4 - CompChem ready", + "5 - Deposition ready", + "6 - Deposited", + "7 - Analysed & Rejected", + ] self.set_xce_logfile(xce_object) @@ -205,87 +252,104 @@ def settings(self, xce_object): xce_object.remote_qsub_submission = "/usr/bin/ssh @nx.diamond.ac.uk 'module load global/cluster; qsub'" xce_object.update_log = XChemLog.updateLog(xce_object.xce_logfile) - xce_object.update_log.insert('new session started') + xce_object.update_log.insert("new session started") xce_object.diffraction_data_directory = xce_object.current_directory - xce_object.diffraction_data_search_info = 'n/a' - xce_object.diffraction_data_reference_mtz = 'ignore' + xce_object.diffraction_data_search_info = "n/a" + xce_object.diffraction_data_reference_mtz = "ignore" xce_object.html_export_directory = os.getcwd() xce_object.external_software = XChemUtils.external_software( - xce_object.xce_logfile).check() + xce_object.xce_logfile + ).check() xce_object.second_cif_file = None - software_list = ['acedrg', 'phenix.elbow', 'grade'] + software_list = ["acedrg", "phenix.elbow", "grade"] for software in software_list: if xce_object.external_software[software]: xce_object.restraints_program = str(software) - xce_object.update_log.insert('will use ' + str(software) + ' for generation of ligand coordinates and' - ' restraints') + xce_object.update_log.insert( + "will use " + + str(software) + + " for generation of ligand coordinates and" + " restraints" + ) else: - xce_object.restraints_program = '' + xce_object.restraints_program = "" xce_object.update_log.warning( - 'No program for generation of ligand coordinates and restraints available!') + "No program for generation of ligand coordinates and restraints available!" + ) def preferences(self, xce_object): # preferences xce_object.preferences_data_to_copy = [ - ['aimless logiles and merged mtz only', 'mtz_log_only'], ] + ["aimless logiles and merged mtz only", "mtz_log_only"], + ] # ['All Files in the respective auto-processing directory','everything'], - xce_object.preferences_selection_mechanism = ['IsigI*Comp*UniqueRefl', - 'highest_resolution', - 'lowest_Rfree', - 'dials - only', - # 'xia2 3d - only', - 'xia2 3dii - only', - 'autoProc - only', - 'autoProc_staraniso - only'] + xce_object.preferences_selection_mechanism = [ + "IsigI*Comp*UniqueRefl", + "highest_resolution", + "lowest_Rfree", + "dials - only", + # 'xia2 3d - only', + "xia2 3dii - only", + "autoProc - only", + "autoProc_staraniso - only", + ] xce_object.allowed_unitcell_difference_percent = 12 xce_object.acceptable_low_resolution_limit_for_data = 3.5 - xce_object.filename_root = '${samplename}' + xce_object.filename_root = "${samplename}" xce_object.max_queue_jobs = 100 xce_object.dimple_twin_mode = False - xce_object.preferences_initial_refinement_pipeline = ['dimple', - 'pipedream', - 'phenix.ligand_pipeline'] + xce_object.preferences_initial_refinement_pipeline = [ + "dimple", + "pipedream", + "phenix.ligand_pipeline", + ] - xce_object.preferences = {'processed_data_to_copy': 'mtz_log_only', - 'dataset_selection_mechanism': 'IsigI*Comp*UniqueRefl', - 'allowed_unitcell_difference_percent': 12, - 'acceptable_low_resolution_limit_for_data': 3.5, - 'acceptable_low_resolution_Rmerge': 0.1, - 'filename_root': '${samplename}', - 'max_queue_jobs': 100, - 'dimple_twin_mode': False, - 'initial_refinement_pipeline': 'dimple'} + xce_object.preferences = { + "processed_data_to_copy": "mtz_log_only", + "dataset_selection_mechanism": "IsigI*Comp*UniqueRefl", + "allowed_unitcell_difference_percent": 12, + "acceptable_low_resolution_limit_for_data": 3.5, + "acceptable_low_resolution_Rmerge": 0.1, + "filename_root": "${samplename}", + "max_queue_jobs": 100, + "dimple_twin_mode": False, + "initial_refinement_pipeline": "dimple", + } # settings - xce_object.settings = {'current_directory': xce_object.current_directory, - 'beamline_directory': xce_object.beamline_directory, - 'datasets_summary': xce_object.datasets_summary_file, - 'initial_model_directory': xce_object.initial_model_directory, - 'panddas_directory': xce_object.panddas_directory, - 'reference_directory': xce_object.reference_directory, - 'database_directory': xce_object.database_directory, - 'data_source': os.path.join(xce_object.database_directory, xce_object.data_source_file), - 'ccp4_scratch': xce_object.ccp4_scratch_directory, - 'unitcell_difference': xce_object.allowed_unitcell_difference_percent, - 'too_low_resolution_data': xce_object.acceptable_low_resolution_limit_for_data, - 'filename_root': xce_object.filename_root, - 'preferences': xce_object.preferences, - 'xce_logfile': xce_object.xce_logfile, - 'max_queue_jobs': xce_object.max_queue_jobs, - 'diffraction_data_directory': xce_object.diffraction_data_directory, - 'html_export_directory': xce_object.html_export_directory, - 'group_deposit_directory': xce_object.group_deposit_directory, - 'remote_qsub': '', - 'dimple_twin_mode': False, - 'agamemnon': False} + xce_object.settings = { + "current_directory": xce_object.current_directory, + "beamline_directory": xce_object.beamline_directory, + "datasets_summary": xce_object.datasets_summary_file, + "initial_model_directory": xce_object.initial_model_directory, + "panddas_directory": xce_object.panddas_directory, + "reference_directory": xce_object.reference_directory, + "database_directory": xce_object.database_directory, + "data_source": os.path.join( + xce_object.database_directory, xce_object.data_source_file + ), + "ccp4_scratch": xce_object.ccp4_scratch_directory, + "unitcell_difference": xce_object.allowed_unitcell_difference_percent, + "too_low_resolution_data": xce_object.acceptable_low_resolution_limit_for_data, + "filename_root": xce_object.filename_root, + "preferences": xce_object.preferences, + "xce_logfile": xce_object.xce_logfile, + "max_queue_jobs": xce_object.max_queue_jobs, + "diffraction_data_directory": xce_object.diffraction_data_directory, + "html_export_directory": xce_object.html_export_directory, + "group_deposit_directory": xce_object.group_deposit_directory, + "remote_qsub": "", + "dimple_twin_mode": False, + "agamemnon": False, + } def tables(self, xce_object): # Table column settings @@ -297,16 +361,18 @@ def tables(self, xce_object): # - populate_and_update_datasource_table() - used within select_datasource_columns_to_display and # update_all_tables() - xce_object.overview_datasource_table_columns = ['Sample ID', - 'Compound ID', - 'Smiles', - 'Visit', - 'Resolution\n[Mn = 1.5]', - 'Refinement\nRfree', - 'Data Collection\nDate', - 'Puck', - 'PuckPosition', - 'Ligand\nConfidence'] + xce_object.overview_datasource_table_columns = [ + "Sample ID", + "Compound ID", + "Smiles", + "Visit", + "Resolution\n[Mn = 1.5]", + "Refinement\nRfree", + "Data Collection\nDate", + "Puck", + "PuckPosition", + "Ligand\nConfidence", + ] # functions that use tables.datasets_summary_table_columns: # @@ -314,110 +380,119 @@ def tables(self, xce_object): # - user_update_selected_autoproc_datasets_summary_table() # - appears in create_widgets_for_autoprocessing_results_only() - xce_object.datasets_summary_table_columns = ['Sample ID', - # 'Resolution\n[Mn = 2.0]', - 'Resolution\nHigh', - 'DataProcessing\nSpaceGroup', - 'DataProcessing\nRfree', - 'SoakDB\nBarcode', - 'GDA\nBarcode', - 'Rmerge\nLow', - 'auto-assigned', - 'DataCollection\nOutcome', - 'img1', - 'img2', - 'img3', - 'img4' - # 'img5', - # 'Show\nDetails', - # 'Show Diffraction\nImage' - ] + xce_object.datasets_summary_table_columns = [ + "Sample ID", + # 'Resolution\n[Mn = 2.0]', + "Resolution\nHigh", + "DataProcessing\nSpaceGroup", + "DataProcessing\nRfree", + "SoakDB\nBarcode", + "GDA\nBarcode", + "Rmerge\nLow", + "auto-assigned", + "DataCollection\nOutcome", + "img1", + "img2", + "img3", + "img4" + # 'img5', + # 'Show\nDetails', + # 'Show Diffraction\nImage' + ] # functions that use tables.data_collection_table_columns: # # - show_results_from_all_pipelines() - appears in populate_datasets_summary_table() - xce_object.data_collection_table_columns = ['Sample ID', - 'Visit', - 'Run', - 'Program', - 'Resolution\nOverall', - 'Resolution\nHigh', - 'DataProcessing\nSpaceGroup', - 'Mn\nHigh', - 'Rmerge\nLow', - 'Completeness\nOverall', - 'DataProcessing\nUnitCell', - 'DataProcessing\nRfree', - 'DataProcessing\nScore' - ] + xce_object.data_collection_table_columns = [ + "Sample ID", + "Visit", + "Run", + "Program", + "Resolution\nOverall", + "Resolution\nHigh", + "DataProcessing\nSpaceGroup", + "Mn\nHigh", + "Rmerge\nLow", + "Completeness\nOverall", + "DataProcessing\nUnitCell", + "DataProcessing\nRfree", + "DataProcessing\nScore", + ] # functions that use tables.datasets_reprocess_columns: # # - update_datasets_reprocess_table() - appears in search_for_datasets() - xce_object.datasets_reprocess_columns = ['Dataset ID', - 'Sample ID', - 'Run\nxia2', - # 'Resolution\n[Mn = 1.5]', - 'Resolution\nHigh', - 'Rmerge\nLow', - 'Dimple\nRfree', - 'DataProcessing\nSpaceGroup', - 'DataProcessing\nUnitCell', - 'DataProcessing\nStatus'] + xce_object.datasets_reprocess_columns = [ + "Dataset ID", + "Sample ID", + "Run\nxia2", + # 'Resolution\n[Mn = 1.5]', + "Resolution\nHigh", + "Rmerge\nLow", + "Dimple\nRfree", + "DataProcessing\nSpaceGroup", + "DataProcessing\nUnitCell", + "DataProcessing\nStatus", + ] # functions that use tables.maps_table_columns: # # - update_datasets_reprocess_table() - appears in create_maps_table() - xce_object.maps_table_columns = ['Sample ID', - 'Select', - 'Compound ID', - 'Smiles', - # 'Resolution\n[Mn = 1.5]', - 'Resolution\nHigh', - 'Dimple\nRcryst', - 'Dimple\nRfree', - 'DataProcessing\nSpaceGroup', - 'Reference\nSpaceGroup', - 'Difference\nUC Volume (%)', - 'Reference File', - 'DataProcessing\nUnitCell', - 'Dimple\nStatus', - 'Compound\nStatus', - 'LastUpdated'] + xce_object.maps_table_columns = [ + "Sample ID", + "Select", + "Compound ID", + "Smiles", + # 'Resolution\n[Mn = 1.5]', + "Resolution\nHigh", + "Dimple\nRcryst", + "Dimple\nRfree", + "DataProcessing\nSpaceGroup", + "Reference\nSpaceGroup", + "Difference\nUC Volume (%)", + "Reference File", + "DataProcessing\nUnitCell", + "Dimple\nStatus", + "Compound\nStatus", + "LastUpdated", + ] # functions that use tables.pandda_table_columns: # # - populate_pandda_analyse_input_table() - appears in update_all_tables() xce_object.pandda_table_columns = [ - 'Sample ID', - 'Export\nSelected', - 'Refinement\nSpace Group', - 'Resolution\n[Mn = 1.5]', - 'Dimple\nRcryst', - 'Dimple\nRfree', - 'Crystal Form\nName', - 'Ignore\ncompletely', - 'Exclude from\n characterisation\n(binds)', - 'Exclude from\n z-map analysis\n(does not bind)'] + "Sample ID", + "Export\nSelected", + "Refinement\nSpace Group", + "Resolution\n[Mn = 1.5]", + "Dimple\nRcryst", + "Dimple\nRfree", + "Crystal Form\nName", + "Ignore\ncompletely", + "Exclude from\n characterisation\n(binds)", + "Exclude from\n z-map analysis\n(does not bind)", + ] # functions that use tables.refinement_table_columns: # # - populate_and_update_refinement_table() - appears in update_all_tables - xce_object.refinement_table_columns = ['Sample ID', - 'Compound ID', - 'Refinement\nSpace Group', - 'Refinement\nResolution', - 'Refinement\nRcryst', - 'Refinement\nRfree', - 'Refinement\nOutcome', - 'buster-reports', - 'Ligand CC', - 'Refinement\nStatus'] + xce_object.refinement_table_columns = [ + "Sample ID", + "Compound ID", + "Refinement\nSpace Group", + "Refinement\nResolution", + "Refinement\nRcryst", + "Refinement\nRfree", + "Refinement\nOutcome", + "buster-reports", + "Ligand CC", + "Refinement\nStatus", + ] def top_menu_dict(self, xce_object): @@ -428,264 +503,347 @@ def top_menu_dict(self, xce_object): # [...], # ]] # } - xce_object.menu_dict = {'A: file': ["&File", - [ - ['Open Config File', 'Ctrl+O', - xce_object.open_config_file], - ['Save Config File', 'Ctrl+S', - xce_object.save_config_file], - ['Quit', 'Ctrl+Q', - xce_object.quit_xce] - ]], - 'B: datasource': ["&Datasource", - [ - ['Reload Samples From Datasource', '', - xce_object.datasource_menu_reload_samples], - ['Save Samples to Datasource', '', - xce_object.datasource_menu_save_samples], - ['Import CSV file into Datasource', '', - xce_object.datasource_menu_import_csv_file], - ['Export CSV file from Datasource', '', - xce_object.datasource_menu_export_csv_file], - ['Update datasource from file system', '', - xce_object.datasource_menu_update_datasource], - ['Select columns to show', '', - xce_object.select_datasource_columns_to_display], - ['Create New Datasource (SQLite)', '', - xce_object.create_new_data_source], - ['Export CSV for wonka', '', - xce_object.export_data_for_WONKA] - ]], - 'C: preferences': ["&Preferences", - [ - ['Edit preferences', '', - xce_object.show_preferences] - ]], - 'D: deposition': ["&Deposition", - [ - ['Edit information', '', - xce_object.deposition_data], - ['Export to HTML', '', - xce_object.export_to_html], - ['Export to HTML - CompChem', '', - xce_object.export_to_html_CompChem], - ['Export to HTML - deposition ready', '', - xce_object.export_to_html_deposition_ready], - # ['Find PanDDA apo structures', '', - # xce_object.create_missing_apo_records_in_depositTable], - # ['Update file info of apo structures', '', - # xce_object.update_file_information_of_apo_records], - # ['Prepare mmcif for apo structures', '', - # xce_object.prepare_models_for_deposition_apo], - # ['Prepare mmcif for ligand bound structures', '', - # xce_object.prepare_models_for_deposition_ligand_bound], - # ['Copy files to group deposition directory (ligand bound)', '', - # xce_object.prepare_for_group_deposition_upload_ligand_bound], - # ['Copy files to group deposition directory (ground state)', '', - # xce_object.prepare_for_group_deposition_upload_ground_state], - ['Update DB with PDB codes', '', - xce_object.enter_pdb_codes], - ['Check SMILES', '', - xce_object.check_smiles_in_db_and_pdb] - ]], - # 'E: proasis': ["Proasis", - # [ - # ['Launch Proasis in browser', '', partial(webbrowser.open, - # url='http://cs04r-sc-vserv-137.diamond.ac.uk/Proasis4_2017/')] - # ]], - 'F: help': ["&Help", - [ - ['Open XCE manual', '', - lambda: setup().openFile( - "/dls/science/groups/i04-1/software/XCE_manual_2018-11-09.pdf" - ) - ], - ['Open XCE tutorial', '', - lambda: setup().openFile( - "/dls/science/groups/i04-1/software/docs/XChemExplorer.pdf")], - ['Troubleshooting', '', - lambda: setup().openFile( - "/dls/science/groups/i04-1/software/xce_troubleshooting.pdf")] - ]], - 'G: labels': ["&Labels", - [ - ['Edit label information', '', - xce_object.add_label_information] - ]] - - } + xce_object.menu_dict = { + "A: file": [ + "&File", + [ + ["Open Config File", "Ctrl+O", xce_object.open_config_file], + ["Save Config File", "Ctrl+S", xce_object.save_config_file], + ["Quit", "Ctrl+Q", xce_object.quit_xce], + ], + ], + "B: datasource": [ + "&Datasource", + [ + [ + "Reload Samples From Datasource", + "", + xce_object.datasource_menu_reload_samples, + ], + [ + "Save Samples to Datasource", + "", + xce_object.datasource_menu_save_samples, + ], + [ + "Import CSV file into Datasource", + "", + xce_object.datasource_menu_import_csv_file, + ], + [ + "Export CSV file from Datasource", + "", + xce_object.datasource_menu_export_csv_file, + ], + [ + "Update datasource from file system", + "", + xce_object.datasource_menu_update_datasource, + ], + [ + "Select columns to show", + "", + xce_object.select_datasource_columns_to_display, + ], + [ + "Create New Datasource (SQLite)", + "", + xce_object.create_new_data_source, + ], + ["Export CSV for wonka", "", xce_object.export_data_for_WONKA], + ], + ], + "C: preferences": [ + "&Preferences", + [["Edit preferences", "", xce_object.show_preferences]], + ], + "D: deposition": [ + "&Deposition", + [ + ["Edit information", "", xce_object.deposition_data], + ["Export to HTML", "", xce_object.export_to_html], + [ + "Export to HTML - CompChem", + "", + xce_object.export_to_html_CompChem, + ], + [ + "Export to HTML - deposition ready", + "", + xce_object.export_to_html_deposition_ready, + ], + # ['Find PanDDA apo structures', '', + # xce_object.create_missing_apo_records_in_depositTable], + # ['Update file info of apo structures', '', + # xce_object.update_file_information_of_apo_records], + # ['Prepare mmcif for apo structures', '', + # xce_object.prepare_models_for_deposition_apo], + # ['Prepare mmcif for ligand bound structures', '', + # xce_object.prepare_models_for_deposition_ligand_bound], + # ['Copy files to group deposition directory (ligand bound)', '', + # xce_object.prepare_for_group_deposition_upload_ligand_bound], + # ['Copy files to group deposition directory (ground state)', '', + # xce_object.prepare_for_group_deposition_upload_ground_state], + ["Update DB with PDB codes", "", xce_object.enter_pdb_codes], + ["Check SMILES", "", xce_object.check_smiles_in_db_and_pdb], + ], + ], + # 'E: proasis': ["Proasis", + # [ + # ['Launch Proasis in browser', '', partial(webbrowser.open, + # url='http://cs04r-sc-vserv-137.diamond.ac.uk/Proasis4_2017/')] + # ]], + "F: help": [ + "&Help", + [ + [ + "Open XCE manual", + "", + lambda: setup().openFile( + "/dls/science/groups/i04-1/software/XCE_manual_2018-11-09.pdf" + ), + ], + [ + "Open XCE tutorial", + "", + lambda: setup().openFile( + "/dls/science/groups/i04-1/software/docs/XChemExplorer.pdf" + ), + ], + [ + "Troubleshooting", + "", + lambda: setup().openFile( + "/dls/science/groups/i04-1/software/xce_troubleshooting.pdf" + ), + ], + ], + ], + "G: labels": [ + "&Labels", + [["Edit label information", "", xce_object.add_label_information]], + ], + } def bottom_box_buttons(self, xce_object): self.dropdown_items(xce_object) - xce_object.datasource_button_dict = {'datasource_button': [r"Update Tables\nFrom Datasource", - [ - [ - 'XChemToolTips.update_from_datasource_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px; ' - 'background: rgb(197,197,197) }', - # stylesheet - 'xce_object.headlineLabelfont', # font - 'xce_object.datasource_menu_reload_samples'] - # action - ]]} - - xce_object.dataset_task_run_button_dict = {'dataset_run_button': - [r"Run", - [ - ['XChemToolTips.dataset_task_run_button_tip()', # tooltip - # stylesheet - 'QPushButton { padding: 1px; margin: 1px }', - '', # font - 'xce_object.button_clicked'] # action - ]]} - - xce_object.dataset_task_status_button_dict = {'dataset_status_button': - [r"Status", - [ - ['XChemToolTips.dataset_task_status_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} - - xce_object.map_cif_file_task_run_button_dict = {'dataset_run_button': - [r"Run", - [ - ['XChemToolTips.map_cif_file_task_run_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} - - xce_object.map_cif_file_task_status_button_dict = {'dataset_status_button': - [r"Status", - [ - [ - 'XChemToolTips.map_cif_file_task_status_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} - - xce_object.panddas_file_task_run_button_dict = {'dataset_run_button': - [r"Run", - [ - ['XChemToolTips.panddas_file_task_run_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} - - xce_object.panddas_file_task_status_button_dict = {'dataset_status_button': - [r"Status", - [ - [ - 'XChemToolTips.panddas_file_task_status_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} - - xce_object.refine_file_task_run_button_dict = {'dataset_run_button': - [r"Run", - [ - ['XChemToolTips.refine_file_task_run_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} - - xce_object.refine_file_task_status_button_dict = {'dataset_status_button': - [r"Status", - [ - [ - 'XChemToolTips.refine_file_task_status_button_tip()', - # tooltip - 'QPushButton { padding: 1px; margin: 1px }', - # stylesheet - '', # font - 'xce_object.button_clicked'] # action - ]]} + xce_object.datasource_button_dict = { + "datasource_button": [ + r"Update Tables\nFrom Datasource", + [ + [ + "XChemToolTips.update_from_datasource_button_tip()", + # tooltip + "QPushButton { padding: 1px; margin: 1px; " + "background: rgb(197,197,197) }", + # stylesheet + "xce_object.headlineLabelfont", # font + "xce_object.datasource_menu_reload_samples", + ] + # action + ], + ] + } + + xce_object.dataset_task_run_button_dict = { + "dataset_run_button": [ + r"Run", + [ + [ + "XChemToolTips.dataset_task_run_button_tip()", # tooltip + # stylesheet + "QPushButton { padding: 1px; margin: 1px }", + "", # font + "xce_object.button_clicked", + ] # action + ], + ] + } + + xce_object.dataset_task_status_button_dict = { + "dataset_status_button": [ + r"Status", + [ + [ + "XChemToolTips.dataset_task_status_button_tip()", + # tooltip + "QPushButton { padding: 1px; margin: 1px }", + # stylesheet + "", # font + "xce_object.button_clicked", + ] # action + ], + ] + } + + xce_object.map_cif_file_task_run_button_dict = { + "dataset_run_button": [ + r"Run", + [ + [ + "XChemToolTips.map_cif_file_task_run_button_tip()", + # tooltip + "QPushButton { padding: 1px; margin: 1px }", + # stylesheet + "", # font + "xce_object.button_clicked", + ] # action + ], + ] + } + + xce_object.map_cif_file_task_status_button_dict = { + "dataset_status_button": [ + r"Status", + [ + [ + "XChemToolTips.map_cif_file_task_status_button_tip()", + # tooltip + "QPushButton { padding: 1px; margin: 1px }", + # stylesheet + "", # font + "xce_object.button_clicked", + ] # action + ], + ] + } + + xce_object.panddas_file_task_run_button_dict = { + "dataset_run_button": [ + r"Run", + [ + [ + "XChemToolTips.panddas_file_task_run_button_tip()", + # tooltip + "QPushButton { padding: 1px; margin: 1px }", + # stylesheet + "", # font + "xce_object.button_clicked", + ] # action + ], + ] + } + + xce_object.panddas_file_task_status_button_dict = { + "dataset_status_button": [ + r"Status", + [ + [ + "XChemToolTips.panddas_file_task_status_button_tip()", + # tooltip + "QPushButton { padding: 1px; margin: 1px }", + # stylesheet + "", # font + "xce_object.button_clicked", + ] # action + ], + ] + } + + xce_object.refine_file_task_run_button_dict = { + "dataset_run_button": [ + r"Run", + [ + [ + "XChemToolTips.refine_file_task_run_button_tip()", + # tooltip + "QPushButton { padding: 1px; margin: 1px }", + # stylesheet + "", # font + "xce_object.button_clicked", + ] # action + ], + ] + } + + xce_object.refine_file_task_status_button_dict = { + "dataset_status_button": [ + r"Status", + [ + [ + "XChemToolTips.refine_file_task_status_button_tip()", + # tooltip + "QPushButton { padding: 1px; margin: 1px }", + # stylesheet + "", # font + "xce_object.button_clicked", + ] # action + ], + ] + } def dropdown_items(self, xce_object): - xce_object.dataset_tasks = ['Get New Results from Autoprocessing', - # 'Run DIMPLE on All Autoprocessing MTZ files', - 'Rescore Datasets', - 'Run xia2 on selected datasets', - 'Run xia2 on selected datasets - overwrite'] + xce_object.dataset_tasks = [ + "Get New Results from Autoprocessing", + # 'Run DIMPLE on All Autoprocessing MTZ files', + "Rescore Datasets", + "Run xia2 on selected datasets", + "Run xia2 on selected datasets - overwrite", + ] xce_object.map_cif_file_tasks = [ # 'Run initial refinement on selected MTZ files', # 'Remove selected initial refinement files', - 'Run DIMPLE on selected MTZ files', - 'Remove selected DIMPLE files', - 'Set DIMPLE output', + "Run DIMPLE on selected MTZ files", + "Remove selected DIMPLE files", + "Set DIMPLE output", # 'Set only results from selected pipeline', # 'Create CIF/PDB/PNG file of ALL compounds', # 'Create CIF/PDB/PNG file of NEW compounds', - '------------------------------------------', - 'Create CIF/PDB/PNG file of SELECTED compounds', - 'Merge ligand CIF file with selected compounds', - 'Restore original CIF file of selected compounds', - 'Fit ligands into maps after initial refinement', - '------------------------------------------', - 'Run PIPEDREAM on selected MTZ files', - 'Remove selected PIPEDREAM files', - 'Set PIPEDREAM output', - '------------------------------------------', - 'Run PHENIX.LIGAND_PIPELINE on selected MTZ files', - 'Remove selected PHENIX.LIGAND_PIPELINE files', - 'Set PHENIX.LIGAND_PIPELINE output' + "------------------------------------------", + "Create CIF/PDB/PNG file of SELECTED compounds", + "Merge ligand CIF file with selected compounds", + "Restore original CIF file of selected compounds", + "Fit ligands into maps after initial refinement", + "------------------------------------------", + "Run PIPEDREAM on selected MTZ files", + "Remove selected PIPEDREAM files", + "Set PIPEDREAM output", + "------------------------------------------", + "Run PHENIX.LIGAND_PIPELINE on selected MTZ files", + "Remove selected PHENIX.LIGAND_PIPELINE files", + "Set PHENIX.LIGAND_PIPELINE output", + ] + + xce_object.panddas_file_tasks = [ + "pandda.analyse", + "pandda.inspect", + "run pandda.inspect at home", + "------------------------------------------", + "Export NEW PANDDA models", + "Export ALL PANDDA models", + "Export SELECTED PANDDA models", + "------------------------------------------", + "Show HTML summary", + # 'Update datasource with results from pandda.inspect', + "cluster datasets", + "Event Map -> SF", + "apo -> mmcif", + "check modelled ligands", + "------------------------------------------", + "refine ALL bound-state models with BUSTER", + "refine NEW bound-state models with BUSTER", + "------------------------------------------", + "refine ALL bound-state models with BUSTER (no sanity check)", + "refine NEW bound-state models with BUSTER (no sanity check)", + "------------------------------------------", + # 'refine NEW bound-state models with BUSTER - NEW', + "pre-run for ground state model", + "Build ground state model", + "------------------------------------------", + "pandda.analyse (PanDDA2)", + ] + + xce_object.refine_file_tasks = [ + "Open COOT - BUSTER refinement -", + "Open COOT - REFMAC refinement -", + "Open COOT - dimple_twin -", + # '-------------------------------', + # 'Reset to last successful refinement (BUSTER or REFMAC)', + "", ] - xce_object.panddas_file_tasks = ['pandda.analyse', - 'pandda.inspect', - 'run pandda.inspect at home', - '------------------------------------------', - 'Export NEW PANDDA models', - 'Export ALL PANDDA models', - 'Export SELECTED PANDDA models', - '------------------------------------------', - 'Show HTML summary', - # 'Update datasource with results from pandda.inspect', - 'cluster datasets', - 'Event Map -> SF', - 'apo -> mmcif', - 'check modelled ligands', - '------------------------------------------', - 'refine ALL bound-state models with BUSTER', - 'refine NEW bound-state models with BUSTER', - '------------------------------------------', - 'refine ALL bound-state models with BUSTER (no sanity check)', - 'refine NEW bound-state models with BUSTER (no sanity check)', - '------------------------------------------', - # 'refine NEW bound-state models with BUSTER - NEW', - 'pre-run for ground state model', - 'Build ground state model', - '------------------------------------------', - 'pandda.analyse (PanDDA2)' - ] - - xce_object.refine_file_tasks = ['Open COOT - BUSTER refinement -', - 'Open COOT - REFMAC refinement -', - 'Open COOT - dimple_twin -', - # '-------------------------------', - # 'Reset to last successful refinement (BUSTER or REFMAC)', - ''] # xce_object.refine_file_tasks = ['Open COOT', # 'Open COOT for old PanDDA', diff --git a/gui_scripts/settings_tab.py b/gui_scripts/settings_tab.py index 00c68e20..cf4c4a6b 100755 --- a/gui_scripts/settings_tab.py +++ b/gui_scripts/settings_tab.py @@ -3,10 +3,10 @@ import os from PyQt4 import QtGui, QtCore, QtWebKit -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'gui_scripts')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) -class SettingsTab(): +class SettingsTab: def __init__(self): self.layout_funcs = layout.LayoutFuncs() @@ -30,41 +30,58 @@ def setup(self, xce_object): # Settings Tab xce_object.data_collection_vbox_for_settings = QtGui.QVBoxLayout() - xce_object.buttons_etc.setLayout( - xce_object.data_collection_vbox_for_settings) + xce_object.buttons_etc.setLayout(xce_object.data_collection_vbox_for_settings) xce_object.scroll.setWidget(xce_object.buttons_etc) - xce_object.initial_model_directory_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, - '\n\nProject Directory: - REQUIRED -', - xce_object.initial_model_directory, - 'Select Project Directory', - xce_object.settings_button_clicked) - - xce_object.reference_directory_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, - '\n\nReference Structure Directory: - OPTIONAL -', - xce_object.reference_directory, - 'Select Reference Structure Directory', - xce_object.settings_button_clicked) - - if xce_object.data_source_file != '': - xce_object.data_source_file_label_text = os.path.join(xce_object.database_directory, - xce_object.data_source_file) - xce_object.data_source_file_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, - '\n\nData Source: - REQUIRED -', - xce_object.data_source_file_label_text, - 'Select Data Source File', - xce_object.settings_button_clicked) + xce_object.initial_model_directory_label = ( + self.layout_funcs.settings_section_setup( + xce_object.data_collection_vbox_for_settings, + "\n\nProject Directory: - REQUIRED -", + xce_object.initial_model_directory, + "Select Project Directory", + xce_object.settings_button_clicked, + ) + ) + + xce_object.reference_directory_label = self.layout_funcs.settings_section_setup( + xce_object.data_collection_vbox_for_settings, + "\n\nReference Structure Directory: - OPTIONAL -", + xce_object.reference_directory, + "Select Reference Structure Directory", + xce_object.settings_button_clicked, + ) + + if xce_object.data_source_file != "": + xce_object.data_source_file_label_text = os.path.join( + xce_object.database_directory, xce_object.data_source_file + ) + xce_object.data_source_file_label = ( + self.layout_funcs.settings_section_setup( + xce_object.data_collection_vbox_for_settings, + "\n\nData Source: - REQUIRED -", + xce_object.data_source_file_label_text, + "Select Data Source File", + xce_object.settings_button_clicked, + ) + ) else: - xce_object.data_source_file_label_text = '' - - xce_object.data_source_file_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, - '\n\nData Source: - REQUIRED -', - xce_object.data_source_file_label_text, - 'Select Data Source File', - xce_object.settings_button_clicked) + xce_object.data_source_file_label_text = "" + + xce_object.data_source_file_label = ( + self.layout_funcs.settings_section_setup( + xce_object.data_collection_vbox_for_settings, + "\n\nData Source: - REQUIRED -", + xce_object.data_source_file_label_text, + "Select Data Source File", + xce_object.settings_button_clicked, + ) + ) xce_object.data_collection_vbox_for_settings.addWidget( - QtGui.QLabel('\n\nData Collection Directory: (e.g. /dls/i04-1/data/2017/lb18145-70) -')) + QtGui.QLabel( + "\n\nData Collection Directory: (e.g. /dls/i04-1/data/2017/lb18145-70) -" + ) + ) settings_beamline_frame = QtGui.QFrame() settings_beamline_frame.setFrameShape(QtGui.QFrame.StyledPanel) @@ -72,70 +89,83 @@ def setup(self, xce_object): settings_hbox_beamline_directory = QtGui.QHBoxLayout() xce_object.beamline_directory_label = QtGui.QLabel( - xce_object.beamline_directory) - settings_hbox_beamline_directory.addWidget( - xce_object.beamline_directory_label) + xce_object.beamline_directory + ) + settings_hbox_beamline_directory.addWidget(xce_object.beamline_directory_label) settings_button_beamline_directory = QtGui.QPushButton( - 'Select Data Collection Directory') + "Select Data Collection Directory" + ) settings_button_beamline_directory.setMaximumWidth(500) settings_button_beamline_directory.clicked.connect( - xce_object.settings_button_clicked) + xce_object.settings_button_clicked + ) - settings_hbox_beamline_directory.addWidget( - settings_button_beamline_directory) + settings_hbox_beamline_directory.addWidget(settings_button_beamline_directory) settings_beamline_vbox.addLayout(settings_hbox_beamline_directory) - xce_object.read_agamemnon = QtGui.QCheckBox( - 'Read Agamemnon data structure') + xce_object.read_agamemnon = QtGui.QCheckBox("Read Agamemnon data structure") settings_beamline_vbox.addWidget(xce_object.read_agamemnon) - -# settings_hbox_datasets_summary_file = QtGui.QHBoxLayout() -# xce_object.datasets_summary_file_label = QtGui.QLabel(xce_object.datasets_summary_file) -# settings_hbox_datasets_summary_file.addWidget(xce_object.datasets_summary_file_label) -# settings_button_datasets_summary_file = QtGui.QPushButton('Select Existing\nCollection Summary File') -# settings_button_datasets_summary_file.setMaximumWidth(247) -# settings_button_datasets_summary_file.clicked.connect(xce_object.settings_button_clicked) -# settings_hbox_datasets_summary_file.addWidget(settings_button_datasets_summary_file) -# -# settings_button_new_datasets_summary_file = QtGui.QPushButton('Assign New\nCollection Summary File') -# settings_button_new_datasets_summary_file.clicked.connect(xce_object.settings_button_clicked) -# settings_button_new_datasets_summary_file.setMaximumWidth(247) -# settings_hbox_datasets_summary_file.addWidget(settings_button_new_datasets_summary_file) -# -# settings_beamline_vbox.addLayout(settings_hbox_datasets_summary_file) + # settings_hbox_datasets_summary_file = QtGui.QHBoxLayout() + # xce_object.datasets_summary_file_label = QtGui.QLabel(xce_object.datasets_summary_file) + # settings_hbox_datasets_summary_file.addWidget(xce_object.datasets_summary_file_label) + # settings_button_datasets_summary_file = QtGui.QPushButton('Select Existing\nCollection Summary File') + # settings_button_datasets_summary_file.setMaximumWidth(247) + # settings_button_datasets_summary_file.clicked.connect(xce_object.settings_button_clicked) + # settings_hbox_datasets_summary_file.addWidget(settings_button_datasets_summary_file) + # + # settings_button_new_datasets_summary_file = QtGui.QPushButton('Assign New\nCollection Summary File') + # settings_button_new_datasets_summary_file.clicked.connect(xce_object.settings_button_clicked) + # settings_button_new_datasets_summary_file.setMaximumWidth(247) + # settings_hbox_datasets_summary_file.addWidget(settings_button_new_datasets_summary_file) + # + # settings_beamline_vbox.addLayout(settings_hbox_datasets_summary_file) settings_beamline_frame.setLayout(settings_beamline_vbox) - xce_object.data_collection_vbox_for_settings.addWidget( - settings_beamline_frame) - - xce_object.ccp4_scratch_directory_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, - '\n\nCCP4_SCR Directory: - OPTIONAL -', - xce_object.ccp4_scratch_directory, - 'Select CCP4_SCR Directory', - xce_object.settings_button_clicked) - - xce_object.panddas_directory_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, - '\n\nPANDDAs directory: - OPTIONAL -', - xce_object.panddas_directory, - 'Select PanDDA Directory', - xce_object.settings_button_clicked) - - xce_object.html_export_directory_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, - '\n\nHTML export directory: - OPTIONAL -', - xce_object.html_export_directory, - 'Select HTML Export Directory', - xce_object.settings_button_clicked) - - xce_object.group_deposition_directory_label = self.layout_funcs.settings_section_setup(xce_object.data_collection_vbox_for_settings, - '\n\nGroup deposition directory: - OPTIONAL -', - xce_object.group_deposit_directory, - 'Select Group deposition Directory', - xce_object.settings_button_clicked) + xce_object.data_collection_vbox_for_settings.addWidget(settings_beamline_frame) + + xce_object.ccp4_scratch_directory_label = ( + self.layout_funcs.settings_section_setup( + xce_object.data_collection_vbox_for_settings, + "\n\nCCP4_SCR Directory: - OPTIONAL -", + xce_object.ccp4_scratch_directory, + "Select CCP4_SCR Directory", + xce_object.settings_button_clicked, + ) + ) + + xce_object.panddas_directory_label = self.layout_funcs.settings_section_setup( + xce_object.data_collection_vbox_for_settings, + "\n\nPANDDAs directory: - OPTIONAL -", + xce_object.panddas_directory, + "Select PanDDA Directory", + xce_object.settings_button_clicked, + ) + + xce_object.html_export_directory_label = ( + self.layout_funcs.settings_section_setup( + xce_object.data_collection_vbox_for_settings, + "\n\nHTML export directory: - OPTIONAL -", + xce_object.html_export_directory, + "Select HTML Export Directory", + xce_object.settings_button_clicked, + ) + ) + + xce_object.group_deposition_directory_label = ( + self.layout_funcs.settings_section_setup( + xce_object.data_collection_vbox_for_settings, + "\n\nGroup deposition directory: - OPTIONAL -", + xce_object.group_deposit_directory, + "Select Group deposition Directory", + xce_object.settings_button_clicked, + ) + ) # xce_object.data_collection_vbox_for_settings.setSpacing(0) - xce_object.data_collection_vbox_for_settings.setContentsMargins( - 30, 30, 30, 30) + xce_object.data_collection_vbox_for_settings.setContentsMargins(30, 30, 30, 30) - xce_object.buttons_etc.resize(xce_object.buttons_etc.sizeHint().width() + 100, xce_object.buttons_etc.sizeHint() - .height()) + xce_object.buttons_etc.resize( + xce_object.buttons_etc.sizeHint().width() + 100, + xce_object.buttons_etc.sizeHint().height(), + ) diff --git a/gui_scripts/stylesheet.py b/gui_scripts/stylesheet.py index 87aa1807..44b217ba 100755 --- a/gui_scripts/stylesheet.py +++ b/gui_scripts/stylesheet.py @@ -8,9 +8,10 @@ def set_stylesheet(xce_object): palette.setColor(QtGui.QPalette.Background, QtGui.QColor("#ececec")) xce_object.setPalette(palette) - icons_directory = os.path.join((os.getenv('XChemExplorer_DIR')), 'icons') + icons_directory = os.path.join((os.getenv("XChemExplorer_DIR")), "icons") - xce_object.setStyleSheet(""" + xce_object.setStyleSheet( + """ QApplication { padding: 0px; } @@ -38,7 +39,9 @@ def set_stylesheet(xce_object): border: 1px solid rgb(184, 192, 210); } QComboBox::down-arrow { - image: url(""" + icons_directory + """/drop-down.png); + image: url(""" + + icons_directory + + """/drop-down.png); background-color: rgb(255, 255, 255); } QComboBox::drop-down { @@ -76,6 +79,7 @@ def set_stylesheet(xce_object): QScrollBar { background: rgb(236, 236, 236); } - """) + """ + ) - QtGui.qApp.setStyle('Cleanlooks') + QtGui.qApp.setStyle("Cleanlooks") diff --git a/helpers/assign_stereochemistry.py b/helpers/assign_stereochemistry.py index 0f0dc3ae..2976a241 100755 --- a/helpers/assign_stereochemistry.py +++ b/helpers/assign_stereochemistry.py @@ -3,41 +3,43 @@ import sys import glob from rdkit import Chem -#from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +# from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions + +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) def enumerateStereoChem(compoundID, sampleDir, db, xtal): # first need to recreate the original CIF file with phenix.elbow because we cannot be sure # which program was used to create the initial restrains # this is because funny things happen to aromatic rings in case the file was made with GRADE - os.chdir(os.path.join(sampleDir, 'compound')) + os.chdir(os.path.join(sampleDir, "compound")) sql = "select CompoundSMILES from mainTable where CrystalName = '%s'" % xtal - print('sqlite query:', sql) + print("sqlite query:", sql) query = db.execute_statement(sql) originalSMILES = query[0][0] print(originalSMILES) cmd = 'phenix.elbow --smiles="%s" --id=LIG --output=tmp' % (originalSMILES) - print('current working directory:', os.getcwd()) - print('runnning:', cmd) + print("current working directory:", os.getcwd()) + print("runnning:", cmd) os.system(cmd) stereosmiles = None pdb = None - if os.path.isfile(os.path.join(sampleDir, 'compound', 'tmp.pdb')): - pdb = os.path.join(sampleDir, 'compound', 'tmp.pdb') + if os.path.isfile(os.path.join(sampleDir, "compound", "tmp.pdb")): + pdb = os.path.join(sampleDir, "compound", "tmp.pdb") else: - print('cannot find tmp.pdb') + print("cannot find tmp.pdb") pass if pdb: mol = Chem.MolFromPDBFile(pdb) Chem.AssignStereochemistry( - mol, cleanIt=True, force=True, flagPossibleStereoCenters=True) + mol, cleanIt=True, force=True, flagPossibleStereoCenters=True + ) if Chem.FindMolChiralCenters(mol, includeUnassigned=True) == []: - print('no chiral centres found') + print("no chiral centres found") db_dict = {} - db_dict['CompoundStereo'] = 'FALSE' + db_dict["CompoundStereo"] = "FALSE" updateDB(db, db_dict, xtal) else: stereosmiles = Chem.MolToSmiles(mol, isomericSmiles=True) @@ -46,25 +48,27 @@ def enumerateStereoChem(compoundID, sampleDir, db, xtal): def generateRestraints(compoundID, sampleDir, db, stereosmiles, xtal): cmd = 'phenix.elbow --smiles="%s" --chiral=enumerate --id=LIG --output=%s' % ( - stereosmiles, compoundID) + stereosmiles, + compoundID, + ) os.system(cmd) checkFiles(compoundID, sampleDir, db, stereosmiles, xtal) def checkFiles(compoundID, sampleDir, db, stereosmiles, xtal): foundCIF = False - allCIF = '' - for cif in glob.glob(os.path.join(compoundID + '_*.cif')): + allCIF = "" + for cif in glob.glob(os.path.join(compoundID + "_*.cif")): foundCIF = True - allCIF += cif+';' - print('---', cif, '===', allCIF) + allCIF += cif + ";" + print("---", cif, "===", allCIF) if foundCIF: db_dict = {} - db_dict['CompoundStereo'] = 'TRUE' - db_dict['CompoundStereoSMILES'] = stereosmiles - db_dict['CompoundStereoCIFprogram'] = 'phenix.elbow' - db_dict['CompoundStereoCIFs'] = allCIF[:-1] - print('>>>', db_dict) + db_dict["CompoundStereo"] = "TRUE" + db_dict["CompoundStereoSMILES"] = stereosmiles + db_dict["CompoundStereoCIFprogram"] = "phenix.elbow" + db_dict["CompoundStereoCIFs"] = allCIF[:-1] + print(">>>", db_dict) updateDB(db, db_dict, xtal) @@ -75,12 +79,12 @@ def updateDB(db, db_dict, xtal): db.update_data_source(xtal, db_dict) -if __name__ == '__main__': +if __name__ == "__main__": compoundID = sys.argv[1] sampleDir = sys.argv[2] - xtal = sampleDir[sampleDir.rfind('/')+1:] - print('sampleID:', xtal) + xtal = sampleDir[sampleDir.rfind("/") + 1 :] + print("sampleID:", xtal) database = sys.argv[3] - print('database:', database) + print("database:", database) db = XChemDB.data_source(database) enumerateStereoChem(compoundID, sampleDir, db, xtal) diff --git a/helpers/change_residues_in_ground_and_bound-state.py b/helpers/change_residues_in_ground_and_bound-state.py index 833672ec..1a8d52ca 100755 --- a/helpers/change_residues_in_ground_and_bound-state.py +++ b/helpers/change_residues_in_ground_and_bound-state.py @@ -4,55 +4,52 @@ def replace_residues(): - for dirs in glob.glob(os.path.join(projectDir, '*')): - xtal = dirs[dirs.rfind('/')+1:] + for dirs in glob.glob(os.path.join(projectDir, "*")): + xtal = dirs[dirs.rfind("/") + 1 :] os.chdir(dirs) if xtal == test: continue for mol in toEdit: if os.path.isfile(mol): - if not os.path.isfile(mol+'_original'): - os.system('/bin/cp %s %s' % (mol, mol+'_original')) - print('%s: found %s' % (xtal, mol)) - os.system('phenix.superpose_pdbs %s %s' % (mol, newModel)) - out = '' + if not os.path.isfile(mol + "_original"): + os.system("/bin/cp %s %s" % (mol, mol + "_original")) + print("%s: found %s" % (xtal, mol)) + os.system("phenix.superpose_pdbs %s %s" % (mol, newModel)) + out = "" changeResi = None for line in open(mol): - if line.startswith('ATOM') or line.startswith('HETATM'): - chainID = str(line[21:23]).replace(' ', '') - resseq = str(line[23:26]).replace(' ', '') - occupancy = str(line[56:60]).replace(' ', '') + if line.startswith("ATOM") or line.startswith("HETATM"): + chainID = str(line[21:23]).replace(" ", "") + resseq = str(line[23:26]).replace(" ", "") + occupancy = str(line[56:60]).replace(" ", "") resi = chainID + resseq if changeResi != None: if resi == changeResi: - print('here', changeResi) + print("here", changeResi) continue else: changeResi = None if resi in residues_to_change: changeResi = resi - print('changeResi', changeResi) - for line in open(newModelName+'_fitted.pdb'): - if line.startswith('ATOM') or line.startswith('HETATM'): - chainIDFitted = str( - line[21:23]).replace(' ', '') - resseqFitted = str( - line[23:26]).replace(' ', '') + print("changeResi", changeResi) + for line in open(newModelName + "_fitted.pdb"): + if line.startswith("ATOM") or line.startswith("HETATM"): + chainIDFitted = str(line[21:23]).replace(" ", "") + resseqFitted = str(line[23:26]).replace(" ", "") residFitted = chainIDFitted + resseqFitted if residFitted == changeResi: - out += line[:56] + \ - occupancy + line[60:] + out += line[:56] + occupancy + line[60:] else: out += line else: out += line - print('saving file', mol, '...') - newFile = open(mol, 'w') + print("saving file", mol, "...") + newFile = open(mol, "w") newFile.write(out) newFile.close() -if __name__ == '__main__': +if __name__ == "__main__": # newModel = '/dls/labxchem/data/2019/lb22717-1/processing/INPP5DA/processing/reference/INPP5DA-x0080-ground-state-corrected.pdb' # residues_to_change = ['A567', 'A812', 'A851'] # projectDir = '/dls/labxchem/data/2019/lb22717-1/processing/INPP5DA/processing/analysis/model_building' @@ -62,5 +59,5 @@ def replace_residues(): newModel = sys.argv[1] residues_to_change = sys.argv[2] projectDir = sys.argv[3] - toEdit = ['refine.split.ground-state.pdb', 'refine.split.bound-state.pdb'] - newModelName = newModel[newModel.rfind('/') + 1:] + toEdit = ["refine.split.ground-state.pdb", "refine.split.bound-state.pdb"] + newModelName = newModel[newModel.rfind("/") + 1 :] diff --git a/helpers/create_png_of_compound.py b/helpers/create_png_of_compound.py index 421f377c..c63c59ed 100755 --- a/helpers/create_png_of_compound.py +++ b/helpers/create_png_of_compound.py @@ -3,10 +3,11 @@ from rdkit import Chem import os import sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) -if __name__ == '__main__': + +if __name__ == "__main__": smiles = sys.argv[1] compoundID = sys.argv[2] @@ -16,5 +17,5 @@ mol = Chem.MolFromSmiles(smiles) AllChem.Compute2DCoords(mol) - os.chdir(os.path.join(inital_model_directory, xtal, 'compound')) - Draw.MolToFile(mol, "{0!s}.png".format(compoundID.replace(' ', ''))) + os.chdir(os.path.join(inital_model_directory, xtal, "compound")) + Draw.MolToFile(mol, "{0!s}.png".format(compoundID.replace(" ", ""))) diff --git a/helpers/find_best_fitting_ligand.py b/helpers/find_best_fitting_ligand.py index 5e358f46..16f71224 100755 --- a/helpers/find_best_fitting_ligand.py +++ b/helpers/find_best_fitting_ligand.py @@ -3,21 +3,27 @@ import os import glob -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) def parse_autofit_folder(sampleDir, compoundID): - filenames = ['best.pdb', 'ligand_fit_1.pdb'] + filenames = ["best.pdb", "ligand_fit_1.pdb"] pdbList = [] - for files in glob.glob(os.path.join(sampleDir, 'autofit_ligand', compoundID+'_*', '*')): - pdb = files[files.rfind('/')+1:] + for files in glob.glob( + os.path.join(sampleDir, "autofit_ligand", compoundID + "_*", "*") + ): + pdb = files[files.rfind("/") + 1 :] if pdb in filenames: pdbList.append(files) return pdbList def find_input_mtz(sampleDir): - possibleMTZ = ['refine.mtz', 'init.mtz', 'dimple.mtz', ] + possibleMTZ = [ + "refine.mtz", + "init.mtz", + "dimple.mtz", + ] mtzin = None for mtz in possibleMTZ: if os.path.isfile(os.path.join(sampleDir, mtz)): @@ -27,56 +33,60 @@ def find_input_mtz(sampleDir): def calculate_cc(sampleDir, compoundID, db): - xtal = sampleDir[sampleDir.rfind('/') + 1:] + xtal = sampleDir[sampleDir.rfind("/") + 1 :] pdbList = parse_autofit_folder(sampleDir, compoundID) mtzin = find_input_mtz(sampleDir) for pdb in pdbList: - autofitDir = pdb[:pdb.rfind('/')] + autofitDir = pdb[: pdb.rfind("/")] os.chdir(autofitDir) os.system( - 'phenix.get_cc_mtz_pdb %s %s > phenix.get_cc_mtz_pdb.log' % (pdb, mtzin)) + "phenix.get_cc_mtz_pdb %s %s > phenix.get_cc_mtz_pdb.log" % (pdb, mtzin) + ) new_file_links(pdbList) bestRun, bestCC = parse_cc_log(sampleDir, compoundID) changeLinks(sampleDir, pdbList, bestRun, compoundID) fitting_program = None - if 'phenix' in bestRun: - fitting_program = 'phenix.ligandfit' - elif 'rhofit' in bestRun: - fitting_program = 'rhofit' + if "phenix" in bestRun: + fitting_program = "phenix.ligandfit" + elif "rhofit" in bestRun: + fitting_program = "rhofit" db_dict = {} - db_dict['CompoundAutofitprogram'] = fitting_program - db_dict['CompoundAutofitCC'] = str(bestCC) + db_dict["CompoundAutofitprogram"] = fitting_program + db_dict["CompoundAutofitCC"] = str(bestCC) updateDB(db, db_dict, xtal) def new_file_links(pdbList): for pdb in pdbList: - autofitDir = pdb[:pdb.rfind('/')] - autofitRun = pdb.split('/')[len(pdb.split('/')) - 2] - pdbFile = pdb[pdb.rfind('/')+1:] + autofitDir = pdb[: pdb.rfind("/")] + autofitRun = pdb.split("/")[len(pdb.split("/")) - 2] + pdbFile = pdb[pdb.rfind("/") + 1 :] os.chdir(autofitDir) - if not os.path.isfile(autofitRun+'.pdb'): - os.system('ln -s %s %s.pdb' % (pdbFile, autofitRun)) + if not os.path.isfile(autofitRun + ".pdb"): + os.system("ln -s %s %s.pdb" % (pdbFile, autofitRun)) def changeLinks(sampleDir, pdbList, bestRun, compoundID): os.chdir(sampleDir) for pdb in pdbList: - autofitDir = pdb.split('/')[len(pdb.split('/')) - 2] + autofitDir = pdb.split("/")[len(pdb.split("/")) - 2] if autofitDir == bestRun: - if os.path.isfile(pdb.replace(sampleDir, '.')): - os.system('/bin/rm %s.pdb' % compoundID) - os.system('ln -s %s %s.pdb' % - (pdb.replace(sampleDir, '.'), compoundID)) + if os.path.isfile(pdb.replace(sampleDir, ".")): + os.system("/bin/rm %s.pdb" % compoundID) + os.system("ln -s %s %s.pdb" % (pdb.replace(sampleDir, "."), compoundID)) def parse_cc_log(sampleDir, compoundID): ccDict = {} ccList = [] - for ccLog in glob.glob(os.path.join(sampleDir, 'autofit_ligand', compoundID+'_*', 'phenix.get_cc_mtz_pdb.log')): - autofitDir = ccLog.split('/')[len(ccLog.split('/'))-2] + for ccLog in glob.glob( + os.path.join( + sampleDir, "autofit_ligand", compoundID + "_*", "phenix.get_cc_mtz_pdb.log" + ) + ): + autofitDir = ccLog.split("/")[len(ccLog.split("/")) - 2] for line in open(ccLog): - if line.startswith('local CC:') and len(line.split()) > 2: + if line.startswith("local CC:") and len(line.split()) > 2: cc = line.split()[2] ccList.append(float(cc)) ccDict[autofitDir] = cc @@ -98,7 +108,7 @@ def updateDB(db, db_dict, xtal): db.update_data_source(xtal, db_dict) -if __name__ == '__main__': +if __name__ == "__main__": compoundID = sys.argv[1] sampleDir = sys.argv[2] database = sys.argv[3] diff --git a/helpers/make_ligand_links_after_pandda.py b/helpers/make_ligand_links_after_pandda.py index a2ec0cc1..f7a345d8 100755 --- a/helpers/make_ligand_links_after_pandda.py +++ b/helpers/make_ligand_links_after_pandda.py @@ -9,8 +9,8 @@ def make_links(projectDir, panddaDir): - os.chdir(os.path.join(panddaDir, 'processed_datasets')) - for xtal in glob.glob('*'): + os.chdir(os.path.join(panddaDir, "processed_datasets")) + for xtal in glob.glob("*"): # for cif in glob.glob(os.path.join(xtal,'ligand_files','*.cif')): # print cif # os.system('/bin/rm %s' %cif) @@ -18,12 +18,12 @@ def make_links(projectDir, panddaDir): # print pdb # os.system('/bin/rm %s' %pdb) - for pdb in glob.glob(os.path.join(projectDir, xtal, 'compound', '*.pdb')): - os.system('ln -s %s %s/ligand_files' % (pdb, xtal)) - for cif in glob.glob(os.path.join(projectDir, xtal, 'compound', '*.cif')): - os.system('ln -s %s %s/ligand_files' % (cif, xtal)) + for pdb in glob.glob(os.path.join(projectDir, xtal, "compound", "*.pdb")): + os.system("ln -s %s %s/ligand_files" % (pdb, xtal)) + for cif in glob.glob(os.path.join(projectDir, xtal, "compound", "*.cif")): + os.system("ln -s %s %s/ligand_files" % (cif, xtal)) -if __name__ == '__main__': +if __name__ == "__main__": projectDir = sys.argv[1] panddaDir = sys.argv[2] diff --git a/helpers/merge_ligand_cif_files.py b/helpers/merge_ligand_cif_files.py index db2116aa..5ddaedd8 100644 --- a/helpers/merge_ligand_cif_files.py +++ b/helpers/merge_ligand_cif_files.py @@ -5,15 +5,15 @@ def merge_cifs(cpdDir): os.chdir(cpdDir) - out = '' - for cif in glob.glob('*.cif'): + out = "" + for cif in glob.glob("*.cif"): for line in open(cif): out += line - f = open('merged.cif', 'w') + f = open("merged.cif", "w") f.write(out) f.close() -if __name__ == '__main__': +if __name__ == "__main__": cpdDir = sys.argv[1] merge_cifs(cpdDir) diff --git a/helpers/phenix_find_TLS_groups.py b/helpers/phenix_find_TLS_groups.py index ac7d6087..08e81852 100755 --- a/helpers/phenix_find_TLS_groups.py +++ b/helpers/phenix_find_TLS_groups.py @@ -4,44 +4,80 @@ def FindTLSgroups(pdbFile): - print('\n==> XCE @ helpers: running phenix.find_tls_groups on new pdb file') + print("\n==> XCE @ helpers: running phenix.find_tls_groups on new pdb file") os.system( - 'phenix.find_tls_groups {0!s} > phenix.find_tls_groups.out'.format(pdbFile)) - GroupNames = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', - 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'] - OutRefmac = '' + "phenix.find_tls_groups {0!s} > phenix.find_tls_groups.out".format(pdbFile) + ) + GroupNames = [ + "A", + "B", + "C", + "D", + "E", + "F", + "G", + "H", + "I", + "J", + "K", + "L", + "M", + "N", + "O", + "P", + "Q", + "R", + "S", + "T", + "U", + "V", + "W", + "X", + "Y", + "Z", + ] + OutRefmac = "" found = 0 i = 0 - for line in open('phenix.find_tls_groups.out'): + for line in open("phenix.find_tls_groups.out"): if found: - if line.startswith('}'): + if line.startswith("}"): break temp = [line.split()] - OutRefmac = OutRefmac + '\nTLS {0!s}\nRANGE '.format((GroupNames)[i]) + str(temp[0][3])[:-1] + ' ' + \ - str(temp[0][6]) + '.\' ' + str(temp[0][3])[:-1] + \ - ' ' + str(temp[0][8]) + '.\' ALL\n' + OutRefmac = ( + OutRefmac + + "\nTLS {0!s}\nRANGE ".format((GroupNames)[i]) + + str(temp[0][3])[:-1] + + " " + + str(temp[0][6]) + + ".' " + + str(temp[0][3])[:-1] + + " " + + str(temp[0][8]) + + ".' ALL\n" + ) i += 1 - if line.startswith('refinement.refine.adp {'): + if line.startswith("refinement.refine.adp {"): found = 1 - f = open('refmac.tls', 'w') + f = open("refmac.tls", "w") f.write(OutRefmac) f.close() - OutPhenix = '' + OutPhenix = "" found = 0 - for line in open('phenix.find_tls_groups.out'): + for line in open("phenix.find_tls_groups.out"): if found: - OutPhenix = OutPhenix+line - if line.startswith('}'): + OutPhenix = OutPhenix + line + if line.startswith("}"): break - if line.startswith('refinement.refine.adp {'): + if line.startswith("refinement.refine.adp {"): found = 1 - OutPhenix = OutPhenix+line - f = open('phenix.tls', 'w') + OutPhenix = OutPhenix + line + f = open("phenix.tls", "w") f.write(OutPhenix) f.close() -if __name__ == '__main__': +if __name__ == "__main__": pdbFile = sys.argv[1] FindTLSgroups(pdbFile) diff --git a/helpers/prepare_for_zenodo_upload.py b/helpers/prepare_for_zenodo_upload.py index 5f425bce..4f3a4e2e 100755 --- a/helpers/prepare_for_zenodo_upload.py +++ b/helpers/prepare_for_zenodo_upload.py @@ -7,98 +7,115 @@ def copy_files(htmlDir): os.chdir(htmlDir) - if not os.path.isdir('zenodo'): - os.mkdir('zenodo') - os.chdir(os.path.join(htmlDir, 'zenodo')) + if not os.path.isdir("zenodo"): + os.mkdir("zenodo") + os.chdir(os.path.join(htmlDir, "zenodo")) - print('copying compoundImages') - os.system('/bin/cp ../compoundImages/* .') + print("copying compoundImages") + os.system("/bin/cp ../compoundImages/* .") - print('copying pdbs') - os.system('/bin/cp ../pdbs/* .') + print("copying pdbs") + os.system("/bin/cp ../pdbs/* .") - print('copying maps') - os.system('/bin/cp ../maps/* .') + print("copying maps") + os.system("/bin/cp ../maps/* .") - print('copying residueplots') - os.system('/bin/cp ../residueplots/* .') + print("copying residueplots") + os.system("/bin/cp ../residueplots/* .") - print('copying mapImages') - os.system('/bin/cp ../mapImages/* .') + print("copying mapImages") + os.system("/bin/cp ../mapImages/* .") - print('copying icbs') - os.system('/bin/cp ../icbs/* .') + print("copying icbs") + os.system("/bin/cp ../icbs/* .") - print('copying css') - os.system('/bin/cp ../css/* .') + print("copying css") + os.system("/bin/cp ../css/* .") - print('copying js') - os.system('/bin/cp ../js/* .') + print("copying js") + os.system("/bin/cp ../js/* .") def edit_index_html(htmlDir, uploadID): - os.chdir(os.path.join(htmlDir, 'zenodo')) + os.chdir(os.path.join(htmlDir, "zenodo")) - out = '' - for line in open('../index.html'): - if 'compoundImages/' in line: + out = "" + for line in open("../index.html"): + if "compoundImages/" in line: line = line.replace( - 'compoundImages/', 'https://zenodo.org/record/'+uploadID+'/files/') - if 'pdbs/' in line: + "compoundImages/", "https://zenodo.org/record/" + uploadID + "/files/" + ) + if "pdbs/" in line: line = line.replace( - 'pdbs/', 'https://zenodo.org/record/'+uploadID+'/files/') - if 'maps/' in line: + "pdbs/", "https://zenodo.org/record/" + uploadID + "/files/" + ) + if "maps/" in line: line = line.replace( - 'maps/', 'https://zenodo.org/record/'+uploadID+'/files/') - if 'residueplots/' in line: + "maps/", "https://zenodo.org/record/" + uploadID + "/files/" + ) + if "residueplots/" in line: line = line.replace( - 'residueplots/', 'https://zenodo.org/record/'+uploadID+'/files/') - if 'mapImages/' in line: + "residueplots/", "https://zenodo.org/record/" + uploadID + "/files/" + ) + if "mapImages/" in line: line = line.replace( - 'mapImages/', 'https://zenodo.org/record/'+uploadID+'/files/') - if 'icbs/' in line: + "mapImages/", "https://zenodo.org/record/" + uploadID + "/files/" + ) + if "icbs/" in line: line = line.replace( - 'icbs/', 'https://zenodo.org/record/'+uploadID+'/files/') - if 'css/' in line: + "icbs/", "https://zenodo.org/record/" + uploadID + "/files/" + ) + if "css/" in line: line = line.replace( - 'css/', 'https://zenodo.org/record/'+uploadID+'/files/') - if 'js/' in line: + "css/", "https://zenodo.org/record/" + uploadID + "/files/" + ) + if "js/" in line: line = line.replace( - 'js/', 'https://zenodo.org/record/'+uploadID+'/files/') + "js/", "https://zenodo.org/record/" + uploadID + "/files/" + ) out += line - print('writing index.html to', os.path.join(htmlDir, 'zenodo')) - f = open('0_index.html', 'w') + print("writing index.html to", os.path.join(htmlDir, "zenodo")) + f = open("0_index.html", "w") f.write(out) f.close() def edit_icb_html_files(htmlDir, uploadID): # https://zenodo.org/record/48768/files/README.txt - os.chdir(os.path.join(htmlDir, 'zenodo')) - for file in glob.glob('*event*html'): - out = '' + os.chdir(os.path.join(htmlDir, "zenodo")) + for file in glob.glob("*event*html"): + out = "" for line in open(file): if 'src="http://molsoft.com/lib/acticm.js">' in line: - line = line.replace('src="http://molsoft.com/lib/acticm.js">', - 'src="https://molsoft.com/lib/acticm.js">') - if '../mapImages/' in line: line = line.replace( - '../mapImages/', 'https://zenodo.org/record/'+uploadID+'/files/') - if '../compoundImages/' in line: + 'src="http://molsoft.com/lib/acticm.js">', + 'src="https://molsoft.com/lib/acticm.js">', + ) + if "../mapImages/" in line: line = line.replace( - '../compoundImages/', 'https://zenodo.org/record/'+uploadID+'/files/') + "../mapImages/", "https://zenodo.org/record/" + uploadID + "/files/" + ) + if "../compoundImages/" in line: + line = line.replace( + "../compoundImages/", + "https://zenodo.org/record/" + uploadID + "/files/", + ) if ' act.projectFile = "' in line: line = line.replace( - ' act.projectFile = "', ' act.projectFile = "https://zenodo.org/record/'+uploadID+'/files/') + ' act.projectFile = "', + ' act.projectFile = "https://zenodo.org/record/' + + uploadID + + "/files/", + ) out += line - print('updating', file) - f = open(file, 'w') + print("updating", file) + f = open(file, "w") f.write(out) f.close() -if __name__ == '__main__': +if __name__ == "__main__": print(len(sys.argv)) @@ -115,4 +132,4 @@ def edit_icb_html_files(htmlDir, uploadID): edit_icb_html_files(htmlDir, uploadID) else: - print('wrong input!') + print("wrong input!") diff --git a/helpers/reset_interesting_datasets.py b/helpers/reset_interesting_datasets.py index 1d1043ef..d1d91f08 100755 --- a/helpers/reset_interesting_datasets.py +++ b/helpers/reset_interesting_datasets.py @@ -6,38 +6,76 @@ def relink_interesting_datasets(panddaDir): - os.chdir(os.path.join(panddaDir, 'interesting_datasets')) + os.chdir(os.path.join(panddaDir, "interesting_datasets")) dirList = [] - for dirs in glob.glob('*'): + for dirs in glob.glob("*"): if os.path.isdir(dirs): dirList.append(dirs) for dirs in dirList: - print('/bin/rm -fr {0!s}'.format(dirs)) - os.system('/bin/rm -fr {0!s}'.format(dirs)) - print('ln -s ../processed_datasets/{0!s} .'.format(dirs)) - os.system('ln -s ../processed_datasets/{0!s} .'.format(dirs)) + print("/bin/rm -fr {0!s}".format(dirs)) + os.system("/bin/rm -fr {0!s}".format(dirs)) + print("ln -s ../processed_datasets/{0!s} .".format(dirs)) + os.system("ln -s ../processed_datasets/{0!s} .".format(dirs)) def check_interesting_datasets(panddaDir): - os.chdir(os.path.join(panddaDir, 'interesting_datasets')) - for xtal in sorted(glob.glob('*')): + os.chdir(os.path.join(panddaDir, "interesting_datasets")) + for xtal in sorted(glob.glob("*")): if not os.path.islink(xtal): # print xtal # print os.path.join(panddaDir,'interesting_datasets',xtal,'modelled_structures',xtal+'-pandda-model.pdb') - if os.path.isfile(os.path.join(panddaDir, 'interesting_datasets', xtal, 'modelled_structures', xtal+'-pandda-model.pdb')): - print('mv --backup=numbered {0!s} {1!s}'.format(os.path.join( - panddaDir, 'interesting_datasets', xtal, 'modelled_structures'), os.path.join(panddaDir, 'processed_datasets', xtal))) - os.system('mv --backup=numbered {0!s} {1!s}'.format(os.path.join(panddaDir, 'interesting_datasets', - xtal, 'modelled_structures'), os.path.join(panddaDir, 'processed_datasets', xtal))) - print('cp {0!s} {1!s}'.format(os.path.join( - panddaDir, 'interesting_datasets', xtal, '*params'), os.path.join(panddaDir, 'processed_datasets', xtal))) - os.system('cp {0!s} {1!s}'.format(os.path.join(panddaDir, 'interesting_datasets', - xtal, '*params'), os.path.join(panddaDir, 'processed_datasets', xtal))) - - -if __name__ == '__main__': + if os.path.isfile( + os.path.join( + panddaDir, + "interesting_datasets", + xtal, + "modelled_structures", + xtal + "-pandda-model.pdb", + ) + ): + print( + "mv --backup=numbered {0!s} {1!s}".format( + os.path.join( + panddaDir, + "interesting_datasets", + xtal, + "modelled_structures", + ), + os.path.join(panddaDir, "processed_datasets", xtal), + ) + ) + os.system( + "mv --backup=numbered {0!s} {1!s}".format( + os.path.join( + panddaDir, + "interesting_datasets", + xtal, + "modelled_structures", + ), + os.path.join(panddaDir, "processed_datasets", xtal), + ) + ) + print( + "cp {0!s} {1!s}".format( + os.path.join( + panddaDir, "interesting_datasets", xtal, "*params" + ), + os.path.join(panddaDir, "processed_datasets", xtal), + ) + ) + os.system( + "cp {0!s} {1!s}".format( + os.path.join( + panddaDir, "interesting_datasets", xtal, "*params" + ), + os.path.join(panddaDir, "processed_datasets", xtal), + ) + ) + + +if __name__ == "__main__": panddaDir = sys.argv[1] check_interesting_datasets(panddaDir) relink_interesting_datasets(panddaDir) diff --git a/helpers/reset_occupancy_protein_to_one.py b/helpers/reset_occupancy_protein_to_one.py index 7c20c482..7ddbea30 100644 --- a/helpers/reset_occupancy_protein_to_one.py +++ b/helpers/reset_occupancy_protein_to_one.py @@ -4,35 +4,35 @@ def reset_residues(projectDir): - for dirs in glob.glob(os.path.join(projectDir, '*')): - xtal = dirs[dirs.rfind('/')+1:] + for dirs in glob.glob(os.path.join(projectDir, "*")): + xtal = dirs[dirs.rfind("/") + 1 :] os.chdir(dirs) for mol in toEdit: if os.path.isfile(mol): - if not os.path.isfile(mol+'_original'): - os.system('/bin/cp %s %s' % (mol, mol+'_original')) - print('%s: found %s' % (xtal, mol)) - out = '' + if not os.path.isfile(mol + "_original"): + os.system("/bin/cp %s %s" % (mol, mol + "_original")) + print("%s: found %s" % (xtal, mol)) + out = "" changeResi = None for line in open(mol): - if line.startswith('ATOM'): - chainID = str(line[21:23]).replace(' ', '') - resseq = str(line[23:26]).replace(' ', '') - occupancy = str(line[56:60]).replace(' ', '') - altLoc = str(line[16:17]).replace(' ', '') - if altLoc != '': + if line.startswith("ATOM"): + chainID = str(line[21:23]).replace(" ", "") + resseq = str(line[23:26]).replace(" ", "") + occupancy = str(line[56:60]).replace(" ", "") + altLoc = str(line[16:17]).replace(" ", "") + if altLoc != "": out += line else: - out += line[:56] + '1.00' + line[60:] + out += line[:56] + "1.00" + line[60:] else: out += line - print('saving file', mol, '...') - newFile = open(mol, 'w') + print("saving file", mol, "...") + newFile = open(mol, "w") newFile.write(out) newFile.close() -if __name__ == '__main__': +if __name__ == "__main__": projectDir = sys.argv[1] - toEdit = ['refine.split.bound-state.pdb'] + toEdit = ["refine.split.bound-state.pdb"] reset_residues(projectDir) diff --git a/helpers/reset_to_last_successful_refinement.py b/helpers/reset_to_last_successful_refinement.py index 1ce5118c..ab47ab02 100644 --- a/helpers/reset_to_last_successful_refinement.py +++ b/helpers/reset_to_last_successful_refinement.py @@ -4,13 +4,13 @@ def find_refine_folder(projectDir): - for xtalDir in sorted(glob.glob(os.path.join(projectDir, '*'))): - xtal = xtalDir[xtalDir.rfind('/')+1:] + for xtalDir in sorted(glob.glob(os.path.join(projectDir, "*"))): + xtal = xtalDir[xtalDir.rfind("/") + 1 :] os.chdir(xtalDir) dirList = [] - for dirs in sorted(glob.glob('*')): - if dirs.startswith('Refine_') and os.path.isdir(dirs): - if not os.path.isfile('refine.pdb'): + for dirs in sorted(glob.glob("*")): + if dirs.startswith("Refine_") and os.path.isdir(dirs): + if not os.path.isfile("refine.pdb"): dirList.append([dirs, os.path.getctime(dirs)]) if dirList != []: find_refine_pdb(xtal, dirList) @@ -20,40 +20,40 @@ def find_refine_pdb(xtal, dirList): sorted_list = sorted(dirList, key=lambda x: x[1], reverse=True) foundRefinePDB = False for d in sorted_list: - serial = int(d[0].split('_')[1]) - if os.path.isfile(os.path.join(d[0], 'refine.pdb')): - print(xtal + ': found refine.pdb in ' + d[0]) - pdbLink = os.path.join(d[0], 'refine.pdb') - mtzLink = os.path.join(d[0], 'refine.mtz') + serial = int(d[0].split("_")[1]) + if os.path.isfile(os.path.join(d[0], "refine.pdb")): + print(xtal + ": found refine.pdb in " + d[0]) + pdbLink = os.path.join(d[0], "refine.pdb") + mtzLink = os.path.join(d[0], "refine.mtz") foundRefinePDB = True break - elif os.path.isfile(os.path.join(d[0], 'refine_%s.pdb' % str(serial))): - print(xtal + ': found refine_%s.pdb in %s' % (str(serial), d[0])) + elif os.path.isfile(os.path.join(d[0], "refine_%s.pdb" % str(serial))): + print(xtal + ": found refine_%s.pdb in %s" % (str(serial), d[0])) foundRefinePDB = True - pdbLink = os.path.join(d[0], 'refine_%s.pdb' % str(serial)) - mtzLink = os.path.join(d[0], 'refine_%s.mtz' % str(serial)) + pdbLink = os.path.join(d[0], "refine_%s.pdb" % str(serial)) + mtzLink = os.path.join(d[0], "refine_%s.mtz" % str(serial)) break if not foundRefinePDB: - print(xtal + ': ERROR -> cannot find refine.pdb') + print(xtal + ": ERROR -> cannot find refine.pdb") else: print(os.getcwd(), pdbLink, mtzLink) reset_links(xtal, pdbLink, mtzLink) def find_pandda_refine_pdb(xtal, dirList): - print('hallp') + print("hallp") def reset_links(xtal, pdbLink, mtzLink): - print(xtal + ': resetting links...') - os.system('/bin/rm refine.pdb') - os.system('/bin/rm refine.mtz') - os.system('/bin/rm refine.split.bound-state.pdb') - os.system('ln -s %s refine.pdb' % pdbLink) - os.system('ln -s %s refine.mtz' % mtzLink) - os.system('ln -s refine.pdb refine.split.bound-state.pdb') + print(xtal + ": resetting links...") + os.system("/bin/rm refine.pdb") + os.system("/bin/rm refine.mtz") + os.system("/bin/rm refine.split.bound-state.pdb") + os.system("ln -s %s refine.pdb" % pdbLink) + os.system("ln -s %s refine.mtz" % mtzLink) + os.system("ln -s refine.pdb refine.split.bound-state.pdb") -if __name__ == '__main__': +if __name__ == "__main__": projectDir = sys.argv[1] find_refine_folder(projectDir) diff --git a/helpers/resort_ligand_atoms.py b/helpers/resort_ligand_atoms.py index c271ed58..9db616fd 100755 --- a/helpers/resort_ligand_atoms.py +++ b/helpers/resort_ligand_atoms.py @@ -2,56 +2,76 @@ import os import sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) def get_atom_order_of_ensemble_model(ensembleModel): - ligandResnames = ['LIG', 'FRS', 'DRG', 'UNL'] + ligandResnames = ["LIG", "FRS", "DRG", "UNL"] ensembleLIGdir = {} for line in open(ensembleModel): - if line.startswith('ATOM') or line.startswith('HETATM'): + if line.startswith("ATOM") or line.startswith("HETATM"): atomName_line = str(line[11:16]) altLoc_line = str(line[16:17]) resname_line = str(line[17:20]) chainID_line = str(line[20:23]) resseq_line = str(line[23:26]) - residueID = resname_line.replace(' ', '')+'-' +\ - chainID_line.replace(' ', '')+'-' +\ - resseq_line.replace(' ', '')+'-' +\ - chainID_line.replace(' ', '')+'-' +\ - altLoc_line + residueID = ( + resname_line.replace(" ", "") + + "-" + + chainID_line.replace(" ", "") + + "-" + + resseq_line.replace(" ", "") + + "-" + + chainID_line.replace(" ", "") + + "-" + + altLoc_line + ) if resname_line in ligandResnames: if residueID not in ensembleLIGdir: ensembleLIGdir[residueID] = [] ensembleLIGdir[residueID].append( - [atomName_line, altLoc_line, resname_line, chainID_line, resseq_line]) + [ + atomName_line, + altLoc_line, + resname_line, + chainID_line, + resseq_line, + ] + ) return ensembleLIGdir def resort_ligand_atoms_in_refined_model(refinedModel, ensembleLIGdir): - ligandResnames = ['LIG', 'FRS', 'DRG', 'UNL'] - out = '' + ligandResnames = ["LIG", "FRS", "DRG", "UNL"] + out = "" refineLIGDir = {} - LIGlineAdditional = '' + LIGlineAdditional = "" LIGlist = [] for line in open(refinedModel): - if line.startswith('ATOM') or line.startswith('HETATM'): + if line.startswith("ATOM") or line.startswith("HETATM"): altLoc_line = str(line[16:17]) resname_line = str(line[17:20]) chainID_line = str(line[20:23]) resseq_line = str(line[23:26]) - residueID = resname_line.replace(' ', '')+'-' +\ - chainID_line.replace(' ', '')+'-' +\ - resseq_line.replace(' ', '')+'-' +\ - chainID_line.replace(' ', '')+'-' +\ - altLoc_line + residueID = ( + resname_line.replace(" ", "") + + "-" + + chainID_line.replace(" ", "") + + "-" + + resseq_line.replace(" ", "") + + "-" + + chainID_line.replace(" ", "") + + "-" + + altLoc_line + ) if residueID in ensembleLIGdir: if residueID not in refineLIGDir: @@ -61,7 +81,7 @@ def resort_ligand_atoms_in_refined_model(refinedModel, ensembleLIGdir): LIGlineAdditional += line refineLIGDir[residueID].append(line) - LIGline = '' + LIGline = "" for ligand in ensembleLIGdir: for atomLine in ensembleLIGdir[ligand]: atomName = atomLine[0] @@ -72,33 +92,35 @@ def resort_ligand_atoms_in_refined_model(refinedModel, ensembleLIGdir): break for line in open(refinedModel): - if line.startswith('ATOM') or line.startswith('HETATM'): + if line.startswith("ATOM") or line.startswith("HETATM"): resname_line = str(line[17:20]) if resname_line in ligandResnames: continue else: out += line - elif line.startswith('END'): + elif line.startswith("END"): continue - elif line.startswith('TER'): + elif line.startswith("TER"): continue else: out += line out += LIGline - out += 'END\n' + out += "END\n" - os.system('/bin/mv %s %s' % (refinedModel, - refinedModel.replace('.pdb', '_original_atom_order.pdb'))) - f = open(refinedModel, 'w') + os.system( + "/bin/mv %s %s" + % (refinedModel, refinedModel.replace(".pdb", "_original_atom_order.pdb")) + ) + f = open(refinedModel, "w") f.write(out) f.close() -if __name__ == '__main__': +if __name__ == "__main__": ensembleModel = sys.argv[1] refinedModel = sys.argv[2] ensembleLIGdir = get_atom_order_of_ensemble_model(ensembleModel) diff --git a/helpers/select_ground_state_dataset.py b/helpers/select_ground_state_dataset.py index 0e1e7c35..07e8be5b 100755 --- a/helpers/select_ground_state_dataset.py +++ b/helpers/select_ground_state_dataset.py @@ -5,7 +5,8 @@ import os import sys import glob -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) # - select datasets with highest resolution @@ -16,20 +17,27 @@ def find_highest_resolution_datasets(panddaDir): found = False datasetList = [] - for logFile in glob.glob(os.path.join(panddaDir, 'logs', '*.log')): + for logFile in glob.glob(os.path.join(panddaDir, "logs", "*.log")): for n, line in enumerate(open(logFile)): - if line.startswith('Statistical Electron Density Characterisation') and len(line.split()) == 6: + if ( + line.startswith("Statistical Electron Density Characterisation") + and len(line.split()) == 6 + ): resolution = line.split()[5] found = True foundLine = n - if found and n >= foundLine+3: - if line.startswith('---'): + if found and n >= foundLine + 3: + if line.startswith("---"): break else: - tmpLine = line.replace(' ', '').replace( - '\t', '').replace('\n', '').replace('\r', '') - for item in tmpLine.split(','): - if item != '': + tmpLine = ( + line.replace(" ", "") + .replace("\t", "") + .replace("\n", "") + .replace("\r", "") + ) + for item in tmpLine.split(","): + if item != "": datasetList.append(item) print(datasetList) return datasetList @@ -39,8 +47,10 @@ def get_datasets_without_event_map(panddaDir, datasetList): datasetListwithoutEvent = [] for dataset in datasetList: noEvent = True - for files in glob.glob(os.path.join(panddaDir, 'processed_datasets', dataset, '*')): - if 'event' in files: + for files in glob.glob( + os.path.join(panddaDir, "processed_datasets", dataset, "*") + ): + if "event" in files: noEvent = False break if noEvent: @@ -51,14 +61,24 @@ def get_datasets_without_event_map(panddaDir, datasetList): def select_dataset_with_lowest_Rfree(panddaDir, datasetListwithoutEvent): datasetList = [] - lowestRfree = '' + lowestRfree = "" for dataset in datasetListwithoutEvent: - if os.path.isfile(os.path.join(panddaDir, 'processed_datasets', dataset, dataset+'-pandda-input.pdb')): - stats = parse().PDBheader(os.path.join( - panddaDir, 'processed_datasets', dataset, dataset+'-pandda-input.pdb')) - Rfree = stats['Rfree'] + if os.path.isfile( + os.path.join( + panddaDir, "processed_datasets", dataset, dataset + "-pandda-input.pdb" + ) + ): + stats = parse().PDBheader( + os.path.join( + panddaDir, + "processed_datasets", + dataset, + dataset + "-pandda-input.pdb", + ) + ) + Rfree = stats["Rfree"] try: - print(dataset, Rfree, stats['ResolutionHigh']) + print(dataset, Rfree, stats["ResolutionHigh"]) datasetList.append([dataset, float(Rfree)]) except ValueError: pass @@ -68,60 +88,121 @@ def select_dataset_with_lowest_Rfree(panddaDir, datasetListwithoutEvent): def link_pdb_mtz_files(panddaDir, lowestRfree): - targetDir = '/'.join(panddaDir.split('/')[:len(panddaDir.split('/'))-1]) - panddaFolder = panddaDir.split('/')[len(panddaDir.split('/'))-1] + targetDir = "/".join(panddaDir.split("/")[: len(panddaDir.split("/")) - 1]) + panddaFolder = panddaDir.split("/")[len(panddaDir.split("/")) - 1] print(targetDir) print(panddaFolder) os.chdir(targetDir) - if os.path.isfile(os.path.join(panddaDir, 'processed_datasets', lowestRfree, lowestRfree+'-pandda-input.pdb')): - os.system('/bin/rm %s-ground-state.pdb 2> /dev/null' % lowestRfree) - os.symlink(os.path.join(panddaFolder, 'processed_datasets', lowestRfree, - lowestRfree+'-pandda-input.pdb'), lowestRfree+'-ground-state.pdb') - if os.path.isfile(os.path.join(panddaDir, 'processed_datasets', lowestRfree, lowestRfree+'-pandda-input.mtz')): - os.system('/bin/rm %s-ground-state.free.mtz 2> /dev/null' % - lowestRfree) - os.symlink(os.path.join(panddaFolder, 'processed_datasets', lowestRfree, - lowestRfree+'-pandda-input.mtz'), lowestRfree+'-ground-state.free.mtz') - - if os.path.isfile(os.path.join(panddaDir, 'processed_datasets', lowestRfree, lowestRfree+'-ground-state-mean-map.native.ccp4')): + if os.path.isfile( + os.path.join( + panddaDir, + "processed_datasets", + lowestRfree, + lowestRfree + "-pandda-input.pdb", + ) + ): + os.system("/bin/rm %s-ground-state.pdb 2> /dev/null" % lowestRfree) + os.symlink( + os.path.join( + panddaFolder, + "processed_datasets", + lowestRfree, + lowestRfree + "-pandda-input.pdb", + ), + lowestRfree + "-ground-state.pdb", + ) + if os.path.isfile( + os.path.join( + panddaDir, + "processed_datasets", + lowestRfree, + lowestRfree + "-pandda-input.mtz", + ) + ): + os.system("/bin/rm %s-ground-state.free.mtz 2> /dev/null" % lowestRfree) + os.symlink( + os.path.join( + panddaFolder, + "processed_datasets", + lowestRfree, + lowestRfree + "-pandda-input.mtz", + ), + lowestRfree + "-ground-state.free.mtz", + ) + + if os.path.isfile( + os.path.join( + panddaDir, + "processed_datasets", + lowestRfree, + lowestRfree + "-ground-state-mean-map.native.ccp4", + ) + ): os.system( - '/bin/rm %s-ground-state-mean-map.native.ccp4 2> /dev/null' % lowestRfree) - os.symlink(os.path.join(panddaFolder, 'processed_datasets', lowestRfree, lowestRfree + - '-ground-state-mean-map.native.ccp4'), lowestRfree+'-ground-state-mean-map.native.ccp4') - elif os.path.isfile(os.path.join(panddaDir, 'processed_datasets', lowestRfree, lowestRfree+'-ground-state-average-map.native.ccp4')): + "/bin/rm %s-ground-state-mean-map.native.ccp4 2> /dev/null" % lowestRfree + ) + os.symlink( + os.path.join( + panddaFolder, + "processed_datasets", + lowestRfree, + lowestRfree + "-ground-state-mean-map.native.ccp4", + ), + lowestRfree + "-ground-state-mean-map.native.ccp4", + ) + elif os.path.isfile( + os.path.join( + panddaDir, + "processed_datasets", + lowestRfree, + lowestRfree + "-ground-state-average-map.native.ccp4", + ) + ): os.system( - '/bin/rm %s-ground-state-mean-map.native.ccp4 2> /dev/null' % lowestRfree) - os.symlink(os.path.join(panddaFolder, 'processed_datasets', lowestRfree, lowestRfree + - '-ground-state-average-map.native.ccp4'), lowestRfree+'-ground-state-mean-map.native.ccp4') + "/bin/rm %s-ground-state-mean-map.native.ccp4 2> /dev/null" % lowestRfree + ) + os.symlink( + os.path.join( + panddaFolder, + "processed_datasets", + lowestRfree, + lowestRfree + "-ground-state-average-map.native.ccp4", + ), + lowestRfree + "-ground-state-mean-map.native.ccp4", + ) convert_mean_map_to_mtz( - lowestRfree+'-ground-state-mean-map.native.ccp4', lowestRfree+'-ground-state.free.mtz') + lowestRfree + "-ground-state-mean-map.native.ccp4", + lowestRfree + "-ground-state.free.mtz", + ) def convert_mean_map_to_mtz(emap, mtz): - print('converting ground-state-mean-map to MTZ') - cmd = ('mapmask MAPIN %s MAPOUT %s << eof\n' % (emap, emap.replace('.ccp4', '.P1.ccp4')) + - ' XYZLIM CELL\n' - ' PAD 0.0\n' - ' SYMMETRY 1\n' - 'eof\n') + print("converting ground-state-mean-map to MTZ") + cmd = ( + "mapmask MAPIN %s MAPOUT %s << eof\n" + % (emap, emap.replace(".ccp4", ".P1.ccp4")) + + " XYZLIM CELL\n" + " PAD 0.0\n" + " SYMMETRY 1\n" + "eof\n" + ) print(cmd) os.system(cmd) - print('--->', mtz) + print("--->", mtz) reso = mtztools(mtz).get_dmin() - print('-> resolution:', reso) - cmd = ('module load phenix\n' - 'phenix.map_to_structure_factors %s d_min=%s\n' % (emap.replace('.ccp4', '.P1.ccp4'), reso) + - '/bin/mv map_to_structure_factors.mtz %s' % emap.replace('.ccp4', '.mtz')) + print("-> resolution:", reso) + cmd = "module load phenix\n" "phenix.map_to_structure_factors %s d_min=%s\n" % ( + emap.replace(".ccp4", ".P1.ccp4"), + reso, + ) + "/bin/mv map_to_structure_factors.mtz %s" % emap.replace(".ccp4", ".mtz") print(cmd) os.system(cmd) -if __name__ == '__main__': +if __name__ == "__main__": panddaDir = sys.argv[1] datasetList = find_highest_resolution_datasets(panddaDir) - datasetListwithoutEvent = get_datasets_without_event_map( - panddaDir, datasetList) - lowestRfree = select_dataset_with_lowest_Rfree( - panddaDir, datasetListwithoutEvent) + datasetListwithoutEvent = get_datasets_without_event_map(panddaDir, datasetList) + lowestRfree = select_dataset_with_lowest_Rfree(panddaDir, datasetListwithoutEvent) link_pdb_mtz_files(panddaDir, lowestRfree) diff --git a/helpers/update_data_source_after_refinement.py b/helpers/update_data_source_after_refinement.py index ca9218d6..7ab5af0d 100755 --- a/helpers/update_data_source_after_refinement.py +++ b/helpers/update_data_source_after_refinement.py @@ -10,38 +10,47 @@ import os import sys import glob -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) def parse_pdb(inital_model_directory, xtal, db_dict): - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.pdb')): - db_dict['RefinementPDB_latest'] = os.path.realpath( - os.path.join(inital_model_directory, xtal, 'refine.pdb')) - pdb = parse().PDBheader(os.path.join(inital_model_directory, xtal, 'refine.pdb')) - db_dict['RefinementRcryst'] = pdb['Rcryst'] - db_dict['RefinementRcrystTraficLight'] = pdb['RcrystTL'] - db_dict['RefinementRfree'] = pdb['Rfree'] - db_dict['RefinementRfreeTraficLight'] = pdb['RfreeTL'] - db_dict['RefinementRmsdBonds'] = pdb['rmsdBonds'] - db_dict['RefinementRmsdBondsTL'] = pdb['rmsdBondsTL'] - db_dict['RefinementRmsdAngles'] = pdb['rmsdAngles'] - db_dict['RefinementRmsdAnglesTL'] = pdb['rmsdAnglesTL'] - db_dict['RefinementSpaceGroup'] = pdb['SpaceGroup'] - db_dict['RefinementResolution'] = pdb['ResolutionHigh'] - db_dict['RefinementResolutionTL'] = pdb['ResolutionColor'] - db_dict['RefinementStatus'] = 'finished' + if os.path.isfile(os.path.join(inital_model_directory, xtal, "refine.pdb")): + db_dict["RefinementPDB_latest"] = os.path.realpath( + os.path.join(inital_model_directory, xtal, "refine.pdb") + ) + pdb = parse().PDBheader( + os.path.join(inital_model_directory, xtal, "refine.pdb") + ) + db_dict["RefinementRcryst"] = pdb["Rcryst"] + db_dict["RefinementRcrystTraficLight"] = pdb["RcrystTL"] + db_dict["RefinementRfree"] = pdb["Rfree"] + db_dict["RefinementRfreeTraficLight"] = pdb["RfreeTL"] + db_dict["RefinementRmsdBonds"] = pdb["rmsdBonds"] + db_dict["RefinementRmsdBondsTL"] = pdb["rmsdBondsTL"] + db_dict["RefinementRmsdAngles"] = pdb["rmsdAngles"] + db_dict["RefinementRmsdAnglesTL"] = pdb["rmsdAnglesTL"] + db_dict["RefinementSpaceGroup"] = pdb["SpaceGroup"] + db_dict["RefinementResolution"] = pdb["ResolutionHigh"] + db_dict["RefinementResolutionTL"] = pdb["ResolutionColor"] + db_dict["RefinementStatus"] = "finished" else: - db_dict['RefinementStatus'] = 'failed' - - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.bound.pdb')): - db_dict['RefinementBoundConformation'] = os.path.realpath( - os.path.join(inital_model_directory, xtal, 'refine.bound.pdb')) - elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.split.bound-state.pdb')): - db_dict['RefinementBoundConformation'] = os.path.realpath( - os.path.join(inital_model_directory, xtal, 'refine.split.bound-state.pdb')) - elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.pdb')): - db_dict['RefinementBoundConformation'] = os.path.realpath( - os.path.join(inital_model_directory, xtal, 'refine.pdb')) + db_dict["RefinementStatus"] = "failed" + + if os.path.isfile(os.path.join(inital_model_directory, xtal, "refine.bound.pdb")): + db_dict["RefinementBoundConformation"] = os.path.realpath( + os.path.join(inital_model_directory, xtal, "refine.bound.pdb") + ) + elif os.path.isfile( + os.path.join(inital_model_directory, xtal, "refine.split.bound-state.pdb") + ): + db_dict["RefinementBoundConformation"] = os.path.realpath( + os.path.join(inital_model_directory, xtal, "refine.split.bound-state.pdb") + ) + elif os.path.isfile(os.path.join(inital_model_directory, xtal, "refine.pdb")): + db_dict["RefinementBoundConformation"] = os.path.realpath( + os.path.join(inital_model_directory, xtal, "refine.pdb") + ) print(db_dict) @@ -49,134 +58,169 @@ def parse_pdb(inital_model_directory, xtal, db_dict): def parse_mtz(inital_model_directory, xtal, db_dict): - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.mtz')): - db_dict['RefinementMTZ_latest'] = os.path.realpath( - os.path.join(inital_model_directory, xtal, 'refine.mtz')) + if os.path.isfile(os.path.join(inital_model_directory, xtal, "refine.mtz")): + db_dict["RefinementMTZ_latest"] = os.path.realpath( + os.path.join(inital_model_directory, xtal, "refine.mtz") + ) return db_dict def check_refmac_matrix_weight(refinement_directory, db_dict): - if os.path.isfile(os.path.join(refinement_directory, 'refmac.log')): - logFile = os.path.join(refinement_directory, 'refmac.log') + if os.path.isfile(os.path.join(refinement_directory, "refmac.log")): + logFile = os.path.join(refinement_directory, "refmac.log") else: - logFile = '' - for files in glob.glob(os.path.join(refinement_directory, '*refine.log')): + logFile = "" + for files in glob.glob(os.path.join(refinement_directory, "*refine.log")): logFile = files break if os.path.isfile(logFile): for line in open(logFile): - if line.startswith(' Weight matrix') and len(line.split()) == 3: - db_dict['RefinementMatrixWeight'] = line.split()[2] + if line.startswith(" Weight matrix") and len(line.split()) == 3: + db_dict["RefinementMatrixWeight"] = line.split()[2] return db_dict def check_refmac_logfile(refinement_directory, db_dict): - if os.path.isfile(os.path.join(refinement_directory, 'refmac.log')): - logFile = os.path.join(refinement_directory, 'refmac.log') + if os.path.isfile(os.path.join(refinement_directory, "refmac.log")): + logFile = os.path.join(refinement_directory, "refmac.log") else: - logFile = '' - for files in glob.glob(os.path.join(refinement_directory, '*refine.log')): + logFile = "" + for files in glob.glob(os.path.join(refinement_directory, "*refine.log")): logFile = files break if os.path.isfile(logFile): for line in open(logFile): - if 'Your coordinate file has a ligand which has either minimum or no description in the library' in line: - db_dict['RefinementStatus'] = 'CIF problem' + if ( + "Your coordinate file has a ligand which has either minimum or no description in the library" + in line + ): + db_dict["RefinementStatus"] = "CIF problem" return db_dict def parse_molprobity_output(inital_model_directory, xtal, db_dict): - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'validation_summary.txt')): - for line in open(os.path.join(inital_model_directory, xtal, 'validation_summary.txt')): - if 'molprobity score' in line.lower(): + if os.path.isfile( + os.path.join(inital_model_directory, xtal, "validation_summary.txt") + ): + for line in open( + os.path.join(inital_model_directory, xtal, "validation_summary.txt") + ): + if "molprobity score" in line.lower(): if len(line.split()) >= 4: - db_dict['RefinementMolProbityScore'] = line.split()[3] + db_dict["RefinementMolProbityScore"] = line.split()[3] if float(line.split()[3]) < 2: - db_dict['RefinementMolProbityScoreTL'] = 'green' + db_dict["RefinementMolProbityScoreTL"] = "green" if 2 <= float(line.split()[3]) < 3: - db_dict['RefinementMolProbityScoreTL'] = 'orange' + db_dict["RefinementMolProbityScoreTL"] = "orange" if float(line.split()[3]) >= 3: - db_dict['RefinementMolProbityScoreTL'] = 'red' + db_dict["RefinementMolProbityScoreTL"] = "red" - if 'ramachandran outliers' in line.lower(): + if "ramachandran outliers" in line.lower(): if len(line.split()) >= 4: - db_dict['RefinementRamachandranOutliers'] = line.split()[3] + db_dict["RefinementRamachandranOutliers"] = line.split()[3] if float(line.split()[3]) < 0.3: - db_dict['RefinementRamachandranOutliersTL'] = 'green' + db_dict["RefinementRamachandranOutliersTL"] = "green" if 0.3 <= float(line.split()[3]) < 1: - db_dict['RefinementRamachandranOutliersTL'] = 'orange' + db_dict["RefinementRamachandranOutliersTL"] = "orange" if float(line.split()[3]) >= 1: - db_dict['RefinementRamachandranOutliersTL'] = 'red' + db_dict["RefinementRamachandranOutliersTL"] = "red" - if 'favored' in line.lower(): + if "favored" in line.lower(): if len(line.split()) >= 3: - db_dict['RefinementRamachandranFavored'] = line.split()[2] + db_dict["RefinementRamachandranFavored"] = line.split()[2] if float(line.split()[2]) < 90: - db_dict['RefinementRamachandranFavoredTL'] = 'red' + db_dict["RefinementRamachandranFavoredTL"] = "red" if 90 <= float(line.split()[2]) < 98: - db_dict['RefinementRamachandranFavoredTL'] = 'orange' + db_dict["RefinementRamachandranFavoredTL"] = "orange" if float(line.split()[2]) >= 98: - db_dict['RefinementRamachandranFavoredTL'] = 'green' + db_dict["RefinementRamachandranFavoredTL"] = "green" return db_dict def parse_ligand_validation(inital_model_directory, refinement_directory, xtal): - if os.path.isfile(os.path.join(refinement_directory, 'residue_scores.csv')): - with open(os.path.join(refinement_directory, 'residue_scores.csv'), 'rb') as csv_import: + if os.path.isfile(os.path.join(refinement_directory, "residue_scores.csv")): + with open( + os.path.join(refinement_directory, "residue_scores.csv"), "rb" + ) as csv_import: csv_dict = csv.DictReader(csv_import) for i, line in enumerate(csv_dict): db_pandda_dict = {} - residue = line[''].replace(' ', '') - residueFilename = line[''] - if len(residue.split('-')) == 2: + residue = line[""].replace(" ", "") + residueFilename = line[""] + if len(residue.split("-")) == 2: # residue_name = residue.split('-')[0] # print residue_name - residue_chain = residue.split('-')[0] - residue_number = residue.split('-')[1] - residue_xyz = pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb') - ).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) + residue_chain = residue.split("-")[0] + residue_number = residue.split("-")[1] + residue_xyz = pdbtools( + os.path.join(inital_model_directory, xtal, "refine.pdb") + ).get_center_of_gravity_of_residue_ish( + residue_chain, residue_number + ) event = db.execute_statement( - "select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='{0!s}'".format(xtal)) + "select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='{0!s}'".format( + xtal + ) + ) for coord in event: db_pandda_dict = {} event_x = float(str(coord[0])) event_y = float(str(coord[1])) event_z = float(str(coord[2])) site_index = str(coord[3]) - distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1], residue_xyz[2], - event_x, event_y, event_z) - print('distance', distance) + distance = misc().calculate_distance_between_coordinates( + residue_xyz[0], + residue_xyz[1], + residue_xyz[2], + event_x, + event_y, + event_z, + ) + print("distance", distance) # if coordinate of ligand and event are closer than 7A, then we assume they belong together if distance < 7: - db_pandda_dict['PANDDA_site_ligand_id'] = residue - db_pandda_dict['PANDDA_site_occupancy'] = line['Occupancy'] - db_pandda_dict['PANDDA_site_B_average'] = line[ - 'Average B-factor (Residue)'] - db_pandda_dict['PANDDA_site_B_ratio_residue_surroundings'] = line['Surroundings B-factor Ratio'] - db_pandda_dict['PANDDA_site_rmsd'] = line['Model RMSD'] - db_pandda_dict['PANDDA_site_RSCC'] = line['RSCC'] - db_pandda_dict['PANDDA_site_RSR'] = line['RSR'] - db_pandda_dict['PANDDA_site_RSZD'] = line['RSZD'] - if os.path.isfile(os.path.join(refinement_directory, 'residue_plots', residueFilename + '.png')): - db_pandda_dict['PANDDA_site_spider_plot'] = os.path.join(refinement_directory, - 'residue_plots', - residueFilename + '.png') + db_pandda_dict["PANDDA_site_ligand_id"] = residue + db_pandda_dict["PANDDA_site_occupancy"] = line["Occupancy"] + db_pandda_dict["PANDDA_site_B_average"] = line[ + "Average B-factor (Residue)" + ] + db_pandda_dict[ + "PANDDA_site_B_ratio_residue_surroundings" + ] = line["Surroundings B-factor Ratio"] + db_pandda_dict["PANDDA_site_rmsd"] = line["Model RMSD"] + db_pandda_dict["PANDDA_site_RSCC"] = line["RSCC"] + db_pandda_dict["PANDDA_site_RSR"] = line["RSR"] + db_pandda_dict["PANDDA_site_RSZD"] = line["RSZD"] + if os.path.isfile( + os.path.join( + refinement_directory, + "residue_plots", + residueFilename + ".png", + ) + ): + db_pandda_dict[ + "PANDDA_site_spider_plot" + ] = os.path.join( + refinement_directory, + "residue_plots", + residueFilename + ".png", + ) else: - db_pandda_dict['PANDDA_site_spider_plot'] = '' + db_pandda_dict["PANDDA_site_spider_plot"] = "" if db_pandda_dict != {}: - print('==> XCE: updating pandda Table of data source') - db.update_panddaTable( - xtal, site_index, db_pandda_dict) + print("==> XCE: updating pandda Table of data source") + db.update_panddaTable(xtal, site_index, db_pandda_dict) def update_ligand_information_in_panddaTable(inital_model_directory, xtal): - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.pdb')): + if os.path.isfile(os.path.join(inital_model_directory, xtal, "refine.pdb")): # ligands_in_file=pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb')).find_xce_ligand_details() - ligands_in_file = pdbtools(os.path.join( - inital_model_directory, xtal, 'refine.pdb')).get_residues_with_resname('LIG') + ligands_in_file = pdbtools( + os.path.join(inital_model_directory, xtal, "refine.pdb") + ).get_residues_with_resname("LIG") for ligand in ligands_in_file: # residue_name= ligand[0] # residue_chain= ligand[1] @@ -185,104 +229,125 @@ def update_ligand_information_in_panddaTable(inital_model_directory, xtal): residue_name = ligand[0] residue_chain = ligand[2] residue_number = ligand[1] - residue_altLoc = 'X' - residue_xyz = pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb') - ).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) + residue_altLoc = "X" + residue_xyz = pdbtools( + os.path.join(inital_model_directory, xtal, "refine.pdb") + ).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) event = db.execute_statement( - "select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='{0!s}'".format(xtal)) + "select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='{0!s}'".format( + xtal + ) + ) for coord in event: db_pandda_dict = {} event_x = float(str(coord[0])) event_y = float(str(coord[1])) event_z = float(str(coord[2])) site_index = str(coord[3]) - distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1], residue_xyz[2], - event_x, event_y, event_z) + distance = misc().calculate_distance_between_coordinates( + residue_xyz[0], + residue_xyz[1], + residue_xyz[2], + event_x, + event_y, + event_z, + ) # if coordinate of ligand and event are closer than 7A, then we assume they belong together if distance < 7: - db_pandda_dict['PANDDA_site_ligand_resname'] = residue_name - db_pandda_dict['PANDDA_site_ligand_chain'] = residue_chain - db_pandda_dict['PANDDA_site_ligand_sequence_number'] = residue_number - db_pandda_dict['PANDDA_site_ligand_altLoc'] = residue_altLoc - db_pandda_dict['PANDDA_site_ligand_placed'] = 'True' + db_pandda_dict["PANDDA_site_ligand_resname"] = residue_name + db_pandda_dict["PANDDA_site_ligand_chain"] = residue_chain + db_pandda_dict[ + "PANDDA_site_ligand_sequence_number" + ] = residue_number + db_pandda_dict["PANDDA_site_ligand_altLoc"] = residue_altLoc + db_pandda_dict["PANDDA_site_ligand_placed"] = "True" if db_pandda_dict != {}: - print('==> XCE: updating pandda Table of data source') + print("==> XCE: updating pandda Table of data source") db.update_panddaTable(xtal, site_index, db_pandda_dict) def update_data_source(db_dict): if db_dict != {}: - print('==> xce: updating mainTable of data source') + print("==> xce: updating mainTable of data source") db.update_data_source(xtal, db_dict) # update refinement outcome if necessary sqlite = ( - "update mainTable set RefinementOutcome = '3 - In Refinement' where CrystalName is '{0!s}' ".format(xtal) + - "and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending' or RefinementOutcome is '2 - PANDDA model')" + "update mainTable set RefinementOutcome = '3 - In Refinement' where CrystalName is '{0!s}' ".format( + xtal + ) + + "and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending' or RefinementOutcome is '2 - PANDDA model')" ) db.execute_statement(sqlite) # now do the same for each site in the pandda table sqlite = ( - "update panddaTable set RefinementOutcome = '3 - In Refinement' where CrystalName is '{0!s}' ".format(xtal) + - "and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending' or RefinementOutcome is '2 - PANDDA model')" + "update panddaTable set RefinementOutcome = '3 - In Refinement' where CrystalName is '{0!s}' ".format( + xtal + ) + + "and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending' or RefinementOutcome is '2 - PANDDA model')" ) db.execute_statement(sqlite) def update_buster_report_index_html(refinement_directory, db_dict): - if os.path.isfile(refinement_directory+'-report/index.html'): - db_dict['RefinementBusterReportHTML'] = refinement_directory + \ - '-report/index.html' + if os.path.isfile(refinement_directory + "-report/index.html"): + db_dict["RefinementBusterReportHTML"] = ( + refinement_directory + "-report/index.html" + ) return db_dict def update_mmcif_file_location(refinement_directory, db_dict): - if os.path.isfile(os.path.join(refinement_directory, 'BUSTER_model.cif')): - db_dict['RefinementMMCIFmodel_latest'] = os.path.join( - refinement_directory, 'BUSTER_model.cif') - if os.path.isfile(os.path.join(refinement_directory, 'BUSTER_refln.cif')): - db_dict['RefinementMMCIFreflections_latest'] = os.path.join( - refinement_directory, 'BUSTER_refln.cif') + if os.path.isfile(os.path.join(refinement_directory, "BUSTER_model.cif")): + db_dict["RefinementMMCIFmodel_latest"] = os.path.join( + refinement_directory, "BUSTER_model.cif" + ) + if os.path.isfile(os.path.join(refinement_directory, "BUSTER_refln.cif")): + db_dict["RefinementMMCIFreflections_latest"] = os.path.join( + refinement_directory, "BUSTER_refln.cif" + ) return db_dict def generate_cut_maps_around_ligand(xtal): - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.pdb')) and \ - os.path.isfile(os.path.join(inital_model_directory, xtal, '2fofc.map')) and \ - os.path.isfile(os.path.join(inital_model_directory, xtal, 'fofc.map')): - ligandDict = pdbtools_gemmi( - 'refine.pdb').center_of_mass_ligand_dict('LIG') - pdbtools_gemmi('refine.pdb').save_ligands_to_pdb('LIG') + if ( + os.path.isfile(os.path.join(inital_model_directory, xtal, "refine.pdb")) + and os.path.isfile(os.path.join(inital_model_directory, xtal, "2fofc.map")) + and os.path.isfile(os.path.join(inital_model_directory, xtal, "fofc.map")) + ): + ligandDict = pdbtools_gemmi("refine.pdb").center_of_mass_ligand_dict("LIG") + pdbtools_gemmi("refine.pdb").save_ligands_to_pdb("LIG") for ligand in ligandDict: - maptools().cut_map_around_ligand('2fofc.map', ligand+'.pdb', '7') - os.system('/bin/mv 2fofc_mapmask.map %s_%s_2fofc_cut.ccp4' % - (xtal, ligand)) - maptools().cut_map_around_ligand('fofc.map', ligand+'.pdb', '7') - os.system('/bin/mv fofc_mapmask.map %s_%s_fofc_cut.ccp4' % - (xtal, ligand)) + maptools().cut_map_around_ligand("2fofc.map", ligand + ".pdb", "7") + os.system("/bin/mv 2fofc_mapmask.map %s_%s_2fofc_cut.ccp4" % (xtal, ligand)) + maptools().cut_map_around_ligand("fofc.map", ligand + ".pdb", "7") + os.system("/bin/mv fofc_mapmask.map %s_%s_fofc_cut.ccp4" % (xtal, ligand)) def read_ligand_cc_from_edstats(xtal, db_dict): - ligCC = '' - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'refine.edstats')): - ligandDict = pdbtools_gemmi( - 'refine.pdb').center_of_mass_ligand_dict('LIG') + ligCC = "" + if os.path.isfile(os.path.join(inital_model_directory, xtal, "refine.edstats")): + ligandDict = pdbtools_gemmi("refine.pdb").center_of_mass_ligand_dict("LIG") for ligand in ligandDict: - lig = ligand.split('-')[0] - chain = ligand.split('-')[1] - resn = ligand.split('-')[2] - for line in open('refine.edstats'): - if line.startswith(lig) and line.split()[1] == chain and line.split()[2] == str(resn): + lig = ligand.split("-")[0] + chain = ligand.split("-")[1] + resn = ligand.split("-")[2] + for line in open("refine.edstats"): + if ( + line.startswith(lig) + and line.split()[1] == chain + and line.split()[2] == str(resn) + ): try: cc = line.split()[8] - ligCC += ligand + ': ' + cc + '\n' + ligCC += ligand + ": " + cc + "\n" except IndexError: continue break - db_dict['RefinementLigandCC'] = ligCC.rstrip() + db_dict["RefinementLigandCC"] = ligCC.rstrip() return db_dict -if __name__ == '__main__': +if __name__ == "__main__": db_file = sys.argv[1] xtal = sys.argv[2] @@ -293,8 +358,8 @@ def read_ligand_cc_from_edstats(xtal, db_dict): db = XChemDB.data_source(db_file) db_dict = {} - db_dict['RefinementRefiner'] = refiner - db_dict['RefinementDate'] = date + db_dict["RefinementRefiner"] = refiner + db_dict["RefinementDate"] = date db_dict = parse_pdb(inital_model_directory, xtal, db_dict) db_dict = parse_mtz(inital_model_directory, xtal, db_dict) diff --git a/helpers/update_data_source_for_new_cif_files.py b/helpers/update_data_source_for_new_cif_files.py index 3ee2dba1..ad936e04 100755 --- a/helpers/update_data_source_for_new_cif_files.py +++ b/helpers/update_data_source_for_new_cif_files.py @@ -4,10 +4,11 @@ from XChemUtils import parse import os import sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) -if __name__ == '__main__': + +if __name__ == "__main__": db_file = sys.argv[1] xtal = sys.argv[2] initial_model_directory = sys.argv[3] @@ -15,19 +16,39 @@ db = XChemDB.data_source(db_file) db_dict = {} - if os.path.isfile(os.path.join(initial_model_directory, xtal, 'compound', compoundID+'.cif')) and \ - os.path.getsize(os.path.join(initial_model_directory, xtal, 'compound', compoundID+'.cif')) > 20: - db_dict['RefinementCIF'] = os.path.join( - initial_model_directory, xtal, 'compound', compoundID+'.cif') - db_dict['RefinementCIFStatus'] = 'restraints generated' + if ( + os.path.isfile( + os.path.join(initial_model_directory, xtal, "compound", compoundID + ".cif") + ) + and os.path.getsize( + os.path.join(initial_model_directory, xtal, "compound", compoundID + ".cif") + ) + > 20 + ): + db_dict["RefinementCIF"] = os.path.join( + initial_model_directory, xtal, "compound", compoundID + ".cif" + ) + db_dict["RefinementCIFStatus"] = "restraints generated" else: - db_dict['RefinementCIF'] = '' - db_dict['RefinementCIFStatus'] = 'restraints failed' - os.system('/bin/rm '+os.path.join(initial_model_directory, - xtal, compoundID.replace(' ', '')+'.pdb')) - os.system('/bin/rm '+os.path.join(initial_model_directory, - xtal, compoundID.replace(' ', '')+'.cif')) - os.system('/bin/rm '+os.path.join(initial_model_directory, - xtal, compoundID.replace(' ', '')+'.png')) + db_dict["RefinementCIF"] = "" + db_dict["RefinementCIFStatus"] = "restraints failed" + os.system( + "/bin/rm " + + os.path.join( + initial_model_directory, xtal, compoundID.replace(" ", "") + ".pdb" + ) + ) + os.system( + "/bin/rm " + + os.path.join( + initial_model_directory, xtal, compoundID.replace(" ", "") + ".cif" + ) + ) + os.system( + "/bin/rm " + + os.path.join( + initial_model_directory, xtal, compoundID.replace(" ", "") + ".png" + ) + ) db.update_data_source(xtal, db_dict) diff --git a/helpers/update_data_source_for_new_dimple_pdb.py b/helpers/update_data_source_for_new_dimple_pdb.py index 73415541..ff13f109 100755 --- a/helpers/update_data_source_for_new_dimple_pdb.py +++ b/helpers/update_data_source_for_new_dimple_pdb.py @@ -6,100 +6,165 @@ import glob import os import sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) -if __name__ == '__main__': + +if __name__ == "__main__": db_file = sys.argv[1] xtal = sys.argv[2] inital_model_directory = sys.argv[3] db = XChemDB.data_source(db_file) - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple.pdb')): - db_dict = {'DimplePathToPDB': os.path.join( - inital_model_directory, xtal, 'dimple.pdb')} + if os.path.isfile(os.path.join(inital_model_directory, xtal, "dimple.pdb")): + db_dict = { + "DimplePathToPDB": os.path.join(inital_model_directory, xtal, "dimple.pdb") + } dimple_ran_successfully = False - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple.mtz')): - db_dict['DimplePathToMTZ'] = os.path.join( - inital_model_directory, xtal, 'dimple.mtz') + if os.path.isfile(os.path.join(inital_model_directory, xtal, "dimple.mtz")): + db_dict["DimplePathToMTZ"] = os.path.join( + inital_model_directory, xtal, "dimple.mtz" + ) dimple_ran_successfully = True - db_dict['DataProcessingDimpleSuccessful'] = 'True' - db_dict['DimpleStatus'] = 'finished' + db_dict["DataProcessingDimpleSuccessful"] = "True" + db_dict["DimpleStatus"] = "finished" if not dimple_ran_successfully: - db_dict['DataProcessingDimpleSuccessful'] = 'False' - db_dict['DimpleStatus'] = 'failed' - pdb = parse().PDBheader(os.path.join(inital_model_directory, xtal, 'dimple.pdb')) - db_dict['DimpleRcryst'] = pdb['Rcryst'] - db_dict['DimpleRfree'] = pdb['Rfree'] - db_dict['RefinementOutcome'] = '1 - Analysis Pending' - db_dict['RefinementSpaceGroup'] = pdb['SpaceGroup'] -# if not os.path.isfile(xtal+'.free.mtz'): -# os.chdir(os.path.join(inital_model_directory,xtal)) -# os.system('/bin/rm '+xtal+'.free.mtz') -# if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz')): -# os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz'),xtal+'.free.mtz') -# db_dict['RefinementMTZfree']=xtal+'.free.mtz' -# elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz')): -# os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz'),xtal+'.free.mtz') -# db_dict['RefinementMTZfree']=xtal+'.free.mtz' + db_dict["DataProcessingDimpleSuccessful"] = "False" + db_dict["DimpleStatus"] = "failed" + pdb = parse().PDBheader( + os.path.join(inital_model_directory, xtal, "dimple.pdb") + ) + db_dict["DimpleRcryst"] = pdb["Rcryst"] + db_dict["DimpleRfree"] = pdb["Rfree"] + db_dict["RefinementOutcome"] = "1 - Analysis Pending" + db_dict["RefinementSpaceGroup"] = pdb["SpaceGroup"] + # if not os.path.isfile(xtal+'.free.mtz'): + # os.chdir(os.path.join(inital_model_directory,xtal)) + # os.system('/bin/rm '+xtal+'.free.mtz') + # if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz')): + # os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz'),xtal+'.free.mtz') + # db_dict['RefinementMTZfree']=xtal+'.free.mtz' + # elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz')): + # os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz'),xtal+'.free.mtz') + # db_dict['RefinementMTZfree']=xtal+'.free.mtz' # setting free.mtz file os.chdir(os.path.join(inital_model_directory, xtal)) - os.system('/bin/rm -f %s.free.mtz' % xtal) + os.system("/bin/rm -f %s.free.mtz" % xtal) mtzFree = None - db_dict['RefinementMTZfree'] = '' - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple', 'dimple_rerun_on_selected_file', 'dimple', 'prepared2.mtz')): - mtzFree = os.path.join(inital_model_directory, xtal, 'dimple', - 'dimple_rerun_on_selected_file', 'dimple', 'prepared2.mtz') - elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple', 'dimple_rerun_on_selected_file', 'dimple', 'prepared.mtz')): - mtzFree = os.path.join(inital_model_directory, xtal, 'dimple', - 'dimple_rerun_on_selected_file', 'dimple', 'prepared.mtz') - elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple', 'dimple', 'prepared.mtz')): + db_dict["RefinementMTZfree"] = "" + if os.path.isfile( + os.path.join( + inital_model_directory, + xtal, + "dimple", + "dimple_rerun_on_selected_file", + "dimple", + "prepared2.mtz", + ) + ): + mtzFree = os.path.join( + inital_model_directory, + xtal, + "dimple", + "dimple_rerun_on_selected_file", + "dimple", + "prepared2.mtz", + ) + elif os.path.isfile( + os.path.join( + inital_model_directory, + xtal, + "dimple", + "dimple_rerun_on_selected_file", + "dimple", + "prepared.mtz", + ) + ): + mtzFree = os.path.join( + inital_model_directory, + xtal, + "dimple", + "dimple_rerun_on_selected_file", + "dimple", + "prepared.mtz", + ) + elif os.path.isfile( + os.path.join( + inital_model_directory, xtal, "dimple", "dimple", "prepared.mtz" + ) + ): + mtzFree = os.path.join( + inital_model_directory, xtal, "dimple", "dimple", "prepared.mtz" + ) + elif os.path.isfile( + os.path.join( + inital_model_directory, xtal, "dimple", "dimple", "prepared2.mtz" + ) + ): mtzFree = os.path.join( - inital_model_directory, xtal, 'dimple', 'dimple', 'prepared.mtz') - elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple', 'dimple', 'prepared2.mtz')): + inital_model_directory, xtal, "dimple", "dimple", "prepared2.mtz" + ) + elif os.path.isfile( + os.path.join( + inital_model_directory, + xtal, + "dimple", + "dimple_rerun_on_selected_file", + "dimple", + "free.mtz", + ) + ): mtzFree = os.path.join( - inital_model_directory, xtal, 'dimple', 'dimple', 'prepared2.mtz') - elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple', 'dimple_rerun_on_selected_file', 'dimple', 'free.mtz')): - mtzFree = os.path.join(inital_model_directory, xtal, 'dimple', - 'dimple_rerun_on_selected_file', 'dimple', 'free.mtz') - elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple', 'dimple', 'free.mtz')): + inital_model_directory, + xtal, + "dimple", + "dimple_rerun_on_selected_file", + "dimple", + "free.mtz", + ) + elif os.path.isfile( + os.path.join(inital_model_directory, xtal, "dimple", "dimple", "free.mtz") + ): mtzFree = os.path.join( - inital_model_directory, xtal, 'dimple', 'dimple', 'free.mtz') + inital_model_directory, xtal, "dimple", "dimple", "free.mtz" + ) if mtzFree is not None: - if 'F_unique' in mtz.object(mtzFree).column_labels(): - cmd = ('cad hklin1 %s hklout %s.free.mtz << eof\n' % (mtzFree, xtal) + - ' monitor BRIEF\n' - ' labin file 1 E1=F E2=SIGF E3=FreeR_flag\n' - ' labout file 1 E1=F E2=SIGF E3=FreeR_flag\n' - 'eof\n') + if "F_unique" in mtz.object(mtzFree).column_labels(): + cmd = ( + "cad hklin1 %s hklout %s.free.mtz << eof\n" % (mtzFree, xtal) + + " monitor BRIEF\n" + " labin file 1 E1=F E2=SIGF E3=FreeR_flag\n" + " labout file 1 E1=F E2=SIGF E3=FreeR_flag\n" + "eof\n" + ) os.system(cmd) else: - os.symlink(mtzFree, xtal+'.free.mtz') + os.symlink(mtzFree, xtal + ".free.mtz") - db_dict['RefinementMTZfree'] = xtal+'.free.mtz' + db_dict["RefinementMTZfree"] = xtal + ".free.mtz" # if no refinement was carried out yet, then we also want to link the dimple files to refine.pdb/refine.log # so that we can look at them with the COOT plugin # 15/11/2016: obsolete since COOT will now read dimple.pdb/dimple.mtz if no refine.pdb/refine.mtz is present -# found_previous_refinement=False -# os.chdir(os.path.join(inital_model_directory,xtal)) -# for dirs in glob.glob('*'): -# if os.path.isdir(dirs) and dirs.startswith('Refine_'): -# found_previous_refinement=True -# break -# if not found_previous_refinement: -# # first delete possible old symbolic links -# if os.path.isfile('refine.pdb'): os.system('/bin/rm refine.pdb') -# os.symlink('dimple.pdb','refine.pdb') -# if os.path.isfile('refine.mtz'): os.system('/bin/rm refine.mtz') -# os.symlink('dimple.mtz','refine.mtz') + # found_previous_refinement=False + # os.chdir(os.path.join(inital_model_directory,xtal)) + # for dirs in glob.glob('*'): + # if os.path.isdir(dirs) and dirs.startswith('Refine_'): + # found_previous_refinement=True + # break + # if not found_previous_refinement: + # # first delete possible old symbolic links + # if os.path.isfile('refine.pdb'): os.system('/bin/rm refine.pdb') + # os.symlink('dimple.pdb','refine.pdb') + # if os.path.isfile('refine.mtz'): os.system('/bin/rm refine.mtz') + # os.symlink('dimple.mtz','refine.mtz') # finally, update data source - print('==> xce: updating data source after DIMPLE run') + print("==> xce: updating data source after DIMPLE run") db.update_data_source(xtal, db_dict) else: @@ -107,7 +172,7 @@ # python os.path.isfile is False if symbolic link points to non existing file # so we remove all of them! os.chdir(os.path.join(inital_model_directory, xtal)) - os.system('/bin/rm dimple.pdb') - os.system('/bin/rm dimple.mtz') - os.system('/bin/rm 2fofc.map') - os.system('/bin/rm fofc.map') + os.system("/bin/rm dimple.pdb") + os.system("/bin/rm dimple.mtz") + os.system("/bin/rm 2fofc.map") + os.system("/bin/rm fofc.map") diff --git a/helpers/update_data_source_for_new_dimple_twin_pdb.py b/helpers/update_data_source_for_new_dimple_twin_pdb.py index 8129344e..af72677e 100755 --- a/helpers/update_data_source_for_new_dimple_twin_pdb.py +++ b/helpers/update_data_source_for_new_dimple_twin_pdb.py @@ -6,101 +6,188 @@ import glob import os import sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) -if __name__ == '__main__': + +if __name__ == "__main__": db_file = sys.argv[1] xtal = sys.argv[2] inital_model_directory = sys.argv[3] db = XChemDB.data_source(db_file) - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin.pdb')): - db_dict = {'DimpleTwinPathToPDB': os.path.join( - inital_model_directory, xtal, 'dimple_twin.pdb')} + if os.path.isfile(os.path.join(inital_model_directory, xtal, "dimple_twin.pdb")): + db_dict = { + "DimpleTwinPathToPDB": os.path.join( + inital_model_directory, xtal, "dimple_twin.pdb" + ) + } dimple_ran_successfully = False - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin.mtz')): - db_dict['DimpleTwinPathToMTZ'] = os.path.join( - inital_model_directory, xtal, 'dimple_twin.mtz') + if os.path.isfile( + os.path.join(inital_model_directory, xtal, "dimple_twin.mtz") + ): + db_dict["DimpleTwinPathToMTZ"] = os.path.join( + inital_model_directory, xtal, "dimple_twin.mtz" + ) dimple_ran_successfully = True - db_dict['DataProcessingDimpleTwinSuccessful'] = 'True' - db_dict['DimpleTwinStatus'] = 'finished' + db_dict["DataProcessingDimpleTwinSuccessful"] = "True" + db_dict["DimpleTwinStatus"] = "finished" if not dimple_ran_successfully: - db_dict['DataProcessingDimpleTwinSuccessful'] = 'False' - db_dict['DimpleTwinStatus'] = 'failed' - pdb = parse().PDBheader(os.path.join(inital_model_directory, xtal, 'dimple_twin.pdb')) - db_dict['DimpleTwinRcryst'] = pdb['Rcryst'] - db_dict['DimpleTwinRfree'] = pdb['Rfree'] - db_dict['RefinementOutcome'] = '1 - Analysis Pending' - db_dict['RefinementSpaceGroup'] = pdb['SpaceGroup'] - db_dict['DimpleTwinFraction'] = pdb['TwinFraction'] -# if not os.path.isfile(xtal+'.free.mtz'): -# os.chdir(os.path.join(inital_model_directory,xtal)) -# os.system('/bin/rm '+xtal+'.free.mtz') -# if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz')): -# os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz'),xtal+'.free.mtz') -# db_dict['RefinementMTZfree']=xtal+'.free.mtz' -# elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz')): -# os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz'),xtal+'.free.mtz') -# db_dict['RefinementMTZfree']=xtal+'.free.mtz' + db_dict["DataProcessingDimpleTwinSuccessful"] = "False" + db_dict["DimpleTwinStatus"] = "failed" + pdb = parse().PDBheader( + os.path.join(inital_model_directory, xtal, "dimple_twin.pdb") + ) + db_dict["DimpleTwinRcryst"] = pdb["Rcryst"] + db_dict["DimpleTwinRfree"] = pdb["Rfree"] + db_dict["RefinementOutcome"] = "1 - Analysis Pending" + db_dict["RefinementSpaceGroup"] = pdb["SpaceGroup"] + db_dict["DimpleTwinFraction"] = pdb["TwinFraction"] + # if not os.path.isfile(xtal+'.free.mtz'): + # os.chdir(os.path.join(inital_model_directory,xtal)) + # os.system('/bin/rm '+xtal+'.free.mtz') + # if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz')): + # os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz'),xtal+'.free.mtz') + # db_dict['RefinementMTZfree']=xtal+'.free.mtz' + # elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz')): + # os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz'),xtal+'.free.mtz') + # db_dict['RefinementMTZfree']=xtal+'.free.mtz' # setting free.mtz file os.chdir(os.path.join(inital_model_directory, xtal)) - os.system('/bin/rm -f %s.free.mtz' % xtal) + os.system("/bin/rm -f %s.free.mtz" % xtal) mtzFree = None - db_dict['RefinementTwinMTZfree'] = '' - if os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin', 'dimple_rerun_on_selected_file', 'dimple_twin', 'prepared2.mtz')): - mtzFree = os.path.join(inital_model_directory, xtal, 'dimple_twin', - 'dimple_rerun_on_selected_file', 'dimple_twin', 'prepared2.mtz') - elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin', 'dimple_rerun_on_selected_file', 'dimple_twin', 'prepared.mtz')): - mtzFree = os.path.join(inital_model_directory, xtal, 'dimple_twin', - 'dimple_rerun_on_selected_file', 'dimple_twin', 'prepared.mtz') - elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin', 'dimple_twin', 'prepared.mtz')): + db_dict["RefinementTwinMTZfree"] = "" + if os.path.isfile( + os.path.join( + inital_model_directory, + xtal, + "dimple_twin", + "dimple_rerun_on_selected_file", + "dimple_twin", + "prepared2.mtz", + ) + ): + mtzFree = os.path.join( + inital_model_directory, + xtal, + "dimple_twin", + "dimple_rerun_on_selected_file", + "dimple_twin", + "prepared2.mtz", + ) + elif os.path.isfile( + os.path.join( + inital_model_directory, + xtal, + "dimple_twin", + "dimple_rerun_on_selected_file", + "dimple_twin", + "prepared.mtz", + ) + ): + mtzFree = os.path.join( + inital_model_directory, + xtal, + "dimple_twin", + "dimple_rerun_on_selected_file", + "dimple_twin", + "prepared.mtz", + ) + elif os.path.isfile( + os.path.join( + inital_model_directory, + xtal, + "dimple_twin", + "dimple_twin", + "prepared.mtz", + ) + ): + mtzFree = os.path.join( + inital_model_directory, + xtal, + "dimple_twin", + "dimple_twin", + "prepared.mtz", + ) + elif os.path.isfile( + os.path.join( + inital_model_directory, + xtal, + "dimple_twin", + "dimple_twin", + "prepared2.mtz", + ) + ): mtzFree = os.path.join( - inital_model_directory, xtal, 'dimple_twin', 'dimple_twin', 'prepared.mtz') - elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin', 'dimple_twin', 'prepared2.mtz')): + inital_model_directory, + xtal, + "dimple_twin", + "dimple_twin", + "prepared2.mtz", + ) + elif os.path.isfile( + os.path.join( + inital_model_directory, + xtal, + "dimple_twin", + "dimple_rerun_on_selected_file", + "dimple_twin", + "free.mtz", + ) + ): mtzFree = os.path.join( - inital_model_directory, xtal, 'dimple_twin', 'dimple_twin', 'prepared2.mtz') - elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin', 'dimple_rerun_on_selected_file', 'dimple_twin', 'free.mtz')): - mtzFree = os.path.join(inital_model_directory, xtal, 'dimple_twin', - 'dimple_rerun_on_selected_file', 'dimple_twin', 'free.mtz') - elif os.path.isfile(os.path.join(inital_model_directory, xtal, 'dimple_twin', 'dimple_twin', 'free.mtz')): + inital_model_directory, + xtal, + "dimple_twin", + "dimple_rerun_on_selected_file", + "dimple_twin", + "free.mtz", + ) + elif os.path.isfile( + os.path.join( + inital_model_directory, xtal, "dimple_twin", "dimple_twin", "free.mtz" + ) + ): mtzFree = os.path.join( - inital_model_directory, xtal, 'dimple_twin', 'dimple_twin', 'free.mtz') + inital_model_directory, xtal, "dimple_twin", "dimple_twin", "free.mtz" + ) if mtzFree is not None: - if 'F_unique' in mtz.object(mtzFree).column_labels(): - cmd = ('cad hklin1 %s hklout %s.free.mtz << eof\n' % (mtzFree, xtal) + - ' monitor BRIEF\n' - ' labin file 1 E1=F E2=SIGF E3=FreeR_flag\n' - ' labout file 1 E1=F E2=SIGF E3=FreeR_flag\n' - 'eof\n') + if "F_unique" in mtz.object(mtzFree).column_labels(): + cmd = ( + "cad hklin1 %s hklout %s.free.mtz << eof\n" % (mtzFree, xtal) + + " monitor BRIEF\n" + " labin file 1 E1=F E2=SIGF E3=FreeR_flag\n" + " labout file 1 E1=F E2=SIGF E3=FreeR_flag\n" + "eof\n" + ) os.system(cmd) else: - os.symlink(mtzFree, xtal+'.free.mtz') + os.symlink(mtzFree, xtal + ".free.mtz") - db_dict['RefinementTwinMTZfree'] = xtal+'.free.mtz' + db_dict["RefinementTwinMTZfree"] = xtal + ".free.mtz" # if no refinement was carried out yet, then we also want to link the dimple files to refine.pdb/refine.log # so that we can look at them with the COOT plugin # 15/11/2016: obsolete since COOT will now read dimple.pdb/dimple.mtz if no refine.pdb/refine.mtz is present -# found_previous_refinement=False -# os.chdir(os.path.join(inital_model_directory,xtal)) -# for dirs in glob.glob('*'): -# if os.path.isdir(dirs) and dirs.startswith('Refine_'): -# found_previous_refinement=True -# break -# if not found_previous_refinement: -# # first delete possible old symbolic links -# if os.path.isfile('refine.pdb'): os.system('/bin/rm refine.pdb') -# os.symlink('dimple.pdb','refine.pdb') -# if os.path.isfile('refine.mtz'): os.system('/bin/rm refine.mtz') -# os.symlink('dimple.mtz','refine.mtz') + # found_previous_refinement=False + # os.chdir(os.path.join(inital_model_directory,xtal)) + # for dirs in glob.glob('*'): + # if os.path.isdir(dirs) and dirs.startswith('Refine_'): + # found_previous_refinement=True + # break + # if not found_previous_refinement: + # # first delete possible old symbolic links + # if os.path.isfile('refine.pdb'): os.system('/bin/rm refine.pdb') + # os.symlink('dimple.pdb','refine.pdb') + # if os.path.isfile('refine.mtz'): os.system('/bin/rm refine.mtz') + # os.symlink('dimple.mtz','refine.mtz') # finally, update data source - print('==> xce: updating data source after DIMPLE run') + print("==> xce: updating data source after DIMPLE run") db.update_data_source(xtal, db_dict) else: @@ -108,7 +195,7 @@ # python os.path.isfile is False if symbolic link points to non existing file # so we remove all of them! os.chdir(os.path.join(inital_model_directory, xtal)) - os.system('/bin/rm dimple_twin.pdb') - os.system('/bin/rm dimple_twin.mtz') - os.system('/bin/rm 2fofc_twin.map') - os.system('/bin/rm fofc_twin.map') + os.system("/bin/rm dimple_twin.pdb") + os.system("/bin/rm dimple_twin.mtz") + os.system("/bin/rm 2fofc_twin.map") + os.system("/bin/rm fofc_twin.map") diff --git a/helpers/update_pandda_status_flag.py b/helpers/update_pandda_status_flag.py index 4f5606af..07a26d5e 100755 --- a/helpers/update_pandda_status_flag.py +++ b/helpers/update_pandda_status_flag.py @@ -3,19 +3,26 @@ import XChemDB import os import sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) def update_data_source(db_file, crystalString, status): db = XChemDB.data_source(db_file) - print("update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format( - status, "'"+crystalString.replace(",", "','")+"'")) - db.execute_statement("update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format( - status, "'"+crystalString.replace(",", "','")+"'")) + print( + "update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format( + status, "'" + crystalString.replace(",", "','") + "'" + ) + ) + db.execute_statement( + "update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format( + status, "'" + crystalString.replace(",", "','") + "'" + ) + ) -if __name__ == '__main__': +if __name__ == "__main__": db_file = sys.argv[1] crystalString = sys.argv[2] status = sys.argv[3] diff --git a/helpers/update_status_flag.py b/helpers/update_status_flag.py index 1ca8714f..1ac3b71c 100755 --- a/helpers/update_status_flag.py +++ b/helpers/update_status_flag.py @@ -3,7 +3,8 @@ import XChemDB import os import sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) + +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) def update_data_source(db_file, xtal, db_column, status): @@ -12,7 +13,7 @@ def update_data_source(db_file, xtal, db_column, status): db.update_data_source(xtal, db_dict) -if __name__ == '__main__': +if __name__ == "__main__": db_file = sys.argv[1] xtal = sys.argv[2] db_column = sys.argv[3] diff --git a/lib/PuckDB.py b/lib/PuckDB.py index 622f08f3..5c35ea61 100755 --- a/lib/PuckDB.py +++ b/lib/PuckDB.py @@ -2,26 +2,25 @@ import os import sys -sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") class puck_db(object): - def __init__(self, data_base): self.data_base = data_base def get_all_pucks_from_DB(self): - print('hello') + print("hello") def insert_mounted_crystals(self): - print('hello') + print("hello") def kill_mounted_cryatsl(self): - print('hello') + print("hello") def change_puck_location(self): - print('hello') + print("hello") def execute_sqlite(self): - print('hello') + print("hello") diff --git a/lib/XChemCoot.py b/lib/XChemCoot.py index 63dea5da..8acc92e0 100755 --- a/lib/XChemCoot.py +++ b/lib/XChemCoot.py @@ -20,7 +20,7 @@ # from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas # XCE libraries -sys.path.append(os.getenv('XChemExplorer_DIR') + '/lib') +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") # libraries from COOT @@ -40,57 +40,60 @@ def __init__(self): # read in settings file from XChemExplorer to set the relevant paths self.settings = pickle.load(open(".xce_settings.pkl", "rb")) - remote_qsub_submission = self.settings['remote_qsub'] - self.database_directory = self.settings['database_directory'] - self.xce_logfile = self.settings['xce_logfile'] + remote_qsub_submission = self.settings["remote_qsub"] + self.database_directory = self.settings["database_directory"] + self.xce_logfile = self.settings["xce_logfile"] self.Logfile = XChemLog.updateLog(self.xce_logfile) - self.Logfile.insert('==> COOT: starting coot plugin...') - self.data_source = self.settings['data_source'] + self.Logfile.insert("==> COOT: starting coot plugin...") + self.data_source = self.settings["data_source"] self.db = XChemDB.data_source(self.data_source) print(self.settings) # checking for external software packages - self.external_software = XChemUtils.external_software( - self.xce_logfile).check() - self.external_software['qsub_remote'] = remote_qsub_submission - - self.selection_criteria = ['0 - All Datasets', - '1 - Analysis Pending', - '2 - PANDDA model', - '3 - In Refinement', - '4 - CompChem ready', - '5 - Deposition ready', - '6 - Deposited', - '7 - Analysed & Rejected'] - - self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], - ['In Refinement', '3 - In Refinement', 65000, 0, 0], - ['Comp Chem Ready!', - '4 - CompChem ready', 65000, 0, 0], - ['Ready for Deposition!', - '5 - Deposition ready', 65000, 0, 0], - ['In PDB', '6 - Deposited', 65000, 0, 0], - ['Analysed & Rejected', '7 - Analysed & Rejected', 65000, 0, 0]] - - self.ligand_confidence_category = ['0 - no ligand present', - '1 - Low Confidence', - '2 - Correct ligand, weak density', - '3 - Clear density, unexpected ligand', - '4 - High Confidence'] + self.external_software = XChemUtils.external_software(self.xce_logfile).check() + self.external_software["qsub_remote"] = remote_qsub_submission + + self.selection_criteria = [ + "0 - All Datasets", + "1 - Analysis Pending", + "2 - PANDDA model", + "3 - In Refinement", + "4 - CompChem ready", + "5 - Deposition ready", + "6 - Deposited", + "7 - Analysed & Rejected", + ] + + self.experiment_stage = [ + ["Review PANDDA export", "2 - PANDDA model", 65000, 0, 0], + ["In Refinement", "3 - In Refinement", 65000, 0, 0], + ["Comp Chem Ready!", "4 - CompChem ready", 65000, 0, 0], + ["Ready for Deposition!", "5 - Deposition ready", 65000, 0, 0], + ["In PDB", "6 - Deposited", 65000, 0, 0], + ["Analysed & Rejected", "7 - Analysed & Rejected", 65000, 0, 0], + ] + + self.ligand_confidence_category = [ + "0 - no ligand present", + "1 - Low Confidence", + "2 - Correct ligand, weak density", + "3 - Clear density, unexpected ligand", + "4 - High Confidence", + ] self.ligand_site_information = self.db.get_list_of_pandda_sites_for_coot() # this decides which samples will be looked at - self.selection_mode = '' + self.selection_mode = "" # self.selected_site='' self.pandda_index = -1 # refers to the number of sites - self.site_index = '0' - self.event_index = '0' + self.site_index = "0" + self.event_index = "0" # the Folder is kind of a legacy thing because my inital idea was to have separate folders # for Data Processing and Refinement - self.project_directory = self.settings['initial_model_directory'] + self.project_directory = self.settings["initial_model_directory"] self.Serial = 0 self.panddaSerial = 0 self.Refine = None @@ -98,26 +101,28 @@ def __init__(self): self.Todo = [] self.siteDict = {} - self.xtalID = '' - self.compoundID = '' - self.ground_state_mean_map = '' - self.spider_plot = '' - self.ligand_confidence = '' - self.refinement_folder = '' - self.refinementProtocol = 'pandda_refmac' + self.xtalID = "" + self.compoundID = "" + self.ground_state_mean_map = "" + self.spider_plot = "" + self.ligand_confidence = "" + self.refinement_folder = "" + self.refinementProtocol = "pandda_refmac" # self.datasetOutcome='' - self.pdb_style = 'refine.pdb' - self.mtz_style = 'refine.mtz' + self.pdb_style = "refine.pdb" + self.mtz_style = "refine.mtz" self.label = None # stores imol of currently loaded molecules and maps - self.mol_dict = {'protein': -1, - 'ligand': -1, - '2fofc': -1, - 'fofc': -1, - 'event': -1} + self.mol_dict = { + "protein": -1, + "ligand": -1, + "2fofc": -1, + "fofc": -1, + "event": -1, + } # two dictionaries which are flushed when a new crystal is loaded # and which contain information to update the data source if necessary @@ -132,51 +137,61 @@ def __init__(self): coot.set_colour_map_rotation_for_map(0) # coot.set_colour_map_rotation_on_read_pdb_flag(21) - self.QualityIndicators = {'RefinementRcryst': '-', - 'RefinementRfree': '-', - 'RefinementRfreeTraficLight': 'gray', - 'RefinementResolution': '-', - 'RefinementResolutionTL': 'gray', - 'RefinementMolProbityScore': '-', - 'RefinementMolProbityScoreTL': 'gray', - 'RefinementRamachandranOutliers': '-', - 'RefinementRamachandranOutliersTL': 'gray', - 'RefinementRamachandranFavored': '-', - 'RefinementRamachandranFavoredTL': 'gray', - 'RefinementRmsdBonds': '-', - 'RefinementRmsdBondsTL': 'gray', - 'RefinementRmsdAngles': '-', - 'RefinementRmsdAnglesTL': 'gray', - 'RefinementMatrixWeight': '-'} - - self.spider_plot_data = {'PANDDA_site_ligand_id': '-', - 'PANDDA_site_occupancy': '-', - 'PANDDA_site_B_average': '-', - 'PANDDA_site_B_ratio_residue_surroundings': '-', - 'PANDDA_site_RSCC': '-', - 'PANDDA_site_rmsd': '-', - 'PANDDA_site_RSR': '-', - 'PANDDA_site_RSZD': '-'} + self.QualityIndicators = { + "RefinementRcryst": "-", + "RefinementRfree": "-", + "RefinementRfreeTraficLight": "gray", + "RefinementResolution": "-", + "RefinementResolutionTL": "gray", + "RefinementMolProbityScore": "-", + "RefinementMolProbityScoreTL": "gray", + "RefinementRamachandranOutliers": "-", + "RefinementRamachandranOutliersTL": "gray", + "RefinementRamachandranFavored": "-", + "RefinementRamachandranFavoredTL": "gray", + "RefinementRmsdBonds": "-", + "RefinementRmsdBondsTL": "gray", + "RefinementRmsdAngles": "-", + "RefinementRmsdAnglesTL": "gray", + "RefinementMatrixWeight": "-", + } + + self.spider_plot_data = { + "PANDDA_site_ligand_id": "-", + "PANDDA_site_occupancy": "-", + "PANDDA_site_B_average": "-", + "PANDDA_site_B_ratio_residue_surroundings": "-", + "PANDDA_site_RSCC": "-", + "PANDDA_site_rmsd": "-", + "PANDDA_site_RSR": "-", + "PANDDA_site_RSZD": "-", + } # default refmac parameters - self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': ''} + self.RefmacParams = { + "HKLIN": "", + "HKLOUT": "", + "XYZIN": "", + "XYZOUT": "", + "LIBIN": "", + "LIBOUT": "", + "TLSIN": "", + "TLSOUT": "", + "TLSADD": "", + "NCYCLES": "10", + "MATRIX_WEIGHT": "AUTO", + "BREF": " bref ISOT\n", + "TLS": "", + "NCS": "", + "TWIN": "", + } # XCE menu menu = coot_menubar_menu("XCE") add_simple_coot_menu_menuitem( - menu, "set all occupanicies to 1", - lambda func: self.reset_occupancy()) + menu, "set all occupanicies to 1", lambda func: self.reset_occupancy() + ) def StartGUI(self): @@ -191,7 +206,7 @@ def StartGUI(self): # --- Sample Selection --- # self.vbox.add(gtk.Label('Select Samples')) - frame = gtk.Frame(label='Select Samples') + frame = gtk.Frame(label="Select Samples") self.hbox_select_samples = gtk.HBox() # vbox=gtk.VBox() @@ -208,8 +223,7 @@ def StartGUI(self): # self.hbox_select_samples.add(self.cb_select_sites) self.select_samples_button = gtk.Button(label="GO") - self.select_samples_button.connect( - "clicked", self.get_samples_to_look_at) + self.select_samples_button.connect("clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) @@ -224,25 +238,24 @@ def StartGUI(self): ################################################################################# # --- refinement protocol --- frame = gtk.Frame() - self.refinementProtocolcheckbox = gtk.CheckButton( - 'PanDDA model refinement)') + self.refinementProtocolcheckbox = gtk.CheckButton("PanDDA model refinement)") # callback is defined later -# self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) + # self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) self.refinementProtocolcheckbox.set_active(True) frame.add(self.refinementProtocolcheckbox) self.vbox.pack_start(frame) ################################################################################# # --- refinement program --- -# frame = gtk.Frame() -# self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') -# self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) -# self.refinementProgramcheckbox.set_active(False) -# frame.add(self.refinementProgramcheckbox) -# self.vbox.pack_start(frame) + # frame = gtk.Frame() + # self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') + # self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) + # self.refinementProgramcheckbox.set_active(False) + # frame.add(self.refinementProgramcheckbox) + # self.vbox.pack_start(frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# # --- Refinement Statistics --- @@ -250,163 +263,162 @@ def StartGUI(self): # a combination of labels and textview widgets, arranged in a table RRfreeLabel_frame = gtk.Frame() - self.RRfreeLabel = gtk.Label('R/Rfree') + self.RRfreeLabel = gtk.Label("R/Rfree") RRfreeLabel_frame.add(self.RRfreeLabel) self.RRfreeValue = gtk.Label( - self.QualityIndicators['RefinementRcryst'] + '/' + self.QualityIndicators['RefinementRfree']) + self.QualityIndicators["RefinementRcryst"] + + "/" + + self.QualityIndicators["RefinementRfree"] + ) RRfreeBox_frame = gtk.Frame() self.RRfreeBox = gtk.EventBox() self.RRfreeBox.add(self.RRfreeValue) RRfreeBox_frame.add(self.RRfreeBox) ResolutionLabel_frame = gtk.Frame() - self.ResolutionLabel = gtk.Label('Resolution') + self.ResolutionLabel = gtk.Label("Resolution") ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label( - self.QualityIndicators['RefinementResolution']) + self.ResolutionValue = gtk.Label(self.QualityIndicators["RefinementResolution"]) ResolutionBox_frame = gtk.Frame() self.ResolutionBox = gtk.EventBox() self.ResolutionBox.add(self.ResolutionValue) ResolutionBox_frame.add(self.ResolutionBox) MolprobityScoreLabel_frame = gtk.Frame() - self.MolprobityScoreLabel = gtk.Label('MolprobityScore') + self.MolprobityScoreLabel = gtk.Label("MolprobityScore") MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) self.MolprobityScoreValue = gtk.Label( - self.QualityIndicators['RefinementMolProbityScore']) + self.QualityIndicators["RefinementMolProbityScore"] + ) MolprobityScoreBox_frame = gtk.Frame() self.MolprobityScoreBox = gtk.EventBox() self.MolprobityScoreBox.add(self.MolprobityScoreValue) MolprobityScoreBox_frame.add(self.MolprobityScoreBox) RamachandranOutliersLabel_frame = gtk.Frame() - self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') + self.RamachandranOutliersLabel = gtk.Label("Rama Outliers") RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) self.RamachandranOutliersValue = gtk.Label( - self.QualityIndicators['RefinementRamachandranOutliers']) + self.QualityIndicators["RefinementRamachandranOutliers"] + ) RamachandranOutliersBox_frame = gtk.Frame() self.RamachandranOutliersBox = gtk.EventBox() self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) RamachandranOutliersBox_frame.add(self.RamachandranOutliersBox) RamachandranFavoredLabel_frame = gtk.Frame() - self.RamachandranFavoredLabel = gtk.Label('Rama Favored') + self.RamachandranFavoredLabel = gtk.Label("Rama Favored") RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) self.RamachandranFavoredValue = gtk.Label( - self.QualityIndicators['RefinementRamachandranFavored']) + self.QualityIndicators["RefinementRamachandranFavored"] + ) RamachandranFavoredBox_frame = gtk.Frame() self.RamachandranFavoredBox = gtk.EventBox() self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) RamachandranFavoredBox_frame.add(self.RamachandranFavoredBox) rmsdBondsLabel_frame = gtk.Frame() - self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') + self.rmsdBondsLabel = gtk.Label("rmsd(Bonds)") rmsdBondsLabel_frame.add(self.rmsdBondsLabel) - self.rmsdBondsValue = gtk.Label( - self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue = gtk.Label(self.QualityIndicators["RefinementRmsdBonds"]) rmsdBondsBox_frame = gtk.Frame() self.rmsdBondsBox = gtk.EventBox() self.rmsdBondsBox.add(self.rmsdBondsValue) rmsdBondsBox_frame.add(self.rmsdBondsBox) rmsdAnglesLabel_frame = gtk.Frame() - self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') + self.rmsdAnglesLabel = gtk.Label("rmsd(Angles)") rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) - self.rmsdAnglesValue = gtk.Label( - self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue = gtk.Label(self.QualityIndicators["RefinementRmsdAngles"]) rmsdAnglesBox_frame = gtk.Frame() self.rmsdAnglesBox = gtk.EventBox() self.rmsdAnglesBox.add(self.rmsdAnglesValue) rmsdAnglesBox_frame.add(self.rmsdAnglesBox) MatrixWeightLabel_frame = gtk.Frame() - self.MatrixWeightLabel = gtk.Label('Matrix Weight') + self.MatrixWeightLabel = gtk.Label("Matrix Weight") MatrixWeightLabel_frame.add(self.MatrixWeightLabel) self.MatrixWeightValue = gtk.Label( - self.QualityIndicators['RefinementMatrixWeight']) + self.QualityIndicators["RefinementMatrixWeight"] + ) MatrixWeightBox_frame = gtk.Frame() self.MatrixWeightBox = gtk.EventBox() self.MatrixWeightBox.add(self.MatrixWeightValue) MatrixWeightBox_frame.add(self.MatrixWeightBox) ligandIDLabel_frame = gtk.Frame() - self.ligandIDLabel = gtk.Label('Ligand ID') + self.ligandIDLabel = gtk.Label("Ligand ID") ligandIDLabel_frame.add(self.ligandIDLabel) - self.ligandIDValue = gtk.Label( - self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue = gtk.Label(self.spider_plot_data["PANDDA_site_ligand_id"]) ligandIDBox_frame = gtk.Frame() self.ligandIDBox = gtk.EventBox() self.ligandIDBox.add(self.ligandIDValue) ligandIDBox_frame.add(self.ligandIDBox) ligand_occupancyLabel_frame = gtk.Frame() - self.ligand_occupancyLabel = gtk.Label('occupancy') + self.ligand_occupancyLabel = gtk.Label("occupancy") ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) self.ligand_occupancyValue = gtk.Label( - self.spider_plot_data['PANDDA_site_occupancy']) + self.spider_plot_data["PANDDA_site_occupancy"] + ) ligand_occupancyBox_frame = gtk.Frame() self.ligand_occupancyBox = gtk.EventBox() self.ligand_occupancyBox.add(self.ligand_occupancyValue) ligand_occupancyBox_frame.add(self.ligand_occupancyBox) ligand_BaverageLabel_frame = gtk.Frame() - self.ligand_BaverageLabel = gtk.Label('B average') + self.ligand_BaverageLabel = gtk.Label("B average") ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) self.ligand_BaverageValue = gtk.Label( - self.spider_plot_data['PANDDA_site_B_average']) + self.spider_plot_data["PANDDA_site_B_average"] + ) ligand_BaverageBox_frame = gtk.Frame() self.ligand_BaverageBox = gtk.EventBox() self.ligand_BaverageBox.add(self.ligand_BaverageValue) ligand_BaverageBox_frame.add(self.ligand_BaverageBox) ligand_BratioSurroundingsLabel_frame = gtk.Frame() - self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') - ligand_BratioSurroundingsLabel_frame.add( - self.ligand_BratioSurroundingsLabel) + self.ligand_BratioSurroundingsLabel = gtk.Label("B ratio") + ligand_BratioSurroundingsLabel_frame.add(self.ligand_BratioSurroundingsLabel) self.ligand_BratioSurroundingsValue = gtk.Label( - self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) + self.spider_plot_data["PANDDA_site_B_ratio_residue_surroundings"] + ) ligand_BratioSurroundingsBox_frame = gtk.Frame() self.ligand_BratioSurroundingsBox = gtk.EventBox() - self.ligand_BratioSurroundingsBox.add( - self.ligand_BratioSurroundingsValue) - ligand_BratioSurroundingsBox_frame.add( - self.ligand_BratioSurroundingsBox) + self.ligand_BratioSurroundingsBox.add(self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add(self.ligand_BratioSurroundingsBox) ligand_RSCCLabel_frame = gtk.Frame() - self.ligand_RSCCLabel = gtk.Label('RSCC') + self.ligand_RSCCLabel = gtk.Label("RSCC") ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) - self.ligand_RSCCValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSCC']) + self.ligand_RSCCValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSCC"]) ligand_RSCCBox_frame = gtk.Frame() self.ligand_RSCCBox = gtk.EventBox() self.ligand_RSCCBox.add(self.ligand_RSCCValue) ligand_RSCCBox_frame.add(self.ligand_RSCCBox) ligand_rmsdLabel_frame = gtk.Frame() - self.ligand_rmsdLabel = gtk.Label('rmsd') + self.ligand_rmsdLabel = gtk.Label("rmsd") ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) - self.ligand_rmsdValue = gtk.Label( - self.spider_plot_data['PANDDA_site_rmsd']) + self.ligand_rmsdValue = gtk.Label(self.spider_plot_data["PANDDA_site_rmsd"]) ligand_rmsdBox_frame = gtk.Frame() self.ligand_rmsdBox = gtk.EventBox() self.ligand_rmsdBox.add(self.ligand_rmsdValue) ligand_rmsdBox_frame.add(self.ligand_rmsdBox) ligand_RSRLabel_frame = gtk.Frame() - self.ligand_RSRLabel = gtk.Label('RSR') + self.ligand_RSRLabel = gtk.Label("RSR") ligand_RSRLabel_frame.add(self.ligand_RSRLabel) - self.ligand_RSRValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSR']) + self.ligand_RSRValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSR"]) ligand_RSRBox_frame = gtk.Frame() self.ligand_RSRBox = gtk.EventBox() self.ligand_RSRBox.add(self.ligand_RSRValue) ligand_RSRBox_frame.add(self.ligand_RSRBox) ligand_RSZDLabel_frame = gtk.Frame() - self.ligand_RSZDLabel = gtk.Label('RSZD') + self.ligand_RSZDLabel = gtk.Label("RSZD") ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) - self.ligand_RSZDValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSZD']) + self.ligand_RSZDValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSZD"]) ligand_RSZDBox_frame = gtk.Frame() self.ligand_RSZDBox = gtk.EventBox() self.ligand_RSZDBox.add(self.ligand_RSZDValue) @@ -441,8 +453,7 @@ def StartGUI(self): self.table_right.attach(ligandIDLabel_frame, 0, 1, 0, 1) self.table_right.attach(ligand_occupancyLabel_frame, 0, 1, 1, 2) self.table_right.attach(ligand_BaverageLabel_frame, 0, 1, 2, 3) - self.table_right.attach( - ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach(ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) self.table_right.attach(ligand_RSCCLabel_frame, 0, 1, 4, 5) self.table_right.attach(ligand_rmsdLabel_frame, 0, 1, 5, 6) self.table_right.attach(ligand_RSRLabel_frame, 0, 1, 6, 7) @@ -467,17 +478,19 @@ def StartGUI(self): hbox.add(button) # --- ground state mean map --- self.ground_state_mean_map_button = gtk.Button( - label="Show ground state mean map") + label="Show ground state mean map" + ) self.ground_state_mean_map_button.connect( - "clicked", self.show_ground_state_mean_map) + "clicked", self.show_ground_state_mean_map + ) hbox.add(self.ground_state_mean_map_button) -# self.vbox.add(self.ground_state_mean_map_button) + # self.vbox.add(self.ground_state_mean_map_button) self.vbox.add(hbox) self.vbox.pack_start(frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# # --- hbox for compound picture & spider_plot (formerly: refinement history) --- @@ -487,7 +500,12 @@ def StartGUI(self): # --- compound picture --- compound_frame = gtk.Frame() pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_COMPOUND_IMAGE_AVAILABLE.png", + ) + ) self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.image = gtk.Image() self.image.set_from_pixbuf(self.pic) @@ -502,9 +520,11 @@ def StartGUI(self): # --- Spider Plot --- spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + os.path.join( + os.getenv("XChemExplorer_DIR"), "image", "NO_SPIDER_PLOT_AVAILABLE.png" + ) + ) + self.spider_plot_pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image = gtk.Image() self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) spider_plot_frame.add(self.spider_plot_image) @@ -515,54 +535,54 @@ def StartGUI(self): ################################################################################# # --- pandda.inspect user comments --- -# outer_frame = gtk.Frame(label='pandda.inspect comments') -# vbox = gtk.VBox() -# ligand_site_name_label_frame = gtk.Frame() -# ligand_site_name_label = gtk.Label('Site Name') -# ligand_site_name_label_frame.add(ligand_site_name_label) -# ligand_inspect_confidence_label_frame = gtk.Frame() -# ligand_inspect_confidence_label = gtk.Label('Confidence') -# ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) -# ligand_inspect_interesting_label_frame = gtk.Frame() -# ligand_inspect_interesting_label = gtk.Label('Interesting') -# ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) -# ligand_inspect_comment_label_frame = gtk.Frame() -# ligand_inspect_comment_label = gtk.Label('Comment') -# ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) -# ligand_site_name_value_frame = gtk.Frame() -# self.ligand_site_name_value = gtk.Label('-') -# ligand_site_name_value_frame.add(self.ligand_site_name_value) -# ligand_inspect_confidence_value_frame = gtk.Frame() -# self.ligand_inspect_confidence_value = gtk.Label('-') -# ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) -# ligand_inspect_interesting_value_frame = gtk.Frame() -# self.ligand_inspect_interesting_value = gtk.Label('-') -# ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) -# ligand_inspect_comment_value_frame = gtk.Frame() -# self.ligand_inspect_comment_value = gtk.Label('-') -# ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) -# -# frame_pandda_inspect_comments_table = gtk.Frame() -# pandda_inspect_comments_table = gtk.Table(2, 6, False) -# pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) -# pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) -# pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) -# -# frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) -# vbox.add(frame_pandda_inspect_comments_table) -# outer_frame.add(vbox) -# self.vbox.pack_start(outer_frame) + # outer_frame = gtk.Frame(label='pandda.inspect comments') + # vbox = gtk.VBox() + # ligand_site_name_label_frame = gtk.Frame() + # ligand_site_name_label = gtk.Label('Site Name') + # ligand_site_name_label_frame.add(ligand_site_name_label) + # ligand_inspect_confidence_label_frame = gtk.Frame() + # ligand_inspect_confidence_label = gtk.Label('Confidence') + # ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) + # ligand_inspect_interesting_label_frame = gtk.Frame() + # ligand_inspect_interesting_label = gtk.Label('Interesting') + # ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) + # ligand_inspect_comment_label_frame = gtk.Frame() + # ligand_inspect_comment_label = gtk.Label('Comment') + # ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) + # ligand_site_name_value_frame = gtk.Frame() + # self.ligand_site_name_value = gtk.Label('-') + # ligand_site_name_value_frame.add(self.ligand_site_name_value) + # ligand_inspect_confidence_value_frame = gtk.Frame() + # self.ligand_inspect_confidence_value = gtk.Label('-') + # ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) + # ligand_inspect_interesting_value_frame = gtk.Frame() + # self.ligand_inspect_interesting_value = gtk.Label('-') + # ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) + # ligand_inspect_comment_value_frame = gtk.Frame() + # self.ligand_inspect_comment_value = gtk.Label('-') + # ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) + # + # frame_pandda_inspect_comments_table = gtk.Frame() + # pandda_inspect_comments_table = gtk.Table(2, 6, False) + # pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) + # pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) + # pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) + # + # frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) + # vbox.add(frame_pandda_inspect_comments_table) + # outer_frame.add(vbox) + # self.vbox.pack_start(outer_frame) # # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# - outer_frame = gtk.Frame(label='Sample Navigator') + outer_frame = gtk.Frame(label="Sample Navigator") hboxSample = gtk.HBox() # --- crystal navigator combobox --- @@ -605,51 +625,51 @@ def StartGUI(self): self.vbox.add(outer_frame) # # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# -# outer_frame = gtk.Frame(label='Label') -# hboxlabel = gtk.HBox() -# -# frame = gtk.Frame() -# hbox = gtk.HBox() -# self.vbox_label = gtk.VBox() -# labels = self.db.get_labels_from_db() -# if len(labels) > 5: -# print '==> sorry, too many labels; cannot display them in panel' -# labels = labels[:5] -# # with radiobuttons, one of them needs to be always on -# # but there will be cases when the user has not assigned a label yet -# # hence, the not_shown button is not shown but gets active -# # if the label has not been set yet -# labels.append('not_shown') -# for n, l in enumerate(labels): -# print n,l -# if n == 0: -# new_button = gtk.RadioButton(None, l) -# else: -# new_button = gtk.RadioButton(new_button, l) -# new_button.connect("toggled", self.label_button_clicked, l) -# if not l == 'not_shown': -# hbox.add(new_button) -# self.label_button_list.append(new_button) -# self.vbox_label.add(hbox) -# frame.add(self.vbox_label) -# -# hboxlabel.add(frame) -# -# outer_frame.add(hboxlabel) -# self.vbox.add(outer_frame) + # outer_frame = gtk.Frame(label='Label') + # hboxlabel = gtk.HBox() + # + # frame = gtk.Frame() + # hbox = gtk.HBox() + # self.vbox_label = gtk.VBox() + # labels = self.db.get_labels_from_db() + # if len(labels) > 5: + # print '==> sorry, too many labels; cannot display them in panel' + # labels = labels[:5] + # # with radiobuttons, one of them needs to be always on + # # but there will be cases when the user has not assigned a label yet + # # hence, the not_shown button is not shown but gets active + # # if the label has not been set yet + # labels.append('not_shown') + # for n, l in enumerate(labels): + # print n,l + # if n == 0: + # new_button = gtk.RadioButton(None, l) + # else: + # new_button = gtk.RadioButton(new_button, l) + # new_button.connect("toggled", self.label_button_clicked, l) + # if not l == 'not_shown': + # hbox.add(new_button) + # self.label_button_list.append(new_button) + # self.vbox_label.add(hbox) + # frame.add(self.vbox_label) + # + # hboxlabel.add(frame) + # + # outer_frame.add(hboxlabel) + # self.vbox.add(outer_frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# # --- current refinement stage --- outer_frame = gtk.Frame() hbox = gtk.HBox() - frame = gtk.Frame(label='Analysis Status') + frame = gtk.Frame(label="Analysis Status") vbox = gtk.VBox() self.experiment_stage_button_list = [] for n, button in enumerate(self.experiment_stage): @@ -658,15 +678,16 @@ def StartGUI(self): else: new_button = gtk.RadioButton(new_button, button[0]) new_button.connect( - "toggled", self.experiment_stage_button_clicked, button[1]) + "toggled", self.experiment_stage_button_clicked, button[1] + ) vbox.pack_start(new_button, False, False, 0) -# vbox.add(new_button) + # vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) # --- ligand confidence --- - frame = gtk.Frame(label='Ligand Confidence') + frame = gtk.Frame(label="Ligand Confidence") vbox = gtk.VBox() self.ligand_confidence_button_list = [] for n, criteria in enumerate(self.ligand_confidence_category): @@ -675,56 +696,55 @@ def StartGUI(self): else: new_button = gtk.RadioButton(new_button, criteria) new_button.connect( - "toggled", self.ligand_confidence_button_clicked, criteria) + "toggled", self.ligand_confidence_button_clicked, criteria + ) vbox.pack_start(new_button, False, False, 0) -# vbox.add(new_button) + # vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) # label section --> start -# frame = gtk.Frame(label='Label') -# vbox = gtk.VBox() -# labels = self.db.get_labels_from_db() -# if len(labels) > 5: -# print '==> sorry, too many labels; cannot display them in panel' -# labels = labels[:5] -# # with radiobuttons, one of them needs to be always on -# # but there will be cases when the user has not assigned a label yet -# # hence, the not_shown button is not shown but gets active -# # if the label has not been set yet -# labels.append('not_shown') -# for n, l in enumerate(labels): -# print n,l -# if n == 0: -# new_button = gtk.RadioButton(None, l) -# else: -# new_button = gtk.RadioButton(new_button, l) -# new_button.connect("toggled", self.label_button_clicked, l) -# if not l == 'not_shown': -# vbox.add(new_button) -# self.label_button_list.append(new_button) -# frame.add(vbox) -# hbox.pack_start(frame) -# # label section <-- end + # frame = gtk.Frame(label='Label') + # vbox = gtk.VBox() + # labels = self.db.get_labels_from_db() + # if len(labels) > 5: + # print '==> sorry, too many labels; cannot display them in panel' + # labels = labels[:5] + # # with radiobuttons, one of them needs to be always on + # # but there will be cases when the user has not assigned a label yet + # # hence, the not_shown button is not shown but gets active + # # if the label has not been set yet + # labels.append('not_shown') + # for n, l in enumerate(labels): + # print n,l + # if n == 0: + # new_button = gtk.RadioButton(None, l) + # else: + # new_button = gtk.RadioButton(new_button, l) + # new_button.connect("toggled", self.label_button_clicked, l) + # if not l == 'not_shown': + # vbox.add(new_button) + # self.label_button_list.append(new_button) + # frame.add(vbox) + # hbox.pack_start(frame) + # # label section <-- end outer_frame.add(hbox) self.vbox.pack_start(outer_frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) # --- ligand modeling --- - frame = gtk.Frame(label='Ligand Modeling') + frame = gtk.Frame(label="Ligand Modeling") self.hbox_for_modeling = gtk.HBox() self.merge_ligand_button = gtk.Button(label="Merge Ligand") self.place_ligand_here_button = gtk.Button(label="Place Ligand here") self.hbox_for_modeling.add(self.place_ligand_here_button) - self.place_ligand_here_button.connect( - "clicked", self.place_ligand_here) + self.place_ligand_here_button.connect("clicked", self.place_ligand_here) self.hbox_for_modeling.add(self.merge_ligand_button) - self.merge_ligand_button.connect( - "clicked", self.merge_ligand_into_protein) + self.merge_ligand_button.connect("clicked", self.merge_ligand_into_protein) frame.add(self.hbox_for_modeling) self.vbox.pack_start(frame) @@ -751,7 +771,8 @@ def StartGUI(self): # need to put it here, because attributes within refinementProtocolCallback function # are defined after checkbox is defined self.refinementProtocolcheckbox.connect( - "toggled", self.refinementProtocolCallback) + "toggled", self.refinementProtocolCallback + ) # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") @@ -781,10 +802,10 @@ def ChooseXtal(self, widget): self.merge_ligand_button.set_sensitive(True) self.place_ligand_here_button.set_sensitive(True) -# self.ligand_site_name_value.set_label('-') -# self.ligand_inspect_confidence_value.set_label('-') -# self.ligand_inspect_interesting_value.set_label('-') -# self.ligand_inspect_comment_value.set_label('-') + # self.ligand_site_name_value.set_label('-') + # self.ligand_inspect_confidence_value.set_label('-') + # self.ligand_inspect_interesting_value.set_label('-') + # self.ligand_inspect_comment_value.set_label('-') self.refresh_site_combobox() self.db_dict_mainTable = {} @@ -794,13 +815,15 @@ def ChooseXtal(self, widget): self.refinement_folder = str(self.Todo[self.index][4]) self.refinement_outcome = str(self.Todo[self.index][5]) self.label = self.db.get_label_of_sample(self.xtalID) -# self.update_label_radiobutton() + # self.update_label_radiobutton() self.update_RefinementOutcome_radiobutton() - if self.xtalID not in self.siteDict: # i.e. we are not working with a PanDDA model + if ( + self.xtalID not in self.siteDict + ): # i.e. we are not working with a PanDDA model self.ligand_confidence = str(self.Todo[self.index][6]) self.update_LigandConfidence_radiobutton() self.label = self.db.get_label_of_sample(self.xtalID) -# self.update_label_radiobutton() + # self.update_label_radiobutton() self.RefreshData() @@ -824,7 +847,7 @@ def update_label_radiobutton(self): found = True if not found: for button in self.label_button_list: - if button.get_label() == 'not_shown': + if button.get_label() == "not_shown": button.set_active(True) break @@ -832,7 +855,7 @@ def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 for i, entry in enumerate(self.ligand_confidence_category): - print('--->', entry, self.ligand_confidence) + print("--->", entry, self.ligand_confidence) try: if entry.split()[0] == self.ligand_confidence.split()[0]: current_stage = i @@ -850,13 +873,14 @@ def refresh_site_combobox(self): # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites for n in range(-1, 100): self.cb_site.remove_text(0) - self.site_index = '0' - self.event_index = '0' + self.site_index = "0" + self.event_index = "0" # only repopulate if site exists if self.xtalID in self.siteDict: for item in sorted(self.siteDict[self.xtalID]): self.cb_site.append_text( - 'site: {0!s} - event: {1!s}'.format(item[5], item[6])) + "site: {0!s} - event: {1!s}".format(item[5], item[6]) + ) def ChangeSite(self, widget, data=None): if self.xtalID in self.siteDict: @@ -889,83 +913,100 @@ def RefreshSiteData(self): # and remove ligand molecule so that there is no temptation to merge it if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): - if self.compoundID + '.pdb' in coot.molecule_name(imol): + if self.compoundID + ".pdb" in coot.molecule_name(imol): coot.close_molecule(imol) for w in self.label_button_list: w.set_active(False) - print('pandda index', self.pandda_index) + print("pandda index", self.pandda_index) self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] - print('new spider plot:', self.spider_plot) + print("new spider plot:", self.spider_plot) self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] - print('new event map:', self.event_map) - self.ligand_confidence = str( - self.siteDict[self.xtalID][self.pandda_index][7]) + print("new event map:", self.event_map) + self.ligand_confidence = str(self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) - print('new site coordinates:', site_x, site_y, site_z) + print("new site coordinates:", site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) -# self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) -# self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) -# self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) -# self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) - - self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, - self.event_index) - print('>>>>> spider plot data', self.spider_plot_data) - self.ligandIDValue.set_label( - self.spider_plot_data['PANDDA_site_ligand_id']) + # self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) + # self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) + # self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) + # self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) + + self.spider_plot_data = ( + self.db.get_db_pandda_dict_for_sample_and_site_and_event( + self.xtalID, self.site_index, self.event_index + ) + ) + print(">>>>> spider plot data", self.spider_plot_data) + self.ligandIDValue.set_label(self.spider_plot_data["PANDDA_site_ligand_id"]) try: self.ligand_occupancyValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_occupancy"]), 2)) + ) except ValueError: - self.ligand_occupancyValue.set_label('-') + self.ligand_occupancyValue.set_label("-") try: self.ligand_BaverageValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_B_average"]), 2)) + ) except ValueError: - self.ligand_BaverageValue.set_label('-') + self.ligand_BaverageValue.set_label("-") try: self.ligand_BratioSurroundingsValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']), 2))) + str( + round( + float( + self.spider_plot_data[ + "PANDDA_site_B_ratio_residue_surroundings" + ] + ), + 2, + ) + ) + ) except ValueError: - self.ligand_BratioSurroundingsValue.set_label('-') + self.ligand_BratioSurroundingsValue.set_label("-") try: self.ligand_RSCCValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSCC"]), 2)) + ) except ValueError: - self.ligand_RSCCValue.set_label('-') + self.ligand_RSCCValue.set_label("-") try: self.ligand_rmsdValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_rmsd"]), 2)) + ) except ValueError: - self.ligand_rmsdValue.set_label('-') + self.ligand_rmsdValue.set_label("-") try: self.ligand_RSRValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSR"]), 2)) + ) except ValueError: - self.ligand_RSRValue.set_label('-') + self.ligand_RSRValue.set_label("-") try: self.ligand_RSZDValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSZD"]), 2)) + ) except ValueError: - self.ligand_RSZDValue.set_label('-') + self.ligand_RSZDValue.set_label("-") ######################################################################################### # delete old Event MAPs if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): - if 'map.native.ccp4' in coot.molecule_name(imol): + if "map.native.ccp4" in coot.molecule_name(imol): coot.close_molecule(imol) ######################################################################################### @@ -975,9 +1016,15 @@ def RefreshSiteData(self): spider_plot_pic = gtk.gdk.pixbuf_new_from_file(self.spider_plot) else: spider_plot_pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_SPIDER_PLOT_AVAILABLE.png", + ) + ) self.spider_plot_pic = spider_plot_pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + 190, 190, gtk.gdk.INTERP_BILINEAR + ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) ######################################################################################### @@ -993,116 +1040,176 @@ def RefreshSiteData(self): coot.set_last_map_colour(0.74, 0.44, 0.02) def experiment_stage_button_clicked(self, widget, data=None): - if data == '4 - CompChem ready' and self.refinementProtocol.startswith('pandda'): - print("==> XCE: removing refine.pdb and linking refine_.split.bound-state.pdb to refine.pdb") + if data == "4 - CompChem ready" and self.refinementProtocol.startswith( + "pandda" + ): + print( + "==> XCE: removing refine.pdb and linking refine_.split.bound-state.pdb to refine.pdb" + ) os.chdir(os.path.join(self.project_directory, self.xtalID)) - if os.path.realpath('refine.pdb').replace('.pdb', '.split.bound-state.pdb'): - newPDB = os.path.realpath('refine.pdb').replace( - '.pdb', '.split.bound-state.pdb') - os.system('/bin/rm refine.pdb') - os.system('ln -s .%s refine.pdb' % - newPDB.replace(os.getcwd(), '')) + if os.path.realpath("refine.pdb").replace(".pdb", ".split.bound-state.pdb"): + newPDB = os.path.realpath("refine.pdb").replace( + ".pdb", ".split.bound-state.pdb" + ) + os.system("/bin/rm refine.pdb") + os.system("ln -s .%s refine.pdb" % newPDB.replace(os.getcwd(), "")) self.refinementProtocolcheckbox.set_active(False) - self.refinementProtocol = 'refmac' + self.refinementProtocol = "refmac" else: - print('==> XCE ERROR: cannot find refine.output.bound-state.pdb') + print("==> XCE ERROR: cannot find refine.output.bound-state.pdb") pass - self.db_dict_mainTable['RefinementOutcome'] = data - print('==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( - data) + ' in mainTable of datasource') + self.db_dict_mainTable["RefinementOutcome"] = data + print( + "==> XCE: setting Refinement Outcome for " + + self.xtalID + + " to " + + str(data) + + " in mainTable of datasource" + ) # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - self.db.create_or_remove_missing_records_in_depositTable(self.xce_logfile, self.xtalID, 'ligand_bound', - self.db_dict_mainTable) + self.db.create_or_remove_missing_records_in_depositTable( + self.xce_logfile, self.xtalID, "ligand_bound", self.db_dict_mainTable + ) def ligand_confidence_button_clicked(self, widget, data=None): - print('PANDDA_index', self.pandda_index) + print("PANDDA_index", self.pandda_index) if self.pandda_index == -1: - self.db_dict_mainTable['RefinementLigandConfidence'] = data - print('==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( - data) + ' in mainTable of datasource') + self.db_dict_mainTable["RefinementLigandConfidence"] = data + print( + "==> XCE: setting Ligand Confidence for " + + self.xtalID + + " to " + + str(data) + + " in mainTable of datasource" + ) self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.Todo[self.index][6] = data else: - self.db_dict_panddaTable['PANDDA_site_confidence'] = data - print('==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( - self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( - data) + ' in panddaTable of datasource') - self.db.update_site_event_panddaTable(self.xtalID, self.site_index, self.event_index, - self.db_dict_panddaTable) + self.db_dict_panddaTable["PANDDA_site_confidence"] = data + print( + "==> XCE: setting Ligand Confidence for " + + self.xtalID + + " (site=" + + str(self.site_index) + + ", event=" + + str(self.event_index) + + ") to " + + str(data) + + " in panddaTable of datasource" + ) + self.db.update_site_event_panddaTable( + self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable + ) self.siteDict[self.xtalID][self.pandda_index][7] = data -# def update_label(self, widget): -# print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' -# # widget.pressed() -# for w in self.label_button_list: -# print w.get_label(), w.get_active() -# if w != widget: -# w.set_active(False) -# print '<<<<<<<<<<<<<<<<<<<<<<<<<<' -# self.db_dict_mainTable['label'] = widget.get_label() -# print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( -# widget.get_label()) + ' in mainTable of datasource' -# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - -# def label_button_clicked(self, widget, data=None): -# print '............',data -# if data == 'not_shown': -# self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) -# else: -# self.db_dict_mainTable['label'] = data -# print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' -# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + # def update_label(self, widget): + # print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' + # # widget.pressed() + # for w in self.label_button_list: + # print w.get_label(), w.get_active() + # if w != widget: + # w.set_active(False) + # print '<<<<<<<<<<<<<<<<<<<<<<<<<<' + # self.db_dict_mainTable['label'] = widget.get_label() + # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( + # widget.get_label()) + ' in mainTable of datasource' + # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + + # def label_button_clicked(self, widget, data=None): + # print '............',data + # if data == 'not_shown': + # self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) + # else: + # self.db_dict_mainTable['label'] = data + # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' + # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) def RefreshData(self): # reset spider plot image spider_plot_pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), "image", "NO_SPIDER_PLOT_AVAILABLE.png" + ) + ) self.spider_plot_pic = spider_plot_pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + 190, 190, gtk.gdk.INTERP_BILINEAR + ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) # reset ground state mean map - self.ground_state_mean_map = '' + self.ground_state_mean_map = "" self.ground_state_mean_map_button.set_sensitive(False) - self.ground_state_mean_map_button.set_label( - 'Show ground state mean map') + self.ground_state_mean_map_button.set_label("Show ground state mean map") if os.path.isfile( - os.path.join(self.project_directory, self.xtalID, self.xtalID + '-ground-state-mean-map.native.ccp4')): + os.path.join( + self.project_directory, + self.xtalID, + self.xtalID + "-ground-state-mean-map.native.ccp4", + ) + ): self.ground_state_mean_map_button.set_sensitive(True) - self.ground_state_mean_map = os.path.join(self.project_directory, self.xtalID, - self.xtalID + '-ground-state-mean-map.native.ccp4') + self.ground_state_mean_map = os.path.join( + self.project_directory, + self.xtalID, + self.xtalID + "-ground-state-mean-map.native.ccp4", + ) # initialize Refinement library self.Refine = XChemRefine.Refine( - self.project_directory, self.xtalID, self.compoundID, self.data_source) - self.Serial = XChemRefine.GetSerial( - self.project_directory, self.xtalID) - self.panddaSerial = panddaSerial = m = ( - 4 - len(str(self.Serial))) * '0' + str(self.Serial) + self.project_directory, self.xtalID, self.compoundID, self.data_source + ) + self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) + self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * "0" + str( + self.Serial + ) # self.Serial=self.Refine.GetSerial() if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): - print('==> XCE: updating quality indicators in data source for ' + self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, - self.pdb_style)) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, - '') # '' because file does not exist - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.pdb')): - print('==> XCE: updating quality indicators in data source for ' + self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, - 'init.pdb')) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, - '') # '' because file does not exist - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): - print('==> XCE: updating quality indicators in data source for ' + self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, - 'dimple.pdb')) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, - '') # '' because file does not exist + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, self.pdb_style), + ) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, "" + ) # '' because file does not exist + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "init.pdb") + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, "init.pdb"), + ) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, "" + ) # '' because file does not exist + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple.pdb") + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, "dimple.pdb"), + ) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, "" + ) # '' because file does not exist # all this information is now updated in the datasource after each refinement cycle self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) @@ -1112,9 +1219,8 @@ def RefreshData(self): # if the structure was previously refined, try to read the parameters # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: - self.RefmacParams = self.Refine.ParamsFromPreviousCycle( - self.Serial - 1) - print('==> REFMAC params:', self.RefmacParams) + self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) + print("==> REFMAC params:", self.RefmacParams) # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) # else: @@ -1138,23 +1244,44 @@ def RefreshData(self): # read new PDB files # read protein molecule after ligand so that this one is the active molecule coot.set_nomenclature_errors_on_read("ignore") - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.compoundID + ".pdb") + ): coot.set_colour_map_rotation_on_read_pdb(0) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb'), 0) - self.mol_dict['ligand'] = imol - coot.read_cif_dictionary(os.path.join( - self.project_directory, self.xtalID, self.compoundID + '.cif')) - if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".pdb" + ), + 0, + ) + self.mol_dict["ligand"] = imol + coot.read_cif_dictionary( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".cif" + ) + ) + if not os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) - if self.refinementProtocol.startswith('pandda'): - print('=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', - '') + '.split.ground-state.pdb')) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): - print('=> XCE: found ground-state model') + if self.refinementProtocol.startswith("pandda"): + print( + "=> XCE: looking for ground-state model", + os.path.join( + self.project_directory, + self.xtalID, + self.pdb_style.replace(".pdb", "") + ".split.ground-state.pdb", + ), + ) + if os.path.isfile( + os.path.join( + self.project_directory, + self.xtalID, + self.pdb_style.replace(".pdb", "") + ".split.ground-state.pdb", + ) + ): + print("=> XCE: found ground-state model") os.chdir(os.path.join(self.project_directory, self.xtalID)) coot.set_colour_map_rotation_on_read_pdb(0) try: @@ -1162,53 +1289,85 @@ def RefreshData(self): except UnboundLocalError: color_wheel_rotation = 80 coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) - imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', - '') + '.split.ground-state.pdb'), - 0) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join( + self.project_directory, + self.xtalID, + self.pdb_style.replace(".pdb", "") + ".split.ground-state.pdb", + ), + 0, + ) coot.set_colour_by_molecule(imol) coot.set_mol_active(imol, 0) else: - print('=> XCE - ERROR: cannot find ground-state model') - print('=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', - '') + '.split.bound-state.pdb')) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb')): - print('=> XCE: found bound-state model') + print("=> XCE - ERROR: cannot find ground-state model") + print( + "=> XCE: looking for bound-state model", + os.path.join( + self.project_directory, + self.xtalID, + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb", + ), + ) + if os.path.isfile( + os.path.join( + self.project_directory, + self.xtalID, + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb", + ) + ): + print("=> XCE: found bound-state model") os.chdir(os.path.join(self.project_directory, self.xtalID)) coot.set_colour_map_rotation_on_read_pdb(0) color_wheel_rotation = 21 / float(imol + 2) coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) - imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', - '') + '.split.bound-state.pdb'), - 0) - self.mol_dict['protein'] = imol + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join( + self.project_directory, + self.xtalID, + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb", + ), + 0, + ) + self.mol_dict["protein"] = imol else: - print('=> XCE - ERROR: cannot find bound-state model') - print('=> XCE: moving to next crystal...') + print("=> XCE - ERROR: cannot find bound-state model") + print("=> XCE: moving to next crystal...") self.go_to_next_xtal() else: - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.pdb')): + os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0 + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "init.pdb") + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, 'init.pdb'), 0) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): + os.path.join(self.project_directory, self.xtalID, "init.pdb"), 0 + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple.pdb") + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, 'dimple.pdb'), 0) + os.path.join(self.project_directory, self.xtalID, "dimple.pdb"), 0 + ) else: self.go_to_next_xtal() - self.mol_dict['protein'] = imol + self.mol_dict["protein"] = imol # read any one event map if present for event_map in glob.glob( - os.path.join(self.project_directory, self.xtalID, self.xtalID + '-event_*.native.ccp4')): + os.path.join( + self.project_directory, + self.xtalID, + self.xtalID + "-event_*.native.ccp4", + ) + ): coot.handle_read_ccp4_map((event_map), 0) coot.set_contour_level_in_sigma(imol, 2) coot.set_last_map_colour(0.74, 0.44, 0.02) @@ -1216,8 +1375,8 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( - item).endswith(self.pdb_style): + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb" + ) or coot.molecule_name(item).endswith(self.pdb_style): # master switch to show symmetry molecules coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model @@ -1226,14 +1385,18 @@ def RefreshData(self): # read fofc maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "2fofc.map") + ): coot.set_colour_map_rotation_on_read_pdb(0) coot.set_default_initial_contour_level_for_difference_map(3) - coot.handle_read_ccp4_map(os.path.join( - self.project_directory, self.xtalID, 'fofc.map'), 1) + coot.handle_read_ccp4_map( + os.path.join(self.project_directory, self.xtalID, "fofc.map"), 1 + ) coot.set_default_initial_contour_level_for_map(1) - coot.handle_read_ccp4_map(os.path.join( - self.project_directory, self.xtalID, '2fofc.map'), 0) + coot.handle_read_ccp4_map( + os.path.join(self.project_directory, self.xtalID, "2fofc.map"), 0 + ) coot.set_last_map_colour(0, 0, 1) else: # try to open mtz file with same name as pdb file @@ -1245,80 +1408,123 @@ def RefreshData(self): # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): # os.symlink('dimple.mtz',self.mtz_style) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, self.mtz_style)) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, 'init.mtz')) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, 'dimple.mtz')) + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.mtz_style) + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, self.mtz_style) + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "init.mtz") + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, "init.mtz") + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple.mtz") + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, "dimple.mtz") + ) ######################################################################################### # update Quality Indicator table try: - self.RRfreeValue.set_label(str(round(float(self.QualityIndicators['RefinementRcryst']), 3)) + ' / ' + str( - round(float(self.QualityIndicators['RefinementRfree']), 3))) + self.RRfreeValue.set_label( + str(round(float(self.QualityIndicators["RefinementRcryst"]), 3)) + + " / " + + str(round(float(self.QualityIndicators["RefinementRfree"]), 3)) + ) except ValueError: - self.RRfreeValue.set_label('-') + self.RRfreeValue.set_label("-") try: - self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementRfreeTraficLight'])) + self.RRfreeBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRfreeTraficLight"] + ), + ) except ValueError: pass - self.ResolutionValue.set_label( - self.QualityIndicators['RefinementResolution']) + self.ResolutionValue.set_label(self.QualityIndicators["RefinementResolution"]) try: - self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementResolutionTL'])) + self.ResolutionBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementResolutionTL"]), + ) except ValueError: pass self.MolprobityScoreValue.set_label( - self.QualityIndicators['RefinementMolProbityScore']) + self.QualityIndicators["RefinementMolProbityScore"] + ) try: - self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementMolProbityScoreTL'])) + self.MolprobityScoreBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementMolProbityScoreTL"] + ), + ) except ValueError: pass self.RamachandranOutliersValue.set_label( - self.QualityIndicators['RefinementRamachandranOutliers']) + self.QualityIndicators["RefinementRamachandranOutliers"] + ) try: - self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRamachandranOutliersTL'])) + self.RamachandranOutliersBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRamachandranOutliersTL"] + ), + ) except ValueError: pass self.RamachandranFavoredValue.set_label( - self.QualityIndicators['RefinementRamachandranFavored']) + self.QualityIndicators["RefinementRamachandranFavored"] + ) try: - self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRamachandranFavoredTL'])) + self.RamachandranFavoredBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRamachandranFavoredTL"] + ), + ) except ValueError: pass - self.rmsdBondsValue.set_label( - self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue.set_label(self.QualityIndicators["RefinementRmsdBonds"]) try: - self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdBondsTL'])) + self.rmsdBondsBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementRmsdBondsTL"]), + ) except ValueError: pass - self.rmsdAnglesValue.set_label( - self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue.set_label(self.QualityIndicators["RefinementRmsdAngles"]) try: - self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdAnglesTL'])) + self.rmsdAnglesBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementRmsdAnglesTL"]), + ) except ValueError: pass self.MatrixWeightValue.set_label( - self.QualityIndicators['RefinementMatrixWeight']) + self.QualityIndicators["RefinementMatrixWeight"] + ) try: pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(self.project_directory, self.xtalID, self.compoundID + '.png')) + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".png" + ) + ) except gobject.GError: pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_COMPOUND_IMAGE_AVAILABLE.png", + ) + ) self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.image.set_from_pixbuf(self.pic) @@ -1350,18 +1556,25 @@ def REFINE(self, widget): # ####################################################### - if self.refinementProtocol.startswith('pandda'): + if self.refinementProtocol.startswith("pandda"): ####################################################### - if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): - os.mkdir(os.path.join( - self.project_directory, self.xtalID, 'cootOut')) + if not os.path.isdir( + os.path.join(self.project_directory, self.xtalID, "cootOut") + ): + os.mkdir(os.path.join(self.project_directory, self.xtalID, "cootOut")) # create folder for new refinement cycle try: - os.mkdir(os.path.join(self.project_directory, - self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + os.mkdir( + os.path.join( + self.project_directory, + self.xtalID, + "cootOut", + "Refine_" + str(self.Serial), + ) + ) except OSError: - print('==> XCE: WARNING -> folder exists; will overwrite contents!') + print("==> XCE: WARNING -> folder exists; will overwrite contents!") ####################################################### # write PDB file @@ -1369,27 +1582,49 @@ def REFINE(self, widget): # note: the user has to make sure that the ligand file was merged into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( - item).endswith(self.pdb_style): - coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', - 'Refine_' + str(self.Serial), 'refine.modified.pdb')) + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb" + ) or coot.molecule_name(item).endswith(self.pdb_style): + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "cootOut", + "Refine_" + str(self.Serial), + "refine.modified.pdb", + ), + ) break # elif coot.molecule_name(item).endswith('dimple.pdb'): # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) # break - XChemRefine.panddaRefine(self.project_directory, self.xtalID, self.compoundID, - self.data_source).RunQuickRefine(self.Serial, self.RefmacParams, - self.external_software, self.xce_logfile, - self.refinementProtocol) + XChemRefine.panddaRefine( + self.project_directory, self.xtalID, self.compoundID, self.data_source + ).RunQuickRefine( + self.Serial, + self.RefmacParams, + self.external_software, + self.xce_logfile, + self.refinementProtocol, + ) else: ####################################################### # create folder for new refinement cycle and check if free.mtz exists if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): os.mkdir(os.path.join(self.project_directory, self.xtalID)) - if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): - os.mkdir(os.path.join(self.project_directory, - self.xtalID, 'Refine_' + str(self.Serial))) + if not os.path.isdir( + os.path.join( + self.project_directory, self.xtalID, "Refine_" + str(self.Serial) + ) + ): + os.mkdir( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial), + ) + ) ####################################################### # write PDB file @@ -1397,30 +1632,53 @@ def REFINE(self, widget): # note: the user has to make sure that the ligand file was merged into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith(self.pdb_style): - coot.write_pdb_file(item, - os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial), - 'in.pdb')) + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) break - elif coot.molecule_name(item).endswith('refine.split.bound-state.pdb'): - coot.write_pdb_file(item, - os.path.join(self.project_directory, self.xtalID, - 'Refine_' + - str(self.Serial), - 'in.pdb')) + elif coot.molecule_name(item).endswith("refine.split.bound-state.pdb"): + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) break - elif coot.molecule_name(item).endswith('init.pdb'): - coot.write_pdb_file(item, - os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial), - 'in.pdb')) + elif coot.molecule_name(item).endswith("init.pdb"): + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) break - elif coot.molecule_name(item).endswith('dimple.pdb'): - coot.write_pdb_file(item, - os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial), - 'in.pdb')) + elif coot.molecule_name(item).endswith("dimple.pdb"): + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) break self.Refine.RunRefmac( - self.Serial, self.RefmacParams, self.external_software, self.xce_logfile) + self.Serial, self.RefmacParams, self.external_software, self.xce_logfile + ) self.index += 1 if self.index >= len(self.Todo): @@ -1429,30 +1687,30 @@ def REFINE(self, widget): self.cb.set_active(self.index) def RefinementParams(self, widget): - print('\n==> XCE: changing refinement parameters') - self.RefmacParams = XChemRefine.RefineParams(self.project_directory, self.xtalID, self.compoundID, - self.data_source).RefmacRefinementParams(self.RefmacParams) + print("\n==> XCE: changing refinement parameters") + self.RefmacParams = XChemRefine.RefineParams( + self.project_directory, self.xtalID, self.compoundID, self.data_source + ).RefmacRefinementParams(self.RefmacParams) def set_selection_mode(self, widget): self.selection_mode = widget.get_active_text() def get_samples_to_look_at(self, widget): - if self.selection_mode == '': - self.status_label.set_text('select model stage') + if self.selection_mode == "": + self.status_label.set_text("select model stage") return - self.status_label.set_text('checking datasource for samples... ') + self.status_label.set_text("checking datasource for samples... ") # first remove old samples if present if len(self.Todo) != 0: for n, item in enumerate(self.Todo): self.cb.remove_text(0) self.Todo = [] self.siteDict = {} - self.Todo, self.siteDict = self.db.get_todoList_for_coot( - self.selection_mode) -# self.status_label.set_text('found {0!s} samples'.format(len(self.Todo))) + self.Todo, self.siteDict = self.db.get_todoList_for_coot(self.selection_mode) + # self.status_label.set_text('found {0!s} samples'.format(len(self.Todo))) # refresh sample CB for item in sorted(self.Todo): - self.cb.append_text('{0!s}'.format(item[0])) + self.cb.append_text("{0!s}".format(item[0])) if self.siteDict == {}: self.cb_site.set_sensitive(False) self.PREVbuttonSite.set_sensitive(False) @@ -1461,68 +1719,113 @@ def get_samples_to_look_at(self, widget): self.cb_site.set_sensitive(True) self.PREVbuttonSite.set_sensitive(True) self.NEXTbuttonSite.set_sensitive(True) - print('===========>', self.cb_select_samples.get_active_text()) + print("===========>", self.cb_select_samples.get_active_text()) if int(self.cb_select_samples.get_active_text().split()[0]) > 3: - print('==> XCE: sorry cannot change refinement protocol since you are at a stage when we refine the ligand bound state only') - self.refinementProtocol = 'refmac' + print( + "==> XCE: sorry cannot change refinement protocol since you are at a stage when we refine the ligand bound state only" + ) + self.refinementProtocol = "refmac" self.refinementProtocolcheckbox.set_active(False) def update_plot(self, refinement_cycle, Rfree, Rcryst): fig = Figure(figsize=(2, 2), dpi=50) Plot = fig.add_subplot(111) Plot.set_ylim([0, max(Rcryst + Rfree)]) - Plot.set_xlabel('Refinement Cycle', fontsize=12) - Plot.plot(refinement_cycle, Rfree, label='Rfree', linewidth=2) - Plot.plot(refinement_cycle, Rcryst, label='Rcryst', linewidth=2) - Plot.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, - ncol=2, mode="expand", borderaxespad=0., fontsize=12) + Plot.set_xlabel("Refinement Cycle", fontsize=12) + Plot.plot(refinement_cycle, Rfree, label="Rfree", linewidth=2) + Plot.plot(refinement_cycle, Rcryst, label="Rcryst", linewidth=2) + Plot.legend( + bbox_to_anchor=(0.0, 1.02, 1.0, 0.102), + loc=3, + ncol=2, + mode="expand", + borderaxespad=0.0, + fontsize=12, + ) return fig def place_ligand_here(self, widget): - print('===> XCE: moving ligand to pointer') + print("===> XCE: moving ligand to pointer") # coot.move_molecule_here() - print('LIGAND: ', self.mol_dict['ligand']) - coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) + print("LIGAND: ", self.mol_dict["ligand"]) + coot_utils_XChem.move_molecule_here(self.mol_dict["ligand"]) def merge_ligand_into_protein(self, widget): - print('===> XCE: merge ligand into protein structure') + print("===> XCE: merge ligand into protein structure") # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) - coot.merge_molecules_py( - [self.mol_dict['ligand']], self.mol_dict['protein']) - print('===> XCE: deleting ligand molecule') - coot.close_molecule(self.mol_dict['ligand']) + coot.merge_molecules_py([self.mol_dict["ligand"]], self.mol_dict["protein"]) + print("===> XCE: deleting ligand molecule") + coot.close_molecule(self.mol_dict["ligand"]) def show_molprobity_to_do(self, widget): print(self.panddaSerial) - AdjPanddaSerial = (4 - len(str(self.Serial))) * \ - '0' + str(int(self.panddaSerial) - 1) - print(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), - 'molprobity_coot.py')) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), - 'molprobity_coot.py')): - print('==> XCE: running MolProbity Summary for', self.xtalID) - coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), - 'molprobity_coot.py')) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), - 'molprobity_coot.py')): - print('==> XCE: running MolProbity Summary for', self.xtalID) - coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), - 'molprobity_coot.py')) + AdjPanddaSerial = (4 - len(str(self.Serial))) * "0" + str( + int(self.panddaSerial) - 1 + ) + print( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.panddaSerial), + "molprobity_coot.py", + ) + ) + if os.path.isfile( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ): + print("==> XCE: running MolProbity Summary for", self.xtalID) + coot.run_script( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ) + elif os.path.isfile( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(AdjPanddaSerial), + "molprobity_coot.py", + ) + ): + print("==> XCE: running MolProbity Summary for", self.xtalID) + coot.run_script( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(AdjPanddaSerial), + "molprobity_coot.py", + ) + ) else: - print('==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')) + print( + "==> XCE: cannot find " + + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ) def refinementProtocolCallback(self, widget): if widget.get_active(): if self.refinementProtocolcheckbox.get_active(): - self.refinementProtocol = 'pandda_phenix' + self.refinementProtocol = "pandda_phenix" else: - self.refinementProtocol = 'pandda_refmac' + self.refinementProtocol = "pandda_refmac" self.PREVbuttonSite.set_sensitive(True) self.NEXTbuttonSite.set_sensitive(True) else: self.refinementProtocolcheckbox.set_active(False) - self.refinementProtocol = 'refmac' + self.refinementProtocol = "refmac" self.PREVbuttonSite.set_sensitive(False) self.NEXTbuttonSite.set_sensitive(False) print(self.refinementProtocol) @@ -1530,28 +1833,30 @@ def refinementProtocolCallback(self, widget): def refinementProgramCallback(self, widget): if widget.get_active(): if self.refinementProtocolcheckbox.get_active(): - self.refinementProtocol = 'pandda_phenix' + self.refinementProtocol = "pandda_phenix" self.RefinementParamsButton.set_sensitive(False) else: self.refinementProgramcheckbox.set_active(False) - self.refinementProtocol = 'refmac' + self.refinementProtocol = "refmac" else: self.RefinementParamsButton.set_sensitive(True) if self.refinementProtocolcheckbox.get_active(): - self.refinementProtocol = 'pandda_refmac' + self.refinementProtocol = "pandda_refmac" else: - self.refinementProtocol = 'refmac' + self.refinementProtocol = "refmac" if int(self.refinement_outcome.split()[0]) > 3: - print('==> XCE: sorry cannot change refinement protocol since you are at a stage when we refine the ligand bound state only') - self.refinementProtocol = 'refmac' + print( + "==> XCE: sorry cannot change refinement protocol since you are at a stage when we refine the ligand bound state only" + ) + self.refinementProtocol = "refmac" self.refinementProtocolcheckbox.set_active(False) print(self.refinementProtocol) def show_ground_state_mean_map(self, widget): - if widget.get_label().startswith('Show'): + if widget.get_label().startswith("Show"): loaded = False for imol in coot_utils_XChem.molecule_number_list(): - if 'ground-state-mean-map' in coot.molecule_name(imol): + if "ground-state-mean-map" in coot.molecule_name(imol): coot.set_map_displayed(imol, 1) loaded = True break @@ -1559,34 +1864,41 @@ def show_ground_state_mean_map(self, widget): coot.set_default_initial_contour_level_for_map(1) coot.handle_read_ccp4_map(self.ground_state_mean_map, 0) coot.set_last_map_colour(0.6, 0.6, 0) - widget.set_label('Undisplay ground state mean map') + widget.set_label("Undisplay ground state mean map") else: for imol in coot_utils_XChem.molecule_number_list(): - if 'ground-state-mean-map' in coot.molecule_name(imol): + if "ground-state-mean-map" in coot.molecule_name(imol): coot.set_map_displayed(imol, 0) - widget.set_label('Show ground state mean map') + widget.set_label("Show ground state mean map") def reset_occupancy(self): self.Logfile.warning( - '==> COOT: trying to set occupancies of all residues to 1.0') - if self.refinementProtocol.startswith('pandda'): + "==> COOT: trying to set occupancies of all residues to 1.0" + ) + if self.refinementProtocol.startswith("pandda"): self.Logfile.warning( - '==> COOT: you cannot reset occupancies while working in PanDDA refine mode') + "==> COOT: you cannot reset occupancies while working in PanDDA refine mode" + ) else: for imol in coot_utils_XChem.molecule_number_list(): - if coot.molecule_name(imol).endswith(self.pdb_style) or \ - coot.molecule_name(imol).endswith('refine.split.bound-state.pdb') or \ - coot.molecule_name(imol).endswith('ini.pdb') or \ - coot.molecule_name(imol).endswith('dimple.pdb'): + if ( + coot.molecule_name(imol).endswith(self.pdb_style) + or coot.molecule_name(imol).endswith("refine.split.bound-state.pdb") + or coot.molecule_name(imol).endswith("ini.pdb") + or coot.molecule_name(imol).endswith("dimple.pdb") + ): self.Logfile.warning( - '==> COOT: setting occupancies of all protein residues in %s to 1.0' % coot.molecule_name(imol)) -# coot.fill_occupancy_residue_range(imol,"A",1,10000) + "==> COOT: setting occupancies of all protein residues in %s to 1.0" + % coot.molecule_name(imol) + ) + # coot.fill_occupancy_residue_range(imol,"A",1,10000) chains = chain_ids(imol) resiDict = {} for chain in chains: resiDict[chain] = residues_in_chain(imol, chain) amino_acids = XChemUtils.pdbtools( - coot.molecule_name(imol)).amino_acids() + coot.molecule_name(imol) + ).amino_acids() resetDict = {} for chain in resiDict: @@ -1594,11 +1906,11 @@ def reset_occupancy(self): resid_prev = -1000 n_res = 0 for resid in resiDict[chain]: - if residue_name(imol, chain, resid[1], '') in amino_acids: + if residue_name(imol, chain, resid[1], "") in amino_acids: n_res += 1 counter = 0 for n, resid in enumerate(resiDict[chain]): - if residue_name(imol, chain, resid[1], '') in amino_acids: + if residue_name(imol, chain, resid[1], "") in amino_acids: counter += 1 if chain not in resetDict: resetDict[chain] = None @@ -1613,9 +1925,15 @@ def reset_occupancy(self): resetDict[chain] = residRange for chain in resetDict: for resid_range in resetDict[chain]: - print('setting occupancy to 1: ->', chain, resid_range[0], resid_range[1]) + print( + "setting occupancy to 1: ->", + chain, + resid_range[0], + resid_range[1], + ) coot.fill_occupancy_residue_range( - imol, chain, resid_range[0], resid_range[1]) + imol, chain, resid_range[0], resid_range[1] + ) # @@ -1624,5 +1942,5 @@ def reset_occupancy(self): # for residue in residues_in_chain(imol, chain): # print residue -if __name__ == '__main__': +if __name__ == "__main__": GUI().StartGUI() diff --git a/lib/XChemCootBuster.py b/lib/XChemCootBuster.py index dedd65a7..6298aecb 100755 --- a/lib/XChemCootBuster.py +++ b/lib/XChemCootBuster.py @@ -23,7 +23,7 @@ # from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas # XCE libraries -sys.path.append(os.getenv('XChemExplorer_DIR') + '/lib') +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") # libraries from COOT @@ -43,57 +43,60 @@ def __init__(self): # read in settings file from XChemExplorer to set the relevant paths self.settings = pickle.load(open(".xce_settings.pkl", "rb")) - remote_qsub_submission = self.settings['remote_qsub'] - self.database_directory = self.settings['database_directory'] - self.xce_logfile = self.settings['xce_logfile'] + remote_qsub_submission = self.settings["remote_qsub"] + self.database_directory = self.settings["database_directory"] + self.xce_logfile = self.settings["xce_logfile"] self.Logfile = XChemLog.updateLog(self.xce_logfile) - self.Logfile.insert('==> COOT: starting coot plugin...') - self.data_source = self.settings['data_source'] + self.Logfile.insert("==> COOT: starting coot plugin...") + self.data_source = self.settings["data_source"] self.db = XChemDB.data_source(self.data_source) print(self.settings) # checking for external software packages - self.external_software = XChemUtils.external_software( - self.xce_logfile).check() - self.external_software['qsub_remote'] = remote_qsub_submission - - self.selection_criteria = ['0 - All Datasets', - '1 - Analysis Pending', - '2 - PANDDA model', - '3 - In Refinement', - '4 - CompChem ready', - '5 - Deposition ready', - '6 - Deposited', - '7 - Analysed & Rejected'] - - self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], - ['In Refinement', '3 - In Refinement', 65000, 0, 0], - ['Comp Chem Ready!', - '4 - CompChem ready', 65000, 0, 0], - ['Ready for Deposition!', - '5 - Deposition ready', 65000, 0, 0], - ['In PDB', '6 - Deposited', 65000, 0, 0], - ['Analysed & Rejected', '7 - Analysed & Rejected', 65000, 0, 0]] - - self.ligand_confidence_category = ['0 - no ligand present', - '1 - Low Confidence', - '2 - Correct ligand, weak density', - '3 - Clear density, unexpected ligand', - '4 - High Confidence'] + self.external_software = XChemUtils.external_software(self.xce_logfile).check() + self.external_software["qsub_remote"] = remote_qsub_submission + + self.selection_criteria = [ + "0 - All Datasets", + "1 - Analysis Pending", + "2 - PANDDA model", + "3 - In Refinement", + "4 - CompChem ready", + "5 - Deposition ready", + "6 - Deposited", + "7 - Analysed & Rejected", + ] + + self.experiment_stage = [ + ["Review PANDDA export", "2 - PANDDA model", 65000, 0, 0], + ["In Refinement", "3 - In Refinement", 65000, 0, 0], + ["Comp Chem Ready!", "4 - CompChem ready", 65000, 0, 0], + ["Ready for Deposition!", "5 - Deposition ready", 65000, 0, 0], + ["In PDB", "6 - Deposited", 65000, 0, 0], + ["Analysed & Rejected", "7 - Analysed & Rejected", 65000, 0, 0], + ] + + self.ligand_confidence_category = [ + "0 - no ligand present", + "1 - Low Confidence", + "2 - Correct ligand, weak density", + "3 - Clear density, unexpected ligand", + "4 - High Confidence", + ] self.ligand_site_information = self.db.get_list_of_pandda_sites_for_coot() # this decides which samples will be looked at - self.selection_mode = '' + self.selection_mode = "" # self.selected_site='' self.pandda_index = -1 # refers to the number of sites - self.site_index = '0' - self.event_index = '0' + self.site_index = "0" + self.event_index = "0" # the Folder is kind of a legacy thing because my inital idea was to have separate folders # for Data Processing and Refinement - self.project_directory = self.settings['initial_model_directory'] + self.project_directory = self.settings["initial_model_directory"] self.Serial = 0 self.panddaSerial = 0 self.Refine = None @@ -101,31 +104,33 @@ def __init__(self): self.Todo = [] self.siteDict = {} - self.xtalID = '' - self.compoundID = '' - self.ground_state_mean_map = '' - self.spider_plot = '' - self.ligand_confidence = '' - self.refinement_folder = '' -# self.refinementProtocol = 'pandda_refmac' + self.xtalID = "" + self.compoundID = "" + self.ground_state_mean_map = "" + self.spider_plot = "" + self.ligand_confidence = "" + self.refinement_folder = "" + # self.refinementProtocol = 'pandda_refmac' # self.datasetOutcome='' - self.pdb_style = 'refine.pdb' - self.mtz_style = 'refine.mtz' + self.pdb_style = "refine.pdb" + self.mtz_style = "refine.mtz" - self.covLink = ['X', 'X', 'X', 'X'] + self.covLink = ["X", "X", "X", "X"] self.covLinkObject = coot.new_generic_object_number("covalent bond") self.covLinkAtomSpec = None self.label = None # stores imol of currently loaded molecules and maps - self.mol_dict = {'protein': -1, - 'ligand': -1, - '2fofc': -1, - 'fofc': -1, - 'event': -1, - 'ligand_stereo': []} + self.mol_dict = { + "protein": -1, + "ligand": -1, + "2fofc": -1, + "fofc": -1, + "event": -1, + "ligand_stereo": [], + } # two dictionaries which are flushed when a new crystal is loaded # and which contain information to update the data source if necessary @@ -140,47 +145,57 @@ def __init__(self): coot.set_colour_map_rotation_for_map(0) # coot.set_colour_map_rotation_on_read_pdb_flag(21) - self.QualityIndicators = {'RefinementRcryst': '-', - 'RefinementRfree': '-', - 'RefinementRfreeTraficLight': 'gray', - 'RefinementResolution': '-', - 'RefinementResolutionTL': 'gray', - 'RefinementMolProbityScore': '-', - 'RefinementMolProbityScoreTL': 'gray', - 'RefinementRamachandranOutliers': '-', - 'RefinementRamachandranOutliersTL': 'gray', - 'RefinementRamachandranFavored': '-', - 'RefinementRamachandranFavoredTL': 'gray', - 'RefinementRmsdBonds': '-', - 'RefinementRmsdBondsTL': 'gray', - 'RefinementRmsdAngles': '-', - 'RefinementRmsdAnglesTL': 'gray', - 'RefinementMatrixWeight': '-'} - - self.spider_plot_data = {'PANDDA_site_ligand_id': '-', - 'PANDDA_site_occupancy': '-', - 'PANDDA_site_B_average': '-', - 'PANDDA_site_B_ratio_residue_surroundings': '-', - 'PANDDA_site_RSCC': '-', - 'PANDDA_site_rmsd': '-', - 'PANDDA_site_RSR': '-', - 'PANDDA_site_RSZD': '-'} + self.QualityIndicators = { + "RefinementRcryst": "-", + "RefinementRfree": "-", + "RefinementRfreeTraficLight": "gray", + "RefinementResolution": "-", + "RefinementResolutionTL": "gray", + "RefinementMolProbityScore": "-", + "RefinementMolProbityScoreTL": "gray", + "RefinementRamachandranOutliers": "-", + "RefinementRamachandranOutliersTL": "gray", + "RefinementRamachandranFavored": "-", + "RefinementRamachandranFavoredTL": "gray", + "RefinementRmsdBonds": "-", + "RefinementRmsdBondsTL": "gray", + "RefinementRmsdAngles": "-", + "RefinementRmsdAnglesTL": "gray", + "RefinementMatrixWeight": "-", + } + + self.spider_plot_data = { + "PANDDA_site_ligand_id": "-", + "PANDDA_site_occupancy": "-", + "PANDDA_site_B_average": "-", + "PANDDA_site_B_ratio_residue_surroundings": "-", + "PANDDA_site_RSCC": "-", + "PANDDA_site_rmsd": "-", + "PANDDA_site_RSR": "-", + "PANDDA_site_RSZD": "-", + } # default refmac parameters - self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '', - 'WATER': '', - 'LIGOCC': '', - 'SANITY': ''} + self.RefmacParams = { + "HKLIN": "", + "HKLOUT": "", + "XYZIN": "", + "XYZOUT": "", + "LIBIN": "", + "LIBOUT": "", + "TLSIN": "", + "TLSOUT": "", + "TLSADD": "", + "NCYCLES": "10", + "MATRIX_WEIGHT": "AUTO", + "BREF": " bref ISOT\n", + "TLS": "", + "NCS": "", + "TWIN": "", + "WATER": "", + "LIGOCC": "", + "SANITY": "", + } def StartGUI(self): @@ -195,7 +210,7 @@ def StartGUI(self): # --- Sample Selection --- # self.vbox.add(gtk.Label('Select Samples')) - frame = gtk.Frame(label='Select Samples') + frame = gtk.Frame(label="Select Samples") self.hbox_select_samples = gtk.HBox() # vbox=gtk.VBox() @@ -212,8 +227,7 @@ def StartGUI(self): # self.hbox_select_samples.add(self.cb_select_sites) self.select_samples_button = gtk.Button(label="GO") - self.select_samples_button.connect( - "clicked", self.get_samples_to_look_at) + self.select_samples_button.connect("clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) @@ -227,25 +241,25 @@ def StartGUI(self): ################################################################################# # --- refinement protocol --- -# frame = gtk.Frame() -# self.refinementProtocolcheckbox = gtk.CheckButton('PanDDA model refinement)') -# # callback is defined later -## self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) -# self.refinementProtocolcheckbox.set_active(True) -# frame.add(self.refinementProtocolcheckbox) -# self.vbox.pack_start(frame) + # frame = gtk.Frame() + # self.refinementProtocolcheckbox = gtk.CheckButton('PanDDA model refinement)') + # # callback is defined later + ## self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) + # self.refinementProtocolcheckbox.set_active(True) + # frame.add(self.refinementProtocolcheckbox) + # self.vbox.pack_start(frame) ################################################################################# # --- refinement program --- -# frame = gtk.Frame() -# self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') -# self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) -# self.refinementProgramcheckbox.set_active(False) -# frame.add(self.refinementProgramcheckbox) -# self.vbox.pack_start(frame) + # frame = gtk.Frame() + # self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') + # self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) + # self.refinementProgramcheckbox.set_active(False) + # frame.add(self.refinementProgramcheckbox) + # self.vbox.pack_start(frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# # --- Refinement Statistics --- @@ -253,163 +267,162 @@ def StartGUI(self): # a combination of labels and textview widgets, arranged in a table RRfreeLabel_frame = gtk.Frame() - self.RRfreeLabel = gtk.Label('R/Rfree') + self.RRfreeLabel = gtk.Label("R/Rfree") RRfreeLabel_frame.add(self.RRfreeLabel) self.RRfreeValue = gtk.Label( - self.QualityIndicators['RefinementRcryst'] + '/' + self.QualityIndicators['RefinementRfree']) + self.QualityIndicators["RefinementRcryst"] + + "/" + + self.QualityIndicators["RefinementRfree"] + ) RRfreeBox_frame = gtk.Frame() self.RRfreeBox = gtk.EventBox() self.RRfreeBox.add(self.RRfreeValue) RRfreeBox_frame.add(self.RRfreeBox) ResolutionLabel_frame = gtk.Frame() - self.ResolutionLabel = gtk.Label('Resolution') + self.ResolutionLabel = gtk.Label("Resolution") ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label( - self.QualityIndicators['RefinementResolution']) + self.ResolutionValue = gtk.Label(self.QualityIndicators["RefinementResolution"]) ResolutionBox_frame = gtk.Frame() self.ResolutionBox = gtk.EventBox() self.ResolutionBox.add(self.ResolutionValue) ResolutionBox_frame.add(self.ResolutionBox) MolprobityScoreLabel_frame = gtk.Frame() - self.MolprobityScoreLabel = gtk.Label('MolprobityScore') + self.MolprobityScoreLabel = gtk.Label("MolprobityScore") MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) self.MolprobityScoreValue = gtk.Label( - self.QualityIndicators['RefinementMolProbityScore']) + self.QualityIndicators["RefinementMolProbityScore"] + ) MolprobityScoreBox_frame = gtk.Frame() self.MolprobityScoreBox = gtk.EventBox() self.MolprobityScoreBox.add(self.MolprobityScoreValue) MolprobityScoreBox_frame.add(self.MolprobityScoreBox) RamachandranOutliersLabel_frame = gtk.Frame() - self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') + self.RamachandranOutliersLabel = gtk.Label("Rama Outliers") RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) self.RamachandranOutliersValue = gtk.Label( - self.QualityIndicators['RefinementRamachandranOutliers']) + self.QualityIndicators["RefinementRamachandranOutliers"] + ) RamachandranOutliersBox_frame = gtk.Frame() self.RamachandranOutliersBox = gtk.EventBox() self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) RamachandranOutliersBox_frame.add(self.RamachandranOutliersBox) RamachandranFavoredLabel_frame = gtk.Frame() - self.RamachandranFavoredLabel = gtk.Label('Rama Favored') + self.RamachandranFavoredLabel = gtk.Label("Rama Favored") RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) self.RamachandranFavoredValue = gtk.Label( - self.QualityIndicators['RefinementRamachandranFavored']) + self.QualityIndicators["RefinementRamachandranFavored"] + ) RamachandranFavoredBox_frame = gtk.Frame() self.RamachandranFavoredBox = gtk.EventBox() self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) RamachandranFavoredBox_frame.add(self.RamachandranFavoredBox) rmsdBondsLabel_frame = gtk.Frame() - self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') + self.rmsdBondsLabel = gtk.Label("rmsd(Bonds)") rmsdBondsLabel_frame.add(self.rmsdBondsLabel) - self.rmsdBondsValue = gtk.Label( - self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue = gtk.Label(self.QualityIndicators["RefinementRmsdBonds"]) rmsdBondsBox_frame = gtk.Frame() self.rmsdBondsBox = gtk.EventBox() self.rmsdBondsBox.add(self.rmsdBondsValue) rmsdBondsBox_frame.add(self.rmsdBondsBox) rmsdAnglesLabel_frame = gtk.Frame() - self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') + self.rmsdAnglesLabel = gtk.Label("rmsd(Angles)") rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) - self.rmsdAnglesValue = gtk.Label( - self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue = gtk.Label(self.QualityIndicators["RefinementRmsdAngles"]) rmsdAnglesBox_frame = gtk.Frame() self.rmsdAnglesBox = gtk.EventBox() self.rmsdAnglesBox.add(self.rmsdAnglesValue) rmsdAnglesBox_frame.add(self.rmsdAnglesBox) MatrixWeightLabel_frame = gtk.Frame() - self.MatrixWeightLabel = gtk.Label('Matrix Weight') + self.MatrixWeightLabel = gtk.Label("Matrix Weight") MatrixWeightLabel_frame.add(self.MatrixWeightLabel) self.MatrixWeightValue = gtk.Label( - self.QualityIndicators['RefinementMatrixWeight']) + self.QualityIndicators["RefinementMatrixWeight"] + ) MatrixWeightBox_frame = gtk.Frame() self.MatrixWeightBox = gtk.EventBox() self.MatrixWeightBox.add(self.MatrixWeightValue) MatrixWeightBox_frame.add(self.MatrixWeightBox) ligandIDLabel_frame = gtk.Frame() - self.ligandIDLabel = gtk.Label('Ligand ID') + self.ligandIDLabel = gtk.Label("Ligand ID") ligandIDLabel_frame.add(self.ligandIDLabel) - self.ligandIDValue = gtk.Label( - self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue = gtk.Label(self.spider_plot_data["PANDDA_site_ligand_id"]) ligandIDBox_frame = gtk.Frame() self.ligandIDBox = gtk.EventBox() self.ligandIDBox.add(self.ligandIDValue) ligandIDBox_frame.add(self.ligandIDBox) ligand_occupancyLabel_frame = gtk.Frame() - self.ligand_occupancyLabel = gtk.Label('occupancy') + self.ligand_occupancyLabel = gtk.Label("occupancy") ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) self.ligand_occupancyValue = gtk.Label( - self.spider_plot_data['PANDDA_site_occupancy']) + self.spider_plot_data["PANDDA_site_occupancy"] + ) ligand_occupancyBox_frame = gtk.Frame() self.ligand_occupancyBox = gtk.EventBox() self.ligand_occupancyBox.add(self.ligand_occupancyValue) ligand_occupancyBox_frame.add(self.ligand_occupancyBox) ligand_BaverageLabel_frame = gtk.Frame() - self.ligand_BaverageLabel = gtk.Label('B average') + self.ligand_BaverageLabel = gtk.Label("B average") ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) self.ligand_BaverageValue = gtk.Label( - self.spider_plot_data['PANDDA_site_B_average']) + self.spider_plot_data["PANDDA_site_B_average"] + ) ligand_BaverageBox_frame = gtk.Frame() self.ligand_BaverageBox = gtk.EventBox() self.ligand_BaverageBox.add(self.ligand_BaverageValue) ligand_BaverageBox_frame.add(self.ligand_BaverageBox) ligand_BratioSurroundingsLabel_frame = gtk.Frame() - self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') - ligand_BratioSurroundingsLabel_frame.add( - self.ligand_BratioSurroundingsLabel) + self.ligand_BratioSurroundingsLabel = gtk.Label("B ratio") + ligand_BratioSurroundingsLabel_frame.add(self.ligand_BratioSurroundingsLabel) self.ligand_BratioSurroundingsValue = gtk.Label( - self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) + self.spider_plot_data["PANDDA_site_B_ratio_residue_surroundings"] + ) ligand_BratioSurroundingsBox_frame = gtk.Frame() self.ligand_BratioSurroundingsBox = gtk.EventBox() - self.ligand_BratioSurroundingsBox.add( - self.ligand_BratioSurroundingsValue) - ligand_BratioSurroundingsBox_frame.add( - self.ligand_BratioSurroundingsBox) + self.ligand_BratioSurroundingsBox.add(self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add(self.ligand_BratioSurroundingsBox) ligand_RSCCLabel_frame = gtk.Frame() - self.ligand_RSCCLabel = gtk.Label('RSCC') + self.ligand_RSCCLabel = gtk.Label("RSCC") ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) - self.ligand_RSCCValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSCC']) + self.ligand_RSCCValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSCC"]) ligand_RSCCBox_frame = gtk.Frame() self.ligand_RSCCBox = gtk.EventBox() self.ligand_RSCCBox.add(self.ligand_RSCCValue) ligand_RSCCBox_frame.add(self.ligand_RSCCBox) ligand_rmsdLabel_frame = gtk.Frame() - self.ligand_rmsdLabel = gtk.Label('rmsd') + self.ligand_rmsdLabel = gtk.Label("rmsd") ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) - self.ligand_rmsdValue = gtk.Label( - self.spider_plot_data['PANDDA_site_rmsd']) + self.ligand_rmsdValue = gtk.Label(self.spider_plot_data["PANDDA_site_rmsd"]) ligand_rmsdBox_frame = gtk.Frame() self.ligand_rmsdBox = gtk.EventBox() self.ligand_rmsdBox.add(self.ligand_rmsdValue) ligand_rmsdBox_frame.add(self.ligand_rmsdBox) ligand_RSRLabel_frame = gtk.Frame() - self.ligand_RSRLabel = gtk.Label('RSR') + self.ligand_RSRLabel = gtk.Label("RSR") ligand_RSRLabel_frame.add(self.ligand_RSRLabel) - self.ligand_RSRValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSR']) + self.ligand_RSRValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSR"]) ligand_RSRBox_frame = gtk.Frame() self.ligand_RSRBox = gtk.EventBox() self.ligand_RSRBox.add(self.ligand_RSRValue) ligand_RSRBox_frame.add(self.ligand_RSRBox) ligand_RSZDLabel_frame = gtk.Frame() - self.ligand_RSZDLabel = gtk.Label('RSZD') + self.ligand_RSZDLabel = gtk.Label("RSZD") ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) - self.ligand_RSZDValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSZD']) + self.ligand_RSZDValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSZD"]) ligand_RSZDBox_frame = gtk.Frame() self.ligand_RSZDBox = gtk.EventBox() self.ligand_RSZDBox.add(self.ligand_RSZDValue) @@ -444,8 +457,7 @@ def StartGUI(self): self.table_right.attach(ligandIDLabel_frame, 0, 1, 0, 1) self.table_right.attach(ligand_occupancyLabel_frame, 0, 1, 1, 2) self.table_right.attach(ligand_BaverageLabel_frame, 0, 1, 2, 3) - self.table_right.attach( - ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach(ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) self.table_right.attach(ligand_RSCCLabel_frame, 0, 1, 4, 5) self.table_right.attach(ligand_rmsdLabel_frame, 0, 1, 5, 6) self.table_right.attach(ligand_RSRLabel_frame, 0, 1, 6, 7) @@ -470,17 +482,19 @@ def StartGUI(self): hbox.add(button) # --- ground state mean map --- self.ground_state_mean_map_button = gtk.Button( - label="Show ground state mean map") + label="Show ground state mean map" + ) self.ground_state_mean_map_button.connect( - "clicked", self.show_ground_state_mean_map) + "clicked", self.show_ground_state_mean_map + ) hbox.add(self.ground_state_mean_map_button) -# self.vbox.add(self.ground_state_mean_map_button) + # self.vbox.add(self.ground_state_mean_map_button) self.vbox.add(hbox) self.vbox.pack_start(frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# # --- hbox for compound picture & spider_plot (formerly: refinement history) --- @@ -490,7 +504,12 @@ def StartGUI(self): # --- compound picture --- compound_frame = gtk.Frame() pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_COMPOUND_IMAGE_AVAILABLE.png", + ) + ) self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.image = gtk.Image() self.image.set_from_pixbuf(self.pic) @@ -505,9 +524,11 @@ def StartGUI(self): # --- Spider Plot --- spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + os.path.join( + os.getenv("XChemExplorer_DIR"), "image", "NO_SPIDER_PLOT_AVAILABLE.png" + ) + ) + self.spider_plot_pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image = gtk.Image() self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) spider_plot_frame.add(self.spider_plot_image) @@ -518,54 +539,54 @@ def StartGUI(self): ################################################################################# # --- pandda.inspect user comments --- -# outer_frame = gtk.Frame(label='pandda.inspect comments') -# vbox = gtk.VBox() -# ligand_site_name_label_frame = gtk.Frame() -# ligand_site_name_label = gtk.Label('Site Name') -# ligand_site_name_label_frame.add(ligand_site_name_label) -# ligand_inspect_confidence_label_frame = gtk.Frame() -# ligand_inspect_confidence_label = gtk.Label('Confidence') -# ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) -# ligand_inspect_interesting_label_frame = gtk.Frame() -# ligand_inspect_interesting_label = gtk.Label('Interesting') -# ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) -# ligand_inspect_comment_label_frame = gtk.Frame() -# ligand_inspect_comment_label = gtk.Label('Comment') -# ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) -# ligand_site_name_value_frame = gtk.Frame() -# self.ligand_site_name_value = gtk.Label('-') -# ligand_site_name_value_frame.add(self.ligand_site_name_value) -# ligand_inspect_confidence_value_frame = gtk.Frame() -# self.ligand_inspect_confidence_value = gtk.Label('-') -# ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) -# ligand_inspect_interesting_value_frame = gtk.Frame() -# self.ligand_inspect_interesting_value = gtk.Label('-') -# ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) -# ligand_inspect_comment_value_frame = gtk.Frame() -# self.ligand_inspect_comment_value = gtk.Label('-') -# ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) -# -# frame_pandda_inspect_comments_table = gtk.Frame() -# pandda_inspect_comments_table = gtk.Table(2, 6, False) -# pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) -# pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) -# pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) -# -# frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) -# vbox.add(frame_pandda_inspect_comments_table) -# outer_frame.add(vbox) -# self.vbox.pack_start(outer_frame) + # outer_frame = gtk.Frame(label='pandda.inspect comments') + # vbox = gtk.VBox() + # ligand_site_name_label_frame = gtk.Frame() + # ligand_site_name_label = gtk.Label('Site Name') + # ligand_site_name_label_frame.add(ligand_site_name_label) + # ligand_inspect_confidence_label_frame = gtk.Frame() + # ligand_inspect_confidence_label = gtk.Label('Confidence') + # ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) + # ligand_inspect_interesting_label_frame = gtk.Frame() + # ligand_inspect_interesting_label = gtk.Label('Interesting') + # ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) + # ligand_inspect_comment_label_frame = gtk.Frame() + # ligand_inspect_comment_label = gtk.Label('Comment') + # ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) + # ligand_site_name_value_frame = gtk.Frame() + # self.ligand_site_name_value = gtk.Label('-') + # ligand_site_name_value_frame.add(self.ligand_site_name_value) + # ligand_inspect_confidence_value_frame = gtk.Frame() + # self.ligand_inspect_confidence_value = gtk.Label('-') + # ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) + # ligand_inspect_interesting_value_frame = gtk.Frame() + # self.ligand_inspect_interesting_value = gtk.Label('-') + # ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) + # ligand_inspect_comment_value_frame = gtk.Frame() + # self.ligand_inspect_comment_value = gtk.Label('-') + # ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) + # + # frame_pandda_inspect_comments_table = gtk.Frame() + # pandda_inspect_comments_table = gtk.Table(2, 6, False) + # pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) + # pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) + # pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) + # + # frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) + # vbox.add(frame_pandda_inspect_comments_table) + # outer_frame.add(vbox) + # self.vbox.pack_start(outer_frame) # # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# - outer_frame = gtk.Frame(label='Sample Navigator') + outer_frame = gtk.Frame(label="Sample Navigator") hboxSample = gtk.HBox() # --- crystal navigator combobox --- @@ -608,51 +629,51 @@ def StartGUI(self): self.vbox.add(outer_frame) # # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# -# outer_frame = gtk.Frame(label='Label') -# hboxlabel = gtk.HBox() -# -# frame = gtk.Frame() -# hbox = gtk.HBox() -# self.vbox_label = gtk.VBox() -# labels = self.db.get_labels_from_db() -# if len(labels) > 5: -# print '==> sorry, too many labels; cannot display them in panel' -# labels = labels[:5] -# # with radiobuttons, one of them needs to be always on -# # but there will be cases when the user has not assigned a label yet -# # hence, the not_shown button is not shown but gets active -# # if the label has not been set yet -# labels.append('not_shown') -# for n, l in enumerate(labels): -# print n,l -# if n == 0: -# new_button = gtk.RadioButton(None, l) -# else: -# new_button = gtk.RadioButton(new_button, l) -# new_button.connect("toggled", self.label_button_clicked, l) -# if not l == 'not_shown': -# hbox.add(new_button) -# self.label_button_list.append(new_button) -# self.vbox_label.add(hbox) -# frame.add(self.vbox_label) -# -# hboxlabel.add(frame) -# -# outer_frame.add(hboxlabel) -# self.vbox.add(outer_frame) + # outer_frame = gtk.Frame(label='Label') + # hboxlabel = gtk.HBox() + # + # frame = gtk.Frame() + # hbox = gtk.HBox() + # self.vbox_label = gtk.VBox() + # labels = self.db.get_labels_from_db() + # if len(labels) > 5: + # print '==> sorry, too many labels; cannot display them in panel' + # labels = labels[:5] + # # with radiobuttons, one of them needs to be always on + # # but there will be cases when the user has not assigned a label yet + # # hence, the not_shown button is not shown but gets active + # # if the label has not been set yet + # labels.append('not_shown') + # for n, l in enumerate(labels): + # print n,l + # if n == 0: + # new_button = gtk.RadioButton(None, l) + # else: + # new_button = gtk.RadioButton(new_button, l) + # new_button.connect("toggled", self.label_button_clicked, l) + # if not l == 'not_shown': + # hbox.add(new_button) + # self.label_button_list.append(new_button) + # self.vbox_label.add(hbox) + # frame.add(self.vbox_label) + # + # hboxlabel.add(frame) + # + # outer_frame.add(hboxlabel) + # self.vbox.add(outer_frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# # --- current refinement stage --- outer_frame = gtk.Frame() hbox = gtk.HBox() - frame = gtk.Frame(label='Analysis Status') + frame = gtk.Frame(label="Analysis Status") vbox = gtk.VBox() self.experiment_stage_button_list = [] for n, button in enumerate(self.experiment_stage): @@ -661,15 +682,16 @@ def StartGUI(self): else: new_button = gtk.RadioButton(new_button, button[0]) new_button.connect( - "toggled", self.experiment_stage_button_clicked, button[1]) + "toggled", self.experiment_stage_button_clicked, button[1] + ) vbox.pack_start(new_button, False, False, 0) -# vbox.add(new_button) + # vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) # --- ligand confidence --- - frame = gtk.Frame(label='Ligand Confidence') + frame = gtk.Frame(label="Ligand Confidence") vbox = gtk.VBox() self.ligand_confidence_button_list = [] for n, criteria in enumerate(self.ligand_confidence_category): @@ -678,56 +700,55 @@ def StartGUI(self): else: new_button = gtk.RadioButton(new_button, criteria) new_button.connect( - "toggled", self.ligand_confidence_button_clicked, criteria) + "toggled", self.ligand_confidence_button_clicked, criteria + ) vbox.pack_start(new_button, False, False, 0) -# vbox.add(new_button) + # vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) -# # label section --> start -# frame = gtk.Frame(label='Label') -# vbox = gtk.VBox() -# labels = self.db.get_labels_from_db() -# if len(labels) > 5: -# print '==> sorry, too many labels; cannot display them in panel' -# labels = labels[:5] -# # with radiobuttons, one of them needs to be always on -# # but there will be cases when the user has not assigned a label yet -# # hence, the not_shown button is not shown but gets active -# # if the label has not been set yet -# labels.append('not_shown') -# for n, l in enumerate(labels): -# print n,l -# if n == 0: -# new_button = gtk.RadioButton(None, l) -# else: -# new_button = gtk.RadioButton(new_button, l) -# new_button.connect("toggled", self.label_button_clicked, l) -# if not l == 'not_shown': -# vbox.add(new_button) -# self.label_button_list.append(new_button) -# frame.add(vbox) -# hbox.pack_start(frame) -# # label section <-- end + # # label section --> start + # frame = gtk.Frame(label='Label') + # vbox = gtk.VBox() + # labels = self.db.get_labels_from_db() + # if len(labels) > 5: + # print '==> sorry, too many labels; cannot display them in panel' + # labels = labels[:5] + # # with radiobuttons, one of them needs to be always on + # # but there will be cases when the user has not assigned a label yet + # # hence, the not_shown button is not shown but gets active + # # if the label has not been set yet + # labels.append('not_shown') + # for n, l in enumerate(labels): + # print n,l + # if n == 0: + # new_button = gtk.RadioButton(None, l) + # else: + # new_button = gtk.RadioButton(new_button, l) + # new_button.connect("toggled", self.label_button_clicked, l) + # if not l == 'not_shown': + # vbox.add(new_button) + # self.label_button_list.append(new_button) + # frame.add(vbox) + # hbox.pack_start(frame) + # # label section <-- end outer_frame.add(hbox) self.vbox.pack_start(outer_frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) # --- ligand modeling --- - frame = gtk.Frame(label='Ligand Modeling') + frame = gtk.Frame(label="Ligand Modeling") self.hbox_for_modeling = gtk.HBox() self.merge_ligand_button = gtk.Button(label="Merge Ligand") self.place_ligand_here_button = gtk.Button(label="Place Ligand here") self.hbox_for_modeling.add(self.place_ligand_here_button) - self.place_ligand_here_button.connect( - "clicked", self.place_ligand_here) + self.place_ligand_here_button.connect("clicked", self.place_ligand_here) self.hbox_for_modeling.add(self.merge_ligand_button) - self.merge_ligand_button.connect( - "clicked", self.merge_ligand_into_protein) + self.merge_ligand_button.connect("clicked", self.merge_ligand_into_protein) self.select_cpd_cb = gtk.combo_box_new_text() self.select_cpd_cb.connect("changed", self.select_cpd) self.hbox_for_modeling.add(self.select_cpd_cb) @@ -747,13 +768,13 @@ def StartGUI(self): self.RefinementParamsButton = gtk.Button(label="refinement parameters") self.covalentLinksbutton = gtk.Button(label="covalent links\n-define-") self.covalentLinksCreatebutton = gtk.Button( - label="covalent links\n-create & refine-") + label="covalent links\n-create & refine-" + ) self.REFINEbutton.connect("clicked", self.REFINE) self.hbox_for_refinement.add(self.REFINEbutton) self.RefinementParamsButton.connect("clicked", self.RefinementParams) self.covalentLinksbutton.connect("clicked", self.covalentLinkDef) - self.covalentLinksCreatebutton.connect( - "clicked", self.covalentLinkCreate) + self.covalentLinksCreatebutton.connect("clicked", self.covalentLinkCreate) self.hbox_for_refinement.add(self.RefinementParamsButton) self.hbox_for_refinement.add(self.covalentLinksbutton) self.hbox_for_refinement.add(self.covalentLinksCreatebutton) @@ -762,10 +783,9 @@ def StartGUI(self): # self.VALIDATEbutton = gtk.Button(label="validate structure") # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") - -# # need to put it here, because attributes within refinementProtocolCallback function -# # are defined after checkbox is defined -# self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) + # # need to put it here, because attributes within refinementProtocolCallback function + # # are defined after checkbox is defined + # self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") @@ -795,10 +815,10 @@ def ChooseXtal(self, widget): self.merge_ligand_button.set_sensitive(True) self.place_ligand_here_button.set_sensitive(True) -# self.ligand_site_name_value.set_label('-') -# self.ligand_inspect_confidence_value.set_label('-') -# self.ligand_inspect_interesting_value.set_label('-') -# self.ligand_inspect_comment_value.set_label('-') + # self.ligand_site_name_value.set_label('-') + # self.ligand_inspect_confidence_value.set_label('-') + # self.ligand_inspect_interesting_value.set_label('-') + # self.ligand_inspect_comment_value.set_label('-') self.refresh_site_combobox() self.db_dict_mainTable = {} @@ -807,36 +827,58 @@ def ChooseXtal(self, widget): self.compoundID = str(self.Todo[self.index][1]) self.refinement_folder = str(self.Todo[self.index][4]) self.refinement_outcome = str(self.Todo[self.index][5]) -# self.label = self.db.get_label_of_sample(self.xtalID) -# self.update_label_radiobutton() + # self.label = self.db.get_label_of_sample(self.xtalID) + # self.update_label_radiobutton() self.update_RefinementOutcome_radiobutton() - if self.xtalID not in self.siteDict: # i.e. we are not working with a PanDDA model + if ( + self.xtalID not in self.siteDict + ): # i.e. we are not working with a PanDDA model self.ligand_confidence = str(self.Todo[self.index][6]) -# self.update_LigandConfidence_radiobutton() -# self.label = self.db.get_label_of_sample(self.xtalID) -# self.update_label_radiobutton() + # self.update_LigandConfidence_radiobutton() + # self.label = self.db.get_label_of_sample(self.xtalID) + # self.update_label_radiobutton() self.RefreshData() def select_cpd(self, widget): cpd = str(widget.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): - if imol not in self.mol_dict['ligand_stereo']: + if imol not in self.mol_dict["ligand_stereo"]: continue - molName = coot.molecule_name(imol)[coot.molecule_name( - imol).rfind('/')+1:].replace('.pdb', '') - if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): - molNameCIF = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( - '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') + molName = coot.molecule_name(imol)[ + coot.molecule_name(imol).rfind("/") + 1 : + ].replace(".pdb", "") + if "rhofit" in coot.molecule_name(imol) or "phenix" in coot.molecule_name( + imol + ): + molNameCIF = ( + coot.molecule_name(imol)[coot.molecule_name(imol).rfind("/") + 1 :] + .replace(".pdb", "") + .replace("_phenix", "") + .replace("_rhofit", "") + ) else: molNameCIF = molName - print(cpd, '-', imol, '-', coot.molecule_name(imol)) + print(cpd, "-", imol, "-", coot.molecule_name(imol)) if molName == cpd: coot.set_mol_displayed(imol, 1) - print('reading', os.path.join( - self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) - coot.read_cif_dictionary(os.path.join( - self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) + print( + "reading", + os.path.join( + self.project_directory, + self.xtalID, + "compound", + molNameCIF + ".cif", + ), + ) + coot.read_cif_dictionary( + os.path.join( + self.project_directory, + self.xtalID, + "compound", + molNameCIF + ".cif", + ) + ) else: coot.set_mol_displayed(imol, 0) @@ -852,23 +894,23 @@ def update_RefinementOutcome_radiobutton(self): button.set_active(True) break -# def update_label_radiobutton(self): -# found = False -# for button in self.label_button_list: -# if button.get_label() == self.label: -# button.set_active(True) -# found = True -# if not found: -# for button in self.label_button_list: -# if button.get_label() == 'not_shown': -# button.set_active(True) -# break + # def update_label_radiobutton(self): + # found = False + # for button in self.label_button_list: + # if button.get_label() == self.label: + # button.set_active(True) + # found = True + # if not found: + # for button in self.label_button_list: + # if button.get_label() == 'not_shown': + # button.set_active(True) + # break def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 for i, entry in enumerate(self.ligand_confidence_category): - print('--->', entry, self.ligand_confidence) + print("--->", entry, self.ligand_confidence) try: if entry.split()[0] == self.ligand_confidence.split()[0]: current_stage = i @@ -886,13 +928,14 @@ def refresh_site_combobox(self): # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites for n in range(-1, 100): self.cb_site.remove_text(0) - self.site_index = '0' - self.event_index = '0' + self.site_index = "0" + self.event_index = "0" # only repopulate if site exists if self.xtalID in self.siteDict: for item in sorted(self.siteDict[self.xtalID]): self.cb_site.append_text( - 'site: {0!s} - event: {1!s}'.format(item[5], item[6])) + "site: {0!s} - event: {1!s}".format(item[5], item[6]) + ) def ChangeSite(self, widget, data=None): if self.xtalID in self.siteDict: @@ -925,83 +968,100 @@ def RefreshSiteData(self): # and remove ligand molecule so that there is no temptation to merge it if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): - if self.compoundID + '.pdb' in coot.molecule_name(imol): + if self.compoundID + ".pdb" in coot.molecule_name(imol): coot.close_molecule(imol) -# for w in self.label_button_list: -# w.set_active(False) + # for w in self.label_button_list: + # w.set_active(False) - print('pandda index', self.pandda_index) + print("pandda index", self.pandda_index) self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] - print('new spider plot:', self.spider_plot) + print("new spider plot:", self.spider_plot) self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] - print('new event map:', self.event_map) - self.ligand_confidence = str( - self.siteDict[self.xtalID][self.pandda_index][7]) + print("new event map:", self.event_map) + self.ligand_confidence = str(self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) - print('new site coordinates:', site_x, site_y, site_z) + print("new site coordinates:", site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) -# self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) -# self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) -# self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) -# self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) - - self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, - self.event_index) - print('>>>>> spider plot data', self.spider_plot_data) - self.ligandIDValue.set_label( - self.spider_plot_data['PANDDA_site_ligand_id']) + # self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) + # self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) + # self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) + # self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) + + self.spider_plot_data = ( + self.db.get_db_pandda_dict_for_sample_and_site_and_event( + self.xtalID, self.site_index, self.event_index + ) + ) + print(">>>>> spider plot data", self.spider_plot_data) + self.ligandIDValue.set_label(self.spider_plot_data["PANDDA_site_ligand_id"]) try: self.ligand_occupancyValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_occupancy"]), 2)) + ) except ValueError: - self.ligand_occupancyValue.set_label('-') + self.ligand_occupancyValue.set_label("-") try: self.ligand_BaverageValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_B_average"]), 2)) + ) except ValueError: - self.ligand_BaverageValue.set_label('-') + self.ligand_BaverageValue.set_label("-") try: self.ligand_BratioSurroundingsValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']), 2))) + str( + round( + float( + self.spider_plot_data[ + "PANDDA_site_B_ratio_residue_surroundings" + ] + ), + 2, + ) + ) + ) except ValueError: - self.ligand_BratioSurroundingsValue.set_label('-') + self.ligand_BratioSurroundingsValue.set_label("-") try: self.ligand_RSCCValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSCC"]), 2)) + ) except ValueError: - self.ligand_RSCCValue.set_label('-') + self.ligand_RSCCValue.set_label("-") try: self.ligand_rmsdValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_rmsd"]), 2)) + ) except ValueError: - self.ligand_rmsdValue.set_label('-') + self.ligand_rmsdValue.set_label("-") try: self.ligand_RSRValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSR"]), 2)) + ) except ValueError: - self.ligand_RSRValue.set_label('-') + self.ligand_RSRValue.set_label("-") try: self.ligand_RSZDValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSZD"]), 2)) + ) except ValueError: - self.ligand_RSZDValue.set_label('-') + self.ligand_RSZDValue.set_label("-") ######################################################################################### # delete old Event MAPs if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): - if 'map.native.ccp4' in coot.molecule_name(imol): + if "map.native.ccp4" in coot.molecule_name(imol): coot.close_molecule(imol) ######################################################################################### @@ -1011,9 +1071,15 @@ def RefreshSiteData(self): spider_plot_pic = gtk.gdk.pixbuf_new_from_file(self.spider_plot) else: spider_plot_pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_SPIDER_PLOT_AVAILABLE.png", + ) + ) self.spider_plot_pic = spider_plot_pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + 190, 190, gtk.gdk.INTERP_BILINEAR + ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) ######################################################################################### @@ -1029,114 +1095,171 @@ def RefreshSiteData(self): coot.set_last_map_colour(0.74, 0.44, 0.02) def experiment_stage_button_clicked(self, widget, data=None): - self.db_dict_mainTable['RefinementOutcome'] = data - self.db_dict_mainTable['RefinementOutcomePerson'] = getpass.getuser() - self.db_dict_mainTable['RefinementOutcomeDate'] = datetime.strftime( - datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] - - self.Logfile.insert('==> COOT: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( - data) + ' in mainTable of datasource') -# print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( -# data) + ' in mainTable of datasource' -# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + self.db_dict_mainTable["RefinementOutcome"] = data + self.db_dict_mainTable["RefinementOutcomePerson"] = getpass.getuser() + self.db_dict_mainTable["RefinementOutcomeDate"] = datetime.strftime( + datetime.now(), "%Y-%m-%d_%H-%M-%S.%f" + )[:-4] + + self.Logfile.insert( + "==> COOT: setting Refinement Outcome for " + + self.xtalID + + " to " + + str(data) + + " in mainTable of datasource" + ) + # print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( + # data) + ' in mainTable of datasource' + # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.db.create_or_remove_missing_records_in_depositTable( - self.xce_logfile, self.xtalID, 'ligand_bound', self.db_dict_mainTable) + self.xce_logfile, self.xtalID, "ligand_bound", self.db_dict_mainTable + ) def ligand_confidence_button_clicked(self, widget, data=None): - print('PANDDA_index', self.pandda_index) + print("PANDDA_index", self.pandda_index) if self.pandda_index == -1: - self.db_dict_mainTable['RefinementLigandConfidence'] = data - self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( - data) + ' in mainTable of datasource') -# print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( -# data) + ' in mainTable of datasource' + self.db_dict_mainTable["RefinementLigandConfidence"] = data + self.Logfile.insert( + "==> COOT: setting Ligand Confidence for " + + self.xtalID + + " to " + + str(data) + + " in mainTable of datasource" + ) + # print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( + # data) + ' in mainTable of datasource' self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.Todo[self.index][6] = data else: - self.db_dict_panddaTable['PANDDA_site_confidence'] = data - self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( - self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( - data) + ' in panddaTable of datasource') -# print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( -# self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( -# data) + ' in panddaTable of datasource' - self.db.update_site_event_panddaTable(self.xtalID, self.site_index, self.event_index, - self.db_dict_panddaTable) + self.db_dict_panddaTable["PANDDA_site_confidence"] = data + self.Logfile.insert( + "==> COOT: setting Ligand Confidence for " + + self.xtalID + + " (site=" + + str(self.site_index) + + ", event=" + + str(self.event_index) + + ") to " + + str(data) + + " in panddaTable of datasource" + ) + # print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( + # self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( + # data) + ' in panddaTable of datasource' + self.db.update_site_event_panddaTable( + self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable + ) self.siteDict[self.xtalID][self.pandda_index][7] = data -# def update_label(self, widget): -# print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' -# # widget.pressed() -# for w in self.label_button_list: -# print w.get_label(), w.get_active() -# if w != widget: -# w.set_active(False) -# print '<<<<<<<<<<<<<<<<<<<<<<<<<<' -# self.db_dict_mainTable['label'] = widget.get_label() -# print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( -# widget.get_label()) + ' in mainTable of datasource' -# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - -# def label_button_clicked(self, widget, data=None): -# print '............',data -# if data == 'not_shown': -# self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) -# else: -# self.db_dict_mainTable['label'] = data -# print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' -# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + # def update_label(self, widget): + # print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' + # # widget.pressed() + # for w in self.label_button_list: + # print w.get_label(), w.get_active() + # if w != widget: + # w.set_active(False) + # print '<<<<<<<<<<<<<<<<<<<<<<<<<<' + # self.db_dict_mainTable['label'] = widget.get_label() + # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( + # widget.get_label()) + ' in mainTable of datasource' + # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + + # def label_button_clicked(self, widget, data=None): + # print '............',data + # if data == 'not_shown': + # self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) + # else: + # self.db_dict_mainTable['label'] = data + # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' + # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) def RefreshData(self): # reset spider plot image spider_plot_pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), "image", "NO_SPIDER_PLOT_AVAILABLE.png" + ) + ) self.spider_plot_pic = spider_plot_pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + 190, 190, gtk.gdk.INTERP_BILINEAR + ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) # reset ground state mean map - self.ground_state_mean_map = '' + self.ground_state_mean_map = "" self.ground_state_mean_map_button.set_sensitive(False) - self.ground_state_mean_map_button.set_label( - 'Show ground state mean map') + self.ground_state_mean_map_button.set_label("Show ground state mean map") if os.path.isfile( - os.path.join(self.project_directory, self.xtalID, self.xtalID + '-ground-state-mean-map.native.ccp4')): + os.path.join( + self.project_directory, + self.xtalID, + self.xtalID + "-ground-state-mean-map.native.ccp4", + ) + ): self.ground_state_mean_map_button.set_sensitive(True) - self.ground_state_mean_map = os.path.join(self.project_directory, self.xtalID, - self.xtalID + '-ground-state-mean-map.native.ccp4') + self.ground_state_mean_map = os.path.join( + self.project_directory, + self.xtalID, + self.xtalID + "-ground-state-mean-map.native.ccp4", + ) # initialize Refinement library -# self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) + # self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) self.Refine = XChemRefine.Refine( - self.project_directory, self.xtalID, self.compoundID, self.data_source) - self.Serial = XChemRefine.GetSerial( - self.project_directory, self.xtalID) - self.panddaSerial = panddaSerial = m = ( - 4 - len(str(self.Serial))) * '0' + str(self.Serial) + self.project_directory, self.xtalID, self.compoundID, self.data_source + ) + self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) + self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * "0" + str( + self.Serial + ) # self.Serial=self.Refine.GetSerial() if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): - print('==> XCE: updating quality indicators in data source for ' + self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, - self.pdb_style)) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, - '') # '' because file does not exist - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.pdb')): - print('==> XCE: updating quality indicators in data source for ' + self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, - 'init.pdb')) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, - '') # '' because file does not exist - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): - print('==> XCE: updating quality indicators in data source for ' + self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, - 'dimple.pdb')) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, - '') # '' because file does not exist + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, self.pdb_style), + ) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, "" + ) # '' because file does not exist + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "init.pdb") + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, "init.pdb"), + ) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, "" + ) # '' because file does not exist + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple.pdb") + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, "dimple.pdb"), + ) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, "" + ) # '' because file does not exist # all this information is now updated in the datasource after each refinement cycle self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) @@ -1146,9 +1269,8 @@ def RefreshData(self): # if the structure was previously refined, try to read the parameters # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: - self.RefmacParams = self.Refine.ParamsFromPreviousCycle( - self.Serial - 1) - print('==> REFMAC params:', self.RefmacParams) + self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) + print("==> REFMAC params:", self.RefmacParams) # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) # else: @@ -1160,11 +1282,11 @@ def RefreshData(self): ######################################################################################### # ligand files # first remove old samples if present - print('>>>', self.mol_dict['ligand_stereo']) - for n, item in enumerate(self.mol_dict['ligand_stereo']): - print('__', item) + print(">>>", self.mol_dict["ligand_stereo"]) + for n, item in enumerate(self.mol_dict["ligand_stereo"]): + print("__", item) self.select_cpd_cb.remove_text(0) - print('done') + print("done") ######################################################################################### # remove potential generic line which indicates a possible covalent link @@ -1173,7 +1295,7 @@ def RefreshData(self): ######################################################################################### # reset covalent links - self.covLinks = ['X', 'X', 'X', 'X'] + self.covLinks = ["X", "X", "X", "X"] ######################################################################################### # update pdb & maps @@ -1190,116 +1312,159 @@ def RefreshData(self): # read new PDB files # read protein molecule after ligand so that this one is the active molecule coot.set_nomenclature_errors_on_read("ignore") - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.compoundID + ".pdb") + ): coot.set_colour_map_rotation_on_read_pdb(0) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb'), 0) - self.mol_dict['ligand'] = imol - coot.read_cif_dictionary(os.path.join( - self.project_directory, self.xtalID, self.compoundID + '.cif')) + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".pdb" + ), + 0, + ) + self.mol_dict["ligand"] = imol + coot.read_cif_dictionary( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".cif" + ) + ) self.select_cpd_cb.append_text(self.compoundID) - self.mol_dict['ligand_stereo'] = [] - self.mol_dict['ligand_stereo'].append(imol) + self.mol_dict["ligand_stereo"] = [] + self.mol_dict["ligand_stereo"].append(imol) # ligands in compound directory - for cifFile in sorted(glob.glob(os.path.join(self.project_directory, self.xtalID, 'compound', self.compoundID+'_*.pdb'))): - cif = cifFile[cifFile.rfind('/')+1:] - if '_with_H' in cif: + for cifFile in sorted( + glob.glob( + os.path.join( + self.project_directory, + self.xtalID, + "compound", + self.compoundID + "_*.pdb", + ) + ) + ): + cif = cifFile[cifFile.rfind("/") + 1 :] + if "_with_H" in cif: continue - self.select_cpd_cb.append_text(cif.replace('.pdb', '')) + self.select_cpd_cb.append_text(cif.replace(".pdb", "")) imol = coot.handle_read_draw_molecule_with_recentre(cifFile, 0) - self.mol_dict['ligand_stereo'].append(imol) + self.mol_dict["ligand_stereo"].append(imol) coot.set_mol_displayed(imol, 0) # autofitted ligands - for pdbFile in sorted(glob.glob(os.path.join(self.project_directory, self.xtalID, 'autofit_ligand', '*', '*.pdb'))): - autofitRun = pdbFile.split('/')[len(pdbFile.split('/')) - 2] - if pdbFile.endswith(autofitRun+'.pdb'): + for pdbFile in sorted( + glob.glob( + os.path.join( + self.project_directory, + self.xtalID, + "autofit_ligand", + "*", + "*.pdb", + ) + ) + ): + autofitRun = pdbFile.split("/")[len(pdbFile.split("/")) - 2] + if pdbFile.endswith(autofitRun + ".pdb"): self.select_cpd_cb.append_text(autofitRun) - imol = coot.handle_read_draw_molecule_with_recentre( - pdbFile, 0) - self.mol_dict['ligand_stereo'].append(imol) + imol = coot.handle_read_draw_molecule_with_recentre(pdbFile, 0) + self.mol_dict["ligand_stereo"].append(imol) coot.set_mol_displayed(imol, 0) self.select_cpd_cb.set_sensitive(True) self.select_cpd_cb.set_active(0) else: - print('no compound found in sample directory') -# self.select_cpd_cb.append_text('') + print("no compound found in sample directory") + # self.select_cpd_cb.append_text('') self.select_cpd_cb.set_sensitive(False) - if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + if not os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) -# if self.refinementProtocol.startswith('pandda'): -# self.Logfile.insert('==> COOT: looking for ground-state model ' + os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.ground-state.pdb')) -# print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.ground-state.pdb') -# if os.path.isfile(os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): -# self.Logfile.insert('==> COOT: found ground-state model') -## print '=> XCE: found ground-state model' -# os.chdir(os.path.join(self.project_directory, self.xtalID)) -# coot.set_colour_map_rotation_on_read_pdb(0) -# try: -# color_wheel_rotation = 160 / float(imol + 2) -# except UnboundLocalError: -# color_wheel_rotation = 80 -# coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) -# imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.ground-state.pdb'), -# 0) -# coot.set_colour_by_molecule(imol) -# coot.set_mol_active(imol, 0) -# else: -# self.Logfile.error('==> COOT - cannot find ground-state model') -## print '=> XCE - ERROR: cannot find ground-state model' -# self.Logfile.insert('==> COOT: looking for bound-state model '+ os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.bound-state.pdb')) -# print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.bound-state.pdb') -# if os.path.isfile(os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb')): -# self.Logfile.insert('==> COOT: found bound-state model') -## print '=> XCE: found bound-state model' -# os.chdir(os.path.join(self.project_directory, self.xtalID)) -# coot.set_colour_map_rotation_on_read_pdb(0) -# color_wheel_rotation = 21 / float(imol + 2) -# coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) -# imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.bound-state.pdb'), -# 0) -# self.mol_dict['protein'] = imol -# else: -# self.Logfile.error('==> COOT: cannot find bound-state model') -## print '=> XCE - ERROR: cannot find bound-state model' -# self.Logfile.warning('==> COOT: moving to next crystal...') -## print '=> XCE: moving to next crystal...' -# self.go_to_next_xtal() -# else: - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + # if self.refinementProtocol.startswith('pandda'): + # self.Logfile.insert('==> COOT: looking for ground-state model ' + os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.ground-state.pdb')) + # print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.ground-state.pdb') + # if os.path.isfile(os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): + # self.Logfile.insert('==> COOT: found ground-state model') + ## print '=> XCE: found ground-state model' + # os.chdir(os.path.join(self.project_directory, self.xtalID)) + # coot.set_colour_map_rotation_on_read_pdb(0) + # try: + # color_wheel_rotation = 160 / float(imol + 2) + # except UnboundLocalError: + # color_wheel_rotation = 80 + # coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) + # imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.ground-state.pdb'), + # 0) + # coot.set_colour_by_molecule(imol) + # coot.set_mol_active(imol, 0) + # else: + # self.Logfile.error('==> COOT - cannot find ground-state model') + ## print '=> XCE - ERROR: cannot find ground-state model' + # self.Logfile.insert('==> COOT: looking for bound-state model '+ os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.bound-state.pdb')) + # print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.bound-state.pdb') + # if os.path.isfile(os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb')): + # self.Logfile.insert('==> COOT: found bound-state model') + ## print '=> XCE: found bound-state model' + # os.chdir(os.path.join(self.project_directory, self.xtalID)) + # coot.set_colour_map_rotation_on_read_pdb(0) + # color_wheel_rotation = 21 / float(imol + 2) + # coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) + # imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.bound-state.pdb'), + # 0) + # self.mol_dict['protein'] = imol + # else: + # self.Logfile.error('==> COOT: cannot find bound-state model') + ## print '=> XCE - ERROR: cannot find bound-state model' + # self.Logfile.warning('==> COOT: moving to next crystal...') + ## print '=> XCE: moving to next crystal...' + # self.go_to_next_xtal() + # else: + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.pdb')): + os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0 + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "init.pdb") + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, 'init.pdb'), 0) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): + os.path.join(self.project_directory, self.xtalID, "init.pdb"), 0 + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple.pdb") + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, 'dimple.pdb'), 0) + os.path.join(self.project_directory, self.xtalID, "dimple.pdb"), 0 + ) else: self.go_to_next_xtal() - self.mol_dict['protein'] = imol + self.mol_dict["protein"] = imol # read any one event map if present for event_map in glob.glob( - os.path.join(self.project_directory, self.xtalID, self.xtalID + '-event_*.native.ccp4')): + os.path.join( + self.project_directory, + self.xtalID, + self.xtalID + "-event_*.native.ccp4", + ) + ): coot.handle_read_ccp4_map((event_map), 0) coot.set_contour_level_in_sigma(imol, 2) coot.set_last_map_colour(0.74, 0.44, 0.02) @@ -1307,8 +1472,8 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( - item).endswith(self.pdb_style): + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb" + ) or coot.molecule_name(item).endswith(self.pdb_style): # master switch to show symmetry molecules coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model @@ -1317,17 +1482,21 @@ def RefreshData(self): # read fofc maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level -# if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): + # if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): # coot 0.9 does not handle P1 maps well, so now looking for non-existent map in order to trigger # map calculation from mtz file - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc_??????.map')): + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "2fofc_??????.map") + ): coot.set_colour_map_rotation_on_read_pdb(0) coot.set_default_initial_contour_level_for_difference_map(3) - coot.handle_read_ccp4_map(os.path.join( - self.project_directory, self.xtalID, 'fofc.map'), 1) + coot.handle_read_ccp4_map( + os.path.join(self.project_directory, self.xtalID, "fofc.map"), 1 + ) coot.set_default_initial_contour_level_for_map(1) - coot.handle_read_ccp4_map(os.path.join( - self.project_directory, self.xtalID, '2fofc.map'), 0) + coot.handle_read_ccp4_map( + os.path.join(self.project_directory, self.xtalID, "2fofc.map"), 0 + ) coot.set_last_map_colour(0, 0, 1) else: # try to open mtz file with same name as pdb file @@ -1340,80 +1509,123 @@ def RefreshData(self): # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): # os.symlink('dimple.mtz',self.mtz_style) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, self.mtz_style)) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, 'init.mtz')) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, 'dimple.mtz')) + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.mtz_style) + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, self.mtz_style) + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "init.mtz") + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, "init.mtz") + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple.mtz") + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, "dimple.mtz") + ) ######################################################################################### # update Quality Indicator table try: - self.RRfreeValue.set_label(str(round(float(self.QualityIndicators['RefinementRcryst']), 3)) + ' / ' + str( - round(float(self.QualityIndicators['RefinementRfree']), 3))) + self.RRfreeValue.set_label( + str(round(float(self.QualityIndicators["RefinementRcryst"]), 3)) + + " / " + + str(round(float(self.QualityIndicators["RefinementRfree"]), 3)) + ) except ValueError: - self.RRfreeValue.set_label('-') + self.RRfreeValue.set_label("-") try: - self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementRfreeTraficLight'])) + self.RRfreeBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRfreeTraficLight"] + ), + ) except ValueError: pass - self.ResolutionValue.set_label( - self.QualityIndicators['RefinementResolution']) + self.ResolutionValue.set_label(self.QualityIndicators["RefinementResolution"]) try: - self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementResolutionTL'])) + self.ResolutionBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementResolutionTL"]), + ) except ValueError: pass self.MolprobityScoreValue.set_label( - self.QualityIndicators['RefinementMolProbityScore']) + self.QualityIndicators["RefinementMolProbityScore"] + ) try: - self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementMolProbityScoreTL'])) + self.MolprobityScoreBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementMolProbityScoreTL"] + ), + ) except ValueError: pass self.RamachandranOutliersValue.set_label( - self.QualityIndicators['RefinementRamachandranOutliers']) + self.QualityIndicators["RefinementRamachandranOutliers"] + ) try: - self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRamachandranOutliersTL'])) + self.RamachandranOutliersBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRamachandranOutliersTL"] + ), + ) except ValueError: pass self.RamachandranFavoredValue.set_label( - self.QualityIndicators['RefinementRamachandranFavored']) + self.QualityIndicators["RefinementRamachandranFavored"] + ) try: - self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRamachandranFavoredTL'])) + self.RamachandranFavoredBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRamachandranFavoredTL"] + ), + ) except ValueError: pass - self.rmsdBondsValue.set_label( - self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue.set_label(self.QualityIndicators["RefinementRmsdBonds"]) try: - self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdBondsTL'])) + self.rmsdBondsBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementRmsdBondsTL"]), + ) except ValueError: pass - self.rmsdAnglesValue.set_label( - self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue.set_label(self.QualityIndicators["RefinementRmsdAngles"]) try: - self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdAnglesTL'])) + self.rmsdAnglesBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementRmsdAnglesTL"]), + ) except ValueError: pass self.MatrixWeightValue.set_label( - self.QualityIndicators['RefinementMatrixWeight']) + self.QualityIndicators["RefinementMatrixWeight"] + ) try: pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(self.project_directory, self.xtalID, self.compoundID + '.png')) + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".png" + ) + ) except gobject.GError: pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_COMPOUND_IMAGE_AVAILABLE.png", + ) + ) self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.image.set_from_pixbuf(self.pic) @@ -1483,28 +1695,42 @@ def start_refinement(self): # else: ####################################################### - if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): - os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) + if not os.path.isdir( + os.path.join(self.project_directory, self.xtalID, "cootOut") + ): + os.mkdir(os.path.join(self.project_directory, self.xtalID, "cootOut")) # create folder for new refinement cycle try: - self.Logfile.insert('==> COOT: trying to make folder: %s' % os.path.join( - self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) - os.mkdir(os.path.join(self.project_directory, self.xtalID, - 'cootOut', 'Refine_' + str(self.Serial))) + self.Logfile.insert( + "==> COOT: trying to make folder: %s" + % os.path.join( + self.project_directory, + self.xtalID, + "cootOut", + "Refine_" + str(self.Serial), + ) + ) + os.mkdir( + os.path.join( + self.project_directory, + self.xtalID, + "cootOut", + "Refine_" + str(self.Serial), + ) + ) except OSError: + self.Logfile.warning("==> COOT: folder exists; will overwrite contents!") + # print '==> XCE: WARNING -> folder exists; will overwrite contents!' self.Logfile.warning( - '==> COOT: folder exists; will overwrite contents!') -# print '==> XCE: WARNING -> folder exists; will overwrite contents!' - self.Logfile.warning( - '==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') - + "==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem" + ) -# ####################################################### -# # create folder for new refinement cycle and check if free.mtz exists -# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): -# os.mkdir(os.path.join(self.project_directory, self.xtalID)) -# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): -# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) + # ####################################################### + # # create folder for new refinement cycle and check if free.mtz exists + # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): + # os.mkdir(os.path.join(self.project_directory, self.xtalID)) + # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): + # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) ####################################################### # write PDB file @@ -1515,23 +1741,36 @@ def start_refinement(self): if coot.molecule_name(item).endswith(self.pdb_style): foundPDB = True break - elif coot.molecule_name(item).endswith('refine.split.bound-state.pdb'): + elif coot.molecule_name(item).endswith("refine.split.bound-state.pdb"): foundPDB = True break - elif coot.molecule_name(item).endswith('init.pdb'): + elif coot.molecule_name(item).endswith("init.pdb"): foundPDB = True break - elif coot.molecule_name(item).endswith('dimple.pdb'): + elif coot.molecule_name(item).endswith("dimple.pdb"): foundPDB = True break if foundPDB: coot.delete_hydrogens(item) - coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', - 'Refine_' + str(self.Serial), 'in.pdb')) - -# self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) - self.Refine.RunBuster(self.Serial, self.RefmacParams, - self.external_software, self.xce_logfile, self.covLinkAtomSpec) + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "cootOut", + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) + + # self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) + self.Refine.RunBuster( + self.Serial, + self.RefmacParams, + self.external_software, + self.xce_logfile, + self.covLinkAtomSpec, + ) self.index += 1 if self.index >= len(self.Todo): # self.index = len(self.Todo) @@ -1539,9 +1778,10 @@ def start_refinement(self): self.cb.set_active(self.index) def RefinementParams(self, widget): - print('\n==> XCE: changing refinement parameters') - self.RefmacParams = XChemRefine.RefineParams(self.project_directory, self.xtalID, self.compoundID, - self.data_source).RefmacRefinementParams(self.RefmacParams) + print("\n==> XCE: changing refinement parameters") + self.RefmacParams = XChemRefine.RefineParams( + self.project_directory, self.xtalID, self.compoundID, self.data_source + ).RefmacRefinementParams(self.RefmacParams) print(self.RefmacParams) def covalentLinkDef(self, widget): @@ -1552,40 +1792,70 @@ def show_potential_link(self, *clicks): # it's a prerequisite that the ligand is merged into the protein imol_protein = None for imol in coot_utils_XChem.molecule_number_list(): - print('>', coot.molecule_name(imol)) - if coot.molecule_name(imol).endswith(self.pdb_style) or \ - coot.molecule_name(imol).endswith('init.pdb') or \ - coot.molecule_name(imol).endswith('dimple.pdb') or \ - coot.molecule_name(imol).endswith(self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb'): + print(">", coot.molecule_name(imol)) + if ( + coot.molecule_name(imol).endswith(self.pdb_style) + or coot.molecule_name(imol).endswith("init.pdb") + or coot.molecule_name(imol).endswith("dimple.pdb") + or coot.molecule_name(imol).endswith( + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb" + ) + ): imol_protein = imol break - print('please click on the two atoms you want to link') - if (len(clicks) == 2): + print("please click on the two atoms you want to link") + if len(clicks) == 2: click_1 = clicks[0] click_2 = clicks[1] imol_1 = click_1[1] imol_2 = click_2[1] - print('imolp', imol, 'imo11', imol_1, 'imol2', imol_2) + print("imolp", imol, "imo11", imol_1, "imol2", imol_2) if imol_1 == imol_2 and imol_1 == imol_protein: - print('click_1', click_1) + print("click_1", click_1) self.covLinkAtomSpec = None xyz_1 = atom_info_string( - click_1[1], click_1[2], click_1[3], click_1[4], click_1[5], click_1[6]) - residue_1 = residue_name( - click_1[1], click_1[2], click_1[3], click_1[4]) + click_1[1], + click_1[2], + click_1[3], + click_1[4], + click_1[5], + click_1[6], + ) + residue_1 = residue_name(click_1[1], click_1[2], click_1[3], click_1[4]) xyz_2 = atom_info_string( - click_2[1], click_2[2], click_2[3], click_2[4], click_2[5], click_2[6]) - residue_2 = residue_name( - click_2[1], click_2[2], click_2[3], click_2[4]) + click_2[1], + click_2[2], + click_2[3], + click_2[4], + click_2[5], + click_2[6], + ) + residue_2 = residue_name(click_2[1], click_2[2], click_2[3], click_2[4]) thick = 4 to_generic_object_add_line( - self.covLinkObject, "yellowtint", thick, xyz_1[3], xyz_1[4], xyz_1[5], xyz_2[3], xyz_2[4], xyz_2[5]) + self.covLinkObject, + "yellowtint", + thick, + xyz_1[3], + xyz_1[4], + xyz_1[5], + xyz_2[3], + xyz_2[4], + xyz_2[5], + ) set_display_generic_object(self.covLinkObject, 1) - self.covLinkAtomSpec = [imol_protein, - click_1, click_2, residue_1, residue_2] + self.covLinkAtomSpec = [ + imol_protein, + click_1, + click_2, + residue_1, + residue_2, + ] else: - print('error: both atoms must belong to the same object; did you merge the ligand with your protein?') + print( + "error: both atoms must belong to the same object; did you merge the ligand with your protein?" + ) def covalentLinkCreate(self, widget): if self.covLinkAtomSpec is not None: @@ -1594,33 +1864,31 @@ def covalentLinkCreate(self, widget): atom2 = self.covLinkAtomSpec[2][1:] residue_1 = self.covLinkAtomSpec[3] residue_2 = self.covLinkAtomSpec[4] - make_link(imol, atom1, atom2, residue_1+'-'+residue_2, 1.7) + make_link(imol, atom1, atom2, residue_1 + "-" + residue_2, 1.7) generic_object_clear(self.covLinkObject) self.start_refinement() else: - print('error: no covalent link defined') + print("error: no covalent link defined") def set_selection_mode(self, widget): self.selection_mode = widget.get_active_text() def get_samples_to_look_at(self, widget): - if self.selection_mode == '': - self.status_label.set_text('select model stage') + if self.selection_mode == "": + self.status_label.set_text("select model stage") return - self.status_label.set_text('checking datasource for samples... ') + self.status_label.set_text("checking datasource for samples... ") # first remove old samples if present if len(self.Todo) != 0: for n, item in enumerate(self.Todo): self.cb.remove_text(0) self.Todo = [] self.siteDict = {} - self.Todo, self.siteDict = self.db.get_todoList_for_coot( - self.selection_mode) - self.status_label.set_text( - 'found {0!s} samples'.format(len(self.Todo))) + self.Todo, self.siteDict = self.db.get_todoList_for_coot(self.selection_mode) + self.status_label.set_text("found {0!s} samples".format(len(self.Todo))) # refresh sample CB for item in sorted(self.Todo): - self.cb.append_text('{0!s}'.format(item[0])) + self.cb.append_text("{0!s}".format(item[0])) if self.siteDict == {}: self.cb_site.set_sensitive(False) self.PREVbuttonSite.set_sensitive(False) @@ -1634,130 +1902,209 @@ def update_plot(self, refinement_cycle, Rfree, Rcryst): fig = Figure(figsize=(2, 2), dpi=50) Plot = fig.add_subplot(111) Plot.set_ylim([0, max(Rcryst + Rfree)]) - Plot.set_xlabel('Refinement Cycle', fontsize=12) - Plot.plot(refinement_cycle, Rfree, label='Rfree', linewidth=2) - Plot.plot(refinement_cycle, Rcryst, label='Rcryst', linewidth=2) - Plot.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, - ncol=2, mode="expand", borderaxespad=0., fontsize=12) + Plot.set_xlabel("Refinement Cycle", fontsize=12) + Plot.plot(refinement_cycle, Rfree, label="Rfree", linewidth=2) + Plot.plot(refinement_cycle, Rcryst, label="Rcryst", linewidth=2) + Plot.legend( + bbox_to_anchor=(0.0, 1.02, 1.0, 0.102), + loc=3, + ncol=2, + mode="expand", + borderaxespad=0.0, + fontsize=12, + ) return fig def place_ligand_here(self, widget): cpd = str(self.select_cpd_cb.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): - if imol not in self.mol_dict['ligand_stereo']: + if imol not in self.mol_dict["ligand_stereo"]: continue - molName = coot.molecule_name(imol)[coot.molecule_name( - imol).rfind('/')+1:].replace('.pdb', '') + molName = coot.molecule_name(imol)[ + coot.molecule_name(imol).rfind("/") + 1 : + ].replace(".pdb", "") if molName == cpd: - print('===> XCE: moving ligand to pointer') + print("===> XCE: moving ligand to pointer") coot_utils_XChem.move_molecule_here(imol) - print('LIGAND: ', molName) -# print '===> XCE: moving ligand to pointer' -# # coot.move_molecule_here() -# print 'LIGAND: ', self.mol_dict['ligand'] -# coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) + print("LIGAND: ", molName) + + # print '===> XCE: moving ligand to pointer' + # # coot.move_molecule_here() + # print 'LIGAND: ', self.mol_dict['ligand'] + # coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) def merge_ligand_into_protein(self, widget): cpd = str(self.select_cpd_cb.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): - if imol not in self.mol_dict['ligand_stereo']: + if imol not in self.mol_dict["ligand_stereo"]: continue - molName = coot.molecule_name(imol)[coot.molecule_name( - imol).rfind('/')+1:].replace('.pdb', '') + molName = coot.molecule_name(imol)[ + coot.molecule_name(imol).rfind("/") + 1 : + ].replace(".pdb", "") if molName == cpd: - print('===> XCE: merge ligand into protein structure -->', cpd) - coot.merge_molecules_py([imol], self.mol_dict['protein']) - if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( - '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')): - os.system('/bin/rm %s' % os.path.join(self.project_directory, - self.xtalID, self.compoundID + '.cif')) - print('XCE: changing directory', os.path.join( - self.project_directory, self.xtalID)) + print("===> XCE: merge ligand into protein structure -->", cpd) + coot.merge_molecules_py([imol], self.mol_dict["protein"]) + if "rhofit" in coot.molecule_name( + imol + ) or "phenix" in coot.molecule_name(imol): + molName = ( + coot.molecule_name(imol)[ + coot.molecule_name(imol).rfind("/") + 1 : + ] + .replace(".pdb", "") + .replace("_phenix", "") + .replace("_rhofit", "") + ) + if os.path.isfile( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".cif" + ) + ): + os.system( + "/bin/rm %s" + % os.path.join( + self.project_directory, + self.xtalID, + self.compoundID + ".cif", + ) + ) + print( + "XCE: changing directory", + os.path.join(self.project_directory, self.xtalID), + ) os.chdir(os.path.join(self.project_directory, self.xtalID)) - print('XCE: changing symlink ln -s %s %s.cif' % ( - os.path.join('compound', molName + '.cif'), self.compoundID)) + print( + "XCE: changing symlink ln -s %s %s.cif" + % (os.path.join("compound", molName + ".cif"), self.compoundID) + ) + os.system( + "ln -s %s %s.cif" + % (os.path.join("compound", molName + ".cif"), self.compoundID) + ) + if os.path.isfile( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".pdb" + ) + ): os.system( - 'ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): - os.system('/bin/rm %s' % os.path.join(self.project_directory, - self.xtalID, self.compoundID + '.pdb')) - print('XCE: changing directory', os.path.join( - self.project_directory, self.xtalID)) + "/bin/rm %s" + % os.path.join( + self.project_directory, + self.xtalID, + self.compoundID + ".pdb", + ) + ) + print( + "XCE: changing directory", + os.path.join(self.project_directory, self.xtalID), + ) os.chdir(os.path.join(self.project_directory, self.xtalID)) - print('XCE: changing symlink ln -s %s %s.pdb' % ( - os.path.join('compound', molName + '.pdb'), self.compoundID)) - os.system('ln -s %s %s.pdb' % (os.path.join('compound', molName - + '.pdb'), self.compoundID)) - print('===> XCE: deleting ligand molecule', molName) + print( + "XCE: changing symlink ln -s %s %s.pdb" + % (os.path.join("compound", molName + ".pdb"), self.compoundID) + ) + os.system( + "ln -s %s %s.pdb" + % (os.path.join("compound", molName + ".pdb"), self.compoundID) + ) + print("===> XCE: deleting ligand molecule", molName) coot.close_molecule(imol) self.select_cpd_cb.set_sensitive(False) -# print '===> XCE: merge ligand into protein structure' -# # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) -# coot.merge_molecules_py([self.mol_dict['ligand']], self.mol_dict['protein']) -# print '===> XCE: deleting ligand molecule' -# coot.close_molecule(self.mol_dict['ligand']) + # print '===> XCE: merge ligand into protein structure' + # # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) + # coot.merge_molecules_py([self.mol_dict['ligand']], self.mol_dict['protein']) + # print '===> XCE: deleting ligand molecule' + # coot.close_molecule(self.mol_dict['ligand']) def show_molprobity_to_do(self, widget): print(self.panddaSerial) - AdjPanddaSerial = (4 - len(str(self.Serial))) * \ - '0' + str(int(self.panddaSerial) - 1) - - print('==> XCE COOT: trying to find ' + os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py')) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py')): - print('==> XCE: running MolProbity Summary for', self.xtalID) - coot.run_script(os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1)+'-report/molprobe/molprobity_coot.py')) -# elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), -# 'molprobity_coot.py')): -# print '==> XCE: running MolProbity Summary for', self.xtalID -# coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), -# 'molprobity_coot.py')) + AdjPanddaSerial = (4 - len(str(self.Serial))) * "0" + str( + int(self.panddaSerial) - 1 + ) + + print( + "==> XCE COOT: trying to find " + + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + + str(self.Serial - 1) + + "-report/molprobe/molprobity_coot.py", + ) + ) + if os.path.isfile( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + + str(self.Serial - 1) + + "-report/molprobe/molprobity_coot.py", + ) + ): + print("==> XCE: running MolProbity Summary for", self.xtalID) + coot.run_script( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + + str(self.Serial - 1) + + "-report/molprobe/molprobity_coot.py", + ) + ) + # elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), + # 'molprobity_coot.py')): + # print '==> XCE: running MolProbity Summary for', self.xtalID + # coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), + # 'molprobity_coot.py')) else: - print('==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')) - -# def refinementProtocolCallback(self, widget): -# if widget.get_active(): -# if self.refinementProtocolcheckbox.get_active(): -# self.refinementProtocol = 'pandda_phenix' -# else: -# self.refinementProtocol = 'pandda_refmac' -# self.PREVbuttonSite.set_sensitive(True) -# self.NEXTbuttonSite.set_sensitive(True) -# else: -# self.refinementProtocolcheckbox.set_active(False) -# self.refinementProtocol = 'refmac' -# self.PREVbuttonSite.set_sensitive(False) -# self.NEXTbuttonSite.set_sensitive(False) -# print self.refinementProtocol - -# def refinementProgramCallback(self, widget): -# if widget.get_active(): -# if self.refinementProtocolcheckbox.get_active(): -# self.refinementProtocol = 'pandda_phenix' -# self.RefinementParamsButton.set_sensitive(False) -# else: -# self.refinementProgramcheckbox.set_active(False) -# self.refinementProtocol = 'refmac' -# else: -# self.RefinementParamsButton.set_sensitive(True) -# if self.refinementProtocolcheckbox.get_active(): -# self.refinementProtocol = 'pandda_refmac' -# else: -# self.refinementProtocol = 'refmac' -# print self.refinementProtocol + print( + "==> XCE: cannot find " + + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ) + + # def refinementProtocolCallback(self, widget): + # if widget.get_active(): + # if self.refinementProtocolcheckbox.get_active(): + # self.refinementProtocol = 'pandda_phenix' + # else: + # self.refinementProtocol = 'pandda_refmac' + # self.PREVbuttonSite.set_sensitive(True) + # self.NEXTbuttonSite.set_sensitive(True) + # else: + # self.refinementProtocolcheckbox.set_active(False) + # self.refinementProtocol = 'refmac' + # self.PREVbuttonSite.set_sensitive(False) + # self.NEXTbuttonSite.set_sensitive(False) + # print self.refinementProtocol + + # def refinementProgramCallback(self, widget): + # if widget.get_active(): + # if self.refinementProtocolcheckbox.get_active(): + # self.refinementProtocol = 'pandda_phenix' + # self.RefinementParamsButton.set_sensitive(False) + # else: + # self.refinementProgramcheckbox.set_active(False) + # self.refinementProtocol = 'refmac' + # else: + # self.RefinementParamsButton.set_sensitive(True) + # if self.refinementProtocolcheckbox.get_active(): + # self.refinementProtocol = 'pandda_refmac' + # else: + # self.refinementProtocol = 'refmac' + # print self.refinementProtocol def show_ground_state_mean_map(self, widget): - if widget.get_label().startswith('Show'): + if widget.get_label().startswith("Show"): loaded = False for imol in coot_utils_XChem.molecule_number_list(): - if 'ground-state-mean-map' in coot.molecule_name(imol): + if "ground-state-mean-map" in coot.molecule_name(imol): coot.set_map_displayed(imol, 1) loaded = True break @@ -1765,13 +2112,13 @@ def show_ground_state_mean_map(self, widget): coot.set_default_initial_contour_level_for_map(1) coot.handle_read_ccp4_map(self.ground_state_mean_map, 0) coot.set_last_map_colour(0.6, 0.6, 0) - widget.set_label('Undisplay ground state mean map') + widget.set_label("Undisplay ground state mean map") else: for imol in coot_utils_XChem.molecule_number_list(): - if 'ground-state-mean-map' in coot.molecule_name(imol): + if "ground-state-mean-map" in coot.molecule_name(imol): coot.set_map_displayed(imol, 0) - widget.set_label('Show ground state mean map') + widget.set_label("Show ground state mean map") -if __name__ == '__main__': +if __name__ == "__main__": GUI().StartGUI() diff --git a/lib/XChemCootNew.py b/lib/XChemCootNew.py index c3acad77..652b688d 100755 --- a/lib/XChemCootNew.py +++ b/lib/XChemCootNew.py @@ -23,7 +23,7 @@ # from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas # XCE libraries -sys.path.append(os.getenv('XChemExplorer_DIR') + '/lib') +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") # libraries from COOT @@ -43,57 +43,60 @@ def __init__(self): # read in settings file from XChemExplorer to set the relevant paths self.settings = pickle.load(open(".xce_settings.pkl", "rb")) - remote_qsub_submission = self.settings['remote_qsub'] - self.database_directory = self.settings['database_directory'] - self.xce_logfile = self.settings['xce_logfile'] + remote_qsub_submission = self.settings["remote_qsub"] + self.database_directory = self.settings["database_directory"] + self.xce_logfile = self.settings["xce_logfile"] self.Logfile = XChemLog.updateLog(self.xce_logfile) - self.Logfile.insert('==> COOT: starting coot plugin...') - self.data_source = self.settings['data_source'] + self.Logfile.insert("==> COOT: starting coot plugin...") + self.data_source = self.settings["data_source"] self.db = XChemDB.data_source(self.data_source) print(self.settings) # checking for external software packages - self.external_software = XChemUtils.external_software( - self.xce_logfile).check() - self.external_software['qsub_remote'] = remote_qsub_submission - - self.selection_criteria = ['0 - All Datasets', - '1 - Analysis Pending', - '2 - PANDDA model', - '3 - In Refinement', - '4 - CompChem ready', - '5 - Deposition ready', - '6 - Deposited', - '7 - Analysed & Rejected'] - - self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], - ['In Refinement', '3 - In Refinement', 65000, 0, 0], - ['Comp Chem Ready!', - '4 - CompChem ready', 65000, 0, 0], - ['Ready for Deposition!', - '5 - Deposition ready', 65000, 0, 0], - ['In PDB', '6 - Deposited', 65000, 0, 0], - ['Analysed & Rejected', '7 - Analysed & Rejected', 65000, 0, 0]] - - self.ligand_confidence_category = ['0 - no ligand present', - '1 - Low Confidence', - '2 - Correct ligand, weak density', - '3 - Clear density, unexpected ligand', - '4 - High Confidence'] + self.external_software = XChemUtils.external_software(self.xce_logfile).check() + self.external_software["qsub_remote"] = remote_qsub_submission + + self.selection_criteria = [ + "0 - All Datasets", + "1 - Analysis Pending", + "2 - PANDDA model", + "3 - In Refinement", + "4 - CompChem ready", + "5 - Deposition ready", + "6 - Deposited", + "7 - Analysed & Rejected", + ] + + self.experiment_stage = [ + ["Review PANDDA export", "2 - PANDDA model", 65000, 0, 0], + ["In Refinement", "3 - In Refinement", 65000, 0, 0], + ["Comp Chem Ready!", "4 - CompChem ready", 65000, 0, 0], + ["Ready for Deposition!", "5 - Deposition ready", 65000, 0, 0], + ["In PDB", "6 - Deposited", 65000, 0, 0], + ["Analysed & Rejected", "7 - Analysed & Rejected", 65000, 0, 0], + ] + + self.ligand_confidence_category = [ + "0 - no ligand present", + "1 - Low Confidence", + "2 - Correct ligand, weak density", + "3 - Clear density, unexpected ligand", + "4 - High Confidence", + ] self.ligand_site_information = self.db.get_list_of_pandda_sites_for_coot() # this decides which samples will be looked at - self.selection_mode = '' + self.selection_mode = "" # self.selected_site='' self.pandda_index = -1 # refers to the number of sites - self.site_index = '0' - self.event_index = '0' + self.site_index = "0" + self.event_index = "0" # the Folder is kind of a legacy thing because my inital idea was to have separate folders # for Data Processing and Refinement - self.project_directory = self.settings['initial_model_directory'] + self.project_directory = self.settings["initial_model_directory"] self.Serial = 0 self.panddaSerial = 0 self.Refine = None @@ -101,31 +104,33 @@ def __init__(self): self.Todo = [] self.siteDict = {} - self.xtalID = '' - self.compoundID = '' - self.ground_state_mean_map = '' - self.spider_plot = '' - self.ligand_confidence = '' - self.refinement_folder = '' - self.refinementProtocol = 'pandda_refmac' + self.xtalID = "" + self.compoundID = "" + self.ground_state_mean_map = "" + self.spider_plot = "" + self.ligand_confidence = "" + self.refinement_folder = "" + self.refinementProtocol = "pandda_refmac" # self.datasetOutcome='' - self.pdb_style = 'refine.pdb' - self.mtz_style = 'refine.mtz' + self.pdb_style = "refine.pdb" + self.mtz_style = "refine.mtz" - self.covLink = ['X', 'X', 'X', 'X'] + self.covLink = ["X", "X", "X", "X"] self.covLinkObject = coot.new_generic_object_number("covalent bond") self.covLinkAtomSpec = None self.label = None # stores imol of currently loaded molecules and maps - self.mol_dict = {'protein': -1, - 'ligand': -1, - '2fofc': -1, - 'fofc': -1, - 'event': -1, - 'ligand_stereo': []} + self.mol_dict = { + "protein": -1, + "ligand": -1, + "2fofc": -1, + "fofc": -1, + "event": -1, + "ligand_stereo": [], + } # two dictionaries which are flushed when a new crystal is loaded # and which contain information to update the data source if necessary @@ -140,47 +145,57 @@ def __init__(self): coot.set_colour_map_rotation_for_map(0) # coot.set_colour_map_rotation_on_read_pdb_flag(21) - self.QualityIndicators = {'RefinementRcryst': '-', - 'RefinementRfree': '-', - 'RefinementRfreeTraficLight': 'gray', - 'RefinementResolution': '-', - 'RefinementResolutionTL': 'gray', - 'RefinementMolProbityScore': '-', - 'RefinementMolProbityScoreTL': 'gray', - 'RefinementRamachandranOutliers': '-', - 'RefinementRamachandranOutliersTL': 'gray', - 'RefinementRamachandranFavored': '-', - 'RefinementRamachandranFavoredTL': 'gray', - 'RefinementRmsdBonds': '-', - 'RefinementRmsdBondsTL': 'gray', - 'RefinementRmsdAngles': '-', - 'RefinementRmsdAnglesTL': 'gray', - 'RefinementMatrixWeight': '-'} - - self.spider_plot_data = {'PANDDA_site_ligand_id': '-', - 'PANDDA_site_occupancy': '-', - 'PANDDA_site_B_average': '-', - 'PANDDA_site_B_ratio_residue_surroundings': '-', - 'PANDDA_site_RSCC': '-', - 'PANDDA_site_rmsd': '-', - 'PANDDA_site_RSR': '-', - 'PANDDA_site_RSZD': '-'} + self.QualityIndicators = { + "RefinementRcryst": "-", + "RefinementRfree": "-", + "RefinementRfreeTraficLight": "gray", + "RefinementResolution": "-", + "RefinementResolutionTL": "gray", + "RefinementMolProbityScore": "-", + "RefinementMolProbityScoreTL": "gray", + "RefinementRamachandranOutliers": "-", + "RefinementRamachandranOutliersTL": "gray", + "RefinementRamachandranFavored": "-", + "RefinementRamachandranFavoredTL": "gray", + "RefinementRmsdBonds": "-", + "RefinementRmsdBondsTL": "gray", + "RefinementRmsdAngles": "-", + "RefinementRmsdAnglesTL": "gray", + "RefinementMatrixWeight": "-", + } + + self.spider_plot_data = { + "PANDDA_site_ligand_id": "-", + "PANDDA_site_occupancy": "-", + "PANDDA_site_B_average": "-", + "PANDDA_site_B_ratio_residue_surroundings": "-", + "PANDDA_site_RSCC": "-", + "PANDDA_site_rmsd": "-", + "PANDDA_site_RSR": "-", + "PANDDA_site_RSZD": "-", + } # default refmac parameters - self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '', - 'WATER': '', - 'LIGOCC': '', - 'SANITY': ''} + self.RefmacParams = { + "HKLIN": "", + "HKLOUT": "", + "XYZIN": "", + "XYZOUT": "", + "LIBIN": "", + "LIBOUT": "", + "TLSIN": "", + "TLSOUT": "", + "TLSADD": "", + "NCYCLES": "10", + "MATRIX_WEIGHT": "AUTO", + "BREF": " bref ISOT\n", + "TLS": "", + "NCS": "", + "TWIN": "", + "WATER": "", + "LIGOCC": "", + "SANITY": "", + } def StartGUI(self): @@ -195,7 +210,7 @@ def StartGUI(self): # --- Sample Selection --- # self.vbox.add(gtk.Label('Select Samples')) - frame = gtk.Frame(label='Select Samples') + frame = gtk.Frame(label="Select Samples") self.hbox_select_samples = gtk.HBox() # vbox=gtk.VBox() @@ -212,8 +227,7 @@ def StartGUI(self): # self.hbox_select_samples.add(self.cb_select_sites) self.select_samples_button = gtk.Button(label="GO") - self.select_samples_button.connect( - "clicked", self.get_samples_to_look_at) + self.select_samples_button.connect("clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) @@ -228,25 +242,24 @@ def StartGUI(self): ################################################################################# # --- refinement protocol --- frame = gtk.Frame() - self.refinementProtocolcheckbox = gtk.CheckButton( - 'PanDDA model refinement)') + self.refinementProtocolcheckbox = gtk.CheckButton("PanDDA model refinement)") # callback is defined later -# self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) + # self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) self.refinementProtocolcheckbox.set_active(True) frame.add(self.refinementProtocolcheckbox) self.vbox.pack_start(frame) ################################################################################# # --- refinement program --- -# frame = gtk.Frame() -# self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') -# self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) -# self.refinementProgramcheckbox.set_active(False) -# frame.add(self.refinementProgramcheckbox) -# self.vbox.pack_start(frame) + # frame = gtk.Frame() + # self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') + # self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) + # self.refinementProgramcheckbox.set_active(False) + # frame.add(self.refinementProgramcheckbox) + # self.vbox.pack_start(frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# # --- Refinement Statistics --- @@ -254,163 +267,162 @@ def StartGUI(self): # a combination of labels and textview widgets, arranged in a table RRfreeLabel_frame = gtk.Frame() - self.RRfreeLabel = gtk.Label('R/Rfree') + self.RRfreeLabel = gtk.Label("R/Rfree") RRfreeLabel_frame.add(self.RRfreeLabel) self.RRfreeValue = gtk.Label( - self.QualityIndicators['RefinementRcryst'] + '/' + self.QualityIndicators['RefinementRfree']) + self.QualityIndicators["RefinementRcryst"] + + "/" + + self.QualityIndicators["RefinementRfree"] + ) RRfreeBox_frame = gtk.Frame() self.RRfreeBox = gtk.EventBox() self.RRfreeBox.add(self.RRfreeValue) RRfreeBox_frame.add(self.RRfreeBox) ResolutionLabel_frame = gtk.Frame() - self.ResolutionLabel = gtk.Label('Resolution') + self.ResolutionLabel = gtk.Label("Resolution") ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label( - self.QualityIndicators['RefinementResolution']) + self.ResolutionValue = gtk.Label(self.QualityIndicators["RefinementResolution"]) ResolutionBox_frame = gtk.Frame() self.ResolutionBox = gtk.EventBox() self.ResolutionBox.add(self.ResolutionValue) ResolutionBox_frame.add(self.ResolutionBox) MolprobityScoreLabel_frame = gtk.Frame() - self.MolprobityScoreLabel = gtk.Label('MolprobityScore') + self.MolprobityScoreLabel = gtk.Label("MolprobityScore") MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) self.MolprobityScoreValue = gtk.Label( - self.QualityIndicators['RefinementMolProbityScore']) + self.QualityIndicators["RefinementMolProbityScore"] + ) MolprobityScoreBox_frame = gtk.Frame() self.MolprobityScoreBox = gtk.EventBox() self.MolprobityScoreBox.add(self.MolprobityScoreValue) MolprobityScoreBox_frame.add(self.MolprobityScoreBox) RamachandranOutliersLabel_frame = gtk.Frame() - self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') + self.RamachandranOutliersLabel = gtk.Label("Rama Outliers") RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) self.RamachandranOutliersValue = gtk.Label( - self.QualityIndicators['RefinementRamachandranOutliers']) + self.QualityIndicators["RefinementRamachandranOutliers"] + ) RamachandranOutliersBox_frame = gtk.Frame() self.RamachandranOutliersBox = gtk.EventBox() self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) RamachandranOutliersBox_frame.add(self.RamachandranOutliersBox) RamachandranFavoredLabel_frame = gtk.Frame() - self.RamachandranFavoredLabel = gtk.Label('Rama Favored') + self.RamachandranFavoredLabel = gtk.Label("Rama Favored") RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) self.RamachandranFavoredValue = gtk.Label( - self.QualityIndicators['RefinementRamachandranFavored']) + self.QualityIndicators["RefinementRamachandranFavored"] + ) RamachandranFavoredBox_frame = gtk.Frame() self.RamachandranFavoredBox = gtk.EventBox() self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) RamachandranFavoredBox_frame.add(self.RamachandranFavoredBox) rmsdBondsLabel_frame = gtk.Frame() - self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') + self.rmsdBondsLabel = gtk.Label("rmsd(Bonds)") rmsdBondsLabel_frame.add(self.rmsdBondsLabel) - self.rmsdBondsValue = gtk.Label( - self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue = gtk.Label(self.QualityIndicators["RefinementRmsdBonds"]) rmsdBondsBox_frame = gtk.Frame() self.rmsdBondsBox = gtk.EventBox() self.rmsdBondsBox.add(self.rmsdBondsValue) rmsdBondsBox_frame.add(self.rmsdBondsBox) rmsdAnglesLabel_frame = gtk.Frame() - self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') + self.rmsdAnglesLabel = gtk.Label("rmsd(Angles)") rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) - self.rmsdAnglesValue = gtk.Label( - self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue = gtk.Label(self.QualityIndicators["RefinementRmsdAngles"]) rmsdAnglesBox_frame = gtk.Frame() self.rmsdAnglesBox = gtk.EventBox() self.rmsdAnglesBox.add(self.rmsdAnglesValue) rmsdAnglesBox_frame.add(self.rmsdAnglesBox) MatrixWeightLabel_frame = gtk.Frame() - self.MatrixWeightLabel = gtk.Label('Matrix Weight') + self.MatrixWeightLabel = gtk.Label("Matrix Weight") MatrixWeightLabel_frame.add(self.MatrixWeightLabel) self.MatrixWeightValue = gtk.Label( - self.QualityIndicators['RefinementMatrixWeight']) + self.QualityIndicators["RefinementMatrixWeight"] + ) MatrixWeightBox_frame = gtk.Frame() self.MatrixWeightBox = gtk.EventBox() self.MatrixWeightBox.add(self.MatrixWeightValue) MatrixWeightBox_frame.add(self.MatrixWeightBox) ligandIDLabel_frame = gtk.Frame() - self.ligandIDLabel = gtk.Label('Ligand ID') + self.ligandIDLabel = gtk.Label("Ligand ID") ligandIDLabel_frame.add(self.ligandIDLabel) - self.ligandIDValue = gtk.Label( - self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue = gtk.Label(self.spider_plot_data["PANDDA_site_ligand_id"]) ligandIDBox_frame = gtk.Frame() self.ligandIDBox = gtk.EventBox() self.ligandIDBox.add(self.ligandIDValue) ligandIDBox_frame.add(self.ligandIDBox) ligand_occupancyLabel_frame = gtk.Frame() - self.ligand_occupancyLabel = gtk.Label('occupancy') + self.ligand_occupancyLabel = gtk.Label("occupancy") ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) self.ligand_occupancyValue = gtk.Label( - self.spider_plot_data['PANDDA_site_occupancy']) + self.spider_plot_data["PANDDA_site_occupancy"] + ) ligand_occupancyBox_frame = gtk.Frame() self.ligand_occupancyBox = gtk.EventBox() self.ligand_occupancyBox.add(self.ligand_occupancyValue) ligand_occupancyBox_frame.add(self.ligand_occupancyBox) ligand_BaverageLabel_frame = gtk.Frame() - self.ligand_BaverageLabel = gtk.Label('B average') + self.ligand_BaverageLabel = gtk.Label("B average") ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) self.ligand_BaverageValue = gtk.Label( - self.spider_plot_data['PANDDA_site_B_average']) + self.spider_plot_data["PANDDA_site_B_average"] + ) ligand_BaverageBox_frame = gtk.Frame() self.ligand_BaverageBox = gtk.EventBox() self.ligand_BaverageBox.add(self.ligand_BaverageValue) ligand_BaverageBox_frame.add(self.ligand_BaverageBox) ligand_BratioSurroundingsLabel_frame = gtk.Frame() - self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') - ligand_BratioSurroundingsLabel_frame.add( - self.ligand_BratioSurroundingsLabel) + self.ligand_BratioSurroundingsLabel = gtk.Label("B ratio") + ligand_BratioSurroundingsLabel_frame.add(self.ligand_BratioSurroundingsLabel) self.ligand_BratioSurroundingsValue = gtk.Label( - self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) + self.spider_plot_data["PANDDA_site_B_ratio_residue_surroundings"] + ) ligand_BratioSurroundingsBox_frame = gtk.Frame() self.ligand_BratioSurroundingsBox = gtk.EventBox() - self.ligand_BratioSurroundingsBox.add( - self.ligand_BratioSurroundingsValue) - ligand_BratioSurroundingsBox_frame.add( - self.ligand_BratioSurroundingsBox) + self.ligand_BratioSurroundingsBox.add(self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add(self.ligand_BratioSurroundingsBox) ligand_RSCCLabel_frame = gtk.Frame() - self.ligand_RSCCLabel = gtk.Label('RSCC') + self.ligand_RSCCLabel = gtk.Label("RSCC") ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) - self.ligand_RSCCValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSCC']) + self.ligand_RSCCValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSCC"]) ligand_RSCCBox_frame = gtk.Frame() self.ligand_RSCCBox = gtk.EventBox() self.ligand_RSCCBox.add(self.ligand_RSCCValue) ligand_RSCCBox_frame.add(self.ligand_RSCCBox) ligand_rmsdLabel_frame = gtk.Frame() - self.ligand_rmsdLabel = gtk.Label('rmsd') + self.ligand_rmsdLabel = gtk.Label("rmsd") ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) - self.ligand_rmsdValue = gtk.Label( - self.spider_plot_data['PANDDA_site_rmsd']) + self.ligand_rmsdValue = gtk.Label(self.spider_plot_data["PANDDA_site_rmsd"]) ligand_rmsdBox_frame = gtk.Frame() self.ligand_rmsdBox = gtk.EventBox() self.ligand_rmsdBox.add(self.ligand_rmsdValue) ligand_rmsdBox_frame.add(self.ligand_rmsdBox) ligand_RSRLabel_frame = gtk.Frame() - self.ligand_RSRLabel = gtk.Label('RSR') + self.ligand_RSRLabel = gtk.Label("RSR") ligand_RSRLabel_frame.add(self.ligand_RSRLabel) - self.ligand_RSRValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSR']) + self.ligand_RSRValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSR"]) ligand_RSRBox_frame = gtk.Frame() self.ligand_RSRBox = gtk.EventBox() self.ligand_RSRBox.add(self.ligand_RSRValue) ligand_RSRBox_frame.add(self.ligand_RSRBox) ligand_RSZDLabel_frame = gtk.Frame() - self.ligand_RSZDLabel = gtk.Label('RSZD') + self.ligand_RSZDLabel = gtk.Label("RSZD") ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) - self.ligand_RSZDValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSZD']) + self.ligand_RSZDValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSZD"]) ligand_RSZDBox_frame = gtk.Frame() self.ligand_RSZDBox = gtk.EventBox() self.ligand_RSZDBox.add(self.ligand_RSZDValue) @@ -445,8 +457,7 @@ def StartGUI(self): self.table_right.attach(ligandIDLabel_frame, 0, 1, 0, 1) self.table_right.attach(ligand_occupancyLabel_frame, 0, 1, 1, 2) self.table_right.attach(ligand_BaverageLabel_frame, 0, 1, 2, 3) - self.table_right.attach( - ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach(ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) self.table_right.attach(ligand_RSCCLabel_frame, 0, 1, 4, 5) self.table_right.attach(ligand_rmsdLabel_frame, 0, 1, 5, 6) self.table_right.attach(ligand_RSRLabel_frame, 0, 1, 6, 7) @@ -471,17 +482,19 @@ def StartGUI(self): hbox.add(button) # --- ground state mean map --- self.ground_state_mean_map_button = gtk.Button( - label="Show ground state mean map") + label="Show ground state mean map" + ) self.ground_state_mean_map_button.connect( - "clicked", self.show_ground_state_mean_map) + "clicked", self.show_ground_state_mean_map + ) hbox.add(self.ground_state_mean_map_button) -# self.vbox.add(self.ground_state_mean_map_button) + # self.vbox.add(self.ground_state_mean_map_button) self.vbox.add(hbox) self.vbox.pack_start(frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# # --- hbox for compound picture & spider_plot (formerly: refinement history) --- @@ -491,7 +504,12 @@ def StartGUI(self): # --- compound picture --- compound_frame = gtk.Frame() pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_COMPOUND_IMAGE_AVAILABLE.png", + ) + ) self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.image = gtk.Image() self.image.set_from_pixbuf(self.pic) @@ -506,9 +524,11 @@ def StartGUI(self): # --- Spider Plot --- spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + os.path.join( + os.getenv("XChemExplorer_DIR"), "image", "NO_SPIDER_PLOT_AVAILABLE.png" + ) + ) + self.spider_plot_pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image = gtk.Image() self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) spider_plot_frame.add(self.spider_plot_image) @@ -519,54 +539,54 @@ def StartGUI(self): ################################################################################# # --- pandda.inspect user comments --- -# outer_frame = gtk.Frame(label='pandda.inspect comments') -# vbox = gtk.VBox() -# ligand_site_name_label_frame = gtk.Frame() -# ligand_site_name_label = gtk.Label('Site Name') -# ligand_site_name_label_frame.add(ligand_site_name_label) -# ligand_inspect_confidence_label_frame = gtk.Frame() -# ligand_inspect_confidence_label = gtk.Label('Confidence') -# ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) -# ligand_inspect_interesting_label_frame = gtk.Frame() -# ligand_inspect_interesting_label = gtk.Label('Interesting') -# ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) -# ligand_inspect_comment_label_frame = gtk.Frame() -# ligand_inspect_comment_label = gtk.Label('Comment') -# ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) -# ligand_site_name_value_frame = gtk.Frame() -# self.ligand_site_name_value = gtk.Label('-') -# ligand_site_name_value_frame.add(self.ligand_site_name_value) -# ligand_inspect_confidence_value_frame = gtk.Frame() -# self.ligand_inspect_confidence_value = gtk.Label('-') -# ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) -# ligand_inspect_interesting_value_frame = gtk.Frame() -# self.ligand_inspect_interesting_value = gtk.Label('-') -# ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) -# ligand_inspect_comment_value_frame = gtk.Frame() -# self.ligand_inspect_comment_value = gtk.Label('-') -# ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) -# -# frame_pandda_inspect_comments_table = gtk.Frame() -# pandda_inspect_comments_table = gtk.Table(2, 6, False) -# pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) -# pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) -# pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) -# -# frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) -# vbox.add(frame_pandda_inspect_comments_table) -# outer_frame.add(vbox) -# self.vbox.pack_start(outer_frame) + # outer_frame = gtk.Frame(label='pandda.inspect comments') + # vbox = gtk.VBox() + # ligand_site_name_label_frame = gtk.Frame() + # ligand_site_name_label = gtk.Label('Site Name') + # ligand_site_name_label_frame.add(ligand_site_name_label) + # ligand_inspect_confidence_label_frame = gtk.Frame() + # ligand_inspect_confidence_label = gtk.Label('Confidence') + # ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) + # ligand_inspect_interesting_label_frame = gtk.Frame() + # ligand_inspect_interesting_label = gtk.Label('Interesting') + # ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) + # ligand_inspect_comment_label_frame = gtk.Frame() + # ligand_inspect_comment_label = gtk.Label('Comment') + # ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) + # ligand_site_name_value_frame = gtk.Frame() + # self.ligand_site_name_value = gtk.Label('-') + # ligand_site_name_value_frame.add(self.ligand_site_name_value) + # ligand_inspect_confidence_value_frame = gtk.Frame() + # self.ligand_inspect_confidence_value = gtk.Label('-') + # ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) + # ligand_inspect_interesting_value_frame = gtk.Frame() + # self.ligand_inspect_interesting_value = gtk.Label('-') + # ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) + # ligand_inspect_comment_value_frame = gtk.Frame() + # self.ligand_inspect_comment_value = gtk.Label('-') + # ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) + # + # frame_pandda_inspect_comments_table = gtk.Frame() + # pandda_inspect_comments_table = gtk.Table(2, 6, False) + # pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) + # pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) + # pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) + # + # frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) + # vbox.add(frame_pandda_inspect_comments_table) + # outer_frame.add(vbox) + # self.vbox.pack_start(outer_frame) # # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# - outer_frame = gtk.Frame(label='Sample Navigator') + outer_frame = gtk.Frame(label="Sample Navigator") hboxSample = gtk.HBox() # --- crystal navigator combobox --- @@ -609,51 +629,51 @@ def StartGUI(self): self.vbox.add(outer_frame) # # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# -# outer_frame = gtk.Frame(label='Label') -# hboxlabel = gtk.HBox() -# -# frame = gtk.Frame() -# hbox = gtk.HBox() -# self.vbox_label = gtk.VBox() -# labels = self.db.get_labels_from_db() -# if len(labels) > 5: -# print '==> sorry, too many labels; cannot display them in panel' -# labels = labels[:5] -# # with radiobuttons, one of them needs to be always on -# # but there will be cases when the user has not assigned a label yet -# # hence, the not_shown button is not shown but gets active -# # if the label has not been set yet -# labels.append('not_shown') -# for n, l in enumerate(labels): -# print n,l -# if n == 0: -# new_button = gtk.RadioButton(None, l) -# else: -# new_button = gtk.RadioButton(new_button, l) -# new_button.connect("toggled", self.label_button_clicked, l) -# if not l == 'not_shown': -# hbox.add(new_button) -# self.label_button_list.append(new_button) -# self.vbox_label.add(hbox) -# frame.add(self.vbox_label) -# -# hboxlabel.add(frame) -# -# outer_frame.add(hboxlabel) -# self.vbox.add(outer_frame) + # outer_frame = gtk.Frame(label='Label') + # hboxlabel = gtk.HBox() + # + # frame = gtk.Frame() + # hbox = gtk.HBox() + # self.vbox_label = gtk.VBox() + # labels = self.db.get_labels_from_db() + # if len(labels) > 5: + # print '==> sorry, too many labels; cannot display them in panel' + # labels = labels[:5] + # # with radiobuttons, one of them needs to be always on + # # but there will be cases when the user has not assigned a label yet + # # hence, the not_shown button is not shown but gets active + # # if the label has not been set yet + # labels.append('not_shown') + # for n, l in enumerate(labels): + # print n,l + # if n == 0: + # new_button = gtk.RadioButton(None, l) + # else: + # new_button = gtk.RadioButton(new_button, l) + # new_button.connect("toggled", self.label_button_clicked, l) + # if not l == 'not_shown': + # hbox.add(new_button) + # self.label_button_list.append(new_button) + # self.vbox_label.add(hbox) + # frame.add(self.vbox_label) + # + # hboxlabel.add(frame) + # + # outer_frame.add(hboxlabel) + # self.vbox.add(outer_frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# # --- current refinement stage --- outer_frame = gtk.Frame() hbox = gtk.HBox() - frame = gtk.Frame(label='Analysis Status') + frame = gtk.Frame(label="Analysis Status") vbox = gtk.VBox() self.experiment_stage_button_list = [] for n, button in enumerate(self.experiment_stage): @@ -662,15 +682,16 @@ def StartGUI(self): else: new_button = gtk.RadioButton(new_button, button[0]) new_button.connect( - "toggled", self.experiment_stage_button_clicked, button[1]) + "toggled", self.experiment_stage_button_clicked, button[1] + ) vbox.pack_start(new_button, False, False, 0) -# vbox.add(new_button) + # vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) # --- ligand confidence --- - frame = gtk.Frame(label='Ligand Confidence') + frame = gtk.Frame(label="Ligand Confidence") vbox = gtk.VBox() self.ligand_confidence_button_list = [] for n, criteria in enumerate(self.ligand_confidence_category): @@ -679,56 +700,55 @@ def StartGUI(self): else: new_button = gtk.RadioButton(new_button, criteria) new_button.connect( - "toggled", self.ligand_confidence_button_clicked, criteria) + "toggled", self.ligand_confidence_button_clicked, criteria + ) vbox.pack_start(new_button, False, False, 0) -# vbox.add(new_button) + # vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) -# # label section --> start -# frame = gtk.Frame(label='Label') -# vbox = gtk.VBox() -# labels = self.db.get_labels_from_db() -# if len(labels) > 5: -# print '==> sorry, too many labels; cannot display them in panel' -# labels = labels[:5] -# # with radiobuttons, one of them needs to be always on -# # but there will be cases when the user has not assigned a label yet -# # hence, the not_shown button is not shown but gets active -# # if the label has not been set yet -# labels.append('not_shown') -# for n, l in enumerate(labels): -# print n,l -# if n == 0: -# new_button = gtk.RadioButton(None, l) -# else: -# new_button = gtk.RadioButton(new_button, l) -# new_button.connect("toggled", self.label_button_clicked, l) -# if not l == 'not_shown': -# vbox.add(new_button) -# self.label_button_list.append(new_button) -# frame.add(vbox) -# hbox.pack_start(frame) -# # label section <-- end + # # label section --> start + # frame = gtk.Frame(label='Label') + # vbox = gtk.VBox() + # labels = self.db.get_labels_from_db() + # if len(labels) > 5: + # print '==> sorry, too many labels; cannot display them in panel' + # labels = labels[:5] + # # with radiobuttons, one of them needs to be always on + # # but there will be cases when the user has not assigned a label yet + # # hence, the not_shown button is not shown but gets active + # # if the label has not been set yet + # labels.append('not_shown') + # for n, l in enumerate(labels): + # print n,l + # if n == 0: + # new_button = gtk.RadioButton(None, l) + # else: + # new_button = gtk.RadioButton(new_button, l) + # new_button.connect("toggled", self.label_button_clicked, l) + # if not l == 'not_shown': + # vbox.add(new_button) + # self.label_button_list.append(new_button) + # frame.add(vbox) + # hbox.pack_start(frame) + # # label section <-- end outer_frame.add(hbox) self.vbox.pack_start(outer_frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) # --- ligand modeling --- - frame = gtk.Frame(label='Ligand Modeling') + frame = gtk.Frame(label="Ligand Modeling") self.hbox_for_modeling = gtk.HBox() self.merge_ligand_button = gtk.Button(label="Merge Ligand") self.place_ligand_here_button = gtk.Button(label="Place Ligand here") self.hbox_for_modeling.add(self.place_ligand_here_button) - self.place_ligand_here_button.connect( - "clicked", self.place_ligand_here) + self.place_ligand_here_button.connect("clicked", self.place_ligand_here) self.hbox_for_modeling.add(self.merge_ligand_button) - self.merge_ligand_button.connect( - "clicked", self.merge_ligand_into_protein) + self.merge_ligand_button.connect("clicked", self.merge_ligand_into_protein) self.select_cpd_cb = gtk.combo_box_new_text() self.select_cpd_cb.connect("changed", self.select_cpd) self.hbox_for_modeling.add(self.select_cpd_cb) @@ -748,13 +768,13 @@ def StartGUI(self): self.RefinementParamsButton = gtk.Button(label="refinement parameters") self.covalentLinksbutton = gtk.Button(label="covalent links\n-define-") self.covalentLinksCreatebutton = gtk.Button( - label="covalent links\n-create & refine-") + label="covalent links\n-create & refine-" + ) self.REFINEbutton.connect("clicked", self.REFINE) self.hbox_for_refinement.add(self.REFINEbutton) self.RefinementParamsButton.connect("clicked", self.RefinementParams) self.covalentLinksbutton.connect("clicked", self.covalentLinkDef) - self.covalentLinksCreatebutton.connect( - "clicked", self.covalentLinkCreate) + self.covalentLinksCreatebutton.connect("clicked", self.covalentLinkCreate) self.hbox_for_refinement.add(self.RefinementParamsButton) self.hbox_for_refinement.add(self.covalentLinksbutton) self.hbox_for_refinement.add(self.covalentLinksCreatebutton) @@ -766,7 +786,8 @@ def StartGUI(self): # need to put it here, because attributes within refinementProtocolCallback function # are defined after checkbox is defined self.refinementProtocolcheckbox.connect( - "toggled", self.refinementProtocolCallback) + "toggled", self.refinementProtocolCallback + ) # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") @@ -796,10 +817,10 @@ def ChooseXtal(self, widget): self.merge_ligand_button.set_sensitive(True) self.place_ligand_here_button.set_sensitive(True) -# self.ligand_site_name_value.set_label('-') -# self.ligand_inspect_confidence_value.set_label('-') -# self.ligand_inspect_interesting_value.set_label('-') -# self.ligand_inspect_comment_value.set_label('-') + # self.ligand_site_name_value.set_label('-') + # self.ligand_inspect_confidence_value.set_label('-') + # self.ligand_inspect_interesting_value.set_label('-') + # self.ligand_inspect_comment_value.set_label('-') self.refresh_site_combobox() self.db_dict_mainTable = {} @@ -808,36 +829,58 @@ def ChooseXtal(self, widget): self.compoundID = str(self.Todo[self.index][1]) self.refinement_folder = str(self.Todo[self.index][4]) self.refinement_outcome = str(self.Todo[self.index][5]) -# self.label = self.db.get_label_of_sample(self.xtalID) -# self.update_label_radiobutton() + # self.label = self.db.get_label_of_sample(self.xtalID) + # self.update_label_radiobutton() self.update_RefinementOutcome_radiobutton() - if self.xtalID not in self.siteDict: # i.e. we are not working with a PanDDA model + if ( + self.xtalID not in self.siteDict + ): # i.e. we are not working with a PanDDA model self.ligand_confidence = str(self.Todo[self.index][6]) -# self.update_LigandConfidence_radiobutton() -# self.label = self.db.get_label_of_sample(self.xtalID) -# self.update_label_radiobutton() + # self.update_LigandConfidence_radiobutton() + # self.label = self.db.get_label_of_sample(self.xtalID) + # self.update_label_radiobutton() self.RefreshData() def select_cpd(self, widget): cpd = str(widget.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): - if imol not in self.mol_dict['ligand_stereo']: + if imol not in self.mol_dict["ligand_stereo"]: continue - molName = coot.molecule_name(imol)[coot.molecule_name( - imol).rfind('/')+1:].replace('.pdb', '') - if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): - molNameCIF = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( - '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') + molName = coot.molecule_name(imol)[ + coot.molecule_name(imol).rfind("/") + 1 : + ].replace(".pdb", "") + if "rhofit" in coot.molecule_name(imol) or "phenix" in coot.molecule_name( + imol + ): + molNameCIF = ( + coot.molecule_name(imol)[coot.molecule_name(imol).rfind("/") + 1 :] + .replace(".pdb", "") + .replace("_phenix", "") + .replace("_rhofit", "") + ) else: molNameCIF = molName - print(cpd, '-', imol, '-', coot.molecule_name(imol)) + print(cpd, "-", imol, "-", coot.molecule_name(imol)) if molName == cpd: coot.set_mol_displayed(imol, 1) - print('reading', os.path.join( - self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) - coot.read_cif_dictionary(os.path.join( - self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) + print( + "reading", + os.path.join( + self.project_directory, + self.xtalID, + "compound", + molNameCIF + ".cif", + ), + ) + coot.read_cif_dictionary( + os.path.join( + self.project_directory, + self.xtalID, + "compound", + molNameCIF + ".cif", + ) + ) else: coot.set_mol_displayed(imol, 0) @@ -853,23 +896,23 @@ def update_RefinementOutcome_radiobutton(self): button.set_active(True) break -# def update_label_radiobutton(self): -# found = False -# for button in self.label_button_list: -# if button.get_label() == self.label: -# button.set_active(True) -# found = True -# if not found: -# for button in self.label_button_list: -# if button.get_label() == 'not_shown': -# button.set_active(True) -# break + # def update_label_radiobutton(self): + # found = False + # for button in self.label_button_list: + # if button.get_label() == self.label: + # button.set_active(True) + # found = True + # if not found: + # for button in self.label_button_list: + # if button.get_label() == 'not_shown': + # button.set_active(True) + # break def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 for i, entry in enumerate(self.ligand_confidence_category): - print('--->', entry, self.ligand_confidence) + print("--->", entry, self.ligand_confidence) try: if entry.split()[0] == self.ligand_confidence.split()[0]: current_stage = i @@ -887,13 +930,14 @@ def refresh_site_combobox(self): # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites for n in range(-1, 100): self.cb_site.remove_text(0) - self.site_index = '0' - self.event_index = '0' + self.site_index = "0" + self.event_index = "0" # only repopulate if site exists if self.xtalID in self.siteDict: for item in sorted(self.siteDict[self.xtalID]): self.cb_site.append_text( - 'site: {0!s} - event: {1!s}'.format(item[5], item[6])) + "site: {0!s} - event: {1!s}".format(item[5], item[6]) + ) def ChangeSite(self, widget, data=None): if self.xtalID in self.siteDict: @@ -926,83 +970,100 @@ def RefreshSiteData(self): # and remove ligand molecule so that there is no temptation to merge it if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): - if self.compoundID + '.pdb' in coot.molecule_name(imol): + if self.compoundID + ".pdb" in coot.molecule_name(imol): coot.close_molecule(imol) -# for w in self.label_button_list: -# w.set_active(False) + # for w in self.label_button_list: + # w.set_active(False) - print('pandda index', self.pandda_index) + print("pandda index", self.pandda_index) self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] - print('new spider plot:', self.spider_plot) + print("new spider plot:", self.spider_plot) self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] - print('new event map:', self.event_map) - self.ligand_confidence = str( - self.siteDict[self.xtalID][self.pandda_index][7]) + print("new event map:", self.event_map) + self.ligand_confidence = str(self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) - print('new site coordinates:', site_x, site_y, site_z) + print("new site coordinates:", site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) -# self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) -# self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) -# self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) -# self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) - - self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, - self.event_index) - print('>>>>> spider plot data', self.spider_plot_data) - self.ligandIDValue.set_label( - self.spider_plot_data['PANDDA_site_ligand_id']) + # self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) + # self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) + # self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) + # self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) + + self.spider_plot_data = ( + self.db.get_db_pandda_dict_for_sample_and_site_and_event( + self.xtalID, self.site_index, self.event_index + ) + ) + print(">>>>> spider plot data", self.spider_plot_data) + self.ligandIDValue.set_label(self.spider_plot_data["PANDDA_site_ligand_id"]) try: self.ligand_occupancyValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_occupancy"]), 2)) + ) except ValueError: - self.ligand_occupancyValue.set_label('-') + self.ligand_occupancyValue.set_label("-") try: self.ligand_BaverageValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_B_average"]), 2)) + ) except ValueError: - self.ligand_BaverageValue.set_label('-') + self.ligand_BaverageValue.set_label("-") try: self.ligand_BratioSurroundingsValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']), 2))) + str( + round( + float( + self.spider_plot_data[ + "PANDDA_site_B_ratio_residue_surroundings" + ] + ), + 2, + ) + ) + ) except ValueError: - self.ligand_BratioSurroundingsValue.set_label('-') + self.ligand_BratioSurroundingsValue.set_label("-") try: self.ligand_RSCCValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSCC"]), 2)) + ) except ValueError: - self.ligand_RSCCValue.set_label('-') + self.ligand_RSCCValue.set_label("-") try: self.ligand_rmsdValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_rmsd"]), 2)) + ) except ValueError: - self.ligand_rmsdValue.set_label('-') + self.ligand_rmsdValue.set_label("-") try: self.ligand_RSRValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSR"]), 2)) + ) except ValueError: - self.ligand_RSRValue.set_label('-') + self.ligand_RSRValue.set_label("-") try: self.ligand_RSZDValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSZD"]), 2)) + ) except ValueError: - self.ligand_RSZDValue.set_label('-') + self.ligand_RSZDValue.set_label("-") ######################################################################################### # delete old Event MAPs if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): - if 'map.native.ccp4' in coot.molecule_name(imol): + if "map.native.ccp4" in coot.molecule_name(imol): coot.close_molecule(imol) ######################################################################################### @@ -1012,9 +1073,15 @@ def RefreshSiteData(self): spider_plot_pic = gtk.gdk.pixbuf_new_from_file(self.spider_plot) else: spider_plot_pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_SPIDER_PLOT_AVAILABLE.png", + ) + ) self.spider_plot_pic = spider_plot_pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + 190, 190, gtk.gdk.INTERP_BILINEAR + ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) ######################################################################################### @@ -1030,112 +1097,169 @@ def RefreshSiteData(self): coot.set_last_map_colour(0.74, 0.44, 0.02) def experiment_stage_button_clicked(self, widget, data=None): - self.db_dict_mainTable['RefinementOutcome'] = data - self.db_dict_mainTable['RefinementOutcomePerson'] = getpass.getuser() - self.db_dict_mainTable['RefinementOutcomeDate'] = datetime.strftime( - datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] - self.Logfile.insert('==> COOT: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( - data) + ' in mainTable of datasource') -# print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( -# data) + ' in mainTable of datasource' -# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + self.db_dict_mainTable["RefinementOutcome"] = data + self.db_dict_mainTable["RefinementOutcomePerson"] = getpass.getuser() + self.db_dict_mainTable["RefinementOutcomeDate"] = datetime.strftime( + datetime.now(), "%Y-%m-%d_%H-%M-%S.%f" + )[:-4] + self.Logfile.insert( + "==> COOT: setting Refinement Outcome for " + + self.xtalID + + " to " + + str(data) + + " in mainTable of datasource" + ) + # print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( + # data) + ' in mainTable of datasource' + # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.db.create_or_remove_missing_records_in_depositTable( - self.xce_logfile, self.xtalID, 'ligand_bound', self.db_dict_mainTable) + self.xce_logfile, self.xtalID, "ligand_bound", self.db_dict_mainTable + ) def ligand_confidence_button_clicked(self, widget, data=None): - print('PANDDA_index', self.pandda_index) + print("PANDDA_index", self.pandda_index) if self.pandda_index == -1: - self.db_dict_mainTable['RefinementLigandConfidence'] = data - self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( - data) + ' in mainTable of datasource') -# print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( -# data) + ' in mainTable of datasource' + self.db_dict_mainTable["RefinementLigandConfidence"] = data + self.Logfile.insert( + "==> COOT: setting Ligand Confidence for " + + self.xtalID + + " to " + + str(data) + + " in mainTable of datasource" + ) + # print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( + # data) + ' in mainTable of datasource' self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.Todo[self.index][6] = data else: - self.db_dict_panddaTable['PANDDA_site_confidence'] = data - self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( - self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( - data) + ' in panddaTable of datasource') -# print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( -# self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( -# data) + ' in panddaTable of datasource' - self.db.update_site_event_panddaTable(self.xtalID, self.site_index, self.event_index, - self.db_dict_panddaTable) + self.db_dict_panddaTable["PANDDA_site_confidence"] = data + self.Logfile.insert( + "==> COOT: setting Ligand Confidence for " + + self.xtalID + + " (site=" + + str(self.site_index) + + ", event=" + + str(self.event_index) + + ") to " + + str(data) + + " in panddaTable of datasource" + ) + # print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( + # self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( + # data) + ' in panddaTable of datasource' + self.db.update_site_event_panddaTable( + self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable + ) self.siteDict[self.xtalID][self.pandda_index][7] = data -# def update_label(self, widget): -# print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' -# # widget.pressed() -# for w in self.label_button_list: -# print w.get_label(), w.get_active() -# if w != widget: -# w.set_active(False) -# print '<<<<<<<<<<<<<<<<<<<<<<<<<<' -# self.db_dict_mainTable['label'] = widget.get_label() -# print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( -# widget.get_label()) + ' in mainTable of datasource' -# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - -# def label_button_clicked(self, widget, data=None): -# print '............',data -# if data == 'not_shown': -# self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) -# else: -# self.db_dict_mainTable['label'] = data -# print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' -# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + # def update_label(self, widget): + # print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' + # # widget.pressed() + # for w in self.label_button_list: + # print w.get_label(), w.get_active() + # if w != widget: + # w.set_active(False) + # print '<<<<<<<<<<<<<<<<<<<<<<<<<<' + # self.db_dict_mainTable['label'] = widget.get_label() + # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( + # widget.get_label()) + ' in mainTable of datasource' + # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + + # def label_button_clicked(self, widget, data=None): + # print '............',data + # if data == 'not_shown': + # self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) + # else: + # self.db_dict_mainTable['label'] = data + # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' + # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) def RefreshData(self): # reset spider plot image spider_plot_pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), "image", "NO_SPIDER_PLOT_AVAILABLE.png" + ) + ) self.spider_plot_pic = spider_plot_pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + 190, 190, gtk.gdk.INTERP_BILINEAR + ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) # reset ground state mean map - self.ground_state_mean_map = '' + self.ground_state_mean_map = "" self.ground_state_mean_map_button.set_sensitive(False) - self.ground_state_mean_map_button.set_label( - 'Show ground state mean map') + self.ground_state_mean_map_button.set_label("Show ground state mean map") if os.path.isfile( - os.path.join(self.project_directory, self.xtalID, self.xtalID + '-ground-state-mean-map.native.ccp4')): + os.path.join( + self.project_directory, + self.xtalID, + self.xtalID + "-ground-state-mean-map.native.ccp4", + ) + ): self.ground_state_mean_map_button.set_sensitive(True) - self.ground_state_mean_map = os.path.join(self.project_directory, self.xtalID, - self.xtalID + '-ground-state-mean-map.native.ccp4') + self.ground_state_mean_map = os.path.join( + self.project_directory, + self.xtalID, + self.xtalID + "-ground-state-mean-map.native.ccp4", + ) # initialize Refinement library self.Refine = XChemRefine.Refine( - self.project_directory, self.xtalID, self.compoundID, self.data_source) - self.Serial = XChemRefine.GetSerial( - self.project_directory, self.xtalID) - self.panddaSerial = panddaSerial = m = ( - 4 - len(str(self.Serial))) * '0' + str(self.Serial) + self.project_directory, self.xtalID, self.compoundID, self.data_source + ) + self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) + self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * "0" + str( + self.Serial + ) # self.Serial=self.Refine.GetSerial() if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): - print('==> XCE: updating quality indicators in data source for ' + self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, - self.pdb_style)) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, - '') # '' because file does not exist - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.pdb')): - print('==> XCE: updating quality indicators in data source for ' + self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, - 'init.pdb')) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, - '') # '' because file does not exist - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): - print('==> XCE: updating quality indicators in data source for ' + self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, - 'dimple.pdb')) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, - '') # '' because file does not exist + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, self.pdb_style), + ) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, "" + ) # '' because file does not exist + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "init.pdb") + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, "init.pdb"), + ) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, "" + ) # '' because file does not exist + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple.pdb") + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, "dimple.pdb"), + ) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, "" + ) # '' because file does not exist # all this information is now updated in the datasource after each refinement cycle self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) @@ -1145,9 +1269,8 @@ def RefreshData(self): # if the structure was previously refined, try to read the parameters # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: - self.RefmacParams = self.Refine.ParamsFromPreviousCycle( - self.Serial - 1) - print('==> REFMAC params:', self.RefmacParams) + self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) + print("==> REFMAC params:", self.RefmacParams) # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) # else: @@ -1159,11 +1282,11 @@ def RefreshData(self): ######################################################################################### # ligand files # first remove old samples if present - print('>>>', self.mol_dict['ligand_stereo']) - for n, item in enumerate(self.mol_dict['ligand_stereo']): - print('__', item) + print(">>>", self.mol_dict["ligand_stereo"]) + for n, item in enumerate(self.mol_dict["ligand_stereo"]): + print("__", item) self.select_cpd_cb.remove_text(0) - print('done') + print("done") ######################################################################################### # remove potential generic line which indicates a possible covalent link @@ -1172,7 +1295,7 @@ def RefreshData(self): ######################################################################################### # reset covalent links - self.covLinks = ['X', 'X', 'X', 'X'] + self.covLinks = ["X", "X", "X", "X"] ######################################################################################### # update pdb & maps @@ -1189,55 +1312,94 @@ def RefreshData(self): # read new PDB files # read protein molecule after ligand so that this one is the active molecule coot.set_nomenclature_errors_on_read("ignore") - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.compoundID + ".pdb") + ): coot.set_colour_map_rotation_on_read_pdb(0) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb'), 0) - self.mol_dict['ligand'] = imol - coot.read_cif_dictionary(os.path.join( - self.project_directory, self.xtalID, self.compoundID + '.cif')) + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".pdb" + ), + 0, + ) + self.mol_dict["ligand"] = imol + coot.read_cif_dictionary( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".cif" + ) + ) self.select_cpd_cb.append_text(self.compoundID) - self.mol_dict['ligand_stereo'] = [] - self.mol_dict['ligand_stereo'].append(imol) + self.mol_dict["ligand_stereo"] = [] + self.mol_dict["ligand_stereo"].append(imol) # ligands in compound directory - for cifFile in sorted(glob.glob(os.path.join(self.project_directory, self.xtalID, 'compound', self.compoundID+'_*.pdb'))): - cif = cifFile[cifFile.rfind('/')+1:] - if '_with_H' in cif: + for cifFile in sorted( + glob.glob( + os.path.join( + self.project_directory, + self.xtalID, + "compound", + self.compoundID + "_*.pdb", + ) + ) + ): + cif = cifFile[cifFile.rfind("/") + 1 :] + if "_with_H" in cif: continue - self.select_cpd_cb.append_text(cif.replace('.pdb', '')) + self.select_cpd_cb.append_text(cif.replace(".pdb", "")) imol = coot.handle_read_draw_molecule_with_recentre(cifFile, 0) - self.mol_dict['ligand_stereo'].append(imol) + self.mol_dict["ligand_stereo"].append(imol) coot.set_mol_displayed(imol, 0) # autofitted ligands - for pdbFile in sorted(glob.glob(os.path.join(self.project_directory, self.xtalID, 'autofit_ligand', '*', '*.pdb'))): - autofitRun = pdbFile.split('/')[len(pdbFile.split('/')) - 2] - if pdbFile.endswith(autofitRun+'.pdb'): + for pdbFile in sorted( + glob.glob( + os.path.join( + self.project_directory, + self.xtalID, + "autofit_ligand", + "*", + "*.pdb", + ) + ) + ): + autofitRun = pdbFile.split("/")[len(pdbFile.split("/")) - 2] + if pdbFile.endswith(autofitRun + ".pdb"): self.select_cpd_cb.append_text(autofitRun) - imol = coot.handle_read_draw_molecule_with_recentre( - pdbFile, 0) - self.mol_dict['ligand_stereo'].append(imol) + imol = coot.handle_read_draw_molecule_with_recentre(pdbFile, 0) + self.mol_dict["ligand_stereo"].append(imol) coot.set_mol_displayed(imol, 0) self.select_cpd_cb.set_sensitive(True) self.select_cpd_cb.set_active(0) else: - print('no compound found in sample directory') -# self.select_cpd_cb.append_text('') + print("no compound found in sample directory") + # self.select_cpd_cb.append_text('') self.select_cpd_cb.set_sensitive(False) - if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + if not os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) - if self.refinementProtocol.startswith('pandda'): - self.Logfile.insert('==> COOT: looking for ground-state model ' + os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', - '') + '.split.ground-state.pdb')) -# print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.ground-state.pdb') - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): - self.Logfile.insert('==> COOT: found ground-state model') -# print '=> XCE: found ground-state model' + if self.refinementProtocol.startswith("pandda"): + self.Logfile.insert( + "==> COOT: looking for ground-state model " + + os.path.join( + self.project_directory, + self.xtalID, + self.pdb_style.replace(".pdb", "") + ".split.ground-state.pdb", + ) + ) + # print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.ground-state.pdb') + if os.path.isfile( + os.path.join( + self.project_directory, + self.xtalID, + self.pdb_style.replace(".pdb", "") + ".split.ground-state.pdb", + ) + ): + self.Logfile.insert("==> COOT: found ground-state model") + # print '=> XCE: found ground-state model' os.chdir(os.path.join(self.project_directory, self.xtalID)) coot.set_colour_map_rotation_on_read_pdb(0) try: @@ -1245,60 +1407,92 @@ def RefreshData(self): except UnboundLocalError: color_wheel_rotation = 80 coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) - imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', - '') + '.split.ground-state.pdb'), - 0) + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join( + self.project_directory, + self.xtalID, + self.pdb_style.replace(".pdb", "") + ".split.ground-state.pdb", + ), + 0, + ) coot.set_colour_by_molecule(imol) coot.set_mol_active(imol, 0) else: - self.Logfile.error('==> COOT - cannot find ground-state model') -# print '=> XCE - ERROR: cannot find ground-state model' - self.Logfile.insert('==> COOT: looking for bound-state model ' + os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', - '') + '.split.bound-state.pdb')) -# print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.bound-state.pdb') - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb')): - self.Logfile.insert('==> COOT: found bound-state model') -# print '=> XCE: found bound-state model' + self.Logfile.error("==> COOT - cannot find ground-state model") + # print '=> XCE - ERROR: cannot find ground-state model' + self.Logfile.insert( + "==> COOT: looking for bound-state model " + + os.path.join( + self.project_directory, + self.xtalID, + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb", + ) + ) + # print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.bound-state.pdb') + if os.path.isfile( + os.path.join( + self.project_directory, + self.xtalID, + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb", + ) + ): + self.Logfile.insert("==> COOT: found bound-state model") + # print '=> XCE: found bound-state model' os.chdir(os.path.join(self.project_directory, self.xtalID)) coot.set_colour_map_rotation_on_read_pdb(0) color_wheel_rotation = 21 / float(imol + 2) coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) - imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, - self.pdb_style.replace('.pdb', - '') + '.split.bound-state.pdb'), - 0) - self.mol_dict['protein'] = imol + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join( + self.project_directory, + self.xtalID, + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb", + ), + 0, + ) + self.mol_dict["protein"] = imol else: - self.Logfile.error('==> COOT: cannot find bound-state model') -# print '=> XCE - ERROR: cannot find bound-state model' - self.Logfile.warning('==> COOT: moving to next crystal...') -# print '=> XCE: moving to next crystal...' + self.Logfile.error("==> COOT: cannot find bound-state model") + # print '=> XCE - ERROR: cannot find bound-state model' + self.Logfile.warning("==> COOT: moving to next crystal...") + # print '=> XCE: moving to next crystal...' self.go_to_next_xtal() else: - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.pdb')): + os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0 + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "init.pdb") + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, 'init.pdb'), 0) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): + os.path.join(self.project_directory, self.xtalID, "init.pdb"), 0 + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple.pdb") + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, 'dimple.pdb'), 0) + os.path.join(self.project_directory, self.xtalID, "dimple.pdb"), 0 + ) else: self.go_to_next_xtal() - self.mol_dict['protein'] = imol + self.mol_dict["protein"] = imol # read any one event map if present for event_map in glob.glob( - os.path.join(self.project_directory, self.xtalID, self.xtalID + '-event_*.native.ccp4')): + os.path.join( + self.project_directory, + self.xtalID, + self.xtalID + "-event_*.native.ccp4", + ) + ): coot.handle_read_ccp4_map((event_map), 0) coot.set_contour_level_in_sigma(imol, 2) coot.set_last_map_colour(0.74, 0.44, 0.02) @@ -1306,8 +1500,8 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( - item).endswith(self.pdb_style): + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb" + ) or coot.molecule_name(item).endswith(self.pdb_style): # master switch to show symmetry molecules coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model @@ -1318,14 +1512,18 @@ def RefreshData(self): # read 2fofc map last so that one can change its contour level # coot 0.9 does not handle P1 maps well, so now looking for non-existent map in order to trigger # map calculation from mtz file - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc_??????.map')): + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "2fofc_??????.map") + ): coot.set_colour_map_rotation_on_read_pdb(0) coot.set_default_initial_contour_level_for_difference_map(3) - coot.handle_read_ccp4_map(os.path.join( - self.project_directory, self.xtalID, 'fofc.map'), 1) + coot.handle_read_ccp4_map( + os.path.join(self.project_directory, self.xtalID, "fofc.map"), 1 + ) coot.set_default_initial_contour_level_for_map(1) - coot.handle_read_ccp4_map(os.path.join( - self.project_directory, self.xtalID, '2fofc.map'), 0) + coot.handle_read_ccp4_map( + os.path.join(self.project_directory, self.xtalID, "2fofc.map"), 0 + ) coot.set_last_map_colour(0, 0, 1) else: # try to open mtz file with same name as pdb file @@ -1337,80 +1535,123 @@ def RefreshData(self): # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): # os.symlink('dimple.mtz',self.mtz_style) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, self.mtz_style)) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, 'init.mtz')) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, 'dimple.mtz')) + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.mtz_style) + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, self.mtz_style) + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "init.mtz") + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, "init.mtz") + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple.mtz") + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, "dimple.mtz") + ) ######################################################################################### # update Quality Indicator table try: - self.RRfreeValue.set_label(str(round(float(self.QualityIndicators['RefinementRcryst']), 3)) + ' / ' + str( - round(float(self.QualityIndicators['RefinementRfree']), 3))) + self.RRfreeValue.set_label( + str(round(float(self.QualityIndicators["RefinementRcryst"]), 3)) + + " / " + + str(round(float(self.QualityIndicators["RefinementRfree"]), 3)) + ) except ValueError: - self.RRfreeValue.set_label('-') + self.RRfreeValue.set_label("-") try: - self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementRfreeTraficLight'])) + self.RRfreeBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRfreeTraficLight"] + ), + ) except ValueError: pass - self.ResolutionValue.set_label( - self.QualityIndicators['RefinementResolution']) + self.ResolutionValue.set_label(self.QualityIndicators["RefinementResolution"]) try: - self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementResolutionTL'])) + self.ResolutionBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementResolutionTL"]), + ) except ValueError: pass self.MolprobityScoreValue.set_label( - self.QualityIndicators['RefinementMolProbityScore']) + self.QualityIndicators["RefinementMolProbityScore"] + ) try: - self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementMolProbityScoreTL'])) + self.MolprobityScoreBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementMolProbityScoreTL"] + ), + ) except ValueError: pass self.RamachandranOutliersValue.set_label( - self.QualityIndicators['RefinementRamachandranOutliers']) + self.QualityIndicators["RefinementRamachandranOutliers"] + ) try: - self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRamachandranOutliersTL'])) + self.RamachandranOutliersBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRamachandranOutliersTL"] + ), + ) except ValueError: pass self.RamachandranFavoredValue.set_label( - self.QualityIndicators['RefinementRamachandranFavored']) + self.QualityIndicators["RefinementRamachandranFavored"] + ) try: - self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRamachandranFavoredTL'])) + self.RamachandranFavoredBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRamachandranFavoredTL"] + ), + ) except ValueError: pass - self.rmsdBondsValue.set_label( - self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue.set_label(self.QualityIndicators["RefinementRmsdBonds"]) try: - self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdBondsTL'])) + self.rmsdBondsBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementRmsdBondsTL"]), + ) except ValueError: pass - self.rmsdAnglesValue.set_label( - self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue.set_label(self.QualityIndicators["RefinementRmsdAngles"]) try: - self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdAnglesTL'])) + self.rmsdAnglesBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementRmsdAnglesTL"]), + ) except ValueError: pass self.MatrixWeightValue.set_label( - self.QualityIndicators['RefinementMatrixWeight']) + self.QualityIndicators["RefinementMatrixWeight"] + ) try: pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(self.project_directory, self.xtalID, self.compoundID + '.png')) + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".png" + ) + ) except gobject.GError: pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_COMPOUND_IMAGE_AVAILABLE.png", + ) + ) self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.image.set_from_pixbuf(self.pic) @@ -1452,24 +1693,40 @@ def start_refinement(self): # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) - if self.refinementProtocol.startswith('pandda'): + if self.refinementProtocol.startswith("pandda"): ####################################################### - if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): - os.mkdir(os.path.join( - self.project_directory, self.xtalID, 'cootOut')) + if not os.path.isdir( + os.path.join(self.project_directory, self.xtalID, "cootOut") + ): + os.mkdir(os.path.join(self.project_directory, self.xtalID, "cootOut")) # create folder for new refinement cycle try: - self.Logfile.insert('==> COOT: trying to make folder: %s' % os.path.join( - self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) - os.mkdir(os.path.join(self.project_directory, - self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) + self.Logfile.insert( + "==> COOT: trying to make folder: %s" + % os.path.join( + self.project_directory, + self.xtalID, + "cootOut", + "Refine_" + str(self.Serial), + ) + ) + os.mkdir( + os.path.join( + self.project_directory, + self.xtalID, + "cootOut", + "Refine_" + str(self.Serial), + ) + ) except OSError: self.Logfile.warning( - '==> COOT: folder exists; will overwrite contents!') -# print '==> XCE: WARNING -> folder exists; will overwrite contents!' + "==> COOT: folder exists; will overwrite contents!" + ) + # print '==> XCE: WARNING -> folder exists; will overwrite contents!' self.Logfile.warning( - '==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') + "==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem" + ) ####################################################### # write PDB file @@ -1477,27 +1734,50 @@ def start_refinement(self): # note: the user has to make sure that the ligand file was merged into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( - item).endswith(self.pdb_style): - coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', - 'Refine_' + str(self.Serial), 'refine.modified.pdb')) + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb" + ) or coot.molecule_name(item).endswith(self.pdb_style): + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "cootOut", + "Refine_" + str(self.Serial), + "refine.modified.pdb", + ), + ) break # elif coot.molecule_name(item).endswith('dimple.pdb'): # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) # break - XChemRefine.panddaRefine(self.project_directory, self.xtalID, self.compoundID, - self.data_source).RunQuickRefine(self.Serial, self.RefmacParams, - self.external_software, self.xce_logfile, - self.refinementProtocol, self.covLinkAtomSpec) + XChemRefine.panddaRefine( + self.project_directory, self.xtalID, self.compoundID, self.data_source + ).RunQuickRefine( + self.Serial, + self.RefmacParams, + self.external_software, + self.xce_logfile, + self.refinementProtocol, + self.covLinkAtomSpec, + ) else: ####################################################### # create folder for new refinement cycle and check if free.mtz exists if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): os.mkdir(os.path.join(self.project_directory, self.xtalID)) - if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): - os.mkdir(os.path.join(self.project_directory, - self.xtalID, 'Refine_' + str(self.Serial))) + if not os.path.isdir( + os.path.join( + self.project_directory, self.xtalID, "Refine_" + str(self.Serial) + ) + ): + os.mkdir( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial), + ) + ) ####################################################### # write PDB file @@ -1505,30 +1785,57 @@ def start_refinement(self): # note: the user has to make sure that the ligand file was merged into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith(self.pdb_style): - coot.write_pdb_file(item, - os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial), - 'in.pdb')) + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) break - elif coot.molecule_name(item).endswith('refine.split.bound-state.pdb'): - coot.write_pdb_file(item, - os.path.join(self.project_directory, self.xtalID, - 'Refine_' + - str(self.Serial), - 'in.pdb')) + elif coot.molecule_name(item).endswith("refine.split.bound-state.pdb"): + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) break - elif coot.molecule_name(item).endswith('init.pdb'): - coot.write_pdb_file(item, - os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial), - 'in.pdb')) + elif coot.molecule_name(item).endswith("init.pdb"): + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) break - elif coot.molecule_name(item).endswith('dimple.pdb'): - coot.write_pdb_file(item, - os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial), - 'in.pdb')) + elif coot.molecule_name(item).endswith("dimple.pdb"): + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) break - self.Refine.RunRefmac(self.Serial, self.RefmacParams, - self.external_software, self.xce_logfile, self.covLinkAtomSpec) + self.Refine.RunRefmac( + self.Serial, + self.RefmacParams, + self.external_software, + self.xce_logfile, + self.covLinkAtomSpec, + ) self.index += 1 if self.index >= len(self.Todo): @@ -1537,9 +1844,10 @@ def start_refinement(self): self.cb.set_active(self.index) def RefinementParams(self, widget): - print('\n==> XCE: changing refinement parameters') - self.RefmacParams = XChemRefine.RefineParams(self.project_directory, self.xtalID, self.compoundID, - self.data_source).RefmacRefinementParams(self.RefmacParams) + print("\n==> XCE: changing refinement parameters") + self.RefmacParams = XChemRefine.RefineParams( + self.project_directory, self.xtalID, self.compoundID, self.data_source + ).RefmacRefinementParams(self.RefmacParams) def covalentLinkDef(self, widget): coot.user_defined_click_py(2, self.show_potential_link) @@ -1549,40 +1857,70 @@ def show_potential_link(self, *clicks): # it's a prerequisite that the ligand is merged into the protein imol_protein = None for imol in coot_utils_XChem.molecule_number_list(): - print('>', coot.molecule_name(imol)) - if coot.molecule_name(imol).endswith(self.pdb_style) or \ - coot.molecule_name(imol).endswith('init.pdb') or \ - coot.molecule_name(imol).endswith('dimple.pdb') or \ - coot.molecule_name(imol).endswith(self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb'): + print(">", coot.molecule_name(imol)) + if ( + coot.molecule_name(imol).endswith(self.pdb_style) + or coot.molecule_name(imol).endswith("init.pdb") + or coot.molecule_name(imol).endswith("dimple.pdb") + or coot.molecule_name(imol).endswith( + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb" + ) + ): imol_protein = imol break - print('please click on the two atoms you want to link') - if (len(clicks) == 2): + print("please click on the two atoms you want to link") + if len(clicks) == 2: click_1 = clicks[0] click_2 = clicks[1] imol_1 = click_1[1] imol_2 = click_2[1] - print('imolp', imol, 'imo11', imol_1, 'imol2', imol_2) + print("imolp", imol, "imo11", imol_1, "imol2", imol_2) if imol_1 == imol_2 and imol_1 == imol_protein: - print('click_1', click_1) + print("click_1", click_1) self.covLinkAtomSpec = None xyz_1 = atom_info_string( - click_1[1], click_1[2], click_1[3], click_1[4], click_1[5], click_1[6]) - residue_1 = residue_name( - click_1[1], click_1[2], click_1[3], click_1[4]) + click_1[1], + click_1[2], + click_1[3], + click_1[4], + click_1[5], + click_1[6], + ) + residue_1 = residue_name(click_1[1], click_1[2], click_1[3], click_1[4]) xyz_2 = atom_info_string( - click_2[1], click_2[2], click_2[3], click_2[4], click_2[5], click_2[6]) - residue_2 = residue_name( - click_2[1], click_2[2], click_2[3], click_2[4]) + click_2[1], + click_2[2], + click_2[3], + click_2[4], + click_2[5], + click_2[6], + ) + residue_2 = residue_name(click_2[1], click_2[2], click_2[3], click_2[4]) thick = 4 to_generic_object_add_line( - self.covLinkObject, "yellowtint", thick, xyz_1[3], xyz_1[4], xyz_1[5], xyz_2[3], xyz_2[4], xyz_2[5]) + self.covLinkObject, + "yellowtint", + thick, + xyz_1[3], + xyz_1[4], + xyz_1[5], + xyz_2[3], + xyz_2[4], + xyz_2[5], + ) set_display_generic_object(self.covLinkObject, 1) - self.covLinkAtomSpec = [imol_protein, - click_1, click_2, residue_1, residue_2] + self.covLinkAtomSpec = [ + imol_protein, + click_1, + click_2, + residue_1, + residue_2, + ] else: - print('error: both atoms must belong to the same object; did you merge the ligand with your protein?') + print( + "error: both atoms must belong to the same object; did you merge the ligand with your protein?" + ) def covalentLinkCreate(self, widget): if self.covLinkAtomSpec is not None: @@ -1591,33 +1929,31 @@ def covalentLinkCreate(self, widget): atom2 = self.covLinkAtomSpec[2][1:] residue_1 = self.covLinkAtomSpec[3] residue_2 = self.covLinkAtomSpec[4] - make_link(imol, atom1, atom2, residue_1+'-'+residue_2, 1.7) + make_link(imol, atom1, atom2, residue_1 + "-" + residue_2, 1.7) generic_object_clear(self.covLinkObject) self.start_refinement() else: - print('error: no covalent link defined') + print("error: no covalent link defined") def set_selection_mode(self, widget): self.selection_mode = widget.get_active_text() def get_samples_to_look_at(self, widget): - if self.selection_mode == '': - self.status_label.set_text('select model stage') + if self.selection_mode == "": + self.status_label.set_text("select model stage") return - self.status_label.set_text('checking datasource for samples... ') + self.status_label.set_text("checking datasource for samples... ") # first remove old samples if present if len(self.Todo) != 0: for n, item in enumerate(self.Todo): self.cb.remove_text(0) self.Todo = [] self.siteDict = {} - self.Todo, self.siteDict = self.db.get_todoList_for_coot( - self.selection_mode) - self.status_label.set_text( - 'found {0!s} samples'.format(len(self.Todo))) + self.Todo, self.siteDict = self.db.get_todoList_for_coot(self.selection_mode) + self.status_label.set_text("found {0!s} samples".format(len(self.Todo))) # refresh sample CB for item in sorted(self.Todo): - self.cb.append_text('{0!s}'.format(item[0])) + self.cb.append_text("{0!s}".format(item[0])) if self.siteDict == {}: self.cb_site.set_sensitive(False) self.PREVbuttonSite.set_sensitive(False) @@ -1631,104 +1967,191 @@ def update_plot(self, refinement_cycle, Rfree, Rcryst): fig = Figure(figsize=(2, 2), dpi=50) Plot = fig.add_subplot(111) Plot.set_ylim([0, max(Rcryst + Rfree)]) - Plot.set_xlabel('Refinement Cycle', fontsize=12) - Plot.plot(refinement_cycle, Rfree, label='Rfree', linewidth=2) - Plot.plot(refinement_cycle, Rcryst, label='Rcryst', linewidth=2) - Plot.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, - ncol=2, mode="expand", borderaxespad=0., fontsize=12) + Plot.set_xlabel("Refinement Cycle", fontsize=12) + Plot.plot(refinement_cycle, Rfree, label="Rfree", linewidth=2) + Plot.plot(refinement_cycle, Rcryst, label="Rcryst", linewidth=2) + Plot.legend( + bbox_to_anchor=(0.0, 1.02, 1.0, 0.102), + loc=3, + ncol=2, + mode="expand", + borderaxespad=0.0, + fontsize=12, + ) return fig def place_ligand_here(self, widget): cpd = str(self.select_cpd_cb.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): - if imol not in self.mol_dict['ligand_stereo']: + if imol not in self.mol_dict["ligand_stereo"]: continue - molName = coot.molecule_name(imol)[coot.molecule_name( - imol).rfind('/')+1:].replace('.pdb', '') + molName = coot.molecule_name(imol)[ + coot.molecule_name(imol).rfind("/") + 1 : + ].replace(".pdb", "") if molName == cpd: - print('===> XCE: moving ligand to pointer') + print("===> XCE: moving ligand to pointer") coot_utils_XChem.move_molecule_here(imol) - print('LIGAND: ', molName) -# print '===> XCE: moving ligand to pointer' -# # coot.move_molecule_here() -# print 'LIGAND: ', self.mol_dict['ligand'] -# coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) + print("LIGAND: ", molName) + + # print '===> XCE: moving ligand to pointer' + # # coot.move_molecule_here() + # print 'LIGAND: ', self.mol_dict['ligand'] + # coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) def merge_ligand_into_protein(self, widget): cpd = str(self.select_cpd_cb.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): - if imol not in self.mol_dict['ligand_stereo']: + if imol not in self.mol_dict["ligand_stereo"]: continue - molName = coot.molecule_name(imol)[coot.molecule_name( - imol).rfind('/')+1:].replace('.pdb', '') + molName = coot.molecule_name(imol)[ + coot.molecule_name(imol).rfind("/") + 1 : + ].replace(".pdb", "") if molName == cpd: - print('===> XCE: merge ligand into protein structure -->', cpd) - coot.merge_molecules_py([imol], self.mol_dict['protein']) - if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( - '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')): - os.system('/bin/rm %s' % os.path.join(self.project_directory, - self.xtalID, self.compoundID + '.cif')) - print('XCE: changing directory', os.path.join( - self.project_directory, self.xtalID)) + print("===> XCE: merge ligand into protein structure -->", cpd) + coot.merge_molecules_py([imol], self.mol_dict["protein"]) + if "rhofit" in coot.molecule_name( + imol + ) or "phenix" in coot.molecule_name(imol): + molName = ( + coot.molecule_name(imol)[ + coot.molecule_name(imol).rfind("/") + 1 : + ] + .replace(".pdb", "") + .replace("_phenix", "") + .replace("_rhofit", "") + ) + if os.path.isfile( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".cif" + ) + ): + os.system( + "/bin/rm %s" + % os.path.join( + self.project_directory, + self.xtalID, + self.compoundID + ".cif", + ) + ) + print( + "XCE: changing directory", + os.path.join(self.project_directory, self.xtalID), + ) os.chdir(os.path.join(self.project_directory, self.xtalID)) - print('XCE: changing symlink ln -s %s %s.cif' % ( - os.path.join('compound', molName + '.cif'), self.compoundID)) + print( + "XCE: changing symlink ln -s %s %s.cif" + % (os.path.join("compound", molName + ".cif"), self.compoundID) + ) os.system( - 'ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): - os.system('/bin/rm %s' % os.path.join(self.project_directory, - self.xtalID, self.compoundID + '.pdb')) - print('XCE: changing directory', os.path.join( - self.project_directory, self.xtalID)) + "ln -s %s %s.cif" + % (os.path.join("compound", molName + ".cif"), self.compoundID) + ) + if os.path.isfile( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".pdb" + ) + ): + os.system( + "/bin/rm %s" + % os.path.join( + self.project_directory, + self.xtalID, + self.compoundID + ".pdb", + ) + ) + print( + "XCE: changing directory", + os.path.join(self.project_directory, self.xtalID), + ) os.chdir(os.path.join(self.project_directory, self.xtalID)) - print('XCE: changing symlink ln -s %s %s.pdb' % ( - os.path.join('compound', molName + '.pdb'), self.compoundID)) - os.system('ln -s %s %s.pdb' % (os.path.join('compound', molName - + '.pdb'), self.compoundID)) - print('===> XCE: deleting ligand molecule', molName) + print( + "XCE: changing symlink ln -s %s %s.pdb" + % (os.path.join("compound", molName + ".pdb"), self.compoundID) + ) + os.system( + "ln -s %s %s.pdb" + % (os.path.join("compound", molName + ".pdb"), self.compoundID) + ) + print("===> XCE: deleting ligand molecule", molName) coot.close_molecule(imol) self.select_cpd_cb.set_sensitive(False) -# print '===> XCE: merge ligand into protein structure' -# # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) -# coot.merge_molecules_py([self.mol_dict['ligand']], self.mol_dict['protein']) -# print '===> XCE: deleting ligand molecule' -# coot.close_molecule(self.mol_dict['ligand']) + # print '===> XCE: merge ligand into protein structure' + # # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) + # coot.merge_molecules_py([self.mol_dict['ligand']], self.mol_dict['protein']) + # print '===> XCE: deleting ligand molecule' + # coot.close_molecule(self.mol_dict['ligand']) def show_molprobity_to_do(self, widget): print(self.panddaSerial) - AdjPanddaSerial = (4 - len(str(self.Serial))) * \ - '0' + str(int(self.panddaSerial) - 1) - print(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), - 'molprobity_coot.py')) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), - 'molprobity_coot.py')): - print('==> XCE: running MolProbity Summary for', self.xtalID) - coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), - 'molprobity_coot.py')) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), - 'molprobity_coot.py')): - print('==> XCE: running MolProbity Summary for', self.xtalID) - coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), - 'molprobity_coot.py')) + AdjPanddaSerial = (4 - len(str(self.Serial))) * "0" + str( + int(self.panddaSerial) - 1 + ) + print( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.panddaSerial), + "molprobity_coot.py", + ) + ) + if os.path.isfile( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ): + print("==> XCE: running MolProbity Summary for", self.xtalID) + coot.run_script( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ) + elif os.path.isfile( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(AdjPanddaSerial), + "molprobity_coot.py", + ) + ): + print("==> XCE: running MolProbity Summary for", self.xtalID) + coot.run_script( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(AdjPanddaSerial), + "molprobity_coot.py", + ) + ) else: - print('==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')) + print( + "==> XCE: cannot find " + + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ) def refinementProtocolCallback(self, widget): if widget.get_active(): if self.refinementProtocolcheckbox.get_active(): - self.refinementProtocol = 'pandda_phenix' + self.refinementProtocol = "pandda_phenix" else: - self.refinementProtocol = 'pandda_refmac' + self.refinementProtocol = "pandda_refmac" self.PREVbuttonSite.set_sensitive(True) self.NEXTbuttonSite.set_sensitive(True) else: self.refinementProtocolcheckbox.set_active(False) - self.refinementProtocol = 'refmac' + self.refinementProtocol = "refmac" self.PREVbuttonSite.set_sensitive(False) self.NEXTbuttonSite.set_sensitive(False) print(self.refinementProtocol) @@ -1736,24 +2159,24 @@ def refinementProtocolCallback(self, widget): def refinementProgramCallback(self, widget): if widget.get_active(): if self.refinementProtocolcheckbox.get_active(): - self.refinementProtocol = 'pandda_phenix' + self.refinementProtocol = "pandda_phenix" self.RefinementParamsButton.set_sensitive(False) else: self.refinementProgramcheckbox.set_active(False) - self.refinementProtocol = 'refmac' + self.refinementProtocol = "refmac" else: self.RefinementParamsButton.set_sensitive(True) if self.refinementProtocolcheckbox.get_active(): - self.refinementProtocol = 'pandda_refmac' + self.refinementProtocol = "pandda_refmac" else: - self.refinementProtocol = 'refmac' + self.refinementProtocol = "refmac" print(self.refinementProtocol) def show_ground_state_mean_map(self, widget): - if widget.get_label().startswith('Show'): + if widget.get_label().startswith("Show"): loaded = False for imol in coot_utils_XChem.molecule_number_list(): - if 'ground-state-mean-map' in coot.molecule_name(imol): + if "ground-state-mean-map" in coot.molecule_name(imol): coot.set_map_displayed(imol, 1) loaded = True break @@ -1761,13 +2184,13 @@ def show_ground_state_mean_map(self, widget): coot.set_default_initial_contour_level_for_map(1) coot.handle_read_ccp4_map(self.ground_state_mean_map, 0) coot.set_last_map_colour(0.6, 0.6, 0) - widget.set_label('Undisplay ground state mean map') + widget.set_label("Undisplay ground state mean map") else: for imol in coot_utils_XChem.molecule_number_list(): - if 'ground-state-mean-map' in coot.molecule_name(imol): + if "ground-state-mean-map" in coot.molecule_name(imol): coot.set_map_displayed(imol, 0) - widget.set_label('Show ground state mean map') + widget.set_label("Show ground state mean map") -if __name__ == '__main__': +if __name__ == "__main__": GUI().StartGUI() diff --git a/lib/XChemCootOld.py b/lib/XChemCootOld.py index b4198760..8deb0644 100755 --- a/lib/XChemCootOld.py +++ b/lib/XChemCootOld.py @@ -14,10 +14,11 @@ import pickle from matplotlib.figure import Figure -#from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas + +# from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas # XCE libraries -sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") # libraries from COOT @@ -36,78 +37,82 @@ def __init__(self): ########################################################################################### # read in settings file from XChemExplorer to set the relevant paths - print('current dir', os.getcwd()) + print("current dir", os.getcwd()) self.settings = pickle.load(open(".xce_settings.pkl", "rb")) - remote_qsub_submission = self.settings['remote_qsub'] - print('setting', self.settings) -# self.refine_model_directory=self.settings['refine_model_directory'] - self.database_directory = self.settings['database_directory'] - self.xce_logfile = self.settings['xce_logfile'] - self.data_source = self.settings['data_source'] + remote_qsub_submission = self.settings["remote_qsub"] + print("setting", self.settings) + # self.refine_model_directory=self.settings['refine_model_directory'] + self.database_directory = self.settings["database_directory"] + self.xce_logfile = self.settings["xce_logfile"] + self.data_source = self.settings["data_source"] self.db = XChemDB.data_source(self.data_source) # checking for external software packages - self.external_software = XChemUtils.external_software( - self.xce_logfile).check() - self.external_software['qsub_remote'] = remote_qsub_submission - - self.selection_criteria = ['0 - All Datasets', - '1 - Analysis Pending', - '2 - PANDDA model', - '3 - In Refinement', - '4 - CompChem ready', - '5 - Deposition ready', - '6 - Deposited'] - - self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], - ['In Refinement', - '3 - In Refinement', 65000, 0, 0], - ['Comp Chem Ready!', - '4 - CompChem ready', 65000, 0, 0], - ['Ready for Deposition!', - '5 - Deposition ready', 65000, 0, 0], - ['In PDB', '6 - Deposited', 65000, 0, 0]] - - self.ligand_confidence_category = ['0 - no ligand present', - '1 - Low Confidence', - '2 - Correct ligand, weak density', - '3 - Clear density, unexpected ligand', - '4 - High Confidence'] + self.external_software = XChemUtils.external_software(self.xce_logfile).check() + self.external_software["qsub_remote"] = remote_qsub_submission + + self.selection_criteria = [ + "0 - All Datasets", + "1 - Analysis Pending", + "2 - PANDDA model", + "3 - In Refinement", + "4 - CompChem ready", + "5 - Deposition ready", + "6 - Deposited", + ] + + self.experiment_stage = [ + ["Review PANDDA export", "2 - PANDDA model", 65000, 0, 0], + ["In Refinement", "3 - In Refinement", 65000, 0, 0], + ["Comp Chem Ready!", "4 - CompChem ready", 65000, 0, 0], + ["Ready for Deposition!", "5 - Deposition ready", 65000, 0, 0], + ["In PDB", "6 - Deposited", 65000, 0, 0], + ] + + self.ligand_confidence_category = [ + "0 - no ligand present", + "1 - Low Confidence", + "2 - Correct ligand, weak density", + "3 - Clear density, unexpected ligand", + "4 - High Confidence", + ] self.ligand_site_information = self.db.get_list_of_pandda_sites_for_coot() # this decides which samples will be looked at - self.selection_mode = '' -# self.selected_site='' - self.pandda_index = -1 # refers to the number of sites - self.site_index = '0' - self.event_index = '0' + self.selection_mode = "" + # self.selected_site='' + self.pandda_index = -1 # refers to the number of sites + self.site_index = "0" + self.event_index = "0" # the Folder is kind of a legacy thing because my inital idea was to have separate folders # for Data Processing and Refinement - self.project_directory = self.settings['initial_model_directory'] + self.project_directory = self.settings["initial_model_directory"] self.Serial = 0 self.Refine = None self.index = -1 self.Todo = [] self.siteDict = {} - self.xtalID = '' - self.compoundID = '' - self.spider_plot = '' - self.ligand_confidence = '' - self.refinement_folder = '' -# self.datasetOutcome='' + self.xtalID = "" + self.compoundID = "" + self.spider_plot = "" + self.ligand_confidence = "" + self.refinement_folder = "" + # self.datasetOutcome='' - self.pdb_style = 'refine.pdb' - self.mtz_style = 'refine.mtz' + self.pdb_style = "refine.pdb" + self.mtz_style = "refine.mtz" # stores imol of currently loaded molecules and maps - self.mol_dict = {'protein': -1, - 'ligand': -1, - '2fofc': -1, - 'fofc': -1, - 'event': -1} + self.mol_dict = { + "protein": -1, + "ligand": -1, + "2fofc": -1, + "fofc": -1, + "event": -1, + } # two dictionaries which are flushed when a new crystal is loaded # and which contain information to update the data source if necessary @@ -120,44 +125,54 @@ def __init__(self): coot.set_colour_map_rotation_for_map(0) coot.set_colour_map_rotation_on_read_pdb_flag(0) - self.QualityIndicators = {'RefinementRcryst': '-', - 'RefinementRfree': '-', - 'RefinementRfreeTraficLight': 'gray', - 'RefinementResolution': '-', - 'RefinementResolutionTL': 'gray', - 'RefinementMolProbityScore': '-', - 'RefinementMolProbityScoreTL': 'gray', - 'RefinementRamachandranOutliers': '-', - 'RefinementRamachandranOutliersTL': 'gray', - 'RefinementRamachandranFavored': '-', - 'RefinementRamachandranFavoredTL': 'gray', - 'RefinementRmsdBonds': '-', - 'RefinementRmsdBondsTL': 'gray', - 'RefinementRmsdAngles': '-', - 'RefinementRmsdAnglesTL': 'gray', - 'RefinementMatrixWeight': '-'} - - self.spider_plot_data = {'PANDDA_site_ligand_id': '-', - 'PANDDA_site_occupancy': '-', - 'PANDDA_site_B_average': '-', - 'PANDDA_site_B_ratio_residue_surroundings': '-', - 'PANDDA_site_RSCC': '-', - 'PANDDA_site_rmsd': '-', - 'PANDDA_site_RSR': '-', - 'PANDDA_site_RSZD': '-'} + self.QualityIndicators = { + "RefinementRcryst": "-", + "RefinementRfree": "-", + "RefinementRfreeTraficLight": "gray", + "RefinementResolution": "-", + "RefinementResolutionTL": "gray", + "RefinementMolProbityScore": "-", + "RefinementMolProbityScoreTL": "gray", + "RefinementRamachandranOutliers": "-", + "RefinementRamachandranOutliersTL": "gray", + "RefinementRamachandranFavored": "-", + "RefinementRamachandranFavoredTL": "gray", + "RefinementRmsdBonds": "-", + "RefinementRmsdBondsTL": "gray", + "RefinementRmsdAngles": "-", + "RefinementRmsdAnglesTL": "gray", + "RefinementMatrixWeight": "-", + } + + self.spider_plot_data = { + "PANDDA_site_ligand_id": "-", + "PANDDA_site_occupancy": "-", + "PANDDA_site_B_average": "-", + "PANDDA_site_B_ratio_residue_surroundings": "-", + "PANDDA_site_RSCC": "-", + "PANDDA_site_rmsd": "-", + "PANDDA_site_RSR": "-", + "PANDDA_site_RSZD": "-", + } # default refmac parameters - self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': ''} + self.RefmacParams = { + "HKLIN": "", + "HKLOUT": "", + "XYZIN": "", + "XYZOUT": "", + "LIBIN": "", + "LIBOUT": "", + "TLSIN": "", + "TLSOUT": "", + "TLSADD": "", + "NCYCLES": "10", + "MATRIX_WEIGHT": "AUTO", + "BREF": " bref ISOT\n", + "TLS": "", + "NCS": "", + "TWIN": "", + } def StartGUI(self): @@ -166,15 +181,15 @@ def StartGUI(self): self.window.set_border_width(10) self.window.set_default_size(400, 800) self.window.set_title("XChemExplorer") - self.vbox = gtk.VBox() # this is the main container + self.vbox = gtk.VBox() # this is the main container ################################################################################# # --- Sample Selection --- -# self.vbox.add(gtk.Label('Select Samples')) + # self.vbox.add(gtk.Label('Select Samples')) - frame = gtk.Frame(label='Select Samples') + frame = gtk.Frame(label="Select Samples") self.hbox_select_samples = gtk.HBox() -# vbox=gtk.VBox() + # vbox=gtk.VBox() self.cb_select_samples = gtk.combo_box_new_text() self.cb_select_samples.connect("changed", self.set_selection_mode) @@ -182,15 +197,14 @@ def StartGUI(self): self.cb_select_samples.append_text(citeria) self.hbox_select_samples.add(self.cb_select_samples) -# self.cb_select_sites = gtk.combo_box_new_text() -# self.cb_select_sites.connect("changed", self.set_site) -# for site in self.ligand_site_information: -# self.cb_select_sites.append_text(str(site[0])+' - '+str(site[1])) -# self.hbox_select_samples.add(self.cb_select_sites) + # self.cb_select_sites = gtk.combo_box_new_text() + # self.cb_select_sites.connect("changed", self.set_site) + # for site in self.ligand_site_information: + # self.cb_select_sites.append_text(str(site[0])+' - '+str(site[1])) + # self.hbox_select_samples.add(self.cb_select_sites) self.select_samples_button = gtk.Button(label="GO") - self.select_samples_button.connect( - "clicked", self.get_samples_to_look_at) + self.select_samples_button.connect("clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) @@ -203,7 +217,7 @@ def StartGUI(self): self.vbox.pack_start(frame) # SPACER - self.vbox.add(gtk.Label(' ')) + self.vbox.add(gtk.Label(" ")) ################################################################################# # --- Refinement Statistics --- @@ -211,163 +225,162 @@ def StartGUI(self): # a combination of labels and textview widgets, arranged in a table RRfreeLabel_frame = gtk.Frame() - self.RRfreeLabel = gtk.Label('R/Rfree') + self.RRfreeLabel = gtk.Label("R/Rfree") RRfreeLabel_frame.add(self.RRfreeLabel) self.RRfreeValue = gtk.Label( - self.QualityIndicators['RefinementRcryst']+'/'+self.QualityIndicators['RefinementRfree']) + self.QualityIndicators["RefinementRcryst"] + + "/" + + self.QualityIndicators["RefinementRfree"] + ) RRfreeBox_frame = gtk.Frame() self.RRfreeBox = gtk.EventBox() self.RRfreeBox.add(self.RRfreeValue) RRfreeBox_frame.add(self.RRfreeBox) ResolutionLabel_frame = gtk.Frame() - self.ResolutionLabel = gtk.Label('Resolution') + self.ResolutionLabel = gtk.Label("Resolution") ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label( - self.QualityIndicators['RefinementResolution']) + self.ResolutionValue = gtk.Label(self.QualityIndicators["RefinementResolution"]) ResolutionBox_frame = gtk.Frame() self.ResolutionBox = gtk.EventBox() self.ResolutionBox.add(self.ResolutionValue) ResolutionBox_frame.add(self.ResolutionBox) MolprobityScoreLabel_frame = gtk.Frame() - self.MolprobityScoreLabel = gtk.Label('MolprobityScore') + self.MolprobityScoreLabel = gtk.Label("MolprobityScore") MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) self.MolprobityScoreValue = gtk.Label( - self.QualityIndicators['RefinementMolProbityScore']) + self.QualityIndicators["RefinementMolProbityScore"] + ) MolprobityScoreBox_frame = gtk.Frame() self.MolprobityScoreBox = gtk.EventBox() self.MolprobityScoreBox.add(self.MolprobityScoreValue) MolprobityScoreBox_frame.add(self.MolprobityScoreBox) RamachandranOutliersLabel_frame = gtk.Frame() - self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') + self.RamachandranOutliersLabel = gtk.Label("Rama Outliers") RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) self.RamachandranOutliersValue = gtk.Label( - self.QualityIndicators['RefinementRamachandranOutliers']) + self.QualityIndicators["RefinementRamachandranOutliers"] + ) RamachandranOutliersBox_frame = gtk.Frame() self.RamachandranOutliersBox = gtk.EventBox() self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) RamachandranOutliersBox_frame.add(self.RamachandranOutliersBox) RamachandranFavoredLabel_frame = gtk.Frame() - self.RamachandranFavoredLabel = gtk.Label('Rama Favored') + self.RamachandranFavoredLabel = gtk.Label("Rama Favored") RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) self.RamachandranFavoredValue = gtk.Label( - self.QualityIndicators['RefinementRamachandranFavored']) + self.QualityIndicators["RefinementRamachandranFavored"] + ) RamachandranFavoredBox_frame = gtk.Frame() self.RamachandranFavoredBox = gtk.EventBox() self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) RamachandranFavoredBox_frame.add(self.RamachandranFavoredBox) rmsdBondsLabel_frame = gtk.Frame() - self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') + self.rmsdBondsLabel = gtk.Label("rmsd(Bonds)") rmsdBondsLabel_frame.add(self.rmsdBondsLabel) - self.rmsdBondsValue = gtk.Label( - self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue = gtk.Label(self.QualityIndicators["RefinementRmsdBonds"]) rmsdBondsBox_frame = gtk.Frame() self.rmsdBondsBox = gtk.EventBox() self.rmsdBondsBox.add(self.rmsdBondsValue) rmsdBondsBox_frame.add(self.rmsdBondsBox) rmsdAnglesLabel_frame = gtk.Frame() - self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') + self.rmsdAnglesLabel = gtk.Label("rmsd(Angles)") rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) - self.rmsdAnglesValue = gtk.Label( - self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue = gtk.Label(self.QualityIndicators["RefinementRmsdAngles"]) rmsdAnglesBox_frame = gtk.Frame() self.rmsdAnglesBox = gtk.EventBox() self.rmsdAnglesBox.add(self.rmsdAnglesValue) rmsdAnglesBox_frame.add(self.rmsdAnglesBox) MatrixWeightLabel_frame = gtk.Frame() - self.MatrixWeightLabel = gtk.Label('Matrix Weight') + self.MatrixWeightLabel = gtk.Label("Matrix Weight") MatrixWeightLabel_frame.add(self.MatrixWeightLabel) self.MatrixWeightValue = gtk.Label( - self.QualityIndicators['RefinementMatrixWeight']) + self.QualityIndicators["RefinementMatrixWeight"] + ) MatrixWeightBox_frame = gtk.Frame() self.MatrixWeightBox = gtk.EventBox() self.MatrixWeightBox.add(self.MatrixWeightValue) MatrixWeightBox_frame.add(self.MatrixWeightBox) ligandIDLabel_frame = gtk.Frame() - self.ligandIDLabel = gtk.Label('Ligand ID') + self.ligandIDLabel = gtk.Label("Ligand ID") ligandIDLabel_frame.add(self.ligandIDLabel) - self.ligandIDValue = gtk.Label( - self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue = gtk.Label(self.spider_plot_data["PANDDA_site_ligand_id"]) ligandIDBox_frame = gtk.Frame() self.ligandIDBox = gtk.EventBox() self.ligandIDBox.add(self.ligandIDValue) ligandIDBox_frame.add(self.ligandIDBox) ligand_occupancyLabel_frame = gtk.Frame() - self.ligand_occupancyLabel = gtk.Label('occupancy') + self.ligand_occupancyLabel = gtk.Label("occupancy") ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) self.ligand_occupancyValue = gtk.Label( - self.spider_plot_data['PANDDA_site_occupancy']) + self.spider_plot_data["PANDDA_site_occupancy"] + ) ligand_occupancyBox_frame = gtk.Frame() self.ligand_occupancyBox = gtk.EventBox() self.ligand_occupancyBox.add(self.ligand_occupancyValue) ligand_occupancyBox_frame.add(self.ligand_occupancyBox) ligand_BaverageLabel_frame = gtk.Frame() - self.ligand_BaverageLabel = gtk.Label('B average') + self.ligand_BaverageLabel = gtk.Label("B average") ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) self.ligand_BaverageValue = gtk.Label( - self.spider_plot_data['PANDDA_site_B_average']) + self.spider_plot_data["PANDDA_site_B_average"] + ) ligand_BaverageBox_frame = gtk.Frame() self.ligand_BaverageBox = gtk.EventBox() self.ligand_BaverageBox.add(self.ligand_BaverageValue) ligand_BaverageBox_frame.add(self.ligand_BaverageBox) ligand_BratioSurroundingsLabel_frame = gtk.Frame() - self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') - ligand_BratioSurroundingsLabel_frame.add( - self.ligand_BratioSurroundingsLabel) + self.ligand_BratioSurroundingsLabel = gtk.Label("B ratio") + ligand_BratioSurroundingsLabel_frame.add(self.ligand_BratioSurroundingsLabel) self.ligand_BratioSurroundingsValue = gtk.Label( - self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) + self.spider_plot_data["PANDDA_site_B_ratio_residue_surroundings"] + ) ligand_BratioSurroundingsBox_frame = gtk.Frame() self.ligand_BratioSurroundingsBox = gtk.EventBox() - self.ligand_BratioSurroundingsBox.add( - self.ligand_BratioSurroundingsValue) - ligand_BratioSurroundingsBox_frame.add( - self.ligand_BratioSurroundingsBox) + self.ligand_BratioSurroundingsBox.add(self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add(self.ligand_BratioSurroundingsBox) ligand_RSCCLabel_frame = gtk.Frame() - self.ligand_RSCCLabel = gtk.Label('RSCC') + self.ligand_RSCCLabel = gtk.Label("RSCC") ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) - self.ligand_RSCCValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSCC']) + self.ligand_RSCCValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSCC"]) ligand_RSCCBox_frame = gtk.Frame() self.ligand_RSCCBox = gtk.EventBox() self.ligand_RSCCBox.add(self.ligand_RSCCValue) ligand_RSCCBox_frame.add(self.ligand_RSCCBox) ligand_rmsdLabel_frame = gtk.Frame() - self.ligand_rmsdLabel = gtk.Label('rmsd') + self.ligand_rmsdLabel = gtk.Label("rmsd") ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) - self.ligand_rmsdValue = gtk.Label( - self.spider_plot_data['PANDDA_site_rmsd']) + self.ligand_rmsdValue = gtk.Label(self.spider_plot_data["PANDDA_site_rmsd"]) ligand_rmsdBox_frame = gtk.Frame() self.ligand_rmsdBox = gtk.EventBox() self.ligand_rmsdBox.add(self.ligand_rmsdValue) ligand_rmsdBox_frame.add(self.ligand_rmsdBox) ligand_RSRLabel_frame = gtk.Frame() - self.ligand_RSRLabel = gtk.Label('RSR') + self.ligand_RSRLabel = gtk.Label("RSR") ligand_RSRLabel_frame.add(self.ligand_RSRLabel) - self.ligand_RSRValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSR']) + self.ligand_RSRValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSR"]) ligand_RSRBox_frame = gtk.Frame() self.ligand_RSRBox = gtk.EventBox() self.ligand_RSRBox.add(self.ligand_RSRValue) ligand_RSRBox_frame.add(self.ligand_RSRBox) ligand_RSZDLabel_frame = gtk.Frame() - self.ligand_RSZDLabel = gtk.Label('RSZD') + self.ligand_RSZDLabel = gtk.Label("RSZD") ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) - self.ligand_RSZDValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSZD']) + self.ligand_RSZDValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSZD"]) ligand_RSZDBox_frame = gtk.Frame() self.ligand_RSZDBox = gtk.EventBox() self.ligand_RSZDBox.add(self.ligand_RSZDValue) @@ -378,59 +391,43 @@ def StartGUI(self): frame = gtk.Frame() self.table_left = gtk.Table(8, 2, False) - self.table_left.attach(RRfreeLabel_frame, 0, 1, 0, 1) - self.table_left.attach(ResolutionLabel_frame, 0, 1, 1, 2) - self.table_left.attach(MolprobityScoreLabel_frame, 0, 1, 2, 3) - self.table_left.attach(RamachandranOutliersLabel_frame, 0, 1, 3, 4) - self.table_left.attach(RamachandranFavoredLabel_frame, 0, 1, 4, 5) - self.table_left.attach(rmsdBondsLabel_frame, 0, 1, 5, 6) - self.table_left.attach(rmsdAnglesLabel_frame, 0, 1, 6, 7) - self.table_left.attach(MatrixWeightLabel_frame, 0, 1, 7, 8) - self.table_left.attach(RRfreeBox_frame, 1, 2, 0, 1) - self.table_left.attach(ResolutionBox_frame, 1, 2, 1, 2) - self.table_left.attach(MolprobityScoreBox_frame, 1, 2, 2, 3) - self.table_left.attach(RamachandranOutliersBox_frame, 1, 2, 3, 4) - self.table_left.attach(RamachandranFavoredBox_frame, 1, 2, 4, 5) - self.table_left.attach(rmsdBondsBox_frame, 1, 2, 5, 6) - self.table_left.attach(rmsdAnglesBox_frame, 1, 2, 6, 7) - self.table_left.attach(MatrixWeightBox_frame, 1, 2, 7, 8) + self.table_left.attach(RRfreeLabel_frame, 0, 1, 0, 1) + self.table_left.attach(ResolutionLabel_frame, 0, 1, 1, 2) + self.table_left.attach(MolprobityScoreLabel_frame, 0, 1, 2, 3) + self.table_left.attach(RamachandranOutliersLabel_frame, 0, 1, 3, 4) + self.table_left.attach(RamachandranFavoredLabel_frame, 0, 1, 4, 5) + self.table_left.attach(rmsdBondsLabel_frame, 0, 1, 5, 6) + self.table_left.attach(rmsdAnglesLabel_frame, 0, 1, 6, 7) + self.table_left.attach(MatrixWeightLabel_frame, 0, 1, 7, 8) + self.table_left.attach(RRfreeBox_frame, 1, 2, 0, 1) + self.table_left.attach(ResolutionBox_frame, 1, 2, 1, 2) + self.table_left.attach(MolprobityScoreBox_frame, 1, 2, 2, 3) + self.table_left.attach(RamachandranOutliersBox_frame, 1, 2, 3, 4) + self.table_left.attach(RamachandranFavoredBox_frame, 1, 2, 4, 5) + self.table_left.attach(rmsdBondsBox_frame, 1, 2, 5, 6) + self.table_left.attach(rmsdAnglesBox_frame, 1, 2, 6, 7) + self.table_left.attach(MatrixWeightBox_frame, 1, 2, 7, 8) frame.add(self.table_left) hbox.add(frame) frame = gtk.Frame() self.table_right = gtk.Table(8, 2, False) - self.table_right.attach(ligandIDLabel_frame, - 0, 1, 0, 1) - self.table_right.attach( - ligand_occupancyLabel_frame, 0, 1, 1, 2) - self.table_right.attach( - ligand_BaverageLabel_frame, 0, 1, 2, 3) - self.table_right.attach( - ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) - self.table_right.attach( - ligand_RSCCLabel_frame, 0, 1, 4, 5) - self.table_right.attach( - ligand_rmsdLabel_frame, 0, 1, 5, 6) - self.table_right.attach( - ligand_RSRLabel_frame, 0, 1, 6, 7) - self.table_right.attach( - ligand_RSZDLabel_frame, 0, 1, 7, 8) - self.table_right.attach(ligandIDBox_frame, - 1, 2, 0, 1) - self.table_right.attach( - ligand_occupancyBox_frame, 1, 2, 1, 2) - self.table_right.attach( - ligand_BaverageBox_frame, 1, 2, 2, 3) - self.table_right.attach( - ligand_BratioSurroundingsBox_frame, 1, 2, 3, 4) - self.table_right.attach( - ligand_RSCCBox_frame, 1, 2, 4, 5) - self.table_right.attach( - ligand_rmsdBox_frame, 1, 2, 5, 6) - self.table_right.attach(ligand_RSRBox_frame, - 1, 2, 6, 7) - self.table_right.attach( - ligand_RSZDBox_frame, 1, 2, 7, 8) + self.table_right.attach(ligandIDLabel_frame, 0, 1, 0, 1) + self.table_right.attach(ligand_occupancyLabel_frame, 0, 1, 1, 2) + self.table_right.attach(ligand_BaverageLabel_frame, 0, 1, 2, 3) + self.table_right.attach(ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach(ligand_RSCCLabel_frame, 0, 1, 4, 5) + self.table_right.attach(ligand_rmsdLabel_frame, 0, 1, 5, 6) + self.table_right.attach(ligand_RSRLabel_frame, 0, 1, 6, 7) + self.table_right.attach(ligand_RSZDLabel_frame, 0, 1, 7, 8) + self.table_right.attach(ligandIDBox_frame, 1, 2, 0, 1) + self.table_right.attach(ligand_occupancyBox_frame, 1, 2, 1, 2) + self.table_right.attach(ligand_BaverageBox_frame, 1, 2, 2, 3) + self.table_right.attach(ligand_BratioSurroundingsBox_frame, 1, 2, 3, 4) + self.table_right.attach(ligand_RSCCBox_frame, 1, 2, 4, 5) + self.table_right.attach(ligand_rmsdBox_frame, 1, 2, 5, 6) + self.table_right.attach(ligand_RSRBox_frame, 1, 2, 6, 7) + self.table_right.attach(ligand_RSZDBox_frame, 1, 2, 7, 8) frame.add(self.table_right) hbox.add(frame) @@ -443,7 +440,7 @@ def StartGUI(self): self.vbox.pack_start(frame) # SPACER - self.vbox.add(gtk.Label(' ')) + self.vbox.add(gtk.Label(" ")) ################################################################################# # --- hbox for compound picture & spider_plot (formerly: refinement history) --- @@ -452,8 +449,13 @@ def StartGUI(self): # --- compound picture --- compound_frame = gtk.Frame() - pic = gtk.gdk.pixbuf_new_from_file(os.path.join( - os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + pic = gtk.gdk.pixbuf_new_from_file( + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_COMPOUND_IMAGE_AVAILABLE.png", + ) + ) self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.image = gtk.Image() self.image.set_from_pixbuf(self.pic) @@ -461,16 +463,18 @@ def StartGUI(self): self.hbox_for_info_graphics.add(compound_frame) # --- Refinement History --- -# self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) -# self.canvas.set_size_request(190, 190) -# self.hbox_for_info_graphics.add(self.canvas) + # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) + # self.canvas.set_size_request(190, 190) + # self.hbox_for_info_graphics.add(self.canvas) # --- Spider Plot --- spider_plot_frame = gtk.Frame() - spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join( - os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + spider_plot_pic = gtk.gdk.pixbuf_new_from_file( + os.path.join( + os.getenv("XChemExplorer_DIR"), "image", "NO_SPIDER_PLOT_AVAILABLE.png" + ) + ) + self.spider_plot_pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image = gtk.Image() self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) spider_plot_frame.add(self.spider_plot_image) @@ -481,67 +485,68 @@ def StartGUI(self): ################################################################################# # --- pandda.inspect user comments --- - outer_frame = gtk.Frame(label='pandda.inspect comments') + outer_frame = gtk.Frame(label="pandda.inspect comments") vbox = gtk.VBox() ligand_site_name_label_frame = gtk.Frame() - ligand_site_name_label = gtk.Label('Site Name') + ligand_site_name_label = gtk.Label("Site Name") ligand_site_name_label_frame.add(ligand_site_name_label) ligand_inspect_confidence_label_frame = gtk.Frame() - ligand_inspect_confidence_label = gtk.Label('Confidence') - ligand_inspect_confidence_label_frame.add( - ligand_inspect_confidence_label) + ligand_inspect_confidence_label = gtk.Label("Confidence") + ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) ligand_inspect_interesting_label_frame = gtk.Frame() - ligand_inspect_interesting_label = gtk.Label('Interesting') - ligand_inspect_interesting_label_frame.add( - ligand_inspect_interesting_label) + ligand_inspect_interesting_label = gtk.Label("Interesting") + ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) ligand_inspect_comment_label_frame = gtk.Frame() - ligand_inspect_comment_label = gtk.Label('Comment') + ligand_inspect_comment_label = gtk.Label("Comment") ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) ligand_site_name_value_frame = gtk.Frame() - self.ligand_site_name_value = gtk.Label('-') + self.ligand_site_name_value = gtk.Label("-") ligand_site_name_value_frame.add(self.ligand_site_name_value) ligand_inspect_confidence_value_frame = gtk.Frame() - self.ligand_inspect_confidence_value = gtk.Label('-') - ligand_inspect_confidence_value_frame.add( - self.ligand_inspect_confidence_value) + self.ligand_inspect_confidence_value = gtk.Label("-") + ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) ligand_inspect_interesting_value_frame = gtk.Frame() - self.ligand_inspect_interesting_value = gtk.Label('-') + self.ligand_inspect_interesting_value = gtk.Label("-") ligand_inspect_interesting_value_frame.add( - self.ligand_inspect_interesting_value) + self.ligand_inspect_interesting_value + ) ligand_inspect_comment_value_frame = gtk.Frame() - self.ligand_inspect_comment_value = gtk.Label('-') - ligand_inspect_comment_value_frame.add( - self.ligand_inspect_comment_value) + self.ligand_inspect_comment_value = gtk.Label("-") + ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) frame_pandda_inspect_comments_table = gtk.Frame() pandda_inspect_comments_table = gtk.Table(2, 6, False) + pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) + pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) pandda_inspect_comments_table.attach( - ligand_site_name_label_frame, 0, 1, 0, 1) - pandda_inspect_comments_table.attach( - ligand_site_name_value_frame, 1, 2, 0, 1) + ligand_inspect_confidence_label_frame, 2, 3, 0, 1 + ) pandda_inspect_comments_table.attach( - ligand_inspect_confidence_label_frame, 2, 3, 0, 1) + ligand_inspect_confidence_value_frame, 3, 4, 0, 1 + ) pandda_inspect_comments_table.attach( - ligand_inspect_confidence_value_frame, 3, 4, 0, 1) + ligand_inspect_interesting_label_frame, 4, 5, 0, 1 + ) pandda_inspect_comments_table.attach( - ligand_inspect_interesting_label_frame, 4, 5, 0, 1) + ligand_inspect_interesting_value_frame, 5, 6, 0, 1 + ) pandda_inspect_comments_table.attach( - ligand_inspect_interesting_value_frame, 5, 6, 0, 1) + ligand_inspect_comment_label_frame, 0, 1, 1, 2 + ) pandda_inspect_comments_table.attach( - ligand_inspect_comment_label_frame, 0, 1, 1, 2) - pandda_inspect_comments_table.attach( - ligand_inspect_comment_value_frame, 1, 6, 1, 2) + ligand_inspect_comment_value_frame, 1, 6, 1, 2 + ) frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) vbox.add(frame_pandda_inspect_comments_table) outer_frame.add(vbox) self.vbox.pack_start(outer_frame) -# # SPACER - self.vbox.add(gtk.Label(' ')) + # # SPACER + self.vbox.add(gtk.Label(" ")) ################################################################################# - outer_frame = gtk.Frame(label='Sample Navigator') + outer_frame = gtk.Frame(label="Sample Navigator") hboxSample = gtk.HBox() # --- crystal navigator combobox --- @@ -584,14 +589,14 @@ def StartGUI(self): self.vbox.add(outer_frame) # SPACER - self.vbox.add(gtk.Label(' ')) + self.vbox.add(gtk.Label(" ")) ################################################################################# # --- current refinement stage --- outer_frame = gtk.Frame() hbox = gtk.HBox() - frame = gtk.Frame(label='Analysis Status') + frame = gtk.Frame(label="Analysis Status") vbox = gtk.VBox() self.experiment_stage_button_list = [] for n, button in enumerate(self.experiment_stage): @@ -600,14 +605,15 @@ def StartGUI(self): else: new_button = gtk.RadioButton(new_button, button[0]) new_button.connect( - "toggled", self.experiment_stage_button_clicked, button[1]) + "toggled", self.experiment_stage_button_clicked, button[1] + ) vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) # --- ligand confidence --- - frame = gtk.Frame(label='Ligand Confidence') + frame = gtk.Frame(label="Ligand Confidence") vbox = gtk.VBox() self.ligand_confidence_button_list = [] for n, criteria in enumerate(self.ligand_confidence_category): @@ -616,7 +622,8 @@ def StartGUI(self): else: new_button = gtk.RadioButton(new_button, criteria) new_button.connect( - "toggled", self.ligand_confidence_button_clicked, criteria) + "toggled", self.ligand_confidence_button_clicked, criteria + ) vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) @@ -626,29 +633,26 @@ def StartGUI(self): self.vbox.pack_start(outer_frame) # SPACER - self.vbox.add(gtk.Label(' ')) + self.vbox.add(gtk.Label(" ")) # --- ligand modeling --- - frame = gtk.Frame(label='Ligand Modeling') + frame = gtk.Frame(label="Ligand Modeling") self.hbox_for_modeling = gtk.HBox() self.merge_ligand_button = gtk.Button(label="Merge Ligand") self.place_ligand_here_button = gtk.Button(label="Place Ligand here") self.hbox_for_modeling.add(self.place_ligand_here_button) - self.place_ligand_here_button.connect( - "clicked", self.place_ligand_here) + self.place_ligand_here_button.connect("clicked", self.place_ligand_here) self.hbox_for_modeling.add(self.merge_ligand_button) - self.merge_ligand_button.connect( - "clicked", self.merge_ligand_into_protein) + self.merge_ligand_button.connect("clicked", self.merge_ligand_into_protein) frame.add(self.hbox_for_modeling) self.vbox.pack_start(frame) - -# # --- ligand confidence --- -# self.cb_ligand_confidence = gtk.combo_box_new_text() -# self.cb_ligand_confidence.connect("changed", self.set_ligand_confidence) -# for citeria in self.ligand_confidence: -# self.cb_ligand_confidence.append_text(citeria) -# self.vbox.add(self.cb_ligand_confidence) + # # --- ligand confidence --- + # self.cb_ligand_confidence = gtk.combo_box_new_text() + # self.cb_ligand_confidence.connect("changed", self.set_ligand_confidence) + # for citeria in self.ligand_confidence: + # self.cb_ligand_confidence.append_text(citeria) + # self.vbox.add(self.cb_ligand_confidence) # --- refinement & options --- self.hbox_for_refinement = gtk.HBox() @@ -660,8 +664,8 @@ def StartGUI(self): self.hbox_for_refinement.add(self.RefinementParamsButton) self.vbox.add(self.hbox_for_refinement) -# self.VALIDATEbutton = gtk.Button(label="validate structure") -# self.DEPOSITbutton = gtk.Button(label="prepare for deposition") + # self.VALIDATEbutton = gtk.Button(label="validate structure") + # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") @@ -691,10 +695,10 @@ def ChooseXtal(self, widget): self.merge_ligand_button.set_sensitive(True) self.place_ligand_here_button.set_sensitive(True) - self.ligand_site_name_value.set_label('-') - self.ligand_inspect_confidence_value.set_label('-') - self.ligand_inspect_interesting_value.set_label('-') - self.ligand_inspect_comment_value.set_label('-') + self.ligand_site_name_value.set_label("-") + self.ligand_inspect_confidence_value.set_label("-") + self.ligand_inspect_interesting_value.set_label("-") + self.ligand_inspect_comment_value.set_label("-") self.refresh_site_combobox() self.db_dict_mainTable = {} @@ -704,7 +708,9 @@ def ChooseXtal(self, widget): self.refinement_folder = str(self.Todo[self.index][4]) self.refinement_outcome = str(self.Todo[self.index][5]) self.update_RefinementOutcome_radiobutton() - if self.xtalID not in self.siteDict: # i.e. we are not working with a PanDDA model + if ( + self.xtalID not in self.siteDict + ): # i.e. we are not working with a PanDDA model self.ligand_confidence = str(self.Todo[self.index][6]) self.update_LigandConfidence_radiobutton() @@ -726,7 +732,7 @@ def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 for i, entry in enumerate(self.ligand_confidence_category): - print('--->', entry, self.ligand_confidence) + print("--->", entry, self.ligand_confidence) try: if entry.split()[0] == self.ligand_confidence.split()[0]: current_stage = i @@ -744,13 +750,12 @@ def refresh_site_combobox(self): # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites for n in range(-1, 100): self.cb_site.remove_text(0) - self.site_index = '0' - self.event_index = '0' + self.site_index = "0" + self.event_index = "0" # only repopulate if site exists if self.xtalID in self.siteDict: for item in sorted(self.siteDict[self.xtalID]): - self.cb_site.append_text( - 'site: %s - event: %s' % (item[5], item[6])) + self.cb_site.append_text("site: %s - event: %s" % (item[5], item[6])) def ChangeSite(self, widget, data=None): if self.xtalID in self.siteDict: @@ -781,84 +786,105 @@ def RefreshSiteData(self): # and remove ligand molecule so that there is no temptation to merge it if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): - if self.compoundID+'.pdb' in coot.molecule_name(imol): + if self.compoundID + ".pdb" in coot.molecule_name(imol): coot.close_molecule(imol) - print('pandda index', self.pandda_index) + print("pandda index", self.pandda_index) self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] - print('new spider plot:', self.spider_plot) + print("new spider plot:", self.spider_plot) self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] - print('new event map:', self.event_map) - self.ligand_confidence = str( - self.siteDict[self.xtalID][self.pandda_index][7]) + print("new event map:", self.event_map) + self.ligand_confidence = str(self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) - print('new site coordinates:', site_x, site_y, site_z) + print("new site coordinates:", site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) self.ligand_site_name_value.set_label( - str(self.siteDict[self.xtalID][self.pandda_index][8])) + str(self.siteDict[self.xtalID][self.pandda_index][8]) + ) self.ligand_inspect_confidence_value.set_label( - str(self.siteDict[self.xtalID][self.pandda_index][9])) + str(self.siteDict[self.xtalID][self.pandda_index][9]) + ) self.ligand_inspect_interesting_value.set_label( - str(self.siteDict[self.xtalID][self.pandda_index][10])) + str(self.siteDict[self.xtalID][self.pandda_index][10]) + ) self.ligand_inspect_comment_value.set_label( - str(self.siteDict[self.xtalID][self.pandda_index][11])) - - self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event( - self.xtalID, self.site_index, self.event_index) - print('>>>>> spider plot data', self.spider_plot_data) - self.ligandIDValue.set_label( - self.spider_plot_data['PANDDA_site_ligand_id']) + str(self.siteDict[self.xtalID][self.pandda_index][11]) + ) + + self.spider_plot_data = ( + self.db.get_db_pandda_dict_for_sample_and_site_and_event( + self.xtalID, self.site_index, self.event_index + ) + ) + print(">>>>> spider plot data", self.spider_plot_data) + self.ligandIDValue.set_label(self.spider_plot_data["PANDDA_site_ligand_id"]) try: self.ligand_occupancyValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_occupancy"]), 2)) + ) except ValueError: - self.ligand_occupancyValue.set_label('-') + self.ligand_occupancyValue.set_label("-") try: self.ligand_BaverageValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_B_average"]), 2)) + ) except ValueError: - self.ligand_BaverageValue.set_label('-') + self.ligand_BaverageValue.set_label("-") try: - self.ligand_BratioSurroundingsValue.set_label(str(round( - float(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']), 2))) + self.ligand_BratioSurroundingsValue.set_label( + str( + round( + float( + self.spider_plot_data[ + "PANDDA_site_B_ratio_residue_surroundings" + ] + ), + 2, + ) + ) + ) except ValueError: - self.ligand_BratioSurroundingsValue.set_label('-') + self.ligand_BratioSurroundingsValue.set_label("-") try: self.ligand_RSCCValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSCC"]), 2)) + ) except ValueError: - self.ligand_RSCCValue.set_label('-') + self.ligand_RSCCValue.set_label("-") try: self.ligand_rmsdValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_rmsd"]), 2)) + ) except ValueError: - self.ligand_rmsdValue.set_label('-') + self.ligand_rmsdValue.set_label("-") try: self.ligand_RSRValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSR"]), 2)) + ) except ValueError: - self.ligand_RSRValue.set_label('-') + self.ligand_RSRValue.set_label("-") try: self.ligand_RSZDValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSZD"]), 2)) + ) except ValueError: - self.ligand_RSZDValue.set_label('-') + self.ligand_RSZDValue.set_label("-") ######################################################################################### # delete old Event MAPs if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): - if 'map.native.ccp4' in coot.molecule_name(imol): + if "map.native.ccp4" in coot.molecule_name(imol): coot.close_molecule(imol) ######################################################################################### @@ -867,10 +893,16 @@ def RefreshSiteData(self): if os.path.isfile(self.spider_plot): spider_plot_pic = gtk.gdk.pixbuf_new_from_file(self.spider_plot) else: - spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join( - os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + spider_plot_pic = gtk.gdk.pixbuf_new_from_file( + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_SPIDER_PLOT_AVAILABLE.png", + ) + ) self.spider_plot_pic = spider_plot_pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + 190, 190, gtk.gdk.INTERP_BILINEAR + ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) ######################################################################################### @@ -880,59 +912,101 @@ def RefreshSiteData(self): for imol in coot_utils_XChem.molecule_number_list(): if self.event_map in coot.molecule_name(imol): coot.set_contour_level_in_sigma(imol, 2) -# coot.set_contour_level_absolute(imol,0.5) -# coot.set_last_map_colour(0.4,0,0.4) + # coot.set_contour_level_absolute(imol,0.5) + # coot.set_last_map_colour(0.4,0,0.4) coot.set_last_map_colour(0.74, 0.44, 0.02) def experiment_stage_button_clicked(self, widget, data=None): - self.db_dict_mainTable['RefinementOutcome'] = data - print('==> XCE: setting Refinement Outcome for ' + \ - self.xtalID+' to '+str(data)+' in mainTable of datasource') + self.db_dict_mainTable["RefinementOutcome"] = data + print( + "==> XCE: setting Refinement Outcome for " + + self.xtalID + + " to " + + str(data) + + " in mainTable of datasource" + ) self.db.update_data_source(self.xtalID, self.db_dict_mainTable) def ligand_confidence_button_clicked(self, widget, data=None): - print('PANDDA_index', self.pandda_index) + print("PANDDA_index", self.pandda_index) if self.pandda_index == -1: - self.db_dict_mainTable['RefinementLigandConfidence'] = data - print('==> XCE: setting Ligand Confidence for ' + \ - self.xtalID+' to '+str(data)+' in mainTable of datasource') + self.db_dict_mainTable["RefinementLigandConfidence"] = data + print( + "==> XCE: setting Ligand Confidence for " + + self.xtalID + + " to " + + str(data) + + " in mainTable of datasource" + ) self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.Todo[self.index][6] = data else: - self.db_dict_panddaTable['PANDDA_site_confidence'] = data - print('==> XCE: setting Ligand Confidence for '+self.xtalID + \ - ' (site='+str(self.site_index)+', event='+str(self.event_index) + \ - ') to '+str(data)+' in panddaTable of datasource') + self.db_dict_panddaTable["PANDDA_site_confidence"] = data + print( + "==> XCE: setting Ligand Confidence for " + + self.xtalID + + " (site=" + + str(self.site_index) + + ", event=" + + str(self.event_index) + + ") to " + + str(data) + + " in panddaTable of datasource" + ) self.db.update_site_event_panddaTable( - self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable) + self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable + ) self.siteDict[self.xtalID][self.pandda_index][7] = data def RefreshData(self): # reset spider plot image - spider_plot_pic = gtk.gdk.pixbuf_new_from_file(os.path.join( - os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + spider_plot_pic = gtk.gdk.pixbuf_new_from_file( + os.path.join( + os.getenv("XChemExplorer_DIR"), "image", "NO_SPIDER_PLOT_AVAILABLE.png" + ) + ) self.spider_plot_pic = spider_plot_pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + 190, 190, gtk.gdk.INTERP_BILINEAR + ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) # initialize Refinement library self.Refine = XChemRefine.RefineOld( - self.project_directory, self.xtalID, self.compoundID, self.data_source) + self.project_directory, self.xtalID, self.compoundID, self.data_source + ) self.Serial = self.Refine.GetSerial() if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): - print('==> XCE: updating quality indicators in data source for '+self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, self.pdb_style)) + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, self.pdb_style), + ) XChemUtils.parse().update_datasource_with_phenix_validation_summary( - self.xtalID, self.data_source, '') # '' because file does not exist - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): - print('==> XCE: updating quality indicators in data source for '+self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')) + self.xtalID, self.data_source, "" + ) # '' because file does not exist + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple.pdb") + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, "dimple.pdb"), + ) XChemUtils.parse().update_datasource_with_phenix_validation_summary( - self.xtalID, self.data_source, '') # '' because file does not exist + self.xtalID, self.data_source, "" + ) # '' because file does not exist # all this information is now updated in the datasource after each refinement cycle self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) @@ -940,17 +1014,16 @@ def RefreshData(self): ######################################################################################### # history # if the structure was previously refined, try to read the parameters -# self.hbox_for_info_graphics.remove(self.canvas) + # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: - self.RefmacParams = self.Refine.ParamsFromPreviousCycle( - self.Serial-1) -# refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() -# self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) -# else: -# self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea -# self.canvas.set_size_request(190, 190) -# self.hbox_for_info_graphics.add(self.canvas) -# self.canvas.show() + self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) + # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() + # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) + # else: + # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea + # self.canvas.set_size_request(190, 190) + # self.hbox_for_info_graphics.add(self.canvas) + # self.canvas.show() ######################################################################################### # update pdb & maps @@ -967,33 +1040,50 @@ def RefreshData(self): # read new PDB files # read protein molecule after ligand so that this one is the active molecule coot.set_nomenclature_errors_on_read("ignore") - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID+'.pdb')): - imol = coot.handle_read_draw_molecule_with_recentre(os.path.join( - self.project_directory, self.xtalID, self.compoundID+'.pdb'), 0) - self.mol_dict['ligand'] = imol - coot.read_cif_dictionary(os.path.join( - self.project_directory, self.xtalID, self.compoundID+'.cif')) - if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.compoundID + ".pdb") + ): + imol = coot.handle_read_draw_molecule_with_recentre( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".pdb" + ), + 0, + ) + self.mol_dict["ligand"] = imol + coot.read_cif_dictionary( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".cif" + ) + ) + if not os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) # we want to be able to check dimple results immediately, but don't want to interfere with refinement -# if not os.path.isfile('REFINEMENT_IN_PROGRESS'): -# if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-ensemble-model.pdb')): -# os.symlink(self.xtalID+'-ensemble-model.pdb',self.pdb_style) -# elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.pdb')): -# os.symlink('dimple.pdb',self.pdb_style) -# else: -# self.go_to_next_xtal() - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + # if not os.path.isfile('REFINEMENT_IN_PROGRESS'): + # if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-ensemble-model.pdb')): + # os.symlink(self.xtalID+'-ensemble-model.pdb',self.pdb_style) + # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.pdb')): + # os.symlink('dimple.pdb',self.pdb_style) + # else: + # self.go_to_next_xtal() + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.pdb')): + os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0 + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple.pdb") + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, 'dimple.pdb'), 0) + os.path.join(self.project_directory, self.xtalID, "dimple.pdb"), 0 + ) else: self.go_to_next_xtal() - self.mol_dict['protein'] = imol + self.mol_dict["protein"] = imol for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith(self.pdb_style): # master switch to show symmetry molecules @@ -1004,95 +1094,139 @@ def RefreshData(self): # read fofo maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "2fofc.map") + ): coot.set_default_initial_contour_level_for_difference_map(3) - coot.handle_read_ccp4_map(os.path.join( - self.project_directory, self.xtalID, 'fofc.map'), 1) + coot.handle_read_ccp4_map( + os.path.join(self.project_directory, self.xtalID, "fofc.map"), 1 + ) coot.set_default_initial_contour_level_for_map(1) - coot.handle_read_ccp4_map(os.path.join( - self.project_directory, self.xtalID, '2fofc.map'), 0) + coot.handle_read_ccp4_map( + os.path.join(self.project_directory, self.xtalID, "2fofc.map"), 0 + ) coot.set_last_map_colour(0, 0, 1) else: # try to open mtz file with same name as pdb file coot.set_default_initial_contour_level_for_map(1) -# if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): -# os.chdir(os.path.join(self.project_directory,self.xtalID)) -# if not os.path.isfile('REFINEMENT_IN_PROGRESS'): -# if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-pandda-input.mtz')): -# os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) -# elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): -# os.symlink('dimple.mtz',self.mtz_style) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, self.mtz_style)) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, 'dimple.mtz')) + # if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): + # os.chdir(os.path.join(self.project_directory,self.xtalID)) + # if not os.path.isfile('REFINEMENT_IN_PROGRESS'): + # if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-pandda-input.mtz')): + # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) + # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): + # os.symlink('dimple.mtz',self.mtz_style) + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.mtz_style) + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, self.mtz_style) + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple.mtz") + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, "dimple.mtz") + ) ######################################################################################### # update Quality Indicator table try: - self.RRfreeValue.set_label(str(round(float(self.QualityIndicators['RefinementRcryst']), 3)) + ' / '+str( - round(float(self.QualityIndicators['RefinementRfree']), 3))) + self.RRfreeValue.set_label( + str(round(float(self.QualityIndicators["RefinementRcryst"]), 3)) + + " / " + + str(round(float(self.QualityIndicators["RefinementRfree"]), 3)) + ) except ValueError: - self.RRfreeValue.set_label('-') + self.RRfreeValue.set_label("-") try: - self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRfreeTraficLight'])) + self.RRfreeBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRfreeTraficLight"] + ), + ) except ValueError: pass - self.ResolutionValue.set_label( - self.QualityIndicators['RefinementResolution']) + self.ResolutionValue.set_label(self.QualityIndicators["RefinementResolution"]) try: - self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementResolutionTL'])) + self.ResolutionBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementResolutionTL"]), + ) except ValueError: pass self.MolprobityScoreValue.set_label( - self.QualityIndicators['RefinementMolProbityScore']) + self.QualityIndicators["RefinementMolProbityScore"] + ) try: - self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementMolProbityScoreTL'])) + self.MolprobityScoreBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementMolProbityScoreTL"] + ), + ) except ValueError: pass self.RamachandranOutliersValue.set_label( - self.QualityIndicators['RefinementRamachandranOutliers']) + self.QualityIndicators["RefinementRamachandranOutliers"] + ) try: - self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRamachandranOutliersTL'])) + self.RamachandranOutliersBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRamachandranOutliersTL"] + ), + ) except ValueError: pass self.RamachandranFavoredValue.set_label( - self.QualityIndicators['RefinementRamachandranFavored']) + self.QualityIndicators["RefinementRamachandranFavored"] + ) try: - self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRamachandranFavoredTL'])) + self.RamachandranFavoredBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRamachandranFavoredTL"] + ), + ) except ValueError: pass - self.rmsdBondsValue.set_label( - self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue.set_label(self.QualityIndicators["RefinementRmsdBonds"]) try: - self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRmsdBondsTL'])) + self.rmsdBondsBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementRmsdBondsTL"]), + ) except ValueError: pass - self.rmsdAnglesValue.set_label( - self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue.set_label(self.QualityIndicators["RefinementRmsdAngles"]) try: - self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRmsdAnglesTL'])) + self.rmsdAnglesBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementRmsdAnglesTL"]), + ) except ValueError: pass self.MatrixWeightValue.set_label( - self.QualityIndicators['RefinementMatrixWeight']) + self.QualityIndicators["RefinementMatrixWeight"] + ) try: - pic = gtk.gdk.pixbuf_new_from_file(os.path.join( - self.project_directory, self.xtalID, self.compoundID+'.png')) + pic = gtk.gdk.pixbuf_new_from_file( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".png" + ) + ) except gobject.GError: - pic = gtk.gdk.pixbuf_new_from_file(os.path.join( - os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + pic = gtk.gdk.pixbuf_new_from_file( + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_COMPOUND_IMAGE_AVAILABLE.png", + ) + ) self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.image.set_from_pixbuf(self.pic) @@ -1106,8 +1240,11 @@ def REFINE(self, widget): ####################################################### # create folder for new refinement cycle - os.mkdir(os.path.join(self.project_directory, - self.xtalID, 'Refine_'+str(self.Serial))) + os.mkdir( + os.path.join( + self.project_directory, self.xtalID, "Refine_" + str(self.Serial) + ) + ) ####################################################### # write PDB file @@ -1115,18 +1252,33 @@ def REFINE(self, widget): # note: the user has to make sure that the ligand file was merged into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith(self.pdb_style): - coot.write_pdb_file(item, os.path.join( - self.project_directory, self.xtalID, 'Refine_'+str(self.Serial), 'in.pdb')) + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) break - elif coot.molecule_name(item).endswith('dimple.pdb'): - coot.write_pdb_file(item, os.path.join( - self.project_directory, self.xtalID, 'Refine_'+str(self.Serial), 'in.pdb')) + elif coot.molecule_name(item).endswith("dimple.pdb"): + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) break ####################################################### # run REFMAC - self.Refine.RunRefmac(self.Serial, self.RefmacParams, - self.external_software, self.xce_logfile) + self.Refine.RunRefmac( + self.Serial, self.RefmacParams, self.external_software, self.xce_logfile + ) self.index += 1 if self.index >= len(self.Todo): @@ -1135,29 +1287,28 @@ def REFINE(self, widget): self.cb.set_active(self.index) def RefinementParams(self, widget): - print('\n==> XCE: changing refinement parameters') + print("\n==> XCE: changing refinement parameters") self.RefmacParams = self.Refine.RefinementParams(self.RefmacParams) def set_selection_mode(self, widget): self.selection_mode = widget.get_active_text() def get_samples_to_look_at(self, widget): - if self.selection_mode == '': - self.status_label.set_text('select model stage') + if self.selection_mode == "": + self.status_label.set_text("select model stage") return - self.status_label.set_text('checking datasource for samples... ') + self.status_label.set_text("checking datasource for samples... ") # first remove old samples if present if len(self.Todo) != 0: for n, item in enumerate(self.Todo): self.cb.remove_text(0) self.Todo = [] self.siteDict = {} - self.Todo, self.siteDict = self.db.get_todoList_for_coot( - self.selection_mode) - self.status_label.set_text('found %s samples' % len(self.Todo)) + self.Todo, self.siteDict = self.db.get_todoList_for_coot(self.selection_mode) + self.status_label.set_text("found %s samples" % len(self.Todo)) # refresh sample CB for item in sorted(self.Todo): - self.cb.append_text('%s' % item[0]) + self.cb.append_text("%s" % item[0]) if self.siteDict == {}: self.cb_site.set_sensitive(False) self.PREVbuttonSite.set_sensitive(False) @@ -1170,41 +1321,66 @@ def get_samples_to_look_at(self, widget): def update_plot(self, refinement_cycle, Rfree, Rcryst): fig = Figure(figsize=(2, 2), dpi=50) Plot = fig.add_subplot(111) - Plot.set_ylim([0, max(Rcryst+Rfree)]) - Plot.set_xlabel('Refinement Cycle', fontsize=12) - Plot.plot(refinement_cycle, Rfree, label='Rfree', linewidth=2) - Plot.plot(refinement_cycle, Rcryst, label='Rcryst', linewidth=2) - Plot.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, - ncol=2, mode="expand", borderaxespad=0., fontsize=12) + Plot.set_ylim([0, max(Rcryst + Rfree)]) + Plot.set_xlabel("Refinement Cycle", fontsize=12) + Plot.plot(refinement_cycle, Rfree, label="Rfree", linewidth=2) + Plot.plot(refinement_cycle, Rcryst, label="Rcryst", linewidth=2) + Plot.legend( + bbox_to_anchor=(0.0, 1.02, 1.0, 0.102), + loc=3, + ncol=2, + mode="expand", + borderaxespad=0.0, + fontsize=12, + ) return fig def place_ligand_here(self, widget): - print('===> XCE: moving ligand to pointer') -# coot.move_molecule_here() - print('LIGAND: ', self.mol_dict['ligand']) - coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) + print("===> XCE: moving ligand to pointer") + # coot.move_molecule_here() + print("LIGAND: ", self.mol_dict["ligand"]) + coot_utils_XChem.move_molecule_here(self.mol_dict["ligand"]) def merge_ligand_into_protein(self, widget): - print('===> XCE: merge ligand into protein structure') + print("===> XCE: merge ligand into protein structure") # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) - coot.merge_molecules_py( - [self.mol_dict['ligand']], self.mol_dict['protein']) - print('===> XCE: deleting ligand molecule') - coot.close_molecule(self.mol_dict['ligand']) + coot.merge_molecules_py([self.mol_dict["ligand"]], self.mol_dict["protein"]) + print("===> XCE: deleting ligand molecule") + coot.close_molecule(self.mol_dict["ligand"]) def show_molprobity_to_do(self, widget): - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')): - print('==> XCE: running MolProbity Summary for', self.xtalID) - coot.run_script(os.path.join(self.project_directory, self.xtalID, - 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')) + if os.path.isfile( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ): + print("==> XCE: running MolProbity Summary for", self.xtalID) + coot.run_script( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ) else: - print('==> XCE: cannot find ' + \ - os.path.join(self.project_directory, self.xtalID, - 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')) + print( + "==> XCE: cannot find " + + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ) + # def fit_ligand(self,widget): # print 'fit' -if __name__ == '__main__': +if __name__ == "__main__": GUI().StartGUI() diff --git a/lib/XChemCootReference.py b/lib/XChemCootReference.py index c291fbeb..da710406 100755 --- a/lib/XChemCootReference.py +++ b/lib/XChemCootReference.py @@ -11,18 +11,19 @@ import pickle import time import gtk -#import threading -#import gobject + +# import threading +# import gobject # gtk.gdk.threads_init() from matplotlib.figure import Figure from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas # XCE libraries -sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") # libraries from COOT -#import pygtk, gtk, pango +# import pygtk, gtk, pango # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. @@ -40,41 +41,42 @@ def __init__(self): ########################################################################################### # read in settings file from XChemExplorer to set the relevant paths self.settings = pickle.load(open(".xce_settings.pkl", "rb")) - remote_qsub_submission = self.settings['remote_qsub'] - self.database_directory = self.settings['database_directory'] - self.xce_logfile = self.settings['xce_logfile'] + remote_qsub_submission = self.settings["remote_qsub"] + self.database_directory = self.settings["database_directory"] + self.xce_logfile = self.settings["xce_logfile"] self.Logfile = XChemLog.updateLog(self.xce_logfile) - self.Logfile.insert('starting COOT gui for reference model refinement') - self.data_source = self.settings['data_source'] + self.Logfile.insert("starting COOT gui for reference model refinement") + self.data_source = self.settings["data_source"] # checking for external software packages - self.external_software = XChemUtils.external_software( - self.xce_logfile).check() - self.external_software['qsub_remote'] = remote_qsub_submission + self.external_software = XChemUtils.external_software(self.xce_logfile).check() + self.external_software["qsub_remote"] = remote_qsub_submission # the Folder is kind of a legacy thing because my inital idea was to have separate folders # for Data Processing and Refinement - self.reference_directory = self.settings['reference_directory'] - self.refinementDir = '' + self.reference_directory = self.settings["reference_directory"] + self.refinementDir = "" self.Serial = 0 self.Refine = None - self.xtalID = '' - self.compoundID = '' - self.spider_plot = '' - self.refinement_folder = '' - self.pdbFile = '' - self.mtzFree = '' + self.xtalID = "" + self.compoundID = "" + self.spider_plot = "" + self.refinement_folder = "" + self.pdbFile = "" + self.mtzFree = "" - self.pdb_style = 'refine.pdb' - self.mtz_style = 'refine.mtz' + self.pdb_style = "refine.pdb" + self.mtz_style = "refine.mtz" # stores imol of currently loaded molecules and maps - self.mol_dict = {'protein': -1, - 'ligand': -1, - '2fofc': -1, - 'fofc': -1, - 'event': -1} + self.mol_dict = { + "protein": -1, + "ligand": -1, + "2fofc": -1, + "fofc": -1, + "event": -1, + } self.ground_state_map_List = [] self.job_running = False @@ -83,37 +85,45 @@ def __init__(self): # some COOT settings coot.set_map_radius(17) coot.set_colour_map_rotation_for_map(0) -# coot.set_colour_map_rotation_on_read_pdb_flag(21) - - self.QualityIndicators = {'Rcryst': '-', - 'Rfree': '-', - 'RfreeTL': 'gray', - 'ResolutionHigh': '-', - 'ResolutionColor': 'gray', - 'MolprobityScore': '-', - 'MolprobityScoreColor': 'gray', - 'RamachandranOutliers': '-', - 'RamachandranOutliersColor': 'gray', - 'RamachandranFavored': '-', - 'RamachandranFavoredColor': 'gray', - 'rmsdBonds': '-', - 'rmsdBondsTL': 'gray', - 'rmsdAngles': '-', - 'rmsdAnglesTL': 'gray', - 'MatrixWeight': '-'} + # coot.set_colour_map_rotation_on_read_pdb_flag(21) + + self.QualityIndicators = { + "Rcryst": "-", + "Rfree": "-", + "RfreeTL": "gray", + "ResolutionHigh": "-", + "ResolutionColor": "gray", + "MolprobityScore": "-", + "MolprobityScoreColor": "gray", + "RamachandranOutliers": "-", + "RamachandranOutliersColor": "gray", + "RamachandranFavored": "-", + "RamachandranFavoredColor": "gray", + "rmsdBonds": "-", + "rmsdBondsTL": "gray", + "rmsdAngles": "-", + "rmsdAnglesTL": "gray", + "MatrixWeight": "-", + } # default refmac parameters - self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': ''} + self.RefmacParams = { + "HKLIN": "", + "HKLOUT": "", + "XYZIN": "", + "XYZOUT": "", + "LIBIN": "", + "LIBOUT": "", + "TLSIN": "", + "TLSOUT": "", + "TLSADD": "", + "NCYCLES": "10", + "MATRIX_WEIGHT": "AUTO", + "BREF": " bref ISOT\n", + "TLS": "", + "NCS": "", + "TWIN": "", + } def StartGUI(self): @@ -122,19 +132,21 @@ def StartGUI(self): self.window.set_border_width(10) self.window.set_default_size(400, 800) self.window.set_title("Reference Model Builder") - self.vbox = gtk.VBox() # this is the main container + self.vbox = gtk.VBox() # this is the main container ################################################################################# # --- PDB file selection --- # checking for pdb files in reference directory referenceFiles = [] - for files in glob.glob(os.path.join(self.reference_directory, '*-ground-state.pdb')): - pdbFile = files[files.rfind('/')+1:] + for files in glob.glob( + os.path.join(self.reference_directory, "*-ground-state.pdb") + ): + pdbFile = files[files.rfind("/") + 1 :] referenceFiles.append(pdbFile) - frame = gtk.Frame(label='Select PDB file') + frame = gtk.Frame(label="Select PDB file") hbox = gtk.HBox() self.cb_select_pdb = gtk.combo_box_new_text() -# self.cb_select_pdb.connect("changed", self.set_selection_mode) + # self.cb_select_pdb.connect("changed", self.set_selection_mode) for pdbFile in referenceFiles: self.cb_select_pdb.append_text(pdbFile) hbox.add(self.cb_select_pdb) @@ -142,27 +154,27 @@ def StartGUI(self): self.vbox.pack_start(frame) self.load_pdb_file_button = gtk.Button(label="Load") -# self.load_pdb_file_button.connect("clicked",self.get_samples_to_look_at) + # self.load_pdb_file_button.connect("clicked",self.get_samples_to_look_at) self.load_pdb_file_button.connect("clicked", self.load_pdb_file) hbox.add(self.load_pdb_file_button) frame.add(hbox) self.vbox.pack_start(frame) # SPACER - self.vbox.add(gtk.Label(' ')) + self.vbox.add(gtk.Label(" ")) - frame = gtk.Frame(label='MTZ file to refine against') + frame = gtk.Frame(label="MTZ file to refine against") hbox = gtk.HBox() - self.mtzFree = '' + self.mtzFree = "" self.mtzFree_label = gtk.Label() hbox.add(self.mtzFree_label) frame.add(hbox) self.vbox.pack_start(frame) # SPACER - self.vbox.add(gtk.Label(' ')) + self.vbox.add(gtk.Label(" ")) - frame = gtk.Frame(label='MTZ file after refinement') + frame = gtk.Frame(label="MTZ file after refinement") hbox = gtk.HBox() self.mtzRefine_label = gtk.Label() hbox.add(self.mtzRefine_label) @@ -170,51 +182,51 @@ def StartGUI(self): self.vbox.pack_start(frame) # SPACER - self.vbox.add(gtk.Label(' \n ')) + self.vbox.add(gtk.Label(" \n ")) ################################################################################# # --- ground state mean map --- # checking for ground state mean map in reference folder -# self.meanMaps = {} -# for dirs in glob.glob(os.path.join(self.reference_directory,'pandda_*')): -# panddaDir=dirs.split('/')[len(dirs.split('/'))-1] -# for files in glob.glob(os.path.join(dirs,'processed_datasets','*','*ground-state-mean-map.native.ccp4')): -# if os.path.isfile(files): -# self.meanMaps[panddaDir]=files -# break - -# frame = gtk.Frame(label='Load ground-state-mean-map files') -# hbox=gtk.HBox() -# self.cb_select_mean_map = gtk.combo_box_new_text() -# for item in self.meanMaps: -# self.cb_select_mean_map.append_text(item) -# hbox.add(self.cb_select_mean_map) -# self.load_ground_state_map_button = gtk.Button(label="Load") -# self.load_ground_state_map_button.connect("clicked",self.load_ground_state_map) -# hbox.add(self.load_ground_state_map_button) -# frame.add(hbox) -# self.vbox.pack_start(frame) - -# frame = gtk.Frame() -# hbox=gtk.HBox() -# self.cb_select_mean_map_by_resolution = gtk.combo_box_new_text() -# self.cb_select_mean_map_by_resolution.connect("changed", self.show_selected_mean_map) -# hbox.add(self.cb_select_mean_map_by_resolution) -## self.show_highres_ground_state_map_button = gtk.Button(label="Show Highest\nResolution Map") -# self.show_highres_ground_state_map_button.connect("clicked",self.show_highres_ground_state_map) -# hbox.add(self.show_highres_ground_state_map_button) -## self.show_all_ground_state_map_button = gtk.Button(label="Show All Maps") -# self.show_all_ground_state_map_button.connect("clicked",self.show_all_ground_state_map) -# hbox.add(self.show_all_ground_state_map_button) -# frame.add(hbox) -# self.vbox.pack_start(frame) + # self.meanMaps = {} + # for dirs in glob.glob(os.path.join(self.reference_directory,'pandda_*')): + # panddaDir=dirs.split('/')[len(dirs.split('/'))-1] + # for files in glob.glob(os.path.join(dirs,'processed_datasets','*','*ground-state-mean-map.native.ccp4')): + # if os.path.isfile(files): + # self.meanMaps[panddaDir]=files + # break + + # frame = gtk.Frame(label='Load ground-state-mean-map files') + # hbox=gtk.HBox() + # self.cb_select_mean_map = gtk.combo_box_new_text() + # for item in self.meanMaps: + # self.cb_select_mean_map.append_text(item) + # hbox.add(self.cb_select_mean_map) + # self.load_ground_state_map_button = gtk.Button(label="Load") + # self.load_ground_state_map_button.connect("clicked",self.load_ground_state_map) + # hbox.add(self.load_ground_state_map_button) + # frame.add(hbox) + # self.vbox.pack_start(frame) + + # frame = gtk.Frame() + # hbox=gtk.HBox() + # self.cb_select_mean_map_by_resolution = gtk.combo_box_new_text() + # self.cb_select_mean_map_by_resolution.connect("changed", self.show_selected_mean_map) + # hbox.add(self.cb_select_mean_map_by_resolution) + ## self.show_highres_ground_state_map_button = gtk.Button(label="Show Highest\nResolution Map") + # self.show_highres_ground_state_map_button.connect("clicked",self.show_highres_ground_state_map) + # hbox.add(self.show_highres_ground_state_map_button) + ## self.show_all_ground_state_map_button = gtk.Button(label="Show All Maps") + # self.show_all_ground_state_map_button.connect("clicked",self.show_all_ground_state_map) + # hbox.add(self.show_all_ground_state_map_button) + # frame.add(hbox) + # self.vbox.pack_start(frame) # SPACER -# self.vbox.add(gtk.Label(' \n ')) + # self.vbox.add(gtk.Label(' \n ')) ################################################################################# # --- Refinement History --- - frame = gtk.Frame(label='Refinement History') + frame = gtk.Frame(label="Refinement History") self.hbox_for_info_graphics = gtk.HBox() self.canvas = FigureCanvas(self.update_plot([0], [0], [0])) self.canvas.set_size_request(190, 190) @@ -224,18 +236,18 @@ def StartGUI(self): ################################################################################# # --- status window --- - frame = gtk.Frame(label='Status') + frame = gtk.Frame(label="Status") vbox = gtk.VBox() self.spinnerBox = gtk.VBox() self.refinementRunning = gtk.Spinner() vbox.add(self.spinnerBox) -# hbox.add(self.refinementRunning) + # hbox.add(self.refinementRunning) self.status_label = gtk.Label() vbox.add(self.status_label) frame.add(vbox) - self.status_label.set_text('idle') + self.status_label.set_text("idle") -# frame.add(self.status_label) + # frame.add(self.status_label) self.vbox.pack_start(frame) ################################################################################# @@ -244,78 +256,78 @@ def StartGUI(self): # a combination of labels and textview widgets, arranged in a table RRfreeLabel_frame = gtk.Frame() - self.RRfreeLabel = gtk.Label('R/Rfree') + self.RRfreeLabel = gtk.Label("R/Rfree") RRfreeLabel_frame.add(self.RRfreeLabel) self.RRfreeValue = gtk.Label( - self.QualityIndicators['Rcryst']+'/'+self.QualityIndicators['Rfree']) + self.QualityIndicators["Rcryst"] + "/" + self.QualityIndicators["Rfree"] + ) RRfreeBox_frame = gtk.Frame() self.RRfreeBox = gtk.EventBox() self.RRfreeBox.add(self.RRfreeValue) RRfreeBox_frame.add(self.RRfreeBox) ResolutionLabel_frame = gtk.Frame() - self.ResolutionLabel = gtk.Label('Resolution') + self.ResolutionLabel = gtk.Label("Resolution") ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label( - self.QualityIndicators['ResolutionHigh']) + self.ResolutionValue = gtk.Label(self.QualityIndicators["ResolutionHigh"]) ResolutionBox_frame = gtk.Frame() self.ResolutionBox = gtk.EventBox() self.ResolutionBox.add(self.ResolutionValue) ResolutionBox_frame.add(self.ResolutionBox) MolprobityScoreLabel_frame = gtk.Frame() - self.MolprobityScoreLabel = gtk.Label('MolprobityScore') + self.MolprobityScoreLabel = gtk.Label("MolprobityScore") MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) - self.MolprobityScoreValue = gtk.Label( - self.QualityIndicators['MolprobityScore']) + self.MolprobityScoreValue = gtk.Label(self.QualityIndicators["MolprobityScore"]) MolprobityScoreBox_frame = gtk.Frame() self.MolprobityScoreBox = gtk.EventBox() self.MolprobityScoreBox.add(self.MolprobityScoreValue) MolprobityScoreBox_frame.add(self.MolprobityScoreBox) RamachandranOutliersLabel_frame = gtk.Frame() - self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') + self.RamachandranOutliersLabel = gtk.Label("Rama Outliers") RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) self.RamachandranOutliersValue = gtk.Label( - self.QualityIndicators['RamachandranOutliers']) + self.QualityIndicators["RamachandranOutliers"] + ) RamachandranOutliersBox_frame = gtk.Frame() self.RamachandranOutliersBox = gtk.EventBox() self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) RamachandranOutliersBox_frame.add(self.RamachandranOutliersBox) RamachandranFavoredLabel_frame = gtk.Frame() - self.RamachandranFavoredLabel = gtk.Label('Rama Favored') + self.RamachandranFavoredLabel = gtk.Label("Rama Favored") RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) self.RamachandranFavoredValue = gtk.Label( - self.QualityIndicators['RamachandranFavoredColor']) + self.QualityIndicators["RamachandranFavoredColor"] + ) RamachandranFavoredBox_frame = gtk.Frame() self.RamachandranFavoredBox = gtk.EventBox() self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) RamachandranFavoredBox_frame.add(self.RamachandranFavoredBox) rmsdBondsLabel_frame = gtk.Frame() - self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') + self.rmsdBondsLabel = gtk.Label("rmsd(Bonds)") rmsdBondsLabel_frame.add(self.rmsdBondsLabel) - self.rmsdBondsValue = gtk.Label(self.QualityIndicators['rmsdBonds']) + self.rmsdBondsValue = gtk.Label(self.QualityIndicators["rmsdBonds"]) rmsdBondsBox_frame = gtk.Frame() self.rmsdBondsBox = gtk.EventBox() self.rmsdBondsBox.add(self.rmsdBondsValue) rmsdBondsBox_frame.add(self.rmsdBondsBox) rmsdAnglesLabel_frame = gtk.Frame() - self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') + self.rmsdAnglesLabel = gtk.Label("rmsd(Angles)") rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) - self.rmsdAnglesValue = gtk.Label(self.QualityIndicators['rmsdAngles']) + self.rmsdAnglesValue = gtk.Label(self.QualityIndicators["rmsdAngles"]) rmsdAnglesBox_frame = gtk.Frame() self.rmsdAnglesBox = gtk.EventBox() self.rmsdAnglesBox.add(self.rmsdAnglesValue) rmsdAnglesBox_frame.add(self.rmsdAnglesBox) MatrixWeightLabel_frame = gtk.Frame() - self.MatrixWeightLabel = gtk.Label('Matrix Weight') + self.MatrixWeightLabel = gtk.Label("Matrix Weight") MatrixWeightLabel_frame.add(self.MatrixWeightLabel) - self.MatrixWeightValue = gtk.Label( - self.QualityIndicators['MatrixWeight']) + self.MatrixWeightValue = gtk.Label(self.QualityIndicators["MatrixWeight"]) MatrixWeightBox_frame = gtk.Frame() self.MatrixWeightBox = gtk.EventBox() self.MatrixWeightBox.add(self.MatrixWeightValue) @@ -326,22 +338,22 @@ def StartGUI(self): frame = gtk.Frame() self.table_left = gtk.Table(8, 2, False) - self.table_left.attach(RRfreeLabel_frame, 0, 1, 0, 1) - self.table_left.attach(ResolutionLabel_frame, 0, 1, 1, 2) - self.table_left.attach(MolprobityScoreLabel_frame, 0, 1, 2, 3) - self.table_left.attach(RamachandranOutliersLabel_frame, 0, 1, 3, 4) - self.table_left.attach(RamachandranFavoredLabel_frame, 0, 1, 4, 5) - self.table_left.attach(rmsdBondsLabel_frame, 0, 1, 5, 6) - self.table_left.attach(rmsdAnglesLabel_frame, 0, 1, 6, 7) - self.table_left.attach(MatrixWeightLabel_frame, 0, 1, 7, 8) - self.table_left.attach(RRfreeBox_frame, 1, 2, 0, 1) - self.table_left.attach(ResolutionBox_frame, 1, 2, 1, 2) - self.table_left.attach(MolprobityScoreBox_frame, 1, 2, 2, 3) - self.table_left.attach(RamachandranOutliersBox_frame, 1, 2, 3, 4) - self.table_left.attach(RamachandranFavoredBox_frame, 1, 2, 4, 5) - self.table_left.attach(rmsdBondsBox_frame, 1, 2, 5, 6) - self.table_left.attach(rmsdAnglesBox_frame, 1, 2, 6, 7) - self.table_left.attach(MatrixWeightBox_frame, 1, 2, 7, 8) + self.table_left.attach(RRfreeLabel_frame, 0, 1, 0, 1) + self.table_left.attach(ResolutionLabel_frame, 0, 1, 1, 2) + self.table_left.attach(MolprobityScoreLabel_frame, 0, 1, 2, 3) + self.table_left.attach(RamachandranOutliersLabel_frame, 0, 1, 3, 4) + self.table_left.attach(RamachandranFavoredLabel_frame, 0, 1, 4, 5) + self.table_left.attach(rmsdBondsLabel_frame, 0, 1, 5, 6) + self.table_left.attach(rmsdAnglesLabel_frame, 0, 1, 6, 7) + self.table_left.attach(MatrixWeightLabel_frame, 0, 1, 7, 8) + self.table_left.attach(RRfreeBox_frame, 1, 2, 0, 1) + self.table_left.attach(ResolutionBox_frame, 1, 2, 1, 2) + self.table_left.attach(MolprobityScoreBox_frame, 1, 2, 2, 3) + self.table_left.attach(RamachandranOutliersBox_frame, 1, 2, 3, 4) + self.table_left.attach(RamachandranFavoredBox_frame, 1, 2, 4, 5) + self.table_left.attach(rmsdBondsBox_frame, 1, 2, 5, 6) + self.table_left.attach(rmsdAnglesBox_frame, 1, 2, 6, 7) + self.table_left.attach(MatrixWeightBox_frame, 1, 2, 7, 8) frame.add(self.table_left) hbox.add(frame) @@ -354,7 +366,7 @@ def StartGUI(self): self.vbox.pack_start(frame) # SPACER - self.vbox.add(gtk.Label(' ')) + self.vbox.add(gtk.Label(" ")) # --- refinement & options --- self.hbox_for_refinement = gtk.HBox() @@ -381,23 +393,28 @@ def RefreshData(self): # initialize Refinement library self.Refine = XChemRefine.Refine( - self.reference_directory, self.refinementDir, 'dummy_compound_ID', 'dummy_database') + self.reference_directory, + self.refinementDir, + "dummy_compound_ID", + "dummy_database", + ) self.Serial = self.Refine.GetSerial() - print('====> Serial', self.Serial) + print("====> Serial", self.Serial) ######################################################################################### # history # if the structure was previously refined, try to read the parameters self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: - self.RefmacParams = self.Refine.ParamsFromPreviousCycle( - self.Serial-1) + self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) refinement_cycle, Rfree, Rcryst = self.Refine.GetRefinementHistory() self.canvas = FigureCanvas( - self.update_plot(refinement_cycle, Rfree, Rcryst)) + self.update_plot(refinement_cycle, Rfree, Rcryst) + ) else: - self.canvas = FigureCanvas(self.update_plot( - [0], [0], [0])) # a gtk.DrawingArea + self.canvas = FigureCanvas( + self.update_plot([0], [0], [0]) + ) # a gtk.DrawingArea self.canvas.set_size_request(190, 190) self.hbox_for_info_graphics.add(self.canvas) self.canvas.show() @@ -406,75 +423,111 @@ def RefreshData(self): # update Quality Indicator table print(self.QualityIndicators) try: - self.RRfreeValue.set_label(str(round(float( - self.QualityIndicators['Rcryst']), 3)) + ' / '+str(round(float(self.QualityIndicators['Rfree']), 3))) + self.RRfreeValue.set_label( + str(round(float(self.QualityIndicators["Rcryst"]), 3)) + + " / " + + str(round(float(self.QualityIndicators["Rfree"]), 3)) + ) except ValueError: - self.RRfreeValue.set_label('-') + self.RRfreeValue.set_label("-") try: - self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RfreeTL'])) + self.RRfreeBox.modify_bg( + gtk.STATE_NORMAL, gtk.gdk.color_parse(self.QualityIndicators["RfreeTL"]) + ) except ValueError: pass - self.ResolutionValue.set_label( - self.QualityIndicators['ResolutionHigh']) + self.ResolutionValue.set_label(self.QualityIndicators["ResolutionHigh"]) try: - self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['ResolutionColor'])) + self.ResolutionBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["ResolutionColor"]), + ) except ValueError: pass - self.MolprobityScoreValue.set_label( - self.QualityIndicators['MolprobityScore']) + self.MolprobityScoreValue.set_label(self.QualityIndicators["MolprobityScore"]) try: - self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['MolprobityScoreColor'])) + self.MolprobityScoreBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["MolprobityScoreColor"]), + ) except ValueError: pass self.RamachandranOutliersValue.set_label( - self.QualityIndicators['RamachandranOutliers']) + self.QualityIndicators["RamachandranOutliers"] + ) try: - self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RamachandranOutliersColor'])) + self.RamachandranOutliersBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RamachandranOutliersColor"] + ), + ) except ValueError: pass self.RamachandranFavoredValue.set_label( - self.QualityIndicators['RamachandranFavored']) + self.QualityIndicators["RamachandranFavored"] + ) try: - self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RamachandranFavoredColor'])) + self.RamachandranFavoredBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RamachandranFavoredColor"]), + ) except ValueError: pass - self.rmsdBondsValue.set_label(self.QualityIndicators['rmsdBonds']) + self.rmsdBondsValue.set_label(self.QualityIndicators["rmsdBonds"]) try: - self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['rmsdBondsTL'])) + self.rmsdBondsBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["rmsdBondsTL"]), + ) except ValueError: pass - self.rmsdAnglesValue.set_label(self.QualityIndicators['rmsdAngles']) + self.rmsdAnglesValue.set_label(self.QualityIndicators["rmsdAngles"]) try: - self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['rmsdAnglesTL'])) + self.rmsdAnglesBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["rmsdAnglesTL"]), + ) except ValueError: pass - self.MatrixWeightValue.set_label( - self.QualityIndicators['MatrixWeight']) + self.MatrixWeightValue.set_label(self.QualityIndicators["MatrixWeight"]) def REFINE(self, widget): if self.job_running: - coot.info_dialog('*** refinement in progress ***') + coot.info_dialog("*** refinement in progress ***") return None ####################################################### # create folder for new refinement cycle and check if free.mtz exists - if not os.path.isdir(os.path.join(self.reference_directory, self.refinementDir)): + if not os.path.isdir( + os.path.join(self.reference_directory, self.refinementDir) + ): os.mkdir(os.path.join(self.reference_directory, self.refinementDir)) - if not os.path.isdir(os.path.join(self.reference_directory, self.refinementDir, 'Refine_'+str(self.Serial))): - os.mkdir(os.path.join(self.reference_directory, - self.refinementDir, 'Refine_'+str(self.Serial))) - if not os.path.isfile(os.path.join(self.reference_directory, self.refinementDir, self.refinementDir+'.free.mtz')): + if not os.path.isdir( + os.path.join( + self.reference_directory, + self.refinementDir, + "Refine_" + str(self.Serial), + ) + ): + os.mkdir( + os.path.join( + self.reference_directory, + self.refinementDir, + "Refine_" + str(self.Serial), + ) + ) + if not os.path.isfile( + os.path.join( + self.reference_directory, + self.refinementDir, + self.refinementDir + ".free.mtz", + ) + ): os.chdir(os.path.join(self.reference_directory, self.refinementDir)) - os.symlink(self.mtzFree, self.refinementDir+'.free.mtz') + os.symlink(self.mtzFree, self.refinementDir + ".free.mtz") ####################################################### # write PDB file @@ -482,49 +535,69 @@ def REFINE(self, widget): # note: the user has to make sure that the ligand file was merged into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item) in self.pdbFile: - coot.write_pdb_file(item, os.path.join( - self.reference_directory, self.refinementDir, 'Refine_'+str(self.Serial), 'in.pdb')) + coot.write_pdb_file( + item, + os.path.join( + self.reference_directory, + self.refinementDir, + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) break - self.Refine.RunRefmac(self.Serial, self.RefmacParams, - self.external_software, self.xce_logfile, None) -# self.spinnerBox.add(self.refinementRunning) -# self.refinementRunning.start() - self.status_label.set_text('Refinement running...') + self.Refine.RunRefmac( + self.Serial, + self.RefmacParams, + self.external_software, + self.xce_logfile, + None, + ) + # self.spinnerBox.add(self.refinementRunning) + # self.refinementRunning.start() + self.status_label.set_text("Refinement running...") # waiting 1s to make sure that REFINEMENT_IN_PROGRESS is written time.sleep(1) snooze = 0 - while os.path.exists(os.path.join(self.reference_directory, self.refinementDir, 'REFINEMENT_IN_PROGRESS')): + while os.path.exists( + os.path.join( + self.reference_directory, self.refinementDir, "REFINEMENT_IN_PROGRESS" + ) + ): time.sleep(10) - print('==> XCE: waiting for refinement to finish; elapsed time = ' + \ - str(snooze) + 's') + print( + "==> XCE: waiting for refinement to finish; elapsed time = " + + str(snooze) + + "s" + ) snooze += 10 - self.update_pdb_mtz_files('') + self.update_pdb_mtz_files("") # launch refinement -# time.sleep(1) # waiting 1s to make sure that REFINEMENT_IN_PROGRESS is written -# self.source_id = gobject.timeout_add(100, self.wait_for_refined_pdb) - -# def wait_for_refined_pdb(self): -# self.spinnerBox.add(self.refinementRunning) -# self.refinementRunning.show() -# self.refinementRunning.start() -# if not os.path.isfile(os.path.join(self.reference_directory,self.refinementDir,'REFINEMENT_IN_PROGRESS')): -# self.job_running=False -# self.end_thread('update_pdb_mtz') -# return True - -# def end_thread(self,action): -# self.refinementRunning.stop() -# self.spinnerBox.remove(self.refinementRunning) -# self.status_label.set_text('idle') -# gobject.source_remove(self.source_id) -# if action=='update_pdb_mtz': -# self.update_pdb_mtz_files('') + + # time.sleep(1) # waiting 1s to make sure that REFINEMENT_IN_PROGRESS is written + # self.source_id = gobject.timeout_add(100, self.wait_for_refined_pdb) + + # def wait_for_refined_pdb(self): + # self.spinnerBox.add(self.refinementRunning) + # self.refinementRunning.show() + # self.refinementRunning.start() + # if not os.path.isfile(os.path.join(self.reference_directory,self.refinementDir,'REFINEMENT_IN_PROGRESS')): + # self.job_running=False + # self.end_thread('update_pdb_mtz') + # return True + + # def end_thread(self,action): + # self.refinementRunning.stop() + # self.spinnerBox.remove(self.refinementRunning) + # self.status_label.set_text('idle') + # gobject.source_remove(self.source_id) + # if action=='update_pdb_mtz': + # self.update_pdb_mtz_files('') def RefinementParams(self, widget): - print('\n==> XCE: changing refinement parameters') + print("\n==> XCE: changing refinement parameters") self.RefmacParams = self.Refine.RefinementParams(self.RefmacParams) def set_selection_mode(self, widget): @@ -532,205 +605,290 @@ def set_selection_mode(self, widget): def load_pdb_file(self, widget): pdbRoot = self.cb_select_pdb.get_active_text() - if self.pdbFile != '': + if self.pdbFile != "": self.Logfile.error( - 'sorry, you need to close the current instance of COOT and start again') + "sorry, you need to close the current instance of COOT and start again" + ) return None - self.refinementDir = pdbRoot.replace('.pdb', '') + self.refinementDir = pdbRoot.replace(".pdb", "") self.update_pdb_mtz_files(pdbRoot) def update_pdb_mtz_files(self, pdbRoot): # first remove all pdb and mtz files from memory - self.Logfile.insert('removing all PDB and MTZ files from memory') + self.Logfile.insert("removing all PDB and MTZ files from memory") if len(coot_utils_XChem.molecule_number_list()) > 0: for item in coot_utils_XChem.molecule_number_list(): - if coot.molecule_name(item).endswith('.pdb') or '.mtz' in coot.molecule_name(item): - self.Logfile.insert('removing %s' % - coot.molecule_name(item)) + if coot.molecule_name(item).endswith( + ".pdb" + ) or ".mtz" in coot.molecule_name(item): + self.Logfile.insert("removing %s" % coot.molecule_name(item)) coot.close_molecule(item) coot.set_nomenclature_errors_on_read("ignore") # first we check if there is a refinement folder and the respective refine.pdb # from previous refinement cycles Root = self.cb_select_pdb.get_active_text() - print('ROOT', Root) - print('REFI_DIR', os.path.join( - self.reference_directory, self.refinementDir, 'refine.pdb')) - if os.path.isfile(os.path.join(self.reference_directory, self.refinementDir, 'refine.pdb')): + print("ROOT", Root) + print( + "REFI_DIR", + os.path.join(self.reference_directory, self.refinementDir, "refine.pdb"), + ) + if os.path.isfile( + os.path.join(self.reference_directory, self.refinementDir, "refine.pdb") + ): os.chdir(self.reference_directory) - print('CURRENT DIR', os.getcwd()) - os.system('/bin/rm %s 2> /dev/null' % Root) - os.symlink(os.path.realpath(os.path.join( - self.refinementDir, 'refine.pdb')), '%s' % Root) + print("CURRENT DIR", os.getcwd()) + os.system("/bin/rm %s 2> /dev/null" % Root) + os.symlink( + os.path.realpath(os.path.join(self.refinementDir, "refine.pdb")), + "%s" % Root, + ) self.pdbFile = os.path.join( - self.reference_directory, self.refinementDir, 'refine.pdb') + self.reference_directory, self.refinementDir, "refine.pdb" + ) elif os.path.isfile(os.path.join(self.reference_directory, Root)): self.pdbFile = os.path.join(self.reference_directory, Root) else: - self.Logfile.error('cannot find PDB file') + self.Logfile.error("cannot find PDB file") - if self.pdbFile != '': + if self.pdbFile != "": # os.chdir(os.path.join(self.reference_directory,self.refinementDir)) coot.set_colour_map_rotation_on_read_pdb(0) - imol = coot.handle_read_draw_molecule_with_recentre( - self.pdbFile, 0) - self.QualityIndicators = XChemUtils.parse().PDBheader(os.path.join(self.pdbFile)) - self.QualityIndicators.update(XChemUtils.logtools(os.path.join( - self.reference_directory, self.refinementDir, 'refine_molprobity.log')).phenix_molprobity()) - self.QualityIndicators.update(XChemUtils.logtools(os.path.join( - self.reference_directory, self.refinementDir, 'Refine_'+str(self.Serial), 'refmac.log')).refmac_log()) - self.mol_dict['protein'] = imol - - if self.mtzFree == '': - print('FREE', os.path.join( - self.reference_directory, pdbRoot.replace('.pdb', '')+'.free.mtz')) - if os.path.isfile(os.path.join(self.reference_directory, pdbRoot.replace('.pdb', '')+'.free.mtz')): + imol = coot.handle_read_draw_molecule_with_recentre(self.pdbFile, 0) + self.QualityIndicators = XChemUtils.parse().PDBheader( + os.path.join(self.pdbFile) + ) + self.QualityIndicators.update( + XChemUtils.logtools( + os.path.join( + self.reference_directory, + self.refinementDir, + "refine_molprobity.log", + ) + ).phenix_molprobity() + ) + self.QualityIndicators.update( + XChemUtils.logtools( + os.path.join( + self.reference_directory, + self.refinementDir, + "Refine_" + str(self.Serial), + "refmac.log", + ) + ).refmac_log() + ) + self.mol_dict["protein"] = imol + + if self.mtzFree == "": + print( + "FREE", + os.path.join( + self.reference_directory, pdbRoot.replace(".pdb", "") + ".free.mtz" + ), + ) + if os.path.isfile( + os.path.join( + self.reference_directory, pdbRoot.replace(".pdb", "") + ".free.mtz" + ) + ): self.mtzFree = os.path.join( - self.reference_directory, pdbRoot.replace('.pdb', '')+'.free.mtz') - self.mtzFree_label.set_text( - pdbRoot.replace('.pdb', '')+'.free.mtz') + self.reference_directory, pdbRoot.replace(".pdb", "") + ".free.mtz" + ) + self.mtzFree_label.set_text(pdbRoot.replace(".pdb", "") + ".free.mtz") self.REFINEbutton.set_sensitive(True) else: - self.mtzFree_label.set_text('missing file') + self.mtzFree_label.set_text("missing file") self.Logfile.error( - 'cannot find file with F,SIGF and FreeR_flag; cannot start refinement') + "cannot find file with F,SIGF and FreeR_flag; cannot start refinement" + ) self.REFINEbutton.set_sensitive(False) - self.mtzRefine = '' - if os.path.isfile(os.path.join(self.reference_directory, self.refinementDir, 'refine.mtz')): + self.mtzRefine = "" + if os.path.isfile( + os.path.join(self.reference_directory, self.refinementDir, "refine.mtz") + ): self.mtzRefine = os.path.join( - self.reference_directory, self.refinementDir, 'refine.mtz') - mtzRefineReal = os.path.realpath(os.path.join( - self.reference_directory, self.refinementDir, 'refine.mtz')) - mtzRefineCurrent = mtzRefineReal.replace(os.path.join( - self.reference_directory, self.refinementDir+'/'), '') + self.reference_directory, self.refinementDir, "refine.mtz" + ) + mtzRefineReal = os.path.realpath( + os.path.join(self.reference_directory, self.refinementDir, "refine.mtz") + ) + mtzRefineCurrent = mtzRefineReal.replace( + os.path.join(self.reference_directory, self.refinementDir + "/"), "" + ) self.mtzRefine_label.set_text(mtzRefineCurrent) coot.set_default_initial_contour_level_for_map(1) - if os.path.isfile(os.path.join(self.reference_directory, self.refinementDir, self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join( - self.reference_directory, self.refinementDir, self.mtz_style)) + if os.path.isfile( + os.path.join( + self.reference_directory, self.refinementDir, self.mtz_style + ) + ): + coot.auto_read_make_and_draw_maps( + os.path.join( + self.reference_directory, self.refinementDir, self.mtz_style + ) + ) else: - self.mtzRefine_label.set_text('missing file') + self.mtzRefine_label.set_text("missing file") self.Logfile.warning( - 'cannot find file with F,SIGF and FreeR_flag; cannot start refinement') + "cannot find file with F,SIGF and FreeR_flag; cannot start refinement" + ) groundStateMap = os.path.join( - self.reference_directory, Root+'-mean-map.native.ccp4').replace('.pdb', '') - print('===>', groundStateMap) + self.reference_directory, Root + "-mean-map.native.ccp4" + ).replace(".pdb", "") + print("===>", groundStateMap) if os.path.isfile(groundStateMap): imol = coot.handle_read_ccp4_map(groundStateMap, 0) coot.set_contour_level_in_sigma(imol, 1) coot.set_last_map_colour(0.6, 0.6, 0) else: - print('==> XCE: ERROR - cannot find ground state mean map!') + print("==> XCE: ERROR - cannot find ground state mean map!") self.RefreshData() -# def load_ground_state_map(self,widget): -# self.spinnerBox.add(self.refinementRunning) -# self.refinementRunning.start() -# self.status_label.set_text('loading ground state maps by reso...') -# self.source_id = gobject.timeout_add(100, self.load_ground_state_map_thread) - - -# def load_ground_state_map_thread(self): -# self.spinnerBox.add(self.refinementRunning) -# self.refinementRunning.show() -# self.refinementRunning.start() -# -# # first remove all ground state maps files -# if len(coot_utils_XChem.molecule_number_list()) > 0: -# for item in coot_utils_XChem.molecule_number_list(): -# if 'ground-state-mean-map' in coot.molecule_name(item): -# coot.close_molecule(item) -# -# # first remove all entries for self.cb_select_mean_map_by_resolution -# # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 maps -# for n in range(-1,100): -# self.cb_select_mean_map_by_resolution.remove_text(0) -# -# self.status_label.set_text('loading ground state maps') -# self.get_highest_reso_ground_state_map() -# blueStart=0.02 -# for map in self.ground_state_map_List: -# self.cb_select_mean_map_by_resolution.append_text(map[0]) -# imol=coot.handle_read_ccp4_map((map[1]),0) -# coot.set_contour_level_in_sigma(imol,1) -# coot.set_last_map_colour(0.74,0.44,blueStart) -# blueStart+=0.05 -# # show only highest resolution map to start with -# self.show_highres_ground_state_map() -# self.cb_select_mean_map_by_resolution.set_active(0) -# self.end_thread('') - -# def show_highres_ground_state_map(self): -# if len(self.ground_state_map_List) >= 1: -# for imol in coot_utils_XChem.molecule_number_list(): -# if coot.molecule_name(imol) in self.ground_state_map_List[0][1]: -# coot.set_map_displayed(imol,1) -# elif 'ground-state-mean-map' in coot.molecule_name(imol): -# coot.set_map_displayed(imol,0) - -# def show_all_ground_state_map(self): -# if len(self.ground_state_map_List) >= 1: -# for imol in coot_utils_XChem.molecule_number_list(): -# if 'ground-state-mean-map' in coot.molecule_name(imol): -# coot.set_map_displayed(imol,1) - -# def show_selected_mean_map(self,widget): -# reso=str(self.cb_select_mean_map_by_resolution.get_active_text()) -# mapToshow='' -# for maps in self.ground_state_map_List: -# if maps[0]==reso: -# mapToshow=maps[1] -# for imol in coot_utils_XChem.molecule_number_list(): -# if coot.molecule_name(imol) in mapToshow: -# coot.set_map_displayed(imol,1) -# elif 'ground-state-mean-map' in coot.molecule_name(imol): -# coot.set_map_displayed(imol,0) - + # def load_ground_state_map(self,widget): + # self.spinnerBox.add(self.refinementRunning) + # self.refinementRunning.start() + # self.status_label.set_text('loading ground state maps by reso...') + # self.source_id = gobject.timeout_add(100, self.load_ground_state_map_thread) + + # def load_ground_state_map_thread(self): + # self.spinnerBox.add(self.refinementRunning) + # self.refinementRunning.show() + # self.refinementRunning.start() + # + # # first remove all ground state maps files + # if len(coot_utils_XChem.molecule_number_list()) > 0: + # for item in coot_utils_XChem.molecule_number_list(): + # if 'ground-state-mean-map' in coot.molecule_name(item): + # coot.close_molecule(item) + # + # # first remove all entries for self.cb_select_mean_map_by_resolution + # # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 maps + # for n in range(-1,100): + # self.cb_select_mean_map_by_resolution.remove_text(0) + # + # self.status_label.set_text('loading ground state maps') + # self.get_highest_reso_ground_state_map() + # blueStart=0.02 + # for map in self.ground_state_map_List: + # self.cb_select_mean_map_by_resolution.append_text(map[0]) + # imol=coot.handle_read_ccp4_map((map[1]),0) + # coot.set_contour_level_in_sigma(imol,1) + # coot.set_last_map_colour(0.74,0.44,blueStart) + # blueStart+=0.05 + # # show only highest resolution map to start with + # self.show_highres_ground_state_map() + # self.cb_select_mean_map_by_resolution.set_active(0) + # self.end_thread('') + + # def show_highres_ground_state_map(self): + # if len(self.ground_state_map_List) >= 1: + # for imol in coot_utils_XChem.molecule_number_list(): + # if coot.molecule_name(imol) in self.ground_state_map_List[0][1]: + # coot.set_map_displayed(imol,1) + # elif 'ground-state-mean-map' in coot.molecule_name(imol): + # coot.set_map_displayed(imol,0) + + # def show_all_ground_state_map(self): + # if len(self.ground_state_map_List) >= 1: + # for imol in coot_utils_XChem.molecule_number_list(): + # if 'ground-state-mean-map' in coot.molecule_name(imol): + # coot.set_map_displayed(imol,1) + + # def show_selected_mean_map(self,widget): + # reso=str(self.cb_select_mean_map_by_resolution.get_active_text()) + # mapToshow='' + # for maps in self.ground_state_map_List: + # if maps[0]==reso: + # mapToshow=maps[1] + # for imol in coot_utils_XChem.molecule_number_list(): + # if coot.molecule_name(imol) in mapToshow: + # coot.set_map_displayed(imol,1) + # elif 'ground-state-mean-map' in coot.molecule_name(imol): + # coot.set_map_displayed(imol,0) def show_molprobity_to_do(self, widget): - if os.path.isfile(os.path.join(self.reference_directory, self.refinementDir, 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')): - coot.run_script(os.path.join(self.reference_directory, self.refinementDir, - 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')) + if os.path.isfile( + os.path.join( + self.reference_directory, + self.refinementDir, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ): + coot.run_script( + os.path.join( + self.reference_directory, + self.refinementDir, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ) else: - print('==> XCE: cannot find ' + \ - os.path.join(self.reference_directory, self.xtalID, - 'Refine_'+str(self.Serial-1), 'molprobity_coot.py')) + print( + "==> XCE: cannot find " + + os.path.join( + self.reference_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ) def update_plot(self, refinement_cycle, Rfree, Rcryst): fig = Figure(figsize=(2, 2), dpi=50) Plot = fig.add_subplot(111) - Plot.set_ylim([0, max(Rcryst+Rfree)]) - Plot.set_xlabel('Refinement Cycle', fontsize=12) - Plot.plot(refinement_cycle, Rfree, label='Rfree', linewidth=2) - Plot.plot(refinement_cycle, Rcryst, label='Rcryst', linewidth=2) - Plot.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, - ncol=2, mode="expand", borderaxespad=0., fontsize=12) + Plot.set_ylim([0, max(Rcryst + Rfree)]) + Plot.set_xlabel("Refinement Cycle", fontsize=12) + Plot.plot(refinement_cycle, Rfree, label="Rfree", linewidth=2) + Plot.plot(refinement_cycle, Rcryst, label="Rcryst", linewidth=2) + Plot.legend( + bbox_to_anchor=(0.0, 1.02, 1.0, 0.102), + loc=3, + ncol=2, + mode="expand", + borderaxespad=0.0, + fontsize=12, + ) return fig def get_ground_state_maps_by_resolution(self): found = False mapList = [] - for logFile in glob.glob(os.path.join(self.reference_directory, str(self.cb_select_mean_map.get_active_text()), 'logs', '*.log')): + for logFile in glob.glob( + os.path.join( + self.reference_directory, + str(self.cb_select_mean_map.get_active_text()), + "logs", + "*.log", + ) + ): for n, line in enumerate(open(logFile)): - if line.startswith('Statistical Electron Density Characterisation') and len(line.split()) == 6: + if ( + line.startswith("Statistical Electron Density Characterisation") + and len(line.split()) == 6 + ): # try: # resolution=float(line.split()[5]) resolution = line.split()[5] print(resolution) found = True foundLine = n -# except ValueError: -# print 'error' -# break - if found and n == foundLine+3: - xtal = line.split(',')[0].replace( - ' ', '').replace('\t', '') - meanmap = os.path.join(self.reference_directory, self.cb_select_mean_map.get_active_text( - ), 'processed_datasets', xtal, xtal+'-ground-state-mean-map.native.ccp4') + # except ValueError: + # print 'error' + # break + if found and n == foundLine + 3: + xtal = line.split(",")[0].replace(" ", "").replace("\t", "") + meanmap = os.path.join( + self.reference_directory, + self.cb_select_mean_map.get_active_text(), + "processed_datasets", + xtal, + xtal + "-ground-state-mean-map.native.ccp4", + ) mapList.append([resolution, meanmap]) found = False return mapList @@ -743,5 +901,5 @@ def get_highest_reso_ground_state_map(self): return self.ground_state_map_List -if __name__ == '__main__': +if __name__ == "__main__": GUI().StartGUI() diff --git a/lib/XChemCootTwin.py b/lib/XChemCootTwin.py index f8117e06..691b336c 100755 --- a/lib/XChemCootTwin.py +++ b/lib/XChemCootTwin.py @@ -20,7 +20,7 @@ # from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas # XCE libraries -sys.path.append(os.getenv('XChemExplorer_DIR') + '/lib') +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") # libraries from COOT @@ -40,57 +40,60 @@ def __init__(self): # read in settings file from XChemExplorer to set the relevant paths self.settings = pickle.load(open(".xce_settings.pkl", "rb")) - remote_qsub_submission = self.settings['remote_qsub'] - self.database_directory = self.settings['database_directory'] - self.xce_logfile = self.settings['xce_logfile'] + remote_qsub_submission = self.settings["remote_qsub"] + self.database_directory = self.settings["database_directory"] + self.xce_logfile = self.settings["xce_logfile"] self.Logfile = XChemLog.updateLog(self.xce_logfile) - self.Logfile.insert('==> COOT: starting coot plugin...') - self.data_source = self.settings['data_source'] + self.Logfile.insert("==> COOT: starting coot plugin...") + self.data_source = self.settings["data_source"] self.db = XChemDB.data_source(self.data_source) print(self.settings) # checking for external software packages - self.external_software = XChemUtils.external_software( - self.xce_logfile).check() - self.external_software['qsub_remote'] = remote_qsub_submission - - self.selection_criteria = ['0 - All Datasets', - '1 - Analysis Pending', - '2 - PANDDA model', - '3 - In Refinement', - '4 - CompChem ready', - '5 - Deposition ready', - '6 - Deposited', - '7 - Analysed & Rejected'] - - self.experiment_stage = [['Review PANDDA export', '2 - PANDDA model', 65000, 0, 0], - ['In Refinement', '3 - In Refinement', 65000, 0, 0], - ['Comp Chem Ready!', - '4 - CompChem ready', 65000, 0, 0], - ['Ready for Deposition!', - '5 - Deposition ready', 65000, 0, 0], - ['In PDB', '6 - Deposited', 65000, 0, 0], - ['Analysed & Rejected', '7 - Analysed & Rejected', 65000, 0, 0]] - - self.ligand_confidence_category = ['0 - no ligand present', - '1 - Low Confidence', - '2 - Correct ligand, weak density', - '3 - Clear density, unexpected ligand', - '4 - High Confidence'] + self.external_software = XChemUtils.external_software(self.xce_logfile).check() + self.external_software["qsub_remote"] = remote_qsub_submission + + self.selection_criteria = [ + "0 - All Datasets", + "1 - Analysis Pending", + "2 - PANDDA model", + "3 - In Refinement", + "4 - CompChem ready", + "5 - Deposition ready", + "6 - Deposited", + "7 - Analysed & Rejected", + ] + + self.experiment_stage = [ + ["Review PANDDA export", "2 - PANDDA model", 65000, 0, 0], + ["In Refinement", "3 - In Refinement", 65000, 0, 0], + ["Comp Chem Ready!", "4 - CompChem ready", 65000, 0, 0], + ["Ready for Deposition!", "5 - Deposition ready", 65000, 0, 0], + ["In PDB", "6 - Deposited", 65000, 0, 0], + ["Analysed & Rejected", "7 - Analysed & Rejected", 65000, 0, 0], + ] + + self.ligand_confidence_category = [ + "0 - no ligand present", + "1 - Low Confidence", + "2 - Correct ligand, weak density", + "3 - Clear density, unexpected ligand", + "4 - High Confidence", + ] self.ligand_site_information = self.db.get_list_of_pandda_sites_for_coot() # this decides which samples will be looked at - self.selection_mode = '' + self.selection_mode = "" # self.selected_site='' self.pandda_index = -1 # refers to the number of sites - self.site_index = '0' - self.event_index = '0' + self.site_index = "0" + self.event_index = "0" # the Folder is kind of a legacy thing because my inital idea was to have separate folders # for Data Processing and Refinement - self.project_directory = self.settings['initial_model_directory'] + self.project_directory = self.settings["initial_model_directory"] self.Serial = 0 self.panddaSerial = 0 self.Refine = None @@ -98,31 +101,33 @@ def __init__(self): self.Todo = [] self.siteDict = {} - self.xtalID = '' - self.compoundID = '' - self.ground_state_mean_map = '' - self.spider_plot = '' - self.ligand_confidence = '' - self.refinement_folder = '' -# self.refinementProtocol = 'pandda_refmac' + self.xtalID = "" + self.compoundID = "" + self.ground_state_mean_map = "" + self.spider_plot = "" + self.ligand_confidence = "" + self.refinement_folder = "" + # self.refinementProtocol = 'pandda_refmac' # self.datasetOutcome='' - self.pdb_style = 'refine.pdb' - self.mtz_style = 'refine.mtz' + self.pdb_style = "refine.pdb" + self.mtz_style = "refine.mtz" - self.covLink = ['X', 'X', 'X', 'X'] + self.covLink = ["X", "X", "X", "X"] self.covLinkObject = coot.new_generic_object_number("covalent bond") self.covLinkAtomSpec = None self.label = None # stores imol of currently loaded molecules and maps - self.mol_dict = {'protein': -1, - 'ligand': -1, - '2fofc': -1, - 'fofc': -1, - 'event': -1, - 'ligand_stereo': []} + self.mol_dict = { + "protein": -1, + "ligand": -1, + "2fofc": -1, + "fofc": -1, + "event": -1, + "ligand_stereo": [], + } # two dictionaries which are flushed when a new crystal is loaded # and which contain information to update the data source if necessary @@ -137,44 +142,54 @@ def __init__(self): coot.set_colour_map_rotation_for_map(0) # coot.set_colour_map_rotation_on_read_pdb_flag(21) - self.QualityIndicators = {'RefinementRcryst': '-', - 'RefinementRfree': '-', - 'RefinementRfreeTraficLight': 'gray', - 'RefinementResolution': '-', - 'RefinementResolutionTL': 'gray', - 'RefinementMolProbityScore': '-', - 'RefinementMolProbityScoreTL': 'gray', - 'RefinementRamachandranOutliers': '-', - 'RefinementRamachandranOutliersTL': 'gray', - 'RefinementRamachandranFavored': '-', - 'RefinementRamachandranFavoredTL': 'gray', - 'RefinementRmsdBonds': '-', - 'RefinementRmsdBondsTL': 'gray', - 'RefinementRmsdAngles': '-', - 'RefinementRmsdAnglesTL': 'gray', - 'RefinementMatrixWeight': '-'} - - self.spider_plot_data = {'PANDDA_site_ligand_id': '-', - 'PANDDA_site_occupancy': '-', - 'PANDDA_site_B_average': '-', - 'PANDDA_site_B_ratio_residue_surroundings': '-', - 'PANDDA_site_RSCC': '-', - 'PANDDA_site_rmsd': '-', - 'PANDDA_site_RSR': '-', - 'PANDDA_site_RSZD': '-'} + self.QualityIndicators = { + "RefinementRcryst": "-", + "RefinementRfree": "-", + "RefinementRfreeTraficLight": "gray", + "RefinementResolution": "-", + "RefinementResolutionTL": "gray", + "RefinementMolProbityScore": "-", + "RefinementMolProbityScoreTL": "gray", + "RefinementRamachandranOutliers": "-", + "RefinementRamachandranOutliersTL": "gray", + "RefinementRamachandranFavored": "-", + "RefinementRamachandranFavoredTL": "gray", + "RefinementRmsdBonds": "-", + "RefinementRmsdBondsTL": "gray", + "RefinementRmsdAngles": "-", + "RefinementRmsdAnglesTL": "gray", + "RefinementMatrixWeight": "-", + } + + self.spider_plot_data = { + "PANDDA_site_ligand_id": "-", + "PANDDA_site_occupancy": "-", + "PANDDA_site_B_average": "-", + "PANDDA_site_B_ratio_residue_surroundings": "-", + "PANDDA_site_RSCC": "-", + "PANDDA_site_rmsd": "-", + "PANDDA_site_RSR": "-", + "PANDDA_site_RSZD": "-", + } # default refmac parameters - self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': ''} + self.RefmacParams = { + "HKLIN": "", + "HKLOUT": "", + "XYZIN": "", + "XYZOUT": "", + "LIBIN": "", + "LIBOUT": "", + "TLSIN": "", + "TLSOUT": "", + "TLSADD": "", + "NCYCLES": "10", + "MATRIX_WEIGHT": "AUTO", + "BREF": " bref ISOT\n", + "TLS": "", + "NCS": "", + "TWIN": "", + } def StartGUI(self): @@ -189,7 +204,7 @@ def StartGUI(self): # --- Sample Selection --- # self.vbox.add(gtk.Label('Select Samples')) - frame = gtk.Frame(label='Select Samples') + frame = gtk.Frame(label="Select Samples") self.hbox_select_samples = gtk.HBox() # vbox=gtk.VBox() @@ -206,8 +221,7 @@ def StartGUI(self): # self.hbox_select_samples.add(self.cb_select_sites) self.select_samples_button = gtk.Button(label="GO") - self.select_samples_button.connect( - "clicked", self.get_samples_to_look_at) + self.select_samples_button.connect("clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) @@ -221,25 +235,25 @@ def StartGUI(self): ################################################################################# # --- refinement protocol --- -# frame = gtk.Frame() -# self.refinementProtocolcheckbox = gtk.CheckButton('PanDDA model refinement)') -# # callback is defined later -## self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) -# self.refinementProtocolcheckbox.set_active(True) -# frame.add(self.refinementProtocolcheckbox) -# self.vbox.pack_start(frame) + # frame = gtk.Frame() + # self.refinementProtocolcheckbox = gtk.CheckButton('PanDDA model refinement)') + # # callback is defined later + ## self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) + # self.refinementProtocolcheckbox.set_active(True) + # frame.add(self.refinementProtocolcheckbox) + # self.vbox.pack_start(frame) ################################################################################# # --- refinement program --- -# frame = gtk.Frame() -# self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') -# self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) -# self.refinementProgramcheckbox.set_active(False) -# frame.add(self.refinementProgramcheckbox) -# self.vbox.pack_start(frame) + # frame = gtk.Frame() + # self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') + # self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) + # self.refinementProgramcheckbox.set_active(False) + # frame.add(self.refinementProgramcheckbox) + # self.vbox.pack_start(frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# # --- Refinement Statistics --- @@ -247,163 +261,162 @@ def StartGUI(self): # a combination of labels and textview widgets, arranged in a table RRfreeLabel_frame = gtk.Frame() - self.RRfreeLabel = gtk.Label('R/Rfree') + self.RRfreeLabel = gtk.Label("R/Rfree") RRfreeLabel_frame.add(self.RRfreeLabel) self.RRfreeValue = gtk.Label( - self.QualityIndicators['RefinementRcryst'] + '/' + self.QualityIndicators['RefinementRfree']) + self.QualityIndicators["RefinementRcryst"] + + "/" + + self.QualityIndicators["RefinementRfree"] + ) RRfreeBox_frame = gtk.Frame() self.RRfreeBox = gtk.EventBox() self.RRfreeBox.add(self.RRfreeValue) RRfreeBox_frame.add(self.RRfreeBox) ResolutionLabel_frame = gtk.Frame() - self.ResolutionLabel = gtk.Label('Resolution') + self.ResolutionLabel = gtk.Label("Resolution") ResolutionLabel_frame.add(self.ResolutionLabel) - self.ResolutionValue = gtk.Label( - self.QualityIndicators['RefinementResolution']) + self.ResolutionValue = gtk.Label(self.QualityIndicators["RefinementResolution"]) ResolutionBox_frame = gtk.Frame() self.ResolutionBox = gtk.EventBox() self.ResolutionBox.add(self.ResolutionValue) ResolutionBox_frame.add(self.ResolutionBox) MolprobityScoreLabel_frame = gtk.Frame() - self.MolprobityScoreLabel = gtk.Label('MolprobityScore') + self.MolprobityScoreLabel = gtk.Label("MolprobityScore") MolprobityScoreLabel_frame.add(self.MolprobityScoreLabel) self.MolprobityScoreValue = gtk.Label( - self.QualityIndicators['RefinementMolProbityScore']) + self.QualityIndicators["RefinementMolProbityScore"] + ) MolprobityScoreBox_frame = gtk.Frame() self.MolprobityScoreBox = gtk.EventBox() self.MolprobityScoreBox.add(self.MolprobityScoreValue) MolprobityScoreBox_frame.add(self.MolprobityScoreBox) RamachandranOutliersLabel_frame = gtk.Frame() - self.RamachandranOutliersLabel = gtk.Label('Rama Outliers') + self.RamachandranOutliersLabel = gtk.Label("Rama Outliers") RamachandranOutliersLabel_frame.add(self.RamachandranOutliersLabel) self.RamachandranOutliersValue = gtk.Label( - self.QualityIndicators['RefinementRamachandranOutliers']) + self.QualityIndicators["RefinementRamachandranOutliers"] + ) RamachandranOutliersBox_frame = gtk.Frame() self.RamachandranOutliersBox = gtk.EventBox() self.RamachandranOutliersBox.add(self.RamachandranOutliersValue) RamachandranOutliersBox_frame.add(self.RamachandranOutliersBox) RamachandranFavoredLabel_frame = gtk.Frame() - self.RamachandranFavoredLabel = gtk.Label('Rama Favored') + self.RamachandranFavoredLabel = gtk.Label("Rama Favored") RamachandranFavoredLabel_frame.add(self.RamachandranFavoredLabel) self.RamachandranFavoredValue = gtk.Label( - self.QualityIndicators['RefinementRamachandranFavored']) + self.QualityIndicators["RefinementRamachandranFavored"] + ) RamachandranFavoredBox_frame = gtk.Frame() self.RamachandranFavoredBox = gtk.EventBox() self.RamachandranFavoredBox.add(self.RamachandranFavoredValue) RamachandranFavoredBox_frame.add(self.RamachandranFavoredBox) rmsdBondsLabel_frame = gtk.Frame() - self.rmsdBondsLabel = gtk.Label('rmsd(Bonds)') + self.rmsdBondsLabel = gtk.Label("rmsd(Bonds)") rmsdBondsLabel_frame.add(self.rmsdBondsLabel) - self.rmsdBondsValue = gtk.Label( - self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue = gtk.Label(self.QualityIndicators["RefinementRmsdBonds"]) rmsdBondsBox_frame = gtk.Frame() self.rmsdBondsBox = gtk.EventBox() self.rmsdBondsBox.add(self.rmsdBondsValue) rmsdBondsBox_frame.add(self.rmsdBondsBox) rmsdAnglesLabel_frame = gtk.Frame() - self.rmsdAnglesLabel = gtk.Label('rmsd(Angles)') + self.rmsdAnglesLabel = gtk.Label("rmsd(Angles)") rmsdAnglesLabel_frame.add(self.rmsdAnglesLabel) - self.rmsdAnglesValue = gtk.Label( - self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue = gtk.Label(self.QualityIndicators["RefinementRmsdAngles"]) rmsdAnglesBox_frame = gtk.Frame() self.rmsdAnglesBox = gtk.EventBox() self.rmsdAnglesBox.add(self.rmsdAnglesValue) rmsdAnglesBox_frame.add(self.rmsdAnglesBox) MatrixWeightLabel_frame = gtk.Frame() - self.MatrixWeightLabel = gtk.Label('Matrix Weight') + self.MatrixWeightLabel = gtk.Label("Matrix Weight") MatrixWeightLabel_frame.add(self.MatrixWeightLabel) self.MatrixWeightValue = gtk.Label( - self.QualityIndicators['RefinementMatrixWeight']) + self.QualityIndicators["RefinementMatrixWeight"] + ) MatrixWeightBox_frame = gtk.Frame() self.MatrixWeightBox = gtk.EventBox() self.MatrixWeightBox.add(self.MatrixWeightValue) MatrixWeightBox_frame.add(self.MatrixWeightBox) ligandIDLabel_frame = gtk.Frame() - self.ligandIDLabel = gtk.Label('Ligand ID') + self.ligandIDLabel = gtk.Label("Ligand ID") ligandIDLabel_frame.add(self.ligandIDLabel) - self.ligandIDValue = gtk.Label( - self.spider_plot_data['PANDDA_site_ligand_id']) + self.ligandIDValue = gtk.Label(self.spider_plot_data["PANDDA_site_ligand_id"]) ligandIDBox_frame = gtk.Frame() self.ligandIDBox = gtk.EventBox() self.ligandIDBox.add(self.ligandIDValue) ligandIDBox_frame.add(self.ligandIDBox) ligand_occupancyLabel_frame = gtk.Frame() - self.ligand_occupancyLabel = gtk.Label('occupancy') + self.ligand_occupancyLabel = gtk.Label("occupancy") ligand_occupancyLabel_frame.add(self.ligand_occupancyLabel) self.ligand_occupancyValue = gtk.Label( - self.spider_plot_data['PANDDA_site_occupancy']) + self.spider_plot_data["PANDDA_site_occupancy"] + ) ligand_occupancyBox_frame = gtk.Frame() self.ligand_occupancyBox = gtk.EventBox() self.ligand_occupancyBox.add(self.ligand_occupancyValue) ligand_occupancyBox_frame.add(self.ligand_occupancyBox) ligand_BaverageLabel_frame = gtk.Frame() - self.ligand_BaverageLabel = gtk.Label('B average') + self.ligand_BaverageLabel = gtk.Label("B average") ligand_BaverageLabel_frame.add(self.ligand_BaverageLabel) self.ligand_BaverageValue = gtk.Label( - self.spider_plot_data['PANDDA_site_B_average']) + self.spider_plot_data["PANDDA_site_B_average"] + ) ligand_BaverageBox_frame = gtk.Frame() self.ligand_BaverageBox = gtk.EventBox() self.ligand_BaverageBox.add(self.ligand_BaverageValue) ligand_BaverageBox_frame.add(self.ligand_BaverageBox) ligand_BratioSurroundingsLabel_frame = gtk.Frame() - self.ligand_BratioSurroundingsLabel = gtk.Label('B ratio') - ligand_BratioSurroundingsLabel_frame.add( - self.ligand_BratioSurroundingsLabel) + self.ligand_BratioSurroundingsLabel = gtk.Label("B ratio") + ligand_BratioSurroundingsLabel_frame.add(self.ligand_BratioSurroundingsLabel) self.ligand_BratioSurroundingsValue = gtk.Label( - self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']) + self.spider_plot_data["PANDDA_site_B_ratio_residue_surroundings"] + ) ligand_BratioSurroundingsBox_frame = gtk.Frame() self.ligand_BratioSurroundingsBox = gtk.EventBox() - self.ligand_BratioSurroundingsBox.add( - self.ligand_BratioSurroundingsValue) - ligand_BratioSurroundingsBox_frame.add( - self.ligand_BratioSurroundingsBox) + self.ligand_BratioSurroundingsBox.add(self.ligand_BratioSurroundingsValue) + ligand_BratioSurroundingsBox_frame.add(self.ligand_BratioSurroundingsBox) ligand_RSCCLabel_frame = gtk.Frame() - self.ligand_RSCCLabel = gtk.Label('RSCC') + self.ligand_RSCCLabel = gtk.Label("RSCC") ligand_RSCCLabel_frame.add(self.ligand_RSCCLabel) - self.ligand_RSCCValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSCC']) + self.ligand_RSCCValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSCC"]) ligand_RSCCBox_frame = gtk.Frame() self.ligand_RSCCBox = gtk.EventBox() self.ligand_RSCCBox.add(self.ligand_RSCCValue) ligand_RSCCBox_frame.add(self.ligand_RSCCBox) ligand_rmsdLabel_frame = gtk.Frame() - self.ligand_rmsdLabel = gtk.Label('rmsd') + self.ligand_rmsdLabel = gtk.Label("rmsd") ligand_rmsdLabel_frame.add(self.ligand_rmsdLabel) - self.ligand_rmsdValue = gtk.Label( - self.spider_plot_data['PANDDA_site_rmsd']) + self.ligand_rmsdValue = gtk.Label(self.spider_plot_data["PANDDA_site_rmsd"]) ligand_rmsdBox_frame = gtk.Frame() self.ligand_rmsdBox = gtk.EventBox() self.ligand_rmsdBox.add(self.ligand_rmsdValue) ligand_rmsdBox_frame.add(self.ligand_rmsdBox) ligand_RSRLabel_frame = gtk.Frame() - self.ligand_RSRLabel = gtk.Label('RSR') + self.ligand_RSRLabel = gtk.Label("RSR") ligand_RSRLabel_frame.add(self.ligand_RSRLabel) - self.ligand_RSRValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSR']) + self.ligand_RSRValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSR"]) ligand_RSRBox_frame = gtk.Frame() self.ligand_RSRBox = gtk.EventBox() self.ligand_RSRBox.add(self.ligand_RSRValue) ligand_RSRBox_frame.add(self.ligand_RSRBox) ligand_RSZDLabel_frame = gtk.Frame() - self.ligand_RSZDLabel = gtk.Label('RSZD') + self.ligand_RSZDLabel = gtk.Label("RSZD") ligand_RSZDLabel_frame.add(self.ligand_RSZDLabel) - self.ligand_RSZDValue = gtk.Label( - self.spider_plot_data['PANDDA_site_RSZD']) + self.ligand_RSZDValue = gtk.Label(self.spider_plot_data["PANDDA_site_RSZD"]) ligand_RSZDBox_frame = gtk.Frame() self.ligand_RSZDBox = gtk.EventBox() self.ligand_RSZDBox.add(self.ligand_RSZDValue) @@ -438,8 +451,7 @@ def StartGUI(self): self.table_right.attach(ligandIDLabel_frame, 0, 1, 0, 1) self.table_right.attach(ligand_occupancyLabel_frame, 0, 1, 1, 2) self.table_right.attach(ligand_BaverageLabel_frame, 0, 1, 2, 3) - self.table_right.attach( - ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) + self.table_right.attach(ligand_BratioSurroundingsLabel_frame, 0, 1, 3, 4) self.table_right.attach(ligand_RSCCLabel_frame, 0, 1, 4, 5) self.table_right.attach(ligand_rmsdLabel_frame, 0, 1, 5, 6) self.table_right.attach(ligand_RSRLabel_frame, 0, 1, 6, 7) @@ -464,17 +476,19 @@ def StartGUI(self): hbox.add(button) # --- ground state mean map --- self.ground_state_mean_map_button = gtk.Button( - label="Show ground state mean map") + label="Show ground state mean map" + ) self.ground_state_mean_map_button.connect( - "clicked", self.show_ground_state_mean_map) + "clicked", self.show_ground_state_mean_map + ) hbox.add(self.ground_state_mean_map_button) -# self.vbox.add(self.ground_state_mean_map_button) + # self.vbox.add(self.ground_state_mean_map_button) self.vbox.add(hbox) self.vbox.pack_start(frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# # --- hbox for compound picture & spider_plot (formerly: refinement history) --- @@ -484,7 +498,12 @@ def StartGUI(self): # --- compound picture --- compound_frame = gtk.Frame() pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_COMPOUND_IMAGE_AVAILABLE.png", + ) + ) self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.image = gtk.Image() self.image.set_from_pixbuf(self.pic) @@ -499,9 +518,11 @@ def StartGUI(self): # --- Spider Plot --- spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) - self.spider_plot_pic = pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + os.path.join( + os.getenv("XChemExplorer_DIR"), "image", "NO_SPIDER_PLOT_AVAILABLE.png" + ) + ) + self.spider_plot_pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.spider_plot_image = gtk.Image() self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) spider_plot_frame.add(self.spider_plot_image) @@ -512,54 +533,54 @@ def StartGUI(self): ################################################################################# # --- pandda.inspect user comments --- -# outer_frame = gtk.Frame(label='pandda.inspect comments') -# vbox = gtk.VBox() -# ligand_site_name_label_frame = gtk.Frame() -# ligand_site_name_label = gtk.Label('Site Name') -# ligand_site_name_label_frame.add(ligand_site_name_label) -# ligand_inspect_confidence_label_frame = gtk.Frame() -# ligand_inspect_confidence_label = gtk.Label('Confidence') -# ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) -# ligand_inspect_interesting_label_frame = gtk.Frame() -# ligand_inspect_interesting_label = gtk.Label('Interesting') -# ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) -# ligand_inspect_comment_label_frame = gtk.Frame() -# ligand_inspect_comment_label = gtk.Label('Comment') -# ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) -# ligand_site_name_value_frame = gtk.Frame() -# self.ligand_site_name_value = gtk.Label('-') -# ligand_site_name_value_frame.add(self.ligand_site_name_value) -# ligand_inspect_confidence_value_frame = gtk.Frame() -# self.ligand_inspect_confidence_value = gtk.Label('-') -# ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) -# ligand_inspect_interesting_value_frame = gtk.Frame() -# self.ligand_inspect_interesting_value = gtk.Label('-') -# ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) -# ligand_inspect_comment_value_frame = gtk.Frame() -# self.ligand_inspect_comment_value = gtk.Label('-') -# ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) -# -# frame_pandda_inspect_comments_table = gtk.Frame() -# pandda_inspect_comments_table = gtk.Table(2, 6, False) -# pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) -# pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) -# pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) -# pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) -# -# frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) -# vbox.add(frame_pandda_inspect_comments_table) -# outer_frame.add(vbox) -# self.vbox.pack_start(outer_frame) + # outer_frame = gtk.Frame(label='pandda.inspect comments') + # vbox = gtk.VBox() + # ligand_site_name_label_frame = gtk.Frame() + # ligand_site_name_label = gtk.Label('Site Name') + # ligand_site_name_label_frame.add(ligand_site_name_label) + # ligand_inspect_confidence_label_frame = gtk.Frame() + # ligand_inspect_confidence_label = gtk.Label('Confidence') + # ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) + # ligand_inspect_interesting_label_frame = gtk.Frame() + # ligand_inspect_interesting_label = gtk.Label('Interesting') + # ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) + # ligand_inspect_comment_label_frame = gtk.Frame() + # ligand_inspect_comment_label = gtk.Label('Comment') + # ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) + # ligand_site_name_value_frame = gtk.Frame() + # self.ligand_site_name_value = gtk.Label('-') + # ligand_site_name_value_frame.add(self.ligand_site_name_value) + # ligand_inspect_confidence_value_frame = gtk.Frame() + # self.ligand_inspect_confidence_value = gtk.Label('-') + # ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) + # ligand_inspect_interesting_value_frame = gtk.Frame() + # self.ligand_inspect_interesting_value = gtk.Label('-') + # ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) + # ligand_inspect_comment_value_frame = gtk.Frame() + # self.ligand_inspect_comment_value = gtk.Label('-') + # ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) + # + # frame_pandda_inspect_comments_table = gtk.Frame() + # pandda_inspect_comments_table = gtk.Table(2, 6, False) + # pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) + # pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) + # pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) + # pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) + # + # frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) + # vbox.add(frame_pandda_inspect_comments_table) + # outer_frame.add(vbox) + # self.vbox.pack_start(outer_frame) # # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# - outer_frame = gtk.Frame(label='Sample Navigator') + outer_frame = gtk.Frame(label="Sample Navigator") hboxSample = gtk.HBox() # --- crystal navigator combobox --- @@ -602,51 +623,51 @@ def StartGUI(self): self.vbox.add(outer_frame) # # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# -# outer_frame = gtk.Frame(label='Label') -# hboxlabel = gtk.HBox() -# -# frame = gtk.Frame() -# hbox = gtk.HBox() -# self.vbox_label = gtk.VBox() -# labels = self.db.get_labels_from_db() -# if len(labels) > 5: -# print '==> sorry, too many labels; cannot display them in panel' -# labels = labels[:5] -# # with radiobuttons, one of them needs to be always on -# # but there will be cases when the user has not assigned a label yet -# # hence, the not_shown button is not shown but gets active -# # if the label has not been set yet -# labels.append('not_shown') -# for n, l in enumerate(labels): -# print n,l -# if n == 0: -# new_button = gtk.RadioButton(None, l) -# else: -# new_button = gtk.RadioButton(new_button, l) -# new_button.connect("toggled", self.label_button_clicked, l) -# if not l == 'not_shown': -# hbox.add(new_button) -# self.label_button_list.append(new_button) -# self.vbox_label.add(hbox) -# frame.add(self.vbox_label) -# -# hboxlabel.add(frame) -# -# outer_frame.add(hboxlabel) -# self.vbox.add(outer_frame) + # outer_frame = gtk.Frame(label='Label') + # hboxlabel = gtk.HBox() + # + # frame = gtk.Frame() + # hbox = gtk.HBox() + # self.vbox_label = gtk.VBox() + # labels = self.db.get_labels_from_db() + # if len(labels) > 5: + # print '==> sorry, too many labels; cannot display them in panel' + # labels = labels[:5] + # # with radiobuttons, one of them needs to be always on + # # but there will be cases when the user has not assigned a label yet + # # hence, the not_shown button is not shown but gets active + # # if the label has not been set yet + # labels.append('not_shown') + # for n, l in enumerate(labels): + # print n,l + # if n == 0: + # new_button = gtk.RadioButton(None, l) + # else: + # new_button = gtk.RadioButton(new_button, l) + # new_button.connect("toggled", self.label_button_clicked, l) + # if not l == 'not_shown': + # hbox.add(new_button) + # self.label_button_list.append(new_button) + # self.vbox_label.add(hbox) + # frame.add(self.vbox_label) + # + # hboxlabel.add(frame) + # + # outer_frame.add(hboxlabel) + # self.vbox.add(outer_frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) ################################################################################# # --- current refinement stage --- outer_frame = gtk.Frame() hbox = gtk.HBox() - frame = gtk.Frame(label='Analysis Status') + frame = gtk.Frame(label="Analysis Status") vbox = gtk.VBox() self.experiment_stage_button_list = [] for n, button in enumerate(self.experiment_stage): @@ -655,15 +676,16 @@ def StartGUI(self): else: new_button = gtk.RadioButton(new_button, button[0]) new_button.connect( - "toggled", self.experiment_stage_button_clicked, button[1]) + "toggled", self.experiment_stage_button_clicked, button[1] + ) vbox.pack_start(new_button, False, False, 0) -# vbox.add(new_button) + # vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) # --- ligand confidence --- - frame = gtk.Frame(label='Ligand Confidence') + frame = gtk.Frame(label="Ligand Confidence") vbox = gtk.VBox() self.ligand_confidence_button_list = [] for n, criteria in enumerate(self.ligand_confidence_category): @@ -672,56 +694,55 @@ def StartGUI(self): else: new_button = gtk.RadioButton(new_button, criteria) new_button.connect( - "toggled", self.ligand_confidence_button_clicked, criteria) + "toggled", self.ligand_confidence_button_clicked, criteria + ) vbox.pack_start(new_button, False, False, 0) -# vbox.add(new_button) + # vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) -# # label section --> start -# frame = gtk.Frame(label='Label') -# vbox = gtk.VBox() -# labels = self.db.get_labels_from_db() -# if len(labels) > 5: -# print '==> sorry, too many labels; cannot display them in panel' -# labels = labels[:5] -# # with radiobuttons, one of them needs to be always on -# # but there will be cases when the user has not assigned a label yet -# # hence, the not_shown button is not shown but gets active -# # if the label has not been set yet -# labels.append('not_shown') -# for n, l in enumerate(labels): -# print n,l -# if n == 0: -# new_button = gtk.RadioButton(None, l) -# else: -# new_button = gtk.RadioButton(new_button, l) -# new_button.connect("toggled", self.label_button_clicked, l) -# if not l == 'not_shown': -# vbox.add(new_button) -# self.label_button_list.append(new_button) -# frame.add(vbox) -# hbox.pack_start(frame) -# # label section <-- end + # # label section --> start + # frame = gtk.Frame(label='Label') + # vbox = gtk.VBox() + # labels = self.db.get_labels_from_db() + # if len(labels) > 5: + # print '==> sorry, too many labels; cannot display them in panel' + # labels = labels[:5] + # # with radiobuttons, one of them needs to be always on + # # but there will be cases when the user has not assigned a label yet + # # hence, the not_shown button is not shown but gets active + # # if the label has not been set yet + # labels.append('not_shown') + # for n, l in enumerate(labels): + # print n,l + # if n == 0: + # new_button = gtk.RadioButton(None, l) + # else: + # new_button = gtk.RadioButton(new_button, l) + # new_button.connect("toggled", self.label_button_clicked, l) + # if not l == 'not_shown': + # vbox.add(new_button) + # self.label_button_list.append(new_button) + # frame.add(vbox) + # hbox.pack_start(frame) + # # label section <-- end outer_frame.add(hbox) self.vbox.pack_start(outer_frame) # SPACER -# self.vbox.add(gtk.Label(' ')) + # self.vbox.add(gtk.Label(' ')) # --- ligand modeling --- - frame = gtk.Frame(label='Ligand Modeling') + frame = gtk.Frame(label="Ligand Modeling") self.hbox_for_modeling = gtk.HBox() self.merge_ligand_button = gtk.Button(label="Merge Ligand") self.place_ligand_here_button = gtk.Button(label="Place Ligand here") self.hbox_for_modeling.add(self.place_ligand_here_button) - self.place_ligand_here_button.connect( - "clicked", self.place_ligand_here) + self.place_ligand_here_button.connect("clicked", self.place_ligand_here) self.hbox_for_modeling.add(self.merge_ligand_button) - self.merge_ligand_button.connect( - "clicked", self.merge_ligand_into_protein) + self.merge_ligand_button.connect("clicked", self.merge_ligand_into_protein) self.select_cpd_cb = gtk.combo_box_new_text() self.select_cpd_cb.connect("changed", self.select_cpd) self.hbox_for_modeling.add(self.select_cpd_cb) @@ -741,13 +762,13 @@ def StartGUI(self): self.RefinementParamsButton = gtk.Button(label="refinement parameters") self.covalentLinksbutton = gtk.Button(label="covalent links\n-define-") self.covalentLinksCreatebutton = gtk.Button( - label="covalent links\n-create & refine-") + label="covalent links\n-create & refine-" + ) self.REFINEbutton.connect("clicked", self.REFINE) self.hbox_for_refinement.add(self.REFINEbutton) self.RefinementParamsButton.connect("clicked", self.RefinementParams) self.covalentLinksbutton.connect("clicked", self.covalentLinkDef) - self.covalentLinksCreatebutton.connect( - "clicked", self.covalentLinkCreate) + self.covalentLinksCreatebutton.connect("clicked", self.covalentLinkCreate) self.hbox_for_refinement.add(self.RefinementParamsButton) self.hbox_for_refinement.add(self.covalentLinksbutton) self.hbox_for_refinement.add(self.covalentLinksCreatebutton) @@ -756,10 +777,9 @@ def StartGUI(self): # self.VALIDATEbutton = gtk.Button(label="validate structure") # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") - -# # need to put it here, because attributes within refinementProtocolCallback function -# # are defined after checkbox is defined -# self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) + # # need to put it here, because attributes within refinementProtocolCallback function + # # are defined after checkbox is defined + # self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") @@ -789,10 +809,10 @@ def ChooseXtal(self, widget): self.merge_ligand_button.set_sensitive(True) self.place_ligand_here_button.set_sensitive(True) -# self.ligand_site_name_value.set_label('-') -# self.ligand_inspect_confidence_value.set_label('-') -# self.ligand_inspect_interesting_value.set_label('-') -# self.ligand_inspect_comment_value.set_label('-') + # self.ligand_site_name_value.set_label('-') + # self.ligand_inspect_confidence_value.set_label('-') + # self.ligand_inspect_interesting_value.set_label('-') + # self.ligand_inspect_comment_value.set_label('-') self.refresh_site_combobox() self.db_dict_mainTable = {} @@ -801,36 +821,58 @@ def ChooseXtal(self, widget): self.compoundID = str(self.Todo[self.index][1]) self.refinement_folder = str(self.Todo[self.index][4]) self.refinement_outcome = str(self.Todo[self.index][5]) -# self.label = self.db.get_label_of_sample(self.xtalID) -# self.update_label_radiobutton() + # self.label = self.db.get_label_of_sample(self.xtalID) + # self.update_label_radiobutton() self.update_RefinementOutcome_radiobutton() - if self.xtalID not in self.siteDict: # i.e. we are not working with a PanDDA model + if ( + self.xtalID not in self.siteDict + ): # i.e. we are not working with a PanDDA model self.ligand_confidence = str(self.Todo[self.index][6]) -# self.update_LigandConfidence_radiobutton() -# self.label = self.db.get_label_of_sample(self.xtalID) -# self.update_label_radiobutton() + # self.update_LigandConfidence_radiobutton() + # self.label = self.db.get_label_of_sample(self.xtalID) + # self.update_label_radiobutton() self.RefreshData() def select_cpd(self, widget): cpd = str(widget.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): - if imol not in self.mol_dict['ligand_stereo']: + if imol not in self.mol_dict["ligand_stereo"]: continue - molName = coot.molecule_name(imol)[coot.molecule_name( - imol).rfind('/')+1:].replace('.pdb', '') - if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): - molNameCIF = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( - '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') + molName = coot.molecule_name(imol)[ + coot.molecule_name(imol).rfind("/") + 1 : + ].replace(".pdb", "") + if "rhofit" in coot.molecule_name(imol) or "phenix" in coot.molecule_name( + imol + ): + molNameCIF = ( + coot.molecule_name(imol)[coot.molecule_name(imol).rfind("/") + 1 :] + .replace(".pdb", "") + .replace("_phenix", "") + .replace("_rhofit", "") + ) else: molNameCIF = molName - print(cpd, '-', imol, '-', coot.molecule_name(imol)) + print(cpd, "-", imol, "-", coot.molecule_name(imol)) if molName == cpd: coot.set_mol_displayed(imol, 1) - print('reading', os.path.join( - self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) - coot.read_cif_dictionary(os.path.join( - self.project_directory, self.xtalID, 'compound', molNameCIF+'.cif')) + print( + "reading", + os.path.join( + self.project_directory, + self.xtalID, + "compound", + molNameCIF + ".cif", + ), + ) + coot.read_cif_dictionary( + os.path.join( + self.project_directory, + self.xtalID, + "compound", + molNameCIF + ".cif", + ) + ) else: coot.set_mol_displayed(imol, 0) @@ -846,23 +888,23 @@ def update_RefinementOutcome_radiobutton(self): button.set_active(True) break -# def update_label_radiobutton(self): -# found = False -# for button in self.label_button_list: -# if button.get_label() == self.label: -# button.set_active(True) -# found = True -# if not found: -# for button in self.label_button_list: -# if button.get_label() == 'not_shown': -# button.set_active(True) -# break + # def update_label_radiobutton(self): + # found = False + # for button in self.label_button_list: + # if button.get_label() == self.label: + # button.set_active(True) + # found = True + # if not found: + # for button in self.label_button_list: + # if button.get_label() == 'not_shown': + # button.set_active(True) + # break def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 for i, entry in enumerate(self.ligand_confidence_category): - print('--->', entry, self.ligand_confidence) + print("--->", entry, self.ligand_confidence) try: if entry.split()[0] == self.ligand_confidence.split()[0]: current_stage = i @@ -880,13 +922,14 @@ def refresh_site_combobox(self): # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites for n in range(-1, 100): self.cb_site.remove_text(0) - self.site_index = '0' - self.event_index = '0' + self.site_index = "0" + self.event_index = "0" # only repopulate if site exists if self.xtalID in self.siteDict: for item in sorted(self.siteDict[self.xtalID]): self.cb_site.append_text( - 'site: {0!s} - event: {1!s}'.format(item[5], item[6])) + "site: {0!s} - event: {1!s}".format(item[5], item[6]) + ) def ChangeSite(self, widget, data=None): if self.xtalID in self.siteDict: @@ -919,83 +962,100 @@ def RefreshSiteData(self): # and remove ligand molecule so that there is no temptation to merge it if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): - if self.compoundID + '.pdb' in coot.molecule_name(imol): + if self.compoundID + ".pdb" in coot.molecule_name(imol): coot.close_molecule(imol) -# for w in self.label_button_list: -# w.set_active(False) + # for w in self.label_button_list: + # w.set_active(False) - print('pandda index', self.pandda_index) + print("pandda index", self.pandda_index) self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] - print('new spider plot:', self.spider_plot) + print("new spider plot:", self.spider_plot) self.event_map = self.siteDict[self.xtalID][self.pandda_index][0] - print('new event map:', self.event_map) - self.ligand_confidence = str( - self.siteDict[self.xtalID][self.pandda_index][7]) + print("new event map:", self.event_map) + self.ligand_confidence = str(self.siteDict[self.xtalID][self.pandda_index][7]) self.update_LigandConfidence_radiobutton() site_x = float(self.siteDict[self.xtalID][self.pandda_index][1]) site_y = float(self.siteDict[self.xtalID][self.pandda_index][2]) site_z = float(self.siteDict[self.xtalID][self.pandda_index][3]) - print('new site coordinates:', site_x, site_y, site_z) + print("new site coordinates:", site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) -# self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) -# self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) -# self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) -# self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) - - self.spider_plot_data = self.db.get_db_pandda_dict_for_sample_and_site_and_event(self.xtalID, self.site_index, - self.event_index) - print('>>>>> spider plot data', self.spider_plot_data) - self.ligandIDValue.set_label( - self.spider_plot_data['PANDDA_site_ligand_id']) + # self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) + # self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) + # self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) + # self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) + + self.spider_plot_data = ( + self.db.get_db_pandda_dict_for_sample_and_site_and_event( + self.xtalID, self.site_index, self.event_index + ) + ) + print(">>>>> spider plot data", self.spider_plot_data) + self.ligandIDValue.set_label(self.spider_plot_data["PANDDA_site_ligand_id"]) try: self.ligand_occupancyValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_occupancy']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_occupancy"]), 2)) + ) except ValueError: - self.ligand_occupancyValue.set_label('-') + self.ligand_occupancyValue.set_label("-") try: self.ligand_BaverageValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_B_average']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_B_average"]), 2)) + ) except ValueError: - self.ligand_BaverageValue.set_label('-') + self.ligand_BaverageValue.set_label("-") try: self.ligand_BratioSurroundingsValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_B_ratio_residue_surroundings']), 2))) + str( + round( + float( + self.spider_plot_data[ + "PANDDA_site_B_ratio_residue_surroundings" + ] + ), + 2, + ) + ) + ) except ValueError: - self.ligand_BratioSurroundingsValue.set_label('-') + self.ligand_BratioSurroundingsValue.set_label("-") try: self.ligand_RSCCValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSCC']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSCC"]), 2)) + ) except ValueError: - self.ligand_RSCCValue.set_label('-') + self.ligand_RSCCValue.set_label("-") try: self.ligand_rmsdValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_rmsd']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_rmsd"]), 2)) + ) except ValueError: - self.ligand_rmsdValue.set_label('-') + self.ligand_rmsdValue.set_label("-") try: self.ligand_RSRValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSR']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSR"]), 2)) + ) except ValueError: - self.ligand_RSRValue.set_label('-') + self.ligand_RSRValue.set_label("-") try: self.ligand_RSZDValue.set_label( - str(round(float(self.spider_plot_data['PANDDA_site_RSZD']), 2))) + str(round(float(self.spider_plot_data["PANDDA_site_RSZD"]), 2)) + ) except ValueError: - self.ligand_RSZDValue.set_label('-') + self.ligand_RSZDValue.set_label("-") ######################################################################################### # delete old Event MAPs if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): - if 'map.native.ccp4' in coot.molecule_name(imol): + if "map.native.ccp4" in coot.molecule_name(imol): coot.close_molecule(imol) ######################################################################################### @@ -1005,9 +1065,15 @@ def RefreshSiteData(self): spider_plot_pic = gtk.gdk.pixbuf_new_from_file(self.spider_plot) else: spider_plot_pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_SPIDER_PLOT_AVAILABLE.png", + ) + ) self.spider_plot_pic = spider_plot_pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + 190, 190, gtk.gdk.INTERP_BILINEAR + ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) ######################################################################################### @@ -1023,110 +1089,168 @@ def RefreshSiteData(self): coot.set_last_map_colour(0.74, 0.44, 0.02) def experiment_stage_button_clicked(self, widget, data=None): - self.db_dict_mainTable['RefinementOutcome'] = data - self.Logfile.insert('==> COOT: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( - data) + ' in mainTable of datasource') -# print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( -# data) + ' in mainTable of datasource' -# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + self.db_dict_mainTable["RefinementOutcome"] = data + self.Logfile.insert( + "==> COOT: setting Refinement Outcome for " + + self.xtalID + + " to " + + str(data) + + " in mainTable of datasource" + ) + # print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( + # data) + ' in mainTable of datasource' + # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.db.create_or_remove_missing_records_in_depositTable( - self.xce_logfile, self.xtalID, 'ligand_bound', self.db_dict_mainTable) + self.xce_logfile, self.xtalID, "ligand_bound", self.db_dict_mainTable + ) def ligand_confidence_button_clicked(self, widget, data=None): - print('PANDDA_index', self.pandda_index) + print("PANDDA_index", self.pandda_index) if self.pandda_index == -1: - self.db_dict_mainTable['RefinementLigandConfidence'] = data - self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( - data) + ' in mainTable of datasource') -# print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( -# data) + ' in mainTable of datasource' + self.db_dict_mainTable["RefinementLigandConfidence"] = data + self.Logfile.insert( + "==> COOT: setting Ligand Confidence for " + + self.xtalID + + " to " + + str(data) + + " in mainTable of datasource" + ) + # print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( + # data) + ' in mainTable of datasource' self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.Todo[self.index][6] = data else: - self.db_dict_panddaTable['PANDDA_site_confidence'] = data - self.Logfile.insert('==> COOT: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( - self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( - data) + ' in panddaTable of datasource') -# print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( -# self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( -# data) + ' in panddaTable of datasource' - self.db.update_site_event_panddaTable(self.xtalID, self.site_index, self.event_index, - self.db_dict_panddaTable) + self.db_dict_panddaTable["PANDDA_site_confidence"] = data + self.Logfile.insert( + "==> COOT: setting Ligand Confidence for " + + self.xtalID + + " (site=" + + str(self.site_index) + + ", event=" + + str(self.event_index) + + ") to " + + str(data) + + " in panddaTable of datasource" + ) + # print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( + # self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( + # data) + ' in panddaTable of datasource' + self.db.update_site_event_panddaTable( + self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable + ) self.siteDict[self.xtalID][self.pandda_index][7] = data -# def update_label(self, widget): -# print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' -# # widget.pressed() -# for w in self.label_button_list: -# print w.get_label(), w.get_active() -# if w != widget: -# w.set_active(False) -# print '<<<<<<<<<<<<<<<<<<<<<<<<<<' -# self.db_dict_mainTable['label'] = widget.get_label() -# print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( -# widget.get_label()) + ' in mainTable of datasource' -# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - -# def label_button_clicked(self, widget, data=None): -# print '............',data -# if data == 'not_shown': -# self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) -# else: -# self.db_dict_mainTable['label'] = data -# print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' -# self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + # def update_label(self, widget): + # print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' + # # widget.pressed() + # for w in self.label_button_list: + # print w.get_label(), w.get_active() + # if w != widget: + # w.set_active(False) + # print '<<<<<<<<<<<<<<<<<<<<<<<<<<' + # self.db_dict_mainTable['label'] = widget.get_label() + # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( + # widget.get_label()) + ' in mainTable of datasource' + # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) + + # def label_button_clicked(self, widget, data=None): + # print '............',data + # if data == 'not_shown': + # self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) + # else: + # self.db_dict_mainTable['label'] = data + # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' + # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) def RefreshData(self): # reset spider plot image spider_plot_pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), "image", "NO_SPIDER_PLOT_AVAILABLE.png" + ) + ) self.spider_plot_pic = spider_plot_pic.scale_simple( - 190, 190, gtk.gdk.INTERP_BILINEAR) + 190, 190, gtk.gdk.INTERP_BILINEAR + ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) # reset ground state mean map - self.ground_state_mean_map = '' + self.ground_state_mean_map = "" self.ground_state_mean_map_button.set_sensitive(False) - self.ground_state_mean_map_button.set_label( - 'Show ground state mean map') + self.ground_state_mean_map_button.set_label("Show ground state mean map") if os.path.isfile( - os.path.join(self.project_directory, self.xtalID, self.xtalID + '-ground-state-mean-map.native.ccp4')): + os.path.join( + self.project_directory, + self.xtalID, + self.xtalID + "-ground-state-mean-map.native.ccp4", + ) + ): self.ground_state_mean_map_button.set_sensitive(True) - self.ground_state_mean_map = os.path.join(self.project_directory, self.xtalID, - self.xtalID + '-ground-state-mean-map.native.ccp4') + self.ground_state_mean_map = os.path.join( + self.project_directory, + self.xtalID, + self.xtalID + "-ground-state-mean-map.native.ccp4", + ) # initialize Refinement library -# self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) + # self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) self.Refine = XChemRefine.Refine( - self.project_directory, self.xtalID, self.compoundID, self.data_source) - self.Serial = XChemRefine.GetSerial( - self.project_directory, self.xtalID) - self.panddaSerial = panddaSerial = m = ( - 4 - len(str(self.Serial))) * '0' + str(self.Serial) + self.project_directory, self.xtalID, self.compoundID, self.data_source + ) + self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) + self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * "0" + str( + self.Serial + ) # self.Serial=self.Refine.GetSerial() if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): - print('==> XCE: updating quality indicators in data source for ' + self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, - self.pdb_style)) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, - '') # '' because file does not exist - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init_twin.pdb')): - print('==> XCE: updating quality indicators in data source for ' + self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, - 'init_twin.pdb')) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, - '') # '' because file does not exist - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple_twin.pdb')): - print('==> XCE: updating quality indicators in data source for ' + self.xtalID) - XChemUtils.parse().update_datasource_with_PDBheader(self.xtalID, self.data_source, - os.path.join(self.project_directory, self.xtalID, - 'dimple_twin.pdb')) - XChemUtils.parse().update_datasource_with_phenix_validation_summary(self.xtalID, self.data_source, - '') # '' because file does not exist + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, self.pdb_style), + ) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, "" + ) # '' because file does not exist + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "init_twin.pdb") + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join(self.project_directory, self.xtalID, "init_twin.pdb"), + ) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, "" + ) # '' because file does not exist + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple_twin.pdb") + ): + print( + "==> XCE: updating quality indicators in data source for " + + self.xtalID + ) + XChemUtils.parse().update_datasource_with_PDBheader( + self.xtalID, + self.data_source, + os.path.join( + self.project_directory, self.xtalID, "dimple_twin.pdb" + ), + ) + XChemUtils.parse().update_datasource_with_phenix_validation_summary( + self.xtalID, self.data_source, "" + ) # '' because file does not exist # all this information is now updated in the datasource after each refinement cycle self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) @@ -1136,9 +1260,8 @@ def RefreshData(self): # if the structure was previously refined, try to read the parameters # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: - self.RefmacParams = self.Refine.ParamsFromPreviousCycle( - self.Serial - 1) - print('==> REFMAC params:', self.RefmacParams) + self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) + print("==> REFMAC params:", self.RefmacParams) # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) # else: @@ -1150,11 +1273,11 @@ def RefreshData(self): ######################################################################################### # ligand files # first remove old samples if present - print('>>>', self.mol_dict['ligand_stereo']) - for n, item in enumerate(self.mol_dict['ligand_stereo']): - print('__', item) + print(">>>", self.mol_dict["ligand_stereo"]) + for n, item in enumerate(self.mol_dict["ligand_stereo"]): + print("__", item) self.select_cpd_cb.remove_text(0) - print('done') + print("done") ######################################################################################### # remove potential generic line which indicates a possible covalent link @@ -1163,7 +1286,7 @@ def RefreshData(self): ######################################################################################### # reset covalent links - self.covLinks = ['X', 'X', 'X', 'X'] + self.covLinks = ["X", "X", "X", "X"] ######################################################################################### # update pdb & maps @@ -1180,116 +1303,159 @@ def RefreshData(self): # read new PDB files # read protein molecule after ligand so that this one is the active molecule coot.set_nomenclature_errors_on_read("ignore") - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.compoundID + ".pdb") + ): coot.set_colour_map_rotation_on_read_pdb(0) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb'), 0) - self.mol_dict['ligand'] = imol - coot.read_cif_dictionary(os.path.join( - self.project_directory, self.xtalID, self.compoundID + '.cif')) + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".pdb" + ), + 0, + ) + self.mol_dict["ligand"] = imol + coot.read_cif_dictionary( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".cif" + ) + ) self.select_cpd_cb.append_text(self.compoundID) - self.mol_dict['ligand_stereo'] = [] - self.mol_dict['ligand_stereo'].append(imol) + self.mol_dict["ligand_stereo"] = [] + self.mol_dict["ligand_stereo"].append(imol) # ligands in compound directory - for cifFile in sorted(glob.glob(os.path.join(self.project_directory, self.xtalID, 'compound', self.compoundID+'_*.pdb'))): - cif = cifFile[cifFile.rfind('/')+1:] - if '_with_H' in cif: + for cifFile in sorted( + glob.glob( + os.path.join( + self.project_directory, + self.xtalID, + "compound", + self.compoundID + "_*.pdb", + ) + ) + ): + cif = cifFile[cifFile.rfind("/") + 1 :] + if "_with_H" in cif: continue - self.select_cpd_cb.append_text(cif.replace('.pdb', '')) + self.select_cpd_cb.append_text(cif.replace(".pdb", "")) imol = coot.handle_read_draw_molecule_with_recentre(cifFile, 0) - self.mol_dict['ligand_stereo'].append(imol) + self.mol_dict["ligand_stereo"].append(imol) coot.set_mol_displayed(imol, 0) # autofitted ligands - for pdbFile in sorted(glob.glob(os.path.join(self.project_directory, self.xtalID, 'autofit_ligand', '*', '*.pdb'))): - autofitRun = pdbFile.split('/')[len(pdbFile.split('/')) - 2] - if pdbFile.endswith(autofitRun+'.pdb'): + for pdbFile in sorted( + glob.glob( + os.path.join( + self.project_directory, + self.xtalID, + "autofit_ligand", + "*", + "*.pdb", + ) + ) + ): + autofitRun = pdbFile.split("/")[len(pdbFile.split("/")) - 2] + if pdbFile.endswith(autofitRun + ".pdb"): self.select_cpd_cb.append_text(autofitRun) - imol = coot.handle_read_draw_molecule_with_recentre( - pdbFile, 0) - self.mol_dict['ligand_stereo'].append(imol) + imol = coot.handle_read_draw_molecule_with_recentre(pdbFile, 0) + self.mol_dict["ligand_stereo"].append(imol) coot.set_mol_displayed(imol, 0) self.select_cpd_cb.set_sensitive(True) self.select_cpd_cb.set_active(0) else: - print('no compound found in sample directory') -# self.select_cpd_cb.append_text('') + print("no compound found in sample directory") + # self.select_cpd_cb.append_text('') self.select_cpd_cb.set_sensitive(False) - if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + if not os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) -# if self.refinementProtocol.startswith('pandda'): -# self.Logfile.insert('==> COOT: looking for ground-state model ' + os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.ground-state.pdb')) -# print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.ground-state.pdb') -# if os.path.isfile(os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): -# self.Logfile.insert('==> COOT: found ground-state model') -## print '=> XCE: found ground-state model' -# os.chdir(os.path.join(self.project_directory, self.xtalID)) -# coot.set_colour_map_rotation_on_read_pdb(0) -# try: -# color_wheel_rotation = 160 / float(imol + 2) -# except UnboundLocalError: -# color_wheel_rotation = 80 -# coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) -# imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.ground-state.pdb'), -# 0) -# coot.set_colour_by_molecule(imol) -# coot.set_mol_active(imol, 0) -# else: -# self.Logfile.error('==> COOT - cannot find ground-state model') -## print '=> XCE - ERROR: cannot find ground-state model' -# self.Logfile.insert('==> COOT: looking for bound-state model '+ os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.bound-state.pdb')) -# print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.bound-state.pdb') -# if os.path.isfile(os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb')): -# self.Logfile.insert('==> COOT: found bound-state model') -## print '=> XCE: found bound-state model' -# os.chdir(os.path.join(self.project_directory, self.xtalID)) -# coot.set_colour_map_rotation_on_read_pdb(0) -# color_wheel_rotation = 21 / float(imol + 2) -# coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) -# imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, -# self.pdb_style.replace('.pdb', -# '') + '.split.bound-state.pdb'), -# 0) -# self.mol_dict['protein'] = imol -# else: -# self.Logfile.error('==> COOT: cannot find bound-state model') -## print '=> XCE - ERROR: cannot find bound-state model' -# self.Logfile.warning('==> COOT: moving to next crystal...') -## print '=> XCE: moving to next crystal...' -# self.go_to_next_xtal() -# else: - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.pdb_style)): + # if self.refinementProtocol.startswith('pandda'): + # self.Logfile.insert('==> COOT: looking for ground-state model ' + os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.ground-state.pdb')) + # print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.ground-state.pdb') + # if os.path.isfile(os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): + # self.Logfile.insert('==> COOT: found ground-state model') + ## print '=> XCE: found ground-state model' + # os.chdir(os.path.join(self.project_directory, self.xtalID)) + # coot.set_colour_map_rotation_on_read_pdb(0) + # try: + # color_wheel_rotation = 160 / float(imol + 2) + # except UnboundLocalError: + # color_wheel_rotation = 80 + # coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) + # imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.ground-state.pdb'), + # 0) + # coot.set_colour_by_molecule(imol) + # coot.set_mol_active(imol, 0) + # else: + # self.Logfile.error('==> COOT - cannot find ground-state model') + ## print '=> XCE - ERROR: cannot find ground-state model' + # self.Logfile.insert('==> COOT: looking for bound-state model '+ os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.bound-state.pdb')) + # print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.bound-state.pdb') + # if os.path.isfile(os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb')): + # self.Logfile.insert('==> COOT: found bound-state model') + ## print '=> XCE: found bound-state model' + # os.chdir(os.path.join(self.project_directory, self.xtalID)) + # coot.set_colour_map_rotation_on_read_pdb(0) + # color_wheel_rotation = 21 / float(imol + 2) + # coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) + # imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, + # self.pdb_style.replace('.pdb', + # '') + '.split.bound-state.pdb'), + # 0) + # self.mol_dict['protein'] = imol + # else: + # self.Logfile.error('==> COOT: cannot find bound-state model') + ## print '=> XCE - ERROR: cannot find bound-state model' + # self.Logfile.warning('==> COOT: moving to next crystal...') + ## print '=> XCE: moving to next crystal...' + # self.go_to_next_xtal() + # else: + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.pdb_style) + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init_twin.pdb')): + os.path.join(self.project_directory, self.xtalID, self.pdb_style), 0 + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "init_twin.pdb") + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, 'init_twin.pdb'), 0) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple_twin.pdb')): + os.path.join(self.project_directory, self.xtalID, "init_twin.pdb"), 0 + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple_twin.pdb") + ): os.chdir(os.path.join(self.project_directory, self.xtalID)) imol = coot.handle_read_draw_molecule_with_recentre( - os.path.join(self.project_directory, self.xtalID, 'dimple_twin.pdb'), 0) + os.path.join(self.project_directory, self.xtalID, "dimple_twin.pdb"), 0 + ) else: self.go_to_next_xtal() - self.mol_dict['protein'] = imol + self.mol_dict["protein"] = imol # read any one event map if present for event_map in glob.glob( - os.path.join(self.project_directory, self.xtalID, self.xtalID + '-event_*.native.ccp4')): + os.path.join( + self.project_directory, + self.xtalID, + self.xtalID + "-event_*.native.ccp4", + ) + ): coot.handle_read_ccp4_map((event_map), 0) coot.set_contour_level_in_sigma(imol, 2) coot.set_last_map_colour(0.74, 0.44, 0.02) @@ -1297,8 +1463,8 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( - self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( - item).endswith(self.pdb_style): + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb" + ) or coot.molecule_name(item).endswith(self.pdb_style): # master switch to show symmetry molecules coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model @@ -1307,14 +1473,18 @@ def RefreshData(self): # read fofc maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc_twin.map')): + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "2fofc_twin.map") + ): coot.set_colour_map_rotation_on_read_pdb(0) coot.set_default_initial_contour_level_for_difference_map(3) - coot.handle_read_ccp4_map(os.path.join( - self.project_directory, self.xtalID, 'fofc_twin.map'), 1) + coot.handle_read_ccp4_map( + os.path.join(self.project_directory, self.xtalID, "fofc_twin.map"), 1 + ) coot.set_default_initial_contour_level_for_map(1) - coot.handle_read_ccp4_map(os.path.join( - self.project_directory, self.xtalID, '2fofc_twin.map'), 0) + coot.handle_read_ccp4_map( + os.path.join(self.project_directory, self.xtalID, "2fofc_twin.map"), 0 + ) coot.set_last_map_colour(0, 0, 1) else: # try to open mtz file with same name as pdb file @@ -1326,80 +1496,123 @@ def RefreshData(self): # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): # os.symlink('dimple.mtz',self.mtz_style) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_style)): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, self.mtz_style)) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'init_twin.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, 'init_twin.mtz')) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'dimple_twin.mtz')): - coot.auto_read_make_and_draw_maps(os.path.join( - self.project_directory, self.xtalID, 'dimple_twin.mtz')) + if os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.mtz_style) + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, self.mtz_style) + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "init_twin.mtz") + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, "init_twin.mtz") + ) + elif os.path.isfile( + os.path.join(self.project_directory, self.xtalID, "dimple_twin.mtz") + ): + coot.auto_read_make_and_draw_maps( + os.path.join(self.project_directory, self.xtalID, "dimple_twin.mtz") + ) ######################################################################################### # update Quality Indicator table try: - self.RRfreeValue.set_label(str(round(float(self.QualityIndicators['RefinementRcryst']), 3)) + ' / ' + str( - round(float(self.QualityIndicators['RefinementRfree']), 3))) + self.RRfreeValue.set_label( + str(round(float(self.QualityIndicators["RefinementRcryst"]), 3)) + + " / " + + str(round(float(self.QualityIndicators["RefinementRfree"]), 3)) + ) except ValueError: - self.RRfreeValue.set_label('-') + self.RRfreeValue.set_label("-") try: - self.RRfreeBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementRfreeTraficLight'])) + self.RRfreeBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRfreeTraficLight"] + ), + ) except ValueError: pass - self.ResolutionValue.set_label( - self.QualityIndicators['RefinementResolution']) + self.ResolutionValue.set_label(self.QualityIndicators["RefinementResolution"]) try: - self.ResolutionBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementResolutionTL'])) + self.ResolutionBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementResolutionTL"]), + ) except ValueError: pass self.MolprobityScoreValue.set_label( - self.QualityIndicators['RefinementMolProbityScore']) + self.QualityIndicators["RefinementMolProbityScore"] + ) try: - self.MolprobityScoreBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementMolProbityScoreTL'])) + self.MolprobityScoreBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementMolProbityScoreTL"] + ), + ) except ValueError: pass self.RamachandranOutliersValue.set_label( - self.QualityIndicators['RefinementRamachandranOutliers']) + self.QualityIndicators["RefinementRamachandranOutliers"] + ) try: - self.RamachandranOutliersBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRamachandranOutliersTL'])) + self.RamachandranOutliersBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRamachandranOutliersTL"] + ), + ) except ValueError: pass self.RamachandranFavoredValue.set_label( - self.QualityIndicators['RefinementRamachandranFavored']) + self.QualityIndicators["RefinementRamachandranFavored"] + ) try: - self.RamachandranFavoredBox.modify_bg(gtk.STATE_NORMAL, gtk.gdk.color_parse( - self.QualityIndicators['RefinementRamachandranFavoredTL'])) + self.RamachandranFavoredBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse( + self.QualityIndicators["RefinementRamachandranFavoredTL"] + ), + ) except ValueError: pass - self.rmsdBondsValue.set_label( - self.QualityIndicators['RefinementRmsdBonds']) + self.rmsdBondsValue.set_label(self.QualityIndicators["RefinementRmsdBonds"]) try: - self.rmsdBondsBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdBondsTL'])) + self.rmsdBondsBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementRmsdBondsTL"]), + ) except ValueError: pass - self.rmsdAnglesValue.set_label( - self.QualityIndicators['RefinementRmsdAngles']) + self.rmsdAnglesValue.set_label(self.QualityIndicators["RefinementRmsdAngles"]) try: - self.rmsdAnglesBox.modify_bg(gtk.STATE_NORMAL, - gtk.gdk.color_parse(self.QualityIndicators['RefinementRmsdAnglesTL'])) + self.rmsdAnglesBox.modify_bg( + gtk.STATE_NORMAL, + gtk.gdk.color_parse(self.QualityIndicators["RefinementRmsdAnglesTL"]), + ) except ValueError: pass self.MatrixWeightValue.set_label( - self.QualityIndicators['RefinementMatrixWeight']) + self.QualityIndicators["RefinementMatrixWeight"] + ) try: pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(self.project_directory, self.xtalID, self.compoundID + '.png')) + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".png" + ) + ) except gobject.GError: pic = gtk.gdk.pixbuf_new_from_file( - os.path.join(os.getenv('XChemExplorer_DIR'), 'image', 'NO_COMPOUND_IMAGE_AVAILABLE.png')) + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_COMPOUND_IMAGE_AVAILABLE.png", + ) + ) self.pic = pic.scale_simple(190, 190, gtk.gdk.INTERP_BILINEAR) self.image.set_from_pixbuf(self.pic) @@ -1469,28 +1682,42 @@ def start_refinement(self): # else: ####################################################### - if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): - os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) + if not os.path.isdir( + os.path.join(self.project_directory, self.xtalID, "cootOut") + ): + os.mkdir(os.path.join(self.project_directory, self.xtalID, "cootOut")) # create folder for new refinement cycle try: - self.Logfile.insert('==> COOT: trying to make folder: %s' % os.path.join( - self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) - os.mkdir(os.path.join(self.project_directory, self.xtalID, - 'cootOut', 'Refine_' + str(self.Serial))) + self.Logfile.insert( + "==> COOT: trying to make folder: %s" + % os.path.join( + self.project_directory, + self.xtalID, + "cootOut", + "Refine_" + str(self.Serial), + ) + ) + os.mkdir( + os.path.join( + self.project_directory, + self.xtalID, + "cootOut", + "Refine_" + str(self.Serial), + ) + ) except OSError: + self.Logfile.warning("==> COOT: folder exists; will overwrite contents!") + # print '==> XCE: WARNING -> folder exists; will overwrite contents!' self.Logfile.warning( - '==> COOT: folder exists; will overwrite contents!') -# print '==> XCE: WARNING -> folder exists; will overwrite contents!' - self.Logfile.warning( - '==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') - + "==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem" + ) -# ####################################################### -# # create folder for new refinement cycle and check if free.mtz exists -# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): -# os.mkdir(os.path.join(self.project_directory, self.xtalID)) -# if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): -# os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) + # ####################################################### + # # create folder for new refinement cycle and check if free.mtz exists + # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): + # os.mkdir(os.path.join(self.project_directory, self.xtalID)) + # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): + # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) ####################################################### # write PDB file @@ -1501,22 +1728,34 @@ def start_refinement(self): if coot.molecule_name(item).endswith(self.pdb_style): foundPDB = True break - elif coot.molecule_name(item).endswith('refine.split.bound-state.pdb'): + elif coot.molecule_name(item).endswith("refine.split.bound-state.pdb"): foundPDB = True break - elif coot.molecule_name(item).endswith('init_twin.pdb'): + elif coot.molecule_name(item).endswith("init_twin.pdb"): foundPDB = True break - elif coot.molecule_name(item).endswith('dimple_twin.pdb'): + elif coot.molecule_name(item).endswith("dimple_twin.pdb"): foundPDB = True break if foundPDB: - coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', - 'Refine_' + str(self.Serial), 'in.pdb')) - -# self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) + coot.write_pdb_file( + item, + os.path.join( + self.project_directory, + self.xtalID, + "cootOut", + "Refine_" + str(self.Serial), + "in.pdb", + ), + ) + + # self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) self.Refine.RunBuster( - self.Serial, self.external_software, self.xce_logfile, self.covLinkAtomSpec) + self.Serial, + self.external_software, + self.xce_logfile, + self.covLinkAtomSpec, + ) self.index += 1 if self.index >= len(self.Todo): # self.index = len(self.Todo) @@ -1524,9 +1763,10 @@ def start_refinement(self): self.cb.set_active(self.index) def RefinementParams(self, widget): - print('\n==> XCE: changing refinement parameters') - self.RefmacParams = XChemRefine.RefineParams(self.project_directory, self.xtalID, self.compoundID, - self.data_source).RefmacRefinementParams(self.RefmacParams) + print("\n==> XCE: changing refinement parameters") + self.RefmacParams = XChemRefine.RefineParams( + self.project_directory, self.xtalID, self.compoundID, self.data_source + ).RefmacRefinementParams(self.RefmacParams) def covalentLinkDef(self, widget): coot.user_defined_click_py(2, self.show_potential_link) @@ -1536,40 +1776,70 @@ def show_potential_link(self, *clicks): # it's a prerequisite that the ligand is merged into the protein imol_protein = None for imol in coot_utils_XChem.molecule_number_list(): - print('>', coot.molecule_name(imol)) - if coot.molecule_name(imol).endswith(self.pdb_style) or \ - coot.molecule_name(imol).endswith('init_twin.pdb') or \ - coot.molecule_name(imol).endswith('dimple_twin.pdb') or \ - coot.molecule_name(imol).endswith(self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb'): + print(">", coot.molecule_name(imol)) + if ( + coot.molecule_name(imol).endswith(self.pdb_style) + or coot.molecule_name(imol).endswith("init_twin.pdb") + or coot.molecule_name(imol).endswith("dimple_twin.pdb") + or coot.molecule_name(imol).endswith( + self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb" + ) + ): imol_protein = imol break - print('please click on the two atoms you want to link') - if (len(clicks) == 2): + print("please click on the two atoms you want to link") + if len(clicks) == 2: click_1 = clicks[0] click_2 = clicks[1] imol_1 = click_1[1] imol_2 = click_2[1] - print('imolp', imol, 'imo11', imol_1, 'imol2', imol_2) + print("imolp", imol, "imo11", imol_1, "imol2", imol_2) if imol_1 == imol_2 and imol_1 == imol_protein: - print('click_1', click_1) + print("click_1", click_1) self.covLinkAtomSpec = None xyz_1 = atom_info_string( - click_1[1], click_1[2], click_1[3], click_1[4], click_1[5], click_1[6]) - residue_1 = residue_name( - click_1[1], click_1[2], click_1[3], click_1[4]) + click_1[1], + click_1[2], + click_1[3], + click_1[4], + click_1[5], + click_1[6], + ) + residue_1 = residue_name(click_1[1], click_1[2], click_1[3], click_1[4]) xyz_2 = atom_info_string( - click_2[1], click_2[2], click_2[3], click_2[4], click_2[5], click_2[6]) - residue_2 = residue_name( - click_2[1], click_2[2], click_2[3], click_2[4]) + click_2[1], + click_2[2], + click_2[3], + click_2[4], + click_2[5], + click_2[6], + ) + residue_2 = residue_name(click_2[1], click_2[2], click_2[3], click_2[4]) thick = 4 to_generic_object_add_line( - self.covLinkObject, "yellowtint", thick, xyz_1[3], xyz_1[4], xyz_1[5], xyz_2[3], xyz_2[4], xyz_2[5]) + self.covLinkObject, + "yellowtint", + thick, + xyz_1[3], + xyz_1[4], + xyz_1[5], + xyz_2[3], + xyz_2[4], + xyz_2[5], + ) set_display_generic_object(self.covLinkObject, 1) - self.covLinkAtomSpec = [imol_protein, - click_1, click_2, residue_1, residue_2] + self.covLinkAtomSpec = [ + imol_protein, + click_1, + click_2, + residue_1, + residue_2, + ] else: - print('error: both atoms must belong to the same object; did you merge the ligand with your protein?') + print( + "error: both atoms must belong to the same object; did you merge the ligand with your protein?" + ) def covalentLinkCreate(self, widget): if self.covLinkAtomSpec is not None: @@ -1578,33 +1848,31 @@ def covalentLinkCreate(self, widget): atom2 = self.covLinkAtomSpec[2][1:] residue_1 = self.covLinkAtomSpec[3] residue_2 = self.covLinkAtomSpec[4] - make_link(imol, atom1, atom2, residue_1+'-'+residue_2, 1.7) + make_link(imol, atom1, atom2, residue_1 + "-" + residue_2, 1.7) generic_object_clear(self.covLinkObject) self.start_refinement() else: - print('error: no covalent link defined') + print("error: no covalent link defined") def set_selection_mode(self, widget): self.selection_mode = widget.get_active_text() def get_samples_to_look_at(self, widget): - if self.selection_mode == '': - self.status_label.set_text('select model stage') + if self.selection_mode == "": + self.status_label.set_text("select model stage") return - self.status_label.set_text('checking datasource for samples... ') + self.status_label.set_text("checking datasource for samples... ") # first remove old samples if present if len(self.Todo) != 0: for n, item in enumerate(self.Todo): self.cb.remove_text(0) self.Todo = [] self.siteDict = {} - self.Todo, self.siteDict = self.db.get_todoList_for_coot( - self.selection_mode) - self.status_label.set_text( - 'found {0!s} samples'.format(len(self.Todo))) + self.Todo, self.siteDict = self.db.get_todoList_for_coot(self.selection_mode) + self.status_label.set_text("found {0!s} samples".format(len(self.Todo))) # refresh sample CB for item in sorted(self.Todo): - self.cb.append_text('{0!s}'.format(item[0])) + self.cb.append_text("{0!s}".format(item[0])) if self.siteDict == {}: self.cb_site.set_sensitive(False) self.PREVbuttonSite.set_sensitive(False) @@ -1618,129 +1886,216 @@ def update_plot(self, refinement_cycle, Rfree, Rcryst): fig = Figure(figsize=(2, 2), dpi=50) Plot = fig.add_subplot(111) Plot.set_ylim([0, max(Rcryst + Rfree)]) - Plot.set_xlabel('Refinement Cycle', fontsize=12) - Plot.plot(refinement_cycle, Rfree, label='Rfree', linewidth=2) - Plot.plot(refinement_cycle, Rcryst, label='Rcryst', linewidth=2) - Plot.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3, - ncol=2, mode="expand", borderaxespad=0., fontsize=12) + Plot.set_xlabel("Refinement Cycle", fontsize=12) + Plot.plot(refinement_cycle, Rfree, label="Rfree", linewidth=2) + Plot.plot(refinement_cycle, Rcryst, label="Rcryst", linewidth=2) + Plot.legend( + bbox_to_anchor=(0.0, 1.02, 1.0, 0.102), + loc=3, + ncol=2, + mode="expand", + borderaxespad=0.0, + fontsize=12, + ) return fig def place_ligand_here(self, widget): cpd = str(self.select_cpd_cb.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): - if imol not in self.mol_dict['ligand_stereo']: + if imol not in self.mol_dict["ligand_stereo"]: continue - molName = coot.molecule_name(imol)[coot.molecule_name( - imol).rfind('/')+1:].replace('.pdb', '') + molName = coot.molecule_name(imol)[ + coot.molecule_name(imol).rfind("/") + 1 : + ].replace(".pdb", "") if molName == cpd: - print('===> XCE: moving ligand to pointer') + print("===> XCE: moving ligand to pointer") coot_utils_XChem.move_molecule_here(imol) - print('LIGAND: ', molName) -# print '===> XCE: moving ligand to pointer' -# # coot.move_molecule_here() -# print 'LIGAND: ', self.mol_dict['ligand'] -# coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) + print("LIGAND: ", molName) + + # print '===> XCE: moving ligand to pointer' + # # coot.move_molecule_here() + # print 'LIGAND: ', self.mol_dict['ligand'] + # coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) def merge_ligand_into_protein(self, widget): cpd = str(self.select_cpd_cb.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): - if imol not in self.mol_dict['ligand_stereo']: + if imol not in self.mol_dict["ligand_stereo"]: continue - molName = coot.molecule_name(imol)[coot.molecule_name( - imol).rfind('/')+1:].replace('.pdb', '') + molName = coot.molecule_name(imol)[ + coot.molecule_name(imol).rfind("/") + 1 : + ].replace(".pdb", "") if molName == cpd: - print('===> XCE: merge ligand into protein structure -->', cpd) - coot.merge_molecules_py([imol], self.mol_dict['protein']) - if 'rhofit' in coot.molecule_name(imol) or 'phenix' in coot.molecule_name(imol): - molName = coot.molecule_name(imol)[coot.molecule_name(imol).rfind( - '/') + 1:].replace('.pdb', '').replace('_phenix', '').replace('_rhofit', '') - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.cif')): - os.system('/bin/rm %s' % os.path.join(self.project_directory, - self.xtalID, self.compoundID + '.cif')) - print('XCE: changing directory', os.path.join( - self.project_directory, self.xtalID)) + print("===> XCE: merge ligand into protein structure -->", cpd) + coot.merge_molecules_py([imol], self.mol_dict["protein"]) + if "rhofit" in coot.molecule_name( + imol + ) or "phenix" in coot.molecule_name(imol): + molName = ( + coot.molecule_name(imol)[ + coot.molecule_name(imol).rfind("/") + 1 : + ] + .replace(".pdb", "") + .replace("_phenix", "") + .replace("_rhofit", "") + ) + if os.path.isfile( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".cif" + ) + ): + os.system( + "/bin/rm %s" + % os.path.join( + self.project_directory, + self.xtalID, + self.compoundID + ".cif", + ) + ) + print( + "XCE: changing directory", + os.path.join(self.project_directory, self.xtalID), + ) os.chdir(os.path.join(self.project_directory, self.xtalID)) - print('XCE: changing symlink ln -s %s %s.cif' % ( - os.path.join('compound', molName + '.cif'), self.compoundID)) + print( + "XCE: changing symlink ln -s %s %s.cif" + % (os.path.join("compound", molName + ".cif"), self.compoundID) + ) + os.system( + "ln -s %s %s.cif" + % (os.path.join("compound", molName + ".cif"), self.compoundID) + ) + if os.path.isfile( + os.path.join( + self.project_directory, self.xtalID, self.compoundID + ".pdb" + ) + ): os.system( - 'ln -s %s %s.cif' % (os.path.join('compound', molName + '.cif'), self.compoundID)) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.compoundID + '.pdb')): - os.system('/bin/rm %s' % os.path.join(self.project_directory, - self.xtalID, self.compoundID + '.pdb')) - print('XCE: changing directory', os.path.join( - self.project_directory, self.xtalID)) + "/bin/rm %s" + % os.path.join( + self.project_directory, + self.xtalID, + self.compoundID + ".pdb", + ) + ) + print( + "XCE: changing directory", + os.path.join(self.project_directory, self.xtalID), + ) os.chdir(os.path.join(self.project_directory, self.xtalID)) - print('XCE: changing symlink ln -s %s %s.pdb' % ( - os.path.join('compound', molName + '.pdb'), self.compoundID)) - os.system('ln -s %s %s.pdb' % (os.path.join('compound', molName - + '.pdb'), self.compoundID)) - print('===> XCE: deleting ligand molecule', molName) + print( + "XCE: changing symlink ln -s %s %s.pdb" + % (os.path.join("compound", molName + ".pdb"), self.compoundID) + ) + os.system( + "ln -s %s %s.pdb" + % (os.path.join("compound", molName + ".pdb"), self.compoundID) + ) + print("===> XCE: deleting ligand molecule", molName) coot.close_molecule(imol) self.select_cpd_cb.set_sensitive(False) -# print '===> XCE: merge ligand into protein structure' -# # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) -# coot.merge_molecules_py([self.mol_dict['ligand']], self.mol_dict['protein']) -# print '===> XCE: deleting ligand molecule' -# coot.close_molecule(self.mol_dict['ligand']) + # print '===> XCE: merge ligand into protein structure' + # # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) + # coot.merge_molecules_py([self.mol_dict['ligand']], self.mol_dict['protein']) + # print '===> XCE: deleting ligand molecule' + # coot.close_molecule(self.mol_dict['ligand']) def show_molprobity_to_do(self, widget): print(self.panddaSerial) - AdjPanddaSerial = (4 - len(str(self.Serial))) * \ - '0' + str(int(self.panddaSerial) - 1) - print(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.panddaSerial), - 'molprobity_coot.py')) - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), - 'molprobity_coot.py')): - print('==> XCE: running MolProbity Summary for', self.xtalID) - coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial - 1), - 'molprobity_coot.py')) - elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), - 'molprobity_coot.py')): - print('==> XCE: running MolProbity Summary for', self.xtalID) - coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), - 'molprobity_coot.py')) + AdjPanddaSerial = (4 - len(str(self.Serial))) * "0" + str( + int(self.panddaSerial) - 1 + ) + print( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.panddaSerial), + "molprobity_coot.py", + ) + ) + if os.path.isfile( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ): + print("==> XCE: running MolProbity Summary for", self.xtalID) + coot.run_script( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ) + elif os.path.isfile( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(AdjPanddaSerial), + "molprobity_coot.py", + ) + ): + print("==> XCE: running MolProbity Summary for", self.xtalID) + coot.run_script( + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(AdjPanddaSerial), + "molprobity_coot.py", + ) + ) else: - print('==> XCE: cannot find ' + os.path.join(self.project_directory, self.xtalID, - 'Refine_' + str(self.Serial - 1), 'molprobity_coot.py')) - -# def refinementProtocolCallback(self, widget): -# if widget.get_active(): -# if self.refinementProtocolcheckbox.get_active(): -# self.refinementProtocol = 'pandda_phenix' -# else: -# self.refinementProtocol = 'pandda_refmac' -# self.PREVbuttonSite.set_sensitive(True) -# self.NEXTbuttonSite.set_sensitive(True) -# else: -# self.refinementProtocolcheckbox.set_active(False) -# self.refinementProtocol = 'refmac' -# self.PREVbuttonSite.set_sensitive(False) -# self.NEXTbuttonSite.set_sensitive(False) -# print self.refinementProtocol - -# def refinementProgramCallback(self, widget): -# if widget.get_active(): -# if self.refinementProtocolcheckbox.get_active(): -# self.refinementProtocol = 'pandda_phenix' -# self.RefinementParamsButton.set_sensitive(False) -# else: -# self.refinementProgramcheckbox.set_active(False) -# self.refinementProtocol = 'refmac' -# else: -# self.RefinementParamsButton.set_sensitive(True) -# if self.refinementProtocolcheckbox.get_active(): -# self.refinementProtocol = 'pandda_refmac' -# else: -# self.refinementProtocol = 'refmac' -# print self.refinementProtocol + print( + "==> XCE: cannot find " + + os.path.join( + self.project_directory, + self.xtalID, + "Refine_" + str(self.Serial - 1), + "molprobity_coot.py", + ) + ) + + # def refinementProtocolCallback(self, widget): + # if widget.get_active(): + # if self.refinementProtocolcheckbox.get_active(): + # self.refinementProtocol = 'pandda_phenix' + # else: + # self.refinementProtocol = 'pandda_refmac' + # self.PREVbuttonSite.set_sensitive(True) + # self.NEXTbuttonSite.set_sensitive(True) + # else: + # self.refinementProtocolcheckbox.set_active(False) + # self.refinementProtocol = 'refmac' + # self.PREVbuttonSite.set_sensitive(False) + # self.NEXTbuttonSite.set_sensitive(False) + # print self.refinementProtocol + + # def refinementProgramCallback(self, widget): + # if widget.get_active(): + # if self.refinementProtocolcheckbox.get_active(): + # self.refinementProtocol = 'pandda_phenix' + # self.RefinementParamsButton.set_sensitive(False) + # else: + # self.refinementProgramcheckbox.set_active(False) + # self.refinementProtocol = 'refmac' + # else: + # self.RefinementParamsButton.set_sensitive(True) + # if self.refinementProtocolcheckbox.get_active(): + # self.refinementProtocol = 'pandda_refmac' + # else: + # self.refinementProtocol = 'refmac' + # print self.refinementProtocol def show_ground_state_mean_map(self, widget): - if widget.get_label().startswith('Show'): + if widget.get_label().startswith("Show"): loaded = False for imol in coot_utils_XChem.molecule_number_list(): - if 'ground-state-mean-map' in coot.molecule_name(imol): + if "ground-state-mean-map" in coot.molecule_name(imol): coot.set_map_displayed(imol, 1) loaded = True break @@ -1748,13 +2103,13 @@ def show_ground_state_mean_map(self, widget): coot.set_default_initial_contour_level_for_map(1) coot.handle_read_ccp4_map(self.ground_state_mean_map, 0) coot.set_last_map_colour(0.6, 0.6, 0) - widget.set_label('Undisplay ground state mean map') + widget.set_label("Undisplay ground state mean map") else: for imol in coot_utils_XChem.molecule_number_list(): - if 'ground-state-mean-map' in coot.molecule_name(imol): + if "ground-state-mean-map" in coot.molecule_name(imol): coot.set_map_displayed(imol, 0) - widget.set_label('Show ground state mean map') + widget.set_label("Show ground state mean map") -if __name__ == '__main__': +if __name__ == "__main__": GUI().StartGUI() diff --git a/lib/XChemDB.py b/lib/XChemDB.py index 635ccc6a..f68da6e0 100755 --- a/lib/XChemDB.py +++ b/lib/XChemDB.py @@ -9,12 +9,11 @@ from datetime import datetime import getpass -sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') -#from XChemUtils import parse +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") +# from XChemUtils import parse class data_source: - def __init__(self, data_source_file): self.data_source_file = data_source_file @@ -23,935 +22,712 @@ def __init__(self, data_source_file): self.column_list = [ # SQLite column name XCE column name SQLite type display in overview tab # from Lab36 - ['ID', 'ID', - 'INTEGER PRIMARY KEY', 0], - ['LabVisit', 'LabVisit', - 'TEXT', 1], - ['LibraryPlate', 'LibraryPlate', - 'TEXT', 0], - ['SourceWell', 'SourceWell', - 'TEXT', 0], - ['LibraryName', 'LibraryName', - 'TEXT', 1], - ['CompoundSMILES', 'Smiles', - 'TEXT', 1], - ['CompoundSMILESproduct', 'Smiles - Product', - 'TEXT', 1], - ['CompoundCode', 'Compound ID', - 'TEXT', 1], - ['CompoundStereo', 'Compound Stereo', - 'TEXT', 1], - ['CompoundStereoSMILES', 'Stereo SMILES', - 'TEXT', 1], - ['CompoundStereoCIFprogram', 'Stereo CIF program', - 'TEXT', 1], - ['CompoundStereoCIFs', 'Compound Stereo IDs', - 'TEXT', 1], - ['CompoundAutofitCC', 'autofit CC', - 'TEXT', 1], - ['CompoundAutofitprogram', 'autofit program', - 'TEXT', 1], - ['CrystalPlate', 'CrystalPlate', - 'TEXT', 1], - ['CrystalWell', 'CrystalWell', - 'TEXT', 1], - ['EchoX', 'EchoX', - 'TEXT', 0], - ['EchoY', 'EchoY', - 'TEXT', 0], - ['DropVolume', 'DropVolume', - 'TEXT', 0], - ['ProteinName', 'ProteinName', - 'TEXT', 1], - ['BatchNumber', 'BatchNumber', - 'TEXT', 0], - ['CompoundStockConcentration', 'CompoundStockConcentration', - 'TEXT', 0], - ['CompoundConcentration', 'CompoundConcentration', - 'TEXT', 1], - ['SolventFraction', 'SolventFraction', - 'TEXT', 1], - ['SoakTransferVol', 'SoakTransferVol', - 'TEXT', 0], - ['SoakStatus', 'SoakStatus', - 'TEXT', 0], - ['SoakTimestamp', 'SoakTimestamp', - 'TEXT', 0], - ['CryoStockFraction', 'CryoStockFraction', - 'TEXT', 0], - ['CryoFraction', 'CryoFraction', - 'TEXT', 0], - ['CryoWell', 'CryoWell', - 'TEXT', 0], - ['CryoTransferVolume', 'CryoTransferVolume', - 'TEXT', 0], - ['CryoStatus', 'CryoStatus', - 'TEXT', 0], - ['CryoTimestamp', 'CryoTimestamp', - 'TEXT', 0], - ['SoakingTime', 'SoakingTime', - 'TEXT', 1], - ['HarvestStatus', 'HarvestStatus', - 'TEXT', 0], - ['CrystalName', 'Sample ID', - 'TEXT', 0], - ['Puck', 'Puck', - 'TEXT', 1], - ['PuckPosition', 'PuckPosition', - 'TEXT', 1], - ['PinBarcode', 'SoakDB\nBarcode', - 'TEXT', 1], - ['MountingResult', 'MountingResult', - 'TEXT', 0], - ['MountingArrivalTime', 'MountingArrivalTime', - 'TEXT', 0], - ['MountedTimestamp', 'MountedTimestamp', - 'TEXT', 0], - ['MountingTime', 'MountingTime', - 'TEXT', 0], - ['ispybStatus', 'ispybStatus', - 'TEXT', 0], - ['DataCollectionVisit', 'Visit', - 'TEXT', 1], - + ["ID", "ID", "INTEGER PRIMARY KEY", 0], + ["LabVisit", "LabVisit", "TEXT", 1], + ["LibraryPlate", "LibraryPlate", "TEXT", 0], + ["SourceWell", "SourceWell", "TEXT", 0], + ["LibraryName", "LibraryName", "TEXT", 1], + ["CompoundSMILES", "Smiles", "TEXT", 1], + ["CompoundSMILESproduct", "Smiles - Product", "TEXT", 1], + ["CompoundCode", "Compound ID", "TEXT", 1], + ["CompoundStereo", "Compound Stereo", "TEXT", 1], + ["CompoundStereoSMILES", "Stereo SMILES", "TEXT", 1], + ["CompoundStereoCIFprogram", "Stereo CIF program", "TEXT", 1], + ["CompoundStereoCIFs", "Compound Stereo IDs", "TEXT", 1], + ["CompoundAutofitCC", "autofit CC", "TEXT", 1], + ["CompoundAutofitprogram", "autofit program", "TEXT", 1], + ["CrystalPlate", "CrystalPlate", "TEXT", 1], + ["CrystalWell", "CrystalWell", "TEXT", 1], + ["EchoX", "EchoX", "TEXT", 0], + ["EchoY", "EchoY", "TEXT", 0], + ["DropVolume", "DropVolume", "TEXT", 0], + ["ProteinName", "ProteinName", "TEXT", 1], + ["BatchNumber", "BatchNumber", "TEXT", 0], + ["CompoundStockConcentration", "CompoundStockConcentration", "TEXT", 0], + ["CompoundConcentration", "CompoundConcentration", "TEXT", 1], + ["SolventFraction", "SolventFraction", "TEXT", 1], + ["SoakTransferVol", "SoakTransferVol", "TEXT", 0], + ["SoakStatus", "SoakStatus", "TEXT", 0], + ["SoakTimestamp", "SoakTimestamp", "TEXT", 0], + ["CryoStockFraction", "CryoStockFraction", "TEXT", 0], + ["CryoFraction", "CryoFraction", "TEXT", 0], + ["CryoWell", "CryoWell", "TEXT", 0], + ["CryoTransferVolume", "CryoTransferVolume", "TEXT", 0], + ["CryoStatus", "CryoStatus", "TEXT", 0], + ["CryoTimestamp", "CryoTimestamp", "TEXT", 0], + ["SoakingTime", "SoakingTime", "TEXT", 1], + ["HarvestStatus", "HarvestStatus", "TEXT", 0], + ["CrystalName", "Sample ID", "TEXT", 0], + ["Puck", "Puck", "TEXT", 1], + ["PuckPosition", "PuckPosition", "TEXT", 1], + ["PinBarcode", "SoakDB\nBarcode", "TEXT", 1], + ["MountingResult", "MountingResult", "TEXT", 0], + ["MountingArrivalTime", "MountingArrivalTime", "TEXT", 0], + ["MountedTimestamp", "MountedTimestamp", "TEXT", 0], + ["MountingTime", "MountingTime", "TEXT", 0], + ["ispybStatus", "ispybStatus", "TEXT", 0], + ["DataCollectionVisit", "Visit", "TEXT", 1], # from XChemExplorer - - ['ProjectDirectory', 'ProjectDirectory', - 'TEXT', 0], - - ['CrystalTag', 'Tag', - 'TEXT', 0], - ['CrystalFormName', 'Crystal Form\nName', - 'TEXT', 0], - ['CrystalFormSpaceGroup', 'Space\nGroup', - 'TEXT', 0], - ['CrystalFormPointGroup', 'Point\nGroup', - 'TEXT', 0], - ['CrystalFormA', 'a', - 'TEXT', 0], - ['CrystalFormB', 'b', - 'TEXT', 0], - ['CrystalFormC', 'c', - 'TEXT', 0], - ['CrystalFormAlpha', 'alpha', - 'TEXT', 0], - ['CrystalFormBeta', 'beta', - 'TEXT', 0], - ['CrystalFormGamma', 'gamma', - 'TEXT', 0], - ['CrystalFormVolume', 'Crystal Form\nVolume', - 'TEXT', 0], - - ['DataCollectionBeamline', 'Beamline', - 'TEXT', 0], - ['DataCollectionDate', 'Data Collection\nDate', - 'TEXT', 1], - ['DataCollectionOutcome', 'DataCollection\nOutcome', - 'TEXT', 1], - ['DataCollectionRun', 'Run', - 'TEXT', 0], - ['DataCollectionSubdir', 'SubDir', - 'TEXT', 0], - ['DataCollectionComment', 'DataCollection\nComment', - 'TEXT', 0], - ['DataCollectionWavelength', 'Wavelength', - 'TEXT', 0], - ['DataCollectionPinBarcode', 'GDA\nBarcode', - 'TEXT', 1], - - ['DataCollectionCrystalImage1', 'img1', 'TEXT', 1], - ['DataCollectionCrystalImage2', 'img2', 'TEXT', 1], - ['DataCollectionCrystalImage3', 'img3', 'TEXT', 1], - ['DataCollectionCrystalImage4', 'img4', 'TEXT', 1], - - ['DataProcessingPathToImageFiles', - 'Path to diffraction\nimage files', 'TEXT', 1], - ['DataProcessingProgram', 'Program', - 'TEXT', 1], - ['DataProcessingSpaceGroup', 'DataProcessing\nSpaceGroup', - 'TEXT', 1], - ['DataProcessingUnitCell', 'DataProcessing\nUnitCell', - 'TEXT', 0], - ['DataProcessingAutoAssigned', 'auto-assigned', - 'TEXT', 0], - - ['DataProcessingA', 'DataProcessing\nA', - 'TEXT', 0], - ['DataProcessingB', 'DataProcessing\nB', - 'TEXT', 0], - ['DataProcessingC', 'DataProcessing\nC', - 'TEXT', 0], - ['DataProcessingAlpha', 'DataProcessing\nAlpha', - 'TEXT', 0], - ['DataProcessingBeta', 'DataProcessing\nBeta', - 'TEXT', 0], - ['DataProcessingGamma', 'DataProcessing\nGamma', - 'TEXT', 0], - + ["ProjectDirectory", "ProjectDirectory", "TEXT", 0], + ["CrystalTag", "Tag", "TEXT", 0], + ["CrystalFormName", "Crystal Form\nName", "TEXT", 0], + ["CrystalFormSpaceGroup", "Space\nGroup", "TEXT", 0], + ["CrystalFormPointGroup", "Point\nGroup", "TEXT", 0], + ["CrystalFormA", "a", "TEXT", 0], + ["CrystalFormB", "b", "TEXT", 0], + ["CrystalFormC", "c", "TEXT", 0], + ["CrystalFormAlpha", "alpha", "TEXT", 0], + ["CrystalFormBeta", "beta", "TEXT", 0], + ["CrystalFormGamma", "gamma", "TEXT", 0], + ["CrystalFormVolume", "Crystal Form\nVolume", "TEXT", 0], + ["DataCollectionBeamline", "Beamline", "TEXT", 0], + ["DataCollectionDate", "Data Collection\nDate", "TEXT", 1], + ["DataCollectionOutcome", "DataCollection\nOutcome", "TEXT", 1], + ["DataCollectionRun", "Run", "TEXT", 0], + ["DataCollectionSubdir", "SubDir", "TEXT", 0], + ["DataCollectionComment", "DataCollection\nComment", "TEXT", 0], + ["DataCollectionWavelength", "Wavelength", "TEXT", 0], + ["DataCollectionPinBarcode", "GDA\nBarcode", "TEXT", 1], + ["DataCollectionCrystalImage1", "img1", "TEXT", 1], + ["DataCollectionCrystalImage2", "img2", "TEXT", 1], + ["DataCollectionCrystalImage3", "img3", "TEXT", 1], + ["DataCollectionCrystalImage4", "img4", "TEXT", 1], + [ + "DataProcessingPathToImageFiles", + "Path to diffraction\nimage files", + "TEXT", + 1, + ], + ["DataProcessingProgram", "Program", "TEXT", 1], + ["DataProcessingSpaceGroup", "DataProcessing\nSpaceGroup", "TEXT", 1], + ["DataProcessingUnitCell", "DataProcessing\nUnitCell", "TEXT", 0], + ["DataProcessingAutoAssigned", "auto-assigned", "TEXT", 0], + ["DataProcessingA", "DataProcessing\nA", "TEXT", 0], + ["DataProcessingB", "DataProcessing\nB", "TEXT", 0], + ["DataProcessingC", "DataProcessing\nC", "TEXT", 0], + ["DataProcessingAlpha", "DataProcessing\nAlpha", "TEXT", 0], + ["DataProcessingBeta", "DataProcessing\nBeta", "TEXT", 0], + ["DataProcessingGamma", "DataProcessing\nGamma", "TEXT", 0], # True or False depending on whether user changed automatic selection # ['DataProcessingUserSelected', 'DataProcessingUserSelected', 'TEXT', 0], - - ['DataProcessingResolutionOverall', 'Resolution\nOverall', - 'TEXT', 0], - ['DataProcessingResolutionLow', 'Resolution\nLow', - 'TEXT', 0], - ['DataProcessingResolutionLowInnerShell', - 'Resolution\nLow (Inner Shell)', 'TEXT', 0], - ['DataProcessingResolutionHigh', 'Resolution\nHigh', - 'TEXT', 1], - ['DataProcessingResolutionHigh15sigma', - 'Resolution\n[Mn = 1.5]', 'TEXT', 1], - ['DataProcessingResolutionHigh20sigma', - 'Resolution\n[Mn = 2.0]', 'TEXT', 1], - ['DataProcessingResolutionHighOuterShell', - 'Resolution\nHigh (Outer Shell)', 'TEXT', 0], - ['DataProcessingRmergeOverall', 'Rmerge\nOverall', - 'TEXT', 1], - ['DataProcessingRmergeLow', 'Rmerge\nLow', - 'TEXT', 1], - ['DataProcessingRmergeHigh', 'Rmerge\nHigh', - 'TEXT', 1], - ['DataProcessingIsigOverall', - 'Mn\nOverall', 'TEXT', 1], - ['DataProcessingIsigLow', - 'Mn\nLow', 'TEXT', 1], - ['DataProcessingIsigHigh', - 'Mn\nHigh', 'TEXT', 1], - ['DataProcessingCompletenessOverall', 'Completeness\nOverall', - 'TEXT', 1], - ['DataProcessingCompletenessLow', 'Completeness\nLow', - 'TEXT', 1], - ['DataProcessingCompletenessHigh', 'Completeness\nHigh', - 'TEXT', 1], - ['DataProcessingMultiplicityOverall', 'Multiplicity\nOverall', - 'TEXT', 1], - ['DataProcessingMultiplicityLow', 'Multiplicity\nLow', - 'TEXT', 1], - ['DataProcessingMultiplicityHigh', 'Multiplicity\nHigh', - 'TEXT', 1], - ['DataProcessingCChalfOverall', - 'CC(1/2)\nOverall', 'TEXT', 1], - ['DataProcessingCChalfLow', - 'CC(1/2)\nLow', 'TEXT', 1], - ['DataProcessingCChalfHigh', - 'CC(1/2)\nHigh', 'TEXT', 1], - + ["DataProcessingResolutionOverall", "Resolution\nOverall", "TEXT", 0], + ["DataProcessingResolutionLow", "Resolution\nLow", "TEXT", 0], + [ + "DataProcessingResolutionLowInnerShell", + "Resolution\nLow (Inner Shell)", + "TEXT", + 0, + ], + ["DataProcessingResolutionHigh", "Resolution\nHigh", "TEXT", 1], + [ + "DataProcessingResolutionHigh15sigma", + "Resolution\n[Mn = 1.5]", + "TEXT", + 1, + ], + [ + "DataProcessingResolutionHigh20sigma", + "Resolution\n[Mn = 2.0]", + "TEXT", + 1, + ], + [ + "DataProcessingResolutionHighOuterShell", + "Resolution\nHigh (Outer Shell)", + "TEXT", + 0, + ], + ["DataProcessingRmergeOverall", "Rmerge\nOverall", "TEXT", 1], + ["DataProcessingRmergeLow", "Rmerge\nLow", "TEXT", 1], + ["DataProcessingRmergeHigh", "Rmerge\nHigh", "TEXT", 1], + ["DataProcessingIsigOverall", "Mn\nOverall", "TEXT", 1], + ["DataProcessingIsigLow", "Mn\nLow", "TEXT", 1], + ["DataProcessingIsigHigh", "Mn\nHigh", "TEXT", 1], + ["DataProcessingCompletenessOverall", "Completeness\nOverall", "TEXT", 1], + ["DataProcessingCompletenessLow", "Completeness\nLow", "TEXT", 1], + ["DataProcessingCompletenessHigh", "Completeness\nHigh", "TEXT", 1], + ["DataProcessingMultiplicityOverall", "Multiplicity\nOverall", "TEXT", 1], + ["DataProcessingMultiplicityLow", "Multiplicity\nLow", "TEXT", 1], + ["DataProcessingMultiplicityHigh", "Multiplicity\nHigh", "TEXT", 1], + ["DataProcessingCChalfOverall", "CC(1/2)\nOverall", "TEXT", 1], + ["DataProcessingCChalfLow", "CC(1/2)\nLow", "TEXT", 1], + ["DataProcessingCChalfHigh", "CC(1/2)\nHigh", "TEXT", 1], # the data source is a bit exploding with entries like the ones below, # but the many different filenames and folder structures of Diamond autoprocessing makes it necessary - ['DataProcessingPathToLogfile', - 'DataProcessingPathToLogfile', 'TEXT', 1], - ['DataProcessingPathToMTZfile', - 'DataProcessingPathToMTZfile', 'TEXT', 1], - ['DataProcessingLOGfileName', 'DataProcessingLOGfileName', - 'TEXT', 0], - ['DataProcessingMTZfileName', 'DataProcessingMTZfileName', - 'TEXT', 0], - ['DataProcessingDirectoryOriginal', - 'DataProcessingDirectoryOriginal', 'TEXT', 0], - ['DataProcessingUniqueReflectionsOverall', - 'Unique Reflections\nOverall', 'TEXT', 1], - ['DataProcessingUniqueReflectionsLow', 'Unique Reflections\nlow', - 'TEXT', 1], - ['DataProcessingUniqueReflectionsHigh', - 'Unique Reflections\nhigh', 'TEXT', 1], - ['DataProcessingLattice', 'DataProcessing\nLattice', - 'TEXT', 0], - ['DataProcessingPointGroup', - 'DataProcessing\nPointGroup', 'TEXT', 0], - ['DataProcessingUnitCellVolume', - 'DataProcessing\nUnit Cell Volume', 'TEXT', 0], - ['DataProcessingAlert', 'DataProcessing\nAlert', - 'TEXT', 0], - ['DataProcessingScore', 'DataProcessing\nScore', - 'TEXT', 1], - - - ['DataProcessingStatus', 'DataProcessing\nStatus', - 'TEXT', 1], - - ['DataProcessingRcryst', 'DataProcessing\nRcryst', - 'TEXT', 0], - ['DataProcessingRfree', 'DataProcessing\nRfree', - 'TEXT', 0], - ['DataProcessingPathToDimplePDBfile', - 'DataProcessingPathToDimplePDBfile', 'TEXT', 0], - ['DataProcessingPathToDimpleMTZfile', - 'DataProcessingPathToDimpleMTZfile', 'TEXT', 0], - ['DataProcessingDimpleSuccessful', - 'DataProcessingDimpleSuccessful', 'TEXT', 0], - - ['DimpleResolutionHigh', 'Dimple\nResolution High', - 'TEXT', 1], - ['DimpleRcryst', 'Dimple\nRcryst', - 'TEXT', 1], - ['DimpleRfree', 'Dimple\nRfree', - 'TEXT', 1], - ['DimplePathToPDB', 'Dimple\nPath to PDB file', - 'TEXT', 1], - ['DimplePathToMTZ', 'Dimple\nPath to MTZ file', - 'TEXT', 1], - ['DimpleReferencePDB', 'Dimple\nReference PDB', - 'TEXT', 1], - ['DimpleStatus', 'Dimple\nStatus', - 'TEXT', 1], - - ['DimpleTwinResolutionHigh', - 'Dimple - twin\nResolution High', 'TEXT', 1], - ['DimpleTwinRcryst', 'Dimple - twin\nRcryst', - 'TEXT', 1], - ['DimpleTwinRfree', 'Dimple - twin\nRfree', - 'TEXT', 1], - ['DimpleTwinPathToPDB', - 'Dimple - twin\nPath to PDB file', 'TEXT', 1], - ['DimpleTwinPathToMTZ', - 'Dimple - twin\nPath to MTZ file', 'TEXT', 1], - ['DimpleTwinReferencePDB', - 'Dimple - twin\nReference PDB', 'TEXT', 1], - ['DimpleTwinStatus', 'Dimple - twin\nStatus', - 'TEXT', 1], - ['DimpleTwinFraction', 'Dimple - twin\nFraction', - 'TEXT', 1], - ['DataProcessingDimpleTwinSuccessful', - 'DataProcessingDimpleTwinSuccessful', 'TEXT', 0], - - - ['DimplePANDDAwasRun', 'PanDDA\nlaunched?', - 'TEXT', 1], - ['DimplePANDDAhit', 'PanDDA\nhit?', - 'TEXT', 1], - ['DimplePANDDAreject', 'PanDDA\nreject?', - 'TEXT', 1], - ['DimplePANDDApath', 'PanDDA\npath?', - 'TEXT', 1], - ['PANDDAStatus', 'PanDDA\nStatus', - 'TEXT', 1], - - ['DatePanDDAModelCreated', 'DatePanDDAModelCreated', - 'TEXT', 0], - - ['RefinementResolution', 'Refinement\nResolution', - 'TEXT', 1], - ['RefinementResolutionTL', 'RefinementResolutionTL', - 'TEXT', 0], - ['RefinementRcryst', 'Refinement\nRcryst', - 'TEXT', 1], - ['RefinementRcrystTraficLight', - 'RefinementRcrystTraficLight', 'TEXT', 0], - ['RefinementRfree', 'Refinement\nRfree', - 'TEXT', 1], - ['RefinementRfreeTraficLight', - 'RefinementRfreeTraficLight', 'TEXT', 0], - ['RefinementSpaceGroup', 'Refinement\nSpace Group', - 'TEXT', 1], - ['RefinementLigandCC', 'Ligand CC', - 'TEXT', 0], - ['RefinementRmsdBonds', 'RefinementRmsdBonds', - 'TEXT', 1], - ['RefinementRmsdBondsTL', 'RefinementRmsdBondsTL', - 'TEXT', 0], - ['RefinementRmsdAngles', 'RefinementRmsdAngles', - 'TEXT', 1], - ['RefinementRmsdAnglesTL', 'RefinementRmsdAnglesTL', - 'TEXT', 0], - ['RefinementOutcome', 'Refinement\nOutcome', - 'TEXT', 1], - ['RefinementOutcomePerson', 'RefinementOutcomePerson', - 'TEXT', 1], - ['RefinementOutcomeDate', 'RefinementOutcomeDate', - 'TEXT', 1], - - ['RefinementMTZfree', 'RefinementMTZfree', - 'TEXT', 1], - ['RefinementTwinMTZfree', 'RefinementTwinMTZfree', - 'TEXT', 1], - - ['RefinementCIF', 'RefinementCIF', - 'TEXT', 1], - ['RefinementCIFStatus', 'Compound\nStatus', - 'TEXT', 1], - ['RefinementCIFprogram', 'RefinementCIFprogram', - 'TEXT', 1], - ['RefinementPDB_latest', 'RefinementPDB_latest', - 'TEXT', 1], - ['RefinementMTZ_latest', 'RefinementMTZ_latest', - 'TEXT', 1], - ['RefinementMMCIFmodel_latest', - 'RefinementMMCIFmodel_latest', 'TEXT', 1], - ['RefinementMMCIFreflections_latest', - 'RefinementMMCIFreflections_latest', 'TEXT', 1], - - ['RefinementMatrixWeight', 'RefinementMatrixWeight', - 'TEXT', 0], - ['RefinementComment', 'RefinementComment', - 'TEXT', 0], - ['RefinementPathToRefinementFolder', - 'RefinementPathToRefinementFolder', 'TEXT', 0], - ['RefinementLigandConfidence', 'Ligand\nConfidence', - 'TEXT', 0], - ['RefinementLigandBoundConformation', - 'RefinementLigandBoundConformation', 'TEXT', 0], - ['RefinementBoundConformation', - 'RefinementBoundConformation', 'TEXT', 0], - ['RefinementMolProbityScore', 'MolProbity Score', - 'TEXT', 1], - ['RefinementMolProbityScoreTL', - 'RefinementMolProbityScoreTL', 'TEXT', 0], - ['RefinementRamachandranOutliers', 'Ramachandran\nOutliers', - 'TEXT', 1], - ['RefinementRamachandranOutliersTL', - 'RefinementRamachandranOutliersTL', 'TEXT', 0], - ['RefinementRamachandranFavored', 'Ramachandran\nFavored', - 'TEXT', 1], - ['RefinementRamachandranFavoredTL', - 'RefinementRamachandranFavoredTL', 'TEXT', 0], - ['RefinementProgram', 'RefinementProgram', - 'TEXT', 1], - ['RefinementStatus', 'Refinement\nStatus', - 'TEXT', 1], - ['RefinementBusterReportHTML', 'buster-reports', - 'TEXT', 1], - ['RefinementRefiner', 'RefinementRefiner', - 'TEXT', 1], - ['RefinementDate', 'RefinementDate', - 'TEXT', 1], - - - ['Deposition_PDB_ID', 'Deposition_PDB_ID', - 'TEXT', 1], - ['Deposition_PDB_file', 'Deposition_PDB_file', - 'TEXT', 0], - ['Deposition_Date', 'Deposition_Date', - 'TEXT', 1], - ['Deposition_mmCIF_model_file', - 'Deposition_mmCIF_model_file', 'TEXT', 0], - ['Deposition_mmCIF_SF_file', 'Deposition_mmCIF_SF_file', - 'TEXT', 0], - - ['Label', 'Label', - 'TEXT', 0], - ['table_one', 'table_one', - 'TEXT', 0], - - ['AssayIC50', 'AssayIC50', - 'TEXT', 0], - ['LastUpdated', 'LastUpdated', - 'TEXT', 0], - ['LastUpdated_by', 'LastUpdated_by', - 'TEXT', 0] + ["DataProcessingPathToLogfile", "DataProcessingPathToLogfile", "TEXT", 1], + ["DataProcessingPathToMTZfile", "DataProcessingPathToMTZfile", "TEXT", 1], + ["DataProcessingLOGfileName", "DataProcessingLOGfileName", "TEXT", 0], + ["DataProcessingMTZfileName", "DataProcessingMTZfileName", "TEXT", 0], + [ + "DataProcessingDirectoryOriginal", + "DataProcessingDirectoryOriginal", + "TEXT", + 0, + ], + [ + "DataProcessingUniqueReflectionsOverall", + "Unique Reflections\nOverall", + "TEXT", + 1, + ], + [ + "DataProcessingUniqueReflectionsLow", + "Unique Reflections\nlow", + "TEXT", + 1, + ], + [ + "DataProcessingUniqueReflectionsHigh", + "Unique Reflections\nhigh", + "TEXT", + 1, + ], + ["DataProcessingLattice", "DataProcessing\nLattice", "TEXT", 0], + ["DataProcessingPointGroup", "DataProcessing\nPointGroup", "TEXT", 0], + [ + "DataProcessingUnitCellVolume", + "DataProcessing\nUnit Cell Volume", + "TEXT", + 0, + ], + ["DataProcessingAlert", "DataProcessing\nAlert", "TEXT", 0], + ["DataProcessingScore", "DataProcessing\nScore", "TEXT", 1], + ["DataProcessingStatus", "DataProcessing\nStatus", "TEXT", 1], + ["DataProcessingRcryst", "DataProcessing\nRcryst", "TEXT", 0], + ["DataProcessingRfree", "DataProcessing\nRfree", "TEXT", 0], + [ + "DataProcessingPathToDimplePDBfile", + "DataProcessingPathToDimplePDBfile", + "TEXT", + 0, + ], + [ + "DataProcessingPathToDimpleMTZfile", + "DataProcessingPathToDimpleMTZfile", + "TEXT", + 0, + ], + [ + "DataProcessingDimpleSuccessful", + "DataProcessingDimpleSuccessful", + "TEXT", + 0, + ], + ["DimpleResolutionHigh", "Dimple\nResolution High", "TEXT", 1], + ["DimpleRcryst", "Dimple\nRcryst", "TEXT", 1], + ["DimpleRfree", "Dimple\nRfree", "TEXT", 1], + ["DimplePathToPDB", "Dimple\nPath to PDB file", "TEXT", 1], + ["DimplePathToMTZ", "Dimple\nPath to MTZ file", "TEXT", 1], + ["DimpleReferencePDB", "Dimple\nReference PDB", "TEXT", 1], + ["DimpleStatus", "Dimple\nStatus", "TEXT", 1], + ["DimpleTwinResolutionHigh", "Dimple - twin\nResolution High", "TEXT", 1], + ["DimpleTwinRcryst", "Dimple - twin\nRcryst", "TEXT", 1], + ["DimpleTwinRfree", "Dimple - twin\nRfree", "TEXT", 1], + ["DimpleTwinPathToPDB", "Dimple - twin\nPath to PDB file", "TEXT", 1], + ["DimpleTwinPathToMTZ", "Dimple - twin\nPath to MTZ file", "TEXT", 1], + ["DimpleTwinReferencePDB", "Dimple - twin\nReference PDB", "TEXT", 1], + ["DimpleTwinStatus", "Dimple - twin\nStatus", "TEXT", 1], + ["DimpleTwinFraction", "Dimple - twin\nFraction", "TEXT", 1], + [ + "DataProcessingDimpleTwinSuccessful", + "DataProcessingDimpleTwinSuccessful", + "TEXT", + 0, + ], + ["DimplePANDDAwasRun", "PanDDA\nlaunched?", "TEXT", 1], + ["DimplePANDDAhit", "PanDDA\nhit?", "TEXT", 1], + ["DimplePANDDAreject", "PanDDA\nreject?", "TEXT", 1], + ["DimplePANDDApath", "PanDDA\npath?", "TEXT", 1], + ["PANDDAStatus", "PanDDA\nStatus", "TEXT", 1], + ["DatePanDDAModelCreated", "DatePanDDAModelCreated", "TEXT", 0], + ["RefinementResolution", "Refinement\nResolution", "TEXT", 1], + ["RefinementResolutionTL", "RefinementResolutionTL", "TEXT", 0], + ["RefinementRcryst", "Refinement\nRcryst", "TEXT", 1], + ["RefinementRcrystTraficLight", "RefinementRcrystTraficLight", "TEXT", 0], + ["RefinementRfree", "Refinement\nRfree", "TEXT", 1], + ["RefinementRfreeTraficLight", "RefinementRfreeTraficLight", "TEXT", 0], + ["RefinementSpaceGroup", "Refinement\nSpace Group", "TEXT", 1], + ["RefinementLigandCC", "Ligand CC", "TEXT", 0], + ["RefinementRmsdBonds", "RefinementRmsdBonds", "TEXT", 1], + ["RefinementRmsdBondsTL", "RefinementRmsdBondsTL", "TEXT", 0], + ["RefinementRmsdAngles", "RefinementRmsdAngles", "TEXT", 1], + ["RefinementRmsdAnglesTL", "RefinementRmsdAnglesTL", "TEXT", 0], + ["RefinementOutcome", "Refinement\nOutcome", "TEXT", 1], + ["RefinementOutcomePerson", "RefinementOutcomePerson", "TEXT", 1], + ["RefinementOutcomeDate", "RefinementOutcomeDate", "TEXT", 1], + ["RefinementMTZfree", "RefinementMTZfree", "TEXT", 1], + ["RefinementTwinMTZfree", "RefinementTwinMTZfree", "TEXT", 1], + ["RefinementCIF", "RefinementCIF", "TEXT", 1], + ["RefinementCIFStatus", "Compound\nStatus", "TEXT", 1], + ["RefinementCIFprogram", "RefinementCIFprogram", "TEXT", 1], + ["RefinementPDB_latest", "RefinementPDB_latest", "TEXT", 1], + ["RefinementMTZ_latest", "RefinementMTZ_latest", "TEXT", 1], + ["RefinementMMCIFmodel_latest", "RefinementMMCIFmodel_latest", "TEXT", 1], + [ + "RefinementMMCIFreflections_latest", + "RefinementMMCIFreflections_latest", + "TEXT", + 1, + ], + ["RefinementMatrixWeight", "RefinementMatrixWeight", "TEXT", 0], + ["RefinementComment", "RefinementComment", "TEXT", 0], + [ + "RefinementPathToRefinementFolder", + "RefinementPathToRefinementFolder", + "TEXT", + 0, + ], + ["RefinementLigandConfidence", "Ligand\nConfidence", "TEXT", 0], + [ + "RefinementLigandBoundConformation", + "RefinementLigandBoundConformation", + "TEXT", + 0, + ], + ["RefinementBoundConformation", "RefinementBoundConformation", "TEXT", 0], + ["RefinementMolProbityScore", "MolProbity Score", "TEXT", 1], + ["RefinementMolProbityScoreTL", "RefinementMolProbityScoreTL", "TEXT", 0], + ["RefinementRamachandranOutliers", "Ramachandran\nOutliers", "TEXT", 1], + [ + "RefinementRamachandranOutliersTL", + "RefinementRamachandranOutliersTL", + "TEXT", + 0, + ], + ["RefinementRamachandranFavored", "Ramachandran\nFavored", "TEXT", 1], + [ + "RefinementRamachandranFavoredTL", + "RefinementRamachandranFavoredTL", + "TEXT", + 0, + ], + ["RefinementProgram", "RefinementProgram", "TEXT", 1], + ["RefinementStatus", "Refinement\nStatus", "TEXT", 1], + ["RefinementBusterReportHTML", "buster-reports", "TEXT", 1], + ["RefinementRefiner", "RefinementRefiner", "TEXT", 1], + ["RefinementDate", "RefinementDate", "TEXT", 1], + ["Deposition_PDB_ID", "Deposition_PDB_ID", "TEXT", 1], + ["Deposition_PDB_file", "Deposition_PDB_file", "TEXT", 0], + ["Deposition_Date", "Deposition_Date", "TEXT", 1], + ["Deposition_mmCIF_model_file", "Deposition_mmCIF_model_file", "TEXT", 0], + ["Deposition_mmCIF_SF_file", "Deposition_mmCIF_SF_file", "TEXT", 0], + ["Label", "Label", "TEXT", 0], + ["table_one", "table_one", "TEXT", 0], + ["AssayIC50", "AssayIC50", "TEXT", 0], + ["LastUpdated", "LastUpdated", "TEXT", 0], + ["LastUpdated_by", "LastUpdated_by", "TEXT", 0], ] self.pandda_table_columns = [ - ['ID', 'ID', - 'INTEGER PRIMARY KEY'], - ['CrystalName', - 'Sample ID', 'TEXT'], - ['PANDDApath', - 'PANDDApath', 'TEXT'], - ['PANDDA_site_index', - 'PANDDA_site_index', 'TEXT'], - ['PANDDA_site_name', - 'PANDDA_site_name', 'TEXT'], - ['PANDDA_site_comment', - 'PANDDA_site_comment', 'TEXT'], - ['PANDDA_site_event_index', - 'PANDDA_site_event_index', 'TEXT'], - ['PANDDA_site_event_comment', - 'PANDDA_site_event_comment', 'TEXT'], - ['PANDDA_site_confidence', - 'PANDDA_site_confidence', 'TEXT'], - ['PANDDA_site_InspectConfidence', - 'PANDDA_site_InspectConfidence', 'TEXT'], - ['PANDDA_site_ligand_placed', - 'PANDDA_site_ligand_placed', 'TEXT'], - ['PANDDA_site_viewed', - 'PANDDA_site_viewed', 'TEXT'], - ['PANDDA_site_interesting', - 'PANDDA_site_interesting', 'TEXT'], - ['PANDDA_site_z_peak', - 'PANDDA_site_z_peak', 'TEXT'], - ['PANDDA_site_x', - 'PANDDA_site_x', 'TEXT'], - ['PANDDA_site_y', - 'PANDDA_site_y', 'TEXT'], - ['PANDDA_site_z', - 'PANDDA_site_z', 'TEXT'], - ['PANDDA_site_ligand_id', - 'PANDDA_site_ligand_id', 'TEXT'], - - ['PANDDA_site_ligand_resname', - 'PANDDA_site_ligand_resname', 'TEXT'], - ['PANDDA_site_ligand_chain', - 'PANDDA_site_ligand_chain', 'TEXT'], - ['PANDDA_site_ligand_sequence_number', - 'PANDDA_site_ligand_sequence_number', 'TEXT'], - ['PANDDA_site_ligand_altLoc', - 'PANDDA_site_ligand_altLoc', 'TEXT'], - - ['PANDDA_site_event_map', - 'PANDDA_site_event_map', 'TEXT'], - ['PANDDA_site_event_map_mtz', - 'PANDDA_site_event_map_mtz', 'TEXT'], - ['PANDDA_site_initial_model', - 'PANDDA_site_initial_model', 'TEXT'], - ['PANDDA_site_initial_mtz', - 'PANDDA_site_initial_mtz', 'TEXT'], - ['PANDDA_site_spider_plot', - 'PANDDA_site_spider_plot', 'TEXT'], - ['PANDDA_site_occupancy', - 'PANDDA_site_occupancy', 'TEXT'], - ['PANDDA_site_B_average', - 'PANDDA_site_B_average', 'TEXT'], - ['PANDDA_site_B_ratio_residue_surroundings', - 'PANDDA_site_B_ratio_residue_surroundings', 'TEXT'], - ['PANDDA_site_RSCC', - 'PANDDA_site_RSCC', 'TEXT'], - ['PANDDA_site_RSR', - 'PANDDA_site_RSR', 'TEXT'], - ['PANDDA_site_RSZD', - 'PANDDA_site_RSZD', 'TEXT'], - ['PANDDA_site_rmsd', - 'PANDDA_site_rmsd', 'TEXT'], - ['RefinementOutcome', - 'RefinementOutcome', 'TEXT'], - ['ApoStructures', - 'ApoStructures', 'TEXT'], - ['LastUpdated', - 'LastUpdated', 'TEXT'], - ['LastUpdated_by', - 'LastUpdated_by', 'TEXT'] + ["ID", "ID", "INTEGER PRIMARY KEY"], + ["CrystalName", "Sample ID", "TEXT"], + ["PANDDApath", "PANDDApath", "TEXT"], + ["PANDDA_site_index", "PANDDA_site_index", "TEXT"], + ["PANDDA_site_name", "PANDDA_site_name", "TEXT"], + ["PANDDA_site_comment", "PANDDA_site_comment", "TEXT"], + ["PANDDA_site_event_index", "PANDDA_site_event_index", "TEXT"], + ["PANDDA_site_event_comment", "PANDDA_site_event_comment", "TEXT"], + ["PANDDA_site_confidence", "PANDDA_site_confidence", "TEXT"], + ["PANDDA_site_InspectConfidence", "PANDDA_site_InspectConfidence", "TEXT"], + ["PANDDA_site_ligand_placed", "PANDDA_site_ligand_placed", "TEXT"], + ["PANDDA_site_viewed", "PANDDA_site_viewed", "TEXT"], + ["PANDDA_site_interesting", "PANDDA_site_interesting", "TEXT"], + ["PANDDA_site_z_peak", "PANDDA_site_z_peak", "TEXT"], + ["PANDDA_site_x", "PANDDA_site_x", "TEXT"], + ["PANDDA_site_y", "PANDDA_site_y", "TEXT"], + ["PANDDA_site_z", "PANDDA_site_z", "TEXT"], + ["PANDDA_site_ligand_id", "PANDDA_site_ligand_id", "TEXT"], + ["PANDDA_site_ligand_resname", "PANDDA_site_ligand_resname", "TEXT"], + ["PANDDA_site_ligand_chain", "PANDDA_site_ligand_chain", "TEXT"], + [ + "PANDDA_site_ligand_sequence_number", + "PANDDA_site_ligand_sequence_number", + "TEXT", + ], + ["PANDDA_site_ligand_altLoc", "PANDDA_site_ligand_altLoc", "TEXT"], + ["PANDDA_site_event_map", "PANDDA_site_event_map", "TEXT"], + ["PANDDA_site_event_map_mtz", "PANDDA_site_event_map_mtz", "TEXT"], + ["PANDDA_site_initial_model", "PANDDA_site_initial_model", "TEXT"], + ["PANDDA_site_initial_mtz", "PANDDA_site_initial_mtz", "TEXT"], + ["PANDDA_site_spider_plot", "PANDDA_site_spider_plot", "TEXT"], + ["PANDDA_site_occupancy", "PANDDA_site_occupancy", "TEXT"], + ["PANDDA_site_B_average", "PANDDA_site_B_average", "TEXT"], + [ + "PANDDA_site_B_ratio_residue_surroundings", + "PANDDA_site_B_ratio_residue_surroundings", + "TEXT", + ], + ["PANDDA_site_RSCC", "PANDDA_site_RSCC", "TEXT"], + ["PANDDA_site_RSR", "PANDDA_site_RSR", "TEXT"], + ["PANDDA_site_RSZD", "PANDDA_site_RSZD", "TEXT"], + ["PANDDA_site_rmsd", "PANDDA_site_rmsd", "TEXT"], + ["RefinementOutcome", "RefinementOutcome", "TEXT"], + ["ApoStructures", "ApoStructures", "TEXT"], + ["LastUpdated", "LastUpdated", "TEXT"], + ["LastUpdated_by", "LastUpdated_by", "TEXT"], ] self.deposition_table_columns = [ - ['ID', 'ID', - 'INTEGER PRIMARY KEY'], - - ['CrystalName', - 'Sample ID', 'TEXT'], - ['StructureType', 'StructureType', - 'TEXT'], # apo/model - - ['PDB_file', - 'PDB_file', 'TEXT'], - ['MTZ_file', - 'MTZ_file', 'TEXT'], - - ['mmCIF_model_file', - 'mmCIF_model_file', 'TEXT'], - ['mmCIF_SF_file', - 'mmCIF_SF_file', 'TEXT'], - ['label', 'label', - 'TEXT'], # for index.txt - ['description', 'description', - 'TEXT'], # for index.txt - - ['DimplePANDDApath', - 'DimplePANDDApath', 'TEXT'], - - ['contact_author_PI_salutation', - 'contact_author_PI_salutation', 'TEXT'], - ['contact_author_PI_first_name', - 'contact_author_PI_first_name', 'TEXT'], - ['contact_author_PI_last_name', - 'contact_author_PI_last_name', 'TEXT'], - ['contact_author_PI_middle_name', - 'contact_author_PI_middle_name', 'TEXT'], - ['contact_author_PI_role', - 'contact_author_PI_role', 'TEXT'], - ['contact_author_PI_organization_type', - 'contact_author_PI_organization_type', 'TEXT'], - ['contact_author_PI_organization_name', - 'contact_author_PI_organization_name', 'TEXT'], - ['contact_author_PI_email', - 'contact_author_PI_email', 'TEXT'], - ['contact_author_PI_address', - 'contact_author_PI_address', 'TEXT'], - ['contact_author_PI_city', - 'contact_author_PI_city', 'TEXT'], - ['contact_author_PI_State_or_Province', - 'contact_author_PI_State_or_Province', 'TEXT'], - ['contact_author_PI_Zip_Code', - 'contact_author_PI_Zip_Code', 'TEXT'], - ['contact_author_PI_Country', - 'contact_author_PI_Country', 'TEXT'], - ['contact_author_PI_fax_number', - 'contact_author_PI_fax_number', 'TEXT'], - ['contact_author_PI_phone_number', - 'contact_author_PI_phone_number', 'TEXT'], - ['contact_author_PI_ORCID', - 'contact_author_PI_ORCID', 'TEXT'], - - ['contact_author_salutation', - 'contact_author_salutation', 'TEXT'], - ['contact_author_first_name', - 'contact_author_first_name', 'TEXT'], - ['contact_author_last_name', - 'contact_author_last_name', 'TEXT'], - ['contact_author_middle_name', - 'contact_author_middle_name', 'TEXT'], - ['contact_author_role', - 'contact_author_role', 'TEXT'], - ['contact_author_organization_type', - 'contact_author_organization_type', 'TEXT'], - ['contact_author_organization_name', - 'contact_author_organization_name', 'TEXT'], - ['contact_author_email', - 'contact_author_email', 'TEXT'], - ['contact_author_address', - 'contact_author_address', 'TEXT'], - ['contact_author_city', - 'contact_author_city', 'TEXT'], - ['contact_author_State_or_Province', - 'contact_author_State_or_Province', 'TEXT'], - ['contact_author_Zip_Code', - 'contact_author_Zip_Code', 'TEXT'], - ['contact_author_Country', - 'contact_author_Country', 'TEXT'], - ['contact_author_fax_number', - 'contact_author_fax_number', 'TEXT'], - ['contact_author_phone_number', - 'contact_author_phone_number', 'TEXT'], - ['contact_author_ORCID', - 'contact_author_ORCID', 'TEXT'], - - ['Release_status_for_coordinates', - 'Release_status_for_coordinates', 'TEXT'], - ['Release_status_for_structure_factor', - 'Release_status_for_structure_factor', 'TEXT'], - ['Release_status_for_sequence', - 'Release_status_for_sequence', 'TEXT'], - - ['group_deposition_title', - 'group_deposition_title', 'TEXT'], - ['group_description', - 'group_description', 'TEXT'], - ['structure_title', - 'structure_title', 'TEXT'], - ['structure_details', - 'structure_details', 'TEXT'], - ['group_deposition_title_apo', - 'group_deposition_title_apo', 'TEXT'], - ['structure_title_apo', - 'structure_title_apo', 'TEXT'], - - ['structure_author_name', - 'structure_author_name', 'TEXT'], - ['primary_citation_author_name', - 'primary_citation_author_name', 'TEXT'], - - ['primary_citation_id', - 'primary_citation_id', 'TEXT'], - ['primary_citation_journal_abbrev', - 'primary_citation_journal_abbrev', 'TEXT'], - ['primary_citation_title', - 'primary_citation_title', 'TEXT'], - ['primary_citation_year', - 'primary_citation_year', 'TEXT'], - ['primary_citation_journal_volume', - 'primary_citation_journal_volume', 'TEXT'], - ['primary_citation_page_first', - 'primary_citation_page_first', 'TEXT'], - ['primary_citation_page_last', - 'primary_citation_page_last', 'TEXT'], - - ['molecule_name', - 'molecule_name', 'TEXT'], - ['Fragment_name', - 'Fragment_name', 'TEXT'], - ['Specific_mutation', - 'Specific_mutation', 'TEXT'], - ['Enzyme_Comission_number', - 'Enzyme_Comission_number', 'TEXT'], - ['Source_organism_scientific_name', - 'Source_organism_scientific_name', 'TEXT'], - ['Source_organism_gene', - 'Source_organism_gene', 'TEXT'], - ['Source_organism_strain', - 'Source_organism_strain', 'TEXT'], - ['Expression_system_scientific_name', - 'Expression_system_scientific_name', 'TEXT'], - ['Expression_system_strain', - 'Expression_system_strain', 'TEXT'], - ['Expression_system_vector_type', - 'Expression_system_vector_type', 'TEXT'], - ['Expression_system_plasmid_name', - 'Expression_system_plasmid_name', 'TEXT'], - ['Manipulated_source_details', - 'Manipulated_source_details', 'TEXT'], - ['fragment_name_one_specific_mutation', - 'fragment_name_one_specific_mutation', 'TEXT'], - ['molecule_chain_one', - 'molecule_chain_one', 'TEXT'], - - ['molecule_name_two', - 'molecule_name_two', 'TEXT'], - ['Fragment_name_two', - 'Fragment_name_two', 'TEXT'], - ['Specific_mutation_two', - 'Specific_mutation_two', 'TEXT'], - ['Enzyme_Comission_number_two', - 'Enzyme_Comission_number_two', 'TEXT'], - ['Source_organism_scientific_name_two', - 'Source_organism_scientific_name_two', 'TEXT'], - ['Source_organism_gene_two', - 'Source_organism_gene_two', 'TEXT'], - ['Source_organism_strain_two', - 'Source_organism_strain_two', 'TEXT'], - ['Expression_system_scientific_name_two', - 'Expression_system_scientific_name_two', 'TEXT'], - ['Expression_system_strain_two', - 'Expression_system_strain_two', 'TEXT'], - ['Expression_system_vector_type_two', - 'Expression_system_vector_type_two', 'TEXT'], - ['Expression_system_plasmid_name_two', - 'Expression_system_plasmid_name_two', 'TEXT'], - ['Manipulated_source_details_two', - 'Manipulated_source_details_two', 'TEXT'], - ['fragment_name_two_specific_mutation', - 'fragment_name_one_specific_mutation_two', 'TEXT'], - ['molecule_chain_two', - 'molecule_chain_two', 'TEXT'], - - ['structure_keywords', - 'structure_keywords', 'TEXT'], - ['biological_assembly_chain_number', - 'biological_assembly_chain_number', 'TEXT'], - - - ['crystallization_id', - 'crystallization_id', 'TEXT'], - ['crystallization_method', - 'crystallization_method', 'TEXT'], - ['crystallization_pH', - 'crystallization_pH', 'TEXT'], - ['crystallization_temperature', - 'crystallization_temperature', 'TEXT'], - ['crystallization_details', - 'crystallization_details', 'TEXT'], - - ['radiation_source', - 'radiation_source', 'TEXT'], - ['radiation_source_type', - 'radiation_source_type', 'TEXT'], - ['radiation_wavelengths', - 'radiation_wavelengths', 'TEXT'], - ['radiation_detector', - 'radiation_detector', 'TEXT'], - ['radiation_detector_type', - 'radiation_detector_type', 'TEXT'], - ['data_collection_date', - 'data_collection_date', 'TEXT'], - ['data_collection_temperature', - 'data_collection_temperature', 'TEXT'], - ['data_collection_protocol', - 'data_collection_protocol', 'TEXT'], - - ['SG_project_name', - 'SG_project_name', 'TEXT'], - ['full_name_of_SG_center', - 'full_name_of_SG_center', 'TEXT'], - - ['molecule_one_letter_sequence', - 'molecule_one_letter_sequence', 'TEXT'], - ['molecule_one_letter_sequence_uniprot_id', - 'molecule_one_letter_sequence_uniprot_id', 'TEXT'], - ['molecule_two_letter_sequence', - 'molecule_two_letter_sequence', 'TEXT'], - ['molecule_two_letter_sequence_uniprot_id', - 'molecule_two_letter_sequence_uniprot_id', 'TEXT'], - - ['CrystalName_of_pandda_input', - 'CrystalName_of_pandda_input', 'TEXT'], - - ['pdbx_starting_model', - 'pdbx_starting_model', 'TEXT'], - ['data_integration_software', - 'data_integration_software', 'TEXT'], - ['phasing_software', - 'phasing_software', 'TEXT'], - - ['pdbx_funding_ordinal_one', - 'pdbx_funding_ordinal_one', 'TEXT'], - ['pdbx_funding_organization_one', - 'pdbx_funding_organization_one', 'TEXT'], - ['pdbx_grant_number_one', - 'pdbx_grant_number_one', 'TEXT'], - ['pdbx_grant_country_one', - 'pdbx_grant_country_one', 'TEXT'], - - ['pdbx_funding_ordinal_two', - 'pdbx_funding_ordinal_two', 'TEXT'], - ['pdbx_funding_organization_two', - 'pdbx_funding_organization_two', 'TEXT'], - ['pdbx_grant_number_two', - 'pdbx_grant_number_two', 'TEXT'], - ['pdbx_grant_country_two', - 'pdbx_grant_country_two', 'TEXT'], - - ['pdbx_funding_ordinal_three', - 'pdbx_funding_ordinal_three', 'TEXT'], - ['pdbx_funding_organization_three', - 'pdbx_funding_organization_three', 'TEXT'], - ['pdbx_grant_number_three', - 'pdbx_grant_number_three', 'TEXT'], - ['pdbx_grant_country_three', - 'pdbx_grant_country_three', 'TEXT'], - - ['LastUpdated', - 'LastUpdated', 'TEXT'], - ['LastUpdated_by', - 'LastUpdated_by', 'TEXT'] + ["ID", "ID", "INTEGER PRIMARY KEY"], + ["CrystalName", "Sample ID", "TEXT"], + ["StructureType", "StructureType", "TEXT"], # apo/model + ["PDB_file", "PDB_file", "TEXT"], + ["MTZ_file", "MTZ_file", "TEXT"], + ["mmCIF_model_file", "mmCIF_model_file", "TEXT"], + ["mmCIF_SF_file", "mmCIF_SF_file", "TEXT"], + ["label", "label", "TEXT"], # for index.txt + ["description", "description", "TEXT"], # for index.txt + ["DimplePANDDApath", "DimplePANDDApath", "TEXT"], + ["contact_author_PI_salutation", "contact_author_PI_salutation", "TEXT"], + ["contact_author_PI_first_name", "contact_author_PI_first_name", "TEXT"], + ["contact_author_PI_last_name", "contact_author_PI_last_name", "TEXT"], + ["contact_author_PI_middle_name", "contact_author_PI_middle_name", "TEXT"], + ["contact_author_PI_role", "contact_author_PI_role", "TEXT"], + [ + "contact_author_PI_organization_type", + "contact_author_PI_organization_type", + "TEXT", + ], + [ + "contact_author_PI_organization_name", + "contact_author_PI_organization_name", + "TEXT", + ], + ["contact_author_PI_email", "contact_author_PI_email", "TEXT"], + ["contact_author_PI_address", "contact_author_PI_address", "TEXT"], + ["contact_author_PI_city", "contact_author_PI_city", "TEXT"], + [ + "contact_author_PI_State_or_Province", + "contact_author_PI_State_or_Province", + "TEXT", + ], + ["contact_author_PI_Zip_Code", "contact_author_PI_Zip_Code", "TEXT"], + ["contact_author_PI_Country", "contact_author_PI_Country", "TEXT"], + ["contact_author_PI_fax_number", "contact_author_PI_fax_number", "TEXT"], + [ + "contact_author_PI_phone_number", + "contact_author_PI_phone_number", + "TEXT", + ], + ["contact_author_PI_ORCID", "contact_author_PI_ORCID", "TEXT"], + ["contact_author_salutation", "contact_author_salutation", "TEXT"], + ["contact_author_first_name", "contact_author_first_name", "TEXT"], + ["contact_author_last_name", "contact_author_last_name", "TEXT"], + ["contact_author_middle_name", "contact_author_middle_name", "TEXT"], + ["contact_author_role", "contact_author_role", "TEXT"], + [ + "contact_author_organization_type", + "contact_author_organization_type", + "TEXT", + ], + [ + "contact_author_organization_name", + "contact_author_organization_name", + "TEXT", + ], + ["contact_author_email", "contact_author_email", "TEXT"], + ["contact_author_address", "contact_author_address", "TEXT"], + ["contact_author_city", "contact_author_city", "TEXT"], + [ + "contact_author_State_or_Province", + "contact_author_State_or_Province", + "TEXT", + ], + ["contact_author_Zip_Code", "contact_author_Zip_Code", "TEXT"], + ["contact_author_Country", "contact_author_Country", "TEXT"], + ["contact_author_fax_number", "contact_author_fax_number", "TEXT"], + ["contact_author_phone_number", "contact_author_phone_number", "TEXT"], + ["contact_author_ORCID", "contact_author_ORCID", "TEXT"], + [ + "Release_status_for_coordinates", + "Release_status_for_coordinates", + "TEXT", + ], + [ + "Release_status_for_structure_factor", + "Release_status_for_structure_factor", + "TEXT", + ], + ["Release_status_for_sequence", "Release_status_for_sequence", "TEXT"], + ["group_deposition_title", "group_deposition_title", "TEXT"], + ["group_description", "group_description", "TEXT"], + ["structure_title", "structure_title", "TEXT"], + ["structure_details", "structure_details", "TEXT"], + ["group_deposition_title_apo", "group_deposition_title_apo", "TEXT"], + ["structure_title_apo", "structure_title_apo", "TEXT"], + ["structure_author_name", "structure_author_name", "TEXT"], + ["primary_citation_author_name", "primary_citation_author_name", "TEXT"], + ["primary_citation_id", "primary_citation_id", "TEXT"], + [ + "primary_citation_journal_abbrev", + "primary_citation_journal_abbrev", + "TEXT", + ], + ["primary_citation_title", "primary_citation_title", "TEXT"], + ["primary_citation_year", "primary_citation_year", "TEXT"], + [ + "primary_citation_journal_volume", + "primary_citation_journal_volume", + "TEXT", + ], + ["primary_citation_page_first", "primary_citation_page_first", "TEXT"], + ["primary_citation_page_last", "primary_citation_page_last", "TEXT"], + ["molecule_name", "molecule_name", "TEXT"], + ["Fragment_name", "Fragment_name", "TEXT"], + ["Specific_mutation", "Specific_mutation", "TEXT"], + ["Enzyme_Comission_number", "Enzyme_Comission_number", "TEXT"], + [ + "Source_organism_scientific_name", + "Source_organism_scientific_name", + "TEXT", + ], + ["Source_organism_gene", "Source_organism_gene", "TEXT"], + ["Source_organism_strain", "Source_organism_strain", "TEXT"], + [ + "Expression_system_scientific_name", + "Expression_system_scientific_name", + "TEXT", + ], + ["Expression_system_strain", "Expression_system_strain", "TEXT"], + ["Expression_system_vector_type", "Expression_system_vector_type", "TEXT"], + [ + "Expression_system_plasmid_name", + "Expression_system_plasmid_name", + "TEXT", + ], + ["Manipulated_source_details", "Manipulated_source_details", "TEXT"], + [ + "fragment_name_one_specific_mutation", + "fragment_name_one_specific_mutation", + "TEXT", + ], + ["molecule_chain_one", "molecule_chain_one", "TEXT"], + ["molecule_name_two", "molecule_name_two", "TEXT"], + ["Fragment_name_two", "Fragment_name_two", "TEXT"], + ["Specific_mutation_two", "Specific_mutation_two", "TEXT"], + ["Enzyme_Comission_number_two", "Enzyme_Comission_number_two", "TEXT"], + [ + "Source_organism_scientific_name_two", + "Source_organism_scientific_name_two", + "TEXT", + ], + ["Source_organism_gene_two", "Source_organism_gene_two", "TEXT"], + ["Source_organism_strain_two", "Source_organism_strain_two", "TEXT"], + [ + "Expression_system_scientific_name_two", + "Expression_system_scientific_name_two", + "TEXT", + ], + ["Expression_system_strain_two", "Expression_system_strain_two", "TEXT"], + [ + "Expression_system_vector_type_two", + "Expression_system_vector_type_two", + "TEXT", + ], + [ + "Expression_system_plasmid_name_two", + "Expression_system_plasmid_name_two", + "TEXT", + ], + [ + "Manipulated_source_details_two", + "Manipulated_source_details_two", + "TEXT", + ], + [ + "fragment_name_two_specific_mutation", + "fragment_name_one_specific_mutation_two", + "TEXT", + ], + ["molecule_chain_two", "molecule_chain_two", "TEXT"], + ["structure_keywords", "structure_keywords", "TEXT"], + [ + "biological_assembly_chain_number", + "biological_assembly_chain_number", + "TEXT", + ], + ["crystallization_id", "crystallization_id", "TEXT"], + ["crystallization_method", "crystallization_method", "TEXT"], + ["crystallization_pH", "crystallization_pH", "TEXT"], + ["crystallization_temperature", "crystallization_temperature", "TEXT"], + ["crystallization_details", "crystallization_details", "TEXT"], + ["radiation_source", "radiation_source", "TEXT"], + ["radiation_source_type", "radiation_source_type", "TEXT"], + ["radiation_wavelengths", "radiation_wavelengths", "TEXT"], + ["radiation_detector", "radiation_detector", "TEXT"], + ["radiation_detector_type", "radiation_detector_type", "TEXT"], + ["data_collection_date", "data_collection_date", "TEXT"], + ["data_collection_temperature", "data_collection_temperature", "TEXT"], + ["data_collection_protocol", "data_collection_protocol", "TEXT"], + ["SG_project_name", "SG_project_name", "TEXT"], + ["full_name_of_SG_center", "full_name_of_SG_center", "TEXT"], + ["molecule_one_letter_sequence", "molecule_one_letter_sequence", "TEXT"], + [ + "molecule_one_letter_sequence_uniprot_id", + "molecule_one_letter_sequence_uniprot_id", + "TEXT", + ], + ["molecule_two_letter_sequence", "molecule_two_letter_sequence", "TEXT"], + [ + "molecule_two_letter_sequence_uniprot_id", + "molecule_two_letter_sequence_uniprot_id", + "TEXT", + ], + ["CrystalName_of_pandda_input", "CrystalName_of_pandda_input", "TEXT"], + ["pdbx_starting_model", "pdbx_starting_model", "TEXT"], + ["data_integration_software", "data_integration_software", "TEXT"], + ["phasing_software", "phasing_software", "TEXT"], + ["pdbx_funding_ordinal_one", "pdbx_funding_ordinal_one", "TEXT"], + ["pdbx_funding_organization_one", "pdbx_funding_organization_one", "TEXT"], + ["pdbx_grant_number_one", "pdbx_grant_number_one", "TEXT"], + ["pdbx_grant_country_one", "pdbx_grant_country_one", "TEXT"], + ["pdbx_funding_ordinal_two", "pdbx_funding_ordinal_two", "TEXT"], + ["pdbx_funding_organization_two", "pdbx_funding_organization_two", "TEXT"], + ["pdbx_grant_number_two", "pdbx_grant_number_two", "TEXT"], + ["pdbx_grant_country_two", "pdbx_grant_country_two", "TEXT"], + ["pdbx_funding_ordinal_three", "pdbx_funding_ordinal_three", "TEXT"], + [ + "pdbx_funding_organization_three", + "pdbx_funding_organization_three", + "TEXT", + ], + ["pdbx_grant_number_three", "pdbx_grant_number_three", "TEXT"], + ["pdbx_grant_country_three", "pdbx_grant_country_three", "TEXT"], + ["LastUpdated", "LastUpdated", "TEXT"], + ["LastUpdated_by", "LastUpdated_by", "TEXT"], ] self.data_collection_columns = [ - ['ID', 'ID', - 'INTEGER PRIMARY KEY'], - ['CrystalName', 'Sample ID', - 'TEXT', 0], - ['ProteinName', 'ProteinName', - 'TEXT', 1], - - ['DataCollectionVisit', 'Visit', - 'TEXT', 0], - ['DataCollectionRun', 'Run', - 'TEXT', 0], - ['DataCollectionSubdir', 'SubDir', - 'TEXT', 0], - ['DataCollectionBeamline', 'Beamline', - 'TEXT', 0], - ['DataCollectionOutcome', 'DataCollection\nOutcome', - 'TEXT', 1], - ['DataCollectionDate', 'Data Collection\nDate', - 'TEXT', 1], - ['DataCollectionWavelength', 'Wavelength', - 'TEXT', 0], - ['DataCollectionPinBarcode', 'GDA\nBarcode', - 'TEXT', 1], - - ['DataCollectionCrystalImage1', 'img1', - 'TEXT', 1], - ['DataCollectionCrystalImage2', 'img2', - 'TEXT', 1], - ['DataCollectionCrystalImage3', 'img3', - 'TEXT', 1], - ['DataCollectionCrystalImage4', 'img4', - 'TEXT', 1], - - ['DataProcessingPathToImageFiles', - 'Path to diffraction\nimage files', 'TEXT', 1], - ['DataProcessingProgram', 'Program', - 'TEXT', 1], - ['DataProcessingSpaceGroup', 'DataProcessing\nSpaceGroup', - 'TEXT', 1], - ['DataProcessingUnitCell', 'DataProcessing\nUnitCell', - 'TEXT', 0], - ['DataProcessingAutoAssigned', 'auto-assigned', - 'TEXT', 0], - ['DataProcessingA', 'DataProcessing\nA', - 'TEXT', 0], - ['DataProcessingB', 'DataProcessing\nB', - 'TEXT', 0], - ['DataProcessingC', 'DataProcessing\nC', - 'TEXT', 0], - ['DataProcessingAlpha', 'DataProcessing\nAlpha', - 'TEXT', 0], - ['DataProcessingBeta', 'DataProcessing\nBeta', - 'TEXT', 0], - ['DataProcessingGamma', 'DataProcessing\nGamma', - 'TEXT', 0], - ['DataProcessingResolutionOverall', 'Resolution\nOverall', - 'TEXT', 0], - ['DataProcessingResolutionLow', 'Resolution\nLow', - 'TEXT', 0], - ['DataProcessingResolutionLowInnerShell', - 'Resolution\nLow (Inner Shell)', 'TEXT', 0], - ['DataProcessingResolutionHigh', 'Resolution\nHigh', - 'TEXT', 1], - ['DataProcessingResolutionHigh15sigma', - 'Resolution\n[Mn = 1.5]', 'TEXT', 1], - ['DataProcessingResolutionHigh20sigma', - 'Resolution\n[Mn = 2.0]', 'TEXT', 1], - ['DataProcessingResolutionHighOuterShell', - 'Resolution\nHigh (Outer Shell)', 'TEXT', 0], - ['DataProcessingRmergeOverall', 'Rmerge\nOverall', - 'TEXT', 1], - ['DataProcessingRmergeLow', 'Rmerge\nLow', - 'TEXT', 1], - ['DataProcessingRmergeHigh', 'Rmerge\nHigh', - 'TEXT', 1], - ['DataProcessingIsigOverall', - 'Mn\nOverall', 'TEXT', 1], - ['DataProcessingIsigLow', - 'Mn\nLow', 'TEXT', 1], - ['DataProcessingIsigHigh', - 'Mn\nHigh', 'TEXT', 1], - ['DataProcessingCompletenessOverall', 'Completeness\nOverall', - 'TEXT', 1], - ['DataProcessingCompletenessLow', 'Completeness\nLow', - 'TEXT', 1], - ['DataProcessingCompletenessHigh', 'Completeness\nHigh', - 'TEXT', 1], - ['DataProcessingMultiplicityOverall', 'Multiplicity\nOverall', - 'TEXT', 1], - ['DataProcessingMultiplicityLow', 'Multiplicity\nLow', - 'TEXT', 1], - ['DataProcessingMultiplicityHigh', 'Multiplicity\nHigh', - 'TEXT', 1], - ['DataProcessingCChalfOverall', - 'CC(1/2)\nOverall', 'TEXT', 1], - ['DataProcessingCChalfLow', - 'CC(1/2)\nLow', 'TEXT', 1], - ['DataProcessingCChalfHigh', - 'CC(1/2)\nHigh', 'TEXT', 1], - ['DataProcessingPathToLogfile', - 'DataProcessingPathToLogfile', 'TEXT', 1], - ['DataProcessingPathToMTZfile', - 'DataProcessingPathToMTZfile', 'TEXT', 1], - ['DataProcessingLOGfileName', 'DataProcessingLOGfileName', - 'TEXT', 0], - ['DataProcessingMTZfileName', 'DataProcessingMTZfileName', - 'TEXT', 0], - ['DataProcessingDirectoryOriginal', - 'DataProcessingDirectoryOriginal', 'TEXT', 0], - ['DataProcessingUniqueReflectionsOverall', - 'Unique Reflections\nOverall', 'TEXT', 1], - ['DataProcessingUniqueReflectionsLow', 'Unique Reflections\nlow', - 'TEXT', 1], - ['DataProcessingUniqueReflectionsHigh', - 'Unique Reflections\nhigh', 'TEXT', 1], - ['DataProcessingLattice', 'DataProcessing\nLattice', - 'TEXT', 0], - ['DataProcessingPointGroup', - 'DataProcessing\nPointGroup', 'TEXT', 0], - ['DataProcessingUnitCellVolume', - 'DataProcessing\nUnit Cell Volume', 'TEXT', 0], - ['DataProcessingAlert', 'DataProcessing\nAlert', - 'TEXT', 0], - ['DataProcessingScore', 'DataProcessing\nScore', - 'TEXT', 1], - ['DataProcessingStatus', 'DataProcessing\nStatus', - 'TEXT', 1], - ['LastUpdated', 'LastUpdated', - 'TEXT', 0], - ['LastUpdated_by', 'LastUpdated_by', - 'TEXT', 0] + ["ID", "ID", "INTEGER PRIMARY KEY"], + ["CrystalName", "Sample ID", "TEXT", 0], + ["ProteinName", "ProteinName", "TEXT", 1], + ["DataCollectionVisit", "Visit", "TEXT", 0], + ["DataCollectionRun", "Run", "TEXT", 0], + ["DataCollectionSubdir", "SubDir", "TEXT", 0], + ["DataCollectionBeamline", "Beamline", "TEXT", 0], + ["DataCollectionOutcome", "DataCollection\nOutcome", "TEXT", 1], + ["DataCollectionDate", "Data Collection\nDate", "TEXT", 1], + ["DataCollectionWavelength", "Wavelength", "TEXT", 0], + ["DataCollectionPinBarcode", "GDA\nBarcode", "TEXT", 1], + ["DataCollectionCrystalImage1", "img1", "TEXT", 1], + ["DataCollectionCrystalImage2", "img2", "TEXT", 1], + ["DataCollectionCrystalImage3", "img3", "TEXT", 1], + ["DataCollectionCrystalImage4", "img4", "TEXT", 1], + [ + "DataProcessingPathToImageFiles", + "Path to diffraction\nimage files", + "TEXT", + 1, + ], + ["DataProcessingProgram", "Program", "TEXT", 1], + ["DataProcessingSpaceGroup", "DataProcessing\nSpaceGroup", "TEXT", 1], + ["DataProcessingUnitCell", "DataProcessing\nUnitCell", "TEXT", 0], + ["DataProcessingAutoAssigned", "auto-assigned", "TEXT", 0], + ["DataProcessingA", "DataProcessing\nA", "TEXT", 0], + ["DataProcessingB", "DataProcessing\nB", "TEXT", 0], + ["DataProcessingC", "DataProcessing\nC", "TEXT", 0], + ["DataProcessingAlpha", "DataProcessing\nAlpha", "TEXT", 0], + ["DataProcessingBeta", "DataProcessing\nBeta", "TEXT", 0], + ["DataProcessingGamma", "DataProcessing\nGamma", "TEXT", 0], + ["DataProcessingResolutionOverall", "Resolution\nOverall", "TEXT", 0], + ["DataProcessingResolutionLow", "Resolution\nLow", "TEXT", 0], + [ + "DataProcessingResolutionLowInnerShell", + "Resolution\nLow (Inner Shell)", + "TEXT", + 0, + ], + ["DataProcessingResolutionHigh", "Resolution\nHigh", "TEXT", 1], + [ + "DataProcessingResolutionHigh15sigma", + "Resolution\n[Mn = 1.5]", + "TEXT", + 1, + ], + [ + "DataProcessingResolutionHigh20sigma", + "Resolution\n[Mn = 2.0]", + "TEXT", + 1, + ], + [ + "DataProcessingResolutionHighOuterShell", + "Resolution\nHigh (Outer Shell)", + "TEXT", + 0, + ], + ["DataProcessingRmergeOverall", "Rmerge\nOverall", "TEXT", 1], + ["DataProcessingRmergeLow", "Rmerge\nLow", "TEXT", 1], + ["DataProcessingRmergeHigh", "Rmerge\nHigh", "TEXT", 1], + ["DataProcessingIsigOverall", "Mn\nOverall", "TEXT", 1], + ["DataProcessingIsigLow", "Mn\nLow", "TEXT", 1], + ["DataProcessingIsigHigh", "Mn\nHigh", "TEXT", 1], + ["DataProcessingCompletenessOverall", "Completeness\nOverall", "TEXT", 1], + ["DataProcessingCompletenessLow", "Completeness\nLow", "TEXT", 1], + ["DataProcessingCompletenessHigh", "Completeness\nHigh", "TEXT", 1], + ["DataProcessingMultiplicityOverall", "Multiplicity\nOverall", "TEXT", 1], + ["DataProcessingMultiplicityLow", "Multiplicity\nLow", "TEXT", 1], + ["DataProcessingMultiplicityHigh", "Multiplicity\nHigh", "TEXT", 1], + ["DataProcessingCChalfOverall", "CC(1/2)\nOverall", "TEXT", 1], + ["DataProcessingCChalfLow", "CC(1/2)\nLow", "TEXT", 1], + ["DataProcessingCChalfHigh", "CC(1/2)\nHigh", "TEXT", 1], + ["DataProcessingPathToLogfile", "DataProcessingPathToLogfile", "TEXT", 1], + ["DataProcessingPathToMTZfile", "DataProcessingPathToMTZfile", "TEXT", 1], + ["DataProcessingLOGfileName", "DataProcessingLOGfileName", "TEXT", 0], + ["DataProcessingMTZfileName", "DataProcessingMTZfileName", "TEXT", 0], + [ + "DataProcessingDirectoryOriginal", + "DataProcessingDirectoryOriginal", + "TEXT", + 0, + ], + [ + "DataProcessingUniqueReflectionsOverall", + "Unique Reflections\nOverall", + "TEXT", + 1, + ], + [ + "DataProcessingUniqueReflectionsLow", + "Unique Reflections\nlow", + "TEXT", + 1, + ], + [ + "DataProcessingUniqueReflectionsHigh", + "Unique Reflections\nhigh", + "TEXT", + 1, + ], + ["DataProcessingLattice", "DataProcessing\nLattice", "TEXT", 0], + ["DataProcessingPointGroup", "DataProcessing\nPointGroup", "TEXT", 0], + [ + "DataProcessingUnitCellVolume", + "DataProcessing\nUnit Cell Volume", + "TEXT", + 0, + ], + ["DataProcessingAlert", "DataProcessing\nAlert", "TEXT", 0], + ["DataProcessingScore", "DataProcessing\nScore", "TEXT", 1], + ["DataProcessingStatus", "DataProcessing\nStatus", "TEXT", 1], + ["LastUpdated", "LastUpdated", "TEXT", 0], + ["LastUpdated_by", "LastUpdated_by", "TEXT", 0], ] self.zenodo_table_columns = [ - ['ID', 'ID', - 'INTEGER PRIMARY KEY'], - ['DimplePANDDApath', 'DimplePANDDApath', 'TEXT'], - ['ZenodoTitle', 'ZenodoTitle', 'TEXT'], - ['ZenodoHTTPS', 'ZenodoHTTPS', 'TEXT'], - ['ZenodoDOI', 'ZenodoDOI', 'TEXT'], - ['LastUpdated', 'LastUpdated', 'TEXT'], - ['LastUpdated_by', 'LastUpdated_by', 'TEXT'] + ["ID", "ID", "INTEGER PRIMARY KEY"], + ["DimplePANDDApath", "DimplePANDDApath", "TEXT"], + ["ZenodoTitle", "ZenodoTitle", "TEXT"], + ["ZenodoHTTPS", "ZenodoHTTPS", "TEXT"], + ["ZenodoDOI", "ZenodoDOI", "TEXT"], + ["LastUpdated", "LastUpdated", "TEXT"], + ["LastUpdated_by", "LastUpdated_by", "TEXT"], ] self.label_table_columns = [ - ['ID', 'ID', - 'INTEGER PRIMARY KEY'], - ['Label', 'Label', 'TEXT'], - ['Description', 'Description', 'TEXT'], + ["ID", "ID", "INTEGER PRIMARY KEY"], + ["Label", "Label", "TEXT"], + ["Description", "Description", "TEXT"], ] def columns_not_to_display(self): @@ -964,8 +740,8 @@ def columns_not_to_display(self): def get_empty_db_dict(self): db_dict = {} for column in self.column_list: - if column[0] != 'ID': - db_dict[column[0]] = '' + if column[0] != "ID": + db_dict[column[0]] = "" return db_dict def create_missing_columns(self): @@ -974,64 +750,73 @@ def create_missing_columns(self): connect.row_factory = sqlite3.Row cursor = connect.cursor() - tableDict = {'mainTable': self.column_list, - 'panddaTable': self.pandda_table_columns, - 'depositTable': self.deposition_table_columns, - 'collectionTable': self.data_collection_columns, - 'zenodoTable': self.zenodo_table_columns, - 'labelTable': self.label_table_columns} + tableDict = { + "mainTable": self.column_list, + "panddaTable": self.pandda_table_columns, + "depositTable": self.deposition_table_columns, + "collectionTable": self.data_collection_columns, + "zenodoTable": self.zenodo_table_columns, + "labelTable": self.label_table_columns, + } for table in tableDict: - cursor.execute("create table if not exists " + - table+" (ID INTEGER);") + cursor.execute("create table if not exists " + table + " (ID INTEGER);") existing_columns = [] - cursor.execute("SELECT * FROM "+table) + cursor.execute("SELECT * FROM " + table) for column in cursor.description: existing_columns.append(column[0]) for column in tableDict[table]: if column[0] not in existing_columns: cursor.execute( - "alter table " + table + " add column '" + column[0] + "' '" + column[2] + "'") + "alter table " + + table + + " add column '" + + column[0] + + "' '" + + column[2] + + "'" + ) connect.commit() - if table == 'labelTable': - cursor.execute('select ID from labelTable') + if table == "labelTable": + cursor.execute("select ID from labelTable") id = cursor.fetchall() if id == []: for idx in range(5): cursor.execute( - "insert into labelTable (ID) Values (%s)" % str(idx+1)) - -# existing_columns=[] -# connect=sqlite3.connect(self.data_source_file) -# connect.row_factory = sqlite3.Row -# cursor = connect.cursor() -# cursor.execute("SELECT * FROM mainTable") -# for column in cursor.description: -# existing_columns.append(column[0]) -# for column in self.column_list: -# if column[0] not in existing_columns: -# cursor.execute("alter table mainTable add column '"+column[0]+"' '"+column[2]+"'") -# connect.commit() -# # create PANDDA table if not exists -# cursor.execute("create table if not exists panddaTable (ID INTEGER);") -# existing_columns=[] -# cursor.execute("SELECT * FROM panddaTable") -# for column in cursor.description: -# existing_columns.append(column[0]) -# for column in self.pandda_table_columns: -# if column[0] not in existing_columns: -# cursor.execute("alter table panddaTable add column '"+column[0]+"' '"+column[2]+"'") -# connect.commit() -# # create DEPOSIT table if not exists -# cursor.execute("create table if not exists depositTable (ID INTEGER);") -# existing_columns=[] -# cursor.execute("SELECT * FROM depositTable") -# for column in cursor.description: -# existing_columns.append(column[0]) -# for column in self.deposition_table_columns: -# if column[0] not in existing_columns: -# cursor.execute("alter table depositTable add column '"+column[0]+"' '"+column[2]+"'") -# connect.commit() + "insert into labelTable (ID) Values (%s)" % str(idx + 1) + ) + + # existing_columns=[] + # connect=sqlite3.connect(self.data_source_file) + # connect.row_factory = sqlite3.Row + # cursor = connect.cursor() + # cursor.execute("SELECT * FROM mainTable") + # for column in cursor.description: + # existing_columns.append(column[0]) + # for column in self.column_list: + # if column[0] not in existing_columns: + # cursor.execute("alter table mainTable add column '"+column[0]+"' '"+column[2]+"'") + # connect.commit() + # # create PANDDA table if not exists + # cursor.execute("create table if not exists panddaTable (ID INTEGER);") + # existing_columns=[] + # cursor.execute("SELECT * FROM panddaTable") + # for column in cursor.description: + # existing_columns.append(column[0]) + # for column in self.pandda_table_columns: + # if column[0] not in existing_columns: + # cursor.execute("alter table panddaTable add column '"+column[0]+"' '"+column[2]+"'") + # connect.commit() + # # create DEPOSIT table if not exists + # cursor.execute("create table if not exists depositTable (ID INTEGER);") + # existing_columns=[] + # cursor.execute("SELECT * FROM depositTable") + # for column in cursor.description: + # existing_columns.append(column[0]) + # for column in self.deposition_table_columns: + # if column[0] not in existing_columns: + # cursor.execute("alter table depositTable add column '"+column[0]+"' '"+column[2]+"'") + # connect.commit() def return_column_list(self): return self.column_list @@ -1043,19 +828,30 @@ def create_empty_data_source_file(self): with connect: cursor = connect.cursor() cursor.execute( - "CREATE TABLE mainTable("+self.column_list[0][0]+' '+self.column_list[0][2]+")") + "CREATE TABLE mainTable(" + + self.column_list[0][0] + + " " + + self.column_list[0][2] + + ")" + ) for i in range(1, len(self.column_list)): - cursor.execute("alter table mainTable add column '" + - self.column_list[i][0]+"' '"+self.column_list[i][2]+"'") + cursor.execute( + "alter table mainTable add column '" + + self.column_list[i][0] + + "' '" + + self.column_list[i][2] + + "'" + ) connect.commit() # Don't need to create panddaTable at this point, because table will be created by create_missing_columns # which is called the first time a data source in specified in XCE -# with connect: -# cursor = connect.cursor() -# cursor.execute("CREATE TABLE panddaTable("+self.pandda_table_columns[0][0]+' '+self.pandda_table_columns[0][2]+")") -# for i in range(1,len(self.pandda_table_columns)): -# cursor.execute("alter table mainTable add column '"+self.pandda_table_columns[i][0]+"' '"+self.pandda_table_columns[i][2]+"'") -# connect.commit() + + # with connect: + # cursor = connect.cursor() + # cursor.execute("CREATE TABLE panddaTable("+self.pandda_table_columns[0][0]+' '+self.pandda_table_columns[0][2]+")") + # for i in range(1,len(self.pandda_table_columns)): + # cursor.execute("alter table mainTable add column '"+self.pandda_table_columns[i][0]+"' '"+self.pandda_table_columns[i][2]+"'") + # connect.commit() def get_all_samples_in_data_source_as_list(self): # creates sqlite file if non existent @@ -1085,9 +881,15 @@ def get_db_dict_for_sample(self, sampleID): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - "select * from mainTable where CrystalName='{0!s}';".format(sampleID)) - print(( - "SQLITE: select * from mainTable where CrystalName='{0!s}';".format(sampleID))) + "select * from mainTable where CrystalName='{0!s}';".format(sampleID) + ) + print( + ( + "SQLITE: select * from mainTable where CrystalName='{0!s}';".format( + sampleID + ) + ) + ) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() @@ -1103,12 +905,13 @@ def get_deposit_dict_for_sample(self, sampleID): # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() -# if sampleID == 'ground-state': # just select first row in depositTable -# cursor.execute("SELECT * FROM depositTable ORDER BY ROWID ASC LIMIT 1;") -# else: -# cursor.execute("select * from depositTable where CrystalName='{0!s}';".format(sampleID)) + # if sampleID == 'ground-state': # just select first row in depositTable + # cursor.execute("SELECT * FROM depositTable ORDER BY ROWID ASC LIMIT 1;") + # else: + # cursor.execute("select * from depositTable where CrystalName='{0!s}';".format(sampleID)) cursor.execute( - "select * from depositTable where CrystalName='{0!s}';".format(sampleID)) + "select * from depositTable where CrystalName='{0!s}';".format(sampleID) + ) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() @@ -1128,7 +931,10 @@ def get_zenodo_dict_for_pandda_analysis(self, panddaPath): cursor = connect.cursor() try: cursor.execute( - "select * from zenodoTable where DimplePANDDApath='{0!s}';".format(panddaPath)) + "select * from zenodoTable where DimplePANDDApath='{0!s}';".format( + panddaPath + ) + ) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() @@ -1149,7 +955,10 @@ def get_db_pandda_dict_for_sample_and_site(self, sampleID, site_index): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - "select * from panddaTable where CrystalName='{0!s}' and PANDDA_site_index='{1!s}';".format(sampleID, site_index)) + "select * from panddaTable where CrystalName='{0!s}' and PANDDA_site_index='{1!s}';".format( + sampleID, site_index + ) + ) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() @@ -1157,15 +966,20 @@ def get_db_pandda_dict_for_sample_and_site(self, sampleID, site_index): db_dict[header[n]] = str(item) return db_dict - def get_db_pandda_dict_for_sample_and_site_and_event(self, sampleID, site_index, event_index): + def get_db_pandda_dict_for_sample_and_site_and_event( + self, sampleID, site_index, event_index + ): db_dict = {} header = [] data = [] # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("select * from panddaTable where CrystalName='{0!s}' and PANDDA_site_index='{1!s}' and PANDDA_site_event_index='{2!s}' and PANDDA_site_ligand_placed='True';".format( - sampleID, site_index, event_index)) + cursor.execute( + "select * from panddaTable where CrystalName='{0!s}' and PANDDA_site_index='{1!s}' and PANDDA_site_event_index='{2!s}' and PANDDA_site_ligand_placed='True';".format( + sampleID, site_index, event_index + ) + ) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() @@ -1186,448 +1000,613 @@ def import_csv_file(self, csv_file): cursor = connect.cursor() available_columns = [] cursor.execute("SELECT * FROM mainTable") - for column in cursor.description: # only update existing columns in data source + for column in cursor.description: # only update existing columns in data source available_columns.append(column[0]) - with open(csv_file, 'rb') as csv_import: # `with` statement available in 2.5+ + with open(csv_file, "rb") as csv_import: # `with` statement available in 2.5+ # csv.DictReader uses first line in file for column headings by default csv_dict = csv.DictReader(csv_import) # comma is default delimiter for line in csv_dict: - sampleID = line['CrystalName'] - if str(sampleID).replace(' ', '') == '': + sampleID = line["CrystalName"] + if str(sampleID).replace(" ", "") == "": continue if self.check_if_sample_exists_in_data_source(sampleID): - update_string = '' + update_string = "" for key, value in line.items(): - if key == 'ID' or key == 'CrystalName': + if key == "ID" or key == "CrystalName": continue if key not in available_columns: continue # this is how I had it originally, so it would ignore empty fields # the problem is that if the user wants to set all values to Null, # if will ignore it and leave the inital value in the datasource -# if not str(value).replace(' ','')=='': # ignore if nothing in csv field -# update_string+=str(key)+'='+"'"+str(value)+"'"+',' -# print "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';" -# cursor.execute("UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';") + # if not str(value).replace(' ','')=='': # ignore if nothing in csv field + # update_string+=str(key)+'='+"'"+str(value)+"'"+',' + # print "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';" + # cursor.execute("UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';") # now try this instead; not sure what will break now... - update_string += str(key)+'='+"'"+str(value)+"'"+',' -# print "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';" + update_string += str(key) + "=" + "'" + str(value) + "'" + "," + # print "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';" cursor.execute( - "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';") + "UPDATE mainTable SET " + + update_string[:-1] + + " WHERE CrystalName=" + + "'" + + sampleID + + "';" + ) else: - column_string = '' - value_string = '' + column_string = "" + value_string = "" for key, value in line.items(): - if key == 'ID': + if key == "ID": continue if key not in available_columns: continue # ignore if nothing in csv field - if not str(value).replace(' ', '') == '': - value_string += "'"+value+"'"+',' - column_string += key+',' -# print sampleID -# print "INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");" + if not str(value).replace(" ", "") == "": + value_string += "'" + value + "'" + "," + column_string += key + "," + # print sampleID + # print "INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");" cursor.execute( - "INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");") + "INSERT INTO mainTable (" + + column_string[:-1] + + ") VALUES (" + + value_string[:-1] + + ");" + ) connect.commit() def update_data_source(self, sampleID, data_dict): - print('here') - data_dict['LastUpdated'] = str( - datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by'] = getpass.getuser() + print("here") + data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict["LastUpdated_by"] = getpass.getuser() # need to do this since some older sqlite files contain a columnn called # DataProcessingResolutionHigh1.5sigma # and this does not go down well with the SQLite statement below - removeKey = '' + removeKey = "" for key in data_dict: - if '.5' in key: + if ".5" in key: removeKey = key break - if removeKey != '': + if removeKey != "": del data_dict[removeKey] connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - update_string = '' + update_string = "" for key in data_dict: value = data_dict[key] - if key == 'ID' or key == 'CrystalName': + if key == "ID" or key == "CrystalName": continue - if not str(value).replace(' ', '') == '': # ignore empty fields - update_string += str(key)+'='+"'"+str(value)+"'"+',' + if not str(value).replace(" ", "") == "": # ignore empty fields + update_string += str(key) + "=" + "'" + str(value) + "'" + "," else: - update_string += str(key)+' = null,' - if update_string != '': + update_string += str(key) + " = null," + if update_string != "": # print "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"'" - cursor.execute("UPDATE mainTable SET " + - update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"'") + cursor.execute( + "UPDATE mainTable SET " + + update_string[:-1] + + " WHERE CrystalName=" + + "'" + + sampleID + + "'" + ) connect.commit() def update_panddaTable(self, sampleID, site_index, data_dict): - data_dict['LastUpdated'] = str( - datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by'] = getpass.getuser() + data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict["LastUpdated_by"] = getpass.getuser() connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - update_string = '' + update_string = "" for key in data_dict: value = data_dict[key] - if key == 'ID' or key == 'CrystalName' or key == 'PANDDA_site_index': + if key == "ID" or key == "CrystalName" or key == "PANDDA_site_index": continue - if not str(value).replace(' ', '') == '': # ignore empty fields - update_string += str(key)+'='+"'"+str(value)+"'"+',' + if not str(value).replace(" ", "") == "": # ignore empty fields + update_string += str(key) + "=" + "'" + str(value) + "'" + "," else: - update_string += str(key)+' = null,' - if update_string != '': - cursor.execute("UPDATE panddaTable SET " + - update_string[:-1]+" WHERE CrystalName='{0!s}' and PANDDA_site_index='{1!s}'".format(sampleID, site_index)) + update_string += str(key) + " = null," + if update_string != "": + cursor.execute( + "UPDATE panddaTable SET " + + update_string[:-1] + + " WHERE CrystalName='{0!s}' and PANDDA_site_index='{1!s}'".format( + sampleID, site_index + ) + ) connect.commit() - def update_site_event_panddaTable(self, sampleID, site_index, event_index, data_dict): - data_dict['LastUpdated'] = str( - datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by'] = getpass.getuser() + def update_site_event_panddaTable( + self, sampleID, site_index, event_index, data_dict + ): + data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict["LastUpdated_by"] = getpass.getuser() connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - update_string = '' + update_string = "" for key in data_dict: value = data_dict[key] - if key == 'ID' or key == 'CrystalName' or key == 'PANDDA_site_index' or key == 'PANDDA_site_event_index': + if ( + key == "ID" + or key == "CrystalName" + or key == "PANDDA_site_index" + or key == "PANDDA_site_event_index" + ): continue - if not str(value).replace(' ', '') == '': # ignore empty fields - update_string += str(key)+'='+"'"+str(value)+"'"+',' + if not str(value).replace(" ", "") == "": # ignore empty fields + update_string += str(key) + "=" + "'" + str(value) + "'" + "," else: - update_string += str(key)+' = null,' - if update_string != '': - cursor.execute("UPDATE panddaTable SET " + - update_string[:-1]+" WHERE CrystalName='{0!s}' and PANDDA_site_index='{1!s}' and PANDDA_site_event_index='{2!s}'".format(sampleID, site_index, event_index)) + update_string += str(key) + " = null," + if update_string != "": + cursor.execute( + "UPDATE panddaTable SET " + + update_string[:-1] + + " WHERE CrystalName='{0!s}' and PANDDA_site_index='{1!s}' and PANDDA_site_event_index='{2!s}'".format( + sampleID, site_index, event_index + ) + ) connect.commit() def update_depositTable(self, sampleID, structure_type, data_dict): - data_dict['LastUpdated'] = str( - datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by'] = getpass.getuser() + data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict["LastUpdated_by"] = getpass.getuser() connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - update_string = '' + update_string = "" for key in data_dict: value = data_dict[key] - if key == 'ID' or key == 'CrystalName' or key == 'StructureType': + if key == "ID" or key == "CrystalName" or key == "StructureType": continue - if not str(value).replace(' ', '') == '': # ignore empty fields + if not str(value).replace(" ", "") == "": # ignore empty fields # update_string+=str(key)+'='+"'"+str(value)+"'"+',' # update_string+=str(key)+'='+'"'+str(value)+'"'+',' - update_string += str(key)+'='+'"' + \ - str(value).replace('\r', '').replace('\n', '')+'"'+',' + update_string += ( + str(key) + + "=" + + '"' + + str(value).replace("\r", "").replace("\n", "") + + '"' + + "," + ) else: - update_string += str(key)+' = null,' - if update_string != '': + update_string += str(key) + " = null," + if update_string != "": # print '-->',"UPDATE depositTable SET "+update_string[:-1]+" WHERE CrystalName='{0!s}' and StructureType='{1!s}'".format(sampleID, structure_type) # cursor.execute("UPDATE depositTable SET "+update_string[:-1]+" WHERE CrystalName='{0!s}' and StructureType='{1!s}'".format(sampleID, structure_type)) - cursor.execute('UPDATE depositTable SET ' + - update_string[:-1]+' WHERE CrystalName="{0!s}" and StructureType="{1!s}"'.format(sampleID, structure_type)) + cursor.execute( + "UPDATE depositTable SET " + + update_string[:-1] + + ' WHERE CrystalName="{0!s}" and StructureType="{1!s}"'.format( + sampleID, structure_type + ) + ) connect.commit() def update_specified_table(self, sampleID, data_dict, table): - data_dict['LastUpdated'] = str( - datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by'] = getpass.getuser() + data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict["LastUpdated_by"] = getpass.getuser() connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - update_string = '' + update_string = "" for key in data_dict: value = data_dict[key] - if key == 'ID' or key == 'CrystalName': + if key == "ID" or key == "CrystalName": continue - if not str(value).replace(' ', '') == '': # ignore empty fields - update_string += str(key)+'='+"'"+str(value)+"'"+',' - if update_string != '': - cursor.execute("UPDATE "+table+" SET " + - update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"'") + if not str(value).replace(" ", "") == "": # ignore empty fields + update_string += str(key) + "=" + "'" + str(value) + "'" + "," + if update_string != "": + cursor.execute( + "UPDATE " + + table + + " SET " + + update_string[:-1] + + " WHERE CrystalName=" + + "'" + + sampleID + + "'" + ) connect.commit() def update_insert_data_source(self, sampleID, data_dict): - data_dict['LastUpdated'] = str( - datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by'] = getpass.getuser() + data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict["LastUpdated_by"] = getpass.getuser() connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute('Select CrystalName FROM mainTable') + cursor.execute("Select CrystalName FROM mainTable") available_columns = [] cursor.execute("SELECT * FROM mainTable") - for column in cursor.description: # only update existing columns in data source + for column in cursor.description: # only update existing columns in data source available_columns.append(column[0]) if self.check_if_sample_exists_in_data_source(sampleID): for key in data_dict: value = data_dict[key] - if key == 'ID' or key == 'CrystalName': + if key == "ID" or key == "CrystalName": continue - if not str(value).replace(' ', '') == '': # ignore empty fields - update_string = str(key)+'='+"'"+str(value)+"'" - cursor.execute("UPDATE mainTable SET "+update_string + - " WHERE CrystalName="+"'"+sampleID+"';") + if not str(value).replace(" ", "") == "": # ignore empty fields + update_string = str(key) + "=" + "'" + str(value) + "'" + cursor.execute( + "UPDATE mainTable SET " + + update_string + + " WHERE CrystalName=" + + "'" + + sampleID + + "';" + ) else: - column_string = 'CrystalName'+',' - value_string = "'"+sampleID+"'"+',' + column_string = "CrystalName" + "," + value_string = "'" + sampleID + "'" + "," for key in data_dict: value = data_dict[key] - if key == 'ID': + if key == "ID": continue if key not in available_columns: continue - if not str(value).replace(' ', '') == '': # ignore if nothing in csv field - value_string += "'"+str(value)+"'"+',' - column_string += key+',' + if ( + not str(value).replace(" ", "") == "" + ): # ignore if nothing in csv field + value_string += "'" + str(value) + "'" + "," + column_string += key + "," cursor.execute( - "INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");") + "INSERT INTO mainTable (" + + column_string[:-1] + + ") VALUES (" + + value_string[:-1] + + ");" + ) connect.commit() def update_insert_panddaTable(self, sampleID, data_dict): - data_dict['LastUpdated'] = str( - datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by'] = getpass.getuser() + data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict["LastUpdated_by"] = getpass.getuser() connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute('Select CrystalName,PANDDA_site_index FROM panddaTable') -# available_columns=[] -# cursor.execute("SELECT * FROM panddaTable") -# for column in cursor.description: # only update existing columns in data source -# available_columns.append(column[0]) + cursor.execute("Select CrystalName,PANDDA_site_index FROM panddaTable") + # available_columns=[] + # cursor.execute("SELECT * FROM panddaTable") + # for column in cursor.description: # only update existing columns in data source + # available_columns.append(column[0]) samples_sites_in_table = [] tmp = cursor.fetchall() for item in tmp: - line = [x.encode('UTF8') for x in list(item)] + line = [x.encode("UTF8") for x in list(item)] samples_sites_in_table.append(line) found_sample_site = False for entry in samples_sites_in_table: - if entry[0] == sampleID and entry[1] == data_dict['PANDDA_site_index']: + if entry[0] == sampleID and entry[1] == data_dict["PANDDA_site_index"]: found_sample_site = True if found_sample_site: for key in data_dict: value = data_dict[key] - if key == 'ID' or key == 'CrystalName' or key == 'PANDDA_site_index': + if key == "ID" or key == "CrystalName" or key == "PANDDA_site_index": continue - if not str(value).replace(' ', '') == '': # ignore empty fields - update_string = str(key)+'='+"'"+str(value)+"'" -# print "UPDATE panddaTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and PANDDA_site_index is '"+data_dict['PANDDA_site_index']+"';" - cursor.execute("UPDATE panddaTable SET "+update_string+" WHERE CrystalName=" + - "'"+sampleID+"' and PANDDA_site_index is '"+data_dict['PANDDA_site_index']+"';") + if not str(value).replace(" ", "") == "": # ignore empty fields + update_string = str(key) + "=" + "'" + str(value) + "'" + # print "UPDATE panddaTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and PANDDA_site_index is '"+data_dict['PANDDA_site_index']+"';" + cursor.execute( + "UPDATE panddaTable SET " + + update_string + + " WHERE CrystalName=" + + "'" + + sampleID + + "' and PANDDA_site_index is '" + + data_dict["PANDDA_site_index"] + + "';" + ) else: - column_string = '' - value_string = '' + column_string = "" + value_string = "" for key in data_dict: value = data_dict[key] - if key == 'ID': + if key == "ID": continue -# if key not in available_columns: -# continue - if not str(value).replace(' ', '') == '': # ignore if nothing in csv field - value_string += "'"+str(value)+"'"+',' - column_string += key+',' - print("INSERT INTO panddaTable (" + \ - column_string[:-1]+") VALUES ("+value_string[:-1]+");") - cursor.execute("INSERT INTO panddaTable (" + - column_string[:-1]+") VALUES ("+value_string[:-1]+");") + # if key not in available_columns: + # continue + if ( + not str(value).replace(" ", "") == "" + ): # ignore if nothing in csv field + value_string += "'" + str(value) + "'" + "," + column_string += key + "," + print( + "INSERT INTO panddaTable (" + + column_string[:-1] + + ") VALUES (" + + value_string[:-1] + + ");" + ) + cursor.execute( + "INSERT INTO panddaTable (" + + column_string[:-1] + + ") VALUES (" + + value_string[:-1] + + ");" + ) connect.commit() def update_insert_any_table(self, table, data_dict, condition_dict): - data_dict['LastUpdated'] = str( - datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by'] = getpass.getuser() + data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict["LastUpdated_by"] = getpass.getuser() connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() # columns - columns = '' + columns = "" for c in condition_dict: - columns += c+',' + columns += c + "," # condition - condition_string = '' + condition_string = "" for key in condition_dict: condition = condition_dict[key] - condition_string += str(key) + '=' + "'" + \ - str(condition) + "' and " + condition_string += str(key) + "=" + "'" + str(condition) + "' and " - cursor.execute('Select %s FROM %s where %s' % - (columns[:-1], table, condition_string[:-5])) + cursor.execute( + "Select %s FROM %s where %s" % (columns[:-1], table, condition_string[:-5]) + ) tmp = cursor.fetchall() if not tmp: data_dict.update(condition_dict) - value_string = '' - column_string = '' + value_string = "" + column_string = "" for key in data_dict: value = data_dict[key] - value_string += "'" + str(value) + "'" + ',' - column_string += key + ',' - cursor.execute("INSERT INTO "+table+" (" + - column_string[:-1] + ") VALUES (" + value_string[:-1] + ");") + value_string += "'" + str(value) + "'" + "," + column_string += key + "," + cursor.execute( + "INSERT INTO " + + table + + " (" + + column_string[:-1] + + ") VALUES (" + + value_string[:-1] + + ");" + ) else: - update_string = '' + update_string = "" for key in data_dict: value = data_dict[key] - update_string += str(key) + '=' + "'" + str(value) + "'," + update_string += str(key) + "=" + "'" + str(value) + "'," cursor.execute( - "UPDATE " + table + - " SET " + update_string[:-1] + - " WHERE " + condition_string[:-5] + ";") + "UPDATE " + + table + + " SET " + + update_string[:-1] + + " WHERE " + + condition_string[:-5] + + ";" + ) connect.commit() def update_insert_site_event_panddaTable(self, sampleID, data_dict): - data_dict['LastUpdated'] = str( - datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by'] = getpass.getuser() + data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict["LastUpdated_by"] = getpass.getuser() connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - 'Select CrystalName,PANDDA_site_index,PANDDA_site_event_index FROM panddaTable') -# available_columns=[] -# cursor.execute("SELECT * FROM panddaTable") -# for column in cursor.description: # only update existing columns in data source -# available_columns.append(column[0]) + "Select CrystalName,PANDDA_site_index,PANDDA_site_event_index FROM panddaTable" + ) + # available_columns=[] + # cursor.execute("SELECT * FROM panddaTable") + # for column in cursor.description: # only update existing columns in data source + # available_columns.append(column[0]) samples_sites_in_table = [] tmp = cursor.fetchall() for item in tmp: - line = [x.encode('UTF8') for x in list(item)] + line = [x.encode("UTF8") for x in list(item)] samples_sites_in_table.append(line) found_sample_site = False for entry in samples_sites_in_table: - if entry[0] == sampleID and entry[1] == data_dict['PANDDA_site_index'] and entry[2] == data_dict['PANDDA_site_event_index']: + if ( + entry[0] == sampleID + and entry[1] == data_dict["PANDDA_site_index"] + and entry[2] == data_dict["PANDDA_site_event_index"] + ): found_sample_site = True if found_sample_site: for key in data_dict: value = data_dict[key] - if key == 'ID' or key == 'CrystalName' or key == 'PANDDA_site_index' or key == 'PANDDA_site_event_index': + if ( + key == "ID" + or key == "CrystalName" + or key == "PANDDA_site_index" + or key == "PANDDA_site_event_index" + ): continue - if not str(value).replace(' ', '') == '': # ignore empty fields - update_string = str(key)+'='+"'"+str(value)+"'" -# print "UPDATE panddaTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and PANDDA_site_index is '"+data_dict['PANDDA_site_index']+"';" - cursor.execute("UPDATE panddaTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and PANDDA_site_index is '" + - data_dict['PANDDA_site_index']+"' and PANDDA_site_event_index is '"+data_dict['PANDDA_site_event_index']+"';") + if not str(value).replace(" ", "") == "": # ignore empty fields + update_string = str(key) + "=" + "'" + str(value) + "'" + # print "UPDATE panddaTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and PANDDA_site_index is '"+data_dict['PANDDA_site_index']+"';" + cursor.execute( + "UPDATE panddaTable SET " + + update_string + + " WHERE CrystalName=" + + "'" + + sampleID + + "' and PANDDA_site_index is '" + + data_dict["PANDDA_site_index"] + + "' and PANDDA_site_event_index is '" + + data_dict["PANDDA_site_event_index"] + + "';" + ) else: - column_string = '' - value_string = '' + column_string = "" + value_string = "" for key in data_dict: value = data_dict[key] - if key == 'ID': + if key == "ID": continue -# if key not in available_columns: -# continue - if not str(value).replace(' ', '') == '': # ignore if nothing in csv field - value_string += "'"+str(value)+"'"+',' - column_string += key+',' - print("INSERT INTO panddaTable (" + \ - column_string[:-1]+") VALUES ("+value_string[:-1]+");") - cursor.execute("INSERT INTO panddaTable (" + - column_string[:-1]+") VALUES ("+value_string[:-1]+");") + # if key not in available_columns: + # continue + if ( + not str(value).replace(" ", "") == "" + ): # ignore if nothing in csv field + value_string += "'" + str(value) + "'" + "," + column_string += key + "," + print( + "INSERT INTO panddaTable (" + + column_string[:-1] + + ") VALUES (" + + value_string[:-1] + + ");" + ) + cursor.execute( + "INSERT INTO panddaTable (" + + column_string[:-1] + + ") VALUES (" + + value_string[:-1] + + ");" + ) connect.commit() def update_insert_depositTable(self, sampleID, data_dict): - data_dict['LastUpdated'] = str( - datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by'] = getpass.getuser() + data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict["LastUpdated_by"] = getpass.getuser() connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() available_columns = [] cursor.execute("SELECT * FROM depositTable") - for column in cursor.description: # only update existing columns in data source + for column in cursor.description: # only update existing columns in data source available_columns.append(column[0]) - cursor.execute('Select CrystalName FROM depositTable') + cursor.execute("Select CrystalName FROM depositTable") samples_in_table = [] tmp = cursor.fetchall() for item in tmp: - line = [x.encode('UTF8') for x in list(item)] -# print 'a',item -# print 'b',str(item) -# print 'c',line -# print 'd',line[0] -# print 'e',str(line[0]) + line = [x.encode("UTF8") for x in list(item)] + # print 'a',item + # print 'b',str(item) + # print 'c',line + # print 'd',line[0] + # print 'e',str(line[0]) if str(item) not in samples_in_table: samples_in_table.append(str(line[0])) -# samples_in_table.append(line) + # samples_in_table.append(line) if sampleID in samples_in_table: for key in data_dict: value = data_dict[key] - if key == 'ID' or key == 'CrystalName': + if key == "ID" or key == "CrystalName": continue - if not str(value).replace(' ', '') == '': # ignore empty fields - update_string = str(key)+'='+"'"+str(value)+"'" - print("UPDATE depositTable SET "+update_string + \ - " WHERE CrystalName="+"'"+sampleID+"';") + if not str(value).replace(" ", "") == "": # ignore empty fields + update_string = str(key) + "=" + "'" + str(value) + "'" + print( + "UPDATE depositTable SET " + + update_string + + " WHERE CrystalName=" + + "'" + + sampleID + + "';" + ) cursor.execute( - "UPDATE depositTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"';") + "UPDATE depositTable SET " + + update_string + + " WHERE CrystalName=" + + "'" + + sampleID + + "';" + ) else: - column_string = 'CrystalName'+',' - value_string = "'"+sampleID+"'"+',' + column_string = "CrystalName" + "," + value_string = "'" + sampleID + "'" + "," for key in data_dict: value = data_dict[key] - if key == 'ID': + if key == "ID": continue if key not in available_columns: continue - if not str(value).replace(' ', '') == '': # ignore if nothing in csv field - value_string += "'"+str(value)+"'"+',' - column_string += key+',' - print("INSERT INTO depositTable (" + \ - column_string[:-1]+") VALUES ("+value_string[:-1]+");") - cursor.execute("INSERT INTO depositTable (" + - column_string[:-1]+") VALUES ("+value_string[:-1]+");") + if ( + not str(value).replace(" ", "") == "" + ): # ignore if nothing in csv field + value_string += "'" + str(value) + "'" + "," + column_string += key + "," + print( + "INSERT INTO depositTable (" + + column_string[:-1] + + ") VALUES (" + + value_string[:-1] + + ");" + ) + cursor.execute( + "INSERT INTO depositTable (" + + column_string[:-1] + + ") VALUES (" + + value_string[:-1] + + ");" + ) connect.commit() def update_insert_not_null_fields_only(self, sampleID, data_dict): - data_dict['LastUpdated'] = str( - datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict['LastUpdated_by'] = getpass.getuser() + data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) + data_dict["LastUpdated_by"] = getpass.getuser() connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute('Select CrystalName FROM mainTable') + cursor.execute("Select CrystalName FROM mainTable") available_columns = [] cursor.execute("SELECT * FROM mainTable") - for column in cursor.description: # only update existing columns in data source + for column in cursor.description: # only update existing columns in data source available_columns.append(column[0]) if self.check_if_sample_exists_in_data_source(sampleID): for key in data_dict: value = data_dict[key] -# print value - if key == 'ID' or key == 'CrystalName': + # print value + if key == "ID" or key == "CrystalName": continue - if not str(value).replace(' ', '') == '': # ignore empty fields - update_string = str(key)+'='+"'"+str(value)+"'" -# cursor.execute("UPDATE mainTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and "+str(key)+" is null;") - cursor.execute("UPDATE mainTable SET "+update_string+" WHERE CrystalName=" + - "'"+sampleID+"' and ("+str(key)+" is null or "+str(key)+"='');") + if not str(value).replace(" ", "") == "": # ignore empty fields + update_string = str(key) + "=" + "'" + str(value) + "'" + # cursor.execute("UPDATE mainTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and "+str(key)+" is null;") + cursor.execute( + "UPDATE mainTable SET " + + update_string + + " WHERE CrystalName=" + + "'" + + sampleID + + "' and (" + + str(key) + + " is null or " + + str(key) + + "='');" + ) else: - column_string = 'CrystalName'+',' - value_string = "'"+sampleID+"'"+',' + column_string = "CrystalName" + "," + value_string = "'" + sampleID + "'" + "," for key in data_dict: value = data_dict[key] - if key == 'ID': + if key == "ID": continue if key not in available_columns: continue - if not str(value).replace(' ', '') == '': # ignore if nothing in csv field - value_string += "'"+str(value)+"'"+',' - column_string += key+',' + if ( + not str(value).replace(" ", "") == "" + ): # ignore if nothing in csv field + value_string += "'" + str(value) + "'" + "," + column_string += key + "," cursor.execute( - "INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");") + "INSERT INTO mainTable (" + + column_string[:-1] + + ") VALUES (" + + value_string[:-1] + + ");" + ) connect.commit() def get_value_from_field(self, sampleID, column): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute("SELECT "+column + - " FROM mainTable WHERE CrystalName='"+sampleID+"';") + cursor.execute( + "SELECT " + + column + + " FROM mainTable WHERE CrystalName='" + + sampleID + + "';" + ) return cursor.fetchone() def export_to_csv_file(self, csv_file): @@ -1639,19 +1618,18 @@ def export_to_csv_file(self, csv_file): header += (column[0],) rows = cursor.fetchall() csvWriter = csv.writer(open(csv_file, "w")) - csvWriter.writerows([header]+rows) - - -# def load_samples_from_data_source(self): -# header=[] -# data=[] -# connect=sqlite3.connect(self.data_source_file) -# cursor = connect.cursor() -# cursor.execute("SELECT * FROM mainTable") -# for column in cursor.description: -# header.append(column[0]) -# data = cursor.fetchall() -# return ([header,data]) + csvWriter.writerows([header] + rows) + + # def load_samples_from_data_source(self): + # header=[] + # data=[] + # connect=sqlite3.connect(self.data_source_file) + # cursor = connect.cursor() + # cursor.execute("SELECT * FROM mainTable") + # for column in cursor.description: + # header.append(column[0]) + # data = cursor.fetchall() + # return ([header,data]) def load_samples_from_data_source(self): header = [] @@ -1664,68 +1642,67 @@ def load_samples_from_data_source(self): data = cursor.fetchall() return header, data - -# def get_samples_for_coot(self,RefinementOutcome,pandda_site): -# sample_list_for_coot=[] -# connect=sqlite3.connect(self.data_source_file) -# cursor = connect.cursor() -# -# if RefinementOutcome=='0 - All Datasets': -# outcome = " not null " -# else: -# outcome = " '%s' " %RefinementOutcome -# -# if int(pandda_site) > 0: -# sqlite = ( -# "select" -# " mainTable.CrystalName," -# " mainTable.CompoundCode," -# " mainTable.RefinementCIF," -# " mainTable.RefinementMTZfree," -# " mainTable.RefinementPathToRefinementFolder," -# " panddaTable.RefinementOutcome, " -# " panddaTable.PANDDA_site_event_map," -# " panddaTable.PANDDA_site_confidence," -# " panddaTable.PANDDA_site_x," -# " panddaTable.PANDDA_site_y," -# " panddaTable.PANDDA_site_z," -# " panddaTable.PANDDA_site_initial_model," -# " panddaTable.PANDDA_site_initial_mtz," -# " panddaTable.PANDDA_site_spider_plot, " -# " panddaTable.PANDDA_site_index " -# "from mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " -# "where panddaTable.PANDDA_site_index is '%s'" %pandda_site+ -# " and panddaTable.PANDDA_site_ligand_placed is 'True'" -# " and panddaTable.RefinementOutcome is %s;" %outcome -# ) -# -# else: -# sqlite = ( -# "select" -# " CrystalName," -# " CompoundCode," -# " RefinementCIF," -# " RefinementMTZfree," -# " RefinementPathToRefinementFolder," -# " RefinementOutcome " -# "from mainTable " -# "where RefinementOutcome is %s;" %outcome -# ) -# -# cursor.execute(sqlite) -# -# tmp = cursor.fetchall() -# for item in tmp: -# tmpx=[] -# for i in list(item): -# if i==None: -# tmpx.append('None') -# else: -# tmpx.append(i) -# line=[x.encode('UTF8') for x in tmpx] -# sample_list_for_coot.append(line) -# -# return sample_list_for_coot + # def get_samples_for_coot(self,RefinementOutcome,pandda_site): + # sample_list_for_coot=[] + # connect=sqlite3.connect(self.data_source_file) + # cursor = connect.cursor() + # + # if RefinementOutcome=='0 - All Datasets': + # outcome = " not null " + # else: + # outcome = " '%s' " %RefinementOutcome + # + # if int(pandda_site) > 0: + # sqlite = ( + # "select" + # " mainTable.CrystalName," + # " mainTable.CompoundCode," + # " mainTable.RefinementCIF," + # " mainTable.RefinementMTZfree," + # " mainTable.RefinementPathToRefinementFolder," + # " panddaTable.RefinementOutcome, " + # " panddaTable.PANDDA_site_event_map," + # " panddaTable.PANDDA_site_confidence," + # " panddaTable.PANDDA_site_x," + # " panddaTable.PANDDA_site_y," + # " panddaTable.PANDDA_site_z," + # " panddaTable.PANDDA_site_initial_model," + # " panddaTable.PANDDA_site_initial_mtz," + # " panddaTable.PANDDA_site_spider_plot, " + # " panddaTable.PANDDA_site_index " + # "from mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " + # "where panddaTable.PANDDA_site_index is '%s'" %pandda_site+ + # " and panddaTable.PANDDA_site_ligand_placed is 'True'" + # " and panddaTable.RefinementOutcome is %s;" %outcome + # ) + # + # else: + # sqlite = ( + # "select" + # " CrystalName," + # " CompoundCode," + # " RefinementCIF," + # " RefinementMTZfree," + # " RefinementPathToRefinementFolder," + # " RefinementOutcome " + # "from mainTable " + # "where RefinementOutcome is %s;" %outcome + # ) + # + # cursor.execute(sqlite) + # + # tmp = cursor.fetchall() + # for item in tmp: + # tmpx=[] + # for i in list(item): + # if i==None: + # tmpx.append('None') + # else: + # tmpx.append(i) + # line=[x.encode('UTF8') for x in tmpx] + # sample_list_for_coot.append(line) + # + # return sample_list_for_coot def get_pandda_info_for_coot(self, xtalID, pandda_site): pandda_info_for_coot = [] @@ -1741,8 +1718,8 @@ def get_pandda_info_for_coot(self, xtalID, pandda_site): " PANDDA_site_spider_plot " "from panddaTable " "where " - " CrystalName is '%s'" % xtalID + - " and PANDDA_site_index is '{0!s}';".format(pandda_site) + " CrystalName is '%s'" % xtalID + + " and PANDDA_site_index is '{0!s}';".format(pandda_site) ) cursor.execute(sqlite) @@ -1752,10 +1729,10 @@ def get_pandda_info_for_coot(self, xtalID, pandda_site): tmpx = [] for i in list(item): if i is None: - tmpx.append('None') + tmpx.append("None") else: tmpx.append(i) - line = [x.encode('UTF8') for x in tmpx] + line = [x.encode("UTF8") for x in tmpx] pandda_info_for_coot.append(line) return pandda_info_for_coot @@ -1765,7 +1742,7 @@ def get_todo_list_for_coot(self, RefinementOutcome, pandda_site): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - if RefinementOutcome == '0 - All Datasets': + if RefinementOutcome == "0 - All Datasets": outcome = " not null " else: outcome = " '{0!s}' ".format(RefinementOutcome) @@ -1795,24 +1772,23 @@ def get_todo_list_for_coot(self, RefinementOutcome, pandda_site): " panddaTable.RefinementOutcome, " " panddaTable.PANDDA_site_confidence " "from mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " - "where panddaTable.PANDDA_site_index is '%s'" % pandda_site + - " and panddaTable.PANDDA_site_ligand_placed is 'True'" - " and panddaTable.RefinementOutcome like " + - outcome.split()[0]+"%';" + "where panddaTable.PANDDA_site_index is '%s'" % pandda_site + + " and panddaTable.PANDDA_site_ligand_placed is 'True'" + " and panddaTable.RefinementOutcome like " + outcome.split()[0] + "%';" ) -# sqlite = ( -# "select" -# " mainTable.CrystalName," -# " mainTable.CompoundCode," -# " mainTable.RefinementCIF," -# " mainTable.RefinementMTZfree," -# " mainTable.RefinementPathToRefinementFolder," -# " panddaTable.RefinementOutcome, " -# " panddaTable.PANDDA_site_confidence " -# "from mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " -# "where panddaTable.PANDDA_site_index is '%s'" %pandda_site+ -# " and panddaTable.RefinementOutcome like "+outcome.split()[0]+"%';" -# ) + # sqlite = ( + # "select" + # " mainTable.CrystalName," + # " mainTable.CompoundCode," + # " mainTable.RefinementCIF," + # " mainTable.RefinementMTZfree," + # " mainTable.RefinementPathToRefinementFolder," + # " panddaTable.RefinementOutcome, " + # " panddaTable.PANDDA_site_confidence " + # "from mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " + # "where panddaTable.PANDDA_site_index is '%s'" %pandda_site+ + # " and panddaTable.RefinementOutcome like "+outcome.split()[0]+"%';" + # ) else: sqlite = ( "select" @@ -1833,10 +1809,10 @@ def get_todo_list_for_coot(self, RefinementOutcome, pandda_site): tmpx = [] for i in list(item): if i is None: - tmpx.append('None') + tmpx.append("None") else: tmpx.append(i) - line = [x.encode('UTF8') for x in tmpx] + line = [x.encode("UTF8") for x in tmpx] sample_list_for_coot.append(line) return sample_list_for_coot @@ -1846,7 +1822,7 @@ def get_todoList_for_coot(self, RefinementOutcome): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - if RefinementOutcome == '0 - All Datasets': + if RefinementOutcome == "0 - All Datasets": outcome = " not null " else: outcome = " '{0!s}' ".format(RefinementOutcome) @@ -1861,7 +1837,8 @@ def get_todoList_for_coot(self, RefinementOutcome): " RefinementOutcome," " RefinementLigandConfidence " "from mainTable " - "where RefinementOutcome is %s and (DimpleRfree is not Null or RefinementRfree is not Null) order by CrystalName ASC;" % outcome + "where RefinementOutcome is %s and (DimpleRfree is not Null or RefinementRfree is not Null) order by CrystalName ASC;" + % outcome ) cursor.execute(sqlite) @@ -1871,82 +1848,113 @@ def get_todoList_for_coot(self, RefinementOutcome): tmpx = [] for i in list(item): if i is None: - tmpx.append('None') + tmpx.append("None") else: tmpx.append(i) - line = [x.encode('UTF8') for x in tmpx] + line = [x.encode("UTF8") for x in tmpx] sample_list_for_coot.append(line) crystalDict = {} for entry in sample_list_for_coot: if entry[0] not in crystalDict: - sqlite = ("select" - " PANDDA_site_event_map," - " PANDDA_site_x," - " PANDDA_site_y," - " PANDDA_site_z," - " PANDDA_site_spider_plot," - " PANDDA_site_index," - " PANDDA_site_event_index," - " PANDDA_site_confidence," - " PANDDA_site_name," - " PANDDA_site_InspectConfidence," - " PANDDA_site_interesting," - " PANDDA_site_event_comment " - "from panddaTable " - "where " - " CrystalName is '%s';" % entry[0]) + sqlite = ( + "select" + " PANDDA_site_event_map," + " PANDDA_site_x," + " PANDDA_site_y," + " PANDDA_site_z," + " PANDDA_site_spider_plot," + " PANDDA_site_index," + " PANDDA_site_event_index," + " PANDDA_site_confidence," + " PANDDA_site_name," + " PANDDA_site_InspectConfidence," + " PANDDA_site_interesting," + " PANDDA_site_event_comment " + "from panddaTable " + "where " + " CrystalName is '%s';" % entry[0] + ) cursor.execute(sqlite) tmp = cursor.fetchall() if tmp: crystalDict[entry[0]] = [] for item in tmp: - print([entry[0], str(item[0]), str(item[1]), str(item[2]), str(item[3]), str(item[4]), str( - item[5]), str(item[6]), str(item[7]), str(item[8]), str(item[9]), str(item[10]), str(item[11])]) - crystalDict[entry[0]].append([str(item[0]), str(item[1]), str(item[2]), str(item[3]), str(item[4]), str( - item[5]), str(item[6]), str(item[7]), str(item[8]), str(item[9]), str(item[10]), str(item[11])]) + print( + [ + entry[0], + str(item[0]), + str(item[1]), + str(item[2]), + str(item[3]), + str(item[4]), + str(item[5]), + str(item[6]), + str(item[7]), + str(item[8]), + str(item[9]), + str(item[10]), + str(item[11]), + ] + ) + crystalDict[entry[0]].append( + [ + str(item[0]), + str(item[1]), + str(item[2]), + str(item[3]), + str(item[4]), + str(item[5]), + str(item[6]), + str(item[7]), + str(item[8]), + str(item[9]), + str(item[10]), + str(item[11]), + ] + ) return sample_list_for_coot, crystalDict def translate_xce_column_list_to_sqlite(self, column_list): out_list = [] for item in column_list: - if item.startswith('Exclude'): - out_list.append(['Exclude']) - if item.startswith('Ignore'): - out_list.append(['Ignore']) -# if item.startswith('img'): -# out_list.append([item,item]) -# continue - if item.startswith('Export'): + if item.startswith("Exclude"): + out_list.append(["Exclude"]) + if item.startswith("Ignore"): + out_list.append(["Ignore"]) + # if item.startswith('img'): + # out_list.append([item,item]) + # continue + if item.startswith("Export"): # out_list.append('Export') - out_list.append(['Export', item]) + out_list.append(["Export", item]) continue - if item.startswith('Show'): + if item.startswith("Show"): out_list.append([item, item]) continue - if item.startswith('Run\nDimple'): + if item.startswith("Run\nDimple"): out_list.append([item, item]) continue - if item.startswith('Select'): + if item.startswith("Select"): out_list.append([item, item]) continue - if item.startswith('Run\nxia2'): + if item.startswith("Run\nxia2"): out_list.append([item, item]) continue - if item.startswith('Dataset ID'): + if item.startswith("Dataset ID"): out_list.append([item, item]) continue - if item.startswith('Reference\nSpaceGroup'): + if item.startswith("Reference\nSpaceGroup"): out_list.append([item, item]) continue - if item.startswith('Difference\nUC Volume (%)'): + if item.startswith("Difference\nUC Volume (%)"): out_list.append([item, item]) continue - if item.startswith('Reference File'): + if item.startswith("Reference File"): out_list.append([item, item]) continue - if item.startswith('PanDDA site details'): + if item.startswith("PanDDA site details"): out_list.append([item, item]) continue for entry in self.column_list: @@ -1956,16 +1964,16 @@ def translate_xce_column_list_to_sqlite(self, column_list): return out_list def get_list_of_pandda_sites_for_coot(self): - site_list = [['0', 'any site']] + site_list = [["0", "any site"]] sqlite = ( - 'select distinct' - ' panddaTable.PANDDA_site_index,' - ' panddaTable.PANDDA_site_name ' - 'from panddaTable ' - 'order by cast (panddaTable.PANDDA_site_index as integer) ASC;' + "select distinct" + " panddaTable.PANDDA_site_index," + " panddaTable.PANDDA_site_name " + "from panddaTable " + "order by cast (panddaTable.PANDDA_site_index as integer) ASC;" ) - print('data source', self.data_source_file) + print("data source", self.data_source_file) connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute(sqlite) @@ -1980,21 +1988,23 @@ def get_list_of_pandda_sites_for_coot(self): return site_list def export_csv_for_WONKA(self): - SQLite = ("select" - " panddaTable.PANDDA_site_ligand_resname," - " panddaTable.PANDDA_site_ligand_sequence_number," - " panddaTable.PANDDA_site_ligand_chain," - " panddaTable.RefinementOutcome," - " mainTable.CompoundSMILES," - " mainTable.RefinementBoundConformation," - " panddaTable.PANDDA_site_initial_mtz," - " panddaTable.PANDDA_site_event_map," - " panddaTable.CrystalName," - " mainTable.CompoundCode " - "from" - " mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " - "where" - " (panddaTable.RefinementOutcome like '3%' or panddaTable.RefinementOutcome like '4%' or panddaTable.RefinementOutcome like '5%')") + SQLite = ( + "select" + " panddaTable.PANDDA_site_ligand_resname," + " panddaTable.PANDDA_site_ligand_sequence_number," + " panddaTable.PANDDA_site_ligand_chain," + " panddaTable.RefinementOutcome," + " mainTable.CompoundSMILES," + " mainTable.RefinementBoundConformation," + " panddaTable.PANDDA_site_initial_mtz," + " panddaTable.PANDDA_site_event_map," + " panddaTable.CrystalName," + " mainTable.CompoundCode " + "from" + " mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " + "where" + " (panddaTable.RefinementOutcome like '3%' or panddaTable.RefinementOutcome like '4%' or panddaTable.RefinementOutcome like '5%')" + ) connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute(SQLite) @@ -2002,181 +2012,250 @@ def export_csv_for_WONKA(self): for column in cursor.description: header += (column[0],) rows = cursor.fetchall() - csvWriter = csv.writer(open('for_wonka.csv', "w")) - csvWriter.writerows([header]+rows) + csvWriter = csv.writer(open("for_wonka.csv", "w")) + csvWriter.writerows([header] + rows) def create_missing_apo_records_in_depositTable(self, xce_logfile): Logfile = XChemLog.updateLog(xce_logfile) connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - "select panddaTable.ApoStructures from panddaTable where panddaTable.ApoStructures is not Null") + "select panddaTable.ApoStructures from panddaTable where panddaTable.ApoStructures is not Null" + ) tmp = cursor.fetchall() -# print str(tmp) + # print str(tmp) apoStructureList = [] for item in tmp: - for xtal in str(item[0]).split(';'): + for xtal in str(item[0]).split(";"): if xtal not in apoStructureList: apoStructureList.append(xtal) if not apoStructureList: - Logfile.insert( - 'no apo structures were assigned to your pandda models') + Logfile.insert("no apo structures were assigned to your pandda models") else: Logfile.insert( - 'the following datasets were at some point used as apo structures for pandda.analyse: '+str(apoStructureList)) + "the following datasets were at some point used as apo structures for pandda.analyse: " + + str(apoStructureList) + ) apoInDB = [] cursor.execute( - "select CrystalName from depositTable where StructureType is 'apo'") + "select CrystalName from depositTable where StructureType is 'apo'" + ) tmp = cursor.fetchall() for xtal in tmp: Logfile.insert( - str(xtal[0])+' exists as entry for apo structure in database') + str(xtal[0]) + " exists as entry for apo structure in database" + ) apoInDB.append(str(xtal[0])) - newEntries = '' + newEntries = "" for xtal in apoStructureList: if xtal not in apoInDB: - Logfile.insert('no entry for '+xtal+' in depositTable') + Logfile.insert("no entry for " + xtal + " in depositTable") newEntries += "('{0!s}','apo'),".format(xtal) - if newEntries != '': - sqlite = 'insert into depositTable (CrystalName,StructureType) values {0!s};'.format( - newEntries[:-1]) + if newEntries != "": + sqlite = "insert into depositTable (CrystalName,StructureType) values {0!s};".format( + newEntries[:-1] + ) Logfile.insert( - 'creating new entries with the following SQLite command:\n'+sqlite) + "creating new entries with the following SQLite command:\n" + sqlite + ) cursor.execute(sqlite) connect.commit() - def create_missing_apo_records_for_all_structures_in_depositTable(self, projectDir, xce_logfile): + def create_missing_apo_records_for_all_structures_in_depositTable( + self, projectDir, xce_logfile + ): Logfile = XChemLog.updateLog(xce_logfile) connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - "select CrystalName from depositTable where StructureType is 'apo'") + "select CrystalName from depositTable where StructureType is 'apo'" + ) tmp = cursor.fetchall() -# print str(tmp) + # print str(tmp) apoStructureList = [] for item in tmp: apoStructureList.append(str(item[0])) - counter = 0 # there is a SQLite limit which does not allow to insert more than 500 records at once - newEntries = '' - for files in glob.glob(os.path.join(projectDir, '*')): - xtal = files[files.rfind('/')+1:] + counter = 0 # there is a SQLite limit which does not allow to insert more than 500 records at once + newEntries = "" + for files in glob.glob(os.path.join(projectDir, "*")): + xtal = files[files.rfind("/") + 1 :] if xtal not in apoStructureList: dimple_pdb = False dimple_mtz = False aimless_log = False - if os.path.isfile(os.path.join(files, 'dimple.pdb')): + if os.path.isfile(os.path.join(files, "dimple.pdb")): dimple_pdb = True - if os.path.isfile(os.path.join(files, 'dimple.mtz')): + if os.path.isfile(os.path.join(files, "dimple.mtz")): dimple_mtz = True - if os.path.isfile(os.path.join(files, xtal+'.log')) or os.path.isfile(os.path.join('aimless.log')): + if os.path.isfile(os.path.join(files, xtal + ".log")) or os.path.isfile( + os.path.join("aimless.log") + ): aimless_log = True if dimple_mtz == False or dimple_pdb == False or aimless_log == False: - Logfile.insert('{0!s}: missing files -> dimple.pdb: {1!s}, dimple.mtz: {2!s}, {3!s}.log: {4!s}'.format( - xtal, str(dimple_pdb), str(dimple_mtz), xtal, str(aimless_log))) + Logfile.insert( + "{0!s}: missing files -> dimple.pdb: {1!s}, dimple.mtz: {2!s}, {3!s}.log: {4!s}".format( + xtal, + str(dimple_pdb), + str(dimple_mtz), + xtal, + str(aimless_log), + ) + ) else: newEntries += "('{0!s}','apo'),".format(xtal) counter += 1 if counter == 450: # set to 450 to stay well below 500 records limit - sqlite = 'insert into depositTable (CrystalName,StructureType) values {0!s};'.format( - newEntries[:-1]) + sqlite = "insert into depositTable (CrystalName,StructureType) values {0!s};".format( + newEntries[:-1] + ) Logfile.insert( - 'creating new entries with the following SQLite command:\n'+sqlite) + "creating new entries with the following SQLite command:\n" + + sqlite + ) cursor.execute(sqlite) connect.commit() counter = 0 - newEntries = '' + newEntries = "" - if newEntries != '': - sqlite = 'insert into depositTable (CrystalName,StructureType) values {0!s};'.format( - newEntries[:-1]) + if newEntries != "": + sqlite = "insert into depositTable (CrystalName,StructureType) values {0!s};".format( + newEntries[:-1] + ) Logfile.insert( - 'creating new entries with the following SQLite command:\n'+sqlite) + "creating new entries with the following SQLite command:\n" + sqlite + ) cursor.execute(sqlite) connect.commit() else: - Logfile.insert('did not find any new apo structures') - -# if apoStructureList==[]: -# Logfile.insert('no apo structures were assigned to your pandda models') -# else: -# Logfile.insert('the following datasets were at some point used as apo structures for pandda.analyse: '+str(apoStructureList)) -# apoInDB=[] -# cursor.execute("select CrystalName from depositTable where StructureType is 'apo'") -# tmp = cursor.fetchall() -# for xtal in tmp: -# Logfile.insert(str(xtal[0])+' exists as entry for apo structure in database') -# apoInDB.append(str(xtal[0])) -# newEntries='' -# for xtal in apoStructureList: -# if xtal not in apoInDB: -# Logfile.insert('no entry for '+xtal+' in depositTable') -# newEntries+="('%s','apo')," %xtal -# if newEntries != '': -# sqlite='insert into depositTable (CrystalName,StructureType) values %s;' %newEntries[:-1] -# Logfile.insert('creating new entries with the following SQLite command:\n'+sqlite) -# cursor.execute(sqlite) -# connect.commit() - -# def get_deposit_dict_for_xtal(self,sampleID,structure_type): - - def create_or_remove_missing_records_in_depositTable(self, xce_logfile, xtal, type, db_dict): + Logfile.insert("did not find any new apo structures") + + # if apoStructureList==[]: + # Logfile.insert('no apo structures were assigned to your pandda models') + # else: + # Logfile.insert('the following datasets were at some point used as apo structures for pandda.analyse: '+str(apoStructureList)) + # apoInDB=[] + # cursor.execute("select CrystalName from depositTable where StructureType is 'apo'") + # tmp = cursor.fetchall() + # for xtal in tmp: + # Logfile.insert(str(xtal[0])+' exists as entry for apo structure in database') + # apoInDB.append(str(xtal[0])) + # newEntries='' + # for xtal in apoStructureList: + # if xtal not in apoInDB: + # Logfile.insert('no entry for '+xtal+' in depositTable') + # newEntries+="('%s','apo')," %xtal + # if newEntries != '': + # sqlite='insert into depositTable (CrystalName,StructureType) values %s;' %newEntries[:-1] + # Logfile.insert('creating new entries with the following SQLite command:\n'+sqlite) + # cursor.execute(sqlite) + # connect.commit() + + # def get_deposit_dict_for_xtal(self,sampleID,structure_type): + + def create_or_remove_missing_records_in_depositTable( + self, xce_logfile, xtal, type, db_dict + ): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() Logfile = XChemLog.updateLog(xce_logfile) - oldRefiStage = '' - if type == 'ligand_bound': + oldRefiStage = "" + if type == "ligand_bound": cursor.execute( - "select RefinementOutcome from mainTable where CrystalName is '{0!s}'".format(xtal)) + "select RefinementOutcome from mainTable where CrystalName is '{0!s}'".format( + xtal + ) + ) tmp = cursor.fetchall() oldRefiStage = str(tmp[0][0]) - Logfile.insert('setting RefinementOutcome field to "' + - db_dict['RefinementOutcome']+'" for '+xtal) + Logfile.insert( + 'setting RefinementOutcome field to "' + + db_dict["RefinementOutcome"] + + '" for ' + + xtal + ) self.update_insert_data_source(xtal, db_dict) - elif type == 'ground_state': - cursor.execute("select DimplePANDDApath from depositTable where StructureType is '{0!s}' and DimplePANDDApath is '{1!s}'".format( - type, db_dict['DimplePANDDApath'])) + elif type == "ground_state": + cursor.execute( + "select DimplePANDDApath from depositTable where StructureType is '{0!s}' and DimplePANDDApath is '{1!s}'".format( + type, db_dict["DimplePANDDApath"] + ) + ) tmp = cursor.fetchall() if not tmp: Logfile.insert( - 'entry for ground-state model in depositTable does not exist') + "entry for ground-state model in depositTable does not exist" + ) else: Logfile.warning( - 'entry for ground-state model in depositTable does already exist') + "entry for ground-state model in depositTable does already exist" + ) Logfile.warning( - 'updating PDB, MTZ and DimplePANDDApath for ground-state entry') - cursor.execute("update depositTable set PDB_file='%s', MTZ_file='%s', DimplePANDDApath='%s' where StructureType='ground_state'" % ( - db_dict['PDB_file'], db_dict['MTZ_file'], db_dict['DimplePANDDApath'])) + "updating PDB, MTZ and DimplePANDDApath for ground-state entry" + ) + cursor.execute( + "update depositTable set PDB_file='%s', MTZ_file='%s', DimplePANDDApath='%s' where StructureType='ground_state'" + % ( + db_dict["PDB_file"], + db_dict["MTZ_file"], + db_dict["DimplePANDDApath"], + ) + ) connect.commit() return cursor.execute( - "select CrystalName,StructureType from depositTable where CrystalName is '{0!s}' and StructureType is '{1!s}'".format(xtal, type)) + "select CrystalName,StructureType from depositTable where CrystalName is '{0!s}' and StructureType is '{1!s}'".format( + xtal, type + ) + ) tmp = cursor.fetchall() - if type == 'ligand_bound': - if not tmp and int(db_dict['RefinementOutcome'].split()[0]) == 5: + if type == "ligand_bound": + if not tmp and int(db_dict["RefinementOutcome"].split()[0]) == 5: sqlite = "insert into depositTable (CrystalName,StructureType) values ('{0!s}','{1!s}');".format( - xtal, type) - Logfile.insert('creating new entry for '+str(type) + - ' structure of '+xtal+' in depositTable') + xtal, type + ) + Logfile.insert( + "creating new entry for " + + str(type) + + " structure of " + + xtal + + " in depositTable" + ) cursor.execute(sqlite) connect.commit() else: - if int(db_dict['RefinementOutcome'].split()[0]) != 5: + if int(db_dict["RefinementOutcome"].split()[0]) != 5: sqlite = "delete from depositTable where CrystalName is '{0!s}' and StructureType is '{1!s}'".format( - xtal, type) - if oldRefiStage.startswith('5'): + xtal, type + ) + if oldRefiStage.startswith("5"): Logfile.insert( - 'removing entry for '+str(type)+' structure of '+xtal+' from depositTable') + "removing entry for " + + str(type) + + " structure of " + + xtal + + " from depositTable" + ) cursor.execute(sqlite) connect.commit() - elif type == 'ground_state': + elif type == "ground_state": sqlite = "insert into depositTable (CrystalName,StructureType,DimplePANDDApath,PDB_file,MTZ_file) values ('{0!s}','{1!s}','{2!s}','{3!s}','{4!s}');".format( - xtal, type, db_dict['DimplePANDDApath'], db_dict['PDB_file'], db_dict['MTZ_file']) - Logfile.insert('creating new entry for ' + str(type) + - ' structure of ' + xtal + ' in depositTable') + xtal, + type, + db_dict["DimplePANDDApath"], + db_dict["PDB_file"], + db_dict["MTZ_file"], + ) + Logfile.insert( + "creating new entry for " + + str(type) + + " structure of " + + xtal + + " in depositTable" + ) cursor.execute(sqlite) connect.commit() @@ -2186,54 +2265,57 @@ def remove_selected_apo_structures_from_depositTable(self, xce_logfile, xtalList Logfile = XChemLog.updateLog(xce_logfile) - Logfile.insert( - 'removing the following apo structures from depositTable') + Logfile.insert("removing the following apo structures from depositTable") deleteStrg = "(" for xtal in xtalList: Logfile.insert(xtal) - deleteStrg += "Crystalname is '"+xtal+"' or " - deleteStrg = deleteStrg[:-4]+")" + deleteStrg += "Crystalname is '" + xtal + "' or " + deleteStrg = deleteStrg[:-4] + ")" - sqlite = "delete from depositTable where {0!s} and StructureType is 'apo'".format( - deleteStrg) - Logfile.insert('executing the following SQLite command:\n'+sqlite) + sqlite = ( + "delete from depositTable where {0!s} and StructureType is 'apo'".format( + deleteStrg + ) + ) + Logfile.insert("executing the following SQLite command:\n" + sqlite) cursor.execute(sqlite) connect.commit() - -# for item in tmp: -# print item -# for xtal in str(item[0]).split(';'): -# if xtal not in apoStructureList: apoStructureList.append(xtal) -# if apoStructureList==[]: -# Logfile.insert('no apo structures were assigned to your pandda models') -# else: -# Logfile.insert('the following datasets were at some point used as apo structures for pandda.analyse: '+str(apoStructureList)) -# apoInDB=[] -# cursor.execute("select CrystalName from depositTable where StructureType is 'apo'") -# tmp = cursor.fetchall() -# for xtal in tmp: -# Logfile.insert(str(xtal[0])+' exists as entry for apo structure in database') -# apoInDB.append(str(xtal[0])) -# newEntries='' -# for xtal in apoStructureList: -# if xtal not in apoInDB: -# Logfile.insert('no entry for '+xtal+' in depositTable') -# newEntries+="('%s','apo')," %xtal -# if newEntries != '': -# sqlite='insert into depositTable (CrystalName,StructureType) values %s;' %newEntries[:-1] -# Logfile.insert('creating new entries with the following SQLite command:\n'+sqlite) -# cursor.execute(sqlite) -# connect.commit() -# - + # for item in tmp: + # print item + # for xtal in str(item[0]).split(';'): + # if xtal not in apoStructureList: apoStructureList.append(xtal) + # if apoStructureList==[]: + # Logfile.insert('no apo structures were assigned to your pandda models') + # else: + # Logfile.insert('the following datasets were at some point used as apo structures for pandda.analyse: '+str(apoStructureList)) + # apoInDB=[] + # cursor.execute("select CrystalName from depositTable where StructureType is 'apo'") + # tmp = cursor.fetchall() + # for xtal in tmp: + # Logfile.insert(str(xtal[0])+' exists as entry for apo structure in database') + # apoInDB.append(str(xtal[0])) + # newEntries='' + # for xtal in apoStructureList: + # if xtal not in apoInDB: + # Logfile.insert('no entry for '+xtal+' in depositTable') + # newEntries+="('%s','apo')," %xtal + # if newEntries != '': + # sqlite='insert into depositTable (CrystalName,StructureType) values %s;' %newEntries[:-1] + # Logfile.insert('creating new entries with the following SQLite command:\n'+sqlite) + # cursor.execute(sqlite) + # connect.commit() + # def collected_xtals_during_visit(self, visitID): # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - "select CrystalName from collectionTable where DataCollectionVisit = '{0!s}'".format(visitID)) + "select CrystalName from collectionTable where DataCollectionVisit = '{0!s}'".format( + visitID + ) + ) collectedXtals = [] samples = cursor.fetchall() for sample in samples: @@ -2246,12 +2328,14 @@ def collected_xtals_during_visit_for_scoring(self, visit): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() xtalList = [] -# if rescore == True: -# cursor.execute("select CrystalName from mainTable where DataCollectionVisit = '%s'" %visit) -# else: -# cursor.execute("select CrystalName from mainTable where DataProcessingAutoAssigned = 'True' and DataCollectionVisit = '%s'" %visit) + # if rescore == True: + # cursor.execute("select CrystalName from mainTable where DataCollectionVisit = '%s'" %visit) + # else: + # cursor.execute("select CrystalName from mainTable where DataProcessingAutoAssigned = 'True' and DataCollectionVisit = '%s'" %visit) cursor.execute( - "select distinct CrystalName from collectionTable where DataCollectionVisit = '%s'" % visit) + "select distinct CrystalName from collectionTable where DataCollectionVisit = '%s'" + % visit + ) samples = cursor.fetchall() for sample in samples: if str(sample[0]) not in xtalList: @@ -2264,14 +2348,21 @@ def autoprocessing_result_user_assigned(self, sample): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - "select DataProcessingAutoAssigned from mainTable where CrystalName = '%s'" % sample) + "select DataProcessingAutoAssigned from mainTable where CrystalName = '%s'" + % sample + ) outcome = cursor.fetchall() try: - if 'false' in str(outcome[0]).lower() or str(outcome[0]).encode('ascii', 'ignore') == '': - userassigned = True # a bit counterintuitive, but here we ask about userassigned + if ( + "false" in str(outcome[0]).lower() + or str(outcome[0]).encode("ascii", "ignore") == "" + ): + userassigned = ( + True # a bit counterintuitive, but here we ask about userassigned + ) # whereas DB records autoassigned except IndexError: - pass # this is the case when sample is encountered the first time + pass # this is the case when sample is encountered the first time # and not yet in mainTable return userassigned @@ -2286,26 +2377,38 @@ def all_results_of_xtals_collected_during_visit_as_dict(self, visitID): for xtal in sorted(collectedXtals): if xtal not in xtalDict: xtalDict[xtal] = [] - sqlite = ("select DataCollectionVisit," - " DataCollectionRun," - " DataProcessingProgram," - " DataCollectionDate," - " DataProcessingResolutionHigh," - " DataProcessingRmergeLow," - " DataCollectionCrystalImage1," - " DataCollectionCrystalImage2," - " DataCollectionCrystalImage3," - " DataCollectionCrystalImage4 " - "from collectionTable " - "where CrystalName = '%s'" % xtal) -# print sqlite + sqlite = ( + "select DataCollectionVisit," + " DataCollectionRun," + " DataProcessingProgram," + " DataCollectionDate," + " DataProcessingResolutionHigh," + " DataProcessingRmergeLow," + " DataCollectionCrystalImage1," + " DataCollectionCrystalImage2," + " DataCollectionCrystalImage3," + " DataCollectionCrystalImage4 " + "from collectionTable " + "where CrystalName = '%s'" % xtal + ) + # print sqlite cursor.execute(sqlite) sq = cursor.fetchall() -# print sq + # print sq for s in sq: # print s - t = [str(s[0]), str(s[1]), str(s[2]), str(s[3]), str(s[4]), str( - s[5]), str(s[6]), str(s[7]), str(s[8]), str(s[9])] + t = [ + str(s[0]), + str(s[1]), + str(s[2]), + str(s[3]), + str(s[4]), + str(s[5]), + str(s[6]), + str(s[7]), + str(s[8]), + str(s[9]), + ] inDict = False for entry in xtalDict[xtal]: if t[0] == entry[0] and t[1] == entry[1] and t[2] == entry[2]: @@ -2322,7 +2425,8 @@ def all_autoprocessing_results_for_xtal_as_dict(self, xtal): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - "select * from collectionTable where CrystalName='{0!s}';".format(xtal)) + "select * from collectionTable where CrystalName='{0!s}';".format(xtal) + ) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() @@ -2340,7 +2444,8 @@ def get_db_list_for_sample_in_panddaTable(self, xtal): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - "select * from panddaTable where CrystalName='{0!s}';".format(xtal)) + "select * from panddaTable where CrystalName='{0!s}';".format(xtal) + ) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() @@ -2357,12 +2462,14 @@ def get_db_dict_for_visit_run_autoproc(self, xtal, visit, run, autoproc): # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - sqlite = ('select * ' - 'from collectionTable ' - "where CrystalName ='%s' and" % xtal + - " DataCollectionVisit = '%s' and" % visit + - " DataCollectionRun = '%s' and" % run + - " DataProcessingProgram = '%s'" % autoproc) + sqlite = ( + "select * " + "from collectionTable " + "where CrystalName ='%s' and" % xtal + + " DataCollectionVisit = '%s' and" % visit + + " DataCollectionRun = '%s' and" % run + + " DataProcessingProgram = '%s'" % autoproc + ) cursor.execute(sqlite) for column in cursor.description: header.append(column[0]) @@ -2371,32 +2478,36 @@ def get_db_dict_for_visit_run_autoproc(self, xtal, visit, run, autoproc): db_dict[header[n]] = str(item) return db_dict - def get_db_dict_for_visit_run_autoproc_score(self, xtal, visit, run, autoproc, score): + def get_db_dict_for_visit_run_autoproc_score( + self, xtal, visit, run, autoproc, score + ): db_dict = {} header = [] # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - sqlite = ('select * ' - 'from collectionTable ' - "where CrystalName ='%s' and" % xtal + - " DataCollectionVisit = '%s' and" % visit + - " DataCollectionRun = '%s' and" % run + - " DataProcessingProgram = '%s' and" % autoproc + - " DataProcessingScore = '%s'" % score) + sqlite = ( + "select * " + "from collectionTable " + "where CrystalName ='%s' and" % xtal + + " DataCollectionVisit = '%s' and" % visit + + " DataCollectionRun = '%s' and" % run + + " DataProcessingProgram = '%s' and" % autoproc + + " DataProcessingScore = '%s'" % score + ) cursor.execute(sqlite) for column in cursor.description: header.append(column[0]) data = cursor.fetchall() - print(('SQLITE: {0!s}'.format(sqlite))) - print(('DATA: {0!s}'.format(data))) + print(("SQLITE: {0!s}".format(sqlite))) + print(("DATA: {0!s}".format(data))) for n, item in enumerate(data[0]): db_dict[header[n]] = str(item) return db_dict def xtals_collected_during_visit_as_dict(self, visitID): # first get all collected xtals as list - if isinstance(visitID, list): # for Agamemnon data structure + if isinstance(visitID, list): # for Agamemnon data structure collectedXtals = [] for visit in visitID: x = self.collected_xtals_during_visit(visit) @@ -2419,35 +2530,40 @@ def getCrystalImageDict(self, visit, xtalList): cursor = connect.cursor() imageDict = {} for xtal in xtalList: - sqlite = ("select CrystalName," - " min(DataCollectionDate)," - " DataCollectionCrystalImage1," - " DataCollectionCrystalImage2," - " DataCollectionCrystalImage3," - " DataCollectionCrystalImage4 " - "from collectionTable " - "where DataCollectionVisit = '%s'" % visit + - " and CrystalName = '%s'" % xtal) + sqlite = ( + "select CrystalName," + " min(DataCollectionDate)," + " DataCollectionCrystalImage1," + " DataCollectionCrystalImage2," + " DataCollectionCrystalImage3," + " DataCollectionCrystalImage4 " + "from collectionTable " + "where DataCollectionVisit = '%s'" % visit + + " and CrystalName = '%s'" % xtal + ) cursor.execute(sqlite) img = cursor.fetchall() - imageDict[xtal] = [str(img[1]), str( - img[2]), str(img[3]), str(img[4])] + imageDict[xtal] = [str(img[1]), str(img[2]), str(img[3]), str(img[4])] return imageDict def samples_for_html_summary(self, whichSamples): # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - if whichSamples.startswith('4'): + if whichSamples.startswith("4"): cursor.execute( - "select CrystalName from mainTable where RefinementOutcome like '4%' order by CrystalName ASC") - elif whichSamples.startswith('5'): + "select CrystalName from mainTable where RefinementOutcome like '4%' order by CrystalName ASC" + ) + elif whichSamples.startswith("5"): cursor.execute( - "select CrystalName from mainTable where RefinementOutcome like '5%' order by CrystalName ASC") + "select CrystalName from mainTable where RefinementOutcome like '5%' order by CrystalName ASC" + ) else: - cursor.execute("select CrystalName from mainTable where RefinementOutcome like '4%' or " - "RefinementOutcome like '5%' or " - "RefinementOutcome like '6%' order by CrystalName ASC") + cursor.execute( + "select CrystalName from mainTable where RefinementOutcome like '4%' or " + "RefinementOutcome like '5%' or " + "RefinementOutcome like '6%' order by CrystalName ASC" + ) xtalList = [] samples = cursor.fetchall() for sample in samples: @@ -2461,20 +2577,20 @@ def get_event_map_for_ligand(self, xtal, ligChain, ligNumber, ligName): cursor = connect.cursor() sql = ( - 'select ' - ' PANDDA_site_event_map ' - 'from ' - ' panddaTable ' - 'where ' - " CrystalName = '%s' and " % xtal + - " PANDDA_site_ligand_chain='%s' and " % ligChain + - " PANDDA_site_ligand_sequence_number='%s' and " % ligNumber + - " PANDDA_site_ligand_resname='%s'" % ligName + "select " + " PANDDA_site_event_map " + "from " + " panddaTable " + "where " + " CrystalName = '%s' and " % xtal + + " PANDDA_site_ligand_chain='%s' and " % ligChain + + " PANDDA_site_ligand_sequence_number='%s' and " % ligNumber + + " PANDDA_site_ligand_resname='%s'" % ligName ) cursor.execute(sql) - eventMap = '' + eventMap = "" maps = cursor.fetchall() for map in maps: eventMap = map[0] @@ -2487,20 +2603,20 @@ def get_ligand_confidence_for_ligand(self, xtal, ligChain, ligNumber, ligName): cursor = connect.cursor() sql = ( - 'select ' - ' PANDDA_site_confidence ' - 'from ' - ' panddaTable ' - 'where ' - " CrystalName = '%s' and " % xtal + - " PANDDA_site_ligand_chain='%s' and " % ligChain + - " PANDDA_site_ligand_sequence_number='%s' and " % ligNumber + - " PANDDA_site_ligand_resname='%s'" % ligName + "select " + " PANDDA_site_confidence " + "from " + " panddaTable " + "where " + " CrystalName = '%s' and " % xtal + + " PANDDA_site_ligand_chain='%s' and " % ligChain + + " PANDDA_site_ligand_sequence_number='%s' and " % ligNumber + + " PANDDA_site_ligand_resname='%s'" % ligName ) cursor.execute(sql) - ligConfidence = 'not assigned' + ligConfidence = "not assigned" ligs = cursor.fetchall() for lig in ligs: ligConfidence = lig[0] @@ -2511,7 +2627,7 @@ def get_labels_from_db(self): # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute('select Label from labelTable') + cursor.execute("select Label from labelTable") labels = cursor.fetchall() labelList = [] for l in labels: @@ -2522,7 +2638,7 @@ def get_label_info_from_db(self): # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute('select Label,Description from labelTable') + cursor.execute("select Label,Description from labelTable") labels = cursor.fetchall() labelList = [] for l in labels: @@ -2533,8 +2649,7 @@ def get_label_of_sample(self, xtalID): # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - cursor.execute( - "select label from mainTable where CrystalName is '%s'" % xtalID) + cursor.execute("select label from mainTable where CrystalName is '%s'" % xtalID) label = None lab = cursor.fetchall() for l in lab: diff --git a/lib/XChemDeposit.py b/lib/XChemDeposit.py index e101e5d8..3bcce791 100755 --- a/lib/XChemDeposit.py +++ b/lib/XChemDeposit.py @@ -17,31 +17,31 @@ from lxml import etree -sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") def create_SF_mmcif(outDir, mtzList): - print('hallo') + print("hallo") def get_protein_sequence(database, xtalID): - print('hallo') + print("hallo") def check_depositDict(depositDict): # check depositDict for entry in depositDict: - if 'middle_name' in depositDict[entry]: + if "middle_name" in depositDict[entry]: continue - elif 'State_or_Province' in depositDict[entry]: + elif "State_or_Province" in depositDict[entry]: continue - elif depositDict[entry] == '': - print('ERROR') + elif depositDict[entry] == "": + print("ERROR") def update_title(depositDict): - print('hallo') + print("hallo") def create_data_template_text(): @@ -50,7 +50,8 @@ def create_data_template_text(): def create_Model_mmcif(outDir, pdbList): - print('hallo') + print("hallo") + # def update_file_locations_of_apo_structuresin_DB(database,projectDir,xce_logfile): # Logfile=XChemLog.updateLog(xce_logfile) @@ -71,174 +72,244 @@ def create_Model_mmcif(outDir, pdbList): class templates: - def data_template_cif(self, depositDict): taxonomy_dict = XChemMain.NCBI_taxonomy_ID() for key in taxonomy_dict: - if taxonomy_dict[key] == depositDict['Source_organism_scientific_name']: + if taxonomy_dict[key] == depositDict["Source_organism_scientific_name"]: pdbx_gene_src_ncbi_taxonomy_id = key - if taxonomy_dict[key] == depositDict['Expression_system_scientific_name']: + if taxonomy_dict[key] == depositDict["Expression_system_scientific_name"]: pdbx_host_org_ncbi_taxonomy_id = key -# structure_author_name='' -# for name in depositDict['structure_author_name'].split(';'): -# structure_author_name+='\n' %name + # structure_author_name='' + # for name in depositDict['structure_author_name'].split(';'): + # structure_author_name+='\n' %name - audit_author_name = '' + audit_author_name = "" # one name must be within quotation, last name and first initial must be separated by comma and space - for name in depositDict['structure_author_name'].split(';'): - if name.replace(' ', '') == '': + for name in depositDict["structure_author_name"].split(";"): + if name.replace(" ", "") == "": continue - if name[name.find(',')+1:name.find(',')+2] != ' ': - name = name.replace(',', ', ') + if name[name.find(",") + 1 : name.find(",") + 2] != " ": + name = name.replace(",", ", ") audit_author_name += "'{0!s}'\n".format(name) - primary_citation_author_name = '' + primary_citation_author_name = "" # one name must be within quotation, last name and first initial must be separated by comma and space - for name in depositDict['primary_citation_author_name'].split(';'): - if name.replace(' ', '') == '': + for name in depositDict["primary_citation_author_name"].split(";"): + if name.replace(" ", "") == "": continue - if name[name.find(',')+1:name.find(',')+2] != ' ': - name = name.replace(',', ', ') + if name[name.find(",") + 1 : name.find(",") + 2] != " ": + name = name.replace(",", ", ") primary_citation_author_name += "primary '{0!s}'\n".format(name) - molecule_one_letter_sequence = ';' + molecule_one_letter_sequence = ";" counter = 1 - for aa in depositDict['molecule_one_letter_sequence']: + for aa in depositDict["molecule_one_letter_sequence"]: if counter < 70: molecule_one_letter_sequence += aa if counter == 70: - molecule_one_letter_sequence += '\n'+aa + molecule_one_letter_sequence += "\n" + aa counter = 0 counter += 1 - if depositDict['molecule_name_two'].replace(' ', '') == '' or depositDict['molecule_name_two'].replace(' ', '').lower() == 'none': + if ( + depositDict["molecule_name_two"].replace(" ", "") == "" + or depositDict["molecule_name_two"].replace(" ", "").lower() == "none" + ): try: entity = ( - 'loop_\n' - '_entity.id\n' - '_entity.type\n' - '_entity.src_method\n' - '_entity.pdbx_description\n' - '_entity.pdbx_mutation\n' - '1 polymer man "%s" %s\n' % (depositDict['Source_organism_gene'], depositDict['fragment_name_one_specific_mutation']) + - '#\n' - 'loop_\n' - '_entity_poly.entity_id\n' - '_entity_poly.type\n' - '_entity_poly.pdbx_seq_one_letter_code\n' - '_entity_poly.pdbx_strand_id\n' - '_entity_poly.pdbx_seq_db_id\n' - '_entity_poly.pdbx_seq_db_name\n' - '1 "polypeptide(L)"\n' - + molecule_one_letter_sequence + '\n' - ';\n' - '%s %s UNP\n' % (depositDict['protein_chains'], depositDict['molecule_one_letter_sequence_uniprot_id']) + - '#\n' - 'loop_\n' - '_entity_src_gen.entity_id\n' - '_entity_src_gen.gene_src_strain\n' - '_entity_src_gen.pdbx_gene_src_scientific_name\n' - '_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id\n' - '_entity_src_gen.pdbx_host_org_scientific_name\n' - '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n' - '1 ? "%s" %s "%s" %s\n' % (depositDict['Source_organism_scientific_name'], pdbx_gene_src_ncbi_taxonomy_id, depositDict['Expression_system_scientific_name'], pdbx_host_org_ncbi_taxonomy_id) + - '#\n' + "loop_\n" + "_entity.id\n" + "_entity.type\n" + "_entity.src_method\n" + "_entity.pdbx_description\n" + "_entity.pdbx_mutation\n" + '1 polymer man "%s" %s\n' + % ( + depositDict["Source_organism_gene"], + depositDict["fragment_name_one_specific_mutation"], + ) + + "#\n" + "loop_\n" + "_entity_poly.entity_id\n" + "_entity_poly.type\n" + "_entity_poly.pdbx_seq_one_letter_code\n" + "_entity_poly.pdbx_strand_id\n" + "_entity_poly.pdbx_seq_db_id\n" + "_entity_poly.pdbx_seq_db_name\n" + '1 "polypeptide(L)"\n' + molecule_one_letter_sequence + "\n" + ";\n" + "%s %s UNP\n" + % ( + depositDict["protein_chains"], + depositDict["molecule_one_letter_sequence_uniprot_id"], + ) + + "#\n" + "loop_\n" + "_entity_src_gen.entity_id\n" + "_entity_src_gen.gene_src_strain\n" + "_entity_src_gen.pdbx_gene_src_scientific_name\n" + "_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id\n" + "_entity_src_gen.pdbx_host_org_scientific_name\n" + "_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n" + '1 ? "%s" %s "%s" %s\n' + % ( + depositDict["Source_organism_scientific_name"], + pdbx_gene_src_ncbi_taxonomy_id, + depositDict["Expression_system_scientific_name"], + pdbx_host_org_ncbi_taxonomy_id, + ) + + "#\n" ) except UnboundLocalError: - print('Error: Something went wrong! Please check if you have saved the .deposit file to the database: Menu Deposition -> Edit Information') + print( + "Error: Something went wrong! Please check if you have saved the .deposit file to the database: Menu Deposition -> Edit Information" + ) else: - molecule_two_letter_sequence = ';' + molecule_two_letter_sequence = ";" counter = 1 - for aa in depositDict['molecule_two_letter_sequence']: + for aa in depositDict["molecule_two_letter_sequence"]: if counter < 70: molecule_two_letter_sequence += aa if counter == 70: - molecule_two_letter_sequence += '\n'+aa + molecule_two_letter_sequence += "\n" + aa counter = 0 counter += 1 entity = ( - 'loop_\n' - '_entity.id\n' - '_entity.type\n' - '_entity.src_method\n' - '_entity.pdbx_description\n' - '_entity.pdbx_mutation\n' - '1 polymer man "%s" %s\n' % (depositDict['Source_organism_gene'], depositDict['fragment_name_one_specific_mutation']) + - '2 polymer man "%s" %s\n' % (depositDict['Source_organism_gene_two'], depositDict['fragment_name_two_specific_mutation']) + - '#\n' - 'loop_\n' - '_entity_poly.entity_id\n' - '_entity_poly.type\n' - '_entity_poly.pdbx_seq_one_letter_code\n' - '_entity_poly.pdbx_strand_id\n' - '_entity_poly.pdbx_seq_db_id\n' - '_entity_poly.pdbx_seq_db_name\n' - '1 "polypeptide(L)"\n' - + molecule_one_letter_sequence + '\n' - ';\n' - '%s %s UNP\n' % (depositDict['molecule_chain_one'], depositDict['molecule_one_letter_sequence_uniprot_id']) + + "loop_\n" + "_entity.id\n" + "_entity.type\n" + "_entity.src_method\n" + "_entity.pdbx_description\n" + "_entity.pdbx_mutation\n" + '1 polymer man "%s" %s\n' + % ( + depositDict["Source_organism_gene"], + depositDict["fragment_name_one_specific_mutation"], + ) + + '2 polymer man "%s" %s\n' + % ( + depositDict["Source_organism_gene_two"], + depositDict["fragment_name_two_specific_mutation"], + ) + + "#\n" + "loop_\n" + "_entity_poly.entity_id\n" + "_entity_poly.type\n" + "_entity_poly.pdbx_seq_one_letter_code\n" + "_entity_poly.pdbx_strand_id\n" + "_entity_poly.pdbx_seq_db_id\n" + "_entity_poly.pdbx_seq_db_name\n" + '1 "polypeptide(L)"\n' + molecule_one_letter_sequence + "\n" + ";\n" + "%s %s UNP\n" + % ( + depositDict["molecule_chain_one"], + depositDict["molecule_one_letter_sequence_uniprot_id"], + ) + + # ';\n' - '2 "polypeptide(L)"\n' - + molecule_two_letter_sequence + '\n' - ';\n' - '%s %s UNP\n' % (depositDict['molecule_chain_two'], depositDict['molecule_two_letter_sequence_uniprot_id']) + - '#\n' - 'loop_\n' - '_entity_src_gen.entity_id\n' - '_entity_src_gen.gene_src_strain\n' - '_entity_src_gen.pdbx_gene_src_scientific_name\n' - '_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id\n' - '_entity_src_gen.pdbx_host_org_scientific_name\n' - '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n' - '1 ? "%s" %s "%s" %s\n' % (depositDict['Source_organism_scientific_name'], pdbx_gene_src_ncbi_taxonomy_id, depositDict['Expression_system_scientific_name'], pdbx_host_org_ncbi_taxonomy_id) + - '2 ? "%s" %s "%s" %s\n' % (depositDict['Source_organism_scientific_name'], pdbx_gene_src_ncbi_taxonomy_id, depositDict['Expression_system_scientific_name'], pdbx_host_org_ncbi_taxonomy_id) + - '#\n' + '2 "polypeptide(L)"\n' + molecule_two_letter_sequence + "\n" + ";\n" + "%s %s UNP\n" + % ( + depositDict["molecule_chain_two"], + depositDict["molecule_two_letter_sequence_uniprot_id"], + ) + + "#\n" + "loop_\n" + "_entity_src_gen.entity_id\n" + "_entity_src_gen.gene_src_strain\n" + "_entity_src_gen.pdbx_gene_src_scientific_name\n" + "_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id\n" + "_entity_src_gen.pdbx_host_org_scientific_name\n" + "_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n" + '1 ? "%s" %s "%s" %s\n' + % ( + depositDict["Source_organism_scientific_name"], + pdbx_gene_src_ncbi_taxonomy_id, + depositDict["Expression_system_scientific_name"], + pdbx_host_org_ncbi_taxonomy_id, + ) + + '2 ? "%s" %s "%s" %s\n' + % ( + depositDict["Source_organism_scientific_name"], + pdbx_gene_src_ncbi_taxonomy_id, + depositDict["Expression_system_scientific_name"], + pdbx_host_org_ncbi_taxonomy_id, + ) + + "#\n" ) data_template_cif = ( - 'data_UNNAMED\n' - '#\n' - '_pdbx_database_status.entry_id UNNAMED\n' - "_pdbx_database_status.dep_release_code_coordinates '%s'\n" % depositDict['Release_status_for_coordinates'] + - "_pdbx_database_status.dep_release_code_sequence '{0!s}'\n".format(depositDict['Release_status_for_sequence']) + - '#\n' - '_pdbx_deposit_group.group_id UNNAMED\n' - '_pdbx_deposit_group.group_description "%s"\n' % depositDict['group_description'] + - '_pdbx_deposit_group.group_title "{0!s}"\n'.format(depositDict['group_title']) + - '_pdbx_deposit_group.group_type "{0!s}"\n'.format(depositDict['group_type']) + - '#\n' - '_exptl_crystal_grow.crystal_id 1\n' - "_exptl_crystal_grow.method '%s'\n" % depositDict['crystallization_method'] + - '_exptl_crystal_grow.pH {0!s}\n'.format(depositDict['crystallization_pH']) + - '_exptl_crystal_grow.temp {0!s}\n'.format(depositDict['crystallization_temperature']) + - '_exptl_crystal_grow.pdbx_details "{0!s}"\n'.format(depositDict['crystallization_details']) + - '#\n' - '_diffrn.id 1\n' - '_diffrn.ambient_temp %s\n' % depositDict['data_collection_temperature'] + - '_diffrn.crystal_id 1\n' - '#\n' - '_diffrn_source.diffrn_id 1\n' - '_diffrn_source.source %s\n' % depositDict['radiation_source'] + - '_diffrn_source.type "{0!s}"\n'.format(depositDict['radiation_source_type']) + - '_diffrn_source.pdbx_wavelength_list {0!s}\n'.format(depositDict['radiation_wavelengths']) + - '#\n' - '_diffrn_detector.detector %s\n' % depositDict['radiation_detector'] + - "_diffrn_detector.type '{0!s}'\n".format(depositDict['radiation_detector_type']) + - '_diffrn_detector.pdbx_collection_date {0!s}\n'.format(depositDict['data_collection_date']) + - '_diffrn_detector.diffrn_id 1\n' - '#\n' - '_diffrn_radiation.diffrn_id 1\n' - '_diffrn_radiation.wavelength_id 1\n' + "data_UNNAMED\n" + "#\n" + "_pdbx_database_status.entry_id UNNAMED\n" + "_pdbx_database_status.dep_release_code_coordinates '%s'\n" + % depositDict["Release_status_for_coordinates"] + + "_pdbx_database_status.dep_release_code_sequence '{0!s}'\n".format( + depositDict["Release_status_for_sequence"] + ) + + "#\n" + "_pdbx_deposit_group.group_id UNNAMED\n" + '_pdbx_deposit_group.group_description "%s"\n' + % depositDict["group_description"] + + '_pdbx_deposit_group.group_title "{0!s}"\n'.format( + depositDict["group_title"] + ) + + '_pdbx_deposit_group.group_type "{0!s}"\n'.format( + depositDict["group_type"] + ) + + "#\n" + "_exptl_crystal_grow.crystal_id 1\n" + "_exptl_crystal_grow.method '%s'\n" + % depositDict["crystallization_method"] + + "_exptl_crystal_grow.pH {0!s}\n".format( + depositDict["crystallization_pH"] + ) + + "_exptl_crystal_grow.temp {0!s}\n".format( + depositDict["crystallization_temperature"] + ) + + '_exptl_crystal_grow.pdbx_details "{0!s}"\n'.format( + depositDict["crystallization_details"] + ) + + "#\n" + "_diffrn.id 1\n" + "_diffrn.ambient_temp %s\n" + % depositDict["data_collection_temperature"] + + "_diffrn.crystal_id 1\n" + "#\n" + "_diffrn_source.diffrn_id 1\n" + "_diffrn_source.source %s\n" + % depositDict["radiation_source"] + + '_diffrn_source.type "{0!s}"\n'.format( + depositDict["radiation_source_type"] + ) + + "_diffrn_source.pdbx_wavelength_list {0!s}\n".format( + depositDict["radiation_wavelengths"] + ) + + "#\n" + "_diffrn_detector.detector %s\n" + % depositDict["radiation_detector"] + + "_diffrn_detector.type '{0!s}'\n".format( + depositDict["radiation_detector_type"] + ) + + "_diffrn_detector.pdbx_collection_date {0!s}\n".format( + depositDict["data_collection_date"] + ) + + "_diffrn_detector.diffrn_id 1\n" + "#\n" + "_diffrn_radiation.diffrn_id 1\n" + "_diffrn_radiation.wavelength_id 1\n" "_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'\n" - '#\n' - '_diffrn_radiation_wavelength.id 1\n' - '_diffrn_radiation_wavelength.wavelength %s\n' % depositDict['radiation_wavelengths'] + - '#\n' - '#\n' - + entity + + "#\n" + "_diffrn_radiation_wavelength.id 1\n" + "_diffrn_radiation_wavelength.wavelength %s\n" + % depositDict["radiation_wavelengths"] + + "#\n" + "#\n" + entity + # 'loop_\n' # '_entity.id\n' # '_entity.type\n' @@ -268,52 +339,78 @@ def data_template_cif(self, depositDict): # '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n' # '1 ? "%s" %s "%s" %s\n' %(depositDict['Source_organism_scientific_name'],pdbx_gene_src_ncbi_taxonomy_id,depositDict['Expression_system_scientific_name'],pdbx_host_org_ncbi_taxonomy_id)+ # '#\n' - 'loop_\n' - '_pdbx_contact_author.id \n' + "loop_\n" + "_pdbx_contact_author.id \n" "_pdbx_contact_author.address_1 \n" - '_pdbx_contact_author.address_2 \n' - '_pdbx_contact_author.city \n' + "_pdbx_contact_author.address_2 \n" + "_pdbx_contact_author.city \n" "_pdbx_contact_author.state_province \n" - '_pdbx_contact_author.postal_code \n' - '_pdbx_contact_author.email \n' - '_pdbx_contact_author.name_first \n' - '_pdbx_contact_author.name_last \n' - '_pdbx_contact_author.country \n' - '_pdbx_contact_author.phone \n' - '_pdbx_contact_author.role \n' - '_pdbx_contact_author.organization_type \n' - '_pdbx_contact_author.identifier_ORCID \n' - "1 '%s' '%s' '%s' '?' '%s' %s %s '%s' '%s' '%s' '%s' %s %s\n" % (depositDict['contact_author_PI_address'], depositDict['contact_author_PI_organization_name'], depositDict['contact_author_PI_city'], depositDict['contact_author_PI_Zip_Code'], depositDict['contact_author_PI_email'], depositDict['contact_author_PI_first_name'], depositDict['contact_author_PI_last_name'], depositDict['contact_author_PI_Country'], depositDict['contact_author_PI_phone_number'], depositDict['contact_author_PI_role'], depositDict['contact_author_PI_organization_type'], depositDict['contact_author_PI_ORCID']) + - "2 '{0!s}' '{1!s}' '{2!s}' '?' '{3!s}' '{4!s}' {5!s} {6!s} '{7!s}' '{8!s}' '{9!s}' '{10!s}' {11!s}\n".format(depositDict['contact_author_address'], depositDict['contact_author_organization_name'], depositDict['contact_author_city'], depositDict['contact_author_Zip_Code'].replace(' ', ''), depositDict['contact_author_email'], depositDict['contact_author_first_name'], depositDict['contact_author_last_name'], depositDict['contact_author_Country'], depositDict['contact_author_phone_number'], depositDict['contact_author_role'], depositDict['contact_author_organization_type'], depositDict['contact_author_ORCID']) + - '#\n' - 'loop_\n' - '_audit_author.name\n' - + audit_author_name + + "_pdbx_contact_author.postal_code \n" + "_pdbx_contact_author.email \n" + "_pdbx_contact_author.name_first \n" + "_pdbx_contact_author.name_last \n" + "_pdbx_contact_author.country \n" + "_pdbx_contact_author.phone \n" + "_pdbx_contact_author.role \n" + "_pdbx_contact_author.organization_type \n" + "_pdbx_contact_author.identifier_ORCID \n" + "1 '%s' '%s' '%s' '?' '%s' %s %s '%s' '%s' '%s' '%s' %s %s\n" + % ( + depositDict["contact_author_PI_address"], + depositDict["contact_author_PI_organization_name"], + depositDict["contact_author_PI_city"], + depositDict["contact_author_PI_Zip_Code"], + depositDict["contact_author_PI_email"], + depositDict["contact_author_PI_first_name"], + depositDict["contact_author_PI_last_name"], + depositDict["contact_author_PI_Country"], + depositDict["contact_author_PI_phone_number"], + depositDict["contact_author_PI_role"], + depositDict["contact_author_PI_organization_type"], + depositDict["contact_author_PI_ORCID"], + ) + + "2 '{0!s}' '{1!s}' '{2!s}' '?' '{3!s}' '{4!s}' {5!s} {6!s} '{7!s}' '{8!s}' '{9!s}' '{10!s}' {11!s}\n".format( + depositDict["contact_author_address"], + depositDict["contact_author_organization_name"], + depositDict["contact_author_city"], + depositDict["contact_author_Zip_Code"].replace(" ", ""), + depositDict["contact_author_email"], + depositDict["contact_author_first_name"], + depositDict["contact_author_last_name"], + depositDict["contact_author_Country"], + depositDict["contact_author_phone_number"], + depositDict["contact_author_role"], + depositDict["contact_author_organization_type"], + depositDict["contact_author_ORCID"], + ) + + "#\n" + "loop_\n" + "_audit_author.name\n" + audit_author_name + # "'%s, %s.'\n" %(depositDict['contact_author_last_name'],depositDict['contact_author_first_name'][0])+ - '#\n' - '_citation.id primary\n' - "_citation.title '%s'\n" % depositDict['group_title'] + - "_citation.journal_abbrev 'To Be Published'\n" - '#\n' - 'loop_\n' - '_citation_author.citation_id\n' - '_citation_author.name\n' - + primary_citation_author_name + + "#\n" + "_citation.id primary\n" + "_citation.title '%s'\n" % depositDict["group_title"] + + "_citation.journal_abbrev 'To Be Published'\n" + "#\n" + "loop_\n" + "_citation_author.citation_id\n" + "_citation_author.name\n" + primary_citation_author_name + # "primary 'Krojer, T.'\n" # "primary 'Von Delft, F.'\n" - '#\n' - '_struct.entry_id UNNAMED\n' - '_struct.title\n' - ';%s\n' % depositDict['title'] + - ';\n' - '#\n' - '_struct_keywords.entry_id UNNAMED\n' - '_struct_keywords.text "%s"\n' % depositDict['structure_keywords'] + - '#\n' - '_pdbx_struct_assembly_depositor_info.id 1\n' + "#\n" + "_struct.entry_id UNNAMED\n" + "_struct.title\n" + ";%s\n" % depositDict["title"] + ";\n" + "#\n" + "_struct_keywords.entry_id UNNAMED\n" + '_struct_keywords.text "%s"\n' + % depositDict["structure_keywords"] + + "#\n" + "_pdbx_struct_assembly_depositor_info.id 1\n" "_pdbx_struct_assembly_depositor_info.method_details PISA\n" - '_pdbx_struct_assembly_depositor_info.oligomeric_count %s\n' % depositDict['biological_assembly_chain_number'] + - '#\n' + "_pdbx_struct_assembly_depositor_info.oligomeric_count %s\n" + % depositDict["biological_assembly_chain_number"] + + "#\n" ) return data_template_cif @@ -329,11 +426,13 @@ def __init__(self, deposit_dict, database, xce_logfile): def run(self): self.Logfile.insert( - 'all entries in the depositTable will be updated with the following values:') + "all entries in the depositTable will be updated with the following values:" + ) for key in self.deposit_dict: - self.Logfile.insert(key+': '+self.deposit_dict[key]) + self.Logfile.insert(key + ": " + self.deposit_dict[key]) dbEntries = self.db.execute_statement( - "select CrystalName,StructureType from depositTable;") + "select CrystalName,StructureType from depositTable;" + ) for item in dbEntries: xtal = str(item[0]) type = str(item[1]) @@ -343,46 +442,66 @@ def run(self): # try to get information about the diffraction experiment try: diffractionExperiment = self.db.execute_statement( - "select DataCollectionBeamline,DataCollectionDate from mainTable where CrystalName is '{0!s}'".format(xtal)) + "select DataCollectionBeamline,DataCollectionDate from mainTable where CrystalName is '{0!s}'".format( + xtal + ) + ) beamline = str(diffractionExperiment[0][0]) date = str(diffractionExperiment[0][1]) except (UnboundLocalError, IndexError): self.Logfile.warning( - '%s: cannot find details about diffraction experiment in mainTable' % xtal) - beamline = db_dict['radiation_source'] - date = db_dict['data_collection_date'] + "%s: cannot find details about diffraction experiment in mainTable" + % xtal + ) + beamline = db_dict["radiation_source"] + date = db_dict["data_collection_date"] self.Logfile.warning( - '%s: using values provided in depositTable for beamline and data collection date' % xtal) - if beamline.lower() != 'none': + "%s: using values provided in depositTable for beamline and data collection date" + % xtal + ) + if beamline.lower() != "none": db_dict = self.tweak_deposit_dict(xtal, db_dict) - if date.lower() != 'none': - db_dict['data_collection_date'] = date.split()[0] + if date.lower() != "none": + db_dict["data_collection_date"] = date.split()[0] - self.Logfile.insert('updating depositTable for '+xtal+' @ '+type) + self.Logfile.insert("updating depositTable for " + xtal + " @ " + type) self.db.update_depositTable(xtal, type, db_dict) - self.Logfile.insert('Note: use DBbrowser to edit individual entries') + self.Logfile.insert("Note: use DBbrowser to edit individual entries") def tweak_deposit_dict(self, xtal, db_dict): - dls_beamlines = ['i02', 'i03', 'i04', 'i04-1', 'i23', 'i24'] - dls_beamline_dict = {'i02': ['DIAMOND BEAMLINE I02', 'DECTRIS PILATUS 6M'], - 'i03': ['DIAMOND BEAMLINE I03', 'DECTRIS PILATUS 6M'], - 'i04': ['DIAMOND BEAMLINE I04', 'DECTRIS PILATUS 6M'], - 'i04-1': ['DIAMOND BEAMLINE I04-1', 'DECTRIS PILATUS 6M'], - 'i23': ['DIAMOND BEAMLINE I23', 'DECTRIS PILATUS 12M'], - 'i24': ['DIAMOND BEAMLINE I24', 'DECTRIS PILATUS 6M'], } - - if db_dict['radiation_source_type'] in dls_beamlines: - db_dict['radiation_source_type'] = dls_beamline_dict[db_dict['radiation_source_type']][0] - db_dict['radiation_detector_type'] = dls_beamline_dict[db_dict['radiation_source_type']][1] - db_dict['radiation_detector'] = 'PIXEL' - db_dict['radiation_source'] = 'SYNCHROTRON' + dls_beamlines = ["i02", "i03", "i04", "i04-1", "i23", "i24"] + dls_beamline_dict = { + "i02": ["DIAMOND BEAMLINE I02", "DECTRIS PILATUS 6M"], + "i03": ["DIAMOND BEAMLINE I03", "DECTRIS PILATUS 6M"], + "i04": ["DIAMOND BEAMLINE I04", "DECTRIS PILATUS 6M"], + "i04-1": ["DIAMOND BEAMLINE I04-1", "DECTRIS PILATUS 6M"], + "i23": ["DIAMOND BEAMLINE I23", "DECTRIS PILATUS 12M"], + "i24": ["DIAMOND BEAMLINE I24", "DECTRIS PILATUS 6M"], + } + + if db_dict["radiation_source_type"] in dls_beamlines: + db_dict["radiation_source_type"] = dls_beamline_dict[ + db_dict["radiation_source_type"] + ][0] + db_dict["radiation_detector_type"] = dls_beamline_dict[ + db_dict["radiation_source_type"] + ][1] + db_dict["radiation_detector"] = "PIXEL" + db_dict["radiation_source"] = "SYNCHROTRON" return db_dict class prepare_mmcif_files_for_deposition(QtCore.QThread): - - def __init__(self, database, xce_logfile, overwrite_existing_mmcif, projectDir, ground_state, ignore_event_map): + def __init__( + self, + database, + xce_logfile, + overwrite_existing_mmcif, + projectDir, + ground_state, + ignore_event_map, + ): QtCore.QThread.__init__(self) self.database = database self.xce_logfile = xce_logfile @@ -402,9 +521,9 @@ def __init__(self, database, xce_logfile, overwrite_existing_mmcif, projectDir, self.logDir = None self.ground_state = False - self.ground_state_pdb = '' -# self.ground_state_mean_mtz = '' - self.panddaDir = '' + self.ground_state_pdb = "" + # self.ground_state_mean_mtz = '' + self.panddaDir = "" self.ignore_event_map = ignore_event_map if ground_state: self.ground_state = True @@ -415,29 +534,35 @@ def __init__(self, database, xce_logfile, overwrite_existing_mmcif, projectDir, self.projectDir = self.panddaDir self.pdb = pdbtools(self.ground_state_pdb) self.mtz = mtztools(self.ground_state_mtz) -# self.mtz = mtztools(self.ground_state_mean_mtz) + + # self.mtz = mtztools(self.ground_state_mean_mtz) def run(self): self.Logfile.insert( - '======= preparing mmcif files for wwPDB deposition =======') - self.Logfile.insert('checking DB for structures to deposit...') + "======= preparing mmcif files for wwPDB deposition =======" + ) + self.Logfile.insert("checking DB for structures to deposit...") if self.ground_state: toDeposit = self.db.execute_statement( - "select CrystalName from depositTable where DimplePANDDApath = '%s';" % self.panddaDir) + "select CrystalName from depositTable where DimplePANDDApath = '%s';" + % self.panddaDir + ) else: toDeposit = self.db.execute_statement( - "select CrystalName from mainTable where RefinementOutcome like '5%';") - self.Logfile.insert('found ' + str(len(toDeposit)) + - ' samples ready for deposition') + "select CrystalName from mainTable where RefinementOutcome like '5%';" + ) + self.Logfile.insert( + "found " + str(len(toDeposit)) + " samples ready for deposition" + ) progress_step = 1 if len(toDeposit) != 0: - progress_step = 100/float(len(toDeposit)) + progress_step = 100 / float(len(toDeposit)) else: progress_step = 1 progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) for item in sorted(toDeposit): xtal = str(item[0]) @@ -446,15 +571,14 @@ def run(self): os.chdir(self.projectDir) else: os.chdir(os.path.join(self.projectDir, xtal)) - self.Logfile.insert( - '%s: ----- preparing files for deposition -----' % xtal) + self.Logfile.insert("%s: ----- preparing files for deposition -----" % xtal) if self.ground_state: if not self.data_template_dict_exists(xtal): continue -# if not self.zenodo_dict_exists(xtal): -# continue + # if not self.zenodo_dict_exists(xtal): + # continue if not self.save_data_template_dict(xtal): continue @@ -464,8 +588,8 @@ def run(self): self.add_funding_information(xtal) -# if not self.create_sf_mmcif(xtal): -# continue + # if not self.create_sf_mmcif(xtal): + # continue if not self.apo_mmcif_exists(): continue @@ -486,8 +610,8 @@ def run(self): if not self.db_dict_exists(xtal): continue -# if not self.zenodo_dict_exists(xtal): -# continue + # if not self.zenodo_dict_exists(xtal): + # continue if not self.refine_bound_exists(xtal): continue @@ -531,15 +655,15 @@ def run(self): self.print_errorlist() self.Logfile.insert( - '======= finished preparing mmcif files for wwPDB deposition =======') + "======= finished preparing mmcif files for wwPDB deposition =======" + ) def ground_state_mmcif_exists(self): mmcifStatus = False - for dirs in glob.glob(os.path.join(self.panddaDir, 'processed_datasets', '*')): - xtal = dirs[dirs.rfind('/') + 1:] - if os.path.isfile(os.path.join(dirs, xtal + '_sf.mmcif')): - self.Logfile.insert( - '%s: found mmcif file for apo structure' % xtal) + for dirs in glob.glob(os.path.join(self.panddaDir, "processed_datasets", "*")): + xtal = dirs[dirs.rfind("/") + 1 :] + if os.path.isfile(os.path.join(dirs, xtal + "_sf.mmcif")): + self.Logfile.insert("%s: found mmcif file for apo structure" % xtal) mmcifStatus = True return mmcifStatus @@ -548,48 +672,62 @@ def data_template_dict_exists(self, xtal): dictStatus = False self.data_template_dict = None self.Logfile.insert( - '%s: reading information from depositTable for sample' % xtal) + "%s: reading information from depositTable for sample" % xtal + ) self.data_template_dict = self.db.get_deposit_dict_for_sample(xtal) if self.data_template_dict == {}: self.Logfile.error( - '%s: cannot find data_template dictionary in depositTable; moving to next dataset...' % xtal) + "%s: cannot find data_template dictionary in depositTable; moving to next dataset..." + % xtal + ) self.add_to_errorList(xtal) else: self.Logfile.insert( - '%s: found data_template dictionary in depositTable' % xtal) + "%s: found data_template dictionary in depositTable" % xtal + ) dictStatus = True return dictStatus def update_beamline_info_data_template_dict(self, xtal): - dls_beamlines = ['i02', 'i03', 'i04', 'i04-1', 'i23', 'i24'] - dls_beamline_dict = {'i02': ['DIAMOND BEAMLINE I02', 'DECTRIS PILATUS 6M'], - 'i03': ['DIAMOND BEAMLINE I03', 'DECTRIS PILATUS 6M'], - 'i04': ['DIAMOND BEAMLINE I04', 'DECTRIS PILATUS 6M'], - 'i04-1': ['DIAMOND BEAMLINE I04-1', 'DECTRIS PILATUS 6M'], - 'i23': ['DIAMOND BEAMLINE I23', 'DECTRIS PILATUS 12M'], - 'i24': ['DIAMOND BEAMLINE I24', 'DECTRIS PILATUS 6M'], } - - if self.db_dict['DataCollectionBeamline'] in dls_beamlines: - self.data_template_dict['radiation_source_type'] = dls_beamline_dict[self.db_dict['DataCollectionBeamline']][0] - self.data_template_dict['radiation_detector_type'] = dls_beamline_dict[self.db_dict['DataCollectionBeamline']][1] - self.data_template_dict['radiation_detector'] = 'PIXEL' - self.data_template_dict['radiation_source'] = 'SYNCHROTRON' - self.Logfile.insert(('%s: setting data collection beamline to %s' % ( - xtal, self.data_template_dict['radiation_source_type']))) + dls_beamlines = ["i02", "i03", "i04", "i04-1", "i23", "i24"] + dls_beamline_dict = { + "i02": ["DIAMOND BEAMLINE I02", "DECTRIS PILATUS 6M"], + "i03": ["DIAMOND BEAMLINE I03", "DECTRIS PILATUS 6M"], + "i04": ["DIAMOND BEAMLINE I04", "DECTRIS PILATUS 6M"], + "i04-1": ["DIAMOND BEAMLINE I04-1", "DECTRIS PILATUS 6M"], + "i23": ["DIAMOND BEAMLINE I23", "DECTRIS PILATUS 12M"], + "i24": ["DIAMOND BEAMLINE I24", "DECTRIS PILATUS 6M"], + } + + if self.db_dict["DataCollectionBeamline"] in dls_beamlines: + self.data_template_dict["radiation_source_type"] = dls_beamline_dict[ + self.db_dict["DataCollectionBeamline"] + ][0] + self.data_template_dict["radiation_detector_type"] = dls_beamline_dict[ + self.db_dict["DataCollectionBeamline"] + ][1] + self.data_template_dict["radiation_detector"] = "PIXEL" + self.data_template_dict["radiation_source"] = "SYNCHROTRON" + self.Logfile.insert( + ( + "%s: setting data collection beamline to %s" + % (xtal, self.data_template_dict["radiation_source_type"]) + ) + ) def db_dict_exists(self, xtal): dictStatus = False self.db_dict = None - self.Logfile.insert( - '%s: reading information from mainTable for sample' % xtal) + self.Logfile.insert("%s: reading information from mainTable for sample" % xtal) self.db_dict = self.db.get_db_dict_for_sample(xtal) if self.db_dict == {}: self.Logfile.error( - '%s: cannot find db_dict dictionary in mainTable; moving to next dataset...' % xtal) + "%s: cannot find db_dict dictionary in mainTable; moving to next dataset..." + % xtal + ) self.add_to_errorList(xtal) else: - self.Logfile.insert( - '%s: found db_dict dictionary in mainTable' % xtal) + self.Logfile.insert("%s: found db_dict dictionary in mainTable" % xtal) self.update_beamline_info_data_template_dict(xtal) dictStatus = True return dictStatus @@ -599,22 +737,29 @@ def zenodo_dict_exists(self, xtal): self.zenodo_dict = None if self.ground_state: self.zenodo_dict = self.db.get_zenodo_dict_for_pandda_analysis( - self.panddaDir) + self.panddaDir + ) else: - self.Logfile.insert('%s: reading information from zenodoTable for pandda run: %s' % ( - xtal, self.db_dict['DimplePANDDApath'])) + self.Logfile.insert( + "%s: reading information from zenodoTable for pandda run: %s" + % (xtal, self.db_dict["DimplePANDDApath"]) + ) self.zenodo_dict = self.db.get_zenodo_dict_for_pandda_analysis( - self.db_dict['DimplePANDDApath']) + self.db_dict["DimplePANDDApath"] + ) if self.zenodo_dict == {}: dictStatus = True - self.zenodo_dict['ZenodoDOI'] = '' + self.zenodo_dict["ZenodoDOI"] = "" self.Logfile.warning( - '%s: cannot find information about zenodo deposition in zenodoTable!!!' % xtal) -# self.Logfile.error('%s: cannot find information about zenodo deposition in zenodoTable; moving to next dataset...' %xtal) -# self.add_to_errorList(xtal) + "%s: cannot find information about zenodo deposition in zenodoTable!!!" + % xtal + ) + # self.Logfile.error('%s: cannot find information about zenodo deposition in zenodoTable; moving to next dataset...' %xtal) + # self.add_to_errorList(xtal) else: self.Logfile.insert( - '%s: found zenodo_dict dictionary in zenodoTable' % xtal) + "%s: found zenodo_dict dictionary in zenodoTable" % xtal + ) dictStatus = True return dictStatus @@ -622,211 +767,247 @@ def mmcif_files_can_be_replaced(self, xtal): status = True if self.overwrite_existing_mmcif: self.Logfile.insert( - '%s: removing existing mmcif files as chosen by user' % xtal) + "%s: removing existing mmcif files as chosen by user" % xtal + ) self.db.execute_statement( - "update depositTable set mmCIF_model_file='',mmCIF_SF_file='' where CrystalName is '{0!s}'".format(xtal)) - for mmcif in glob.glob('*.mmcif'): - self.Logfile.warning('%s: removing %s' % (xtal, mmcif)) - os.system('/bin/rm ' + mmcif) + "update depositTable set mmCIF_model_file='',mmCIF_SF_file='' where CrystalName is '{0!s}'".format( + xtal + ) + ) + for mmcif in glob.glob("*.mmcif"): + self.Logfile.warning("%s: removing %s" % (xtal, mmcif)) + os.system("/bin/rm " + mmcif) else: - for mmcif in glob.glob('*.mmcif'): - self.Logfile.warning( - '%s: %s exists; skipping...' % (xtal, mmcif)) + for mmcif in glob.glob("*.mmcif"): + self.Logfile.warning("%s: %s exists; skipping..." % (xtal, mmcif)) status = False return status def refine_bound_exists(self, xtal): self.pdb = None self.Logfile.insert( - '%s: checking if refine.split.bound-state.pdb exists' % xtal) + "%s: checking if refine.split.bound-state.pdb exists" % xtal + ) fileStatus = False - if os.path.isfile('refine.split.bound-state.pdb'): - self.Logfile.insert( - '%s: found refine.split.bound-state.pdb' % xtal) - self.pdb = pdbtools('refine.split.bound-state.pdb') + if os.path.isfile("refine.split.bound-state.pdb"): + self.Logfile.insert("%s: found refine.split.bound-state.pdb" % xtal) + self.pdb = pdbtools("refine.split.bound-state.pdb") fileStatus = True else: self.Logfile.error( - '%s: cannot find refine.split.bound-state.pdb; moving to next dataset...' % xtal) + "%s: cannot find refine.split.bound-state.pdb; moving to next dataset..." + % xtal + ) self.add_to_errorList(xtal) return fileStatus def refine_mtz_exists(self, xtal): self.mtz = None - self.Logfile.insert('%s: checking if refine.mtz exists' % xtal) + self.Logfile.insert("%s: checking if refine.mtz exists" % xtal) fileStatus = False - if os.path.isfile('refine.mtz'): - self.Logfile.insert('%s: found refine.mtz' % xtal) - self.mtz = mtztools('refine.mtz') + if os.path.isfile("refine.mtz"): + self.Logfile.insert("%s: found refine.mtz" % xtal) + self.mtz = mtztools("refine.mtz") fileStatus = True else: self.Logfile.error( - '%s: cannot find refine.mtz; moving to next dataset...' % xtal) + "%s: cannot find refine.mtz; moving to next dataset..." % xtal + ) self.add_to_errorList(xtal) return fileStatus def run_aimless_merge_only(self, xtal, unmerged, APpath): cmd = ( - 'aimless hklin %s hklout mergeonly.mtz << eof > %s\n' % (unmerged, unmerged.replace('.mtz', '.log')) + - ' onlymerge\n' - 'eof' + "aimless hklin %s hklout mergeonly.mtz << eof > %s\n" + % (unmerged, unmerged.replace(".mtz", ".log")) + + " onlymerge\n" + "eof" ) - self.Logfile.insert('%s: running AIMLESS in onlymerge mode...' % xtal) + self.Logfile.insert("%s: running AIMLESS in onlymerge mode..." % xtal) os.system(cmd) os.chdir(os.path.join(self.projectDir, xtal)) - os.system('/bin/rm %s.log' % xtal) - os.system('ln -s %s/%s %s.log' % - (APpath, unmerged.replace('.mtz', '.log'), xtal)) - self.Logfile.insert('%s: finished running AIMLESS' % xtal) - if os.path.isfile(xtal+'.log'): - self.Logfile.insert( - '%s: AIMLESS logfile successfully created' % xtal) + os.system("/bin/rm %s.log" % xtal) + os.system( + "ln -s %s/%s %s.log" % (APpath, unmerged.replace(".mtz", ".log"), xtal) + ) + self.Logfile.insert("%s: finished running AIMLESS" % xtal) + if os.path.isfile(xtal + ".log"): + self.Logfile.insert("%s: AIMLESS logfile successfully created" % xtal) else: - self.Logfile.error('%s: cannot find AIMLESS logfile...' % xtal) + self.Logfile.error("%s: cannot find AIMLESS logfile..." % xtal) def prepare_aimless_log(self, xtal): - parse().make_pseudo_aimless_log_from_json(xtal + '.log') + parse().make_pseudo_aimless_log_from_json(xtal + ".log") def aimless_logfile_exists(self, xtal): self.Logfile.insert( - '%s: checking if aimless logfile, i.e. %s.log, exists' % (xtal, xtal)) + "%s: checking if aimless logfile, i.e. %s.log, exists" % (xtal, xtal) + ) fileStatus = False - if os.path.isfile('%s.log' % xtal): - self.Logfile.insert('%s: found %s.log' % (xtal, xtal)) - for n, line in enumerate(open('%s.log' % xtal)): - if 'AIMLESS' in line: + if os.path.isfile("%s.log" % xtal): + self.Logfile.insert("%s: found %s.log" % (xtal, xtal)) + for n, line in enumerate(open("%s.log" % xtal)): + if "AIMLESS" in line: fileStatus = True break -# if n < 10: -# print line + # if n < 10: + # print line if not fileStatus: - if os.path.realpath('%s.log' % xtal).endswith('.table1'): + if os.path.realpath("%s.log" % xtal).endswith(".table1"): self.Logfile.warning( - '{0!s}: {1!s}.log seems to be a staraniso .table1 file'.format(xtal, xtal)) + "{0!s}: {1!s}.log seems to be a staraniso .table1 file".format( + xtal, xtal + ) + ) fileStatus = True if not fileStatus: self.Logfile.warning( - '%s: this does not seem to be an AIMLESS logfile' % xtal) - Filepath = os.path.relpath(os.path.realpath('%s.log' % xtal)) - APpath = Filepath[:Filepath.rfind('/')] - self.Logfile.insert( - '%s: relative path to logfile %s' % (xtal, APpath)) - self.Logfile.insert( - '%s: file path to logfile %s' % (xtal, Filepath)) + "%s: this does not seem to be an AIMLESS logfile" % xtal + ) + Filepath = os.path.relpath(os.path.realpath("%s.log" % xtal)) + APpath = Filepath[: Filepath.rfind("/")] + self.Logfile.insert("%s: relative path to logfile %s" % (xtal, APpath)) + self.Logfile.insert("%s: file path to logfile %s" % (xtal, Filepath)) if os.path.isdir(APpath): os.chdir(APpath) - for unmerged in glob.glob('*_scaled_unmerged.mtz'): - self.Logfile.insert('%s: found %s in %s' % - (xtal, unmerged, APpath)) + for unmerged in glob.glob("*_scaled_unmerged.mtz"): + self.Logfile.insert( + "%s: found %s in %s" % (xtal, unmerged, APpath) + ) self.run_aimless_merge_only(xtal, unmerged, APpath) fileStatus = True break else: - self.Logfile.error( - '%s: %s is not a directory' % (xtal, APpath)) + self.Logfile.error("%s: %s is not a directory" % (xtal, APpath)) self.add_to_errorList(xtal) if not fileStatus: os.chdir(os.path.join(self.projectDir, xtal)) self.Logfile.insert( - '%s: trying to prepare a pseudo-aimless file from json file...' % xtal) + "%s: trying to prepare a pseudo-aimless file from json file..." + % xtal + ) self.prepare_aimless_log(xtal) - if os.path.isfile('aimless_dials.log'): - self.Logfile.insert( - '%s: found aimless_dials.log' % xtal) + if os.path.isfile("aimless_dials.log"): + self.Logfile.insert("%s: found aimless_dials.log" % xtal) fileStatus = True if not fileStatus: self.Logfile.error( - '%s: cannot find a suitable AIMLESS logfile' % xtal) + "%s: cannot find a suitable AIMLESS logfile" % xtal + ) self.add_to_errorList(xtal) -# fileStatus = True + # fileStatus = True else: self.Logfile.error( - '%s: cannot find %s.log; moving to next dataset...' % (xtal, xtal)) + "%s: cannot find %s.log; moving to next dataset..." % (xtal, xtal) + ) self.add_to_errorList(xtal) return fileStatus def mtzFree_exists(self, xtal): - self.Logfile.insert( - '%s: checking if %s.free.mtz exists' % (xtal, xtal)) + self.Logfile.insert("%s: checking if %s.free.mtz exists" % (xtal, xtal)) fileStatus = False - if os.path.isfile('%s.free.mtz' % xtal): - self.Logfile.insert('%s: found %s.free.mtz' % (xtal, xtal)) + if os.path.isfile("%s.free.mtz" % xtal): + self.Logfile.insert("%s: found %s.free.mtz" % (xtal, xtal)) fileStatus = True else: self.Logfile.error( - '%s: cannot find %s.free.mtz; moving to next dataset...' % (xtal, xtal)) + "%s: cannot find %s.free.mtz; moving to next dataset..." % (xtal, xtal) + ) self.add_to_errorList(xtal) return fileStatus def ligand_in_pdb_file(self, xtal): self.Logfile.insert( - '%s: checking if refine.split.bound-state.pdb contains ligands of type LIG' % xtal) + "%s: checking if refine.split.bound-state.pdb contains ligands of type LIG" + % xtal + ) ligandStatus = False - ligList = pdbtools( - 'refine.split.bound-state.pdb').get_residues_with_resname('LIG') + ligList = pdbtools("refine.split.bound-state.pdb").get_residues_with_resname( + "LIG" + ) if ligList is []: self.Logfile.error( - '%s: refine.split.bound-state.pdb does not contain any modelled ligands of type LIG' % xtal) + "%s: refine.split.bound-state.pdb does not contain any modelled ligands of type LIG" + % xtal + ) self.add_to_errorList(xtal) else: - self.Logfile.insert(xtal + ': found ' + - str(len(ligList)) + ' ligands of type LIG') + self.Logfile.insert( + xtal + ": found " + str(len(ligList)) + " ligands of type LIG" + ) ligandStatus = True return ligandStatus def eventMTZ_exists(self, xtal): - self.Logfile.insert('%s: checking if mtz of event maps exists' % xtal) + self.Logfile.insert("%s: checking if mtz of event maps exists" % xtal) eventMTZlist = [] eventMTZexists = False - if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: + if os.path.isfile("no_pandda_analysis_performed") or self.ignore_event_map: self.Logfile.warning( - '%s: found empty file named "no_pandda_analysis_performed" which suggests we will ignore event maps for this sample' % xtal) + '%s: found empty file named "no_pandda_analysis_performed" which suggests we will ignore event maps for this sample' + % xtal + ) eventMTZexists = True elif self.ignore_event_map: self.Logfile.warning( - '%s: user selected to not include event map in SF mmcif file' % xtal) + "%s: user selected to not include event map in SF mmcif file" % xtal + ) eventMTZexists = True else: - for mtz in glob.glob('*event*.native*.mtz'): - eventMTZlist.append(mtz[mtz.rfind('/')+1:]) + for mtz in glob.glob("*event*.native*.mtz"): + eventMTZlist.append(mtz[mtz.rfind("/") + 1 :]) if eventMTZlist is []: self.Logfile.error( - '%s: MTZ files of event maps do not exists! Go to PANDDA tab and run "Event Map -> SF"' % xtal) + '%s: MTZ files of event maps do not exists! Go to PANDDA tab and run "Event Map -> SF"' + % xtal + ) self.add_to_errorList(xtal) else: self.Logfile.insert( - xtal + ': found ' + str(len(eventMTZlist)) + ' MTZ files of event maps') + xtal + + ": found " + + str(len(eventMTZlist)) + + " MTZ files of event maps" + ) eventMTZexists = True return eventMTZexists def find_matching_event_map(self, xtal): self.eventList = [] self.Logfile.insert( - '%s: trying to find fitting event maps for modelled ligands' % xtal) + "%s: trying to find fitting event maps for modelled ligands" % xtal + ) ligList = self.pdb.save_residues_with_resname( - os.path.join(self.projectDir, xtal), 'LIG') + os.path.join(self.projectDir, xtal), "LIG" + ) foundMatchingMap = None - if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: + if os.path.isfile("no_pandda_analysis_performed") or self.ignore_event_map: self.Logfile.warning( - '%s: found empty file named "no_pandda_analysis_performed" which suggests we will ignore event maps for this sample' % xtal) + '%s: found empty file named "no_pandda_analysis_performed" which suggests we will ignore event maps for this sample' + % xtal + ) foundMatchingMap = True ligList = [] self.Logfile.insert( - '%s: looking for event maps for the following ligands -> %s' % (xtal, str(ligList))) + "%s: looking for event maps for the following ligands -> %s" + % (xtal, str(ligList)) + ) for lig in sorted(ligList): - ligID = lig.replace('.pdb', '') -# if os.path.isfile('no_pandda_analysis_performed'): -# self.Logfile.warning('%s: no pandda analysis performed; skipping this step...' %xtal) -# foundMatchingMap = True -# break + ligID = lig.replace(".pdb", "") + # if os.path.isfile('no_pandda_analysis_performed'): + # self.Logfile.warning('%s: no pandda analysis performed; skipping this step...' %xtal) + # foundMatchingMap = True + # break ligCC = [] # for newer BUSTER export -# print '>>>> %s-event_*.native_%s.mtz' %(xtal,lig.replace('.pdb','')) - for mtz in glob.glob(('%s-event_*.native_%s.mtz' % (xtal, lig.replace('.pdb', '')))): - self.Logfile.insert(xtal + ': found ' + mtz) + # print '>>>> %s-event_*.native_%s.mtz' %(xtal,lig.replace('.pdb','')) + for mtz in glob.glob( + ("%s-event_*.native_%s.mtz" % (xtal, lig.replace(".pdb", ""))) + ): + self.Logfile.insert(xtal + ": found " + mtz) foundMatchingMap = True self.eventList.append(mtz) break @@ -834,52 +1015,69 @@ def find_matching_event_map(self, xtal): if foundMatchingMap: continue - for mtz in sorted(glob.glob('*event*.native.mtz')): + for mtz in sorted(glob.glob("*event*.native.mtz")): self.get_lig_cc(xtal, mtz, lig) - cc = self.check_lig_cc(mtz.replace('.mtz', '_CC'+ligID+'.log')) - self.Logfile.insert('%s: %s -> CC = %s for %s' % - (xtal, ligID, cc, mtz)) + cc = self.check_lig_cc(mtz.replace(".mtz", "_CC" + ligID + ".log")) + self.Logfile.insert("%s: %s -> CC = %s for %s" % (xtal, ligID, cc, mtz)) try: ligCC.append([mtz, float(cc)]) except ValueError: ligCC.append([mtz, 0.00]) - for mtz in sorted(glob.glob('*event*.native*P1.mtz')): + for mtz in sorted(glob.glob("*event*.native*P1.mtz")): self.get_lig_cc(xtal, mtz, lig) - cc = self.check_lig_cc(mtz.replace('.mtz', '_CC'+ligID+'.log')) - self.Logfile.insert('%s: %s -> CC = %s for %s' % - (xtal, ligID, cc, mtz)) + cc = self.check_lig_cc(mtz.replace(".mtz", "_CC" + ligID + ".log")) + self.Logfile.insert("%s: %s -> CC = %s for %s" % (xtal, ligID, cc, mtz)) try: ligCC.append([mtz, float(cc)]) except ValueError: ligCC.append([mtz, 0.00]) try: for cm in ligCC: - self.Logfile.insert('%s: cc = %s - %s' % - (xtal, cm[1], cm[0])) -# highestCC = max(ligCC, key=lambda x: x[0])[1] + self.Logfile.insert("%s: cc = %s - %s" % (xtal, cm[1], cm[0])) + # highestCC = max(ligCC, key=lambda x: x[0])[1] highestCCeventmap = max(ligCC, key=lambda x: float(x[1]))[0] except ValueError: highestCC = 0.00 highestCCeventmap = None -# if highestCC == 0.00 or ligCC is []: + # if highestCC == 0.00 or ligCC is []: if highestCCeventmap is None or ligCC is []: self.Logfile.error( - '%s: best CC of ligand %s for any event map is 0!' % (xtal, lig)) + "%s: best CC of ligand %s for any event map is 0!" % (xtal, lig) + ) self.add_to_errorList(xtal) foundMatchingMap = False else: - self.Logfile.insert('%s: selected event map for ligand %s is %s' % ( - xtal, lig, highestCCeventmap)) - if os.path.isfile(highestCCeventmap.replace('.mtz', '_'+ligID+'.mtz')): - self.Logfile.warning('%s: symlink exists %s' % ( - xtal, highestCCeventmap.replace('.mtz', '_'+ligID+'.mtz'))) + self.Logfile.insert( + "%s: selected event map for ligand %s is %s" + % (xtal, lig, highestCCeventmap) + ) + if os.path.isfile( + highestCCeventmap.replace(".mtz", "_" + ligID + ".mtz") + ): + self.Logfile.warning( + "%s: symlink exists %s" + % ( + xtal, + highestCCeventmap.replace(".mtz", "_" + ligID + ".mtz"), + ) + ) else: - self.Logfile.insert('%s: making symlink %s' % ( - xtal, highestCCeventmap.replace('.mtz', '_'+ligID+'.mtz'))) - os.system('ln -s %s %s' % (highestCCeventmap, - highestCCeventmap.replace('.mtz', '_'+ligID+'.mtz'))) + self.Logfile.insert( + "%s: making symlink %s" + % ( + xtal, + highestCCeventmap.replace(".mtz", "_" + ligID + ".mtz"), + ) + ) + os.system( + "ln -s %s %s" + % ( + highestCCeventmap, + highestCCeventmap.replace(".mtz", "_" + ligID + ".mtz"), + ) + ) if highestCCeventmap not in self.eventList: self.eventList.append(highestCCeventmap) if foundMatchingMap is None: @@ -887,127 +1085,170 @@ def find_matching_event_map(self, xtal): return foundMatchingMap def get_lig_cc(self, xtal, mtz, lig): - ligID = lig.replace('.pdb', '') - self.Logfile.insert('%s: calculating CC for %s in %s' % - (xtal, lig, mtz)) - if os.path.isfile(mtz.replace('.mtz', '_CC'+ligID+'.log')): - self.Logfile.warning('logfile of CC analysis exists; skipping...') + ligID = lig.replace(".pdb", "") + self.Logfile.insert("%s: calculating CC for %s in %s" % (xtal, lig, mtz)) + if os.path.isfile(mtz.replace(".mtz", "_CC" + ligID + ".log")): + self.Logfile.warning("logfile of CC analysis exists; skipping...") return - cmd = ('module load phenix\n' - 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log'))) + cmd = "module load phenix\n" "phenix.get_cc_mtz_pdb %s %s > %s" % ( + mtz, + lig, + mtz.replace(".mtz", "_CC" + ligID + ".log"), + ) os.system(cmd) def check_lig_cc(self, log): - cc = 'n/a' + cc = "n/a" if os.path.isfile(log): for line in open(log): - if line.startswith('local'): + if line.startswith("local"): cc = line.split()[len(line.split()) - 1] else: - self.Logfile.error('logfile does not exist: %s' % log) + self.Logfile.error("logfile does not exist: %s" % log) return cc def add_to_errorList(self, xtal): - if xtal.replace(' ', '') == '': + if xtal.replace(" ", "") == "": self.Logfile.warning( - 'trying to add xtal to error list, but xtal string is empty') + "trying to add xtal to error list, but xtal string is empty" + ) else: if xtal not in self.errorList: self.errorList.append(xtal) def print_errorlist(self): if not self.errorList: - self.Logfile.insert('XCE did not detect any problems during mmcif file preparation. ' - 'It is however recommended to check the logfile.') + self.Logfile.insert( + "XCE did not detect any problems during mmcif file preparation. " + "It is however recommended to check the logfile." + ) else: - self.Logfile.warning('The following samples had problems during mmcif creation. ' - 'Please check the logfile for details!') + self.Logfile.warning( + "The following samples had problems during mmcif creation. " + "Please check the logfile for details!" + ) for xtal in self.errorList: self.Logfile.error(xtal) def save_data_template_dict(self, xtal): # check if file exists noError = True - self.Logfile.insert('%s: preparing data_template.cif file' % xtal) + self.Logfile.insert("%s: preparing data_template.cif file" % xtal) if self.overwrite_existing_mmcif: - self.data_template_dict['radiation_wavelengths'] = self.mtz.get_wavelength( - ) - if str(self.data_template_dict['radiation_wavelengths']).startswith('0.0'): - self.Logfile.error('%s: this does not seem to be the true experimental wavelength: %s' % ( - xtal, str(self.data_template_dict['radiation_wavelengths']))) + self.data_template_dict["radiation_wavelengths"] = self.mtz.get_wavelength() + if str(self.data_template_dict["radiation_wavelengths"]).startswith("0.0"): + self.Logfile.error( + "%s: this does not seem to be the true experimental wavelength: %s" + % (xtal, str(self.data_template_dict["radiation_wavelengths"])) + ) self.Logfile.insert( - '%s: trying to find it from %s.free.mtz...' % (xtal, xtal)) - if os.path.isfile('%s.free.mtz' % xtal): - self.data_template_dict['radiation_wavelengths'] = mtztools( - xtal+'.free.mtz').get_wavelength() - self.Logfile.warning('%s: found the following wavelength -> %s' % ( - xtal, str(self.data_template_dict['radiation_wavelengths']))) - self.Logfile.insert('%s: experimental wavelength according to %s is %s' % ( - xtal, self.mtz, self.data_template_dict['radiation_wavelengths'])) + "%s: trying to find it from %s.free.mtz..." % (xtal, xtal) + ) + if os.path.isfile("%s.free.mtz" % xtal): + self.data_template_dict["radiation_wavelengths"] = mtztools( + xtal + ".free.mtz" + ).get_wavelength() + self.Logfile.warning( + "%s: found the following wavelength -> %s" + % (xtal, str(self.data_template_dict["radiation_wavelengths"])) + ) + self.Logfile.insert( + "%s: experimental wavelength according to %s is %s" + % (xtal, self.mtz, self.data_template_dict["radiation_wavelengths"]) + ) if self.ground_state: os.chdir(self.projectDir) -# self.data_template_dict['radiation_wavelengths'] = '1.000' - self.data_template_dict['group_type'] = 'ground state' - self.data_template_dict['group_title'] = 'PanDDA analysis group deposition of ground-state model' - self.data_template_dict['group_description'] = self.data_template_dict['group_description'].replace('$ProteinName', - self.data_template_dict[ - 'Source_organism_gene']) - self.data_template_dict['title'] = self.data_template_dict['structure_title_apo'].replace('$ProteinName', - self.data_template_dict[ - 'Source_organism_gene']) + # self.data_template_dict['radiation_wavelengths'] = '1.000' + self.data_template_dict["group_type"] = "ground state" + self.data_template_dict[ + "group_title" + ] = "PanDDA analysis group deposition of ground-state model" + self.data_template_dict["group_description"] = self.data_template_dict[ + "group_description" + ].replace( + "$ProteinName", self.data_template_dict["Source_organism_gene"] + ) + self.data_template_dict["title"] = self.data_template_dict[ + "structure_title_apo" + ].replace( + "$ProteinName", self.data_template_dict["Source_organism_gene"] + ) else: os.chdir(os.path.join(self.projectDir, xtal)) # edit wavelength -# self.data_template_dict['radiation_wavelengths'] = self.mtz.get_wavelength() - - title = self.data_template_dict['structure_title'].replace('$ProteinName', self.data_template_dict[ - 'Source_organism_gene']).replace('$CompoundName', self.db_dict['CompoundCode']).replace('($SampleID)', '('+xtal+')') + # self.data_template_dict['radiation_wavelengths'] = self.mtz.get_wavelength() + + title = ( + self.data_template_dict["structure_title"] + .replace( + "$ProteinName", self.data_template_dict["Source_organism_gene"] + ) + .replace("$CompoundName", self.db_dict["CompoundCode"]) + .replace("($SampleID)", "(" + xtal + ")") + ) - self.data_template_dict['group_type'] = 'changed state' + self.data_template_dict["group_type"] = "changed state" # edit title - self.data_template_dict['group_title'] = self.data_template_dict['group_deposition_title'].replace('$ProteinName', - self.data_template_dict[ - 'Source_organism_gene']).replace( - '$CompoundName', self.db_dict['CompoundCode']) - -# self.data_template_dict[ -# 'group_title'] = 'PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)' - self.data_template_dict['group_description'] = self.data_template_dict['group_description'].replace('$ProteinName', - self.data_template_dict[ - 'Source_organism_gene']) - self.data_template_dict['title'] = self.data_template_dict['group_title'] + ' -- ' + title - - if ('$ProteinName' or '$CompoundName') in self.data_template_dict['title']: + self.data_template_dict["group_title"] = ( + self.data_template_dict["group_deposition_title"] + .replace( + "$ProteinName", self.data_template_dict["Source_organism_gene"] + ) + .replace("$CompoundName", self.db_dict["CompoundCode"]) + ) + + # self.data_template_dict[ + # 'group_title'] = 'PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)' + self.data_template_dict["group_description"] = self.data_template_dict[ + "group_description" + ].replace( + "$ProteinName", self.data_template_dict["Source_organism_gene"] + ) + self.data_template_dict["title"] = ( + self.data_template_dict["group_title"] + " -- " + title + ) + + if ("$ProteinName" or "$CompoundName") in self.data_template_dict[ + "title" + ]: self.Logfile.error( - '%s: data_template - title not correctly formatted') + "%s: data_template - title not correctly formatted" + ) self.add_to_errorList(xtal) noError = False # mutations - mutations = self.data_template_dict['fragment_name_one_specific_mutation'] - if mutations.lower().replace(' ', '').replace('none', '').replace('null', '') == '': - self.data_template_dict['fragment_name_one_specific_mutation'] = '?' + mutations = self.data_template_dict["fragment_name_one_specific_mutation"] + if ( + mutations.lower() + .replace(" ", "") + .replace("none", "") + .replace("null", "") + == "" + ): + self.data_template_dict["fragment_name_one_specific_mutation"] = "?" else: - self.data_template_dict['fragment_name_one_specific_mutation'] = '"' + \ - mutations.replace(' ', '') + '"' + self.data_template_dict["fragment_name_one_specific_mutation"] = ( + '"' + mutations.replace(" ", "") + '"' + ) # get protein chains - self.data_template_dict['protein_chains'] = '' + self.data_template_dict["protein_chains"] = "" chains = self.pdb.GetProteinChains() for item in chains: - self.data_template_dict['protein_chains'] += item + ',' - self.data_template_dict['protein_chains'] = self.data_template_dict['protein_chains'][:-1] + self.data_template_dict["protein_chains"] += item + "," + self.data_template_dict["protein_chains"] = self.data_template_dict[ + "protein_chains" + ][:-1] data_template = templates().data_template_cif(self.data_template_dict) -# site_details = self.make_site_description(xtal) -# data_template += site_details + # site_details = self.make_site_description(xtal) + # data_template += site_details if self.ground_state: - f = open(os.path.join(self.projectDir, - 'data_template.cif'), 'w') + f = open(os.path.join(self.projectDir, "data_template.cif"), "w") else: - f = open(os.path.join(self.projectDir, - xtal, 'data_template.cif'), 'w') + f = open(os.path.join(self.projectDir, xtal, "data_template.cif"), "w") f.write(data_template) f.close() @@ -1022,76 +1263,103 @@ def create_model_mmcif(self, xtal): os.chdir(os.path.join(self.projectDir, xtal)) refSoft = self.pdb.get_refinement_program() - if os.path.isdir('/dls'): + if os.path.isdir("/dls"): # if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): # pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-v3.26/pdb-extract-v3.26-prod-src/setup.sh\n' # pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-v3.26/pdb-extract-v3.26-prod-src/bin/pdb_extract' # else: - pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n' - pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-prod/bin/pdb_extract' + pdb_extract_init = ( + "source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n" + ) + pdb_extract_init += ( + "/dls/science/groups/i04-1/software/pdb-extract-prod/bin/pdb_extract" + ) else: - if os.path.isfile(os.path.join(os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/bin/pdb_extract')): - pdb_extract_init = 'source ' + \ - os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' + if os.path.isfile( + os.path.join( + os.getenv("XChemExplorer_DIR"), + "pdb_extract/pdb-extract-prod/bin/pdb_extract", + ) + ): + pdb_extract_init = ( + "source " + + os.path.join( + os.getenv("XChemExplorer_DIR"), + "pdb_extract/pdb-extract-prod/setup.sh", + ) + + "\n" + ) pdb_extract_init += os.path.join( - os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/bin/pdb_extract') + os.getenv("XChemExplorer_DIR"), + "pdb_extract/pdb-extract-prod/bin/pdb_extract", + ) else: - pdb_extract_init = 'pdb_extract' + pdb_extract_init = "pdb_extract" if self.ground_state: - refXtal = self.ground_state_pdb.split( - '/')[len(self.ground_state_pdb.split('/')) - 2] + refXtal = self.ground_state_pdb.split("/")[ + len(self.ground_state_pdb.split("/")) - 2 + ] self.Logfile.insert( - 'ground_state deposition reference dataset: {0!s}'.format(refXtal)) - aimless = os.path.join(self.logDir, refXtal, refXtal+'.log') + "ground_state deposition reference dataset: {0!s}".format(refXtal) + ) + aimless = os.path.join(self.logDir, refXtal, refXtal + ".log") else: - aimless = '%s.log' % xtal + aimless = "%s.log" % xtal isAimlessFile = False for n, line in enumerate(open(aimless)): - if 'AIMLESS' in line: + if "AIMLESS" in line: isAimlessFile = True break if not isAimlessFile: self.Logfile.warning( - 'processing log file does not seem to be an aimless file: {0!s}'.format(aimless)) - self.Logfile.insert('realpath of processing logfile: {0!s}'.format( - os.path.realpath(aimless))) - if os.path.realpath(aimless).endswith('.table1'): + "processing log file does not seem to be an aimless file: {0!s}".format( + aimless + ) + ) + self.Logfile.insert( + "realpath of processing logfile: {0!s}".format( + os.path.realpath(aimless) + ) + ) + if os.path.realpath(aimless).endswith(".table1"): self.Logfile.warning( - '{0!s}: {1!s}.log seems to be a staraniso .table1 file'.format(xtal, xtal)) + "{0!s}: {1!s}.log seems to be a staraniso .table1 file".format( + xtal, xtal + ) + ) isAimlessFile = True - self.Logfile.warning( - 'it does not seem to originate from staraniso either') + self.Logfile.warning("it does not seem to originate from staraniso either") if not isAimlessFile: - if os.path.isfile('aimless_dials.log'): - aimless = 'aimless_dials.log' + if os.path.isfile("aimless_dials.log"): + aimless = "aimless_dials.log" else: parse().make_pseudo_aimless_log_from_json(aimless) - aimless = 'aimless_dials.log' + aimless = "aimless_dials.log" -# aimless = None -# for n,line in enumerate(open('%s.log' %xtal)): -# if 'AIMLESS' in line: -# aimless = '%s.log' %xtal -# break -# if not aimless: -# if os.path.isfile('aimless_dials.log'): -# aimless = 'aimless_dials.log' + # aimless = None + # for n,line in enumerate(open('%s.log' %xtal)): + # if 'AIMLESS' in line: + # aimless = '%s.log' %xtal + # break + # if not aimless: + # if os.path.isfile('aimless_dials.log'): + # aimless = 'aimless_dials.log' if self.ground_state: # refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] # aimless = os.path.join(self.logDir,refXtal,refXtal+'.log') - self.Logfile.insert('aimless.log file: ' + aimless) - Cmd = (pdb_extract_init + - ' -r {0!s}'.format(refSoft) + - ' -iPDB {0!s}'.format(self.ground_state_pdb) + - ' -e MR' - ' -s AIMLESS' - ' -iLOG {0!s}'.format(aimless) + - ' -iENT data_template.cif' - ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) + self.Logfile.insert("aimless.log file: " + aimless) + Cmd = ( + pdb_extract_init + + " -r {0!s}".format(refSoft) + + " -iPDB {0!s}".format(self.ground_state_pdb) + + " -e MR" + " -s AIMLESS" + " -iLOG {0!s}".format(aimless) + " -iENT data_template.cif" + " -o {0!s}.mmcif > {1!s}.mmcif.log".format(xtal, xtal) + ) else: # if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): # self.Logfile.insert('%s: found MMCIF file; will use instead of PDB: %s' %(xtal,self.db_dict['RefinementMMCIFmodel_latest'])) @@ -1104,89 +1372,103 @@ def create_model_mmcif(self, xtal): # ' -iENT data_template.cif' # ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) # else: - Cmd = (pdb_extract_init + - ' -r {0!s}'.format(refSoft) + - ' -iPDB {0!s}'.format('refine.split.bound-state.pdb') + - ' -e MR' - ' -s AIMLESS' - ' -iLOG {0!s}'.format(aimless) + - ' -iENT data_template.cif' - ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) - - self.Logfile.insert(xtal + ': running pdb_extract: ' + Cmd) + Cmd = ( + pdb_extract_init + + " -r {0!s}".format(refSoft) + + " -iPDB {0!s}".format("refine.split.bound-state.pdb") + + " -e MR" + " -s AIMLESS" + " -iLOG {0!s}".format(aimless) + " -iENT data_template.cif" + " -o {0!s}.mmcif > {1!s}.mmcif.log".format(xtal, xtal) + ) + + self.Logfile.insert(xtal + ": running pdb_extract: " + Cmd) os.system(Cmd) self.update_model_mmcif_header(xtal) - if os.path.isfile(xtal+'.mmcif') and os.path.getsize(xtal+'.mmcif') > 20000: - self.Logfile.insert( - '%s: model mmcif file successfully created' % xtal) + if os.path.isfile(xtal + ".mmcif") and os.path.getsize(xtal + ".mmcif") > 20000: + self.Logfile.insert("%s: model mmcif file successfully created" % xtal) if self.ground_state: self.db.execute_statement( - "update depositTable set mmCIF_model_file='{0!s}.mmcif' where CrystalName is '{1!s}' and DimplePANDDApath is '{2!s}'".format(xtal, - xtal, self.panddaDir)) + "update depositTable set mmCIF_model_file='{0!s}.mmcif' where CrystalName is '{1!s}' and DimplePANDDApath is '{2!s}'".format( + xtal, xtal, self.panddaDir + ) + ) else: self.db.execute_statement( - "update depositTable set mmCIF_model_file='{0!s}.mmcif' where CrystalName is '{1!s}'".format(xtal, xtal)) + "update depositTable set mmCIF_model_file='{0!s}.mmcif' where CrystalName is '{1!s}'".format( + xtal, xtal + ) + ) fileStatus = True else: - self.Logfile.error( - '%s: model mmcif file was not created successfully') + self.Logfile.error("%s: model mmcif file was not created successfully") self.add_to_errorList(xtal) return fileStatus def update_model_mmcif_header(self, xtal): - self.Logfile.insert('%s: updating header of model mmcif file' % xtal) + self.Logfile.insert("%s: updating header of model mmcif file" % xtal) foundSoftwareBlock = False amendSoftwareBlock = False softwareEntry = [] - for i, line in enumerate(fileinput.input(xtal + '.mmcif', inplace=1)): + for i, line in enumerate(fileinput.input(xtal + ".mmcif", inplace=1)): # if i == 4: sys.stdout.write('\n') # write a blank line after the 5th line - if '_software.pdbx_ordinal' in line: + if "_software.pdbx_ordinal" in line: foundSoftwareBlock = True if foundSoftwareBlock: - if not line.startswith('_'): + if not line.startswith("_"): try: softwareEntry.append(int(line.split()[0])) except (ValueError, IndexError): pass - if '#' in line: + if "#" in line: amendSoftwareBlock = True foundSoftwareBlock = False - if '_refine.pdbx_ls_cross_valid_method' in line: + if "_refine.pdbx_ls_cross_valid_method" in line: sys.stdout.write( - '_refine.pdbx_ls_cross_valid_method THROUGHOUT \n') + "_refine.pdbx_ls_cross_valid_method THROUGHOUT \n" + ) - elif '_refine.pdbx_starting_model' in line: - sys.stdout.write('_refine.pdbx_starting_model {0!s} \n'.format( - self.data_template_dict['pdbx_starting_model'])) + elif "_refine.pdbx_starting_model" in line: + sys.stdout.write( + "_refine.pdbx_starting_model {0!s} \n".format( + self.data_template_dict["pdbx_starting_model"] + ) + ) - elif '_refine.pdbx_method_to_determine_struct' in line: + elif "_refine.pdbx_method_to_determine_struct" in line: sys.stdout.write( - "_refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS'\n") - elif '_struct.title ---' in line: + "_refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS'\n" + ) + elif "_struct.title ---" in line: # self.Logfile.warning('structure title was not created by pdb_extract; there might be an issue with REFMAC 5.8.0238') # self.Logfile.insert('trying to get title from data_template.cif file') - Title = '' + Title = "" foundTitle = False - for li in open('data_template.cif'): - if li.startswith('_struct.title'): + for li in open("data_template.cif"): + if li.startswith("_struct.title"): foundTitle = True if foundTitle: - if li.replace(' ', '').replace('\n', '').replace('\r', '') == ';': + if ( + li.replace(" ", "").replace("\n", "").replace("\r", "") + == ";" + ): Title += li break Title += li sys.stdout.write(Title) elif amendSoftwareBlock: cifItem = ( - "{0!s} {1!s} ? ? program ? ? 'data reduction' ? ?\n".format(str(max(softwareEntry) + 1), - self.data_template_dict[ - 'data_integration_software']) + - '{0!s} {1!s} ? ? program ? ? phasing ? ?\n'.format(str(max(softwareEntry) + 2), - self.data_template_dict[ - 'phasing_software']) + "{0!s} {1!s} ? ? program ? ? 'data reduction' ? ?\n".format( + str(max(softwareEntry) + 1), + self.data_template_dict["data_integration_software"], + ) + + "{0!s} {1!s} ? ? program ? ? phasing ? ?\n".format( + str(max(softwareEntry) + 2), + self.data_template_dict["phasing_software"], + ) # '#\n' # "loop_\n" # "_pdbx_related_exp_data_set.ordinal\n" @@ -1208,114 +1490,166 @@ def update_model_mmcif_header(self, xtal): else: sys.stdout.write(line) - -# elif '_reflns.d_resolution_low' in line and len(line.split()) == 2: -# sys.stdout.write('_reflns.d_resolution_low {0!s}\n'.format(min(low_reso_list))) -# -# elif '_refine.ls_d_res_low' in line and len(line.split()) == 2: -# sys.stdout.write('_refine.ls_d_res_low {0!s}\n'.format(min(low_reso_list))) + # elif '_reflns.d_resolution_low' in line and len(line.split()) == 2: + # sys.stdout.write('_reflns.d_resolution_low {0!s}\n'.format(min(low_reso_list))) + # + # elif '_refine.ls_d_res_low' in line and len(line.split()) == 2: + # sys.stdout.write('_refine.ls_d_res_low {0!s}\n'.format(min(low_reso_list))) def add_funding_information(self, xtal): - pdbx_funding_ordinal_one = self.data_template_dict['pdbx_funding_ordinal_one'] - if pdbx_funding_ordinal_one.lower().replace(' ', '').replace('none', '').replace('null', '') == '': - self.data_template_dict['pdbx_funding_ordinal_one'] = '' - self.data_template_dict['pdbx_funding_organization_one'] = '' - self.data_template_dict['pdbx_grant_number_one'] = '' - self.data_template_dict['pdbx_grant_country_one'] = '' - funding_one = '' + pdbx_funding_ordinal_one = self.data_template_dict["pdbx_funding_ordinal_one"] + if ( + pdbx_funding_ordinal_one.lower() + .replace(" ", "") + .replace("none", "") + .replace("null", "") + == "" + ): + self.data_template_dict["pdbx_funding_ordinal_one"] = "" + self.data_template_dict["pdbx_funding_organization_one"] = "" + self.data_template_dict["pdbx_grant_number_one"] = "" + self.data_template_dict["pdbx_grant_country_one"] = "" + funding_one = "" else: - funding_one = "%s '%s' '%s' '%s'\n" % (self.data_template_dict['pdbx_funding_ordinal_one'], self.data_template_dict[ - 'pdbx_funding_organization_one'], self.data_template_dict['pdbx_grant_number_one'], self.data_template_dict['pdbx_grant_country_one']) - - pdbx_funding_ordinal_two = self.data_template_dict['pdbx_funding_ordinal_two'] - if pdbx_funding_ordinal_two.lower().replace(' ', '').replace('none', '').replace('null', '') == '': - self.data_template_dict['pdbx_funding_ordinal_two'] = '' - self.data_template_dict['pdbx_funding_organization_two'] = '' - self.data_template_dict['pdbx_grant_number_two'] = '' - self.data_template_dict['pdbx_grant_country_two'] = '' - funding_two = '' + funding_one = "%s '%s' '%s' '%s'\n" % ( + self.data_template_dict["pdbx_funding_ordinal_one"], + self.data_template_dict["pdbx_funding_organization_one"], + self.data_template_dict["pdbx_grant_number_one"], + self.data_template_dict["pdbx_grant_country_one"], + ) + + pdbx_funding_ordinal_two = self.data_template_dict["pdbx_funding_ordinal_two"] + if ( + pdbx_funding_ordinal_two.lower() + .replace(" ", "") + .replace("none", "") + .replace("null", "") + == "" + ): + self.data_template_dict["pdbx_funding_ordinal_two"] = "" + self.data_template_dict["pdbx_funding_organization_two"] = "" + self.data_template_dict["pdbx_grant_number_two"] = "" + self.data_template_dict["pdbx_grant_country_two"] = "" + funding_two = "" else: - funding_two = "%s '%s' '%s' '%s'\n" % (self.data_template_dict['pdbx_funding_ordinal_two'], self.data_template_dict[ - 'pdbx_funding_organization_two'], self.data_template_dict['pdbx_grant_number_two'], self.data_template_dict['pdbx_grant_country_two']) - - pdbx_funding_ordinal_three = self.data_template_dict['pdbx_funding_ordinal_three'] - if pdbx_funding_ordinal_three.lower().replace(' ', '').replace('none', '').replace('null', '') == '': - self.data_template_dict['pdbx_funding_ordinal_three'] = '' - self.data_template_dict['pdbx_funding_organization_three'] = '' - self.data_template_dict['pdbx_grant_number_three'] = '' - self.data_template_dict['pdbx_grant_country_three'] = '' - funding_three = '' + funding_two = "%s '%s' '%s' '%s'\n" % ( + self.data_template_dict["pdbx_funding_ordinal_two"], + self.data_template_dict["pdbx_funding_organization_two"], + self.data_template_dict["pdbx_grant_number_two"], + self.data_template_dict["pdbx_grant_country_two"], + ) + + pdbx_funding_ordinal_three = self.data_template_dict[ + "pdbx_funding_ordinal_three" + ] + if ( + pdbx_funding_ordinal_three.lower() + .replace(" ", "") + .replace("none", "") + .replace("null", "") + == "" + ): + self.data_template_dict["pdbx_funding_ordinal_three"] = "" + self.data_template_dict["pdbx_funding_organization_three"] = "" + self.data_template_dict["pdbx_grant_number_three"] = "" + self.data_template_dict["pdbx_grant_country_three"] = "" + funding_three = "" else: - funding_three = "%s '%s' '%s' '%s'\n" % (self.data_template_dict['pdbx_funding_ordinal_three'], self.data_template_dict[ - 'pdbx_funding_organization_three'], self.data_template_dict['pdbx_grant_number_three'], self.data_template_dict['pdbx_grant_country_three']) + funding_three = "%s '%s' '%s' '%s'\n" % ( + self.data_template_dict["pdbx_funding_ordinal_three"], + self.data_template_dict["pdbx_funding_organization_three"], + self.data_template_dict["pdbx_grant_number_three"], + self.data_template_dict["pdbx_grant_country_three"], + ) funding_info = ( - '#\n' - 'loop_\n' - '_pdbx_audit_support.ordinal \n' - '_pdbx_audit_support.funding_organization \n' - '_pdbx_audit_support.grant_number \n' - '_pdbx_audit_support.country \n' - + funding_one + funding_two + funding_three + - '#\n' + "#\n" + "loop_\n" + "_pdbx_audit_support.ordinal \n" + "_pdbx_audit_support.funding_organization \n" + "_pdbx_audit_support.grant_number \n" + "_pdbx_audit_support.country \n" + + funding_one + + funding_two + + funding_three + + "#\n" ) - f = open(xtal + '.mmcif', 'a') + f = open(xtal + ".mmcif", "a") f.write(funding_info) f.close() def add_ligand_cif_to_model_mmcif(self, xtal): filestatus = False - self.Logfile.insert('%s: looking for ligand restraints file...' % xtal) + self.Logfile.insert("%s: looking for ligand restraints file..." % xtal) os.chdir(os.path.join(self.projectDir, xtal)) - if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): - self.Logfile.insert('%s: found %s; assuming that ligand cif dictionary is already included...' % ( - xtal, self.db_dict['RefinementMMCIFmodel_latest'])) + if os.path.isfile(self.db_dict["RefinementMMCIFmodel_latest"]): + self.Logfile.insert( + "%s: found %s; assuming that ligand cif dictionary is already included..." + % (xtal, self.db_dict["RefinementMMCIFmodel_latest"]) + ) filestatus = True else: - if os.path.isfile(self.db_dict['CompoundCode']+'.cif'): - self.Logfile.insert('%s: found ligand restraints file -> %s' % - (xtal, self.db_dict['CompoundCode']+'.cif')) + if os.path.isfile(self.db_dict["CompoundCode"] + ".cif"): + self.Logfile.insert( + "%s: found ligand restraints file -> %s" + % (xtal, self.db_dict["CompoundCode"] + ".cif") + ) self.Logfile.insert( - '%s: adding ligand restraints file to model mmcif' % xtal) - cif = '' - for line in open(self.db_dict['CompoundCode']+'.cif'): + "%s: adding ligand restraints file to model mmcif" % xtal + ) + cif = "" + for line in open(self.db_dict["CompoundCode"] + ".cif"): cif += line - f = open(xtal+'.mmcif', 'a') + f = open(xtal + ".mmcif", "a") f.write(cif) f.close() filestatus = True else: - self.Logfile.warning('%s: could not find %s' % ( - xtal, self.db_dict['CompoundCode']+'.cif')) + self.Logfile.warning( + "%s: could not find %s" + % (xtal, self.db_dict["CompoundCode"] + ".cif") + ) return filestatus def make_table_one(self, xtal): os.chdir(os.path.join(self.projectDir, xtal)) - if os.path.isfile(xtal + '.mmcif') and os.path.getsize(xtal + '.mmcif') > 20000: - self.Logfile.insert('making table_1 for %s.mmcif' % xtal) - if os.path.isdir('/dls'): - extract_table_init = 'source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n' - extract_table_init += '/dls/science/groups/i04-1/software/pdb-extract-prod/bin/extract_table' + if os.path.isfile(xtal + ".mmcif") and os.path.getsize(xtal + ".mmcif") > 20000: + self.Logfile.insert("making table_1 for %s.mmcif" % xtal) + if os.path.isdir("/dls"): + extract_table_init = "source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n" + extract_table_init += "/dls/science/groups/i04-1/software/pdb-extract-prod/bin/extract_table" else: - extract_table_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' - extract_table_init += os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/bin/extract_table') + extract_table_init = ( + "source " + + os.path.join( + os.getenv("XChemExplorer_DIR"), + "pdb_extract/pdb-extract-prod/setup.sh", + ) + + "\n" + ) + extract_table_init += os.path.join( + os.getenv("XChemExplorer_DIR"), + "pdb_extract/pdb-extract-prod/bin/extract_table", + ) - Cmd = extract_table_init + ' ' + xtal + '.mmcif' + Cmd = extract_table_init + " " + xtal + ".mmcif" - self.Logfile.insert(xtal + ': running sf_convert: ' + Cmd) + self.Logfile.insert(xtal + ": running sf_convert: " + Cmd) os.system(Cmd) - if os.path.isfile('cryst-table-1.out'): - os.system('/bin/mv cryst-table-1.out %s-table-1.txt' % xtal) + if os.path.isfile("cryst-table-1.out"): + os.system("/bin/mv cryst-table-1.out %s-table-1.txt" % xtal) self.Logfile.insert( - '%s: table_1 successfully created; updating database...' % xtal) + "%s: table_1 successfully created; updating database..." % xtal + ) self.db.execute_statement( - "update mainTable set table_one='{0!s}-table-1.txt' where CrystalName is '{1!s}'".format(xtal, xtal)) + "update mainTable set table_one='{0!s}-table-1.txt' where CrystalName is '{1!s}'".format( + xtal, xtal + ) + ) else: - self.Logfile.warning('%s: could not create table_1' % xtal) + self.Logfile.warning("%s: could not create table_1" % xtal) def create_sf_mmcif(self, xtal): fileStatus = False @@ -1324,132 +1658,193 @@ def create_sf_mmcif(self, xtal): else: os.chdir(os.path.join(self.projectDir, xtal)) - if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: - mtzin = 'refine.mtz ' + if os.path.isfile("no_pandda_analysis_performed") or self.ignore_event_map: + mtzin = "refine.mtz " else: - mtzin = 'refine.mtz ' + xtal + '.free.mtz ' + mtzin = "refine.mtz " + xtal + ".free.mtz " for event in self.eventList: - mtzin += event + ' ' + mtzin += event + " " -# if self.ground_state: -# mtzin = self.ground_state_mean_mtz + # if self.ground_state: + # mtzin = self.ground_state_mean_mtz - if os.path.isdir('/dls'): - pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n' - pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-prod/bin/sf_convert' + if os.path.isdir("/dls"): + pdb_extract_init = ( + "source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n" + ) + pdb_extract_init += ( + "/dls/science/groups/i04-1/software/pdb-extract-prod/bin/sf_convert" + ) else: - if os.path.isfile(os.path.join(os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/bin/sf_convert')): - pdb_extract_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' + if os.path.isfile( + os.path.join( + os.getenv("XChemExplorer_DIR"), + "pdb_extract/pdb-extract-prod/bin/sf_convert", + ) + ): + pdb_extract_init = ( + "source " + + os.path.join( + os.getenv("XChemExplorer_DIR"), + "pdb_extract/pdb-extract-prod/setup.sh", + ) + + "\n" + ) pdb_extract_init += os.path.join( - os.getenv('XChemExplorer_DIR'), 'pdb_extract/pdb-extract-prod/bin/sf_convert') + os.getenv("XChemExplorer_DIR"), + "pdb_extract/pdb-extract-prod/bin/sf_convert", + ) else: - pdb_extract_init = 'sf_convert' + pdb_extract_init = "sf_convert" - Cmd = (pdb_extract_init + - ' -o mmcif' - ' -sf %s' % mtzin + - ' -out {0!s}_sf.mmcif > {1!s}.sf_mmcif.log'.format(xtal, xtal)) + Cmd = ( + pdb_extract_init + " -o mmcif" + " -sf %s" % mtzin + + " -out {0!s}_sf.mmcif > {1!s}.sf_mmcif.log".format(xtal, xtal) + ) - self.Logfile.insert(xtal + ': running sf_convert: ' + Cmd) + self.Logfile.insert(xtal + ": running sf_convert: " + Cmd) os.system(Cmd) os.system( - '/bin/rm sf_format_guess.text mtzdmp.log SF_4_validate.cif sf_information.cif') + "/bin/rm sf_format_guess.text mtzdmp.log SF_4_validate.cif sf_information.cif" + ) self.update_sf_mmcif_file(xtal) - if os.path.isfile(xtal+'_sf.mmcif') and os.path.getsize(xtal+'_sf.mmcif') > 20000: - self.Logfile.insert( - '%s: SF mmcif file successfully created' % xtal) + if ( + os.path.isfile(xtal + "_sf.mmcif") + and os.path.getsize(xtal + "_sf.mmcif") > 20000 + ): + self.Logfile.insert("%s: SF mmcif file successfully created" % xtal) if self.ground_state: self.db.execute_statement( - "update depositTable set mmCIF_SF_file='{0!s}_sf.mmcif' where CrystalName is '{1!s}' and DimplePANDDApath is '{2!s}'".format(xtal, xtal, self.panddaDir)) + "update depositTable set mmCIF_SF_file='{0!s}_sf.mmcif' where CrystalName is '{1!s}' and DimplePANDDApath is '{2!s}'".format( + xtal, xtal, self.panddaDir + ) + ) else: self.db.execute_statement( - "update depositTable set mmCIF_SF_file='{0!s}_sf.mmcif' where CrystalName is '{1!s}'".format(xtal, xtal)) + "update depositTable set mmCIF_SF_file='{0!s}_sf.mmcif' where CrystalName is '{1!s}'".format( + xtal, xtal + ) + ) fileStatus = True else: - self.Logfile.error( - '%s: SF mmcif file was not created successfully') + self.Logfile.error("%s: SF mmcif file was not created successfully") self.add_to_errorList(xtal) return fileStatus def apo_mmcif_exists(self): fileStatus = False - self.Logfile.insert('checking if mmcif files of apo structures exist') + self.Logfile.insert("checking if mmcif files of apo structures exist") counter = 0 - for mmcif in glob.glob(os.path.join(self.panddaDir, 'processed_datasets', '*', '*.mmcif')): + for mmcif in glob.glob( + os.path.join(self.panddaDir, "processed_datasets", "*", "*.mmcif") + ): if os.path.isfile(mmcif): counter += 1 if counter < 40: - self.Logfile.error('found only %s apo mmcif files' % str(counter)) - self.Logfile.warning( - 'you may need to run "PanDDA tab"/"apo -> mmcif"') + self.Logfile.error("found only %s apo mmcif files" % str(counter)) + self.Logfile.warning('you may need to run "PanDDA tab"/"apo -> mmcif"') else: - self.Logfile.insert( - 'found %s apo mmcif files; seems OK!' % str(counter)) + self.Logfile.insert("found %s apo mmcif files; seems OK!" % str(counter)) fileStatus = True return fileStatus def add_apo_sf_mmcif_to_ground_state_mmcif(self): os.chdir(self.projectDir) self.Logfile.insert( - 'checking pandda directory for apo mmcif files: '+self.panddaDir) - f = open('ground_state_sf.mmcif', 'w') + "checking pandda directory for apo mmcif files: " + self.panddaDir + ) + f = open("ground_state_sf.mmcif", "w") - refXtal = self.ground_state_pdb.split( - '/')[len(self.ground_state_pdb.split('/'))-2] + refXtal = self.ground_state_pdb.split("/")[ + len(self.ground_state_pdb.split("/")) - 2 + ] # make sure that mmcof belonging to ref PDB file is first xtalList = [refXtal] - for dirs in glob.glob(os.path.join(self.panddaDir, 'processed_datasets', '*')): - xtal = dirs[dirs.rfind('/') + 1:] + for dirs in glob.glob(os.path.join(self.panddaDir, "processed_datasets", "*")): + xtal = dirs[dirs.rfind("/") + 1 :] if xtal not in xtalList: xtalList.append(xtal) counter = 1 for xtal in xtalList: # this is needed in case single files are in processed_datasets - if not os.path.isdir(os.path.join(self.panddaDir, 'processed_datasets', xtal)): + if not os.path.isdir( + os.path.join(self.panddaDir, "processed_datasets", xtal) + ): continue else: - dirs = os.path.join(self.panddaDir, 'processed_datasets', xtal) + dirs = os.path.join(self.panddaDir, "processed_datasets", xtal) self.Logfile.insert( - '%s: reading saoked compound information from database' % xtal) + "%s: reading saoked compound information from database" % xtal + ) xtalDict = self.db.get_db_dict_for_sample(xtal) - if xtalDict['CompoundSMILES'].lower().replace(' ', '') == '': - smiles = 'none' - elif 'none' in xtalDict['CompoundSMILES'].lower().replace(' ', ''): - smiles = 'none' - elif 'null' in xtalDict['CompoundSMILES'].lower().replace(' ', ''): - smiles = 'none' + if xtalDict["CompoundSMILES"].lower().replace(" ", "") == "": + smiles = "none" + elif "none" in xtalDict["CompoundSMILES"].lower().replace(" ", ""): + smiles = "none" + elif "null" in xtalDict["CompoundSMILES"].lower().replace(" ", ""): + smiles = "none" else: - smiles = xtalDict['CompoundSMILES'].replace(' ', '') - self.Logfile.insert('%s: compound SMILES -> %s' % (xtal, smiles)) - if os.path.isfile(os.path.join(dirs, xtal+'_sf.mmcif')): + smiles = xtalDict["CompoundSMILES"].replace(" ", "") + self.Logfile.insert("%s: compound SMILES -> %s" % (xtal, smiles)) + if os.path.isfile(os.path.join(dirs, xtal + "_sf.mmcif")): self.Logfile.insert( - 'adding %s_sf.mmcif to ground-state_sf.mmcif' % xtal) - for line in open(os.path.join(dirs, xtal+'_sf.mmcif')): - if line.startswith('_cell.angle_gamma'): + "adding %s_sf.mmcif to ground-state_sf.mmcif" % xtal + ) + for line in open(os.path.join(dirs, xtal + "_sf.mmcif")): + if line.startswith("_cell.angle_gamma"): newLine = line - newLine += '#\n' - newLine += '_diffrn.id 1\n' - newLine += '_diffrn.details "diffraction data from crystal %s; soaked compound: %s"\n' % ( - str(counter), smiles.replace('\n', '').replace('\r', '')) + newLine += "#\n" + newLine += "_diffrn.id 1\n" + newLine += ( + '_diffrn.details "diffraction data from crystal %s; soaked compound: %s"\n' + % (str(counter), smiles.replace("\n", "").replace("\r", "")) + ) f.write(newLine) counter += 1 else: f.write(line) f.close() self.Logfile.insert( - 'added %s apo mmcif files to ground-state mmcif' % str(counter)) + "added %s apo mmcif files to ground-state mmcif" % str(counter) + ) return True def add_data_increment_to_apo_mmcif(self): - self.Logfile.insert( - 'inrementing data_rxxxxsf in ground-state_sf.mmcif') - x = ['', 'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', - 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'] + self.Logfile.insert("inrementing data_rxxxxsf in ground-state_sf.mmcif") + x = [ + "", + "A", + "B", + "C", + "D", + "E", + "F", + "G", + "H", + "I", + "J", + "K", + "L", + "M", + "N", + "O", + "P", + "Q", + "R", + "S", + "T", + "U", + "V", + "W", + "X", + "Y", + "Z", + ] a = 0 b = 0 c = 0 @@ -1457,14 +1852,16 @@ def add_data_increment_to_apo_mmcif(self): foundFirstLine = False foundCulprit = False datasetCounter = 0 - if os.path.isfile(os.path.join(self.panddaDir, 'ground_state_sf.mmcif')): - f = open('ground_state_sf_tmp.mmcif', 'w') - for n, line in enumerate(open(os.path.join(self.panddaDir, 'ground_state_sf.mmcif'))): - if line.startswith('data_rxxxxsf') and not foundFirstLine: + if os.path.isfile(os.path.join(self.panddaDir, "ground_state_sf.mmcif")): + f = open("ground_state_sf_tmp.mmcif", "w") + for n, line in enumerate( + open(os.path.join(self.panddaDir, "ground_state_sf.mmcif")) + ): + if line.startswith("data_rxxxxsf") and not foundFirstLine: foundFirstLine = True a += 1 f.write(line) - elif line.startswith('data_rxxxxsf') and foundFirstLine: + elif line.startswith("data_rxxxxsf") and foundFirstLine: if a == len(x): a = 1 b += 1 @@ -1472,29 +1869,37 @@ def add_data_increment_to_apo_mmcif(self): a = 1 b = 1 c += 1 - newLine = line.replace('xsf', 's%ssf' % - str(x[a]+x[b]+x[c])) + newLine = line.replace("xsf", "s%ssf" % str(x[a] + x[b] + x[c])) datasetCounter += 1 f.write(newLine) a += 1 - self.Logfile.insert('new dataset block: %s -> %s' % ( - str(datasetCounter), newLine.replace('\n', '').replace('\r', ''))) -# if datasetCounter % 50 == 0: -# self.Logfile.insert('%s data_rxxxxsf records edited...' %str(datasetCounter)) + self.Logfile.insert( + "new dataset block: %s -> %s" + % ( + str(datasetCounter), + newLine.replace("\n", "").replace("\r", ""), + ) + ) + # if datasetCounter % 50 == 0: + # self.Logfile.insert('%s data_rxxxxsf records edited...' %str(datasetCounter)) else: f.write(line) f.close() os.chdir(self.panddaDir) - os.system('/bin/mv ground_state_sf_tmp.mmcif ground_state_sf.mmcif') + os.system("/bin/mv ground_state_sf_tmp.mmcif ground_state_sf.mmcif") - if os.path.isfile('ground_state_sf.mmcif') and os.path.getsize('ground_state_sf.mmcif') > 20000: - self.Logfile.insert( - 'ground_state: SF mmcif file successfully created') + if ( + os.path.isfile("ground_state_sf.mmcif") + and os.path.getsize("ground_state_sf.mmcif") > 20000 + ): + self.Logfile.insert("ground_state: SF mmcif file successfully created") self.db.execute_statement( - "update depositTable set mmCIF_SF_file='ground_state_sf.mmcif' where CrystalName is 'ground_state' and DimplePANDDApath is '{0!s}'".format(self.panddaDir)) + "update depositTable set mmCIF_SF_file='ground_state_sf.mmcif' where CrystalName is 'ground_state' and DimplePANDDApath is '{0!s}'".format( + self.panddaDir + ) + ) else: - self.Logfile.error( - '%s: SF mmcif file was not created successfully') + self.Logfile.error("%s: SF mmcif file was not created successfully") self.add_to_errorList(xtal) return True @@ -1503,68 +1908,82 @@ def event_maps_exist_in_sf_mmcif(self, xtal): fileOK = False # set to -2 since first two data blocks are initial/final.mtz and data.mtz n_eventMTZ_found = -2 - if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: + if os.path.isfile("no_pandda_analysis_performed") or self.ignore_event_map: self.Logfile.warning( - '%s: no pandda analysis performed; skipping this step...' % xtal) + "%s: no pandda analysis performed; skipping this step..." % xtal + ) fileOK = True else: - for line in open(xtal + '_sf.mmcif'): - if line.startswith('_refln.crystal_id'): + for line in open(xtal + "_sf.mmcif"): + if line.startswith("_refln.crystal_id"): n_eventMTZ_found += 1 if n_eventMTZ_found == len(self.eventList): fileOK = True - self.Logfile.insert('%s: %s_sf.mmcif should contains %s of %s event maps' % ( - xtal, xtal, n_eventMTZ_found, len(self.eventList))) + self.Logfile.insert( + "%s: %s_sf.mmcif should contains %s of %s event maps" + % (xtal, xtal, n_eventMTZ_found, len(self.eventList)) + ) else: - self.Logfile.error('%s: %s_sf.mmcif should contains only %s of %s event maps' % ( - xtal, xtal, n_eventMTZ_found, len(self.eventList))) + self.Logfile.error( + "%s: %s_sf.mmcif should contains only %s of %s event maps" + % (xtal, xtal, n_eventMTZ_found, len(self.eventList)) + ) self.add_to_errorList(xtal) return fileOK def update_sf_mmcif_file(self, xtal): - self.Logfile.insert('%s: updating %s_sf.mmcif' % (xtal, xtal)) + self.Logfile.insert("%s: updating %s_sf.mmcif" % (xtal, xtal)) if self.ground_state: bound = ["data for PanDDA ground-state-mean-map"] else: - bound = ["data from final refinement with ligand, final.mtz", - "data from original reflections, data.mtz", - "data for ligand evidence map (PanDDA event map), event_map_$.mtz"] + bound = [ + "data from final refinement with ligand, final.mtz", + "data from original reflections, data.mtz", + "data for ligand evidence map (PanDDA event map), event_map_$.mtz", + ] block = -1 - self.Logfile.insert('%s: reading wavelength from mtz file; lambda = %s' % ( - xtal, str(self.data_template_dict['radiation_wavelengths']))) + self.Logfile.insert( + "%s: reading wavelength from mtz file; lambda = %s" + % (xtal, str(self.data_template_dict["radiation_wavelengths"])) + ) - if os.path.isfile('no_pandda_analysis_performed') or self.ignore_event_map: + if os.path.isfile("no_pandda_analysis_performed") or self.ignore_event_map: self.Logfile.warning( - '%s: apparently not a pandda deposition; will skip this step...' % xtal) + "%s: apparently not a pandda deposition; will skip this step..." % xtal + ) return None - for i, line in enumerate(fileinput.input(xtal + '_sf.mmcif', inplace=1)): + for i, line in enumerate(fileinput.input(xtal + "_sf.mmcif", inplace=1)): - if line.startswith('_cell.length_a'): + if line.startswith("_cell.length_a"): block += 1 - if line.startswith('_cell.angle_gamma'): + if line.startswith("_cell.angle_gamma"): if block >= 2: n = 2 else: n = block sys.stdout.write(line) - newLines = ('#\n' - '_diffrn.id 1\n' - '_diffrn.details "%s"\n' % bound[n]).replace('$', str(block-1)) + newLines = ( + "#\n" + "_diffrn.id 1\n" + '_diffrn.details "%s"\n' % bound[n] + ).replace("$", str(block - 1)) sys.stdout.write(newLines) - elif line.startswith('_diffrn_radiation_wavelength.wavelength'): - sys.stdout.write('_diffrn_radiation_wavelength.wavelength {0!s}\n'.format( - str(self.data_template_dict['radiation_wavelengths']))) + elif line.startswith("_diffrn_radiation_wavelength.wavelength"): + sys.stdout.write( + "_diffrn_radiation_wavelength.wavelength {0!s}\n".format( + str(self.data_template_dict["radiation_wavelengths"]) + ) + ) else: sys.stdout.write(line) class prepare_for_group_deposition_upload(QtCore.QThread): - def __init__(self, database, xce_logfile, depositDir, projectDir, type): QtCore.QThread.__init__(self) self.database = database @@ -1576,99 +1995,127 @@ def __init__(self, database, xce_logfile, depositDir, projectDir, type): def run(self): - TextIndex = '' + TextIndex = "" os.chdir(self.depositDir) # ligand bound structures - if self.type == 'ligand_bound': + if self.type == "ligand_bound": self.Logfile.insert( - 'checking depositionTable for mmcif files of ligand-bound structures') + "checking depositionTable for mmcif files of ligand-bound structures" + ) depositList = self.db.execute_statement( - "select CrystalName from mainTable where RefinementOutcome like '5%';") - xtalString = '(' + "select CrystalName from mainTable where RefinementOutcome like '5%';" + ) + xtalString = "(" for item in depositList: xtal = str(item[0]) self.Logfile.insert( - '%s: adding mmcif files to final tar.bz2 file' % xtal) - xtalString += "CrystalName = '"+xtal+"' or " - xtalString = xtalString[:-4] + ')' + "%s: adding mmcif files to final tar.bz2 file" % xtal + ) + xtalString += "CrystalName = '" + xtal + "' or " + xtalString = xtalString[:-4] + ")" toDeposit = self.db.execute_statement( - "select CrystalName,mmCIF_model_file,mmCIF_SF_file,DimplePANDDApath from depositTable where StructureType is 'ligand_bound' and %s;" % xtalString) - elif self.type == 'ground_state': + "select CrystalName,mmCIF_model_file,mmCIF_SF_file,DimplePANDDApath from depositTable where StructureType is 'ligand_bound' and %s;" + % xtalString + ) + elif self.type == "ground_state": self.Logfile.insert( - 'checking depositionTable for mmcif files of ground-state structures') + "checking depositionTable for mmcif files of ground-state structures" + ) toDeposit = self.db.execute_statement( - "select CrystalName,mmCIF_model_file,mmCIF_SF_file,DimplePANDDApath from depositTable where StructureType is 'ground_state';") + "select CrystalName,mmCIF_model_file,mmCIF_SF_file,DimplePANDDApath from depositTable where StructureType is 'ground_state';" + ) else: return for n, item in enumerate(sorted(toDeposit)): xtal = str(item[0]) - if self.type == 'ligand_bound': + if self.type == "ligand_bound": mmcif = os.path.join(self.projectDir, xtal, str(item[1])) mmcif_sf = os.path.join(self.projectDir, xtal, str(item[2])) - elif self.type == 'ground_state': + elif self.type == "ground_state": mmcif = os.path.join(str(item[3]), str(item[1])) mmcif_sf = os.path.join(str(item[3]), str(item[2])) else: continue - self.Logfile.insert('%s: %s/ %s' % (xtal, mmcif, mmcif_sf)) + self.Logfile.insert("%s: %s/ %s" % (xtal, mmcif, mmcif_sf)) if os.path.isfile(mmcif) and os.path.isfile(mmcif_sf): self.Logfile.insert( - 'copying {0!s} to {1!s}'.format(mmcif, self.depositDir)) - os.system('/bin/cp {0!s} .'.format(mmcif)) - if self.type == 'ground_state': + "copying {0!s} to {1!s}".format(mmcif, self.depositDir) + ) + os.system("/bin/cp {0!s} .".format(mmcif)) + if self.type == "ground_state": os.system( - '/bin/mv ground_state.mmcif ground_state_{0!s}.mmcif'.format(str(n))) + "/bin/mv ground_state.mmcif ground_state_{0!s}.mmcif".format( + str(n) + ) + ) mmcif = mmcif.replace( - 'ground_state.mmcif', 'ground_state_{0!s}.mmcif'.format(str(n))) - self.Logfile.insert('copying {0!s} to {1!s}'.format( - mmcif_sf, self.depositDir)) - os.system('/bin/cp {0!s} .'.format(mmcif_sf)) - if self.type == 'ground_state': + "ground_state.mmcif", "ground_state_{0!s}.mmcif".format(str(n)) + ) + self.Logfile.insert( + "copying {0!s} to {1!s}".format(mmcif_sf, self.depositDir) + ) + os.system("/bin/cp {0!s} .".format(mmcif_sf)) + if self.type == "ground_state": os.system( - '/bin/mv ground_state_sf.mmcif ground_state_{0!s}_sf.mmcif'.format(str(n))) + "/bin/mv ground_state_sf.mmcif ground_state_{0!s}_sf.mmcif".format( + str(n) + ) + ) mmcif_sf = mmcif_sf.replace( - 'ground_state_sf.mmcif', 'ground_state_{0!s}_sf.mmcif'.format(str(n))) + "ground_state_sf.mmcif", + "ground_state_{0!s}_sf.mmcif".format(str(n)), + ) else: - self.Logfile.error('cannot find mmcif file for '+xtal) + self.Logfile.error("cannot find mmcif file for " + xtal) - text = ('label: {0!s}-{1!s}\n'.format(xtal, self.type) + - 'description: {0!s} structure of {1!s}\n'.format(self.type, xtal) + - 'model: {0!s}\n'.format(mmcif[mmcif.rfind('/')+1:]) + - 'sf: {0!s}\n\n'.format(mmcif_sf[mmcif_sf.rfind('/')+1:])) + text = ( + "label: {0!s}-{1!s}\n".format(xtal, self.type) + + "description: {0!s} structure of {1!s}\n".format(self.type, xtal) + + "model: {0!s}\n".format(mmcif[mmcif.rfind("/") + 1 :]) + + "sf: {0!s}\n\n".format(mmcif_sf[mmcif_sf.rfind("/") + 1 :]) + ) TextIndex += text - f = open('index.txt', 'w') + f = open("index.txt", "w") f.write(TextIndex) f.close() # checking of tar.bz2 files exisit fileList = [] - for i in sorted(glob.glob('%s_structures.tar.bz2.*' % self.type)): - fileList.append(int(i[i.rfind('.')+1:])) + for i in sorted(glob.glob("%s_structures.tar.bz2.*" % self.type)): + fileList.append(int(i[i.rfind(".") + 1 :])) - if os.path.isfile('%s_structures.tar.bz2' % self.type): + if os.path.isfile("%s_structures.tar.bz2" % self.type): if fileList == []: self.Logfile.warning( - 'moving existing %s_structures.tar.bz2 to %s_structures.tar.bz2.1' % (self.type, self.type)) + "moving existing %s_structures.tar.bz2 to %s_structures.tar.bz2.1" + % (self.type, self.type) + ) os.system( - '/bin/mv %s_structures.tar.bz2 %s_structures.tar.bz2.1' % (self.type, self.type)) + "/bin/mv %s_structures.tar.bz2 %s_structures.tar.bz2.1" + % (self.type, self.type) + ) else: - self.Logfile.warning('moving existing %s_structures.tar.bz2 %s_structures.tar.bz2.%s' % ( - self.type, self.type, str(max(fileList)+1))) - os.system('/bin/mv %s_structures.tar.bz2 %s_structures.tar.bz2.%s' % - (self.type, self.type, str(max(fileList)+1))) + self.Logfile.warning( + "moving existing %s_structures.tar.bz2 %s_structures.tar.bz2.%s" + % (self.type, self.type, str(max(fileList) + 1)) + ) + os.system( + "/bin/mv %s_structures.tar.bz2 %s_structures.tar.bz2.%s" + % (self.type, self.type, str(max(fileList) + 1)) + ) - self.Logfile.insert('preparing tar archive...') - os.system( - 'tar -cvf {0!s}_structures.tar *mmcif index.txt'.format(self.type)) - self.Logfile.insert('bzipping archive...') - os.system('bzip2 {0!s}_structures.tar'.format(self.type)) + self.Logfile.insert("preparing tar archive...") + os.system("tar -cvf {0!s}_structures.tar *mmcif index.txt".format(self.type)) + self.Logfile.insert("bzipping archive...") + os.system("bzip2 {0!s}_structures.tar".format(self.type)) self.Logfile.insert( - 'removing all bound mmcif files and index.txt file from '+self.depositDir) - os.system('/bin/rm -f *mmcif index.txt') - self.Logfile.insert('done!') + "removing all bound mmcif files and index.txt file from " + self.depositDir + ) + os.system("/bin/rm -f *mmcif index.txt") + self.Logfile.insert("done!") # # apo structures @@ -1716,13 +2163,14 @@ def __init__(self, pdbCodes, database, xce_logfile): def run(self): - for line in self.pdbCodes.split('\n'): - if len(line.split('/')) == 2 and '-ligand_bound' in line: - xtal = line[:line.rfind('-ligand_bound')].replace(' ', '') - pdbID = line.split('/')[1].replace(' ', '') - self.Logfile.insert('setting PDB ID for '+xtal+' to '+pdbID) + for line in self.pdbCodes.split("\n"): + if len(line.split("/")) == 2 and "-ligand_bound" in line: + xtal = line[: line.rfind("-ligand_bound")].replace(" ", "") + pdbID = line.split("/")[1].replace(" ", "") + self.Logfile.insert("setting PDB ID for " + xtal + " to " + pdbID) sqlite = "UPDATE mainTable SET Deposition_PDB_ID='{0!s}',RefinementOutcome='6 - Deposited' where CrystalName is '{1!s}';".format( - pdbID, xtal) + pdbID, xtal + ) self.db.execute_statement(sqlite) @@ -1745,28 +2193,33 @@ def run(self): os.chdir(self.projectDir) progress_step = 1 - if len(glob.glob('*')) != 0: - progress_step = 100/float(len(glob.glob('*'))) + if len(glob.glob("*")) != 0: + progress_step = 100 / float(len(glob.glob("*"))) else: progress_step = 1 progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) - for xtal in sorted(glob.glob('*')): - if os.path.isfile(os.path.join(xtal, 'refine.pdb')): + for xtal in sorted(glob.glob("*")): + if os.path.isfile(os.path.join(xtal, "refine.pdb")): smiles = self.db.execute_statement( - "select CompoundSmiles,CompoundCode from mainTable where CrystalName is '{0!s}'".format(xtal)) + "select CompoundSmiles,CompoundCode from mainTable where CrystalName is '{0!s}'".format( + xtal + ) + ) try: LigandSmiles = str(smiles[0][0]) LigandCode = str(smiles[0][1]) - elementDict_smiles = smilestools( - LigandSmiles).ElementDict() + elementDict_smiles = smilestools(LigandSmiles).ElementDict() except IndexError: self.Logfile.error( - "{0!s}: something is seems to be wrong with the CompoundCode or SMILES string: {1!s}".format(xtal, str(smiles))) + "{0!s}: something is seems to be wrong with the CompoundCode or SMILES string: {1!s}".format( + xtal, str(smiles) + ) + ) continue - pdb = pdbtools(os.path.join(xtal, 'refine.pdb')) + pdb = pdbtools(os.path.join(xtal, "refine.pdb")) ligandList = pdb.ligand_details_as_list() for ligand in ligandList: resname = ligand[0] @@ -1774,16 +2227,30 @@ def run(self): resseq = ligand[2] altLoc = ligand[3] elementDict_ligand = pdb.ElementDict( - resname, chainID, resseq, altLoc) + resname, chainID, resseq, altLoc + ) for element in elementDict_ligand: if elementDict_ligand[element] != elementDict_smiles[element]: - self.Logfile.error('{0!s}: {1!s} {2!s} {3!s} {4!s} contains different number of atoms than smiles in DB: {5!s} -> {6!s}'.format( - xtal, resname, chainID, resseq, altLoc, LigandSmiles, LigandCode)) - self.update_ErrorDict(xtal, '{0!s} {1!s} {2!s} {3!s} contains different number of atoms than smiles in DB'.format( - resname, chainID, resseq, altLoc)) + self.Logfile.error( + "{0!s}: {1!s} {2!s} {3!s} {4!s} contains different number of atoms than smiles in DB: {5!s} -> {6!s}".format( + xtal, + resname, + chainID, + resseq, + altLoc, + LigandSmiles, + LigandCode, + ) + ) + self.update_ErrorDict( + xtal, + "{0!s} {1!s} {2!s} {3!s} contains different number of atoms than smiles in DB".format( + resname, chainID, resseq, altLoc + ), + ) break progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) - self.emit(QtCore.SIGNAL('show_error_dict'), self.ErrorDict) + self.emit(QtCore.SIGNAL("show_error_dict"), self.ErrorDict) diff --git a/lib/XChemDialogs.py b/lib/XChemDialogs.py index 7d333f6e..5986a356 100755 --- a/lib/XChemDialogs.py +++ b/lib/XChemDialogs.py @@ -8,7 +8,8 @@ class select_columns_to_show(QtGui.QDialog): def __init__(self, data_source_file, parent=None): super(select_columns_to_show, self).__init__(parent) self.columns_in_data_source = XChemDB.data_source( - data_source_file).return_column_list() + data_source_file + ).return_column_list() self.column_dict = {} @@ -18,13 +19,14 @@ def __init__(self, data_source_file, parent=None): grid = QtGui.QGridLayout() x = 0 y = 0 - columns_to_ignore = ['Sample ID', 'ID'] + columns_to_ignore = ["Sample ID", "ID"] for entries_added in range(number_of_entries): if not self.columns_in_data_source[entries_added][1] in columns_to_ignore: data_source_column = QtGui.QCheckBox( - self.columns_in_data_source[entries_added][1]) + self.columns_in_data_source[entries_added][1] + ) self.column_dict[entries_added] = data_source_column -# data_source_column.toggle() + # data_source_column.toggle() grid.addWidget(data_source_column, y, x) y += 1 if y == columns_shown_in_dialog_column: @@ -35,13 +37,15 @@ def __init__(self, data_source_file, parent=None): # OK and Cancel buttons buttons = QtGui.QDialogButtonBox( QtGui.QDialogButtonBox.Ok | QtGui.QDialogButtonBox.Cancel, - QtCore.Qt.Horizontal, self) + QtCore.Qt.Horizontal, + self, + ) buttons.accepted.connect(self.accept) buttons.rejected.connect(self.reject) layout.addWidget(buttons) def data_source_column_active(self): - columns_to_show = ['Sample ID'] + columns_to_show = ["Sample ID"] for key in self.column_dict: if self.column_dict[key].isChecked(): columns_to_show.append(self.columns_in_data_source[key][1]) diff --git a/lib/XChemLigand.py b/lib/XChemLigand.py index 857cc0b9..9432f2c8 100755 --- a/lib/XChemLigand.py +++ b/lib/XChemLigand.py @@ -9,5 +9,6 @@ def generate_steroisomers(input_smiles): """ mol = Chem.MolFromSmiles(input_smiles) out_mols = AllChem.EnumerateStereoisomers( - mol, AllChem.StereoEnumerationOptions(onlyUnassigned=False, tryEmbedding=True)) + mol, AllChem.StereoEnumerationOptions(onlyUnassigned=False, tryEmbedding=True) + ) return [Chem.MolToSmiles(x, isomericSmiles=True) for x in out_mols] diff --git a/lib/XChemLog.py b/lib/XChemLog.py index f576ae69..fa370117 100755 --- a/lib/XChemLog.py +++ b/lib/XChemLog.py @@ -6,48 +6,59 @@ import sys from datetime import datetime -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) class startLog: - def __init__(self, logfile): self.logfile = logfile def create_logfile(self, version): pasteVersion = version - for i in range(0, 20-len(version)): - pasteVersion += ' ' + for i in range(0, 20 - len(version)): + pasteVersion += " " message = ( - '\n\n' - ' #######################################################################\n' - ' # #\n' - ' # XCHEMEXPLORER - multi dataset analysis #\n' - ' # #\n' - ' # Version: %s #\n' % pasteVersion + - ' # #\n' - ' # Date: 10/10/2022 #\n' - ' # #\n' - ' # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n' - ' # tobias.krojer@maxiv.lu.se #\n' - ' # #\n' - ' #######################################################################\n' - '\n' + "\n\n" + " #######################################################################\n" + " # #\n" + " # XCHEMEXPLORER - multi dataset analysis #\n" + " # #\n" + " # Version: %s #\n" + % pasteVersion + + " # #\n" + " # Date: 10/10/2022 #\n" + " # #\n" + " # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n" + " # tobias.krojer@maxiv.lu.se #\n" + " # #\n" + " #######################################################################\n" + "\n" ) if not os.path.isfile(self.logfile): - os.system('touch '+self.logfile) - message += 'creating new logfile for the current XChemExplorer (' + \ - version+') session:\n'+self.logfile+'\n' + os.system("touch " + self.logfile) + message += ( + "creating new logfile for the current XChemExplorer (" + + version + + ") session:\n" + + self.logfile + + "\n" + ) else: - message += 'writing into existing logfile for current XChemExplorer (' + \ - version+') session:\n'+self.logfile+'\n' + message += ( + "writing into existing logfile for current XChemExplorer (" + + version + + ") session:\n" + + self.logfile + + "\n" + ) updateLog(self.logfile).insert(message) # print(message) + # class depositLog: # # def __init__(self,logfile): @@ -108,30 +119,25 @@ def create_logfile(self, version): class updateLog: - def __init__(self, logfile): self.logfile = open(logfile, "a") def insert(self, message): - present_time = datetime.strftime( - datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] - print(str(present_time)+' ==> XCE: '+message, file=self.logfile) - print('==> XCE: '+message) + present_time = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S.%f")[:-4] + print(str(present_time) + " ==> XCE: " + message, file=self.logfile) + print("==> XCE: " + message) def warning(self, message): - present_time = datetime.strftime( - datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] - print(str(present_time)+' ==> XCE: WARNING! '+message, file=self.logfile) - print('==> XCE: WARNING! '+message) + present_time = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S.%f")[:-4] + print(str(present_time) + " ==> XCE: WARNING! " + message, file=self.logfile) + print("==> XCE: WARNING! " + message) def error(self, message): - present_time = datetime.strftime( - datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] - print(str(present_time)+' ==> XCE: ERROR!!! '+message, file=self.logfile) - print('==> XCE: ERROR!!! '+message) + present_time = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S.%f")[:-4] + print(str(present_time) + " ==> XCE: ERROR!!! " + message, file=self.logfile) + print("==> XCE: ERROR!!! " + message) def hint(self, message): - present_time = datetime.strftime( - datetime.now(), '%Y-%m-%d %H:%M:%S.%f')[:-4] - print(str(present_time)+' ==> XCE: HINT -> '+message, file=self.logfile) - print('==> XCE: HINT -> '+message) + present_time = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S.%f")[:-4] + print(str(present_time) + " ==> XCE: HINT -> " + message, file=self.logfile) + print("==> XCE: HINT -> " + message) diff --git a/lib/XChemMain.py b/lib/XChemMain.py index dfd6ca55..2e6c9d28 100755 --- a/lib/XChemMain.py +++ b/lib/XChemMain.py @@ -11,70 +11,142 @@ from datetime import datetime from PyQt4 import QtGui, QtCore -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) def space_group_list(): - space_group_list = ['P1', - 'P2', 'P21', 'C121', 'P1211', 'P121', 'I2', 'I121', - 'P222', 'P2122', 'P2212', 'P2221', - 'P21212', 'P21221', 'P22121', 'P212121', - 'C222', 'C2221', 'F222', 'I222', 'I212121', - 'P4', 'P41', 'P42', 'P43', 'I4', 'I41', - 'P422', 'P4212', 'P4122', 'P41212', 'P4222', - 'P42212', 'P4322', 'P43212', 'I422', 'I4122', - 'P3', 'P31', 'P32', - 'P312', 'P321', 'P3112', 'P3121', 'P3212', 'P3221', - 'P6', 'P61', 'P65', 'P62', 'P64', 'P63', - 'P622', 'P6122', 'P6522', 'P6222', 'P6422', 'P6322', - 'H3', 'H32', - 'P23', 'F23', 'I23', 'P213', 'I213', - 'P432', 'P4232', 'F432', 'F4132', 'I432', 'P4332', 'P4132', 'I4132'] + space_group_list = [ + "P1", + "P2", + "P21", + "C121", + "P1211", + "P121", + "I2", + "I121", + "P222", + "P2122", + "P2212", + "P2221", + "P21212", + "P21221", + "P22121", + "P212121", + "C222", + "C2221", + "F222", + "I222", + "I212121", + "P4", + "P41", + "P42", + "P43", + "I4", + "I41", + "P422", + "P4212", + "P4122", + "P41212", + "P4222", + "P42212", + "P4322", + "P43212", + "I422", + "I4122", + "P3", + "P31", + "P32", + "P312", + "P321", + "P3112", + "P3121", + "P3212", + "P3221", + "P6", + "P61", + "P65", + "P62", + "P64", + "P63", + "P622", + "P6122", + "P6522", + "P6222", + "P6422", + "P6322", + "H3", + "H32", + "P23", + "F23", + "I23", + "P213", + "I213", + "P432", + "P4232", + "F432", + "F4132", + "I432", + "P4332", + "P4132", + "I4132", + ] return space_group_list def get_target_and_visit_list(beamline_directory, agamemnon): # target_list=['*'] # always give the option to read in all targets - target_list = ['=== SELECT TARGET ===', '=== project directory ==='] + target_list = ["=== SELECT TARGET ===", "=== project directory ==="] visit_list = [] # the beamline directory could be a the real directory or # a directory where the visits are linked into -# if agamemnon: -# # /dls/i03/data/2019/lb18145-136 -# for target in glob.glob(beamline_directory[:beamline_directory.rfind('-') + 1] + '*/agamemnon/*'): -# visit_list.append(beamline_directory[:beamline_directory.rfind('/')].replace('/agamemnon','')) -# if target[target.rfind('/') + 1:] not in ['results', 'README-log', 'edna-latest.html']: -# if target[target.rfind('/') + 1:] not in target_list: -# target_list.append(target[target.rfind('/') + 1:]) -# for target in glob.glob(beamline_directory[:beamline_directory.rfind('-') + 1] + '*/auto/*'): -# visit_list.append(beamline_directory[:beamline_directory.rfind('/')].replace('/auto', '')) -# if target[target.rfind('/') + 1:] not in ['results', 'README-log', 'edna-latest.html']: -# if target[target.rfind('/') + 1:] not in target_list: -# target_list.append(target[target.rfind('/') + 1:]) -# else: - if len(beamline_directory.split('/')) and \ - beamline_directory.split('/')[1] == 'dls' and beamline_directory.split('/')[3] == 'data' \ - and not 'labxchem' in beamline_directory: + # if agamemnon: + # # /dls/i03/data/2019/lb18145-136 + # for target in glob.glob(beamline_directory[:beamline_directory.rfind('-') + 1] + '*/agamemnon/*'): + # visit_list.append(beamline_directory[:beamline_directory.rfind('/')].replace('/agamemnon','')) + # if target[target.rfind('/') + 1:] not in ['results', 'README-log', 'edna-latest.html']: + # if target[target.rfind('/') + 1:] not in target_list: + # target_list.append(target[target.rfind('/') + 1:]) + # for target in glob.glob(beamline_directory[:beamline_directory.rfind('-') + 1] + '*/auto/*'): + # visit_list.append(beamline_directory[:beamline_directory.rfind('/')].replace('/auto', '')) + # if target[target.rfind('/') + 1:] not in ['results', 'README-log', 'edna-latest.html']: + # if target[target.rfind('/') + 1:] not in target_list: + # target_list.append(target[target.rfind('/') + 1:]) + # else: + if ( + len(beamline_directory.split("/")) + and beamline_directory.split("/")[1] == "dls" + and beamline_directory.split("/")[3] == "data" + and not "labxchem" in beamline_directory + ): visit_list.append(beamline_directory) else: visit_list.append(os.path.realpath(beamline_directory)) for visit in visit_list: - print('-->', os.path.join(visit, 'processed', '*')) + print("-->", os.path.join(visit, "processed", "*")) if agamemnon: - for target in glob.glob(os.path.join(visit, 'processed', 'auto', '*')): + for target in glob.glob(os.path.join(visit, "processed", "auto", "*")): print(target) - if target[target.rfind('/')+1:] not in ['results', 'README-log', 'edna-latest.html']: - if target[target.rfind('/')+1:] not in target_list: - target_list.append(target[target.rfind('/')+1:]) + if target[target.rfind("/") + 1 :] not in [ + "results", + "README-log", + "edna-latest.html", + ]: + if target[target.rfind("/") + 1 :] not in target_list: + target_list.append(target[target.rfind("/") + 1 :]) else: - for target in glob.glob(os.path.join(visit, 'processed', '*')): + for target in glob.glob(os.path.join(visit, "processed", "*")): print(target) - if target[target.rfind('/')+1:] not in ['results', 'README-log', 'edna-latest.html']: - if target[target.rfind('/')+1:] not in target_list: - target_list.append(target[target.rfind('/')+1:]) + if target[target.rfind("/") + 1 :] not in [ + "results", + "README-log", + "edna-latest.html", + ]: + if target[target.rfind("/") + 1 :] not in target_list: + target_list.append(target[target.rfind("/") + 1 :]) return target_list, visit_list + # def get_target_and_visit_list_for_Pietro(beamline_directory): # target_list=['*'] # always give the option to read in all targets # target_list=['=== SELECT TARGET ==='] # always give the option to read in all targets @@ -95,19 +167,22 @@ def get_target_and_visit_list(beamline_directory, agamemnon): def get_dewar_configuration(beamline_directory): dewar_sample_configuration_dict = {} # need to do it like this for now until we got a way to query ispyb - for xml in glob.glob(os.path.join(beamline_directory, 'xml', 'exptTableParams-*.xml')): - prefix = '' - container_reference = '' - sample_location = '' + for xml in glob.glob( + os.path.join(beamline_directory, "xml", "exptTableParams-*.xml") + ): + prefix = "" + container_reference = "" + sample_location = "" for line in open(xml): - if 'prefix' in line: - prefix = line[line.find('>')+1:line.rfind('<')] - if 'container_reference' in line: - container_reference = line[line.find('>')+1:line.rfind('<')] - if 'sample_location' in line: - sample_location = line[line.find('>')+1:line.rfind('<')] - dewar_sample_configuration_dict[str( - container_reference)+'-'+str(sample_location)] = prefix + if "prefix" in line: + prefix = line[line.find(">") + 1 : line.rfind("<")] + if "container_reference" in line: + container_reference = line[line.find(">") + 1 : line.rfind("<")] + if "sample_location" in line: + sample_location = line[line.find(">") + 1 : line.rfind("<")] + dewar_sample_configuration_dict[ + str(container_reference) + "-" + str(sample_location) + ] = prefix return dewar_sample_configuration_dict @@ -123,8 +198,8 @@ def get_jobs_running_on_cluster(): # note: each job_details list contains a list with # [job_ID, status, run_time] - out = subprocess.Popen(['qstat'], stdout=subprocess.PIPE) - for n, line in enumerate(iter(out.stdout.readline, '')): + out = subprocess.Popen(["qstat"], stdout=subprocess.PIPE) + for n, line in enumerate(iter(out.stdout.readline, "")): if len(line.split()) >= 7: if line.split()[3] == getpass.getuser(): @@ -134,57 +209,65 @@ def get_jobs_running_on_cluster(): ########################################################## # determine run time of each job in minutes - start_date = '' - start_time = '' - run_time_minutes = '' + start_date = "" + start_time = "" + run_time_minutes = "" start_date = line.split()[5] - if len(start_date.split('/')) == 3: - month_start = start_date.split('/')[0] - day_start = start_date.split('/')[1] - year_start = start_date.split('/')[2] + if len(start_date.split("/")) == 3: + month_start = start_date.split("/")[0] + day_start = start_date.split("/")[1] + year_start = start_date.split("/")[2] start_time = line.split()[6] - if len(start_time.split(':')) == 3: - hour_start = start_time.split(':')[0] - minute_start = start_time.split(':')[1] - second_start = start_time.split(':')[2] - - if start_time != '' and start_date != '': - start = '{0!s}-{1!s}-{2!s} {3!s}:{4!s}:{5!s}'.format( - year_start, month_start, day_start, hour_start, minute_start, second_start) - run_time = datetime.now()-datetime.strptime(start, "%Y-%m-%d %H:%M:%S") + if len(start_time.split(":")) == 3: + hour_start = start_time.split(":")[0] + minute_start = start_time.split(":")[1] + second_start = start_time.split(":")[2] + + if start_time != "" and start_date != "": + start = "{0!s}-{1!s}-{2!s} {3!s}:{4!s}:{5!s}".format( + year_start, + month_start, + day_start, + hour_start, + minute_start, + second_start, + ) + run_time = datetime.now() - datetime.strptime( + start, "%Y-%m-%d %H:%M:%S" + ) run_time_seconds = int(run_time.total_seconds()) run_time_minutes = int(run_time.total_seconds() / 60) run_time_hours = int(run_time.total_seconds() / 3600) ########################################################## # determine run time of each job in minutes - if 'dimple' in job_name: + if "dimple" in job_name: dimple_jobs.append([job_id, job_status, run_time_minutes]) - elif 'acedrg' in job_name: + elif "acedrg" in job_name: acedrg_jobs.append([job_id, job_status, run_time_minutes]) - elif 'pandda' in job_name: + elif "pandda" in job_name: pandda_jobs.append([job_id, job_status, run_time_minutes]) - elif 'refmac' in job_name: + elif "refmac" in job_name: refmac_jobs.append([job_id, job_status, run_time_minutes]) - elif 'xia2' in job_name: + elif "xia2" in job_name: xia2_jobs.append([job_id, job_status, run_time_minutes]) else: others_jobs.append([job_id, job_status, run_time_minutes]) - out_dict['dimple'] = dimple_jobs - out_dict['acedrg'] = acedrg_jobs - out_dict['pandda'] = pandda_jobs - out_dict['refmac'] = refmac_jobs - out_dict['xia2'] = xia2_jobs - out_dict['others'] = others_jobs + out_dict["dimple"] = dimple_jobs + out_dict["acedrg"] = acedrg_jobs + out_dict["pandda"] = pandda_jobs + out_dict["refmac"] = refmac_jobs + out_dict["xia2"] = xia2_jobs + out_dict["others"] = others_jobs return out_dict def print_acedrg_status(xce_logfile, xtal_db_dict): Logfile = XChemLog.updateLog(xce_logfile) - Logfile.insert('compound restraints summary:') + Logfile.insert("compound restraints summary:") pending = 0 started = 0 running = 0 @@ -194,42 +277,40 @@ def print_acedrg_status(xce_logfile, xtal_db_dict): unknown = 0 for xtal in xtal_db_dict: db_dict = xtal_db_dict[xtal] - status = db_dict['RefinementCIFStatus'] - if 'pending' in status: + status = db_dict["RefinementCIFStatus"] + if "pending" in status: pending += 1 - elif 'started' in status: + elif "started" in status: started += 1 - elif 'running' in status: + elif "running" in status: running += 1 - elif 'missing' in status: + elif "missing" in status: missing_smiles += 1 - elif 'failed' in status: + elif "failed" in status: failed += 1 - elif 'generated' in status: + elif "generated" in status: success += 1 else: unknown += 1 + Logfile.insert("restraint generation pending: ...... {0!s}".format(str(pending))) + Logfile.insert("restraint generation started: ...... {0!s}".format(str(started))) + Logfile.insert("restraint generation running: ...... {0!s}".format(str(running))) Logfile.insert( - 'restraint generation pending: ...... {0!s}'.format(str(pending))) - Logfile.insert( - 'restraint generation started: ...... {0!s}'.format(str(started))) - Logfile.insert( - 'restraint generation running: ...... {0!s}'.format(str(running))) - Logfile.insert( - 'missing smiles string: ............. {0!s}'.format(str(missing_smiles))) - Logfile.insert( - 'restraint generation failed: ....... {0!s}'.format(str(failed))) - Logfile.insert( - 'restraints successfully created: ... {0!s}'.format(str(success))) - Logfile.insert( - 'unknown status: .................... {0!s}'.format(str(unknown))) + "missing smiles string: ............. {0!s}".format(str(missing_smiles)) + ) + Logfile.insert("restraint generation failed: ....... {0!s}".format(str(failed))) + Logfile.insert("restraints successfully created: ... {0!s}".format(str(success))) + Logfile.insert("unknown status: .................... {0!s}".format(str(unknown))) def print_cluster_status_message(program, cluster_dict, xce_logfile): Logfile = XChemLog.updateLog(xce_logfile) - Logfile.insert('cluster status summary:') - Logfile.insert('{0!s} {1!s} jobs are running on the cluster'.format( - len(cluster_dict[program]), program)) + Logfile.insert("cluster status summary:") + Logfile.insert( + "{0!s} {1!s} jobs are running on the cluster".format( + len(cluster_dict[program]), program + ) + ) if len(cluster_dict[program]) > 0: cumulative_runtime = 0 job_ids = [] @@ -237,26 +318,41 @@ def print_cluster_status_message(program, cluster_dict, xce_logfile): cumulative_runtime += item[2] if not item[0] in job_ids: job_ids.append(item[0]) - average_runtime = round(float(cumulative_runtime)/float(n+1), 0) - Logfile.insert('average run time '+str(average_runtime)+' minutes') + average_runtime = round(float(cumulative_runtime) / float(n + 1), 0) + Logfile.insert("average run time " + str(average_runtime) + " minutes") if job_ids: Logfile.insert( - 'you can kill them by pasting the following line into a new terminal window:') - out = 'qdel ' + "you can kill them by pasting the following line into a new terminal window:" + ) + out = "qdel " for job in job_ids: - out += str(job)+' ' + out += str(job) + " " Logfile.insert(out) def display_queue_status_in_terminal(in_dict): # latest_run=max(tmp,key=lambda x: x[1])[0] - max_dimple_runtime = max(in_dict['dimple'], key=lambda x: x[2])[2] - print('----------------------------------------------------------------------------') - print('| Task | Nr. Jobs | Max. Runtime (minutes) |') - print('----------------------------------------------------------------------------') - print('{0:24} {1:24} {2:24} {3:1}'.format('| DIMPLE', '| {0!s}'.format( - len(in_dict['dimple'])), '| %s' & max_dimple_runtime, '|')) - print('----------------------------------------------------------------------------') + max_dimple_runtime = max(in_dict["dimple"], key=lambda x: x[2])[2] + print( + "----------------------------------------------------------------------------" + ) + print( + "| Task | Nr. Jobs | Max. Runtime (minutes) |" + ) + print( + "----------------------------------------------------------------------------" + ) + print( + "{0:24} {1:24} {2:24} {3:1}".format( + "| DIMPLE", + "| {0!s}".format(len(in_dict["dimple"])), + "| %s" & max_dimple_runtime, + "|", + ) + ) + print( + "----------------------------------------------------------------------------" + ) def get_datasource_summary(db_file): @@ -264,158 +360,275 @@ def get_datasource_summary(db_file): out_dict = {} - out_dict['nr_samples'] = len(db.execute_statement( - "select CrystalName from mainTable where CrystalName is not NULL;")) - out_dict['nr_samples_failed_to_mount'] = len(db.execute_statement( - "select HarvestStatus from mainTable where HarvestStatus is 'fail';")) - - out_dict['nr_smiles_for_samples'] = len(db.execute_statement( - "select compoundSMILES from mainTable where compoundSMILES is not (NULL or '')")) - - out_dict['nr_data_collection_success'] = len(db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'success';")) - out_dict['nr_data_collection_centring_fail'] = len(db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - centring failed';")) - out_dict['nr_data_collection_no-diffraction'] = len(db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - no diffraction';")) - out_dict['nr_data_collection_processing_fail'] = len(db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - processing';")) - out_dict['nr_data_collection_loop-empty'] = len(db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - loop empty';")) - out_dict['nr_data_collection_loop-broken'] = len(db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - loop broken';")) - out_dict['nr_data_collection_low-resolution'] = len(db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - low resolution';")) - out_dict['nr_data_collection_no-X-rays'] = len(db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - no X-rays';")) - out_dict['nr_data_collection_unknown'] = len(db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - unknown';")) - - out_dict['nr_data_collection_failed'] = out_dict['nr_data_collection_centring_fail'] + \ - out_dict['nr_data_collection_no-diffraction'] + \ - out_dict['nr_data_collection_processing_fail'] + \ - out_dict['nr_data_collection_loop-empty'] + \ - out_dict['nr_data_collection_loop-broken'] + \ - out_dict['nr_data_collection_low-resolution'] + \ - out_dict['nr_data_collection_no-X-rays'] + \ - out_dict['nr_data_collection_unknown'] - - out_dict['nr_data_collection_pending'] = out_dict['nr_samples'] - out_dict['nr_data_collection_success'] - \ - out_dict['nr_data_collection_centring_fail'] - \ - out_dict['nr_data_collection_no-diffraction'] - \ - out_dict['nr_data_collection_processing_fail'] - \ - out_dict['nr_data_collection_loop-empty'] - \ - out_dict['nr_data_collection_loop-broken'] - \ - out_dict['nr_data_collection_low-resolution'] - \ - out_dict['nr_data_collection_no-X-rays'] - \ - out_dict['nr_data_collection_unknown'] - - out_dict['nr_initial_maps_available'] = len(db.execute_statement( - "select DimplePathToMTZ from mainTable where DimplePathToMTZ is not '';")) - out_dict['nr_initial_maps_fail'] = len(db.execute_statement( - "select DataProcessingDimpleSuccessful from mainTable where DataProcessingDimpleSuccessful = 'False';")) - out_dict['nr_initial_maps_pending'] = out_dict['nr_data_collection_success'] - \ - out_dict['nr_initial_maps_available']-out_dict['nr_initial_maps_fail'] - - out_dict['nr_pandda_hits'] = len(db.execute_statement( - "select DimplePANDDAhit from mainTable where DimplePANDDAhit = 'True';")) - out_dict['nr_pandda_reject'] = len(db.execute_statement( - "select DimplePANDDAreject from mainTable where DimplePANDDAreject = 'True';")) - out_dict['nr_pandda_processed'] = len(db.execute_statement( - "select DimplePANDDAwasRun from mainTable where DimplePANDDAwasRun = 'True';"))-out_dict['nr_pandda_hits']-out_dict['nr_pandda_reject'] - out_dict['nr_pandda_pending'] = out_dict['nr_initial_maps_available'] - \ - out_dict['nr_pandda_hits']-out_dict['nr_pandda_reject'] - \ - out_dict['nr_pandda_processed'] - - out_dict['nr_cif_files'] = len(db.execute_statement( - "select RefinementCIF from mainTable where RefinementCIF is not (Null or '');")) - - out_dict['nr_analysis-pending'] = len(db.execute_statement( - "select RefinementOutcome from mainTable where RefinementOutcome is '1 - Analysis Pending';")) - out_dict['nr_pandda-models'] = len(db.execute_statement( - "select RefinementOutcome from mainTable where RefinementOutcome is '2 - PANDDA model';")) - out_dict['nr_in-refinement'] = len(db.execute_statement( - "select RefinementOutcome from mainTable where RefinementOutcome is '3 - In Refinement';")) - out_dict['nr_comp-chem-ready'] = len(db.execute_statement( - "select RefinementOutcome from mainTable where RefinementOutcome is '4 - ComChem ready';")) - out_dict['nr_deposition-ready'] = len(db.execute_statement( - "select RefinementOutcome from mainTable where RefinementOutcome is '5 - Deposition ready';")) + out_dict["nr_samples"] = len( + db.execute_statement( + "select CrystalName from mainTable where CrystalName is not NULL;" + ) + ) + out_dict["nr_samples_failed_to_mount"] = len( + db.execute_statement( + "select HarvestStatus from mainTable where HarvestStatus is 'fail';" + ) + ) - return out_dict + out_dict["nr_smiles_for_samples"] = len( + db.execute_statement( + "select compoundSMILES from mainTable where compoundSMILES is not (NULL or '')" + ) + ) + + out_dict["nr_data_collection_success"] = len( + db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'success';" + ) + ) + out_dict["nr_data_collection_centring_fail"] = len( + db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - centring failed';" + ) + ) + out_dict["nr_data_collection_no-diffraction"] = len( + db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - no diffraction';" + ) + ) + out_dict["nr_data_collection_processing_fail"] = len( + db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - processing';" + ) + ) + out_dict["nr_data_collection_loop-empty"] = len( + db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - loop empty';" + ) + ) + out_dict["nr_data_collection_loop-broken"] = len( + db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - loop broken';" + ) + ) + out_dict["nr_data_collection_low-resolution"] = len( + db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - low resolution';" + ) + ) + out_dict["nr_data_collection_no-X-rays"] = len( + db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - no X-rays';" + ) + ) + out_dict["nr_data_collection_unknown"] = len( + db.execute_statement( + "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - unknown';" + ) + ) + out_dict["nr_data_collection_failed"] = ( + out_dict["nr_data_collection_centring_fail"] + + out_dict["nr_data_collection_no-diffraction"] + + out_dict["nr_data_collection_processing_fail"] + + out_dict["nr_data_collection_loop-empty"] + + out_dict["nr_data_collection_loop-broken"] + + out_dict["nr_data_collection_low-resolution"] + + out_dict["nr_data_collection_no-X-rays"] + + out_dict["nr_data_collection_unknown"] + ) -def remove_all_refmac_jobs_from_cluster_and_reinstate_last_stable_state(): - print('hallo') + out_dict["nr_data_collection_pending"] = ( + out_dict["nr_samples"] + - out_dict["nr_data_collection_success"] + - out_dict["nr_data_collection_centring_fail"] + - out_dict["nr_data_collection_no-diffraction"] + - out_dict["nr_data_collection_processing_fail"] + - out_dict["nr_data_collection_loop-empty"] + - out_dict["nr_data_collection_loop-broken"] + - out_dict["nr_data_collection_low-resolution"] + - out_dict["nr_data_collection_no-X-rays"] + - out_dict["nr_data_collection_unknown"] + ) + + out_dict["nr_initial_maps_available"] = len( + db.execute_statement( + "select DimplePathToMTZ from mainTable where DimplePathToMTZ is not '';" + ) + ) + out_dict["nr_initial_maps_fail"] = len( + db.execute_statement( + "select DataProcessingDimpleSuccessful from mainTable where DataProcessingDimpleSuccessful = 'False';" + ) + ) + out_dict["nr_initial_maps_pending"] = ( + out_dict["nr_data_collection_success"] + - out_dict["nr_initial_maps_available"] + - out_dict["nr_initial_maps_fail"] + ) + out_dict["nr_pandda_hits"] = len( + db.execute_statement( + "select DimplePANDDAhit from mainTable where DimplePANDDAhit = 'True';" + ) + ) + out_dict["nr_pandda_reject"] = len( + db.execute_statement( + "select DimplePANDDAreject from mainTable where DimplePANDDAreject = 'True';" + ) + ) + out_dict["nr_pandda_processed"] = ( + len( + db.execute_statement( + "select DimplePANDDAwasRun from mainTable where DimplePANDDAwasRun = 'True';" + ) + ) + - out_dict["nr_pandda_hits"] + - out_dict["nr_pandda_reject"] + ) + out_dict["nr_pandda_pending"] = ( + out_dict["nr_initial_maps_available"] + - out_dict["nr_pandda_hits"] + - out_dict["nr_pandda_reject"] + - out_dict["nr_pandda_processed"] + ) -def change_links_to_selected_data_collection_outcome(sample, data_collection_dict, data_collection_column_three_dict, dataset_outcome_dict, initial_model_directory, data_source_file, xce_logfile): + out_dict["nr_cif_files"] = len( + db.execute_statement( + "select RefinementCIF from mainTable where RefinementCIF is not (Null or '');" + ) + ) + + out_dict["nr_analysis-pending"] = len( + db.execute_statement( + "select RefinementOutcome from mainTable where RefinementOutcome is '1 - Analysis Pending';" + ) + ) + out_dict["nr_pandda-models"] = len( + db.execute_statement( + "select RefinementOutcome from mainTable where RefinementOutcome is '2 - PANDDA model';" + ) + ) + out_dict["nr_in-refinement"] = len( + db.execute_statement( + "select RefinementOutcome from mainTable where RefinementOutcome is '3 - In Refinement';" + ) + ) + out_dict["nr_comp-chem-ready"] = len( + db.execute_statement( + "select RefinementOutcome from mainTable where RefinementOutcome is '4 - ComChem ready';" + ) + ) + out_dict["nr_deposition-ready"] = len( + db.execute_statement( + "select RefinementOutcome from mainTable where RefinementOutcome is '5 - Deposition ready';" + ) + ) + + return out_dict + + +def remove_all_refmac_jobs_from_cluster_and_reinstate_last_stable_state(): + print("hallo") + + +def change_links_to_selected_data_collection_outcome( + sample, + data_collection_dict, + data_collection_column_three_dict, + dataset_outcome_dict, + initial_model_directory, + data_source_file, + xce_logfile, +): Logfile = XChemLog.updateLog(xce_logfile) # find out which row was selected in respective data collection table - selected_processing_result = 'n/a' - indexes = data_collection_column_three_dict[sample][0].selectionModel( - ).selectedRows() - if indexes: # i.e. logfile exists + selected_processing_result = "n/a" + indexes = ( + data_collection_column_three_dict[sample][0].selectionModel().selectedRows() + ) + if indexes: # i.e. logfile exists for index in sorted(indexes): selected_processing_result = index.row() for n, entry in enumerate(data_collection_dict[sample]): - if entry[0] == 'logfile': + if entry[0] == "logfile": if entry[7] == selected_processing_result: visit = entry[1] run = entry[2] autoproc = entry[4] db_dict = entry[6] outcome = dataset_outcome_dict[sample] - path_to_logfile = db_dict['DataProcessingPathToLogfile'] - path_to_mtzfile = db_dict['DataProcessingPathToMTZfile'] - mtz_filename = db_dict['DataProcessingMTZfileName'] - log_filename = db_dict['DataProcessingLOGfileName'] -# relative_path_to_mtzfile='./'+path_to_mtzfile.replace(initial_model_directory,'') - relative_path_to_mtzfile = './' + \ - path_to_mtzfile.replace(os.path.join( - initial_model_directory, sample), '') - if relative_path_to_mtzfile.startswith('.//'): + path_to_logfile = db_dict["DataProcessingPathToLogfile"] + path_to_mtzfile = db_dict["DataProcessingPathToMTZfile"] + mtz_filename = db_dict["DataProcessingMTZfileName"] + log_filename = db_dict["DataProcessingLOGfileName"] + # relative_path_to_mtzfile='./'+path_to_mtzfile.replace(initial_model_directory,'') + relative_path_to_mtzfile = "./" + path_to_mtzfile.replace( + os.path.join(initial_model_directory, sample), "" + ) + if relative_path_to_mtzfile.startswith(".//"): relative_path_to_mtzfile = relative_path_to_mtzfile.replace( - './/', './') - relative_path_to_logfile = './' + \ - path_to_logfile.replace(os.path.join( - initial_model_directory, sample), '') - if relative_path_to_logfile.startswith('.//'): + ".//", "./" + ) + relative_path_to_logfile = "./" + path_to_logfile.replace( + os.path.join(initial_model_directory, sample), "" + ) + if relative_path_to_logfile.startswith(".//"): relative_path_to_logfile = relative_path_to_logfile.replace( - './/', './') + ".//", "./" + ) # first check if folders and files exist # since user might do this before data are actually copied over - if os.path.isdir(os.path.join(initial_model_directory, sample, 'autoprocessing', visit+'-'+run+autoproc)): - db_dict['DataProcessingAutoAssigned'] = 'False' - Logfile.insert('changing directory to: ' + - os.path.join(initial_model_directory, sample)) + if os.path.isdir( + os.path.join( + initial_model_directory, + sample, + "autoprocessing", + visit + "-" + run + autoproc, + ) + ): + db_dict["DataProcessingAutoAssigned"] = "False" + Logfile.insert( + "changing directory to: " + + os.path.join(initial_model_directory, sample) + ) os.chdir(os.path.join(initial_model_directory, sample)) # first remove old links - os.system('/bin/rm '+sample+'.mtz 2> /dev/null') - os.system('/bin/rm '+sample+'.log 2> /dev/null') + os.system("/bin/rm " + sample + ".mtz 2> /dev/null") + os.system("/bin/rm " + sample + ".log 2> /dev/null") # make new links -# Logfile.insert('setting symlink: '+os.path.join(path_to_logfile,log_filename)+' -> '+sample+'.log') -# os.symlink(os.path.join(path_to_logfile,log_filename),sample+'.log') -# Logfile.insert('setting symlink: '+os.path.join(path_to_mtzfile,mtz_filename)+' -> '+sample+'.mtz') -# os.symlink(os.path.join(path_to_mtzfile,mtz_filename),sample+'.mtz') - Logfile.insert('setting relative symlink: '+os.path.join( - relative_path_to_logfile, log_filename)+' -> '+sample+'.log') - os.symlink(os.path.join(relative_path_to_logfile, - log_filename), sample+'.log') - Logfile.insert('setting relative symlink: '+os.path.join( - relative_path_to_mtzfile, mtz_filename)+' -> '+sample+'.mtz') - os.symlink(os.path.join(relative_path_to_mtzfile, - mtz_filename), sample+'.mtz') + # Logfile.insert('setting symlink: '+os.path.join(path_to_logfile,log_filename)+' -> '+sample+'.log') + # os.symlink(os.path.join(path_to_logfile,log_filename),sample+'.log') + # Logfile.insert('setting symlink: '+os.path.join(path_to_mtzfile,mtz_filename)+' -> '+sample+'.mtz') + # os.symlink(os.path.join(path_to_mtzfile,mtz_filename),sample+'.mtz') + Logfile.insert( + "setting relative symlink: " + + os.path.join(relative_path_to_logfile, log_filename) + + " -> " + + sample + + ".log" + ) + os.symlink( + os.path.join(relative_path_to_logfile, log_filename), + sample + ".log", + ) + Logfile.insert( + "setting relative symlink: " + + os.path.join(relative_path_to_mtzfile, mtz_filename) + + " -> " + + sample + + ".mtz" + ) + os.symlink( + os.path.join(relative_path_to_mtzfile, mtz_filename), + sample + ".mtz", + ) # update data source data_source = XChemDB.data_source(data_source_file) data_source.update_insert_data_source(sample, db_dict) else: - Logfile.insert( - 'please copy data to PROJECT DIRECTORY first!') + Logfile.insert("please copy data to PROJECT DIRECTORY first!") # def find_diffraction_image_directory(diffraction_data_directory): @@ -436,39 +649,40 @@ def change_links_to_selected_data_collection_outcome(sample, data_collection_dic # del data_dict[xtal] # return data_dict + def get_nr_files_from_gda_log_folder(beamline): - n = len(glob.glob(os.path.join('/dls_sw', beamline, 'logs', 'gda_server*'))) + n = len(glob.glob(os.path.join("/dls_sw", beamline, "logs", "gda_server*"))) return n def get_dict_of_gda_barcodes(beamline): out_dict = {} - for files in glob.glob(os.path.join('/dls_sw', beamline, 'logs', '*')): + for files in glob.glob(os.path.join("/dls_sw", beamline, "logs", "*")): found_barcode_entry = False - gda_log = files[files.rfind('/')+1:] - if gda_log.startswith('gda_server.') and gda_log.endswith('.gz'): - with gzip.open(files, 'r') as f: - print('parsing', files) -# for line in fin: + gda_log = files[files.rfind("/") + 1 :] + if gda_log.startswith("gda_server.") and gda_log.endswith(".gz"): + with gzip.open(files, "r") as f: + print("parsing", files) + # for line in fin: for line in f: - if 'BART SampleChanger - getBarcode() returning' in line: - barcode = line.split()[len(line.split())-1] + if "BART SampleChanger - getBarcode() returning" in line: + barcode = line.split()[len(line.split()) - 1] found_barcode_entry = True if found_barcode_entry: - if 'Snapshots will be saved' in line: - sampleID = line.split()[len( - line.split())-1].split('/')[-1] + if "Snapshots will be saved" in line: + sampleID = line.split()[len(line.split()) - 1].split("/")[ + -1 + ] out_dict[sampleID] = barcode found_barcode_entry = False - elif gda_log.startswith('gda_server.') and gda_log.endswith('.log'): + elif gda_log.startswith("gda_server.") and gda_log.endswith(".log"): for line in files: - if 'BART SampleChanger - getBarcode() returning' in line: - barcode = line.split()[len(line.split())-1] + if "BART SampleChanger - getBarcode() returning" in line: + barcode = line.split()[len(line.split()) - 1] found_barcode_entry = True if found_barcode_entry: - if 'Snapshots will be saved' in line: - sampleID = line.split()[len( - line.split())-1].split('/')[-1] + if "Snapshots will be saved" in line: + sampleID = line.split()[len(line.split()) - 1].split("/")[-1] out_dict[sampleID] = barcode found_barcode_entry = False @@ -480,87 +694,118 @@ def append_dict_of_gda_barcodes(out_dict, files, xce_logfile): # for files in glob.glob(os.path.join('/dls_sw',beamline,'logs','*')): Logfile = XChemLog.updateLog(xce_logfile) found_barcode_entry = False - gda_log = files[files.rfind('/')+1:] - if gda_log.startswith('gda_server.') or gda_log.startswith('gda-server.') and gda_log.endswith('.gz'): - with gzip.open(files, 'r') as f: + gda_log = files[files.rfind("/") + 1 :] + if ( + gda_log.startswith("gda_server.") + or gda_log.startswith("gda-server.") + and gda_log.endswith(".gz") + ): + with gzip.open(files, "r") as f: for line in f: - if 'BART SampleChanger - getBarcode() returning' in line: - barcode = line.split()[len(line.split())-1] + if "BART SampleChanger - getBarcode() returning" in line: + barcode = line.split()[len(line.split()) - 1] found_barcode_entry = True if found_barcode_entry: - if 'Snapshots will be saved' in line: - sampleID = line.split()[len( - line.split())-1].split('/')[-1] + if "Snapshots will be saved" in line: + sampleID = line.split()[len(line.split()) - 1].split("/")[-1] out_dict[sampleID] = barcode - Logfile.insert('found: sample={0!s}, barcode={1!s}, file={2!s}'.format( - sampleID, barcode, files)) + Logfile.insert( + "found: sample={0!s}, barcode={1!s}, file={2!s}".format( + sampleID, barcode, files + ) + ) found_barcode_entry = False - elif gda_log.startswith('gda_server') or gda_log.startswith('gda-server') and gda_log.endswith('txt'): + elif ( + gda_log.startswith("gda_server") + or gda_log.startswith("gda-server") + and gda_log.endswith("txt") + ): for line in open(files): - if 'BART SampleChanger - getBarcode() returning' in line: - barcode = line.split()[len(line.split())-1] + if "BART SampleChanger - getBarcode() returning" in line: + barcode = line.split()[len(line.split()) - 1] found_barcode_entry = True if found_barcode_entry: - if 'Snapshots will be saved' in line: - sampleID = line.split()[len(line.split())-1].split('/')[-1] + if "Snapshots will be saved" in line: + sampleID = line.split()[len(line.split()) - 1].split("/")[-1] out_dict[sampleID] = barcode - Logfile.insert('found: sample={0!s}, barcode={1!s}, file={2!s}'.format( - sampleID, barcode, files)) + Logfile.insert( + "found: sample={0!s}, barcode={1!s}, file={2!s}".format( + sampleID, barcode, files + ) + ) found_barcode_entry = False return out_dict -def get_gda_barcodes(sampleList, gzipped_logs_parsed, gda_log_start_line, beamline, xce_logfile): +def get_gda_barcodes( + sampleList, gzipped_logs_parsed, gda_log_start_line, beamline, xce_logfile +): Logfile = XChemLog.updateLog(xce_logfile) - Logfile.insert('checking GDA logfile in {0!s}'.format( - os.path.join('/dls_sw', beamline, 'logs'))) + Logfile.insert( + "checking GDA logfile in {0!s}".format( + os.path.join("/dls_sw", beamline, "logs") + ) + ) pinDict = {} found_barcode_entry = False - for gdaLogFile in glob.glob(os.path.join('/dls_sw', beamline, 'logs', 'gda-server*log*')): - if gdaLogFile.endswith('tmp'): - Logfile.warning('ignoring temporary file ' + gdaLogFile) + for gdaLogFile in glob.glob( + os.path.join("/dls_sw", beamline, "logs", "gda-server*log*") + ): + if gdaLogFile.endswith("tmp"): + Logfile.warning("ignoring temporary file " + gdaLogFile) continue - Logfile.insert('parsing {0!s}'.format(gdaLogFile)) - if gzipped_logs_parsed and gdaLogFile.endswith('.gz'): + Logfile.insert("parsing {0!s}".format(gdaLogFile)) + if gzipped_logs_parsed and gdaLogFile.endswith(".gz"): Logfile.insert( - '{0!s} was already parsed during this visit'.format(gdaLogFile)) + "{0!s} was already parsed during this visit".format(gdaLogFile) + ) continue - if gdaLogFile.endswith('.gz'): + if gdaLogFile.endswith(".gz"): try: - with gzip.open(gdaLogFile, 'r') as f: + with gzip.open(gdaLogFile, "r") as f: for line in f: - if 'BART SampleChanger - getBarcode() returning' in line: + if "BART SampleChanger - getBarcode() returning" in line: barcode = line.split()[len(line.split()) - 1] found_barcode_entry = True if found_barcode_entry: - if 'Snapshots will be saved' in line: - sampleID = line.split()[len( - line.split()) - 1].split('/')[-1] + if "Snapshots will be saved" in line: + sampleID = line.split()[len(line.split()) - 1].split( + "/" + )[-1] if sampleID in sampleList: pinDict[sampleID] = barcode Logfile.insert( - 'found: sample={0!s}, barcode={1!s}, file={2!s}'.format(sampleID, barcode, gdaLogFile)) + "found: sample={0!s}, barcode={1!s}, file={2!s}".format( + sampleID, barcode, gdaLogFile + ) + ) found_barcode_entry = False except IOError: - Logfile.warning('cannot open file %s' % gdaLogFile) + Logfile.warning("cannot open file %s" % gdaLogFile) else: try: - for n, line in enumerate(open(gdaLogFile).readlines()[gda_log_start_line:]): - if 'BART SampleChanger - getBarcode() returning' in line: + for n, line in enumerate( + open(gdaLogFile).readlines()[gda_log_start_line:] + ): + if "BART SampleChanger - getBarcode() returning" in line: barcode = line.split()[len(line.split()) - 1] found_barcode_entry = True if found_barcode_entry: - if 'Snapshots will be saved' in line: - sampleID = line.split()[len( - line.split()) - 1].split('/')[-1] + if "Snapshots will be saved" in line: + sampleID = line.split()[len(line.split()) - 1].split("/")[ + -1 + ] if sampleID in sampleList: pinDict[sampleID] = barcode Logfile.insert( - 'found: sample={0!s}, barcode={1!s}, file={2!s}'.format(sampleID, barcode, gdaLogFile)) + "found: sample={0!s}, barcode={1!s}, file={2!s}".format( + sampleID, barcode, gdaLogFile + ) + ) found_barcode_entry = False except IOError: - Logfile.error('IOError -> ' + gdaLogFile) + Logfile.error("IOError -> " + gdaLogFile) try: gda_log_start_line = gda_log_start_line + n - 1 @@ -573,46 +818,80 @@ def get_gda_barcodes(sampleList, gzipped_logs_parsed, gda_log_start_line, beamli def linkAutoProcessingResult(xtal, dbDict, projectDir, xce_logfile): Logfile = XChemLog.updateLog(xce_logfile) - run = dbDict['DataCollectionRun'] - subDir = dbDict['DataCollectionSubdir'] - if subDir != '': - procCode = '_' + subDir + run = dbDict["DataCollectionRun"] + subDir = dbDict["DataCollectionSubdir"] + if subDir != "": + procCode = "_" + subDir else: - procCode = '' - visit = dbDict['DataCollectionVisit'] - autoproc = dbDict['DataProcessingProgram'] - mtzFileAbs = dbDict['DataProcessingPathToMTZfile'] - mtzfile = mtzFileAbs[mtzFileAbs.rfind('/')+1:] - logFileAbs = dbDict['DataProcessingPathToLogfile'] - logfile = logFileAbs[logFileAbs.rfind('/')+1:] - - Logfile.insert('changing directory to ' + os.path.join(projectDir, xtal)) + procCode = "" + visit = dbDict["DataCollectionVisit"] + autoproc = dbDict["DataProcessingProgram"] + mtzFileAbs = dbDict["DataProcessingPathToMTZfile"] + mtzfile = mtzFileAbs[mtzFileAbs.rfind("/") + 1 :] + logFileAbs = dbDict["DataProcessingPathToLogfile"] + logfile = logFileAbs[logFileAbs.rfind("/") + 1 :] + + Logfile.insert("changing directory to " + os.path.join(projectDir, xtal)) os.chdir(os.path.join(projectDir, xtal)) # MTZ file - Logfile.warning('removing %s.mtz' % xtal) - os.system('/bin/rm %s.mtz' % xtal) - Logfile.insert(xtal+': looking for '+os.path.join('autoprocessing', - visit + '-' + run + autoproc + procCode, mtzfile)) - if os.path.isfile(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, mtzfile)): - os.symlink(os.path.join('autoprocessing', visit + '-' + - run + autoproc + procCode, mtzfile), xtal + '.mtz') + Logfile.warning("removing %s.mtz" % xtal) + os.system("/bin/rm %s.mtz" % xtal) + Logfile.insert( + xtal + + ": looking for " + + os.path.join( + "autoprocessing", visit + "-" + run + autoproc + procCode, mtzfile + ) + ) + if os.path.isfile( + os.path.join("autoprocessing", visit + "-" + run + autoproc + procCode, mtzfile) + ): + os.symlink( + os.path.join( + "autoprocessing", visit + "-" + run + autoproc + procCode, mtzfile + ), + xtal + ".mtz", + ) + Logfile.insert("linking MTZ file from different auto-processing pipeline:") Logfile.insert( - 'linking MTZ file from different auto-processing pipeline:') - Logfile.insert('ln -s ' + os.path.join('autoprocessing', visit + - '-' + run + autoproc + procCode, mtzfile) + ' ' + xtal + '.mtz') + "ln -s " + + os.path.join( + "autoprocessing", visit + "-" + run + autoproc + procCode, mtzfile + ) + + " " + + xtal + + ".mtz" + ) # LOG file - Logfile.warning('removing %s.log' % xtal) - os.system('/bin/rm %s.log' % xtal) - Logfile.insert(xtal+': looking for '+os.path.join('autoprocessing', - visit + '-' + run + autoproc + procCode, logfile)) - if os.path.isfile(os.path.join('autoprocessing', visit + '-' + run + autoproc + procCode, logfile)): - os.symlink(os.path.join('autoprocessing', visit + '-' + - run + autoproc + procCode, logfile), xtal + '.log') + Logfile.warning("removing %s.log" % xtal) + os.system("/bin/rm %s.log" % xtal) + Logfile.insert( + xtal + + ": looking for " + + os.path.join( + "autoprocessing", visit + "-" + run + autoproc + procCode, logfile + ) + ) + if os.path.isfile( + os.path.join("autoprocessing", visit + "-" + run + autoproc + procCode, logfile) + ): + os.symlink( + os.path.join( + "autoprocessing", visit + "-" + run + autoproc + procCode, logfile + ), + xtal + ".log", + ) + Logfile.insert("linking LOG file from different auto-processing pipeline:") Logfile.insert( - 'linking LOG file from different auto-processing pipeline:') - Logfile.insert('ln -s ' + os.path.join('autoprocessing', visit + - '-' + run + autoproc + procCode, logfile) + ' ' + xtal + '.log') + "ln -s " + + os.path.join( + "autoprocessing", visit + "-" + run + autoproc + procCode, logfile + ) + + " " + + xtal + + ".log" + ) def getProgressSteps(iterations): @@ -624,134 +903,133 @@ def getProgressSteps(iterations): def getVisitAndBeamline(visitDirectory): - visit = 'unknown' - beamline = 'unknown' - if 'attic' in visitDirectory: + visit = "unknown" + beamline = "unknown" + if "attic" in visitDirectory: try: - visit = visitDirectory.split('/')[6] - beamline = visitDirectory.split('/')[3] + visit = visitDirectory.split("/")[6] + beamline = visitDirectory.split("/")[3] except IndexError: pass else: try: - visit = visitDirectory.split('/')[5] - beamline = visitDirectory.split('/')[2] + visit = visitDirectory.split("/")[5] + beamline = visitDirectory.split("/")[2] except IndexError: pass - if not visitDirectory.startswith('/dls'): + if not visitDirectory.startswith("/dls"): # this is all a bit of a fudge in case someone transfers a DLS visit directory back home # does most certainly not catch all possible scenarios - if visitDirectory.split('/')[len(visitDirectory.split('/')) - 2] == 'processed': - visit = visitDirectory.split( - '/')[len(visitDirectory.split('/')) - 3] + if visitDirectory.split("/")[len(visitDirectory.split("/")) - 2] == "processed": + visit = visitDirectory.split("/")[len(visitDirectory.split("/")) - 3] else: - visit = visitDirectory.split('/')[len(visitDirectory.split('/'))-1] - beamline = 'unknown' + visit = visitDirectory.split("/")[len(visitDirectory.split("/")) - 1] + beamline = "unknown" return visit, beamline def crystal_growth_methods(): - methods = ['VAPOR DIFFUSION, SITTING DROP', - 'VAPOR DIFFUSION, HANGING DROP', - 'BATCH MODE', - 'LIPIDIC CUBIC PHASE', - 'MICROBATCH', - 'MICROFLUIDIC'] + methods = [ + "VAPOR DIFFUSION, SITTING DROP", + "VAPOR DIFFUSION, HANGING DROP", + "BATCH MODE", + "LIPIDIC CUBIC PHASE", + "MICROBATCH", + "MICROFLUIDIC", + ] return methods def wwBeamlines(): - beamlines = ['DIAMOND BEAMLINE I02', - 'DIAMOND BEAMLINE I03', - 'DIAMOND BEAMLINE I04', - 'DIAMOND BEAMLINE I04-1', - 'DIAMOND BEAMLINE I23', - 'DIAMOND BEAMLINE I24'] + beamlines = [ + "DIAMOND BEAMLINE I02", + "DIAMOND BEAMLINE I03", + "DIAMOND BEAMLINE I04", + "DIAMOND BEAMLINE I04-1", + "DIAMOND BEAMLINE I23", + "DIAMOND BEAMLINE I24", + ] return beamlines def radiationSource(): - source = ['SYNCHROTRON', - 'ROTATING ANODE', - 'SEALED TUBE'] + source = ["SYNCHROTRON", "ROTATING ANODE", "SEALED TUBE"] return source def detector(): - detectorPrinciple = ['PIXEL', - 'CCD', - 'IMAGE PLATE', - 'CMOS'] + detectorPrinciple = ["PIXEL", "CCD", "IMAGE PLATE", "CMOS"] return detectorPrinciple def detectorType(): - detector = ['DECTRIS PILATUS 2M', - 'DECTRIS PILATUS 2M-F', - 'DECTRIS PILATUS 6M', - 'DECTRIS PILATUS 6M-F', - 'DECTRIS PILATUS 12M', - 'DECTRIS PILATUS3 2M', - 'DECTRIS PILATUS3 6M', - 'DECTRIS EIGER X 9M', - 'DECTRIS EIGER X 16M', - 'ADSC QUANTUM 315', - 'ADSC QUANTUM 315r'] + detector = [ + "DECTRIS PILATUS 2M", + "DECTRIS PILATUS 2M-F", + "DECTRIS PILATUS 6M", + "DECTRIS PILATUS 6M-F", + "DECTRIS PILATUS 12M", + "DECTRIS PILATUS3 2M", + "DECTRIS PILATUS3 6M", + "DECTRIS EIGER X 9M", + "DECTRIS EIGER X 16M", + "ADSC QUANTUM 315", + "ADSC QUANTUM 315r", + ] return detector def NCBI_taxonomy_ID(): - taxonomy_dict = {'9606': 'Homo sapiens', - '10090': 'Mus musculus', - '7108': 'SPODOPTERA FRUGIPERDA', - '5693 ': 'Trypanosoma cruzi', - '1508227': 'BAT SARS-LIKE CORONAVIRUS', - '2697049': 'SARS-CoV-2', - '562': 'Escherichia coli', - '837': 'Porphyromonas gingivalis' - } + taxonomy_dict = { + "9606": "Homo sapiens", + "10090": "Mus musculus", + "7108": "SPODOPTERA FRUGIPERDA", + "5693 ": "Trypanosoma cruzi", + "1508227": "BAT SARS-LIKE CORONAVIRUS", + "2697049": "SARS-CoV-2", + "562": "Escherichia coli", + "837": "Porphyromonas gingivalis", + } return taxonomy_dict def data_integration_software(): - software = ['XDS', - 'HKL', - 'DENZO', - 'DTREK', - 'MOSFLM'] + software = ["XDS", "HKL", "DENZO", "DTREK", "MOSFLM"] return software def phasing_software(): - software = ['REFMAC', - 'PHENIX', - 'SOLVE', - 'PHASER', - 'CNS', - 'XPLOR', - 'MLPHARE', - 'SHELX', - 'SNB', - 'BnP', - 'BP3', - 'SHARP', - 'PHASES', - 'WARP'] + software = [ + "REFMAC", + "PHENIX", + "SOLVE", + "PHASER", + "CNS", + "XPLOR", + "MLPHARE", + "SHELX", + "SNB", + "BnP", + "BP3", + "SHARP", + "PHASES", + "WARP", + ] return software @@ -759,89 +1037,89 @@ def phasing_software(): def pdbx_keywords(): keywords = [ - '', - 'ALLERGEN', - 'ANTIBIOTIC', - 'ANTIFREEZE PROTEIN', - 'ANTIFUNGAL PROTEIN', - 'ANTIMICROBIAL PROTEIN', - 'ANTITOXIN', - 'ANTITUMOR PROTEIN', - 'ANTIVIRAL PROTEIN', - 'APOPTOSIS', - 'ATTRACTANT', - 'BIOSYNTHETIC PROTEIN', - 'BLOOD CLOTTING', - 'CARBOHYDRATE', - 'CELL ADHESION', - 'CELL CYCLE', - 'CELL INVASION', - 'CHAPERONE', - 'CHOLINE - BINDING PROTEIN', - 'CIRCADIAN CLOCK PROTEIN', - 'CONTRACTILE PROTEIN', - 'CYTOKINE', - 'CYTOSOLIC PROTEIN', - 'DE NOVO PROTEIN', - 'DNA', - 'DNA BINDING PROTEIN', - 'DNA - RNA HYBRID', - 'ELECTRON TRANSPORT', - 'ENDOCYTOSIS', - 'EXOCYTOSIS', - 'FLAVOPROTEIN', - 'FLUORESCENT PROTEIN', - 'GENE REGULATION', - 'HORMONE', - 'HYDROLASE', - 'IMMUNE SYSTEM', - 'IMMUNOSUPPRESSANT', - 'ISOMERASE', - 'LIGASE', - 'LIPID BINDING PROTEIN', - 'LIPID TRANSPORT', - 'LUMINESCENT PROTEIN', - 'LYASE', - 'MEMBRANE PROTEIN', - 'METAL BINDING PROTEIN', - 'METAL TRANSPORT', - 'MOTOR PROTEIN', - 'NEUROPEPTIDE', - 'NUCLEAR PROTEIN', - 'ONCOPROTEIN', - 'OXIDOREDUCTASE', - 'OXYGEN BINDING', - 'OXYGEN STORAGE', - 'OXYGEN TRANSPORT', - 'PEPTIDE BINDING PROTEIN', - 'PHOTOSYNTHESIS', - 'PLANT PROTEIN', - 'PROTEIN BINDING', - 'PROTEIN FIBRIL', - 'PROTEIN TRANSPORT', - 'PROTON TRANSPORT', - 'RECOMBINATION', - 'REPLICATION', - 'RIBOSOMAL PROTEIN', - 'RIBOSOME', - 'RNA', - 'RNA BINDING PROTEIN', - 'SIGNALING PROTEIN', - 'SPLICING', - 'STRUCTURAL GENOMICS', - 'STRUCTURAL PROTEIN', - 'SUGAR BINDING PROTEIN', - 'SURFACTANT PROTEIN', - 'TOXIN', - 'TRANSCRIPTION', - 'TRANSFERASE', - 'TRANSLATION', - 'TRANSLOCASE', - 'TRANSPORT PROTEIN', - 'UNKNOWN FUNCTION', - 'VIRAL PROTEIN', - 'VIRUS', - 'VIRUS LIKE PARTICLE' + "", + "ALLERGEN", + "ANTIBIOTIC", + "ANTIFREEZE PROTEIN", + "ANTIFUNGAL PROTEIN", + "ANTIMICROBIAL PROTEIN", + "ANTITOXIN", + "ANTITUMOR PROTEIN", + "ANTIVIRAL PROTEIN", + "APOPTOSIS", + "ATTRACTANT", + "BIOSYNTHETIC PROTEIN", + "BLOOD CLOTTING", + "CARBOHYDRATE", + "CELL ADHESION", + "CELL CYCLE", + "CELL INVASION", + "CHAPERONE", + "CHOLINE - BINDING PROTEIN", + "CIRCADIAN CLOCK PROTEIN", + "CONTRACTILE PROTEIN", + "CYTOKINE", + "CYTOSOLIC PROTEIN", + "DE NOVO PROTEIN", + "DNA", + "DNA BINDING PROTEIN", + "DNA - RNA HYBRID", + "ELECTRON TRANSPORT", + "ENDOCYTOSIS", + "EXOCYTOSIS", + "FLAVOPROTEIN", + "FLUORESCENT PROTEIN", + "GENE REGULATION", + "HORMONE", + "HYDROLASE", + "IMMUNE SYSTEM", + "IMMUNOSUPPRESSANT", + "ISOMERASE", + "LIGASE", + "LIPID BINDING PROTEIN", + "LIPID TRANSPORT", + "LUMINESCENT PROTEIN", + "LYASE", + "MEMBRANE PROTEIN", + "METAL BINDING PROTEIN", + "METAL TRANSPORT", + "MOTOR PROTEIN", + "NEUROPEPTIDE", + "NUCLEAR PROTEIN", + "ONCOPROTEIN", + "OXIDOREDUCTASE", + "OXYGEN BINDING", + "OXYGEN STORAGE", + "OXYGEN TRANSPORT", + "PEPTIDE BINDING PROTEIN", + "PHOTOSYNTHESIS", + "PLANT PROTEIN", + "PROTEIN BINDING", + "PROTEIN FIBRIL", + "PROTEIN TRANSPORT", + "PROTON TRANSPORT", + "RECOMBINATION", + "REPLICATION", + "RIBOSOMAL PROTEIN", + "RIBOSOME", + "RNA", + "RNA BINDING PROTEIN", + "SIGNALING PROTEIN", + "SPLICING", + "STRUCTURAL GENOMICS", + "STRUCTURAL PROTEIN", + "SUGAR BINDING PROTEIN", + "SURFACTANT PROTEIN", + "TOXIN", + "TRANSCRIPTION", + "TRANSFERASE", + "TRANSLATION", + "TRANSLOCASE", + "TRANSPORT PROTEIN", + "UNKNOWN FUNCTION", + "VIRAL PROTEIN", + "VIRUS", + "VIRUS LIKE PARTICLE", ] return keywords @@ -850,81 +1128,81 @@ def pdbx_keywords(): def pdbx_country(): countries = [ - 'United Kingdom', - 'United States', - 'Japan', - 'Albania', - 'Andorra', - 'Argentina', - 'Armenia', - 'Australia', - 'Austria', - 'Azerbaijan', - 'Bahamas', - 'Bangladesh', - 'Barbados', - 'Belarus', - 'Belgium', - 'Brazil', - 'Bulgaria', - 'Canada', - 'Chile', - 'China', - 'Croatia', - 'Cuba', - 'Cyprus', - 'Czech Republic', - 'Denmark', - 'Estonia', - 'Finland', - 'France', - 'Germany', - 'Greece', - 'Hungary', - 'Iceland', - 'India', - 'Indonesia', - 'Iran, Islamic Republic Of', - 'Iraq', - 'Ireland', - 'Israel', - 'Italy', - 'Jamaica', - 'Jordan', - 'Kazakhstan', - 'Kenya', - 'Kiribati', - 'Korea, Republic Of', - 'Latvia', - 'Lithuania', - 'Luxembourg', - 'Malta', - 'Mexico', - 'Netherlands', - 'New Zealand', - 'Norway', - 'Pakistan', - 'Paraguay', - 'Peru', - 'Philippines', - 'Poland', - 'Portugal', - 'Romania', - 'Russian Federation', - 'Serbia', - 'Singapore', - 'Slovakia', - 'Slovenia', - 'South Africa', - 'Spain', - 'Sweden', - 'Switzerland', - 'Taiwan', - 'Thailand', - 'Turkey', - 'Ukraine', - 'United Arab Emirates', - 'Uruguay' + "United Kingdom", + "United States", + "Japan", + "Albania", + "Andorra", + "Argentina", + "Armenia", + "Australia", + "Austria", + "Azerbaijan", + "Bahamas", + "Bangladesh", + "Barbados", + "Belarus", + "Belgium", + "Brazil", + "Bulgaria", + "Canada", + "Chile", + "China", + "Croatia", + "Cuba", + "Cyprus", + "Czech Republic", + "Denmark", + "Estonia", + "Finland", + "France", + "Germany", + "Greece", + "Hungary", + "Iceland", + "India", + "Indonesia", + "Iran, Islamic Republic Of", + "Iraq", + "Ireland", + "Israel", + "Italy", + "Jamaica", + "Jordan", + "Kazakhstan", + "Kenya", + "Kiribati", + "Korea, Republic Of", + "Latvia", + "Lithuania", + "Luxembourg", + "Malta", + "Mexico", + "Netherlands", + "New Zealand", + "Norway", + "Pakistan", + "Paraguay", + "Peru", + "Philippines", + "Poland", + "Portugal", + "Romania", + "Russian Federation", + "Serbia", + "Singapore", + "Slovakia", + "Slovenia", + "South Africa", + "Spain", + "Sweden", + "Switzerland", + "Taiwan", + "Thailand", + "Turkey", + "Ukraine", + "United Arab Emirates", + "Uruguay", ] return countries @@ -932,23 +1210,23 @@ def pdbx_country(): def html_header(): header = ( - '\n' - '\n' + "\n" + "\n" ' \n' ' \n' ' \n' ' \n' - ' Summary Fragment Hits\n' + " Summary Fragment Hits\n" ' \n' + " \n" ' \n' + " \n" ' \n' + " ]\n" + " } )\n" + " });\n" + " stage = undefined;\n" + " \n" ' \n' - '\n' - '\n' + "\n" + "\n" ) return header @@ -977,159 +1255,159 @@ def html_header(): def html_ngl(firstPDB, firstEvent, firstMap, firstDiffMap, ligID): - ligChain = ligID.split('-')[1] - ligResid = ligID.split('-')[2] + ligChain = ligID.split("-")[1] + ligResid = ligID.split("-")[2] ngl = ( "\n" - ' \n' - '\n' + " }\n" + " }\n" + " \n" + " \n" + "\n" ) return ngl @@ -1277,8 +1555,8 @@ def html_download(protein_name): download = ( '
\n' - '

%s - XChem results

\n' % protein_name + - " \n" + "

%s - XChem results

\n" % protein_name + + " \n" ' \n' - '
\n' - '\n' + " \n" + "
\n" + "
\n" + "
\n" + "
\n" + "
\n" + "\n" ) return download @@ -1319,23 +1601,23 @@ def html_guide(): " \n" "
\n" "

Ligand-bound models for Summary

Interpreting 'Ligand confidence'

\n" - '

4 - High Confidence: The expected ligand was easily interpretable from clear density, and subsequent refinement was well-behaved. This ligand can be trusted.\n' - '
3 - Clear density, unexpected ligand: Density very clearly showed a well-defined ligand, but that ligand was unexpected in that crystal/dataset. The observed ligand was modelled anyway, because its presence could be explained in some way.\n' - '
2 - Correct ligand, weak density: Though density was weak, it was possible to model the expected ligand, possibly including other circumstantial evidence (e.g. similar ligand in another model).\n' - '
1 - Low Confidence: The ligand model is to be treated with scepticism, because the evidence (density, identity, pose) were not convincing.\n' + "

4 - High Confidence: The expected ligand was easily interpretable from clear density, and subsequent refinement was well-behaved. This ligand can be trusted.\n" + "
3 - Clear density, unexpected ligand: Density very clearly showed a well-defined ligand, but that ligand was unexpected in that crystal/dataset. The observed ligand was modelled anyway, because its presence could be explained in some way.\n" + "
2 - Correct ligand, weak density: Though density was weak, it was possible to model the expected ligand, possibly including other circumstantial evidence (e.g. similar ligand in another model).\n" + "
1 - Low Confidence: The ligand model is to be treated with scepticism, because the evidence (density, identity, pose) were not convincing.\n" "

Interpreting 'Model status':

\n" - '

6 - Deposited: The model has been deposited in the PDB.\n' - '
5 - Deposition ready: The model is fully error-free, in every residue, and is ready for deposition.\n' - '
4 - CompChem ready: The model is complete and correct in the region of the bound ligand. There may be remaining small errors elsewhere in the structure, but they are far away and unlikely to be relevant to any computational analysis or compound design.\n' + "

6 - Deposited: The model has been deposited in the PDB.\n" + "
5 - Deposition ready: The model is fully error-free, in every residue, and is ready for deposition.\n" + "
4 - CompChem ready: The model is complete and correct in the region of the bound ligand. There may be remaining small errors elsewhere in the structure, but they are far away and unlikely to be relevant to any computational analysis or compound design.\n" "

Interpreting 'Ligand validation' spider plots:

Each axis represents one of the values described below; small is better, and large values on any axis implies that further investigation is warranted.\n" - '

Quality (RSCC) reflects the fit of the atoms to the experimental density, and should typically be greater than 0.7.\n' - '
Accuracy (RSZD) measures the amount of difference density that is found around these atoms, and should be below 3.\n' - '
B-factor ratio measures the consistency of the model with surrounding protein, and is calculated from the B factors of respectively the changed atoms and all side-chain atoms within 4Å. Large values (>3) reflect poor evidence for the model, and intermediate values (1.5+) indicate errors in refinement or modelling; for weakly-binding ligands, systematically large ratios may be justifiable.\n' - '
RMSD compares the positions of all atoms built into event density, with their positions after final refinement, and should be below 1Å.\n' - '
Precision (RSZO/OCC) measures how clear the density is after refinement. (This is not a quality indicator, but is related to strength of binding but not in a straightforward way.)\n' - '

\n' - '

\n' - '\n' + "

Quality (RSCC) reflects the fit of the atoms to the experimental density, and should typically be greater than 0.7.\n" + "
Accuracy (RSZD) measures the amount of difference density that is found around these atoms, and should be below 3.\n" + "
B-factor ratio measures the consistency of the model with surrounding protein, and is calculated from the B factors of respectively the changed atoms and all side-chain atoms within 4Å. Large values (>3) reflect poor evidence for the model, and intermediate values (1.5+) indicate errors in refinement or modelling; for weakly-binding ligands, systematically large ratios may be justifiable.\n" + "
RMSD compares the positions of all atoms built into event density, with their positions after final refinement, and should be below 1Å.\n" + "
Precision (RSZO/OCC) measures how clear the density is after refinement. (This is not a quality indicator, but is related to strength of binding but not in a straightforward way.)\n" + " \n" + "

\n" + "\n" ) return guide @@ -1345,65 +1627,83 @@ def html_table_header(): table = ( "\n" - '\n' + "\n" '\n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - ' \n' - + " \n" + " \n" + " \n" + " \n" + " \n" + " \n" + " \n" + " \n" + " \n" + " \n" + " \n" + " \n" + " \n" + " \n" + " \n" + " \n" ) return table -def html_table_row(xtalID, pdbID, ligID, compoundImage, residuePlot, pdb, event, thumbNail, resoHigh, spg, unitCell, FWT, DELFWT, ligConfidence, modelStatus): - - ligChain = ligID.split('-')[1] - ligResid = ligID.split('-')[2] - -# row = ( -# '\n' -# '\n' %xtalID + -# '\n' %(pdbID,pdbID) + -# '\n' %ligID + -# '\n' % ligConfidence + -# '\n' % modelStatus + -# "\n" %compoundImage + -# "\n" %residuePlot + -# "\n" %(pdbID,pdb,event,FWT,DELFWT,ligChain,ligResid,thumbNail) + -# '\n' %resoHigh + -# '\n' %(spg,unitCell) + -# "\n" %(pdb.replace('.pdb',''),ligID) + -# '\n' -# ) +def html_table_row( + xtalID, + pdbID, + ligID, + compoundImage, + residuePlot, + pdb, + event, + thumbNail, + resoHigh, + spg, + unitCell, + FWT, + DELFWT, + ligConfidence, + modelStatus, +): + + ligChain = ligID.split("-")[1] + ligResid = ligID.split("-")[2] + + # row = ( + # '\n' + # '\n' %xtalID + + # '\n' %(pdbID,pdbID) + + # '\n' %ligID + + # '\n' % ligConfidence + + # '\n' % modelStatus + + # "\n" %compoundImage + + # "\n" %residuePlot + + # "\n" %(pdbID,pdb,event,FWT,DELFWT,ligChain,ligResid,thumbNail) + + # '\n' %resoHigh + + # '\n' %(spg,unitCell) + + # "\n" %(pdb.replace('.pdb',''),ligID) + + # '\n' + # ) row = ( - ' \n' - ' \n' % xtalID + - ' \n' % (pdbID, pdbID) + - ' \n' % ligID + - ' \n' % ligConfidence + - ' \n' % modelStatus + - " \n" % compoundImage + - " \n" % residuePlot + - " \n" % (pdbID, pdb, event, FWT, DELFWT, ligChain, ligResid, thumbNail) + - ' \n' % resoHigh + - ' \n' % (spg, unitCell) + - " \n" % (pdb.replace('.pdb', ''), ligID) + - ' \n' + " \n" + " \n" % xtalID + + ' \n' + % (pdbID, pdbID) + + " \n" % ligID + + " \n" % ligConfidence + + " \n" % modelStatus + + " \n" % compoundImage + + " \n" % residuePlot + + " \n" + % (pdbID, pdb, event, FWT, DELFWT, ligChain, ligResid, thumbNail) + + " \n" % resoHigh + + " \n" % (spg, unitCell) + + " \n" + % (pdb.replace(".pdb", ""), ligID) + + " \n" ) return row @@ -1411,12 +1711,7 @@ def html_table_row(xtalID, pdbID, ligID, compoundImage, residuePlot, pdb, event, def html_footer(): - footer = ( - '\n' - '
Crystal IDPDB IDLigand IDLigand confidenceModel statusCompoundLigand ValidationEvent Map 3DResolSPG/ CellFiles
Crystal IDPDB IDLigand IDLigand confidenceModel statusCompoundLigand ValidationEvent Map 3DResolSPG/ CellFiles
%s%s%s%s%s
%s%s
%s		Save
%s%s%s%s%s
%s%s
%s		Save
%s%s%s%s%s
%s%s
%s		Save
%s%s%s%s%s
%s%s
%s		Save
\n' - '\n' - '\n' - ) + footer = "\n" "\n" "\n" "\n" return footer @@ -1425,48 +1720,54 @@ def coot_prepare_input(x, y, z, ligID, sampleDir, eventMap): os.chdir(sampleDir) cmd = ( - '# !/usr/bin/env coot\n' - '# python script for coot - generated by dimple\n' - 'import coot\n' + "# !/usr/bin/env coot\n" + "# python script for coot - generated by dimple\n" + "import coot\n" 'set_nomenclature_errors_on_read("ignore")\n' 'molecule = read_pdb("refine.split.bound-state.pdb")\n' - 'set_rotation_centre(%s, %s, %s)\n' % (x, y, z) + - 'set_zoom(30.)\n' - 'set_view_quaternion(-0.180532, -0.678828, 0, 0.711759)\n' + "set_rotation_centre(%s, %s, %s)\n" % (x, y, z) + "set_zoom(30.)\n" + "set_view_quaternion(-0.180532, -0.678828, 0, 0.711759)\n" 'coot.handle_read_ccp4_map(("%s"),0)\n' % eventMap + # 'mtz = "final.mtz"\n' # 'map21 = make_and_draw_map(mtz, "FWT", "PHWT", "", 0, 0)\n' # 'map11 = make_and_draw_map(mtz, "DELFWT", "PHDELWT", "", 0, 1)\n' - 'coot.raster3d("%s.r3d")\n' % ligID + - 'coot_real_exit(0)\n' + 'coot.raster3d("%s.r3d")\n' % ligID + "coot_real_exit(0)\n" ) - f = open(ligID+'.py', 'w') + f = open(ligID + ".py", "w") f.write(cmd) f.close() def coot_write_raster_file(ligID, sampleDir): os.chdir(sampleDir) - os.system('coot --no-graphics --no-guano --script %s.py' % ligID) + os.system("coot --no-graphics --no-guano --script %s.py" % ligID) def render_scene(xtal, ligID, sampleDir): os.chdir(sampleDir) - os.system('render < %s.r3d -png %s_%s.png' % (ligID, xtal, ligID)) + os.system("render < %s.r3d -png %s_%s.png" % (ligID, xtal, ligID)) def make_thumbnail(xtal, ligID, sampleDir): os.chdir(sampleDir) - os.system('convert -thumbnail 150x150 %s_%s.png %s_%s_thumb.png' % - (xtal, ligID, xtal, ligID)) + os.system( + "convert -thumbnail 150x150 %s_%s.png %s_%s_thumb.png" + % (xtal, ligID, xtal, ligID) + ) def backup_soakDB(database, xce_logfile): Logfile = XChemLog.updateLog(xce_logfile) - Logfile.insert('backing up soakDB: ' + database + - str(datetime.now()).replace(' ', '_')) - os.system('/bin/cp %s %s' % (database, database+'.' + - str(datetime.now()).replace(' ', '_').replace(':', '-'))) + Logfile.insert( + "backing up soakDB: " + database + str(datetime.now()).replace(" ", "_") + ) + os.system( + "/bin/cp %s %s" + % ( + database, + database + "." + str(datetime.now()).replace(" ", "_").replace(":", "-"), + ) + ) class find_diffraction_image_directory(QtCore.QThread): @@ -1475,44 +1776,57 @@ def __init__(self, diffraction_data_directory): self.diffraction_data_directory = diffraction_data_directory self.data_dict = {} self.diffraction_image_extension = [ - '.img', '.cbf', '.mccd', '.mar2560', '.mar2300'] -# self.datasetID_to_sampleID_conversion='*' + ".img", + ".cbf", + ".mccd", + ".mar2560", + ".mar2300", + ] + + # self.datasetID_to_sampleID_conversion='*' def run(self): os.chdir(self.diffraction_data_directory) - if len(glob.glob(os.path.join(self.diffraction_data_directory, '*'))) != 0: - progress_step = 100 / \ - float(len(glob.glob(os.path.join(self.diffraction_data_directory, '*')))) + if len(glob.glob(os.path.join(self.diffraction_data_directory, "*"))) != 0: + progress_step = 100 / float( + len(glob.glob(os.path.join(self.diffraction_data_directory, "*"))) + ) else: progress_step = 100 progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'searching diffraction data directory') - for xtal in glob.glob('*'): + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "searching diffraction data directory", + ) + for xtal in glob.glob("*"): self.data_dict[xtal] = [[], []] for root, dirs, files in os.walk(xtal): - if 'screening' in root: + if "screening" in root: continue image_file_list = [] - for n, image_file in enumerate(glob.glob(os.path.join(root, '*'))): - file_extension = image_file[image_file.rfind('.'):] + for n, image_file in enumerate(glob.glob(os.path.join(root, "*"))): + file_extension = image_file[image_file.rfind(".") :] if file_extension in self.diffraction_image_extension: image_file_list.append(image_file) if n > 20 and file_extension in self.diffraction_image_extension: - if os.path.join(self.diffraction_data_directory, root) not in self.data_dict[xtal][0]: - self.data_dict[xtal][0].append(os.path.join( - self.diffraction_data_directory, root)) -# break + if ( + os.path.join(self.diffraction_data_directory, root) + not in self.data_dict[xtal][0] + ): + self.data_dict[xtal][0].append( + os.path.join(self.diffraction_data_directory, root) + ) + # break if self.data_dict[xtal][0]: found_new_file_root = False run_list = [] counter = 0 - current_file_root = '' + current_file_root = "" for image in image_file_list: - file_root = image[image.rfind('/')+1:image.rfind('_')] + file_root = image[image.rfind("/") + 1 : image.rfind("_")] if file_root not in run_list and not found_new_file_root: counter = 0 found_new_file_root = True @@ -1532,10 +1846,9 @@ def run(self): del self.data_dict[xtal] progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) - self.emit(QtCore.SIGNAL( - 'update_datasets_reprocess_table'), self.data_dict) + self.emit(QtCore.SIGNAL("update_datasets_reprocess_table"), self.data_dict) class find_diffraction_image_directory_fast(QtCore.QThread): @@ -1544,43 +1857,56 @@ def __init__(self, diffraction_data_directory): self.diffraction_data_directory = diffraction_data_directory self.data_dict = {} self.diffraction_image_extension = [ - '.img', '.cbf', '.mccd', '.mar2560', '.mar2300'] -# self.datasetID_to_sampleID_conversion='*' + ".img", + ".cbf", + ".mccd", + ".mar2560", + ".mar2300", + ] + + # self.datasetID_to_sampleID_conversion='*' def run(self): - print(('Running diffraction image search in ' + - str(self.diffraction_data_directory))) + print( + ( + "Running diffraction image search in " + + str(self.diffraction_data_directory) + ) + ) os.chdir(self.diffraction_data_directory) - if len(glob.glob(os.path.join(self.diffraction_data_directory, '*'))) != 0: - progress_step = 100 / \ - float(len(glob.glob(os.path.join(self.diffraction_data_directory, '*')))) + if len(glob.glob(os.path.join(self.diffraction_data_directory, "*"))) != 0: + progress_step = 100 / float( + len(glob.glob(os.path.join(self.diffraction_data_directory, "*"))) + ) else: progress_step = 100 progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'searching diffraction data directory') - for xtal in glob.glob('*'): - #print xtal - if 'screening' in xtal: + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) + + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "searching diffraction data directory", + ) + for xtal in glob.glob("*"): + # print xtal + if "screening" in xtal: continue self.data_dict[xtal] = [] rootList = [] imageCounter = 0 # find image file extension; the assumption is that there is only one file type - imageExtension = 'cbf' - for files in sorted(glob.glob(os.path.join(xtal, '*'))): + imageExtension = "cbf" + for files in sorted(glob.glob(os.path.join(xtal, "*"))): fileName = os.path.join(self.diffraction_data_directory, files) - file_extension = fileName[fileName.rfind('.'):] + file_extension = fileName[fileName.rfind(".") :] if file_extension in self.diffraction_image_extension: imageExtension = file_extension break - for files in sorted(glob.glob(os.path.join(xtal, '*'+imageExtension))): - fileName = files[files.rfind('/')+1:] - file_root = fileName[:fileName.rfind('_')] + for files in sorted(glob.glob(os.path.join(xtal, "*" + imageExtension))): + fileName = files[files.rfind("/") + 1 :] + file_root = fileName[: fileName.rfind("_")] if file_root not in rootList: rootList.append(file_root) @@ -1589,8 +1915,9 @@ def run(self): if imageCounter == 20: self.data_dict[xtal].append( - [os.path.join(self.diffraction_data_directory, xtal), file_root]) -# self.data_dict[xtal][1].append(file_root) + [os.path.join(self.diffraction_data_directory, xtal), file_root] + ) + # self.data_dict[xtal][1].append(file_root) imageCounter += 1 @@ -1598,7 +1925,6 @@ def run(self): del self.data_dict[xtal] progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) - self.emit(QtCore.SIGNAL( - 'update_datasets_reprocess_table'), self.data_dict) + self.emit(QtCore.SIGNAL("update_datasets_reprocess_table"), self.data_dict) diff --git a/lib/XChemPANDDA.py b/lib/XChemPANDDA.py index 72d4749f..feca2f49 100755 --- a/lib/XChemPANDDA.py +++ b/lib/XChemPANDDA.py @@ -7,7 +7,8 @@ from datetime import datetime from PyQt4 import QtGui, QtCore import math -#from XChemUtils import mtztools + +# from XChemUtils import mtztools import XChemDB import XChemRefine import XChemUtils @@ -41,8 +42,9 @@ class export_and_refine_ligand_bound_models(QtCore.QThread): - - def __init__(self, PanDDA_directory, datasource, project_directory, xce_logfile, which_models): + def __init__( + self, PanDDA_directory, datasource, project_directory, xce_logfile, which_models + ): QtCore.QThread.__init__(self) self.PanDDA_directory = PanDDA_directory self.datasource = datasource @@ -51,62 +53,70 @@ def __init__(self, PanDDA_directory, datasource, project_directory, xce_logfile, self.xce_logfile = xce_logfile self.project_directory = project_directory self.which_models = which_models - self.external_software = XChemUtils.external_software( - xce_logfile).check() + self.external_software = XChemUtils.external_software(xce_logfile).check() -# self.initial_model_directory=initial_model_directory -# self.db.create_missing_columns() -# self.db_list=self.db.get_empty_db_dict() -# self.external_software=XChemUtils.external_software(xce_logfile).check() -# self.xce_logfile=xce_logfile + # self.initial_model_directory=initial_model_directory + # self.db.create_missing_columns() + # self.db_list=self.db.get_empty_db_dict() + # self.external_software=XChemUtils.external_software(xce_logfile).check() + # self.xce_logfile=xce_logfile -# self.already_exported_models=[] + # self.already_exported_models=[] def run(self): self.Logfile.warning( - XChemToolTips.pandda_export_ligand_bound_models_only_disclaimer()) + XChemToolTips.pandda_export_ligand_bound_models_only_disclaimer() + ) # find all folders with *-pandda-model.pdb modelsDict = self.find_modeled_structures_and_timestamps() # if only NEW models shall be exported, check timestamps - if not self.which_models.startswith('all'): + if not self.which_models.startswith("all"): modelsDict = self.find_new_models(modelsDict) # find pandda_inspect_events.csv and read in as pandas dataframe inspect_csv = None - if os.path.isfile(os.path.join(self.PanDDA_directory, 'analyses', 'pandda_inspect_events.csv')): - inspect_csv = pandas.read_csv(os.path.join( - self.PanDDA_directory, 'analyses', 'pandda_inspect_events.csv')) + if os.path.isfile( + os.path.join(self.PanDDA_directory, "analyses", "pandda_inspect_events.csv") + ): + inspect_csv = pandas.read_csv( + os.path.join( + self.PanDDA_directory, "analyses", "pandda_inspect_events.csv" + ) + ) progress = 0 try: - progress_step = float(1/len(modelsDict)) + progress_step = float(1 / len(modelsDict)) except TypeError: - self.Logfile.error('DID NOT FIND ANY MODELS TO EXPORT') + self.Logfile.error("DID NOT FIND ANY MODELS TO EXPORT") return None for xtal in sorted(modelsDict): - os.chdir(os.path.join(self.PanDDA_directory, - 'processed_datasets', xtal)) + os.chdir(os.path.join(self.PanDDA_directory, "processed_datasets", xtal)) pandda_model = os.path.join( - 'modelled_structures', xtal + '-pandda-model.pdb') + "modelled_structures", xtal + "-pandda-model.pdb" + ) pdb = gemmi.read_structure(pandda_model) # find out ligand event map relationship ligandDict = XChemUtils.pdbtools_gemmi( - pandda_model).center_of_mass_ligand_dict('LIG') + pandda_model + ).center_of_mass_ligand_dict("LIG") if ligandDict == {}: self.Logfile.error( - xtal + ': cannot find ligand of type LIG; skipping...') + xtal + ": cannot find ligand of type LIG; skipping..." + ) continue self.show_ligands_in_model(xtal, ligandDict) emapLigandDict = self.find_ligands_matching_event_map( - inspect_csv, xtal, ligandDict) + inspect_csv, xtal, ligandDict + ) - self.Logfile.warning('emapLigandDict' + str(emapLigandDict)) + self.Logfile.warning("emapLigandDict" + str(emapLigandDict)) # convert event map to SF self.event_map_to_sf(pdb.resolution, emapLigandDict) @@ -130,114 +140,166 @@ def run(self): self.refine_exported_model(xtal) progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) def update_database(self, xtal, modelsDict): db_dict = {} timestamp_file = modelsDict[xtal] - db_dict['DatePanDDAModelCreated'] = timestamp_file - db_dict['RefinementOutcome'] = '3 - In Refinement' - self.Logfile.insert('updating database for '+xtal + - ' setting time model was created to '+db_dict['DatePanDDAModelCreated']) + db_dict["DatePanDDAModelCreated"] = timestamp_file + db_dict["RefinementOutcome"] = "3 - In Refinement" + self.Logfile.insert( + "updating database for " + + xtal + + " setting time model was created to " + + db_dict["DatePanDDAModelCreated"] + ) self.db.update_data_source(xtal, db_dict) def make_and_cut_map(self, xtal, emapLigandDict): - self.Logfile.insert('changing directory to ' + - os.path.join(self.project_directory, xtal)) + self.Logfile.insert( + "changing directory to " + os.path.join(self.project_directory, xtal) + ) os.chdir(os.path.join(self.project_directory, xtal)) - XChemUtils.pdbtools_gemmi( - xtal + '-pandda-model.pdb').save_ligands_to_pdb('LIG') + XChemUtils.pdbtools_gemmi(xtal + "-pandda-model.pdb").save_ligands_to_pdb("LIG") for ligID in emapLigandDict: m = emapLigandDict[ligID] - emtz = m.replace('.ccp4', '_' + ligID + '.mtz') - emap = m.replace('.ccp4', '_' + ligID + '.ccp4') - XChemUtils.maptools().calculate_map(emtz, 'FWT', 'PHWT') - XChemUtils.maptools().cut_map_around_ligand(emap, ligID+'.pdb', '7') - if os.path.isfile(emap.replace('.ccp4', '_mapmask.ccp4')): - os.system('/bin/mv %s %s_%s_event.ccp4' % - (emap.replace('.ccp4', '_mapmask.ccp4'), xtal, ligID)) - os.system('ln -s %s_%s_event.ccp4 %s_%s_event_cut.ccp4' % - (xtal, ligID, xtal, ligID)) + emtz = m.replace(".ccp4", "_" + ligID + ".mtz") + emap = m.replace(".ccp4", "_" + ligID + ".ccp4") + XChemUtils.maptools().calculate_map(emtz, "FWT", "PHWT") + XChemUtils.maptools().cut_map_around_ligand(emap, ligID + ".pdb", "7") + if os.path.isfile(emap.replace(".ccp4", "_mapmask.ccp4")): + os.system( + "/bin/mv %s %s_%s_event.ccp4" + % (emap.replace(".ccp4", "_mapmask.ccp4"), xtal, ligID) + ) + os.system( + "ln -s %s_%s_event.ccp4 %s_%s_event_cut.ccp4" + % (xtal, ligID, xtal, ligID) + ) def copy_pandda_model_to_project_directory(self, xtal): os.chdir(os.path.join(self.project_directory, xtal)) - model = os.path.join(self.PanDDA_directory, 'processed_datasets', - xtal, 'modelled_structures', xtal+'-pandda-model.pdb') - self.Logfile.insert('copying %s to project directory' % model) - os.system('/bin/cp %s .' % model) + model = os.path.join( + self.PanDDA_directory, + "processed_datasets", + xtal, + "modelled_structures", + xtal + "-pandda-model.pdb", + ) + self.Logfile.insert("copying %s to project directory" % model) + os.system("/bin/cp %s ." % model) def copy_event_mtz_to_project_directory(self, xtal): - self.Logfile.insert('changing directory to ' + - os.path.join(self.PanDDA_directory, 'processed_datasets', xtal)) - os.chdir(os.path.join(self.PanDDA_directory, 'processed_datasets', xtal)) - for emap in glob.glob('*-BDC_*.mtz'): - self.Logfile.insert('copying %s to %s...' % ( - emap, os.path.join(self.project_directory, xtal))) - os.system('/bin/cp %s %s' % - (emap, os.path.join(self.project_directory, xtal))) + self.Logfile.insert( + "changing directory to " + + os.path.join(self.PanDDA_directory, "processed_datasets", xtal) + ) + os.chdir(os.path.join(self.PanDDA_directory, "processed_datasets", xtal)) + for emap in glob.glob("*-BDC_*.mtz"): + self.Logfile.insert( + "copying %s to %s..." + % (emap, os.path.join(self.project_directory, xtal)) + ) + os.system( + "/bin/cp %s %s" % (emap, os.path.join(self.project_directory, xtal)) + ) def move_old_event_to_backup_folder(self, xtal): - self.Logfile.insert('changing directory to ' + - os.path.join(self.project_directory, xtal)) + self.Logfile.insert( + "changing directory to " + os.path.join(self.project_directory, xtal) + ) os.chdir(os.path.join(self.project_directory, xtal)) - if not os.path.isdir('event_map_backup'): - os.mkdir('event_map_backup') - self.Logfile.insert('moving existing event maps to event_map_backup') - for emap in glob.glob('*-BDC_*.ccp4'): - os.system('/bin/mv %s event_map_backup/%s' % (emap, emap + - '.'+str(datetime.now()).replace(' ', '_').replace(':', '-'))) + if not os.path.isdir("event_map_backup"): + os.mkdir("event_map_backup") + self.Logfile.insert("moving existing event maps to event_map_backup") + for emap in glob.glob("*-BDC_*.ccp4"): + os.system( + "/bin/mv %s event_map_backup/%s" + % ( + emap, + emap + + "." + + str(datetime.now()).replace(" ", "_").replace(":", "-"), + ) + ) def show_ligands_in_model(self, xtal, ligandDict): - self.Logfile.insert(xtal + ': found the following ligands...') + self.Logfile.insert(xtal + ": found the following ligands...") for lig in ligandDict: - self.Logfile.insert( - lig + ' -> coordinates ' + str(ligandDict[lig])) + self.Logfile.insert(lig + " -> coordinates " + str(ligandDict[lig])) def find_modeled_structures_and_timestamps(self): self.Logfile.insert( - 'finding out modelled structures in ' + self.PanDDA_directory) + "finding out modelled structures in " + self.PanDDA_directory + ) modelsDict = {} - for model in sorted(glob.glob(os.path.join(self.PanDDA_directory, 'processed_datasets', '*', 'modelled_structures', '*-pandda-model.pdb'))): - sample = model[model.rfind( - '/')+1:].replace('-pandda-model.pdb', '') - timestamp = datetime.fromtimestamp( - os.path.getmtime(model)).strftime('%Y-%m-%d %H:%M:%S') + for model in sorted( + glob.glob( + os.path.join( + self.PanDDA_directory, + "processed_datasets", + "*", + "modelled_structures", + "*-pandda-model.pdb", + ) + ) + ): + sample = model[model.rfind("/") + 1 :].replace("-pandda-model.pdb", "") + timestamp = datetime.fromtimestamp(os.path.getmtime(model)).strftime( + "%Y-%m-%d %H:%M:%S" + ) self.Logfile.insert( - sample+'-pandda-model.pdb was created on '+str(timestamp)) + sample + "-pandda-model.pdb was created on " + str(timestamp) + ) modelsDict[sample] = timestamp return modelsDict def find_new_models(self, modelsDict): samples_to_export = {} self.Logfile.hint( - 'XCE will never export/ refine models that are "5-deposition ready" or "6-deposited"') + 'XCE will never export/ refine models that are "5-deposition ready" or "6-deposited"' + ) self.Logfile.hint( - 'Please change the RefinementOutcome flag in the Refinement table if you wish to re-export them') - self.Logfile.insert('checking timestamps of models in database...') + "Please change the RefinementOutcome flag in the Refinement table if you wish to re-export them" + ) + self.Logfile.insert("checking timestamps of models in database...") for xtal in modelsDict: timestamp_file = modelsDict[xtal] - db_query = self.db.execute_statement("select DatePanDDAModelCreated from mainTable where CrystalName is '" + - xtal+"' and (RefinementOutcome like '3%' or RefinementOutcome like '4%')") + db_query = self.db.execute_statement( + "select DatePanDDAModelCreated from mainTable where CrystalName is '" + + xtal + + "' and (RefinementOutcome like '3%' or RefinementOutcome like '4%')" + ) try: timestamp_db = str(db_query[0][0]) except IndexError: self.Logfile.warning( - '%s: database query gave no results for DatePanDDAModelCreated; skipping...' % xtal) + "%s: database query gave no results for DatePanDDAModelCreated; skipping..." + % xtal + ) self.Logfile.warning( - '%s: this might be a brand new model; will continue with export!' % xtal) + "%s: this might be a brand new model; will continue with export!" + % xtal + ) samples_to_export[xtal] = timestamp_file # some time in the future... timestamp_db = "2100-01-01 00:00:00" try: - difference = (datetime.strptime(timestamp_file, '%Y-%m-%d %H:%M:%S') - - datetime.strptime(timestamp_db, '%Y-%m-%d %H:%M:%S')) + difference = datetime.strptime( + timestamp_file, "%Y-%m-%d %H:%M:%S" + ) - datetime.strptime(timestamp_db, "%Y-%m-%d %H:%M:%S") if difference.seconds != 0: self.Logfile.insert( - 'exporting '+xtal+' -> was already refined, but newer PanDDA model available') + "exporting " + + xtal + + " -> was already refined, but newer PanDDA model available" + ) samples_to_export[xtal] = timestamp_file else: self.Logfile.insert( - '%s: model has not changed since it was created on %s' % (xtal, timestamp_db)) + "%s: model has not changed since it was created on %s" + % (xtal, timestamp_db) + ) except (ValueError, IndexError) as e: self.Logfile.error(str(e)) return samples_to_export @@ -245,42 +307,46 @@ def find_new_models(self, modelsDict): def event_map_to_sf(self, resolution, emapLigandDict): for lig in emapLigandDict: emap = emapLigandDict[lig] - emtz = emap.replace('.ccp4', '.mtz') - emtz_ligand = emap.replace('.ccp4', '_' + lig + '.mtz') + emtz = emap.replace(".ccp4", ".mtz") + emtz_ligand = emap.replace(".ccp4", "_" + lig + ".mtz") self.Logfile.insert( - 'trying to convert %s to SF -> %s' % (emap, emtz_ligand)) - self.Logfile.insert('>>> ' + emtz) + "trying to convert %s to SF -> %s" % (emap, emtz_ligand) + ) + self.Logfile.insert(">>> " + emtz) XChemUtils.maptools_gemmi(emap).map_to_sf(resolution) if os.path.isfile(emtz): - os.system('/bin/mv %s %s' % (emtz, emtz_ligand)) - self.Logfile.insert('success; %s exists' % emtz_ligand) + os.system("/bin/mv %s %s" % (emtz, emtz_ligand)) + self.Logfile.insert("success; %s exists" % emtz_ligand) else: self.Logfile.warning( - 'something went wrong; %s could not be created...' % emtz_ligand) + "something went wrong; %s could not be created..." % emtz_ligand + ) def find_ligands_matching_event_map(self, inspect_csv, xtal, ligandDict): emapLigandDict = {} for index, row in inspect_csv.iterrows(): - if row['dtag'] == xtal: - for emap in glob.glob('*-BDC_*.ccp4'): + if row["dtag"] == xtal: + for emap in glob.glob("*-BDC_*.ccp4"): self.Logfile.insert( - 'checking if event and ligand are within 7A of each other') - x = float(row['x']) - y = float(row['y']) - z = float(row['z']) + "checking if event and ligand are within 7A of each other" + ) + x = float(row["x"]) + y = float(row["y"]) + z = float(row["z"]) matching_ligand = self.calculate_distance_to_ligands( - ligandDict, x, y, z) + ligandDict, x, y, z + ) if matching_ligand is not None: emapLigandDict[matching_ligand] = emap self.Logfile.insert( - 'found matching ligand (%s) for %s' % (matching_ligand, emap)) + "found matching ligand (%s) for %s" + % (matching_ligand, emap) + ) break else: - self.Logfile.warning( - 'current ligand not close to event...') + self.Logfile.warning("current ligand not close to event...") if emapLigandDict == {}: - self.Logfile.error( - 'could not find ligands within 7A of PanDDA events') + self.Logfile.error("could not find ligands within 7A of PanDDA events") return emapLigandDict def calculate_distance_to_ligands(self, ligandDict, x, y, z): @@ -289,13 +355,16 @@ def calculate_distance_to_ligands(self, ligandDict, x, y, z): for ligand in ligandDict: c = ligandDict[ligand] p_ligand = gemmi.Position(c[0], c[1], c[2]) - self.Logfile.insert('coordinates ligand: ' + - str(c[0])+' ' + str(c[1])+' '+str(c[2])) - self.Logfile.insert('coordinates event: ' + - str(x)+' ' + str(y)+' '+str(z)) + self.Logfile.insert( + "coordinates ligand: " + str(c[0]) + " " + str(c[1]) + " " + str(c[2]) + ) + self.Logfile.insert( + "coordinates event: " + str(x) + " " + str(y) + " " + str(z) + ) distance = p_event.dist(p_ligand) self.Logfile.insert( - 'distance between ligand and event: %s A' % str(distance)) + "distance between ligand and event: %s A" % str(distance) + ) if distance < 7: matching_ligand = ligand break @@ -303,65 +372,120 @@ def calculate_distance_to_ligands(self, ligandDict, x, y, z): def refine_exported_model(self, xtal): - RefmacParams = {'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '', - 'WATER': '', - 'LIGOCC': '', - 'SANITY': ''} - - if 'nocheck' in self.which_models: - RefmacParams['SANITY'] = 'off' - - self.Logfile.insert('trying to refine ' + xtal + '...') - self.Logfile.insert('%s: getting compound code from database' % xtal) + RefmacParams = { + "HKLIN": "", + "HKLOUT": "", + "XYZIN": "", + "XYZOUT": "", + "LIBIN": "", + "LIBOUT": "", + "TLSIN": "", + "TLSOUT": "", + "TLSADD": "", + "NCYCLES": "10", + "MATRIX_WEIGHT": "AUTO", + "BREF": " bref ISOT\n", + "TLS": "", + "NCS": "", + "TWIN": "", + "WATER": "", + "LIGOCC": "", + "SANITY": "", + } + + if "nocheck" in self.which_models: + RefmacParams["SANITY"] = "off" + + self.Logfile.insert("trying to refine " + xtal + "...") + self.Logfile.insert("%s: getting compound code from database" % xtal) query = self.db.execute_statement( - "select CompoundCode from mainTable where CrystalName='%s';" % xtal) + "select CompoundCode from mainTable where CrystalName='%s';" % xtal + ) compoundID = str(query[0][0]) - self.Logfile.insert('%s: compounds code = %s' % (xtal, compoundID)) - if os.path.isfile(os.path.join(self.project_directory, xtal, xtal+'.free.mtz')): - if os.path.isfile(os.path.join(self.project_directory, xtal, xtal+'-pandda-model.pdb')): + self.Logfile.insert("%s: compounds code = %s" % (xtal, compoundID)) + if os.path.isfile( + os.path.join(self.project_directory, xtal, xtal + ".free.mtz") + ): + if os.path.isfile( + os.path.join(self.project_directory, xtal, xtal + "-pandda-model.pdb") + ): self.Logfile.insert( - 'running inital refinement on PANDDA model of '+xtal) + "running inital refinement on PANDDA model of " + xtal + ) Serial = XChemRefine.GetSerial(self.project_directory, xtal) - if not os.path.isdir(os.path.join(self.project_directory, xtal, 'cootOut')): - os.mkdir(os.path.join( - self.project_directory, xtal, 'cootOut')) + if not os.path.isdir( + os.path.join(self.project_directory, xtal, "cootOut") + ): + os.mkdir(os.path.join(self.project_directory, xtal, "cootOut")) # create folder for new refinement cycle - if os.path.isdir(os.path.join(self.project_directory, xtal, 'cootOut', 'Refine_'+str(Serial))): - os.chdir(os.path.join(self.project_directory, - xtal, 'cootOut', 'Refine_'+str(Serial))) + if os.path.isdir( + os.path.join( + self.project_directory, xtal, "cootOut", "Refine_" + str(Serial) + ) + ): + os.chdir( + os.path.join( + self.project_directory, + xtal, + "cootOut", + "Refine_" + str(Serial), + ) + ) else: - os.mkdir(os.path.join(self.project_directory, - xtal, 'cootOut', 'Refine_'+str(Serial))) - os.chdir(os.path.join(self.project_directory, - xtal, 'cootOut', 'Refine_'+str(Serial))) - os.system('/bin/cp %s in.pdb' % - os.path.join(self.project_directory, xtal, xtal+'-pandda-model.pdb')) + os.mkdir( + os.path.join( + self.project_directory, + xtal, + "cootOut", + "Refine_" + str(Serial), + ) + ) + os.chdir( + os.path.join( + self.project_directory, + xtal, + "cootOut", + "Refine_" + str(Serial), + ) + ) + os.system( + "/bin/cp %s in.pdb" + % os.path.join( + self.project_directory, xtal, xtal + "-pandda-model.pdb" + ) + ) Refine = XChemRefine.Refine( - self.project_directory, xtal, compoundID, self.datasource) - Refine.RunBuster(str(Serial), RefmacParams, - self.external_software, self.xce_logfile, None) + self.project_directory, xtal, compoundID, self.datasource + ) + Refine.RunBuster( + str(Serial), + RefmacParams, + self.external_software, + self.xce_logfile, + None, + ) else: self.Logfile.error( - '%s: cannot find %s-pandda-model.pdb; cannot start refinement...' % (xtal, xtal)) + "%s: cannot find %s-pandda-model.pdb; cannot start refinement..." + % (xtal, xtal) + ) else: - self.Logfile.error('%s: cannot start refinement because %s.free.mtz is missing in %s' % ( - xtal, xtal, os.path.join(self.project_directory, xtal))) + self.Logfile.error( + "%s: cannot start refinement because %s.free.mtz is missing in %s" + % (xtal, xtal, os.path.join(self.project_directory, xtal)) + ) class refine_bound_state_with_buster(QtCore.QThread): - - def __init__(self, panddas_directory, datasource, initial_model_directory, xce_logfile, which_models): + def __init__( + self, + panddas_directory, + datasource, + initial_model_directory, + xce_logfile, + which_models, + ): QtCore.QThread.__init__(self) self.panddas_directory = panddas_directory self.datasource = datasource @@ -369,8 +493,7 @@ def __init__(self, panddas_directory, datasource, initial_model_directory, xce_l self.db = XChemDB.data_source(self.datasource) self.db.create_missing_columns() self.db_list = self.db.get_empty_db_dict() - self.external_software = XChemUtils.external_software( - xce_logfile).check() + self.external_software = XChemUtils.external_software(xce_logfile).check() self.xce_logfile = xce_logfile self.Logfile = XChemLog.updateLog(xce_logfile) self.which_models = which_models @@ -383,159 +506,278 @@ def run(self): self.refine_exported_models(samples_to_export) def refine_exported_models(self, samples_to_export): - self.Logfile.insert('will try to refine the following crystals:') + self.Logfile.insert("will try to refine the following crystals:") for xtal in sorted(samples_to_export): self.Logfile.insert(xtal) for xtal in sorted(samples_to_export): - self.Logfile.insert( - '%s: getting compound code from database' % xtal) + self.Logfile.insert("%s: getting compound code from database" % xtal) query = self.db.execute_statement( - "select CompoundCode from mainTable where CrystalName='%s';" % xtal) + "select CompoundCode from mainTable where CrystalName='%s';" % xtal + ) compoundID = str(query[0][0]) - self.Logfile.insert('%s: compounds code = %s' % (xtal, compoundID)) -# compoundID=str(item[1]) - if os.path.isfile(os.path.join(self.initial_model_directory, xtal, xtal+'.free.mtz')): - if os.path.isfile(os.path.join(self.initial_model_directory, xtal, xtal+'-pandda-model.pdb')): + self.Logfile.insert("%s: compounds code = %s" % (xtal, compoundID)) + # compoundID=str(item[1]) + if os.path.isfile( + os.path.join(self.initial_model_directory, xtal, xtal + ".free.mtz") + ): + if os.path.isfile( + os.path.join( + self.initial_model_directory, xtal, xtal + "-pandda-model.pdb" + ) + ): self.Logfile.insert( - 'running inital refinement on PANDDA model of '+xtal) - Serial = XChemRefine.GetSerial( - self.initial_model_directory, xtal) + "running inital refinement on PANDDA model of " + xtal + ) + Serial = XChemRefine.GetSerial(self.initial_model_directory, xtal) ####################################################### - if not os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'cootOut')): - os.mkdir(os.path.join( - self.initial_model_directory, xtal, 'cootOut')) + if not os.path.isdir( + os.path.join(self.initial_model_directory, xtal, "cootOut") + ): + os.mkdir( + os.path.join(self.initial_model_directory, xtal, "cootOut") + ) # create folder for new refinement cycle - if os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'cootOut', 'Refine_'+str(Serial))): - os.chdir(os.path.join(self.initial_model_directory, - xtal, 'cootOut', 'Refine_'+str(Serial))) + if os.path.isdir( + os.path.join( + self.initial_model_directory, + xtal, + "cootOut", + "Refine_" + str(Serial), + ) + ): + os.chdir( + os.path.join( + self.initial_model_directory, + xtal, + "cootOut", + "Refine_" + str(Serial), + ) + ) else: - os.mkdir(os.path.join(self.initial_model_directory, - xtal, 'cootOut', 'Refine_'+str(Serial))) - os.chdir(os.path.join(self.initial_model_directory, - xtal, 'cootOut', 'Refine_'+str(Serial))) - os.system('/bin/cp %s in.pdb' % os.path.join( - self.initial_model_directory, xtal, xtal+'-pandda-model.pdb')) + os.mkdir( + os.path.join( + self.initial_model_directory, + xtal, + "cootOut", + "Refine_" + str(Serial), + ) + ) + os.chdir( + os.path.join( + self.initial_model_directory, + xtal, + "cootOut", + "Refine_" + str(Serial), + ) + ) + os.system( + "/bin/cp %s in.pdb" + % os.path.join( + self.initial_model_directory, + xtal, + xtal + "-pandda-model.pdb", + ) + ) Refine = XChemRefine.Refine( - self.initial_model_directory, xtal, compoundID, self.datasource) + self.initial_model_directory, xtal, compoundID, self.datasource + ) Refine.RunBuster( - str(Serial), self.external_software, self.xce_logfile, None) + str(Serial), self.external_software, self.xce_logfile, None + ) else: self.Logfile.error( - '%s: cannot find %s-pandda-model.pdb; cannot start refinement...' % (xtal, xtal)) + "%s: cannot find %s-pandda-model.pdb; cannot start refinement..." + % (xtal, xtal) + ) elif xtal in samples_to_export and not os.path.isfile( - os.path.join(self.initial_model_directory, xtal, xtal + '.free.mtz')): - self.Logfile.error('%s: cannot start refinement because %s.free.mtz is missing in %s' % ( - xtal, xtal, os.path.join(self.initial_model_directory, xtal))) + os.path.join(self.initial_model_directory, xtal, xtal + ".free.mtz") + ): + self.Logfile.error( + "%s: cannot start refinement because %s.free.mtz is missing in %s" + % (xtal, xtal, os.path.join(self.initial_model_directory, xtal)) + ) else: - self.Logfile.insert('%s: nothing to refine' % (xtal)) + self.Logfile.insert("%s: nothing to refine" % (xtal)) def export_models(self): - self.Logfile.insert( - 'finding out which PanDDA models need to be exported') + self.Logfile.insert("finding out which PanDDA models need to be exported") # first find which samples are in interesting datasets and have a model # and determine the timestamp fileModelsDict = {} - queryModels = '' - for model in glob.glob(os.path.join(self.panddas_directory, 'processed_datasets', '*', 'modelled_structures', '*-pandda-model.pdb')): - sample = model[model.rfind( - '/')+1:].replace('-pandda-model.pdb', '') - timestamp = datetime.fromtimestamp( - os.path.getmtime(model)).strftime('%Y-%m-%d %H:%M:%S') + queryModels = "" + for model in glob.glob( + os.path.join( + self.panddas_directory, + "processed_datasets", + "*", + "modelled_structures", + "*-pandda-model.pdb", + ) + ): + sample = model[model.rfind("/") + 1 :].replace("-pandda-model.pdb", "") + timestamp = datetime.fromtimestamp(os.path.getmtime(model)).strftime( + "%Y-%m-%d %H:%M:%S" + ) self.Logfile.insert( - sample+'-pandda-model.pdb was created on '+str(timestamp)) - queryModels += "'"+sample+"'," + sample + "-pandda-model.pdb was created on " + str(timestamp) + ) + queryModels += "'" + sample + "'," fileModelsDict[sample] = timestamp # now get these models from the database and compare the datestamps # Note: only get the models that underwent some form of refinement, # because only if the model was updated in pandda.inspect will it be exported and refined dbModelsDict = {} - if queryModels != '': - dbEntries = self.db.execute_statement("select CrystalName,DatePanDDAModelCreated from mainTable where CrystalName in (" + - queryModels[:-1]+") and (RefinementOutcome like '3%' or RefinementOutcome like '4%' or RefinementOutcome like '5%')") + if queryModels != "": + dbEntries = self.db.execute_statement( + "select CrystalName,DatePanDDAModelCreated from mainTable where CrystalName in (" + + queryModels[:-1] + + ") and (RefinementOutcome like '3%' or RefinementOutcome like '4%' or RefinementOutcome like '5%')" + ) for item in dbEntries: xtal = str(item[0]) timestamp = str(item[1]) dbModelsDict[xtal] = timestamp self.Logfile.insert( - 'PanDDA model for '+xtal+' is in database and was created on '+str(timestamp)) + "PanDDA model for " + + xtal + + " is in database and was created on " + + str(timestamp) + ) # compare timestamps and only export the ones where the timestamp of the file is newer than the one in the DB samples_to_export = {} self.Logfile.insert( - 'checking which PanDDA models were newly created or updated') - if self.which_models == 'all': - self.Logfile.insert( - 'Note: you chose to export ALL available PanDDA!') + "checking which PanDDA models were newly created or updated" + ) + if self.which_models == "all": + self.Logfile.insert("Note: you chose to export ALL available PanDDA!") for sample in fileModelsDict: - if self.which_models == 'all': - self.Logfile.insert('exporting '+sample) + if self.which_models == "all": + self.Logfile.insert("exporting " + sample) samples_to_export[sample] = fileModelsDict[sample] else: if sample in dbModelsDict: try: - difference = (datetime.strptime( - fileModelsDict[sample], '%Y-%m-%d %H:%M:%S') - datetime.strptime(dbModelsDict[sample], '%Y-%m-%d %H:%M:%S')) + difference = datetime.strptime( + fileModelsDict[sample], "%Y-%m-%d %H:%M:%S" + ) - datetime.strptime(dbModelsDict[sample], "%Y-%m-%d %H:%M:%S") if difference.seconds != 0: self.Logfile.insert( - 'exporting '+sample+' -> was already refined, but newer PanDDA model available') + "exporting " + + sample + + " -> was already refined, but newer PanDDA model available" + ) samples_to_export[sample] = fileModelsDict[sample] except ValueError: # this will be raised if timestamp is not properly formatted; # which will usually be the case when respective field in database is blank # these are hopefully legacy cases which are from before this extensive check was introduced (13/01/2017) - advice = ('The pandda model of '+xtal+' was changed, but it was already refined! ' - 'This is most likely because this was done with an older version of XCE. ' - 'If you really want to export and refine this model, you need to open the database ' - 'with DBbroweser (sqlitebrowser.org); then change the RefinementOutcome field ' - 'of the respective sample to "2 - PANDDA model", save the database and repeat the export prodedure.') + advice = ( + "The pandda model of " + + xtal + + " was changed, but it was already refined! " + "This is most likely because this was done with an older version of XCE. " + "If you really want to export and refine this model, you need to open the database " + "with DBbroweser (sqlitebrowser.org); then change the RefinementOutcome field " + 'of the respective sample to "2 - PANDDA model", save the database and repeat the export prodedure.' + ) self.Logfile.insert(advice) else: self.Logfile.insert( - 'exporting '+sample+' -> first time to be exported and refined') + "exporting " + + sample + + " -> first time to be exported and refined" + ) samples_to_export[sample] = fileModelsDict[sample] # update the DB: # set timestamp to current timestamp of file and set RefinementOutcome to '2-pandda...' if samples_to_export != {}: - select_dir_string = '' - select_dir_string_new_pannda = ' ' + select_dir_string = "" + select_dir_string_new_pannda = " " for sample in samples_to_export: self.Logfile.insert( - 'changing directory to ' + os.path.join(self.initial_model_directory, sample)) + "changing directory to " + + os.path.join(self.initial_model_directory, sample) + ) os.chdir(os.path.join(self.initial_model_directory, sample)) - self.Logfile.insert(sample + ': copying ' + os.path.join(self.panddas_directory, - 'processed_datasets', sample, 'modelled_structures', sample+'-pandda-model.pdb')) - os.system('/bin/cp %s .' % os.path.join(self.panddas_directory, - 'processed_datasets', sample, 'modelled_structures', sample+'-pandda-model.pdb')) - db_dict = {'RefinementOutcome': '2 - PANDDA model', - 'DatePanDDAModelCreated': samples_to_export[sample]} - for old_event_map in glob.glob('*-BDC_*.ccp4'): - if not os.path.isdir('old_event_maps'): - os.mkdir('old_event_maps') + self.Logfile.insert( + sample + + ": copying " + + os.path.join( + self.panddas_directory, + "processed_datasets", + sample, + "modelled_structures", + sample + "-pandda-model.pdb", + ) + ) + os.system( + "/bin/cp %s ." + % os.path.join( + self.panddas_directory, + "processed_datasets", + sample, + "modelled_structures", + sample + "-pandda-model.pdb", + ) + ) + db_dict = { + "RefinementOutcome": "2 - PANDDA model", + "DatePanDDAModelCreated": samples_to_export[sample], + } + for old_event_map in glob.glob("*-BDC_*.ccp4"): + if not os.path.isdir("old_event_maps"): + os.mkdir("old_event_maps") self.Logfile.warning( - sample + ': moving ' + old_event_map + ' to old_event_maps folder') - os.system('/bin/mv %s old_event_maps' % old_event_map) - for event_map in glob.glob(os.path.join(self.panddas_directory, 'processed_datasets', sample, '*-BDC_*.ccp4')): - self.Logfile.insert(sample + ': copying ' + event_map) - os.system('/bin/cp %s .' % event_map) + sample + + ": moving " + + old_event_map + + " to old_event_maps folder" + ) + os.system("/bin/mv %s old_event_maps" % old_event_map) + for event_map in glob.glob( + os.path.join( + self.panddas_directory, + "processed_datasets", + sample, + "*-BDC_*.ccp4", + ) + ): + self.Logfile.insert(sample + ": copying " + event_map) + os.system("/bin/cp %s ." % event_map) select_dir_string += "select_dir={0!s} ".format(sample) - select_dir_string_new_pannda += '{0!s} '.format(sample) - self.Logfile.insert('updating database for '+sample+' setting time model was created to ' + - db_dict['DatePanDDAModelCreated']+' and RefinementOutcome to '+db_dict['RefinementOutcome']) + select_dir_string_new_pannda += "{0!s} ".format(sample) + self.Logfile.insert( + "updating database for " + + sample + + " setting time model was created to " + + db_dict["DatePanDDAModelCreated"] + + " and RefinementOutcome to " + + db_dict["RefinementOutcome"] + ) self.db.update_data_source(sample, db_dict) return samples_to_export class run_pandda_export(QtCore.QThread): - - def __init__(self, panddas_directory, datasource, initial_model_directory, xce_logfile, update_datasource_only, which_models, pandda_params): + def __init__( + self, + panddas_directory, + datasource, + initial_model_directory, + xce_logfile, + update_datasource_only, + which_models, + pandda_params, + ): QtCore.QThread.__init__(self) self.panddas_directory = panddas_directory self.datasource = datasource @@ -543,26 +785,31 @@ def __init__(self, panddas_directory, datasource, initial_model_directory, xce_l self.db = XChemDB.data_source(self.datasource) self.db.create_missing_columns() self.db_list = self.db.get_empty_db_dict() - self.external_software = XChemUtils.external_software( - xce_logfile).check() + self.external_software = XChemUtils.external_software(xce_logfile).check() self.xce_logfile = xce_logfile self.Logfile = XChemLog.updateLog(xce_logfile) self.update_datasource_only = update_datasource_only self.which_models = which_models self.already_exported_models = [] - self.pandda_analyse_data_table = pandda_params['pandda_table'] - - self.RefmacParams = {'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': ''} + self.pandda_analyse_data_table = pandda_params["pandda_table"] + + self.RefmacParams = { + "HKLIN": "", + "HKLOUT": "", + "XYZIN": "", + "XYZOUT": "", + "LIBIN": "", + "LIBOUT": "", + "TLSIN": "", + "TLSOUT": "", + "TLSADD": "", + "NCYCLES": "10", + "MATRIX_WEIGHT": "AUTO", + "BREF": " bref ISOT\n", + "TLS": "", + "NCS": "", + "TWIN": "", + } def run(self): @@ -572,137 +819,221 @@ def run(self): self.import_samples_into_datasouce(samples_to_export) -# if not self.update_datasource_only: + # if not self.update_datasource_only: self.refine_exported_models(samples_to_export) def refine_exported_models(self, samples_to_export): - self.Logfile.insert('will try to refine the following crystals:') + self.Logfile.insert("will try to refine the following crystals:") for xtal in samples_to_export: self.Logfile.insert(xtal) -# sample_list=self.db.execute_statement("select CrystalName,CompoundCode from mainTable where RefinementOutcome='2 - PANDDA model';") -# for item in sample_list: -# xtal=str(item[0]) + # sample_list=self.db.execute_statement("select CrystalName,CompoundCode from mainTable where RefinementOutcome='2 - PANDDA model';") + # for item in sample_list: + # xtal=str(item[0]) for xtal in sorted(samples_to_export): - self.Logfile.insert( - '%s: getting compound code from database' % xtal) + self.Logfile.insert("%s: getting compound code from database" % xtal) query = self.db.execute_statement( - "select CompoundCode from mainTable where CrystalName='%s';" % xtal) + "select CompoundCode from mainTable where CrystalName='%s';" % xtal + ) compoundID = str(query[0][0]) - self.Logfile.insert('%s: compounds code = %s' % (xtal, compoundID)) -# compoundID=str(item[1]) - if os.path.isfile(os.path.join(self.initial_model_directory, xtal, xtal+'.free.mtz')): - if os.path.isfile(os.path.join(self.initial_model_directory, xtal, xtal+'-ensemble-model.pdb')): + self.Logfile.insert("%s: compounds code = %s" % (xtal, compoundID)) + # compoundID=str(item[1]) + if os.path.isfile( + os.path.join(self.initial_model_directory, xtal, xtal + ".free.mtz") + ): + if os.path.isfile( + os.path.join( + self.initial_model_directory, xtal, xtal + "-ensemble-model.pdb" + ) + ): self.Logfile.insert( - 'running inital refinement on PANDDA model of '+xtal) - Serial = XChemRefine.GetSerial( - self.initial_model_directory, xtal) + "running inital refinement on PANDDA model of " + xtal + ) + Serial = XChemRefine.GetSerial(self.initial_model_directory, xtal) ####################################################### - if not os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'cootOut')): - os.mkdir(os.path.join( - self.initial_model_directory, xtal, 'cootOut')) + if not os.path.isdir( + os.path.join(self.initial_model_directory, xtal, "cootOut") + ): + os.mkdir( + os.path.join(self.initial_model_directory, xtal, "cootOut") + ) # create folder for new refinement cycle - if os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'cootOut', 'Refine_'+str(Serial))): - os.chdir(os.path.join(self.initial_model_directory, - xtal, 'cootOut', 'Refine_'+str(Serial))) + if os.path.isdir( + os.path.join( + self.initial_model_directory, + xtal, + "cootOut", + "Refine_" + str(Serial), + ) + ): + os.chdir( + os.path.join( + self.initial_model_directory, + xtal, + "cootOut", + "Refine_" + str(Serial), + ) + ) try: - os.system( - '/bin/rm *-ensemble-model.pdb *restraints*') + os.system("/bin/rm *-ensemble-model.pdb *restraints*") except: self.Logfile.error( - "Restraint files didn't exist to remove. Will try to continue") + "Restraint files didn't exist to remove. Will try to continue" + ) else: - os.mkdir(os.path.join(self.initial_model_directory, - xtal, 'cootOut', 'Refine_'+str(Serial))) - os.chdir(os.path.join(self.initial_model_directory, - xtal, 'cootOut', 'Refine_'+str(Serial))) + os.mkdir( + os.path.join( + self.initial_model_directory, + xtal, + "cootOut", + "Refine_" + str(Serial), + ) + ) + os.chdir( + os.path.join( + self.initial_model_directory, + xtal, + "cootOut", + "Refine_" + str(Serial), + ) + ) Refine = XChemRefine.panddaRefine( - self.initial_model_directory, xtal, compoundID, self.datasource) - os.symlink(os.path.join(self.initial_model_directory, xtal, - xtal+'-ensemble-model.pdb'), xtal+'-ensemble-model.pdb') + self.initial_model_directory, xtal, compoundID, self.datasource + ) + os.symlink( + os.path.join( + self.initial_model_directory, + xtal, + xtal + "-ensemble-model.pdb", + ), + xtal + "-ensemble-model.pdb", + ) Refine.RunQuickRefine( - Serial, self.RefmacParams, self.external_software, self.xce_logfile, 'pandda_refmac', None) - -# elif xtal in os.path.join(self.panddas_directory,'processed_datasets',xtal,'modelled_structures', -# '{}-pandda-model.pdb'.format(xtal)): -# self.Logfile.insert('{}: cannot start refinement because {}'.format(xtal,xtal) + -# ' does not have a modelled structure. Check whether you expect this dataset to ' + -# ' have a modelled structure, compare pandda.inspect and datasource,' -# ' then tell XCHEMBB ') + Serial, + self.RefmacParams, + self.external_software, + self.xce_logfile, + "pandda_refmac", + None, + ) + + # elif xtal in os.path.join(self.panddas_directory,'processed_datasets',xtal,'modelled_structures', + # '{}-pandda-model.pdb'.format(xtal)): + # self.Logfile.insert('{}: cannot start refinement because {}'.format(xtal,xtal) + + # ' does not have a modelled structure. Check whether you expect this dataset to ' + + # ' have a modelled structure, compare pandda.inspect and datasource,' + # ' then tell XCHEMBB ') else: self.Logfile.error( - '%s: cannot find %s-ensemble-model.pdb; cannot start refinement...' % (xtal, xtal)) + "%s: cannot find %s-ensemble-model.pdb; cannot start refinement..." + % (xtal, xtal) + ) self.Logfile.error( - 'Please check terminal window for any PanDDA related tracebacks') + "Please check terminal window for any PanDDA related tracebacks" + ) elif xtal in samples_to_export and not os.path.isfile( - os.path.join(self.initial_model_directory, xtal, xtal + '.free.mtz')): - self.Logfile.error('%s: cannot start refinement because %s.free.mtz is missing in %s' % ( - xtal, xtal, os.path.join(self.initial_model_directory, xtal))) + os.path.join(self.initial_model_directory, xtal, xtal + ".free.mtz") + ): + self.Logfile.error( + "%s: cannot start refinement because %s.free.mtz is missing in %s" + % (xtal, xtal, os.path.join(self.initial_model_directory, xtal)) + ) else: - self.Logfile.insert('%s: nothing to refine' % (xtal)) + self.Logfile.insert("%s: nothing to refine" % (xtal)) def import_samples_into_datasouce(self, samples_to_export): # first make a note of all the datasets which were used in pandda directory - os.chdir(os.path.join(self.panddas_directory, 'processed_datasets')) - for xtal in glob.glob('*'): - self.db.execute_statement("update mainTable set DimplePANDDAwasRun = 'True',DimplePANDDAreject = 'False',DimplePANDDApath='{0!s}' where CrystalName is '{1!s}'".format( - self.panddas_directory, xtal)) + os.chdir(os.path.join(self.panddas_directory, "processed_datasets")) + for xtal in glob.glob("*"): + self.db.execute_statement( + "update mainTable set DimplePANDDAwasRun = 'True',DimplePANDDAreject = 'False',DimplePANDDApath='{0!s}' where CrystalName is '{1!s}'".format( + self.panddas_directory, xtal + ) + ) # do the same as before, but look for rejected datasets try: - os.chdir(os.path.join(self.panddas_directory, 'rejected_datasets')) - for xtal in glob.glob('*'): - self.db.execute_statement("update mainTable set DimplePANDDAwasRun = 'True',DimplePANDDAreject = 'True',DimplePANDDApath='{0!s}',DimplePANDDAhit = 'False' where CrystalName is '{1!s}'".format( - self.panddas_directory, xtal)) + os.chdir(os.path.join(self.panddas_directory, "rejected_datasets")) + for xtal in glob.glob("*"): + self.db.execute_statement( + "update mainTable set DimplePANDDAwasRun = 'True',DimplePANDDAreject = 'True',DimplePANDDApath='{0!s}',DimplePANDDAhit = 'False' where CrystalName is '{1!s}'".format( + self.panddas_directory, xtal + ) + ) except OSError: pass site_list = [] pandda_hit_list = [] - with open(os.path.join(self.panddas_directory, 'analyses', 'pandda_inspect_sites.csv'), 'rb') as csv_import: + with open( + os.path.join( + self.panddas_directory, "analyses", "pandda_inspect_sites.csv" + ), + "rb", + ) as csv_import: csv_dict = csv.DictReader(csv_import) - self.Logfile.insert('reding pandda_inspect_sites.csv') + self.Logfile.insert("reding pandda_inspect_sites.csv") for i, line in enumerate(csv_dict): - self.Logfile.insert(str(line).replace( - '\n', '').replace('\r', '')) - site_index = line['site_idx'] - name = line['Name'].replace("'", "") - comment = line['Comment'] + self.Logfile.insert(str(line).replace("\n", "").replace("\r", "")) + site_index = line["site_idx"] + name = line["Name"].replace("'", "") + comment = line["Comment"] site_list.append([site_index, name, comment]) - self.Logfile.insert('add to site_list_:' + - str([site_index, name, comment])) + self.Logfile.insert( + "add to site_list_:" + str([site_index, name, comment]) + ) progress_step = 1 - for i, line in enumerate(open(os.path.join(self.panddas_directory, 'analyses', 'pandda_inspect_events.csv'))): + for i, line in enumerate( + open( + os.path.join( + self.panddas_directory, "analyses", "pandda_inspect_events.csv" + ) + ) + ): n_lines = i if n_lines != 0: - progress_step = 100/float(n_lines) + progress_step = 100 / float(n_lines) else: progress_step = 0 progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) - self.Logfile.insert('reading '+os.path.join(self.panddas_directory, - 'analyses', 'pandda_inspect_events.csv')) - with open(os.path.join(self.panddas_directory, 'analyses', 'pandda_inspect_events.csv'), 'rb') as csv_import: + self.Logfile.insert( + "reading " + + os.path.join( + self.panddas_directory, "analyses", "pandda_inspect_events.csv" + ) + ) + with open( + os.path.join( + self.panddas_directory, "analyses", "pandda_inspect_events.csv" + ), + "rb", + ) as csv_import: csv_dict = csv.DictReader(csv_import) for i, line in enumerate(csv_dict): db_dict = {} - sampleID = line['dtag'] + sampleID = line["dtag"] if sampleID not in samples_to_export: self.Logfile.warning( - '%s: not to be exported; will not add to panddaTable...' % sampleID) + "%s: not to be exported; will not add to panddaTable..." + % sampleID + ) continue if sampleID not in pandda_hit_list: pandda_hit_list.append(sampleID) - site_index = str(line['site_idx']).replace('.0', '') - event_index = str(line['event_idx']).replace('.0', '') + site_index = str(line["site_idx"]).replace(".0", "") + event_index = str(line["event_idx"]).replace(".0", "") self.Logfile.insert(str(line)) self.Logfile.insert( - 'reading {0!s} -> site {1!s} -> event {2!s}'.format(sampleID, site_index, event_index)) + "reading {0!s} -> site {1!s} -> event {2!s}".format( + sampleID, site_index, event_index + ) + ) for entry in site_list: if entry[0] == site_index: @@ -711,53 +1042,63 @@ def import_samples_into_datasouce(self, samples_to_export): break # check if EVENT map exists in project directory - event_map = '' - for file in glob.glob(os.path.join(self.initial_model_directory, sampleID, '*ccp4')): - filename = file[file.rfind('/')+1:] - if filename.startswith(sampleID+'-event_'+event_index) and filename.endswith('map.native.ccp4'): + event_map = "" + for file in glob.glob( + os.path.join(self.initial_model_directory, sampleID, "*ccp4") + ): + filename = file[file.rfind("/") + 1 :] + if filename.startswith( + sampleID + "-event_" + event_index + ) and filename.endswith("map.native.ccp4"): event_map = file - self.Logfile.insert('found respective event maps in {0!s}: {1!s}'.format( - self.initial_model_directory, event_map)) + self.Logfile.insert( + "found respective event maps in {0!s}: {1!s}".format( + self.initial_model_directory, event_map + ) + ) break # initial pandda model and mtz file - pandda_model = '' - for file in glob.glob(os.path.join(self.initial_model_directory, sampleID, '*pdb')): - filename = file[file.rfind('/')+1:] - if filename.endswith('-ensemble-model.pdb'): + pandda_model = "" + for file in glob.glob( + os.path.join(self.initial_model_directory, sampleID, "*pdb") + ): + filename = file[file.rfind("/") + 1 :] + if filename.endswith("-ensemble-model.pdb"): pandda_model = file if sampleID not in self.already_exported_models: self.already_exported_models.append(sampleID) break - inital_mtz = '' - for file in glob.glob(os.path.join(self.initial_model_directory, sampleID, '*mtz')): - filename = file[file.rfind('/')+1:] - if filename.endswith('pandda-input.mtz'): + inital_mtz = "" + for file in glob.glob( + os.path.join(self.initial_model_directory, sampleID, "*mtz") + ): + filename = file[file.rfind("/") + 1 :] + if filename.endswith("pandda-input.mtz"): inital_mtz = file break - db_dict['CrystalName'] = sampleID - db_dict['PANDDApath'] = self.panddas_directory - db_dict['PANDDA_site_index'] = site_index - db_dict['PANDDA_site_name'] = site_name - db_dict['PANDDA_site_comment'] = site_comment - db_dict['PANDDA_site_event_index'] = event_index - db_dict['PANDDA_site_event_comment'] = line['Comment'].replace( - "'", "") - db_dict['PANDDA_site_confidence'] = line['Ligand Confidence'] - db_dict['PANDDA_site_InspectConfidence'] = line['Ligand Confidence'] - db_dict['PANDDA_site_ligand_placed'] = line['Ligand Placed'] - db_dict['PANDDA_site_viewed'] = line['Viewed'] - db_dict['PANDDA_site_interesting'] = line['Interesting'] - db_dict['PANDDA_site_z_peak'] = line['z_peak'] - db_dict['PANDDA_site_x'] = line['x'] - db_dict['PANDDA_site_y'] = line['y'] - db_dict['PANDDA_site_z'] = line['z'] - db_dict['PANDDA_site_ligand_id'] = '' - db_dict['PANDDA_site_event_map'] = event_map - db_dict['PANDDA_site_initial_model'] = pandda_model - db_dict['PANDDA_site_initial_mtz'] = inital_mtz - db_dict['PANDDA_site_spider_plot'] = '' + db_dict["CrystalName"] = sampleID + db_dict["PANDDApath"] = self.panddas_directory + db_dict["PANDDA_site_index"] = site_index + db_dict["PANDDA_site_name"] = site_name + db_dict["PANDDA_site_comment"] = site_comment + db_dict["PANDDA_site_event_index"] = event_index + db_dict["PANDDA_site_event_comment"] = line["Comment"].replace("'", "") + db_dict["PANDDA_site_confidence"] = line["Ligand Confidence"] + db_dict["PANDDA_site_InspectConfidence"] = line["Ligand Confidence"] + db_dict["PANDDA_site_ligand_placed"] = line["Ligand Placed"] + db_dict["PANDDA_site_viewed"] = line["Viewed"] + db_dict["PANDDA_site_interesting"] = line["Interesting"] + db_dict["PANDDA_site_z_peak"] = line["z_peak"] + db_dict["PANDDA_site_x"] = line["x"] + db_dict["PANDDA_site_y"] = line["y"] + db_dict["PANDDA_site_z"] = line["z"] + db_dict["PANDDA_site_ligand_id"] = "" + db_dict["PANDDA_site_event_map"] = event_map + db_dict["PANDDA_site_initial_model"] = pandda_model + db_dict["PANDDA_site_initial_mtz"] = inital_mtz + db_dict["PANDDA_site_spider_plot"] = "" # find apo structures which were used # XXX missing XXX @@ -766,195 +1107,251 @@ def import_samples_into_datasouce(self, samples_to_export): # this is necessary, otherwise RefinementOutcome will be reset for samples that are actually already in refinement self.db.execute_statement( - "update panddaTable set RefinementOutcome = '2 - PANDDA model' where CrystalName is '{0!s}' and RefinementOutcome is null".format(sampleID)) + "update panddaTable set RefinementOutcome = '2 - PANDDA model' where CrystalName is '{0!s}' and RefinementOutcome is null".format( + sampleID + ) + ) self.db.execute_statement( - "update mainTable set RefinementOutcome = '2 - PANDDA model' where CrystalName is '{0!s}' and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending')".format(sampleID)) + "update mainTable set RefinementOutcome = '2 - PANDDA model' where CrystalName is '{0!s}' and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending')".format( + sampleID + ) + ) self.db.execute_statement( - "update mainTable set DimplePANDDAhit = 'True' where CrystalName is '{0!s}'".format(sampleID)) + "update mainTable set DimplePANDDAhit = 'True' where CrystalName is '{0!s}'".format( + sampleID + ) + ) progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) - self.Logfile.insert('done reading pandda_inspect_sites.csv') + self.Logfile.insert("done reading pandda_inspect_sites.csv") # finally find all samples which do not have a pandda hit - os.chdir(os.path.join(self.panddas_directory, 'processed_datasets')) - self.Logfile.insert('check which datasets are not interesting') + os.chdir(os.path.join(self.panddas_directory, "processed_datasets")) + self.Logfile.insert("check which datasets are not interesting") # DimplePANDDAhit -# for xtal in glob.glob('*'): -# if xtal not in pandda_hit_list: -# self.Logfile.insert(xtal+': not in interesting_datasets; updating database...') -# self.db.execute_statement("update mainTable set DimplePANDDAhit = 'False' where CrystalName is '{0!s}'".format(xtal)) + + # for xtal in glob.glob('*'): + # if xtal not in pandda_hit_list: + # self.Logfile.insert(xtal+': not in interesting_datasets; updating database...') + # self.db.execute_statement("update mainTable set DimplePANDDAhit = 'False' where CrystalName is '{0!s}'".format(xtal)) def export_models(self): - self.Logfile.insert( - 'finding out which PanDDA models need to be exported') + self.Logfile.insert("finding out which PanDDA models need to be exported") # first find which samples are in interesting datasets and have a model # and determine the timestamp fileModelsDict = {} - queryModels = '' - for model in glob.glob(os.path.join(self.panddas_directory, 'processed_datasets', '*', 'modelled_structures', '*-pandda-model.pdb')): - sample = model[model.rfind( - '/')+1:].replace('-pandda-model.pdb', '') - timestamp = datetime.fromtimestamp( - os.path.getmtime(model)).strftime('%Y-%m-%d %H:%M:%S') + queryModels = "" + for model in glob.glob( + os.path.join( + self.panddas_directory, + "processed_datasets", + "*", + "modelled_structures", + "*-pandda-model.pdb", + ) + ): + sample = model[model.rfind("/") + 1 :].replace("-pandda-model.pdb", "") + timestamp = datetime.fromtimestamp(os.path.getmtime(model)).strftime( + "%Y-%m-%d %H:%M:%S" + ) self.Logfile.insert( - sample+'-pandda-model.pdb was created on '+str(timestamp)) - queryModels += "'"+sample+"'," + sample + "-pandda-model.pdb was created on " + str(timestamp) + ) + queryModels += "'" + sample + "'," fileModelsDict[sample] = timestamp # now get these models from the database and compare the datestamps # Note: only get the models that underwent some form of refinement, # because only if the model was updated in pandda.inspect will it be exported and refined dbModelsDict = {} - if queryModels != '': - dbEntries = self.db.execute_statement("select CrystalName,DatePanDDAModelCreated from mainTable where CrystalName in (" + - queryModels[:-1]+") and (RefinementOutcome like '3%' or RefinementOutcome like '4%' or RefinementOutcome like '5%')") + if queryModels != "": + dbEntries = self.db.execute_statement( + "select CrystalName,DatePanDDAModelCreated from mainTable where CrystalName in (" + + queryModels[:-1] + + ") and (RefinementOutcome like '3%' or RefinementOutcome like '4%' or RefinementOutcome like '5%')" + ) for item in dbEntries: xtal = str(item[0]) timestamp = str(item[1]) dbModelsDict[xtal] = timestamp self.Logfile.insert( - 'PanDDA model for '+xtal+' is in database and was created on '+str(timestamp)) + "PanDDA model for " + + xtal + + " is in database and was created on " + + str(timestamp) + ) # compare timestamps and only export the ones where the timestamp of the file is newer than the one in the DB samples_to_export = {} self.Logfile.insert( - 'checking which PanDDA models were newly created or updated') - if self.which_models == 'all': - self.Logfile.insert( - 'Note: you chose to export ALL available PanDDA!') + "checking which PanDDA models were newly created or updated" + ) + if self.which_models == "all": + self.Logfile.insert("Note: you chose to export ALL available PanDDA!") for sample in fileModelsDict: - if self.which_models == 'all': - self.Logfile.insert('exporting '+sample) + if self.which_models == "all": + self.Logfile.insert("exporting " + sample) samples_to_export[sample] = fileModelsDict[sample] - elif self.which_models == 'selected': + elif self.which_models == "selected": for i in range(0, self.pandda_analyse_data_table.rowCount()): if str(self.pandda_analyse_data_table.item(i, 0).text()) == sample: if self.pandda_analyse_data_table.cellWidget(i, 1).isChecked(): self.Logfile.insert( - 'Dataset selected by user -> exporting '+sample) + "Dataset selected by user -> exporting " + sample + ) samples_to_export[sample] = fileModelsDict[sample] break else: if sample in dbModelsDict: try: - difference = (datetime.strptime( - fileModelsDict[sample], '%Y-%m-%d %H:%M:%S') - datetime.strptime(dbModelsDict[sample], '%Y-%m-%d %H:%M:%S')) + difference = datetime.strptime( + fileModelsDict[sample], "%Y-%m-%d %H:%M:%S" + ) - datetime.strptime(dbModelsDict[sample], "%Y-%m-%d %H:%M:%S") if difference.seconds != 0: self.Logfile.insert( - 'exporting '+sample+' -> was already refined, but newer PanDDA model available') + "exporting " + + sample + + " -> was already refined, but newer PanDDA model available" + ) samples_to_export[sample] = fileModelsDict[sample] except ValueError: # this will be raised if timestamp is not properly formatted; # which will usually be the case when respective field in database is blank # these are hopefully legacy cases which are from before this extensive check was introduced (13/01/2017) - advice = ('The pandda model of '+xtal+' was changed, but it was already refined! ' - 'This is most likely because this was done with an older version of XCE. ' - 'If you really want to export and refine this model, you need to open the database ' - 'with DBbroweser (sqlitebrowser.org); then change the RefinementOutcome field ' - 'of the respective sample to "2 - PANDDA model", save the database and repeat the export prodedure.') + advice = ( + "The pandda model of " + + xtal + + " was changed, but it was already refined! " + "This is most likely because this was done with an older version of XCE. " + "If you really want to export and refine this model, you need to open the database " + "with DBbroweser (sqlitebrowser.org); then change the RefinementOutcome field " + 'of the respective sample to "2 - PANDDA model", save the database and repeat the export prodedure.' + ) self.Logfile.insert(advice) else: self.Logfile.insert( - 'exporting '+sample+' -> first time to be exported and refined') + "exporting " + + sample + + " -> first time to be exported and refined" + ) samples_to_export[sample] = fileModelsDict[sample] # update the DB: # set timestamp to current timestamp of file and set RefinementOutcome to '2-pandda...' if samples_to_export != {}: - select_dir_string = '' - select_dir_string_new_pannda = ' ' + select_dir_string = "" + select_dir_string_new_pannda = " " for sample in samples_to_export: - db_dict = {'RefinementOutcome': '2 - PANDDA model', - 'DatePanDDAModelCreated': samples_to_export[sample]} + db_dict = { + "RefinementOutcome": "2 - PANDDA model", + "DatePanDDAModelCreated": samples_to_export[sample], + } select_dir_string += "select_dir={0!s} ".format(sample) - select_dir_string_new_pannda += '{0!s} '.format(sample) - self.Logfile.insert('updating database for '+sample+' setting time model was created to ' + - db_dict['DatePanDDAModelCreated']+' and RefinementOutcome to '+db_dict['RefinementOutcome']) + select_dir_string_new_pannda += "{0!s} ".format(sample) + self.Logfile.insert( + "updating database for " + + sample + + " setting time model was created to " + + db_dict["DatePanDDAModelCreated"] + + " and RefinementOutcome to " + + db_dict["RefinementOutcome"] + ) self.db.update_data_source(sample, db_dict) - if os.path.isdir(os.path.join(self.panddas_directory, 'rejected_datasets')): + if os.path.isdir(os.path.join(self.panddas_directory, "rejected_datasets")): Cmds = ( - - 'pandda.export' - ' pandda_dir=%s' % self.panddas_directory + - ' export_dir={0!s}'.format(self.initial_model_directory) + - ' {0!s}'.format(select_dir_string) + - ' export_ligands=False' - ' generate_occupancy_groupings=True\n' + "pandda.export" + " pandda_dir=%s" % self.panddas_directory + + " export_dir={0!s}".format(self.initial_model_directory) + + " {0!s}".format(select_dir_string) + + " export_ligands=False" + " generate_occupancy_groupings=True\n" ) else: Cmds = ( - 'module load ccp4/7.1.016\n' + "module load ccp4/7.1.016\n" # 'source /dls/science/groups/i04-1/software/pandda-update/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' # 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' - 'pandda.export' - ' pandda_dir=%s' % self.panddas_directory + - ' export_dir={0!s}'.format(self.initial_model_directory) + - ' {0!s}'.format(select_dir_string_new_pannda) + - ' generate_restraints=True\n' + "pandda.export" + " pandda_dir=%s" % self.panddas_directory + + " export_dir={0!s}".format(self.initial_model_directory) + + " {0!s}".format(select_dir_string_new_pannda) + + " generate_restraints=True\n" ) self.Logfile.insert( - 'running pandda.export with the following settings:\n'+Cmds) + "running pandda.export with the following settings:\n" + Cmds + ) os.system(Cmds) return samples_to_export class run_pandda_analyse(QtCore.QThread): - def __init__(self, pandda_params, xce_logfile, datasource): QtCore.QThread.__init__(self) - self.data_directory = pandda_params['data_dir'] - self.panddas_directory = pandda_params['out_dir'] - self.submit_mode = pandda_params['submit_mode'] - - self.pandda_analyse_data_table = pandda_params['pandda_table'] - self.nproc = pandda_params['nproc'] - self.min_build_datasets = pandda_params['min_build_datasets'] - self.pdb_style = pandda_params['pdb_style'] - self.mtz_style = pandda_params['mtz_style'] - self.sort_event = pandda_params['sort_event'] - self.number_of_datasets = pandda_params['N_datasets'] - self.max_new_datasets = pandda_params['max_new_datasets'] - self.grid_spacing = pandda_params['grid_spacing'] - self.reference_dir = pandda_params['reference_dir'] - self.filter_pdb = os.path.join( - self.reference_dir, pandda_params['filter_pdb']) - self.wilson_scaling = pandda_params['perform_diffraction_data_scaling'] + self.data_directory = pandda_params["data_dir"] + self.panddas_directory = pandda_params["out_dir"] + self.submit_mode = pandda_params["submit_mode"] + + self.pandda_analyse_data_table = pandda_params["pandda_table"] + self.nproc = pandda_params["nproc"] + self.min_build_datasets = pandda_params["min_build_datasets"] + self.pdb_style = pandda_params["pdb_style"] + self.mtz_style = pandda_params["mtz_style"] + self.sort_event = pandda_params["sort_event"] + self.number_of_datasets = pandda_params["N_datasets"] + self.max_new_datasets = pandda_params["max_new_datasets"] + self.grid_spacing = pandda_params["grid_spacing"] + self.reference_dir = pandda_params["reference_dir"] + self.filter_pdb = os.path.join(self.reference_dir, pandda_params["filter_pdb"]) + self.wilson_scaling = pandda_params["perform_diffraction_data_scaling"] self.Logfile = XChemLog.updateLog(xce_logfile) self.datasource = datasource self.db = XChemDB.data_source(datasource) - self.appendix = pandda_params['appendix'] - self.write_mean_maps = pandda_params['write_mean_map'] - self.calc_map_by = pandda_params['average_map'] - self.select_ground_state_model = '' - projectDir = self.data_directory.replace('/*', '') - self.make_ligand_links = '$CCP4/bin/ccp4-python %s %s %s\n' % (os.path.join(os.getenv('XChemExplorer_DIR'), - 'helpers', - 'make_ligand_links_after_pandda.py'), projectDir, self.panddas_directory) - self.use_remote = pandda_params['use_remote'] - self.remote_string = pandda_params['remote_string'] - - if self.appendix != '': + self.appendix = pandda_params["appendix"] + self.write_mean_maps = pandda_params["write_mean_map"] + self.calc_map_by = pandda_params["average_map"] + self.select_ground_state_model = "" + projectDir = self.data_directory.replace("/*", "") + self.make_ligand_links = "$CCP4/bin/ccp4-python %s %s %s\n" % ( + os.path.join( + os.getenv("XChemExplorer_DIR"), + "helpers", + "make_ligand_links_after_pandda.py", + ), + projectDir, + self.panddas_directory, + ) + self.use_remote = pandda_params["use_remote"] + self.remote_string = pandda_params["remote_string"] + + if self.appendix != "": self.panddas_directory = os.path.join( - self.reference_dir, 'pandda_'+self.appendix) + self.reference_dir, "pandda_" + self.appendix + ) if os.path.isdir(self.panddas_directory): - os.system('/bin/rm -fr %s' % self.panddas_directory) + os.system("/bin/rm -fr %s" % self.panddas_directory) os.mkdir(self.panddas_directory) - if self.data_directory.startswith('/dls'): - self.select_ground_state_model = 'module load ccp4/7.1.018\n' - self.select_ground_state_model += '$CCP4/bin/ccp4-python %s %s\n' % (os.path.join(os.getenv( - 'XChemExplorer_DIR'), 'helpers', 'select_ground_state_dataset.py'), self.panddas_directory) - self.make_ligand_links = '' + if self.data_directory.startswith("/dls"): + self.select_ground_state_model = "module load ccp4/7.1.018\n" + self.select_ground_state_model += "$CCP4/bin/ccp4-python %s %s\n" % ( + os.path.join( + os.getenv("XChemExplorer_DIR"), + "helpers", + "select_ground_state_dataset.py", + ), + self.panddas_directory, + ) + self.make_ligand_links = "" def run(self): @@ -974,23 +1371,27 @@ def run(self): # # 3) Repeat 2) until you don't add any "new" datasets. Then you can build the models as normal. - number_of_cyles = int(self.number_of_datasets) / \ - int(self.max_new_datasets) + number_of_cyles = int(self.number_of_datasets) / int(self.max_new_datasets) # modulo gives remainder after integer division if int(self.number_of_datasets) % int(self.max_new_datasets) != 0: number_of_cyles += 1 self.Logfile.insert( - 'will run %s rounds of pandda.analyse' % str(number_of_cyles)) + "will run %s rounds of pandda.analyse" % str(number_of_cyles) + ) - if os.path.isfile(os.path.join(self.panddas_directory, 'pandda.running')): + if os.path.isfile(os.path.join(self.panddas_directory, "pandda.running")): self.Logfile.insert( - 'it looks as if a pandda.analyse job is currently running in: '+self.panddas_directory) - msg = ('there are three possibilities:\n' - '1.) choose another PANDDA directory\n' - '2.) - check if the job is really running either on the cluster (qstat) or on your local machine\n' - ' - if so, be patient and wait until the job has finished\n' - '3.) same as 2., but instead of waiting, kill the job and remove at least the pandda.running file\n' - ' (or all the contents in the directory if you want to start from scratch)\n') + "it looks as if a pandda.analyse job is currently running in: " + + self.panddas_directory + ) + msg = ( + "there are three possibilities:\n" + "1.) choose another PANDDA directory\n" + "2.) - check if the job is really running either on the cluster (qstat) or on your local machine\n" + " - if so, be patient and wait until the job has finished\n" + "3.) same as 2., but instead of waiting, kill the job and remove at least the pandda.running file\n" + " (or all the contents in the directory if you want to start from scratch)\n" + ) self.Logfile.insert(msg) return None else: @@ -1004,51 +1405,59 @@ def run(self): # v1.2.1 - pandda.setup files should be obsolete now that pandda is part of ccp4 # 08/10/2020 - pandda v0.2.12 installation at DLS is obsolete # source_file='source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' - source_file = '' - source_file += 'export XChemExplorer_DIR="' + \ - os.getenv('XChemExplorer_DIR') + '"\n' - - if os.path.isfile(self.filter_pdb + '.pdb'): - print('filter pdb located') - filter_pdb = ' filter.pdb='+self.filter_pdb+'.pdb' - print(('will use ' + filter_pdb + - 'as a filter for pandda.analyse')) + source_file = "" + source_file += ( + 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"\n' + ) + + if os.path.isfile(self.filter_pdb + ".pdb"): + print("filter pdb located") + filter_pdb = " filter.pdb=" + self.filter_pdb + ".pdb" + print(("will use " + filter_pdb + "as a filter for pandda.analyse")) else: if self.use_remote: stat_command = self.remote_string.replace( - "qsub'", str('stat ' + self.filter_pdb + "'")) + "qsub'", str("stat " + self.filter_pdb + "'") + ) output = subprocess.Popen( - stat_command, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) + stat_command, + shell=True, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) out, err = output.communicate() - if 'cannot stat' in out: - filter_pdb = '' + if "cannot stat" in out: + filter_pdb = "" else: - filter_pdb = ' filter.pdb=' + self.filter_pdb + '.pdb' + filter_pdb = " filter.pdb=" + self.filter_pdb + ".pdb" else: - filter_pdb = '' + filter_pdb = "" os.chdir(self.panddas_directory) # note: copied latest pandda.setup-sh from XCE2 installation (08/08/2017) - dls = '' - if self.data_directory.startswith('/dls'): + dls = "" + if self.data_directory.startswith("/dls"): dls = ( - source_file + - '\n' - 'module load pymol/1.8.2.0\n' - '\n' - 'module load ccp4/7.0.072\n' - '\n' + source_file + "\n" + "module load pymol/1.8.2.0\n" + "\n" + "module load ccp4/7.0.072\n" + "\n" ) Cmds = ( - '#!'+os.getenv('SHELL')+'\n' + - '\n' + - dls + - 'cd ' + self.panddas_directory + '\n' + - '\n' + "#!" + + os.getenv("SHELL") + + "\n" + + "\n" + + dls + + "cd " + + self.panddas_directory + + "\n" + + "\n" ) ignore = [] @@ -1056,29 +1465,25 @@ def run(self): zmap = [] for i in range(0, self.pandda_analyse_data_table.rowCount()): - ignore_all_checkbox = self.pandda_analyse_data_table.cellWidget( - i, 7) - ignore_characterisation_checkbox = self.pandda_analyse_data_table.cellWidget( - i, 8) - ignore_zmap_checkbox = self.pandda_analyse_data_table.cellWidget( - i, 9) + ignore_all_checkbox = self.pandda_analyse_data_table.cellWidget(i, 7) + ignore_characterisation_checkbox = ( + self.pandda_analyse_data_table.cellWidget(i, 8) + ) + ignore_zmap_checkbox = self.pandda_analyse_data_table.cellWidget(i, 9) if ignore_all_checkbox.isChecked(): - ignore.append( - str(self.pandda_analyse_data_table.item(i, 0).text())) + ignore.append(str(self.pandda_analyse_data_table.item(i, 0).text())) if ignore_characterisation_checkbox.isChecked(): - char.append( - str(self.pandda_analyse_data_table.item(i, 0).text())) + char.append(str(self.pandda_analyse_data_table.item(i, 0).text())) if ignore_zmap_checkbox.isChecked(): - zmap.append( - str(self.pandda_analyse_data_table.item(i, 0).text())) + zmap.append(str(self.pandda_analyse_data_table.item(i, 0).text())) def append_to_ignore_string(datasets_list, append_string): if len(datasets_list) == 0: - append_string = '' + append_string = "" for i in range(0, len(datasets_list)): - if i < len(datasets_list)-1: - append_string += str(datasets_list[i] + ',') + if i < len(datasets_list) - 1: + append_string += str(datasets_list[i] + ",") else: append_string += str(datasets_list[i] + '"') print(append_string) @@ -1095,290 +1500,378 @@ def append_to_ignore_string(datasets_list, append_string): for i in range(number_of_cyles): Cmds += ( - 'pandda.analyse ' + - ' data_dirs="'+self.data_directory.replace('/*', '')+'/*"' + - ' out_dir="'+self.panddas_directory+'"' - ' min_build_datasets='+self.min_build_datasets + - ' max_new_datasets='+self.max_new_datasets + - ' grid_spacing='+self.grid_spacing + - ' cpus='+self.nproc + - ' events.order_by='+self.sort_event + - filter_pdb + - ' pdb_style='+self.pdb_style + - ' mtz_style='+self.mtz_style + - ' lig_style=/compound/*.cif' + - ' apply_b_factor_scaling='+self.wilson_scaling + - ' write_average_map='+self.write_mean_maps + - ' average_map=' + self.calc_map_by + - ' ' + - ignore_string + ' ' + - char_string + ' ' + - zmap_string + ' ' + - '\n' + "pandda.analyse " + + ' data_dirs="' + + self.data_directory.replace("/*", "") + + '/*"' + + ' out_dir="' + + self.panddas_directory + + '"' + " min_build_datasets=" + + self.min_build_datasets + + " max_new_datasets=" + + self.max_new_datasets + + " grid_spacing=" + + self.grid_spacing + + " cpus=" + + self.nproc + + " events.order_by=" + + self.sort_event + + filter_pdb + + " pdb_style=" + + self.pdb_style + + " mtz_style=" + + self.mtz_style + + " lig_style=/compound/*.cif" + + " apply_b_factor_scaling=" + + self.wilson_scaling + + " write_average_map=" + + self.write_mean_maps + + " average_map=" + + self.calc_map_by + + " " + + ignore_string + + " " + + char_string + + " " + + zmap_string + + " " + + "\n" ) Cmds += self.select_ground_state_model Cmds += self.make_ligand_links - Cmds += '\n' + Cmds += "\n" - data_dir_string = self.data_directory.replace('/*', '') + data_dir_string = self.data_directory.replace("/*", "") Cmds += str( - 'find ' + data_dir_string + - '/*/compound -name "*.cif" | while read line; do echo ${line//"' + - data_dir_string + '"/"' + self.panddas_directory + - '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' - 'done; done;') + "find " + + data_dir_string + + '/*/compound -name "*.cif" | while read line; do echo ${line//"' + + data_dir_string + + '"/"' + + self.panddas_directory + + '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' + "done; done;" + ) - Cmds += '\n' + Cmds += "\n" Cmds += str( - 'find ' + data_dir_string + - '/*/compound -name "*.pdb" | while read line; do echo ${line//"' + - data_dir_string + '"/"' + self.panddas_directory + - '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' - 'done; done;') + "find " + + data_dir_string + + '/*/compound -name "*.pdb" | while read line; do echo ${line//"' + + data_dir_string + + '"/"' + + self.panddas_directory + + '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' + "done; done;" + ) self.Logfile.insert( - 'running pandda.analyse with the following command:\n'+Cmds) + "running pandda.analyse with the following command:\n" + Cmds + ) - f = open('pandda.sh', 'w') + f = open("pandda.sh", "w") f.write(Cmds) f.close() -# #>>> for testing -# self.submit_mode='local machine' + # #>>> for testing + # self.submit_mode='local machine' self.Logfile.insert( - 'trying to run pandda.analyse on ' + str(self.submit_mode)) + "trying to run pandda.analyse on " + str(self.submit_mode) + ) - if self.submit_mode == 'local machine': - self.Logfile.insert('running PANDDA on local machine') - os.system('chmod +x pandda.sh') - os.system('./pandda.sh &') + if self.submit_mode == "local machine": + self.Logfile.insert("running PANDDA on local machine") + os.system("chmod +x pandda.sh") + os.system("./pandda.sh &") elif self.use_remote: # handles remote submission of pandda.analyse jobs - submission_string = self.remote_string.replace("qsub'", - str('cd ' + - self.panddas_directory + - '; ' + - "qsub -P labxchem -q medium.q -N pandda 5 -l exclusive,m_mem_free=100G pandda.sh'")) + submission_string = self.remote_string.replace( + "qsub'", + str( + "cd " + + self.panddas_directory + + "; " + + "qsub -P labxchem -q medium.q -N pandda 5 -l exclusive,m_mem_free=100G pandda.sh'" + ), + ) os.system(submission_string) self.Logfile.insert( - str('running PANDDA remotely, using: ' + submission_string)) + str("running PANDDA remotely, using: " + submission_string) + ) else: - self.Logfile.insert('running PANDDA on cluster, using qsub...') + self.Logfile.insert("running PANDDA on cluster, using qsub...") os.system( - 'qsub -P labxchem -q medium.q -N pandda -l exclusive,m_mem_free=100G pandda.sh') + "qsub -P labxchem -q medium.q -N pandda -l exclusive,m_mem_free=100G pandda.sh" + ) - self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) + self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) class run_pandda_two_analyse(QtCore.QThread): - def __init__(self, pandda_params, xce_logfile, datasource): QtCore.QThread.__init__(self) - self.data_directory = pandda_params['data_dir'] - self.panddas_directory = pandda_params['out_dir'] - self.submit_mode = pandda_params['submit_mode'] - - self.pandda_analyse_data_table = pandda_params['pandda_table'] - self.nproc = pandda_params['nproc'] - self.min_build_datasets = pandda_params['min_build_datasets'] - self.pdb_style = pandda_params['pdb_style'] - self.mtz_style = pandda_params['mtz_style'] - self.sort_event = pandda_params['sort_event'] - self.number_of_datasets = pandda_params['N_datasets'] - self.max_new_datasets = pandda_params['max_new_datasets'] - self.grid_spacing = pandda_params['grid_spacing'] - self.keyword_arguments = pandda_params['keyword_arguments'] - self.reference_dir = pandda_params['reference_dir'] - self.filter_pdb = os.path.join( - self.reference_dir, pandda_params['filter_pdb']) - self.wilson_scaling = pandda_params['perform_diffraction_data_scaling'] + self.data_directory = pandda_params["data_dir"] + self.panddas_directory = pandda_params["out_dir"] + self.submit_mode = pandda_params["submit_mode"] + + self.pandda_analyse_data_table = pandda_params["pandda_table"] + self.nproc = pandda_params["nproc"] + self.min_build_datasets = pandda_params["min_build_datasets"] + self.pdb_style = pandda_params["pdb_style"] + self.mtz_style = pandda_params["mtz_style"] + self.sort_event = pandda_params["sort_event"] + self.number_of_datasets = pandda_params["N_datasets"] + self.max_new_datasets = pandda_params["max_new_datasets"] + self.grid_spacing = pandda_params["grid_spacing"] + self.keyword_arguments = pandda_params["keyword_arguments"] + self.reference_dir = pandda_params["reference_dir"] + self.filter_pdb = os.path.join(self.reference_dir, pandda_params["filter_pdb"]) + self.wilson_scaling = pandda_params["perform_diffraction_data_scaling"] self.Logfile = XChemLog.updateLog(xce_logfile) self.datasource = datasource self.db = XChemDB.data_source(datasource) - self.appendix = pandda_params['appendix'] - self.write_mean_maps = pandda_params['write_mean_map'] - self.calc_map_by = pandda_params['average_map'] - self.select_ground_state_model = '' + self.appendix = pandda_params["appendix"] + self.write_mean_maps = pandda_params["write_mean_map"] + self.calc_map_by = pandda_params["average_map"] + self.select_ground_state_model = "" def run(self): - if not self.data_directory.startswith('/dls'): - self.Logfile.error( - 'Sorry, you need to be at DLS for pandda2 to work!') + if not self.data_directory.startswith("/dls"): + self.Logfile.error("Sorry, you need to be at DLS for pandda2 to work!") return None os.chdir(self.panddas_directory) cmd = ( - '#/bin/sh\n' - 'module load ccp4\n' - 'module load phenix\n' - 'module load buster\n' - '__conda_setup="$(\'/dls/science/groups/i04-1/conor_dev/conda/anaconda/bin/conda\' \'shell.bash\' \'hook\' 2> /dev/null)"\n' - 'if [ $? -eq 0 ]; then\n' + "#/bin/sh\n" + "module load ccp4\n" + "module load phenix\n" + "module load buster\n" + "__conda_setup=\"$('/dls/science/groups/i04-1/conor_dev/conda/anaconda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)\"\n" + "if [ $? -eq 0 ]; then\n" ' eval "$__conda_setup"\n' - 'else\n' + "else\n" ' if [ -f "/dls/science/groups/i04-1/conor_dev/conda/anaconda/etc/profile.d/conda.sh" ]; then\n' ' . "/dls/science/groups/i04-1/conor_dev/conda/anaconda/etc/profile.d/conda.sh"\n' - ' else\n' + " else\n" ' export PATH="/dls/science/groups/i04-1/conor_dev/conda/anaconda/bin:$PATH"\n' - ' fi\n' - 'fi\n' - 'unset __conda_setup\n' + " fi\n" + "fi\n" + "unset __conda_setup\n" 'export PYTHONPATH=""\n' - 'conda activate pandda2_ray\n' - 'python -u /dls/science/groups/i04-1/conor_dev/pandda_2_gemmi/pandda_gemmi/analyse.py' - ' --data_dirs={0!s}'.format(self.data_directory.replace('/*', '')) + - ' --out_dir={0!s}'.format(self.panddas_directory) + - ' --pdb_regex="{0!s}" '.format(self.pdb_style) + - ' --mtz_regex="{0!s}" '.format(self.mtz_style) + - ' --autobuild=True ' + "conda activate pandda2_ray\n" + "python -u /dls/science/groups/i04-1/conor_dev/pandda_2_gemmi/pandda_gemmi/analyse.py" + " --data_dirs={0!s}".format(self.data_directory.replace("/*", "")) + + " --out_dir={0!s}".format(self.panddas_directory) + + ' --pdb_regex="{0!s}" '.format(self.pdb_style) + + ' --mtz_regex="{0!s}" '.format(self.mtz_style) + + " --autobuild=True " ' --global_processing="serial" ' - ' --local_cpus=6 ' + " --local_cpus=6 " ' --local_processing="ray" ' - ' --rank_method=autobuild ' + " --rank_method=autobuild " ' --comparison_strategy="hybrid" ' - ' --min_characterisation_datasets=25 ' - ' {0!s} '.format(self.keyword_arguments) + - ' --debug=True --memory_availability="low" | tee livelog_20220324_event_class_old_score\n' + " --min_characterisation_datasets=25 " + " {0!s} ".format(self.keyword_arguments) + + ' --debug=True --memory_availability="low" | tee livelog_20220324_event_class_old_score\n' ) self.Logfile.insert( - 'running pandda.analyse with the following command:\n' + cmd) + "running pandda.analyse with the following command:\n" + cmd + ) - f = open('pandda2.sh', 'w') + f = open("pandda2.sh", "w") f.write(cmd) f.close() - self.Logfile.warning('ignoring selected submission option') + self.Logfile.warning("ignoring selected submission option") - self.Logfile.insert('running PANDDA on cluster, using qsub...') + self.Logfile.insert("running PANDDA on cluster, using qsub...") os.system( - 'qsub -pe smp 6 -l m_mem_free=30G -q medium.q -o log.out -e log.err pandda2.sh') + "qsub -pe smp 6 -l m_mem_free=30G -q medium.q -o log.out -e log.err pandda2.sh" + ) - self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) + self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) class giant_cluster_datasets(QtCore.QThread): - - def __init__(self, initial_model_directory, pandda_params, xce_logfile, datasource,): + def __init__( + self, + initial_model_directory, + pandda_params, + xce_logfile, + datasource, + ): QtCore.QThread.__init__(self) - self.panddas_directory = pandda_params['out_dir'] - self.pdb_style = pandda_params['pdb_style'] - self.mtz_style = pandda_params['mtz_style'] + self.panddas_directory = pandda_params["out_dir"] + self.pdb_style = pandda_params["pdb_style"] + self.mtz_style = pandda_params["mtz_style"] self.Logfile = XChemLog.updateLog(xce_logfile) self.initial_model_directory = initial_model_directory self.db = XChemDB.data_source(datasource) def run(self): - self.emit(QtCore.SIGNAL('update_progress_bar'), 0) + self.emit(QtCore.SIGNAL("update_progress_bar"), 0) - if self.pdb_style.replace(' ', '') == '': - self.Logfile.insert('PDB style is not set in pandda.analyse!') - self.Logfile.insert('cannot start pandda.analyse') - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'PDB style is not set in pandda.analyse!') + if self.pdb_style.replace(" ", "") == "": + self.Logfile.insert("PDB style is not set in pandda.analyse!") + self.Logfile.insert("cannot start pandda.analyse") + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "PDB style is not set in pandda.analyse!", + ) return None - if self.mtz_style.replace(' ', '') == '': - self.Logfile.insert('MTZ style is not set in pandda.analyse!') - self.Logfile.insert('cannot start pandda.analyse') - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'MTZ style is not set in pandda.analyse!') + if self.mtz_style.replace(" ", "") == "": + self.Logfile.insert("MTZ style is not set in pandda.analyse!") + self.Logfile.insert("cannot start pandda.analyse") + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "MTZ style is not set in pandda.analyse!", + ) return None # 1.) prepare output directory os.chdir(self.panddas_directory) - if os.path.isdir('cluster_analysis'): - self.Logfile.insert('removing old cluster_analysis directory in {0!s}'.format( - self.panddas_directory)) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'removing old cluster_analysis directory in {0!s}'.format(self.panddas_directory)) - os.system('/bin/rm -fr cluster_analysis 2> /dev/null') + if os.path.isdir("cluster_analysis"): + self.Logfile.insert( + "removing old cluster_analysis directory in {0!s}".format( + self.panddas_directory + ) + ) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "removing old cluster_analysis directory in {0!s}".format( + self.panddas_directory + ), + ) + os.system("/bin/rm -fr cluster_analysis 2> /dev/null") self.Logfile.insert( - 'creating cluster_analysis directory in {0!s}'.format(self.panddas_directory)) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'creating cluster_analysis directory in {0!s}'.format(self.panddas_directory)) - os.mkdir('cluster_analysis') - self.emit(QtCore.SIGNAL('update_progress_bar'), 10) + "creating cluster_analysis directory in {0!s}".format( + self.panddas_directory + ) + ) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "creating cluster_analysis directory in {0!s}".format( + self.panddas_directory + ), + ) + os.mkdir("cluster_analysis") + self.emit(QtCore.SIGNAL("update_progress_bar"), 10) # 2.) go through project directory and make sure that all pdb files really exist # broken links derail the giant.cluster_mtzs_and_pdbs script - self.Logfile.insert('cleaning up broken links of {0!s} and {1!s} in {2!s}'.format( - self.pdb_style, self.mtz_style, self.initial_model_directory)) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'cleaning up broken links of {0!s} and {1!s} in {2!s}'.format( - self.pdb_style, self.mtz_style, self.initial_model_directory)) + self.Logfile.insert( + "cleaning up broken links of {0!s} and {1!s} in {2!s}".format( + self.pdb_style, self.mtz_style, self.initial_model_directory + ) + ) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "cleaning up broken links of {0!s} and {1!s} in {2!s}".format( + self.pdb_style, self.mtz_style, self.initial_model_directory + ), + ) os.chdir(self.initial_model_directory) - for xtal in glob.glob('*'): + for xtal in glob.glob("*"): if not os.path.isfile(os.path.join(xtal, self.pdb_style)): - self.Logfile.insert('missing {0!s} and {1!s} for {2!s}'.format( - self.pdb_style, self.mtz_style, xtal)) + self.Logfile.insert( + "missing {0!s} and {1!s} for {2!s}".format( + self.pdb_style, self.mtz_style, xtal + ) + ) os.system( - '/bin/rm {0!s}/{1!s} 2> /dev/null'.format(xtal, self.pdb_style)) + "/bin/rm {0!s}/{1!s} 2> /dev/null".format(xtal, self.pdb_style) + ) os.system( - '/bin/rm {0!s}/{1!s} 2> /dev/null'.format(xtal, self.mtz_style)) - self.emit(QtCore.SIGNAL('update_progress_bar'), 20) + "/bin/rm {0!s}/{1!s} 2> /dev/null".format(xtal, self.mtz_style) + ) + self.emit(QtCore.SIGNAL("update_progress_bar"), 20) # 3.) giant.cluster_mtzs_and_pdbs - self.Logfile.insert("running giant.cluster_mtzs_and_pdbs {0!s}/*/{1!s} pdb_regex='{2!s}/(.*)/{3!s}' out_dir='{4!s}/cluster_analysis'".format( - self.initial_model_directory, self.pdb_style, self.initial_model_directory, self.pdb_style, self.panddas_directory)) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'running giant.cluster_mtzs_and_pdbs') + self.Logfile.insert( + "running giant.cluster_mtzs_and_pdbs {0!s}/*/{1!s} pdb_regex='{2!s}/(.*)/{3!s}' out_dir='{4!s}/cluster_analysis'".format( + self.initial_model_directory, + self.pdb_style, + self.initial_model_directory, + self.pdb_style, + self.panddas_directory, + ) + ) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "running giant.cluster_mtzs_and_pdbs", + ) - if os.getenv('SHELL') == '/bin/tcsh' or os.getenv('SHELL') == '/bin/csh': + if os.getenv("SHELL") == "/bin/tcsh" or os.getenv("SHELL") == "/bin/csh": source_file = os.path.join( - os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-csh') - elif os.getenv('SHELL') == '/bin/bash': + os.getenv("XChemExplorer_DIR"), "setup-scripts", "pandda.setup-csh" + ) + elif os.getenv("SHELL") == "/bin/bash": source_file = os.path.join( - os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-sh') + os.getenv("XChemExplorer_DIR"), "setup-scripts", "pandda.setup-sh" + ) else: - source_file = '' + source_file = "" Cmds = ( - '#!'+os.getenv('SHELL')+'\n' - 'unset PYTHONPATH\n' - 'source '+source_file+'\n' - "giant.datasets.cluster %s/*/%s pdb_regex='%s/(.*)/%s' out_dir='%s/cluster_analysis'" % ( - self.initial_model_directory, self.pdb_style, self.initial_model_directory, self.pdb_style, self.panddas_directory) + "#!" + os.getenv("SHELL") + "\n" + "unset PYTHONPATH\n" + "source " + source_file + "\n" + "giant.datasets.cluster %s/*/%s pdb_regex='%s/(.*)/%s' out_dir='%s/cluster_analysis'" + % ( + self.initial_model_directory, + self.pdb_style, + self.initial_model_directory, + self.pdb_style, + self.panddas_directory, + ) ) -# os.system("giant.cluster_mtzs_and_pdbs %s/*/%s pdb_regex='%s/(.*)/%s' out_dir='%s/cluster_analysis'" %(self.initial_model_directory,self.pdb_style,self.initial_model_directory,self.pdb_style,self.panddas_directory)) + # os.system("giant.cluster_mtzs_and_pdbs %s/*/%s pdb_regex='%s/(.*)/%s' out_dir='%s/cluster_analysis'" %(self.initial_model_directory,self.pdb_style,self.initial_model_directory,self.pdb_style,self.panddas_directory)) os.system(Cmds) - self.emit(QtCore.SIGNAL('update_progress_bar'), 80) + self.emit(QtCore.SIGNAL("update_progress_bar"), 80) # 4.) analyse output self.Logfile.insert( - 'parsing {0!s}/cluster_analysis'.format(self.panddas_directory)) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'parsing {0!s}/cluster_analysis'.format(self.panddas_directory)) - os.chdir('{0!s}/cluster_analysis'.format(self.panddas_directory)) + "parsing {0!s}/cluster_analysis".format(self.panddas_directory) + ) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "parsing {0!s}/cluster_analysis".format(self.panddas_directory), + ) + os.chdir("{0!s}/cluster_analysis".format(self.panddas_directory)) cluster_dict = {} - for out_dir in sorted(glob.glob('*')): + for out_dir in sorted(glob.glob("*")): if os.path.isdir(out_dir): cluster_dict[out_dir] = [] - for folder in glob.glob(os.path.join(out_dir, 'pdbs', '*')): - xtal = folder[folder.rfind('/')+1:] + for folder in glob.glob(os.path.join(out_dir, "pdbs", "*")): + xtal = folder[folder.rfind("/") + 1 :] cluster_dict[out_dir].append(xtal) - self.emit(QtCore.SIGNAL('update_progress_bar'), 90) + self.emit(QtCore.SIGNAL("update_progress_bar"), 90) # 5.) update datasource self.Logfile.insert( - 'updating datasource with results from giant.cluster_mtzs_and_pdbs') + "updating datasource with results from giant.cluster_mtzs_and_pdbs" + ) if cluster_dict != {}: for key in cluster_dict: for xtal in cluster_dict[key]: - db_dict = {'CrystalFormName': key} + db_dict = {"CrystalFormName": key} self.db.update_data_source(xtal, db_dict) # 6.) finish - self.emit(QtCore.SIGNAL('update_progress_bar'), 100) - self.Logfile.insert('finished giant.cluster_mtzs_and_pdbs') - self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) + self.emit(QtCore.SIGNAL("update_progress_bar"), 100) + self.Logfile.insert("finished giant.cluster_mtzs_and_pdbs") + self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) class check_if_pandda_can_run: @@ -1390,12 +1883,12 @@ class check_if_pandda_can_run: # - map amplitude and phase labels don't exist def __init__(self, pandda_params, xce_logfile, datasource): - self.data_directory = pandda_params['data_dir'] - self.panddas_directory = pandda_params['out_dir'] - self.min_build_datasets = pandda_params['min_build_datasets'] - self.pdb_style = pandda_params['pdb_style'] - self.mtz_style = pandda_params['mtz_style'] - self.input_dir_structure = pandda_params['pandda_dir_structure'] + self.data_directory = pandda_params["data_dir"] + self.panddas_directory = pandda_params["out_dir"] + self.min_build_datasets = pandda_params["min_build_datasets"] + self.pdb_style = pandda_params["pdb_style"] + self.mtz_style = pandda_params["mtz_style"] + self.input_dir_structure = pandda_params["pandda_dir_structure"] self.problem_found = False self.error_code = -1 self.Logfile = XChemLog.updateLog(xce_logfile) @@ -1407,43 +1900,70 @@ def number_of_available_datasets(self): if os.path.isfile(file): counter += 1 self.Logfile.insert( - 'pandda.analyse: found {0!s} useable datasets'.format(counter)) + "pandda.analyse: found {0!s} useable datasets".format(counter) + ) return counter def get_first_dataset_in_project_directory(self): - first_dataset = '' + first_dataset = "" for file in glob.glob(os.path.join(self.input_dir_structure, self.pdb_style)): if os.path.isfile(file): first_dataset = file break return first_dataset - def compare_number_of_atoms_in_reference_vs_all_datasets(self, refData, dataset_list): + def compare_number_of_atoms_in_reference_vs_all_datasets( + self, refData, dataset_list + ): mismatched_datasets = [] pdbtools = XChemUtils.pdbtools(refData) - refPDB = refData[refData.rfind('/')+1:] + refPDB = refData[refData.rfind("/") + 1 :] refPDBlist = pdbtools.get_init_pdb_as_list() n_atom_ref = len(refPDBlist) for n_datasets, dataset in enumerate(dataset_list): - if os.path.isfile(os.path.join(self.data_directory.replace('*', ''), dataset, self.pdb_style)): - n_atom = len(pdbtools.get_pdb_as_list(os.path.join( - self.data_directory.replace('*', ''), dataset, self.pdb_style))) + if os.path.isfile( + os.path.join( + self.data_directory.replace("*", ""), dataset, self.pdb_style + ) + ): + n_atom = len( + pdbtools.get_pdb_as_list( + os.path.join( + self.data_directory.replace("*", ""), + dataset, + self.pdb_style, + ) + ) + ) if n_atom_ref == n_atom: - self.Logfile.insert('{0!s}: atoms in PDB file ({1!s}): {2!s}; atoms in Reference file: {3!s} ===> OK'.format( - dataset, self.pdb_style, str(n_atom), str(n_atom_ref))) + self.Logfile.insert( + "{0!s}: atoms in PDB file ({1!s}): {2!s}; atoms in Reference file: {3!s} ===> OK".format( + dataset, self.pdb_style, str(n_atom), str(n_atom_ref) + ) + ) if n_atom_ref != n_atom: - self.Logfile.insert('{0!s}: atoms in PDB file ({1!s}): {2!s}; atoms in Reference file: {3!s} ===> ERROR'.format( - dataset, self.pdb_style, str(n_atom), str(n_atom_ref))) + self.Logfile.insert( + "{0!s}: atoms in PDB file ({1!s}): {2!s}; atoms in Reference file: {3!s} ===> ERROR".format( + dataset, self.pdb_style, str(n_atom), str(n_atom_ref) + ) + ) mismatched_datasets.append(dataset) return n_datasets, mismatched_datasets - def get_datasets_which_fit_to_reference_file(self, ref, reference_directory, cluster_dict, allowed_unitcell_difference_percent): + def get_datasets_which_fit_to_reference_file( + self, + ref, + reference_directory, + cluster_dict, + allowed_unitcell_difference_percent, + ): refStructure = XChemUtils.pdbtools( - os.path.join(reference_directory, ref+'.pdb')) + os.path.join(reference_directory, ref + ".pdb") + ) symmRef = refStructure.get_spg_number_from_pdb() ucVolRef = refStructure.calc_unitcell_volume_from_pdb() cluster_dict[ref] = [] - cluster_dict[ref].append(os.path.join(reference_directory, ref+'.pdb')) + cluster_dict[ref].append(os.path.join(reference_directory, ref + ".pdb")) for dataset in glob.glob(os.path.join(self.data_directory, self.pdb_style)): datasetStructure = XChemUtils.pdbtools(dataset) symmDataset = datasetStructure.get_spg_number_from_pdb() @@ -1451,11 +1971,13 @@ def get_datasets_which_fit_to_reference_file(self, ref, reference_directory, clu if symmDataset == symmRef: try: - difference = math.fabs( - 1-(float(ucVolRef)/float(ucVolDataset)))*100 + difference = ( + math.fabs(1 - (float(ucVolRef) / float(ucVolDataset))) * 100 + ) if difference < allowed_unitcell_difference_percent: - sampleID = dataset.replace( - '/'+self.pdb_style, '')[dataset.replace('/'+self.pdb_style, '').rfind('/')+1:] + sampleID = dataset.replace("/" + self.pdb_style, "")[ + dataset.replace("/" + self.pdb_style, "").rfind("/") + 1 : + ] cluster_dict[ref].append(sampleID) except ZeroDivisionError: continue @@ -1464,22 +1986,40 @@ def get_datasets_which_fit_to_reference_file(self, ref, reference_directory, clu def remove_dimple_files(self, dataset_list): for n_datasets, dataset in enumerate(dataset_list): db_dict = {} - if os.path.isfile(os.path.join(self.data_directory.replace('*', ''), dataset, self.pdb_style)): + if os.path.isfile( + os.path.join( + self.data_directory.replace("*", ""), dataset, self.pdb_style + ) + ): os.system( - '/bin/rm '+os.path.join(self.data_directory.replace('*', ''), dataset, self.pdb_style)) + "/bin/rm " + + os.path.join( + self.data_directory.replace("*", ""), dataset, self.pdb_style + ) + ) self.Logfile.insert( - '{0!s}: removing {1!s}'.format(dataset, self.pdb_style)) - db_dict['DimplePathToPDB'] = '' - db_dict['DimpleRcryst'] = '' - db_dict['DimpleRfree'] = '' - db_dict['DimpleResolutionHigh'] = '' - db_dict['DimpleStatus'] = 'pending' - if os.path.isfile(os.path.join(self.data_directory.replace('*', ''), dataset, self.mtz_style)): + "{0!s}: removing {1!s}".format(dataset, self.pdb_style) + ) + db_dict["DimplePathToPDB"] = "" + db_dict["DimpleRcryst"] = "" + db_dict["DimpleRfree"] = "" + db_dict["DimpleResolutionHigh"] = "" + db_dict["DimpleStatus"] = "pending" + if os.path.isfile( + os.path.join( + self.data_directory.replace("*", ""), dataset, self.mtz_style + ) + ): os.system( - '/bin/rm '+os.path.join(self.data_directory.replace('*', ''), dataset, self.mtz_style)) + "/bin/rm " + + os.path.join( + self.data_directory.replace("*", ""), dataset, self.mtz_style + ) + ) self.Logfile.insert( - '{0!s}: removing {1!s}'.format(dataset, self.mtz_style)) - db_dict['DimplePathToMTZ'] = '' + "{0!s}: removing {1!s}".format(dataset, self.mtz_style) + ) + db_dict["DimplePathToMTZ"] = "" if db_dict != {}: self.db.update_data_source(dataset, db_dict) @@ -1516,19 +2056,18 @@ def analyse_min_build_dataset(self): return message def warning_messages(self): - message = '' + message = "" if self.error_code == 1: - message = 'PDB file does not exist' + message = "PDB file does not exist" if self.error_code == 2: - message = 'MTZ file does not exist' + message = "MTZ file does not exist" if self.error_code == 3: - message = 'Not enough datasets available' + message = "Not enough datasets available" return message class convert_all_event_maps_in_database(QtCore.QThread): - def __init__(self, initial_model_directory, xce_logfile, datasource): QtCore.QThread.__init__(self) self.xce_logfile = xce_logfile @@ -1539,14 +2078,14 @@ def __init__(self, initial_model_directory, xce_logfile, datasource): def run(self): sqlite = ( - 'select' - ' CrystalName,' - ' PANDDA_site_event_map,' - ' PANDDA_site_ligand_resname,' - ' PANDDA_site_ligand_chain,' - ' PANDDA_site_ligand_sequence_number,' - ' PANDDA_site_ligand_altLoc ' - 'from panddaTable ' + "select" + " CrystalName," + " PANDDA_site_event_map," + " PANDDA_site_ligand_resname," + " PANDDA_site_ligand_chain," + " PANDDA_site_ligand_sequence_number," + " PANDDA_site_ligand_altLoc " + "from panddaTable " 'where PANDDA_site_event_map not like "event%"' ) @@ -1554,11 +2093,11 @@ def run(self): progress_step = 1 if len(query) != 0: - progress_step = 100/float(len(query)) + progress_step = 100 / float(len(query)) else: progress_step = 1 progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) for item in query: xtalID = str(item[0]) @@ -1568,58 +2107,97 @@ def run(self): resseq = str(item[4]) altLoc = str(item[5]) - if os.path.isfile(os.path.join(self.initial_model_directory, xtalID, 'refine.pdb')): + if os.path.isfile( + os.path.join(self.initial_model_directory, xtalID, "refine.pdb") + ): os.chdir(os.path.join(self.initial_model_directory, xtalID)) - self.Logfile.insert('extracting ligand ({0!s},{1!s},{2!s},{3!s}) from refine.pdb'.format( - str(resname), str(chainID), str(resseq), str(altLoc))) - XChemUtils.pdbtools(os.path.join(self.initial_model_directory, xtalID, 'refine.pdb') - ).save_specific_ligands_to_pdb(resname, chainID, resseq, altLoc) - if os.path.isfile('ligand_{0!s}_{1!s}_{2!s}_{3!s}.pdb'.format(str(resname), str(chainID), str(resseq), str(altLoc))): - ligand_pdb = 'ligand_{0!s}_{1!s}_{2!s}_{3!s}.pdb'.format( - str(resname), str(chainID), str(resseq), str(altLoc)) + self.Logfile.insert( + "extracting ligand ({0!s},{1!s},{2!s},{3!s}) from refine.pdb".format( + str(resname), str(chainID), str(resseq), str(altLoc) + ) + ) + XChemUtils.pdbtools( + os.path.join(self.initial_model_directory, xtalID, "refine.pdb") + ).save_specific_ligands_to_pdb(resname, chainID, resseq, altLoc) + if os.path.isfile( + "ligand_{0!s}_{1!s}_{2!s}_{3!s}.pdb".format( + str(resname), str(chainID), str(resseq), str(altLoc) + ) + ): + ligand_pdb = "ligand_{0!s}_{1!s}_{2!s}_{3!s}.pdb".format( + str(resname), str(chainID), str(resseq), str(altLoc) + ) else: - self.Logfile.insert( - 'could not extract ligand; trying next...') + self.Logfile.insert("could not extract ligand; trying next...") continue else: - self.Logfile.insert('directory: '+os.path.join( - self.initial_model_directory, xtalID)+' -> cannot find refine.pdb; trying next') + self.Logfile.insert( + "directory: " + + os.path.join(self.initial_model_directory, xtalID) + + " -> cannot find refine.pdb; trying next" + ) continue - if os.path.isfile(os.path.join(self.initial_model_directory, xtalID, 'refine.mtz')): - resolution = XChemUtils.mtztools(os.path.join( - self.initial_model_directory, xtalID, 'refine.mtz')).get_high_resolution_from_mtz() + if os.path.isfile( + os.path.join(self.initial_model_directory, xtalID, "refine.mtz") + ): + resolution = XChemUtils.mtztools( + os.path.join(self.initial_model_directory, xtalID, "refine.mtz") + ).get_high_resolution_from_mtz() else: - self.Logfile.insert('directory: '+os.path.join( - self.initial_model_directory, xtalID)+' -> cannot find refine.mtz; trying next') + self.Logfile.insert( + "directory: " + + os.path.join(self.initial_model_directory, xtalID) + + " -> cannot find refine.mtz; trying next" + ) continue - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'eventMap -> SF for '+event_map) - convert_event_map_to_SF(self.initial_model_directory, xtalID, event_map, - ligand_pdb, self.xce_logfile, self.datasource, resolution).run() + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "eventMap -> SF for " + event_map, + ) + convert_event_map_to_SF( + self.initial_model_directory, + xtalID, + event_map, + ligand_pdb, + self.xce_logfile, + self.datasource, + resolution, + ).run() progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) class convert_event_map_to_SF: - def __init__(self, project_directory, xtalID, event_map, ligand_pdb, xce_logfile, db_file, resolution): + def __init__( + self, + project_directory, + xtalID, + event_map, + ligand_pdb, + xce_logfile, + db_file, + resolution, + ): self.Logfile = XChemLog.updateLog(xce_logfile) self.event_map = event_map if not os.path.isfile(self.event_map): - self.Logfile.insert('cannot find Event map: '+self.event_map) - self.Logfile.insert( - 'cannot convert event_map to structure factors!') + self.Logfile.insert("cannot find Event map: " + self.event_map) + self.Logfile.insert("cannot convert event_map to structure factors!") return None self.project_directory = project_directory self.xtalID = xtalID self.event_map = event_map self.ligand_pdb = ligand_pdb - self.event = event_map[event_map.rfind( - '/')+1:].replace('.map', '').replace('.ccp4', '') + self.event = ( + event_map[event_map.rfind("/") + 1 :] + .replace(".map", "") + .replace(".ccp4", "") + ) self.db = XChemDB.data_source(db_file) self.resolution = resolution @@ -1627,9 +2205,9 @@ def run(self): os.chdir(os.path.join(self.project_directory, self.xtalID)) # remove exisiting mtz file - if os.path.isfile(self.event+'.mtz'): - self.Logfile.insert('removing existing '+self.event+'.mtz') - os.system('/bin/rm '+self.event+'.mtz') + if os.path.isfile(self.event + ".mtz"): + self.Logfile.insert("removing existing " + self.event + ".mtz") + os.system("/bin/rm " + self.event + ".mtz") # event maps generated with pandda v0.2 or higher have the same symmetry as the crystal # but phenix.map_to_structure_facors only accepts maps in spg P1 @@ -1643,36 +2221,32 @@ def run(self): self.remove_and_rename_column_labels() # check if output files exist - if not os.path.isfile('{0!s}.mtz'.format(self.event)): - self.Logfile.insert('cannot find {0!s}.mtz'.format(self.event)) + if not os.path.isfile("{0!s}.mtz".format(self.event)): + self.Logfile.insert("cannot find {0!s}.mtz".format(self.event)) else: self.Logfile.insert( - 'conversion successful, {0!s}.mtz exists'.format(self.event)) + "conversion successful, {0!s}.mtz exists".format(self.event) + ) # update datasource with event_map_mtz information self.update_database() def calculate_electron_density_map(self, mtzin): missing_columns = False column_dict = XChemUtils.mtztools(mtzin).get_all_columns_as_dict() - if 'FWT' in column_dict['F'] and 'PHWT' in column_dict['PHS']: - labin = ' labin F1=FWT PHI=PHWT\n' - elif '2FOFCWT' in column_dict['F'] and 'PH2FOFCWT' in column_dict['PHS']: - labin = ' labin F1=2FOFCWT PHI=PH2FOFCWT\n' + if "FWT" in column_dict["F"] and "PHWT" in column_dict["PHS"]: + labin = " labin F1=FWT PHI=PHWT\n" + elif "2FOFCWT" in column_dict["F"] and "PH2FOFCWT" in column_dict["PHS"]: + labin = " labin F1=2FOFCWT PHI=PH2FOFCWT\n" else: missing_columns = True if not missing_columns: os.chdir(os.path.join(self.project_directory, self.xtalID)) - cmd = ( - 'fft hklin '+mtzin+' mapout 2fofc.map << EOF\n' - + labin + - 'EOF\n' - ) - self.Logfile.insert('calculating 2fofc map from '+mtzin) + cmd = "fft hklin " + mtzin + " mapout 2fofc.map << EOF\n" + labin + "EOF\n" + self.Logfile.insert("calculating 2fofc map from " + mtzin) os.system(cmd) else: - self.Logfile.insert( - 'cannot calculate 2fofc.map; missing map coefficients') + self.Logfile.insert("cannot calculate 2fofc.map; missing map coefficients") def prepare_conversion_script(self): @@ -1681,224 +2255,264 @@ def prepare_conversion_script(self): # see also: # http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model - if os.getcwd().startswith('/dls'): - phenix_module = 'module_load_phenix\n' + if os.getcwd().startswith("/dls"): + phenix_module = "module_load_phenix\n" else: - phenix_module = '' + phenix_module = "" cmd = ( - '#!'+os.getenv('SHELL')+'\n' - '\n' - + phenix_module + - '\n' - 'pdbset XYZIN %s XYZOUT mask_ligand.pdb << eof\n' % self.ligand_pdb + - ' SPACEGROUP {0!s}\n'.format(self.space_group) + - ' CELL {0!s}\n'.format((' '.join(self.unit_cell))) + - ' END\n' - 'eof\n' - '\n' - 'ncsmask XYZIN mask_ligand.pdb MSKOUT mask_ligand.msk << eof\n' - ' GRID %s\n' % (' '.join(self.gridElectronDensityMap)) + - ' RADIUS 10\n' - ' PEAK 1\n' - 'eof\n' - '\n' - 'mapmask MAPIN %s MAPOUT onecell_event_map.map << eof\n' % self.event_map + - ' XYZLIM CELL\n' - 'eof\n' - '\n' - 'maprot MAPIN onecell_event_map.map MSKIN mask_ligand.msk WRKOUT masked_event_map.map << eof\n' - ' MODE FROM\n' - ' SYMMETRY WORK %s\n' % self.space_group_numberElectronDensityMap + - ' AVERAGE\n' - ' ROTATE EULER 0 0 0\n' - ' TRANSLATE 0 0 0\n' - 'eof\n' - '\n' - 'mapmask MAPIN masked_event_map.map MAPOUT masked_event_map_fullcell.map << eof\n' - ' XYZLIM CELL\n' - ' PAD 0.0\n' - 'eof\n' - '\n' - 'sfall HKLOUT %s.mtz MAPIN masked_event_map_fullcell.map << eof\n' % self.event + - ' LABOUT FC=FC_event PHIC=PHIC_event\n' - ' MODE SFCALC MAPIN\n' - ' RESOLUTION %s\n' % self.resolution + - ' END\n' + "#!" + os.getenv("SHELL") + "\n" + "\n" + phenix_module + "\n" + "pdbset XYZIN %s XYZOUT mask_ligand.pdb << eof\n" % self.ligand_pdb + + " SPACEGROUP {0!s}\n".format(self.space_group) + + " CELL {0!s}\n".format((" ".join(self.unit_cell))) + + " END\n" + "eof\n" + "\n" + "ncsmask XYZIN mask_ligand.pdb MSKOUT mask_ligand.msk << eof\n" + " GRID %s\n" % (" ".join(self.gridElectronDensityMap)) + " RADIUS 10\n" + " PEAK 1\n" + "eof\n" + "\n" + "mapmask MAPIN %s MAPOUT onecell_event_map.map << eof\n" % self.event_map + + " XYZLIM CELL\n" + "eof\n" + "\n" + "maprot MAPIN onecell_event_map.map MSKIN mask_ligand.msk WRKOUT masked_event_map.map << eof\n" + " MODE FROM\n" + " SYMMETRY WORK %s\n" % self.space_group_numberElectronDensityMap + + " AVERAGE\n" + " ROTATE EULER 0 0 0\n" + " TRANSLATE 0 0 0\n" + "eof\n" + "\n" + "mapmask MAPIN masked_event_map.map MAPOUT masked_event_map_fullcell.map << eof\n" + " XYZLIM CELL\n" + " PAD 0.0\n" + "eof\n" + "\n" + "sfall HKLOUT %s.mtz MAPIN masked_event_map_fullcell.map << eof\n" + % self.event + + " LABOUT FC=FC_event PHIC=PHIC_event\n" + " MODE SFCALC MAPIN\n" + " RESOLUTION %s\n" % self.resolution + " END\n" ) - self.Logfile.insert( - 'preparing script for conversion of Event map to SF') - f = open('eventMap2sf.sh', 'w') + self.Logfile.insert("preparing script for conversion of Event map to SF") + f = open("eventMap2sf.sh", "w") f.write(cmd) f.close() - os.system('chmod +x eventMap2sf.sh') + os.system("chmod +x eventMap2sf.sh") def run_conversion_script(self): - self.Logfile.insert('running conversion script...') - os.system('./eventMap2sf.sh') + self.Logfile.insert("running conversion script...") + os.system("./eventMap2sf.sh") def convert_map_to_p1(self): - self.Logfile.insert('running mapmask -> converting map to p1...') - cmd = ('#!'+os.getenv('SHELL')+'\n' - '\n' - 'mapmask mapin %s mapout %s_p1.map << eof\n' % (self.event_map, self.event) + - 'xyzlin cell\n' - 'symmetry p1\n') - self.Logfile.insert('mapmask command:\n%s' % cmd) + self.Logfile.insert("running mapmask -> converting map to p1...") + cmd = ( + "#!" + os.getenv("SHELL") + "\n" + "\n" + "mapmask mapin %s mapout %s_p1.map << eof\n" % (self.event_map, self.event) + + "xyzlin cell\n" + "symmetry p1\n" + ) + self.Logfile.insert("mapmask command:\n%s" % cmd) os.system(cmd) def run_phenix_map_to_structure_factors(self): - if float(self.resolution) < 1.21: # program complains if resolution is 1.2 or higher - self.resolution = '1.21' - self.Logfile.insert('running phenix.map_to_structure_factors {0!s}_p1.map d_min={1!s} output_file_name={2!s}_tmp.mtz'.format( - self.event, self.resolution, self.event)) - os.system('phenix.map_to_structure_factors {0!s}_p1.map d_min={1!s} output_file_name={2!s}_tmp.mtz'.format( - self.event, self.resolution, self.event)) + if ( + float(self.resolution) < 1.21 + ): # program complains if resolution is 1.2 or higher + self.resolution = "1.21" + self.Logfile.insert( + "running phenix.map_to_structure_factors {0!s}_p1.map d_min={1!s} output_file_name={2!s}_tmp.mtz".format( + self.event, self.resolution, self.event + ) + ) + os.system( + "phenix.map_to_structure_factors {0!s}_p1.map d_min={1!s} output_file_name={2!s}_tmp.mtz".format( + self.event, self.resolution, self.event + ) + ) def run_cinvfft(self, mtzin): # mtzin is usually refine.mtz self.Logfile.insert( - 'running cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz -colout event'.format(self.event_map, mtzin, self.event)) - os.system('cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz -colout event'.format( - self.event_map, mtzin, self.event)) + "running cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz -colout event".format( + self.event_map, mtzin, self.event + ) + ) + os.system( + "cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz -colout event".format( + self.event_map, mtzin, self.event + ) + ) def remove_and_rename_column_labels(self): - cmd = ('#!'+os.getenv('SHELL')+'\n' - '\n' - 'cad hklin1 %s_tmp.mtz hklout %s.mtz << eof\n' % (self.event, self.event) + - ' labin file_number 1 E1=F-obs E2=PHIF\n' - ' labout file_number 1 E1=F_ampl E2=PHIF\n' - 'eof\n' - '\n') - self.Logfile.insert('running CAD: new column labels F_ampl,PHIF') + cmd = ( + "#!" + os.getenv("SHELL") + "\n" + "\n" + "cad hklin1 %s_tmp.mtz hklout %s.mtz << eof\n" % (self.event, self.event) + + " labin file_number 1 E1=F-obs E2=PHIF\n" + " labout file_number 1 E1=F_ampl E2=PHIF\n" + "eof\n" + "\n" + ) + self.Logfile.insert("running CAD: new column labels F_ampl,PHIF") os.system(cmd) def remove_and_rename_column_labels_after_cinvfft(self): - cmd = ('#!'+os.getenv('SHELL')+'\n' - '\n' - 'cad hklin1 %s_tmp.mtz hklout %s.mtz << eof\n' % (self.event, self.event) + - ' labin file_number 1 E1=event.F_phi.F E2=event.F_phi.phi\n' - ' labout file_number 1 E1=F_ampl E2=PHIF\n' - 'eof\n' - '\n') + cmd = ( + "#!" + os.getenv("SHELL") + "\n" + "\n" + "cad hklin1 %s_tmp.mtz hklout %s.mtz << eof\n" % (self.event, self.event) + + " labin file_number 1 E1=event.F_phi.F E2=event.F_phi.phi\n" + " labout file_number 1 E1=F_ampl E2=PHIF\n" + "eof\n" + "\n" + ) self.Logfile.insert( - 'running CAD: renaming event.F_phi.F -> F_ampl and event.F_phi.phi -> PHIF') + "running CAD: renaming event.F_phi.F -> F_ampl and event.F_phi.phi -> PHIF" + ) os.system(cmd) def update_database(self): - sqlite = ("update panddaTable set " - " PANDDA_site_event_map_mtz = '%s' " % os.path.join(self.project_directory, self.xtalID, self.event+'.mtz') + - " where PANDDA_site_event_map is '{0!s}' ".format( - self.event_map) - ) + sqlite = ( + "update panddaTable set " + " PANDDA_site_event_map_mtz = '%s' " + % os.path.join(self.project_directory, self.xtalID, self.event + ".mtz") + + " where PANDDA_site_event_map is '{0!s}' ".format(self.event_map) + ) self.db.execute_statement(sqlite) - self.Logfile.insert('updating data source: '+sqlite) + self.Logfile.insert("updating data source: " + sqlite) def clean_output_directory(self): - os.system('/bin/rm mask_targetcell.pdb') - os.system('/bin/rm mask_targetcell.msk') - os.system('/bin/rm onecell.map') - os.system('/bin/rm masked_targetcell.map') - os.system('/bin/rm masked_fullcell.map') - os.system('/bin/rm eventMap2sf.sh') - os.system('/bin/rm '+self.ligand_pdb) + os.system("/bin/rm mask_targetcell.pdb") + os.system("/bin/rm mask_targetcell.msk") + os.system("/bin/rm onecell.map") + os.system("/bin/rm masked_targetcell.map") + os.system("/bin/rm masked_fullcell.map") + os.system("/bin/rm eventMap2sf.sh") + os.system("/bin/rm " + self.ligand_pdb) class run_pandda_inspect_at_home(QtCore.QThread): - def __init__(self, panddaDir, xce_logfile): QtCore.QThread.__init__(self) self.panddaDir = panddaDir self.Logfile = XChemLog.updateLog(xce_logfile) def run(self): - os.chdir(os.path.join(self.panddaDir, 'processed_datasets')) + os.chdir(os.path.join(self.panddaDir, "processed_datasets")) progress_step = 1 - if len(glob.glob('*')) != 0: - progress_step = 100/float(len(glob.glob('*'))) + if len(glob.glob("*")) != 0: + progress_step = 100 / float(len(glob.glob("*"))) else: progress_step = 1 progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) - self.Logfile.insert('parsing '+self.panddaDir) - for xtal in sorted(glob.glob('*')): - for files in glob.glob(xtal+'/ligand_files/*'): + self.Logfile.insert("parsing " + self.panddaDir) + for xtal in sorted(glob.glob("*")): + for files in glob.glob(xtal + "/ligand_files/*"): if os.path.islink(files): - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'replacing symlink for {0!s} with real file'.format(files)) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "replacing symlink for {0!s} with real file".format(files), + ) self.Logfile.insert( - 'replacing symlink for {0!s} with real file'.format(files)) + "replacing symlink for {0!s} with real file".format(files) + ) os.system( - 'cp --remove-destination {0!s} {1!s}/ligand_files'.format(os.path.realpath(files), xtal)) + "cp --remove-destination {0!s} {1!s}/ligand_files".format( + os.path.realpath(files), xtal + ) + ) progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) XChemToolTips.run_pandda_inspect_at_home(self.panddaDir) class convert_apo_structures_to_mmcif(QtCore.QThread): - def __init__(self, panddaDir, xce_logfile): QtCore.QThread.__init__(self) self.panddaDir = panddaDir self.Logfile = XChemLog.updateLog(xce_logfile) def sf_convert_environment(self): - pdb_extract_init = '' - if os.path.isdir('/dls'): - pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n' - pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-prod/bin/sf_convert' + pdb_extract_init = "" + if os.path.isdir("/dls"): + pdb_extract_init = ( + "source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n" + ) + pdb_extract_init += ( + "/dls/science/groups/i04-1/software/pdb-extract-prod/bin/sf_convert" + ) else: - pdb_extract_init = 'source ' + os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/setup.sh') + '\n' - pdb_extract_init += +os.path.join(os.getenv('XChemExplorer_DIR'), - 'pdb_extract/pdb-extract-prod/bin/sf_convert') + pdb_extract_init = ( + "source " + + os.path.join( + os.getenv("XChemExplorer_DIR"), + "pdb_extract/pdb-extract-prod/setup.sh", + ) + + "\n" + ) + pdb_extract_init += +os.path.join( + os.getenv("XChemExplorer_DIR"), + "pdb_extract/pdb-extract-prod/bin/sf_convert", + ) return pdb_extract_init def run(self): self.Logfile.insert( - 'converting apo structures in pandda directory to mmcif files') - self.Logfile.insert('chanfing to '+self.panddaDir) + "converting apo structures in pandda directory to mmcif files" + ) + self.Logfile.insert("chanfing to " + self.panddaDir) progress_step = 1 - if len(glob.glob('*')) != 0: - progress_step = 100 / \ - float( - len(glob.glob(os.path.join(self.panddaDir, 'processed_datasets', '*')))) + if len(glob.glob("*")) != 0: + progress_step = 100 / float( + len(glob.glob(os.path.join(self.panddaDir, "processed_datasets", "*"))) + ) else: progress_step = 1 progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) pdb_extract_init = self.sf_convert_environment() - self.Logfile.insert('parsing '+self.panddaDir) - for dirs in glob.glob(os.path.join(self.panddaDir, 'processed_datasets', '*')): - xtal = dirs[dirs.rfind('/')+1:] - self.Logfile.insert('%s: converting %s to mmcif' % - (xtal, xtal+'-pandda-input.mtz')) - if os.path.isfile(os.path.join(dirs, xtal+'-pandda-input.mtz')): - if os.path.isfile(os.path.join(dirs, xtal+'_sf.mmcif')): + self.Logfile.insert("parsing " + self.panddaDir) + for dirs in glob.glob(os.path.join(self.panddaDir, "processed_datasets", "*")): + xtal = dirs[dirs.rfind("/") + 1 :] + self.Logfile.insert( + "%s: converting %s to mmcif" % (xtal, xtal + "-pandda-input.mtz") + ) + if os.path.isfile(os.path.join(dirs, xtal + "-pandda-input.mtz")): + if os.path.isfile(os.path.join(dirs, xtal + "_sf.mmcif")): self.Logfile.insert( - '%s: %s_sf.mmcif exists; skipping...' % (xtal, xtal)) + "%s: %s_sf.mmcif exists; skipping..." % (xtal, xtal) + ) else: os.chdir(dirs) - Cmd = (pdb_extract_init + - ' -o mmcif' - ' -sf %s' % xtal+'-pandda-input.mtz' + - ' -out {0!s}_sf.mmcif > {1!s}.sf_mmcif.log'.format(xtal, xtal)) - self.Logfile.insert('running command: '+Cmd) + Cmd = ( + pdb_extract_init + " -o mmcif" + " -sf %s" % xtal + + "-pandda-input.mtz" + + " -out {0!s}_sf.mmcif > {1!s}.sf_mmcif.log".format( + xtal, xtal + ) + ) + self.Logfile.insert("running command: " + Cmd) os.system(Cmd) progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) class check_number_of_modelled_ligands(QtCore.QThread): - def __init__(self, project_directory, xce_logfile, db_file): QtCore.QThread.__init__(self) self.Logfile = XChemLog.updateLog(xce_logfile) @@ -1927,7 +2541,11 @@ def insert_new_row_in_panddaTable(self, xtal, ligand, site, dbDict): siteList = [] for entry in dbDict[xtal]: siteList.append(str(entry[0])) - if entry[4] == resnameSimilarSite and entry[5] == chainSimilarSite and entry[6] == seqnumSimilarSite: + if ( + entry[4] == resnameSimilarSite + and entry[5] == chainSimilarSite + and entry[6] == seqnumSimilarSite + ): eventMap = str(entry[7]) eventMap_mtz = str(entry[8]) initialPDB = str(entry[9]) @@ -1936,45 +2554,48 @@ def insert_new_row_in_panddaTable(self, xtal, ligand, site, dbDict): PanDDApath = str(entry[13]) db_dict = { - 'PANDDA_site_index': str(int(max(siteList))+1), - 'PANDDApath': PanDDApath, - 'PANDDA_site_ligand_id': resname+'-'+chain+'-'+seqnum, - 'PANDDA_site_ligand_resname': resname, - 'PANDDA_site_ligand_chain': chain, - 'PANDDA_site_ligand_sequence_number': seqnum, - 'PANDDA_site_ligand_altLoc': 'D', - 'PANDDA_site_event_index': event_id, - 'PANDDA_site_event_map': eventMap, - 'PANDDA_site_event_map_mtz': eventMap_mtz, - 'PANDDA_site_initial_model': initialPDB, - 'PANDDA_site_initial_mtz': initialMTZ, - 'PANDDA_site_ligand_placed': 'True', - 'PANDDA_site_x': x_site, - 'PANDDA_site_y': y_site, - 'PANDDA_site_z': z_site} + "PANDDA_site_index": str(int(max(siteList)) + 1), + "PANDDApath": PanDDApath, + "PANDDA_site_ligand_id": resname + "-" + chain + "-" + seqnum, + "PANDDA_site_ligand_resname": resname, + "PANDDA_site_ligand_chain": chain, + "PANDDA_site_ligand_sequence_number": seqnum, + "PANDDA_site_ligand_altLoc": "D", + "PANDDA_site_event_index": event_id, + "PANDDA_site_event_map": eventMap, + "PANDDA_site_event_map_mtz": eventMap_mtz, + "PANDDA_site_initial_model": initialPDB, + "PANDDA_site_initial_mtz": initialMTZ, + "PANDDA_site_ligand_placed": "True", + "PANDDA_site_x": x_site, + "PANDDA_site_y": y_site, + "PANDDA_site_z": z_site, + } def run(self): - self.Logfile.insert('reading modelled ligands from panddaTable') + self.Logfile.insert("reading modelled ligands from panddaTable") dbDict = {} - sqlite = ("select " - " CrystalName," - " PANDDA_site_index," - " PANDDA_site_x," - " PANDDA_site_y," - " PANDDA_site_z," - " PANDDA_site_ligand_resname," - " PANDDA_site_ligand_chain," - " PANDDA_site_ligand_sequence_number," - " PANDDA_site_event_map," - " PANDDA_site_event_map_mtz," - " PANDDA_site_initial_model," - " PANDDA_site_initial_mtz," - " RefinementOutcome," - " PANDDA_site_event_index," - " PANDDApath " - "from panddaTable ") + sqlite = ( + "select " + " CrystalName," + " PANDDA_site_index," + " PANDDA_site_x," + " PANDDA_site_y," + " PANDDA_site_z," + " PANDDA_site_ligand_resname," + " PANDDA_site_ligand_chain," + " PANDDA_site_ligand_sequence_number," + " PANDDA_site_event_map," + " PANDDA_site_event_map_mtz," + " PANDDA_site_initial_model," + " PANDDA_site_initial_mtz," + " RefinementOutcome," + " PANDDA_site_event_index," + " PANDDApath " + "from panddaTable " + ) dbEntries = self.db.execute_statement(sqlite) for item in dbEntries: @@ -1996,33 +2617,53 @@ def run(self): if xtal not in dbDict: dbDict[xtal] = [] - dbDict[xtal].append([site, x, y, z, resname, chain, seqnum, eventMap, - eventMap_mtz, initialPDB, initialMTZ, outcome, event, PanDDApath]) + dbDict[xtal].append( + [ + site, + x, + y, + z, + resname, + chain, + seqnum, + eventMap, + eventMap_mtz, + initialPDB, + initialMTZ, + outcome, + event, + PanDDApath, + ] + ) os.chdir(self.project_directory) progress_step = 1 - if len(glob.glob('*')) != 0: - progress_step = 100/float(len(glob.glob('*'))) + if len(glob.glob("*")) != 0: + progress_step = 100 / float(len(glob.glob("*"))) else: progress_step = 1 progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - - for xtal in sorted(glob.glob('*')): - if os.path.isfile(os.path.join(xtal, 'refine.pdb')): - ligands = XChemUtils.pdbtools(os.path.join( - xtal, 'refine.pdb')).ligand_details_as_list() - self.Logfile.insert( - '{0!s}: found file refine.pdb'.format(xtal)) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) + + for xtal in sorted(glob.glob("*")): + if os.path.isfile(os.path.join(xtal, "refine.pdb")): + ligands = XChemUtils.pdbtools( + os.path.join(xtal, "refine.pdb") + ).ligand_details_as_list() + self.Logfile.insert("{0!s}: found file refine.pdb".format(xtal)) if ligands: - if os.path.isdir(os.path.join(xtal, 'xceTmp')): + if os.path.isdir(os.path.join(xtal, "xceTmp")): os.system( - '/bin/rm -fr {0!s}'.format(os.path.join(xtal, 'xceTmp'))) - os.mkdir(os.path.join(xtal, 'xceTmp')) + "/bin/rm -fr {0!s}".format(os.path.join(xtal, "xceTmp")) + ) + os.mkdir(os.path.join(xtal, "xceTmp")) else: self.Logfile.warning( - '{0!s}: cannot find ligand molecule in refine.pdb; skipping...'.format(xtal)) + "{0!s}: cannot find ligand molecule in refine.pdb; skipping...".format( + xtal + ) + ) continue made_sym_copies = False @@ -2033,11 +2674,16 @@ def run(self): seqnumLIG = item[2] altLocLIG = item[3] occupancyLig = item[4] - if altLocLIG.replace(' ', '') == '': + if altLocLIG.replace(" ", "") == "": self.Logfile.insert( - xtal+': found a ligand not modelled with pandda.inspect -> {0!s} {1!s} {2!s}'.format(resnameLIG, chainLIG, seqnumLIG)) - residue_xyz = XChemUtils.pdbtools(os.path.join( - xtal, 'refine.pdb')).get_center_of_gravity_of_residue_ish(item[1], item[2]) + xtal + + ": found a ligand not modelled with pandda.inspect -> {0!s} {1!s} {2!s}".format( + resnameLIG, chainLIG, seqnumLIG + ) + ) + residue_xyz = XChemUtils.pdbtools( + os.path.join(xtal, "refine.pdb") + ).get_center_of_gravity_of_residue_ish(item[1], item[2]) ligands[n].append(residue_xyz) foundLigand = False if xtal in dbDict: @@ -2045,52 +2691,104 @@ def run(self): resnameTable = entry[4] chainTable = entry[5] seqnumTable = entry[6] - self.Logfile.insert('panddaTable: {0!s} {1!s} {2!s} {3!s}'.format( - xtal, resnameTable, chainTable, seqnumTable)) - if resnameLIG == resnameTable and chainLIG == chainTable and seqnumLIG == seqnumTable: - self.Logfile.insert('{0!s}: found ligand in database -> {1!s} {2!s} {3!s}'.format( - xtal, resnameTable, chainTable, seqnumTable)) + self.Logfile.insert( + "panddaTable: {0!s} {1!s} {2!s} {3!s}".format( + xtal, resnameTable, chainTable, seqnumTable + ) + ) + if ( + resnameLIG == resnameTable + and chainLIG == chainTable + and seqnumLIG == seqnumTable + ): + self.Logfile.insert( + "{0!s}: found ligand in database -> {1!s} {2!s} {3!s}".format( + xtal, resnameTable, chainTable, seqnumTable + ) + ) foundLigand = True if not foundLigand: - self.Logfile.error('{0!s}: did NOT find ligand in database -> {1!s} {2!s} {3!s}'.format( - xtal, resnameLIG, chainLIG, seqnumLIG)) + self.Logfile.error( + "{0!s}: did NOT find ligand in database -> {1!s} {2!s} {3!s}".format( + xtal, resnameLIG, chainLIG, seqnumLIG + ) + ) ligands_not_in_panddaTable.append( - [resnameLIG, chainLIG, seqnumLIG, altLocLIG, occupancyLig, residue_xyz]) + [ + resnameLIG, + chainLIG, + seqnumLIG, + altLocLIG, + occupancyLig, + residue_xyz, + ] + ) else: self.Logfile.warning( - 'ligand in PDB file, but dataset not listed in panddaTable: {0!s} -> {1!s} {2!s} {3!s}'.format(xtal, item[0], item[1], item[2])) + "ligand in PDB file, but dataset not listed in panddaTable: {0!s} -> {1!s} {2!s} {3!s}".format( + xtal, item[0], item[1], item[2] + ) + ) for entry in ligands_not_in_panddaTable: - self.Logfile.error('{0!s}: refine.pdb contains a ligand that is not assigned in the panddaTable: {1!s} {2!s} {3!s} {4!s}'.format( - xtal, entry[0], entry[1], entry[2], entry[3])) + self.Logfile.error( + "{0!s}: refine.pdb contains a ligand that is not assigned in the panddaTable: {1!s} {2!s} {3!s} {4!s}".format( + xtal, entry[0], entry[1], entry[2], entry[3] + ) + ) for site in ligands_not_in_panddaTable: - for files in glob.glob(os.path.join(self.project_directory, xtal, 'xceTmp', 'ligand_*_*.pdb')): + for files in glob.glob( + os.path.join( + self.project_directory, xtal, "xceTmp", "ligand_*_*.pdb" + ) + ): mol_xyz = XChemUtils.pdbtools( - files).get_center_of_gravity_of_molecule_ish() + files + ).get_center_of_gravity_of_molecule_ish() # now need to check if there is a unassigned entry in panddaTable that is close for entry in dbDict[xtal]: distance = XChemUtils.misc().calculate_distance_between_coordinates( - mol_xyz[0], mol_xyz[1], mol_xyz[2], entry[1], entry[2], entry[3]) - self.Logfile.insert('{0!s}: {1!s} {2!s} {3!s} <---> {4!s} {5!s} {6!s}'.format( - xtal, mol_xyz[0], mol_xyz[1], mol_xyz[2], entry[1], entry[2], entry[3])) + mol_xyz[0], + mol_xyz[1], + mol_xyz[2], + entry[1], + entry[2], + entry[3], + ) self.Logfile.insert( - '{0!s}: symm equivalent molecule: {1!s}'.format(xtal, files)) + "{0!s}: {1!s} {2!s} {3!s} <---> {4!s} {5!s} {6!s}".format( + xtal, + mol_xyz[0], + mol_xyz[1], + mol_xyz[2], + entry[1], + entry[2], + entry[3], + ) + ) self.Logfile.insert( - '{0!s}: distance: {1!s}'.format(xtal, str(distance))) + "{0!s}: symm equivalent molecule: {1!s}".format( + xtal, files + ) + ) + self.Logfile.insert( + "{0!s}: distance: {1!s}".format(xtal, str(distance)) + ) progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) if self.errorDict != {}: self.update_errorDict( - 'General', 'The aforementioned PDB files were automatically changed by XCE!\nPlease check and refine them!!!') - self.emit(QtCore.SIGNAL('show_error_dict'), self.errorDict) + "General", + "The aforementioned PDB files were automatically changed by XCE!\nPlease check and refine them!!!", + ) + self.emit(QtCore.SIGNAL("show_error_dict"), self.errorDict) class find_event_map_for_ligand(QtCore.QThread): - def __init__(self, project_directory, xce_logfile, external_software): QtCore.QThread.__init__(self) self.Logfile = XChemLog.updateLog(xce_logfile) @@ -2098,108 +2796,133 @@ def __init__(self, project_directory, xce_logfile, external_software): self.external_software = external_software try: import gemmi - self.Logfile.insert('found gemmi library in ccp4-python') + + self.Logfile.insert("found gemmi library in ccp4-python") except ImportError: - self.external_software['gemmi'] = False + self.external_software["gemmi"] = False self.Logfile.warning( - 'cannot import gemmi; will use phenix.map_to_structure_factors instead') + "cannot import gemmi; will use phenix.map_to_structure_factors instead" + ) def run(self): - self.Logfile.insert( - '======== checking ligand CC in event maps ========') - for dirs in sorted(glob.glob(os.path.join(self.project_directory, '*'))): - xtal = dirs[dirs.rfind('/')+1:] - if os.path.isfile(os.path.join(dirs, 'refine.pdb')) and \ - os.path.isfile(os.path.join(dirs, 'refine.mtz')): - self.Logfile.insert('%s: found refine.pdb' % xtal) + self.Logfile.insert("======== checking ligand CC in event maps ========") + for dirs in sorted(glob.glob(os.path.join(self.project_directory, "*"))): + xtal = dirs[dirs.rfind("/") + 1 :] + if os.path.isfile(os.path.join(dirs, "refine.pdb")) and os.path.isfile( + os.path.join(dirs, "refine.mtz") + ): + self.Logfile.insert("%s: found refine.pdb" % xtal) os.chdir(dirs) try: - p = gemmi.read_structure('refine.pdb') + p = gemmi.read_structure("refine.pdb") except: - self.Logfile.error('gemmi library not available') - self.external_software['gemmi'] = False - reso = XChemUtils.mtztools('refine.mtz').get_dmin() - ligList = XChemUtils.pdbtools( - 'refine.pdb').save_residues_with_resname(dirs, 'LIG') + self.Logfile.error("gemmi library not available") + self.external_software["gemmi"] = False + reso = XChemUtils.mtztools("refine.mtz").get_dmin() + ligList = XChemUtils.pdbtools("refine.pdb").save_residues_with_resname( + dirs, "LIG" + ) self.Logfile.insert( - '%s: found %s ligands of type LIG in refine.pdb' % (xtal, str(len(ligList)))) + "%s: found %s ligands of type LIG in refine.pdb" + % (xtal, str(len(ligList))) + ) - for maps in glob.glob(os.path.join(dirs, '*event*.native.ccp4')): - if self.external_software['gemmi']: + for maps in glob.glob(os.path.join(dirs, "*event*.native.ccp4")): + if self.external_software["gemmi"]: self.convert_map_to_sf_with_gemmi(maps, p) else: self.expand_map_to_p1(maps) - self.convert_map_to_sf( - maps.replace('.ccp4', '.P1.ccp4'), reso) + self.convert_map_to_sf(maps.replace(".ccp4", ".P1.ccp4"), reso) - summary = '' + summary = "" for lig in sorted(ligList): - if self.external_software['gemmi']: - for mtz in sorted(glob.glob(os.path.join(dirs, '*event*.native.mtz'))): + if self.external_software["gemmi"]: + for mtz in sorted( + glob.glob(os.path.join(dirs, "*event*.native.mtz")) + ): self.get_lig_cc(mtz, lig) - cc = self.check_lig_cc( - mtz.replace('.mtz', '_CC.log')) - summary += '%s: %s LIG CC = %s (%s)\n' % ( - xtal, lig, cc, mtz[mtz.rfind('/')+1:]) + cc = self.check_lig_cc(mtz.replace(".mtz", "_CC.log")) + summary += "%s: %s LIG CC = %s (%s)\n" % ( + xtal, + lig, + cc, + mtz[mtz.rfind("/") + 1 :], + ) else: - for mtz in sorted(glob.glob(os.path.join(dirs, '*event*.native*P1.mtz'))): + for mtz in sorted( + glob.glob(os.path.join(dirs, "*event*.native*P1.mtz")) + ): self.get_lig_cc(mtz, lig) - cc = self.check_lig_cc( - mtz.replace('.mtz', '_CC.log')) - summary += '%s: %s LIG CC = %s (%s)\n' % ( - xtal, lig, cc, mtz[mtz.rfind('/')+1:]) + cc = self.check_lig_cc(mtz.replace(".mtz", "_CC.log")) + summary += "%s: %s LIG CC = %s (%s)\n" % ( + xtal, + lig, + cc, + mtz[mtz.rfind("/") + 1 :], + ) self.Logfile.insert( - '\nsummary of CC analysis:\n======================:\n'+summary) + "\nsummary of CC analysis:\n======================:\n" + summary + ) def expand_map_to_p1(self, emap): - self.Logfile.insert('expanding map to P1: %s' % emap) - if os.path.isfile(emap.replace('.ccp4', '.P1.ccp4')): - self.Logfile.warning('P1 map exists; skipping...') + self.Logfile.insert("expanding map to P1: %s" % emap) + if os.path.isfile(emap.replace(".ccp4", ".P1.ccp4")): + self.Logfile.warning("P1 map exists; skipping...") return - cmd = ('mapmask MAPIN %s MAPOUT %s << eof\n' % (emap, emap.replace('.ccp4', '.P1.ccp4')) + - ' XYZLIM CELL\n' - ' PAD 0.0\n' - ' SYMMETRY 1\n' - 'eof\n') + cmd = ( + "mapmask MAPIN %s MAPOUT %s << eof\n" + % (emap, emap.replace(".ccp4", ".P1.ccp4")) + + " XYZLIM CELL\n" + " PAD 0.0\n" + " SYMMETRY 1\n" + "eof\n" + ) os.system(cmd) def convert_map_to_sf(self, emap, reso): self.Logfile.insert( - 'converting ccp4 map to mtz with phenix.map_to_structure_factors: %s' % emap) - if os.path.isfile(emap.replace('.ccp4', '.mtz')): - self.Logfile.warning('mtz file of event map exists; skipping...') + "converting ccp4 map to mtz with phenix.map_to_structure_factors: %s" % emap + ) + if os.path.isfile(emap.replace(".ccp4", ".mtz")): + self.Logfile.warning("mtz file of event map exists; skipping...") return - cmd = ('module load phenix\n' - 'phenix.map_to_structure_factors %s d_min=%s\n' % (emap, reso) + - '/bin/mv map_to_structure_factors.mtz %s' % emap.replace('.ccp4', '.mtz')) + cmd = "module load phenix\n" "phenix.map_to_structure_factors %s d_min=%s\n" % ( + emap, + reso, + ) + "/bin/mv map_to_structure_factors.mtz %s" % emap.replace(".ccp4", ".mtz") os.system(cmd) def get_lig_cc(self, mtz, lig): - self.Logfile.insert('calculating CC for %s in %s' % (lig, mtz)) - if os.path.isfile(mtz.replace('.mtz', '_CC.log')): - self.Logfile.warning('logfile of CC analysis exists; skipping...') + self.Logfile.insert("calculating CC for %s in %s" % (lig, mtz)) + if os.path.isfile(mtz.replace(".mtz", "_CC.log")): + self.Logfile.warning("logfile of CC analysis exists; skipping...") return - cmd = ('module load phenix\n' - 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC.log'))) + cmd = "module load phenix\n" "phenix.get_cc_mtz_pdb %s %s > %s" % ( + mtz, + lig, + mtz.replace(".mtz", "_CC.log"), + ) os.system(cmd) def check_lig_cc(self, log): - cc = 'n/a' + cc = "n/a" if os.path.isfile(log): for line in open(log): - if line.startswith('local'): + if line.startswith("local"): cc = line.split()[len(line.split()) - 1] else: - self.Logfile.error('logfile does not exist: %s' % log) + self.Logfile.error("logfile does not exist: %s" % log) return cc def convert_map_to_sf_with_gemmi(self, emap, p): - self.Logfile.insert( - 'converting ccp4 map to mtz with gemmi map2sf: %s' % emap) - if os.path.isfile(emap.replace('.ccp4', '.mtz')): - self.Logfile.warning('mtz file of event map exists; skipping...') + self.Logfile.insert("converting ccp4 map to mtz with gemmi map2sf: %s" % emap) + if os.path.isfile(emap.replace(".ccp4", ".mtz")): + self.Logfile.warning("mtz file of event map exists; skipping...") return - cmd = 'gemmi map2sf %s %s FWT PHWT --dmin=%s' % ( - emap, emap.replace('.ccp4', '.mtz'), p.resolution) - self.Logfile.insert('converting map with command:\n' + cmd) + cmd = "gemmi map2sf %s %s FWT PHWT --dmin=%s" % ( + emap, + emap.replace(".ccp4", ".mtz"), + p.resolution, + ) + self.Logfile.insert("converting map with command:\n" + cmd) os.system(cmd) diff --git a/lib/XChemPlots.py b/lib/XChemPlots.py index 5f48f218..46f2e568 100755 --- a/lib/XChemPlots.py +++ b/lib/XChemPlots.py @@ -7,7 +7,7 @@ import os import sys -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) class summary_plot(object): @@ -19,58 +19,69 @@ def update_overview(self): db_dict = XChemMain.get_datasource_summary(self.datasource) - category = ('Crystals mounted', - 'Data Collection', - 'Maps', - 'PANDDA', - 'Refinement', - 'Comp Chem') + category = ( + "Crystals mounted", + "Data Collection", + "Maps", + "PANDDA", + "Refinement", + "Comp Chem", + ) N = len(category) - Success = np.array([db_dict['nr_samples'], - db_dict['nr_data_collection_success'], - db_dict['nr_initial_maps_available'], - db_dict['nr_pandda_hits'], - 5, - 6]) + Success = np.array( + [ + db_dict["nr_samples"], + db_dict["nr_data_collection_success"], + db_dict["nr_initial_maps_available"], + db_dict["nr_pandda_hits"], + 5, + 6, + ] + ) - Processed = np.array([0, - 0, - 0, - db_dict['nr_pandda_processed'], - 0, - 0]) + Processed = np.array([0, 0, 0, db_dict["nr_pandda_processed"], 0, 0]) - Pending = np.array([0, - db_dict['nr_data_collection_pending'], - db_dict['nr_initial_maps_pending'], - db_dict['nr_pandda_pending'], - 2, - 1]) + Pending = np.array( + [ + 0, + db_dict["nr_data_collection_pending"], + db_dict["nr_initial_maps_pending"], + db_dict["nr_pandda_pending"], + 2, + 1, + ] + ) - Failure = np.array([db_dict['nr_samples_failed_to_mount'], - db_dict['nr_data_collection_failed'], - db_dict['nr_initial_maps_fail'], - db_dict['nr_pandda_reject'], - 2, - 3]) + Failure = np.array( + [ + db_dict["nr_samples_failed_to_mount"], + db_dict["nr_data_collection_failed"], + db_dict["nr_initial_maps_fail"], + db_dict["nr_pandda_reject"], + 2, + 3, + ] + ) ind = np.arange(N) # the x locations for the groups - width = 0.35 # the width of the bars + width = 0.35 # the width of the bars - p0 = self.overview_axes.bar(ind, Success, width, color='g') - p1 = self.overview_axes.bar( - ind, Processed, width, color='b', bottom=Success) + p0 = self.overview_axes.bar(ind, Success, width, color="g") + p1 = self.overview_axes.bar(ind, Processed, width, color="b", bottom=Success) p2 = self.overview_axes.bar( - ind, Pending, width, color='y', bottom=Success+Processed) + ind, Pending, width, color="y", bottom=Success + Processed + ) p3 = self.overview_axes.bar( - ind, Failure, width, color='r', bottom=Pending+Success+Processed) + ind, Failure, width, color="r", bottom=Pending + Success + Processed + ) # add some text for labels, title and axes ticks - self.overview_axes.set_ylabel('N') - self.overview_axes.set_title('Overview') + self.overview_axes.set_ylabel("N") + self.overview_axes.set_title("Overview") self.overview_axes.set_xticks(ind + width) self.overview_axes.set_xticklabels(category) self.overview_axes.legend( - (p0[0], p1[0], p2[0], p3[0]), ('Success', 'Processed', 'Pending', 'Failure')) + (p0[0], p1[0], p2[0], p3[0]), ("Success", "Processed", "Pending", "Failure") + ) diff --git a/lib/XChemProcess.py b/lib/XChemProcess.py index c4f00518..67c32c8a 100755 --- a/lib/XChemProcess.py +++ b/lib/XChemProcess.py @@ -7,11 +7,26 @@ import glob from PyQt4 import QtGui, QtCore -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) class run_xia2(QtCore.QThread): - def __init__(self, initial_model_directory, run_dict, protocol, spg, ref, reso_limit, cc_half, xce_logfile, external_software, ccp4_scratch_directory, max_queue_jobs, database, overwrite): + def __init__( + self, + initial_model_directory, + run_dict, + protocol, + spg, + ref, + reso_limit, + cc_half, + xce_logfile, + external_software, + ccp4_scratch_directory, + max_queue_jobs, + database, + overwrite, + ): QtCore.QThread.__init__(self) self.initial_model_directory = initial_model_directory self.run_dict = run_dict @@ -34,184 +49,294 @@ def run(self): # first create directories if they do not exist if not self.protocol: - self.Logfile.insert( - 'please select data processing protocol first!') + self.Logfile.insert("please select data processing protocol first!") return None for i, xtal in enumerate(self.run_dict): - script = '' + script = "" - if self.external_software['qsub']: - script += '#PBS -joe -N XCE_reprocess\n' + if self.external_software["qsub"]: + script += "#PBS -joe -N XCE_reprocess\n" else: - script += '#!'+os.getenv('SHELL')+'\n' + script += "#!" + os.getenv("SHELL") + "\n" - if 'bash' in os.getenv('SHELL'): - script += 'export XChemExplorer_DIR="' + \ - os.getenv('XChemExplorer_DIR')+'"\n' - elif 'csh' in os.getenv('SHELL'): - script += 'setenv XChemExplorer_DIR ' + \ - os.getenv('XChemExplorer_DIR')+'\n' + if "bash" in os.getenv("SHELL"): + script += ( + 'export XChemExplorer_DIR="' + + os.getenv("XChemExplorer_DIR") + + '"\n' + ) + elif "csh" in os.getenv("SHELL"): + script += ( + "setenv XChemExplorer_DIR " + os.getenv("XChemExplorer_DIR") + "\n" + ) - if os.getcwd().startswith('/dls'): - script += 'module load ccp4/7.1.018\n' - script += 'module load XDS\n' -# script += 'module load phenix\n' + if os.getcwd().startswith("/dls"): + script += "module load ccp4/7.1.018\n" + script += "module load XDS\n" + # script += 'module load phenix\n' -# 2018-09-19 - removed this for Joe's test -# script += 'module load ccp4\n' -# script += 'module load XDS\n' -# script += 'module load ccp4 xia2\n' -# print 'hallo' + # 2018-09-19 - removed this for Joe's test + # script += 'module load ccp4\n' + # script += 'module load XDS\n' + # script += 'module load ccp4 xia2\n' + # print 'hallo' if not self.spg: - spg_option = '' + spg_option = "" else: - spg_option = 'space_group='+str(self.spg[0]) + spg_option = "space_group=" + str(self.spg[0]) if not self.ref: - ref_option = '' + ref_option = "" else: - ref_option = 'reference_reflection_file='+str(self.ref[0]) + ref_option = "reference_reflection_file=" + str(self.ref[0]) if not self.reso_limit: - reso_limit_option = '' + reso_limit_option = "" else: - reso_limit_option = 'misigma='+str(self.reso_limit[0]) + reso_limit_option = "misigma=" + str(self.reso_limit[0]) if not self.cc_half: - cc_half_option = '' + cc_half_option = "" else: - cc_half_option = 'cc_half='+str(self.cc_half[0]) + cc_half_option = "cc_half=" + str(self.cc_half[0]) # first link diffraction images into directory if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): os.mkdir(os.path.join(self.initial_model_directory, xtal)) - if not os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'diffraction_images')): - os.mkdir(os.path.join(self.initial_model_directory, - xtal, 'diffraction_images')) + if not os.path.isdir( + os.path.join(self.initial_model_directory, xtal, "diffraction_images") + ): + os.mkdir( + os.path.join( + self.initial_model_directory, xtal, "diffraction_images" + ) + ) - if not os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'processed')): - os.mkdir(os.path.join( - self.initial_model_directory, xtal, 'processed')) -# 2018-09-19 - disabled this for Joe's test -# if os.path.isfile(os.path.join(self.initial_model_directory,xtal,'processed','run_in_progress')): -# self.Logfile.insert('data processing is in progress; skipping...') -# continue + if not os.path.isdir( + os.path.join(self.initial_model_directory, xtal, "processed") + ): + os.mkdir(os.path.join(self.initial_model_directory, xtal, "processed")) + # 2018-09-19 - disabled this for Joe's test + # if os.path.isfile(os.path.join(self.initial_model_directory,xtal,'processed','run_in_progress')): + # self.Logfile.insert('data processing is in progress; skipping...') + # continue f = True if f: - print('hallo') + print("hallo") else: if self.overwrite: - os.chdir(os.path.join(self.initial_model_directory, - xtal, 'diffraction_images')) - self.Logfile.insert('removing all links to diffraction images in '+os.path.join( - self.initial_model_directory, xtal, 'diffraction_images')) - os.system('/bin/rm -fr *') - os.chdir(os.path.join( - self.initial_model_directory, xtal, 'processed')) - self.Logfile.insert('removing all links to diffraction images in '+os.path.join( - self.initial_model_directory, xtal, 'processed')) - os.system('/bin/rm -fr *') - os.chdir(os.path.join( - self.initial_model_directory, xtal, 'processed')) -# 2018-09-19 - disabled this for Joe's test -# os.system('touch run_in_progress') + os.chdir( + os.path.join( + self.initial_model_directory, xtal, "diffraction_images" + ) + ) + self.Logfile.insert( + "removing all links to diffraction images in " + + os.path.join( + self.initial_model_directory, xtal, "diffraction_images" + ) + ) + os.system("/bin/rm -fr *") + os.chdir( + os.path.join(self.initial_model_directory, xtal, "processed") + ) + self.Logfile.insert( + "removing all links to diffraction images in " + + os.path.join(self.initial_model_directory, xtal, "processed") + ) + os.system("/bin/rm -fr *") + os.chdir(os.path.join(self.initial_model_directory, xtal, "processed")) + # 2018-09-19 - disabled this for Joe's test + # os.system('touch run_in_progress') for n, entry in enumerate(sorted(self.run_dict[xtal])): newRun = 1 - for runDir in sorted(glob.glob(os.path.join(self.initial_model_directory, xtal, 'diffraction_images', 'run_*'))): - newRun = int(runDir[runDir.rfind('_')+1:])+1 + for runDir in sorted( + glob.glob( + os.path.join( + self.initial_model_directory, + xtal, + "diffraction_images", + "run_*", + ) + ) + ): + newRun = int(runDir[runDir.rfind("_") + 1 :]) + 1 - os.mkdir(os.path.join(self.initial_model_directory, - xtal, 'diffraction_images', 'run_'+str(newRun))) + os.mkdir( + os.path.join( + self.initial_model_directory, + xtal, + "diffraction_images", + "run_" + str(newRun), + ) + ) image_dir = os.path.join( - self.initial_model_directory, xtal, 'diffraction_images', 'run_'+str(newRun)) - os.chdir(os.path.join(self.initial_model_directory, - xtal, 'diffraction_images', 'run_'+str(newRun))) - os.system('ln -s '+os.path.join(entry[0], entry[1])+'* .') + self.initial_model_directory, + xtal, + "diffraction_images", + "run_" + str(newRun), + ) + os.chdir( + os.path.join( + self.initial_model_directory, + xtal, + "diffraction_images", + "run_" + str(newRun), + ) + ) + os.system("ln -s " + os.path.join(entry[0], entry[1]) + "* .") - os.chdir(os.path.join( - self.initial_model_directory, xtal, 'processed')) - os.mkdir(os.path.join(self.initial_model_directory, - xtal, 'processed', 'run_'+str(newRun))) + os.chdir(os.path.join(self.initial_model_directory, xtal, "processed")) + os.mkdir( + os.path.join( + self.initial_model_directory, + xtal, + "processed", + "run_" + str(newRun), + ) + ) for pipeline in self.protocol: - script += 'cd ' + \ - os.path.join(self.initial_model_directory, xtal, - 'processed', 'run_'+str(newRun), pipeline)+'\n' - if not os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'processed', 'run_'+str(newRun), pipeline)): - os.mkdir(os.path.join(self.initial_model_directory, - xtal, 'processed', 'run_'+str(newRun), pipeline)) + script += ( + "cd " + + os.path.join( + self.initial_model_directory, + xtal, + "processed", + "run_" + str(newRun), + pipeline, + ) + + "\n" + ) + if not os.path.isdir( + os.path.join( + self.initial_model_directory, + xtal, + "processed", + "run_" + str(newRun), + pipeline, + ) + ): + os.mkdir( + os.path.join( + self.initial_model_directory, + xtal, + "processed", + "run_" + str(newRun), + pipeline, + ) + ) - script += '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_status_flag.py') + \ - ' {0!s} {1!s} {2!s} {3!s}\n'.format( - self.database, xtal, 'DataProcessingStatus', 'running') + script += ( + "$CCP4/bin/ccp4-python " + + os.path.join( + os.getenv("XChemExplorer_DIR"), + "helpers", + "update_status_flag.py", + ) + + " {0!s} {1!s} {2!s} {3!s}\n".format( + self.database, xtal, "DataProcessingStatus", "running" + ) + ) -# 2018-09-19 - changed this for Joe's test -# script+='$CCP4/bin/xia2 pipeline='+pipeline+' '+ref_option+' '+spg_option+' '+reso_limit_option+' '+cc_half_option+' '+image_dir+'\n' - script += 'xia2 pipeline='+pipeline+' '+ref_option+' '+spg_option + \ - ' '+reso_limit_option+' '+cc_half_option+' '+image_dir+'\n' + # 2018-09-19 - changed this for Joe's test + # script+='$CCP4/bin/xia2 pipeline='+pipeline+' '+ref_option+' '+spg_option+' '+reso_limit_option+' '+cc_half_option+' '+image_dir+'\n' + script += ( + "xia2 pipeline=" + + pipeline + + " " + + ref_option + + " " + + spg_option + + " " + + reso_limit_option + + " " + + cc_half_option + + " " + + image_dir + + "\n" + ) - script += '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_status_flag.py') + \ - ' {0!s} {1!s} {2!s} {3!s}\n'.format( - self.database, xtal, 'DataProcessingStatus', 'finished') - script += 'cd ' + \ - os.path.join(self.initial_model_directory, - xtal, 'processed')+'\n' - script += '/bin/rm run_in_progress\n' + script += ( + "$CCP4/bin/ccp4-python " + + os.path.join( + os.getenv("XChemExplorer_DIR"), "helpers", "update_status_flag.py" + ) + + " {0!s} {1!s} {2!s} {3!s}\n".format( + self.database, xtal, "DataProcessingStatus", "finished" + ) + ) + script += ( + "cd " + + os.path.join(self.initial_model_directory, xtal, "processed") + + "\n" + ) + script += "/bin/rm run_in_progress\n" os.chdir(self.ccp4_scratch_directory) - f = open('xce_xia2_{0!s}.sh'.format(str(i+1)), 'w') + f = open("xce_xia2_{0!s}.sh".format(str(i + 1)), "w") f.write(script) f.close() - os.system('chmod +x xce_xia2_{0!s}.sh'.format(str(i+1))) - db_dict = {'DataProcessingStatus': 'started'} + os.system("chmod +x xce_xia2_{0!s}.sh".format(str(i + 1))) + db_dict = {"DataProcessingStatus": "started"} self.Logfile.insert( - '{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) + "{0!s}: setting DataProcessingStatus flag to started".format(xtal) + ) self.db.update_data_source(xtal, db_dict) # submit job - self.Logfile.insert('created input scripts for ' + - str(n+1)+' in '+self.ccp4_scratch_directory) + self.Logfile.insert( + "created input scripts for " + + str(n + 1) + + " in " + + self.ccp4_scratch_directory + ) os.chdir(self.ccp4_scratch_directory) - if os.getcwd().startswith('/dls'): - if self.external_software['qsub_array']: - Cmds = ( - '#PBS -joe -N xce_xia2_master\n' - './xce_xia2_$SGE_TASK_ID.sh\n' - ) - f = open('xia2_master.sh', 'w') + if os.getcwd().startswith("/dls"): + if self.external_software["qsub_array"]: + Cmds = "#PBS -joe -N xce_xia2_master\n" "./xce_xia2_$SGE_TASK_ID.sh\n" + f = open("xia2_master.sh", "w") f.write(Cmds) f.close() self.Logfile.insert( - 'submitting array job with maximal 100 jobs running on cluster') - self.Logfile.insert('using the following command:') + "submitting array job with maximal 100 jobs running on cluster" + ) + self.Logfile.insert("using the following command:") self.Logfile.insert( - 'qsub -t 1:{0!s} -tc {1!s} xia2_master.sh'.format(str(i+1), self.max_queue_jobs)) - os.system('qsub -P labxchem -q medium.q -N xia2 -t 1:{0!s} -tc {1!s} xia2_master.sh'.format( - str(i+1), self.max_queue_jobs)) + "qsub -t 1:{0!s} -tc {1!s} xia2_master.sh".format( + str(i + 1), self.max_queue_jobs + ) + ) + os.system( + "qsub -P labxchem -q medium.q -N xia2 -t 1:{0!s} -tc {1!s} xia2_master.sh".format( + str(i + 1), self.max_queue_jobs + ) + ) else: self.Logfile.insert( - "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") - elif self.external_software['qsub']: - self.Logfile.insert( - 'submitting {0!s} individual jobs to cluster'.format((str(i+1)))) + "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file" + ) + elif self.external_software["qsub"]: self.Logfile.insert( - 'WARNING: this could potentially lead to a crash...') - for n in range(i+1): - self.Logfile.insert( - 'qsub xce_xia2_{0!s}.sh'.format((str(n+1)))) + "submitting {0!s} individual jobs to cluster".format((str(i + 1))) + ) + self.Logfile.insert("WARNING: this could potentially lead to a crash...") + for n in range(i + 1): + self.Logfile.insert("qsub xce_xia2_{0!s}.sh".format((str(n + 1)))) os.system( - 'qsub -q medium.q -N xia2 xce_xia2_{0!s}.sh'.format((str(n+1)))) + "qsub -q medium.q -N xia2 xce_xia2_{0!s}.sh".format((str(n + 1))) + ) else: self.Logfile.insert( - 'running %s consecutive XIA2 jobs on your local machine') - for n in range(i+1): - self.Logfile.insert( - 'starting xce_xia2_{0!s}.sh'.format((str(n+1)))) - os.system('./xce_xia2_{0!s}.sh'.format((str(n+1)))) + "running %s consecutive XIA2 jobs on your local machine" + ) + for n in range(i + 1): + self.Logfile.insert("starting xce_xia2_{0!s}.sh".format((str(n + 1)))) + os.system("./xce_xia2_{0!s}.sh".format((str(n + 1)))) # if not os.path.isdir(os.path.join(self.initial_model_directory,xtal)): diff --git a/lib/XChemRefine.py b/lib/XChemRefine.py index d516e3d3..08330e09 100755 --- a/lib/XChemRefine.py +++ b/lib/XChemRefine.py @@ -14,14 +14,14 @@ import os import pygtk -pygtk.require('2.0') +pygtk.require("2.0") # sys.path.append(os.path.join(os.getenv('CCP4'),'lib/python2.7/site-packages')) -#import coot +# import coot # sys.path.append('/usr/local/coot/SoakProc/lib') -#import coot_utils_XChem +# import coot_utils_XChem -sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") def GetSerial(ProjectPath, xtalID): @@ -31,12 +31,12 @@ def GetSerial(ProjectPath, xtalID): temp = [] found = 0 if os.path.isdir(os.path.join(ProjectPath, xtalID)): - for item in glob.glob(os.path.join(ProjectPath, xtalID, '*')): - if item.startswith(os.path.join(ProjectPath, xtalID, 'Refine_')): - if item.endswith('-report'): + for item in glob.glob(os.path.join(ProjectPath, xtalID, "*")): + if item.startswith(os.path.join(ProjectPath, xtalID, "Refine_")): + if item.endswith("-report"): continue try: - temp.append(int(item[item.rfind('_')+1:])) + temp.append(int(item[item.rfind("_") + 1 :])) except ValueError: continue found = 1 @@ -48,12 +48,11 @@ def GetSerial(ProjectPath, xtalID): class RefineParams(object): - def __init__(self, ProjectPath, xtalID, compoundID, datasource): self.ProjectPath = ProjectPath self.xtalID = xtalID self.compoundID = compoundID - self.prefix = 'refine' + self.prefix = "refine" self.datasource = datasource def RefmacRefinementParams(self, RefmacParams): @@ -65,72 +64,72 @@ def RefmacRefinementParams(self, RefmacParams): self.vbox = gtk.VBox() self.hbox1 = gtk.HBox() - self.hbox1.add(gtk.Label('Refine')) + self.hbox1.add(gtk.Label("Refine")) self.cb = gtk.combo_box_new_text() self.cb.connect("changed", self.ChooseBfacRefinement) - for item in ['isotropic', 'anisotropic']: + for item in ["isotropic", "anisotropic"]: self.cb.append_text(item) - if 'ISOT' in self.RefmacParams['BREF']: + if "ISOT" in self.RefmacParams["BREF"]: self.cb.set_active(0) - if 'ANIS' in self.RefmacParams['BREF']: + if "ANIS" in self.RefmacParams["BREF"]: self.cb.set_active(1) self.hbox1.add(self.cb) - self.hbox1.add(gtk.Label('temperature factors')) + self.hbox1.add(gtk.Label("temperature factors")) self.vbox.add(self.hbox1) self.hbox2 = gtk.HBox() - self.hbox2.add(gtk.Label('Number of Cycles: ')) + self.hbox2.add(gtk.Label("Number of Cycles: ")) self.Ncycles = gtk.Entry() self.Ncycles.add_events(gtk.gdk.KEY_RELEASE_MASK) self.Ncycles.connect("key-release-event", self.on_key_release_Ncycles) - self.Ncycles.set_text(self.RefmacParams['NCYCLES']) + self.Ncycles.set_text(self.RefmacParams["NCYCLES"]) self.hbox2.add(self.Ncycles) self.vbox.add(self.hbox2) self.hbox3 = gtk.HBox() - self.hbox3.add(gtk.Label('MATRIX WEIGHT: ')) + self.hbox3.add(gtk.Label("MATRIX WEIGHT: ")) self.MATRIX_WEIGHT = gtk.Entry() self.MATRIX_WEIGHT.add_events(gtk.gdk.KEY_RELEASE_MASK) self.MATRIX_WEIGHT.connect( - "key-release-event", self.on_key_release_MATRIX_WEIGHT) - self.MATRIX_WEIGHT.set_text(self.RefmacParams['MATRIX_WEIGHT']) + "key-release-event", self.on_key_release_MATRIX_WEIGHT + ) + self.MATRIX_WEIGHT.set_text(self.RefmacParams["MATRIX_WEIGHT"]) self.hbox3.add(self.MATRIX_WEIGHT) self.vbox.add(self.hbox3) - self.TLS = gtk.CheckButton( - 'TLS (find TLS groups with phenix.find_tls_groups)') + self.TLS = gtk.CheckButton("TLS (find TLS groups with phenix.find_tls_groups)") self.TLS.connect("toggled", self.TLSCallback) - if self.RefmacParams['TLS'] == 'refi tlsc 10\n': + if self.RefmacParams["TLS"] == "refi tlsc 10\n": self.TLS.set_active(True) self.vbox.pack_start(self.TLS, False) - self.NCS = gtk.CheckButton('NCS (if applicable') + self.NCS = gtk.CheckButton("NCS (if applicable") self.NCS.connect("toggled", self.NCSCallback) - if self.RefmacParams['NCS'] == 'NCSR LOCAL\n': + if self.RefmacParams["NCS"] == "NCSR LOCAL\n": self.NCS.set_active(True) self.vbox.pack_start(self.NCS, False) - self.TWIN = gtk.CheckButton('Twin?') + self.TWIN = gtk.CheckButton("Twin?") self.TWIN.connect("toggled", self.TWINCallback) - if self.RefmacParams['TWIN'] == 'TWIN\n': + if self.RefmacParams["TWIN"] == "TWIN\n": self.TWIN.set_active(True) self.vbox.pack_start(self.TWIN, False) - self.WATER = gtk.CheckButton('Update waters (BUSTER)') + self.WATER = gtk.CheckButton("Update waters (BUSTER)") self.WATER.connect("toggled", self.WATERCallback) - if self.RefmacParams['WATER'] == 'WATER\n': + if self.RefmacParams["WATER"] == "WATER\n": self.WATER.set_active(True) self.vbox.pack_start(self.WATER, False) - self.LIGOCC = gtk.CheckButton('Refine ligand occupancy (BUSTER)') + self.LIGOCC = gtk.CheckButton("Refine ligand occupancy (BUSTER)") self.LIGOCC.connect("toggled", self.LIGOCCCallback) - if self.RefmacParams['LIGOCC'] == 'LIGOCC\n': + if self.RefmacParams["LIGOCC"] == "LIGOCC\n": self.LIGOCC.set_active(True) self.vbox.pack_start(self.LIGOCC, False) - self.SANITY = gtk.CheckButton('Ignore sanity checks (BUSTER)') + self.SANITY = gtk.CheckButton("Ignore sanity checks (BUSTER)") self.SANITY.connect("toggled", self.SANITYCallback) - if self.RefmacParams['SANITY'] == 'off\n': + if self.RefmacParams["SANITY"] == "off\n": self.SANITY.set_active(True) self.vbox.pack_start(self.SANITY, False) @@ -144,66 +143,66 @@ def RefmacRefinementParams(self, RefmacParams): def TLSCallback(self, widget): if widget.get_active(): - self.RefmacParams['TLS'] = 'refi tlsc 10\n' - self.RefmacParams['TLSIN'] = 'refmac.tls\n' - self.RefmacParams['TLSOUT'] = 'out.tls\n' - self.RefmacParams['TLSADD'] = 'TLSO ADDU\n' + self.RefmacParams["TLS"] = "refi tlsc 10\n" + self.RefmacParams["TLSIN"] = "refmac.tls\n" + self.RefmacParams["TLSOUT"] = "out.tls\n" + self.RefmacParams["TLSADD"] = "TLSO ADDU\n" else: - self.RefmacParams['TLS'] = '' - self.RefmacParams['TLSIN'] = '' - self.RefmacParams['TLSOUT'] = '' - self.RefmacParams['TLSADD'] = '' + self.RefmacParams["TLS"] = "" + self.RefmacParams["TLSIN"] = "" + self.RefmacParams["TLSOUT"] = "" + self.RefmacParams["TLSADD"] = "" return self.RefmacParams def NCSCallback(self, widget): if widget.get_active(): - self.RefmacParams['NCS'] = 'NCSR LOCAL\n' + self.RefmacParams["NCS"] = "NCSR LOCAL\n" else: - self.RefmacParams['NCS'] = '' + self.RefmacParams["NCS"] = "" return self.RefmacParams def ChooseBfacRefinement(self, widget): - if widget.get_active_text() == 'isotropic': - self.RefmacParams['BREF'] = ' bref ISOT\n' - if widget.get_active_text() == 'anisotropic': - self.RefmacParams['BREF'] = ' bref ANIS\n' + if widget.get_active_text() == "isotropic": + self.RefmacParams["BREF"] = " bref ISOT\n" + if widget.get_active_text() == "anisotropic": + self.RefmacParams["BREF"] = " bref ANIS\n" return self.RefmacParams def on_key_release_Ncycles(self, widget, event): print(widget.get_text()) - self.RefmacParams['NCYCLES'] = widget.get_text() + self.RefmacParams["NCYCLES"] = widget.get_text() return self.RefmacParams def on_key_release_MATRIX_WEIGHT(self, widget, event): - self.RefmacParams['MATRIX_WEIGHT'] = widget.get_text() + self.RefmacParams["MATRIX_WEIGHT"] = widget.get_text() return self.RefmacParams def TWINCallback(self, widget): if widget.get_active(): - self.RefmacParams['TWIN'] = 'TWIN\n' + self.RefmacParams["TWIN"] = "TWIN\n" else: - self.RefmacParams['TWIN'] = '' + self.RefmacParams["TWIN"] = "" return self.RefmacParams def WATERCallback(self, widget): if widget.get_active(): - self.RefmacParams['WATER'] = 'WATER\n' + self.RefmacParams["WATER"] = "WATER\n" else: - self.RefmacParams['WATER'] = '' + self.RefmacParams["WATER"] = "" return self.RefmacParams def LIGOCCCallback(self, widget): if widget.get_active(): - self.RefmacParams['LIGOCC'] = 'LIGOCC\n' + self.RefmacParams["LIGOCC"] = "LIGOCC\n" else: - self.RefmacParams['LIGOCC'] = '' + self.RefmacParams["LIGOCC"] = "" return self.RefmacParams def SANITYCallback(self, widget): if widget.get_active(): - self.RefmacParams['SANITY'] = 'off\n' + self.RefmacParams["SANITY"] = "off\n" else: - self.RefmacParams['SANITY'] = '' + self.RefmacParams["SANITY"] = "" return self.RefmacParams def OK(self, widget): @@ -211,55 +210,89 @@ def OK(self, widget): def ParamsFromPreviousCycle(self, Serial): - RefmacParams = {'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '', - 'WATER': '', - 'LIGOCC': '', - 'SANITY': ''} - - if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): - for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): - if line.startswith('refi tlsc'): - RefmacParams['TLS'] = line - if line.startswith('TLSO'): - RefmacParams['TLSADD'] = line - if line.startswith('NCSR LOCAL'): - RefmacParams['NCS'] = line - if line.startswith(' bref '): - RefmacParams['BREF'] = line - if line.startswith('ncyc'): - RefmacParams['Ncycles'] = line.split()[1] - if line.startswith('weight'): - RefmacParams['MATRIX_WEIGHT'] = line.split()[ - len(line.split())-1] - if line.startswith('TWIN'): - RefmacParams['TWIN'] = line - elif os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'refmac.csh')): - for line in open(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'refmac.csh')): - if line.startswith('refi tlsc'): - RefmacParams['TLS'] = line - if line.startswith('TLSO'): - RefmacParams['TLSADD'] = line - if line.startswith('NCSR LOCAL'): - RefmacParams['NCS'] = line - if line.startswith(' bref '): - RefmacParams['BREF'] = line - if line.startswith('ncyc'): - RefmacParams['Ncycles'] = line.split()[1] - if line.startswith('weight'): - RefmacParams['MATRIX_WEIGHT'] = line.split()[ - len(line.split())-1] - if line.startswith('TWIN'): - RefmacParams['TWIN'] = line + RefmacParams = { + "HKLIN": "", + "HKLOUT": "", + "XYZIN": "", + "XYZOUT": "", + "LIBIN": "", + "LIBOUT": "", + "TLSIN": "", + "TLSOUT": "", + "TLSADD": "", + "NCYCLES": "10", + "MATRIX_WEIGHT": "AUTO", + "BREF": " bref ISOT\n", + "TLS": "", + "NCS": "", + "TWIN": "", + "WATER": "", + "LIGOCC": "", + "SANITY": "", + } + + if os.path.isfile( + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(Serial) + + "/refmac.csh" + ): + for line in open( + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(Serial) + + "/refmac.csh" + ): + if line.startswith("refi tlsc"): + RefmacParams["TLS"] = line + if line.startswith("TLSO"): + RefmacParams["TLSADD"] = line + if line.startswith("NCSR LOCAL"): + RefmacParams["NCS"] = line + if line.startswith(" bref "): + RefmacParams["BREF"] = line + if line.startswith("ncyc"): + RefmacParams["Ncycles"] = line.split()[1] + if line.startswith("weight"): + RefmacParams["MATRIX_WEIGHT"] = line.split()[len(line.split()) - 1] + if line.startswith("TWIN"): + RefmacParams["TWIN"] = line + elif os.path.isfile( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "refmac.csh", + ) + ): + for line in open( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "refmac.csh", + ) + ): + if line.startswith("refi tlsc"): + RefmacParams["TLS"] = line + if line.startswith("TLSO"): + RefmacParams["TLSADD"] = line + if line.startswith("NCSR LOCAL"): + RefmacParams["NCS"] = line + if line.startswith(" bref "): + RefmacParams["BREF"] = line + if line.startswith("ncyc"): + RefmacParams["Ncycles"] = line.split()[1] + if line.startswith("weight"): + RefmacParams["MATRIX_WEIGHT"] = line.split()[len(line.split()) - 1] + if line.startswith("TWIN"): + RefmacParams["TWIN"] = line return RefmacParams @@ -270,10 +303,10 @@ def GetRefinementHistory(self): RfreeList = [] found = False - for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): - if item.startswith(os.path.join(self.ProjectPath, self.xtalID, 'Refine_')): - print(item[item.rfind('_')+1:]) - RefinementCycle.append(int(item[item.rfind('_')+1:])) + for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, "*")): + if item.startswith(os.path.join(self.ProjectPath, self.xtalID, "Refine_")): + print(item[item.rfind("_") + 1 :]) + RefinementCycle.append(int(item[item.rfind("_") + 1 :])) found = True if found: for cycle in sorted(RefinementCycle): @@ -284,14 +317,29 @@ def GetRefinementHistory(self): try: found_Rcryst = False found_Rfree = False - newestPDB = max(glob.iglob(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str( - cycle)+'/refine_'+str(cycle)+'.pdb'), key=os.path.getctime) + newestPDB = max( + glob.iglob( + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(cycle) + + "/refine_" + + str(cycle) + + ".pdb" + ), + key=os.path.getctime, + ) for line in open(newestPDB): - if line.startswith('REMARK 3 R VALUE (WORKING + TEST SET) :'): + if line.startswith( + "REMARK 3 R VALUE (WORKING + TEST SET) :" + ): Rcryst = line.split()[9] RcrystList.append(float(Rcryst)) found_Rcryst = True - if line.startswith('REMARK 3 FREE R VALUE :'): + if line.startswith( + "REMARK 3 FREE R VALUE :" + ): Rfree = line.split()[6] RfreeList.append(float(Rfree)) found_Rfree = True @@ -299,29 +347,28 @@ def GetRefinementHistory(self): RcrystList.append(0) if not found_Rfree: RfreeList.append(0) -# if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): -# for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): -# if line.startswith('| LIG'): LigandCC = line.split()[6] -# RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' + # if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): + # for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): + # if line.startswith('| LIG'): LigandCC = line.split()[6] + # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' except ValueError: RcrystList.append(0) RfreeList.append(0) -# RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' + # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' else: RefinementCycle = [0] RcrystList = [0] RfreeList = [0] print(RefinementCycle, RcrystList, RfreeList) - return(sorted(RefinementCycle), RcrystList, RfreeList) + return (sorted(RefinementCycle), RcrystList, RfreeList) class Refine(object): - def __init__(self, ProjectPath, xtalID, compoundID, datasource): self.ProjectPath = ProjectPath self.xtalID = xtalID self.compoundID = compoundID - self.prefix = 'refine' + self.prefix = "refine" self.datasource = datasource self.error = False self.Logfile = None @@ -333,10 +380,12 @@ def GetSerial(self): temp = [] found = 0 if os.path.isdir(os.path.join(self.ProjectPath, self.xtalID)): - for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): - if item.startswith(os.path.join(self.ProjectPath, self.xtalID, 'Refine_')): - print(int(item[item.rfind('_')+1:])) - temp.append(int(item[item.rfind('_')+1:])) + for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, "*")): + if item.startswith( + os.path.join(self.ProjectPath, self.xtalID, "Refine_") + ): + print(int(item[item.rfind("_") + 1 :])) + temp.append(int(item[item.rfind("_") + 1 :])) found = 1 if found: Serial = max(temp) + 1 @@ -345,7 +394,7 @@ def GetSerial(self): return Serial def make_covalent_link(self, covLinkAtomSpec, Logfile): - residuesToModify = ['CYS', 'SER'] + residuesToModify = ["CYS", "SER"] atom1 = covLinkAtomSpec[1][5] atom2 = covLinkAtomSpec[2][5] @@ -353,49 +402,58 @@ def make_covalent_link(self, covLinkAtomSpec, Logfile): residue_2 = covLinkAtomSpec[4] if residue_2 in residuesToModify: - bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' % ( - residue_1, self.compoundID, atom1, residue_2, atom2) + bond_text = ( + "LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s" + % (residue_1, self.compoundID, atom1, residue_2, atom2) + ) else: - bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' % ( - residue_2, self.compoundID, atom2, residue_1, atom1) + bond_text = ( + "LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s" + % (residue_2, self.compoundID, atom2, residue_1, atom1) + ) os.chdir(os.path.join(self.ProjectPath, self.xtalID)) - f = open('covalent_bond.txt', 'w') + f = open("covalent_bond.txt", "w") f.write(bond_text) f.close() # seems somewhat unncessary, but acedrg does not like some certain descriptions generated by phenix.elbow - os.system('acedrg -c %s.cif -o %s_acedrg' % - (self.compoundID, self.compoundID)) + os.system("acedrg -c %s.cif -o %s_acedrg" % (self.compoundID, self.compoundID)) - os.system('acedrg -L covalent_bond.txt -o %s' % self.compoundID) + os.system("acedrg -L covalent_bond.txt -o %s" % self.compoundID) - if os.path.isfile('%s_link.cif' % self.compoundID): - Logfile.insert( - 'succefully created link file %s_link.cif' % self.compoundID) - os.system('/bin/rm %s.cif' % self.compoundID) - os.system('ln -s %s_link.cif %s.cif' % - (self.compoundID, self.compoundID)) + if os.path.isfile("%s_link.cif" % self.compoundID): + Logfile.insert("succefully created link file %s_link.cif" % self.compoundID) + os.system("/bin/rm %s.cif" % self.compoundID) + os.system("ln -s %s_link.cif %s.cif" % (self.compoundID, self.compoundID)) else: - Logfile.error('could not create linkfile; please check logs in %s/%s' % - (self.ProjectPath, self.xtalID)) + Logfile.error( + "could not create linkfile; please check logs in %s/%s" + % (self.ProjectPath, self.xtalID) + ) def get_hklin_hklout(self, Serial): ####################################################### # HKLIN & HKLOUT hklin = None hklout = None - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'.free.mtz')): + if os.path.isfile( + os.path.join(self.ProjectPath, self.xtalID, self.xtalID + ".free.mtz") + ): hklin = os.path.join( - self.ProjectPath, self.xtalID, self.xtalID+'.free.mtz') -# elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): -# RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') + self.ProjectPath, self.xtalID, self.xtalID + ".free.mtz" + ) + # elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): + # RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') else: - self.Logfile.error( - '%s: cannot find HKLIN for refinement' % self.xtalID) + self.Logfile.error("%s: cannot find HKLIN for refinement" % self.xtalID) self.error = True - hklout = os.path.join(self.ProjectPath, self.xtalID, - 'Refine_'+Serial, 'refine_'+Serial+'.mtz') + hklout = os.path.join( + self.ProjectPath, + self.xtalID, + "Refine_" + Serial, + "refine_" + Serial + ".mtz", + ) return hklin, hklout def get_xyzin_xyzout(self, Serial): @@ -403,17 +461,36 @@ def get_xyzin_xyzout(self, Serial): # XYZIN & XYZOUT xyzin = None xyzout = None - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'in.pdb')): + if os.path.isfile( + os.path.join(self.ProjectPath, self.xtalID, "Refine_" + Serial, "in.pdb") + ): xyzin = os.path.join( - self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'in.pdb') + self.ProjectPath, self.xtalID, "Refine_" + Serial, "in.pdb" + ) xyzout = os.path.join( - self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'refine_'+Serial+'.pdb') - elif os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'in.pdb')): - xyzin = os.path.join(self.ProjectPath, self.xtalID, - 'cootOut', 'Refine_'+str(Serial), 'in.pdb') + self.ProjectPath, + self.xtalID, + "Refine_" + Serial, + "refine_" + Serial + ".pdb", + ) + elif os.path.isfile( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "in.pdb", + ) + ): + xyzin = os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "in.pdb", + ) else: - self.Logfile.error( - '%s: cannot find XYZIN for refinement' % self.xtalID) + self.Logfile.error("%s: cannot find XYZIN for refinement" % self.xtalID) self.error = True return xyzin, xyzout @@ -422,14 +499,20 @@ def get_libin_libout(self, Serial): # LIBIN & LIBOUT libin = None libout = None - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.compoundID+'.cif')): + if os.path.isfile( + os.path.join(self.ProjectPath, self.xtalID, self.compoundID + ".cif") + ): libin = os.path.join( - self.ProjectPath, self.xtalID, self.compoundID+'.cif') + self.ProjectPath, self.xtalID, self.compoundID + ".cif" + ) libout = os.path.join( - self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'refine_'+Serial+'.cif') + self.ProjectPath, + self.xtalID, + "Refine_" + Serial, + "refine_" + Serial + ".cif", + ) else: - self.Logfile.error( - '%s: cannot find CIF file for refinement' % self.xtalID) + self.Logfile.error("%s: cannot find CIF file for refinement" % self.xtalID) self.error = True return libin, libout @@ -437,219 +520,274 @@ def write_refinement_in_progress(self): ####################################################### # we write 'REFINEMENT_IN_PROGRESS' immediately to avoid unncessary refiment os.chdir(os.path.join(self.ProjectPath, self.xtalID)) - os.system('touch REFINEMENT_IN_PROGRESS') + os.system("touch REFINEMENT_IN_PROGRESS") def clean_up_before_refinement(self): ####################################################### # clean up! # and remove all files which will be re-created by current refinement cycle os.chdir(os.path.join(self.ProjectPath, self.xtalID)) - os.system('/bin/rm refine.pdb refine.mtz refine.split.bound-state.pdb validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log') + os.system( + "/bin/rm refine.pdb refine.mtz refine.split.bound-state.pdb validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log" + ) def get_shebang(self, program, qsub): - cmd = '#!'+os.getenv('SHELL')+'\n' + cmd = "#!" + os.getenv("SHELL") + "\n" if qsub: - cmd += '#PBS -joe -N xce_%s\n' % program + cmd += "#PBS -joe -N xce_%s\n" % program return cmd def load_modules(self, cmd): ####################################################### # PHENIX stuff (if working at DLS) - if os.getcwd().startswith('/dls'): - cmd += 'module load phenix\n' - cmd += 'module load buster\n' + if os.getcwd().startswith("/dls"): + cmd += "module load phenix\n" + cmd += "module load buster\n" return cmd def get_source_line(self, cmd): - if 'bash' in os.getenv('SHELL'): - cmd += 'export XChemExplorer_DIR="' + \ - os.getenv('XChemExplorer_DIR')+'"\n' - elif 'csh' in os.getenv('SHELL'): - cmd += 'setenv XChemExplorer_DIR ' + \ - os.getenv('XChemExplorer_DIR')+'\n' + if "bash" in os.getenv("SHELL"): + cmd += 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"\n' + elif "csh" in os.getenv("SHELL"): + cmd += "setenv XChemExplorer_DIR " + os.getenv("XChemExplorer_DIR") + "\n" return cmd def set_refinement_status(self, cmd): - cmd += ('$CCP4/bin/ccp4-python ' - ' $XChemExplorer_DIR/helpers/update_status_flag.py ' - + self.datasource + ' ' + self.xtalID + ' RefinementStatus running\n') + cmd += ( + "$CCP4/bin/ccp4-python " + " $XChemExplorer_DIR/helpers/update_status_flag.py " + + self.datasource + + " " + + self.xtalID + + " RefinementStatus running\n" + ) return cmd - def add_buster_command(self, cmd, xyzin, hklin, libin, Serial, anisotropic_Bfactor, update_water, refine_ligand_occupancy, ignore_sanity_check): + def add_buster_command( + self, + cmd, + xyzin, + hklin, + libin, + Serial, + anisotropic_Bfactor, + update_water, + refine_ligand_occupancy, + ignore_sanity_check, + ): cmd += ( - 'refine ' - ' -p %s' % xyzin + - ' -m %s' % hklin + - ' -l %s' % libin + - ' -autoncs' - + anisotropic_Bfactor + update_water + refine_ligand_occupancy + ignore_sanity_check + - ' -d Refine_%s\n' % str(Serial) + "refine " + " -p %s" % xyzin + + " -m %s" % hklin + + " -l %s" % libin + + " -autoncs" + + anisotropic_Bfactor + + update_water + + refine_ligand_occupancy + + ignore_sanity_check + + " -d Refine_%s\n" % str(Serial) ) return cmd def run_giant_score_model(self, cmd, cycle): - old_ccp4 = '' - if os.path.isfile('/dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh'): + old_ccp4 = "" + if os.path.isfile( + "/dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh" + ): # giant.score_model does not work with ccp4 7.1-000 - old_ccp4 = 'source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'-pandda-model.pdb')): - cmd += ('cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+cycle+'\n' - + old_ccp4 + - 'giant.score_model ' - ' pdb1=../%s-pandda-model.pdb ' % self.xtalID + - ' mtz1=../dimple.mtz ' - ' pdb2=refine.pdb ' - ' mtz2=refine.mtz\n') + old_ccp4 = "source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n" + if os.path.isfile( + os.path.join( + self.ProjectPath, self.xtalID, self.xtalID + "-pandda-model.pdb" + ) + ): + cmd += ( + "cd " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + cycle + + "\n" + + old_ccp4 + + "giant.score_model " + " pdb1=../%s-pandda-model.pdb " % self.xtalID + " mtz1=../dimple.mtz " + " pdb2=refine.pdb " + " mtz2=refine.mtz\n" + ) return cmd def add_validation(self, cmd, cycle, program): - buster_report = '' - if program == 'refmac': - Serial = '_' + cycle - elif program == 'buster': - Serial = '' - if os.getcwd().startswith('/dls'): - buster_report += 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+cycle+'\n' - buster_report += 'corr -p refine.pdb -m refine.mtz -F 2FOFCWT -P PH2FOFCWT\n' - buster_report += 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' - buster_report += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' - buster_report += 'buster-report -d Refine_%s\n' % cycle + buster_report = "" + if program == "refmac": + Serial = "_" + cycle + elif program == "buster": + Serial = "" + if os.getcwd().startswith("/dls"): + buster_report += ( + "cd " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + cycle + + "\n" + ) + buster_report += ( + "corr -p refine.pdb -m refine.mtz -F 2FOFCWT -P PH2FOFCWT\n" + ) + buster_report += "cd " + self.ProjectPath + "/" + self.xtalID + "\n" + buster_report += ( + "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n" + ) + buster_report += "buster-report -d Refine_%s\n" % cycle cmd += ( - '\n' - + buster_report + - 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' - 'ln -s ./Refine_%s/refine%s.pdb refine.pdb\n' % (cycle, Serial) + - 'ln -s ./Refine_%s/refine%s.mtz refine.mtz\n' % (cycle, Serial) + - 'ln -s refine.pdb refine.split.bound-state.pdb\n' - '\n' - 'phenix.molprobity refine%s.pdb refine%s.mtz\n' % (Serial, Serial) + - '/bin/mv molprobity.out refine_molprobity.log\n' - 'mmtbx.validate_ligands refine%s.pdb refine%s.mtz LIG > validate_ligands.txt\n' % (Serial, Serial) + - '\n' + "\n" + buster_report + "cd " + self.ProjectPath + "/" + self.xtalID + "\n" + "ln -s ./Refine_%s/refine%s.pdb refine.pdb\n" % (cycle, Serial) + + "ln -s ./Refine_%s/refine%s.mtz refine.mtz\n" % (cycle, Serial) + + "ln -s refine.pdb refine.split.bound-state.pdb\n" + "\n" + "phenix.molprobity refine%s.pdb refine%s.mtz\n" % (Serial, Serial) + + "/bin/mv molprobity.out refine_molprobity.log\n" + "mmtbx.validate_ligands refine%s.pdb refine%s.mtz LIG > validate_ligands.txt\n" + % (Serial, Serial) + + "\n" # 'ln -s Refine_%s/validate_ligands.txt .\n' %cycle+ # 'ln -s Refine_%s/refine_molprobity.log .\n' %cycle+ - 'mmtbx.validation_summary refine.pdb > validation_summary.txt\n' - '\n' + "mmtbx.validation_summary refine.pdb > validation_summary.txt\n" + "\n" ) return cmd def calculate_maps(self, cmd, program): - if program == 'refmac': - FWT = 'FWT' - PHWT = 'PHWT' - DELFWT = 'DELFWT' - PHDELWT = 'PHDELWT' - elif program == 'buster': - FWT = '2FOFCWT' - PHWT = 'PH2FOFCWT' - DELFWT = 'FOFCWT' - PHDELWT = 'PHFOFCWT' + if program == "refmac": + FWT = "FWT" + PHWT = "PHWT" + DELFWT = "DELFWT" + PHDELWT = "PHDELWT" + elif program == "buster": + FWT = "2FOFCWT" + PHWT = "PH2FOFCWT" + DELFWT = "FOFCWT" + PHDELWT = "PHFOFCWT" cmd += ( - 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' - '\n' - 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' - ' labin F1=%s PHI=%s\n' % (FWT, PHWT) + - ' grid samp 4.5\n' - 'EOF\n' - '\n' + "cd " + self.ProjectPath + "/" + self.xtalID + "\n" + "\n" + "fft hklin refine.mtz mapout 2fofc.map << EOF\n" + " labin F1=%s PHI=%s\n" % (FWT, PHWT) + " grid samp 4.5\n" + "EOF\n" + "\n" # 'mapmask mapin 2fofc_asu.map xyzin refine.pdb mapout 2fofc.map << EOF\n' # ' border 5\n' # 'EOF\n' # '\n' # '/bin/rm 2fofc_asu.map\n' # '\n' - 'fft hklin refine.mtz mapout fofc.map << EOF\n' - ' labin F1=%s PHI=%s\n' % (DELFWT, PHDELWT) + - ' grid samp 4.5\n' - 'EOF\n' - '\n' + "fft hklin refine.mtz mapout fofc.map << EOF\n" + " labin F1=%s PHI=%s\n" % (DELFWT, PHDELWT) + " grid samp 4.5\n" + "EOF\n" + "\n" # 'mapmask mapin fofc_asu.map xyzin refine.pdb mapout fofc.map << EOF\n' # ' border 5\n' # 'EOF\n' # '\n' # '/bin/rm fofc_asu.map\n' - '\n' + "\n" ) return cmd def run_edstats(self, cmd, resh, resl): cmd += ( - '\n' - 'edstats XYZIN refine.pdb MAPIN1 2fofc.map MAPIN2 fofc.map OUT refine.edstats << eof\n' - ' resl={0!s}\n'.format(resl) + - ' resh={0!s}\n'.format(resh) + - 'eof\n' - '\n' + "\n" + "edstats XYZIN refine.pdb MAPIN1 2fofc.map MAPIN2 fofc.map OUT refine.edstats << eof\n" + " resl={0!s}\n".format(resl) + " resh={0!s}\n".format(resh) + "eof\n" + "\n" ) return cmd def update_database(self, cmd, Serial): - date = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] + date = datetime.strftime(datetime.now(), "%Y-%m-%d_%H-%M-%S.%f")[:-4] user = getpass.getuser() - ccp4_module = '' # need to source again, because giant.score_model still needs outdated version which does not have gemmi - if self.ProjectPath.startswith('/dls'): - ccp4_module = 'module load ccp4/7.1.018' - cmd += ('\n' - + ccp4_module + - '\n' - '$CCP4/bin/ccp4-python ' - + os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_data_source_after_refinement.py') + - ' %s %s %s %s %s %s\n' % (self.datasource, self.xtalID, self.ProjectPath, os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial), user, date)) - cmd += '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' % ( - self.ProjectPath, self.xtalID) + ccp4_module = "" # need to source again, because giant.score_model still needs outdated version which does not have gemmi + if self.ProjectPath.startswith("/dls"): + ccp4_module = "module load ccp4/7.1.018" + cmd += "\n" + ccp4_module + "\n" "$CCP4/bin/ccp4-python " + os.path.join( + os.getenv("XChemExplorer_DIR"), + "helpers", + "update_data_source_after_refinement.py", + ) + " %s %s %s %s %s %s\n" % ( + self.datasource, + self.xtalID, + self.ProjectPath, + os.path.join(self.ProjectPath, self.xtalID, "Refine_" + Serial), + user, + date, + ) + cmd += "/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n" % ( + self.ProjectPath, + self.xtalID, + ) return cmd def write_refinement_script(self, cmd, program): os.chdir(os.path.join(self.ProjectPath, self.xtalID)) - f = open(program + '.sh', 'w') + f = open(program + ".sh", "w") f.write(cmd) f.close() def run_script(self, program, external_software): os.chdir(os.path.join(self.ProjectPath, self.xtalID)) - if external_software['qsub'] and os.path.isdir('/dls'): + if external_software["qsub"] and os.path.isdir("/dls"): self.Logfile.insert( - 'starting refinement with command: qsub -P labxchem -q medium.q %s.sh' % program) + "starting refinement with command: qsub -P labxchem -q medium.q %s.sh" + % program + ) os.system("qsub -P labxchem -q medium.q %s.sh" % program) - elif external_software['qsub'] and not os.path.isdir('/dls'): + elif external_software["qsub"] and not os.path.isdir("/dls"): self.Logfile.insert( - 'starting refinement with command: qsub %s.sh' % program) + "starting refinement with command: qsub %s.sh" % program + ) os.system("qsub %s.sh" % program) - elif external_software['qsub_remote'] != '': - Logfile.insert('starting refinement on remote cluster') - remote_command = external_software['qsub_remote'].replace('qsub', 'cd %s; qsub' % os.path.join( - self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) - self.Logfile.insert( - 'starting refinement with command: %s' % remote_command) - os.system('%s -P labxchem refmac.csh' % remote_command) + elif external_software["qsub_remote"] != "": + Logfile.insert("starting refinement on remote cluster") + remote_command = external_software["qsub_remote"].replace( + "qsub", + "cd %s; qsub" + % os.path.join( + self.ProjectPath, self.xtalID, "cootOut", "Refine_" + str(Serial) + ), + ) + self.Logfile.insert("starting refinement with command: %s" % remote_command) + os.system("%s -P labxchem refmac.csh" % remote_command) else: - self.Logfile.insert( - 'starting refinement with command: ./%s.sh &' % program) - os.system('chmod +x %s.sh' % program) - os.system('./%s.sh &' % program) + self.Logfile.insert("starting refinement with command: ./%s.sh &" % program) + os.system("chmod +x %s.sh" % program) + os.system("./%s.sh &" % program) - def RunBuster(self, Serial, RefmacParams, external_software, xce_logfile, covLinkAtomSpec): + def RunBuster( + self, Serial, RefmacParams, external_software, xce_logfile, covLinkAtomSpec + ): if RefmacParams == None: - anisotropic_Bfactor = ' -M ADP ' - update_water = '' + anisotropic_Bfactor = " -M ADP " + update_water = "" else: - if 'ANIS' in RefmacParams['BREF']: - anisotropic_Bfactor = ' -M ADP ' + if "ANIS" in RefmacParams["BREF"]: + anisotropic_Bfactor = " -M ADP " else: - anisotropic_Bfactor = ' -M TLSbasic ' + anisotropic_Bfactor = " -M TLSbasic " - if 'WATER' in RefmacParams['WATER']: - update_water = ' -WAT ' + if "WATER" in RefmacParams["WATER"]: + update_water = " -WAT " else: - update_water = '' + update_water = "" - if 'off' in RefmacParams['SANITY']: - ignore_sanity_check = ' StopOnGellySanityCheckError=no ' + if "off" in RefmacParams["SANITY"]: + ignore_sanity_check = " StopOnGellySanityCheckError=no " else: - ignore_sanity_check = '' + ignore_sanity_check = "" self.error = False @@ -661,9 +799,13 @@ def RunBuster(self, Serial, RefmacParams, external_software, xce_logfile, covLin self.make_covalent_link(covLinkAtomSpec, self.Logfile) # first check if refinement is ongoing and exit if yes - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'REFINEMENT_IN_PROGRESS')): + if os.path.isfile( + os.path.join(self.ProjectPath, self.xtalID, "REFINEMENT_IN_PROGRESS") + ): self.Logfile.insert( - 'cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' % self.xtalID) + "cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***" + % self.xtalID + ) return None hklin, hklout = self.get_hklin_hklout(Serial) @@ -672,12 +814,12 @@ def RunBuster(self, Serial, RefmacParams, external_software, xce_logfile, covLin xyzin, xyzout = self.get_xyzin_xyzout(Serial) - refine_ligand_occupancy = '' + refine_ligand_occupancy = "" if RefmacParams != None: - if 'LIGOCC' in RefmacParams['LIGOCC']: - ligand_info = pdbtools(xyzin).get_residues_with_resname('LIG') + if "LIGOCC" in RefmacParams["LIGOCC"]: + ligand_info = pdbtools(xyzin).get_residues_with_resname("LIG") if self.prepare_gelly_dat(ligand_info): - refine_ligand_occupancy = ' -B user -Gelly gelly.dat ' + refine_ligand_occupancy = " -B user -Gelly gelly.dat " libin, libout = self.get_libin_libout(Serial) @@ -685,7 +827,7 @@ def RunBuster(self, Serial, RefmacParams, external_software, xce_logfile, covLin self.write_refinement_in_progress() - cmd = self.get_shebang('buster', external_software['qsub']) + cmd = self.get_shebang("buster", external_software["qsub"]) cmd = self.load_modules(cmd) @@ -693,14 +835,23 @@ def RunBuster(self, Serial, RefmacParams, external_software, xce_logfile, covLin cmd = self.set_refinement_status(cmd) - cmd = self.add_buster_command(cmd, xyzin, hklin, libin, Serial, anisotropic_Bfactor, - update_water, refine_ligand_occupancy, ignore_sanity_check) + cmd = self.add_buster_command( + cmd, + xyzin, + hklin, + libin, + Serial, + anisotropic_Bfactor, + update_water, + refine_ligand_occupancy, + ignore_sanity_check, + ) - cmd = self.add_validation(cmd, Serial, 'buster') + cmd = self.add_validation(cmd, Serial, "buster") cmd = self.run_giant_score_model(cmd, Serial) - cmd = self.calculate_maps(cmd, 'buster') + cmd = self.calculate_maps(cmd, "buster") cmd = self.run_edstats(cmd, resh, resl) @@ -708,42 +859,48 @@ def RunBuster(self, Serial, RefmacParams, external_software, xce_logfile, covLin if self.error: self.Logfile.error( - '%s: cannot start refinement; check error message above' % self.xtalID) + "%s: cannot start refinement; check error message above" % self.xtalID + ) else: - self.Logfile.insert('%s: writing buster.sh file in %s' % ( - self.xtalID, os.path.join(self.ProjectPath, self.xtalID))) - self.write_refinement_script(cmd, 'buster') - self.Logfile.insert('%s: starting refinement...' % self.xtalID) - self.run_script('buster', external_software) + self.Logfile.insert( + "%s: writing buster.sh file in %s" + % (self.xtalID, os.path.join(self.ProjectPath, self.xtalID)) + ) + self.write_refinement_script(cmd, "buster") + self.Logfile.insert("%s: starting refinement..." % self.xtalID) + self.run_script("buster", external_software) def prepare_gelly_dat(self, ligand_info): found_ligand = False - gelly = 'NOTE BUSTER_SET Ligand = ' + gelly = "NOTE BUSTER_SET Ligand = " for n, lig in enumerate(ligand_info): resseq = lig[1] chain = lig[2] if n == 0: - gelly += '{ %s|%s }' % (chain.replace(' ', ''), - resseq.replace(' ', '')) + gelly += "{ %s|%s }" % (chain.replace(" ", ""), resseq.replace(" ", "")) else: - gelly += ' + { %s|%s }' % (chain.replace(' ', ''), - resseq.replace(' ', '')) + gelly += " + { %s|%s }" % ( + chain.replace(" ", ""), + resseq.replace(" ", ""), + ) found_ligand = True - if '{' in gelly: - gelly += '\n' + if "{" in gelly: + gelly += "\n" gelly += ( - 'NOTE BUSTER_SET NotLigand = \ Ligand\n' - 'NOTE BUSTER_CONSTANT OCC NotLigand \n' - 'NOTE BUSTER_COMBINE OCC Ligand \n' - 'NOTE BUSTER_COMBINE B Ligand \n' + "NOTE BUSTER_SET NotLigand = \ Ligand\n" + "NOTE BUSTER_CONSTANT OCC NotLigand \n" + "NOTE BUSTER_COMBINE OCC Ligand \n" + "NOTE BUSTER_COMBINE B Ligand \n" ) os.chdir(os.path.join(self.ProjectPath, self.xtalID)) - f = open('gelly.dat', 'w') + f = open("gelly.dat", "w") f.write(gelly) f.close() return found_ligand - def RunRefmac(self, Serial, RefmacParams, external_software, xce_logfile, covLinkAtomSpec): + def RunRefmac( + self, Serial, RefmacParams, external_software, xce_logfile, covLinkAtomSpec + ): if os.path.isfile(xce_logfile): Logfile = XChemLog.updateLog(xce_logfile) @@ -753,274 +910,410 @@ def RunRefmac(self, Serial, RefmacParams, external_software, xce_logfile, covLin self.make_covalent_link(covLinkAtomSpec, Logfile) # first check if refinement is ongoing and exit if yes - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'REFINEMENT_IN_PROGRESS')): + if os.path.isfile( + os.path.join(self.ProjectPath, self.xtalID, "REFINEMENT_IN_PROGRESS") + ): # coot.info_dialog('*** REFINEMENT IN PROGRESS ***') Logfile.insert( - 'cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' % self.xtalID) + "cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***" + % self.xtalID + ) return None ####################################################### # HKLIN & HKLOUT - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'.free.mtz')): - RefmacParams['HKLIN'] = 'HKLIN '+os.path.join( - self.ProjectPath, self.xtalID, self.xtalID+'.free.mtz \\\n') -# elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): -# RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') + if os.path.isfile( + os.path.join(self.ProjectPath, self.xtalID, self.xtalID + ".free.mtz") + ): + RefmacParams["HKLIN"] = "HKLIN " + os.path.join( + self.ProjectPath, self.xtalID, self.xtalID + ".free.mtz \\\n" + ) + # elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): + # RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') else: Logfile.error( - '%s: cannot find HKLIN for refinement; aborting...' % self.xtalID) + "%s: cannot find HKLIN for refinement; aborting..." % self.xtalID + ) return None - RefmacParams['HKLOUT'] = 'HKLOUT '+os.path.join( - self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'refine_'+Serial+'.mtz \\\n') + RefmacParams["HKLOUT"] = "HKLOUT " + os.path.join( + self.ProjectPath, + self.xtalID, + "Refine_" + Serial, + "refine_" + Serial + ".mtz \\\n", + ) ####################################################### # XYZIN & XYZOUT - RefmacParams['XYZIN'] = 'XYZIN ' + \ - os.path.join(self.ProjectPath, self.xtalID, - 'Refine_'+Serial, 'in.pdb \\\n') - RefmacParams['XYZOUT'] = 'XYZOUT '+os.path.join( - self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'refine_'+Serial+'.pdb \\\n') + RefmacParams["XYZIN"] = "XYZIN " + os.path.join( + self.ProjectPath, self.xtalID, "Refine_" + Serial, "in.pdb \\\n" + ) + RefmacParams["XYZOUT"] = "XYZOUT " + os.path.join( + self.ProjectPath, + self.xtalID, + "Refine_" + Serial, + "refine_" + Serial + ".pdb \\\n", + ) ####################################################### # LIBIN & LIBOUT found_cif = False - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.compoundID+'.cif')): - RefmacParams['LIBIN'] = 'LIBIN '+self.ProjectPath + \ - '/'+self.xtalID+'/'+self.compoundID+'.cif \\\n' - RefmacParams['LIBOUT'] = 'LIBOUT '+self.ProjectPath+'/' + \ - self.xtalID+'/Refine_'+Serial+'/refine_'+Serial+'.cif \\\n' + if os.path.isfile( + os.path.join(self.ProjectPath, self.xtalID, self.compoundID + ".cif") + ): + RefmacParams["LIBIN"] = ( + "LIBIN " + + self.ProjectPath + + "/" + + self.xtalID + + "/" + + self.compoundID + + ".cif \\\n" + ) + RefmacParams["LIBOUT"] = ( + "LIBOUT " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + Serial + + "/refine_" + + Serial + + ".cif \\\n" + ) ####################################################### # TLSIN & TLSOUT - findTLS = '\n' - TLSphenix = '' - if RefmacParams['TLS'].startswith('refi'): - if external_software['phenix.find_tls_groups']: - findTLS = os.path.join(os.getenv( - 'XChemExplorer_DIR'), 'helpers', 'phenix_find_TLS_groups.py')+' in.pdb\n' - RefmacParams['TLSIN'] = 'TLSIN '+self.ProjectPath + \ - '/'+self.xtalID+'/Refine_'+Serial+'/refmac.tls \\\n' - RefmacParams['TLSOUT'] = 'TLSOUT '+self.ProjectPath + \ - '/'+self.xtalID+'/Refine_'+Serial+'/refine.tls \\\n' - TLSphenix = ' phenix.tls ' + findTLS = "\n" + TLSphenix = "" + if RefmacParams["TLS"].startswith("refi"): + if external_software["phenix.find_tls_groups"]: + findTLS = ( + os.path.join( + os.getenv("XChemExplorer_DIR"), + "helpers", + "phenix_find_TLS_groups.py", + ) + + " in.pdb\n" + ) + RefmacParams["TLSIN"] = ( + "TLSIN " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + Serial + + "/refmac.tls \\\n" + ) + RefmacParams["TLSOUT"] = ( + "TLSOUT " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + Serial + + "/refine.tls \\\n" + ) + TLSphenix = " phenix.tls " else: - RefmacParams['TLS'] = '\n' + RefmacParams["TLS"] = "\n" - print('==> XCE: assembling refmac.csh') + print("==> XCE: assembling refmac.csh") ####################################################### # we write 'REFINEMENT_IN_PROGRESS' immediately to avoid unncessary refiment os.chdir(os.path.join(self.ProjectPath, self.xtalID)) - os.system('touch REFINEMENT_IN_PROGRESS') + os.system("touch REFINEMENT_IN_PROGRESS") ####################################################### # Database updates: # no DB will be specified when a reference model is built and refined - refinementStatus = '' - updateDB = '' - date = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] + refinementStatus = "" + updateDB = "" + date = datetime.strftime(datetime.now(), "%Y-%m-%d_%H-%M-%S.%f")[:-4] user = getpass.getuser() if os.path.isfile(self.datasource): - refinementStatus = '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' % ( - self.datasource, self.xtalID, 'RefinementStatus', 'running') - updateDB = ('$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_data_source_after_refinement.py') + - ' %s %s %s %s %s %s\n' % (self.datasource, self.xtalID, self.ProjectPath, os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial), user, date)) + refinementStatus = ( + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n" + % (self.datasource, self.xtalID, "RefinementStatus", "running") + ) + updateDB = ( + "$CCP4/bin/ccp4-python " + + os.path.join( + os.getenv("XChemExplorer_DIR"), + "helpers", + "update_data_source_after_refinement.py", + ) + + " %s %s %s %s %s %s\n" + % ( + self.datasource, + self.xtalID, + self.ProjectPath, + os.path.join(self.ProjectPath, self.xtalID, "Refine_" + Serial), + user, + date, + ) + ) ####################################################### # clean up! # and remove all files which will be re-created by current refinement cycle - os.system('/bin/rm refine.pdb refine.mtz refine.split.bound-state.pdb validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log') + os.system( + "/bin/rm refine.pdb refine.mtz refine.split.bound-state.pdb validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log" + ) - if external_software['qsub']: - pbs_line = '#PBS -joe -N XCE_refmac\n' + if external_software["qsub"]: + pbs_line = "#PBS -joe -N XCE_refmac\n" else: - pbs_line = '\n' + pbs_line = "\n" ####################################################### # weight - if str(RefmacParams['MATRIX_WEIGHT']).lower() == 'auto': - weight = 'weight AUTO\n' + if str(RefmacParams["MATRIX_WEIGHT"]).lower() == "auto": + weight = "weight AUTO\n" else: - weight = 'weight matrix '+str(RefmacParams['MATRIX_WEIGHT'])+'\n' + weight = "weight matrix " + str(RefmacParams["MATRIX_WEIGHT"]) + "\n" ####################################################### # PHENIX stuff (if working at DLS) - module_load = '' - if os.getcwd().startswith('/dls'): - module_load = 'module load phenix\n' + module_load = "" + if os.getcwd().startswith("/dls"): + module_load = "module load phenix\n" - source = '' - if 'bash' in os.getenv('SHELL'): + source = "" + if "bash" in os.getenv("SHELL"): source = ( - 'export XChemExplorer_DIR="' + - os.getenv('XChemExplorer_DIR')+'"\n' - '\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'), - 'setup-scripts', 'xce.setup-sh')+'\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-sh')+'\n') - elif 'csh' in os.getenv('SHELL'): + 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"\n' + "\n" + "source " + + os.path.join( + os.getenv("XChemExplorer_DIR"), "setup-scripts", "xce.setup-sh" + ) + + "\n" + "source " + + os.path.join( + os.getenv("XChemExplorer_DIR"), "setup-scripts", "pandda.setup-sh" + ) + + "\n" + ) + elif "csh" in os.getenv("SHELL"): source = ( - 'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n' - '\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'), - 'setup-scripts', 'xce.setup-csh')+'\n' - 'source '+os.path.join(os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-csh')+'\n') - - spider_plot = '' - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'-ensemble-model.pdb')): - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'-pandda-input.mtz')): + "setenv XChemExplorer_DIR " + os.getenv("XChemExplorer_DIR") + "\n" + "\n" + "source " + + os.path.join( + os.getenv("XChemExplorer_DIR"), "setup-scripts", "xce.setup-csh" + ) + + "\n" + "source " + + os.path.join( + os.getenv("XChemExplorer_DIR"), "setup-scripts", "pandda.setup-csh" + ) + + "\n" + ) + + spider_plot = "" + if os.path.isfile( + os.path.join( + self.ProjectPath, self.xtalID, self.xtalID + "-ensemble-model.pdb" + ) + ): + if os.path.isfile( + os.path.join( + self.ProjectPath, self.xtalID, self.xtalID + "-pandda-input.mtz" + ) + ): pdb_two = os.path.join( - self.ProjectPath, self.xtalID, self.xtalID+'-ensemble-model.pdb') + self.ProjectPath, self.xtalID, self.xtalID + "-ensemble-model.pdb" + ) mtz_two = os.path.join( - self.ProjectPath, self.xtalID, self.xtalID+'-pandda-input.mtz') + self.ProjectPath, self.xtalID, self.xtalID + "-pandda-input.mtz" + ) pdb_one = os.path.join( - self.ProjectPath, self.xtalID, 'Refine_'+str(Serial), 'refine_'+str(Serial)+'.pdb') + self.ProjectPath, + self.xtalID, + "Refine_" + str(Serial), + "refine_" + str(Serial) + ".pdb", + ) mtz_one = os.path.join( - self.ProjectPath, self.xtalID, 'Refine_'+str(Serial), 'refine_'+str(Serial)+'.mtz') + self.ProjectPath, + self.xtalID, + "Refine_" + str(Serial), + "refine_" + str(Serial) + ".mtz", + ) spider_plot = ( - 'cd ' + self.ProjectPath + '/' + self.xtalID + '/Refine_' + Serial + '\n' - '\n' + "cd " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + Serial + + "\n" + "\n" # 'giant.merge_conformations ' # ' major=../refine.split.ground-state.pdb' # ' minor=../refine.split.bound-state.pdb' # ' reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0\n' - 'giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' % ( - pdb_one, mtz_one, pdb_two, mtz_two) + "giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n" + % (pdb_one, mtz_one, pdb_two, mtz_two) ) refmacCmds = ( - '#!'+os.getenv('SHELL')+'\n' - + pbs_line + - '\n' - + module_load + - '\n' - + source + - 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'\n' - '\n' - + refinementStatus + - '\n' - + findTLS + - 'refmac5 ' - + RefmacParams['HKLIN'] - + RefmacParams['HKLOUT'] - + RefmacParams['XYZIN'] - + RefmacParams['XYZOUT'] - + RefmacParams['LIBIN'] - + RefmacParams['LIBOUT'] - + RefmacParams['TLSIN'] - + RefmacParams['TLSOUT'] + - ' << EOF > refmac.log\n' - 'make -\n' - ' hydrogen ALL -\n' - ' hout NO -\n' - ' peptide NO -\n' - ' cispeptide YES -\n' - ' ssbridge YES -\n' - ' symmetry YES -\n' - ' sugar YES -\n' - ' connectivity NO -\n' - ' link NO\n' - + RefmacParams['NCS'] + - 'refi -\n' - ' type REST -\n' - ' resi MLKF -\n' - ' meth CGMAT -\n' - + RefmacParams['BREF'] - + RefmacParams['TLS'] - + RefmacParams['TWIN'] + - 'ncyc '+RefmacParams['NCYCLES']+'\n' - 'scal -\n' - ' type SIMP -\n' - ' LSSC -\n' - ' ANISO -\n' - ' EXPE\n' - + weight + - 'solvent YES\n' - 'monitor MEDIUM -\n' - ' torsion 10.0 -\n' - ' distance 10.0 -\n' - ' angle 10.0 -\n' - ' plane 10.0 -\n' - ' chiral 10.0 -\n' - ' bfactor 10.0 -\n' - ' bsphere 10.0 -\n' - ' rbond 10.0 -\n' - ' ncsr 10.0\n' - 'labin FP=F SIGFP=SIGF FREE=FreeR_flag\n' - 'labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM\n' - + RefmacParams['TLSADD']+'\n' - 'DNAME '+self.xtalID+'\n' - 'END\n' - 'EOF\n' - '\n' - 'phenix.molprobity refine_%s.pdb refine_%s.mtz\n' % (Serial, Serial) + - '/bin/mv molprobity.out refine_molprobity.log\n' - 'mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n' % (Serial, Serial) + - 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' - '#ln -s %s/%s/Refine_%s/refine_%s.pdb refine.pdb\n' % (self.ProjectPath, self.xtalID, Serial, Serial) + - '#ln -s %s/%s/Refine_%s/refine_%s.mtz refine.mtz\n' % (self.ProjectPath, self.xtalID, Serial, Serial) + - 'ln -s ./Refine_%s/refine_%s.pdb refine.pdb\n' % (Serial, Serial) + - 'ln -s ./Refine_%s/refine_%s.mtz refine.mtz\n' % (Serial, Serial) + - 'ln -s refine.pdb refine.split.bound-state.pdb\n' - '\n' - 'ln -s Refine_%s/validate_ligands.txt .\n' % Serial + - 'ln -s Refine_%s/refine_molprobity.log .\n' % Serial + - 'mmtbx.validation_summary refine.pdb > validation_summary.txt\n' - '\n' - 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' - 'labin F1=FWT PHI=PHWT\n' - 'EOF\n' - '\n' - 'fft hklin refine.mtz mapout fofc.map << EOF\n' - 'labin F1=DELFWT PHI=PHDELWT\n' - 'EOF\n' - '\n' - + updateDB + - '\n' - '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' % (self.ProjectPath, self.xtalID) + - '\n' - 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'\n' - '\n' - + spider_plot + - '\n' + "#!" + + os.getenv("SHELL") + + "\n" + + pbs_line + + "\n" + + module_load + + "\n" + + source + + "cd " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + Serial + + "\n" + "\n" + + refinementStatus + + "\n" + + findTLS + + "refmac5 " + + RefmacParams["HKLIN"] + + RefmacParams["HKLOUT"] + + RefmacParams["XYZIN"] + + RefmacParams["XYZOUT"] + + RefmacParams["LIBIN"] + + RefmacParams["LIBOUT"] + + RefmacParams["TLSIN"] + + RefmacParams["TLSOUT"] + + " << EOF > refmac.log\n" + "make -\n" + " hydrogen ALL -\n" + " hout NO -\n" + " peptide NO -\n" + " cispeptide YES -\n" + " ssbridge YES -\n" + " symmetry YES -\n" + " sugar YES -\n" + " connectivity NO -\n" + " link NO\n" + RefmacParams["NCS"] + "refi -\n" + " type REST -\n" + " resi MLKF -\n" + " meth CGMAT -\n" + + RefmacParams["BREF"] + + RefmacParams["TLS"] + + RefmacParams["TWIN"] + + "ncyc " + + RefmacParams["NCYCLES"] + + "\n" + "scal -\n" + " type SIMP -\n" + " LSSC -\n" + " ANISO -\n" + " EXPE\n" + weight + "solvent YES\n" + "monitor MEDIUM -\n" + " torsion 10.0 -\n" + " distance 10.0 -\n" + " angle 10.0 -\n" + " plane 10.0 -\n" + " chiral 10.0 -\n" + " bfactor 10.0 -\n" + " bsphere 10.0 -\n" + " rbond 10.0 -\n" + " ncsr 10.0\n" + "labin FP=F SIGFP=SIGF FREE=FreeR_flag\n" + "labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM\n" + + RefmacParams["TLSADD"] + + "\n" + "DNAME " + self.xtalID + "\n" + "END\n" + "EOF\n" + "\n" + "phenix.molprobity refine_%s.pdb refine_%s.mtz\n" % (Serial, Serial) + + "/bin/mv molprobity.out refine_molprobity.log\n" + "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n" + % (Serial, Serial) + + "cd " + + self.ProjectPath + + "/" + + self.xtalID + + "\n" + "#ln -s %s/%s/Refine_%s/refine_%s.pdb refine.pdb\n" + % (self.ProjectPath, self.xtalID, Serial, Serial) + + "#ln -s %s/%s/Refine_%s/refine_%s.mtz refine.mtz\n" + % (self.ProjectPath, self.xtalID, Serial, Serial) + + "ln -s ./Refine_%s/refine_%s.pdb refine.pdb\n" % (Serial, Serial) + + "ln -s ./Refine_%s/refine_%s.mtz refine.mtz\n" % (Serial, Serial) + + "ln -s refine.pdb refine.split.bound-state.pdb\n" + "\n" + "ln -s Refine_%s/validate_ligands.txt .\n" % Serial + + "ln -s Refine_%s/refine_molprobity.log .\n" % Serial + + "mmtbx.validation_summary refine.pdb > validation_summary.txt\n" + "\n" + "fft hklin refine.mtz mapout 2fofc.map << EOF\n" + "labin F1=FWT PHI=PHWT\n" + "EOF\n" + "\n" + "fft hklin refine.mtz mapout fofc.map << EOF\n" + "labin F1=DELFWT PHI=PHDELWT\n" + "EOF\n" + "\n" + updateDB + "\n" + "/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n" % (self.ProjectPath, self.xtalID) + + "\n" + "cd " + self.ProjectPath + "/" + self.xtalID + "/Refine_" + Serial + "\n" + "\n" + spider_plot + "\n" ) if os.path.isfile(xce_logfile): - Logfile.insert('writing refinement shell script to'+os.path.join( - self.ProjectPath, self.xtalID, 'Refine_'+Serial, 'refmac.csh')) - cmd = open(os.path.join(self.ProjectPath, self.xtalID, - 'Refine_'+Serial, 'refmac.csh'), 'w') + Logfile.insert( + "writing refinement shell script to" + + os.path.join( + self.ProjectPath, self.xtalID, "Refine_" + Serial, "refmac.csh" + ) + ) + cmd = open( + os.path.join( + self.ProjectPath, self.xtalID, "Refine_" + Serial, "refmac.csh" + ), + "w", + ) cmd.write(refmacCmds) cmd.close() - os.chdir(os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial)) -# os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) + os.chdir(os.path.join(self.ProjectPath, self.xtalID, "Refine_" + Serial)) + # os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) if os.path.isfile(xce_logfile): - Logfile.insert('changing directory to %s' % ( - os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial))) - if external_software['qsub_remote'] != '': - print(os.getenv('LD_LIBRARY_PATH')) + Logfile.insert( + "changing directory to %s" + % (os.path.join(self.ProjectPath, self.xtalID, "Refine_" + Serial)) + ) + if external_software["qsub_remote"] != "": + print(os.getenv("LD_LIBRARY_PATH")) if os.path.isfile(xce_logfile): - Logfile.insert('starting refinement on remote cluster') - remote_command = external_software['qsub_remote'].replace( - "qsub'", 'cd %s; qsub' % os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+Serial)) - os.system("%s -P labxchem -q medium.q refmac.csh'" % - remote_command) - print('%s -P labxchem -q medium.q refmac.csh' % remote_command) - - elif external_software['qsub'] and os.path.isdir('/dls'): + Logfile.insert("starting refinement on remote cluster") + remote_command = external_software["qsub_remote"].replace( + "qsub'", + "cd %s; qsub" + % os.path.join(self.ProjectPath, self.xtalID, "Refine_" + Serial), + ) + os.system("%s -P labxchem -q medium.q refmac.csh'" % remote_command) + print("%s -P labxchem -q medium.q refmac.csh" % remote_command) + + elif external_software["qsub"] and os.path.isdir("/dls"): Logfile.insert( - 'starting refinement on cluster with command "qsub -P labxchem -q medium.q refmac.csh"') + 'starting refinement on cluster with command "qsub -P labxchem -q medium.q refmac.csh"' + ) os.system("qsub -P labxchem -q medium.q refmac.csh") - elif external_software['qsub'] and not os.path.isdir('/dls'): + elif external_software["qsub"] and not os.path.isdir("/dls"): Logfile.insert( - 'starting refinement on cluster with command "qsub refmac.csh"') + 'starting refinement on cluster with command "qsub refmac.csh"' + ) os.system("qsub refmac.csh") else: - os.system('chmod +x refmac.csh') + os.system("chmod +x refmac.csh") if os.path.isfile(xce_logfile): - Logfile.insert('starting refinement on local machine') - os.system('./refmac.csh &') + Logfile.insert("starting refinement on local machine") + os.system("./refmac.csh &") def RefinementParams(self, RefmacParams): self.RefmacParams = RefmacParams @@ -1031,54 +1324,54 @@ def RefinementParams(self, RefmacParams): self.vbox = gtk.VBox() self.hbox1 = gtk.HBox() - self.hbox1.add(gtk.Label('Refine')) + self.hbox1.add(gtk.Label("Refine")) self.cb = gtk.combo_box_new_text() self.cb.connect("changed", self.ChooseBfacRefinement) - for item in ['isotropic', 'anisotropic']: + for item in ["isotropic", "anisotropic"]: self.cb.append_text(item) - if 'ISOT' in self.RefmacParams['BREF']: + if "ISOT" in self.RefmacParams["BREF"]: self.cb.set_active(0) - if 'ANIS' in self.RefmacParams['BREF']: + if "ANIS" in self.RefmacParams["BREF"]: self.cb.set_active(1) self.hbox1.add(self.cb) - self.hbox1.add(gtk.Label('temperature factors')) + self.hbox1.add(gtk.Label("temperature factors")) self.vbox.add(self.hbox1) self.hbox2 = gtk.HBox() - self.hbox2.add(gtk.Label('Number of Cycles: ')) + self.hbox2.add(gtk.Label("Number of Cycles: ")) self.Ncycles = gtk.Entry() self.Ncycles.add_events(gtk.gdk.KEY_RELEASE_MASK) self.Ncycles.connect("key-release-event", self.on_key_release_Ncycles) - self.Ncycles.set_text(self.RefmacParams['NCYCLES']) + self.Ncycles.set_text(self.RefmacParams["NCYCLES"]) self.hbox2.add(self.Ncycles) self.vbox.add(self.hbox2) self.hbox3 = gtk.HBox() - self.hbox3.add(gtk.Label('MATRIX WEIGHT: ')) + self.hbox3.add(gtk.Label("MATRIX WEIGHT: ")) self.MATRIX_WEIGHT = gtk.Entry() self.MATRIX_WEIGHT.add_events(gtk.gdk.KEY_RELEASE_MASK) self.MATRIX_WEIGHT.connect( - "key-release-event", self.on_key_release_MATRIX_WEIGHT) - self.MATRIX_WEIGHT.set_text(self.RefmacParams['MATRIX_WEIGHT']) + "key-release-event", self.on_key_release_MATRIX_WEIGHT + ) + self.MATRIX_WEIGHT.set_text(self.RefmacParams["MATRIX_WEIGHT"]) self.hbox3.add(self.MATRIX_WEIGHT) self.vbox.add(self.hbox3) - self.TLS = gtk.CheckButton( - 'TLS (find TLS groups with phenix.find_tls_groups)') + self.TLS = gtk.CheckButton("TLS (find TLS groups with phenix.find_tls_groups)") self.TLS.connect("toggled", self.TLSCallback) - if self.RefmacParams['TLS'] == 'refi tlsc 10\n': + if self.RefmacParams["TLS"] == "refi tlsc 10\n": self.TLS.set_active(True) self.vbox.pack_start(self.TLS, False) - self.NCS = gtk.CheckButton('NCS (if applicable') + self.NCS = gtk.CheckButton("NCS (if applicable") self.NCS.connect("toggled", self.NCSCallback) - if self.RefmacParams['NCS'] == 'NCSR LOCAL\n': + if self.RefmacParams["NCS"] == "NCSR LOCAL\n": self.NCS.set_active(True) self.vbox.pack_start(self.NCS, False) - self.TWIN = gtk.CheckButton('Twin?') + self.TWIN = gtk.CheckButton("Twin?") self.TWIN.connect("toggled", self.TWINCallback) - if self.RefmacParams['TWIN'] == 'TWIN\n': + if self.RefmacParams["TWIN"] == "TWIN\n": self.TWIN.set_active(True) self.vbox.pack_start(self.TWIN, False) @@ -1092,45 +1385,45 @@ def RefinementParams(self, RefmacParams): def TLSCallback(self, widget): if widget.get_active(): - self.RefmacParams['TLS'] = 'refi tlsc 10\n' - self.RefmacParams['TLSIN'] = 'refmac.tls\n' - self.RefmacParams['TLSOUT'] = 'out.tls\n' - self.RefmacParams['TLSADD'] = 'TLSO ADDU\n' + self.RefmacParams["TLS"] = "refi tlsc 10\n" + self.RefmacParams["TLSIN"] = "refmac.tls\n" + self.RefmacParams["TLSOUT"] = "out.tls\n" + self.RefmacParams["TLSADD"] = "TLSO ADDU\n" else: - self.RefmacParams['TLS'] = '' - self.RefmacParams['TLSIN'] = '' - self.RefmacParams['TLSOUT'] = '' - self.RefmacParams['TLSADD'] = '' + self.RefmacParams["TLS"] = "" + self.RefmacParams["TLSIN"] = "" + self.RefmacParams["TLSOUT"] = "" + self.RefmacParams["TLSADD"] = "" return self.RefmacParams def NCSCallback(self, widget): if widget.get_active(): - self.RefmacParams['NCS'] = 'NCSR LOCAL\n' + self.RefmacParams["NCS"] = "NCSR LOCAL\n" else: - self.RefmacParams['NCS'] = '' + self.RefmacParams["NCS"] = "" return self.RefmacParams def ChooseBfacRefinement(self, widget): - if widget.get_active_text() == 'isotropic': - self.RefmacParams['BREF'] = ' bref ISOT\n' - if widget.get_active_text() == 'anisotropic': - self.RefmacParams['BREF'] = ' bref ANIS\n' + if widget.get_active_text() == "isotropic": + self.RefmacParams["BREF"] = " bref ISOT\n" + if widget.get_active_text() == "anisotropic": + self.RefmacParams["BREF"] = " bref ANIS\n" return self.RefmacParams def on_key_release_Ncycles(self, widget, event): print(widget.get_text()) - self.RefmacParams['NCYCLES'] = widget.get_text() + self.RefmacParams["NCYCLES"] = widget.get_text() return self.RefmacParams def on_key_release_MATRIX_WEIGHT(self, widget, event): - self.RefmacParams['MATRIX_WEIGHT'] = widget.get_text() + self.RefmacParams["MATRIX_WEIGHT"] = widget.get_text() return self.RefmacParams def TWINCallback(self, widget): if widget.get_active(): - self.RefmacParams['TWIN'] = 'TWIN\n' + self.RefmacParams["TWIN"] = "TWIN\n" else: - self.RefmacParams['TWIN'] = '' + self.RefmacParams["TWIN"] = "" return self.RefmacParams def OK(self, widget): @@ -1138,55 +1431,89 @@ def OK(self, widget): def ParamsFromPreviousCycle(self, Serial): - RefmacParams = {'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': '', - 'WATER': '', - 'LIGOCC': '', - 'SANITY': ''} - - if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): - for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): - if line.startswith('refi tlsc'): - RefmacParams['TLS'] = line - if line.startswith('TLSO'): - RefmacParams['TLSADD'] = line - if line.startswith('NCSR LOCAL'): - RefmacParams['NCS'] = line - if line.startswith(' bref '): - RefmacParams['BREF'] = line - if line.startswith('ncyc'): - RefmacParams['Ncycles'] = line.split()[1] - if line.startswith('weight'): - RefmacParams['MATRIX_WEIGHT'] = line.split()[ - len(line.split())-1] - if line.startswith('TWIN'): - RefmacParams['TWIN'] = line - elif os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-restraints.refmac.params')): - for line in open(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-restraints.refmac.params')): - if 'refi tlsc' in line: - RefmacParams['TLS'] = line - if 'TLSO' in line: - RefmacParams['TLSADD'] = line - if 'NCSR LOCAL' in line: - RefmacParams['NCS'] = line - if 'bref' in line: - RefmacParams['BREF'] = line - if 'ncyc' in line: - RefmacParams['Ncycles'] = line.split()[1] - if 'weight' in line: - RefmacParams['MATRIX_WEIGHT'] = line.split()[ - len(line.split())-1] - if 'TWIN' in line: - RefmacParams['TWIN'] = line + RefmacParams = { + "HKLIN": "", + "HKLOUT": "", + "XYZIN": "", + "XYZOUT": "", + "LIBIN": "", + "LIBOUT": "", + "TLSIN": "", + "TLSOUT": "", + "TLSADD": "", + "NCYCLES": "10", + "MATRIX_WEIGHT": "AUTO", + "BREF": " bref ISOT\n", + "TLS": "", + "NCS": "", + "TWIN": "", + "WATER": "", + "LIGOCC": "", + "SANITY": "", + } + + if os.path.isfile( + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(Serial) + + "/refmac.csh" + ): + for line in open( + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(Serial) + + "/refmac.csh" + ): + if line.startswith("refi tlsc"): + RefmacParams["TLS"] = line + if line.startswith("TLSO"): + RefmacParams["TLSADD"] = line + if line.startswith("NCSR LOCAL"): + RefmacParams["NCS"] = line + if line.startswith(" bref "): + RefmacParams["BREF"] = line + if line.startswith("ncyc"): + RefmacParams["Ncycles"] = line.split()[1] + if line.startswith("weight"): + RefmacParams["MATRIX_WEIGHT"] = line.split()[len(line.split()) - 1] + if line.startswith("TWIN"): + RefmacParams["TWIN"] = line + elif os.path.isfile( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "multi-state-restraints.refmac.params", + ) + ): + for line in open( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "multi-state-restraints.refmac.params", + ) + ): + if "refi tlsc" in line: + RefmacParams["TLS"] = line + if "TLSO" in line: + RefmacParams["TLSADD"] = line + if "NCSR LOCAL" in line: + RefmacParams["NCS"] = line + if "bref" in line: + RefmacParams["BREF"] = line + if "ncyc" in line: + RefmacParams["Ncycles"] = line.split()[1] + if "weight" in line: + RefmacParams["MATRIX_WEIGHT"] = line.split()[len(line.split()) - 1] + if "TWIN" in line: + RefmacParams["TWIN"] = line return RefmacParams @@ -1197,10 +1524,10 @@ def GetRefinementHistory(self): RfreeList = [] found = False - for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): - if item.startswith(os.path.join(self.ProjectPath, self.xtalID, 'Refine_')): - print(item[item.rfind('_')+1:]) - RefinementCycle.append(int(item[item.rfind('_')+1:])) + for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, "*")): + if item.startswith(os.path.join(self.ProjectPath, self.xtalID, "Refine_")): + print(item[item.rfind("_") + 1 :]) + RefinementCycle.append(int(item[item.rfind("_") + 1 :])) found = True if found: for cycle in sorted(RefinementCycle): @@ -1211,14 +1538,29 @@ def GetRefinementHistory(self): try: found_Rcryst = False found_Rfree = False - newestPDB = max(glob.iglob(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str( - cycle)+'/refine_'+str(cycle)+'.pdb'), key=os.path.getctime) + newestPDB = max( + glob.iglob( + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(cycle) + + "/refine_" + + str(cycle) + + ".pdb" + ), + key=os.path.getctime, + ) for line in open(newestPDB): - if line.startswith('REMARK 3 R VALUE (WORKING + TEST SET) :'): + if line.startswith( + "REMARK 3 R VALUE (WORKING + TEST SET) :" + ): Rcryst = line.split()[9] RcrystList.append(float(Rcryst)) found_Rcryst = True - if line.startswith('REMARK 3 FREE R VALUE :'): + if line.startswith( + "REMARK 3 FREE R VALUE :" + ): Rfree = line.split()[6] RfreeList.append(float(Rfree)) found_Rfree = True @@ -1226,33 +1568,32 @@ def GetRefinementHistory(self): RcrystList.append(0) if not found_Rfree: RfreeList.append(0) -# if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): -# for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): -# if line.startswith('| LIG'): LigandCC = line.split()[6] -# RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' + # if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): + # for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): + # if line.startswith('| LIG'): LigandCC = line.split()[6] + # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' except ValueError: RcrystList.append(0) RfreeList.append(0) -# RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' + # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' else: RefinementCycle = [0] RcrystList = [0] RfreeList = [0] print(RefinementCycle, RcrystList, RfreeList) - return(sorted(RefinementCycle), RcrystList, RfreeList) + return (sorted(RefinementCycle), RcrystList, RfreeList) class panddaRefine(object): - def __init__(self, ProjectPath, xtalID, compoundID, datasource): self.ProjectPath = ProjectPath self.xtalID = xtalID self.compoundID = compoundID - self.prefix = 'refine' + self.prefix = "refine" self.datasource = datasource def make_covalent_link(self, covLinkAtomSpec, Logfile): - residuesToModify = ['CYS', 'SER'] + residuesToModify = ["CYS", "SER"] atom1 = covLinkAtomSpec[1][5] atom2 = covLinkAtomSpec[2][5] @@ -1260,444 +1601,717 @@ def make_covalent_link(self, covLinkAtomSpec, Logfile): residue_2 = covLinkAtomSpec[4] if residue_2 in residuesToModify: - bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' % ( - residue_1, self.compoundID, atom1, residue_2, atom2) + bond_text = ( + "LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s" + % (residue_1, self.compoundID, atom1, residue_2, atom2) + ) else: - bond_text = 'LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s' % ( - residue_2, self.compoundID, atom2, residue_1, atom1) + bond_text = ( + "LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s" + % (residue_2, self.compoundID, atom2, residue_1, atom1) + ) os.chdir(os.path.join(self.ProjectPath, self.xtalID)) - f = open('covalent_bond.txt', 'w') + f = open("covalent_bond.txt", "w") f.write(bond_text) f.close() # seems somewhat unncessary, but acedrg does not like some certain descriptions generated by phenix.elbow - os.system('acedrg -c %s.cif -o %s_acedrg' % - (self.compoundID, self.compoundID)) + os.system("acedrg -c %s.cif -o %s_acedrg" % (self.compoundID, self.compoundID)) - os.system('acedrg -L covalent_bond.txt -o %s' % self.compoundID) + os.system("acedrg -L covalent_bond.txt -o %s" % self.compoundID) - if os.path.isfile('%s_link.cif' % self.compoundID): - Logfile.insert( - 'succefully created link file %s_link.cif' % self.compoundID) - os.system('/bin/rm %s.cif' % self.compoundID) - os.system('ln -s %s_link.cif %s.cif' % - (self.compoundID, self.compoundID)) + if os.path.isfile("%s_link.cif" % self.compoundID): + Logfile.insert("succefully created link file %s_link.cif" % self.compoundID) + os.system("/bin/rm %s.cif" % self.compoundID) + os.system("ln -s %s_link.cif %s.cif" % (self.compoundID, self.compoundID)) else: - Logfile.error('could not create linkfile; please check logs in %s/%s' % - (self.ProjectPath, self.xtalID)) + Logfile.error( + "could not create linkfile; please check logs in %s/%s" + % (self.ProjectPath, self.xtalID) + ) - def RunQuickRefine(self, Serial, RefmacParams, external_software, xce_logfile, refinementProtocol, covLinkAtomSpec): + def RunQuickRefine( + self, + Serial, + RefmacParams, + external_software, + xce_logfile, + refinementProtocol, + covLinkAtomSpec, + ): Logfile = XChemLog.updateLog(xce_logfile) - Logfile.insert('preparing files for giant.quick_refine') + Logfile.insert("preparing files for giant.quick_refine") # panddaSerial because giant.quick_refine writes Refine_0001 instead of Refine_1 - panddaSerial = (4-len(str(Serial)))*'0'+str(Serial) + panddaSerial = (4 - len(str(Serial))) * "0" + str(Serial) make_all_links = True - add_links_line = '' + add_links_line = "" if covLinkAtomSpec is not None: self.make_covalent_link(covLinkAtomSpec, Logfile) # first check if refinement is ongoing and exit if yes - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'REFINEMENT_IN_PROGRESS')): + if os.path.isfile( + os.path.join(self.ProjectPath, self.xtalID, "REFINEMENT_IN_PROGRESS") + ): # coot.info_dialog('*** REFINEMENT IN PROGRESS ***') Logfile.insert( - 'cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' % self.xtalID) + "cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***" + % self.xtalID + ) return None ####################################################### # HKLIN & HKLOUT - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'.free.mtz')): - RefmacParams['HKLIN'] = os.path.join( - self.ProjectPath, self.xtalID, self.xtalID+'.free.mtz') - elif os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'-pandda-input.mtz')): - RefmacParams['HKLIN'] = os.path.join( - self.ProjectPath, self.xtalID, self.xtalID+'-pandda-input.mtz') + if os.path.isfile( + os.path.join(self.ProjectPath, self.xtalID, self.xtalID + ".free.mtz") + ): + RefmacParams["HKLIN"] = os.path.join( + self.ProjectPath, self.xtalID, self.xtalID + ".free.mtz" + ) + elif os.path.isfile( + os.path.join( + self.ProjectPath, self.xtalID, self.xtalID + "-pandda-input.mtz" + ) + ): + RefmacParams["HKLIN"] = os.path.join( + self.ProjectPath, self.xtalID, self.xtalID + "-pandda-input.mtz" + ) else: Logfile.error( - '%s: cannot find HKLIN for refinement; aborting...' % self.xtalID) + "%s: cannot find HKLIN for refinement; aborting..." % self.xtalID + ) return None ####################################################### # LIBIN & LIBOUT found_cif = False - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.compoundID+'.cif')): + if os.path.isfile( + os.path.join(self.ProjectPath, self.xtalID, self.compoundID + ".cif") + ): found_cif = True - RefmacParams['LIBIN'] = os.path.join( - self.ProjectPath, self.xtalID, self.compoundID+'.cif') + RefmacParams["LIBIN"] = os.path.join( + self.ProjectPath, self.xtalID, self.compoundID + ".cif" + ) if not found_cif: # this should actually not be necessary, but the following scenario can happen: # if a new data source is created from a file system, but smiles and compoundID where not updated; # so the ligand may still be in the structure, but since the compoundID is unknown to the datasource, # its restraints won't be read in and refmac will fail - for file in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): - if file.endswith('.cif'): - RefmacParams['LIBIN'] = file + for file in glob.glob(os.path.join(self.ProjectPath, self.xtalID, "*")): + if file.endswith(".cif"): + RefmacParams["LIBIN"] = file break ####################################################### # giant_merge_conformations - Logfile.insert( - 'trying to merge modified bound state with ground state') - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), self.xtalID+'-ensemble-model.pdb')): + Logfile.insert("trying to merge modified bound state with ground state") + if os.path.isfile( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + self.xtalID + "-ensemble-model.pdb", + ) + ): + Logfile.insert( + "seems to be an initial refinement after pandda.export, no need to merge the conformations" + ) + os.chdir( + os.path.join( + self.ProjectPath, self.xtalID, "cootOut", "Refine_" + str(Serial) + ) + ) Logfile.insert( - 'seems to be an initial refinement after pandda.export, no need to merge the conformations') - os.chdir(os.path.join(self.ProjectPath, self.xtalID, - 'cootOut', 'Refine_'+str(Serial))) - Logfile.insert('running giant.make_restraints %s:' % - self.xtalID+'-ensemble-model.pdb') -# os.system('giant.make_restraints %s' %self.xtalID+'-ensemble-model.pdb') + "running giant.make_restraints %s:" % self.xtalID + + "-ensemble-model.pdb" + ) + # os.system('giant.make_restraints %s' %self.xtalID+'-ensemble-model.pdb') cmd = ( - 'export XChemExplorer_DIR="%s"\n' % os.getenv('XChemExplorer_DIR') + - 'source %s\n' % os.path.join(os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-sh\n') + - 'giant.make_restraints %s-ensemble-model.pdb' % self.xtalID + 'export XChemExplorer_DIR="%s"\n' % os.getenv("XChemExplorer_DIR") + + "source %s\n" + % os.path.join( + os.getenv("XChemExplorer_DIR"), "setup-scripts", "pandda.setup-sh\n" + ) + + "giant.make_restraints %s-ensemble-model.pdb" % self.xtalID ) - Logfile.insert(cmd+'\n') + Logfile.insert(cmd + "\n") os.system(cmd) - elif os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'refine.split.ground-state.pdb')): - Logfile.insert('found model of ground state: '+os.path.join( - self.ProjectPath, self.xtalID, 'refine.split.ground-state.pdb')) - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'refine.modified.pdb')): - Logfile.insert('found model of modified bound state') - os.chdir(os.path.join(self.ProjectPath, self.xtalID, - 'cootOut', 'Refine_'+str(Serial))) + elif os.path.isfile( + os.path.join(self.ProjectPath, self.xtalID, "refine.split.ground-state.pdb") + ): + Logfile.insert( + "found model of ground state: " + + os.path.join( + self.ProjectPath, self.xtalID, "refine.split.ground-state.pdb" + ) + ) + if os.path.isfile( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "refine.modified.pdb", + ) + ): + Logfile.insert("found model of modified bound state") + os.chdir( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + ) + ) ground_state = os.path.join( - self.ProjectPath, self.xtalID, 'refine.split.ground-state.pdb') - bound_state = 'refine.modified.pdb' - Logfile.insert('running giant.merge_conformations major=%s minor=%s' % ( - ground_state, bound_state)) - if os.getcwd().startswith('/dls'): + self.ProjectPath, self.xtalID, "refine.split.ground-state.pdb" + ) + bound_state = "refine.modified.pdb" + Logfile.insert( + "running giant.merge_conformations major=%s minor=%s" + % (ground_state, bound_state) + ) + if os.getcwd().startswith("/dls"): cmd = ( - 'export XChemExplorer_DIR="%s"\n' % os.getenv('XChemExplorer_DIR') + + 'export XChemExplorer_DIR="%s"\n' + % os.getenv("XChemExplorer_DIR") + + # 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') + - 'module load ccp4/7.1.018\n' - 'giant.merge_conformations major=%s minor=%s reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0' % ( - ground_state, bound_state) + "module load ccp4/7.1.018\n" + "giant.merge_conformations major=%s minor=%s reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0" + % (ground_state, bound_state) ) else: cmd = ( - 'giant.merge_conformations major=%s minor=%s reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0' % ( - ground_state, bound_state) + "giant.merge_conformations major=%s minor=%s reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0" + % (ground_state, bound_state) ) - Logfile.insert(cmd+'\n') + Logfile.insert(cmd + "\n") os.system(cmd) - link_line = '' + link_line = "" for line in open(bound_state): - if line.startswith('LINK'): - Logfile.insert('found LINK: ' + line[:-1]) + if line.startswith("LINK"): + Logfile.insert("found LINK: " + line[:-1]) link_line += line - if link_line != '': - if os.path.isfile('multi-state-model.pdb'): - for line in open('multi-state-model.pdb'): - if line.startswith('CRYST'): + if link_line != "": + if os.path.isfile("multi-state-model.pdb"): + for line in open("multi-state-model.pdb"): + if line.startswith("CRYST"): Logfile.insert( - 'adding LINK lines to multi-state-model.pdb') + "adding LINK lines to multi-state-model.pdb" + ) out = link_line + line else: out += line - Logfile.insert('writing updated multi-state-model.pdb') - f = open('multi-state-model.pdb', 'w') + Logfile.insert("writing updated multi-state-model.pdb") + f = open("multi-state-model.pdb", "w") f.write(out) f.close() else: - Logfile.error('cannot find multi-state-model.pdb') + Logfile.error("cannot find multi-state-model.pdb") else: - Logfile.error('cannot find modified version of bound state in %s' % os.path.join( - self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) + Logfile.error( + "cannot find modified version of bound state in %s" + % os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + ) + ) return None else: - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'refine.modified.pdb')): - os.chdir(os.path.join(self.ProjectPath, self.xtalID, - 'cootOut', 'Refine_'+str(Serial))) + if os.path.isfile( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "refine.modified.pdb", + ) + ): + os.chdir( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + ) + ) Logfile.warning( - '%s: ground-state model does not exist, but refine.modified.pdb does exist' % self.xtalID) + "%s: ground-state model does not exist, but refine.modified.pdb does exist" + % self.xtalID + ) Logfile.warning( - 'This may be a case where there are no differences between bound and ground state') + "This may be a case where there are no differences between bound and ground state" + ) Logfile.warning( - 'creating symbolic link: ln -s refine.modified.pdb %s-ensemble-model.pdb' % self.xtalID) + "creating symbolic link: ln -s refine.modified.pdb %s-ensemble-model.pdb" + % self.xtalID + ) os.system( - 'ln -s refine.modified.pdb %s-ensemble-model.pdb' % self.xtalID) + "ln -s refine.modified.pdb %s-ensemble-model.pdb" % self.xtalID + ) # note: after first cycle of refinement, REFMAC will remove alternate conformer from the ligand # i.e. need to link refine.pdb to refine.split.bound-state.pdb make_all_links = False - add_links_line = 'ln -s refine.pdb refine.split.bound-state.pdb' - Logfile.insert('trying to continue with refinement') + add_links_line = "ln -s refine.pdb refine.split.bound-state.pdb" + Logfile.insert("trying to continue with refinement") else: Logfile.error( - 'cannot find any suitable PDB file for refinement, aborting...') + "cannot find any suitable PDB file for refinement, aborting..." + ) return None ####################################################### # checking if input PDB files are present - Logfile.insert('checking if input PDB files for REFMAC are present') - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), self.xtalID+'-ensemble-model.pdb')): - RefmacParams['XYZIN'] = os.path.join( - self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), self.xtalID+'-ensemble-model.pdb') - elif os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-model.pdb')): - RefmacParams['XYZIN'] = os.path.join( - self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-model.pdb') + Logfile.insert("checking if input PDB files for REFMAC are present") + if os.path.isfile( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + self.xtalID + "-ensemble-model.pdb", + ) + ): + RefmacParams["XYZIN"] = os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + self.xtalID + "-ensemble-model.pdb", + ) + elif os.path.isfile( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "multi-state-model.pdb", + ) + ): + RefmacParams["XYZIN"] = os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "multi-state-model.pdb", + ) else: - Logfile.error('cannot find multi-state-model.pdb in %s; aborting...' % - os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) + Logfile.error( + "cannot find multi-state-model.pdb in %s; aborting..." + % os.path.join( + self.ProjectPath, self.xtalID, "cootOut", "Refine_" + str(Serial) + ) + ) return None ####################################################### # checking if multi-state-restraints.refmac.params file is present - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-restraints.refmac.params')): + if os.path.isfile( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "multi-state-restraints.refmac.params", + ) + ): # add REFMAC keywords to multi-state-restraints.refmac.params - with open('multi-state-restraints.refmac.params', 'a') as refmacParams: - refmacParams.write(RefmacParams['BREF']+'\n') - refmacParams.write(RefmacParams['TLS']+'\n') - refmacParams.write(RefmacParams['TWIN']+'\n') - refmacParams.write('ncyc '+RefmacParams['NCYCLES']+'\n') - if str(RefmacParams['MATRIX_WEIGHT']).lower() == 'auto': - refmacParams.write('weight AUTO' + '\n') + with open("multi-state-restraints.refmac.params", "a") as refmacParams: + refmacParams.write(RefmacParams["BREF"] + "\n") + refmacParams.write(RefmacParams["TLS"] + "\n") + refmacParams.write(RefmacParams["TWIN"] + "\n") + refmacParams.write("ncyc " + RefmacParams["NCYCLES"] + "\n") + if str(RefmacParams["MATRIX_WEIGHT"]).lower() == "auto": + refmacParams.write("weight AUTO" + "\n") else: refmacParams.write( - 'weight matrix '+str(RefmacParams['MATRIX_WEIGHT'])+'\n') - refmacParams.write(RefmacParams['TLSADD']+'\n') + "weight matrix " + str(RefmacParams["MATRIX_WEIGHT"]) + "\n" + ) + refmacParams.write(RefmacParams["TLSADD"] + "\n") else: - Logfile.warning('cannot find multi-state-restraints.refmac.params in %s!' % - os.path.join(self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) + Logfile.warning( + "cannot find multi-state-restraints.refmac.params in %s!" + % os.path.join( + self.ProjectPath, self.xtalID, "cootOut", "Refine_" + str(Serial) + ) + ) try: - os.chdir(os.path.join(self.ProjectPath, self.xtalID, - 'cootOut', 'Refine_'+str(Serial))) + os.chdir( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + ) + ) Logfile.insert( - 'checking if %s-ensemble-model.pdb contains residue of type LIG, DRG, FRG, UNK or UNL' % self.xtalID) - knowLigandIDs = ['LIG', 'DRG', 'FRG', 'UNK', 'UNL'] + "checking if %s-ensemble-model.pdb contains residue of type LIG, DRG, FRG, UNK or UNL" + % self.xtalID + ) + knowLigandIDs = ["LIG", "DRG", "FRG", "UNK", "UNL"] ligandsInFile = pdbtools( - self.xtalID+'-ensemble-model.pdb').find_ligands() + self.xtalID + "-ensemble-model.pdb" + ).find_ligands() found_lig = False for lig in ligandsInFile: if lig[0] in knowLigandIDs: - Logfile.insert('found ligand of type: ' + lig[0]) + Logfile.insert("found ligand of type: " + lig[0]) found_lig = True if found_lig: - Logfile.warning('giant.make_restraints was not able to create multi-state-restraints.refmac.params. ' + - 'Something may have gone wrong, but it could be that ligand binding did not lead to ' + - 'displacement of water molecules or rearrangement of protein side-chains. ' + - 'Hence, there is no difference between the bound-state and the ground-state. ' + - 'We will create an empty multi-state-restraints.refmac.params which may contain ' + - 'additional REFMAC keywords and otherwise try to continue with refinement') - os.system('touch multi-state-restraints.refmac.params') + Logfile.warning( + "giant.make_restraints was not able to create multi-state-restraints.refmac.params. " + + "Something may have gone wrong, but it could be that ligand binding did not lead to " + + "displacement of water molecules or rearrangement of protein side-chains. " + + "Hence, there is no difference between the bound-state and the ground-state. " + + "We will create an empty multi-state-restraints.refmac.params which may contain " + + "additional REFMAC keywords and otherwise try to continue with refinement" + ) + os.system("touch multi-state-restraints.refmac.params") else: Logfile.error( - '%s-ensemble-model.pdb does not contain any modelled ligand; aborting refinement' % self.xtalID) + "%s-ensemble-model.pdb does not contain any modelled ligand; aborting refinement" + % self.xtalID + ) return None except OSError: - Logfile.error('directory does not exisit: %s' % os.path.join( - self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) - Logfile.error('aborting refinement...') + Logfile.error( + "directory does not exisit: %s" + % os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + ) + ) + Logfile.error("aborting refinement...") return None ####################################################### # we write 'REFINEMENT_IN_PROGRESS' immediately to avoid unncessary refinement os.chdir(os.path.join(self.ProjectPath, self.xtalID)) - os.system('touch REFINEMENT_IN_PROGRESS') + os.system("touch REFINEMENT_IN_PROGRESS") ####################################################### # clean up! # and remove all files which will be re-created by current refinement cycle os.chdir(os.path.join(self.ProjectPath, self.xtalID)) - files_to_remove = ('refine.pdb ' - 'refine.mtz ' - 'refine.split.bound-state.pdb ' - 'refine.split.ground-state.pdb ' - 'validation_summary.txt ' - 'validate_ligands.txt ' - '2fofc.map ' - 'fofc.map ' - 'refine_molprobity.log') - os.system('/bin/rm %s' % files_to_remove) - - if external_software['qsub']: - pbs_line = '#PBS -joe -N XCE_refmac\n' + files_to_remove = ( + "refine.pdb " + "refine.mtz " + "refine.split.bound-state.pdb " + "refine.split.ground-state.pdb " + "validation_summary.txt " + "validate_ligands.txt " + "2fofc.map " + "fofc.map " + "refine_molprobity.log" + ) + os.system("/bin/rm %s" % files_to_remove) + + if external_software["qsub"]: + pbs_line = "#PBS -joe -N XCE_refmac\n" else: - pbs_line = '\n' + pbs_line = "\n" ####################################################### # PANDDA validation @ spider plot - spider_plot = '' - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'-ensemble-model.pdb')): - if os.path.isfile(os.path.join(self.ProjectPath, self.xtalID, self.xtalID+'-pandda-input.mtz')): + spider_plot = "" + if os.path.isfile( + os.path.join( + self.ProjectPath, self.xtalID, self.xtalID + "-ensemble-model.pdb" + ) + ): + if os.path.isfile( + os.path.join( + self.ProjectPath, self.xtalID, self.xtalID + "-pandda-input.mtz" + ) + ): pdb_two = os.path.join( - self.ProjectPath, self.xtalID, self.xtalID+'-ensemble-model.pdb') + self.ProjectPath, self.xtalID, self.xtalID + "-ensemble-model.pdb" + ) mtz_two = os.path.join( - self.ProjectPath, self.xtalID, self.xtalID+'-pandda-input.mtz') + self.ProjectPath, self.xtalID, self.xtalID + "-pandda-input.mtz" + ) pdb_one = os.path.join( - self.ProjectPath, self.xtalID, 'Refine_'+str(panddaSerial), 'refine_'+str(Serial)+'.pdb') + self.ProjectPath, + self.xtalID, + "Refine_" + str(panddaSerial), + "refine_" + str(Serial) + ".pdb", + ) mtz_one = os.path.join( - self.ProjectPath, self.xtalID, 'Refine_'+str(panddaSerial), 'refine_'+str(Serial)+'.mtz') - spider_plot += 'giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' % ( - pdb_one, mtz_one, pdb_two, mtz_two) + self.ProjectPath, + self.xtalID, + "Refine_" + str(panddaSerial), + "refine_" + str(Serial) + ".mtz", + ) + spider_plot += ( + "giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n" + % (pdb_one, mtz_one, pdb_two, mtz_two) + ) ####################################################### # CCP4 & PHENIX stuff (if working at DLS) - module_load = '' - if os.getcwd().startswith('/dls'): - module_load = 'module load ccp4/7.1.018\n' - module_load += 'module load phenix\n' + module_load = "" + if os.getcwd().startswith("/dls"): + module_load = "module load ccp4/7.1.018\n" + module_load += "module load phenix\n" # 2017-07-20: for the time being this will explicitly source pandda since version 0.2 really only works at DLS # 2020-11-02: will start using default ccp4 installation at DLS otherwise gemmi does not work - source = '' - if 'bash' in os.getenv('SHELL'): + source = "" + if "bash" in os.getenv("SHELL"): source = ( - 'export XChemExplorer_DIR="' + - os.getenv('XChemExplorer_DIR')+'"\n' - '\n' + 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"\n' + "\n" # 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') ) - elif 'csh' in os.getenv('SHELL'): + elif "csh" in os.getenv("SHELL"): source = ( - 'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n' - '\n' + "setenv XChemExplorer_DIR " + os.getenv("XChemExplorer_DIR") + "\n" + "\n" # 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh\n') ) - if refinementProtocol == 'pandda_refmac': - refinementProgram = 'refmac' + if refinementProtocol == "pandda_refmac": + refinementProgram = "refmac" refinementParams = os.path.join( - self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-restraints.refmac.params') + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "multi-state-restraints.refmac.params", + ) mapCalculation = ( - 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' - 'labin F1=FWT PHI=PHWT\n' - 'EOF\n' - '\n' - 'fft hklin refine.mtz mapout fofc.map << EOF\n' - 'labin F1=DELFWT PHI=PHDELWT\n' - 'EOF\n') - elif refinementProtocol == 'pandda_phenix': - - if os.getcwd().startswith('/dls'): - module_load = 'module load phenix/1.13\n' - - refinementProgram = 'phenix' + "fft hklin refine.mtz mapout 2fofc.map << EOF\n" + "labin F1=FWT PHI=PHWT\n" + "EOF\n" + "\n" + "fft hklin refine.mtz mapout fofc.map << EOF\n" + "labin F1=DELFWT PHI=PHDELWT\n" + "EOF\n" + ) + elif refinementProtocol == "pandda_phenix": + + if os.getcwd().startswith("/dls"): + module_load = "module load phenix/1.13\n" + + refinementProgram = "phenix" refinementParams = os.path.join( - self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'multi-state-restraints.phenix.params') + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "multi-state-restraints.phenix.params", + ) mapCalculation = ( - 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' - 'labin F1=2FOFCWT PHI=PH2FOFCWT\n' - 'EOF\n' - '\n' - 'fft hklin refine.mtz mapout fofc.map << EOF\n' - 'labin F1=FOFCWT PHI=PHFOFCWT\n' - 'EOF\n') + "fft hklin refine.mtz mapout 2fofc.map << EOF\n" + "labin F1=2FOFCWT PHI=PH2FOFCWT\n" + "EOF\n" + "\n" + "fft hklin refine.mtz mapout fofc.map << EOF\n" + "labin F1=FOFCWT PHI=PHFOFCWT\n" + "EOF\n" + ) if make_all_links: add_links_line = ( - 'ln -s Refine_%s/refine_%s.split.bound-state.pdb ./refine.split.bound-state.pdb\n' % (panddaSerial, Serial) + - 'ln -s Refine_%s/refine_%s.split.ground-state.pdb ./refine.split.ground-state.pdb\n' % ( - panddaSerial, Serial) + "ln -s Refine_%s/refine_%s.split.bound-state.pdb ./refine.split.bound-state.pdb\n" + % (panddaSerial, Serial) + + "ln -s Refine_%s/refine_%s.split.ground-state.pdb ./refine.split.ground-state.pdb\n" + % (panddaSerial, Serial) # 'ln -s Refine_%s/refine_%s.output.bound-state.pdb ./refine.output.bound-state.pdb\n' %(panddaSerial,Serial)+ # 'ln -s Refine_%s/refine_%s.output.ground-state.pdb ./refine.output.ground-state.pdb\n' %(panddaSerial,Serial) ) - date = datetime.strftime(datetime.now(), '%Y-%m-%d_%H-%M-%S.%f')[:-4] + date = datetime.strftime(datetime.now(), "%Y-%m-%d_%H-%M-%S.%f")[:-4] user = getpass.getuser() refmacCmds = ( - '#!'+os.getenv('SHELL')+'\n' - + pbs_line + - '\n' - + module_load + - '\n' - + source + - 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' - '\n' - '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' % (self.datasource, self.xtalID, 'RefinementStatus', 'running') + - '\n' - 'giant.quick_refine' - ' input.pdb=%s' % RefmacParams['XYZIN'] + - ' mtz=%s' % RefmacParams['HKLIN'] + - ' cif=%s' % RefmacParams['LIBIN'] + - ' program=%s' % refinementProgram + - ' params=%s' % refinementParams + - " dir_prefix='Refine_'" - " out_prefix='refine_%s'" % str(Serial) + - " split_conformations='False'" - '\n' - 'cd '+self.ProjectPath+'/'+self.xtalID + - '/Refine_'+str(panddaSerial)+'\n' - - 'ln -s '+self.ProjectPath+'/'+self.xtalID+'/Refine_' + - str(panddaSerial)+'/refine_'+str(Serial)+'_001.pdb ' - + self.ProjectPath+'/'+self.xtalID+'/Refine_' + - str(panddaSerial)+'/refine_'+str(Serial)+'.pdb' + '\n' - - 'ln -s '+self.ProjectPath+'/'+self.xtalID+'/Refine_' + - str(panddaSerial)+'/refine_'+str(Serial)+'_001.mtz ' - + self.ProjectPath+'/'+self.xtalID+'/Refine_' + - str(panddaSerial)+'/refine_'+str(Serial)+'.mtz' + '\n' - - 'giant.split_conformations' - " input.pdb='refine_%s.pdb'" % str(Serial) + - ' reset_occupancies=False' - ' suffix_prefix=split' - '\n' - 'giant.split_conformations' - " input.pdb='refine_%s.pdb'" % str(Serial) + - ' reset_occupancies=True' - ' suffix_prefix=output ' - '\n' - + spider_plot + - '\n' - 'phenix.molprobity refine_%s.pdb refine_%s.mtz\n' % (Serial, Serial) + - '/bin/mv molprobity.out refine_molprobity.log\n' - 'module load phenix\n' - 'mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n' % (Serial, Serial) + - 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' - '\n' - 'ln -s Refine_%s/validate_ligands.txt .\n' % panddaSerial + - 'ln -s Refine_%s/refine_molprobity.log .\n' % panddaSerial + - '\n' - + add_links_line + - '\n' - 'mmtbx.validation_summary refine.pdb > validation_summary.txt\n' - '\n' - + mapCalculation + - '\n' - '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_data_source_after_refinement.py') + - ' %s %s %s %s %s %s\n' % (self.datasource, self.xtalID, self.ProjectPath, os.path.join(self.ProjectPath, self.xtalID, 'Refine_'+str(panddaSerial)), user, date) + - '\n' - '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' % (self.ProjectPath, self.xtalID) + - '\n' + "#!" + + os.getenv("SHELL") + + "\n" + + pbs_line + + "\n" + + module_load + + "\n" + + source + + "cd " + + self.ProjectPath + + "/" + + self.xtalID + + "\n" + "\n" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n" + % (self.datasource, self.xtalID, "RefinementStatus", "running") + + "\n" + "giant.quick_refine" + " input.pdb=%s" % RefmacParams["XYZIN"] + + " mtz=%s" % RefmacParams["HKLIN"] + + " cif=%s" % RefmacParams["LIBIN"] + + " program=%s" % refinementProgram + + " params=%s" % refinementParams + + " dir_prefix='Refine_'" + " out_prefix='refine_%s'" % str(Serial) + " split_conformations='False'" + "\n" + "cd " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(panddaSerial) + + "\n" + "ln -s " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(panddaSerial) + + "/refine_" + + str(Serial) + + "_001.pdb " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(panddaSerial) + + "/refine_" + + str(Serial) + + ".pdb" + + "\n" + "ln -s " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(panddaSerial) + + "/refine_" + + str(Serial) + + "_001.mtz " + + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(panddaSerial) + + "/refine_" + + str(Serial) + + ".mtz" + + "\n" + "giant.split_conformations" + " input.pdb='refine_%s.pdb'" % str(Serial) + " reset_occupancies=False" + " suffix_prefix=split" + "\n" + "giant.split_conformations" + " input.pdb='refine_%s.pdb'" % str(Serial) + " reset_occupancies=True" + " suffix_prefix=output " + "\n" + spider_plot + "\n" + "phenix.molprobity refine_%s.pdb refine_%s.mtz\n" % (Serial, Serial) + + "/bin/mv molprobity.out refine_molprobity.log\n" + "module load phenix\n" + "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n" + % (Serial, Serial) + + "cd " + + self.ProjectPath + + "/" + + self.xtalID + + "\n" + "\n" + "ln -s Refine_%s/validate_ligands.txt .\n" % panddaSerial + + "ln -s Refine_%s/refine_molprobity.log .\n" % panddaSerial + + "\n" + + add_links_line + + "\n" + "mmtbx.validation_summary refine.pdb > validation_summary.txt\n" + "\n" + mapCalculation + "\n" + "$CCP4/bin/ccp4-python " + + os.path.join( + os.getenv("XChemExplorer_DIR"), + "helpers", + "update_data_source_after_refinement.py", + ) + + " %s %s %s %s %s %s\n" + % ( + self.datasource, + self.xtalID, + self.ProjectPath, + os.path.join( + self.ProjectPath, self.xtalID, "Refine_" + str(panddaSerial) + ), + user, + date, + ) + + "\n" + "/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n" % (self.ProjectPath, self.xtalID) + + "\n" ) - Logfile.insert('writing refinement shell script to'+os.path.join( - self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial), 'refmac.csh')) - cmd = open(os.path.join(self.ProjectPath, self.xtalID, - 'cootOut', 'Refine_'+str(Serial), 'refmac.csh'), 'w') + Logfile.insert( + "writing refinement shell script to" + + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "refmac.csh", + ) + ) + cmd = open( + os.path.join( + self.ProjectPath, + self.xtalID, + "cootOut", + "Refine_" + str(Serial), + "refmac.csh", + ), + "w", + ) cmd.write(refmacCmds) cmd.close() - os.chdir(os.path.join(self.ProjectPath, self.xtalID, - 'cootOut', 'Refine_'+str(Serial))) -# os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) - Logfile.insert('changing directory to %s' % (os.path.join( - self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial)))) - - if external_software['qsub']: - Logfile.insert('starting refinement on cluster') - os.system('qsub -P labxchem refmac.csh') - elif external_software['qsub_remote'] != '': - Logfile.insert('starting refinement on remote cluster') - remote_command = external_software['qsub_remote'].replace('qsub', 'cd %s; qsub' % os.path.join( - self.ProjectPath, self.xtalID, 'cootOut', 'Refine_'+str(Serial))) - os.system('%s -P labxchem refmac.csh' % remote_command) - print('%s -P labxchem refmac.csh' % remote_command) + os.chdir( + os.path.join( + self.ProjectPath, self.xtalID, "cootOut", "Refine_" + str(Serial) + ) + ) + # os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) + Logfile.insert( + "changing directory to %s" + % ( + os.path.join( + self.ProjectPath, self.xtalID, "cootOut", "Refine_" + str(Serial) + ) + ) + ) + + if external_software["qsub"]: + Logfile.insert("starting refinement on cluster") + os.system("qsub -P labxchem refmac.csh") + elif external_software["qsub_remote"] != "": + Logfile.insert("starting refinement on remote cluster") + remote_command = external_software["qsub_remote"].replace( + "qsub", + "cd %s; qsub" + % os.path.join( + self.ProjectPath, self.xtalID, "cootOut", "Refine_" + str(Serial) + ), + ) + os.system("%s -P labxchem refmac.csh" % remote_command) + print("%s -P labxchem refmac.csh" % remote_command) else: - Logfile.insert( - 'changing permission of refmac.csh: chmod +x refmac.csh') - os.system('chmod +x refmac.csh') - Logfile.insert('starting refinement on local machine') - os.system('./refmac.csh &') + Logfile.insert("changing permission of refmac.csh: chmod +x refmac.csh") + os.system("chmod +x refmac.csh") + Logfile.insert("starting refinement on local machine") + os.system("./refmac.csh &") -# if '/work/' in os.getcwd(): -# os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) -# else: -# os.system('./refmac.csh &') + # if '/work/' in os.getcwd(): + # os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) + # else: + # os.system('./refmac.csh &') def RefinementParams(self, RefmacParams): self.RefmacParams = RefmacParams @@ -1708,54 +2322,54 @@ def RefinementParams(self, RefmacParams): self.vbox = gtk.VBox() self.hbox1 = gtk.HBox() - self.hbox1.add(gtk.Label('Refine')) + self.hbox1.add(gtk.Label("Refine")) self.cb = gtk.combo_box_new_text() self.cb.connect("changed", self.ChooseBfacRefinement) - for item in ['isotropic', 'anisotropic']: + for item in ["isotropic", "anisotropic"]: self.cb.append_text(item) - if 'ISOT' in self.RefmacParams['BREF']: + if "ISOT" in self.RefmacParams["BREF"]: self.cb.set_active(0) - if 'ANIS' in self.RefmacParams['BREF']: + if "ANIS" in self.RefmacParams["BREF"]: self.cb.set_active(1) self.hbox1.add(self.cb) - self.hbox1.add(gtk.Label('temperature factors')) + self.hbox1.add(gtk.Label("temperature factors")) self.vbox.add(self.hbox1) self.hbox2 = gtk.HBox() - self.hbox2.add(gtk.Label('Number of Cycles: ')) + self.hbox2.add(gtk.Label("Number of Cycles: ")) self.Ncycles = gtk.Entry() self.Ncycles.add_events(gtk.gdk.KEY_RELEASE_MASK) self.Ncycles.connect("key-release-event", self.on_key_release_Ncycles) - self.Ncycles.set_text(self.RefmacParams['NCYCLES']) + self.Ncycles.set_text(self.RefmacParams["NCYCLES"]) self.hbox2.add(self.Ncycles) self.vbox.add(self.hbox2) self.hbox3 = gtk.HBox() - self.hbox3.add(gtk.Label('MATRIX WEIGHT: ')) + self.hbox3.add(gtk.Label("MATRIX WEIGHT: ")) self.MATRIX_WEIGHT = gtk.Entry() self.MATRIX_WEIGHT.add_events(gtk.gdk.KEY_RELEASE_MASK) self.MATRIX_WEIGHT.connect( - "key-release-event", self.on_key_release_MATRIX_WEIGHT) - self.MATRIX_WEIGHT.set_text(self.RefmacParams['MATRIX_WEIGHT']) + "key-release-event", self.on_key_release_MATRIX_WEIGHT + ) + self.MATRIX_WEIGHT.set_text(self.RefmacParams["MATRIX_WEIGHT"]) self.hbox3.add(self.MATRIX_WEIGHT) self.vbox.add(self.hbox3) - self.TLS = gtk.CheckButton( - 'TLS (find TLS groups with phenix.find_tls_groups)') + self.TLS = gtk.CheckButton("TLS (find TLS groups with phenix.find_tls_groups)") self.TLS.connect("toggled", self.TLSCallback) - if self.RefmacParams['TLS'] == 'refi tlsc 10\n': + if self.RefmacParams["TLS"] == "refi tlsc 10\n": self.TLS.set_active(True) self.vbox.pack_start(self.TLS, False) - self.NCS = gtk.CheckButton('NCS (if applicable') + self.NCS = gtk.CheckButton("NCS (if applicable") self.NCS.connect("toggled", self.NCSCallback) - if self.RefmacParams['NCS'] == 'NCSR LOCAL\n': + if self.RefmacParams["NCS"] == "NCSR LOCAL\n": self.NCS.set_active(True) self.vbox.pack_start(self.NCS, False) - self.TWIN = gtk.CheckButton('Twin?') + self.TWIN = gtk.CheckButton("Twin?") self.TWIN.connect("toggled", self.TWINCallback) - if self.RefmacParams['TWIN'] == 'TWIN\n': + if self.RefmacParams["TWIN"] == "TWIN\n": self.TWIN.set_active(True) self.vbox.pack_start(self.TWIN, False) @@ -1769,45 +2383,45 @@ def RefinementParams(self, RefmacParams): def TLSCallback(self, widget): if widget.get_active(): - self.RefmacParams['TLS'] = 'refi tlsc 10\n' - self.RefmacParams['TLSIN'] = 'refmac.tls\n' - self.RefmacParams['TLSOUT'] = 'out.tls\n' - self.RefmacParams['TLSADD'] = 'TLSO ADDU\n' + self.RefmacParams["TLS"] = "refi tlsc 10\n" + self.RefmacParams["TLSIN"] = "refmac.tls\n" + self.RefmacParams["TLSOUT"] = "out.tls\n" + self.RefmacParams["TLSADD"] = "TLSO ADDU\n" else: - self.RefmacParams['TLS'] = '' - self.RefmacParams['TLSIN'] = '' - self.RefmacParams['TLSOUT'] = '' - self.RefmacParams['TLSADD'] = '' + self.RefmacParams["TLS"] = "" + self.RefmacParams["TLSIN"] = "" + self.RefmacParams["TLSOUT"] = "" + self.RefmacParams["TLSADD"] = "" return self.RefmacParams def NCSCallback(self, widget): if widget.get_active(): - self.RefmacParams['NCS'] = 'NCSR LOCAL\n' + self.RefmacParams["NCS"] = "NCSR LOCAL\n" else: - self.RefmacParams['NCS'] = '' + self.RefmacParams["NCS"] = "" return self.RefmacParams def ChooseBfacRefinement(self, widget): - if widget.get_active_text() == 'isotropic': - self.RefmacParams['BREF'] = ' bref ISOT\n' - if widget.get_active_text() == 'anisotropic': - self.RefmacParams['BREF'] = ' bref ANIS\n' + if widget.get_active_text() == "isotropic": + self.RefmacParams["BREF"] = " bref ISOT\n" + if widget.get_active_text() == "anisotropic": + self.RefmacParams["BREF"] = " bref ANIS\n" return self.RefmacParams def on_key_release_Ncycles(self, widget, event): print(widget.get_text()) - self.RefmacParams['NCYCLES'] = widget.get_text() + self.RefmacParams["NCYCLES"] = widget.get_text() return self.RefmacParams def on_key_release_MATRIX_WEIGHT(self, widget, event): - self.RefmacParams['MATRIX_WEIGHT'] = widget.get_text() + self.RefmacParams["MATRIX_WEIGHT"] = widget.get_text() return self.RefmacParams def TWINCallback(self, widget): if widget.get_active(): - self.RefmacParams['TWIN'] = 'TWIN\n' + self.RefmacParams["TWIN"] = "TWIN\n" else: - self.RefmacParams['TWIN'] = '' + self.RefmacParams["TWIN"] = "" return self.RefmacParams def OK(self, widget): @@ -1815,35 +2429,54 @@ def OK(self, widget): def ParamsFromPreviousCycle(self, Serial): - RefmacParams = {'HKLIN': '', 'HKLOUT': '', - 'XYZIN': '', 'XYZOUT': '', - 'LIBIN': '', 'LIBOUT': '', - 'TLSIN': '', 'TLSOUT': '', - 'TLSADD': '', - 'NCYCLES': '10', - 'MATRIX_WEIGHT': 'AUTO', - 'BREF': ' bref ISOT\n', - 'TLS': '', - 'NCS': '', - 'TWIN': ''} - - if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): - for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): - if line.startswith('refi tlsc'): - RefmacParams['TLS'] = line - if line.startswith('TLSO'): - RefmacParams['TLSADD'] = line - if line.startswith('NCSR LOCAL'): - RefmacParams['NCS'] = line - if line.startswith(' bref '): - RefmacParams['BREF'] = line - if line.startswith('ncyc'): - RefmacParams['Ncycles'] = line.split()[1] - if line.startswith('weight'): - RefmacParams['MATRIX_WEIGHT'] = line.split()[ - len(line.split())-1] - if line.startswith('TWIN'): - RefmacParams['TWIN'] = line + RefmacParams = { + "HKLIN": "", + "HKLOUT": "", + "XYZIN": "", + "XYZOUT": "", + "LIBIN": "", + "LIBOUT": "", + "TLSIN": "", + "TLSOUT": "", + "TLSADD": "", + "NCYCLES": "10", + "MATRIX_WEIGHT": "AUTO", + "BREF": " bref ISOT\n", + "TLS": "", + "NCS": "", + "TWIN": "", + } + + if os.path.isfile( + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(Serial) + + "/refmac.csh" + ): + for line in open( + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(Serial) + + "/refmac.csh" + ): + if line.startswith("refi tlsc"): + RefmacParams["TLS"] = line + if line.startswith("TLSO"): + RefmacParams["TLSADD"] = line + if line.startswith("NCSR LOCAL"): + RefmacParams["NCS"] = line + if line.startswith(" bref "): + RefmacParams["BREF"] = line + if line.startswith("ncyc"): + RefmacParams["Ncycles"] = line.split()[1] + if line.startswith("weight"): + RefmacParams["MATRIX_WEIGHT"] = line.split()[len(line.split()) - 1] + if line.startswith("TWIN"): + RefmacParams["TWIN"] = line return RefmacParams @@ -1854,10 +2487,10 @@ def GetRefinementHistory(self): RfreeList = [] found = False - for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, '*')): - if item.startswith(os.path.join(self.ProjectPath, self.xtalID, 'Refine_')): - print(item[item.rfind('_')+1:]) - RefinementCycle.append(int(item[item.rfind('_')+1:])) + for item in glob.glob(os.path.join(self.ProjectPath, self.xtalID, "*")): + if item.startswith(os.path.join(self.ProjectPath, self.xtalID, "Refine_")): + print(item[item.rfind("_") + 1 :]) + RefinementCycle.append(int(item[item.rfind("_") + 1 :])) found = True if found: for cycle in sorted(RefinementCycle): @@ -1868,14 +2501,29 @@ def GetRefinementHistory(self): try: found_Rcryst = False found_Rfree = False - newestPDB = max(glob.iglob(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str( - cycle)+'/refine_'+str(cycle)+'.pdb'), key=os.path.getctime) + newestPDB = max( + glob.iglob( + self.ProjectPath + + "/" + + self.xtalID + + "/Refine_" + + str(cycle) + + "/refine_" + + str(cycle) + + ".pdb" + ), + key=os.path.getctime, + ) for line in open(newestPDB): - if line.startswith('REMARK 3 R VALUE (WORKING + TEST SET) :'): + if line.startswith( + "REMARK 3 R VALUE (WORKING + TEST SET) :" + ): Rcryst = line.split()[9] RcrystList.append(float(Rcryst)) found_Rcryst = True - if line.startswith('REMARK 3 FREE R VALUE :'): + if line.startswith( + "REMARK 3 FREE R VALUE :" + ): Rfree = line.split()[6] RfreeList.append(float(Rfree)) found_Rfree = True @@ -1883,20 +2531,20 @@ def GetRefinementHistory(self): RcrystList.append(0) if not found_Rfree: RfreeList.append(0) -# if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): -# for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): -# if line.startswith('| LIG'): LigandCC = line.split()[6] -# RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' + # if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): + # for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): + # if line.startswith('| LIG'): LigandCC = line.split()[6] + # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' except ValueError: RcrystList.append(0) RfreeList.append(0) -# RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' + # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' else: RefinementCycle = [0] RcrystList = [0] RfreeList = [0] print(RefinementCycle, RcrystList, RfreeList) - return(sorted(RefinementCycle), RcrystList, RfreeList) + return (sorted(RefinementCycle), RcrystList, RfreeList) # class RefineOld(object): diff --git a/lib/XChemThread.py b/lib/XChemThread.py index c7ac90f5..4f7e3f0a 100755 --- a/lib/XChemThread.py +++ b/lib/XChemThread.py @@ -33,32 +33,37 @@ from iotbx import mtz from iotbx.reflection_file_reader import any_reflection_file -sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") class synchronise_db_and_filesystem(QtCore.QThread): - ''' - - remove broken links - - insert new samples in DB - - update data for existing samples - ''' + """ + - remove broken links + - insert new samples in DB + - update data for existing samples + """ - def __init__(self, initial_model_directory, datasource, panddas_directory, xce_logfile, mode): + def __init__( + self, initial_model_directory, datasource, panddas_directory, xce_logfile, mode + ): QtCore.QThread.__init__(self) self.initial_model_directory = initial_model_directory self.datasource = datasource self.db = XChemDB.data_source(self.datasource) - self.all_samples_in_datasource = self.db.get_all_samples_in_data_source_as_list() + self.all_samples_in_datasource = ( + self.db.get_all_samples_in_data_source_as_list() + ) self.panddas_directory = panddas_directory self.xce_logfile = xce_logfile self.Logfile = XChemLog.updateLog(xce_logfile) self.mode = mode def run(self): - self.Logfile.insert('synchronising database and filesystem') - self.Logfile.insert('current project directory: ' + - self.initial_model_directory) + self.Logfile.insert("synchronising database and filesystem") + self.Logfile.insert( + "current project directory: " + self.initial_model_directory + ) XChemMain.backup_soakDB(self.datasource, self.xce_logfile) @@ -69,28 +74,33 @@ def run(self): self.xtal_list = [] progress_step = 1 progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - if self.mode != 'project_directory': + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) + if self.mode != "project_directory": # if only a single xtal is synched, then self.mode==xtalID - self.Logfile.insert('synchronising '+self.mode+' only') + self.Logfile.insert("synchronising " + self.mode + " only") self.xtal_list.append(self.mode) else: - if len(glob.glob(os.path.join(self.initial_model_directory, '*'))) != 0: - progress_step = 100 / \ - float( - len(glob.glob(os.path.join(self.initial_model_directory, '*')))) - self.Logfile.insert('found '+str(len(glob.glob(os.path.join( - self.initial_model_directory, '*'))))+' samples in project directory') - for directory in sorted(glob.glob(os.path.join(self.initial_model_directory, '*'))): + if len(glob.glob(os.path.join(self.initial_model_directory, "*"))) != 0: + progress_step = 100 / float( + len(glob.glob(os.path.join(self.initial_model_directory, "*"))) + ) + self.Logfile.insert( + "found " + + str(len(glob.glob(os.path.join(self.initial_model_directory, "*")))) + + " samples in project directory" + ) + for directory in sorted( + glob.glob(os.path.join(self.initial_model_directory, "*")) + ): try: os.chdir(directory) except OSError: # this could happen if the user accidentaly left a file in the project directory continue if os.listdir(directory) == []: - self.Logfile.warning(directory + ' is empty; skipping...') + self.Logfile.warning(directory + " is empty; skipping...") continue - xtal = directory[directory.rfind('/')+1:] + xtal = directory[directory.rfind("/") + 1 :] self.xtal_list.append(xtal) # @@ -98,19 +108,18 @@ def run(self): # for xtal in self.xtal_list: - self.Logfile.insert('directory name: '+xtal + - ' = sampleID in database') + self.Logfile.insert("directory name: " + xtal + " = sampleID in database") os.chdir(os.path.join(self.initial_model_directory, xtal)) if xtal not in self.all_samples_in_datasource: - self.Logfile.insert( - 'sampleID not found in database: inserting '+xtal) + self.Logfile.insert("sampleID not found in database: inserting " + xtal) self.db.execute_statement( - "insert into mainTable (CrystalName) values ('{0!s}');".format(xtal)) + "insert into mainTable (CrystalName) values ('{0!s}');".format(xtal) + ) self.all_samples_in_datasource.append(xtal) db_dict = self.db.get_db_dict_for_sample(xtal) - db_dict['ProjectDirectory'] = self.initial_model_directory + db_dict["ProjectDirectory"] = self.initial_model_directory db_dict = self.sync_data_processing(xtal, db_dict) @@ -121,59 +130,63 @@ def run(self): db_dict = self.sync_refinement_results(xtal, db_dict) if db_dict != {}: - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'updating datasource for '+xtal) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "updating datasource for " + xtal, + ) self.db.update_data_source(xtal, db_dict) progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) - self.Logfile.insert('database mainTable update finished') - self.Logfile.insert('updating panddaTable') - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'updating panddaTable') -# self.sync_pandda_table() + self.Logfile.insert("database mainTable update finished") + self.Logfile.insert("updating panddaTable") + self.emit(QtCore.SIGNAL("update_status_bar(QString)"), "updating panddaTable") + # self.sync_pandda_table() self.sync_pandda_table_NEW() - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'database panddaTable update finished') - self.Logfile.insert('database panddaTable update finished') + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "database panddaTable update finished", + ) + self.Logfile.insert("database panddaTable update finished") - self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) + self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) def change_absolute_to_relative_links(self, target, filename): os.unlink(filename) os.symlink(os.path.relpath(target), filename) - self.Logfile.insert( - '{0!s} -> {1!s}'.format(os.readlink(filename), target)) + self.Logfile.insert("{0!s} -> {1!s}".format(os.readlink(filename), target)) def find_file(self, filename, xtal): found_file = False - for files in glob.glob('*'): + for files in glob.glob("*"): if files == filename: # at this point, this could ba a file or a (broken) symbolic link try: link = os.readlink(filename) - if link.startswith('/'): - if os.path.isfile(link.replace(link[:link.find(xtal)], self.initial_model_directory+'/')): + if link.startswith("/"): + if os.path.isfile( + link.replace( + link[: link.find(xtal)], + self.initial_model_directory + "/", + ) + ): target = link.replace( - link[:link.find(xtal)], self.initial_model_directory+'/') + link[: link.find(xtal)], + self.initial_model_directory + "/", + ) found_file = True - self.change_absolute_to_relative_links( - target, filename) + self.change_absolute_to_relative_links(target, filename) elif os.path.isfile(files): # this will leave the absolute path found_file = True else: - self.Logfile.insert( - 'removing broken link: '+filename) - os.system( - '/bin/rm {0!s} 2> /dev/null'.format(filename)) + self.Logfile.insert("removing broken link: " + filename) + os.system("/bin/rm {0!s} 2> /dev/null".format(filename)) else: if not os.path.isfile(link): - self.Logfile.insert( - 'removing broken link: '+filename) - os.system( - '/bin/rm {0!s} 2> /dev/null'.format(filename)) + self.Logfile.insert("removing broken link: " + filename) + os.system("/bin/rm {0!s} 2> /dev/null".format(filename)) else: found_file = True except OSError: @@ -187,98 +200,128 @@ def sync_data_processing(self, xtal, db_dict): # AIMLESS logfile # in case the MTZ file which is used for refinement is different to the one used for refinement - if os.path.isfile('refine.mtz'): - if os.path.isfile(xtal+'.free.mtz'): - freeMTZ = mtztools(xtal+'.free.mtz') + if os.path.isfile("refine.mtz"): + if os.path.isfile(xtal + ".free.mtz"): + freeMTZ = mtztools(xtal + ".free.mtz") nREFfree = freeMTZ.get_number_measured_reflections() - if os.path.isfile(xtal+'.mtz'): - procMTZ = mtztools(xtal+'.mtz') + if os.path.isfile(xtal + ".mtz"): + procMTZ = mtztools(xtal + ".mtz") nREF = procMTZ.get_number_measured_reflections() - CC, errorMessage = freeMTZ.calculate_correlaton_between_intensities_in_mtzfiles( - xtal+'.mtz') - self.Logfile.insert('%s: calculating CC between %s.free.mtz (%s refl) and %s.mtz (%s refl): %s' % ( - xtal, xtal, str(nREFfree), xtal, str(nREF), str(CC))) - if errorMessage != '': + ( + CC, + errorMessage, + ) = freeMTZ.calculate_correlaton_between_intensities_in_mtzfiles( + xtal + ".mtz" + ) + self.Logfile.insert( + "%s: calculating CC between %s.free.mtz (%s refl) and %s.mtz (%s refl): %s" + % (xtal, xtal, str(nREFfree), xtal, str(nREF), str(CC)) + ) + if errorMessage != "": self.Logfile.insert( - 'pointless failed with the following error: %s' % errorMessage) + "pointless failed with the following error: %s" + % errorMessage + ) try: if float(CC) < 0.999: self.Logfile.insert( - 'correlation coefficient between the two files is below 0.999; will try to understand from dimple.log which one was used for initial map calculation') - if os.path.isfile('dimple/dimple_rerun_on_selected_file/dimple/dimple.log'): + "correlation coefficient between the two files is below 0.999; will try to understand from dimple.log which one was used for initial map calculation" + ) + if os.path.isfile( + "dimple/dimple_rerun_on_selected_file/dimple/dimple.log" + ): foundLine = False - mtzin = '' - for line in open('dimple/dimple_rerun_on_selected_file/dimple/dimple.log'): + mtzin = "" + for line in open( + "dimple/dimple_rerun_on_selected_file/dimple/dimple.log" + ): if foundLine: - mtzin = line.replace(' ', '').replace( - '\n', '').replace('\r', '') + mtzin = ( + line.replace(" ", "") + .replace("\n", "") + .replace("\r", "") + ) self.Logfile.insert( - '%s was used for inital map calculation' % mtzin) + "%s was used for inital map calculation" + % mtzin + ) break - if line.startswith(' --no-cleanup'): + if line.startswith(" --no-cleanup"): foundLine = True if os.path.isfile(mtzin): self.Logfile.insert( - '%s: mtzfile used for refinement is not the same as the one chosen from autoprocessing' % xtal) - self.Logfile.insert('%s: current mtzfile after autoprocessing: %s' % ( - xtal, os.path.realpath(xtal+'.mtz'))) + "%s: mtzfile used for refinement is not the same as the one chosen from autoprocessing" + % xtal + ) + self.Logfile.insert( + "%s: current mtzfile after autoprocessing: %s" + % (xtal, os.path.realpath(xtal + ".mtz")) + ) + self.Logfile.insert( + "%s: removing links for %s.mtz/%s.log" + % (xtal, xtal, xtal) + ) + os.system("/bin/rm %s.mtz 2> /dev/null" % xtal) + os.system("/bin/rm %s.log 2> /dev/null" % xtal) self.Logfile.insert( - '%s: removing links for %s.mtz/%s.log' % (xtal, xtal, xtal)) - os.system( - '/bin/rm %s.mtz 2> /dev/null' % xtal) - os.system( - '/bin/rm %s.log 2> /dev/null' % xtal) - self.Logfile.insert('linking %s to %s.mtz' % ( - os.path.relpath(mtzin), xtal)) - os.symlink(os.path.relpath( - mtzin), xtal+'.mtz') - for logfile in glob.glob(os.path.join(mtzin[:mtzin.rfind('/')], '*log')): - self.Logfile.insert('linking %s to %s.log' % ( - os.path.relpath(logfile), xtal)) - os.symlink(os.path.relpath( - logfile), xtal+'.log') + "linking %s to %s.mtz" + % (os.path.relpath(mtzin), xtal) + ) + os.symlink(os.path.relpath(mtzin), xtal + ".mtz") + for logfile in glob.glob( + os.path.join(mtzin[: mtzin.rfind("/")], "*log") + ): + self.Logfile.insert( + "linking %s to %s.log" + % (os.path.relpath(logfile), xtal) + ) + os.symlink( + os.path.relpath(logfile), xtal + ".log" + ) break except ValueError: self.Logfile.insert( - 'something went wrong: calculated CC value does not seem to be a floating point number') + "something went wrong: calculated CC value does not seem to be a floating point number" + ) found_logfile = False - if os.path.isfile(xtal+'.log'): + if os.path.isfile(xtal + ".log"): found_logfile = True -# db_dict['DataProcessingPathToLogfile']=os.path.realpath(xtal+'.log').replace(os.getcwd()+'/','') - db_dict['DataProcessingPathToLogfile'] = os.path.realpath( - xtal+'.log') - db_dict['DataProcessingLOGfileName'] = xtal+'.log' - if db_dict['DataCollectionOutcome'] == 'None' or db_dict['DataCollectionOutcome'] == '': - db_dict['DataCollectionOutcome'] = 'success' -# aimless_results=parse().read_aimless_logfile(xtal+'.log') + # db_dict['DataProcessingPathToLogfile']=os.path.realpath(xtal+'.log').replace(os.getcwd()+'/','') + db_dict["DataProcessingPathToLogfile"] = os.path.realpath(xtal + ".log") + db_dict["DataProcessingLOGfileName"] = xtal + ".log" + if ( + db_dict["DataCollectionOutcome"] == "None" + or db_dict["DataCollectionOutcome"] == "" + ): + db_dict["DataCollectionOutcome"] = "success" + # aimless_results=parse().read_aimless_logfile(xtal+'.log') aimless_results = parse().read_aimless_logfile( - db_dict['DataProcessingPathToLogfile']) + db_dict["DataProcessingPathToLogfile"] + ) db_dict.update(aimless_results) else: - db_dict['DataProcessingPathToLogfile'] = '' - db_dict['DataProcessingLOGfileName'] = '' + db_dict["DataProcessingPathToLogfile"] = "" + db_dict["DataProcessingLOGfileName"] = "" # MTZ file -# found_mtzfile=self.find_file(xtal+'.mtz',xtal) -# if found_mtzfile: - if os.path.isfile(xtal+'.mtz'): - db_dict['DataProcessingPathToMTZfile'] = os.path.realpath( - xtal+'.mtz') -# db_dict['DataProcessingPathToMTZfile']=os.path.realpath(xtal+'.mtz').replace(os.getcwd()+'/','') - db_dict['DataProcessingMTZfileName'] = xtal+'.mtz' + # found_mtzfile=self.find_file(xtal+'.mtz',xtal) + # if found_mtzfile: + if os.path.isfile(xtal + ".mtz"): + db_dict["DataProcessingPathToMTZfile"] = os.path.realpath(xtal + ".mtz") + # db_dict['DataProcessingPathToMTZfile']=os.path.realpath(xtal+'.mtz').replace(os.getcwd()+'/','') + db_dict["DataProcessingMTZfileName"] = xtal + ".mtz" if not found_logfile: - mtz_info = mtztools( - xtal+'.mtz').get_information_for_datasource() + mtz_info = mtztools(xtal + ".mtz").get_information_for_datasource() db_dict.update(mtz_info) - db_dict['DataCollectionOutcome'] = 'success' + db_dict["DataCollectionOutcome"] = "success" else: - db_dict['DataProcessingPathToMTZfile'] = '' - db_dict['DataProcessingMTZfileName'] = '' + db_dict["DataProcessingPathToMTZfile"] = "" + db_dict["DataProcessingMTZfileName"] = "" return db_dict @@ -288,121 +331,139 @@ def sync_dimple_results(self, xtal, db_dict): # found_dimple_pdb=self.find_file('dimple.pdb',xtal) # if found_dimple_pdb: - if os.path.isfile('dimple.pdb'): + if os.path.isfile("dimple.pdb"): # db_dict['DimplePathToPDB']=os.path.realpath('dimple.pdb').replace(os.getcwd()+'/','') - db_dict['DimplePathToPDB'] = os.path.realpath('dimple.pdb') - pdb_info = parse().PDBheader('dimple.pdb') - db_dict['DimpleRcryst'] = pdb_info['Rcryst'] - db_dict['DimpleRfree'] = pdb_info['Rfree'] - db_dict['DimpleResolutionHigh'] = pdb_info['ResolutionHigh'] - db_dict['DimpleStatus'] = 'finished' + db_dict["DimplePathToPDB"] = os.path.realpath("dimple.pdb") + pdb_info = parse().PDBheader("dimple.pdb") + db_dict["DimpleRcryst"] = pdb_info["Rcryst"] + db_dict["DimpleRfree"] = pdb_info["Rfree"] + db_dict["DimpleResolutionHigh"] = pdb_info["ResolutionHigh"] + db_dict["DimpleStatus"] = "finished" else: - db_dict['DimplePathToPDB'] = '' - db_dict['DimpleRcryst'] = '' - db_dict['DimpleRfree'] = '' - db_dict['DimpleResolutionHigh'] = '' - db_dict['DimpleStatus'] = 'pending' + db_dict["DimplePathToPDB"] = "" + db_dict["DimpleRcryst"] = "" + db_dict["DimpleRfree"] = "" + db_dict["DimpleResolutionHigh"] = "" + db_dict["DimpleStatus"] = "pending" # DIMPLE mtz - dimple_path = '' -# found_dimple_mtz=self.find_file('dimple.mtz',xtal) -# if found_dimple_mtz: - if os.path.isfile('dimple.mtz'): + dimple_path = "" + # found_dimple_mtz=self.find_file('dimple.mtz',xtal) + # if found_dimple_mtz: + if os.path.isfile("dimple.mtz"): # db_dict['DimplePathToMTZ']=os.path.realpath('dimple.mtz').replace(os.getcwd()+'/','') - db_dict['DimplePathToMTZ'] = os.path.realpath('dimple.mtz') - dimple_mtz = db_dict['DimplePathToMTZ'] - dimple_path = dimple_mtz[:dimple_mtz.rfind('/')] + db_dict["DimplePathToMTZ"] = os.path.realpath("dimple.mtz") + dimple_mtz = db_dict["DimplePathToMTZ"] + dimple_path = dimple_mtz[: dimple_mtz.rfind("/")] else: - db_dict['DimplePathToMTZ'] = '' - db_dict['DimpleStatus'] = 'pending' - - if os.path.isfile(os.path.join(dimple_path, 'dimple', 'dimple_rerun_on_selected_file', 'dimple_run_in_progress')): - db_dict['DimpleStatus'] = 'running' + db_dict["DimplePathToMTZ"] = "" + db_dict["DimpleStatus"] = "pending" + + if os.path.isfile( + os.path.join( + dimple_path, + "dimple", + "dimple_rerun_on_selected_file", + "dimple_run_in_progress", + ) + ): + db_dict["DimpleStatus"] = "running" # MTZ free file -# found_free_mtz=self.find_file(xtal+'.free.mtz',xtal) -# if found_free_mtz: - if os.path.isfile(xtal+'.free.mtz'): - db_dict['RefinementMTZfree'] = os.path.realpath(xtal+'.free.mtz') -# db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz').replace(os.getcwd()+'/','') + # found_free_mtz=self.find_file(xtal+'.free.mtz',xtal) + # if found_free_mtz: + if os.path.isfile(xtal + ".free.mtz"): + db_dict["RefinementMTZfree"] = os.path.realpath(xtal + ".free.mtz") + # db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz').replace(os.getcwd()+'/','') else: - db_dict['RefinementMTZfree'] = '' - os.system('/bin/rm %s.free.mtz 2> /dev/null' % xtal) - if os.path.isfile(os.path.join(dimple_path, 'prepared2.mtz')): - os.symlink(os.path.relpath(os.path.join( - dimple_path, 'prepared2.mtz')), xtal+'.free.mtz') -# db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz').replace(os.getcwd()+'/','') - db_dict['RefinementMTZfree'] = os.path.realpath( - xtal+'.free.mtz') -# db_dict['RefinementMTZfree']=xtal+'.free.mtz' - elif os.path.isfile(os.path.join(dimple_path, 'prepared.mtz')): - os.symlink(os.path.relpath(os.path.join( - dimple_path, 'prepared.mtz')), xtal+'.free.mtz') - db_dict['RefinementMTZfree'] = os.path.realpath( - xtal+'.free.mtz') -# db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz').replace(os.getcwd()+'/','') -# db_dict['RefinementMTZfree']=xtal+'.free.mtz' - elif os.path.isfile(os.path.join(dimple_path, 'free.mtz')): - os.symlink(os.path.relpath(os.path.join( - dimple_path, 'free.mtz')), xtal+'.free.mtz') - db_dict['RefinementMTZfree'] = os.path.realpath( - xtal+'.free.mtz') + db_dict["RefinementMTZfree"] = "" + os.system("/bin/rm %s.free.mtz 2> /dev/null" % xtal) + if os.path.isfile(os.path.join(dimple_path, "prepared2.mtz")): + os.symlink( + os.path.relpath(os.path.join(dimple_path, "prepared2.mtz")), + xtal + ".free.mtz", + ) + # db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz').replace(os.getcwd()+'/','') + db_dict["RefinementMTZfree"] = os.path.realpath(xtal + ".free.mtz") + # db_dict['RefinementMTZfree']=xtal+'.free.mtz' + elif os.path.isfile(os.path.join(dimple_path, "prepared.mtz")): + os.symlink( + os.path.relpath(os.path.join(dimple_path, "prepared.mtz")), + xtal + ".free.mtz", + ) + db_dict["RefinementMTZfree"] = os.path.realpath(xtal + ".free.mtz") + # db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz').replace(os.getcwd()+'/','') + # db_dict['RefinementMTZfree']=xtal+'.free.mtz' + elif os.path.isfile(os.path.join(dimple_path, "free.mtz")): + os.symlink( + os.path.relpath(os.path.join(dimple_path, "free.mtz")), + xtal + ".free.mtz", + ) + db_dict["RefinementMTZfree"] = os.path.realpath(xtal + ".free.mtz") return db_dict def sync_compound_information(self, db_dict): # only update database if SMILES or compoundID field is blank! - compoundID = db_dict['CompoundCode'] - if compoundID == 'None' or compoundID == '': - if os.path.isdir('compound'): - for smiles in glob.glob('compound/*'): - if smiles.endswith('smiles'): + compoundID = db_dict["CompoundCode"] + if compoundID == "None" or compoundID == "": + if os.path.isdir("compound"): + for smiles in glob.glob("compound/*"): + if smiles.endswith("smiles"): for line in open(smiles): if len(line.split()) >= 1: - db_dict['CompoundCode'] = smiles[smiles.rfind( - '/')+1:smiles.rfind('.')] - compoundID = db_dict['CompoundCode'] + db_dict["CompoundCode"] = smiles[ + smiles.rfind("/") + 1 : smiles.rfind(".") + ] + compoundID = db_dict["CompoundCode"] break - if os.path.isfile(compoundID+'.cif') and os.path.getsize(compoundID+'.cif') > 20: - db_dict['RefinementCIF'] = os.path.realpath( - compoundID+'.cif').replace(os.getcwd()+'/', '') - db_dict['RefinementCIFStatus'] = 'restraints generated' + if ( + os.path.isfile(compoundID + ".cif") + and os.path.getsize(compoundID + ".cif") > 20 + ): + db_dict["RefinementCIF"] = os.path.realpath(compoundID + ".cif").replace( + os.getcwd() + "/", "" + ) + db_dict["RefinementCIFStatus"] = "restraints generated" else: - os.system('/bin/rm {0!s}.cif 2> /dev/null'.format(compoundID)) - os.system( - '/bin/rm compound/{0!s}.cif 2> /dev/null'.format(compoundID)) - db_dict['RefinementCIF'] = '' - db_dict['RefinementCIFStatus'] = 'pending' + os.system("/bin/rm {0!s}.cif 2> /dev/null".format(compoundID)) + os.system("/bin/rm compound/{0!s}.cif 2> /dev/null".format(compoundID)) + db_dict["RefinementCIF"] = "" + db_dict["RefinementCIFStatus"] = "pending" - smilesDB = db_dict['CompoundSMILES'] + smilesDB = db_dict["CompoundSMILES"] smiles_found = True - if smilesDB == 'None' or smilesDB == '': + if smilesDB == "None" or smilesDB == "": smiles_found = False - if os.path.isdir('compound'): - for smiles in glob.glob('compound/*'): - if smiles.endswith('smiles'): + if os.path.isdir("compound"): + for smiles in glob.glob("compound/*"): + if smiles.endswith("smiles"): for line in open(smiles): if len(line.split()) >= 1: - db_dict['CompoundSMILES'] = line.split()[0] - smilesDB = db_dict['CompoundSMILES'] + db_dict["CompoundSMILES"] = line.split()[0] + smilesDB = db_dict["CompoundSMILES"] smiles_found = True break if not smiles_found: - db_dict['RefinementCIFStatus'] = 'missing smiles' - - if not os.path.isfile(compoundID+'.pdb') or os.path.getsize(compoundID+'.pdb') < 20: - os.system('/bin/rm {0!s}.pdb 2> /dev/null'.format(compoundID)) - os.system( - '/bin/rm compound/{0!s}.pdb 2> /dev/null'.format(compoundID)) - - if not os.path.isfile(compoundID+'.png') or os.path.getsize(compoundID+'.png') < 20: - os.system('/bin/rm {0!s}.png 2> /dev/null'.format(compoundID)) - os.system( - '/bin/rm compound/{0!s}.png 2> /dev/null'.format(compoundID)) + db_dict["RefinementCIFStatus"] = "missing smiles" + + if ( + not os.path.isfile(compoundID + ".pdb") + or os.path.getsize(compoundID + ".pdb") < 20 + ): + os.system("/bin/rm {0!s}.pdb 2> /dev/null".format(compoundID)) + os.system("/bin/rm compound/{0!s}.pdb 2> /dev/null".format(compoundID)) + + if ( + not os.path.isfile(compoundID + ".png") + or os.path.getsize(compoundID + ".png") < 20 + ): + os.system("/bin/rm {0!s}.png 2> /dev/null".format(compoundID)) + os.system("/bin/rm compound/{0!s}.png 2> /dev/null".format(compoundID)) return db_dict @@ -416,35 +477,39 @@ def sync_refinement_results(self, xtal, db_dict): # if found_refine_pdb and not 'dimple' in os.path.realpath('refine.pdb'): # if os.path.isfile('refine.pdb') and not 'dimple' in os.path.realpath('refine.pdb'): - if os.path.isfile('refine.pdb'): - db_dict['RefinementPDB_latest'] = os.path.realpath('refine.pdb') -# db_dict['RefinementPDB_latest']=os.path.realpath('refine.pdb').replace(os.getcwd()+'/','') - db_dict['RefinementStatus'] = 'finished' - pdb_info = parse().dict_for_datasource_update('refine.pdb') + if os.path.isfile("refine.pdb"): + db_dict["RefinementPDB_latest"] = os.path.realpath("refine.pdb") + # db_dict['RefinementPDB_latest']=os.path.realpath('refine.pdb').replace(os.getcwd()+'/','') + db_dict["RefinementStatus"] = "finished" + pdb_info = parse().dict_for_datasource_update("refine.pdb") db_dict.update(pdb_info) - if db_dict['RefinementOutcome'] == 'None' or db_dict['RefinementOutcome'] == '': - db_dict['RefinementOutcome'] = '3 - In Refinement' - elif str(db_dict['RefinementOutcome']).startswith('1'): - db_dict['RefinementOutcome'] = '3 - In Refinement' - elif str(db_dict['RefinementOutcome']).startswith('2'): - db_dict['RefinementOutcome'] = '3 - In Refinement' + if ( + db_dict["RefinementOutcome"] == "None" + or db_dict["RefinementOutcome"] == "" + ): + db_dict["RefinementOutcome"] = "3 - In Refinement" + elif str(db_dict["RefinementOutcome"]).startswith("1"): + db_dict["RefinementOutcome"] = "3 - In Refinement" + elif str(db_dict["RefinementOutcome"]).startswith("2"): + db_dict["RefinementOutcome"] = "3 - In Refinement" else: - db_dict['RefinementPDB_latest'] = '' - db_dict['RefinementStatus'] = 'pending' - db_dict['RefinementOutcome'] = '1 - Analysis Pending' - os.system('/bin/rm refine.pdb 2> /dev/null') + db_dict["RefinementPDB_latest"] = "" + db_dict["RefinementStatus"] = "pending" + db_dict["RefinementOutcome"] = "1 - Analysis Pending" + os.system("/bin/rm refine.pdb 2> /dev/null") - if os.path.isfile('REFINEMENT_IN_PROGRESS'): - db_dict['RefinementStatus'] = 'running' + if os.path.isfile("REFINEMENT_IN_PROGRESS"): + db_dict["RefinementStatus"] = "running" # # REFINE bound pdb # - if os.path.isfile('refine.split.bound-state.pdb'): - db_dict['RefinementBoundConformation'] = os.path.realpath( - 'refine.split.bound-state.pdb') -# db_dict['RefinementBoundConformation']='refine.bound.pdb' + if os.path.isfile("refine.split.bound-state.pdb"): + db_dict["RefinementBoundConformation"] = os.path.realpath( + "refine.split.bound-state.pdb" + ) + # db_dict['RefinementBoundConformation']='refine.bound.pdb' else: # if os.path.isfile('refine.pdb'): # os.system("giant.strip_conformations pdb=refine.pdb suffix='.bound.pdb'") @@ -454,21 +519,21 @@ def sync_refinement_results(self, xtal, db_dict): # db_dict['RefinementBoundConformation']='' # else: # db_dict['RefinementBoundConformation']='' - db_dict['RefinementBoundConformation'] = '' + db_dict["RefinementBoundConformation"] = "" # # REFINE mtz # -# found_refine_mtz=self.find_file('refine.mtz',xtal) -# if found_refine_mtz and not 'dimple' in os.path.realpath('refine.mtz'): -# if os.path.isfile('refine.mtz') and not 'dimple' in os.path.realpath('refine.mtz'): - if os.path.isfile('refine.mtz'): - db_dict['RefinementMTZ_latest'] = os.path.realpath('refine.mtz') -# db_dict['RefinementMTZ_latest']=os.path.realpath('refine.mtz').replace(os.getcwd()+'/','') + # found_refine_mtz=self.find_file('refine.mtz',xtal) + # if found_refine_mtz and not 'dimple' in os.path.realpath('refine.mtz'): + # if os.path.isfile('refine.mtz') and not 'dimple' in os.path.realpath('refine.mtz'): + if os.path.isfile("refine.mtz"): + db_dict["RefinementMTZ_latest"] = os.path.realpath("refine.mtz") + # db_dict['RefinementMTZ_latest']=os.path.realpath('refine.mtz').replace(os.getcwd()+'/','') else: - db_dict['RefinementMTZ_latest'] = '' - os.system('/bin/rm refine.mtz 2> /dev/null') + db_dict["RefinementMTZ_latest"] = "" + os.system("/bin/rm refine.mtz 2> /dev/null") return db_dict @@ -486,180 +551,191 @@ def find_apo_structures_for_PanDDA(self, panddaPATH): # newer pandda versions seem to have severl copies of pandda.log with names like # pandda-2016-09-01-2139.log - panddaLog = glob.glob(os.path.join(panddaPATH, 'pandda*log')) + panddaLog = glob.glob(os.path.join(panddaPATH, "pandda*log")) panddaLog.sort(key=os.path.getmtime) - panddaVersion = 'unknown' + panddaVersion = "unknown" readindApoStructures = False apoStructures = [] apoStructureDict = {} - apoString = '' + apoString = "" for files in panddaLog: for line in open(files): - if line.startswith('- Pandda Version'): + if line.startswith("- Pandda Version"): if len(line.split()) >= 4: panddaVersion = line.split()[3] - if 'No Statistical Maps Found:' in line: + if "No Statistical Maps Found:" in line: readindApoStructures = True if readindApoStructures: - if 'Pickling Object: processed_datasets' in line: + if "Pickling Object: processed_datasets" in line: if line.split() >= 2: # e.g. line.split() -> ['Pickling', 'Object:', 'processed_datasets/NUDT22A-x0055/pickles/dataset.pickle'] - xtal = line.split()[2].split('/')[1] - if os.path.isfile(os.path.join(panddaPATH, 'processed_datasets', xtal, xtal+'-pandda-input.pdb')): + xtal = line.split()[2].split("/")[1] + if os.path.isfile( + os.path.join( + panddaPATH, + "processed_datasets", + xtal, + xtal + "-pandda-input.pdb", + ) + ): apoStructures.append(xtal) - apoString += xtal+';' - if 'Pre-existing statistical maps (from previous runs) have been found and will be reused:' in line: + apoString += xtal + ";" + if ( + "Pre-existing statistical maps (from previous runs) have been found and will be reused:" + in line + ): readindApoStructures = False apoStructureDict[panddaPATH] = apoStructures return apoString[:-1] -# def sync_pandda_table(self): -# progress_step=1 -# progress=0 -# self.emit(QtCore.SIGNAL('update_progress_bar'), progress) -# -# # also need to update PANDDA table... -# pandda_models=self.db.execute_statement("select CrystalName,PANDDA_site_index,PANDDA_site_event_index,PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDApath,ApoStructures from panddaTable") -# if len(pandda_models) > 0: -# progress_step=100/float(len(pandda_models)) -# -# if pandda_models != []: -# for entry in pandda_models: -# db_pandda_dict={} -# xtal=entry[0] -# site_index=entry[1] -# event_index=entry[2] -# panddaPATH=entry[6] -# apoStructures=entry[7] -# self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'checking %s -> site %s -> event %s ' %(xtal,site_index,event_index)) -# try: -# event_x = float(str(entry[3])) -# event_y = float(str(entry[4])) -# event_z = float(str(entry[5])) -# except ValueError: -# pass -# -# # do not update pandda path since this one is updated during pandda export! -# # instead try to get apo semi-colon separated list of apo structures that were used to -# # calculate event maps; but only if field is blank! -# db_pandda_dict['PANDDApath']=self.panddas_directory -# if str(apoStructures)=='None' or apoStructures=='': -# if panddaPATH != 'None' or panddaPATH != '': -# self.Logfile.insert('trying to find which apo structures were used to calculate the event maps in '+panddaPATH) -# db_pandda_dict['ApoStructures']=self.find_apo_structures_for_PanDDA(panddaPATH) -# else: -# self.Logfile.insert('pandda path for '+xtal+' is empty in database') -# -# # event map -# -# found_event_map=False -# db_pandda_dict['PANDDA_site_event_map']='' -# for file in glob.glob(os.path.join(self.initial_model_directory,xtal,'*ccp4')): -# filename=file[file.rfind('/')+1:] -# if filename.startswith(xtal+'-event_'+event_index) and filename.endswith('map.native.ccp4'): -# event_map=file -# db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map) -# db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map).replace(os.getcwd()+'/','') -# found_event_map=True -# break -# if not found_event_map: -# db_pandda_dict['PANDDA_site_event_map']='' -# -# db_pandda_dict['PANDDA_site_initial_model']='' -# for file in glob.glob(os.path.join(self.initial_model_directory,xtal,'*pdb')): -# filename=file[file.rfind('/')+1:] -# if filename.endswith('-ensemble-model.pdb'): -# db_pandda_dict['PANDDA_site_initial_model']=os.path.realpath(file).replace(os.getcwd()+'/','') -# break -# -# db_pandda_dict['PANDDA_site_initial_mtz']='' -# for file in glob.glob(os.path.join(self.initial_model_directory,xtal,'*mtz')): -# filename=file[file.rfind('/')+1:] -# if filename.endswith('pandda-input.mtz'): -# db_pandda_dict['PANDDA_site_initial_mtz']=os.path.realpath(file).replace(os.getcwd()+'/','') -# break -# -# -# db_pandda_dict['PANDDA_site_ligand_resname'] = '' -# db_pandda_dict['PANDDA_site_ligand_chain'] = '' -# db_pandda_dict['PANDDA_site_ligand_sequence_number'] = '' -# db_pandda_dict['PANDDA_site_ligand_altLoc'] = '' -# db_pandda_dict['PANDDA_site_ligand_placed'] = 'False' -# db_pandda_dict['PANDDA_site_spider_plot'] = '' -# db_pandda_dict['PANDDA_site_ligand_id'] = '' -# -# db_pandda_dict['PANDDA_site_occupancy'] = '' -# db_pandda_dict['PANDDA_site_B_average'] = '' -# db_pandda_dict['PANDDA_site_B_ratio_residue_surroundings'] = '' -# db_pandda_dict['PANDDA_site_rmsd'] = '' -# db_pandda_dict['PANDDA_site_RSCC'] = '' -# db_pandda_dict['PANDDA_site_RSR'] = '' -# db_pandda_dict['PANDDA_site_RSZD'] = '' -# -# if os.path.isfile(os.path.join(self.initial_model_directory,xtal,'refine.pdb')): -# ligands_in_file=pdbtools(os.path.join(self.initial_model_directory,xtal,'refine.pdb')).find_xce_ligand_details() -# -# for ligand in ligands_in_file: -# residue_name= ligand[0] -# residue_chain= ligand[1] -# residue_number= ligand[2] -# residue_altLoc= ligand[3] -# residue_xyz = pdbtools(os.path.join(self.initial_model_directory,xtal,'refine.pdb')).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) -# distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1],residue_xyz[2],event_x, event_y,event_z) -# # if coordinate of ligand and event are closer than 7A, then we assume they belong together -# if distance < 7: -# db_pandda_dict['PANDDA_site_ligand_resname'] = residue_name -# db_pandda_dict['PANDDA_site_ligand_chain'] = residue_chain -# db_pandda_dict['PANDDA_site_ligand_sequence_number'] = residue_number -# db_pandda_dict['PANDDA_site_ligand_altLoc'] = residue_altLoc -# db_pandda_dict['PANDDA_site_ligand_placed'] = 'True' -# db_pandda_dict['PANDDA_site_ligand_id']=residue_name+'-'+residue_chain+'-'+residue_number -# -# if xtal+'/Refine_' in os.path.realpath(os.path.join(self.initial_model_directory,xtal,'refine.pdb')): -# tmp=os.path.realpath(os.path.join(self.initial_model_directory,xtal,'refine.pdb')) -# spider_plot=os.path.join(tmp[:tmp.rfind('/')],'residue_plots',residue_name+'-'+residue_chain+'-'+residue_number+'.png') -# if os.path.isfile(spider_plot): -# db_pandda_dict['PANDDA_site_spider_plot']=os.path.realpath(spider_plot) -# db_pandda_dict['PANDDA_site_spider_plot']=os.path.realpath(spider_plot).replace(os.getcwd()+'/','') -# if os.path.isfile(os.path.join(tmp[:tmp.rfind('/')],'residue_scores.csv')): -# -# with open(os.path.join(tmp[:tmp.rfind('/')],'residue_scores.csv'), 'rb') as csv_import: -# csv_dict = csv.DictReader(csv_import) -# for i, line in enumerate(csv_dict): -# residueNameChainNumber = line[''] -# if residueNameChainNumber == residue_name+'-'+residue_chain+'-'+residue_number: -# db_pandda_dict['PANDDA_site_occupancy'] = line['Occupancy'] -# db_pandda_dict['PANDDA_site_B_average'] = line['Average B-factor (Residue)'] -# db_pandda_dict['PANDDA_site_B_ratio_residue_surroundings'] = line['Surroundings B-factor Ratio'] -# db_pandda_dict['PANDDA_site_rmsd'] = line['Model RMSD'] -# db_pandda_dict['PANDDA_site_RSCC'] = line['RSCC'] -# db_pandda_dict['PANDDA_site_RSR'] = line['RSR'] -# db_pandda_dict['PANDDA_site_RSZD'] = line['RSZD'] -# break -# -# if db_pandda_dict != {}: -## self.db.update_panddaTable(xtal, site_index, db_pandda_dict) -# self.db.update_site_event_panddaTable(xtal, site_index, event_index, db_pandda_dict) -# self.Logfile.insert('updating panddaTable for xtal: %s, site: %s' %(xtal,site_index)) -# -# progress += progress_step -# self.emit(QtCore.SIGNAL('update_progress_bar'), progress) -# + # def sync_pandda_table(self): + # progress_step=1 + # progress=0 + # self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + # + # # also need to update PANDDA table... + # pandda_models=self.db.execute_statement("select CrystalName,PANDDA_site_index,PANDDA_site_event_index,PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDApath,ApoStructures from panddaTable") + # if len(pandda_models) > 0: + # progress_step=100/float(len(pandda_models)) + # + # if pandda_models != []: + # for entry in pandda_models: + # db_pandda_dict={} + # xtal=entry[0] + # site_index=entry[1] + # event_index=entry[2] + # panddaPATH=entry[6] + # apoStructures=entry[7] + # self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'checking %s -> site %s -> event %s ' %(xtal,site_index,event_index)) + # try: + # event_x = float(str(entry[3])) + # event_y = float(str(entry[4])) + # event_z = float(str(entry[5])) + # except ValueError: + # pass + # + # # do not update pandda path since this one is updated during pandda export! + # # instead try to get apo semi-colon separated list of apo structures that were used to + # # calculate event maps; but only if field is blank! + # db_pandda_dict['PANDDApath']=self.panddas_directory + # if str(apoStructures)=='None' or apoStructures=='': + # if panddaPATH != 'None' or panddaPATH != '': + # self.Logfile.insert('trying to find which apo structures were used to calculate the event maps in '+panddaPATH) + # db_pandda_dict['ApoStructures']=self.find_apo_structures_for_PanDDA(panddaPATH) + # else: + # self.Logfile.insert('pandda path for '+xtal+' is empty in database') + # + # # event map + # + # found_event_map=False + # db_pandda_dict['PANDDA_site_event_map']='' + # for file in glob.glob(os.path.join(self.initial_model_directory,xtal,'*ccp4')): + # filename=file[file.rfind('/')+1:] + # if filename.startswith(xtal+'-event_'+event_index) and filename.endswith('map.native.ccp4'): + # event_map=file + # db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map) + # db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map).replace(os.getcwd()+'/','') + # found_event_map=True + # break + # if not found_event_map: + # db_pandda_dict['PANDDA_site_event_map']='' + # + # db_pandda_dict['PANDDA_site_initial_model']='' + # for file in glob.glob(os.path.join(self.initial_model_directory,xtal,'*pdb')): + # filename=file[file.rfind('/')+1:] + # if filename.endswith('-ensemble-model.pdb'): + # db_pandda_dict['PANDDA_site_initial_model']=os.path.realpath(file).replace(os.getcwd()+'/','') + # break + # + # db_pandda_dict['PANDDA_site_initial_mtz']='' + # for file in glob.glob(os.path.join(self.initial_model_directory,xtal,'*mtz')): + # filename=file[file.rfind('/')+1:] + # if filename.endswith('pandda-input.mtz'): + # db_pandda_dict['PANDDA_site_initial_mtz']=os.path.realpath(file).replace(os.getcwd()+'/','') + # break + # + # + # db_pandda_dict['PANDDA_site_ligand_resname'] = '' + # db_pandda_dict['PANDDA_site_ligand_chain'] = '' + # db_pandda_dict['PANDDA_site_ligand_sequence_number'] = '' + # db_pandda_dict['PANDDA_site_ligand_altLoc'] = '' + # db_pandda_dict['PANDDA_site_ligand_placed'] = 'False' + # db_pandda_dict['PANDDA_site_spider_plot'] = '' + # db_pandda_dict['PANDDA_site_ligand_id'] = '' + # + # db_pandda_dict['PANDDA_site_occupancy'] = '' + # db_pandda_dict['PANDDA_site_B_average'] = '' + # db_pandda_dict['PANDDA_site_B_ratio_residue_surroundings'] = '' + # db_pandda_dict['PANDDA_site_rmsd'] = '' + # db_pandda_dict['PANDDA_site_RSCC'] = '' + # db_pandda_dict['PANDDA_site_RSR'] = '' + # db_pandda_dict['PANDDA_site_RSZD'] = '' + # + # if os.path.isfile(os.path.join(self.initial_model_directory,xtal,'refine.pdb')): + # ligands_in_file=pdbtools(os.path.join(self.initial_model_directory,xtal,'refine.pdb')).find_xce_ligand_details() + # + # for ligand in ligands_in_file: + # residue_name= ligand[0] + # residue_chain= ligand[1] + # residue_number= ligand[2] + # residue_altLoc= ligand[3] + # residue_xyz = pdbtools(os.path.join(self.initial_model_directory,xtal,'refine.pdb')).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) + # distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1],residue_xyz[2],event_x, event_y,event_z) + # # if coordinate of ligand and event are closer than 7A, then we assume they belong together + # if distance < 7: + # db_pandda_dict['PANDDA_site_ligand_resname'] = residue_name + # db_pandda_dict['PANDDA_site_ligand_chain'] = residue_chain + # db_pandda_dict['PANDDA_site_ligand_sequence_number'] = residue_number + # db_pandda_dict['PANDDA_site_ligand_altLoc'] = residue_altLoc + # db_pandda_dict['PANDDA_site_ligand_placed'] = 'True' + # db_pandda_dict['PANDDA_site_ligand_id']=residue_name+'-'+residue_chain+'-'+residue_number + # + # if xtal+'/Refine_' in os.path.realpath(os.path.join(self.initial_model_directory,xtal,'refine.pdb')): + # tmp=os.path.realpath(os.path.join(self.initial_model_directory,xtal,'refine.pdb')) + # spider_plot=os.path.join(tmp[:tmp.rfind('/')],'residue_plots',residue_name+'-'+residue_chain+'-'+residue_number+'.png') + # if os.path.isfile(spider_plot): + # db_pandda_dict['PANDDA_site_spider_plot']=os.path.realpath(spider_plot) + # db_pandda_dict['PANDDA_site_spider_plot']=os.path.realpath(spider_plot).replace(os.getcwd()+'/','') + # if os.path.isfile(os.path.join(tmp[:tmp.rfind('/')],'residue_scores.csv')): + # + # with open(os.path.join(tmp[:tmp.rfind('/')],'residue_scores.csv'), 'rb') as csv_import: + # csv_dict = csv.DictReader(csv_import) + # for i, line in enumerate(csv_dict): + # residueNameChainNumber = line[''] + # if residueNameChainNumber == residue_name+'-'+residue_chain+'-'+residue_number: + # db_pandda_dict['PANDDA_site_occupancy'] = line['Occupancy'] + # db_pandda_dict['PANDDA_site_B_average'] = line['Average B-factor (Residue)'] + # db_pandda_dict['PANDDA_site_B_ratio_residue_surroundings'] = line['Surroundings B-factor Ratio'] + # db_pandda_dict['PANDDA_site_rmsd'] = line['Model RMSD'] + # db_pandda_dict['PANDDA_site_RSCC'] = line['RSCC'] + # db_pandda_dict['PANDDA_site_RSR'] = line['RSR'] + # db_pandda_dict['PANDDA_site_RSZD'] = line['RSZD'] + # break + # + # if db_pandda_dict != {}: + ## self.db.update_panddaTable(xtal, site_index, db_pandda_dict) + # self.db.update_site_event_panddaTable(xtal, site_index, event_index, db_pandda_dict) + # self.Logfile.insert('updating panddaTable for xtal: %s, site: %s' %(xtal,site_index)) + # + # progress += progress_step + # self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + # def sync_pandda_table_NEW(self): progress_step = 1 progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) # also need to update PANDDA table... pandda_models = self.db.execute_statement( - "select CrystalName,PANDDA_site_index,PANDDA_site_event_index,PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDApath,ApoStructures from panddaTable") + "select CrystalName,PANDDA_site_index,PANDDA_site_event_index,PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDApath,ApoStructures from panddaTable" + ) if len(pandda_models) > 0: - progress_step = 100/float(len(pandda_models)) + progress_step = 100 / float(len(pandda_models)) else: - self.Logfile.warning('panddaTable seems to be empty!') + self.Logfile.warning("panddaTable seems to be empty!") if pandda_models: for entry in pandda_models: @@ -669,9 +745,13 @@ def sync_pandda_table_NEW(self): event_index = entry[2] panddaPATH = entry[6] apoStructures = entry[7] - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'checking {0!s} -> site {1!s} -> event {2!s} '.format(xtal, site_index, event_index)) - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "checking {0!s} -> site {1!s} -> event {2!s} ".format( + xtal, site_index, event_index + ), + ) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) progress += progress_step try: @@ -684,75 +764,99 @@ def sync_pandda_table_NEW(self): # do not update pandda path since this one is updated during pandda export! # instead try to get apo semi-colon separated list of apo structures that were used to # calculate event maps; but only if field is blank! -# db_pandda_dict['PANDDApath']=self.panddas_directory - if str(apoStructures) == 'None' or apoStructures == '': - if panddaPATH != 'None' or panddaPATH != '': + # db_pandda_dict['PANDDApath']=self.panddas_directory + if str(apoStructures) == "None" or apoStructures == "": + if panddaPATH != "None" or panddaPATH != "": self.Logfile.insert( - 'trying to find which apo structures were used to calculate the event maps in '+panddaPATH) - db_pandda_dict['ApoStructures'] = self.find_apo_structures_for_PanDDA( - panddaPATH) + "trying to find which apo structures were used to calculate the event maps in " + + panddaPATH + ) + db_pandda_dict[ + "ApoStructures" + ] = self.find_apo_structures_for_PanDDA(panddaPATH) else: self.Logfile.insert( - 'pandda path for '+xtal+' is empty in database') + "pandda path for " + xtal + " is empty in database" + ) # event map found_event_map = False - db_pandda_dict['PANDDA_site_event_map'] = '' - for file in glob.glob(os.path.join(self.initial_model_directory, xtal, '*ccp4')): - filename = file[file.rfind('/')+1:] - if filename.startswith(xtal+'-event_'+event_index) and filename.endswith('map.native.ccp4'): + db_pandda_dict["PANDDA_site_event_map"] = "" + for file in glob.glob( + os.path.join(self.initial_model_directory, xtal, "*ccp4") + ): + filename = file[file.rfind("/") + 1 :] + if filename.startswith( + xtal + "-event_" + event_index + ) and filename.endswith("map.native.ccp4"): event_map = file - db_pandda_dict['PANDDA_site_event_map'] = os.path.realpath( - event_map) -# db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map).replace(os.getcwd()+'/','') + db_pandda_dict["PANDDA_site_event_map"] = os.path.realpath( + event_map + ) + # db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map).replace(os.getcwd()+'/','') found_event_map = True break if not found_event_map: - db_pandda_dict['PANDDA_site_event_map'] = '' - - db_pandda_dict['PANDDA_site_initial_model'] = '' - for file in glob.glob(os.path.join(self.initial_model_directory, xtal, '*pdb')): - filename = file[file.rfind('/')+1:] - if filename.endswith('-ensemble-model.pdb'): - db_pandda_dict['PANDDA_site_initial_model'] = os.path.realpath( - file).replace(os.getcwd()+'/', '') + db_pandda_dict["PANDDA_site_event_map"] = "" + + db_pandda_dict["PANDDA_site_initial_model"] = "" + for file in glob.glob( + os.path.join(self.initial_model_directory, xtal, "*pdb") + ): + filename = file[file.rfind("/") + 1 :] + if filename.endswith("-ensemble-model.pdb"): + db_pandda_dict["PANDDA_site_initial_model"] = os.path.realpath( + file + ).replace(os.getcwd() + "/", "") break - db_pandda_dict['PANDDA_site_initial_mtz'] = '' - for file in glob.glob(os.path.join(self.initial_model_directory, xtal, '*mtz')): - filename = file[file.rfind('/')+1:] - if filename.endswith('pandda-input.mtz'): - db_pandda_dict['PANDDA_site_initial_mtz'] = os.path.realpath( - file).replace(os.getcwd()+'/', '') + db_pandda_dict["PANDDA_site_initial_mtz"] = "" + for file in glob.glob( + os.path.join(self.initial_model_directory, xtal, "*mtz") + ): + filename = file[file.rfind("/") + 1 :] + if filename.endswith("pandda-input.mtz"): + db_pandda_dict["PANDDA_site_initial_mtz"] = os.path.realpath( + file + ).replace(os.getcwd() + "/", "") break - db_pandda_dict['PANDDA_site_ligand_resname'] = '' - db_pandda_dict['PANDDA_site_ligand_chain'] = '' - db_pandda_dict['PANDDA_site_ligand_sequence_number'] = '' - db_pandda_dict['PANDDA_site_ligand_altLoc'] = '' - db_pandda_dict['PANDDA_site_ligand_placed'] = 'False' - db_pandda_dict['PANDDA_site_spider_plot'] = '' - db_pandda_dict['PANDDA_site_ligand_id'] = '' - - db_pandda_dict['PANDDA_site_occupancy'] = '' - db_pandda_dict['PANDDA_site_B_average'] = '' - db_pandda_dict['PANDDA_site_B_ratio_residue_surroundings'] = '' - db_pandda_dict['PANDDA_site_rmsd'] = '' - db_pandda_dict['PANDDA_site_RSCC'] = '' - db_pandda_dict['PANDDA_site_RSR'] = '' - db_pandda_dict['PANDDA_site_RSZD'] = '' - - if os.path.isfile(os.path.join(self.initial_model_directory, xtal, 'refine.pdb')): - ligands_in_file = pdbtools(os.path.join( - self.initial_model_directory, xtal, 'refine.pdb')).find_xce_ligand_details() + db_pandda_dict["PANDDA_site_ligand_resname"] = "" + db_pandda_dict["PANDDA_site_ligand_chain"] = "" + db_pandda_dict["PANDDA_site_ligand_sequence_number"] = "" + db_pandda_dict["PANDDA_site_ligand_altLoc"] = "" + db_pandda_dict["PANDDA_site_ligand_placed"] = "False" + db_pandda_dict["PANDDA_site_spider_plot"] = "" + db_pandda_dict["PANDDA_site_ligand_id"] = "" + + db_pandda_dict["PANDDA_site_occupancy"] = "" + db_pandda_dict["PANDDA_site_B_average"] = "" + db_pandda_dict["PANDDA_site_B_ratio_residue_surroundings"] = "" + db_pandda_dict["PANDDA_site_rmsd"] = "" + db_pandda_dict["PANDDA_site_RSCC"] = "" + db_pandda_dict["PANDDA_site_RSR"] = "" + db_pandda_dict["PANDDA_site_RSZD"] = "" + + if os.path.isfile( + os.path.join(self.initial_model_directory, xtal, "refine.pdb") + ): + ligands_in_file = pdbtools( + os.path.join(self.initial_model_directory, xtal, "refine.pdb") + ).find_xce_ligand_details() if not ligands_in_file: self.Logfile.warning( - '{0!s}: could not find any ligands in refine.pdb'.format(xtal)) + "{0!s}: could not find any ligands in refine.pdb".format( + xtal + ) + ) continue else: - self.Logfile.insert('{0!s}: found the following ligands in refine.pdb: {1!s}'.format( - xtal, str(ligands_in_file))) + self.Logfile.insert( + "{0!s}: found the following ligands in refine.pdb: {1!s}".format( + xtal, str(ligands_in_file) + ) + ) distanceList = [] for ligand in ligands_in_file: @@ -760,77 +864,160 @@ def sync_pandda_table_NEW(self): residue_chain = ligand[1] residue_number = ligand[2] residue_altLoc = ligand[3] - residue_xyz = pdbtools(os.path.join(self.initial_model_directory, xtal, 'refine.pdb') - ).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) + residue_xyz = pdbtools( + os.path.join( + self.initial_model_directory, xtal, "refine.pdb" + ) + ).get_center_of_gravity_of_residue_ish( + residue_chain, residue_number + ) distance = misc().calculate_distance_between_coordinates( - residue_xyz[0], residue_xyz[1], residue_xyz[2], event_x, event_y, event_z) + residue_xyz[0], + residue_xyz[1], + residue_xyz[2], + event_x, + event_y, + event_z, + ) distanceList.append( - [distance, residue_name, residue_chain, residue_number, residue_altLoc]) - self.Logfile.insert('{0!s}: calculating distance between event and ligand ({1!s} {2!s} {3!s}): {4!s}'.format( - xtal, residue_name, residue_chain, residue_number, str(distance))) + [ + distance, + residue_name, + residue_chain, + residue_number, + residue_altLoc, + ] + ) + self.Logfile.insert( + "{0!s}: calculating distance between event and ligand ({1!s} {2!s} {3!s}): {4!s}".format( + xtal, + residue_name, + residue_chain, + residue_number, + str(distance), + ) + ) # now take the ligand that is closest to the event try: - smallestDistance = min( - distanceList, key=lambda x: x[0]) + smallestDistance = min(distanceList, key=lambda x: x[0]) except ValueError: self.Logfile.error( - 'could not determine smallest distance between current ligand pandda events') + "could not determine smallest distance between current ligand pandda events" + ) continue distance = smallestDistance[0] residue_name = smallestDistance[1] residue_chain = smallestDistance[2] residue_number = smallestDistance[3] residue_altLoc = smallestDistance[4] - self.Logfile.insert('{0!s}: ligand with the shorted distance ({1!s}A) to the current event (id: {2!s}): {3!s} {4!s} {5!s} {6!s}'.format( - xtal, str(distance), event_index, residue_name, residue_chain, residue_number, residue_altLoc)) - db_pandda_dict['PANDDA_site_ligand_resname'] = residue_name - db_pandda_dict['PANDDA_site_ligand_chain'] = residue_chain - db_pandda_dict['PANDDA_site_ligand_sequence_number'] = residue_number - db_pandda_dict['PANDDA_site_ligand_altLoc'] = residue_altLoc - db_pandda_dict['PANDDA_site_ligand_placed'] = 'True' - db_pandda_dict['PANDDA_site_ligand_id'] = residue_name + \ - '-'+residue_chain+'-'+residue_number - - if xtal+'/Refine_' in os.path.realpath(os.path.join(self.initial_model_directory, xtal, 'refine.pdb')): - tmp = os.path.realpath(os.path.join( - self.initial_model_directory, xtal, 'refine.pdb')) - spider_plot = os.path.join(tmp[:tmp.rfind( - '/')], 'residue_plots', residue_chain+'-'+residue_number+'.png').replace(' ', '') + self.Logfile.insert( + "{0!s}: ligand with the shorted distance ({1!s}A) to the current event (id: {2!s}): {3!s} {4!s} {5!s} {6!s}".format( + xtal, + str(distance), + event_index, + residue_name, + residue_chain, + residue_number, + residue_altLoc, + ) + ) + db_pandda_dict["PANDDA_site_ligand_resname"] = residue_name + db_pandda_dict["PANDDA_site_ligand_chain"] = residue_chain + db_pandda_dict[ + "PANDDA_site_ligand_sequence_number" + ] = residue_number + db_pandda_dict["PANDDA_site_ligand_altLoc"] = residue_altLoc + db_pandda_dict["PANDDA_site_ligand_placed"] = "True" + db_pandda_dict["PANDDA_site_ligand_id"] = ( + residue_name + "-" + residue_chain + "-" + residue_number + ) + + if xtal + "/Refine_" in os.path.realpath( + os.path.join(self.initial_model_directory, xtal, "refine.pdb") + ): + tmp = os.path.realpath( + os.path.join( + self.initial_model_directory, xtal, "refine.pdb" + ) + ) + spider_plot = os.path.join( + tmp[: tmp.rfind("/")], + "residue_plots", + residue_chain + "-" + residue_number + ".png", + ).replace(" ", "") if os.path.isfile(spider_plot): - db_pandda_dict['PANDDA_site_spider_plot'] = os.path.realpath( - spider_plot) - if os.path.isfile(os.path.join(tmp[:tmp.rfind('/')], 'residue_scores.csv')): - with open(os.path.join(tmp[:tmp.rfind('/')], 'residue_scores.csv'), 'rb') as csv_import: + db_pandda_dict[ + "PANDDA_site_spider_plot" + ] = os.path.realpath(spider_plot) + if os.path.isfile( + os.path.join(tmp[: tmp.rfind("/")], "residue_scores.csv") + ): + with open( + os.path.join( + tmp[: tmp.rfind("/")], "residue_scores.csv" + ), + "rb", + ) as csv_import: csv_dict = csv.DictReader(csv_import) for i, line in enumerate(csv_dict): - residueNameChainNumber = line[''] - if residueNameChainNumber == residue_chain+'-'+residue_number: - db_pandda_dict['PANDDA_site_occupancy'] = line['Occupancy'] - db_pandda_dict['PANDDA_site_B_average'] = line[ - 'Average B-factor (Residue)'] - db_pandda_dict['PANDDA_site_B_ratio_residue_surroundings'] = line['Surroundings B-factor Ratio'] - db_pandda_dict['PANDDA_site_rmsd'] = line['Model RMSD'] - db_pandda_dict['PANDDA_site_RSCC'] = line['RSCC'] - db_pandda_dict['PANDDA_site_RSR'] = line['RSR'] - db_pandda_dict['PANDDA_site_RSZD'] = line['RSZD'] -# break + residueNameChainNumber = line[""] + if ( + residueNameChainNumber + == residue_chain + "-" + residue_number + ): + db_pandda_dict["PANDDA_site_occupancy"] = line[ + "Occupancy" + ] + db_pandda_dict["PANDDA_site_B_average"] = line[ + "Average B-factor (Residue)" + ] + db_pandda_dict[ + "PANDDA_site_B_ratio_residue_surroundings" + ] = line["Surroundings B-factor Ratio"] + db_pandda_dict["PANDDA_site_rmsd"] = line[ + "Model RMSD" + ] + db_pandda_dict["PANDDA_site_RSCC"] = line[ + "RSCC" + ] + db_pandda_dict["PANDDA_site_RSR"] = line["RSR"] + db_pandda_dict["PANDDA_site_RSZD"] = line[ + "RSZD" + ] + # break if db_pandda_dict != {}: # self.db.update_panddaTable(xtal, site_index, db_pandda_dict) self.db.update_site_event_panddaTable( - xtal, site_index, event_index, db_pandda_dict) - self.Logfile.insert('updating panddaTable for xtal: {0!s}, site: {1!s}, event: {2!s}'.format( - xtal, site_index, event_index)) + xtal, site_index, event_index, db_pandda_dict + ) self.Logfile.insert( - '-> panddaDict: ' + str(db_pandda_dict)) + "updating panddaTable for xtal: {0!s}, site: {1!s}, event: {2!s}".format( + xtal, site_index, event_index + ) + ) + self.Logfile.insert("-> panddaDict: " + str(db_pandda_dict)) + # progress += progress_step # self.emit(QtCore.SIGNAL('update_progress_bar'), progress) class create_png_and_cif_of_compound(QtCore.QThread): - def __init__(self, external_software, initial_model_directory, compound_list, database_directory, data_source_file, todo, ccp4_scratch_directory, xce_logfile, max_queue_jobs, restraints_program): + def __init__( + self, + external_software, + initial_model_directory, + compound_list, + database_directory, + data_source_file, + todo, + ccp4_scratch_directory, + xce_logfile, + max_queue_jobs, + restraints_program, + ): QtCore.QThread.__init__(self) self.external_software = external_software self.initial_model_directory = initial_model_directory @@ -842,18 +1029,20 @@ def __init__(self, external_software, initial_model_directory, compound_list, da self.xce_logfile = xce_logfile self.Logfile = XChemLog.updateLog(xce_logfile) self.max_queue_jobs = max_queue_jobs - self.db = XChemDB.data_source(os.path.join( - self.database_directory, self.data_source_file)) + self.db = XChemDB.data_source( + os.path.join(self.database_directory, self.data_source_file) + ) self.restraints_program = restraints_program def run(self): # first remove all ACEDRG input scripts in ccp4_scratch directory self.Logfile.insert( - 'removing all xce_acedrg scripts from '+self.ccp4_scratch_directory) + "removing all xce_acedrg scripts from " + self.ccp4_scratch_directory + ) os.chdir(self.ccp4_scratch_directory) - os.system('/bin/rm -f xce_acedrg*') + os.system("/bin/rm -f xce_acedrg*") - progress_step = 100/float(len(self.compound_list)) + progress_step = 100 / float(len(self.compound_list)) progress = 0 counter = 1 for item in self.compound_list: @@ -861,137 +1050,246 @@ def run(self): compoundID = item[1] sm = item[2] # if counterions are present, split and take the longest string in list - smiles = max(sm.split('.'), key=len) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'creating ACEDRG shell script for '+sampleID) - if compoundID == '' or compoundID is None: - compoundID = 'compound' + smiles = max(sm.split("."), key=len) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "creating ACEDRG shell script for " + sampleID, + ) + if compoundID == "" or compoundID is None: + compoundID = "compound" if not os.path.isdir(os.path.join(self.initial_model_directory, sampleID)): os.mkdir(os.path.join(self.initial_model_directory, sampleID)) - if self.todo == 'ALL' or self.todo == 'SELECTED': + if self.todo == "ALL" or self.todo == "SELECTED": # remove symbolic links if present - if os.path.isfile(os.path.join(self.initial_model_directory, sampleID, compoundID.replace(' ', '')+'.pdb')): - os.system('/bin/rm '+os.path.join(self.initial_model_directory, - sampleID, compoundID.replace(' ', '')+'.pdb')) -# commented this out since people found the presence of the old.cif file interfering with pandda.inspect -# if os.path.isfile(os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.cif')): -# # copy existing CIF file to old.cif so that it can be used as input in -# # restraints generating program -# os.chdir(os.path.join(self.initial_model_directory,sampleID)) -# os.system('/bin/cp %s old.cif' %(compoundID.replace(' ','')+'.cif')) -# os.system('/bin/rm '+os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.cif')) - if os.path.isfile(os.path.join(self.initial_model_directory, sampleID, compoundID.replace(' ', '')+'.png')): - os.system('/bin/rm '+os.path.join(self.initial_model_directory, - sampleID, compoundID.replace(' ', '')+'.png')) - if os.path.isdir(os.path.join(self.initial_model_directory, sampleID, 'compound')): + if os.path.isfile( + os.path.join( + self.initial_model_directory, + sampleID, + compoundID.replace(" ", "") + ".pdb", + ) + ): + os.system( + "/bin/rm " + + os.path.join( + self.initial_model_directory, + sampleID, + compoundID.replace(" ", "") + ".pdb", + ) + ) + # commented this out since people found the presence of the old.cif file interfering with pandda.inspect + # if os.path.isfile(os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.cif')): + # # copy existing CIF file to old.cif so that it can be used as input in + # # restraints generating program + # os.chdir(os.path.join(self.initial_model_directory,sampleID)) + # os.system('/bin/cp %s old.cif' %(compoundID.replace(' ','')+'.cif')) + # os.system('/bin/rm '+os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.cif')) + if os.path.isfile( + os.path.join( + self.initial_model_directory, + sampleID, + compoundID.replace(" ", "") + ".png", + ) + ): + os.system( + "/bin/rm " + + os.path.join( + self.initial_model_directory, + sampleID, + compoundID.replace(" ", "") + ".png", + ) + ) + if os.path.isdir( + os.path.join(self.initial_model_directory, sampleID, "compound") + ): os.system( - '/bin/rm -fr '+os.path.join(self.initial_model_directory, sampleID, 'compound')) - db_dict = {'RefinementCIFStatus': 'pending'} + "/bin/rm -fr " + + os.path.join( + self.initial_model_directory, sampleID, "compound" + ) + ) + db_dict = {"RefinementCIFStatus": "pending"} self.Logfile.insert( - '{0!s}: removed compound directory and all its contents'.format(sampleID)) + "{0!s}: removed compound directory and all its contents".format( + sampleID + ) + ) self.Logfile.insert( - '{0!s}: setting RefinementCIFStatus flag to started'.format(sampleID)) + "{0!s}: setting RefinementCIFStatus flag to started".format( + sampleID + ) + ) self.db.update_data_source(sampleID, db_dict) # create 'compound' directory if not present - if not os.path.isdir(os.path.join(self.initial_model_directory, sampleID, 'compound')): - os.mkdir(os.path.join( - self.initial_model_directory, sampleID, 'compound')) + if not os.path.isdir( + os.path.join(self.initial_model_directory, sampleID, "compound") + ): + os.mkdir( + os.path.join(self.initial_model_directory, sampleID, "compound") + ) # create text file which contains the smiles string - if not os.path.isfile(os.path.join(self.initial_model_directory, sampleID, 'compound', compoundID+'.smiles')): - os.chdir(os.path.join( - self.initial_model_directory, sampleID, 'compound')) - f = open(compoundID+'.smiles', 'w') + if not os.path.isfile( + os.path.join( + self.initial_model_directory, + sampleID, + "compound", + compoundID + ".smiles", + ) + ): + os.chdir( + os.path.join(self.initial_model_directory, sampleID, "compound") + ) + f = open(compoundID + ".smiles", "w") f.write(smiles) f.close() - if not os.path.isfile(os.path.join(self.initial_model_directory, sampleID, compoundID.replace(' ', '')+'.cif')) \ - or self.todo == 'SELECTED': + if ( + not os.path.isfile( + os.path.join( + self.initial_model_directory, + sampleID, + compoundID.replace(" ", "") + ".cif", + ) + ) + or self.todo == "SELECTED" + ): os.chdir(os.path.join(self.initial_model_directory, sampleID)) - os.system('/bin/rm -f %s*' % compoundID.replace(' ', '')) - os.chdir(os.path.join( - self.initial_model_directory, sampleID, 'compound')) - - helpers().make_png(self.initial_model_directory, - sampleID, - compoundID, - smiles, - self.external_software, - self.database_directory, - self.data_source_file, - self.ccp4_scratch_directory, - counter, - self.xce_logfile, - self.restraints_program) + os.system("/bin/rm -f %s*" % compoundID.replace(" ", "")) + os.chdir( + os.path.join(self.initial_model_directory, sampleID, "compound") + ) + + helpers().make_png( + self.initial_model_directory, + sampleID, + compoundID, + smiles, + self.external_software, + self.database_directory, + self.data_source_file, + self.ccp4_scratch_directory, + counter, + self.xce_logfile, + self.restraints_program, + ) counter += 1 - db_dict = {'RefinementCIFprogram': self.restraints_program, - 'RefinementCIFStatus': 'started'} + db_dict = { + "RefinementCIFprogram": self.restraints_program, + "RefinementCIFStatus": "started", + } self.Logfile.insert( - '{0!s}: setting RefinementCIFStatus flag to started'.format(sampleID)) + "{0!s}: setting RefinementCIFStatus flag to started".format( + sampleID + ) + ) self.db.update_data_source(sampleID, db_dict) progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) # submit array job at Diamond - self.Logfile.insert('created input scripts for '+str(counter) + - ' ACEDRG jobs in '+self.ccp4_scratch_directory) + self.Logfile.insert( + "created input scripts for " + + str(counter) + + " ACEDRG jobs in " + + self.ccp4_scratch_directory + ) os.chdir(self.ccp4_scratch_directory) - self.Logfile.insert('changing directory to ' + - self.ccp4_scratch_directory) + self.Logfile.insert("changing directory to " + self.ccp4_scratch_directory) if counter > 1: # if os.getcwd().startswith('/dls'): - if os.path.isdir('/dls'): - if self.external_software['qsub_array']: + if os.path.isdir("/dls"): + if self.external_software["qsub_array"]: Cmds = ( - '#PBS -joe -N xce_%s_master\n' % self.restraints_program + - './xce_%s_$SGE_TASK_ID.sh\n' % self.restraints_program + "#PBS -joe -N xce_%s_master\n" % self.restraints_program + + "./xce_%s_$SGE_TASK_ID.sh\n" % self.restraints_program ) - f = open('%s_master.sh' % self.restraints_program, 'w') + f = open("%s_master.sh" % self.restraints_program, "w") f.write(Cmds) f.close() self.Logfile.insert( - 'submitting array job with maximal 100 jobs running on cluster') - self.Logfile.insert('using the following command:') - self.Logfile.insert(' qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh'.format( - str(counter), self.max_queue_jobs, self.restraints_program)) - os.system('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} -N {2!s} {3!s}_master.sh'.format( - str(counter), self.max_queue_jobs, self.restraints_program, self.restraints_program)) + "submitting array job with maximal 100 jobs running on cluster" + ) + self.Logfile.insert("using the following command:") + self.Logfile.insert( + " qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh".format( + str(counter), self.max_queue_jobs, self.restraints_program + ) + ) + os.system( + "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} -N {2!s} {3!s}_master.sh".format( + str(counter), + self.max_queue_jobs, + self.restraints_program, + self.restraints_program, + ) + ) else: self.Logfile.insert( - "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") - elif self.external_software['qsub']: + "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file" + ) + elif self.external_software["qsub"]: self.Logfile.insert( - 'submitting {0!s} individual jobs to cluster'.format((str(counter)))) + "submitting {0!s} individual jobs to cluster".format((str(counter))) + ) self.Logfile.insert( - 'WARNING: this could potentially lead to a crash...') + "WARNING: this could potentially lead to a crash..." + ) for i in range(counter): - self.Logfile.insert('qsub -q medium.q -N {0!s} xce_{1!s}_{2!s}.sh'.format( - self.restraints_program, self.restraints_program, (str(i+1)))) - os.system('qsub -N {0!s} xce_{1!s}_{2!s}.sh'.format( - self.restraints_program, self.restraints_program, (str(i+1)))) + self.Logfile.insert( + "qsub -q medium.q -N {0!s} xce_{1!s}_{2!s}.sh".format( + self.restraints_program, + self.restraints_program, + (str(i + 1)), + ) + ) + os.system( + "qsub -N {0!s} xce_{1!s}_{2!s}.sh".format( + self.restraints_program, + self.restraints_program, + (str(i + 1)), + ) + ) else: - self.Logfile.insert('running %s consecutive %s jobs on your local machine' % ( - str(counter), self.restraints_program)) + self.Logfile.insert( + "running %s consecutive %s jobs on your local machine" + % (str(counter), self.restraints_program) + ) for i in range(counter): - self.Logfile.insert('starting xce_{0!s}_{1!s}.sh'.format( - self.restraints_program, (str(i+1)))) + self.Logfile.insert( + "starting xce_{0!s}_{1!s}.sh".format( + self.restraints_program, (str(i + 1)) + ) + ) os.system( - './xce_{0!s}_{1!s}.sh'.format(self.restraints_program, (str(i+1)))) + "./xce_{0!s}_{1!s}.sh".format( + self.restraints_program, (str(i + 1)) + ) + ) -# self.emit(QtCore.SIGNAL("finished()")) - self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) + # self.emit(QtCore.SIGNAL("finished()")) + self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) class fit_ligands(QtCore.QThread): - def __init__(self, external_software, initial_model_directory, compound_list, database_directory, data_source_file, ccp4_scratch_directory, xce_logfile, max_queue_jobs): + def __init__( + self, + external_software, + initial_model_directory, + compound_list, + database_directory, + data_source_file, + ccp4_scratch_directory, + xce_logfile, + max_queue_jobs, + ): QtCore.QThread.__init__(self) self.external_software = external_software - self.queueing_system_available = external_software['qsub'] + self.queueing_system_available = external_software["qsub"] self.initial_model_directory = initial_model_directory self.compound_list = compound_list self.database_directory = database_directory @@ -1000,18 +1298,25 @@ def __init__(self, external_software, initial_model_directory, compound_list, da self.xce_logfile = xce_logfile self.Logfile = XChemLog.updateLog(xce_logfile) self.max_queue_jobs = max_queue_jobs - self.db = XChemDB.data_source(os.path.join( - self.database_directory, self.data_source_file)) + self.db = XChemDB.data_source( + os.path.join(self.database_directory, self.data_source_file) + ) self.n = 1 def prepareInput(self, cmd, ligList): for cif in ligList: - cmd += 'rhofit -m ../init.mtz -p ../init.pdb -l ../compound/%s.cif -scanchirals -d %s_rhofit\n' % ( - cif, cif) - cmd += 'phenix.ligandfit data=../init.mtz model=../init.pdb ligand=../compound/%s.cif clean_up=True\n' % cif - cmd += '/bin/mv LigandFit_run_1_ %s_phenix\n' % cif - cmd += '/bin/rm -fr PDS\n\n' + cmd += ( + "rhofit -m ../init.mtz -p ../init.pdb -l ../compound/%s.cif -scanchirals -d %s_rhofit\n" + % (cif, cif) + ) + cmd += ( + "phenix.ligandfit data=../init.mtz model=../init.pdb ligand=../compound/%s.cif clean_up=True\n" + % cif + ) + cmd += "/bin/mv LigandFit_run_1_ %s_phenix\n" % cif + cmd += "/bin/rm -fr PDS\n\n" return cmd + # rhofit -m refine.mtz -p refine.pdb -l ../compound/NU074105a.cif -d NU074105a_rhofit # phenix.ligandfit data=refine.mtz model=refine.pdb ligand=../compound/NU074105a.cif # phenix.get_cc_mtz_pdb LigandFit_run_1_/ligand_fit_1_1.pdb refine.mtz > log @@ -1019,58 +1324,75 @@ def prepareInput(self, cmd, ligList): def get_header(self, sampleID): if self.queueing_system_available: - top_line = '#PBS -joe -N XCE_dimple\n' + top_line = "#PBS -joe -N XCE_dimple\n" else: - top_line = '#!' + os.getenv('SHELL') + '\n' + top_line = "#!" + os.getenv("SHELL") + "\n" - module = '' - if os.path.isdir('/dls'): - module = 'module load mx\n' - module += 'module load buster\n' + module = "" + if os.path.isdir("/dls"): + module = "module load mx\n" + module += "module load buster\n" cmd = ( - '{0!s}\n'.format(top_line) + - '\n' - 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' - '\n' - 'cd %s\n' % os.path.join(self.initial_model_directory, sampleID, 'autofit_ligand') + - '\n' + "{0!s}\n".format(top_line) + "\n" + 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"\n' + "\n" + "cd %s\n" + % os.path.join(self.initial_model_directory, sampleID, "autofit_ligand") + + "\n" + module ) return cmd def get_footer(self, cmd, sampleID, compoundID): - cmd += ('$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/find_best_fitting_ligand.py {0!s} {1!s} {2!s}' - .format(compoundID.replace(' ', ''), os.path.join(self.initial_model_directory, sampleID), - os.path.join(self.database_directory, self.data_source_file))) + cmd += "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/find_best_fitting_ligand.py {0!s} {1!s} {2!s}".format( + compoundID.replace(" ", ""), + os.path.join(self.initial_model_directory, sampleID), + os.path.join(self.database_directory, self.data_source_file), + ) return cmd def run(self): # first remove all ACEDRG input scripts in ccp4_scratch directory self.Logfile.insert( - 'removing all xce_fit_ligands scripts from '+self.ccp4_scratch_directory) + "removing all xce_fit_ligands scripts from " + self.ccp4_scratch_directory + ) os.chdir(self.ccp4_scratch_directory) - os.system('/bin/rm -f xce_autofit_ligand*') + os.system("/bin/rm -f xce_autofit_ligand*") - progress_step = 100/float(len(self.compound_list)) + progress_step = 100 / float(len(self.compound_list)) progress = 0 counter = 1 for item in self.compound_list: sampleID = item[0] compoundID = item[1] - if os.path.isdir(os.path.join(self.initial_model_directory, sampleID, 'autofit_ligand')): + if os.path.isdir( + os.path.join(self.initial_model_directory, sampleID, "autofit_ligand") + ): os.system( - '/bin/rm -fr ' + os.path.join(self.initial_model_directory, sampleID, 'autofit_ligand')) - os.mkdir(os.path.join(self.initial_model_directory, - sampleID, 'autofit_ligand')) + "/bin/rm -fr " + + os.path.join( + self.initial_model_directory, sampleID, "autofit_ligand" + ) + ) + os.mkdir( + os.path.join(self.initial_model_directory, sampleID, "autofit_ligand") + ) # find ligands to fit (there might be more than one in case of stereoisomers ligList = [] - for file in glob.glob(os.path.join(self.initial_model_directory, sampleID, 'compound', compoundID+'*.cif')): - cif = file[file.rfind('/')+1:].replace('.cif', '') - if 'with_H' in cif: + for file in glob.glob( + os.path.join( + self.initial_model_directory, + sampleID, + "compound", + compoundID + "*.cif", + ) + ): + cif = file[file.rfind("/") + 1 :].replace(".cif", "") + if "with_H" in cif: continue else: ligList.append(cif) @@ -1084,65 +1406,81 @@ def run(self): self.n += 1 progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) # self.emit(QtCore.SIGNAL("finished()")) - self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) + self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) def write_script(self, cmd): os.chdir(self.ccp4_scratch_directory) - f = open('xce_autofit_ligand_{0!s}.sh'.format(str(self.n)), 'w') + f = open("xce_autofit_ligand_{0!s}.sh".format(str(self.n)), "w") f.write(cmd) f.close() - os.system('chmod +x xce_autofit_ligand_{0!s}.sh'.format(str(self.n))) + os.system("chmod +x xce_autofit_ligand_{0!s}.sh".format(str(self.n))) def run_script(self): # submit job - self.Logfile.insert('created input scripts for ' + - str(self.n) + ' in ' + self.ccp4_scratch_directory) + self.Logfile.insert( + "created input scripts for " + + str(self.n) + + " in " + + self.ccp4_scratch_directory + ) os.chdir(self.ccp4_scratch_directory) - if os.path.isdir('/dls'): - if self.external_software['qsub_array']: + if os.path.isdir("/dls"): + if self.external_software["qsub_array"]: Cmds = ( - '#PBS -joe -N xce_autofit_ligand_master\n' + - './xce_autofit_ligand_$SGE_TASK_ID.sh\n' + "#PBS -joe -N xce_autofit_ligand_master\n" + + "./xce_autofit_ligand_$SGE_TASK_ID.sh\n" ) - f = open('autofit_ligand_master.sh', 'w') + f = open("autofit_ligand_master.sh", "w") f.write(Cmds) f.close() self.Logfile.insert( - 'submitting array job with maximal 100 jobs running on cluster') - self.Logfile.insert('using the following command:') + "submitting array job with maximal 100 jobs running on cluster" + ) + self.Logfile.insert("using the following command:") self.Logfile.insert( - 'qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} autofit_ligand_master.sh'.format(str(self.n), - self.max_queue_jobs)) + "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} autofit_ligand_master.sh".format( + str(self.n), self.max_queue_jobs + ) + ) os.system( - 'qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} autofit_ligand_master.sh'.format(str(self.n - 1), - self.max_queue_jobs)) + "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} autofit_ligand_master.sh".format( + str(self.n - 1), self.max_queue_jobs + ) + ) else: self.Logfile.insert( - "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") - elif self.external_software['qsub']: - self.Logfile.insert( - 'submitting {0!s} individual jobs to cluster'.format((str(self.n)))) + "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file" + ) + elif self.external_software["qsub"]: self.Logfile.insert( - 'WARNING: this could potentially lead to a crash...') + "submitting {0!s} individual jobs to cluster".format((str(self.n))) + ) + self.Logfile.insert("WARNING: this could potentially lead to a crash...") for i in range(1, self.n): self.Logfile.insert( - 'qsub -q medium.q xce_autofit_ligand_{0!s}.sh'.format(str(i))) - os.system( - 'qsub -q medium.q xce_autofit_ligand_{0!s}.sh'.format(str(i))) + "qsub -q medium.q xce_autofit_ligand_{0!s}.sh".format(str(i)) + ) + os.system("qsub -q medium.q xce_autofit_ligand_{0!s}.sh".format(str(i))) else: self.Logfile.insert( - 'running {0!s} consecutive autofit_ligand jobs on your local machine'.format(str(self.n - 1))) - for i in range(1, self.n+1): + "running {0!s} consecutive autofit_ligand jobs on your local machine".format( + str(self.n - 1) + ) + ) + for i in range(1, self.n + 1): self.Logfile.insert( - 'starting xce_autofit_ligand_{0!s}.sh'.format(str(i))) - os.system('./xce_autofit_ligand_{0!s}.sh'.format(str(i))) + "starting xce_autofit_ligand_{0!s}.sh".format(str(i)) + ) + os.system("./xce_autofit_ligand_{0!s}.sh".format(str(i))) class merge_cif_files(QtCore.QThread): - def __init__(self, initial_model_directory, xce_logfile, second_cif_file, compound_list, todo): + def __init__( + self, initial_model_directory, xce_logfile, second_cif_file, compound_list, todo + ): QtCore.QThread.__init__(self) self.initial_model_directory = initial_model_directory self.xce_logfile = xce_logfile @@ -1152,7 +1490,7 @@ def __init__(self, initial_model_directory, xce_logfile, second_cif_file, compou self.todo = todo def run(self): - progress_step = 100/float(len(self.compound_list)) + progress_step = 100 / float(len(self.compound_list)) progress = 0 counter = 1 @@ -1160,64 +1498,89 @@ def run(self): sampleID = item[0] compoundID = item[1] - if os.path.isfile(os.path.join(self.initial_model_directory, sampleID, 'compound', compoundID + '.cif')): + if os.path.isfile( + os.path.join( + self.initial_model_directory, + sampleID, + "compound", + compoundID + ".cif", + ) + ): self.Logfile.insert( - '%s: found %s.cif file in compound sub-directory' % (sampleID, compoundID)) + "%s: found %s.cif file in compound sub-directory" + % (sampleID, compoundID) + ) else: self.Logfile.error( - '%s: %s.cif file does not exist in compound sub-directory; skipping...' % (sampleID, compoundID)) + "%s: %s.cif file does not exist in compound sub-directory; skipping..." + % (sampleID, compoundID) + ) continue os.chdir(os.path.join(self.initial_model_directory, sampleID)) - if os.path.isfile(os.path.join(self.initial_model_directory, sampleID, compoundID+'.cif')): + if os.path.isfile( + os.path.join( + self.initial_model_directory, sampleID, compoundID + ".cif" + ) + ): self.Logfile.warning( - '%s: removing symbolic link to (or file) %s.cif from sample directory' % (sampleID, compoundID)) - os.system('/bin/rm %s.cif 2> /dev/null' % compoundID) + "%s: removing symbolic link to (or file) %s.cif from sample directory" + % (sampleID, compoundID) + ) + os.system("/bin/rm %s.cif 2> /dev/null" % compoundID) - if self.todo == 'merge': - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - sampleID+' merging CIF files') + if self.todo == "merge": + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + sampleID + " merging CIF files", + ) self.run_libcheck(sampleID, compoundID) - elif self.todo == 'restore': - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - sampleID + ' restoring original CIF file') + elif self.todo == "restore": + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + sampleID + " restoring original CIF file", + ) self.Logfile.insert( - '%s: restoring symbolic link -> ln -s compound/%s.cif .' % (sampleID, compoundID)) - os.system('ln -s compound/%s.cif .' % compoundID) + "%s: restoring symbolic link -> ln -s compound/%s.cif ." + % (sampleID, compoundID) + ) + os.system("ln -s compound/%s.cif ." % compoundID) progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) self.emit(QtCore.SIGNAL("finished()")) def run_libcheck(self, sampleID, compoundID): cmd = ( - '#!/bin/bash\n' - '\n' - '$CCP4/bin/libcheck << eof \n' - '_Y\n' - '_FILE_L compound/%s.cif\n' % compoundID + - '_FILE_L2 '+self.second_cif_file+'\n' - '_FILE_O '+compoundID+'.cif\n' - '_END\n' - 'eof\n' + "#!/bin/bash\n" + "\n" + "$CCP4/bin/libcheck << eof \n" + "_Y\n" + "_FILE_L compound/%s.cif\n" % compoundID + + "_FILE_L2 " + + self.second_cif_file + + "\n" + "_FILE_O " + compoundID + ".cif\n" + "_END\n" + "eof\n" ) self.Logfile.insert( - '%s: running libcheck with the following input:\n%s' % (sampleID, cmd)) + "%s: running libcheck with the following input:\n%s" % (sampleID, cmd) + ) os.system(cmd) - if os.path.isfile(compoundID+'.cif.lib'): - self.Logfile.insert( - '%s: merged CIF file successfully created' % sampleID) - os.system('/bin/mv %s %s' % - (compoundID+'.cif.lib', compoundID+'.cif')) + if os.path.isfile(compoundID + ".cif.lib"): + self.Logfile.insert("%s: merged CIF file successfully created" % sampleID) + os.system("/bin/mv %s %s" % (compoundID + ".cif.lib", compoundID + ".cif")) else: - self.Logfile.error( - '%s: could not create merged CIF file' % sampleID) + self.Logfile.error("%s: could not create merged CIF file" % sampleID) self.Logfile.warning( - '%s: will re-create symbolic links to original restraints file' % sampleID) - os.system('ln -s compound/%s.cif .' % compoundID) + "%s: will re-create symbolic links to original restraints file" + % sampleID + ) + os.system("ln -s compound/%s.cif ." % compoundID) # class run_dimple_on_all_autoprocessing_files(QtCore.QThread): @@ -1483,20 +1846,34 @@ def run_libcheck(self, sampleID, compoundID): # # self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) + class run_dimple_on_all_autoprocessing_files_new(QtCore.QThread): - def __init__(self, sample_list, initial_model_directory, external_software, ccp4_scratch_directory, database_directory, - data_source_file, max_queue_jobs, xce_logfile, remote_submission, remote_submission_string, - dimple_twin_mode, pipeline): + def __init__( + self, + sample_list, + initial_model_directory, + external_software, + ccp4_scratch_directory, + database_directory, + data_source_file, + max_queue_jobs, + xce_logfile, + remote_submission, + remote_submission_string, + dimple_twin_mode, + pipeline, + ): QtCore.QThread.__init__(self) self.sample_list = sample_list self.initial_model_directory = initial_model_directory self.external_software = external_software - self.queueing_system_available = external_software['qsub'] + self.queueing_system_available = external_software["qsub"] self.ccp4_scratch_directory = ccp4_scratch_directory self.database_directory = database_directory self.data_source_file = data_source_file - self.db = XChemDB.data_source(os.path.join( - self.database_directory, self.data_source_file)) + self.db = XChemDB.data_source( + os.path.join(self.database_directory, self.data_source_file) + ) self.max_queue_jobs = max_queue_jobs self.xce_logfile = xce_logfile self.Logfile = XChemLog.updateLog(xce_logfile) @@ -1508,17 +1885,18 @@ def __init__(self, sample_list, initial_model_directory, external_software, ccp4 self.n = 1 self.Logfile.insert( - 'running initial refinement with the following pipeline: '+self.pipeline) + "running initial refinement with the following pipeline: " + self.pipeline + ) def run(self): progress_step = 1 if len(self.sample_list) != 0: - progress_step = 100/float(len(self.sample_list)) + progress_step = 100 / float(len(self.sample_list)) progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) os.chdir(self.ccp4_scratch_directory) - os.system('/bin/rm -f xce_{0!s}*sh'.format(self.pipeline)) + os.system("/bin/rm -f xce_{0!s}*sh".format(self.pipeline)) for item in sorted(self.sample_list): @@ -1529,28 +1907,34 @@ def run(self): ref_mtz = item[4] ref_cif = item[5] - if 'dimple_rerun_on_selected_file' in visit_run_autoproc: - if self.pipeline == 'dimple': + if "dimple_rerun_on_selected_file" in visit_run_autoproc: + if self.pipeline == "dimple": twin = self.prepare_dimple_shell_script( - xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif) - elif self.pipeline == 'pipedream': + xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif + ) + elif self.pipeline == "pipedream": twin = self.prepare_pipedream_shell_script( - xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif) - elif self.pipeline == 'phenix.ligand_pipeline': + xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif + ) + elif self.pipeline == "phenix.ligand_pipeline": twin = self.prepare_phenix_ligand_pipeline_shell_script( - xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif) + xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif + ) else: twin = self.prepare_dimple_shell_script( - xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif) + xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif + ) progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) self.run_script(twin) - self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) + self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) - def prepare_phenix_ligand_pipeline_shell_script(self, xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif): + def prepare_phenix_ligand_pipeline_shell_script( + self, xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif + ): # check if reference mtzfile has an Rfree column; if not, then ignore # DIMPLE assumes an Rfree column and barfs if it is not present @@ -1574,718 +1958,850 @@ def prepare_phenix_ligand_pipeline_shell_script(self, xtal, visit_run_autoproc, if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): os.mkdir(os.path.join(self.initial_model_directory, xtal)) os.chdir(os.path.join(self.initial_model_directory, xtal)) - if os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'phenix.ligand_pipeline')): - os.system('/bin/rm -fr phenix.ligand_pipeline') - os.mkdir(os.path.join(self.initial_model_directory, - xtal, 'phenix.ligand_pipeline')) - os.system('touch phenix.ligand_pipeline_run_in_progress') + if os.path.isdir( + os.path.join(self.initial_model_directory, xtal, "phenix.ligand_pipeline") + ): + os.system("/bin/rm -fr phenix.ligand_pipeline") + os.mkdir( + os.path.join(self.initial_model_directory, xtal, "phenix.ligand_pipeline") + ) + os.system("touch phenix.ligand_pipeline_run_in_progress") if self.queueing_system_available: - top_line = '#PBS -joe -N XCE_{0!s}\n'.format(self.pipeline) + top_line = "#PBS -joe -N XCE_{0!s}\n".format(self.pipeline) else: - top_line = '#!'+os.getenv('SHELL')+'\n' + top_line = "#!" + os.getenv("SHELL") + "\n" - if 'csh' in os.getenv('SHELL'): - ccp4_scratch = 'setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' - elif 'bash' in os.getenv('SHELL'): - ccp4_scratch = 'export CCP4_SCR='+self.ccp4_scratch_directory+'\n' + if "csh" in os.getenv("SHELL"): + ccp4_scratch = "setenv CCP4_SCR " + self.ccp4_scratch_directory + "\n" + elif "bash" in os.getenv("SHELL"): + ccp4_scratch = "export CCP4_SCR=" + self.ccp4_scratch_directory + "\n" else: - ccp4_scratch = '' + ccp4_scratch = "" - if os.path.isdir('/dls'): - ccp4_scratch += 'module load phenix\n' - ccp4_scratch += 'module load ccp4/7.1.018\n' + if os.path.isdir("/dls"): + ccp4_scratch += "module load phenix\n" + ccp4_scratch += "module load ccp4/7.1.018\n" mtz_column_list = mtztools(mtzin).get_all_columns_as_list() - rfree = '' - if 'FreeR_flag' in mtz_column_list: + rfree = "" + if "FreeR_flag" in mtz_column_list: rfree = ' xray_data.r_free_flags.label="FreeR_flag"' Cmds = ( - '{0!s}\n'.format(top_line) + - '\n' - 'export XChemExplorer_DIR="' + - os.getenv('XChemExplorer_DIR')+'"\n' - '\n' - 'cd %s\n' % os.path.join(self.initial_model_directory, xtal, 'phenix.ligand_pipeline') + - '\n' - 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' - '\n' - + ccp4_scratch + - '\n' - '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' % (os.path.join(self.database_directory, self.data_source_file), xtal, 'DimpleStatus', 'running') + - '\n' - 'phenix.ligand_pipeline %s %s' % (ref_pdb, mtzin) + - ' mr=False' - ' ligand_copies=0' - ' build=False' - ' prune=False' - ' remove_waters=False' - ' stop_if_r_free_greater_than=0.4' - ' update_waters=False' - + rfree + - ' build_hydrogens=False\n' - '\n' - 'fft hklin pipeline_1/refine_final.mtz mapout 2fofc.map << EOF\n' - ' labin F1=2FOFCWT_filled PHI=PH2FOFCWT\n' - 'EOF\n' - '\n' - 'fft hklin pipeline_1/refine_final.mtz mapout fofc.map << EOF\n' - ' labin F1=FOFCWT PHI=PHFOFCWT\n' - 'EOF\n' - '\n' - 'cd %s\n' % os.path.join(self.initial_model_directory, xtal) + - '\n' - '/bin/rm phenix.ligand_pipeline.pdb\n' - '/bin/rm phenix.ligand_pipeline.mtz\n' - '\n' - 'ln -s phenix.ligand_pipeline/pipeline_1/refine_final.pdb phenix.ligand_pipeline.pdb\n' - 'ln -s phenix.ligand_pipeline/pipeline_1/refine_final.mtz phenix.ligand_pipeline.mtz\n' - '\n' - '/bin/rm init.pdb\n' - '/bin/rm init.mtz\n' - '\n' - 'ln -s phenix.ligand_pipeline.pdb init.pdb\n' - 'ln -s phenix.ligand_pipeline.mtz init.mtz\n' - '\n' - '/bin/rm 2fofc.map\n' - '/bin/rm fofc.map\n' - '\n' - 'ln -s phenix.ligand_pipeline/2fofc.map .\n' - 'ln -s phenix.ligand_pipeline/fofc.map .\n' - '\n' - '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_data_source_for_new_dimple_pdb.py') + - ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory, self.data_source_file), xtal, self.initial_model_directory) + - '\n' - '/bin/rm phenix.ligand_pipeline_run_in_progress\n' + "{0!s}\n".format(top_line) + "\n" + 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"\n' + "\n" + "cd %s\n" + % os.path.join(self.initial_model_directory, xtal, "phenix.ligand_pipeline") + + "\n" + "source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n" + "\n" + ccp4_scratch + "\n" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n" + % ( + os.path.join(self.database_directory, self.data_source_file), + xtal, + "DimpleStatus", + "running", + ) + + "\n" + "phenix.ligand_pipeline %s %s" % (ref_pdb, mtzin) + " mr=False" + " ligand_copies=0" + " build=False" + " prune=False" + " remove_waters=False" + " stop_if_r_free_greater_than=0.4" + " update_waters=False" + rfree + " build_hydrogens=False\n" + "\n" + "fft hklin pipeline_1/refine_final.mtz mapout 2fofc.map << EOF\n" + " labin F1=2FOFCWT_filled PHI=PH2FOFCWT\n" + "EOF\n" + "\n" + "fft hklin pipeline_1/refine_final.mtz mapout fofc.map << EOF\n" + " labin F1=FOFCWT PHI=PHFOFCWT\n" + "EOF\n" + "\n" + "cd %s\n" % os.path.join(self.initial_model_directory, xtal) + "\n" + "/bin/rm phenix.ligand_pipeline.pdb\n" + "/bin/rm phenix.ligand_pipeline.mtz\n" + "\n" + "ln -s phenix.ligand_pipeline/pipeline_1/refine_final.pdb phenix.ligand_pipeline.pdb\n" + "ln -s phenix.ligand_pipeline/pipeline_1/refine_final.mtz phenix.ligand_pipeline.mtz\n" + "\n" + "/bin/rm init.pdb\n" + "/bin/rm init.mtz\n" + "\n" + "ln -s phenix.ligand_pipeline.pdb init.pdb\n" + "ln -s phenix.ligand_pipeline.mtz init.mtz\n" + "\n" + "/bin/rm 2fofc.map\n" + "/bin/rm fofc.map\n" + "\n" + "ln -s phenix.ligand_pipeline/2fofc.map .\n" + "ln -s phenix.ligand_pipeline/fofc.map .\n" + "\n" + "$CCP4/bin/ccp4-python " + + os.path.join( + os.getenv("XChemExplorer_DIR"), + "helpers", + "update_data_source_for_new_dimple_pdb.py", + ) + + " {0!s} {1!s} {2!s}\n".format( + os.path.join(self.database_directory, self.data_source_file), + xtal, + self.initial_model_directory, + ) + + "\n" + "/bin/rm phenix.ligand_pipeline_run_in_progress\n" ) os.chdir(self.ccp4_scratch_directory) - f = open('xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n)), 'w') + f = open("xce_{0!s}_{1!s}.sh".format(self.pipeline, str(self.n)), "w") f.write(Cmds) f.close() - os.system( - 'chmod +x xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n))) + os.system("chmod +x xce_{0!s}_{1!s}.sh".format(self.pipeline, str(self.n))) self.n += 1 - db_dict = {'DimpleStatus': 'started'} + db_dict = {"DimpleStatus": "started"} self.Logfile.insert( - '{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) + "{0!s}: setting DataProcessingStatus flag to started".format(xtal) + ) self.db.update_data_source(xtal, db_dict) - twin = '' + twin = "" return twin - def prepare_pipedream_shell_script(self, xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif): + def prepare_pipedream_shell_script( + self, xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif + ): if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): os.mkdir(os.path.join(self.initial_model_directory, xtal)) - if os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'pipedream')): + if os.path.isdir(os.path.join(self.initial_model_directory, xtal, "pipedream")): os.chdir(os.path.join(self.initial_model_directory, xtal)) - os.system('/bin/rm -fr pipedream') - os.mkdir(os.path.join(self.initial_model_directory, xtal, 'pipedream')) - os.system('touch pipedream_run_in_progress') + os.system("/bin/rm -fr pipedream") + os.mkdir(os.path.join(self.initial_model_directory, xtal, "pipedream")) + os.system("touch pipedream_run_in_progress") if self.queueing_system_available: - top_line = '#PBS -joe -N XCE_{0!s}\n'.format(self.pipeline) + top_line = "#PBS -joe -N XCE_{0!s}\n".format(self.pipeline) else: - top_line = '#!'+os.getenv('SHELL')+'\n' + top_line = "#!" + os.getenv("SHELL") + "\n" - if 'csh' in os.getenv('SHELL'): - ccp4_scratch = 'setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' - elif 'bash' in os.getenv('SHELL'): - ccp4_scratch = 'export CCP4_SCR='+self.ccp4_scratch_directory+'\n' + if "csh" in os.getenv("SHELL"): + ccp4_scratch = "setenv CCP4_SCR " + self.ccp4_scratch_directory + "\n" + elif "bash" in os.getenv("SHELL"): + ccp4_scratch = "export CCP4_SCR=" + self.ccp4_scratch_directory + "\n" else: - ccp4_scratch = '' + ccp4_scratch = "" - if os.path.isdir('/dls'): - ccp4_scratch += 'module load buster\n' - ccp4_scratch += 'module load ccp4/7.1.018\n' + if os.path.isdir("/dls"): + ccp4_scratch += "module load buster\n" + ccp4_scratch += "module load ccp4/7.1.018\n" if os.path.isfile(ref_mtz): - hklref_line = ' -hklref {0!s}'.format(ref_mtz) + hklref_line = " -hklref {0!s}".format(ref_mtz) else: - hklref_line = ' -nofreeref' + hklref_line = " -nofreeref" Cmds = ( - '{0!s}\n'.format(top_line) + - '\n' - 'export XChemExplorer_DIR="' + - os.getenv('XChemExplorer_DIR')+'"\n' - '\n' - 'cd %s\n' % os.path.join(self.initial_model_directory, xtal, 'pipedream') + - '\n' - 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' - '\n' - + ccp4_scratch + - '\n' - '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' % (os.path.join(self.database_directory, self.data_source_file), xtal, 'DimpleStatus', 'running') + - '\n' - 'pointless hklin {0!s} xyzin {1!s} hklout pointless.mtz > pointless.log\n'.format(mtzin, ref_pdb) + - '\n' - 'pipedream ' - ' -d pipedreamDir' - ' -xyzin %s' % ref_pdb + - hklref_line + - ' -hklin pointless.mtz' - ' -keepwater\n' - '\n' - 'fft hklin pipedreamDir/refine/refine.mtz mapout 2fofc.map << EOF\n' - ' labin F1=2FOFCWT PHI=PH2FOFCWT\n' - 'EOF\n' - '\n' - 'fft hklin pipedreamDir/refine/refine.mtz mapout fofc.map << EOF\n' - ' labin F1=FOFCWT PHI=PHFOFCWT\n' - 'EOF\n' - '\n' - 'cd %s\n' % os.path.join(self.initial_model_directory, xtal) + - '\n' - '/bin/rm pipedream.pdb\n' - '/bin/rm pipedream.mtz\n' - '\n' - 'ln -s pipedream/pipedreamDir/refine/refine.pdb pipedream.pdb\n' - 'ln -s pipedream/pipedreamDir/refine/refine.mtz pipedream.mtz\n' - '\n' - '/bin/rm init.pdb\n' - '/bin/rm init.mtz\n' - '\n' - 'ln -s pipedream.pdb init.pdb\n' - 'ln -s pipedream.mtz init.mtz\n' - '\n' - '/bin/rm 2fofc.map\n' - '/bin/rm fofc.map\n' - '\n' - 'ln -s pipedream/2fofc.map .\n' - 'ln -s pipedream/fofc.map .\n' - '\n' - '$CCP4/libexec/python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_data_source_for_new_dimple_pdb.py') + - ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory, self.data_source_file), xtal, self.initial_model_directory) + - '\n' - '/bin/rm pipedream_run_in_progress\n' + "{0!s}\n".format(top_line) + "\n" + 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"\n' + "\n" + "cd %s\n" % os.path.join(self.initial_model_directory, xtal, "pipedream") + + "\n" + "source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n" + "\n" + ccp4_scratch + "\n" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n" + % ( + os.path.join(self.database_directory, self.data_source_file), + xtal, + "DimpleStatus", + "running", + ) + + "\n" + "pointless hklin {0!s} xyzin {1!s} hklout pointless.mtz > pointless.log\n".format( + mtzin, ref_pdb + ) + + "\n" + "pipedream " + " -d pipedreamDir" + " -xyzin %s" % ref_pdb + hklref_line + " -hklin pointless.mtz" + " -keepwater\n" + "\n" + "fft hklin pipedreamDir/refine/refine.mtz mapout 2fofc.map << EOF\n" + " labin F1=2FOFCWT PHI=PH2FOFCWT\n" + "EOF\n" + "\n" + "fft hklin pipedreamDir/refine/refine.mtz mapout fofc.map << EOF\n" + " labin F1=FOFCWT PHI=PHFOFCWT\n" + "EOF\n" + "\n" + "cd %s\n" % os.path.join(self.initial_model_directory, xtal) + "\n" + "/bin/rm pipedream.pdb\n" + "/bin/rm pipedream.mtz\n" + "\n" + "ln -s pipedream/pipedreamDir/refine/refine.pdb pipedream.pdb\n" + "ln -s pipedream/pipedreamDir/refine/refine.mtz pipedream.mtz\n" + "\n" + "/bin/rm init.pdb\n" + "/bin/rm init.mtz\n" + "\n" + "ln -s pipedream.pdb init.pdb\n" + "ln -s pipedream.mtz init.mtz\n" + "\n" + "/bin/rm 2fofc.map\n" + "/bin/rm fofc.map\n" + "\n" + "ln -s pipedream/2fofc.map .\n" + "ln -s pipedream/fofc.map .\n" + "\n" + "$CCP4/libexec/python " + + os.path.join( + os.getenv("XChemExplorer_DIR"), + "helpers", + "update_data_source_for_new_dimple_pdb.py", + ) + + " {0!s} {1!s} {2!s}\n".format( + os.path.join(self.database_directory, self.data_source_file), + xtal, + self.initial_model_directory, + ) + + "\n" + "/bin/rm pipedream_run_in_progress\n" ) os.chdir(self.ccp4_scratch_directory) - f = open('xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n)), 'w') + f = open("xce_{0!s}_{1!s}.sh".format(self.pipeline, str(self.n)), "w") f.write(Cmds) f.close() - os.system( - 'chmod +x xce_{0!s}_{1!s}.sh'.format(self.pipeline, str(self.n))) + os.system("chmod +x xce_{0!s}_{1!s}.sh".format(self.pipeline, str(self.n))) self.n += 1 - db_dict = {'DimpleStatus': 'started'} + db_dict = {"DimpleStatus": "started"} self.Logfile.insert( - '{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) + "{0!s}: setting DataProcessingStatus flag to started".format(xtal) + ) self.db.update_data_source(xtal, db_dict) - twin = '' + twin = "" return twin + # pipedream -d pipedreamDir -xyzin $reference.pdb -hklref $referenceDataset.mtz -hklin $mtzFileUnique.mtz -rhofit $inhib.cif -target $reference.pdb -keepwater -nthreads 12 -postquick -allclusters |tee -a pipedream.log -# pipedream -d pipedreamDir -xyzin $reference.pdb -hklref $referenceDataset.mtz -hklin $mtzFileUnique.mtz -rhofit $inhib.cif -target $reference.pdb -keepwater -nthreads 12 -postquick -allclusters |tee -a pipedream.log - - def prepare_dimple_shell_script(self, xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif): + def prepare_dimple_shell_script( + self, xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif + ): # check if reference mtzfile has an Rfree column; if not, then ignore # DIMPLE assumes an Rfree column and barfs if it is not present # note: ref_mtz looks like this: ref mtz -R reference.mtz if os.path.isfile(ref_mtz): mtz_column_dict = mtztools(ref_mtz).get_all_columns_as_dict() - if 'FreeR_flag' not in mtz_column_dict['RFREE']: + if "FreeR_flag" not in mtz_column_dict["RFREE"]: self.Logfile.insert( - 'cannot find FreeR_flag in reference mtz file: {0!s} -> ignoring reference mtzfile!!!'.format(ref_mtz)) - ref_mtz = '' - if mtz_column_dict['RFREE']: - self.Logfile.insert('found Rfree set with other column name though: {0!s}'.format( - str(mtz_column_dict['RFREE']))) + "cannot find FreeR_flag in reference mtz file: {0!s} -> ignoring reference mtzfile!!!".format( + ref_mtz + ) + ) + ref_mtz = "" + if mtz_column_dict["RFREE"]: + self.Logfile.insert( + "found Rfree set with other column name though: {0!s}".format( + str(mtz_column_dict["RFREE"]) + ) + ) self.Logfile.insert( - 'try renaming Rfree column to FreeR_flag with CAD!') + "try renaming Rfree column to FreeR_flag with CAD!" + ) - db_dict = {'DimpleReferencePDB': ref_pdb} + db_dict = {"DimpleReferencePDB": ref_pdb} self.db.update_data_source(xtal, db_dict) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'creating input script for '+xtal+' in '+visit_run_autoproc) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "creating input script for " + xtal + " in " + visit_run_autoproc, + ) if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): os.mkdir(os.path.join(self.initial_model_directory, xtal)) os.chdir(os.path.join(self.initial_model_directory, xtal)) - twin = '' + twin = "" twinRefmac = "" if self.dimple_twin_mode: twinRefmac = "--refmac-key 'TWIN'" - twin = '_twin' - if os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'dimple_twin')): - os.system('/bin/rm -fr dimple_twin') - os.mkdir(os.path.join( - self.initial_model_directory, xtal, 'dimple_twin')) - os.system('touch dimple_twin_run_in_progress') + twin = "_twin" + if os.path.isdir( + os.path.join(self.initial_model_directory, xtal, "dimple_twin") + ): + os.system("/bin/rm -fr dimple_twin") + os.mkdir(os.path.join(self.initial_model_directory, xtal, "dimple_twin")) + os.system("touch dimple_twin_run_in_progress") else: - if os.path.isdir(os.path.join(self.initial_model_directory, xtal, 'dimple')): - os.system('/bin/rm -fr dimple') - os.mkdir(os.path.join(self.initial_model_directory, xtal, 'dimple')) - os.system('touch dimple_run_in_progress') - os.system('/bin/rm final.mtz 2> /dev/null') - os.system('/bin/rm final.pdb 2> /dev/null') + if os.path.isdir( + os.path.join(self.initial_model_directory, xtal, "dimple") + ): + os.system("/bin/rm -fr dimple") + os.mkdir(os.path.join(self.initial_model_directory, xtal, "dimple")) + os.system("touch dimple_run_in_progress") + os.system("/bin/rm final.mtz 2> /dev/null") + os.system("/bin/rm final.pdb 2> /dev/null") if self.queueing_system_available: - top_line = '#PBS -joe -N XCE_dimple\n' + top_line = "#PBS -joe -N XCE_dimple\n" else: - top_line = '#!'+os.getenv('SHELL')+'\n' + top_line = "#!" + os.getenv("SHELL") + "\n" - if 'csh' in os.getenv('SHELL'): - ccp4_scratch = 'setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' - elif 'bash' in os.getenv('SHELL'): - ccp4_scratch = 'export CCP4_SCR='+self.ccp4_scratch_directory+'\n' + if "csh" in os.getenv("SHELL"): + ccp4_scratch = "setenv CCP4_SCR " + self.ccp4_scratch_directory + "\n" + elif "bash" in os.getenv("SHELL"): + ccp4_scratch = "export CCP4_SCR=" + self.ccp4_scratch_directory + "\n" else: - ccp4_scratch = '' + ccp4_scratch = "" - if os.path.isdir('/dls'): - ccp4_scratch += 'module load ccp4/7.1.018\n' + if os.path.isdir("/dls"): + ccp4_scratch += "module load ccp4/7.1.018\n" hkl = any_reflection_file(file_name=mtzin) miller_arrays = hkl.as_miller_arrays() mtzFile = miller_arrays[0] - if mtzFile.space_group_info().symbol_and_number() == 'R 3 :H (No. 146)': - symNoAbsence = 'H3' - elif mtzFile.space_group_info().symbol_and_number() == 'R 3 2 :H (No. 155)': - symNoAbsence = 'H32' + if mtzFile.space_group_info().symbol_and_number() == "R 3 :H (No. 146)": + symNoAbsence = "H3" + elif mtzFile.space_group_info().symbol_and_number() == "R 3 2 :H (No. 155)": + symNoAbsence = "H32" else: - symNoAbsence = str([x[0] for x in str(mtzFile.space_group_info().symbol_and_number().split( - '(')[0]).split()]).replace('[', '').replace(']', '').replace("'", "").replace(',', '').replace(' ', '') + symNoAbsence = ( + str( + [ + x[0] + for x in str( + mtzFile.space_group_info().symbol_and_number().split("(")[0] + ).split() + ] + ) + .replace("[", "") + .replace("]", "") + .replace("'", "") + .replace(",", "") + .replace(" ", "") + ) Cmds = ( - '{0!s}\n'.format(top_line) + - '\n' - 'export XChemExplorer_DIR="' + - os.getenv('XChemExplorer_DIR')+'"\n' - '\n' - 'cd %s\n' % os.path.join(self.initial_model_directory, xtal, 'dimple%s' % twin) + - '\n' - 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' - '\n' - + ccp4_scratch + - '\n' - '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' % (os.path.join(self.database_directory, self.data_source_file), xtal, 'DimpleStatus', 'running') + - '\n' - 'cd %s\n' % os.path.join(self.initial_model_directory, xtal, 'dimple%s' % twin) + - '\n' - 'unique hklout unique.mtz << eof\n' - ' cell %s\n' % str([round(float(i), 2) for i in mtzFile.unit_cell().parameters()]).replace('[', '').replace(']', '') + - ' symmetry %s\n' % symNoAbsence + - ' resolution %s\n' % str(round(float(mtzFile.d_min()), 3)) + - 'eof\n' - '\n' + "{0!s}\n".format(top_line) + "\n" + 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"\n' + "\n" + "cd %s\n" + % os.path.join(self.initial_model_directory, xtal, "dimple%s" % twin) + + "\n" + "source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n" + "\n" + ccp4_scratch + "\n" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n" + % ( + os.path.join(self.database_directory, self.data_source_file), + xtal, + "DimpleStatus", + "running", + ) + + "\n" + "cd %s\n" + % os.path.join(self.initial_model_directory, xtal, "dimple%s" % twin) + + "\n" + "unique hklout unique.mtz << eof\n" + " cell %s\n" + % str([round(float(i), 2) for i in mtzFile.unit_cell().parameters()]) + .replace("[", "") + .replace("]", "") + + " symmetry %s\n" % symNoAbsence + + " resolution %s\n" % str(round(float(mtzFile.d_min()), 3)) + + "eof\n" + "\n" # 'freerflag hklin unique.mtz hklout free.mtz > freerflag.log\n' - '\n' - 'sftools << eof > sftools.log\n' - ' read unique.mtz\n' - ' calc col F = 10.0\n' - ' calc col SIGF = 1.0\n' - ' write sftools.mtz\n' - 'eof\n' - '\n' - 'cad hklin1 sftools.mtz hklin2 %s hklout %s.999A.mtz << eof\n' % (mtzin, xtal) + - ' monitor BRIEF\n' - ' labin file 1 E1=F E2=SIGF\n' - ' labout file 1 E1=F_unique E2=SIGF_unique\n' - ' labin file 2 ALL\n' - ' resolution file 1 999.0 %s\n' % str(round(float(mtzFile.d_min()), 2)) + - 'eof\n' - '\n' - 'pointless hklin %s.999A.mtz hklout %s.999A.reind.mtz xyzin %s << eof > pointless.reind.log\n' % (xtal, xtal, ref_pdb) + - ' tolerance 5\n' - 'eof\n' - '\n' - "dimple --no-cleanup %s.999A.reind.mtz %s %s %s %s dimple%s\n" % (xtal, ref_pdb, ref_mtz, ref_cif, twinRefmac, twin) + - '\n' - 'fft hklin dimple%s/final.mtz mapout 2fofc%s.map << EOF\n' % (twin, twin) + - ' labin F1=FWT PHI=PHWT\n' - 'EOF\n' - '\n' - 'fft hklin dimple%s/final.mtz mapout fofc%s.map << EOF\n' % (twin, twin) + - ' labin F1=DELFWT PHI=PHDELWT\n' - 'EOF\n' - '\n' - 'cd %s\n' % os.path.join(self.initial_model_directory, xtal) + - '\n' - '/bin/rm dimple%s.pdb\n' % twin + - '/bin/rm dimple%s.mtz\n' % twin + - '\n' - 'ln -s dimple%s/dimple%s/final.pdb dimple%s.pdb\n' % (twin, twin, twin) + - 'ln -s dimple%s/dimple%s/final.mtz dimple%s.mtz\n' % (twin, twin, twin) + - '\n' - '/bin/rm init%s.pdb\n' % twin + - '/bin/rm init%s.mtz\n' % twin + - '\n' - 'ln -s dimple%s.pdb init%s.pdb\n' % (twin, twin) + - 'ln -s dimple%s.mtz init%s.mtz\n' % (twin, twin) + - '\n' - '/bin/rm 2fofc%s.map\n' % twin + - '/bin/rm fofc%s.map\n' % twin + - '\n' - 'ln -s dimple%s/2fofc%s.map .\n' % (twin, twin) + - 'ln -s dimple%s/fofc%s.map .\n' % (twin, twin) + - '\n' - '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'update_data_source_for_new_dimple%s_pdb.py' % twin) + - ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory, self.data_source_file), xtal, self.initial_model_directory) + - '\n' - '/bin/rm dimple_run_in_progress\n' - '\n' + "\n" + "sftools << eof > sftools.log\n" + " read unique.mtz\n" + " calc col F = 10.0\n" + " calc col SIGF = 1.0\n" + " write sftools.mtz\n" + "eof\n" + "\n" + "cad hklin1 sftools.mtz hklin2 %s hklout %s.999A.mtz << eof\n" + % (mtzin, xtal) + + " monitor BRIEF\n" + " labin file 1 E1=F E2=SIGF\n" + " labout file 1 E1=F_unique E2=SIGF_unique\n" + " labin file 2 ALL\n" + " resolution file 1 999.0 %s\n" % str(round(float(mtzFile.d_min()), 2)) + + "eof\n" + "\n" + "pointless hklin %s.999A.mtz hklout %s.999A.reind.mtz xyzin %s << eof > pointless.reind.log\n" + % (xtal, xtal, ref_pdb) + + " tolerance 5\n" + "eof\n" + "\n" + "dimple --no-cleanup %s.999A.reind.mtz %s %s %s %s dimple%s\n" + % (xtal, ref_pdb, ref_mtz, ref_cif, twinRefmac, twin) + + "\n" + "fft hklin dimple%s/final.mtz mapout 2fofc%s.map << EOF\n" % (twin, twin) + + " labin F1=FWT PHI=PHWT\n" + "EOF\n" + "\n" + "fft hklin dimple%s/final.mtz mapout fofc%s.map << EOF\n" % (twin, twin) + + " labin F1=DELFWT PHI=PHDELWT\n" + "EOF\n" + "\n" + "cd %s\n" % os.path.join(self.initial_model_directory, xtal) + "\n" + "/bin/rm dimple%s.pdb\n" % twin + "/bin/rm dimple%s.mtz\n" % twin + "\n" + "ln -s dimple%s/dimple%s/final.pdb dimple%s.pdb\n" % (twin, twin, twin) + + "ln -s dimple%s/dimple%s/final.mtz dimple%s.mtz\n" % (twin, twin, twin) + + "\n" + "/bin/rm init%s.pdb\n" % twin + "/bin/rm init%s.mtz\n" % twin + "\n" + "ln -s dimple%s.pdb init%s.pdb\n" % (twin, twin) + + "ln -s dimple%s.mtz init%s.mtz\n" % (twin, twin) + + "\n" + "/bin/rm 2fofc%s.map\n" % twin + "/bin/rm fofc%s.map\n" % twin + "\n" + "ln -s dimple%s/2fofc%s.map .\n" % (twin, twin) + + "ln -s dimple%s/fofc%s.map .\n" % (twin, twin) + + "\n" + "$CCP4/bin/ccp4-python " + + os.path.join( + os.getenv("XChemExplorer_DIR"), + "helpers", + "update_data_source_for_new_dimple%s_pdb.py" % twin, + ) + + " {0!s} {1!s} {2!s}\n".format( + os.path.join(self.database_directory, self.data_source_file), + xtal, + self.initial_model_directory, + ) + + "\n" + "/bin/rm dimple_run_in_progress\n" + "\n" ) os.chdir(self.ccp4_scratch_directory) - f = open('xce_{0!s}{1!s}_{2!s}.sh'.format( - self.pipeline, twin, str(self.n)), 'w') + f = open( + "xce_{0!s}{1!s}_{2!s}.sh".format(self.pipeline, twin, str(self.n)), "w" + ) f.write(Cmds) f.close() os.system( - 'chmod +x xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline, twin, str(self.n))) + "chmod +x xce_{0!s}{1!s}_{2!s}.sh".format(self.pipeline, twin, str(self.n)) + ) self.n += 1 - db_dict = {'DimpleStatus': 'started'} + db_dict = {"DimpleStatus": "started"} self.Logfile.insert( - '{0!s}: setting DataProcessingStatus flag to started'.format(xtal)) + "{0!s}: setting DataProcessingStatus flag to started".format(xtal) + ) self.db.update_data_source(xtal, db_dict) return twin def run_script(self, twin): # submit job - self.Logfile.insert('created input scripts for ' + - str(self.n)+' in '+self.ccp4_scratch_directory) + self.Logfile.insert( + "created input scripts for " + + str(self.n) + + " in " + + self.ccp4_scratch_directory + ) os.chdir(self.ccp4_scratch_directory) - if os.path.isdir('/dls'): - if self.external_software['qsub_array']: - Cmds = ( - '#PBS -joe -N xce_{0!s}{1!s}_master\n'.format(self.pipeline, twin) + - './xce_{0!s}{1!s}_$SGE_TASK_ID.sh\n'.format( - self.pipeline, twin) - ) - f = open('{0!s}{1!s}_master.sh'.format( - self.pipeline, twin), 'w') + if os.path.isdir("/dls"): + if self.external_software["qsub_array"]: + Cmds = "#PBS -joe -N xce_{0!s}{1!s}_master\n".format( + self.pipeline, twin + ) + "./xce_{0!s}{1!s}_$SGE_TASK_ID.sh\n".format(self.pipeline, twin) + f = open("{0!s}{1!s}_master.sh".format(self.pipeline, twin), "w") f.write(Cmds) f.close() self.Logfile.insert( - 'submitting array job with maximal 100 jobs running on cluster') - self.Logfile.insert('using the following command:') - self.Logfile.insert('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh'.format( - str(self.n), self.max_queue_jobs, self.pipeline)) - os.system('qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}{3!s}_master.sh'.format( - str(self.n-1), self.max_queue_jobs, self.pipeline, twin)) + "submitting array job with maximal 100 jobs running on cluster" + ) + self.Logfile.insert("using the following command:") + self.Logfile.insert( + "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh".format( + str(self.n), self.max_queue_jobs, self.pipeline + ) + ) + os.system( + "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}{3!s}_master.sh".format( + str(self.n - 1), self.max_queue_jobs, self.pipeline, twin + ) + ) else: self.Logfile.insert( - "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file") - elif self.external_software['qsub']: - self.Logfile.insert( - 'submitting {0!s} individual jobs to cluster'.format((str(self.n)))) + "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file" + ) + elif self.external_software["qsub"]: self.Logfile.insert( - 'WARNING: this could potentially lead to a crash...') + "submitting {0!s} individual jobs to cluster".format((str(self.n))) + ) + self.Logfile.insert("WARNING: this could potentially lead to a crash...") for i in range(1, self.n): self.Logfile.insert( - 'qsub -q medium.q xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline, twin, str(i))) + "qsub -q medium.q xce_{0!s}{1!s}_{2!s}.sh".format( + self.pipeline, twin, str(i) + ) + ) os.system( - 'qsub -q medium.q xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline, twin, str(i))) + "qsub -q medium.q xce_{0!s}{1!s}_{2!s}.sh".format( + self.pipeline, twin, str(i) + ) + ) else: - self.Logfile.insert('running {0!s} consecutive {1!s} jobs on your local machine'.format( - str(self.n-1), self.pipeline)) + self.Logfile.insert( + "running {0!s} consecutive {1!s} jobs on your local machine".format( + str(self.n - 1), self.pipeline + ) + ) for i in range(1, self.n): - self.Logfile.insert('starting xce_{0!s}{1!s}_{2!s}.sh'.format( - self.pipeline, twin, str(i))) + self.Logfile.insert( + "starting xce_{0!s}{1!s}_{2!s}.sh".format( + self.pipeline, twin, str(i) + ) + ) os.system( - './xce_{0!s}{1!s}_{2!s}.sh'.format(self.pipeline, twin, str(i))) + "./xce_{0!s}{1!s}_{2!s}.sh".format(self.pipeline, twin, str(i)) + ) class remove_selected_dimple_files(QtCore.QThread): - def __init__(self, sample_list, initial_model_directory, xce_logfile, database_directory, data_source_file, pipeline): + def __init__( + self, + sample_list, + initial_model_directory, + xce_logfile, + database_directory, + data_source_file, + pipeline, + ): QtCore.QThread.__init__(self) self.sample_list = sample_list self.initial_model_directory = initial_model_directory self.xce_logfile = xce_logfile self.Logfile = XChemLog.updateLog(xce_logfile) - self.db = XChemDB.data_source(os.path.join( - database_directory, data_source_file)) + self.db = XChemDB.data_source( + os.path.join(database_directory, data_source_file) + ) self.pipeline = pipeline def run(self): progress_step = 1 if len(self.sample_list) != 0: - progress_step = 100/float(len(self.sample_list)) + progress_step = 100 / float(len(self.sample_list)) progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) for n, xtal in enumerate(self.sample_list): db_dict = {} if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): - self.Logfile.insert( - '{0!s}: directory does not exist'.format(xtal)) + self.Logfile.insert("{0!s}: directory does not exist".format(xtal)) continue os.chdir(os.path.join(self.initial_model_directory, xtal)) - if self.pipeline == 'dimple': - if os.path.isfile('init.pdb'): - if 'dimple' in os.path.realpath('init.pdb'): + if self.pipeline == "dimple": + if os.path.isfile("init.pdb"): + if "dimple" in os.path.realpath("init.pdb"): self.Logfile.warning( - '{0!s}: init.pdb & init.mtz is linked to dimple outcome'.format(xtal)) + "{0!s}: init.pdb & init.mtz is linked to dimple outcome".format( + xtal + ) + ) self.Logfile.warning( - '{0!s}: removing init.pdb & init.mtz & (2)fofc maps'.format(xtal)) + "{0!s}: removing init.pdb & init.mtz & (2)fofc maps".format( + xtal + ) + ) db_dict = self.remove_init(db_dict) else: db_dict = self.remove_init(db_dict) self.Logfile.warning( - '{0!s}: removing dimple folder & dimple.pdb/dimple.mtz'.format(xtal)) - os.system('/bin/rm dimple_run_in_progress 2> /dev/null') - os.system('/bin/rm dimple.pdb 2> /dev/null') - os.system('/bin/rm dimple.mtz 2> /dev/null') - os.system('/bin/rm -fr dimple') - elif self.pipeline == 'pipedream': - if os.path.isfile('init.pdb'): - if 'dimple' in os.path.realpath('init.pdb'): + "{0!s}: removing dimple folder & dimple.pdb/dimple.mtz".format(xtal) + ) + os.system("/bin/rm dimple_run_in_progress 2> /dev/null") + os.system("/bin/rm dimple.pdb 2> /dev/null") + os.system("/bin/rm dimple.mtz 2> /dev/null") + os.system("/bin/rm -fr dimple") + elif self.pipeline == "pipedream": + if os.path.isfile("init.pdb"): + if "dimple" in os.path.realpath("init.pdb"): self.Logfile.warning( - '{0!s}: init.pdb & init.mtz is linked to pipedream outcome'.format(xtal)) + "{0!s}: init.pdb & init.mtz is linked to pipedream outcome".format( + xtal + ) + ) self.Logfile.warning( - '{0!s}: removing init.pdb & init.mtz & (2)fofc maps'.format(xtal)) + "{0!s}: removing init.pdb & init.mtz & (2)fofc maps".format( + xtal + ) + ) db_dict = self.remove_init(db_dict) else: db_dict = self.remove_init(db_dict) self.Logfile.warning( - '{0!s}: removing pipedream folder & pipedream.pdb/pipedream.mtz'.format(xtal)) - os.system('/bin/rm pipedream_run_in_progress 2> /dev/null') - os.system('/bin/rm pipedream.pdb 2> /dev/null') - os.system('/bin/rm pipedream.mtz 2> /dev/null') - os.system('/bin/rm -fr pipedream') - elif self.pipeline == 'phenix.ligand_pipeline': - if os.path.isfile('init.pdb'): - if 'dimple' in os.path.realpath('init.pdb'): + "{0!s}: removing pipedream folder & pipedream.pdb/pipedream.mtz".format( + xtal + ) + ) + os.system("/bin/rm pipedream_run_in_progress 2> /dev/null") + os.system("/bin/rm pipedream.pdb 2> /dev/null") + os.system("/bin/rm pipedream.mtz 2> /dev/null") + os.system("/bin/rm -fr pipedream") + elif self.pipeline == "phenix.ligand_pipeline": + if os.path.isfile("init.pdb"): + if "dimple" in os.path.realpath("init.pdb"): self.Logfile.warning( - '{0!s}: init.pdb & init.mtz is linked to phenix.ligand_pipeline outcome'.format(xtal)) + "{0!s}: init.pdb & init.mtz is linked to phenix.ligand_pipeline outcome".format( + xtal + ) + ) self.Logfile.warning( - '{0!s}: removing init.pdb & init.mtz & (2)fofc maps'.format(xtal)) + "{0!s}: removing init.pdb & init.mtz & (2)fofc maps".format( + xtal + ) + ) db_dict = self.remove_init(db_dict) else: db_dict = self.remove_init(db_dict) self.Logfile.warning( - '{0!s}: removing phenix.ligand_pipeline folder & phenix.ligand_pipeline.pdb/phenix.ligand_pipeline.mtz'.format(xtal)) - os.system( - '/bin/rm phenix.ligand_pipeline_run_in_progress 2> /dev/null') - os.system('/bin/rm phenix.ligand_pipeline.pdb 2> /dev/null') - os.system('/bin/rm phenix.ligand_pipeline.mtz 2> /dev/null') - os.system('/bin/rm -fr phenix.ligand_pipeline') + "{0!s}: removing phenix.ligand_pipeline folder & phenix.ligand_pipeline.pdb/phenix.ligand_pipeline.mtz".format( + xtal + ) + ) + os.system("/bin/rm phenix.ligand_pipeline_run_in_progress 2> /dev/null") + os.system("/bin/rm phenix.ligand_pipeline.pdb 2> /dev/null") + os.system("/bin/rm phenix.ligand_pipeline.mtz 2> /dev/null") + os.system("/bin/rm -fr phenix.ligand_pipeline") if db_dict != {}: - self.Logfile.insert('{0!s}: updating database'.format(xtal)) + self.Logfile.insert("{0!s}: updating database".format(xtal)) self.db.update_data_source(xtal, db_dict) progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) - self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) + self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) def remove_init(self, db_dict): - os.system('/bin/rm init.pdb') - os.system('/bin/rm init.mtz') - os.system('/bin/rm 2fofc.map') - os.system('/bin/rm fofc.map') - db_dict['DimpleResolutionHigh'] = '' - db_dict['DimpleRcryst'] = '' - db_dict['DimpleRfree'] = '' - db_dict['DimplePathToPDB'] = '' - db_dict['DimplePathToMTZ'] = '' - db_dict['DimpleReferencePDB'] = '' - db_dict['DimplePANDDAwasRun'] = 'False' - db_dict['DimplePANDDAhit'] = 'False' - db_dict['DimplePANDDAreject'] = 'False' - db_dict['DimplePANDDApath'] = '' - db_dict['DimpleStatus'] = 'pending' + os.system("/bin/rm init.pdb") + os.system("/bin/rm init.mtz") + os.system("/bin/rm 2fofc.map") + os.system("/bin/rm fofc.map") + db_dict["DimpleResolutionHigh"] = "" + db_dict["DimpleRcryst"] = "" + db_dict["DimpleRfree"] = "" + db_dict["DimplePathToPDB"] = "" + db_dict["DimplePathToMTZ"] = "" + db_dict["DimpleReferencePDB"] = "" + db_dict["DimplePANDDAwasRun"] = "False" + db_dict["DimplePANDDAhit"] = "False" + db_dict["DimplePANDDAreject"] = "False" + db_dict["DimplePANDDApath"] = "" + db_dict["DimpleStatus"] = "pending" return db_dict class set_results_from_selected_pipeline(QtCore.QThread): - def __init__(self, sample_list, initial_model_directory, xce_logfile, database_directory, data_source_file, pipeline): + def __init__( + self, + sample_list, + initial_model_directory, + xce_logfile, + database_directory, + data_source_file, + pipeline, + ): QtCore.QThread.__init__(self) self.sample_list = sample_list self.initial_model_directory = initial_model_directory self.xce_logfile = xce_logfile self.Logfile = XChemLog.updateLog(xce_logfile) - self.db = XChemDB.data_source(os.path.join( - database_directory, data_source_file)) + self.db = XChemDB.data_source( + os.path.join(database_directory, data_source_file) + ) self.pipeline = pipeline def run(self): progress_step = 1 if len(self.sample_list) != 0: - progress_step = 100/float(len(self.sample_list)) + progress_step = 100 / float(len(self.sample_list)) progress = 0 - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) for n, xtal in enumerate(self.sample_list): db_dict = {} if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): - self.Logfile.insert( - '{0!s}: directory does not exist'.format(xtal)) + self.Logfile.insert("{0!s}: directory does not exist".format(xtal)) continue os.chdir(os.path.join(self.initial_model_directory, xtal)) - if os.path.isfile('init.pdb'): + if os.path.isfile("init.pdb"): + self.Logfile.warning("{0!s}: init.pdb & init.mtz exist".format(xtal)) self.Logfile.warning( - '{0!s}: init.pdb & init.mtz exist'.format(xtal)) - self.Logfile.warning( - '{0!s}: removing init.pdb & init.mtz & (2)fofc maps'.format(xtal)) - os.system('/bin/rm init.pdb') - os.system('/bin/rm init.mtz') - os.system('/bin/rm 2fofc.map') - os.system('/bin/rm fofc.map') - db_dict['DimpleResolutionHigh'] = '' - db_dict['DimpleRcryst'] = '' - db_dict['DimpleRfree'] = '' - db_dict['DimplePathToPDB'] = '' - db_dict['DimplePathToMTZ'] = '' - db_dict['DimpleReferencePDB'] = '' - db_dict['DimplePANDDAwasRun'] = 'False' - db_dict['DimplePANDDAhit'] = 'False' - db_dict['DimplePANDDAreject'] = 'False' - db_dict['DimplePANDDApath'] = '' - db_dict['DimpleStatus'] = 'pending' - - if self.pipeline == 'dimple': - if os.path.isfile('dimple.pdb'): - self.Logfile.insert( - '%s: selecting output from dimple' % xtal) - os.system('ln -s dimple.pdb init.pdb') - pdb_info = parse().PDBheader('dimple.pdb') - db_dict['DimpleRcryst'] = pdb_info['Rcryst'] - db_dict['DimpleRfree'] = pdb_info['Rfree'] - db_dict['DimpleResolutionHigh'] = pdb_info['ResolutionHigh'] - db_dict['DimpleStatus'] = 'finished' - db_dict['DimplePathToPDB'] = os.path.realpath('dimple.pdb') - if os.path.isfile('dimple.mtz'): - os.system('ln -s dimple.mtz init.mtz') - db_dict['DimplePathToMTZ'] = os.path.realpath('dimple.mtz') - if os.path.isfile('dimple/2fofc.map'): - os.system('ln -s dimple/2fofc.map .') - if os.path.isfile('dimple/fofc.map'): - os.system('ln -s dimple/fofc.map .') - elif self.pipeline == 'pipedream': - if os.path.isfile('pipedream.pdb'): - self.Logfile.insert( - '%s: selecting output from pipedream' % xtal) - os.system('ln -s pipedream.pdb init.pdb') - pdb_info = parse().PDBheader('pipedream.pdb') - db_dict['DimpleRcryst'] = pdb_info['Rcryst'] - db_dict['DimpleRfree'] = pdb_info['Rfree'] - db_dict['DimpleResolutionHigh'] = pdb_info['ResolutionHigh'] - db_dict['DimpleStatus'] = 'finished' - db_dict['DimplePathToPDB'] = os.path.realpath( - 'pipedream.pdb') - if os.path.isfile('pipedream.mtz'): - os.system('ln -s pipedream.mtz init.mtz') - db_dict['DimplePathToMTZ'] = os.path.realpath( - 'pipedream.mtz') - if os.path.isfile('pipedream/2fofc.map'): - os.system('ln -s pipedream/2fofc.map .') - if os.path.isfile('pipedream/fofc.map'): - os.system('ln -s pipedream/fofc.map .') - elif self.pipeline == 'phenix.ligand_pipeline': - if os.path.isfile('phenix.ligand_pipeline.pdb'): + "{0!s}: removing init.pdb & init.mtz & (2)fofc maps".format(xtal) + ) + os.system("/bin/rm init.pdb") + os.system("/bin/rm init.mtz") + os.system("/bin/rm 2fofc.map") + os.system("/bin/rm fofc.map") + db_dict["DimpleResolutionHigh"] = "" + db_dict["DimpleRcryst"] = "" + db_dict["DimpleRfree"] = "" + db_dict["DimplePathToPDB"] = "" + db_dict["DimplePathToMTZ"] = "" + db_dict["DimpleReferencePDB"] = "" + db_dict["DimplePANDDAwasRun"] = "False" + db_dict["DimplePANDDAhit"] = "False" + db_dict["DimplePANDDAreject"] = "False" + db_dict["DimplePANDDApath"] = "" + db_dict["DimpleStatus"] = "pending" + + if self.pipeline == "dimple": + if os.path.isfile("dimple.pdb"): + self.Logfile.insert("%s: selecting output from dimple" % xtal) + os.system("ln -s dimple.pdb init.pdb") + pdb_info = parse().PDBheader("dimple.pdb") + db_dict["DimpleRcryst"] = pdb_info["Rcryst"] + db_dict["DimpleRfree"] = pdb_info["Rfree"] + db_dict["DimpleResolutionHigh"] = pdb_info["ResolutionHigh"] + db_dict["DimpleStatus"] = "finished" + db_dict["DimplePathToPDB"] = os.path.realpath("dimple.pdb") + if os.path.isfile("dimple.mtz"): + os.system("ln -s dimple.mtz init.mtz") + db_dict["DimplePathToMTZ"] = os.path.realpath("dimple.mtz") + if os.path.isfile("dimple/2fofc.map"): + os.system("ln -s dimple/2fofc.map .") + if os.path.isfile("dimple/fofc.map"): + os.system("ln -s dimple/fofc.map .") + elif self.pipeline == "pipedream": + if os.path.isfile("pipedream.pdb"): + self.Logfile.insert("%s: selecting output from pipedream" % xtal) + os.system("ln -s pipedream.pdb init.pdb") + pdb_info = parse().PDBheader("pipedream.pdb") + db_dict["DimpleRcryst"] = pdb_info["Rcryst"] + db_dict["DimpleRfree"] = pdb_info["Rfree"] + db_dict["DimpleResolutionHigh"] = pdb_info["ResolutionHigh"] + db_dict["DimpleStatus"] = "finished" + db_dict["DimplePathToPDB"] = os.path.realpath("pipedream.pdb") + if os.path.isfile("pipedream.mtz"): + os.system("ln -s pipedream.mtz init.mtz") + db_dict["DimplePathToMTZ"] = os.path.realpath("pipedream.mtz") + if os.path.isfile("pipedream/2fofc.map"): + os.system("ln -s pipedream/2fofc.map .") + if os.path.isfile("pipedream/fofc.map"): + os.system("ln -s pipedream/fofc.map .") + elif self.pipeline == "phenix.ligand_pipeline": + if os.path.isfile("phenix.ligand_pipeline.pdb"): self.Logfile.insert( - '%s: selecting output from phenix.ligand_pipeline' % xtal) - os.system('ln -s phenix.ligand_pipeline.pdb init.pdb') - pdb_info = parse().PDBheader('phenix.ligand_pipeline.pdb') - db_dict['DimpleRcryst'] = pdb_info['Rcryst'] - db_dict['DimpleRfree'] = pdb_info['Rfree'] - db_dict['DimpleResolutionHigh'] = pdb_info['ResolutionHigh'] - db_dict['DimpleStatus'] = 'finished' - db_dict['DimplePathToPDB'] = os.path.realpath( - 'phenix.ligand_pipeline.pdb') - if os.path.isfile('phenix.ligand_pipeline.mtz'): - os.system('ln -s phenix.ligand_pipeline.mtz init.mtz') - db_dict['DimplePathToMTZ'] = os.path.realpath( - 'phenix.ligand_pipeline.mtz') - if os.path.isfile('phenix.ligand_pipeline/2fofc.map'): - os.system('ln -s phenix.ligand_pipeline/2fofc.map .') - if os.path.isfile('phenix.ligand_pipeline/fofc.map'): - os.system('ln -s phenix.ligand_pipeline/fofc.map .') - - self.Logfile.insert('{0!s}: updating database'.format(xtal)) + "%s: selecting output from phenix.ligand_pipeline" % xtal + ) + os.system("ln -s phenix.ligand_pipeline.pdb init.pdb") + pdb_info = parse().PDBheader("phenix.ligand_pipeline.pdb") + db_dict["DimpleRcryst"] = pdb_info["Rcryst"] + db_dict["DimpleRfree"] = pdb_info["Rfree"] + db_dict["DimpleResolutionHigh"] = pdb_info["ResolutionHigh"] + db_dict["DimpleStatus"] = "finished" + db_dict["DimplePathToPDB"] = os.path.realpath( + "phenix.ligand_pipeline.pdb" + ) + if os.path.isfile("phenix.ligand_pipeline.mtz"): + os.system("ln -s phenix.ligand_pipeline.mtz init.mtz") + db_dict["DimplePathToMTZ"] = os.path.realpath( + "phenix.ligand_pipeline.mtz" + ) + if os.path.isfile("phenix.ligand_pipeline/2fofc.map"): + os.system("ln -s phenix.ligand_pipeline/2fofc.map .") + if os.path.isfile("phenix.ligand_pipeline/fofc.map"): + os.system("ln -s phenix.ligand_pipeline/fofc.map .") + + self.Logfile.insert("{0!s}: updating database".format(xtal)) self.db.update_data_source(xtal, db_dict) progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) - self.emit(QtCore.SIGNAL('datasource_menu_reload_samples')) + self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) class start_COOT(QtCore.QThread): - def __init__(self, settings, interface): QtCore.QThread.__init__(self) self.settings = settings - if interface == 'test': - self.pylib = 'XChemCoot.py' - elif interface == 'new': - self.pylib = 'XChemCootNew.py' - elif interface == 'panddaV1': - self.pylib = 'XChemCootOld.py' - elif interface == 'reference': - self.pylib = 'XChemCootReference.py' - elif interface == 'buster': - self.pylib = 'XChemCootBuster.py' - elif interface == 'dimple_twin': - self.pylib = 'XChemCootTwin.py' + if interface == "test": + self.pylib = "XChemCoot.py" + elif interface == "new": + self.pylib = "XChemCootNew.py" + elif interface == "panddaV1": + self.pylib = "XChemCootOld.py" + elif interface == "reference": + self.pylib = "XChemCootReference.py" + elif interface == "buster": + self.pylib = "XChemCootBuster.py" + elif interface == "dimple_twin": + self.pylib = "XChemCootTwin.py" def run(self): cwd = os.getcwd() # coot at Diamond always or sometimes at least open in home directory, so then it won't find the .pkl file - pickle.dump(self.settings, open(os.path.join( - os.getenv('HOME'), '.xce_settings.pkl'), 'wb')) - os.system('cd {0!s}\ncoot --no-guano --no-state-script --script {1!s}'.format( - os.getenv('HOME'), os.path.join(os.getenv('XChemExplorer_DIR'), 'lib', self.pylib))) + pickle.dump( + self.settings, + open(os.path.join(os.getenv("HOME"), ".xce_settings.pkl"), "wb"), + ) + os.system( + "cd {0!s}\ncoot --no-guano --no-state-script --script {1!s}".format( + os.getenv("HOME"), + os.path.join(os.getenv("XChemExplorer_DIR"), "lib", self.pylib), + ) + ) class start_ICM(QtCore.QThread): - def __init__(self, html_export_directory): QtCore.QThread.__init__(self) self.html_export_directory = html_export_directory def run(self): cwd = os.getcwd() - if cwd.startswith('/dls'): + if cwd.startswith("/dls"): # if not os.path.isfile(os.path.join('/home',getpass.getuser(),'.flexlmrc')): # os.system('touch '+os.path.join('/home',getpass.getuser(),'.flexlmrc')) # f=open(os.path.join('/home',getpass.getuser(),'.flexlmrc'),'w') # f.write('MOLSOFTD_LICENSE_FILE=@diamvicmpro.diamond.ac.uk') # f.close() - os.system('nautilus {0!s} &'.format(self.html_export_directory)) - os.system('/dls/science/groups/i04-1/software/icm-3.8-5/icm64 -g') + os.system("nautilus {0!s} &".format(self.html_export_directory)) + os.system("/dls/science/groups/i04-1/software/icm-3.8-5/icm64 -g") class start_pandda_inspect(QtCore.QThread): - def __init__(self, settings, xce_logfile): QtCore.QThread.__init__(self) -# self.settings=settings - self.panddas_directory = settings['panddas_directory'] + # self.settings=settings + self.panddas_directory = settings["panddas_directory"] self.xce_logfile = xce_logfile self.Logfile = XChemLog.updateLog(xce_logfile) def run(self): - if os.getenv('SHELL') == '/bin/tcsh' or os.getenv('SHELL') == '/bin/csh': + if os.getenv("SHELL") == "/bin/tcsh" or os.getenv("SHELL") == "/bin/csh": source_file = os.path.join( - os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-csh') - elif os.getenv('SHELL') == '/bin/bash': + os.getenv("XChemExplorer_DIR"), "setup-scripts", "pandda.setup-csh" + ) + elif os.getenv("SHELL") == "/bin/bash": source_file = os.path.join( - os.getenv('XChemExplorer_DIR'), 'setup-scripts', 'pandda.setup-sh') + os.getenv("XChemExplorer_DIR"), "setup-scripts", "pandda.setup-sh" + ) else: - source_file = '' + source_file = "" Cmds = ( - '#!'+os.getenv('SHELL')+'\n' - 'unset PYTHONPATH\n' - 'source '+source_file+'\n' - 'cd '+self.panddas_directory+'\n' - 'pandda.inspect\n' + "#!" + os.getenv("SHELL") + "\n" + "unset PYTHONPATH\n" + "source " + source_file + "\n" + "cd " + self.panddas_directory + "\n" + "pandda.inspect\n" ) self.Logfile.insert( - 'starting pandda.inspect with the following command:\n'+Cmds) + "starting pandda.inspect with the following command:\n" + Cmds + ) os.system(Cmds) + # Cmds = ( # 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' # 'cd '+self.panddas_directory+'\n' @@ -2298,26 +2814,21 @@ def run(self): class start_dials_image_viewer(QtCore.QThread): - def __init__(self, diffraction_image): QtCore.QThread.__init__(self) self.diffraction_image = diffraction_image def run(self): - os.system('dials.image_viewer '+self.diffraction_image) + os.system("dials.image_viewer " + self.diffraction_image) # # --- new module from hell ------------------------------------------------------------------------------------------- # + class read_pinIDs_from_gda_logs(QtCore.QThread): - def __init__(self, - beamline, - visit, - database, - gdaLogInstructions, - xce_logfile): + def __init__(self, beamline, visit, database, gdaLogInstructions, xce_logfile): QtCore.QThread.__init__(self) self.beamline = beamline self.visit = visit @@ -2326,8 +2837,7 @@ def __init__(self, self.Logfile = XChemLog.updateLog(xce_logfile) self.db = XChemDB.data_source(database) - self.allSamples = self.db.collected_xtals_during_visit_for_scoring( - visit) + self.allSamples = self.db.collected_xtals_during_visit_for_scoring(visit) self.gdaLogInstructions = gdaLogInstructions self.gda_log_start_line = gdaLogInstructions[0] @@ -2335,64 +2845,80 @@ def __init__(self, def run(self): if self.gzipped_logs_parsed: - self.Logfile.insert( - "parsed gzipped gda logfiles before, won't do again...") - self.Logfile.insert("will start parsing of current gda logfile at line {0!s}".format( - str(self.gda_log_start_line))) - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'checking GDA logiles for pinID details') - pinDict, self.gda_log_start_line = XChemMain.get_gda_barcodes(self.allSamples, - self.gzipped_logs_parsed, - self.gda_log_start_line, - self.beamline, - self.xce_logfile) + self.Logfile.insert("parsed gzipped gda logfiles before, won't do again...") + self.Logfile.insert( + "will start parsing of current gda logfile at line {0!s}".format( + str(self.gda_log_start_line) + ) + ) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "checking GDA logiles for pinID details", + ) + pinDict, self.gda_log_start_line = XChemMain.get_gda_barcodes( + self.allSamples, + self.gzipped_logs_parsed, + self.gda_log_start_line, + self.beamline, + self.xce_logfile, + ) self.update_database(pinDict) self.gdaLogInstructions = [self.gda_log_start_line, True] - self.Logfile.insert('====== finished checking GDA logfiles ======') - self.emit(QtCore.SIGNAL( - 'update_gdaLog_parsing_instructions_and_score'), self.gdaLogInstructions) + self.Logfile.insert("====== finished checking GDA logfiles ======") + self.emit( + QtCore.SIGNAL("update_gdaLog_parsing_instructions_and_score"), + self.gdaLogInstructions, + ) self.emit(QtCore.SIGNAL("finished()")) def update_database(self, pinDict): - self.Logfile.insert('updating database with pinDIs from GDA logfiles') + self.Logfile.insert("updating database with pinDIs from GDA logfiles") progress = 0 progress_step = XChemMain.getProgressSteps(len(pinDict)) for sample in pinDict: - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'updating pinID in DB for ' + sample) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "updating pinID in DB for " + sample, + ) dbDict = {} - dbDict['DataCollectionPinBarcode'] = pinDict[sample] -# self.db.update_data_source(sample,dbDict) - self.db.update_specified_table(sample, dbDict, 'collectionTable') + dbDict["DataCollectionPinBarcode"] = pinDict[sample] + # self.db.update_data_source(sample,dbDict) + self.db.update_specified_table(sample, dbDict, "collectionTable") progress += progress_step - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) class choose_autoprocessing_outcome(QtCore.QThread): - def __init__(self, - database, - visit, - reference_file_list, - preferences, - projectDir, - rescore, - xce_logfile, - agamemnon): + def __init__( + self, + database, + visit, + reference_file_list, + preferences, + projectDir, + rescore, + xce_logfile, + agamemnon, + ): QtCore.QThread.__init__(self) self.visit = visit self.projectDir = projectDir self.reference_file_list = reference_file_list self.rescore = rescore - self.selection_mechanism = preferences['dataset_selection_mechanism'] + self.selection_mechanism = preferences["dataset_selection_mechanism"] self.acceptable_unitcell_volume_difference = preferences[ - 'allowed_unitcell_difference_percent'] + "allowed_unitcell_difference_percent" + ] self.acceptable_low_resolution_limit_for_data = preferences[ - 'acceptable_low_resolution_limit_for_data'] - self.acceptable_low_resolution_Rmerge = preferences['acceptable_low_resolution_Rmerge'] + "acceptable_low_resolution_limit_for_data" + ] + self.acceptable_low_resolution_Rmerge = preferences[ + "acceptable_low_resolution_Rmerge" + ] self.agamemnon = agamemnon self.xce_logfile = xce_logfile self.Logfile = XChemLog.updateLog(xce_logfile) @@ -2405,10 +2931,10 @@ def __init__(self, for e in x: self.allSamples.append(e) else: - self.allSamples = self.db.collected_xtals_during_visit_for_scoring( - visit) -# print 'here', self.allSamples -# self.allSamples = self.db.collected_xtals_during_visit_for_scoring(visit,rescore) + self.allSamples = self.db.collected_xtals_during_visit_for_scoring(visit) + + # print 'here', self.allSamples + # self.allSamples = self.db.collected_xtals_during_visit_for_scoring(visit,rescore) def run(self): @@ -2417,32 +2943,43 @@ def run(self): for sample in sorted(self.allSamples): if self.db.autoprocessing_result_user_assigned(sample) and not self.rescore: - if os.path.isfile(os.path.join(self.projectDir, sample, sample+'.mtz')): + if os.path.isfile( + os.path.join(self.projectDir, sample, sample + ".mtz") + ): self.Logfile.warning( - '{0!s}: user has manually selected auto-processing result; will NOT auto-select!'.format(sample)) + "{0!s}: user has manually selected auto-processing result; will NOT auto-select!".format( + sample + ) + ) continue else: self.Logfile.warning( - '{0!s}: user has manually selected auto-processing result before, but {1!s}.mtz does not exist'.format(sample, sample)) - self.Logfile.insert( - '%s: selecting autoprocessing result' % sample) + "{0!s}: user has manually selected auto-processing result before, but {1!s}.mtz does not exist".format( + sample, sample + ) + ) + self.Logfile.insert("%s: selecting autoprocessing result" % sample) elif self.rescore: self.Logfile.warning( - '{0!s}: rescore selected -> might overwrite user selection!'.format(sample)) + "{0!s}: rescore selected -> might overwrite user selection!".format( + sample + ) + ) else: - self.Logfile.insert( - '%s: selecting autoprocessing result' % sample) - dbList = self.db.all_autoprocessing_results_for_xtal_as_dict( - sample) + self.Logfile.insert("%s: selecting autoprocessing result" % sample) + dbList = self.db.all_autoprocessing_results_for_xtal_as_dict(sample) self.Logfile.insert( - '%s: found %s different autoprocessing results' % (sample, str(len(dbList)))) + "%s: found %s different autoprocessing results" + % (sample, str(len(dbList))) + ) # 0.) first check for which results files actually exist # dbList = self.checkExistingFiles(dbList, sample) if not dbList: self.Logfile.error( - sample + ': cannot find any MTZ & LOG files; skipping...') + sample + ": cannot find any MTZ & LOG files; skipping..." + ) continue # 1.) if posssible, only carry forward samples with similar UCvolume and same point group @@ -2453,91 +2990,111 @@ def run(self): dbList = self.selectResultsWithAcceptableLowResoRmerge(dbList) # 3.) Make selection based on speified selection mechanism - if self.selection_mechanism == 'IsigI*Comp*UniqueRefl': + if self.selection_mechanism == "IsigI*Comp*UniqueRefl": dbDict = self.selectHighestScore(dbList) - elif self.selection_mechanism == 'highest_resolution': + elif self.selection_mechanism == "highest_resolution": dbDict = self.selectHighestResolution(dbList) - elif 'only' in self.selection_mechanism: + elif "only" in self.selection_mechanism: dbDict = self.selectSpecificPipelineOnly(dbList) # 4.) Set new symbolic links in project directory XChemMain.linkAutoProcessingResult( - sample, dbDict, self.projectDir, self.xce_logfile) + sample, dbDict, self.projectDir, self.xce_logfile + ) # 5.) Determine DataProcessing Outcome - dbDict['DataCollectionOutcome'] = self.determine_processing_outcome( - dbDict) + dbDict["DataCollectionOutcome"] = self.determine_processing_outcome(dbDict) # 6.) update database - dbDict['DataProcessingAutoAssigned'] = 'True' + dbDict["DataProcessingAutoAssigned"] = "True" self.updateDB(sample, dbDict) progress += progress_step - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'scoring auto-processing results for '+sample) - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - - self.Logfile.insert( - '====== finished scoring data processing results ======') - self.emit(QtCore.SIGNAL('populate_datasets_summary_table_NEW')) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "scoring auto-processing results for " + sample, + ) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) + + self.Logfile.insert("====== finished scoring data processing results ======") + self.emit(QtCore.SIGNAL("populate_datasets_summary_table_NEW")) self.emit(QtCore.SIGNAL("finished()")) def report_forward_carried_pipelines(self, dbListOut, dbList): if not dbListOut: dbListOut = dbList self.Logfile.warning( - 'none of the MTZ files fulfilled criteria; will carry forward all results:') + "none of the MTZ files fulfilled criteria; will carry forward all results:" + ) else: self.Logfile.insert( - 'will carry forward the MTZ files from the following auto-processing pipelines:') - self.Logfile.insert('{0:30} {1:10} {2:10} {3:10}'.format( - 'pipeline', 'Rmerge(Low)', 'PG', 'Score')) + "will carry forward the MTZ files from the following auto-processing pipelines:" + ) + self.Logfile.insert( + "{0:30} {1:10} {2:10} {3:10}".format( + "pipeline", "Rmerge(Low)", "PG", "Score" + ) + ) self.Logfile.insert( - '----------------------------------------------------------------------') + "----------------------------------------------------------------------" + ) for resultDict in dbListOut: - self.Logfile.insert('{0:30} {1:10} {2:10} {3:10}'.format(resultDict['DataProcessingProgram'], - resultDict['DataProcessingRmergeLow'], - resultDict['DataProcessingPointGroup'], - resultDict['DataProcessingScore'])) + self.Logfile.insert( + "{0:30} {1:10} {2:10} {3:10}".format( + resultDict["DataProcessingProgram"], + resultDict["DataProcessingRmergeLow"], + resultDict["DataProcessingPointGroup"], + resultDict["DataProcessingScore"], + ) + ) return dbListOut def checkExistingFiles(self, dbList, xtal): - self.Logfile.insert('checking if MTZ & LOG files exisit') + self.Logfile.insert("checking if MTZ & LOG files exisit") os.chdir(os.path.join(self.projectDir, xtal)) - self.Logfile.insert(xtal + ': changing directory ' + - os.path.join(self.projectDir, xtal)) + self.Logfile.insert( + xtal + ": changing directory " + os.path.join(self.projectDir, xtal) + ) dbListOut = [] for resultDict in dbList: try: - run = resultDict['DataCollectionRun'] - subDir = resultDict['DataCollectionSubdir'] - if subDir != '': - procCode = '_' + subDir + run = resultDict["DataCollectionRun"] + subDir = resultDict["DataCollectionSubdir"] + if subDir != "": + procCode = "_" + subDir else: - procCode = '' - visit = resultDict['DataCollectionVisit'] - autoproc = resultDict['DataProcessingProgram'] - mtzFileAbs = resultDict['DataProcessingPathToMTZfile'] - mtzfileName = mtzFileAbs[mtzFileAbs.rfind('/')+1:] - logFileAbs = resultDict['DataProcessingPathToLogfile'] - logfileName = logFileAbs[logFileAbs.rfind('/')+1:] + procCode = "" + visit = resultDict["DataCollectionVisit"] + autoproc = resultDict["DataProcessingProgram"] + mtzFileAbs = resultDict["DataProcessingPathToMTZfile"] + mtzfileName = mtzFileAbs[mtzFileAbs.rfind("/") + 1 :] + logFileAbs = resultDict["DataProcessingPathToLogfile"] + logfileName = logFileAbs[logFileAbs.rfind("/") + 1 :] mtzfile = os.path.join( - 'autoprocessing', visit + '-' + run + autoproc + procCode, mtzfileName) + "autoprocessing", + visit + "-" + run + autoproc + procCode, + mtzfileName, + ) logfile = os.path.join( - 'autoprocessing', visit + '-' + run + autoproc + procCode, logfileName) + "autoprocessing", + visit + "-" + run + autoproc + procCode, + logfileName, + ) if os.path.isfile(mtzfile): - self.Logfile.insert(xtal + ': found ' + mtzfile) + self.Logfile.insert(xtal + ": found " + mtzfile) if os.path.isfile(logfile): - self.Logfile.insert(xtal + ': found ' + logfile) + self.Logfile.insert(xtal + ": found " + logfile) dbListOut.append(resultDict) else: self.Logfile.error( - xtal + ': cannot find ' + logfile + ' ; skipping...') + xtal + ": cannot find " + logfile + " ; skipping..." + ) else: self.Logfile.error( - xtal + ': cannot find ' + mtzfile + ' ; skipping...') + xtal + ": cannot find " + mtzfile + " ; skipping..." + ) except ValueError: pass @@ -2545,51 +3102,89 @@ def checkExistingFiles(self, dbList, xtal): def selectResultsSimilarToReference(self, dbList): self.Logfile.insert( - 'checking if MTZ files are similar to supplied reference files') + "checking if MTZ files are similar to supplied reference files" + ) dbListOut = [] for resultDict in dbList: try: - if isinstance(float(resultDict['DataProcessingUnitCellVolume']), float): + if isinstance(float(resultDict["DataProcessingUnitCellVolume"]), float): self.Logfile.insert( - 'checking unit cell volume difference and point group:') + "checking unit cell volume difference and point group:" + ) for reference_file in self.reference_file_list: if not reference_file[4] == 0: self.Logfile.insert( - 'unitcell volume reference:' + str(reference_file[4])) + "unitcell volume reference:" + str(reference_file[4]) + ) self.Logfile.insert( - 'unitcell volume dataset: ' + str(resultDict['DataProcessingUnitCellVolume'])) - unitcell_difference = round((math.fabs( - reference_file[4]-float(resultDict['DataProcessingUnitCellVolume']))/reference_file[4])*100, 1) - self.Logfile.insert(resultDict['DataProcessingProgram'] + ': ' + - str(unitcell_difference) + '% difference -> pg(ref): ' + - reference_file[5] + ' -> pg(mtz): ' + resultDict['DataProcessingPointGroup']) - if unitcell_difference < self.acceptable_unitcell_volume_difference and reference_file[5] == resultDict['DataProcessingPointGroup']: + "unitcell volume dataset: " + + str(resultDict["DataProcessingUnitCellVolume"]) + ) + unitcell_difference = round( + ( + math.fabs( + reference_file[4] + - float( + resultDict["DataProcessingUnitCellVolume"] + ) + ) + / reference_file[4] + ) + * 100, + 1, + ) + self.Logfile.insert( + resultDict["DataProcessingProgram"] + + ": " + + str(unitcell_difference) + + "% difference -> pg(ref): " + + reference_file[5] + + " -> pg(mtz): " + + resultDict["DataProcessingPointGroup"] + ) + if ( + unitcell_difference + < self.acceptable_unitcell_volume_difference + and reference_file[5] + == resultDict["DataProcessingPointGroup"] + ): self.Logfile.insert( - '=> passed -> mtz file has same point group as reference file and similar unit cell volume') + "=> passed -> mtz file has same point group as reference file and similar unit cell volume" + ) dbListOut.append(resultDict) else: self.Logfile.warning( - 'mtz file has different point group/ unit cell volume as reference file') + "mtz file has different point group/ unit cell volume as reference file" + ) except ValueError: pass dbListOut = self.report_forward_carried_pipelines(dbListOut, dbList) return dbListOut def selectResultsWithAcceptableLowResoRmerge(self, dbList): - self.Logfile.insert('checking if MTZ files have acceptable low resolution Rmerge values (currently set to %s)' % str( - self.acceptable_low_resolution_Rmerge)) + self.Logfile.insert( + "checking if MTZ files have acceptable low resolution Rmerge values (currently set to %s)" + % str(self.acceptable_low_resolution_Rmerge) + ) dbListOut = [] for resultDict in dbList: try: - if float(resultDict['DataProcessingRmergeLow']) < self.acceptable_low_resolution_Rmerge: - self.Logfile.insert(resultDict['DataProcessingProgram'] + - ': Rmerge(low) of MTZ file is below threshold: ' + - str(resultDict['DataProcessingRmergeLow'])) + if ( + float(resultDict["DataProcessingRmergeLow"]) + < self.acceptable_low_resolution_Rmerge + ): + self.Logfile.insert( + resultDict["DataProcessingProgram"] + + ": Rmerge(low) of MTZ file is below threshold: " + + str(resultDict["DataProcessingRmergeLow"]) + ) dbListOut.append(resultDict) else: - self.Logfile.warning(resultDict['DataProcessingProgram'] + - ': Rmerge(low) of MTZ file is ABOVE threshold: ' + - str(resultDict['DataProcessingRmergeLow'])) + self.Logfile.warning( + resultDict["DataProcessingProgram"] + + ": Rmerge(low) of MTZ file is ABOVE threshold: " + + str(resultDict["DataProcessingRmergeLow"]) + ) except ValueError: pass dbListOut = self.report_forward_carried_pipelines(dbListOut, dbList) @@ -2599,7 +3194,7 @@ def selectHighestScore(self, dbList): tmp = [] for resultDict in dbList: try: - tmp.append(float(resultDict['DataProcessingScore'])) + tmp.append(float(resultDict["DataProcessingScore"])) except ValueError: tmp.append(0.0) highestScoreDict = dbList[tmp.index(max(tmp))] @@ -2609,7 +3204,7 @@ def selectHighestResolution(self, dbList): tmp = [] for resultDict in dbList: try: - tmp.append(float(resultDict['DataProcessingResolutionHigh'])) + tmp.append(float(resultDict["DataProcessingResolutionHigh"])) except ValueError: tmp.append(100.0) highestResoDict = dbList[tmp.index(min(tmp))] @@ -2618,17 +3213,36 @@ def selectHighestResolution(self, dbList): def selectSpecificPipelineOnly(self, dbList): tmp = [] self.Logfile.insert( - 'selecting datasets by auto-processing pipeline: ' + self.selection_mechanism) + "selecting datasets by auto-processing pipeline: " + + self.selection_mechanism + ) for resultDict in dbList: - if self.selection_mechanism == 'dials - only' and 'dials' in resultDict['DataProcessingProgram']: + if ( + self.selection_mechanism == "dials - only" + and "dials" in resultDict["DataProcessingProgram"] + ): tmp.append(resultDict) - if self.selection_mechanism == 'xia2 3d - only' and '3d-' in resultDict['DataProcessingProgram']: + if ( + self.selection_mechanism == "xia2 3d - only" + and "3d-" in resultDict["DataProcessingProgram"] + ): tmp.append(resultDict) - if self.selection_mechanism == 'xia2 3dii - only' and '3dii' in resultDict['DataProcessingProgram']: + if ( + self.selection_mechanism == "xia2 3dii - only" + and "3dii" in resultDict["DataProcessingProgram"] + ): tmp.append(resultDict) - if self.selection_mechanism == 'autoProc - only' and 'autoPROC' in resultDict['DataProcessingProgram'] and not 'staraniso' in resultDict['DataProcessingProgram']: + if ( + self.selection_mechanism == "autoProc - only" + and "autoPROC" in resultDict["DataProcessingProgram"] + and not "staraniso" in resultDict["DataProcessingProgram"] + ): tmp.append(resultDict) - if self.selection_mechanism == 'autoProc_staraniso - only' and 'autoPROC' in resultDict['DataProcessingProgram'] and 'staraniso' in resultDict['DataProcessingProgram']: + if ( + self.selection_mechanism == "autoProc_staraniso - only" + and "autoPROC" in resultDict["DataProcessingProgram"] + and "staraniso" in resultDict["DataProcessingProgram"] + ): tmp.append(resultDict) if not tmp: tmp = dbList @@ -2636,18 +3250,21 @@ def selectSpecificPipelineOnly(self, dbList): return pipelineDict def determine_processing_outcome(self, db_dict): - outcome = 'Failed - unknown' + outcome = "Failed - unknown" try: - if float(db_dict['DataProcessingResolutionHigh']) < self.acceptable_low_resolution_limit_for_data: - outcome = 'success' + if ( + float(db_dict["DataProcessingResolutionHigh"]) + < self.acceptable_low_resolution_limit_for_data + ): + outcome = "success" else: - outcome = 'Failed - low resolution' + outcome = "Failed - low resolution" except ValueError: pass return outcome def updateDB(self, sample, dbDict): - self.Logfile.insert('{0!s}: updating database'.format(sample)) + self.Logfile.insert("{0!s}: updating database".format(sample)) self.db.update_insert_data_source(sample, dbDict) @@ -2670,140 +3287,141 @@ class read_write_autoprocessing_results_from_to_disc(QtCore.QThread): - parsing of pinIDs in gda logfiles is still missing """ - def __init__(self, - processedDir, - database, - projectDir, - xce_logfile, - target, - agamemnon): + def __init__( + self, processedDir, database, projectDir, xce_logfile, target, agamemnon + ): QtCore.QThread.__init__(self) -# self.target = target + # self.target = target self.processedDir = processedDir - self.visit, self.beamline = XChemMain.getVisitAndBeamline( - self.processedDir) -# print 'visit' + self.visit, self.beamline = XChemMain.getVisitAndBeamline(self.processedDir) + # print 'visit' self.projectDir = projectDir self.Logfile = XChemLog.updateLog(xce_logfile) self.target = target self.agamemnon = agamemnon -# if self.agamemnon: -## print 'procDir',self.processedDir -# if len(procDir.split('/')) >= 8: -# if procDir.split('/')[7] == 'agamemnon' -# quit() -# self.visit = 'agamemnon' # this is for trouble-shooting only + # if self.agamemnon: + ## print 'procDir',self.processedDir + # if len(procDir.split('/')) >= 8: + # if procDir.split('/')[7] == 'agamemnon' + # quit() + # self.visit = 'agamemnon' # this is for trouble-shooting only self.db = XChemDB.data_source(os.path.join(database)) self.exisitingSamples = self.getExistingSamples() -# for xtal in self.exisitingSamples: -# print self.exisitingSamples[xtal] -# break -# quit() + # for xtal in self.exisitingSamples: + # print self.exisitingSamples[xtal] + # break + # quit() self.toParse = [ - [os.path.join('*'), - os.path.join('LogFiles', '*aimless.log'), - os.path.join('DataFiles', '*free.mtz')], - [os.path.join('*'), - os.path.join('LogFiles', '*merging-statistics.json'), - os.path.join('DataFiles', '*free.mtz')], - [os.path.join('multi-xia2', '*'), - os.path.join('LogFiles', '*aimless.log'), - os.path.join('DataFiles', '*free.mtz')], + [ + os.path.join("*"), + os.path.join("LogFiles", "*aimless.log"), + os.path.join("DataFiles", "*free.mtz"), + ], + [ + os.path.join("*"), + os.path.join("LogFiles", "*merging-statistics.json"), + os.path.join("DataFiles", "*free.mtz"), + ], + [ + os.path.join("multi-xia2", "*"), + os.path.join("LogFiles", "*aimless.log"), + os.path.join("DataFiles", "*free.mtz"), + ], # [ os.path.join('autoPROC', '*'), # '*aimless.log', # '*truncate-unique.mtz'], # [ os.path.join('autoPROC', '*'), # '*staraniso_alldata-unique.table1', # '*staraniso_alldata-unique.mtz'], - [os.path.join('autoPROC'), - '*aimless.log', - '*truncate-unique.mtz'], - [os.path.join('autoPROC'), - # staraniso_alldata-unique.table1 only available in tar archive - '*summary.tar.gz', - '*staraniso_alldata-unique.mtz'], - [os.path.join('autoPROC-*'), - '*aimless.log', - '*truncate-unique.mtz'], - [os.path.join('autoPROC-*'), - '*summary.tar.gz', - '*staraniso_alldata-unique.mtz'], + [os.path.join("autoPROC"), "*aimless.log", "*truncate-unique.mtz"], + [ + os.path.join("autoPROC"), + # staraniso_alldata-unique.table1 only available in tar archive + "*summary.tar.gz", + "*staraniso_alldata-unique.mtz", + ], + [os.path.join("autoPROC-*"), "*aimless.log", "*truncate-unique.mtz"], + [ + os.path.join("autoPROC-*"), + "*summary.tar.gz", + "*staraniso_alldata-unique.mtz", + ], # [ os.path.join('*'), # os.path.join('LogFiles', '*aimless.log'), # os.path.join('DataFiles', '*free.mtz')] ] -# self.toParse = [ -# [ os.path.join('*'), -# os.path.join('LogFiles', '*aimless.log'), -# os.path.join('DataFiles', '*free.mtz')], -# [ os.path.join('*'), -# os.path.join('LogFiles', '*merging-statistics.json'), -# os.path.join('DataFiles', '*free.mtz')], -# [ os.path.join('multi-xia2', '*'), -# os.path.join('LogFiles', '*aimless.log'), -# os.path.join('DataFiles', '*free.mtz')], -# [ os.path.join('autoPROC', '*'), -# '*aimless.log', -# '*truncate-unique.mtz'], -# [ os.path.join('autoPROC', '*'), -# '*staraniso_alldata-unique.table1', -# '*staraniso_alldata-unique.mtz'], -# [ os.path.join('autoPROC'), -# '*aimless.log', -# '*truncate-unique.mtz'], -# [ os.path.join('autoPROC'), -# '*summary.tar.gz', # staraniso_alldata-unique.table1 only available in tar archive -# '*staraniso_alldata-unique.mtz'], -# [ os.path.join('autoPROC-*'), -# '*aimless.log', -# '*truncate-unique.mtz'], -# [ os.path.join('autoPROC-*'), -# '*summary.tar.gz', -# '*staraniso_alldata-unique.mtz'], -# [ os.path.join('*'), -# os.path.join('LogFiles', '*aimless.log'), -# os.path.join('DataFiles', '*free.mtz')] -# ] - -# self.toParse = [ -# [ os.path.join('xia2', '*'), -# os.path.join('LogFiles', '*aimless.log'), -# os.path.join('DataFiles', '*free.mtz')], -# [ os.path.join('xia2-3*'), -# os.path.join('LogFiles', '*aimless.log'), -# os.path.join('DataFiles', '*free.mtz')], -# [ os.path.join('xia2-dials*'), -# os.path.join('LogFiles', '*merging-statistics.json'), -# os.path.join('DataFiles', '*free.mtz')], -# [ os.path.join('multi-xia2', '*'), -# os.path.join('LogFiles', '*aimless.log'), -# os.path.join('DataFiles', '*free.mtz')], -# [ os.path.join('autoPROC', '*'), -# '*aimless.log', -# '*truncate-unique.mtz'], -# [ os.path.join('autoPROC', '*'), -# '*staraniso_alldata-unique.table1', -# '*staraniso_alldata-unique.mtz'], -# [ os.path.join('autoPROC'), -# '*aimless.log', -# '*truncate-unique.mtz'], -# [ os.path.join('autoPROC'), -# '*summary.tar.gz', # staraniso_alldata-unique.table1 only available in tar archive -# '*staraniso_alldata-unique.mtz'], -# [ os.path.join('autoPROC-*'), -# '*aimless.log', -# '*truncate-unique.mtz'], -# [ os.path.join('autoPROC-*'), -# '*summary.tar.gz', -# '*staraniso_alldata-unique.mtz'], -# [ os.path.join('*'), -# os.path.join('LogFiles', '*aimless.log'), -# os.path.join('DataFiles', '*free.mtz')] -# ] + # self.toParse = [ + # [ os.path.join('*'), + # os.path.join('LogFiles', '*aimless.log'), + # os.path.join('DataFiles', '*free.mtz')], + # [ os.path.join('*'), + # os.path.join('LogFiles', '*merging-statistics.json'), + # os.path.join('DataFiles', '*free.mtz')], + # [ os.path.join('multi-xia2', '*'), + # os.path.join('LogFiles', '*aimless.log'), + # os.path.join('DataFiles', '*free.mtz')], + # [ os.path.join('autoPROC', '*'), + # '*aimless.log', + # '*truncate-unique.mtz'], + # [ os.path.join('autoPROC', '*'), + # '*staraniso_alldata-unique.table1', + # '*staraniso_alldata-unique.mtz'], + # [ os.path.join('autoPROC'), + # '*aimless.log', + # '*truncate-unique.mtz'], + # [ os.path.join('autoPROC'), + # '*summary.tar.gz', # staraniso_alldata-unique.table1 only available in tar archive + # '*staraniso_alldata-unique.mtz'], + # [ os.path.join('autoPROC-*'), + # '*aimless.log', + # '*truncate-unique.mtz'], + # [ os.path.join('autoPROC-*'), + # '*summary.tar.gz', + # '*staraniso_alldata-unique.mtz'], + # [ os.path.join('*'), + # os.path.join('LogFiles', '*aimless.log'), + # os.path.join('DataFiles', '*free.mtz')] + # ] + + # self.toParse = [ + # [ os.path.join('xia2', '*'), + # os.path.join('LogFiles', '*aimless.log'), + # os.path.join('DataFiles', '*free.mtz')], + # [ os.path.join('xia2-3*'), + # os.path.join('LogFiles', '*aimless.log'), + # os.path.join('DataFiles', '*free.mtz')], + # [ os.path.join('xia2-dials*'), + # os.path.join('LogFiles', '*merging-statistics.json'), + # os.path.join('DataFiles', '*free.mtz')], + # [ os.path.join('multi-xia2', '*'), + # os.path.join('LogFiles', '*aimless.log'), + # os.path.join('DataFiles', '*free.mtz')], + # [ os.path.join('autoPROC', '*'), + # '*aimless.log', + # '*truncate-unique.mtz'], + # [ os.path.join('autoPROC', '*'), + # '*staraniso_alldata-unique.table1', + # '*staraniso_alldata-unique.mtz'], + # [ os.path.join('autoPROC'), + # '*aimless.log', + # '*truncate-unique.mtz'], + # [ os.path.join('autoPROC'), + # '*summary.tar.gz', # staraniso_alldata-unique.table1 only available in tar archive + # '*staraniso_alldata-unique.mtz'], + # [ os.path.join('autoPROC-*'), + # '*aimless.log', + # '*truncate-unique.mtz'], + # [ os.path.join('autoPROC-*'), + # '*summary.tar.gz', + # '*staraniso_alldata-unique.mtz'], + # [ os.path.join('*'), + # os.path.join('LogFiles', '*aimless.log'), + # os.path.join('DataFiles', '*free.mtz')] + # ] def run(self): # if self.agamemnon: @@ -2814,17 +3432,18 @@ def run(self): def getExistingSamples(self): existingSamples = {} - self.Logfile.insert('reading existing samples from collectionTable') + self.Logfile.insert("reading existing samples from collectionTable") allEntries = self.db.execute_statement( - 'select CrystalName,DataCollectionVisit,DataCollectionRun,DataProcessingProgram, DataCollectionSubdir from collectionTable where DataCollectionOutcome = "success"') + 'select CrystalName,DataCollectionVisit,DataCollectionRun,DataProcessingProgram, DataCollectionSubdir from collectionTable where DataCollectionOutcome = "success"' + ) for item in allEntries: if str(item[0]) not in existingSamples: existingSamples[str(item[0])] = [] - self.Logfile.insert('%s: adding %s' % - (str(item[0]), str(item[1]))) + self.Logfile.insert("%s: adding %s" % (str(item[0]), str(item[1]))) # visit-runautoproc-subdir existingSamples[str(item[0])].append( - str(item[1]) + '-' + str(item[2])+str(item[3])+'-'+str(item[4])) + str(item[1]) + "-" + str(item[2]) + str(item[3]) + "-" + str(item[4]) + ) return existingSamples def createSampleDir(self, xtal): @@ -2833,219 +3452,391 @@ def createSampleDir(self, xtal): def createAutoprocessingDir(self, xtal, run, autoproc, proc_code): # create all the directories if necessary - self.Logfile.insert('%s: checking if new directory needs to be created for %s' % (xtal, os.path.join( - self.projectDir, xtal, 'autoprocessing', self.visit + '-' + run + autoproc + '_' + proc_code))) - if not os.path.isdir(os.path.join(self.projectDir, xtal, 'autoprocessing')): - os.mkdir(os.path.join(self.projectDir, xtal, 'autoprocessing')) + self.Logfile.insert( + "%s: checking if new directory needs to be created for %s" + % ( + xtal, + os.path.join( + self.projectDir, + xtal, + "autoprocessing", + self.visit + "-" + run + autoproc + "_" + proc_code, + ), + ) + ) + if not os.path.isdir(os.path.join(self.projectDir, xtal, "autoprocessing")): + os.mkdir(os.path.join(self.projectDir, xtal, "autoprocessing")) if not os.path.isdir( - os.path.join(self.projectDir, xtal, 'autoprocessing', self.visit + '-' + run + autoproc + '_' + proc_code)): - self.Logfile.insert('%s: making directory %s' % (xtal, os.path.join( - self.projectDir, xtal, 'autoprocessing', self.visit + '-' + run + autoproc + '_' + proc_code))) - os.mkdir(os.path.join(self.projectDir, xtal, 'autoprocessing', - self.visit + '-' + run + autoproc + '_' + proc_code)) + os.path.join( + self.projectDir, + xtal, + "autoprocessing", + self.visit + "-" + run + autoproc + "_" + proc_code, + ) + ): + self.Logfile.insert( + "%s: making directory %s" + % ( + xtal, + os.path.join( + self.projectDir, + xtal, + "autoprocessing", + self.visit + "-" + run + autoproc + "_" + proc_code, + ), + ) + ) + os.mkdir( + os.path.join( + self.projectDir, + xtal, + "autoprocessing", + self.visit + "-" + run + autoproc + "_" + proc_code, + ) + ) else: - self.Logfile.warning('%s: directory exists; skipping...' % xtal) + self.Logfile.warning("%s: directory exists; skipping..." % xtal) def cleanUpDir(self, xtal, run, autoproc, mtzfile, logfile, proc_code): - toKeep = ['staraniso_alldata-unique.mtz', 'staraniso_alldata-unique.table1', - 'staraniso_alldata.log', xtal+'.mtz', xtal+'.log'] - os.chdir(os.path.join(self.projectDir, xtal, 'autoprocessing', - self.visit + '-' + run + autoproc + '_' + proc_code)) - for files in glob.glob('*'): + toKeep = [ + "staraniso_alldata-unique.mtz", + "staraniso_alldata-unique.table1", + "staraniso_alldata.log", + xtal + ".mtz", + xtal + ".log", + ] + os.chdir( + os.path.join( + self.projectDir, + xtal, + "autoprocessing", + self.visit + "-" + run + autoproc + "_" + proc_code, + ) + ) + for files in glob.glob("*"): if files not in toKeep: - os.system('/bin/rm -f ' + files) + os.system("/bin/rm -f " + files) def copyMTZandLOGfiles(self, xtal, run, autoproc, mtzfile, logfile, proc_code): - mtzNew = '' - logNew = '' - os.chdir(os.path.join(self.projectDir, xtal, 'autoprocessing', - self.visit + '-' + run + autoproc + '_' + proc_code)) + mtzNew = "" + logNew = "" + os.chdir( + os.path.join( + self.projectDir, + xtal, + "autoprocessing", + self.visit + "-" + run + autoproc + "_" + proc_code, + ) + ) # MTZ file - if not os.path.isfile(mtzfile[mtzfile.rfind('/') + 1:]): - self.Logfile.insert('%s: copying %s' % (xtal, mtzfile)) - os.system('/bin/cp ' + mtzfile + ' .') - for mmcif in glob.glob(os.path.join(mtzfile[:mtzfile.rfind('/')], '*')): - if mmcif.endswith('.mmcif'): - self.Logfile.insert('%s: copying %s' % (xtal, mmcif)) - os.system('/bin/cp ' + mmcif + ' .') - elif mmcif.endswith('.mmcif.bz2'): + if not os.path.isfile(mtzfile[mtzfile.rfind("/") + 1 :]): + self.Logfile.insert("%s: copying %s" % (xtal, mtzfile)) + os.system("/bin/cp " + mtzfile + " .") + for mmcif in glob.glob(os.path.join(mtzfile[: mtzfile.rfind("/")], "*")): + if mmcif.endswith(".mmcif"): + self.Logfile.insert("%s: copying %s" % (xtal, mmcif)) + os.system("/bin/cp " + mmcif + " .") + elif mmcif.endswith(".mmcif.bz2"): self.Logfile.insert( - '%s: copying and decompressing %s' % (xtal, mmcif)) - os.system('/bin/cp ' + mmcif + ' .') - os.system('bzip2 -d ./' + mmcif) - if os.path.isfile(mtzfile[mtzfile.rfind('/')+1:]) and not os.path.isfile(xtal+'.mtz'): - os.symlink(mtzfile[mtzfile.rfind('/')+1:], xtal + '.mtz') - if os.path.isfile(mtzfile[mtzfile.rfind('/') + 1:]): - mtzNew = os.path.join(self.projectDir, xtal, 'autoprocessing', self.visit + - '-' + run + autoproc + '_' + proc_code, mtzfile[mtzfile.rfind('/')+1:]) + "%s: copying and decompressing %s" % (xtal, mmcif) + ) + os.system("/bin/cp " + mmcif + " .") + os.system("bzip2 -d ./" + mmcif) + if os.path.isfile(mtzfile[mtzfile.rfind("/") + 1 :]) and not os.path.isfile( + xtal + ".mtz" + ): + os.symlink(mtzfile[mtzfile.rfind("/") + 1 :], xtal + ".mtz") + if os.path.isfile(mtzfile[mtzfile.rfind("/") + 1 :]): + mtzNew = os.path.join( + self.projectDir, + xtal, + "autoprocessing", + self.visit + "-" + run + autoproc + "_" + proc_code, + mtzfile[mtzfile.rfind("/") + 1 :], + ) # MTZ file unmerged - if os.path.isfile(mtzfile.replace('_free.mtz', '_scaled_unmerged.mtz')): - self.Logfile.insert('%s: found unmerged mtz file' % xtal) - if not os.path.isfile(xtal+'_unmerged.mtz'): - self.Logfile.insert('%s: copying %s' % ( - xtal, mtzfile.replace('_free.mtz', '_scaled_unmerged.mtz'))) - os.system('/bin/cp ' + mtzfile.replace('_free.mtz', - '_scaled_unmerged.mtz') + ' .') + if os.path.isfile(mtzfile.replace("_free.mtz", "_scaled_unmerged.mtz")): + self.Logfile.insert("%s: found unmerged mtz file" % xtal) + if not os.path.isfile(xtal + "_unmerged.mtz"): + self.Logfile.insert( + "%s: copying %s" + % (xtal, mtzfile.replace("_free.mtz", "_scaled_unmerged.mtz")) + ) + os.system( + "/bin/cp " + + mtzfile.replace("_free.mtz", "_scaled_unmerged.mtz") + + " ." + ) # AIMLESS logfile - if not os.path.isfile(logfile[logfile.rfind('/')+1:]): - self.Logfile.insert('%s: copying %s' % (xtal, logfile)) - os.system('/bin/cp ' + logfile + ' .') - if logfile.endswith('summary.tar.gz'): - self.Logfile.insert('unpacking summary.tar.gz') - os.system('tar -xzvf summary.tar.gz') + if not os.path.isfile(logfile[logfile.rfind("/") + 1 :]): + self.Logfile.insert("%s: copying %s" % (xtal, logfile)) + os.system("/bin/cp " + logfile + " .") + if logfile.endswith("summary.tar.gz"): + self.Logfile.insert("unpacking summary.tar.gz") + os.system("tar -xzvf summary.tar.gz") logfile = logfile.replace( - 'summary.tar.gz', 'staraniso_alldata-unique.table1') - self.cleanUpDir(xtal, run, autoproc, - mtzfile, logfile, proc_code) - if os.path.isfile(logfile[logfile.rfind('/')+1:]) and not os.path.isfile(xtal+'.log'): - os.symlink(logfile[logfile.rfind('/')+1:], xtal + '.log') - if os.path.isfile(logfile[logfile.rfind('/') + 1:]): - logNew = os.path.join(self.projectDir, xtal, 'autoprocessing', self.visit + - '-' + run + autoproc + '_' + proc_code, logfile[logfile.rfind('/') + 1:]) + "summary.tar.gz", "staraniso_alldata-unique.table1" + ) + self.cleanUpDir(xtal, run, autoproc, mtzfile, logfile, proc_code) + if os.path.isfile(logfile[logfile.rfind("/") + 1 :]) and not os.path.isfile( + xtal + ".log" + ): + os.symlink(logfile[logfile.rfind("/") + 1 :], xtal + ".log") + if os.path.isfile(logfile[logfile.rfind("/") + 1 :]): + logNew = os.path.join( + self.projectDir, + xtal, + "autoprocessing", + self.visit + "-" + run + autoproc + "_" + proc_code, + logfile[logfile.rfind("/") + 1 :], + ) # September 2021: xia2 does not also output a xia2.mmcif and json merging statistics file, even if aimless was used # for scaling, however, the xia2.mmcif file is differently formatted than the one from dials # hence, if xtal.log file already exists, use this one - if 'aimless' in os.readlink(xtal + '.log'): - logNew = os.path.join(self.projectDir, xtal, 'autoprocessing', - self.visit + '-' + run + autoproc + '_' + proc_code, xtal + '.log') + if "aimless" in os.readlink(xtal + ".log"): + logNew = os.path.join( + self.projectDir, + xtal, + "autoprocessing", + self.visit + "-" + run + autoproc + "_" + proc_code, + xtal + ".log", + ) return mtzNew, logNew def makeJPGdir(self, xtal, run): - if not os.path.isdir(os.path.join(self.projectDir, xtal, 'jpg')): - self.Logfile.insert('making jpg directory in '+xtal) - os.mkdir(os.path.join(self.projectDir, xtal, 'jpg')) + if not os.path.isdir(os.path.join(self.projectDir, xtal, "jpg")): + self.Logfile.insert("making jpg directory in " + xtal) + os.mkdir(os.path.join(self.projectDir, xtal, "jpg")) if not os.path.isdir( - os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run)): - os.mkdir(os.path.join(self.projectDir, xtal, - 'jpg', self.visit + '-' + run)) + os.path.join(self.projectDir, xtal, "jpg", self.visit + "-" + run) + ): + os.mkdir(os.path.join(self.projectDir, xtal, "jpg", self.visit + "-" + run)) def copyJPGs(self, xtal, run, auto): # for img in glob.glob(os.path.join(self.processedDir.replace('processed','jpegs'),xtal,run+'*t.png')): # for img in glob.glob(os.path.join(self.processedDir.replace('processed', 'jpegs'), run + '*t.png')): - self.Logfile.insert('%s: trying to copy crystal snapshots...' % xtal) + self.Logfile.insert("%s: trying to copy crystal snapshots..." % xtal) found = False if self.agamemnon: - proposal = self.visit.split('-')[0] - self.Logfile.insert('looking for images in '+os.path.join(self.processedDir.replace( - proposal, self.visit), 'jpegs', auto, self.target, xtal, run + '*.0.png')) - for img in glob.glob(os.path.join(self.processedDir.replace(proposal, self.visit), 'jpegs', auto, self.target, xtal, run + '*.0.png')): - if not os.path.isfile(os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run, img[img.rfind('/')+1:])): - self.Logfile.insert('%s: copying %s' % (xtal, img)) - os.system('/bin/cp %s %s' % (img, os.path.join(self.projectDir, - xtal, 'jpg', self.visit + '-' + auto+'_' + run))) + proposal = self.visit.split("-")[0] + self.Logfile.insert( + "looking for images in " + + os.path.join( + self.processedDir.replace(proposal, self.visit), + "jpegs", + auto, + self.target, + xtal, + run + "*.0.png", + ) + ) + for img in glob.glob( + os.path.join( + self.processedDir.replace(proposal, self.visit), + "jpegs", + auto, + self.target, + xtal, + run + "*.0.png", + ) + ): + if not os.path.isfile( + os.path.join( + self.projectDir, + xtal, + "jpg", + self.visit + "-" + run, + img[img.rfind("/") + 1 :], + ) + ): + self.Logfile.insert("%s: copying %s" % (xtal, img)) + os.system( + "/bin/cp %s %s" + % ( + img, + os.path.join( + self.projectDir, + xtal, + "jpg", + self.visit + "-" + auto + "_" + run, + ), + ) + ) else: - for img in glob.glob(os.path.join(self.processedDir.replace('processed', 'jpegs'), run + '*.0.png')): + for img in glob.glob( + os.path.join( + self.processedDir.replace("processed", "jpegs"), run + "*.0.png" + ) + ): found = True - if not os.path.isfile(os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run, img[img.rfind('/')+1:])): - self.Logfile.insert('%s: copying %s' % (xtal, img)) - os.system('/bin/cp %s %s' % (img, os.path.join(self.projectDir, - xtal, 'jpg', self.visit + '-' + run))) + if not os.path.isfile( + os.path.join( + self.projectDir, + xtal, + "jpg", + self.visit + "-" + run, + img[img.rfind("/") + 1 :], + ) + ): + self.Logfile.insert("%s: copying %s" % (xtal, img)) + os.system( + "/bin/cp %s %s" + % ( + img, + os.path.join( + self.projectDir, xtal, "jpg", self.visit + "-" + run + ), + ) + ) if not found: - for img in glob.glob(os.path.join(self.processedDir.replace('processed', 'jpegs'), xtal, run + '*.0.png')): - if not os.path.isfile(os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run, img[img.rfind('/') + 1:])): - self.Logfile.insert('%s: copying %s' % (xtal, img)) + for img in glob.glob( + os.path.join( + self.processedDir.replace("processed", "jpegs"), + xtal, + run + "*.0.png", + ) + ): + if not os.path.isfile( + os.path.join( + self.projectDir, + xtal, + "jpg", + self.visit + "-" + run, + img[img.rfind("/") + 1 :], + ) + ): + self.Logfile.insert("%s: copying %s" % (xtal, img)) os.system( - '/bin/cp %s %s' % (img, os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run))) + "/bin/cp %s %s" + % ( + img, + os.path.join( + self.projectDir, xtal, "jpg", self.visit + "-" + run + ), + ) + ) def findJPGs(self, xtal, run): jpgDict = {} -# for n,img in enumerate(glob.glob(os.path.join(self.projectDir,xtal,'jpg', self.visit +'-'+ run,'*t.png'))): - for n, img in enumerate(glob.glob(os.path.join(self.projectDir, xtal, 'jpg', self.visit + '-' + run, '*.0.png'))): + # for n,img in enumerate(glob.glob(os.path.join(self.projectDir,xtal,'jpg', self.visit +'-'+ run,'*t.png'))): + for n, img in enumerate( + glob.glob( + os.path.join( + self.projectDir, xtal, "jpg", self.visit + "-" + run, "*.0.png" + ) + ) + ): if n <= 3: - jpgDict['DataCollectionCrystalImage'+str(n+1)] = img + jpgDict["DataCollectionCrystalImage" + str(n + 1)] = img return jpgDict - def readProcessingUpdateResults(self, xtal, folder, log, mtz, timestamp, current_run, autoproc, proc_code): + def readProcessingUpdateResults( + self, xtal, folder, log, mtz, timestamp, current_run, autoproc, proc_code + ): db_dict = {} - self.Logfile.warning('%s: looking for %s' % - (xtal, os.path.join(folder, mtz))) + self.Logfile.warning("%s: looking for %s" % (xtal, os.path.join(folder, mtz))) for mtzfile in glob.glob(os.path.join(folder, mtz)): - self.Logfile.insert('%s: found %s' % (xtal, mtzfile)) - self.Logfile.warning('%s: looking for %s' % - (xtal, os.path.join(folder, log))) + self.Logfile.insert("%s: found %s" % (xtal, mtzfile)) + self.Logfile.warning( + "%s: looking for %s" % (xtal, os.path.join(folder, log)) + ) for logfile in glob.glob(os.path.join(folder, log)): - self.Logfile.insert('%s: found %s' % (xtal, logfile)) - self.createAutoprocessingDir( - xtal, current_run, autoproc, proc_code) + self.Logfile.insert("%s: found %s" % (xtal, logfile)) + self.createAutoprocessingDir(xtal, current_run, autoproc, proc_code) mtzNew, logNew = self.copyMTZandLOGfiles( - xtal, current_run, autoproc, mtzfile, logfile, proc_code) - if self.target == '=== project directory ===': - target = 'unknown' + xtal, current_run, autoproc, mtzfile, logfile, proc_code + ) + if self.target == "=== project directory ===": + target = "unknown" else: target = self.target - db_dict = {'DataCollectionDate': timestamp, - 'DataProcessingPathToLogfile': logNew, - 'DataProcessingPathToMTZfile': mtzNew, - 'DataProcessingDirectoryOriginal': folder, - # success in collection Table only means that a logfile was found - 'DataCollectionOutcome': 'success', - 'ProteinName': target} + db_dict = { + "DataCollectionDate": timestamp, + "DataProcessingPathToLogfile": logNew, + "DataProcessingPathToMTZfile": mtzNew, + "DataProcessingDirectoryOriginal": folder, + # success in collection Table only means that a logfile was found + "DataCollectionOutcome": "success", + "ProteinName": target, + } db_dict.update(parse().read_aimless_logfile(logNew)) # image exist even if data processing failed db_dict.update(self.findJPGs(xtal, current_run)) - db_dict['DataCollectionBeamline'] = self.beamline + db_dict["DataCollectionBeamline"] = self.beamline self.update_data_collection_table( - xtal, current_run, autoproc, db_dict, proc_code) -# return db_dict + xtal, current_run, autoproc, db_dict, proc_code + ) + + # return db_dict def getAutoProc(self, folder_rel, staraniso): - self.Logfile.insert('checking name of auto-processing pipeline...') + self.Logfile.insert("checking name of auto-processing pipeline...") folder = os.path.realpath(folder_rel) - self.Logfile.insert('folder: ' + folder) - autoproc = 'unknown' - if 'ap-run' in folder: - autoproc = 'autoPROC' + self.Logfile.insert("folder: " + folder) + autoproc = "unknown" + if "ap-run" in folder: + autoproc = "autoPROC" else: - for f in folder.split('/'): - if 'autoPROC' in f: + for f in folder.split("/"): + if "autoPROC" in f: autoproc = f + staraniso break - elif 'xia2' in f: + elif "xia2" in f: autoproc = f break - elif 'dials' in f: + elif "dials" in f: autoproc = f break - self.Logfile.insert('name of auto-processing pipeline: %s' % autoproc) + self.Logfile.insert("name of auto-processing pipeline: %s" % autoproc) return autoproc - def update_data_collection_table(self, xtal, current_run, autoproc, db_dict, proc_code): - condition_dict = {'CrystalName': xtal, - 'DataCollectionVisit': self.visit, - 'DataCollectionRun': current_run, - 'DataCollectionSubdir': proc_code, - 'DataProcessingProgram': autoproc} - self.db.update_insert_any_table( - 'collectionTable', db_dict, condition_dict) + def update_data_collection_table( + self, xtal, current_run, autoproc, db_dict, proc_code + ): + condition_dict = { + "CrystalName": xtal, + "DataCollectionVisit": self.visit, + "DataCollectionRun": current_run, + "DataCollectionSubdir": proc_code, + "DataProcessingProgram": autoproc, + } + self.db.update_insert_any_table("collectionTable", db_dict, condition_dict) def alreadyParsed(self, xtal, current_run, proc_code, autoproc): parsed = False - self.Logfile.insert( - 'checking if this processed directory was already parsed') + self.Logfile.insert("checking if this processed directory was already parsed") if xtal in self.exisitingSamples: - self.Logfile.insert(xtal + ' exists in collectionTable') - self.Logfile.insert('current identifier:') - self.Logfile.insert(self.visit + '-' + - current_run + autoproc + '-' + proc_code) - self.Logfile.insert('indentifier in collectionTable') + self.Logfile.insert(xtal + " exists in collectionTable") + self.Logfile.insert("current identifier:") + self.Logfile.insert( + self.visit + "-" + current_run + autoproc + "-" + proc_code + ) + self.Logfile.insert("indentifier in collectionTable") for x in self.exisitingSamples[xtal]: self.Logfile.insert(x) # visit-runautoproc-subdir - if self.visit + '-' + current_run + autoproc + '-' + proc_code in self.exisitingSamples[xtal]: + if ( + self.visit + "-" + current_run + autoproc + "-" + proc_code + in self.exisitingSamples[xtal] + ): self.Logfile.warning( - '%s: results from %s already parsed; skipping...' % ( - xtal, self.visit + '-' + current_run + autoproc)) + "%s: results from %s already parsed; skipping..." + % (xtal, self.visit + "-" + current_run + autoproc) + ) parsed = True return parsed def empty_folder(self, xtal, folder): empty = True stuff = [] - for x in glob.glob(os.path.join(folder, '*')): + for x in glob.glob(os.path.join(folder, "*")): stuff.append(x) if not stuff: self.Logfile.warning( - '{0!s}: {1!s} is empty; probably waiting for autoprocessing to finish; try later!'.format(xtal, folder)) + "{0!s}: {1!s} is empty; probably waiting for autoprocessing to finish; try later!".format( + xtal, folder + ) + ) else: empty = False return empty @@ -3054,123 +3845,144 @@ def junk(self, folder): do_not_parse = False if not os.path.isdir(folder): do_not_parse = True - elif 'dimple' in folder: + elif "dimple" in folder: do_not_parse = True return do_not_parse def parse_file_system(self): if self.agamemnon: - d = self.processedDir[:self.processedDir.rfind('/')] - t = self.processedDir[self.processedDir.rfind('/')+1:] - autoDir = os.path.join(d, 'auto', t) + d = self.processedDir[: self.processedDir.rfind("/")] + t = self.processedDir[self.processedDir.rfind("/") + 1 :] + autoDir = os.path.join(d, "auto", t) else: autoDir = self.processedDir - self.Logfile.insert( - 'checking for new data processing results in '+autoDir) + self.Logfile.insert("checking for new data processing results in " + autoDir) progress = 0 progress_step = XChemMain.getProgressSteps( - len(glob.glob(os.path.join(autoDir, '*')))) + len(glob.glob(os.path.join(autoDir, "*"))) + ) runList = [] -# for auto in autoDir: - self.Logfile.insert('--> ' + os.path.join(autoDir, '*')) - for nx, collected_xtals in enumerate(sorted(glob.glob(os.path.join(autoDir, '*')))): - self.Logfile.insert('%s: %s' % (nx, collected_xtals)) - self.visit = collected_xtals.split('/')[5] - if 'tmp' in collected_xtals or 'results' in collected_xtals or 'scre' in collected_xtals: + # for auto in autoDir: + self.Logfile.insert("--> " + os.path.join(autoDir, "*")) + for nx, collected_xtals in enumerate( + sorted(glob.glob(os.path.join(autoDir, "*"))) + ): + self.Logfile.insert("%s: %s" % (nx, collected_xtals)) + self.visit = collected_xtals.split("/")[5] + if ( + "tmp" in collected_xtals + or "results" in collected_xtals + or "scre" in collected_xtals + ): continue if not os.path.isdir(collected_xtals): continue -# for collected_xtals in sorted(glob.glob(os.path.join(self.processedDir,'*'))): + # for collected_xtals in sorted(glob.glob(os.path.join(self.processedDir,'*'))): # why is this here? self.visit is derived in init function through XChemMain.getVisitAndBeamline -# self.visit = collected_xtals.split('/')[5] - if 'tmp' in collected_xtals or 'results' in collected_xtals or 'scre' in collected_xtals: + # self.visit = collected_xtals.split('/')[5] + if ( + "tmp" in collected_xtals + or "results" in collected_xtals + or "scre" in collected_xtals + ): continue if not os.path.isdir(collected_xtals): - self.Logfile.warning(collected_xtals + ' is not a directory') + self.Logfile.warning(collected_xtals + " is not a directory") continue - xtal = collected_xtals[collected_xtals.rfind('/')+1:] -# if self.agamemnon: -# tmp = xtal[:xtal.rfind('_')] -# xtal = tmp[:tmp.rfind('_')] + xtal = collected_xtals[collected_xtals.rfind("/") + 1 :] + # if self.agamemnon: + # tmp = xtal[:xtal.rfind('_')] + # xtal = tmp[:tmp.rfind('_')] - self.Logfile.insert('%s: checking auto-processing results' % xtal) + self.Logfile.insert("%s: checking auto-processing results" % xtal) self.createSampleDir(xtal) - if self.target == '=== project directory ===': - runDir = os.path.join(collected_xtals, 'processed', '*') -# elif self.agamemnon: -# tmpDir = collected_xtals[:collected_xtals.rfind('/')] -# runDir = os.path.join(tmpDir,xtal+'_*_') + if self.target == "=== project directory ===": + runDir = os.path.join(collected_xtals, "processed", "*") + # elif self.agamemnon: + # tmpDir = collected_xtals[:collected_xtals.rfind('/')] + # runDir = os.path.join(tmpDir,xtal+'_*_') else: - runDir = os.path.join(collected_xtals, '*') - self.Logfile.insert('current runDir: ' + runDir) + runDir = os.path.join(collected_xtals, "*") + self.Logfile.insert("current runDir: " + runDir) for run in sorted(glob.glob(runDir)): - current_run = run[run.rfind('/')+1:] - for code in glob.glob(os.path.join(run, '*')): + current_run = run[run.rfind("/") + 1 :] + for code in glob.glob(os.path.join(run, "*")): if os.path.islink(code): continue -# else: -# proc_code = code[code.rfind('/')+1:] - proc_code = code.split('/')[len(code.split('/'))-1] - self.Logfile.insert( - xtal + ': processed directory -> ' + proc_code) - if current_run+proc_code in runList: + # else: + # proc_code = code[code.rfind('/')+1:] + proc_code = code.split("/")[len(code.split("/")) - 1] + self.Logfile.insert(xtal + ": processed directory -> " + proc_code) + if current_run + proc_code in runList: continue self.Logfile.insert( - '%s -> run: %s -> current run: %s -> %s' % (xtal, run, current_run, proc_code)) - timestamp = datetime.fromtimestamp( - os.path.getmtime(run)).strftime('%Y-%m-%d %H:%M:%S') + "%s -> run: %s -> current run: %s -> %s" + % (xtal, run, current_run, proc_code) + ) + timestamp = datetime.fromtimestamp(os.path.getmtime(run)).strftime( + "%Y-%m-%d %H:%M:%S" + ) # create directory for crystal aligment images in projectDir self.makeJPGdir(xtal, current_run) # 'non-auto' is irrelevant here - self.copyJPGs(xtal, current_run, 'non-auto') + self.copyJPGs(xtal, current_run, "non-auto") for item in self.toParse: procDir = os.path.join(code, item[0]) logfile = item[1] mtzfile = item[2] self.Logfile.insert( - '%s: search template: procDir - logfile - mtzfile' % xtal) - self.Logfile.insert( - '%s: procDir = %s' % (xtal, procDir)) - self.Logfile.insert( - '%s: logfile = %s' % (xtal, logfile)) - self.Logfile.insert( - '%s: mtzfile = %s' % (xtal, mtzfile)) + "%s: search template: procDir - logfile - mtzfile" % xtal + ) + self.Logfile.insert("%s: procDir = %s" % (xtal, procDir)) + self.Logfile.insert("%s: logfile = %s" % (xtal, logfile)) + self.Logfile.insert("%s: mtzfile = %s" % (xtal, mtzfile)) for folder in glob.glob(procDir): - staraniso = '' - self.Logfile.insert( - '%s: searching %s' % (xtal, folder)) + staraniso = "" + self.Logfile.insert("%s: searching %s" % (xtal, folder)) if self.junk(folder): continue if self.empty_folder(xtal, folder): continue - if 'staraniso' in logfile or 'summary.tar.gz' in logfile: - staraniso = '_staraniso' + if "staraniso" in logfile or "summary.tar.gz" in logfile: + staraniso = "_staraniso" autoproc = self.getAutoProc(folder, staraniso) - if self.alreadyParsed(xtal, current_run, proc_code, autoproc): + if self.alreadyParsed( + xtal, current_run, proc_code, autoproc + ): continue self.readProcessingUpdateResults( - xtal, folder, logfile, mtzfile, timestamp, current_run, autoproc, proc_code) - runList.append(current_run+proc_code) - -# quit() + xtal, + folder, + logfile, + mtzfile, + timestamp, + current_run, + autoproc, + proc_code, + ) + runList.append(current_run + proc_code) + + # quit() progress += progress_step - self.emit(QtCore.SIGNAL('update_status_bar(QString)'), - 'parsing auto-processing results for '+xtal) - self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - - self.Logfile.insert( - '====== finished parsing beamline directory ======') - self.emit(QtCore.SIGNAL('read_pinIDs_from_gda_logs')) + self.emit( + QtCore.SIGNAL("update_status_bar(QString)"), + "parsing auto-processing results for " + xtal, + ) + self.emit(QtCore.SIGNAL("update_progress_bar"), progress) + + self.Logfile.insert("====== finished parsing beamline directory ======") + self.emit(QtCore.SIGNAL("read_pinIDs_from_gda_logs")) self.emit(QtCore.SIGNAL("finished()")) + # def parse_agamemnon_file_system(self): # self.Logfile.insert('checking for new data processing results in '+self.processedDir) # progress = 0 diff --git a/lib/XChemToolTips.py b/lib/XChemToolTips.py index ed388045..c31f7318 100755 --- a/lib/XChemToolTips.py +++ b/lib/XChemToolTips.py @@ -5,111 +5,111 @@ def dataset_task_tip(): - tip = ('describes what you can do') + tip = "describes what you can do" return tip def dataset_task_run_button_tip(): - tip = ('Run dataset') + tip = "Run dataset" return tip def dataset_task_status_button_tip(): - tip = ('Status dataset') + tip = "Status dataset" return tip def map_cif_file_task_tip(): - tip = ('describes what you can do') + tip = "describes what you can do" return tip def map_cif_file_task_run_button_tip(): - tip = ('Run map_cif_file') + tip = "Run map_cif_file" return tip def map_cif_file_task_status_button_tip(): - tip = ('Status map_cif_file') + tip = "Status map_cif_file" return tip def panddas_file_task_tip(): - tip = ('describes what you can do') + tip = "describes what you can do" return tip def panddas_file_task_run_button_tip(): - tip = ('Run panddas_file') + tip = "Run panddas_file" return tip def panddas_file_task_status_button_tip(): - tip = ('Status panddas_file') + tip = "Status panddas_file" return tip def refine_file_task_tip(): - tip = ('describes what you can do') + tip = "describes what you can do" return tip def refine_file_task_run_button_tip(): - tip = ('Run refine_file') + tip = "Run refine_file" return tip def refine_file_task_status_button_tip(): - tip = ('Status refine_file') + tip = "Status refine_file" return tip def validation_file_task_tip(): - tip = ('describes what you can do') + tip = "describes what you can do" return tip def validation_file_task_run_button_tip(): - tip = ('Run validation_file') + tip = "Run validation_file" return tip def validation_file_task_status_button_tip(): - tip = ('Status validation_file') + tip = "Status validation_file" return tip def update_from_datasource_button_tip(): - tip = ('Status validation_file') + tip = "Status validation_file" return tip def load_samples_from_datasource(): - tip = ('loads all information\n' - 'which is currently in the\n' - 'data source') + tip = "loads all information\n" "which is currently in the\n" "data source" return tip def save_samples_to_datasource(): - tip = ('saves all changes you made\n' - 'to any of the cells to the\n' - 'data source') + tip = "saves all changes you made\n" "to any of the cells to the\n" "data source" return tip def create_pdb_cif_png_files(): - tip = ('uses ACEDRG to create pdb,cif and png files for all compounds\n' - 'that have a smiles string assigned. The compounds ID\n' - 'serves as name if available.\n' - 'The files are written to initial_model//compound\n' - 'data source') + tip = ( + "uses ACEDRG to create pdb,cif and png files for all compounds\n" + "that have a smiles string assigned. The compounds ID\n" + "serves as name if available.\n" + "The files are written to initial_model//compound\n" + "data source" + ) return tip def check_status_create_pdb_cif_png_files(): - tip = ('the jobs are sent to a computer cluster if available\n' - 'gives you an overview about how it progresses') + tip = ( + "the jobs are sent to a computer cluster if available\n" + "gives you an overview about how it progresses" + ) return tip @@ -141,173 +141,196 @@ def run_pandda_inspect_at_home(pandda_directory): # ' qstat\n\n' # ' 8. At DLS: go to the REFINEMENT tab and run "Open COOT" to review and further refine your models if necessary\n' ) - instruction = ('\n\n' - 'Be sure to have pandda installed at home, and go to a clean subdirectory.\n' - 'From that directory, do the steps below.\n' - 'This moves the relevant files to your site so you can do the model building locally, and then moves the files back to Diamond.\n' - '1. run: rsync -av %s@nx.diamond.ac.uk:%s .\n' % (getpass.getuser(), pandda_directory) + - '2. run: "pandda.inspect", and build all relevant models, etc.\n' - '3. run: rsync -av * %s@nx.diamond.ac.uk:%s\n' % (getpass.getuser(), pandda_directory) + - 'Now proceed within XChemExplorer as before.\n') + instruction = ( + "\n\n" + "Be sure to have pandda installed at home, and go to a clean subdirectory.\n" + "From that directory, do the steps below.\n" + "This moves the relevant files to your site so you can do the model building locally, and then moves the files back to Diamond.\n" + "1. run: rsync -av %s@nx.diamond.ac.uk:%s .\n" + % (getpass.getuser(), pandda_directory) + + '2. run: "pandda.inspect", and build all relevant models, etc.\n' + "3. run: rsync -av * %s@nx.diamond.ac.uk:%s\n" + % (getpass.getuser(), pandda_directory) + + "Now proceed within XChemExplorer as before.\n" + ) print(instruction) def deposition_interface_note(): - note = ('\n\n' - 'Note: you can use this mask to save identical information for ALL structures to be deposited.\n' - 'However, this may not be suitable in cases where the information is different for certain samples.\n' - 'In such cases, please use for example SQLiteBrowser to edit the relevant fields in the depositTable.') + note = ( + "\n\n" + "Note: you can use this mask to save identical information for ALL structures to be deposited.\n" + "However, this may not be suitable in cases where the information is different for certain samples.\n" + "In such cases, please use for example SQLiteBrowser to edit the relevant fields in the depositTable." + ) return note def html_summary_introduction(): - text = ('This section describes how to generate an HTML summary page of the current project. \n' - 'All you need to do is select the HTML output directory where the html and additional auxiliary files \n' - 'and will be written to. ' - 'Then press the "Export to HTML" button and \nall bound structures that are labeled as "4 - compchem ready"' - 'or higher will be included in the final document. \n' - 'Please checkout https://www.thesgc.org/fragment-screening to see what the final pages look like. ') + text = ( + "This section describes how to generate an HTML summary page of the current project. \n" + "All you need to do is select the HTML output directory where the html and additional auxiliary files \n" + "and will be written to. " + 'Then press the "Export to HTML" button and \nall bound structures that are labeled as "4 - compchem ready"' + "or higher will be included in the final document. \n" + "Please checkout https://www.thesgc.org/fragment-screening to see what the final pages look like. " + ) return text def html_export_directory_background(): - text = ('The HTML export directory will contain all files necessary to generate the summary file.\n' - 'It is also makes it easy to share the results with collaborators.') + text = ( + "The HTML export directory will contain all files necessary to generate the summary file.\n" + "It is also makes it easy to share the results with collaborators." + ) return text def html_export_step(): - text = ('This step will create an index.html file and it will copy pdb, mtz and cif files\n' - 'as well as PanDDA event maps into the html export directory.') + text = ( + "This step will create an index.html file and it will copy pdb, mtz and cif files\n" + "as well as PanDDA event maps into the html export directory." + ) return text def icb_file_background(): - text = ('This step will use ICM-pro to create interactive structure thumbnails in the html file (http://www.molsoft.com/activeicmjs.html)') + text = "This step will use ICM-pro to create interactive structure thumbnails in the html file (http://www.molsoft.com/activeicmjs.html)" return text def prepare_ICB_files(): - instruction = ('- Open file browser and navigate to HTML export directory.\n' - '- Open ICM (at DLS: select SERVER and enter diamvicmpro.diamond.ac.uk in case ICM asks).\n' - '- Drag-and-drop dsEvent_sqlite.icm file into ICM main window.\n' - '- In ICM workspace panel: right-click on dsEvent_sqlite.icm and select "RUN".') + instruction = ( + "- Open file browser and navigate to HTML export directory.\n" + "- Open ICM (at DLS: select SERVER and enter diamvicmpro.diamond.ac.uk in case ICM asks).\n" + "- Drag-and-drop dsEvent_sqlite.icm file into ICM main window.\n" + '- In ICM workspace panel: right-click on dsEvent_sqlite.icm and select "RUN".' + ) return instruction def zenodo_upload_start(html_export_directory): - instruction = ('This will copy all files required for ZENODO upload to\n' - '%s' % os.path.join(html_export_directory, 'zenodo')) + instruction = ( + "This will copy all files required for ZENODO upload to\n" + "%s" % os.path.join(html_export_directory, "zenodo") + ) return instruction def zenodo_upload_part_one(html_export_directory): - instruction = ('- Register with ZENODO (www.zenodo.org)\n' - '- Select Upload -> New Upload\n' - '- upload all files from %s/zenodo, BUT NOT any of the .html files!!!' % html_export_directory) + instruction = ( + "- Register with ZENODO (www.zenodo.org)\n" + "- Select Upload -> New Upload\n" + "- upload all files from %s/zenodo, BUT NOT any of the .html files!!!" + % html_export_directory + ) return instruction def zenodo_upload_part_two(): - instruction = ( - 'You might have noticed that once you started uploading files, the address bar in your browser will change to something like this:') + instruction = "You might have noticed that once you started uploading files, the address bar in your browser will change to something like this:" return instruction def zenodo_upload_part_three(): - instruction = ( - 'Please enter the upload ID, i.e. the number at the end of the line, into the field below') + instruction = "Please enter the upload ID, i.e. the number at the end of the line, into the field below" return instruction def zenodo_upload_part_four(html_export_directory): - instruction = ('Upload ALL html files in {0!s} to ZENODO and publish the page.'.format( - os.path.join(html_export_directory, 'zenodo'))) + instruction = ( + "Upload ALL html files in {0!s} to ZENODO and publish the page.".format( + os.path.join(html_export_directory, "zenodo") + ) + ) return instruction def deposition_pandda_site_not_ready(xtal): - msg = ('Please make sure that all placed ligands in '+xtal+' are ready for deposition.\n' - 'Go to the Refinement tab -> Open COOT and either delete the ligand or set the site ' - ' to "5 - Deposition ready"') + msg = ( + "Please make sure that all placed ligands in " + + xtal + + " are ready for deposition.\n" + "Go to the Refinement tab -> Open COOT and either delete the ligand or set the site " + ' to "5 - Deposition ready"' + ) return msg def pandda_pre_run(reference_directory): - msg = ('The aim of the pre-run is NOT to identify bound ligands,\n' - 'but to create mean ground state maps.\n' - 'Hence, the pre-run will only comprise 100 datasets.\n' - 'After the pre-run is finished use the resulting ground state mean maps\n' - 'to build a suitable reference model for the subsequent PanDDA production run.\n' - 'The appendix will determine the name of the folder where the results from\n' - 'the pre-run will be stored. It is used by the COOT plugin to distinguish\n' - 'between different pre-runs.\n' - 'The result from the pre-run will be stored in:\n' - '%s/pannda_'https://openlabnotebooks.org/update-on-batch-deposition-of-xchem-structures'" - ) + lnk = "'https://openlabnotebooks.org/update-on-batch-deposition-of-xchem-structures'" return lnk def deposition_bound_state_prerequisites(): msg = ( - '1. Event map to MTZ conversion.\n' - ' All pandda event maps need to be converted to MTZ format. This is currently not done automatically.\n' + "1. Event map to MTZ conversion.\n" + " All pandda event maps need to be converted to MTZ format. This is currently not done automatically.\n" ' If you have not done so, select and run "Event Map -> SF" from the Hit Identification action box.\n' - ' This may take a while, but you only need to run this once.\n' - '2. Select datasets to be deposited.\n' + " This may take a while, but you only need to run this once.\n" + "2. Select datasets to be deposited.\n" ' Set crystals to "5-ready for deposition" in XCE refinement tab\n' - '3. Enter additional data required for PDB deposition.\n' + "3. Enter additional data required for PDB deposition.\n" ' In the Deposition menu, select "Edit information". Fill out all the required items and press "Save to Database".\n' - ' Note: this needs to be done after the datasets have been selected for deposition.' + " Note: this needs to be done after the datasets have been selected for deposition." ) return msg def deposition_bound_state_preparation_step_one_text(): msg = ( - '1. Press the button below to generate structure and structure factor mmcif files of all selected datasets.\n' - ' Note: all previously generated mmcif files will be overwritten.' + "1. Press the button below to generate structure and structure factor mmcif files of all selected datasets.\n" + " Note: all previously generated mmcif files will be overwritten." ) return msg @@ -315,91 +338,82 @@ def deposition_bound_state_preparation_step_one_text(): def deposition_bound_state_preparation_step_two_text(): msg = ( '2. Press the button below to copy all the mmcif files into the "group deposition directory" (see settings tab).\n' - 'All mmcif files will be bundled into a single, bzipped tar archive which can be uploaded into via the PDB group deposition website.' + "All mmcif files will be bundled into a single, bzipped tar archive which can be uploaded into via the PDB group deposition website." ) return msg def pdb_group_deposition_instruction_one(): - msg = ( - '3. Go to the group deposition website, create a session and upload the ligand-bound.tar.bz2 file from the group deposition directory.' - ) + msg = "3. Go to the group deposition website, create a session and upload the ligand-bound.tar.bz2 file from the group deposition directory." return msg def pdb_group_deposition_link(): - lnk = ( - "'https://deposit-group-1.rcsb.rutgers.edu/groupdeposit'" - ) + lnk = "'https://deposit-group-1.rcsb.rutgers.edu/groupdeposit'" return lnk def pdb_group_deposition_instruction_two(): - msg = ( - ' user: grouptester\n' - ' password: !2016rcsbpdb ' - ) + msg = " user: grouptester\n" " password: !2016rcsbpdb " return msg def deposition_ground_state_prerequisites(): msg = ( - '1. Convert all apo MTZ files to mmcif format.\n' - ' Swtich to the pandda tab, select the PanDDA directory which contains the analysis you want to deposit.\n' + "1. Convert all apo MTZ files to mmcif format.\n" + " Swtich to the pandda tab, select the PanDDA directory which contains the analysis you want to deposit.\n" ' Then select and run "apo -> mmcif" from the Hit Identification action box.\n' - ' Note: you only need to do this once.' + " Note: you only need to do this once." ) return msg def deposition_ground_state_preparation_step_one_text(): msg = ( - '1. Select ground-state PDB file.\n' - ' Note: the file is usually in the reference directory.' + "1. Select ground-state PDB file.\n" + " Note: the file is usually in the reference directory." ) return msg def deposition_ground_state_log_info(): msg = ( - ' IMPORTANT:\n' - ' Make sure that a file or symlink to an AIMLESS logile with the same name root as your ground-state PDB file\n' - ' is present in the same folder. This is currently not generated automatically! ' + " IMPORTANT:\n" + " Make sure that a file or symlink to an AIMLESS logile with the same name root as your ground-state PDB file\n" + " is present in the same folder. This is currently not generated automatically! " ) return msg def deposition_ground_state_preparation_step_two_text(): msg = ( - '2. Select ground-state MTZ file.\n' - ' Notes: - this is the MTZ file of the ground-state mean map\n' - ' - the file should have been created after the pandda pre-run\n' - ' - hence, you will usually find it in the reference directory' + "2. Select ground-state MTZ file.\n" + " Notes: - this is the MTZ file of the ground-state mean map\n" + " - the file should have been created after the pandda pre-run\n" + " - hence, you will usually find it in the reference directory" ) return msg def deposition_ground_state_preparation_step_three_text(): msg = ( - '1. Please check the settings tab that you have selected the correct pandda directory.\n' - ' (Note: we will take all the apo mmcif files from this directory)\n' - ' Current PanDDA directory:' + "1. Please check the settings tab that you have selected the correct pandda directory.\n" + " (Note: we will take all the apo mmcif files from this directory)\n" + " Current PanDDA directory:" ) return msg def deposition_ground_state_preparation_step_four_text(): - msg = ( - '2. Add the ground-state entry to the database.' - ) + msg = "2. Add the ground-state entry to the database." return msg def deposition_ground_state_preparation_step_five_text(): msg = ( - '3. Enter meta-data for ground-state model:\n' + "3. Enter meta-data for ground-state model:\n" ' - Open "Deposition -> Edit information"\n' - ' - Fill out form or load .deposit file\n' + " - Fill out form or load .deposit file\n" ' - Press "Save to Database"\n' ' - Press "OK"' ) @@ -408,8 +422,8 @@ def deposition_ground_state_preparation_step_five_text(): def deposition_ground_state_preparation_step_six_text(): msg = ( - '4. Prepare the ground-state mmcif file.\n' - ' Note: the mmcif files are saved into the selected pandda directory' + "4. Prepare the ground-state mmcif file.\n" + " Note: the mmcif files are saved into the selected pandda directory" ) return msg @@ -417,21 +431,19 @@ def deposition_ground_state_preparation_step_six_text(): def deposition_ground_state_preparation_step_seven_text(): msg = ( '5. Press the button below to copy the structire and structure factor mmcif files into the "group deposition directory" (see settings tab).\n' - 'Both mmcif files will be bundled into a single, bzipped tar archive which can be uploaded into via the PDB group deposition website.' + "Both mmcif files will be bundled into a single, bzipped tar archive which can be uploaded into via the PDB group deposition website." ) return msg def deposition_ground_state_preparation_step_eight_text(): - msg = ( - '6. Go to the group deposition website, create a session and upload the ligand-bound.tar.bz2 file from the group deposition directory.' - ) + msg = "6. Go to the group deposition website, create a session and upload the ligand-bound.tar.bz2 file from the group deposition directory." return msg def after_deposition_step_one_text(): msg = ( - 'After you have successfully submitted the ligand-bound structures via the PDB group deposition interface, you will immediately get\n' + "After you have successfully submitted the ligand-bound structures via the PDB group deposition interface, you will immediately get\n" 'an email with the PDB codes. There will be a single line for each PDB submission. Highlight and copy the text! Then go to the "Deposition" menu\n' 'and select "Update DB with PDB codes". A pop-up window will appear, paste the text into the window and press "Update Database".' ) @@ -439,9 +451,7 @@ def after_deposition_step_one_text(): def deposition_bounnd_state_preparation_ignore_event_map(): - msg = ( - 'do NOT include PanDDA event maps (ONLY USE IN CASE IF DATA WERE NOT ANALYSED WITH PANDDA!)' - ) + msg = "do NOT include PanDDA event maps (ONLY USE IN CASE IF DATA WERE NOT ANALYSED WITH PANDDA!)" return msg @@ -449,61 +459,55 @@ def second_cif_file_info(cif_file): second_cif_file = str(cif_file) if os.path.isfile(second_cif_file): msg = ( - 'You have selected the following restraints file\n' - 'for merging into the the ligand CIF files:\n' - + second_cif_file + - '\n' - 'Press NO in case you do not want to continue\n' - 'In case you want to use another file, open the preferences menu and set it there\n' - 'Please check the XCE logfile in case of unexpected behaviour' - ) - elif second_cif_file.replace(' ', '') == '' or second_cif_file.lower() == 'none': - msg = ( - 'No restraints file was selected!' + "You have selected the following restraints file\n" + "for merging into the the ligand CIF files:\n" + second_cif_file + "\n" + "Press NO in case you do not want to continue\n" + "In case you want to use another file, open the preferences menu and set it there\n" + "Please check the XCE logfile in case of unexpected behaviour" ) + elif second_cif_file.replace(" ", "") == "" or second_cif_file.lower() == "none": + msg = "No restraints file was selected!" else: msg = ( - 'The selected restraints file does not exist:\n' - + second_cif_file + - '\n' - 'Open the preferences menu and set it there\n' + "The selected restraints file does not exist:\n" + second_cif_file + "\n" + "Open the preferences menu and set it there\n" ) return msg def second_cif_file_not_exists(): msg = ( - 'The CIF file for the non-standard ligand does not exist! ' - 'It was either not selected or the file was deleted/ moved in the meantime. ' - 'Please check Menu -> Preferences.' + "The CIF file for the non-standard ligand does not exist! " + "It was either not selected or the file was deleted/ moved in the meantime. " + "Please check Menu -> Preferences." ) return msg def notification_about_changes_to_apo_deposition(): msg = ( - 'The ground-state deposition procedure has changes in XCE v1.5.0!\n\n' - 'Previously, users had to select a specific reference PDB file, which had to have a ground-state mean-map and logfile associated with it.\n' - 'However, there were two main problems: (i) the map to mtz conversion did sometimes lead to strange maps or maps in space group P1 only\n' - 'and (2) occasionally the resulting MTZ files had missing columns. This lead to errors and delays during deposition, while inclusion of\n' - 'ground-state mean maps has little benefit since the mean map can be calculated with the deposited apo datasets. Hence, there is really\n' - 'no need to include it in the deposition.\n\n' - 'All you need to do is to select the relevant PanDDA directory and XCE will arbitrarily select a high resolution structure with low Rfree\n' - 'as the model for the deposition bundle and then put all structure factor MMCIF files into a single file. Note that it does not matter\n' - 'which PDB file gets chosen at this point since the positional modifications during refinement with REFMAC will be minimal.\n' - 'If you still want to make the ground-state mean map available, we would recommend to deposit ground-state mean map and \n' - 'everything else you think is relevant on ZENODO and ask the PDB annotator to include the respective DOI in the deposition\n' + "The ground-state deposition procedure has changes in XCE v1.5.0!\n\n" + "Previously, users had to select a specific reference PDB file, which had to have a ground-state mean-map and logfile associated with it.\n" + "However, there were two main problems: (i) the map to mtz conversion did sometimes lead to strange maps or maps in space group P1 only\n" + "and (2) occasionally the resulting MTZ files had missing columns. This lead to errors and delays during deposition, while inclusion of\n" + "ground-state mean maps has little benefit since the mean map can be calculated with the deposited apo datasets. Hence, there is really\n" + "no need to include it in the deposition.\n\n" + "All you need to do is to select the relevant PanDDA directory and XCE will arbitrarily select a high resolution structure with low Rfree\n" + "as the model for the deposition bundle and then put all structure factor MMCIF files into a single file. Note that it does not matter\n" + "which PDB file gets chosen at this point since the positional modifications during refinement with REFMAC will be minimal.\n" + "If you still want to make the ground-state mean map available, we would recommend to deposit ground-state mean map and \n" + "everything else you think is relevant on ZENODO and ask the PDB annotator to include the respective DOI in the deposition\n" ) return msg def pandda_export_ligand_bound_models_only_disclaimer(): msg = ( - 'You have chosen to export and refine the ligand-bound model only. ' - 'This is different to the original procedure described by Pearce et al. (doi 10.1107/S2059798317003412), ' - 'which is based on refinement of an ensemble model consisting of ligand-bound state and confounding ground-state.' - 'Please note that working with the ligand-bound model only usually works well for reasonably well-defined ' - 'ligands and conformational changes, but it may not be ideal for weakly bound fragments and corresponding ' - 'conformational changes.' + "You have chosen to export and refine the ligand-bound model only. " + "This is different to the original procedure described by Pearce et al. (doi 10.1107/S2059798317003412), " + "which is based on refinement of an ensemble model consisting of ligand-bound state and confounding ground-state." + "Please note that working with the ligand-bound model only usually works well for reasonably well-defined " + "ligands and conformational changes, but it may not be ideal for weakly bound fragments and corresponding " + "conformational changes." ) return msg diff --git a/lib/XChemUtils.py b/lib/XChemUtils.py index 31f72516..7ea28363 100755 --- a/lib/XChemUtils.py +++ b/lib/XChemUtils.py @@ -28,7 +28,7 @@ from iotbx.reflection_file_reader import any_reflection_file from iotbx import mtz -sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") def open_decompress_file(filename, mode="rb"): @@ -44,105 +44,118 @@ def open_decompress_file(filename, mode="rb"): class process: - def __init__(self, dimple): - self.project_directory = dimple['project_directory'] - self.delete_old = dimple['delete_old'] - self.xtalID = dimple['xtalID'] - self.reference = dimple['reference'] - self.queueing_system_available = dimple['queueing_system_available'] - self.ccp4_scratch_directory = dimple['ccp4_scratch'] - self.fileroot_in = dimple['fileroot_in'] - self.mtz_free = self.fileroot_in+'.free.mtz' - self.mtz_in = self.fileroot_in+'.mtz' + self.project_directory = dimple["project_directory"] + self.delete_old = dimple["delete_old"] + self.xtalID = dimple["xtalID"] + self.reference = dimple["reference"] + self.queueing_system_available = dimple["queueing_system_available"] + self.ccp4_scratch_directory = dimple["ccp4_scratch"] + self.fileroot_in = dimple["fileroot_in"] + self.mtz_free = self.fileroot_in + ".free.mtz" + self.mtz_in = self.fileroot_in + ".mtz" # need to set $CCP4_SCR, because the default directory in /home/zqr16691/tmp fills up easily # and then dimple will not run -# if not os.path.isdir(self.project_directory[:self.project_directory.find('processing')+11]+'/tmp'): -# os.mkdir(self.project_directory[:self.project_directory.find('processing')+11]+'/tmp') -# self.ccp4_scratch=self.project_directory[:self.project_directory.find('processing')+11]+'/tmp' + + # if not os.path.isdir(self.project_directory[:self.project_directory.find('processing')+11]+'/tmp'): + # os.mkdir(self.project_directory[:self.project_directory.find('processing')+11]+'/tmp') + # self.ccp4_scratch=self.project_directory[:self.project_directory.find('processing')+11]+'/tmp' def get_Rfree(self): - Cmds = '' - if not os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.mtz_free)): - if os.path.isfile(os.path.join(self.project_directory, self.xtalID, self.reference+'.mtz')): + Cmds = "" + if not os.path.isfile( + os.path.join(self.project_directory, self.xtalID, self.mtz_free) + ): + if os.path.isfile( + os.path.join( + self.project_directory, self.xtalID, self.reference + ".mtz" + ) + ): Cmds = ( # '#!'+os.getenv('SHELL')+'\n' - '\n' - 'cd %s/%s/Dimple\n' % (self.project_directory, self.xtalID) + - '\n' - 'pointless hklin ../%s hklref %s.mtz hklout %s.reind.mtz << EOF > pointless.log\n' % (self.mtz_in, self.reference, self.xtalID) + - ' tolerance 5\n' - 'EOF\n' - '\n' - 'cad hklin1 %s.reind.mtz hklin2 %s.mtz hklout cad.mtz << EOF > cad.log\n' % (self.xtalID, self.reference) + - ' labin file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n' - ' labout file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n' - ' labin file_number 2 E1=FreeR_flag\n' - ' labout file_number 2 E1=FreeR_flag\n' - ' END\n' - 'EOF\n' - '\n' - 'freerflag hklin cad.mtz hklout ../%s << EOF > freerflag.log\n' % self.mtz_free + - ' COMPLETE FREE=FreeR_flag\n' - ' END\n' - 'EOF\n' - '#uniqueify -f FreeR_flag cad.mtz ../%s\n' % self.mtz_free + "\n" + "cd %s/%s/Dimple\n" % (self.project_directory, self.xtalID) + "\n" + "pointless hklin ../%s hklref %s.mtz hklout %s.reind.mtz << EOF > pointless.log\n" + % (self.mtz_in, self.reference, self.xtalID) + + " tolerance 5\n" + "EOF\n" + "\n" + "cad hklin1 %s.reind.mtz hklin2 %s.mtz hklout cad.mtz << EOF > cad.log\n" + % (self.xtalID, self.reference) + + " labin file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" + " labout file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" + " labin file_number 2 E1=FreeR_flag\n" + " labout file_number 2 E1=FreeR_flag\n" + " END\n" + "EOF\n" + "\n" + "freerflag hklin cad.mtz hklout ../%s << EOF > freerflag.log\n" + % self.mtz_free + + " COMPLETE FREE=FreeR_flag\n" + " END\n" + "EOF\n" + "#uniqueify -f FreeR_flag cad.mtz ../%s\n" % self.mtz_free ) else: Cmds = ( # '#!'+os.getenv('SHELL')+'\n' - '\n' - 'cd %s/%s/Dimple\n' % (self.project_directory, self.xtalID) + - '\n' - 'pointless hklin ../%s xyzin %s.pdb hklout %s.reind.mtz << EOF > pointless.log\n' % (self.mtz_in, self.reference, self.xtalID) + - ' tolerance 5\n' - 'EOF\n' - '\n' - 'cad hklin1 %s.reind.mtz hklout cad.mtz << EOF > cad.log\n' % self.xtalID + - ' labin file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n' - ' labout file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n' - ' END\n' - 'EOF\n' - '\n' - 'freerflag hklin cad.mtz hklout ../%s > freerflag.log\n' % self.mtz_free + - '#uniqueify cad.mtz ../{0!s}\n'.format(self.mtz_free) + "\n" + "cd %s/%s/Dimple\n" % (self.project_directory, self.xtalID) + "\n" + "pointless hklin ../%s xyzin %s.pdb hklout %s.reind.mtz << EOF > pointless.log\n" + % (self.mtz_in, self.reference, self.xtalID) + + " tolerance 5\n" + "EOF\n" + "\n" + "cad hklin1 %s.reind.mtz hklout cad.mtz << EOF > cad.log\n" + % self.xtalID + + " labin file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" + " labout file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" + " END\n" + "EOF\n" + "\n" + "freerflag hklin cad.mtz hklout ../%s > freerflag.log\n" + % self.mtz_free + + "#uniqueify cad.mtz ../{0!s}\n".format(self.mtz_free) ) -# os.chdir(os.path.join(self.project_directory,self.xtalID)) -# os.system(Cmds) -# os.symlink(os.path.join('Dimple',self.xtalID+'.free.mtz'),self.xtalID+'.free.mtz') + # os.chdir(os.path.join(self.project_directory,self.xtalID)) + # os.system(Cmds) + # os.symlink(os.path.join('Dimple',self.xtalID+'.free.mtz'),self.xtalID+'.free.mtz') return Cmds def dimple(self): - os.chdir('{0!s}/{1!s}'.format(self.project_directory, self.xtalID)) - generate_Rfree_Cmds = '' - if os.path.isdir('{0!s}/{1!s}/Dimple'.format(self.project_directory, self.xtalID)): + os.chdir("{0!s}/{1!s}".format(self.project_directory, self.xtalID)) + generate_Rfree_Cmds = "" + if os.path.isdir( + "{0!s}/{1!s}/Dimple".format(self.project_directory, self.xtalID) + ): # this 'if not' step is usually not necessary; only if process was stopped in an odd way - if not os.path.isfile(self.project_directory+'/'+self.xtalID+'/'+self.mtz_free): + if not os.path.isfile( + self.project_directory + "/" + self.xtalID + "/" + self.mtz_free + ): generate_Rfree_Cmds = self.get_Rfree() if self.delete_old: - os.system('rm -fr Dimple') + os.system("rm -fr Dimple") os.mkdir( - '{0!s}/{1!s}/Dimple'.format(self.project_directory, self.xtalID)) + "{0!s}/{1!s}/Dimple".format(self.project_directory, self.xtalID) + ) else: return None else: - os.mkdir( - '{0!s}/{1!s}/Dimple'.format(self.project_directory, self.xtalID)) + os.mkdir("{0!s}/{1!s}/Dimple".format(self.project_directory, self.xtalID)) generate_Rfree_Cmds = self.get_Rfree() - os.chdir( - '{0!s}/{1!s}/Dimple'.format(self.project_directory, self.xtalID)) + os.chdir("{0!s}/{1!s}/Dimple".format(self.project_directory, self.xtalID)) if self.queueing_system_available: - top_line = '#PBS -joe -N XCE_dimple' + top_line = "#PBS -joe -N XCE_dimple" else: - top_line = '#!'+os.getenv('SHELL') + top_line = "#!" + os.getenv("SHELL") - if 'csh' in os.getenv('SHELL'): - ccp4_scratch = 'setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' - elif 'bash' in os.getenv('SHELL'): - ccp4_scratch = 'export CCP4_SCR='+self.ccp4_scratch_directory+'\n' + if "csh" in os.getenv("SHELL"): + ccp4_scratch = "setenv CCP4_SCR " + self.ccp4_scratch_directory + "\n" + elif "bash" in os.getenv("SHELL"): + ccp4_scratch = "export CCP4_SCR=" + self.ccp4_scratch_directory + "\n" else: - ccp4_scratch = '' + ccp4_scratch = "" ################################################################################ # in case additional ligands are present in the reference.pdb file, @@ -150,65 +163,61 @@ def dimple(self): # - .pdb # - .cif # this file contains restraints for all the ligands in the respective pdb file - if os.path.isfile(self.reference+'.cif'): - ref_lib = ' --libin '+self.reference+'.cif' + if os.path.isfile(self.reference + ".cif"): + ref_lib = " --libin " + self.reference + ".cif" else: - ref_lib = '' + ref_lib = "" Cmds = ( - '{0!s}\n'.format(top_line) + - generate_Rfree_Cmds + - '\n' - 'cd %s/%s/Dimple\n' % (self.project_directory, self.xtalID) + - '\n' - + ccp4_scratch + - '\n' - 'dimple %s ../%s %s.pdb dimple' % (ref_lib, self.mtz_free, self.reference) + - '\n' - 'cd %s/%s\n' % (self.project_directory, self.xtalID) + - '\n' - '/bin/rm refine.pdb\n' - '/bin/rm refine.mtz\n' - 'ln -s Dimple/dimple/final.pdb refine.pdb\n' - 'ln -s Dimple/dimple/final.mtz refine.mtz\n' - '\n' - 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' - ' labin F1=2FOFCWT PHI=PH2FOFCWT\n' - 'EOF\n' - '\n' - 'fft hklin refine.mtz mapout fofc.map << EOF\n' - ' labin F1=FOFCWT PHI=PHFOFCWT\n' - 'EOF\n' - '\n' - 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' - ' labin F1=FWT PHI=PHWT\n' - 'EOF\n' - '\n' - 'fft hklin refine.mtz mapout fofc.map << EOF\n' - ' labin F1=DELFWT PHI=PHDELWT\n' - 'EOF\n' - '\n' - '/bin/rm dimple_run_in_progress\n' + "{0!s}\n".format(top_line) + generate_Rfree_Cmds + "\n" + "cd %s/%s/Dimple\n" % (self.project_directory, self.xtalID) + + "\n" + + ccp4_scratch + + "\n" + "dimple %s ../%s %s.pdb dimple" % (ref_lib, self.mtz_free, self.reference) + + "\n" + "cd %s/%s\n" % (self.project_directory, self.xtalID) + "\n" + "/bin/rm refine.pdb\n" + "/bin/rm refine.mtz\n" + "ln -s Dimple/dimple/final.pdb refine.pdb\n" + "ln -s Dimple/dimple/final.mtz refine.mtz\n" + "\n" + "fft hklin refine.mtz mapout 2fofc.map << EOF\n" + " labin F1=2FOFCWT PHI=PH2FOFCWT\n" + "EOF\n" + "\n" + "fft hklin refine.mtz mapout fofc.map << EOF\n" + " labin F1=FOFCWT PHI=PHFOFCWT\n" + "EOF\n" + "\n" + "fft hklin refine.mtz mapout 2fofc.map << EOF\n" + " labin F1=FWT PHI=PHWT\n" + "EOF\n" + "\n" + "fft hklin refine.mtz mapout fofc.map << EOF\n" + " labin F1=DELFWT PHI=PHDELWT\n" + "EOF\n" + "\n" + "/bin/rm dimple_run_in_progress\n" ) self.Run(Cmds) def Run(self, Cmds): - os.chdir(self.project_directory+'/'+self.xtalID) - os.system('touch dimple_run_in_progress') - os.chdir(self.project_directory+'/'+self.xtalID+'/Dimple') - f = open('xce_dimple.sh', 'w') + os.chdir(self.project_directory + "/" + self.xtalID) + os.system("touch dimple_run_in_progress") + os.chdir(self.project_directory + "/" + self.xtalID + "/Dimple") + f = open("xce_dimple.sh", "w") f.write(Cmds) f.close() if self.queueing_system_available: - os.system('qsub xce_dimple.sh') + os.system("qsub xce_dimple.sh") else: - os.system('chmod +x xce_dimple.sh') - os.system('./xce_dimple.sh') + os.system("chmod +x xce_dimple.sh") + os.system("./xce_dimple.sh") class helpers: - def __init__(self): try: # this sys path append is only meaningful if non-CCP4 python is used to launch XCE @@ -216,6 +225,7 @@ def __init__(self): from rdkit import Chem from rdkit.Chem import AllChem from rdkit.Chem import Draw + self.pil_rdkit_present = True except ImportError: self.pil_rdkit_present = False @@ -224,173 +234,246 @@ def __init__(self): def pil_rdkit_exist(self): return self.pil_rdkit_present - def make_png(self, initial_model_directory, sample, compoundID, smiles, external_software, database_directory, data_source_file, ccp4_scratch_directory, counter, xce_logfile, restraints_program): + def make_png( + self, + initial_model_directory, + sample, + compoundID, + smiles, + external_software, + database_directory, + data_source_file, + ccp4_scratch_directory, + counter, + xce_logfile, + restraints_program, + ): Logfile = XChemLog.updateLog(xce_logfile) -# if not os.path.isfile(os.path.join(initial_model_directory,sample,'compound','ACEDRG_IN_PROGRESS')): - os.system('touch RESTRAINTS_IN_PROGRESS') + # if not os.path.isfile(os.path.join(initial_model_directory,sample,'compound','ACEDRG_IN_PROGRESS')): + os.system("touch RESTRAINTS_IN_PROGRESS") - header = '#!'+os.getenv('SHELL')+'\n' - if external_software['qsub']: - if not external_software['qsub_array']: - header = '#PBS -joe -N xce_acedrg\n' + header = "#!" + os.getenv("SHELL") + "\n" + if external_software["qsub"]: + if not external_software["qsub_array"]: + header = "#PBS -joe -N xce_acedrg\n" # check for combisoaks/ cocktails # note: compoundIDs and smiles are semi-colon separated - if len(compoundID.split(';')) > 1: + if len(compoundID.split(";")) > 1: Logfile.insert( - 'looks like you are working with cocktails; found the following IDs and smiles:') - if len(compoundID.split(';')) != len(smiles.split(';')): + "looks like you are working with cocktails; found the following IDs and smiles:" + ) + if len(compoundID.split(";")) != len(smiles.split(";")): + Logfile.error("Number of compoundIDs and SMILES does not match:") Logfile.error( - 'Number of compoundIDs and SMILES does not match:') - Logfile.error('N(compoundID): {0!s} -> {1!s}'.format( - len(compoundID.split(';')), compoundID.split(';'))) + "N(compoundID): {0!s} -> {1!s}".format( + len(compoundID.split(";")), compoundID.split(";") + ) + ) Logfile.error( - 'N(SMILES): {0!s} -> {1!s}'.format(len(smiles.split(';')), smiles.split(';'))) - Logfile.error('aborting...') + "N(SMILES): {0!s} -> {1!s}".format( + len(smiles.split(";")), smiles.split(";") + ) + ) + Logfile.error("aborting...") return else: - software = '' - if restraints_program == 'acedrg': - if os.getcwd().startswith('/dls'): - software += 'module load ccp4/7.1.018\n' - elif restraints_program == 'phenix.elbow': - if os.getcwd().startswith('/dls'): - software += 'module load ccp4/7.1.018\n' - software += 'module load phenix\n' - elif restraints_program == 'grade': - if os.getcwd().startswith('/dls'): - software += 'module load ccp4/7.1.018\n' - software += 'module load buster\n' - software += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' + software = "" + if restraints_program == "acedrg": + if os.getcwd().startswith("/dls"): + software += "module load ccp4/7.1.018\n" + elif restraints_program == "phenix.elbow": + if os.getcwd().startswith("/dls"): + software += "module load ccp4/7.1.018\n" + software += "module load phenix\n" + elif restraints_program == "grade": + if os.getcwd().startswith("/dls"): + software += "module load ccp4/7.1.018\n" + software += "module load buster\n" + software += "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n" software += "export BDG_TOOL_OBABEL='none'\n" - for i in range(len(compoundID.split(';'))): + for i in range(len(compoundID.split(";"))): Logfile.insert( - '{0!s} - {1!s}'.format(compoundID.split(';')[i], smiles.split(';')[i])) - cID = 'L' + (2 - len(str(i))) * '0' + str(i) - if restraints_program == 'acedrg': + "{0!s} - {1!s}".format( + compoundID.split(";")[i], smiles.split(";")[i] + ) + ) + cID = "L" + (2 - len(str(i))) * "0" + str(i) + if restraints_program == "acedrg": software += 'acedrg --res {0!s} -i "{1!s}" -o {2!s}\n'.format( - cID, smiles.split(';')[i], compoundID.split(';')[i].replace(' ', '')) - elif restraints_program == 'phenix.elbow': + cID, + smiles.split(";")[i], + compoundID.split(";")[i].replace(" ", ""), + ) + elif restraints_program == "phenix.elbow": software += 'phenix.elbow --smiles="{0!s}" --id {1!s}} --output {2!s}\n'.format( - smiles.split(';')[i], cID, compoundID.split(';')[i].replace(' ', '')) - elif restraints_program == 'grade': - if external_software['mogul']: - mogul = '' + smiles.split(";")[i], + cID, + compoundID.split(";")[i].replace(" ", ""), + ) + elif restraints_program == "grade": + if external_software["mogul"]: + mogul = "" else: - mogul = '-nomogul' + mogul = "-nomogul" software += 'grade -resname {0!s} {1!s} "{2!s}" -ocif {3!s}.cif -opdb {4!s}.pdb\n'.format( - cID, mogul, smiles.split(';')[i], compoundID.split(';')[i].replace(' ', ''), compoundID.split(';')[i].replace(' ', '')) + cID, + mogul, + smiles.split(";")[i], + compoundID.split(";")[i].replace(" ", ""), + compoundID.split(";")[i].replace(" ", ""), + ) else: # check if CompoundSMILEScovalent field is not Null # CompoundSMILESproduct can be used to create only a CIF file for the product to make fitting easier # however, the complete smiles string will be used to make the png file productSmiles = None - db = XChemDB.data_source(os.path.join( - database_directory, data_source_file)) - sql = "select CompoundSMILESproduct from mainTable where CrystalName = '%s'" % sample + db = XChemDB.data_source(os.path.join(database_directory, data_source_file)) + sql = ( + "select CompoundSMILESproduct from mainTable where CrystalName = '%s'" + % sample + ) query = db.execute_statement(sql) productSmiles = query[0][0] - if str(productSmiles).replace(' ', '') == '': + if str(productSmiles).replace(" ", "") == "": productSmiles = smiles - elif 'none' in str(productSmiles).lower(): + elif "none" in str(productSmiles).lower(): productSmiles = smiles - elif 'null' in str(productSmiles).lower(): + elif "null" in str(productSmiles).lower(): productSmiles = smiles else: productSmiles = str(productSmiles) - software = '' - if restraints_program == 'acedrg': - if os.getcwd().startswith('/dls'): - software += 'module load ccp4/7.1.018\n' - if os.path.isfile(os.path.join(initial_model_directory, sample, 'old.cif')): - software += 'acedrg --res LIG -c ../old.cif -o {0!s}\n'.format( - (compoundID.replace(' ', ''))) + software = "" + if restraints_program == "acedrg": + if os.getcwd().startswith("/dls"): + software += "module load ccp4/7.1.018\n" + if os.path.isfile( + os.path.join(initial_model_directory, sample, "old.cif") + ): + software += "acedrg --res LIG -c ../old.cif -o {0!s}\n".format( + (compoundID.replace(" ", "")) + ) else: software += 'acedrg --res LIG -i "{0!s}" -o {1!s}\n'.format( - productSmiles, compoundID.replace(' ', '')) - elif restraints_program == 'phenix.elbow': - if os.getcwd().startswith('/dls'): - software += 'module load ccp4/7.1.018\n' - software += 'module load phenix\n' - if os.path.isfile(os.path.join(initial_model_directory, sample, 'old.cif')): - software += 'phenix.elbow --file=../old.cif --id LIG --output {0!s}\n'.format( - (compoundID.replace(' ', ''))) + productSmiles, compoundID.replace(" ", "") + ) + elif restraints_program == "phenix.elbow": + if os.getcwd().startswith("/dls"): + software += "module load ccp4/7.1.018\n" + software += "module load phenix\n" + if os.path.isfile( + os.path.join(initial_model_directory, sample, "old.cif") + ): + software += "phenix.elbow --file=../old.cif --id LIG --output {0!s}\n".format( + (compoundID.replace(" ", "")) + ) else: - software += 'phenix.elbow --smiles="{0!s}" --id LIG --output {1!s}\n'\ - .format(productSmiles, compoundID.replace(' ', '')) - elif restraints_program == 'grade': - if os.getcwd().startswith('/dls'): - software += 'module load ccp4/7.1.018\n' - software += 'module load buster\n' - software += 'export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n' + software += 'phenix.elbow --smiles="{0!s}" --id LIG --output {1!s}\n'.format( + productSmiles, compoundID.replace(" ", "") + ) + elif restraints_program == "grade": + if os.getcwd().startswith("/dls"): + software += "module load ccp4/7.1.018\n" + software += "module load buster\n" + software += ( + "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n" + ) software += "export BDG_TOOL_OBABEL='none'\n" - if external_software['mogul']: - mogul = '' + if external_software["mogul"]: + mogul = "" else: - mogul = '-nomogul' - if os.path.isfile(os.path.join(initial_model_directory, sample, 'old.cif')): - software += 'grade -resname LIG {0!s} -in ../old.cif -ocif {1!s}.cif -opdb {2!s}.pdb\n'\ - .format(mogul, compoundID.replace(' ', ''), compoundID.replace(' ', '')) + mogul = "-nomogul" + if os.path.isfile( + os.path.join(initial_model_directory, sample, "old.cif") + ): + software += "grade -resname LIG {0!s} -in ../old.cif -ocif {1!s}.cif -opdb {2!s}.pdb\n".format( + mogul, compoundID.replace(" ", ""), compoundID.replace(" ", "") + ) else: - software += 'grade -resname LIG {0!s} "{1!s}" -ocif {2!s}.cif -opdb {3!s}.pdb\n'\ - .format(mogul, productSmiles, compoundID.replace(' ', ''), compoundID.replace(' ', '')) + software += 'grade -resname LIG {0!s} "{1!s}" -ocif {2!s}.cif -opdb {3!s}.pdb\n'.format( + mogul, + productSmiles, + compoundID.replace(" ", ""), + compoundID.replace(" ", ""), + ) # merge all compound CIFs into 1 file called merged.cif - software += '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/merge_ligand_cif_files.py {0!s}\n'.format( - os.path.join(initial_model_directory, sample, 'compound')) + software += "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/merge_ligand_cif_files.py {0!s}\n".format( + os.path.join(initial_model_directory, sample, "compound") + ) # Removal of the hydrogen atoms in PDB files is required for REFMAC 5 run. With hydrogens some ligands fail to # pass the external restraints in pandda.giant.make_restraints. # Copy the file with hydrogens to retain in case needed - check_stereochemistry = '' + check_stereochemistry = "" Cmds = ( - - header + - '\n' - 'export XChemExplorer_DIR="' + os.getenv('XChemExplorer_DIR') + '"' + - '\n' - '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py {0!s} {1!s} {2!s} {3!s}' - .format(os.path.join(database_directory, data_source_file), sample, 'RefinementCIFStatus', 'running') + - '\n' - '$CCP4/bin/ccp4-python {0!s} "{1!s}" {2!s} {3!s} {4!s}\n' - .format(os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', 'create_png_of_compound.py'), - smiles, compoundID.replace(' ', ''), sample, initial_model_directory) + - '\n' - 'cd ' + os.path.join(initial_model_directory, sample, 'compound') + - '\n' - + software + - '\n' - 'cd ' + os.path.join(initial_model_directory, sample) + - '\n' - 'ln -s compound/%s.cif .\n' % compoundID.replace(' ', '') + - 'ln -s compound/{0!s}.pdb .\n'.format(compoundID.replace(' ', '')) + - 'ln -s compound/{0!s}.png .\n'.format(compoundID.replace(' ', '')) + - '\n' - '$CCP4/bin/ccp4-python ' + os.path.join(os.getenv('XChemExplorer_DIR'), 'helpers', - 'update_data_source_for_new_cif_files.py') + - ' {0!s} {1!s} {2!s} {3!s}\n'.format(os.path.join(database_directory, data_source_file), sample, - initial_model_directory, compoundID.replace(' ', '')) + - '\n' - '/bin/rm -f compound/RESTRAINTS_IN_PROGRESS\n' + header + "\n" + 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"' + "\n" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py {0!s} {1!s} {2!s} {3!s}".format( + os.path.join(database_directory, data_source_file), + sample, + "RefinementCIFStatus", + "running", + ) + + "\n" + '$CCP4/bin/ccp4-python {0!s} "{1!s}" {2!s} {3!s} {4!s}\n'.format( + os.path.join( + os.getenv("XChemExplorer_DIR"), + "helpers", + "create_png_of_compound.py", + ), + smiles, + compoundID.replace(" ", ""), + sample, + initial_model_directory, + ) + + "\n" + "cd " + + os.path.join(initial_model_directory, sample, "compound") + + "\n" + + software + + "\n" + "cd " + os.path.join(initial_model_directory, sample) + "\n" + "ln -s compound/%s.cif .\n" % compoundID.replace(" ", "") + + "ln -s compound/{0!s}.pdb .\n".format(compoundID.replace(" ", "")) + + "ln -s compound/{0!s}.png .\n".format(compoundID.replace(" ", "")) + + "\n" + "$CCP4/bin/ccp4-python " + + os.path.join( + os.getenv("XChemExplorer_DIR"), + "helpers", + "update_data_source_for_new_cif_files.py", + ) + + " {0!s} {1!s} {2!s} {3!s}\n".format( + os.path.join(database_directory, data_source_file), + sample, + initial_model_directory, + compoundID.replace(" ", ""), + ) + + "\n" + "/bin/rm -f compound/RESTRAINTS_IN_PROGRESS\n" ) os.chdir(ccp4_scratch_directory) - Logfile.insert('creating ACEDRG shell script for {0!s},{1!s} in {2!s}'.format( - sample, compoundID, ccp4_scratch_directory)) -# print Cmds -# print 'ccp4_scratch',ccp4_scratch_directory - f = open('xce_{0!s}_{1!s}.sh'.format( - restraints_program, str(counter)), 'w') + Logfile.insert( + "creating ACEDRG shell script for {0!s},{1!s} in {2!s}".format( + sample, compoundID, ccp4_scratch_directory + ) + ) + # print Cmds + # print 'ccp4_scratch',ccp4_scratch_directory + f = open("xce_{0!s}_{1!s}.sh".format(restraints_program, str(counter)), "w") f.write(Cmds) f.close() os.system( - 'chmod +x xce_{0!s}_{1!s}.sh'.format(restraints_program, str(counter))) + "chmod +x xce_{0!s}_{1!s}.sh".format(restraints_program, str(counter)) + ) # if queueing_system_available: @@ -412,175 +495,272 @@ def make_png(self, initial_model_directory, sample, compoundID, smiles, external class parse: - def __init__(self): - self.space_group_dict = {'triclinic': ['P1'], - # 'monoclinic': ['P2','P21','C121','P1211','P121'], - 'monoclinic_P': ['P2', 'P21', 'P1211', 'P121'], - 'monoclinic_C': ['C2', 'C121'], - 'orthorhombic': ['P222', 'P2122', 'P2212', 'P2221', - 'P21212', 'P21221', 'P22121', 'P212121', - 'C222', 'C2221', - 'F222', 'I222', 'I212121'], - 'tetragonal': ['P4', 'P41', 'P42', 'P43', 'I4', 'I41', - 'P422', 'P4212', 'P4122', 'P41212', 'P4222', - 'P42212', 'P4322', 'P43212', 'I422', 'I4122'], - 'hexagonal': ['P3', 'P31', 'P32', - 'P312', 'P321', 'P3112', 'P3121', 'P3212', 'P3221', - 'P6', 'P61', 'P65', 'P62', 'P64', 'P63', - 'P622', 'P6122', 'P6522', 'P6222', 'P6422', 'P6322'], - 'rhombohedral': ['H3', 'H32'], - 'cubic': ['P23', 'F23', 'I23', 'P213', 'I213', - 'P432', 'P4232', 'F432', 'F4132', 'I432', 'P4332', 'P4132', 'I4132']} - - self.point_group_dict = {'1': ['P1'], - '2': ['P2', 'P21', 'C121', 'P1211', 'P121', 'C2'], - '222': ['P222', 'P2122', 'P2212', 'P2221', - 'P21212', 'P21221', 'P22121', 'P212121', - 'C222', 'C2221', - 'F222', 'I222', 'I212121'], - '4': ['P4', 'P41', 'P42', 'P43', 'I4', 'I41'], - '422': ['P422', 'P4212', 'P4122', 'P41212', 'P4222', - 'P42212', 'P4322', 'P43212', 'I422', 'I4122'], - '3': ['P3', 'P31', 'P32', 'H3'], - '32': ['P312', 'P321', 'P3112', 'P3121', 'P3212', 'P3221', 'H32'], - '6': ['P6', 'P61', 'P65', 'P62', 'P64', 'P63'], - '622': ['P622', 'P6122', 'P6522', 'P6222', 'P6422', 'P6322'], - '23': ['P23', 'F23', 'I23', 'P213', 'I213'], - '432': ['P432', 'P4232', 'F432', 'F4132', 'I432', 'P4332', 'P4132', 'I4132']} - - self.nr_asu_in_unitcell_for_point_group = {'1': 1, - '2': 2, - '222': 4, - '4': 4, - '422': 8, - '3': 3, - '32': 6, - '6': 6, - '622': 12, - '23': 12, - '432': 24} - - self.aimless = {'DataProcessingProgram': 'n/a', - # 'DataCollectionRun': 'n/a', - 'DataProcessingSpaceGroup': 'n/a', - 'DataProcessingUnitCell': 'n/a', - 'DataProcessingA': 'n/a', - 'DataProcessingB': 'n/a', - 'DataProcessingC': 'n/a', - 'DataProcessingAlpha': 'n/a', - 'DataProcessingBeta': 'n/a', - 'DataProcessingGamma': 'n/a', - 'DataProcessingResolutionLow': 'n/a', - 'DataProcessingResolutionLowInnerShell': 'n/a', - 'DataProcessingResolutionHigh': 'n/a', - 'DataProcessingResolutionHighOuterShell': 'n/a', - 'DataProcessingResolutionOverall': 'n/a', - 'DataProcessingRmergeOverall': 'n/a', - 'DataProcessingRmergeLow': 'n/a', - 'DataProcessingRmergeHigh': 'n/a', - 'DataProcessingIsigOverall': 'n/a', - 'DataProcessingIsigLow': 'n/a', - 'DataProcessingIsigHigh': 'n/a', - 'DataProcessingCompletenessOverall': 'n/a', - 'DataProcessingCompletenessLow': 'n/a', - 'DataProcessingCompletenessHigh': 'n/a', - 'DataProcessingMultiplicityOverall': 'n/a', - 'DataProcessingMultiplicityLow': 'n/a', - 'DataProcessingMultiplicityHigh': 'n/a', - 'DataProcessingCChalfOverall': 'n/a', - 'DataProcessingCChalfLow': 'n/a', - 'DataProcessingCChalfHigh': 'n/a', - 'DataProcessingResolutionHigh15sigma': 'n/a', - 'DataProcessingUniqueReflectionsLow': 'n/a', - 'DataProcessingUniqueReflectionsHigh': 'n/a', - 'DataProcessingUniqueReflectionsOverall': 'n/a', - 'DataProcessingLattice': 'n/a', - 'DataProcessingPointGroup': 'n/a', - 'DataProcessingUnitCellVolume': 0, - 'DataProcessingAlert': '#FF0000', - 'DataCollectionWavelength': 'n/a', - 'DataProcessingScore': 'n/a'} + self.space_group_dict = { + "triclinic": ["P1"], + # 'monoclinic': ['P2','P21','C121','P1211','P121'], + "monoclinic_P": ["P2", "P21", "P1211", "P121"], + "monoclinic_C": ["C2", "C121"], + "orthorhombic": [ + "P222", + "P2122", + "P2212", + "P2221", + "P21212", + "P21221", + "P22121", + "P212121", + "C222", + "C2221", + "F222", + "I222", + "I212121", + ], + "tetragonal": [ + "P4", + "P41", + "P42", + "P43", + "I4", + "I41", + "P422", + "P4212", + "P4122", + "P41212", + "P4222", + "P42212", + "P4322", + "P43212", + "I422", + "I4122", + ], + "hexagonal": [ + "P3", + "P31", + "P32", + "P312", + "P321", + "P3112", + "P3121", + "P3212", + "P3221", + "P6", + "P61", + "P65", + "P62", + "P64", + "P63", + "P622", + "P6122", + "P6522", + "P6222", + "P6422", + "P6322", + ], + "rhombohedral": ["H3", "H32"], + "cubic": [ + "P23", + "F23", + "I23", + "P213", + "I213", + "P432", + "P4232", + "F432", + "F4132", + "I432", + "P4332", + "P4132", + "I4132", + ], + } + + self.point_group_dict = { + "1": ["P1"], + "2": ["P2", "P21", "C121", "P1211", "P121", "C2"], + "222": [ + "P222", + "P2122", + "P2212", + "P2221", + "P21212", + "P21221", + "P22121", + "P212121", + "C222", + "C2221", + "F222", + "I222", + "I212121", + ], + "4": ["P4", "P41", "P42", "P43", "I4", "I41"], + "422": [ + "P422", + "P4212", + "P4122", + "P41212", + "P4222", + "P42212", + "P4322", + "P43212", + "I422", + "I4122", + ], + "3": ["P3", "P31", "P32", "H3"], + "32": ["P312", "P321", "P3112", "P3121", "P3212", "P3221", "H32"], + "6": ["P6", "P61", "P65", "P62", "P64", "P63"], + "622": ["P622", "P6122", "P6522", "P6222", "P6422", "P6322"], + "23": ["P23", "F23", "I23", "P213", "I213"], + "432": [ + "P432", + "P4232", + "F432", + "F4132", + "I432", + "P4332", + "P4132", + "I4132", + ], + } + + self.nr_asu_in_unitcell_for_point_group = { + "1": 1, + "2": 2, + "222": 4, + "4": 4, + "422": 8, + "3": 3, + "32": 6, + "6": 6, + "622": 12, + "23": 12, + "432": 24, + } + + self.aimless = { + "DataProcessingProgram": "n/a", + # 'DataCollectionRun': 'n/a', + "DataProcessingSpaceGroup": "n/a", + "DataProcessingUnitCell": "n/a", + "DataProcessingA": "n/a", + "DataProcessingB": "n/a", + "DataProcessingC": "n/a", + "DataProcessingAlpha": "n/a", + "DataProcessingBeta": "n/a", + "DataProcessingGamma": "n/a", + "DataProcessingResolutionLow": "n/a", + "DataProcessingResolutionLowInnerShell": "n/a", + "DataProcessingResolutionHigh": "n/a", + "DataProcessingResolutionHighOuterShell": "n/a", + "DataProcessingResolutionOverall": "n/a", + "DataProcessingRmergeOverall": "n/a", + "DataProcessingRmergeLow": "n/a", + "DataProcessingRmergeHigh": "n/a", + "DataProcessingIsigOverall": "n/a", + "DataProcessingIsigLow": "n/a", + "DataProcessingIsigHigh": "n/a", + "DataProcessingCompletenessOverall": "n/a", + "DataProcessingCompletenessLow": "n/a", + "DataProcessingCompletenessHigh": "n/a", + "DataProcessingMultiplicityOverall": "n/a", + "DataProcessingMultiplicityLow": "n/a", + "DataProcessingMultiplicityHigh": "n/a", + "DataProcessingCChalfOverall": "n/a", + "DataProcessingCChalfLow": "n/a", + "DataProcessingCChalfHigh": "n/a", + "DataProcessingResolutionHigh15sigma": "n/a", + "DataProcessingUniqueReflectionsLow": "n/a", + "DataProcessingUniqueReflectionsHigh": "n/a", + "DataProcessingUniqueReflectionsOverall": "n/a", + "DataProcessingLattice": "n/a", + "DataProcessingPointGroup": "n/a", + "DataProcessingUnitCellVolume": 0, + "DataProcessingAlert": "#FF0000", + "DataCollectionWavelength": "n/a", + "DataProcessingScore": "n/a", + } def GetAimlessLog(self, Logfile): self.Logfile = Logfile - Aimless = {'AutoProc': 'n/a', - 'Run': 'n/a', - 'SpaceGroup': 'n/a', - 'UnitCell': 'n/a', - 'ResolutionLow': 'n/a', - 'ResolutionLowInnerShell': 'n/a', - 'ResolutionHigh': 'n/a', - 'ResolutionHighOuterShell': 'n/a', - 'RmergeOverall': 'n/a', - 'RmergeLow': 'n/a', - 'RmergeHigh': 'n/a', - 'IsigOverall': 'n/a', - 'IsigLow': 'n/a', - 'IsigHigh': 'n/a', - 'CompletenessOverall': 'n/a', - 'CompletenessLow': 'n/a', - 'CompletenessHigh': 'n/a', - 'MultiplicityOverall': 'n/a', - 'MultiplicityLow': 'n/a', - 'MultiplicityHigh': 'n/a', - 'UniqueReflectionsOverall': 'n/a', - 'Lattice': 'n/a', - 'UnitCellVolume': 0, - 'Alert': '#FF0000'} - - spg = 'n/a' - a = 'n/a' - b = 'n/a' - c = 'n/a' - alpha = 'n/a' - beta = 'n/a' - gamma = 'n/a' - - if 'fast_dp' in self.Logfile: - Aimless['AutoProc'] = 'fast_dp' - if '3d-run' in self.Logfile: - Aimless['AutoProc'] = 'xia2 3d' - if '3dii-run' in self.Logfile: - Aimless['AutoProc'] = 'xia2 3dii' - if 'dials-run' in self.Logfile: - Aimless['AutoProc'] = 'dials' - if 'autoPROC' in self.Logfile: - Aimless['AutoProc'] = 'autoPROC' + Aimless = { + "AutoProc": "n/a", + "Run": "n/a", + "SpaceGroup": "n/a", + "UnitCell": "n/a", + "ResolutionLow": "n/a", + "ResolutionLowInnerShell": "n/a", + "ResolutionHigh": "n/a", + "ResolutionHighOuterShell": "n/a", + "RmergeOverall": "n/a", + "RmergeLow": "n/a", + "RmergeHigh": "n/a", + "IsigOverall": "n/a", + "IsigLow": "n/a", + "IsigHigh": "n/a", + "CompletenessOverall": "n/a", + "CompletenessLow": "n/a", + "CompletenessHigh": "n/a", + "MultiplicityOverall": "n/a", + "MultiplicityLow": "n/a", + "MultiplicityHigh": "n/a", + "UniqueReflectionsOverall": "n/a", + "Lattice": "n/a", + "UnitCellVolume": 0, + "Alert": "#FF0000", + } + + spg = "n/a" + a = "n/a" + b = "n/a" + c = "n/a" + alpha = "n/a" + beta = "n/a" + gamma = "n/a" + + if "fast_dp" in self.Logfile: + Aimless["AutoProc"] = "fast_dp" + if "3d-run" in self.Logfile: + Aimless["AutoProc"] = "xia2 3d" + if "3dii-run" in self.Logfile: + Aimless["AutoProc"] = "xia2 3dii" + if "dials-run" in self.Logfile: + Aimless["AutoProc"] = "dials" + if "autoPROC" in self.Logfile: + Aimless["AutoProc"] = "autoPROC" # get run number from logfile # Note: only works if file is in original directory, but not once it lifes in 'inital_model' -# print self.Logfile.split('/')[9].split('_')[1] -# if len(self.Logfile.split('/'))>8 and len(self.Logfile.split('/')[9].split('_'))==1: + # print self.Logfile.split('/')[9].split('_')[1] + # if len(self.Logfile.split('/'))>8 and len(self.Logfile.split('/')[9].split('_'))==1: try: - Aimless['Run'] = self.Logfile.split('/')[9].split('_')[1] + Aimless["Run"] = self.Logfile.split("/")[9].split("_")[1] except IndexError: pass for line in open(self.Logfile): - if line.startswith('Low resolution limit') and len(line.split()) == 6: - Aimless['ResolutionLow'] = line.split()[3] - Aimless['ResolutionHighOuterShell'] = line.split()[5] - if line.startswith('High resolution limit') and len(line.split()) == 6: - Aimless['ResolutionHigh'] = line.split()[3] - Aimless['ResolutionLowInnerShell'] = line.split()[4] - if line.startswith('Rmerge (all I+ and I-)') and len(line.split()) == 8: - Aimless['RmergeOverall'] = line.split()[5] - Aimless['RmergeLow'] = line.split()[6] - Aimless['RmergeHigh'] = line.split()[7] - if line.startswith('Mean((I)/sd(I))') and len(line.split()) == 4: - Aimless['IsigOverall'] = line.split()[1] - Aimless['IsigHigh'] = line.split()[3] - Aimless['IsigLow'] = line.split()[2] - if line.startswith('Completeness') and len(line.split()) == 4: - Aimless['CompletenessOverall'] = line.split()[1] - Aimless['CompletenessHigh'] = line.split()[3] - Aimless['CompletenessLow'] = line.split()[2] - if line.startswith('Multiplicity') and len(line.split()) == 4: - Aimless['MultiplicityOverall'] = line.split()[1] - Aimless['MultiplicityHigh'] = line.split()[3] - Aimless['MultiplicityLow'] = line.split()[3] - if line.startswith('Average unit cell:') and len(line.split()) == 9: + if line.startswith("Low resolution limit") and len(line.split()) == 6: + Aimless["ResolutionLow"] = line.split()[3] + Aimless["ResolutionHighOuterShell"] = line.split()[5] + if line.startswith("High resolution limit") and len(line.split()) == 6: + Aimless["ResolutionHigh"] = line.split()[3] + Aimless["ResolutionLowInnerShell"] = line.split()[4] + if line.startswith("Rmerge (all I+ and I-)") and len(line.split()) == 8: + Aimless["RmergeOverall"] = line.split()[5] + Aimless["RmergeLow"] = line.split()[6] + Aimless["RmergeHigh"] = line.split()[7] + if line.startswith("Mean((I)/sd(I))") and len(line.split()) == 4: + Aimless["IsigOverall"] = line.split()[1] + Aimless["IsigHigh"] = line.split()[3] + Aimless["IsigLow"] = line.split()[2] + if line.startswith("Completeness") and len(line.split()) == 4: + Aimless["CompletenessOverall"] = line.split()[1] + Aimless["CompletenessHigh"] = line.split()[3] + Aimless["CompletenessLow"] = line.split()[2] + if line.startswith("Multiplicity") and len(line.split()) == 4: + Aimless["MultiplicityOverall"] = line.split()[1] + Aimless["MultiplicityHigh"] = line.split()[3] + Aimless["MultiplicityLow"] = line.split()[3] + if line.startswith("Average unit cell:") and len(line.split()) == 9: tmp = [line.split()] a = int(float(tmp[0][3])) b = int(float(tmp[0][4])) @@ -588,24 +768,44 @@ def GetAimlessLog(self, Logfile): alpha = int(float(tmp[0][6])) beta = int(float(tmp[0][7])) gamma = int(float(tmp[0][8])) - if line.startswith('Total number unique') and len(line.split()) == 6: - Aimless['UniqueReflectionsOverall'] = line.split()[3] - if line.startswith('Space group:'): - Aimless['SpaceGroup'] = line.replace('Space group: ', '')[:-1] - Aimless['Lattice'] = self.get_lattice_from_space_group( - Aimless['SpaceGroup']) - if a != 'n/a' and b != 'n/a' and c != 'n/a' and \ - alpha != 'n/a' and beta != 'n/a' and gamma != 'n/a' and Aimless['Lattice'] != 'n/a': - Aimless['UnitCellVolume'] = self.calc_unitcell_volume_from_logfile(float(a), float(b), float(c), - math.radians( - float(alpha)), - math.radians( - float(beta)), - math.radians( - float(gamma)), - Aimless['Lattice']) - Aimless['UnitCell'] = str( - a)+' '+str(b)+' '+str(c)+' '+str(alpha)+' '+str(beta)+' '+str(gamma) + if line.startswith("Total number unique") and len(line.split()) == 6: + Aimless["UniqueReflectionsOverall"] = line.split()[3] + if line.startswith("Space group:"): + Aimless["SpaceGroup"] = line.replace("Space group: ", "")[:-1] + Aimless["Lattice"] = self.get_lattice_from_space_group( + Aimless["SpaceGroup"] + ) + if ( + a != "n/a" + and b != "n/a" + and c != "n/a" + and alpha != "n/a" + and beta != "n/a" + and gamma != "n/a" + and Aimless["Lattice"] != "n/a" + ): + Aimless["UnitCellVolume"] = self.calc_unitcell_volume_from_logfile( + float(a), + float(b), + float(c), + math.radians(float(alpha)), + math.radians(float(beta)), + math.radians(float(gamma)), + Aimless["Lattice"], + ) + Aimless["UnitCell"] = ( + str(a) + + " " + + str(b) + + " " + + str(c) + + " " + + str(alpha) + + " " + + str(beta) + + " " + + str(gamma) + ) # Hex Color code: # red: #FF0000 @@ -613,16 +813,23 @@ def GetAimlessLog(self, Logfile): # green: #00FF00 # gray: #E0E0E0 - if Aimless['ResolutionHigh'] == 'n/a' or Aimless['RmergeLow'] == 'n/a': - Aimless['Alert'] = '#FF0000' + if Aimless["ResolutionHigh"] == "n/a" or Aimless["RmergeLow"] == "n/a": + Aimless["Alert"] = "#FF0000" else: - if float(Aimless['ResolutionHigh']) > 3.5 or float(Aimless['RmergeLow']) > 0.1: - Aimless['Alert'] = '#FF0000' - if (3.5 >= float(Aimless['ResolutionHigh']) > 2.5) or \ - (0.1 >= float(Aimless['RmergeLow']) > 0.05): - Aimless['Alert'] = '#FF9900' - if float(Aimless['ResolutionHigh']) <= 2.5 and float(Aimless['RmergeLow']) <= 0.05: - Aimless['Alert'] = '#00FF00' + if ( + float(Aimless["ResolutionHigh"]) > 3.5 + or float(Aimless["RmergeLow"]) > 0.1 + ): + Aimless["Alert"] = "#FF0000" + if (3.5 >= float(Aimless["ResolutionHigh"]) > 2.5) or ( + 0.1 >= float(Aimless["RmergeLow"]) > 0.05 + ): + Aimless["Alert"] = "#FF9900" + if ( + float(Aimless["ResolutionHigh"]) <= 2.5 + and float(Aimless["RmergeLow"]) <= 0.05 + ): + Aimless["Alert"] = "#00FF00" return Aimless @@ -633,43 +840,43 @@ def read_aimless_logfile(self, logfile): # essentially same as above, but compatible with datasource # will hopefully supersede function above - spg = 'n/a' - a = 'n/a' - b = 'n/a' - c = 'n/a' - alpha = 'n/a' - beta = 'n/a' - gamma = 'n/a' - - if 'fast_dp' in logfile: - self.aimless['DataProcessingProgram'] = 'fast_dp' - elif '3d-run' in logfile: - self.aimless['DataProcessingProgram'] = 'xia2-3d' - elif '3dii-run' in logfile: - self.aimless['DataProcessingProgram'] = 'xia2-3dii' - elif 'xia2-3dii' in logfile: - self.aimless['DataProcessingProgram'] = 'xia2-3dii' - elif 'dials-run' in logfile: - self.aimless['DataProcessingProgram'] = 'dials' - elif 'dials' in logfile: - self.aimless['DataProcessingProgram'] = 'dials' - elif 'autoPROC' in logfile: - self.aimless['DataProcessingProgram'] = 'autoPROC' - elif 'staraniso' in logfile: - self.aimless['DataProcessingProgram'] = 'aP_staraniso' + spg = "n/a" + a = "n/a" + b = "n/a" + c = "n/a" + alpha = "n/a" + beta = "n/a" + gamma = "n/a" + + if "fast_dp" in logfile: + self.aimless["DataProcessingProgram"] = "fast_dp" + elif "3d-run" in logfile: + self.aimless["DataProcessingProgram"] = "xia2-3d" + elif "3dii-run" in logfile: + self.aimless["DataProcessingProgram"] = "xia2-3dii" + elif "xia2-3dii" in logfile: + self.aimless["DataProcessingProgram"] = "xia2-3dii" + elif "dials-run" in logfile: + self.aimless["DataProcessingProgram"] = "dials" + elif "dials" in logfile: + self.aimless["DataProcessingProgram"] = "dials" + elif "autoPROC" in logfile: + self.aimless["DataProcessingProgram"] = "autoPROC" + elif "staraniso" in logfile: + self.aimless["DataProcessingProgram"] = "aP_staraniso" # get run number from logfile # Note: only works if file is in original directory, but not once it moved to 'inital_model' folder# -## print self.Logfile.split('/')[9].split('_')[1] -# if len(self.Logfile.split('/'))>8 and len(self.Logfile.split('/')[9].split('_'))==1: -# try: -# self.aimless['DataCollectionRun']=logfile.split('/')[9].split('_')[1] -# except IndexError: -# pass - - if logfile.endswith('.log') or logfile.endswith('.table1'): + ## print self.Logfile.split('/')[9].split('_')[1] + # if len(self.Logfile.split('/'))>8 and len(self.Logfile.split('/')[9].split('_'))==1: + # try: + # self.aimless['DataCollectionRun']=logfile.split('/')[9].split('_')[1] + # except IndexError: + # pass + + if logfile.endswith(".log") or logfile.endswith(".table1"): self.aimless_logile(logfile) - elif logfile.endswith('.json'): + elif logfile.endswith(".json"): self.json_logfile(logfile) # Hex Color code: @@ -678,48 +885,84 @@ def read_aimless_logfile(self, logfile): # green: #00FF00 # gray: #E0E0E0 - if self.aimless['DataProcessingA'] != 'n/a' and self.aimless['DataProcessingB'] != 'n/a' and self.aimless['DataProcessingC'] != 'n/a' \ - and self.aimless['DataProcessingAlpha'] != 'n/a' and self.aimless['DataProcessingBeta'] != 'n/a' and self.aimless['DataProcessingGamma'] != 'n/a' \ - and self.aimless['DataProcessingLattice'] != 'n/a': - a = self.aimless['DataProcessingA'] - b = self.aimless['DataProcessingB'] - c = self.aimless['DataProcessingC'] - alpha = self.aimless['DataProcessingAlpha'] - beta = self.aimless['DataProcessingBeta'] - gamma = self.aimless['DataProcessingGamma'] - self.aimless['DataProcessingUnitCellVolume'] = str( - self.calc_unitcell_volume_from_logfile(float(a), float(b), float(c), - math.radians( - float(alpha)), - math.radians( - float(beta)), - math.radians( - float(gamma)), - self.aimless['DataProcessingLattice'])) + if ( + self.aimless["DataProcessingA"] != "n/a" + and self.aimless["DataProcessingB"] != "n/a" + and self.aimless["DataProcessingC"] != "n/a" + and self.aimless["DataProcessingAlpha"] != "n/a" + and self.aimless["DataProcessingBeta"] != "n/a" + and self.aimless["DataProcessingGamma"] != "n/a" + and self.aimless["DataProcessingLattice"] != "n/a" + ): + a = self.aimless["DataProcessingA"] + b = self.aimless["DataProcessingB"] + c = self.aimless["DataProcessingC"] + alpha = self.aimless["DataProcessingAlpha"] + beta = self.aimless["DataProcessingBeta"] + gamma = self.aimless["DataProcessingGamma"] + self.aimless["DataProcessingUnitCellVolume"] = str( + self.calc_unitcell_volume_from_logfile( + float(a), + float(b), + float(c), + math.radians(float(alpha)), + math.radians(float(beta)), + math.radians(float(gamma)), + self.aimless["DataProcessingLattice"], + ) + ) try: high_symmetry_boost = self.nr_asu_in_unitcell_for_point_group[ - self.aimless['DataProcessingPointGroup']] - self.aimless['DataProcessingScore'] = (float( - self.aimless['DataProcessingUniqueReflectionsOverall']) * float(self.aimless['DataProcessingCompletenessOverall']) * high_symmetry_boost * float(self.aimless['DataProcessingIsigOverall'])) / float( - self.aimless['DataProcessingUnitCellVolume']) + self.aimless["DataProcessingPointGroup"] + ] + self.aimless["DataProcessingScore"] = ( + float(self.aimless["DataProcessingUniqueReflectionsOverall"]) + * float(self.aimless["DataProcessingCompletenessOverall"]) + * high_symmetry_boost + * float(self.aimless["DataProcessingIsigOverall"]) + ) / float(self.aimless["DataProcessingUnitCellVolume"]) # When P-6 was accidentally used self.aimless['DataProcessingPointGroup'] through a KeyError, so handling this except (ValueError, KeyError): - self.aimless['DataProcessingScore'] = 0.0 - self.aimless['DataProcessingUnitCell'] = str(a) + ' ' + str(b) + ' ' + str(c) + ' ' + str(alpha) + ' ' + str( - beta) + ' ' + str(gamma) - self.aimless['DataProcessingResolutionOverall'] = str( - self.aimless['DataProcessingResolutionLow']) + ' - ' + str(self.aimless['DataProcessingResolutionHigh']) - - if self.aimless['DataProcessingResolutionHigh'] == 'n/a' or self.aimless['DataProcessingRmergeLow'] == 'n/a': - self.aimless['DataProcessingAlert'] = '#FF0000' + self.aimless["DataProcessingScore"] = 0.0 + self.aimless["DataProcessingUnitCell"] = ( + str(a) + + " " + + str(b) + + " " + + str(c) + + " " + + str(alpha) + + " " + + str(beta) + + " " + + str(gamma) + ) + self.aimless["DataProcessingResolutionOverall"] = ( + str(self.aimless["DataProcessingResolutionLow"]) + + " - " + + str(self.aimless["DataProcessingResolutionHigh"]) + ) + + if ( + self.aimless["DataProcessingResolutionHigh"] == "n/a" + or self.aimless["DataProcessingRmergeLow"] == "n/a" + ): + self.aimless["DataProcessingAlert"] = "#FF0000" else: - if float(self.aimless['DataProcessingResolutionHigh']) > 3.5 or float(self.aimless['DataProcessingRmergeLow']) > 0.1: - self.aimless['DataProcessingAlert'] = '#FF0000' - if (3.5 >= float(self.aimless['DataProcessingResolutionHigh']) > 2.5) or \ - (0.1 >= float(self.aimless['DataProcessingRmergeLow']) > 0.05): - self.aimless['DataProcessingAlert'] = '#FF9900' - if float(self.aimless['DataProcessingResolutionHigh']) <= 2.5 and float(self.aimless['DataProcessingRmergeLow']) <= 0.05: - self.aimless['DataProcessingAlert'] = '#00FF00' + if ( + float(self.aimless["DataProcessingResolutionHigh"]) > 3.5 + or float(self.aimless["DataProcessingRmergeLow"]) > 0.1 + ): + self.aimless["DataProcessingAlert"] = "#FF0000" + if (3.5 >= float(self.aimless["DataProcessingResolutionHigh"]) > 2.5) or ( + 0.1 >= float(self.aimless["DataProcessingRmergeLow"]) > 0.05 + ): + self.aimless["DataProcessingAlert"] = "#FF9900" + if ( + float(self.aimless["DataProcessingResolutionHigh"]) <= 2.5 + and float(self.aimless["DataProcessingRmergeLow"]) <= 0.05 + ): + self.aimless["DataProcessingAlert"] = "#00FF00" return self.aimless @@ -731,75 +974,74 @@ def aimless_logile(self, logfile): # if 'Wavelength' in line: # print 'here' # print line.split() - if 'Wavelength' in line and len(line.split()) >= 2: - self.aimless['DataCollectionWavelength'] = line.split()[1] - if 'Low resolution limit' in line and len(line.split()) == 6: - self.aimless['DataProcessingResolutionLow'] = line.split()[3] - self.aimless['DataProcessingResolutionHighOuterShell'] = line.split()[ - 5] - if 'High resolution limit' in line and len(line.split()) == 6: - self.aimless['DataProcessingResolutionHigh'] = line.split()[3] - self.aimless['DataProcessingResolutionLowInnerShell'] = line.split()[ - 4] - if 'Rmerge (all I+ and I-)' in line and len(line.split()) == 8: - self.aimless['DataProcessingRmergeOverall'] = line.split()[5] - self.aimless['DataProcessingRmergeLow'] = line.split()[6] - self.aimless['DataProcessingRmergeHigh'] = line.split()[7] - if 'Rmerge (all I+ & I-)' in line and len(line.split()) == 8: - self.aimless['DataProcessingRmergeOverall'] = line.split()[5] - self.aimless['DataProcessingRmergeLow'] = line.split()[6] - self.aimless['DataProcessingRmergeHigh'] = line.split()[7] - if 'Mean((I)/sd(I))' in line and len(line.split()) == 4: - self.aimless['DataProcessingIsigOverall'] = line.split()[1] - self.aimless['DataProcessingIsigHigh'] = line.split()[3] - self.aimless['DataProcessingIsigLow'] = line.split()[2] - if 'Mean(I)/sd(I)' in line and len(line.split()) == 4: - self.aimless['DataProcessingIsigOverall'] = line.split()[1] - self.aimless['DataProcessingIsigHigh'] = line.split()[3] - self.aimless['DataProcessingIsigLow'] = line.split()[2] - if line.startswith('Completeness') and len(line.split()) == 4: - self.aimless['DataProcessingCompletenessOverall'] = line.split()[ - 1] - self.aimless['DataProcessingCompletenessHigh'] = line.split()[ - 3] - self.aimless['DataProcessingCompletenessLow'] = line.split()[2] - if 'Completeness (ellipsoidal)' in line and len(line.split()) == 5: - self.aimless['DataProcessingCompletenessOverall'] = line.split()[ - 2] - self.aimless['DataProcessingCompletenessHigh'] = line.split()[ - 4] - self.aimless['DataProcessingCompletenessLow'] = line.split()[3] - if 'Multiplicity' in line and len(line.split()) == 4: - self.aimless['DataProcessingMultiplicityOverall'] = line.split()[ - 1] - self.aimless['DataProcessingMultiplicityHigh'] = line.split()[ - 3] - self.aimless['DataProcessingMultiplicityLow'] = line.split()[3] - if line.startswith('Mn(I) half-set correlation CC(1/2)') and len(line.split()) == 7: - self.aimless['DataProcessingCChalfOverall'] = line.split()[4] - self.aimless['DataProcessingCChalfLow'] = line.split()[5] - self.aimless['DataProcessingCChalfHigh'] = line.split()[6] - if line.startswith(' CC(1/2)') and len(line.split()) == 4: - self.aimless['DataProcessingCChalfOverall'] = line.split()[1] - self.aimless['DataProcessingCChalfLow'] = line.split()[2] - self.aimless['DataProcessingCChalfHigh'] = line.split()[3] - if line.startswith('Estimates of resolution limits: overall'): + if "Wavelength" in line and len(line.split()) >= 2: + self.aimless["DataCollectionWavelength"] = line.split()[1] + if "Low resolution limit" in line and len(line.split()) == 6: + self.aimless["DataProcessingResolutionLow"] = line.split()[3] + self.aimless["DataProcessingResolutionHighOuterShell"] = line.split()[5] + if "High resolution limit" in line and len(line.split()) == 6: + self.aimless["DataProcessingResolutionHigh"] = line.split()[3] + self.aimless["DataProcessingResolutionLowInnerShell"] = line.split()[4] + if "Rmerge (all I+ and I-)" in line and len(line.split()) == 8: + self.aimless["DataProcessingRmergeOverall"] = line.split()[5] + self.aimless["DataProcessingRmergeLow"] = line.split()[6] + self.aimless["DataProcessingRmergeHigh"] = line.split()[7] + if "Rmerge (all I+ & I-)" in line and len(line.split()) == 8: + self.aimless["DataProcessingRmergeOverall"] = line.split()[5] + self.aimless["DataProcessingRmergeLow"] = line.split()[6] + self.aimless["DataProcessingRmergeHigh"] = line.split()[7] + if "Mean((I)/sd(I))" in line and len(line.split()) == 4: + self.aimless["DataProcessingIsigOverall"] = line.split()[1] + self.aimless["DataProcessingIsigHigh"] = line.split()[3] + self.aimless["DataProcessingIsigLow"] = line.split()[2] + if "Mean(I)/sd(I)" in line and len(line.split()) == 4: + self.aimless["DataProcessingIsigOverall"] = line.split()[1] + self.aimless["DataProcessingIsigHigh"] = line.split()[3] + self.aimless["DataProcessingIsigLow"] = line.split()[2] + if line.startswith("Completeness") and len(line.split()) == 4: + self.aimless["DataProcessingCompletenessOverall"] = line.split()[1] + self.aimless["DataProcessingCompletenessHigh"] = line.split()[3] + self.aimless["DataProcessingCompletenessLow"] = line.split()[2] + if "Completeness (ellipsoidal)" in line and len(line.split()) == 5: + self.aimless["DataProcessingCompletenessOverall"] = line.split()[2] + self.aimless["DataProcessingCompletenessHigh"] = line.split()[4] + self.aimless["DataProcessingCompletenessLow"] = line.split()[3] + if "Multiplicity" in line and len(line.split()) == 4: + self.aimless["DataProcessingMultiplicityOverall"] = line.split()[1] + self.aimless["DataProcessingMultiplicityHigh"] = line.split()[3] + self.aimless["DataProcessingMultiplicityLow"] = line.split()[3] + if ( + line.startswith("Mn(I) half-set correlation CC(1/2)") + and len(line.split()) == 7 + ): + self.aimless["DataProcessingCChalfOverall"] = line.split()[4] + self.aimless["DataProcessingCChalfLow"] = line.split()[5] + self.aimless["DataProcessingCChalfHigh"] = line.split()[6] + if line.startswith(" CC(1/2)") and len(line.split()) == 4: + self.aimless["DataProcessingCChalfOverall"] = line.split()[1] + self.aimless["DataProcessingCChalfLow"] = line.split()[2] + self.aimless["DataProcessingCChalfHigh"] = line.split()[3] + if line.startswith("Estimates of resolution limits: overall"): resolution_at_15_sigma_line_overall_found = True resolution_at_20_sigma_line_overall_found = True if resolution_at_15_sigma_line_overall_found: - if 'from Mn(I/sd)' in line and len(line.split()) >= 7: - if '1.5' in line.split()[3]: - self.aimless['DataProcessingResolutionHigh15sigma'] = line.split()[ - 6][:-1] + if "from Mn(I/sd)" in line and len(line.split()) >= 7: + if "1.5" in line.split()[3]: + self.aimless[ + "DataProcessingResolutionHigh15sigma" + ] = line.split()[6][:-1] resolution_at_15_sigma_line_overall_found = False if resolution_at_20_sigma_line_overall_found: - if 'from Mn(I/sd)' in line and len(line.split()) >= 7: - if '2.0' in line.split()[3]: - self.aimless['DataProcessingResolutionHigh20sigma'] = line.split()[ - 6][:-1] + if "from Mn(I/sd)" in line and len(line.split()) >= 7: + if "2.0" in line.split()[3]: + self.aimless[ + "DataProcessingResolutionHigh20sigma" + ] = line.split()[6][:-1] resolution_at_20_sigma_line_overall_found = False - if (line.startswith('Average unit cell:') or line.startswith(' Unit cell parameters')) and len( - line.split()) == 9: + if ( + line.startswith("Average unit cell:") + or line.startswith(" Unit cell parameters") + ) and len(line.split()) == 9: tmp = [line.split()] a = int(float(tmp[0][3])) b = int(float(tmp[0][4])) @@ -807,111 +1049,149 @@ def aimless_logile(self, logfile): alpha = int(float(tmp[0][6])) beta = int(float(tmp[0][7])) gamma = int(float(tmp[0][8])) - self.aimless['DataProcessingA'] = str(a) - self.aimless['DataProcessingB'] = str(b) - self.aimless['DataProcessingC'] = str(c) - self.aimless['DataProcessingAlpha'] = str(alpha) - self.aimless['DataProcessingBeta'] = str(beta) - self.aimless['DataProcessingGamma'] = str(gamma) - if 'Total number unique' in line and len(line.split()) == 6: - self.aimless['DataProcessingUniqueReflectionsOverall'] = line.split()[ - 3] - if line.startswith('Space group:') or line.startswith(' Spacegroup name'): - if 'Laue' in line: + self.aimless["DataProcessingA"] = str(a) + self.aimless["DataProcessingB"] = str(b) + self.aimless["DataProcessingC"] = str(c) + self.aimless["DataProcessingAlpha"] = str(alpha) + self.aimless["DataProcessingBeta"] = str(beta) + self.aimless["DataProcessingGamma"] = str(gamma) + if "Total number unique" in line and len(line.split()) == 6: + self.aimless["DataProcessingUniqueReflectionsOverall"] = line.split()[3] + if line.startswith("Space group:") or line.startswith(" Spacegroup name"): + if "Laue" in line: continue - if 'Spacegroup name' in line: - self.aimless['DataProcessingSpaceGroup'] = line.replace(' Spacegroup name', '')[:-1].replace(' ', - '') + if "Spacegroup name" in line: + self.aimless["DataProcessingSpaceGroup"] = line.replace( + " Spacegroup name", "" + )[:-1].replace(" ", "") else: - self.aimless['DataProcessingSpaceGroup'] = line.replace('Space group: ', '')[ - :-1] - self.aimless['DataProcessingLattice'] = self.get_lattice_from_space_group( - self.aimless['DataProcessingSpaceGroup']) - self.aimless['DataProcessingPointGroup'] = self.get_pointgroup_from_space_group( - self.aimless['DataProcessingSpaceGroup']) + self.aimless["DataProcessingSpaceGroup"] = line.replace( + "Space group: ", "" + )[:-1] + self.aimless[ + "DataProcessingLattice" + ] = self.get_lattice_from_space_group( + self.aimless["DataProcessingSpaceGroup"] + ) + self.aimless[ + "DataProcessingPointGroup" + ] = self.get_pointgroup_from_space_group( + self.aimless["DataProcessingSpaceGroup"] + ) # print a,b,c,alpha,beta,gamma,self.aimless['DataProcessingLattice'] -# if a != 'n/a' and b != 'n/a' and c != 'n/a' and \ -# alpha != 'n/a' and beta != 'n/a' and gamma != 'n/a' and self.aimless[ -# 'DataProcessingLattice'] != 'n/a': -# self.aimless['DataProcessingUnitCellVolume'] = str( -# self.calc_unitcell_volume_from_logfile(float(a), float(b), float(c), -# math.radians(float(alpha)), -# math.radians(float(beta)), -# math.radians(float(gamma)), -# self.aimless['DataProcessingLattice'])) -# try: -# high_symmetry_boost = self.nr_asu_in_unitcell_for_point_group[ -# self.aimless['DataProcessingPointGroup']] -# self.aimless['DataProcessingScore'] = (float( -# self.aimless['DataProcessingUniqueReflectionsOverall']) * float(self.aimless['DataProcessingCompletenessOverall']) * high_symmetry_boost * float(self.aimless['DataProcessingIsigOverall'])) / float( -# self.aimless['DataProcessingUnitCellVolume']) -# except ValueError: -# self.aimless['DataProcessingScore'] = 0.0 -# self.aimless['DataProcessingUnitCell'] = str(a) + ' ' + str(b) + ' ' + str(c) + ' ' + str(alpha) + ' ' + str( -# beta) + ' ' + str(gamma) -# self.aimless['DataProcessingResolutionOverall'] = str( -# self.aimless['DataProcessingResolutionLow']) + ' - ' + str(self.aimless['DataProcessingResolutionHigh']) + + # if a != 'n/a' and b != 'n/a' and c != 'n/a' and \ + # alpha != 'n/a' and beta != 'n/a' and gamma != 'n/a' and self.aimless[ + # 'DataProcessingLattice'] != 'n/a': + # self.aimless['DataProcessingUnitCellVolume'] = str( + # self.calc_unitcell_volume_from_logfile(float(a), float(b), float(c), + # math.radians(float(alpha)), + # math.radians(float(beta)), + # math.radians(float(gamma)), + # self.aimless['DataProcessingLattice'])) + # try: + # high_symmetry_boost = self.nr_asu_in_unitcell_for_point_group[ + # self.aimless['DataProcessingPointGroup']] + # self.aimless['DataProcessingScore'] = (float( + # self.aimless['DataProcessingUniqueReflectionsOverall']) * float(self.aimless['DataProcessingCompletenessOverall']) * high_symmetry_boost * float(self.aimless['DataProcessingIsigOverall'])) / float( + # self.aimless['DataProcessingUnitCellVolume']) + # except ValueError: + # self.aimless['DataProcessingScore'] = 0.0 + # self.aimless['DataProcessingUnitCell'] = str(a) + ' ' + str(b) + ' ' + str(c) + ' ' + str(alpha) + ' ' + str( + # beta) + ' ' + str(gamma) + # self.aimless['DataProcessingResolutionOverall'] = str( + # self.aimless['DataProcessingResolutionLow']) + ' - ' + str(self.aimless['DataProcessingResolutionHigh']) def json_logfile(self, logfile): - with open(logfile, 'r') as log: + with open(logfile, "r") as log: data = log.read() obj = json.loads(data) - self.aimless['DataProcessingResolutionLow'] = str( - round(math.sqrt(1/float(obj['d_star_sq_max'][0])), 2)) - self.aimless['DataProcessingResolutionLowInnerShell'] = str( - round(math.sqrt(1/float(obj['d_star_sq_max'][1])), 2)) - self.aimless['DataProcessingResolutionHigh'] = str( - round(math.sqrt(1/float(obj['d_star_sq_min'][len(obj['d_star_sq_min'])-1])), 2)) - self.aimless['DataProcessingResolutionHighOuterShell'] = str( - round(math.sqrt(1/float(obj['d_star_sq_min'][len(obj['d_star_sq_min'])-2])), 2)) - self.aimless['DataProcessingResolutionOverall'] = self.aimless['DataProcessingResolutionLow'] + \ - '-' + self.aimless['DataProcessingResolutionHigh'] - self.aimless['DataProcessingRmergeOverall'] = str( - round(obj['overall']['r_merge'], 3)) - self.aimless['DataProcessingRmergeLow'] = str( - round(obj['r_merge'][0], 3)) - self.aimless['DataProcessingRmergeHigh'] = str( - round(obj['r_merge'][len(obj['r_merge'])-1], 3)) - self.aimless['DataProcessingIsigOverall'] = str( - round(obj['overall']['i_over_sigma_mean'], 1)) - self.aimless['DataProcessingIsigLow'] = str( - round(obj['i_over_sigma_mean'][0], 1)) - self.aimless['DataProcessingIsigHigh'] = str( - round(obj['i_over_sigma_mean'][len(obj['i_over_sigma_mean'])-1], 1)) - self.aimless['DataProcessingCompletenessOverall'] = str( - round(obj['overall']['completeness'], 1)) - self.aimless['DataProcessingCompletenessLow'] = str( - round(obj['completeness'][0], 1)) - self.aimless['DataProcessingCompletenessHigh'] = str( - round(obj['completeness'][len(obj['completeness'])-1], 1)) - self.aimless['DataProcessingMultiplicityOverall'] = str( - round(obj['overall']['multiplicity'], 1)) - self.aimless['DataProcessingMultiplicityLow'] = str( - round(obj['multiplicity'][0], 1)) - self.aimless['DataProcessingMultiplicityHigh'] = str( - round(obj['multiplicity'][len(obj['multiplicity'])-1], 1)) - self.aimless['DataProcessingCChalfOverall'] = str( - round(obj['overall']['cc_one_half'], 2)) - self.aimless['DataProcessingCChalfLow'] = str( - round(obj['cc_one_half'][0], 2)) - self.aimless['DataProcessingCChalfHigh'] = str( - round(obj['cc_one_half'][len(obj['cc_one_half'])-1], 2)) -# self.aimless['DataProcessingResolutionHigh15sigma'] = - - self.aimless['DataProcessingUniqueReflectionsLow'] = str( - obj['n_uniq'][0]) - self.aimless['DataProcessingUniqueReflectionsHigh'] = str( - obj['n_uniq'][len(obj['n_uniq'])-1]) - - self.aimless['DataProcessingUniqueReflectionsOverall'] = str( - obj['overall']['n_obs']) -# self.aimless['DataProcessingPointGroup'] = -# self.aimless['DataProcessingUnitCellVolume'] = -# self.aimless['DataProcessingAlert'] = -# self.aimless['DataProcessingScore'] = - json_name = logfile[logfile.rfind('/')+1:] - mmcif_file = logfile.replace( - 'LogFiles', 'DataFiles').replace(json_name, 'xia2.mmcif') + self.aimless["DataProcessingResolutionLow"] = str( + round(math.sqrt(1 / float(obj["d_star_sq_max"][0])), 2) + ) + self.aimless["DataProcessingResolutionLowInnerShell"] = str( + round(math.sqrt(1 / float(obj["d_star_sq_max"][1])), 2) + ) + self.aimless["DataProcessingResolutionHigh"] = str( + round( + math.sqrt( + 1 / float(obj["d_star_sq_min"][len(obj["d_star_sq_min"]) - 1]) + ), + 2, + ) + ) + self.aimless["DataProcessingResolutionHighOuterShell"] = str( + round( + math.sqrt( + 1 / float(obj["d_star_sq_min"][len(obj["d_star_sq_min"]) - 2]) + ), + 2, + ) + ) + self.aimless["DataProcessingResolutionOverall"] = ( + self.aimless["DataProcessingResolutionLow"] + + "-" + + self.aimless["DataProcessingResolutionHigh"] + ) + self.aimless["DataProcessingRmergeOverall"] = str( + round(obj["overall"]["r_merge"], 3) + ) + self.aimless["DataProcessingRmergeLow"] = str(round(obj["r_merge"][0], 3)) + self.aimless["DataProcessingRmergeHigh"] = str( + round(obj["r_merge"][len(obj["r_merge"]) - 1], 3) + ) + self.aimless["DataProcessingIsigOverall"] = str( + round(obj["overall"]["i_over_sigma_mean"], 1) + ) + self.aimless["DataProcessingIsigLow"] = str( + round(obj["i_over_sigma_mean"][0], 1) + ) + self.aimless["DataProcessingIsigHigh"] = str( + round(obj["i_over_sigma_mean"][len(obj["i_over_sigma_mean"]) - 1], 1) + ) + self.aimless["DataProcessingCompletenessOverall"] = str( + round(obj["overall"]["completeness"], 1) + ) + self.aimless["DataProcessingCompletenessLow"] = str( + round(obj["completeness"][0], 1) + ) + self.aimless["DataProcessingCompletenessHigh"] = str( + round(obj["completeness"][len(obj["completeness"]) - 1], 1) + ) + self.aimless["DataProcessingMultiplicityOverall"] = str( + round(obj["overall"]["multiplicity"], 1) + ) + self.aimless["DataProcessingMultiplicityLow"] = str( + round(obj["multiplicity"][0], 1) + ) + self.aimless["DataProcessingMultiplicityHigh"] = str( + round(obj["multiplicity"][len(obj["multiplicity"]) - 1], 1) + ) + self.aimless["DataProcessingCChalfOverall"] = str( + round(obj["overall"]["cc_one_half"], 2) + ) + self.aimless["DataProcessingCChalfLow"] = str(round(obj["cc_one_half"][0], 2)) + self.aimless["DataProcessingCChalfHigh"] = str( + round(obj["cc_one_half"][len(obj["cc_one_half"]) - 1], 2) + ) + # self.aimless['DataProcessingResolutionHigh15sigma'] = + + self.aimless["DataProcessingUniqueReflectionsLow"] = str(obj["n_uniq"][0]) + self.aimless["DataProcessingUniqueReflectionsHigh"] = str( + obj["n_uniq"][len(obj["n_uniq"]) - 1] + ) + + self.aimless["DataProcessingUniqueReflectionsOverall"] = str( + obj["overall"]["n_obs"] + ) + # self.aimless['DataProcessingPointGroup'] = + # self.aimless['DataProcessingUnitCellVolume'] = + # self.aimless['DataProcessingAlert'] = + # self.aimless['DataProcessingScore'] = + json_name = logfile[logfile.rfind("/") + 1 :] + mmcif_file = logfile.replace("LogFiles", "DataFiles").replace( + json_name, "xia2.mmcif" + ) if os.path.isfile(mmcif_file): self.read_mmcif(mmcif_file) elif os.path.isfile("%s.bz2" % mmcif_file): @@ -920,82 +1200,130 @@ def json_logfile(self, logfile): def make_pseudo_aimless_log_from_json(self, logfile): self.json_logfile(logfile) template = ( - '==============================================================\n' - '\n' - ' $TEXT:Result: $$ $$\n' - 'Summary data for Project: nt11175v63 Crystal: xPHIPAx17245 Dataset: SAD\n' - '\n' - ' Overall InnerShell OuterShell\n' - 'Low resolution limit {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingResolutionLow'], self.aimless['DataProcessingResolutionLow'], self.aimless['DataProcessingResolutionHighOuterShell']) + - 'High resolution limit {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingResolutionHigh'], self.aimless['DataProcessingResolutionLowInnerShell'], self.aimless['DataProcessingResolutionHigh']) + - '\n' - 'Rmerge (within I+/I-) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingRmergeOverall'], self.aimless['DataProcessingRmergeLow'], self.aimless['DataProcessingRmergeHigh']) + - 'Rmerge (all I+ and I-) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingRmergeOverall'], self.aimless['DataProcessingRmergeLow'], self.aimless['DataProcessingRmergeHigh']) + - 'Rmeas (within I+/I-) - - - \n' - 'Rmeas (all I+ & I-) - - - \n' - 'Rpim (within I+/I-) - - - \n' - 'Rpim (all I+ & I-) - - - \n' - 'Rmerge in top intensity bin - - - \n' - 'Total number of observations - - - \n' - 'Total number unique {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingUniqueReflectionsOverall'], self.aimless['DataProcessingUniqueReflectionsLow'], self.aimless['DataProcessingUniqueReflectionsHigh']) + - 'Mean((I)/sd(I)) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingIsigOverall'], self.aimless['DataProcessingIsigLow'], self.aimless['DataProcessingIsigHigh']) + - 'Mn(I) half-set correlation CC(1/2) {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingCChalfOverall'], self.aimless['DataProcessingCChalfLow'], self.aimless['DataProcessingCChalfHigh']) + - 'Completeness {0!s} {1!s} {2!s}\n'.format(self.aimless['DataProcessingCompletenessOverall'], self.aimless['DataProcessingCompletenessLow'], self.aimless['DataProcessingCompletenessHigh']) + - 'Multiplicity {0!s} {1!s} {2!s}\n'.format( - self.aimless['DataProcessingMultiplicityOverall'], self.aimless['DataProcessingMultiplicityLow'], self.aimless['DataProcessingMultiplicityHigh']) + "==============================================================\n" + "\n" + " $TEXT:Result: $$ $$\n" + "Summary data for Project: nt11175v63 Crystal: xPHIPAx17245 Dataset: SAD\n" + "\n" + " Overall InnerShell OuterShell\n" + "Low resolution limit {0!s} {1!s} {2!s}\n".format( + self.aimless["DataProcessingResolutionLow"], + self.aimless["DataProcessingResolutionLow"], + self.aimless["DataProcessingResolutionHighOuterShell"], + ) + + "High resolution limit {0!s} {1!s} {2!s}\n".format( + self.aimless["DataProcessingResolutionHigh"], + self.aimless["DataProcessingResolutionLowInnerShell"], + self.aimless["DataProcessingResolutionHigh"], + ) + + "\n" + "Rmerge (within I+/I-) {0!s} {1!s} {2!s}\n".format( + self.aimless["DataProcessingRmergeOverall"], + self.aimless["DataProcessingRmergeLow"], + self.aimless["DataProcessingRmergeHigh"], + ) + + "Rmerge (all I+ and I-) {0!s} {1!s} {2!s}\n".format( + self.aimless["DataProcessingRmergeOverall"], + self.aimless["DataProcessingRmergeLow"], + self.aimless["DataProcessingRmergeHigh"], + ) + + "Rmeas (within I+/I-) - - - \n" + "Rmeas (all I+ & I-) - - - \n" + "Rpim (within I+/I-) - - - \n" + "Rpim (all I+ & I-) - - - \n" + "Rmerge in top intensity bin - - - \n" + "Total number of observations - - - \n" + "Total number unique {0!s} {1!s} {2!s}\n".format( + self.aimless["DataProcessingUniqueReflectionsOverall"], + self.aimless["DataProcessingUniqueReflectionsLow"], + self.aimless["DataProcessingUniqueReflectionsHigh"], + ) + + "Mean((I)/sd(I)) {0!s} {1!s} {2!s}\n".format( + self.aimless["DataProcessingIsigOverall"], + self.aimless["DataProcessingIsigLow"], + self.aimless["DataProcessingIsigHigh"], + ) + + "Mn(I) half-set correlation CC(1/2) {0!s} {1!s} {2!s}\n".format( + self.aimless["DataProcessingCChalfOverall"], + self.aimless["DataProcessingCChalfLow"], + self.aimless["DataProcessingCChalfHigh"], + ) + + "Completeness {0!s} {1!s} {2!s}\n".format( + self.aimless["DataProcessingCompletenessOverall"], + self.aimless["DataProcessingCompletenessLow"], + self.aimless["DataProcessingCompletenessHigh"], + ) + + "Multiplicity {0!s} {1!s} {2!s}\n".format( + self.aimless["DataProcessingMultiplicityOverall"], + self.aimless["DataProcessingMultiplicityLow"], + self.aimless["DataProcessingMultiplicityHigh"], + ) ) - f = open('aimless_dials.log', 'w') + f = open("aimless_dials.log", "w") f.write(template) f.close() def read_mmcif(self, mmcif): for line in open_decompress_file(mmcif): - if line.startswith('_cell.angle_alpha '): - self.aimless['DataProcessingAlpha'] = line.split()[1] - elif line.startswith('_cell.angle_beta '): - self.aimless['DataProcessingBeta'] = line.split()[1] - elif line.startswith('_cell.angle_gamma '): - self.aimless['DataProcessingGamma'] = line.split()[1] - elif line.startswith('_cell.length_a '): - self.aimless['DataProcessingA'] = line.split()[1] - elif line.startswith('_cell.length_b '): - self.aimless['DataProcessingB'] = line.split()[1] - elif line.startswith('_cell.length_c '): - self.aimless['DataProcessingC'] = line.split()[1] - elif line.startswith('_diffrn_radiation_wavelength.wavelength'): - self.aimless['DataCollectionWavelength'] = line.split()[1] - elif line.startswith('_symmetry.space_group_name_H-M'): - self.aimless['DataProcessingSpaceGroup'] = line[line.find( - "'")+1:line.rfind("'")].replace(' ', '') - if 'R32:H' in self.aimless['DataProcessingSpaceGroup']: - self.aimless['DataProcessingSpaceGroup'] = 'H32' - if 'R3:H' in self.aimless['DataProcessingSpaceGroup']: - self.aimless['DataProcessingSpaceGroup'] = 'H3' - self.aimless['DataProcessingPointGroup'] = self.get_pointgroup_from_space_group( - self.aimless['DataProcessingSpaceGroup']) - elif line.startswith('_space_group.crystal_system'): - self.aimless['DataProcessingLattice'] = line.split()[1] - if self.aimless['DataProcessingLattice'] == 'trigonal': - self.aimless['DataProcessingLattice'] = 'hexagonal' - self.aimless['DataProcessingUnitCell'] = self.aimless['DataProcessingA'] + ' ' + self.aimless[ - 'DataProcessingA'] + ' ' + self.aimless['DataProcessingA'] + ' ' + self.aimless[ - 'DataProcessingA'] + ' ' + self.aimless[ - 'DataProcessingA'] + ' ' + self.aimless['DataProcessingA'] + if line.startswith("_cell.angle_alpha "): + self.aimless["DataProcessingAlpha"] = line.split()[1] + elif line.startswith("_cell.angle_beta "): + self.aimless["DataProcessingBeta"] = line.split()[1] + elif line.startswith("_cell.angle_gamma "): + self.aimless["DataProcessingGamma"] = line.split()[1] + elif line.startswith("_cell.length_a "): + self.aimless["DataProcessingA"] = line.split()[1] + elif line.startswith("_cell.length_b "): + self.aimless["DataProcessingB"] = line.split()[1] + elif line.startswith("_cell.length_c "): + self.aimless["DataProcessingC"] = line.split()[1] + elif line.startswith("_diffrn_radiation_wavelength.wavelength"): + self.aimless["DataCollectionWavelength"] = line.split()[1] + elif line.startswith("_symmetry.space_group_name_H-M"): + self.aimless["DataProcessingSpaceGroup"] = line[ + line.find("'") + 1 : line.rfind("'") + ].replace(" ", "") + if "R32:H" in self.aimless["DataProcessingSpaceGroup"]: + self.aimless["DataProcessingSpaceGroup"] = "H32" + if "R3:H" in self.aimless["DataProcessingSpaceGroup"]: + self.aimless["DataProcessingSpaceGroup"] = "H3" + self.aimless[ + "DataProcessingPointGroup" + ] = self.get_pointgroup_from_space_group( + self.aimless["DataProcessingSpaceGroup"] + ) + elif line.startswith("_space_group.crystal_system"): + self.aimless["DataProcessingLattice"] = line.split()[1] + if self.aimless["DataProcessingLattice"] == "trigonal": + self.aimless["DataProcessingLattice"] = "hexagonal" + self.aimless["DataProcessingUnitCell"] = ( + self.aimless["DataProcessingA"] + + " " + + self.aimless["DataProcessingA"] + + " " + + self.aimless["DataProcessingA"] + + " " + + self.aimless["DataProcessingA"] + + " " + + self.aimless["DataProcessingA"] + + " " + + self.aimless["DataProcessingA"] + ) def get_lattice_from_space_group(self, logfile_spacegroup): - lattice_type = 'n/a' + lattice_type = "n/a" for lattice in self.space_group_dict: for spacegroup in self.space_group_dict[lattice]: - if logfile_spacegroup.replace(' ', '') == spacegroup: + if logfile_spacegroup.replace(" ", "") == spacegroup: lattice_type = lattice break return lattice_type def get_pointgroup_from_space_group(self, logfile_spacegroup): - pointgroup = 'n/a' + pointgroup = "n/a" for pg in self.point_group_dict: for spacegroup in self.point_group_dict[pg]: - if logfile_spacegroup.replace(' ', '') == spacegroup: + if logfile_spacegroup.replace(" ", "") == spacegroup: pointgroup = pg break return pointgroup @@ -1003,121 +1331,142 @@ def get_pointgroup_from_space_group(self, logfile_spacegroup): def calc_unitcell_volume_from_logfile(self, a, b, c, alpha, beta, gamma, lattice): # print '>>>',a,b,c,alpha,beta,gamma,lattice unitcell_volume = 0 - if lattice == 'triclinic': - unitcell_volume = a*b*c * \ - math.sqrt((1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2) - + 2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma))) -# print 'unit cell volume',unitcell_volume -# if lattice=='monoclinic': - if 'monoclinic' in lattice: - unitcell_volume = round(a*b*c*math.sin(beta), 1) - if lattice == 'orthorhombic' or lattice == 'tetragonal' or lattice == 'cubic': - unitcell_volume = round(a*b*c, 1) - if lattice == 'hexagonal' or lattice == 'rhombohedral': - unitcell_volume = round(a*b*c*(math.sin(math.radians(60))), 1) + if lattice == "triclinic": + unitcell_volume = ( + a + * b + * c + * math.sqrt( + ( + 1 + - math.cos(alpha) ** 2 + - math.cos(beta) ** 2 + - math.cos(gamma) ** 2 + ) + + 2 * (math.cos(alpha) * math.cos(beta) * math.cos(gamma)) + ) + ) + # print 'unit cell volume',unitcell_volume + # if lattice=='monoclinic': + if "monoclinic" in lattice: + unitcell_volume = round(a * b * c * math.sin(beta), 1) + if lattice == "orthorhombic" or lattice == "tetragonal" or lattice == "cubic": + unitcell_volume = round(a * b * c, 1) + if lattice == "hexagonal" or lattice == "rhombohedral": + unitcell_volume = round(a * b * c * (math.sin(math.radians(60))), 1) return unitcell_volume -# def get_all_values_as_dict(self): -# info = { 'unitcell': 'n/a', -# 'spacegroup': 'n/a', -# 'unitcell_volume': 'n/a', -# 'bravais_lattice': 'n/a' } + # def get_all_values_as_dict(self): + # info = { 'unitcell': 'n/a', + # 'spacegroup': 'n/a', + # 'unitcell_volume': 'n/a', + # 'bravais_lattice': 'n/a' } def PDBheader(self, pdbfile): - PDBinfo = {'Rcryst': 'n/a', - 'RcrystTL': 'gray', - 'Rfree': 'n/a', - 'RfreeTL': 'gray', - 'SpaceGroup': 'n/a', - 'PointGroup': 'n/a', - 'UnitCell': 'n/a', - 'ResolutionHigh': 'n/a', - 'ResolutionColor': 'gray', - 'Lattice': 'n/a', - 'UnitCellVolume': 0, - 'Alert': '#E0E0E0', - 'rmsdBonds': 'n/a', - 'rmsdBondsTL': 'gray', - 'rmsdAngles': 'n/a', - 'rmsdAnglesTL': 'gray', - 'TwinFraction': 'n/a'} - - a = 'n/a' - b = 'n/a' - c = 'n/a' - alpha = 'n/a' - beta = 'n/a' - gamma = 'n/a' + PDBinfo = { + "Rcryst": "n/a", + "RcrystTL": "gray", + "Rfree": "n/a", + "RfreeTL": "gray", + "SpaceGroup": "n/a", + "PointGroup": "n/a", + "UnitCell": "n/a", + "ResolutionHigh": "n/a", + "ResolutionColor": "gray", + "Lattice": "n/a", + "UnitCellVolume": 0, + "Alert": "#E0E0E0", + "rmsdBonds": "n/a", + "rmsdBondsTL": "gray", + "rmsdAngles": "n/a", + "rmsdAnglesTL": "gray", + "TwinFraction": "n/a", + } + + a = "n/a" + b = "n/a" + c = "n/a" + alpha = "n/a" + beta = "n/a" + gamma = "n/a" if os.path.isfile(pdbfile): for line in open(pdbfile): try: - if line.startswith('REMARK 3 R VALUE (WORKING + TEST SET) :'): - PDBinfo['Rcryst'] = line.split()[9] - if float(PDBinfo['Rcryst']) > 0.4: - PDBinfo['Alert'] = '#FF0000' - PDBinfo['RcrystTL'] = 'red' - if 0.4 >= float(PDBinfo['Rcryst']) >= 0.3: - PDBinfo['Alert'] = '#FF9900' - PDBinfo['RcrystTL'] = 'orange' - if float(PDBinfo['Rcryst']) < 0.3: - PDBinfo['Alert'] = '#00FF00' - PDBinfo['RcrystTL'] = 'green' - if line.startswith('REMARK 3 FREE R VALUE :'): - PDBinfo['Rfree'] = line.split()[6] - if float(PDBinfo['Rfree']) > 0.4: - PDBinfo['Alert'] = '#FF0000' - PDBinfo['RfreeTL'] = 'red' - if 0.4 >= float(PDBinfo['Rfree']) >= 0.3: - PDBinfo['Alert'] = '#FF9900' - PDBinfo['RfreeTL'] = 'orange' - if float(PDBinfo['Rfree']) < 0.3: - PDBinfo['Alert'] = '#00FF00' - PDBinfo['RfreeTL'] = 'green' + if line.startswith( + "REMARK 3 R VALUE (WORKING + TEST SET) :" + ): + PDBinfo["Rcryst"] = line.split()[9] + if float(PDBinfo["Rcryst"]) > 0.4: + PDBinfo["Alert"] = "#FF0000" + PDBinfo["RcrystTL"] = "red" + if 0.4 >= float(PDBinfo["Rcryst"]) >= 0.3: + PDBinfo["Alert"] = "#FF9900" + PDBinfo["RcrystTL"] = "orange" + if float(PDBinfo["Rcryst"]) < 0.3: + PDBinfo["Alert"] = "#00FF00" + PDBinfo["RcrystTL"] = "green" + if line.startswith( + "REMARK 3 FREE R VALUE :" + ): + PDBinfo["Rfree"] = line.split()[6] + if float(PDBinfo["Rfree"]) > 0.4: + PDBinfo["Alert"] = "#FF0000" + PDBinfo["RfreeTL"] = "red" + if 0.4 >= float(PDBinfo["Rfree"]) >= 0.3: + PDBinfo["Alert"] = "#FF9900" + PDBinfo["RfreeTL"] = "orange" + if float(PDBinfo["Rfree"]) < 0.3: + PDBinfo["Alert"] = "#00FF00" + PDBinfo["RfreeTL"] = "green" except ValueError: pass - if line.startswith('REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) :'): - PDBinfo['ResolutionHigh'] = line.split()[7] + if line.startswith("REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) :"): + PDBinfo["ResolutionHigh"] = line.split()[7] try: if float(line.split()[7]) < 2.4: - PDBinfo['ResolutionColor'] = 'green' + PDBinfo["ResolutionColor"] = "green" if 2.4 <= float(line.split()[7]) < 2.8: - PDBinfo['ResolutionColor'] = 'orange' + PDBinfo["ResolutionColor"] = "orange" if float(line.split()[7]) >= 2.8: - PDBinfo['ResolutionColor'] = 'red' + PDBinfo["ResolutionColor"] = "red" except ValueError: pass - if line.startswith('REMARK 3 BOND LENGTHS REFINED ATOMS (A):'): - PDBinfo['rmsdBonds'] = line.split()[9] + if line.startswith( + "REMARK 3 BOND LENGTHS REFINED ATOMS (A):" + ): + PDBinfo["rmsdBonds"] = line.split()[9] try: if float(line.split()[9]) < 0.02: - PDBinfo['rmsdBondsTL'] = 'green' + PDBinfo["rmsdBondsTL"] = "green" if 0.02 <= float(line.split()[9]) < 0.03: - PDBinfo['rmsdBondsTL'] = 'orange' + PDBinfo["rmsdBondsTL"] = "orange" if float(line.split()[9]) >= 0.03: - PDBinfo['rmsdBondsTL'] = 'red' + PDBinfo["rmsdBondsTL"] = "red" except ValueError: pass - if line.startswith('REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES):'): - PDBinfo['rmsdAngles'] = line.split()[9] + if line.startswith( + "REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES):" + ): + PDBinfo["rmsdAngles"] = line.split()[9] try: if float(line.split()[9]) < 2.0: - PDBinfo['rmsdAnglesTL'] = 'green' + PDBinfo["rmsdAnglesTL"] = "green" if 2.0 <= float(line.split()[9]) < 3.0: - PDBinfo['rmsdAnglesTL'] = 'orange' + PDBinfo["rmsdAnglesTL"] = "orange" if float(line.split()[9]) >= 3.0: - PDBinfo['rmsdAnglesTL'] = 'red' + PDBinfo["rmsdAnglesTL"] = "red" except ValueError: pass - if line.startswith('REMARK 3 TWIN FRACTION'): + if line.startswith("REMARK 3 TWIN FRACTION"): try: - PDBinfo['TwinFraction'] = line.split()[5] + PDBinfo["TwinFraction"] = line.split()[5] except IndexError: pass - if line.startswith('CRYST1'): + if line.startswith("CRYST1"): a = int(float(line.split()[1])) b = int(float(line.split()[2])) c = int(float(line.split()[3])) @@ -1125,98 +1474,136 @@ def PDBheader(self, pdbfile): beta = int(float(line.split()[5])) gamma = int(float(line.split()[6])) - PDBinfo['UnitCell'] = line.split()[1]+' '+line.split()[2]+' '+line.split()[3]+' ' + \ - line.split()[4]+' '+line.split()[5]+' '+line.split()[6] -# PDBinfo['SpaceGroup']=line[55:len(line)-1].replace(' ','').rstrip('\r') - PDBinfo['SpaceGroup'] = str(line[55:65]).rstrip() - - PDBinfo['Lattice'] = self.get_lattice_from_space_group( - PDBinfo['SpaceGroup']) - PDBinfo['PointGroup'] = self.get_pointgroup_from_space_group( - PDBinfo['SpaceGroup']) - if a != 'n/a' and b != 'n/a' and c != 'n/a' and \ - alpha != 'n/a' and beta != 'n/a' and gamma != 'n/a' and PDBinfo['Lattice'] != 'n/a': - PDBinfo['UnitCellVolume'] = self.calc_unitcell_volume_from_logfile(float(a), float(b), float(c), - math.radians( - float(alpha)), - math.radians( - float(beta)), - math.radians( - float(gamma)), - PDBinfo['Lattice']) + PDBinfo["UnitCell"] = ( + line.split()[1] + + " " + + line.split()[2] + + " " + + line.split()[3] + + " " + + line.split()[4] + + " " + + line.split()[5] + + " " + + line.split()[6] + ) + # PDBinfo['SpaceGroup']=line[55:len(line)-1].replace(' ','').rstrip('\r') + PDBinfo["SpaceGroup"] = str(line[55:65]).rstrip() + + PDBinfo["Lattice"] = self.get_lattice_from_space_group( + PDBinfo["SpaceGroup"] + ) + PDBinfo["PointGroup"] = self.get_pointgroup_from_space_group( + PDBinfo["SpaceGroup"] + ) + if ( + a != "n/a" + and b != "n/a" + and c != "n/a" + and alpha != "n/a" + and beta != "n/a" + and gamma != "n/a" + and PDBinfo["Lattice"] != "n/a" + ): + PDBinfo[ + "UnitCellVolume" + ] = self.calc_unitcell_volume_from_logfile( + float(a), + float(b), + float(c), + math.radians(float(alpha)), + math.radians(float(beta)), + math.radians(float(gamma)), + PDBinfo["Lattice"], + ) return PDBinfo def dict_for_datasource_update(self, pdbfile): pdb = self.PDBheader(pdbfile) - db_dict = {'RefinementPDB_latest': os.path.realpath(pdbfile), 'RefinementRcryst': pdb['Rcryst'], - 'RefinementRcrystTraficLight': pdb['RcrystTL'], 'RefinementRfree': pdb['Rfree'], - 'RefinementRfreeTraficLight': pdb['RfreeTL'], 'RefinementRmsdBonds': pdb['rmsdBonds'], - 'RefinementRmsdBondsTL': pdb['rmsdBondsTL'], 'RefinementRmsdAngles': pdb['rmsdAngles'], - 'RefinementRmsdAnglesTL': pdb['rmsdAnglesTL'], 'RefinementSpaceGroup': pdb['SpaceGroup'], - 'RefinementResolution': pdb['ResolutionHigh'], 'RefinementResolutionTL': pdb['ResolutionColor']} + db_dict = { + "RefinementPDB_latest": os.path.realpath(pdbfile), + "RefinementRcryst": pdb["Rcryst"], + "RefinementRcrystTraficLight": pdb["RcrystTL"], + "RefinementRfree": pdb["Rfree"], + "RefinementRfreeTraficLight": pdb["RfreeTL"], + "RefinementRmsdBonds": pdb["rmsdBonds"], + "RefinementRmsdBondsTL": pdb["rmsdBondsTL"], + "RefinementRmsdAngles": pdb["rmsdAngles"], + "RefinementRmsdAnglesTL": pdb["rmsdAnglesTL"], + "RefinementSpaceGroup": pdb["SpaceGroup"], + "RefinementResolution": pdb["ResolutionHigh"], + "RefinementResolutionTL": pdb["ResolutionColor"], + } return db_dict def update_datasource_with_PDBheader(self, xtal, datasource, pdbfile): pdb = self.PDBheader(pdbfile) - db_dict = {'RefinementPDB_latest': os.path.realpath(pdbfile), 'RefinementRcryst': pdb['Rcryst'], - 'RefinementRcrystTraficLight': pdb['RcrystTL'], 'RefinementRfree': pdb['Rfree'], - 'RefinementRfreeTraficLight': pdb['RfreeTL'], 'RefinementRmsdBonds': pdb['rmsdBonds'], - 'RefinementRmsdBondsTL': pdb['rmsdBondsTL'], 'RefinementRmsdAngles': pdb['rmsdAngles'], - 'RefinementRmsdAnglesTL': pdb['rmsdAnglesTL'], 'RefinementSpaceGroup': pdb['SpaceGroup'], - 'RefinementResolution': pdb['ResolutionHigh'], 'RefinementResolutionTL': pdb['ResolutionColor']} + db_dict = { + "RefinementPDB_latest": os.path.realpath(pdbfile), + "RefinementRcryst": pdb["Rcryst"], + "RefinementRcrystTraficLight": pdb["RcrystTL"], + "RefinementRfree": pdb["Rfree"], + "RefinementRfreeTraficLight": pdb["RfreeTL"], + "RefinementRmsdBonds": pdb["rmsdBonds"], + "RefinementRmsdBondsTL": pdb["rmsdBondsTL"], + "RefinementRmsdAngles": pdb["rmsdAngles"], + "RefinementRmsdAnglesTL": pdb["rmsdAnglesTL"], + "RefinementSpaceGroup": pdb["SpaceGroup"], + "RefinementResolution": pdb["ResolutionHigh"], + "RefinementResolutionTL": pdb["ResolutionColor"], + } print(db_dict) db = XChemDB.data_source(datasource) db.update_data_source(xtal, db_dict) - def update_datasource_with_phenix_validation_summary(self, xtal, datasource, validation_summary): + def update_datasource_with_phenix_validation_summary( + self, xtal, datasource, validation_summary + ): db_dict = {} if os.path.isfile(validation_summary): for line in open(validation_summary): - if 'molprobity score' in line.lower(): + if "molprobity score" in line.lower(): if len(line.split()) >= 4: - db_dict['RefinementMolProbityScore'] = line.split()[3] + db_dict["RefinementMolProbityScore"] = line.split()[3] if float(line.split()[3]) < 2: - db_dict['RefinementMolProbityScoreTL'] = 'green' + db_dict["RefinementMolProbityScoreTL"] = "green" if 2 <= float(line.split()[3]) < 3: - db_dict['RefinementMolProbityScoreTL'] = 'orange' + db_dict["RefinementMolProbityScoreTL"] = "orange" if float(line.split()[3]) >= 3: - db_dict['RefinementMolProbityScoreTL'] = 'red' + db_dict["RefinementMolProbityScoreTL"] = "red" - if 'ramachandran outliers' in line.lower(): + if "ramachandran outliers" in line.lower(): if len(line.split()) >= 4: - db_dict['RefinementRamachandranOutliers'] = line.split()[ - 3] + db_dict["RefinementRamachandranOutliers"] = line.split()[3] if float(line.split()[3]) < 0.3: - db_dict['RefinementRamachandranOutliersTL'] = 'green' + db_dict["RefinementRamachandranOutliersTL"] = "green" if 0.3 <= float(line.split()[3]) < 1: - db_dict['RefinementRamachandranOutliersTL'] = 'orange' + db_dict["RefinementRamachandranOutliersTL"] = "orange" if float(line.split()[3]) >= 1: - db_dict['RefinementRamachandranOutliersTL'] = 'red' + db_dict["RefinementRamachandranOutliersTL"] = "red" - if 'favored' in line.lower(): + if "favored" in line.lower(): if len(line.split()) >= 3: - db_dict['RefinementRamachandranFavored'] = line.split()[ - 2] + db_dict["RefinementRamachandranFavored"] = line.split()[2] if float(line.split()[2]) < 90: - db_dict['RefinementRamachandranFavoredTL'] = 'red' + db_dict["RefinementRamachandranFavoredTL"] = "red" if 90 <= float(line.split()[2]) < 98: - db_dict['RefinementRamachandranFavoredTL'] = 'orange' + db_dict["RefinementRamachandranFavoredTL"] = "orange" if float(line.split()[2]) >= 98: - db_dict['RefinementRamachandranFavoredTL'] = 'green' + db_dict["RefinementRamachandranFavoredTL"] = "green" else: - db_dict['RefinementMolProbityScore'] = '-' - db_dict['RefinementMolProbityScoreTL'] = 'gray' - db_dict['RefinementRamachandranOutliers'] = '-' - db_dict['RefinementRamachandranOutliersTL'] = 'gray' - db_dict['RefinementRamachandranFavored'] = '-' - db_dict['RefinementRamachandranFavoredTL'] = 'gray' + db_dict["RefinementMolProbityScore"] = "-" + db_dict["RefinementMolProbityScoreTL"] = "gray" + db_dict["RefinementRamachandranOutliers"] = "-" + db_dict["RefinementRamachandranOutliersTL"] = "gray" + db_dict["RefinementRamachandranFavored"] = "-" + db_dict["RefinementRamachandranFavoredTL"] = "gray" db = XChemDB.data_source(datasource) db.update_data_source(xtal, db_dict) class mtztools: - def __init__(self, mtzfile): self.mtzfile = mtzfile self.hkl = any_reflection_file(file_name=self.mtzfile) @@ -1224,96 +1611,202 @@ def __init__(self, mtzfile): self.mtz = self.miller_arrays[0] self.iotbxMTZ = mtz.object(self.mtzfile) - self.space_group_dict = {'triclinic': [1], - # 'monoclinic': [3,4,5], - 'monoclinic_P': [3, 4], - 'monoclinic_C': [5], - 'orthorhombic': [16, 17, 18, 19, 20, 21, 22, 23, 24], - 'tetragonal': [75, 76, 77, 78, 79, 80, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98], - 'hexagonal': [143, 144, 145, 149, 150, 151, 152, 153, 154, 168, 169, 170, - 171, 172, 173, 177, 178, 179, 180, 181, 182], - 'rhombohedral': [146, 155], - 'cubic': [195, 196, 197, 198, 199, - 207, 208, 209, 210, 211, 212, 213, 214]} + self.space_group_dict = { + "triclinic": [1], + # 'monoclinic': [3,4,5], + "monoclinic_P": [3, 4], + "monoclinic_C": [5], + "orthorhombic": [16, 17, 18, 19, 20, 21, 22, 23, 24], + "tetragonal": [ + 75, + 76, + 77, + 78, + 79, + 80, + 89, + 90, + 91, + 92, + 93, + 94, + 95, + 96, + 97, + 98, + ], + "hexagonal": [ + 143, + 144, + 145, + 149, + 150, + 151, + 152, + 153, + 154, + 168, + 169, + 170, + 171, + 172, + 173, + 177, + 178, + 179, + 180, + 181, + 182, + ], + "rhombohedral": [146, 155], + "cubic": [195, 196, 197, 198, 199, 207, 208, 209, 210, 211, 212, 213, 214], + } self.translate_spg_to_number_dict = { - 'p1': 1, 'p121': 3, 'p1211': 4, 'c2': 5, 'c121': 5, 'i2': 5, 'i121': 5, 'p222': 16, - 'p2122': 17, 'p2212': 17, 'p2221': 17, 'p21212': 18, 'p21221': 18, 'p22121': 18, - 'p212121': 19, 'c2221': 20, 'c222': 21, 'f222': 22, 'i222': 23, 'i212121': 24, - 'p4': 75, 'p41': 76, 'p42': 77, 'p43': 78, 'i4': 79, 'i41': 80, - 'p422': 89, 'p4212': 90, 'p4122': 91, 'p41212': 92, 'p4222': 93, 'p42212': 94, - 'p4322': 95, 'p43212': 96, 'i422': 97, 'i4122': 98, - 'p3': 143, 'p31': 144, 'p32': 145, 'p312': 149, 'p321': 150, 'p3112': 151, 'p3121': 152, - 'p3212': 153, 'p3221': 154, 'p6': 168, 'p61': 169, 'p65': 170, 'p62': 171, 'p64': 172, 'p63': 173, - 'p622': 177, 'p6122': 178, 'p6522': 179, 'p6222': 180, 'p6422': 181, 'p6322': 182, - 'r3': 146, 'h3': 146, 'r32': 155, 'h32': 155, - 'p23': 195, 'f23': 196, 'i23': 197, 'p213': 198, 'i213': 199, - 'p432': 207, 'p4232': 208, 'f432': 209, 'f4132': 210, 'i432': 211, 'p4332': 212, - 'p4132': 213, 'i4132': 214 + "p1": 1, + "p121": 3, + "p1211": 4, + "c2": 5, + "c121": 5, + "i2": 5, + "i121": 5, + "p222": 16, + "p2122": 17, + "p2212": 17, + "p2221": 17, + "p21212": 18, + "p21221": 18, + "p22121": 18, + "p212121": 19, + "c2221": 20, + "c222": 21, + "f222": 22, + "i222": 23, + "i212121": 24, + "p4": 75, + "p41": 76, + "p42": 77, + "p43": 78, + "i4": 79, + "i41": 80, + "p422": 89, + "p4212": 90, + "p4122": 91, + "p41212": 92, + "p4222": 93, + "p42212": 94, + "p4322": 95, + "p43212": 96, + "i422": 97, + "i4122": 98, + "p3": 143, + "p31": 144, + "p32": 145, + "p312": 149, + "p321": 150, + "p3112": 151, + "p3121": 152, + "p3212": 153, + "p3221": 154, + "p6": 168, + "p61": 169, + "p65": 170, + "p62": 171, + "p64": 172, + "p63": 173, + "p622": 177, + "p6122": 178, + "p6522": 179, + "p6222": 180, + "p6422": 181, + "p6322": 182, + "r3": 146, + "h3": 146, + "r32": 155, + "h32": 155, + "p23": 195, + "f23": 196, + "i23": 197, + "p213": 198, + "i213": 199, + "p432": 207, + "p4232": 208, + "f432": 209, + "f4132": 210, + "i432": 211, + "p4332": 212, + "p4132": 213, + "i4132": 214, + } + + self.point_group_dict = { + "1": [1], + "2": [3, 4, 5], + "222": [16, 17, 18, 19, 20, 21, 22, 23, 24], + "4": [75, 76, 77, 78, 79, 80], + "422": [89, 90, 91, 92, 93, 94, 95, 96, 97, 98], + "3": [143, 144, 145, 146], + "32": [149, 150, 151, 152, 153, 154, 155], + "6": [168, 169, 170, 171, 172, 173], + "622": [177, 178, 179, 180, 181, 182], + "23": [195, 196, 197, 198, 199], + "432": [207, 208, 209, 210, 211, 212, 213, 214], + } + + self.nr_asu_in_unitcell_for_point_group = { + "1": 1, + "2": 2, + "222": 4, + "4": 4, + "422": 8, + "3": 3, + "32": 6, + "6": 6, + "622": 12, + "23": 12, + "432": 24, } - self.point_group_dict = {'1': [1], - '2': [3, 4, 5], - '222': [16, 17, 18, 19, 20, 21, 22, 23, 24], - '4': [75, 76, 77, 78, 79, 80], - '422': [89, 90, 91, 92, 93, 94, 95, 96, 97, 98], - '3': [143, 144, 145, 146], - '32': [149, 150, 151, 152, 153, 154, 155], - '6': [168, 169, 170, 171, 172, 173], - '622': [177, 178, 179, 180, 181, 182], - '23': [195, 196, 197, 198, 199], - '432': [207, 208, 209, 210, 211, 212, 213, 214]} - - self.nr_asu_in_unitcell_for_point_group = {'1': 1, - '2': 2, - '222': 4, - '4': 4, - '422': 8, - '3': 3, - '32': 6, - '6': 6, - '622': 12, - '23': 12, - '432': 24} - - self.aimless = {'DataProcessingProgram': 'n/a', - # 'DataCollectionRun': 'n/a', - 'DataProcessingSpaceGroup': 'n/a', - 'DataProcessingUnitCell': 'n/a', - 'DataProcessingA': 'n/a', - 'DataProcessingB': 'n/a', - 'DataProcessingC': 'n/a', - 'DataProcessingAlpha': 'n/a', - 'DataProcessingBeta': 'n/a', - 'DataProcessingGamma': 'n/a', - 'DataProcessingResolutionLow': 'n/a', - 'DataProcessingResolutionLowInnerShell': 'n/a', - 'DataProcessingResolutionHigh': 'n/a', - 'DataProcessingResolutionHighOuterShell': 'n/a', - 'DataProcessingResolutionOverall': 'n/a', - 'DataProcessingRmergeOverall': 'n/a', - 'DataProcessingRmergeLow': 'n/a', - 'DataProcessingRmergeHigh': 'n/a', - 'DataProcessingIsigOverall': 'n/a', - 'DataProcessingIsigLow': 'n/a', - 'DataProcessingIsigHigh': 'n/a', - 'DataProcessingCompletenessOverall': 'n/a', - 'DataProcessingCompletenessLow': 'n/a', - 'DataProcessingCompletenessHigh': 'n/a', - 'DataProcessingMultiplicityOverall': 'n/a', - 'DataProcessingMultiplicityLow': 'n/a', - 'DataProcessingMultiplicityHigh': 'n/a', - 'DataProcessingCChalfOverall': 'n/a', - 'DataProcessingCChalfLow': 'n/a', - 'DataProcessingCChalfHigh': 'n/a', - 'DataProcessingResolutionHigh15sigma': 'n/a', - 'DataProcessingUniqueReflectionsOverall': 'n/a', - 'DataProcessingLattice': 'n/a', - 'DataProcessingPointGroup': 'n/a', - 'DataProcessingUnitCellVolume': 0, - 'DataProcessingAlert': '#FF0000', - 'DataCollectionWavelength': 'n/a', - 'DataProcessingScore': 'n/a'} + self.aimless = { + "DataProcessingProgram": "n/a", + # 'DataCollectionRun': 'n/a', + "DataProcessingSpaceGroup": "n/a", + "DataProcessingUnitCell": "n/a", + "DataProcessingA": "n/a", + "DataProcessingB": "n/a", + "DataProcessingC": "n/a", + "DataProcessingAlpha": "n/a", + "DataProcessingBeta": "n/a", + "DataProcessingGamma": "n/a", + "DataProcessingResolutionLow": "n/a", + "DataProcessingResolutionLowInnerShell": "n/a", + "DataProcessingResolutionHigh": "n/a", + "DataProcessingResolutionHighOuterShell": "n/a", + "DataProcessingResolutionOverall": "n/a", + "DataProcessingRmergeOverall": "n/a", + "DataProcessingRmergeLow": "n/a", + "DataProcessingRmergeHigh": "n/a", + "DataProcessingIsigOverall": "n/a", + "DataProcessingIsigLow": "n/a", + "DataProcessingIsigHigh": "n/a", + "DataProcessingCompletenessOverall": "n/a", + "DataProcessingCompletenessLow": "n/a", + "DataProcessingCompletenessHigh": "n/a", + "DataProcessingMultiplicityOverall": "n/a", + "DataProcessingMultiplicityLow": "n/a", + "DataProcessingMultiplicityHigh": "n/a", + "DataProcessingCChalfOverall": "n/a", + "DataProcessingCChalfLow": "n/a", + "DataProcessingCChalfHigh": "n/a", + "DataProcessingResolutionHigh15sigma": "n/a", + "DataProcessingUniqueReflectionsOverall": "n/a", + "DataProcessingLattice": "n/a", + "DataProcessingPointGroup": "n/a", + "DataProcessingUnitCellVolume": 0, + "DataProcessingAlert": "#FF0000", + "DataCollectionWavelength": "n/a", + "DataProcessingScore": "n/a", + } def get_dmin(self): return str(round(float(self.mtz.d_min()), 2)) @@ -1332,17 +1825,17 @@ def get_information_for_datasource(self): mtz_dict = self.get_all_values_as_dict() pg = self.get_pointgroup_from_mtz() if mtz_dict != {}: - db_dict['DataProcessingResolutionHigh'] = mtz_dict['resolution_high'] - db_dict['DataProcessingUnitCell'] = mtz_dict['unitcell'] - db_dict['DataProcessingSpaceGroup'] = mtz_dict['spacegroup'] - db_dict['DataProcessingUnitCellVolume'] = mtz_dict['unitcell_volume'] - db_dict['DataProcessingLattice'] = mtz_dict['bravais_lattice'] - if pg != '': - db_dict['DataProcessingPointGroup'] = pg + db_dict["DataProcessingResolutionHigh"] = mtz_dict["resolution_high"] + db_dict["DataProcessingUnitCell"] = mtz_dict["unitcell"] + db_dict["DataProcessingSpaceGroup"] = mtz_dict["spacegroup"] + db_dict["DataProcessingUnitCellVolume"] = mtz_dict["unitcell_volume"] + db_dict["DataProcessingLattice"] = mtz_dict["bravais_lattice"] + if pg != "": + db_dict["DataProcessingPointGroup"] = pg return db_dict def get_bravais_lattice_from_spg_number(self, number): - lattice = '' + lattice = "" for bravaislattice in self.space_group_dict: for spg_number in self.space_group_dict[bravaislattice]: if spg_number == number: @@ -1350,7 +1843,7 @@ def get_bravais_lattice_from_spg_number(self, number): return lattice def get_point_group_from_spg_number(self, number): - pointgroup = '' + pointgroup = "" for pg in self.point_group_dict: for spg_number in self.point_group_dict[pg]: if spg_number == number: @@ -1366,11 +1859,10 @@ def get_unit_cell_from_mtz(self): alpha = 0 beta = 0 gamma = 0 - mtzdmp = subprocess.Popen( - ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) - for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): - if line.startswith(' * Cell Dimensions :'): - cell_line = n+2 + mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, "")): + if line.startswith(" * Cell Dimensions :"): + cell_line = n + 2 if n == cell_line and len(line.split()) == 6: a = line.split()[0] b = line.split()[1] @@ -1382,30 +1874,28 @@ def get_unit_cell_from_mtz(self): def get_spg_number_from_mtz(self): spg_number = 0 - mtzdmp = subprocess.Popen( - ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) - for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): - if line.startswith(' * Space group ='): - spg_number = int(line[line.rfind(')')-3:line.rfind(')')]) + mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, "")): + if line.startswith(" * Space group ="): + spg_number = int(line[line.rfind(")") - 3 : line.rfind(")")]) return spg_number def get_spg_from_mtz(self): - spg = '' - mtzdmp = subprocess.Popen( - ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) - for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): - if line.startswith(' * Space group ='): - spg = line[line.find("'")+1:line.rfind("'")] + spg = "" + mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, "")): + if line.startswith(" * Space group ="): + spg = line[line.find("'") + 1 : line.rfind("'")] return spg def get_bravais_lattice_from_mtz(self): - bravais_lattice = '' + bravais_lattice = "" spg_number = self.get_spg_number_from_mtz() bravais_lattice = self.get_bravais_lattice_from_spg_number(spg_number) return bravais_lattice def get_pointgroup_from_mtz(self): - pointgroup = '' + pointgroup = "" spg_number = self.get_spg_number_from_mtz() pointgroup = self.get_point_group_from_spg_number(spg_number) return pointgroup @@ -1421,103 +1911,121 @@ def calc_unitcell_volume_from_mtz(self): beta = math.radians(float(unitcell[4])) gamma = math.radians(float(unitcell[5])) unitcell_volume = 0 - if lattice == 'triclinic': - unitcell_volume = a*b*c * \ - math.sqrt((1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2) - + 2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma))) - if 'monoclinic' in lattice: - unitcell_volume = round(a*b*c*math.sin(beta), 1) - if lattice == 'orthorhombic' or lattice == 'tetragonal' or lattice == 'cubic': - unitcell_volume = round(a*b*c, 1) - if lattice == 'hexagonal' or lattice == 'rhombohedral': - unitcell_volume = round(a*b*c*(math.sin(math.radians(60))), 1) + if lattice == "triclinic": + unitcell_volume = ( + a + * b + * c + * math.sqrt( + ( + 1 + - math.cos(alpha) ** 2 + - math.cos(beta) ** 2 + - math.cos(gamma) ** 2 + ) + + 2 * (math.cos(alpha) * math.cos(beta) * math.cos(gamma)) + ) + ) + if "monoclinic" in lattice: + unitcell_volume = round(a * b * c * math.sin(beta), 1) + if lattice == "orthorhombic" or lattice == "tetragonal" or lattice == "cubic": + unitcell_volume = round(a * b * c, 1) + if lattice == "hexagonal" or lattice == "rhombohedral": + unitcell_volume = round(a * b * c * (math.sin(math.radians(60))), 1) return unitcell_volume def get_high_resolution_from_mtz(self): - resolution_high = 'n/a' + resolution_high = "n/a" resolution_line = 1000000 - mtzdmp = subprocess.Popen( - ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) - for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): - if line.startswith(' * Resolution Range :'): - resolution_line = n+2 + mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, "")): + if line.startswith(" * Resolution Range :"): + resolution_line = n + 2 if n == resolution_line and len(line.split()) == 8: resolution_high = line.split()[5] return resolution_high def get_low_resolution_from_mtz(self): - resolution_low = 'n/a' + resolution_low = "n/a" resolution_line = 1000000 - mtzdmp = subprocess.Popen( - ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) - for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): - if line.startswith(' * Resolution Range :'): - resolution_line = n+2 + mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, "")): + if line.startswith(" * Resolution Range :"): + resolution_line = n + 2 if n == resolution_line and len(line.split()) == 8: resolution_low = line.split()[3] return resolution_low def get_number_measured_reflections(self): - missing_reflections = '0' - all_reflections = '0' - meassured_reflections = '0' + missing_reflections = "0" + all_reflections = "0" + meassured_reflections = "0" resolution_line = 1000000 - mtzdmp = subprocess.Popen( - ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) + mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) foundTable = False - for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): - if line.startswith(' Col Sort Min Max Num % Mean Mean Resolution Type Column'): + for n, line in enumerate(iter(mtzdmp.stdout.readline, "")): + if line.startswith( + " Col Sort Min Max Num % Mean Mean Resolution Type Column" + ): foundTable = True if foundTable and len(line.split()) == 12: - if line.split()[11] == 'F': + if line.split()[11] == "F": missing_reflections = line.split()[4] foundTable = False - if line.startswith(' No. of reflections used in FILE STATISTICS'): + if line.startswith(" No. of reflections used in FILE STATISTICS"): all_reflections = line.split()[7] break try: - meassured_reflections = int( - all_reflections)-int(missing_reflections) + meassured_reflections = int(all_reflections) - int(missing_reflections) except ValueError: pass return meassured_reflections def calculate_correlaton_between_intensities_in_mtzfiles(self, mtzin): - CC = '0.0' - errorMessage = '' -# cmd = ( 'pointless hklin %s hklref %s << eof\n' %(mtzin,self.mtzfile)+ -# 'labref F=F\n' -# 'labin F=F\n' -# 'eof\n' ) - cmd = ('pointless hklin %s hklref %s << eof\n' % (mtzin, self.mtzfile) + - 'labref I=IMEAN\n' - 'labin I=IMEAN\n' - 'eof\n') + CC = "0.0" + errorMessage = "" + # cmd = ( 'pointless hklin %s hklref %s << eof\n' %(mtzin,self.mtzfile)+ + # 'labref F=F\n' + # 'labin F=F\n' + # 'eof\n' ) + cmd = ( + "pointless hklin %s hklref %s << eof\n" % (mtzin, self.mtzfile) + + "labref I=IMEAN\n" + "labin I=IMEAN\n" + "eof\n" + ) pointless = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE) foundLine = False - for line in iter(pointless.stdout.readline, ''): + for line in iter(pointless.stdout.readline, ""): if foundLine: CC = line.split()[3] break - if 'Alternative reindexing Lklhd CC' in line: + if "Alternative reindexing Lklhd CC" in line: foundLine = True - if '**** Incompatible symmetries ****' in line: - errorMessage = '**** Incompatible symmetries ****' + if "**** Incompatible symmetries ****" in line: + errorMessage = "**** Incompatible symmetries ****" break - if 'Merged test dataset (HKLIN) has different Laue symmetry to reference set' in line: - errorMessage = '%s has different Laue symmetry to %s' % ( - mtzin, self.mtzfile) + if ( + "Merged test dataset (HKLIN) has different Laue symmetry to reference set" + in line + ): + errorMessage = "%s has different Laue symmetry to %s" % ( + mtzin, + self.mtzfile, + ) break return CC, errorMessage def get_all_values_as_dict(self): - mtz = {'resolution_high': 'n/a', - 'unitcell': 'n/a', - 'spacegroup': 'n/a', - 'unitcell_volume': 'n/a', - 'bravais_lattice': 'n/a'} + mtz = { + "resolution_high": "n/a", + "unitcell": "n/a", + "spacegroup": "n/a", + "unitcell_volume": "n/a", + "bravais_lattice": "n/a", + } a = 0.0 b = 0.0 c = 0.0 @@ -1526,15 +2034,14 @@ def get_all_values_as_dict(self): gamma_rad = 0.0 resolution_line = 1000000 cell_line = 1000000 - mtzdmp = subprocess.Popen( - ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) - for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): - if line.startswith(' * Resolution Range :'): - resolution_line = n+2 + mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, "")): + if line.startswith(" * Resolution Range :"): + resolution_line = n + 2 if n == resolution_line and len(line.split()) == 8: - mtz['resolution_high'] = round(float(line.split()[5]), 2) - if line.startswith(' * Cell Dimensions :'): - cell_line = n+2 + mtz["resolution_high"] = round(float(line.split()[5]), 2) + if line.startswith(" * Cell Dimensions :"): + cell_line = n + 2 if n == cell_line and len(line.split()) == 6: a = round(float(line.split()[0]), 1) b = round(float(line.split()[1]), 1) @@ -1542,57 +2049,81 @@ def get_all_values_as_dict(self): alpha = round(float(line.split()[3]), 1) beta = round(float(line.split()[4]), 1) gamma = round(float(line.split()[5]), 1) - mtz['unitcell'] = str(a)+' '+str(b)+' '+str(c)+' ' + \ - str(alpha)+' '+str(beta)+' '+str(gamma) + mtz["unitcell"] = ( + str(a) + + " " + + str(b) + + " " + + str(c) + + " " + + str(alpha) + + " " + + str(beta) + + " " + + str(gamma) + ) alpha_rad = math.radians(alpha) beta_rad = math.radians(beta) gamma_rad = math.radians(gamma) - if line.startswith(' * Space group ='): - spg_number = int(line[line.rfind(')')-3:line.rfind(')')]) - mtz['bravais_lattice'] = self.get_bravais_lattice_from_spg_number( - spg_number) - mtz['spacegroup'] = line[line.find("'")+1:line.rfind("'")] - if mtz['bravais_lattice'] == 'triclinic': - mtz['unitcell_volume'] = a*b*c * \ - math.sqrt((1-math.cos(alpha_rad)**2-math.cos(beta_rad)**2-math.cos(gamma_rad)**2) - + 2*(math.cos(alpha_rad)*math.cos(beta_rad)*math.cos(gamma_rad))) -# elif mtz['bravais_lattice']=='monoclinic': - elif 'monoclinic' in mtz['bravais_lattice']: - mtz['unitcell_volume'] = round(a*b*c*math.sin(beta_rad), 1) - elif mtz['bravais_lattice'] == 'orthorhombic' or mtz['bravais_lattice'] == 'tetragonal' or mtz['bravais_lattice'] == 'cubic': - mtz['unitcell_volume'] = round(a*b*c, 1) - elif mtz['bravais_lattice'] == 'hexagonal' or mtz['bravais_lattice'] == 'rhombohedral': - mtz['unitcell_volume'] = round( - a*b*c*(math.sin(math.radians(60))), 1) + if line.startswith(" * Space group ="): + spg_number = int(line[line.rfind(")") - 3 : line.rfind(")")]) + mtz["bravais_lattice"] = self.get_bravais_lattice_from_spg_number( + spg_number + ) + mtz["spacegroup"] = line[line.find("'") + 1 : line.rfind("'")] + if mtz["bravais_lattice"] == "triclinic": + mtz["unitcell_volume"] = ( + a + * b + * c + * math.sqrt( + ( + 1 + - math.cos(alpha_rad) ** 2 + - math.cos(beta_rad) ** 2 + - math.cos(gamma_rad) ** 2 + ) + + 2 + * (math.cos(alpha_rad) * math.cos(beta_rad) * math.cos(gamma_rad)) + ) + ) + # elif mtz['bravais_lattice']=='monoclinic': + elif "monoclinic" in mtz["bravais_lattice"]: + mtz["unitcell_volume"] = round(a * b * c * math.sin(beta_rad), 1) + elif ( + mtz["bravais_lattice"] == "orthorhombic" + or mtz["bravais_lattice"] == "tetragonal" + or mtz["bravais_lattice"] == "cubic" + ): + mtz["unitcell_volume"] = round(a * b * c, 1) + elif ( + mtz["bravais_lattice"] == "hexagonal" + or mtz["bravais_lattice"] == "rhombohedral" + ): + mtz["unitcell_volume"] = round(a * b * c * (math.sin(math.radians(60))), 1) return mtz def get_all_columns_as_dict(self): - column_dict = {'F': [], - 'I': [], - 'SIG': [], - 'PHS': [], - 'FOM': [], - 'RFREE': []} + column_dict = {"F": [], "I": [], "SIG": [], "PHS": [], "FOM": [], "RFREE": []} startline = 1000000 - mtzdmp = subprocess.Popen( - ['mtzdmp', self.mtzfile], stdout=subprocess.PIPE) - for n, line in enumerate(iter(mtzdmp.stdout.readline, '')): - if line.startswith(' Col Sort Min Max Num'): - startline = n+2 + mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) + for n, line in enumerate(iter(mtzdmp.stdout.readline, "")): + if line.startswith(" Col Sort Min Max Num"): + startline = n + 2 if n >= startline and len(line.split()) > 10: - if line.split()[10] == 'F': - column_dict['F'].append(line.split()[11]) - if line.split()[10] == 'J': - column_dict['I'].append(line.split()[11]) - if line.split()[10] == 'Q': - column_dict['SIG'].append(line.split()[11]) - if line.split()[10] == 'I': - column_dict['RFREE'].append(line.split()[11]) - if line.split()[10] == 'P': - column_dict['PHS'].append(line.split()[11]) - if line.split()[10] == 'W': - column_dict['FOM'].append(line.split()[11]) + if line.split()[10] == "F": + column_dict["F"].append(line.split()[11]) + if line.split()[10] == "J": + column_dict["I"].append(line.split()[11]) + if line.split()[10] == "Q": + column_dict["SIG"].append(line.split()[11]) + if line.split()[10] == "I": + column_dict["RFREE"].append(line.split()[11]) + if line.split()[10] == "P": + column_dict["PHS"].append(line.split()[11]) + if line.split()[10] == "W": + column_dict["FOM"].append(line.split()[11]) return column_dict @@ -1602,15 +2133,14 @@ def get_all_columns_as_list(self): class queue: - def jobs_in_queue(self): jobs = [] - qstat = subprocess.Popen(['qstat -r'], stdout=subprocess.PIPE) + qstat = subprocess.Popen(["qstat -r"], stdout=subprocess.PIPE) counter = 0 - for n, line in enumerate(iter(qstat.stdout.readline, '')): - jobID = '' - job_name = '' - user_name = '' + for n, line in enumerate(iter(qstat.stdout.readline, "")): + jobID = "" + job_name = "" + user_name = "" if getpass.getuser() in line: counter += 1 jobID = line.split()[0] @@ -1624,11 +2154,10 @@ def remove_all_jobs_from_queue(self): jobs_in_queue = self.jobs_in_queue() if jobs_in_queue: for job in jobs_in_queue: - os.system('qdel '+job[0]) + os.system("qdel " + job[0]) class external_software: - def __init__(self, xce_logfile): self.available_programs = {} @@ -1636,411 +2165,598 @@ def __init__(self, xce_logfile): def check(self): - self.Logfile.insert('Searching for external software...') + self.Logfile.insert("Searching for external software...") # default is False; user needs to explicitely set this - self.available_programs['qsub_remote'] = '' + self.available_programs["qsub_remote"] = "" - FNULL = open(os.devnull, 'w') + FNULL = open(os.devnull, "w") try: # subprocess.call(['qstat'], stdout=FNULL, stderr=subprocess.STDOUT) - p = subprocess.Popen('qstat', shell=True, stdin=subprocess.PIPE, - stdout=subprocess.PIPE, stderr=subprocess.STDOUT, close_fds=True) - status = 'found' + p = subprocess.Popen( + "qstat", + shell=True, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.STDOUT, + close_fds=True, + ) + status = "found" try: for line in p.stdout: - if 'symbol lookup error:' in line or 'command not found' in line or 'error' in line: - self.available_programs['qsub'] = False - self.available_programs['qsub_array'] = False - status = 'not found' - array_status = 'not found' + if ( + "symbol lookup error:" in line + or "command not found" in line + or "error" in line + ): + self.available_programs["qsub"] = False + self.available_programs["qsub_array"] = False + status = "not found" + array_status = "not found" except IOError: - self.available_programs['qsub'] = False - self.available_programs['qsub_array'] = False - status = 'not found' - array_status = 'not found' - - if status == 'found': - self.available_programs['qsub'] = True -# if os.getcwd().startswith('/dls'): - if os.path.isdir('/dls'): - self.available_programs['qsub_array'] = True - array_status = 'found' + self.available_programs["qsub"] = False + self.available_programs["qsub_array"] = False + status = "not found" + array_status = "not found" + + if status == "found": + self.available_programs["qsub"] = True + # if os.getcwd().startswith('/dls'): + if os.path.isdir("/dls"): + self.available_programs["qsub_array"] = True + array_status = "found" else: - self.available_programs['qsub_array'] = False - array_status = 'not found' + self.available_programs["qsub_array"] = False + array_status = "not found" except OSError: - self.available_programs['qsub'] = False - self.available_programs['qsub_array'] = False - status = 'not found' - array_status = 'not found' - self.Logfile.insert('{0:50} {1:10}'.format( - 'checking for qsub:', status)) -# print '{0:50} {1:10}'.format('-checking for qsub:', status) -# if os.getcwd().startswith('/dls'): - if os.path.isdir('/dls'): - self.Logfile.insert('{0:50} {1:10}'.format( - 'checking for array qsub:', array_status)) + self.available_programs["qsub"] = False + self.available_programs["qsub_array"] = False + status = "not found" + array_status = "not found" + self.Logfile.insert("{0:50} {1:10}".format("checking for qsub:", status)) + # print '{0:50} {1:10}'.format('-checking for qsub:', status) + # if os.getcwd().startswith('/dls'): + if os.path.isdir("/dls"): + self.Logfile.insert( + "{0:50} {1:10}".format("checking for array qsub:", array_status) + ) try: - subprocess.call(['refmac5', 'end'], stdout=FNULL, - stderr=subprocess.STDOUT) - self.available_programs['refmac5'] = True - status = 'found' + subprocess.call(["refmac5", "end"], stdout=FNULL, stderr=subprocess.STDOUT) + self.available_programs["refmac5"] = True + status = "found" except OSError: - self.available_programs['refmac5'] = False - status = 'not found' - self.Logfile.insert('{0:50} {1:10}'.format( - 'checking for refmac5:', status)) + self.available_programs["refmac5"] = False + status = "not found" + self.Logfile.insert("{0:50} {1:10}".format("checking for refmac5:", status)) try: - subprocess.call(['phenix.molprobity'], - stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['phenix.molprobity'] = True - status = 'found' + subprocess.call( + ["phenix.molprobity"], stdout=FNULL, stderr=subprocess.STDOUT + ) + self.available_programs["phenix.molprobity"] = True + status = "found" except OSError: - self.available_programs['phenix.molprobity'] = False - status = 'not found' - self.Logfile.insert('{0:50} {1:10}'.format( - 'checking for phenix.molprobity:', status)) + self.available_programs["phenix.molprobity"] = False + status = "not found" + self.Logfile.insert( + "{0:50} {1:10}".format("checking for phenix.molprobity:", status) + ) try: - subprocess.call(['phenix.find_tls_groups'], - stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['phenix.find_tls_groups'] = True - status = 'found' + subprocess.call( + ["phenix.find_tls_groups"], stdout=FNULL, stderr=subprocess.STDOUT + ) + self.available_programs["phenix.find_tls_groups"] = True + status = "found" except OSError: - self.available_programs['phenix.find_tls_groups'] = False - status = 'not found' - self.Logfile.insert('{0:50} {1:10}'.format( - 'checking for phenix.find_tls_groups:', status)) + self.available_programs["phenix.find_tls_groups"] = False + status = "not found" + self.Logfile.insert( + "{0:50} {1:10}".format("checking for phenix.find_tls_groups:", status) + ) try: - subprocess.call(['mmtbx.validate_ligands'], - stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['mmtbx.validate_ligands'] = True - status = 'found' + subprocess.call( + ["mmtbx.validate_ligands"], stdout=FNULL, stderr=subprocess.STDOUT + ) + self.available_programs["mmtbx.validate_ligands"] = True + status = "found" except OSError: - self.available_programs['mmtbx.validate_ligands'] = False - status = 'not found' - self.Logfile.insert('{0:50} {1:10}'.format( - 'checking for mmtbx.validate_ligands:', status)) + self.available_programs["mmtbx.validate_ligands"] = False + status = "not found" + self.Logfile.insert( + "{0:50} {1:10}".format("checking for mmtbx.validate_ligands:", status) + ) try: - subprocess.call(['acedrg'], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['acedrg'] = True - shutil.rmtree('AcedrgOut_TMP') - status = 'found' + subprocess.call(["acedrg"], stdout=FNULL, stderr=subprocess.STDOUT) + self.available_programs["acedrg"] = True + shutil.rmtree("AcedrgOut_TMP") + status = "found" except OSError: - self.available_programs['acedrg'] = False - status = 'not found' - self.Logfile.insert('{0:50} {1:10}'.format( - 'checking for acedrg:', status)) + self.available_programs["acedrg"] = False + status = "not found" + self.Logfile.insert("{0:50} {1:10}".format("checking for acedrg:", status)) try: - subprocess.call(['phenix.elbow'], stdout=FNULL, - stderr=subprocess.STDOUT) - self.available_programs['phenix.elbow'] = True - status = 'found' + subprocess.call(["phenix.elbow"], stdout=FNULL, stderr=subprocess.STDOUT) + self.available_programs["phenix.elbow"] = True + status = "found" except OSError: - self.available_programs['phenix.elbow'] = False - status = 'not found' - self.Logfile.insert('{0:50} {1:10}'.format( - 'checking for phenix.elbow:', status)) + self.available_programs["phenix.elbow"] = False + status = "not found" + self.Logfile.insert( + "{0:50} {1:10}".format("checking for phenix.elbow:", status) + ) try: - subprocess.call(['grade'], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['grade'] = True - status = 'found' + subprocess.call(["grade"], stdout=FNULL, stderr=subprocess.STDOUT) + self.available_programs["grade"] = True + status = "found" except OSError: - self.available_programs['grade'] = False - status = 'not found' - self.Logfile.insert('{0:50} {1:10}'.format( - 'checking for grade:', status)) + self.available_programs["grade"] = False + status = "not found" + self.Logfile.insert("{0:50} {1:10}".format("checking for grade:", status)) try: - subprocess.call(['giant.create_occupancy_params'], - stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['giant.create_occupancy_params'] = True - status = 'found' + subprocess.call( + ["giant.create_occupancy_params"], + stdout=FNULL, + stderr=subprocess.STDOUT, + ) + self.available_programs["giant.create_occupancy_params"] = True + status = "found" except OSError: - self.available_programs['giant.create_occupancy_params'] = False - status = 'not found' - self.Logfile.insert('{0:50} {1:10}'.format( - 'checking for giant.create_occupancy_params:', status)) + self.available_programs["giant.create_occupancy_params"] = False + status = "not found" + self.Logfile.insert( + "{0:50} {1:10}".format( + "checking for giant.create_occupancy_params:", status + ) + ) - self.Logfile.insert('checking if MOGUL is configured...') - self.available_programs['mogul'] = False + self.Logfile.insert("checking if MOGUL is configured...") + self.available_programs["mogul"] = False if "BDG_TOOL_MOGUL" in os.environ: - self.Logfile.insert('BDG_TOOL_MOGUL is set to ' + - os.environ['BDG_TOOL_MOGUL']) - if str(os.environ['BDG_TOOL_MOGUL']).lower() == 'none': - self.Logfile.warning( - 'BDG_TOOL_MOGUL is not properly configured!') + self.Logfile.insert( + "BDG_TOOL_MOGUL is set to " + os.environ["BDG_TOOL_MOGUL"] + ) + if str(os.environ["BDG_TOOL_MOGUL"]).lower() == "none": + self.Logfile.warning("BDG_TOOL_MOGUL is not properly configured!") self.Logfile.hint( - 'try adding "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul" to your .bashrc file') + 'try adding "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul" to your .bashrc file' + ) else: - if os.path.isfile(os.getenv('BDG_TOOL_MOGUL')): - self.available_programs['mogul'] = True - status = 'found' + if os.path.isfile(os.getenv("BDG_TOOL_MOGUL")): + self.available_programs["mogul"] = True + status = "found" else: - status = 'not found' + status = "not found" self.Logfile.hint( - 'try adding "export PATH=/dls_sw/apps/ccdc/CSD_2020/bin:$PATH" to your .bashrc file') + 'try adding "export PATH=/dls_sw/apps/ccdc/CSD_2020/bin:$PATH" to your .bashrc file' + ) else: - self.Logfile.warning('BDG_TOOL_MOGUL is not set!') + self.Logfile.warning("BDG_TOOL_MOGUL is not set!") self.Logfile.hint( - 'try adding "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul" to your .bashrc file') - status = 'not found' - self.Logfile.insert('{0:50} {1:10}'.format( - 'checking for mogul:', status)) + 'try adding "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul" to your .bashrc file' + ) + status = "not found" + self.Logfile.insert("{0:50} {1:10}".format("checking for mogul:", status)) try: - subprocess.call(['gemmi'], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs['gemmi'] = True - status = 'found' + subprocess.call(["gemmi"], stdout=FNULL, stderr=subprocess.STDOUT) + self.available_programs["gemmi"] = True + status = "found" except OSError: - self.available_programs['gemmi'] = False - status = 'not found' - self.Logfile.insert('{0:50} {1:10}'.format( - 'checking for gemmi:', status)) + self.available_programs["gemmi"] = False + status = "not found" + self.Logfile.insert("{0:50} {1:10}".format("checking for gemmi:", status)) return self.available_programs class ParseFiles: - def __init__(self, DataPath, xtalID): # probably need to read in compoundID, because for custom projects, need to take newest pdb file # that has not same root as compoundID self.DataPath = DataPath self.xtalID = xtalID - if '' in DataPath: - self.newestPDB = max(glob.iglob(self.DataPath.replace( - '', xtalID)+'/*.pdb'), key=os.path.getctime) + if "" in DataPath: + self.newestPDB = max( + glob.iglob(self.DataPath.replace("", xtalID) + "/*.pdb"), + key=os.path.getctime, + ) else: - self.newestPDB = self.DataPath+'/'+self.xtalID+'/refine.pdb' + self.newestPDB = self.DataPath + "/" + self.xtalID + "/refine.pdb" def UpdateQualityIndicators(self): - QualityIndicators = {'R': '-', - 'RRfree': '-', - 'RRfreeColor': 'gray', - 'Resolution': 'n/a', - 'ResolutionColor': 'gray', - 'MolprobityScore': 'n/a', - 'MolprobityScoreColor': 'gray', - 'RamachandranOutliers': 'n/a', - 'RamachandranOutliersColor': 'gray', - 'RamachandranFavored': 'n/a', - 'RamachandranFavoredColor': 'gray', - 'LigandCCcolor': 'gray', - 'LigandCC': 'n/a', - 'rmsdBonds': 'n/a', - 'rmsdBondsColor': 'gray', - 'rmsdAngles': 'n/a', - 'rmsdAnglesColor': 'gray', - 'MatrixWeight': 'n/a'} + QualityIndicators = { + "R": "-", + "RRfree": "-", + "RRfreeColor": "gray", + "Resolution": "n/a", + "ResolutionColor": "gray", + "MolprobityScore": "n/a", + "MolprobityScoreColor": "gray", + "RamachandranOutliers": "n/a", + "RamachandranOutliersColor": "gray", + "RamachandranFavored": "n/a", + "RamachandranFavoredColor": "gray", + "LigandCCcolor": "gray", + "LigandCC": "n/a", + "rmsdBonds": "n/a", + "rmsdBondsColor": "gray", + "rmsdAngles": "n/a", + "rmsdAnglesColor": "gray", + "MatrixWeight": "n/a", + } # R, Rfree, Resolution found = 0 if os.path.isfile(self.newestPDB): for line in open(self.newestPDB): - if line.startswith('REMARK 3 R VALUE (WORKING + TEST SET) :'): - QualityIndicators['R'] = line.split()[9] - if line.startswith('REMARK 3 FREE R VALUE :'): - QualityIndicators['RRfree'] = line.split()[6] + if line.startswith("REMARK 3 R VALUE (WORKING + TEST SET) :"): + QualityIndicators["R"] = line.split()[9] + if line.startswith("REMARK 3 FREE R VALUE :"): + QualityIndicators["RRfree"] = line.split()[6] if float(line.split()[6]) < 0.3: - QualityIndicators['RRfreeColor'] = 'green' + QualityIndicators["RRfreeColor"] = "green" if float(line.split()[6]) >= 0.3 and float(line.split()[6]): - QualityIndicators['RRfreeColor'] = 'orange' + QualityIndicators["RRfreeColor"] = "orange" if float(line.split()[6]) >= 0.4: - QualityIndicators['RRfreeColor'] = 'red' - if line.startswith('REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) :'): - QualityIndicators['Resolution'] = line.split()[7] + QualityIndicators["RRfreeColor"] = "red" + if line.startswith("REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) :"): + QualityIndicators["Resolution"] = line.split()[7] if float(line.split()[7]) < 2.4: - QualityIndicators['ResolutionColor'] = 'green' + QualityIndicators["ResolutionColor"] = "green" if 2.4 <= float(line.split()[7]) < 2.8: - QualityIndicators['ResolutionColor'] = 'orange' + QualityIndicators["ResolutionColor"] = "orange" if float(line.split()[7]) >= 2.8: - QualityIndicators['ResolutionColor'] = 'red' - if line.startswith('REMARK 3 BOND LENGTHS REFINED ATOMS (A):'): - QualityIndicators['rmsdBonds'] = line.split()[9] + QualityIndicators["ResolutionColor"] = "red" + if line.startswith( + "REMARK 3 BOND LENGTHS REFINED ATOMS (A):" + ): + QualityIndicators["rmsdBonds"] = line.split()[9] if float(line.split()[9]) < 0.02: - QualityIndicators['rmsdBondsColor'] = 'green' + QualityIndicators["rmsdBondsColor"] = "green" if 0.02 <= float(line.split()[9]) < 0.03: - QualityIndicators['rmsdBondsColor'] = 'orange' + QualityIndicators["rmsdBondsColor"] = "orange" if float(line.split()[9]) >= 0.03: - QualityIndicators['rmsdBondsColor'] = 'red' - if line.startswith('REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES):'): - QualityIndicators['rmsdAngles'] = line.split()[9] + QualityIndicators["rmsdBondsColor"] = "red" + if line.startswith( + "REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES):" + ): + QualityIndicators["rmsdAngles"] = line.split()[9] if float(line.split()[9]) < 2.0: - QualityIndicators['rmsdAnglesColor'] = 'green' + QualityIndicators["rmsdAnglesColor"] = "green" if 2.0 <= float(line.split()[9]) < 3.0: - QualityIndicators['rmsdAnglesColor'] = 'orange' + QualityIndicators["rmsdAnglesColor"] = "orange" if float(line.split()[9]) >= 3.0: - QualityIndicators['rmsdAnglesColor'] = 'red' + QualityIndicators["rmsdAnglesColor"] = "red" # Molprobity - if os.path.isfile(self.DataPath+'/'+self.xtalID+'/validation_summary.txt'): - for line in open(self.DataPath+'/'+self.xtalID+'/validation_summary.txt'): + if os.path.isfile( + self.DataPath + "/" + self.xtalID + "/validation_summary.txt" + ): + for line in open( + self.DataPath + "/" + self.xtalID + "/validation_summary.txt" + ): # if line.startswith(' Molprobity score ='): # if line.lower().startswith(' molprobity score'): - if 'molprobity score' in line.lower(): + if "molprobity score" in line.lower(): if len(line.split()) >= 4: - QualityIndicators['MolprobityScore'] = line.split()[3] + QualityIndicators["MolprobityScore"] = line.split()[3] try: if float(line.split()[3]) < 2: - QualityIndicators['MolprobityScoreColor'] = 'green' + QualityIndicators["MolprobityScoreColor"] = "green" if 2 <= float(line.split()[3]) < 3: - QualityIndicators['MolprobityScoreColor'] = 'orange' + QualityIndicators["MolprobityScoreColor"] = "orange" if float(line.split()[3]) >= 3: - QualityIndicators['MolprobityScoreColor'] = 'red' + QualityIndicators["MolprobityScoreColor"] = "red" except ValueError: pass -# if line.lower().startswith(' ramachandran outliers ='): - if 'ramachandran outliers' in line.lower(): + # if line.lower().startswith(' ramachandran outliers ='): + if "ramachandran outliers" in line.lower(): if len(line.split()) >= 4: - QualityIndicators['RamachandranOutliers'] = line.split()[ - 3] + QualityIndicators["RamachandranOutliers"] = line.split()[3] try: if float(line.split()[3]) < 0.3: - QualityIndicators['RamachandranOutliersColor'] = 'green' + QualityIndicators["RamachandranOutliersColor"] = "green" if 0.3 <= float(line.split()[3]) < 1: - QualityIndicators['RamachandranOutliersColor'] = 'orange' + QualityIndicators[ + "RamachandranOutliersColor" + ] = "orange" if float(line.split()[3]) >= 1: - QualityIndicators['RamachandranOutliersColor'] = 'red' + QualityIndicators["RamachandranOutliersColor"] = "red" except ValueError: pass -# if line.startswith(' favored ='): - if 'favored' in line.lower(): + # if line.startswith(' favored ='): + if "favored" in line.lower(): if len(line.split()) >= 3: - QualityIndicators['RamachandranFavored'] = line.split()[ - 2] + QualityIndicators["RamachandranFavored"] = line.split()[2] try: if float(line.split()[2]) < 90: - QualityIndicators['RamachandranFavoredColor'] = 'red' + QualityIndicators["RamachandranFavoredColor"] = "red" if 90 <= float(line.split()[2]) < 98: - QualityIndicators['RamachandranFavoredColor'] = 'orange' + QualityIndicators["RamachandranFavoredColor"] = "orange" if float(line.split()[2]) >= 98: - QualityIndicators['RamachandranFavoredColor'] = 'green' + QualityIndicators["RamachandranFavoredColor"] = "green" except ValueError: pass # LigandCC - if os.path.isfile(self.DataPath+'/'+self.xtalID+'/validate_ligands.txt'): - for line in open(self.DataPath+'/'+self.xtalID+'/validate_ligands.txt'): + if os.path.isfile(self.DataPath + "/" + self.xtalID + "/validate_ligands.txt"): + for line in open( + self.DataPath + "/" + self.xtalID + "/validate_ligands.txt" + ): # if line.startswith('| LIG'): - if 'LIG' in line: - QualityIndicators['LigandCC'] = line.split()[6] + if "LIG" in line: + QualityIndicators["LigandCC"] = line.split()[6] if float(line.split()[6]) < 0.8: - QualityIndicators['LigandCCcolor'] = 'red' + QualityIndicators["LigandCCcolor"] = "red" if 0.8 <= float(line.split()[6]) < 0.9: - QualityIndicators['LigandCCcolor'] = 'orange' + QualityIndicators["LigandCCcolor"] = "orange" if float(line.split()[6]) >= 0.9: - QualityIndicators['LigandCCcolor'] = 'green' + QualityIndicators["LigandCCcolor"] = "green" # Matrix Weight temp = [] found = 0 if os.path.isdir(os.path.join(self.DataPath, self.xtalID)): - for item in glob.glob(os.path.join(self.DataPath, self.xtalID, '*')): - if item.startswith(os.path.join(self.DataPath, self.xtalID, 'Refine_')): - temp.append(int(item[item.rfind('_')+1:])) + for item in glob.glob(os.path.join(self.DataPath, self.xtalID, "*")): + if item.startswith(os.path.join(self.DataPath, self.xtalID, "Refine_")): + temp.append(int(item[item.rfind("_") + 1 :])) found = 1 if found: Serial = max(temp) - if os.path.isfile(os.path.join(self.DataPath, self.xtalID, 'Refine_'+str(Serial), 'refmac.log')): - for line in open(os.path.join(self.DataPath, self.xtalID, 'Refine_'+str(Serial), 'refmac.log')): - if line.startswith(' Weight matrix') and len(line.split()) == 3: - QualityIndicators['MatrixWeight'] = line.split()[2] + if os.path.isfile( + os.path.join( + self.DataPath, self.xtalID, "Refine_" + str(Serial), "refmac.log" + ) + ): + for line in open( + os.path.join( + self.DataPath, + self.xtalID, + "Refine_" + str(Serial), + "refmac.log", + ) + ): + if line.startswith(" Weight matrix") and len(line.split()) == 3: + QualityIndicators["MatrixWeight"] = line.split()[2] return QualityIndicators class pdbtools(object): - def __init__(self, pdb): self.pdb = pdb self.pdb_inp = iotbx.pdb.input(file_name=self.pdb) self.hierarchy = self.pdb_inp.construct_hierarchy() - self.AminoAcids = ['ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'GLU', 'GLN', 'GLY', 'HIS', - 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'VAL', 'CSO', 'HYP'] - self.Solvents = ['DMS', 'EDO', 'GOL', 'HOH'] - self.Ions = ['NA', 'MG', 'CL', 'K', 'SO4', 'PO4', 'CA'] - self.AAdict = {'ALA': 'A', 'ARG': 'R', 'ASN': 'N', 'ASP': 'D', 'CYS': 'C', 'GLU': 'E', 'GLN': 'Q', - 'GLY': 'G', 'HIS': 'H', 'ILE': 'I', 'LEU': 'L', 'LYS': 'K', 'MET': 'M', 'PHE': 'F', - 'PRO': 'P', 'SER': 'S', 'THR': 'T', 'TRP': 'W', 'TYR': 'Y', 'VAL': 'V'} - self.xce_ligands = ['LIG', 'DRG', 'FRS'] - - self.space_group_dict = {'triclinic': [1], - # 'monoclinic': [3,4,5], - 'monoclinic_P': [3, 4], - 'monoclinic_C': [5], - 'orthorhombic': [16, 17, 18, 19, 20, 21, 22, 23, 24], - 'tetragonal': [75, 76, 77, 78, 79, 80, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98], - 'hexagonal': [143, 144, 145, 149, 150, 151, 152, 153, 154, 168, 169, 170, - 171, 172, 173, 177, 178, 179, 180, 181, 182], - 'rhombohedral': [146, 155], - 'cubic': [195, 196, 197, 198, 199, - 207, 208, 209, 210, 211, 212, 213, 214]} + self.AminoAcids = [ + "ALA", + "ARG", + "ASN", + "ASP", + "CYS", + "GLU", + "GLN", + "GLY", + "HIS", + "ILE", + "LEU", + "LYS", + "MET", + "PHE", + "PRO", + "SER", + "THR", + "TRP", + "TYR", + "VAL", + "CSO", + "HYP", + ] + self.Solvents = ["DMS", "EDO", "GOL", "HOH"] + self.Ions = ["NA", "MG", "CL", "K", "SO4", "PO4", "CA"] + self.AAdict = { + "ALA": "A", + "ARG": "R", + "ASN": "N", + "ASP": "D", + "CYS": "C", + "GLU": "E", + "GLN": "Q", + "GLY": "G", + "HIS": "H", + "ILE": "I", + "LEU": "L", + "LYS": "K", + "MET": "M", + "PHE": "F", + "PRO": "P", + "SER": "S", + "THR": "T", + "TRP": "W", + "TYR": "Y", + "VAL": "V", + } + self.xce_ligands = ["LIG", "DRG", "FRS"] + + self.space_group_dict = { + "triclinic": [1], + # 'monoclinic': [3,4,5], + "monoclinic_P": [3, 4], + "monoclinic_C": [5], + "orthorhombic": [16, 17, 18, 19, 20, 21, 22, 23, 24], + "tetragonal": [ + 75, + 76, + 77, + 78, + 79, + 80, + 89, + 90, + 91, + 92, + 93, + 94, + 95, + 96, + 97, + 98, + ], + "hexagonal": [ + 143, + 144, + 145, + 149, + 150, + 151, + 152, + 153, + 154, + 168, + 169, + 170, + 171, + 172, + 173, + 177, + 178, + 179, + 180, + 181, + 182, + ], + "rhombohedral": [146, 155], + "cubic": [195, 196, 197, 198, 199, 207, 208, 209, 210, 211, 212, 213, 214], + } self.translate_spg_to_number_dict = { - 'p1': 1, 'p121': 3, 'p1211': 4, 'c2': 5, 'c121': 5, 'i2': 5, 'i121': 5, 'p222': 16, - 'p2122': 17, 'p2212': 17, 'p2221': 17, 'p21212': 18, 'p21221': 18, 'p22121': 18, - 'p212121': 19, 'c2221': 20, 'c222': 21, 'f222': 22, 'i222': 23, 'i212121': 24, - 'p4': 75, 'p41': 76, 'p42': 77, 'p43': 78, 'i4': 79, 'i41': 80, - 'p422': 89, 'p4212': 90, 'p4122': 91, 'p41212': 92, 'p4222': 93, 'p42212': 94, - 'p4322': 95, 'p43212': 96, 'i422': 97, 'i4122': 98, - 'p3': 143, 'p31': 144, 'p32': 145, 'p312': 149, 'p321': 150, 'p3112': 151, 'p3121': 152, - 'p3212': 153, 'p3221': 154, 'p6': 168, 'p61': 169, 'p65': 170, 'p62': 171, 'p64': 172, 'p63': 173, - 'p622': 177, 'p6122': 178, 'p6522': 179, 'p6222': 180, 'p6422': 181, 'p6322': 182, - 'r3': 146, 'h3': 146, 'r32': 155, 'h32': 155, - 'p23': 195, 'f23': 196, 'i23': 197, 'p213': 198, 'i213': 199, - 'p432': 207, 'p4232': 208, 'f432': 209, 'f4132': 210, 'i432': 211, 'p4332': 212, - 'p4132': 213, 'i4132': 214 + "p1": 1, + "p121": 3, + "p1211": 4, + "c2": 5, + "c121": 5, + "i2": 5, + "i121": 5, + "p222": 16, + "p2122": 17, + "p2212": 17, + "p2221": 17, + "p21212": 18, + "p21221": 18, + "p22121": 18, + "p212121": 19, + "c2221": 20, + "c222": 21, + "f222": 22, + "i222": 23, + "i212121": 24, + "p4": 75, + "p41": 76, + "p42": 77, + "p43": 78, + "i4": 79, + "i41": 80, + "p422": 89, + "p4212": 90, + "p4122": 91, + "p41212": 92, + "p4222": 93, + "p42212": 94, + "p4322": 95, + "p43212": 96, + "i422": 97, + "i4122": 98, + "p3": 143, + "p31": 144, + "p32": 145, + "p312": 149, + "p321": 150, + "p3112": 151, + "p3121": 152, + "p3212": 153, + "p3221": 154, + "p6": 168, + "p61": 169, + "p65": 170, + "p62": 171, + "p64": 172, + "p63": 173, + "p622": 177, + "p6122": 178, + "p6522": 179, + "p6222": 180, + "p6422": 181, + "p6322": 182, + "r3": 146, + "h3": 146, + "r32": 155, + "h32": 155, + "p23": 195, + "f23": 196, + "i23": 197, + "p213": 198, + "i213": 199, + "p432": 207, + "p4232": 208, + "f432": 209, + "f4132": 210, + "i432": 211, + "p4332": 212, + "p4132": 213, + "i4132": 214, } - self.point_group_dict = {'1': [1], - '2': [3, 4, 5], - '222': [16, 17, 18, 19, 20, 21, 22, 23, 24], - '4': [75, 76, 77, 78, 79, 80], - '422': [89, 90, 91, 92, 93, 94, 95, 96, 97, 98], - '3': [143, 144, 145, 146], - '32': [149, 150, 151, 152, 153, 154, 155], - '6': [168, 169, 170, 171, 172, 173], - '622': [177, 178, 179, 180, 181, 182], - '23': [195, 196, 197, 198, 199], - '432': [207, 208, 209, 210, 211, 212, 213, 214]} - - self.nr_asu_in_unitcell_for_point_group = {'1': 1, - '2': 2, - '222': 4, - '4': 4, - '422': 8, - '3': 3, - '32': 6, - '6': 6, - '622': 12, - '23': 12, - '432': 24} + self.point_group_dict = { + "1": [1], + "2": [3, 4, 5], + "222": [16, 17, 18, 19, 20, 21, 22, 23, 24], + "4": [75, 76, 77, 78, 79, 80], + "422": [89, 90, 91, 92, 93, 94, 95, 96, 97, 98], + "3": [143, 144, 145, 146], + "32": [149, 150, 151, 152, 153, 154, 155], + "6": [168, 169, 170, 171, 172, 173], + "622": [177, 178, 179, 180, 181, 182], + "23": [195, 196, 197, 198, 199], + "432": [207, 208, 209, 210, 211, 212, 213, 214], + } + + self.nr_asu_in_unitcell_for_point_group = { + "1": 1, + "2": 2, + "222": 4, + "4": 4, + "422": 8, + "3": 3, + "32": 6, + "6": 6, + "622": 12, + "23": 12, + "432": 24, + } def amino_acids(self): return self.AminoAcids def get_refinement_program(self): - program = 'unknown' + program = "unknown" for remark in self.pdb_inp.remark_section(): - if 'PROGRAM' in remark: - if 'refmac' in remark.lower(): - program = 'REFMAC' - elif 'phenix' in remark.lower(): - program = 'PHENIX' - elif 'buster' in remark.lower(): - program = 'BUSTER' + if "PROGRAM" in remark: + if "refmac" in remark.lower(): + program = "REFMAC" + elif "phenix" in remark.lower(): + program = "PHENIX" + elif "buster" in remark.lower(): + program = "BUSTER" return program def get_residues_with_resname(self, resname): @@ -2050,16 +2766,21 @@ def get_residues_with_resname(self, resname): for conformer in chain.conformers(): for residue in conformer.residues(): if residue.resname == resname: - if [residue.resname, residue.resseq, chain.id] not in ligands: + if [ + residue.resname, + residue.resseq, + chain.id, + ] not in ligands: ligands.append( - [residue.resname, residue.resseq, chain.id]) + [residue.resname, residue.resseq, chain.id] + ) return ligands -# def get_centre_of_gravity_of_residue(self,resname_resseq_chain): + # def get_centre_of_gravity_of_residue(self,resname_resseq_chain): def get_centre_of_gravity_of_residue(self, resname_chain_resseq): - resname_x = resname_chain_resseq.split('-')[0] - chain_x = resname_chain_resseq.split('-')[1] - resseq_x = resname_chain_resseq.split('-')[2] + resname_x = resname_chain_resseq.split("-")[0] + chain_x = resname_chain_resseq.split("-")[1] + resseq_x = resname_chain_resseq.split("-")[2] x = [] y = [] z = [] @@ -2067,7 +2788,11 @@ def get_centre_of_gravity_of_residue(self, resname_chain_resseq): for chain in model.chains(): for conformer in chain.conformers(): for residue in conformer.residues(): - if residue.resname.replace(' ', '') == resname_x and residue.resseq.replace(' ', '') == resseq_x and chain.id.replace(' ', '') == chain_x: + if ( + residue.resname.replace(" ", "") == resname_x + and residue.resseq.replace(" ", "") == resseq_x + and chain.id.replace(" ", "") == chain_x + ): for atom in residue.atoms(): x.append(atom.xyz[0]) y.append(atom.xyz[1]) @@ -2086,59 +2811,62 @@ def save_residues_with_resname(self, outDir, resname): for l in ligands: sel_cache = self.hierarchy.atom_selection_cache() lig_sel = sel_cache.selection( - "(resname %s and resseq %s and chain %s)" % (l[0], l[1], l[2])) + "(resname %s and resseq %s and chain %s)" % (l[0], l[1], l[2]) + ) hierarchy_lig = self.hierarchy.select(lig_sel) -# ligName = (l[0] + '-' + l[1] + '-' + l[2] + '.pdb').replace(' ', '') - ligName = (l[0] + '-' + l[2] + '-' + - l[1] + '.pdb').replace(' ', '') + # ligName = (l[0] + '-' + l[1] + '-' + l[2] + '.pdb').replace(' ', '') + ligName = (l[0] + "-" + l[2] + "-" + l[1] + ".pdb").replace(" ", "") ligList.append(ligName) try: f = open(os.path.join(outDir, ligName), "w") - f.write(hierarchy_lig.as_pdb_string( - crystal_symmetry=self.pdb_inp.crystal_symmetry())) + f.write( + hierarchy_lig.as_pdb_string( + crystal_symmetry=self.pdb_inp.crystal_symmetry() + ) + ) f.close() except IOError: - print('ERROR: {0!s} exists; skipping...') + print("ERROR: {0!s} exists; skipping...") return ligList def GetRefinementProgram(self): - program = '' + program = "" for line in open(self.pdb): - if line.startswith('REMARK') and 'REFMAC' in line: - program = 'REFMAC' + if line.startswith("REMARK") and "REFMAC" in line: + program = "REFMAC" break - if line.startswith('REMARK') and 'PHENIX' in line: - program = 'PHENIX' + if line.startswith("REMARK") and "PHENIX" in line: + program = "PHENIX" break - if line.startswith('REMARK') and 'BUSTER' in line: - program = 'BUSTER' + if line.startswith("REMARK") and "BUSTER" in line: + program = "BUSTER" break return program def GetSequence(self): chain = [] - Sequence = '' + Sequence = "" # need to count residue numbers in case of alternative conformations ResiNum = [] for line in open(self.pdb): - if line.startswith('ATOM') and line[17:20] in self.AminoAcids: + if line.startswith("ATOM") and line[17:20] in self.AminoAcids: if line[21:22] not in chain: chain.append(line[21:22]) - Sequence = Sequence+'\n>chain{0!s}.\n'.format(line[21:22]) + Sequence = Sequence + "\n>chain{0!s}.\n".format(line[21:22]) ResiNum = [] - if line[13:15] == 'CA' and line[22:27] not in ResiNum: - Sequence = Sequence+self.AAdict[line[17:20]] + if line[13:15] == "CA" and line[22:27] not in ResiNum: + Sequence = Sequence + self.AAdict[line[17:20]] ResiNum.append(line[22:27]) return Sequence def GetProteinChains(self): chain = [] for line in open(self.pdb): - if line.startswith('ATOM'): + if line.startswith("ATOM"): if line[17:20] in self.AminoAcids: if line[21:22] not in chain: chain.append(line[21:22]) @@ -2146,22 +2874,22 @@ def GetProteinChains(self): def GetSymm(self): unitcell = [] - a = '' - b = '' - c = '' - alpha = '' - beta = '' - gamma = '' - spg = '' + a = "" + b = "" + c = "" + alpha = "" + beta = "" + gamma = "" + spg = "" for line in open(self.pdb): - if line.startswith('CRYST1'): + if line.startswith("CRYST1"): a = line.split()[1] b = line.split()[2] c = line.split()[3] alpha = line.split()[4] beta = line.split()[5] gamma = line.split()[6] -# spg=line[55:len(line)-1] + # spg=line[55:len(line)-1] spg = line[55:65] return [a, b, c, alpha, beta, gamma, spg] @@ -2170,9 +2898,14 @@ def get_spg_from_pdb(self): return spg def get_spg_number_from_pdb(self): - spg = self.get_spg_from_pdb().replace( - ' ', '').lower().replace('\n', '').replace('\r', '') - spg_number = '0' + spg = ( + self.get_spg_from_pdb() + .replace(" ", "") + .lower() + .replace("\n", "") + .replace("\r", "") + ) + spg_number = "0" for key in self.translate_spg_to_number_dict: if key == spg: spg_number = str(self.translate_spg_to_number_dict[key]) @@ -2180,13 +2913,13 @@ def get_spg_number_from_pdb(self): return spg_number def get_bravais_lattice_from_pdb(self): - bravais_lattice = '' + bravais_lattice = "" spg_number = self.get_spg_number_from_pdb() bravais_lattice = self.get_bravais_lattice_from_spg_number(spg_number) return bravais_lattice def get_bravais_lattice_from_spg_number(self, number): - lattice = '' + lattice = "" for bravaislattice in self.space_group_dict: for spg_number in self.space_group_dict[bravaislattice]: if str(spg_number) == str(number): @@ -2194,7 +2927,7 @@ def get_bravais_lattice_from_spg_number(self, number): return lattice def get_pointgroup_from_pdb(self): - pointgroup = '' + pointgroup = "" spg_number = self.get_spg_number_from_pdb() pointgroup = self.get_point_group_from_spg_number(spg_number) return pointgroup @@ -2215,17 +2948,28 @@ def calc_unitcell_volume_from_pdb(self): beta = math.radians(float(unitcell[4])) gamma = math.radians(float(unitcell[5])) unitcell_volume = 0 - if lattice == 'triclinic': - unitcell_volume = a*b*c * \ - math.sqrt((1-math.cos(alpha)**2-math.cos(beta)**2-math.cos(gamma)**2) - + 2*(math.cos(alpha)*math.cos(beta)*math.cos(gamma))) -# if lattice=='monoclinic': - if 'monoclinic' in lattice: - unitcell_volume = round(a*b*c*math.sin(beta), 1) - if lattice == 'orthorhombic' or lattice == 'tetragonal' or lattice == 'cubic': - unitcell_volume = round(a*b*c, 1) - if lattice == 'hexagonal' or lattice == 'rhombohedral': - unitcell_volume = round(a*b*c*(math.sin(math.radians(60))), 1) + if lattice == "triclinic": + unitcell_volume = ( + a + * b + * c + * math.sqrt( + ( + 1 + - math.cos(alpha) ** 2 + - math.cos(beta) ** 2 + - math.cos(gamma) ** 2 + ) + + 2 * (math.cos(alpha) * math.cos(beta) * math.cos(gamma)) + ) + ) + # if lattice=='monoclinic': + if "monoclinic" in lattice: + unitcell_volume = round(a * b * c * math.sin(beta), 1) + if lattice == "orthorhombic" or lattice == "tetragonal" or lattice == "cubic": + unitcell_volume = round(a * b * c, 1) + if lattice == "hexagonal" or lattice == "rhombohedral": + unitcell_volume = round(a * b * c * (math.sin(math.radians(60))), 1) return unitcell_volume def MatthewsCoefficient(self, sequence): @@ -2233,22 +2977,35 @@ def MatthewsCoefficient(self, sequence): symm = self.GetSymm() nres = 0 for char in sequence: - if char != ' ': + if char != " ": nres += 1 cmd = ( - '#!/bin/csh -f\n' - 'matthews_coef << eof\n' - ' cell %s\n' % (symm[0]+' '+symm[1]+' '+symm[2]+' '+symm[3]+' '+symm[4]+' '+symm[5]) + - ' symm {0!s}\n'.format(symm[6].replace(' ', '')) + - ' nres {0!s}\n'.format(nres) + - ' auto\n' - ' end\n' - 'eof\n' + "#!/bin/csh -f\n" + "matthews_coef << eof\n" + " cell %s\n" + % ( + symm[0] + + " " + + symm[1] + + " " + + symm[2] + + " " + + symm[3] + + " " + + symm[4] + + " " + + symm[5] + ) + + " symm {0!s}\n".format(symm[6].replace(" ", "")) + + " nres {0!s}\n".format(nres) + + " auto\n" + " end\n" + "eof\n" ) Log = subprocess.check_output(cmd, shell=True) - MatthewsCoeff = 'n/a' - Solvent = 'n/a' + MatthewsCoeff = "n/a" + Solvent = "n/a" found = 0 for line in Log.split(os.linesep): if found: @@ -2256,7 +3013,7 @@ def MatthewsCoefficient(self, sequence): MatthewsCoeff = line.split()[1] Solvent = line.split()[2] break - if line.startswith('_______________'): + if line.startswith("_______________"): found = 1 return [MatthewsCoeff, Solvent] @@ -2266,8 +3023,9 @@ def find_ligands(self): # need to count residue numbers in case of alternative conformations ResiNum = [] for line in open(self.pdb): - if (line.startswith('ATOM') or line.startswith('HETATM')) \ - and line[17:20].replace(' ', '') not in self.AminoAcids+self.Solvents+self.Ions: + if (line.startswith("ATOM") or line.startswith("HETATM")) and line[ + 17:20 + ].replace(" ", "") not in self.AminoAcids + self.Solvents + self.Ions: if [line[17:20], line[21:22], line[23:26]] not in Ligands: Ligands.append([line[17:20], line[21:22], line[23:26]]) return Ligands @@ -2276,13 +3034,18 @@ def save_ligands_to_pdb(self): Ligands = self.find_ligands() if not Ligands == []: for n, item in enumerate(Ligands): - pdb = '' + pdb = "" for line in open(self.pdb): - if line.startswith('CRYST'): + if line.startswith("CRYST"): pdb += line - if (line.startswith('ATOM') or line.startswith('HETATM')) and line[17:20] == item[0] and line[21:22] == item[1] and line[23:26] == item[2]: - pdb = pdb+line - f = open('ligand_{0!s}.pdb'.format(n), 'w') + if ( + (line.startswith("ATOM") or line.startswith("HETATM")) + and line[17:20] == item[0] + and line[21:22] == item[1] + and line[23:26] == item[2] + ): + pdb = pdb + line + f = open("ligand_{0!s}.pdb".format(n), "w") f.write(pdb) f.close() return Ligands @@ -2291,14 +3054,18 @@ def save_ligands_to_pdb_to_directory(self, outDir): Ligands = self.find_ligands() if not Ligands == []: for n, item in enumerate(Ligands): - pdb = '' + pdb = "" for line in open(self.pdb): - if line.startswith('CRYST'): + if line.startswith("CRYST"): pdb += line - if (line.startswith('ATOM') or line.startswith('HETATM')) and line[17:20] == item[0] and line[21:22] == item[1] and line[23:26] == item[2]: - pdb = pdb+line - f = open(os.path.join( - outDir, 'ligand_{0!s}.pdb'.format(n)), 'w') + if ( + (line.startswith("ATOM") or line.startswith("HETATM")) + and line[17:20] == item[0] + and line[21:22] == item[1] + and line[23:26] == item[2] + ): + pdb = pdb + line + f = open(os.path.join(outDir, "ligand_{0!s}.pdb".format(n)), "w") f.write(pdb) f.close() return Ligands @@ -2306,45 +3073,59 @@ def save_ligands_to_pdb_to_directory(self, outDir): def save_all_ligands_to_pdb(self, outDir): Ligands = self.find_ligands() if not Ligands == []: - pdb = '' + pdb = "" for line in open(self.pdb): - if line.startswith('CRYST'): + if line.startswith("CRYST"): pdb += line for n, item in enumerate(Ligands): for line in open(self.pdb): - if (line.startswith('ATOM') or line.startswith('HETATM')) and line[17:20] == item[0] and line[21:22] == item[1] and line[23:26] == item[2]: + if ( + (line.startswith("ATOM") or line.startswith("HETATM")) + and line[17:20] == item[0] + and line[21:22] == item[1] + and line[23:26] == item[2] + ): pdb += line - f = open(os.path.join(outDir, 'all_ligands.pdb'), 'w') + f = open(os.path.join(outDir, "all_ligands.pdb"), "w") f.write(pdb) f.close() def save_specific_ligands_to_pdb(self, resname, chainID, resseq, altLoc): - pdb = '' - outDir = self.pdb[:self.pdb.rfind('/')] + pdb = "" + outDir = self.pdb[: self.pdb.rfind("/")] for line in open(self.pdb): - if line.startswith('ATOM') or line.startswith('HETATM'): - resname_line = str(line[17:20]).replace(' ', '') - chainID_line = str(line[21:23]).replace(' ', '') - resseq_line = str(line[23:26]).replace(' ', '') - altLoc_line = str(line[16:17]).replace(' ', '') - if resname_line == str(resname) and chainID_line == str(chainID) and resseq_line == str(resseq) and altLoc_line == str(altLoc): - pdb = pdb+line - - if pdb != '': - f = open('{0!s}/ligand_{1!s}_{2!s}_{3!s}_{4!s}.pdb'.format(outDir, - str(resname), str(chainID), str(resseq), str(altLoc)), 'w') + if line.startswith("ATOM") or line.startswith("HETATM"): + resname_line = str(line[17:20]).replace(" ", "") + chainID_line = str(line[21:23]).replace(" ", "") + resseq_line = str(line[23:26]).replace(" ", "") + altLoc_line = str(line[16:17]).replace(" ", "") + if ( + resname_line == str(resname) + and chainID_line == str(chainID) + and resseq_line == str(resseq) + and altLoc_line == str(altLoc) + ): + pdb = pdb + line + + if pdb != "": + f = open( + "{0!s}/ligand_{1!s}_{2!s}_{3!s}_{4!s}.pdb".format( + outDir, str(resname), str(chainID), str(resseq), str(altLoc) + ), + "w", + ) f.write(pdb) f.close() def find_xce_ligand_details(self): Ligands = [] for line in open(self.pdb): - if line.startswith('ATOM') or line.startswith('HETATM'): - resname = str(line[17:20]).replace(' ', '') + if line.startswith("ATOM") or line.startswith("HETATM"): + resname = str(line[17:20]).replace(" ", "") if resname in self.xce_ligands: - chainID = str(line[21:23]).replace(' ', '') - resseq = str(line[23:26]).replace(' ', '') - altLoc = str(line[16:17]).replace(' ', '') + chainID = str(line[21:23]).replace(" ", "") + resseq = str(line[23:26]).replace(" ", "") + altLoc = str(line[16:17]).replace(" ", "") if [resname, chainID, resseq, altLoc] not in Ligands: Ligands.append([resname, chainID, resseq, altLoc]) return Ligands @@ -2352,50 +3133,49 @@ def find_xce_ligand_details(self): def ligand_details_as_list(self): Ligands = [] for line in open(self.pdb): - if line.startswith('ATOM') or line.startswith('HETATM'): - resname = str(line[17:20]).replace(' ', '') + if line.startswith("ATOM") or line.startswith("HETATM"): + resname = str(line[17:20]).replace(" ", "") if resname in self.xce_ligands: - chainID = str(line[21:23]).replace(' ', '') - resseq = str(line[23:26]).replace(' ', '') - altLoc = str(line[16:17]).replace(' ', '') - occupancy = str(line[56:60]).replace(' ', '') + chainID = str(line[21:23]).replace(" ", "") + resseq = str(line[23:26]).replace(" ", "") + altLoc = str(line[16:17]).replace(" ", "") + occupancy = str(line[56:60]).replace(" ", "") if [resname, chainID, resseq, altLoc, occupancy] not in Ligands: - Ligands.append( - [resname, chainID, resseq, altLoc, occupancy]) + Ligands.append([resname, chainID, resseq, altLoc, occupancy]) return Ligands def residue_details_as_list(self, pdbin): residueList = [] for line in open(pdbin): - if line.startswith('ATOM') or line.startswith('HETATM'): - resname = str(line[17:20]).replace(' ', '') - chainID = str(line[21:23]).replace(' ', '') - resseq = str(line[23:26]).replace(' ', '') - altLoc = str(line[16:17]).replace(' ', '') - occupancy = str(line[56:60]).replace(' ', '') + if line.startswith("ATOM") or line.startswith("HETATM"): + resname = str(line[17:20]).replace(" ", "") + chainID = str(line[21:23]).replace(" ", "") + resseq = str(line[23:26]).replace(" ", "") + altLoc = str(line[16:17]).replace(" ", "") + occupancy = str(line[56:60]).replace(" ", "") if [resname, chainID, resseq, altLoc, occupancy] not in residueList: - residueList.append( - [resname, chainID, resseq, altLoc, occupancy]) + residueList.append([resname, chainID, resseq, altLoc, occupancy]) return residueList def check_occupancies(self): - errorText = '' - warningText = '' + errorText = "" + warningText = "" residueDict = {} for line in open(self.pdb): - if line.startswith('ATOM') or line.startswith('HETATM'): - atomname = str(line[12:16]).replace(' ', '') - resname = str(line[17:20]).replace(' ', '') - chainID = str(line[21:22]).replace(' ', '') - resseq = str(line[22:26]).replace(' ', '') - altLoc = str(line[16:17]).replace(' ', '') - occupancy = str(line[56:60]).replace(' ', '') - if resname+'-'+chainID+'-'+resseq not in residueDict: - residueDict[resname+'-'+chainID+'-'+resseq] = [] - if altLoc == '': - altLoc = '0' - residueDict[resname+'-'+chainID+'-'+resseq].append( - [altLoc, occupancy, atomname, resname, chainID, resseq]) + if line.startswith("ATOM") or line.startswith("HETATM"): + atomname = str(line[12:16]).replace(" ", "") + resname = str(line[17:20]).replace(" ", "") + chainID = str(line[21:22]).replace(" ", "") + resseq = str(line[22:26]).replace(" ", "") + altLoc = str(line[16:17]).replace(" ", "") + occupancy = str(line[56:60]).replace(" ", "") + if resname + "-" + chainID + "-" + resseq not in residueDict: + residueDict[resname + "-" + chainID + "-" + resseq] = [] + if altLoc == "": + altLoc = "0" + residueDict[resname + "-" + chainID + "-" + resseq].append( + [altLoc, occupancy, atomname, resname, chainID, resseq] + ) for item in residueDict: altLocDict = {} for atom in residueDict[item]: @@ -2408,10 +3188,17 @@ def check_occupancies(self): if altLoc not in altLocDict: altLocDict[altLoc] = [] altLocDict[altLoc].append( - [occupancy, atomname, resname, chainID, resseq]) + [occupancy, atomname, resname, chainID, resseq] + ) if float(occupancy) > 1: - errorText += 'ERROR: %s %s %s (%s) %s: occupancy is %s\n' % ( - chainID, resname, resseq, altLoc, atomname, occupancy) + errorText += "ERROR: %s %s %s (%s) %s: occupancy is %s\n" % ( + chainID, + resname, + resseq, + altLoc, + atomname, + occupancy, + ) occupancySumList = [] for altLoc in altLocDict: occupancySum = 0.0 @@ -2427,16 +3214,29 @@ def check_occupancies(self): occStart = occupancy else: if occupancy != occStart: - warningText += '%s %s %s (%s) %s: occupancy differs for altLoc -> %s\n' % ( - chainID, resname, resseq, altLoc, atomname, occupancy) - occupancySumList.append(occupancySum/nAtom) + warningText += ( + "%s %s %s (%s) %s: occupancy differs for altLoc -> %s\n" + % ( + chainID, + resname, + resseq, + altLoc, + atomname, + occupancy, + ) + ) + occupancySumList.append(occupancySum / nAtom) occAdd = 0.0 for entry in occupancySumList: occAdd += entry if occAdd > 1: - errorText += 'ERROR: '+item + \ - ' -> summarised occupanies of alternative conformations are > 1.0 ('+str( - occupancySumList)+')\n' + errorText += ( + "ERROR: " + + item + + " -> summarised occupanies of alternative conformations are > 1.0 (" + + str(occupancySumList) + + ")\n" + ) return errorText, warningText @@ -2446,7 +3246,11 @@ def get_xyz_coordinated_of_residue(self, chain, number): Z = 0.0 # pdb definition see: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM for line in open(self.pdb): - if (line.startswith('ATOM') or line.startswith('HETATM')) and line[21:22] == chain and line[22:26].replace(' ', '') == str(number): + if ( + (line.startswith("ATOM") or line.startswith("HETATM")) + and line[21:22] == chain + and line[22:26].replace(" ", "") == str(number) + ): X = float(line[30:38]) Y = float(line[38:46]) Z = float(line[46:54]) @@ -2454,8 +3258,8 @@ def get_xyz_coordinated_of_residue(self, chain, number): return X, Y, Z def get_center_of_gravity_of_residue_ish(self, chain, number): - print('-> chain:', chain) - print('-> number:', number) + print("-> chain:", chain) + print("-> number:", number) X = 0.0 Y = 0.0 Z = 0.0 @@ -2465,7 +3269,11 @@ def get_center_of_gravity_of_residue_ish(self, chain, number): # pdb definition see: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM for line in open(self.pdb): # print line[21:22],line[22:26] - if (line.startswith('ATOM') or line.startswith('HETATM')) and line[21:22].replace(' ', '') == chain.replace(' ', '') and line[22:26].replace(' ', '') == str(number).replace(' ', ''): + if ( + (line.startswith("ATOM") or line.startswith("HETATM")) + and line[21:22].replace(" ", "") == chain.replace(" ", "") + and line[22:26].replace(" ", "") == str(number).replace(" ", "") + ): X = float(line[30:38]) x_list.append(X) Y = float(line[38:46]) @@ -2473,9 +3281,9 @@ def get_center_of_gravity_of_residue_ish(self, chain, number): Z = float(line[46:54]) z_list.append(Z) # 'ish' because it's not really the centre of gravity, but the the middle of the min/max of each x,y,z - X = ((max(x_list)-min(x_list))/2)+min(x_list) - Y = ((max(y_list)-min(y_list))/2)+min(y_list) - Z = ((max(z_list)-min(z_list))/2)+min(z_list) + X = ((max(x_list) - min(x_list)) / 2) + min(x_list) + Y = ((max(y_list) - min(y_list)) / 2) + min(y_list) + Z = ((max(z_list) - min(z_list)) / 2) + min(z_list) return X, Y, Z def get_center_of_gravity_of_molecule_ish(self): @@ -2487,7 +3295,7 @@ def get_center_of_gravity_of_molecule_ish(self): z_list = [] # pdb definition see: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM for line in open(self.pdb): - if (line.startswith('ATOM') or line.startswith('HETATM')): + if line.startswith("ATOM") or line.startswith("HETATM"): X = float(line[30:38]) x_list.append(X) Y = float(line[38:46]) @@ -2495,9 +3303,9 @@ def get_center_of_gravity_of_molecule_ish(self): Z = float(line[46:54]) z_list.append(Z) # 'ish' because it's not really the centre of gravity, but the the middle of the min/max of each x,y,z - X = ((max(x_list)-min(x_list))/2)+min(x_list) - Y = ((max(y_list)-min(y_list))/2)+min(y_list) - Z = ((max(z_list)-min(z_list))/2)+min(z_list) + X = ((max(x_list) - min(x_list)) / 2) + min(x_list) + Y = ((max(y_list) - min(y_list)) / 2) + min(y_list) + Z = ((max(z_list) - min(z_list)) / 2) + min(z_list) return X, Y, Z def get_init_pdb_as_list(self): @@ -2506,47 +3314,66 @@ def get_init_pdb_as_list(self): def get_pdb_as_list(self, pdbin): pdb_list = [] for line in open(pdbin): - if line.startswith('ATOM') or line.startswith('HETATM'): - atom_line = str(line[12:16]).replace(' ', '') - resname_line = str(line[17:20]).replace(' ', '') - chainID_line = str(line[21:23]).replace(' ', '') - resseq_line = str(line[23:26]).replace(' ', '') - altLoc_line = str(line[16:17]).replace(' ', '') + if line.startswith("ATOM") or line.startswith("HETATM"): + atom_line = str(line[12:16]).replace(" ", "") + resname_line = str(line[17:20]).replace(" ", "") + chainID_line = str(line[21:23]).replace(" ", "") + resseq_line = str(line[23:26]).replace(" ", "") + altLoc_line = str(line[16:17]).replace(" ", "") pdb_list.append( - [atom_line, altLoc_line, resname_line, chainID_line, resseq_line]) + [atom_line, altLoc_line, resname_line, chainID_line, resseq_line] + ) return pdb_list def ElementDict(self, resname, chainID, resseq, altLoc): ElementDict = { - 'C': 0, - 'N': 0, - 'O': 0, - 'P': 0, - 'S': 0, - 'BR': 0, - 'CL': 0, - 'I': 0, - 'F': 0} + "C": 0, + "N": 0, + "O": 0, + "P": 0, + "S": 0, + "BR": 0, + "CL": 0, + "I": 0, + "F": 0, + } for line in open(self.pdb): - if line.startswith('ATOM') or line.startswith('HETATM'): - atom_line = str(line[12:16]).replace(' ', '') - resname_line = str(line[17:20]).replace(' ', '') - chainID_line = str(line[21:23]).replace(' ', '') - resseq_line = str(line[23:26]).replace(' ', '') - altLoc_line = str(line[16:17]).replace(' ', '') - element_line = str(line[66:78]).replace(' ', '') - if resname_line == resname and chainID_line == chainID and resseq_line == resseq and altLoc_line == altLoc: + if line.startswith("ATOM") or line.startswith("HETATM"): + atom_line = str(line[12:16]).replace(" ", "") + resname_line = str(line[17:20]).replace(" ", "") + chainID_line = str(line[21:23]).replace(" ", "") + resseq_line = str(line[23:26]).replace(" ", "") + altLoc_line = str(line[16:17]).replace(" ", "") + element_line = str(line[66:78]).replace(" ", "") + if ( + resname_line == resname + and chainID_line == chainID + and resseq_line == resseq + and altLoc_line == altLoc + ): if element_line.upper() in ElementDict: ElementDict[element_line.upper()] += 1 return ElementDict - def update_residue(self, resname_old, chainID_old, resseq_old, altLoc_old, occupancy_old, resname_new, chainID_new, resseq_new, altLoc_new, occupancy_new): - outPDB = '' + def update_residue( + self, + resname_old, + chainID_old, + resseq_old, + altLoc_old, + occupancy_old, + resname_new, + chainID_new, + resseq_new, + altLoc_new, + occupancy_new, + ): + outPDB = "" for line in open(self.pdb): - if line.startswith('ATOM') or line.startswith('HETATM'): + if line.startswith("ATOM") or line.startswith("HETATM"): atom_line = str(line[0:6]) serial_line = str(line[6:11]) atomName_line = str(line[11:16]) @@ -2562,7 +3389,12 @@ def update_residue(self, resname_old, chainID_old, resseq_old, altLoc_old, occup Bfac_line = str(line[60:66]) element_line = str(line[66:78]) charge_line = str(line[78:80]) - if resname_line.replace(' ', '') == resname_old and chainID_line.replace(' ', '') == chainID_old and resseq_line.replace(' ', '') == resseq_old and altLoc_line.replace(' ', '') == altLoc_old: + if ( + resname_line.replace(" ", "") == resname_old + and chainID_line.replace(" ", "") == chainID_old + and resseq_line.replace(" ", "") == resseq_old + and altLoc_line.replace(" ", "") == altLoc_old + ): NewResname = resname_line.replace(resname_old, resname_new) @@ -2570,34 +3402,51 @@ def update_residue(self, resname_old, chainID_old, resseq_old, altLoc_old, occup if len(resseq_old) < len(resseq_new): NewResseq = resseq_line.replace( - resseq_old, ' '*(len(resseq_old)-len(resseq_new))+resseq_new) + resseq_old, + " " * (len(resseq_old) - len(resseq_new)) + resseq_new, + ) elif len(resseq_old) == len(resseq_new): NewResseq = resseq_line.replace(resseq_old, resseq_new) else: - NewResseq = resseq_line[len( - resseq_new)-len(resseq_old):].replace(resseq_old, resseq_new) + NewResseq = resseq_line[ + len(resseq_new) - len(resseq_old) : + ].replace(resseq_old, resseq_new) - if altLoc_line == ' ': - NewAltloc = altLoc_line.replace(' ', altLoc_new) + if altLoc_line == " ": + NewAltloc = altLoc_line.replace(" ", altLoc_new) else: NewAltloc = altLoc_line.replace(altLoc_old, altLoc_new) - NewOccupany = occupancy_line.replace( - occupancy_old, occupancy_new) - - outPDB += atom_line+serial_line+atomName_line+NewAltloc+NewResname+NewChain+NewResseq + \ - insert_line+x_line+y_line+z_line+NewOccupany+Bfac_line+element_line+charge_line + NewOccupany = occupancy_line.replace(occupancy_old, occupancy_new) + + outPDB += ( + atom_line + + serial_line + + atomName_line + + NewAltloc + + NewResname + + NewChain + + NewResseq + + insert_line + + x_line + + y_line + + z_line + + NewOccupany + + Bfac_line + + element_line + + charge_line + ) else: outPDB += line else: outPDB += line - f = open(self.pdb, 'w') + f = open(self.pdb, "w") f.write(outPDB) f.close() def merge_pdb_file(self, pdbin): - outPDB = '' + outPDB = "" # only merge if residue with same resname, chain and resnumber not already in self.pdb!!! residueListReference = self.residue_details_as_list(self.pdb) @@ -2605,40 +3454,42 @@ def merge_pdb_file(self, pdbin): DuplicateResidue = False for entry in residueListPDBin: if entry in residueListReference: - print('residue already exisits in '+self.pdb+':') + print("residue already exisits in " + self.pdb + ":") print(str(entry)) DuplicateResidue = True if not DuplicateResidue: for line in open(self.pdb): - if not line.startswith('END'): + if not line.startswith("END"): outPDB += line for line in open(pdbin): - if not line.startswith('END'): + if not line.startswith("END"): outPDB += line - outPDB += 'END\n' + outPDB += "END\n" - f = open(self.pdb, 'w') + f = open(self.pdb, "w") f.write(outPDB) f.close() else: - print('cannot merge pdb files!') + print("cannot merge pdb files!") def get_symmetry_operators(self): symop = [] spg_number = str(self.get_spg_number_from_pdb()) -# print 'spg',spg_number + # print 'spg',spg_number foundSPG = False - if os.path.isfile(os.path.join(os.getenv('CCP4'), 'lib', 'data', 'symop.lib')): + if os.path.isfile(os.path.join(os.getenv("CCP4"), "lib", "data", "symop.lib")): # print 'a',os.path.join(os.getenv('CCP4'),'lib','data','symop.lib') - for line in open(os.path.join(os.getenv('CCP4'), 'lib', 'data', 'symop.lib')): + for line in open( + os.path.join(os.getenv("CCP4"), "lib", "data", "symop.lib") + ): # print line.split()[0] if foundSPG: - if line.startswith(' '): - tmp = line.replace('\n', '') - symop.append(tmp.split(',')) + if line.startswith(" "): + tmp = line.replace("\n", "") + symop.append(tmp.split(",")) else: break if line.split()[0] == spg_number: @@ -2652,76 +3503,94 @@ def save_sym_equivalents(self): unit_cell = self.get_unit_cell_from_pdb() spg = self.get_spg_from_pdb() symop = self.get_symmetry_operators() - outDir = self.pdb[:self.pdb.rfind('/')] - root = self.pdb[self.pdb.rfind('/')+1:self.pdb.rfind('.')] - outPDB = os.path.join(outDir, root+'_sym.pdb') - pdbset = ('#!'+os.getenv('SHELL')+'\n' - 'pdbset xyzin %s xyzout %s << eof\n' % (self.pdb, outPDB) + - 'cell {0!s}\n'.format((str(','.join(unit_cell)))) + - 'spacegroup {0!s}\n'.format(spg)) + outDir = self.pdb[: self.pdb.rfind("/")] + root = self.pdb[self.pdb.rfind("/") + 1 : self.pdb.rfind(".")] + outPDB = os.path.join(outDir, root + "_sym.pdb") + pdbset = "#!" + os.getenv( + "SHELL" + ) + "\n" "pdbset xyzin %s xyzout %s << eof\n" % ( + self.pdb, + outPDB, + ) + "cell {0!s}\n".format( + (str(",".join(unit_cell))) + ) + "spacegroup {0!s}\n".format( + spg + ) for op in symop: - pdbset += 'SYMGEN '+','.join(op)+'\n' - pdbset += 'eof\n' + pdbset += "SYMGEN " + ",".join(op) + "\n" + pdbset += "eof\n" os.system(pdbset) def save_sym_equivalents_of_ligands_in_pdb(self, pdbIN): unit_cell = self.get_unit_cell_from_pdb() spg = self.get_spg_from_pdb() symop = self.get_symmetry_operators() - outDir = pdbIN[:pdbIN.rfind('/')] - root = pdbIN[pdbIN.rfind('/')+1:pdbIN.rfind('.')] - pdbset = ('#!'+os.getenv('SHELL')+'\n' - 'pdbset xyzin %s xyzout %s/%s_0.pdb << eof\n' % (pdbIN, outDir, root) + - 'cell {0!s}\n'.format((str(','.join(unit_cell)))) + - 'spacegroup {0!s}\n'.format(spg)) + outDir = pdbIN[: pdbIN.rfind("/")] + root = pdbIN[pdbIN.rfind("/") + 1 : pdbIN.rfind(".")] + pdbset = "#!" + os.getenv( + "SHELL" + ) + "\n" "pdbset xyzin %s xyzout %s/%s_0.pdb << eof\n" % ( + pdbIN, + outDir, + root, + ) + "cell {0!s}\n".format( + (str(",".join(unit_cell))) + ) + "spacegroup {0!s}\n".format( + spg + ) for op in symop: - pdbset += 'SYMGEN '+','.join(op)+'\n' - pdbset += 'eof\n' + pdbset += "SYMGEN " + ",".join(op) + "\n" + pdbset += "eof\n" os.system(pdbset) - return os.path.join(outDir, root+'_0.pdb') + return os.path.join(outDir, root + "_0.pdb") def save_sym_equivalents_of_ligands_in_pdb_as_one_file_per_ligand(self, pdbIN): nres = 0 for line in open(pdbIN): - if line.startswith('ATOM') or line.startswith('HETATM'): + if line.startswith("ATOM") or line.startswith("HETATM"): nres += 1 - print('NRES', nres) + print("NRES", nres) unit_cell = self.get_unit_cell_from_pdb() spg = self.get_spg_from_pdb() symop = self.get_symmetry_operators() - outDir = pdbIN[:pdbIN.rfind('/')] - root = pdbIN[pdbIN.rfind('/')+1:pdbIN.rfind('.')] - pdbset = ('#!'+os.getenv('SHELL')+'\n' - 'pdbset xyzin %s xyzout %s/out.pdb << eof 2> /dev/null\n' % (pdbIN, outDir) + - 'cell {0!s}\n'.format((str(','.join(unit_cell)))) + - 'spacegroup {0!s}\n'.format(spg)) + outDir = pdbIN[: pdbIN.rfind("/")] + root = pdbIN[pdbIN.rfind("/") + 1 : pdbIN.rfind(".")] + pdbset = "#!" + os.getenv( + "SHELL" + ) + "\n" "pdbset xyzin %s xyzout %s/out.pdb << eof 2> /dev/null\n" % ( + pdbIN, + outDir, + ) + "cell {0!s}\n".format( + (str(",".join(unit_cell))) + ) + "spacegroup {0!s}\n".format( + spg + ) for op in symop: - pdbset += 'SYMGEN '+','.join(op)+'\n' - pdbset += 'eof\n' + pdbset += "SYMGEN " + ",".join(op) + "\n" + pdbset += "eof\n" os.system(pdbset) pdbList = [] counter = 0 - out = '' - Cryst = '' + out = "" + Cryst = "" n = 0 - for line in open(os.path.join(outDir, 'out.pdb')): - if line.startswith('CRYST'): + for line in open(os.path.join(outDir, "out.pdb")): + if line.startswith("CRYST"): Cryst = line - if line.startswith('ATOM') or line.startswith('HETATM'): - if counter < nres-1: + if line.startswith("ATOM") or line.startswith("HETATM"): + if counter < nres - 1: if counter == 0: out = Cryst out += line counter += 1 else: out += line - pdbList.append(os.path.join( - outDir, root+'_'+str(n)+'.pdb')) - f = open(os.path.join(outDir, root+'_'+str(n)+'.pdb'), 'w') + pdbList.append(os.path.join(outDir, root + "_" + str(n) + ".pdb")) + f = open(os.path.join(outDir, root + "_" + str(n) + ".pdb"), "w") f.write(out) f.close() - out = '' + out = "" counter = 0 n += 1 @@ -2729,161 +3598,172 @@ def save_sym_equivalents_of_ligands_in_pdb_as_one_file_per_ligand(self, pdbIN): def save_surounding_unit_cells(self, pdbIN): translations = [ - - [0, 1, 0], - [0, 1, 1], - [0, 0, 1], - [0, -1, 1], - [0, -1, 0], - [0, -1, -1], - [0, 0, -1], - [0, 1, -1], - - [1, 0, 0], - [1, 1, 0], - [1, 1, 1], - [1, 0, 1], - [1, -1, 1], - [1, -1, 0], - [1, -1, -1], - [1, 0, -1], - [1, 1, -1], - - [-1, 0, 0], - [-1, 1, 0], - [-1, 1, 1], - [-1, 0, 1], + [0, 1, 0], + [0, 1, 1], + [0, 0, 1], + [0, -1, 1], + [0, -1, 0], + [0, -1, -1], + [0, 0, -1], + [0, 1, -1], + [1, 0, 0], + [1, 1, 0], + [1, 1, 1], + [1, 0, 1], + [1, -1, 1], + [1, -1, 0], + [1, -1, -1], + [1, 0, -1], + [1, 1, -1], + [-1, 0, 0], + [-1, 1, 0], + [-1, 1, 1], + [-1, 0, 1], [-1, -1, 1], [-1, -1, 0], [-1, -1, -1], - [-1, 0, -1], - [-1, 1, -1], - + [-1, 0, -1], + [-1, 1, -1], ] unit_cell = self.get_unit_cell_from_pdb() spg = self.get_spg_from_pdb() - outDir = pdbIN[:pdbIN.rfind('/')] - root = pdbIN[pdbIN.rfind('/')+1:pdbIN.rfind('.')] + outDir = pdbIN[: pdbIN.rfind("/")] + root = pdbIN[pdbIN.rfind("/") + 1 : pdbIN.rfind(".")] for n, shift in enumerate(translations): - pdbset = ('#!'+os.getenv('SHELL')+'\n' - 'pdbset xyzin %s/%s.pdb xyzout %s/%s_%s.pdb << eof 2> /dev/null\n' % (outDir, root, outDir, root, str(n+1)) + - 'cell {0!s}\n'.format((str(','.join(unit_cell)))) + - 'spacegroup {0!s}\n'.format(spg) + - 'shift fractional {0!s}\n'.format(str(shift).replace('[', '').replace(']', '')) + - 'eof\n') - print('pdinin', pdbIN) - print('outdir', outDir) - print('root', root) + pdbset = ( + "#!" + os.getenv("SHELL") + "\n" + "pdbset xyzin %s/%s.pdb xyzout %s/%s_%s.pdb << eof 2> /dev/null\n" + % (outDir, root, outDir, root, str(n + 1)) + + "cell {0!s}\n".format((str(",".join(unit_cell)))) + + "spacegroup {0!s}\n".format(spg) + + "shift fractional {0!s}\n".format( + str(shift).replace("[", "").replace("]", "") + ) + + "eof\n" + ) + print("pdinin", pdbIN) + print("outdir", outDir) + print("root", root) print(pdbset) os.system(pdbset) class logtools: - def __init__(self, logfile): self.logfile = logfile def phenix_molprobity(self): - QualityIndicators = {'MolprobityScore': 'n/a', - 'MolprobityScoreColor': 'gray', - 'RamachandranOutliers': 'n/a', - 'RamachandranOutliersColor': 'gray', - 'RamachandranFavored': 'n/a', - 'RamachandranFavoredColor': 'gray'} + QualityIndicators = { + "MolprobityScore": "n/a", + "MolprobityScoreColor": "gray", + "RamachandranOutliers": "n/a", + "RamachandranOutliersColor": "gray", + "RamachandranFavored": "n/a", + "RamachandranFavoredColor": "gray", + } # Molprobity = validation_summary.txt if os.path.isfile(self.logfile): for line in open(self.logfile): - if 'molprobity score' in line.lower(): + if "molprobity score" in line.lower(): if len(line.split()) >= 4: - QualityIndicators['MolprobityScore'] = line.split()[3] + QualityIndicators["MolprobityScore"] = line.split()[3] try: if float(line.split()[3]) < 2: - QualityIndicators['MolprobityScoreColor'] = 'green' + QualityIndicators["MolprobityScoreColor"] = "green" if 2 <= float(line.split()[3]) < 3: - QualityIndicators['MolprobityScoreColor'] = 'orange' + QualityIndicators["MolprobityScoreColor"] = "orange" if float(line.split()[3]) >= 3: - QualityIndicators['MolprobityScoreColor'] = 'red' + QualityIndicators["MolprobityScoreColor"] = "red" except ValueError: pass -# if line.lower().startswith(' ramachandran outliers ='): - if 'ramachandran outliers' in line.lower(): + # if line.lower().startswith(' ramachandran outliers ='): + if "ramachandran outliers" in line.lower(): if len(line.split()) >= 4: - QualityIndicators['RamachandranOutliers'] = line.split()[ - 3] + QualityIndicators["RamachandranOutliers"] = line.split()[3] try: if float(line.split()[3]) < 0.3: - QualityIndicators['RamachandranOutliersColor'] = 'green' + QualityIndicators["RamachandranOutliersColor"] = "green" if 0.3 <= float(line.split()[3]) < 1: - QualityIndicators['RamachandranOutliersColor'] = 'orange' + QualityIndicators[ + "RamachandranOutliersColor" + ] = "orange" if float(line.split()[3]) >= 1: - QualityIndicators['RamachandranOutliersColor'] = 'red' + QualityIndicators["RamachandranOutliersColor"] = "red" except ValueError: pass -# if line.startswith(' favored ='): - if 'favored' in line.lower(): + # if line.startswith(' favored ='): + if "favored" in line.lower(): if len(line.split()) == 4: - QualityIndicators['RamachandranFavored'] = line.split()[ - 2] + QualityIndicators["RamachandranFavored"] = line.split()[2] try: if float(line.split()[2]) < 90: - QualityIndicators['RamachandranFavoredColor'] = 'red' + QualityIndicators["RamachandranFavoredColor"] = "red" if 90 <= float(line.split()[2]) < 98: - QualityIndicators['RamachandranFavoredColor'] = 'orange' + QualityIndicators["RamachandranFavoredColor"] = "orange" if float(line.split()[2]) >= 98: - QualityIndicators['RamachandranFavoredColor'] = 'green' + QualityIndicators["RamachandranFavoredColor"] = "green" except ValueError: pass return QualityIndicators def refmac_log(self): - QualityIndicators = {'MatrixWeight': 'n/a'} + QualityIndicators = {"MatrixWeight": "n/a"} # Matrix Weight if os.path.isfile(self.logfile): for line in open(self.logfile): - if line.startswith(' Weight matrix') and len(line.split()) == 3: - QualityIndicators['MatrixWeight'] = line.split()[2] + if line.startswith(" Weight matrix") and len(line.split()) == 3: + QualityIndicators["MatrixWeight"] = line.split()[2] return QualityIndicators class reference: - def __init__(self, sample_mtz, reference_file_list): self.sample_mtz = sample_mtz self.reference_file_list = reference_file_list -# print reference_file_list + + # print reference_file_list def find_suitable_reference(self, allowed_unitcell_difference_percent): found_suitable_reference = False - unitcell_reference = 'n/a' - reference = '' - spg_reference = 'n/a' - unitcell_difference = 'n/a' - resolution_high = 'n/a' - spg_autoproc = 'n/a' - unitcell_autoproc = 'n/a' + unitcell_reference = "n/a" + reference = "" + spg_reference = "n/a" + unitcell_difference = "n/a" + resolution_high = "n/a" + spg_autoproc = "n/a" + unitcell_autoproc = "n/a" if os.path.isfile(self.sample_mtz): mtz_autoproc = mtztools(self.sample_mtz).get_all_values_as_dict() - resolution_high = mtz_autoproc['resolution_high'] - spg_autoproc = mtz_autoproc['spacegroup'] - unitcell_autoproc = mtz_autoproc['unitcell'] - lattice_autoproc = mtz_autoproc['bravais_lattice'] - unitcell_volume_autoproc = mtz_autoproc['unitcell_volume'] + resolution_high = mtz_autoproc["resolution_high"] + spg_autoproc = mtz_autoproc["spacegroup"] + unitcell_autoproc = mtz_autoproc["unitcell"] + lattice_autoproc = mtz_autoproc["bravais_lattice"] + unitcell_volume_autoproc = mtz_autoproc["unitcell_volume"] # check which reference file is most similar for o, reference_file in enumerate(self.reference_file_list): # print reference_file try: if not reference_file[4] == 0: unitcell_difference = round( - (math.fabs(reference_file[4]-unitcell_volume_autoproc)/reference_file[4])*100, 1) + ( + math.fabs(reference_file[4] - unitcell_volume_autoproc) + / reference_file[4] + ) + * 100, + 1, + ) # reference file is accepted when different in unitcell volume < 5% # and both files have the same lattice type - if unitcell_difference < allowed_unitcell_difference_percent and lattice_autoproc == reference_file[3]: + if ( + unitcell_difference < allowed_unitcell_difference_percent + and lattice_autoproc == reference_file[3] + ): spg_reference = reference_file[1] unitcell_reference = reference_file[2] reference = reference_file[0] @@ -2891,17 +3771,27 @@ def find_suitable_reference(self, allowed_unitcell_difference_percent): break except IndexError: pass - return (spg_reference, unitcell_reference, reference, found_suitable_reference, - resolution_high, spg_autoproc, unitcell_autoproc, unitcell_difference) + return ( + spg_reference, + unitcell_reference, + reference, + found_suitable_reference, + resolution_high, + spg_autoproc, + unitcell_autoproc, + unitcell_difference, + ) class misc: - def calculate_distance_between_coordinates(self, x1, y1, z1, x2, y2, z2): # print '==> XCE: calculating distance between two coordinates' distance = 0.0 - distance = math.sqrt(math.pow(float( - x1)-float(x2), 2)+math.pow(float(y1)-float(y2), 2)+math.pow(float(z1)-float(z2), 2)) + distance = math.sqrt( + math.pow(float(x1) - float(x2), 2) + + math.pow(float(y1) - float(y2), 2) + + math.pow(float(z1) - float(z2), 2) + ) return distance @@ -2911,15 +3801,16 @@ def __init__(self, smiles): def ElementDict(self): ElementDict = { - 'C': 0, - 'N': 0, - 'O': 0, - 'P': 0, - 'S': 0, - 'BR': 0, - 'CL': 0, - 'I': 0, - 'F': 0} + "C": 0, + "N": 0, + "O": 0, + "P": 0, + "S": 0, + "BR": 0, + "CL": 0, + "I": 0, + "F": 0, + } m = Chem.MolFromSmiles(self.smiles) for atom in m.GetAtoms(): @@ -2930,31 +3821,34 @@ def ElementDict(self): class maptools(object): - def calculate_map(self, mtz, F, PH): cmd = ( - 'fft hklin %s mapout %s << EOF\n' % (mtz, mtz.replace('.mtz', '.ccp4')) + - 'labin F1=%s PHI=%s\n' % (F, PH) + - 'EOF\n' + "fft hklin %s mapout %s << EOF\n" % (mtz, mtz.replace(".mtz", ".ccp4")) + + "labin F1=%s PHI=%s\n" % (F, PH) + + "EOF\n" ) os.system(cmd) -# print(cmd) + + # print(cmd) def cut_map_around_ligand(self, map, ligPDB, border): - if map.endswith('.map'): - map_extension = '.map' - elif map.endswith('.ccp4'): - map_extension = '.ccp4' + if map.endswith(".map"): + map_extension = ".map" + elif map.endswith(".ccp4"): + map_extension = ".ccp4" else: - map_extension = '' + map_extension = "" cmd = ( - 'mapmask mapin %s mapout %s xyzin %s << eof\n' % (map, map.replace(map_extension, '_mapmask'+map_extension), ligPDB) + - ' border %s\n' % border + - ' end\n' - 'eof' + "mapmask mapin %s mapout %s xyzin %s << eof\n" + % (map, map.replace(map_extension, "_mapmask" + map_extension), ligPDB) + + " border %s\n" % border + + " end\n" + "eof" ) os.system(cmd) + + # print(cmd) # self.translate_spg_to_number_dict = { @@ -3011,7 +3905,6 @@ def cut_map_around_ligand(self, map, ligPDB, border): class mtztools_gemmi: - def __init__(self, mtz): self.mtz = gemmi.read_mtz_file(mtz) @@ -3024,21 +3917,21 @@ def get_map_labels(self): DELFWT = None PHDELWT = None - if 'FWT' in labelList and 'PHWT' in labelList: - FWT = 'FWT' - PHWT = 'PHWT' + if "FWT" in labelList and "PHWT" in labelList: + FWT = "FWT" + PHWT = "PHWT" - if 'DELFWT' in labelList and 'PHDELWT' in labelList: - DELFWT = 'DELFWT' - PHDELWT = 'PHDELWT' + if "DELFWT" in labelList and "PHDELWT" in labelList: + DELFWT = "DELFWT" + PHDELWT = "PHDELWT" - if '2FOFCWT' in labelList and 'PH2FOFCWT' in labelList: - FWT = '2FOFCWT' - PHWT = 'PH2FOFCWT' + if "2FOFCWT" in labelList and "PH2FOFCWT" in labelList: + FWT = "2FOFCWT" + PHWT = "PH2FOFCWT" - if 'FOFCWT' in labelList and 'PHFOFCWT' in labelList: - DELFWT = 'FOFCWT' - PHDELWT = 'PHFOFCWT' + if "FOFCWT" in labelList and "PHFOFCWT" in labelList: + DELFWT = "FOFCWT" + PHDELWT = "PHFOFCWT" return FWT, PHWT, DELFWT, PHDELWT @@ -3049,36 +3942,43 @@ def get_high_low_resolution_limits(self): class maptools_gemmi: - def __init__(self, emap): self.emap = emap - self.emtz = emap.replace('.ccp4', '.mtz').replace('.map', '.mtz') + self.emtz = emap.replace(".ccp4", ".mtz").replace(".map", ".mtz") def map_to_sf(self, resolution): if os.path.isfile(self.emtz): - print('mtz file of event map exists; skipping...') + print("mtz file of event map exists; skipping...") return - cmd = 'gemmi map2sf %s %s FWT PHWT --dmin=%s' % ( - self.emap, self.emtz, resolution) - print(('converting map with command:\n' + cmd)) + cmd = "gemmi map2sf %s %s FWT PHWT --dmin=%s" % ( + self.emap, + self.emtz, + resolution, + ) + print(("converting map with command:\n" + cmd)) os.system(cmd) if os.path.isfile(self.emtz): - print('event map to SF conversion successful') + print("event map to SF conversion successful") mtz = gemmi.read_mtz_file(self.emtz) - mtz.history += ['date created: ' + - time.ctime(os.path.getmtime(self.emap))] - mtz.history += ['folder: ' + os.getcwd()] - mtz.history += ['file name: ' + self.emap] - if 'BDC' in self.emap: - mtz.history += ['BDC value: ' + self.emap[self.emap.find('BDC')+4:self.emap.find( - 'BDC')+4+self.emap[self.emap.find('BDC')+4:].find('_')]] -# mtz.write_to_file(self.emtz) + mtz.history += ["date created: " + time.ctime(os.path.getmtime(self.emap))] + mtz.history += ["folder: " + os.getcwd()] + mtz.history += ["file name: " + self.emap] + if "BDC" in self.emap: + mtz.history += [ + "BDC value: " + + self.emap[ + self.emap.find("BDC") + + 4 : self.emap.find("BDC") + + 4 + + self.emap[self.emap.find("BDC") + 4 :].find("_") + ] + ] + # mtz.write_to_file(self.emtz) else: - print('failed to convert event map to SF') + print("failed to convert event map to SF") class pdbtools_gemmi: - def __init__(self, pdb): self.pdb = gemmi.read_structure(pdb) @@ -3088,18 +3988,41 @@ def get_ligand_models_as_dict(self, ligandID): for chain in model: for residue in chain: if residue.name == ligandID: - if str(residue.name + '-' + chain.name + '-' + str(residue.seqid.num)) not in ligandDict: - ligandDict[str( - residue.name + '-' + chain.name + '-' + str(residue.seqid.num))] = None - m = gemmi.Model('1') - m.add_chain(gemmi.Chain('X')) - c = m['X'].get_polymer() + if ( + str( + residue.name + + "-" + + chain.name + + "-" + + str(residue.seqid.num) + ) + not in ligandDict + ): + ligandDict[ + str( + residue.name + + "-" + + chain.name + + "-" + + str(residue.seqid.num) + ) + ] = None + m = gemmi.Model("1") + m.add_chain(gemmi.Chain("X")) + c = m["X"].get_polymer() c.add_residue(gemmi.Residue(), 0) c[0].name = residue.name for n, atom in enumerate(residue): c[0].add_atom(atom, n) - ligandDict[str( - residue.name + '-' + chain.name + '-' + str(residue.seqid.num))] = m + ligandDict[ + str( + residue.name + + "-" + + chain.name + + "-" + + str(residue.seqid.num) + ) + ] = m return ligandDict def center_of_mass_ligand_dict(self, ligandID): @@ -3115,4 +4038,4 @@ def save_ligands_to_pdb(self, ligandID): for ligand in ligandDict: s = gemmi.Structure() s.add_model(ligandDict[ligand]) - s.write_pdb(ligand + '.pdb') + s.write_pdb(ligand + ".pdb") diff --git a/lib/coot_utils_XChem.py b/lib/coot_utils_XChem.py index 753dc5ee..b3319889 100755 --- a/lib/coot_utils_XChem.py +++ b/lib/coot_utils_XChem.py @@ -27,7 +27,8 @@ import coot import sys import numbers -sys.path.append('/usr/local/coot/current/lib/python2.7/site-packages') + +sys.path.append("/usr/local/coot/current/lib/python2.7/site-packages") # 3D annotations - a bit of a hack currently @@ -65,8 +66,8 @@ def with_no_backups(imol, *funcs): turn_off_backup(imol) for f in funcs: func = f[0] - args = f[1:len(f)] - #print "BL DEBUG:: func %s and args %s" %(func, args) + args = f[1 : len(f)] + # print "BL DEBUG:: func %s and args %s" %(func, args) func(*args) if backup_mode == 1: turn_on_backup(imol) @@ -86,15 +87,16 @@ def with_auto_accept(*funcs): set_refinement_immediate_replacement(1) for f in funcs: func = f[0] - args = f[1:len(f)] - #print "BL DEBUG:: func %s and args %s" %(func, args) + args = f[1 : len(f)] + # print "BL DEBUG:: func %s and args %s" %(func, args) ret = func(*args) accept_regularizement() - if (replace_state == 0): + if replace_state == 0: set_refinement_immediate_replacement(0) - return ret # returns result of last functions!!!! + return ret # returns result of last functions!!!! + # 'Macro' to run funcs on an active atom # funcs is function, active_atom specifiers and extra args @@ -108,18 +110,21 @@ def with_auto_accept(*funcs): def using_active_atom(*funcs): from types import ListType + active_atom = active_residue() - if (not active_atom): + if not active_atom: add_status_bar_text("No residue found") else: def arg_to_append(item): - aa_dict = {"aa_imol": active_atom[0], - "aa_chain_id": active_atom[1], - "aa_res_no": active_atom[2], - "aa_ins_code": active_atom[3], - "aa_atom_name": active_atom[4], - "aa_alt_conf": active_atom[5]} + aa_dict = { + "aa_imol": active_atom[0], + "aa_chain_id": active_atom[1], + "aa_res_no": active_atom[2], + "aa_ins_code": active_atom[3], + "aa_atom_name": active_atom[4], + "aa_alt_conf": active_atom[5], + } if isinstance(item, list): arg_ls = [] @@ -132,11 +137,11 @@ def arg_to_append(item): else: return item - if (len(funcs) == 1): + if len(funcs) == 1: # we have a list of functions # so use ls_funcs = funcs[0] - elif (type(funcs[0]) is ListType): + elif type(funcs[0]) is ListType: # we have a range of lists # use as is ls_funcs = funcs @@ -155,6 +160,7 @@ def arg_to_append(item): ret = func(*args) return ret + # here some truely pythonic version of the macros. Should replace # them in usage too: @@ -188,9 +194,10 @@ def __enter__(self): turn_off_backup(self.imol) def __exit__(self, type, value, traceback): - if (self.b_state == 1): + if self.b_state == 1: turn_on_backup(self.imol) + # Pythonic 'Macro' to tidy up a set of functions to be run with automatic # accepting of the refinement. # @@ -223,7 +230,7 @@ def __enter__(self): def __exit__(self, type, value, traceback): accept_regularizement() - if (self.replace_state == 0): + if self.replace_state == 0: set_refinement_immediate_replacement(0) @@ -243,10 +250,10 @@ def __init__(self): def __enter__(self): self.active_atom = active_residue() - if (not self.active_atom): + if not self.active_atom: add_status_bar_text("No (active) residue found") self.no_residue = True - #self.__exit__(None, "dummy", None) + # self.__exit__(None, "dummy", None) else: imol = self.active_atom[0] chain_id = self.active_atom[1] @@ -257,7 +264,7 @@ def __enter__(self): return [imol, chain_id, res_no, ins_code, atom_name, alt_conf] def __exit__(self, type, value, traceback): - if (self.no_residue): + if self.no_residue: # internal calling of exit, ignore errors return True pass @@ -266,37 +273,46 @@ def __exit__(self, type, value, traceback): # Pythonize function: return a python boolean. # def molecule_has_hydrogens(imol): - return (molecule_has_hydrogens_raw(imol) == 1) + return molecule_has_hydrogens_raw(imol) == 1 def add_hydrogens_using_refmac(imol): - out_file_name = os.path.join("coot-refmac", - molecule_name_stub(imol, 0) + '-needs-H.pdb') - in_file_name = os.path.join("coot-refmac", - molecule_name_stub(imol, 0) + '-with-H.pdb') - make_directory_maybe('coot-refmac') + out_file_name = os.path.join( + "coot-refmac", molecule_name_stub(imol, 0) + "-needs-H.pdb" + ) + in_file_name = os.path.join( + "coot-refmac", molecule_name_stub(imol, 0) + "-with-H.pdb" + ) + make_directory_maybe("coot-refmac") write_pdb_file(imol, out_file_name) return add_hydrogens_using_refmac_inner(imol, in_file_name, out_file_name) def add_hydrogens_to_chain_using_refmac(imol, chain_id): - out_file_name = os.path.join("coot-refmac", - molecule_name_stub(imol, 0) + '-chain-' + chain_id + '-needs-H.pdb') - in_file_name = os.path.join("coot-refmac", - molecule_name_stub(imol, 0) + '-chain-' + chain_id + '-with-H.pdb') - make_directory_maybe('coot-refmac') + out_file_name = os.path.join( + "coot-refmac", + molecule_name_stub(imol, 0) + "-chain-" + chain_id + "-needs-H.pdb", + ) + in_file_name = os.path.join( + "coot-refmac", + molecule_name_stub(imol, 0) + "-chain-" + chain_id + "-with-H.pdb", + ) + make_directory_maybe("coot-refmac") write_chain_to_pdb_file(imol, chain_id, out_file_name) return add_hydrogens_using_refmac_inner(imol, in_file_name, out_file_name) def add_hydrogens_using_refmac_inner(imol, in_file_name, out_file_name): - status = popen_command("refmac5", - ['XYZIN', out_file_name, 'XYZOUT', in_file_name], - ['MAKE HOUT YES'], - 'refmac-H-addition.log', 0) + status = popen_command( + "refmac5", + ["XYZIN", out_file_name, "XYZOUT", in_file_name], + ["MAKE HOUT YES"], + "refmac-H-addition.log", + 0, + ) try: - if (status == 0): + if status == 0: # all good return add_hydrogens_from_file(imol, in_file_name) except: @@ -335,8 +351,7 @@ def pre_release_qm(): def molecule_number_list(): ret = [] for mol_no in range(coot.graphics_n_molecules()): - if (valid_map_molecule_qm(mol_no) or - valid_model_molecule_qm(mol_no)): + if valid_map_molecule_qm(mol_no) or valid_model_molecule_qm(mol_no): ret.append(mol_no) return ret @@ -344,6 +359,7 @@ def molecule_number_list(): def model_molecule_number_list(): return list(filter(valid_model_molecule_qm, molecule_number_list())) + # Test for prefix-dir (1) being a string (2) existing (3) being a # directory (4-6) modifiable by user (ie. u+rwx). prefix_dir must be a # string. @@ -354,6 +370,7 @@ def model_molecule_number_list(): def directory_is_modifiable_qm(prefix_dir): from types import StringType + ret = False # check string: ret = type(prefix_dir) is StringType @@ -374,6 +391,7 @@ def directory_is_modifiable_qm(prefix_dir): ret = os.access(prefix_dir, os.X_OK) return ret + # return an absolute file-name for file-name or False # # def absolutify(file_name) - exists in python as os.path.abspath use that!! @@ -408,8 +426,7 @@ def most_recently_created_file(glob_str, dir): # FIXME:: to be tested # def residue_spec2atom_selection_string(centre_residue_spec): - ret = "//" + centre_residue_spec[0] + \ - "/" + str(centre_residue_spec[1]) + ret = "//" + centre_residue_spec[0] + "/" + str(centre_residue_spec[1]) return ret @@ -431,10 +448,10 @@ def residue_spec2chain_id(rs): if not isinstance(rs, list): return False else: - if (len(rs) == 3): + if len(rs) == 3: return rs[0] else: - if (len(rs) == 4): + if len(rs) == 4: return rs[1] else: return False @@ -444,10 +461,10 @@ def residue_spec2res_no(rs): if not isinstance(rs, list): return False else: - if (len(rs) == 3): + if len(rs) == 3: return rs[1] else: - if (len(rs) == 4): + if len(rs) == 4: return rs[2] return False @@ -456,31 +473,30 @@ def residue_spec2ins_code(rs): if not isinstance(rs, list): return False else: - if (len(rs) == 3): + if len(rs) == 3: return rs[2] else: - if (len(rs) == 4): + if len(rs) == 4: return rs[3] return False def atom_spec2imol(atom_spec): import types + if not (isinstance(atom_spec, list)): return False else: - if (len(atom_spec) == 6): + if len(atom_spec) == 6: return atom_spec[0] - if (len(atom_spec) == 7): + if len(atom_spec) == 7: return atom_spec[1] return False def residue_spec2residue_name(imol, spec): - return residue_name(imol, - spec[1], - spec[2], - spec[3]) + return residue_name(imol, spec[1], spec[2], spec[3]) + # Return a list of molecules that are maps # @@ -494,6 +510,7 @@ def map_molecule_list(): map_list.append(i) return map_list + # Return a list of molecules that are (coordinate) models # @@ -506,16 +523,18 @@ def model_molecule_list(): model_list.append(i) return model_list + # Return True(False) if @var{imol} is (isn't) a shelx molecule. # def shelx_molecule_qm(imol): - if (is_shelx_molecule(imol) == 1): + if is_shelx_molecule(imol) == 1: return True else: return False + # Set the virtual trackball behaviour. # # trackball @var{type} is a string: either 'flat' or 'spherical-surface' @@ -523,19 +542,21 @@ def shelx_molecule_qm(imol): def set_virtual_trackball_type(type): - if (type == "flat"): + if type == "flat": vt_surface(1) - elif (type == "spherical-surface"): + elif type == "spherical-surface": vt_surface(0) else: print("virtual trackball type", type, "not understood") + # Is ls a list of strings? Return True or False # def list_of_strings_qm(ls): import types + not_str = 0 if type(ls) is not ListType: return False @@ -550,6 +571,7 @@ def list_of_strings_qm(ls): else: return False + # string concat with spaces, @var{ls} must be a list of strings. # @@ -557,11 +579,13 @@ def list_of_strings_qm(ls): def string_append_with_spaces(ls): import string + if ls: return string.join(ls) else: return [""] + # The screen centre. # # return the rotation centre as a 3 membered list of numbers @@ -570,9 +594,12 @@ def string_append_with_spaces(ls): def rotation_centre(): - return [coot.rotation_centre_position(0), - coot.rotation_centre_position(1), - coot.rotation_centre_position(2)] + return [ + coot.rotation_centre_position(0), + coot.rotation_centre_position(1), + coot.rotation_centre_position(2), + ] + # this is actually not essentail since python has these funtion(s) @@ -595,24 +622,25 @@ def file_n_lines(file_name): if not os.path.isfile(file_name): return False else: - fin = open(file_name, 'r') + fin = open(file_name, "r") n_lines = sum(1 for line in fin) fin.close() return n_lines + # backport, so that we can replace once move to Python 2.7 is done def check_output(*popenargs, **kwargs): r"""Run command with arguments and return its output as a byte string. -Backported from Python 2.7 as it's implemented as pure python on stdlib. + Backported from Python 2.7 as it's implemented as pure python on stdlib. ->>> check_output(['/usr/bin/python', '--version']) -Python 2.6.2 -""" + >>> check_output(['/usr/bin/python', '--version']) + Python 2.6.2""" import subprocess + process = subprocess.Popen(stdout=subprocess.PIPE, *popenargs, **kwargs) output, unused_err = process.communicate() retcode = process.poll() @@ -625,6 +653,7 @@ def check_output(*popenargs, **kwargs): raise error return output + # returns false of there is a problem running cmd # @@ -636,7 +665,7 @@ def shell_command_to_string(cmd): major, minor, micro, releaselevel, serial = sys.version_info - if (major >= 2 and minor >= 7): + if major >= 2 and minor >= 7: try: ret = subprocess.check_output(cmd.split()) except: @@ -648,21 +677,25 @@ def shell_command_to_string(cmd): ret = False return ret + # Return True or False # adapted from find_exe # this finds absolute file names too # -def command_in_path_qm(cmd, only_extension_here=None, - add_extensions_here=None): +def command_in_path_qm(cmd, only_extension_here=None, add_extensions_here=None): if add_extensions_here is None: add_extensions_here = [] - exe_path = find_exe(cmd, "PATH", no_disk_search=True, - screen_info=False, - only_extension=only_extension_here, - add_extensions=add_extensions_here) + exe_path = find_exe( + cmd, + "PATH", + no_disk_search=True, + screen_info=False, + only_extension=only_extension_here, + add_extensions=add_extensions_here, + ) if exe_path: return True @@ -679,16 +712,16 @@ def command_in_path_qm_old_version(cmd, only_extension="", add_extensions=None): import string # we shall check for full path names first - if (os.path.isfile(cmd)): + if os.path.isfile(cmd): return True else: extensions = [] cmd_noext = cmd # some windows magic - if (os.name == 'nt'): + if os.name == "nt": file_ext = file_name_extension(cmd) cmd_noext = strip_extension(cmd) - if (file_ext): + if file_ext: extensions = [file_ext] else: tmp_ext = os.environ["PATHEXT"].split(os.pathsep) @@ -710,7 +743,7 @@ def command_in_path_qm_old_version(cmd, only_extension="", add_extensions=None): for path in string.split(primary_path, os.pathsep): program_exe = os.path.join(path, cmd_name) # print "BL DEBUG:: program_exe is", program_exe - if (os.path.isfile(program_exe)): + if os.path.isfile(program_exe): return True return False except: @@ -740,32 +773,33 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): major, minor, micro, releaselevel, serial = sys.version_info - if (os.path.isfile(cmd)): + if os.path.isfile(cmd): cmd_execfile = cmd else: - if not(command_in_path_qm(cmd)): + if not (command_in_path_qm(cmd)): print("command ", cmd, " not found in $PATH!") print("BL INFO:: Maybe we'll find it somewhere else later...") cmd_execfile = find_exe(cmd, "CCP4_BIN", "PATH") - if (cmd_execfile): + if cmd_execfile: # minor = 2 - if (major >= 2 and minor >= 4): + if major >= 2 and minor >= 4: # subprocess import subprocess - log = open(log_file, 'w') + + log = open(log_file, "w") cmd_args = [cmd_execfile] + args - if (screen_flag): + if screen_flag: process = subprocess.Popen( - cmd_args, stdin=subprocess.PIPE, stdout=subprocess.PIPE) + cmd_args, stdin=subprocess.PIPE, stdout=subprocess.PIPE + ) else: - process = subprocess.Popen( - cmd_args, stdin=subprocess.PIPE, stdout=log) + process = subprocess.Popen(cmd_args, stdin=subprocess.PIPE, stdout=log) for data in data_list: process.stdin.write(data + "\n") process.stdin.close() - if (screen_flag): + if screen_flag: for line in process.stdout: print("#", line.rstrip(" \n")) # remove trailing whitespace log.write(line) @@ -782,16 +816,24 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): args_string = string.join(args) # write tmp input file - input = file(data_list_file, 'w') + input = file(data_list_file, "w") for data in data_list: - input.write(data + '\n') + input.write(data + "\n") input.close() # print "BL DEBUG:: popen command is", cmd_execfile + " " + args_string + " < " + data_list_file + " > " + log_file - status = os.popen(cmd_execfile + " " + args_string + - " < " + data_list_file + " > " + log_file, 'r') + status = os.popen( + cmd_execfile + + " " + + args_string + + " < " + + data_list_file + + " > " + + log_file, + "r", + ) cmd_finished = status.close() - if (cmd_finished is not None): + if cmd_finished is not None: print("running command ", cmd, " failed!") return 1 else: @@ -803,6 +845,7 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): print("WARNING:: could not find {0!s}, so not running".format(cmd)) return False + # example usage: # popen_command("mtzdump",["HKLIN","a.mtz"],["HEAD","END"],"test.log",0) @@ -813,7 +856,8 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): def close_float_qm(x1, x2): - return (abs(x1 - x2) < 0.001) + return abs(x1 - x2) < 0.001 + # "a.b.res" -> "a.b" # file_name_sans_extension @@ -822,9 +866,11 @@ def close_float_qm(x1, x2): def strip_extension(s): import os + head, tail = os.path.splitext(s) return head + # What is the extension of file_name? # # "a.pdb" -> "pdb" @@ -836,13 +882,15 @@ def file_name_extension(file_name): import os import string + root, ext = os.path.splitext(file_name) if ext: - ext = string.lstrip(ext, '.') + ext = string.lstrip(ext, ".") return ext else: return "" + # e.g. "a.pdb" -> "a-tmp.pdb" # @@ -850,6 +898,7 @@ def file_name_extension(file_name): def add_tmp_extension_to(file_name): import types + if isinstance(file_name, (str,)): root, ext = os.path.splitext(file_name) f = root + "-tmp" + ext @@ -857,6 +906,7 @@ def add_tmp_extension_to(file_name): else: return "tmp" + # Same function as strip_extension, different name, as per scsh, in fact. # @@ -864,15 +914,18 @@ def add_tmp_extension_to(file_name): def file_name_sans_extension(s): return strip_extension(s) + # /a/b.t -> b.t d/e.ext -> e.ext # file-name-sans-path def strip_path(s): import os + head, tail = os.path.split(s) return tail + # does s start with a "/" ? # return True or False # @@ -882,19 +935,20 @@ def strip_path(s): def slash_start_qm(s): import types import string + if isinstance(s, (str,)): if len(s) > 0: - if (s.startswith("/") or s.startswith("\\")): + if s.startswith("/") or s.startswith("\\"): return True else: - if (os.name == 'nt' and len(s) > 1): + if os.name == "nt" and len(s) > 1: # for windows check if the start is a drive letter - drive_letter_ls = [ - dl + ':' for dl in string.ascii_uppercase] - if (s[0:2] in drive_letter_ls): + drive_letter_ls = [dl + ":" for dl in string.ascii_uppercase] + if s[0:2] in drive_letter_ls: return True return False + # return a string that contains the date/time # e.g. "2006-01-02_2216.03" # @@ -902,9 +956,11 @@ def slash_start_qm(s): def unique_date_time_str(): import time + lt = time.strftime("%Y-%m-%d_%H%M", time.localtime()) return lt + # return a list that has only every-nth members; # e.g. @code{every_nth ([0,1,2,3,4,5,6,7,8],2)} -> [0,2,4,6,8] # @code{every_nth ([0,1,2,3,4,5,6,7,8],3)} -> [0,3,6] @@ -921,6 +977,7 @@ def every_nth(ls, n): a.append(ls[i]) return a + # now usefull in testing # # residue_atoms must be a list @@ -932,11 +989,9 @@ def get_atom_from_residue(atom_name, residue_atoms, alt_conf): residue_atoms must be a list """ - if ((isinstance(residue_atoms, list)) and - (residue_atoms != [])): + if (isinstance(residue_atoms, list)) and (residue_atoms != []): for residue_atom in residue_atoms: - if (residue_atom[0][0] == atom_name and - residue_atom[0][1] == alt_conf): + if residue_atom[0][0] == atom_name and residue_atom[0][1] == alt_conf: return residue_atom # print "BL WARNING:: no atom name %s found in residue" %atom_name return False # no residue name found fail save @@ -948,21 +1003,23 @@ def get_atom(imol, chain_id, resno, ins_code, atom_name, alt_conf_internal=""): res_info = residue_info(imol, chain_id, resno, "") - if (not res_info): + if not res_info: return False else: ret = get_atom_from_residue(atom_name, res_info, alt_conf_internal) return ret + # def residue_info_dialog_displayed_qm(): - if (residue_info_dialog_is_displayed == 1): + if residue_info_dialog_is_displayed == 1: return True else: return False + # multi_read pdb reads all the files matching # @code{@emph{glob_pattern}} in # directory @code{@emph{dir}}. Typical usage of this might be: @@ -974,12 +1031,14 @@ def residue_info_dialog_displayed_qm(): def multi_read_pdb(glob_pattern, dir): import glob import os - patt = os.path.normpath(dir+'/*.'+glob_pattern) + + patt = os.path.normpath(dir + "/*." + glob_pattern) all_files = glob.glob(patt) for file in all_files: print("BL INFO:: reading ", file) read_pdb(file) + # read_pdb_all reads all the "*.pdb" files in the current directory. # @@ -987,36 +1046,45 @@ def multi_read_pdb(glob_pattern, dir): def read_pdb_all(): import glob import os + recentre_status = recentre_on_read_pdb() set_recentre_on_read_pdb(0) - patt = os.path.normpath(os.path.abspath(".")+'/*.pdb') + patt = os.path.normpath(os.path.abspath(".") + "/*.pdb") all_files = glob.glob(patt) for file in all_files: print("BL INFO:: reading ", file) read_pdb(file) set_recentre_on_read_pdb(recentre_status) + # return False if dir_name is a file or we can't do the mkdir def coot_mkdir(dir_name): import os - if (os.path.isfile(dir_name)): + + if os.path.isfile(dir_name): return False else: - if (os.path.isdir(dir_name)): + if os.path.isdir(dir_name): return True else: os.mkdir(dir_name) return True + # return the view matrix (useful for molscript, perhaps). # BL says: like all matrices is a python list [...] # def view_matrix(): - return [get_view_matrix_element(row_number, column_number) for row_number in range(3) for column_number in range(3)] + return [ + get_view_matrix_element(row_number, column_number) + for row_number in range(3) + for column_number in range(3) + ] + # return the transposed view matrix (useful for molscript, perhaps). # BL says: like all matrices is a python list [...] @@ -1024,7 +1092,12 @@ def view_matrix(): def view_matrix_transp(): - return [get_view_matrix_element(column_number, row_number) for row_number in range(3) for column_number in range(3)] + return [ + get_view_matrix_element(column_number, row_number) + for row_number in range(3) + for column_number in range(3) + ] + # return the view quaternion # @@ -1035,6 +1108,7 @@ def view_quaternion(): ret = list(map(get_view_quaternion_internal, [0, 1, 2, 3])) return ret + # Return the view number # @@ -1047,6 +1121,7 @@ def add_view(position, quaternion, zoom, view_name): ret = add_view_raw(*args) return ret + # Convert a view matrix to a view quaternion to set Coot view internals. # @@ -1062,11 +1137,11 @@ def matrix2quaternion(m00, m10, m20, m01, m11, m21, m02, m12, m22): # return x with the sign of y def convert_sign(x, y): - if (x > 0 and y > 0): + if x > 0 and y > 0: return x - elif (x < 0 < y): + elif x < 0 < y: return -x - elif (x > 0 > y): + elif x > 0 > y: return -x else: return x @@ -1090,6 +1165,7 @@ def convert_sign(x, y): return ls + # e.g # matrix2quaternion(0.0347695872187614, 0.773433089256287, 0.632923781871796, # 0.774806916713715, 0.379149734973907, -0.505885183811188, @@ -1105,9 +1181,8 @@ def convert_sign(x, y): def set_view_matrix(m00, m10, m20, m01, m11, m21, m02, m12, m22): - set_view_quaternion(matrix2quaternion(m00, m10, m20, - m01, m11, m21, - m02, m12, m22)) + set_view_quaternion(matrix2quaternion(m00, m10, m20, m01, m11, m21, m02, m12, m22)) + # Miguel's molecular orientation axes # @@ -1117,6 +1192,7 @@ def miguels_axes(): set_axis_orientation_matrix(*view_matrix()) set_axis_orientation_matrix_usage(1) + # Return the molecule centre as a list of 3 numbers. # # Note: mol_cen could contain values less than -9999. @@ -1124,9 +1200,12 @@ def miguels_axes(): def molecule_centre(imol): - return [coot.molecule_centre_internal(imol, 0), - coot.molecule_centre_internal(imol, 1), - coot.molecule_centre_internal(imol, 2)] + return [ + coot.molecule_centre_internal(imol, 0), + coot.molecule_centre_internal(imol, 1), + coot.molecule_centre_internal(imol, 2), + ] + # Move the centre of molecule number imol to the current screen centre # @@ -1135,9 +1214,12 @@ def molecule_centre(imol): def move_molecule_to_screen_centre(imol): if valid_model_molecule_qm(imol): rotate_centre = rotation_centre() - coot.translate_molecule_by(imol, (rotate_centre[0]-molecule_centre(imol)[0]), - (rotate_centre[1]-molecule_centre(imol)[1]), - (rotate_centre[2]-molecule_centre(imol)[2])) + coot.translate_molecule_by( + imol, + (rotate_centre[0] - molecule_centre(imol)[0]), + (rotate_centre[1] - molecule_centre(imol)[1]), + (rotate_centre[2] - molecule_centre(imol)[2]), + ) # This is a short name for the above. @@ -1151,6 +1233,7 @@ def move_molecule_to_screen_centre(imol): def identity_matrix(): return [1, 0, 0, 0, 1, 0, 0, 0, 1] + # e.g. translation('x',2) # -> [2, 0, 0] # Return: False on error @@ -1159,13 +1242,14 @@ def identity_matrix(): def translation(axis, length): import operator -# BL says: we dont check if axis is string, yet at least not directly - if (isinstance(length, numbers.Number)): - if (axis == "x"): + + # BL says: we dont check if axis is string, yet at least not directly + if isinstance(length, numbers.Number): + if axis == "x": return [length, 0, 0] - elif (axis == "y"): + elif axis == "y": return [0, length, 0] - elif (axis == "z"): + elif axis == "z": return [0, 0, length] else: print("symbol axis: ", axis, " incomprehensible") @@ -1174,6 +1258,7 @@ def translation(axis, length): print("incomprehensible length argument: ", length) return False + # Rotate degrees about screen axis, where axis is either 'x', 'y' or 'z'. # @@ -1183,7 +1268,7 @@ def rotate_about_screen_axis(axis, degrees): import operator def deg_to_rad(degs): - return (degs * 3.1415926 / 180.0) + return degs * 3.1415926 / 180.0 def simple_rotation_x(alpha): cos_alpha = math.cos(alpha) @@ -1198,21 +1283,34 @@ def simple_rotation_y(alpha): def simple_rotation_z(alpha): cos_alpha = math.cos(alpha) sin_alpha = math.sin(alpha) - return [cos_alpha, -sin_alpha, 0, sin_alpha, cos_alpha, 0, 0, 0, ] - -# BL says: I dont know what the next 2 defines are for... -# looks not used and/or useless to me -# seems that only 2nd matrix is used and not view_matrix! - def vm(): view_matrix() - def mult(mat1, mat2): mat2 -# end of uselessness... - - if (isinstance(degrees, numbers.Number)): - if (axis == "x"): + return [ + cos_alpha, + -sin_alpha, + 0, + sin_alpha, + cos_alpha, + 0, + 0, + 0, + ] + + # BL says: I dont know what the next 2 defines are for... + # looks not used and/or useless to me + # seems that only 2nd matrix is used and not view_matrix! + def vm(): + view_matrix() + + def mult(mat1, mat2): + mat2 + + # end of uselessness... + + if isinstance(degrees, numbers.Number): + if axis == "x": mult(view_matrix(), simple_rotation_x(deg_to_rad(degrees))) - elif (axis == "y"): + elif axis == "y": mult(view_matrix(), simple_rotation_y(deg_to_rad(degrees))) - elif (axis == "z"): + elif axis == "z": mult(view_matrix(), simple_rotation_z(deg_to_rad(degrees))) else: print("symbol axis: ", axis, " incomprehensible") @@ -1224,31 +1322,34 @@ def mult(mat1, mat2): mat2 # functions use the direct set_displayed functions). # def toggle_display_map(imol, idummy): - if (map_is_displayed(imol) == 0): + if map_is_displayed(imol) == 0: set_map_displayed(imol, 1) else: set_map_displayed(imol, 0) + # toggle the display of imol # def toggle_display_mol(imol): - if (mol_is_displayed(imol) == 0): + if mol_is_displayed(imol) == 0: set_mol_displayed(imol, 1) else: set_mol_displayed(imol, 0) + # toggle the active state (clickability) of imol # def toggle_active_mol(imol): - if (mol_is_active(imol) == 0): + if mol_is_active(imol) == 0: set_mol_active(imol, 1) else: set_mol_active(imol, 0) + # return a python (list) representation of molecule imol, or False if we can't # do it (imol is a map, say) # @@ -1256,7 +1357,7 @@ def toggle_active_mol(imol): def python_representation(imol): - if (not valid_model_molecule_qm(imol)): + if not valid_model_molecule_qm(imol): return False else: ls = [] @@ -1265,12 +1366,28 @@ def r_info(imol, chain_id, n): res_name = resname_from_serial_number(imol, chain_id, n) res_no = seqnum_from_serial_number(imol, chain_id, n) ins_code = insertion_code_from_serial_number(imol, chain_id, n) - return [res_no, ins_code, res_name, residue_info(imol, chain_id, res_no, ins_code)] - - ls = [[[chain_id, [r_info( - imol, chain_id, serial_number) for serial_number in range(chain_n_residues(chain_id, imol))]] for chain_id in chain_ids(imol)]] + return [ + res_no, + ins_code, + res_name, + residue_info(imol, chain_id, res_no, ins_code), + ] + + ls = [ + [ + [ + chain_id, + [ + r_info(imol, chain_id, serial_number) + for serial_number in range(chain_n_residues(chain_id, imol)) + ], + ] + for chain_id in chain_ids(imol) + ] + ] return ls + # reorder chains # @@ -1285,7 +1402,7 @@ def reorder_chains_in_model(chain_list): list(map(lambda model: model.sort(), chain_list)) p_rep = python_representation(imol) - if (type(p_rep) is ListType): + if type(p_rep) is ListType: reorder_chains_in_model(p_rep) clear_and_update_molecule(imol, p_rep) @@ -1303,6 +1420,7 @@ def transform_coords_molecule(imol, rtop): transform_molecule_by(imol, *ls) + # @code{transform_map(imol, mat, trans, about_pt, radius, space_group, cell)} # # where space_group is a HM-symbol and cell is a list of 6 @@ -1322,35 +1440,66 @@ def transform_map(*args): ret = None def tf(imol, mat, trans, about_pt, radius, space_group, cell): - return transform_map_raw(imol, - mat[0], mat[1], mat[2], - mat[3], mat[4], mat[5], - mat[6], mat[7], mat[8], - trans[0], trans[1], trans[2], - about_pt[0], about_pt[1], about_pt[2], - radius, - space_group, - cell[0], cell[1], cell[2], - cell[3], cell[4], cell[5]) + return transform_map_raw( + imol, + mat[0], + mat[1], + mat[2], + mat[3], + mat[4], + mat[5], + mat[6], + mat[7], + mat[8], + trans[0], + trans[1], + trans[2], + about_pt[0], + about_pt[1], + about_pt[2], + radius, + space_group, + cell[0], + cell[1], + cell[2], + cell[3], + cell[4], + cell[5], + ) # main line - if (len(args) == 7): + if len(args) == 7: ret = tf(args[0], args[1], args[2], args[3], args[4], args[5], args[6]) # imol_map mat trans about_pt radius: - elif (len(args) == 5): + elif len(args) == 5: imol = args[0] - ret = tf(imol, args[1], args[2], args[3], args[4], - space_group(imol), cell(imol)) + ret = tf( + imol, args[1], args[2], args[3], args[4], space_group(imol), cell(imol) + ) # no matrix specified: - elif (len(args) == 4): + elif len(args) == 4: imol = args[0] - ret = tf(imol, identity_matrix(), args[1], args[2], args[3], - space_group(imol), cell(imol)) + ret = tf( + imol, + identity_matrix(), + args[1], + args[2], + args[3], + space_group(imol), + cell(imol), + ) # no matrix or about point specified: - elif (len(args) == 3): + elif len(args) == 3: imol = args[0] - ret = tf(args[0], identity_matrix(), args[1], rotation_centre(), - args[2], space_group(imol), cell(imol)) + ret = tf( + args[0], + identity_matrix(), + args[1], + rotation_centre(), + args[2], + space_group(imol), + cell(imol), + ) else: print("arguments to transform-map incomprehensible: args: ", args) return ret @@ -1369,6 +1518,7 @@ def get_first_ncs_master_chain(): return ncs_masters[0] return r + # Define a map transformation function that obeys Lapthorn's Law of # NCS Handling Programs # @@ -1379,28 +1529,51 @@ def get_first_ncs_master_chain(): # -def transform_map_using_lsq_matrix(imol_bref, ref_chain, ref_resno_start, ref_resno_end, - imol_mov, mov_chain, mov_resno_start, mov_resno_end, - imol_map, about_pt, radius): +def transform_map_using_lsq_matrix( + imol_bref, + ref_chain, + ref_resno_start, + ref_resno_end, + imol_mov, + mov_chain, + mov_resno_start, + mov_resno_end, + imol_map, + about_pt, + radius, +): clear_lsq_matches() - add_lsq_match(ref_resno_start, ref_resno_end, ref_chain, - mov_resno_start, mov_resno_end, mov_chain, 1) + add_lsq_match( + ref_resno_start, + ref_resno_end, + ref_chain, + mov_resno_start, + mov_resno_end, + mov_chain, + 1, + ) space_group = symmetry_operators_to_xHM(symmetry_operators(imol_ref)) cell_params = cell(imol_ref) if not (space_group and cell): - message = "Bad cell or symmetry for molecule" + \ - str(cell) + str(space_group) + str(imol_ref) + message = ( + "Bad cell or symmetry for molecule" + + str(cell) + + str(space_group) + + str(imol_ref) + ) print("Bad cell or symmetry for molecule", message) - ret = -1 # invalid mol! or return message!? + ret = -1 # invalid mol! or return message!? else: rtop = apply_lsq_matches(imol_ref, imol_mov) - ret = transform_map(imol_map, rtop[0], rtop[1], about_pt, radius, - space_group, cell_params) + ret = transform_map( + imol_map, rtop[0], rtop[1], about_pt, radius, space_group, cell_params + ) return ret + # Make the imol-th map brighter. # # Scale_factor > 1 makes brighter... @@ -1428,6 +1601,7 @@ def brighten_map(imol, scale_factor): print("bad non-list current-colour ", current_colour) graphics_draw() + # Make all maps brighter # @@ -1435,6 +1609,7 @@ def brighten_map(imol, scale_factor): def brighten_maps(): list(map(lambda imap: brighten_map(imap, 1.25), map_molecule_list())) + # Make all maps darker # @@ -1442,6 +1617,7 @@ def brighten_maps(): def darken_maps(): list(map(lambda imap: brighten_map(imap, 0.8), map_molecule_list())) + # return a list of chain ids for given molecule number @var{imol}. # return empty list on error # @@ -1455,6 +1631,7 @@ def chain_ids(imol): chain_id_is.append(chain_id(imol, chain_no)) return chain_id_is + # convert from interface name to schemisch name to be equivalent to Paul's naming # # return True or False @@ -1462,11 +1639,12 @@ def chain_ids(imol): def is_solvent_chain_qm(imol, chain_id): - if (is_solvent_chain_p(imol, chain_id) == 1): + if is_solvent_chain_p(imol, chain_id) == 1: return True else: return False + # convert from interface name to schemisch name to be equivalent to Paul's naming # # return True or False @@ -1476,6 +1654,7 @@ def is_solvent_chain_qm(imol, chain_id): def is_protein_chain_qm(imol, chain_id): return is_protein_chain_p(imol, chain_id) == 1 + # convert from interface name to schemisch name to be equivalent to Paul's naming # # return True or False @@ -1485,28 +1664,31 @@ def is_protein_chain_qm(imol, chain_id): def is_nucleotide_chain_qm(imol, chain_id): return is_nucleotide_chain_p(imol, chain_id) == 1 + # python (schemeyish) interface to eponymous scripting interface function!? # return True or False # def valid_model_molecule_qm(imol): - if (coot.is_valid_model_molecule(imol) == 1): + if coot.is_valid_model_molecule(imol) == 1: return True else: return False + # python (schemeyish) interface to eponymous scripting interface function. # return True or False # def valid_map_molecule_qm(imol): - if (coot.is_valid_map_molecule(imol) == 1): + if coot.is_valid_map_molecule(imol) == 1: return True else: return False + # convenience function (slightly less typing). # # Return True or False @@ -1516,6 +1698,7 @@ def valid_map_molecule_qm(imol): def valid_refinement_map_qm(): return valid_map_molecule_qm(imol_refinement_map()) + # python (schemeyish) interface to shelx molecule test # # Return True or False @@ -1525,6 +1708,7 @@ def valid_refinement_map_qm(): def shelx_molecule_qm(imol): return is_shelx_molecule(imol) == 1 + # python (schemeyish) interface to the function that returns whether or not a map # is a difference map. # @@ -1533,11 +1717,12 @@ def shelx_molecule_qm(imol): def is_difference_map_qm(imol_map): - if (not valid_map_molecule_qm(imol_map)): + if not valid_map_molecule_qm(imol_map): return False else: return map_is_difference_map(imol_map) == 1 + # Does residue resno with insertion code ins_code of chain chain_id # and in molecule number imol exist? # @@ -1548,6 +1733,7 @@ def is_difference_map_qm(imol_map): def residue_exists_qm(imol, chain_id, resno, ins_code): return does_residue_exist_p(imol, chain_id, resno, ins_code) == 1 + # Does the residue contain hetatoms? # Return True or False. # @@ -1556,6 +1742,7 @@ def residue_exists_qm(imol, chain_id, resno, ins_code): def residue_has_hetatms_qm(imol, chain_id, res_no, ins_code): return residue_has_hetatms(imol, chain_id, res_no, ins_code) == 1 + # Return a list of 3 float for the centre of mas of molecule number imol. # # on failure return False. @@ -1564,7 +1751,7 @@ def residue_has_hetatms_qm(imol, chain_id, res_no, ins_code): def centre_of_mass(imol): centre = eval(centre_of_mass_string(imol)) - if (centre == 0): + if centre == 0: print("molecule number", imol, "is not valid") return False else: @@ -1572,6 +1759,7 @@ def centre_of_mass(imol): # for use somewhere let's return the centre return centre + # Return as a list the occupancy, temperature_factor, x y z coordinates # of the given atom. # (the x,y,z are in Cartesian Angstroms). @@ -1588,6 +1776,7 @@ def atom_specs(imol, chain_id, resno, ins_code, atom_name, alt_conf): def atom_spec2residue_spec(atom_spec): return atom_spec[2:][0:3] + # return a guess at the map to be refined (usually called after # imol_refinement_map returns -1) # @@ -1599,7 +1788,7 @@ def guess_refinement_map(): map_list = map_molecule_list() if not map_list: - return -1 # failed to find a map + return -1 # failed to find a map else: for map_mol in map_list: if map_is_difference_map(map_mol) == 0: @@ -1634,16 +1823,15 @@ def auto_weight_for_refinement(): def sphere_residues(radius): active_atom = active_residue() - if not active_atom: # check for list? + if not active_atom: # check for list? print("No active atom") return False else: centred_residue = active_atom[1:4] imol = active_atom[0] - other_residues = residues_near_residue( - imol, centred_residue, radius) + other_residues = residues_near_residue(imol, centred_residue, radius) all_residues = [centred_residue] - if (isinstance(other_residues, list)): + if isinstance(other_residues, list): all_residues += other_residues return [imol, all_residues] @@ -1674,7 +1862,7 @@ def no_non_bonded(ls): # chi squareds will be about 1.0). # def weight_scale_from_refinement_results(rr): - if not rr: # check for list? + if not rr: # check for list? return False else: nnb_list = no_non_bonded(rr[2]) @@ -1684,7 +1872,7 @@ def weight_scale_from_refinement_results(rr): if n == 0: return False else: - return summ/n + return summ / n # main body # @@ -1693,12 +1881,16 @@ def weight_scale_from_refinement_results(rr): while results: av_rms_d = weight_scale_from_refinement_results(results) print("av_rms_d:", av_rms_d) - if not av_rms_d: # check for number? + if not av_rms_d: # check for number? return False if n_trials > 20: print("BL INFO:: refinement did not converge, bailing out") return False - if ((target_auto_weighting_value * 1.1) > av_rms_d > (target_auto_weighting_value * 0.9)): + if ( + (target_auto_weighting_value * 1.1) + > av_rms_d + > (target_auto_weighting_value * 0.9) + ): # done s = "Success: Set weight matrix to " + str(matrix_state()) add_status_bar_text(s) @@ -1710,18 +1902,21 @@ def weight_scale_from_refinement_results(rr): # as does 1.5. # Simple is overdamped. current_weight = matrix_state() - new_weight = (target_auto_weighting_value * - current_weight) / av_rms_d - print("INFO:: setting refinement weight to {0!s} from * {1!s} / {2!s}".format( - new_weight, current_weight, av_rms_d)) - if (new_weight < 2): + new_weight = (target_auto_weighting_value * current_weight) / av_rms_d + print( + "INFO:: setting refinement weight to {0!s} from * {1!s} / {2!s}".format( + new_weight, current_weight, av_rms_d + ) + ) + if new_weight < 2: # weight refinement not converging print("BL INFO:: not convering, weight to set was", new_weight) set_matrix(new_weight) results = refinement_func() n_trials += 1 - return True # return successful termination... + return True # return successful termination... + # Print the sequence of molecule number @var{imol} # @@ -1734,23 +1929,26 @@ def print_sequence(imol): for chain in chain_ids(imol): print_sequence_chain(imol, chain) + # simple utility function to return the contents of a file as a string. # def pir_file_name2pir_sequence(pir_file_name): import os - if (not os.path.isfile(pir_file_name)): + + if not os.path.isfile(pir_file_name): return False else: try: - fin = open(pir_file_name, 'r') + fin = open(pir_file_name, "r") str = fin.read() fin.close() return str except: return False + # Associate the contents of a PIR file with a molecule. # @@ -1762,6 +1960,7 @@ def associate_pir_file(imol, chain_id, pir_file_name): else: print("WARNING:: associate-pir-file: bad text for", pir_file_name) + # Associate the contents of a fasta file with a molecule. # @@ -1778,12 +1977,14 @@ def associate_fasta_file(imol, chain_id, pir_file_name): def graphics_comma_key_pressed_hook(): pass + # dot key hook def graphics_dot_key_pressed_hook(): pass + # a list of [code, key, name, thunk] # e.g. [103, "g", "Goto Blob", blob_under_pointer_to_screen_centre()] @@ -1799,10 +2000,11 @@ def graphics_dot_key_pressed_hook(): def decode_key(key_val_name): try: import gtk + key_value = int(gtk.gdk.keyval_from_name(key_val_name)) # on some windows: special characters seem to have high value, # so need to convert these properly too - if (not key_value or key_value >= 100000): + if not key_value or key_value >= 100000: # new python needs a long there!? I hope it wont harm old!? new_val = int(ord(key_val_name)) key_value = int(gtk.gdk.unicode_to_keyval(new_val)) @@ -1810,6 +2012,7 @@ def decode_key(key_val_name): except: return key_sym_code(key_val_name) + # Add a key binding # # with a given name, key (e.g. "x" or "S") and the function to run @@ -1819,29 +2022,31 @@ def decode_key(key_val_name): def add_key_binding(name, key, thunk): from types import IntType, StringType + global key_bindings, std_key_bindings std_keys = [] - if (use_gui_qm): + if use_gui_qm: std_keys = [elem[1] for elem in std_key_bindings] keys = [elem[1] for elem in key_bindings] codes = [elem[0] for elem in key_bindings] - if (key in std_keys): - print("INFO:: you shall not overwrite a standard key binding ({0!s})".format( - key)) + if key in std_keys: + print( + "INFO:: you shall not overwrite a standard key binding ({0!s})".format(key) + ) else: - if (type(key) is IntType): - if (key in keys): + if type(key) is IntType: + if key in keys: print("INFO:: you are overwriting existing key", key) key_bindings.pop(keys.index(key)) key_bindings.append([key, key, name, thunk]) - elif (type(key) is StringType): + elif type(key) is StringType: code = decode_key(key) - if (code in codes): + if code in codes: print("INFO:: you are overwriting existing key (from code)", key) key_bindings.pop(codes.index(code)) if "Control_" in key: code = decode_key(key[-1]) - if (("Control_" in key) or not (code == -1)): + if ("Control_" in key) or not (code == -1): key_bindings.append([code, key, name, thunk]) else: print("INFO:: key {0!s} not found in code table".format(key)) @@ -1860,16 +2065,14 @@ def graphics_general_key_press_hook(key, control_flag=0): else: codes = [elem[0] for elem in key_bindings if not "Control_" in elem[1]] funcs = [elem[3] for elem in key_bindings if not "Control_" in elem[1]] - if (key in codes): + if key in codes: index = codes.index(key) func = funcs[index] # print "BL DEBUG:: index and executing:", index, func apply(func) else: if coot_has_guile() and is_windows(): - run_scheme_command("(graphics-general-key-press-hook " + - str(key) + - ")") + run_scheme_command("(graphics-general-key-press-hook " + str(key) + ")") print("Key {0!s} not found in (python) key bindings".format(key)) @@ -1892,7 +2095,7 @@ def colour_from_number(obj): if type(obj) is StringType: return obj elif isNumbertype(obj): - if (obj == 0): + if obj == 0: return "white" else: return "red" @@ -1901,7 +2104,7 @@ def colour_from_number(obj): # main body n = new_generic_object_number(obj_name) - fin = open(filename, 'r') + fin = open(filename, "r") lines = fin.readlines() fin.close() for line in lines: @@ -1911,10 +2114,11 @@ def colour_from_number(obj): try: coords = list(map(float, current_line[0:-1])) except: - print("BL WARNING:: cannot make float from cordinates", current_line[0:-1]) + print( + "BL WARNING:: cannot make float from cordinates", current_line[0:-1] + ) return - to_generic_object_add_line(n, colour, 2, - *coords) + to_generic_object_add_line(n, colour, 2, *coords) set_display_generic_object(n, 1) @@ -1935,8 +2139,7 @@ def residues_matching_criteria(imol, residue_test_func): for chain_id in chain_list: for serial_number in range(chain_n_residues(chain_id, imol)): res_no = seqnum_from_serial_number(imol, chain_id, serial_number) - ins_code = insertion_code_from_serial_number( - imol, chain_id, serial_number) + ins_code = insertion_code_from_serial_number(imol, chain_id, serial_number) r = residue_test_func(chain_id, res_no, ins_code, serial_number) if r: seq_residue_list.append([chain_id, res_no, ins_code]) @@ -1945,12 +2148,16 @@ def residues_matching_criteria(imol, residue_test_func): else: return False + # Return residue specs for all residues in imol (each spec is preceeded by True) # def all_residues(imol): - return residues_matching_criteria(imol, lambda chain_id, resno, ins_code, serial: True) + return residues_matching_criteria( + imol, lambda chain_id, resno, ins_code, serial: True + ) + # Return a list of all residues that have alt confs: where a residue # is specified thusly: [[chain_id, resno, ins_code], [...] ] @@ -1971,7 +2178,13 @@ def alt_func1(chain_id, res_no, ins_code, res_serial_no): break return r - return residues_matching_criteria(imol, lambda chain_id, res_no, ins_code, res_serial_no: alt_func1(chain_id, res_no, ins_code, res_serial_no)) + return residues_matching_criteria( + imol, + lambda chain_id, res_no, ins_code, res_serial_no: alt_func1( + chain_id, res_no, ins_code, res_serial_no + ), + ) + # Return a list of all the altconfs in the residue. # Typically this will return [""] or ["A", "B"] @@ -2001,24 +2214,20 @@ def atoms_with_zero_occ(imol): n_residues = chain_n_residues(chain_id, imol) for serial_number in range(n_residues): - res_name = resname_from_serial_number( - imol, chain_id, serial_number) + res_name = resname_from_serial_number(imol, chain_id, serial_number) res_no = seqnum_from_serial_number(imol, chain_id, serial_number) - ins_code = insertion_code_from_serial_number( - imol, chain_id, serial_number) + ins_code = insertion_code_from_serial_number(imol, chain_id, serial_number) res_info = residue_info(imol, chain_id, res_no, ins_code) for atom_info in res_info: occ = atom_info[1][0] name = atom_info[0][0] alt_conf = atom_info[0][1] - if (occ < 0.01): - text = str(imol) + " " + chain_id + " " + \ - str(res_no) + " " + name - if (alt_conf): + if occ < 0.01: + text = str(imol) + " " + chain_id + " " + str(res_no) + " " + name + if alt_conf: text += " " text += alt_conf - r.append([text, imol, chain_id, res_no, - ins_code, name, alt_conf]) + r.append([text, imol, chain_id, res_no, ins_code, name, alt_conf]) return r @@ -2029,12 +2238,13 @@ def res_spec2chain_id(res_spec): if not res_spec: return False - if (len(res_spec) == 4): + if len(res_spec) == 4: return res_spec[1] - if (len(res_spec) == 3): + if len(res_spec) == 3: return res_spec[0] return False + # simple extraction function @@ -2043,12 +2253,13 @@ def res_spec2res_no(res_spec): if not res_spec: return False - if (len(res_spec) == 4): + if len(res_spec) == 4: return res_spec[2] - if (len(res_spec) == 3): + if len(res_spec) == 3: return res_spec[1] return False + # simple extraction function @@ -2057,9 +2268,9 @@ def res_spec2ins_code(res_spec): if not res_spec: return False - if (len(res_spec) == 4): + if len(res_spec) == 4: return res_spec[3] - if (len(res_spec) == 3): + if len(res_spec) == 3: return res_spec[2] return False @@ -2073,6 +2284,7 @@ def res_spec2ins_code(res_spec): def residue_spec2atom_for_centre(imol, chain_id, res_no, ins_code): from types import ListType + # residue-info can return False atom_ls = residue_info(imol, chain_id, res_no, ins_code) @@ -2082,7 +2294,7 @@ def residue_spec2atom_for_centre(imol, chain_id, res_no, ins_code): for i in range(len(atom_ls)): alt_conf_str = atom_ls[i][0][1] atom = atom_ls[i][0][0] - if (atom == " CA "): + if atom == " CA ": centre_atom_name_alt_conf = [atom, alt_conf_str] break if (not centre_atom_name_alt_conf) and (len(atom_ls) > 0): @@ -2094,9 +2306,8 @@ def residue_spec2atom_for_centre(imol, chain_id, res_no, ins_code): def set_go_to_atom(res_spec): set_go_to_atom_chain_residue_atom_name( - res_spec2chain_id(res_spec), - res_spec2res_no(res_spec), - " CA ") + res_spec2chain_id(res_spec), res_spec2res_no(res_spec), " CA " + ) def update_go_to_atom_from_current_atom(): @@ -2126,6 +2337,7 @@ def flip_active_ligand(): alt_conf = active_atom[5] flip_ligand(imol, chain_id, resno) + # Typically one might want to use this on a water, but it deletes the # nearest CA currently... Needs a re-think. Should active-atom just # return the nearest atom and not be clever about returning a CA. @@ -2138,6 +2350,7 @@ def delete_atom_by_active_residue(): if active_atom: delete_atom(active_atom) + # general mutate # # typically: @@ -2167,16 +2380,16 @@ def get_monomer_and_dictionary(tlc): have_tlc_molecule = False for imol in model_molecule_list(): nc = n_chains(imol) - if (nc == 1): + if nc == 1: ch_id = chain_id(imol, 0) nr = chain_n_residues(ch_id, imol) - if (nr == 1): + if nr == 1: rn = resname_from_serial_number(imol, ch_id, 0) - if (rn == tlc): + if rn == tlc: have_tlc_molecule = imol break have_dict_for_tlc = monomer_restraints(tlc) - if ((not have_tlc_molecule) or (not have_dict_for_tlc)): + if (not have_tlc_molecule) or (not have_dict_for_tlc): return get_monomer(tlc) else: print("we have dict and model for tlc already") @@ -2200,8 +2413,7 @@ def mutate_it(): if merge_status == 1: new_chain_id = new_chain_id_info[1] change_residue_number(imol, new_chain_id, 1, "", resno, "") - change_chain_id(imol, new_chain_id, - chain_id_in, 1, resno, resno) + change_chain_id(imol, new_chain_id, chain_id_in, 1, resno, resno) replacement_state = refinement_immediate_replacement_state() imol_map = imol_refinement_map() @@ -2211,17 +2423,25 @@ def mutate_it(): else: spin_atoms = [" P ", " O1P", " O2P", " O3P"] phos_dir = { - 'PTR': [" CZ ", " OH "], - 'SEP': [" CB ", " OG "], - 'TPO': [" CB ", " OG1"]} + "PTR": [" CZ ", " OH "], + "SEP": [" CB ", " OG "], + "TPO": [" CB ", " OG1"], + } if tlc in list(phos_dir.keys()): dir_atoms = phos_dir[tlc] else: dir_atoms = False refine_zone(imol, chain_id_in, resno, resno, "") if dir_atoms: - spin_search(imol_map, imol, chain_id_in, - resno, "", dir_atoms, spin_atoms) + spin_search( + imol_map, + imol, + chain_id_in, + resno, + "", + dir_atoms, + spin_atoms, + ) refine_zone(imol, chain_id_in, resno, resno, "") accept_regularizement() set_refinement_immediate_replacement(replacement_state) @@ -2239,7 +2459,7 @@ def mutate_it(): # rather than continuing. # imol_map = imol_refinement_map() - if (imol_map == -1): + if imol_map == -1: map_mols = map_molecule_list() if not map_mols: print("BL WARNING:: no valid maps around! Cannot mutate.") @@ -2247,9 +2467,11 @@ def mutate_it(): # BL says:: I dunno how to wait for the input from map selection since there is no return # waiting for mouse/keyboard input may be an option but no curses on windows, maybe # fix later, for now we use the first map - # show_select_map_dialog() + # show_select_map_dialog() if len(map_mols) > 1: - print("BL INFO:: we use the first map! If you wanna use another one, please select from Model/Fit/Refine") + print( + "BL INFO:: we use the first map! If you wanna use another one, please select from Model/Fit/Refine" + ) else: print("BL INFO:: no refinement map set, will set first one for you!") set_imol_refinement_map(map_mols[0]) @@ -2257,6 +2479,7 @@ def mutate_it(): else: mutate_it() + # A bit of fun # @@ -2270,27 +2493,29 @@ def phosphorylate_active_residue(): inscode = active_atom[3] res_name = residue_name(imol, chain_id, resno, inscode) - if res_name == 'TYR': + if res_name == "TYR": mutate_by_overlap(imol, chain_id, resno, "PTR") - elif res_name == 'SER': + elif res_name == "SER": mutate_by_overlap(imol, chain_id, resno, "SEP") - elif res_name == 'THR': + elif res_name == "THR": mutate_by_overlap(imol, chain_id, resno, "TPO") else: s = "Can't Phosphorylate residue of type " + res_name info_dialog(s) + # A function for Overlaying ligands. The transformation is applied # to all the atoms of the molecule that contains the moving ligand. # -def overlay_my_ligands(imol_mov, chain_id_mov, resno_mov, - imol_ref, chain_id_ref, resno_ref): +def overlay_my_ligands( + imol_mov, chain_id_mov, resno_mov, imol_ref, chain_id_ref, resno_ref +): - imol_frag = new_molecule_by_atom_selection(imol_mov, - "//" + chain_id_mov + - "/" + str(resno_mov)) + imol_frag = new_molecule_by_atom_selection( + imol_mov, "//" + chain_id_mov + "/" + str(resno_mov) + ) rtop_i = overlap_ligands(imol_frag, imol_ref, chain_id_ref, resno_ref) set_mol_displayed(imol_frag, 0) transform_coords_molecule(imol_mov, rtop_i[0]) @@ -2302,12 +2527,11 @@ def label_all_CAs(imol): if not (is_solvent_chain_qm(imol, chain_id)): n_residues = chain_n_residues(chain_id, imol) for serial_number in number_list(0, n_residues): - res_name = resname_from_serial_number( - imol, chain_id, serial_number) - res_no = seqnum_from_serial_number( - imol, chain_id, serial_number) + res_name = resname_from_serial_number(imol, chain_id, serial_number) + res_no = seqnum_from_serial_number(imol, chain_id, serial_number) ins_code = insertion_code_from_serial_number( - imol, chain_id, serial_number) + imol, chain_id, serial_number + ) add_atom_label(imol, chain_id, res_no, " CA ") graphics_draw() @@ -2336,6 +2560,7 @@ def label_all_active_residue_atoms(): add_atom_label(imol, chain_id, resno, atom_info[0][0]) graphics_draw() + # Resets alt confs and occupancies of atoms in residue that have # orphan alt-loc attributes # @@ -2352,7 +2577,7 @@ def name_match_qm(atom_1, atom_ls): compound_name_2 = atom[0] atom_name_2 = compound_name_2[0] - if (atom_name_1 == atom_name_2): + if atom_name_1 == atom_name_2: matchers.append(atom) if matchers: @@ -2365,25 +2590,46 @@ def name_match_qm(atom_1, atom_ls): chain_id = atom_info[1] resno = atom_info[2] inscode = atom_info[3] - atom_attribute_settings = [] # add to this + atom_attribute_settings = [] # add to this for atom in atom_ls: compound_name = atom[0] atom_name = compound_name[0] alt_conf = compound_name[1] - if (alt_conf != ""): + if alt_conf != "": matchers = name_match_qm(atom, atom_ls) - if (len(matchers) == 1): - atom_attribute_settings.append([imol, chain_id, resno, inscode, atom_name, - alt_conf, "alt-conf", ""]) + if len(matchers) == 1: + atom_attribute_settings.append( + [ + imol, + chain_id, + resno, + inscode, + atom_name, + alt_conf, + "alt-conf", + "", + ] + ) else: - atom_attribute_settings.append([imol, chain_id, resno, inscode, atom_name, - alt_conf, "occ", ((shelx_molecule_qm(imol) and 11.0) or (1.0))]) - if (atom_attribute_settings != []): + atom_attribute_settings.append( + [ + imol, + chain_id, + resno, + inscode, + atom_name, + alt_conf, + "occ", + ((shelx_molecule_qm(imol) and 11.0) or (1.0)), + ] + ) + if atom_attribute_settings != []: set_atom_attributes(atom_attribute_settings) - if (residue_info_dialog_displayed_qm()): + if residue_info_dialog_displayed_qm(): residue_info_dialog(imol, chain_id, resno, inscode) + # @@ -2393,6 +2639,7 @@ def sanitise_alt_confs_in_residue(imol, chain_id, resno, inscode): atom_ls = residue_info(imol, chain_id, resno, inscode) sanitise_alt_confs(atom_info, atom_ls) + # Resets alt confs and occupancies of atoms in residue that have # orphan alt-loc attributes. Use the active-residue. # @@ -2414,8 +2661,17 @@ def sanitise_alt_confs_active_residue(): def print_molecule_names(): - list(map(lambda molecule_number: printf(" {0!s} {1!s}\n".format(molecule_number, molecule_name(molecule_number))), - molecule_number_list())) + list( + map( + lambda molecule_number: printf( + " {0!s} {1!s}\n".format( + molecule_number, molecule_name(molecule_number) + ) + ), + molecule_number_list(), + ) + ) + # save the dialog positions to the coot_dialog_positions.py file in ./coot-preferences # @@ -2424,38 +2680,35 @@ def print_molecule_names(): def save_dialog_positions_to_init_file(): import os + # return False on failure to find .coot.py (or .coot-preferences) def dump_positions_to_file(positions, preferences=False): - home = 'HOME' + home = "HOME" port = False - if (os.name == 'nt'): - home = 'COOT_HOME' + if os.name == "nt": + home = "COOT_HOME" if preferences: - init_dir = os.path.join(os.getenv(home), - ".coot-preferences") - init_file = os.path.join(init_dir, - "saved_dialog_positions.py") - if (not os.path.isdir(init_dir)): + init_dir = os.path.join(os.getenv(home), ".coot-preferences") + init_file = os.path.join(init_dir, "saved_dialog_positions.py") + if not os.path.isdir(init_dir): return False - port = open(init_file, 'w') - print("BL INFO:: writing dialog positions to .coot-preferences/saved_dialog_positions.py") + port = open(init_file, "w") + print( + "BL INFO:: writing dialog positions to .coot-preferences/saved_dialog_positions.py" + ) else: - init_file = os.path.join(os.getenv(home), - ".coot.py") - if (not os.path.isfile(init_file)): + init_file = os.path.join(os.getenv(home), ".coot.py") + if not os.path.isfile(init_file): return False - port = open(init_file, 'a') + port = open(init_file, "a") print("BL INFO:: writing dialog positions to .coot.py") if port: - port.write( - "# ----------------------------------------------------------") - port.write( - "# the following were written by extraction from a state file") - port.write( - "# ----------------------------------------------------------") + port.write("# ----------------------------------------------------------") + port.write("# the following were written by extraction from a state file") + port.write("# ----------------------------------------------------------") for position in positions: port.write(position) port.write("# -------------------------") @@ -2466,30 +2719,34 @@ def dump_positions_to_file(positions, preferences=False): # main line state_file = "0-coot.state.py" save_state() - if (not os.path.isfile(state_file)): - print("Ooops {0!s} does not exist (either guile enabled or problem writing the file".format( - state_file)) + if not os.path.isfile(state_file): + print( + "Ooops {0!s} does not exist (either guile enabled or problem writing the file".format( + state_file + ) + ) else: - port = open("0-coot.state.py", 'r') + port = open("0-coot.state.py", "r") try: lines = port.readlines() except: lines = [] positions = [] for line in lines: - if ("_dialog_position" in line): + if "_dialog_position" in line: print(" Adding dialog position: ", line) positions.append(line) - elif ("set_go_to_atom_window_position" in line): + elif "set_go_to_atom_window_position" in line: print(" Adding dialog position: ", line) positions.append(line) port.close() write_init_status = dump_positions_to_file(positions) - if (write_init_status == False): + if write_init_status == False: # try to write a file to preferences dump_positions_to_file(positions, preferences=True) + # saves a string to a file! # if the string is already present dont do anything # optional arg: overwrite @@ -2500,20 +2757,20 @@ def dump_positions_to_file(positions, preferences=False): def save_string_to_file(string, filename, overwrite=False): - #home = 'HOME' + # home = 'HOME' # if (os.name == 'nt'): # home = 'COOT_HOME' init_file = filename - if (os.path.isfile(init_file)): + if os.path.isfile(init_file): # init file exists - if (overwrite): - port = open(init_file, 'w') + if overwrite: + port = open(init_file, "w") lines = [] else: - port = open(init_file, 'r+') + port = open(init_file, "r+") lines = port.readlines() else: - port = open(init_file, 'w') + port = open(init_file, "w") lines = [] string_written = False for line in lines: @@ -2521,7 +2778,7 @@ def save_string_to_file(string, filename, overwrite=False): # line exists, dont write string_written = True break - if (not string_written): + if not string_written: # append the string port.write((string + "\n")) port.close() @@ -2530,40 +2787,39 @@ def save_string_to_file(string, filename, overwrite=False): # removes a line containg all strings of the given list from file def remove_line_containing_from_file(remove_str_ls, filename): - #home = 'HOME' + # home = 'HOME' # if (os.name == 'nt'): # home = 'COOT_HOME' - #init_file = os.path.join(os.getenv(home), ".coot.py") + # init_file = os.path.join(os.getenv(home), ".coot.py") init_file = filename - if (os.path.isfile(init_file)): + if os.path.isfile(init_file): # init file exists - port = open(init_file, 'r') + port = open(init_file, "r") lines = port.readlines() port.close() else: - print("BL INFO:: no {0!s} file, so cannot remove line".format( - init_file)) + print("BL INFO:: no {0!s} file, so cannot remove line".format(init_file)) lines = [] - if (lines): - patt = string.join(remove_str_ls, '|') + if lines: + patt = string.join(remove_str_ls, "|") re_patt = re.compile(patt) tmp_ls = [] for line in lines: result = re_patt.findall(line) - if (not len(result) == len(remove_str_ls)): + if not len(result) == len(remove_str_ls): tmp_ls.append(line) - port = open(init_file, 'w') + port = open(init_file, "w") lines = port.writelines(tmp_ls) port.close() + # multiple maps of varying colour from a given map. # def multi_chicken(imol, n_colours=False): - def rotate_colour_map(col, degrees): - ret = [degrees/360, col[1], col[2] - degrees/360] + ret = [degrees / 360, col[1], col[2] - degrees / 360] # ??? not sure about 1st element, think mistake in Paul's scheme script return ret @@ -2572,8 +2828,8 @@ def rotate_colour_map(col, degrees): initial_colour = [0.2, 0.2, 0.8] colour_range = 360 - if (valid_map_molecule_qm(imol)): - if (not n_colours): + if valid_map_molecule_qm(imol): + if not n_colours: n_col = 10 else: n_col = n_colours @@ -2583,18 +2839,19 @@ def rotate_colour_map(col, degrees): for icol in range(n_col): new_map = copy_molecule(imol) - frac = icol / float(n_col) # need a float!! + frac = icol / float(n_col) # need a float!! contour_level_sigma = start + (stop - start) * frac set_last_map_contour_level(sigma * contour_level_sigma) - set_last_map_colour( - *rotate_colour_map(initial_colour, colour_range * frac)) + set_last_map_colour(*rotate_colour_map(initial_colour, colour_range * frac)) else: print("BL INFO:: {0!s} is not valid map".format(imol)) # simple enumeration # -def BALL_AND_STICK(): return 2 +def BALL_AND_STICK(): + return 2 + # hilight-colour is specified in degrees (round the colour wheel - # starting at yellow (e.g. 230 is purple)) @@ -2603,10 +2860,9 @@ def BALL_AND_STICK(): return 2 def hilight_binding_site(imol, centre_residue_spec, hilight_colour, radius): - if (valid_model_molecule_qm(imol)): + if valid_model_molecule_qm(imol): - other_residues = residues_near_residue( - imol, centre_residue_spec, radius) + other_residues = residues_near_residue(imol, centre_residue_spec, radius) atom_sel_str = residue_spec2atom_selection_string(centre_residue_spec) imol_new = new_molecule_by_atom_selection(imol, atom_sel_str) @@ -2616,24 +2872,34 @@ def hilight_binding_site(imol, centre_residue_spec, hilight_colour, radius): set_mol_active(imol_new, 0) set_show_environment_distances(1) set_molecule_bonds_colour_map_rotation(imol_new, hilight_colour) - additional_representation_by_attributes(imol_new, - centre_residue_spec[0], - centre_residue_spec[1], - centre_residue_spec[1], - centre_residue_spec[2], - BALL_AND_STICK(), - bb_type, 6, - draw_hydrogens_flag) - - list(map(lambda spec: additional_representation_by_attributes(imol, - spec[0], - spec[1], - spec[1], - spec[2], - BALL_AND_STICK(), - bb_type, 6, - draw_hydrogens_flag), - other_residues)) + additional_representation_by_attributes( + imol_new, + centre_residue_spec[0], + centre_residue_spec[1], + centre_residue_spec[1], + centre_residue_spec[2], + BALL_AND_STICK(), + bb_type, + 6, + draw_hydrogens_flag, + ) + + list( + map( + lambda spec: additional_representation_by_attributes( + imol, + spec[0], + spec[1], + spec[1], + spec[2], + BALL_AND_STICK(), + bb_type, + 6, + draw_hydrogens_flag, + ), + other_residues, + ) + ) highlight_binding_site = hilight_binding_site # typo? @@ -2676,71 +2942,92 @@ def add_questionable(r): residue_list.append(r) def get_ribose_residue_atom_name(imol, residue_spec, pucker_atom): - r_info = residue_info( - imol, residue_spec[0], residue_spec[1], residue_spec[2]) + r_info = residue_info(imol, residue_spec[0], residue_spec[1], residue_spec[2]) t_pucker_atom = pucker_atom[0:3] + "*" - if (pucker_atom in [at[0][0] for at in r_info]): + if pucker_atom in [at[0][0] for at in r_info]: return pucker_atom else: return t_pucker_atom # main line for chain_id in chain_ids(imol): - if (not is_solvent_chain_qm(imol, chain_id)): + if not is_solvent_chain_qm(imol, chain_id): n_residues = chain_n_residues(chain_id, imol) for serial_number in range(n_residues): - res_name = resname_from_serial_number( - imol, chain_id, serial_number) - res_no = seqnum_from_serial_number( - imol, chain_id, serial_number) + res_name = resname_from_serial_number(imol, chain_id, serial_number) + res_no = seqnum_from_serial_number(imol, chain_id, serial_number) ins_code = insertion_code_from_serial_number( - imol, chain_id, serial_number) + imol, chain_id, serial_number + ) - if (not res_name == "HOH"): + if not res_name == "HOH": residue_spec = [chain_id, res_no, ins_code] pi = pucker_info(imol, residue_spec, 1) - if (pi): - if (type(pi) is ListType): - if (len(pi) == 4): + if pi: + if type(pi) is ListType: + if len(pi) == 4: pucker_atom = pi[1] - if ((abs(pi[0]) > crit_d) and - (pucker_atom == " C2'")): - add_questionable([pucker_atom, residue_spec, - "Inconsistent phosphate distance for C2' pucker"]) - if ((abs(pi[0]) < crit_d) and - (pucker_atom == " C3'")): - add_questionable([pucker_atom, residue_spec, - "Inconsistent phosphate distance for C3' pucker"]) - if not ((pucker_atom == " C2'") or - (pucker_atom == " C3'")): - add_questionable([pucker_atom, residue_spec, - "puckered atom:" + pucker_atom]) - - if (len(residue_list) == 0): + if (abs(pi[0]) > crit_d) and (pucker_atom == " C2'"): + add_questionable( + [ + pucker_atom, + residue_spec, + "Inconsistent phosphate distance for C2' pucker", + ] + ) + if (abs(pi[0]) < crit_d) and (pucker_atom == " C3'"): + add_questionable( + [ + pucker_atom, + residue_spec, + "Inconsistent phosphate distance for C3' pucker", + ] + ) + if not ( + (pucker_atom == " C2'") or (pucker_atom == " C3'") + ): + add_questionable( + [ + pucker_atom, + residue_spec, + "puckered atom:" + pucker_atom, + ] + ) + + if len(residue_list) == 0: info_dialog("No bad puckers.") else: buttons = [] for residue in residue_list: residue_spec = residue[1] pucker_atom = residue[0] - at_name = get_ribose_residue_atom_name( - imol, residue_spec, pucker_atom) - ls = [residue_spec[0] + " " + str(residue_spec[1]) + residue_spec[2] + - ": " + residue[2], - ["set_go_to_atom_molecule(" + str(imol) + ")", - "set_go_to_atom_chain_residue_atom_name(" + - "\"" + str(residue_spec[0]) + "\", " + - str(residue_spec[1]) + ", " + - "\"" + str(at_name) + "\")"] - ] + at_name = get_ribose_residue_atom_name(imol, residue_spec, pucker_atom) + ls = [ + residue_spec[0] + + " " + + str(residue_spec[1]) + + residue_spec[2] + + ": " + + residue[2], + [ + "set_go_to_atom_molecule(" + str(imol) + ")", + "set_go_to_atom_chain_residue_atom_name(" + + '"' + + str(residue_spec[0]) + + '", ' + + str(residue_spec[1]) + + ", " + + '"' + + str(at_name) + + '")', + ], + ] buttons.append(ls) - dialog_box_of_buttons("Non-pukka puckers", - [370, 250], - buttons, - " Close ") + dialog_box_of_buttons("Non-pukka puckers", [370, 250], buttons, " Close ") + # Run libcheck to convert from SMILES string # @@ -2748,48 +3035,51 @@ def get_ribose_residue_atom_name(imol, residue_spec, pucker_atom): def new_molecule_by_smiles_string(tlc_text, smiles_text): import shutil + if len(smiles_text) > 0: - if ((len(tlc_text) > 0) and (len(tlc_text) < 4)): + if (len(tlc_text) > 0) and (len(tlc_text) < 4): three_letter_code = tlc_text - elif (len(tlc_text) > 0): + elif len(tlc_text) > 0: three_letter_code = tlc_text[0:3] else: three_letter_code = "DUM" # ok let's run libcheck smiles_file = "coot-" + three_letter_code + ".smi" - libcheck_data_lines = ["N", - "MON " + three_letter_code, - "FILE_SMILE " + smiles_file, - ""] + libcheck_data_lines = [ + "N", + "MON " + three_letter_code, + "FILE_SMILE " + smiles_file, + "", + ] log_file_name = "libcheck-" + three_letter_code + ".log" pdb_file_name = "libcheck_" + three_letter_code + ".pdb" cif_file_name = "libcheck_" + three_letter_code + ".cif" - smiles_input = file(smiles_file, 'w') + smiles_input = file(smiles_file, "w") smiles_input.write(smiles_text) smiles_input.close() # now let's run libcheck (based on libcheck.py) libcheck_exe_file = find_exe(libcheck_exe, "CCP4_BIN", "PATH") - if (not libcheck_exe_file): + if not libcheck_exe_file: print(" BL WARNING:: libcheck not found!") else: - status = popen_command(libcheck_exe_file, [], - libcheck_data_lines, log_file_name, True) + status = popen_command( + libcheck_exe_file, [], libcheck_data_lines, log_file_name, True + ) # the output of libcheck goes to libcheck.lib, we want it in # (i.e. overwrite the minimal description in cif_file_name - if (status == 0): - if (os.path.isfile("libcheck.lib")): + if status == 0: + if os.path.isfile("libcheck.lib"): # copy rather than rename file to avoid accession issues shutil.copy("libcheck.lib", cif_file_name) sc = rotation_centre() - imol = handle_read_draw_molecule_with_recentre( - pdb_file_name, 0) - if (is_valid_model_molecule(imol)): + imol = handle_read_draw_molecule_with_recentre(pdb_file_name, 0) + if is_valid_model_molecule(imol): mc = molecule_centre(imol) - sc_mc = [sc[i]-mc[i] for i in range(len(mc))] + sc_mc = [sc[i] - mc[i] for i in range(len(mc))] translate_molecule_by(imol, *sc_mc) read_cif_dictionary(cif_file_name) else: @@ -2802,8 +3092,7 @@ def new_molecule_by_smiles_string(tlc_text, smiles_text): # def prodrg_ify(imol, chain_id, res_no, ins_code): - new_mol = new_molecule_by_atom_selection(imol, - "//" + chain_id + "/" + str(res_no)) + new_mol = new_molecule_by_atom_selection(imol, "//" + chain_id + "/" + str(res_no)) set_mol_active(new_mol, 0) set_mol_displayed(new_mol, 0) @@ -2820,42 +3109,46 @@ def prodrg_ify(imol, chain_id, res_no, ins_code): delete_residue_hydrogens(new_mol, chain_id, res_no, ins_code, "") delete_residue_hydrogens( - imol, chain_id, res_no, ins_code, "") # otherwise they fly + imol, chain_id, res_no, ins_code, "" + ) # otherwise they fly write_pdb_file(new_mol, prodrg_xyzin) close_molecule(new_mol) prodrg_exe = find_exe("cprodrg", "CCP4_BIN", "PATH") if not prodrg_exe: - info_dialog( - "Cannot find cprodrg, so no prodrg-ifying of ligand possible") + info_dialog("Cannot find cprodrg, so no prodrg-ifying of ligand possible") else: - print("BL DEBUG:: now run prodrg with", prodrg_exe, \ - "XYZIN", prodrg_xyzin,\ - "XYZOUT", prodrg_xyzout,\ - "LIBOUT", prodrg_cif) - status = popen_command(prodrg_exe, - ["XYZIN", prodrg_xyzin, - "XYZOUT", prodrg_xyzout, - "LIBOUT", prodrg_cif], - ["MINI PREP", "END"], - prodrg_log, - True) + print( + "BL DEBUG:: now run prodrg with", + prodrg_exe, + "XYZIN", + prodrg_xyzin, + "XYZOUT", + prodrg_xyzout, + "LIBOUT", + prodrg_cif, + ) + status = popen_command( + prodrg_exe, + ["XYZIN", prodrg_xyzin, "XYZOUT", prodrg_xyzout, "LIBOUT", prodrg_cif], + ["MINI PREP", "END"], + prodrg_log, + True, + ) if status == 0: read_cif_dictionary(prodrg_cif) - imol_new = handle_read_draw_molecule_with_recentre( - prodrg_xyzout, 0) + imol_new = handle_read_draw_molecule_with_recentre(prodrg_xyzout, 0) rn = residue_name(imol, chain_id, res_no, ins_code) with_auto_accept([regularize_zone, imol_new, "", 1, 1, ""]) overlap_ligands(imol_new, imol, chain_id, res_no) - match_ligand_torsions( - imol_new, imol, chain_id, res_no) # broken? + match_ligand_torsions(imol_new, imol, chain_id, res_no) # broken? overlap_ligands(imol_new, imol, chain_id, res_no) set_residue_name(imol_new, "", 1, "", rn) change_chain_id(imol_new, "", chain_id, 1, 1, 1) renumber_residue_range(imol_new, chain_id, 1, 1, res_no - 1) set_mol_displayed(imol_new, 0) set_mol_active(imol_new, 0) - #set_mol_displayed(imol, 0) - #set_mol_active (imol, 0) + # set_mol_displayed(imol, 0) + # set_mol_active (imol, 0) # I don't think that replace-fragment is the right # function because that does not copy across the hydrogen @@ -2865,7 +3158,8 @@ def prodrg_ify(imol, chain_id, res_no, ins_code): # "//" + chain_id + "/" + str(res_no)) imol_replacing = add_ligand_delete_residue_copy_molecule( - imol_new, chain_id, res_no, imol, chain_id, res_no) + imol_new, chain_id, res_no, imol, chain_id, res_no + ) col = get_molecule_bonds_colour_map_rotation(imol) new_col = col + 5 set_molecule_bonds_colour_map_rotation(imol_replacing, new_col) @@ -2876,6 +3170,7 @@ def prodrg_ify(imol, chain_id, res_no, ins_code): # ---------- annotations --------------------- + def add_annotation_here(text): global annotations rc = rotation_centre() @@ -2902,6 +3197,7 @@ def add_here(*args): annotations.append(ann) place_text(*(ann + [0])) graphics_draw() + user_defined_click(1, add_here) @@ -2916,14 +3212,15 @@ def save_annotations(file_name): def load_annotations(file_name): - if (os.path.isfile(file_name)): + if os.path.isfile(file_name): from types import ListType - port = open(file_name, 'r') + + port = open(file_name, "r") ls = port.readline() port.close() ls = ls.rstrip("\n") ls = eval(ls) - if (type(ls) is ListType): + if type(ls) is ListType: global annotations annotations = ls for ann in annotations: @@ -2936,8 +3233,8 @@ def load_annotations(file_name): global pending_install_in_place pending_install_in_place = False # shall this be global? Currently pass use_curl along? FIXME -#global use_curl -#use_curl = False +# global use_curl +# use_curl = False # Here we construct the url that contains the latest (pre) # release info adding in "pre-release" if this binary is a @@ -2958,12 +3255,7 @@ def make_latest_version_url(): if is_windows(): host = "http://www.ysbl.york.ac.uk/~lohkamp/software/binaries/" pre_dir = "nightlies/pre-release" if pre_release_qm() else "stable" - url = host + \ - pre_dir + \ - "/" + \ - "type-binary-" + \ - build_type + \ - "-latest.txt" + url = host + pre_dir + "/" + "type-binary-" + build_type + "-latest.txt" return url @@ -2977,11 +3269,14 @@ def make_latest_version_url(): # # This is using python/urllib by default, set use_curl to True to use curl # -def run_download_binary_curl(revision, version_string, - pending_install_in_place_func, - set_file_name_func=False, # combine with progress_bar?! - progress_bar=False, - use_curl=False): +def run_download_binary_curl( + revision, + version_string, + pending_install_in_place_func, + set_file_name_func=False, # combine with progress_bar?! + progress_bar=False, + use_curl=False, +): global pending_install_in_place @@ -2991,32 +3286,32 @@ def match_md5sums(tar_file_name, target_md5sum_file_name): return False else: if not os.path.isfile(target_md5sum_file_name): - #print "OOps! %s does not exist" %target_md5sum_file_name - print("OOps! {0!s} does not exist".format( - target_md5sum_file_name)) + # print "OOps! %s does not exist" %target_md5sum_file_name + print("OOps! {0!s} does not exist".format(target_md5sum_file_name)) return False else: - target_md5_string = get_target_md5_string( - target_md5sum_file_name) + target_md5_string = get_target_md5_string(target_md5sum_file_name) # remove the md5sum file (not needed any more) os.remove(target_md5sum_file_name) md5_string = get_md5sum_string(tar_file_name) - if not target_md5_string: # need to test if string? - #print "OOps %s is not a string" %target_md5_string - print("OOps {0!s} is not a string".format( - target_md5_string)) + if not target_md5_string: # need to test if string? + # print "OOps %s is not a string" %target_md5_string + print("OOps {0!s} is not a string".format(target_md5_string)) return False else: - if not md5_string: # as above - #print "OOps %s is not a string" %md5_string + if not md5_string: # as above + # print "OOps %s is not a string" %md5_string print("OOps {0!s} is not a string".format(md5_string)) return False else: if not (target_md5_string == md5_string): - #print "Oops: md5sums do not match %s %s. Doing nothing" \ + # print "Oops: md5sums do not match %s %s. Doing nothing" \ # %(target_md5_string, md5_string) - print("Oops: md5sums do not match {0!s} {1!s}. Doing nothing".format( - target_md5_string, md5_string)) + print( + "Oops: md5sums do not match {0!s} {1!s}. Doing nothing".format( + target_md5_string, md5_string + ) + ) return False else: return True @@ -3028,17 +3323,17 @@ def install_coot_tar_file(tar_file_name, use_tar=False): prefix_dir = os.getenv("COOT_PREFIX") prefix_dir = os.path.normpath(prefix_dir) # FIXME do we need this? if not prefix_dir: - #print "OOps could not get COOT_PREFIX" + # print "OOps could not get COOT_PREFIX" return False if not directory_is_modifiable_qm(prefix_dir): - #print "OOps directory %s is not modifiable" %prefix_dir + # print "OOps directory %s is not modifiable" %prefix_dir return False else: pending_dir = os.path.join(prefix_dir, "pending-install") if not os.path.isdir(pending_dir): os.mkdir(pending_dir) if not os.path.isdir(pending_dir): - #print "OOps could not create", pending_dir + # print "OOps could not create", pending_dir return False else: a_tar_file_name = os.path.abspath(tar_file_name) @@ -3048,12 +3343,14 @@ def install_coot_tar_file(tar_file_name, use_tar=False): print("now current dir is", os.getcwd()) if use_tar: # non-pythonic - popen_command("tar", ["xzf", a_tar_file_name], [], - "untar.log", False) + popen_command( + "tar", ["xzf", a_tar_file_name], [], "untar.log", False + ) else: # pythonic if not is_windows(): import tarfile + tar = tarfile.open(a_tar_file_name) tar.extractall() tar.close() @@ -3072,11 +3369,11 @@ def get_target_md5_string(file_name): if not os.path.isfile(file_name): return False else: - fin = open(file_name, 'r') + fin = open(file_name, "r") lines = fin.readlines() fin.close() first_line = lines[0] - return first_line[0:first_line.find(" ")] + return first_line[0 : first_line.find(" ")] # return a string def get_md5sum_string(file_name): @@ -3084,14 +3381,15 @@ def get_md5sum_string(file_name): return False else: import hashlib - fin = open(file_name, 'rb') + + fin = open(file_name, "rb") md5sum = hashlib.md5(fin.read()).hexdigest() fin.close() return md5sum # main line # - #print "::::: run_download_binary_curl.... with revision %s with version_string %s" \ + # print "::::: run_download_binary_curl.... with revision %s with version_string %s" \ # %(revision, version_string) prefix = os.getenv("COOT_PREFIX") prefix = os.path.normpath(prefix) # FIXME do we need this? @@ -3102,9 +3400,16 @@ def get_md5sum_string(file_name): pre_release_flag = "-pre" in coot_version() ys = "www.ysbl.york.ac.uk/~emsley/software/binaries/" binary_type = coot_sys_build_type() - type_list = ['Linux-i386-fedora-3', 'Linux-i386-fedora-3-python', 'Linux-i386-fedora-8-python-gtk2', - 'Linux-i386-fedora-8-gtk2', 'Linux-i386-fedora-10-python-gtk2', 'Linux-i386-fedora-10-gtk2', - 'Linux-i686-ubuntu-8.04.3', 'Linux-i686-ubuntu-8.04.3-python'] + type_list = [ + "Linux-i386-fedora-3", + "Linux-i386-fedora-3-python", + "Linux-i386-fedora-8-python-gtk2", + "Linux-i386-fedora-8-gtk2", + "Linux-i386-fedora-10-python-gtk2", + "Linux-i386-fedora-10-gtk2", + "Linux-i686-ubuntu-8.04.3", + "Linux-i686-ubuntu-8.04.3-python", + ] if binary_type in type_list: host_dir = ys else: @@ -3120,7 +3425,7 @@ def get_md5sum_string(file_name): tar_file_name += "-binary-" + binary_type + ".tar.gz" release_dir = "releases/" - if ("ysbl.york.ac.uk" in host_dir): # includes windows + if "ysbl.york.ac.uk" in host_dir: # includes windows if pre_release_flag: release_dir = "nightlies/pre-release/" else: @@ -3135,15 +3440,15 @@ def get_md5sum_string(file_name): md5_url = url + ".md5sum" md5_tar_file_name = tar_file_name + ".md5sum" - #print "md5sum url for curl:", md5_url - #print "url for curl:", url + # print "md5sum url for curl:", md5_url + # print "url for curl:", url if set_file_name_func: set_file_name_func(tar_file_name) print("INFO:: getting URL:", url) - if (use_curl): + if use_curl: # this is for curl coot_get_url_and_activate_curl_hook(md5_url, md5_tar_file_name, 1) coot_get_url_and_activate_curl_hook(url, tar_file_name, 1) @@ -3160,18 +3465,18 @@ def get_md5sum_string(file_name): def progress_function(count, blockSize, totalSize): global pending_install_in_place - percent = int(count*blockSize*100/totalSize) + percent = int(count * blockSize * 100 / totalSize) dots = int(percent / 2.5) * "=" if percent < 100: dots += ">" - sys.stdout.write("\rProgress {0:d}%".format( - percent) + " |{0:<40!s}|".format(dots)) + sys.stdout.write( + "\rProgress {0:d}%".format(percent) + " |{0:<40!s}|".format(dots) + ) sys.stdout.flush() if progress_bar: - progress_bar.set_text( - "Downloading {0!s} %".format(percent)) - progress_bar.set_fraction(percent/100.) - if (pending_install_in_place == "cancelled"): + progress_bar.set_text("Downloading {0!s} %".format(percent)) + progress_bar.set_fraction(percent / 100.0) + if pending_install_in_place == "cancelled": # Brute force exit of thread! sys.stdout.write("\nBL INFO:: stopping download\n") sys.stdout.flush() @@ -3179,7 +3484,8 @@ def progress_function(count, blockSize, totalSize): try: md5_url_local_file_name, md5_url_info = urllib.request.urlretrieve( - md5_url, md5_tar_file_name) + md5_url, md5_tar_file_name + ) except: print("BL ERROR:: could not download", md5_url) return False @@ -3187,7 +3493,8 @@ def progress_function(count, blockSize, totalSize): print("\n") print("Downloading: {0!s}".format(tar_file_name)) url_local_file_name, url_info = urllib.request.urlretrieve( - url, tar_file_name, progress_function) + url, tar_file_name, progress_function + ) pending_install_in_place = "full" print("\nDone") except: @@ -3196,11 +3503,11 @@ def progress_function(count, blockSize, totalSize): return False if not os.path.isfile(tar_file_name): - #print "Ooops: %s does not exist after attempted download" %tar_file_name + # print "Ooops: %s does not exist after attempted download" %tar_file_name return False else: if not os.path.isfile(md5_tar_file_name): - #print "Ooops: %s does not exist after attempted download" %md5_tar_file_name + # print "Ooops: %s does not exist after attempted download" %md5_tar_file_name return False else: if not match_md5sums(tar_file_name, md5_tar_file_name): @@ -3212,6 +3519,7 @@ def progress_function(count, blockSize, totalSize): return True return False + # get revision number from string # # (used in downloading new version) @@ -3221,7 +3529,7 @@ def progress_function(count, blockSize, totalSize): def get_revision_from_string(stri): # e.g. str is "coot-0.6-pre-1-revision-2060" (with a newline at the # end too). We want to return 2060 (a number) from here (or False). - if stri: # maybe test for string + if stri: # maybe test for string lss = stri.rsplit("\n") ls = lss[0].split("-") try: @@ -3230,6 +3538,7 @@ def get_revision_from_string(stri): return False return False + # for true pythonic url retrievel # returns url as string or False if error # @@ -3238,6 +3547,7 @@ def get_revision_from_string(stri): def get_url_as_string(my_url): import urllib.request, urllib.parse, urllib.error + try: s = urllib.request.urlopen(my_url).read() except: @@ -3253,11 +3563,12 @@ def get_url_as_string(my_url): # def coot_split_version_string(stri): if not is_windows(): - ls2 = stri[stri.find("c"):-1] # for 'coot' start + ls2 = stri[stri.find("c") : -1] # for 'coot' start else: - ls2 = stri[stri.find("W"):-1] # for 'WinCoot' start + ls2 = stri[stri.find("W") : -1] # for 'WinCoot' start return ls2 + # convert file to string @@ -3270,6 +3581,7 @@ def file2string(file_name): fin.close() return ret + # If "default.seq" (a simple text file with the sequence (not PIR or # FASTA)) exists in the current directory, then try to assign it to # each chain of each molecule. @@ -3302,6 +3614,7 @@ def load_default_sequence(): def update_self(use_curl=False): import operator import time + global file_name_for_progress_bar file_name_for_progress_bar = False @@ -3312,8 +3625,7 @@ def update_self(use_curl=False): else: coot_url = get_url_as_string(url) if not coot_url: - print("BL INFO:: could not get string from URL {0!s}, so no update".format( - url)) + print("BL INFO:: could not get string from URL {0!s}, so no update".format(url)) else: version_string = coot_split_version_string(coot_url) revision = get_revision_from_string(version_string) @@ -3332,10 +3644,13 @@ def pending_install_in_place_func(val): continue_status = True def threaded_func(): - ret = run_download_binary_curl(revision, version_string, - pending_install_in_place_func, - set_file_name_func, - use_curl=use_curl) + ret = run_download_binary_curl( + revision, + version_string, + pending_install_in_place_func, + set_file_name_func, + use_curl=use_curl, + ) global continue_status continue_status = False @@ -3346,14 +3661,14 @@ def threaded_func(): if file_name_for_progress_bar: curl_info = curl_progress_info(file_name_for_progress_bar) if curl_info: - v1 = curl_info['content-length-download'] - v2 = curl_info['size-download'] + v1 = curl_info["content-length-download"] + v2 = curl_info["size-download"] if isinstance(v1, numbers.Number): if isinstance(v2, numbers.Number): f = v2 / v1 - #sys.stdout.write("\rProgress %3.2f%%" %(f*100)) + # sys.stdout.write("\rProgress %3.2f%%" %(f*100)) # sys.stdout.flush() - print("{0:3.2f}%".format((f*100))) + print("{0:3.2f}%".format((f * 100))) if f > 0.999: continue_status = False elif count >= 1500: # about 50 min @@ -3391,14 +3706,17 @@ def chiral_centre_inverter(): def residue_is_close_to_screen_centre_qm(imol, chain_id, res_no, ins_code): - def square(x): return x * x + def square(x): + return x * x + rc = residue_centre(imol, chain_id, res_no, ins_code) if not isinstance(rc, list): return False else: sc = rotation_centre() - dist_sum_sq = sum(square(rcx-scx) for rcx, scx in zip(rc, sc)) - return dist_sum_sq < 25. + dist_sum_sq = sum(square(rcx - scx) for rcx, scx in zip(rc, sc)) + return dist_sum_sq < 25.0 + # return a string "DB00xxxx.mol" or some such - this is the file name # of the mdl mol file from drugbank. Or False/undefined on fail. @@ -3412,7 +3730,7 @@ def get_drug_via_wikipedia(drug_name_in): from xml.etree import ElementTree def get_redirected_drug_name(xml): - return parse_wiki_drug_xml(xml, '#REDIRECT', True) + return parse_wiki_drug_xml(xml, "#REDIRECT", True) def parse_wiki_drug_xml(tree, key, redirect=False): key_re = re.compile(key) @@ -3422,20 +3740,20 @@ def parse_wiki_drug_xml(tree, key, redirect=False): if len(rev_iter) > 0: rev_text = rev_iter[0].text # seems to be in some strange format!? - decode_text = rev_text.encode('ascii', 'ignore') + decode_text = rev_text.encode("ascii", "ignore") for line in decode_text.split("\n"): # if key in line: # too simple, we need a regular expresssion search if key_re.search(line): - if (redirect == False): + if redirect == False: drug_bank_id = line.split(" ")[-1] if not drug_bank_id: # we can get an empty string drug_bank_id = False else: # a REDIRECT was found - drug_bank_id = line[line.find("[[")+2:line.find("]]")] + drug_bank_id = line[line.find("[[") + 2 : line.find("]]")] else: - print('Oops! len rev_text is 0') + print("Oops! len rev_text is 0") return drug_bank_id @@ -3443,9 +3761,11 @@ def parse_wiki_drug_xml(tree, key, redirect=False): if isinstance(drug_name_in, str): if len(drug_name_in) > 0: drug_name = drug_name_in.lower() - url = "http://en.wikipedia.org/w/api.php?format=xml&action=query&titles=" + \ - drug_name + \ - "&prop=revisions&rvprop=content" + url = ( + "http://en.wikipedia.org/w/api.php?format=xml&action=query&titles=" + + drug_name + + "&prop=revisions&rvprop=content" + ) # we want to parse the Etree rather than xml as this is an addurlinfo thingy xml = urllib.request.urlopen(url) @@ -3454,27 +3774,39 @@ def parse_wiki_drug_xml(tree, key, redirect=False): mol_name = parse_wiki_drug_xml(xml_tree, "DrugBank *= ") if not isinstance(mol_name, str): - print("BL WARNING:: mol_name not a string (DrugBank entry from wikipedia)", mol_name) + print( + "BL WARNING:: mol_name not a string (DrugBank entry from wikipedia)", + mol_name, + ) # try pubchem as fallback - mol_name = parse_wiki_drug_xml(xml_tree, "PubChem *= ") + mol_name = parse_wiki_drug_xml(xml_tree, "PubChem *= ") if not isinstance(mol_name, str): - print("BL WARNING:: mol_name not a string (pubchem entry either)", mol_name) + print( + "BL WARNING:: mol_name not a string (pubchem entry either)", + mol_name, + ) # so was there a redirect? # if so, get the name and call get_drug_via_wikipedia with it redirected_drug_name = get_redirected_drug_name(xml_tree) return get_drug_via_wikipedia(redirected_drug_name) else: - pc_mol_uri = "http://pubchem.ncbi.nlm.nih.gov" + \ - "/summary/summary.cgi?cid=" + \ - mol_name + "&disopt=DisplaySDF" + pc_mol_uri = ( + "http://pubchem.ncbi.nlm.nih.gov" + + "/summary/summary.cgi?cid=" + + mol_name + + "&disopt=DisplaySDF" + ) file_name = "pc-" + mol_name + ".mol" coot_get_url(pc_mol_uri, file_name) else: - db_mol_uri = "http://www.drugbank.ca/structures/structures/small_molecule_drugs/" + \ - mol_name + ".mol" + db_mol_uri = ( + "http://www.drugbank.ca/structures/structures/small_molecule_drugs/" + + mol_name + + ".mol" + ) file_name = mol_name + ".mol" coot_get_url(db_mol_uri, file_name) return file_name @@ -3489,16 +3821,17 @@ def get_SMILES_for_comp_id_from_pdbe(comp_id): if isinstance(s, str): return s else: - cif_file_name = os.path.join("coot-download", - "PDBe-" + comp_id + ".cif") - url = "ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/mmcif/" + \ - comp_id + \ - ".cif" + cif_file_name = os.path.join("coot-download", "PDBe-" + comp_id + ".cif") + url = ( + "ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/mmcif/" + + comp_id + + ".cif" + ) make_directory_maybe("coot-download") if os.path.isfile(cif_file_name): # try the filesystem cache l = os.stat(cif_file_name).st_size - if (l > 0): + if l > 0: read_cif_dictionary(cif_file_name) s2 = SMILES_for_comp_id(comp_id) if isinstance(s2, str): @@ -3506,19 +3839,20 @@ def get_SMILES_for_comp_id_from_pdbe(comp_id): else: # give a dialog, saying that the file will not be # overwritten - msg = cif_file_name + \ - " exists but is empty." + \ - "\nNot overwriting." + msg = cif_file_name + " exists but is empty." + "\nNot overwriting." info_dialog(msg) return False # use network then print("BL INFO:: getting url:", url) state = coot_get_url(url, cif_file_name) - if (state != 0): - msg = "Problem downloading\n" + \ - url + "\n to file \n" + \ - cif_file_name + \ - "." + if state != 0: + msg = ( + "Problem downloading\n" + + url + + "\n to file \n" + + cif_file_name + + "." + ) info_dialog(msg) return False else: @@ -3529,6 +3863,7 @@ def get_SMILES_for_comp_id_from_pdbe(comp_id): # something probably went wrong if we got to here return False + # # load the redefining functions # try: # load_from_search_load_path("redefine_functions.py") @@ -3572,20 +3907,23 @@ def file_to_preferences(filename): pref_file = os.path.join(pref_dir, filename) # don't install it if it is already in place. if os.path.isfile(pref_file): - s = "keybinding file " + pref_file + \ - " already exists. Not overwritten." + s = "keybinding file " + pref_file + " already exists. Not overwritten." add_status_bar_text(s) else: shutil.copyfile(ref_py, pref_file) if os.path.isfile(pref_file): - exec(compile(open(pref_file, "rb").read(), pref_file, 'exec'), globals()) + exec( + compile(open(pref_file, "rb").read(), pref_file, "exec"), + globals(), + ) + # add terminal residue is the normal thing we do with an aligned # sequence, but also we can try ton find the residue type of a # residue in the middle of the chain that is modelled as an ALA, say. # # PE comment - not sure why needed. -#find_aligned_residue_type = find_terminal_residue_type +# find_aligned_residue_type = find_terminal_residue_type def using_gui(): @@ -3597,6 +3935,7 @@ def using_gui(): ret = "coot_python" in globals() # coot_main_menubar is not a global var return ret + ############################################################################################ # end of Paul's scripting ############################################################################################ @@ -3614,6 +3953,7 @@ def GL_light_on(): set_do_GL_lighting(1) do_GL_lighting_state() + # and to turn it off # @@ -3632,9 +3972,11 @@ def set_b_factor_molecule(imol, bval): for chain_id in chain_ids(imol): start_res = seqnum_from_serial_number(imol, chain_id, 0) end_res = seqnum_from_serial_number( - imol, chain_id, chain_n_residues(chain_id, imol) - 1) + imol, chain_id, chain_n_residues(chain_id, imol) - 1 + ) set_b_factor_residue_range(imol, chain_id, start_res, end_res, bval) + # reset B-factor for molecule imol to default value # @@ -3644,9 +3986,12 @@ def reset_b_factor_molecule(imol): for chain_id in chain_ids(imol): start_res = seqnum_from_serial_number(imol, chain_id, 0) end_res = seqnum_from_serial_number( - imol, chain_id, chain_n_residues(chain_id, imol) - 1) + imol, chain_id, chain_n_residues(chain_id, imol) - 1 + ) set_b_factor_residue_range( - imol, chain_id, start_res, end_res, default_new_atoms_b_factor()) + imol, chain_id, start_res, end_res, default_new_atoms_b_factor() + ) + # reset B-factor for active residue to default value # @@ -3667,7 +4012,8 @@ def reset_b_factor_active_residue(): alt_conf = active_atom[5] set_b_factor_residue_range( - imol, chain_id, res_no, res_no, default_new_atoms_b_factor()) + imol, chain_id, res_no, res_no, default_new_atoms_b_factor() + ) # BL module to find exe files @@ -3701,20 +4047,21 @@ def find_exe(program_name, *args, **kwargs): info = True # we shall check for full path names first - if (os.path.isfile(program_name)): + if os.path.isfile(program_name): return os.path.abspath(program_name) # if Unix we use which and python's command module to locate the # executable (indepent if PATH was given); commands only available on # unix! May use subprocess at some point... # if the program is not found with which we use the usual way... - if (os.name == 'posix'): + if os.name == "posix": import subprocess - program_exe = subprocess.getoutput('which ' + program_name) - if (os.path.isfile(program_exe)): + + program_exe = subprocess.getoutput("which " + program_name) + if os.path.isfile(program_exe): return program_exe - if (len(args) > 0): + if len(args) > 0: path_ls = args else: # no extra PATH given, should at least check in this dir @@ -3726,13 +4073,13 @@ def find_exe(program_name, *args, **kwargs): drives_ls = ["/"] program_name_noext = program_name # some windows magic - if (os.name == 'nt'): + if os.name == "nt": drives_ls = get_windows_drives() program_name_noext = strip_extension(program_name) file_ext = file_name_extension(program_name) # if extenion is explicitly given - only use this one # otherwise try all possible ones on Windows, i.e PATHEXT - if (file_ext): + if file_ext: extensions = [file_ext] else: tmp_ext = os.environ["PATHEXT"].split(os.pathsep) @@ -3757,10 +4104,10 @@ def find_exe(program_name, *args, **kwargs): # search the extra Paths for search_path in path_ls: - if (os.path.isdir(search_path)): + if os.path.isdir(search_path): # we have a single file name, not environ var program_exe = os.path.join(search_path, file_name) - if (os.path.isfile(program_exe)): + if os.path.isfile(program_exe): if info: print("BL INFO:: We found ", program_exe) return program_exe @@ -3769,14 +4116,13 @@ def find_exe(program_name, *args, **kwargs): primary_path = os.environ[search_path] for path in string.split(primary_path, os.pathsep): program_exe = os.path.join(path, file_name) - if (os.path.isfile(program_exe)): + if os.path.isfile(program_exe): if info: print("BL INFO:: We found ", program_exe) return program_exe except: if info: - print("BL WARNING:: {0!s} not defined!".format( - search_path)) + print("BL WARNING:: {0!s} not defined!".format(search_path)) # BL says: before we search everywhere we might want to ask # the user if he actually wishes to do so! @@ -3787,24 +4133,28 @@ def find_exe(program_name, *args, **kwargs): else: no_search = False search_disk = False - if (use_gui_qm and not no_search): + if use_gui_qm and not no_search: search_disk = search_disk_dialog(program_name, path_ls) if search_disk: # search everywhere for drive in drives_ls: for root, dir, file in os.walk(drive): program_exe = os.path.join(root, program_name) - if (os.path.isfile(program_exe)): + if os.path.isfile(program_exe): return program_exe else: if info: print("BL INFO:: we don't search the whole disk for", program_name_noext) if info: - print("BL WARNING:: We cannot find {0!s} anywhere! Program {1!s} won't run!".format( - program_name_noext, program_name_noext)) + print( + "BL WARNING:: We cannot find {0!s} anywhere! Program {1!s} won't run!".format( + program_name_noext, program_name_noext + ) + ) return False + # for running online docs @@ -3814,23 +4164,29 @@ def open_url(url): try: webbrowser.open(url, 1, 1) except: - print("BL WARNING:: Cannot open the URL {0!s} in webbrowser {1!s}!".format( - url, webbrowser.get())) + print( + "BL WARNING:: Cannot open the URL {0!s} in webbrowser {1!s}!".format( + url, webbrowser.get() + ) + ) # to reload modules def reload_module(name): import os - path = os.getenv('COOT_PYTHON_DIR') + + path = os.getenv("COOT_PYTHON_DIR") file = os.path.join(path, name) - exec(compile(open(file, "rb").read(), file, 'exec')) + exec(compile(open(file, "rb").read(), file, "exec")) + # to make print a function: def printf(*args): for arg in args: - print(arg, end=' ') + print(arg, end=" ") + # to print elements of a list: @@ -3838,6 +4194,7 @@ def printf(*args): def printl(ls): list(map(printf, ls)) + # Where cmd is e.g. "bltwish" # args is list, e.g. [loggraph, "refmac.log"] # @@ -3863,24 +4220,24 @@ def run_concurrently(cmd, args=None, data_list=None, logfile=None, screen_flag=F major, minor, micro, releaselevel, serial = sys.version_info cmd_execfile = "" - if not(command_in_path_qm(cmd)): + if not (command_in_path_qm(cmd)): print("command ", cmd, " not found in $PATH!") print("BL INFO:: Maybe we'll find it somewhere else later...") else: cmd_execfile = find_exe(cmd, "CCP4_BIN", "PATH") - if (cmd_execfile): - if (major >= 2 and minor >= 4): + if cmd_execfile: + if major >= 2 and minor >= 4: # subprocess import subprocess + cmd_args = [cmd_execfile] + args log = logfile - if (logfile): - log = open(logfile, 'w') - process = subprocess.Popen( - cmd_args, stdin=subprocess.PIPE, stdout=log) + if logfile: + log = open(logfile, "w") + process = subprocess.Popen(cmd_args, stdin=subprocess.PIPE, stdout=log) - if (data_list): + if data_list: for data in data_list: process.stdin.write(data + "\n") @@ -3896,10 +4253,10 @@ def run_concurrently(cmd, args=None, data_list=None, logfile=None, screen_flag=F pid = os.spawnv(os.P_NOWAIT, cmd_execfile, [cmd_execfile] + args) return pid else: - print("WARNING:: could not find {0!s}, so not running this program".format( - cmd)) + print("WARNING:: could not find {0!s}, so not running this program".format(cmd)) return False + # python command to see if we have pygtk available # return True if availabel otherwise False # @@ -3907,11 +4264,13 @@ def run_concurrently(cmd, args=None, data_list=None, logfile=None, screen_flag=F def coot_has_pygtk(): import sys - if ('pygtk' in list(sys.modules.keys())): + + if "pygtk" in list(sys.modules.keys()): return True else: return False + # python command to see if we have pygobject available # return True if availabel otherwise False # @@ -3919,7 +4278,8 @@ def coot_has_pygtk(): def coot_has_gobject(): import sys - if ('gobject' in list(sys.modules.keys())): + + if "gobject" in list(sys.modules.keys()): return True else: return False @@ -3933,19 +4293,19 @@ def kill_process(pid): import sys import signal - if (os.name == 'nt'): + if os.name == "nt": # Windows killing tasks try: # for now use subprocess.call, maybe can use Popen.kill?! major, minor, micro, releaselevel, serial = sys.version_info - if (major >= 2 and minor >= 4): + if major >= 2 and minor >= 4: # new style import subprocess - ret = subprocess.call( - "taskkill /F /PID {0:d}".format(pid), shell=True) + + ret = subprocess.call("taskkill /F /PID {0:d}".format(pid), shell=True) else: ret = os.system("taskkill /F /PID {0:d}".format(pid)) - if (ret == 0): + if ret == 0: # success return True else: @@ -3964,7 +4324,7 @@ def kill_process(pid): # maybe should go in coot_gui!? def stereo_mono_toggle(): display_state = stereo_mode_state() - if (display_state == 0): + if display_state == 0: hardware_stereo_mode() else: mono_mode() @@ -3972,7 +4332,7 @@ def stereo_mono_toggle(): def side_by_side_stereo_mono_toggle(): display_state = stereo_mode_state() - if (display_state == 0): + if display_state == 0: side_by_side_stereo_mode(0) else: mono_mode() @@ -3980,19 +4340,19 @@ def side_by_side_stereo_mono_toggle(): def zalman_stereo_mono_toggle(): display_state = stereo_mode_state() - if (display_state == 0): + if display_state == 0: zalman_stereo_mode() else: mono_mode() def switch_stereo_sides(): - factor = -1. * hardware_stereo_angle_factor_state() + factor = -1.0 * hardware_stereo_angle_factor_state() set_hardware_stereo_angle_factor(factor) def toggle_full_screen(widget=None): - """ Toggle between full screen and window mode + """Toggle between full screen and window mode Keyword arguments: widget -- can be passed from the toolbutton @@ -4010,9 +4370,17 @@ def toggle_full_screen(widget=None): def split_active_water(): - with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: + with UsingActiveAtom() as [ + aa_imol, + aa_chain_id, + aa_res_no, + aa_ins_code, + aa_atom_name, + aa_alt_conf, + ]: split_water(aa_imol, aa_chain_id, aa_res_no, aa_ins_code) + # helper function to test for a number # returns True if number, otherwise False # @@ -4023,7 +4391,7 @@ def isNumber(num): helper function to test for a number returns True if number, otherwise False """ - if (isinstance(num, int) or isinstance(num, float)): + if isinstance(num, int) or isinstance(num, float): return True else: return False @@ -4038,27 +4406,26 @@ def merge_solvent_chains(imol): # collect all solvent chains solvent_chains = [] for chain_id in chain_ids(imol): - if (is_solvent_chain_qm(imol, chain_id)): + if is_solvent_chain_qm(imol, chain_id): solvent_chains.append(chain_id) # now renumber - if (len(solvent_chains) > 1): + if len(solvent_chains) > 1: master_chain = solvent_chains[0] last_prev_water = chain_n_residues(master_chain, imol) for chain_id in solvent_chains[1:]: n_residues = chain_n_residues(chain_id, imol) - renumber_residue_range(imol, chain_id, 1, - n_residues, last_prev_water) + renumber_residue_range(imol, chain_id, 1, n_residues, last_prev_water) new_start = last_prev_water + 1 new_end = last_prev_water + n_residues - change_chain_id(imol, chain_id, master_chain, 1, - new_start, new_end) + change_chain_id(imol, chain_id, master_chain, 1, new_start, new_end) last_prev_water = new_end # helper to comvert functions to strings def cmd2str(*args): from types import StringType + func = args[0] if callable(func): ret = args[0].__name__ @@ -4067,7 +4434,7 @@ def cmd2str(*args): ret += "(" for arg in args[1:]: if type(arg) is StringType: - ret += "\"" + arg + "\"" + ret += '"' + arg + '"' else: ret += str(arg) if not arg == args[-1]: @@ -4088,16 +4455,26 @@ def set_alt_conf_occ(imol, chain_id, res_no, ins_code, alt_conf_list): """ # first check if we have alt confs: alt_confs = residue_alt_confs(imol, chain_id, res_no, ins_code) - if (alt_confs > 1): + if alt_confs > 1: atom_ls = residue_info(imol, chain_id, res_no, ins_code) change_list = [] for i in range(len(atom_ls)): alt_conf_str = atom_ls[i][0][1] atom_name = atom_ls[i][0][0] for (alt_conf_name, alt_conf_occ) in alt_conf_list: - if (alt_conf_str == alt_conf_name): - change_list.append([imol, chain_id, res_no, ins_code, atom_name, - alt_conf_str, "occ", alt_conf_occ]) + if alt_conf_str == alt_conf_name: + change_list.append( + [ + imol, + chain_id, + res_no, + ins_code, + atom_name, + alt_conf_str, + "occ", + alt_conf_occ, + ] + ) set_atom_attributes(change_list) else: print("BL INFO:: no alt confs in residue", imol, chain_id, res_no, ins_code) @@ -4105,7 +4482,8 @@ def set_alt_conf_occ(imol, chain_id, res_no, ins_code, alt_conf_list): # simplyfy check for windows def is_windows(): - return os.name == 'nt' + return os.name == "nt" + # find all windows drives # @@ -4113,6 +4491,7 @@ def is_windows(): def get_windows_drives(): from ctypes import windll + drives = [] bitmask = windll.kernel32.GetLogicalDrives() for letter in string.uppercase: @@ -4143,7 +4522,7 @@ def clean_pdb(imol): merge_water_chains = merge_solvent_chains # the python run_thread function if no graphics -#global use_gui_qm +# global use_gui_qm # if not use_gui_qm: # import threading # # this has locked, so that no one else can use it diff --git a/web/XChemWeb.py b/web/XChemWeb.py index 872dcebe..5b74bb90 100755 --- a/web/XChemWeb.py +++ b/web/XChemWeb.py @@ -10,11 +10,10 @@ import sys import glob -sys.path.append(os.getenv('XChemExplorer_DIR')+'/lib') +sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") class export_to_html: - def __init__(self, htmlDir, projectDir, database, xce_logfile): self.htmlDir = htmlDir self.projectDir = projectDir @@ -25,7 +24,7 @@ def __init__(self, htmlDir, projectDir, database, xce_logfile): self.protein_name = None def prepare(self, whichSamples): - self.Logfile.insert('======== preparing HTML summary ========') + self.Logfile.insert("======== preparing HTML summary ========") self.makeFolders() self.copy_jscss() html = XChemMain.html_header() @@ -33,490 +32,574 @@ def prepare(self, whichSamples): for xtal in self.db.samples_for_html_summary(whichSamples): self.db_dict = self.db.get_db_dict_for_sample(xtal) if firstFile: - if self.db_dict['ProteinName'] == 'None': - self.Logfile.warning('could not determine protein name') + if self.db_dict["ProteinName"] == "None": + self.Logfile.warning("could not determine protein name") try: - self.protein_name = xtal.split('-')[0] + self.protein_name = xtal.split("-")[0] self.Logfile.warning( - 'xtal name = %s => setting protein name to %s' % (xtal, self.protein_name)) + "xtal name = %s => setting protein name to %s" + % (xtal, self.protein_name) + ) except IndexError: self.Logfile.warning( - 'could not determine protein name from cystal name; setting to None') - self.protein_name = '' + "could not determine protein name from cystal name; setting to None" + ) + self.protein_name = "" else: - self.protein_name = self.db_dict['ProteinName'] - self.Logfile.insert( - 'protein name is: ' + self.protein_name) + self.protein_name = self.db_dict["ProteinName"] + self.Logfile.insert("protein name is: " + self.protein_name) self.copy_pdb(xtal) self.copy_mtz(xtal) -# self.copy_electron_density(xtal) + # self.copy_electron_density(xtal) self.copy_ligand_files(xtal) os.chdir(os.path.join(self.projectDir, xtal)) ligandDict = XChemUtils.pdbtools_gemmi( - 'refine.pdb').center_of_mass_ligand_dict('LIG') + "refine.pdb" + ).center_of_mass_ligand_dict("LIG") self.Logfile.insert( - xtal + ': saving ligand(s) of type LIG in refine.pdb as PDB files...') - XChemUtils.pdbtools_gemmi('refine.pdb').save_ligands_to_pdb('LIG') + xtal + ": saving ligand(s) of type LIG in refine.pdb as PDB files..." + ) + XChemUtils.pdbtools_gemmi("refine.pdb").save_ligands_to_pdb("LIG") for ligand in ligandDict: - self.Logfile.insert(xtal + ': current ligand -> ' + ligand) + self.Logfile.insert(xtal + ": current ligand -> " + ligand) os.chdir(os.path.join(self.projectDir, xtal)) -# for ligand in self.ligands_in_pdbFile(xtal): - ligName = ligand.split('-')[0] - ligChain = ligand.split('-')[1] - ligNumber = ligand.split('-')[2] -# eventMap = self.find_matching_event_map_from_database(xtal, ligand) -# if eventMap: -# self.Logfile.insert('%s: using the following event map -> %s' %(xtal,eventMap)) -# self.cut_and_copy_map(xtal, ligand+'.pdb', eventMap, xtal + '_' + ligand + '_event.ccp4','F','PHIF') -# eventMap = xtal + '_' + ligand + '_event.ccp4' -# else: -# self.Logfile.error('%s: value of event map -> %s' %(xtal,eventMap)) - eventMap = '' -# self.Logfile.insert(xtal + ': looking for' + xtal + '_' + ligand + '_event.ccp4') - if os.path.isfile(xtal + '_' + ligand + '_event.ccp4'): - eventMap = xtal + '_' + ligand + '_event.ccp4' -# self.Logfile.insert(xtal + ': found ' + eventMap) -# else: -# self.Logfile.error(xtal + ': cannot find' + xtal + '_' + ligand + '_event.ccp4') -# x,y,z = self.pdb.get_centre_of_gravity_of_residue(ligand) + # for ligand in self.ligands_in_pdbFile(xtal): + ligName = ligand.split("-")[0] + ligChain = ligand.split("-")[1] + ligNumber = ligand.split("-")[2] + # eventMap = self.find_matching_event_map_from_database(xtal, ligand) + # if eventMap: + # self.Logfile.insert('%s: using the following event map -> %s' %(xtal,eventMap)) + # self.cut_and_copy_map(xtal, ligand+'.pdb', eventMap, xtal + '_' + ligand + '_event.ccp4','F','PHIF') + # eventMap = xtal + '_' + ligand + '_event.ccp4' + # else: + # self.Logfile.error('%s: value of event map -> %s' %(xtal,eventMap)) + eventMap = "" + # self.Logfile.insert(xtal + ': looking for' + xtal + '_' + ligand + '_event.ccp4') + if os.path.isfile(xtal + "_" + ligand + "_event.ccp4"): + eventMap = xtal + "_" + ligand + "_event.ccp4" + # self.Logfile.insert(xtal + ': found ' + eventMap) + # else: + # self.Logfile.error(xtal + ': cannot find' + xtal + '_' + ligand + '_event.ccp4') + # x,y,z = self.pdb.get_centre_of_gravity_of_residue(ligand) x = ligandDict[ligand][0] y = ligandDict[ligand][1] z = ligandDict[ligand][2] self.copy_spider_plot(xtal, ligand) - pdbID = self.db_dict['Deposition_PDB_ID'] - compoundImage = xtal + '_' + \ - self.db_dict['CompoundCode'] + '.png' - compoundCIF = xtal + '_' + \ - self.db_dict['CompoundCode'] + '.cif' - residuePlot = xtal + '_' + ligand + '.png' - pdb = xtal + '.pdb' - event = xtal + '_' + ligand + '_event.ccp4' - thumbNail = xtal + '_' + ligand + '_thumb.png' - resoHigh = self.db_dict['DataProcessingResolutionHigh'] - spg = self.db_dict['RefinementSpaceGroup'] - unitCell = self.db_dict['DataProcessingUnitCell'] - t = '' + pdbID = self.db_dict["Deposition_PDB_ID"] + compoundImage = xtal + "_" + self.db_dict["CompoundCode"] + ".png" + compoundCIF = xtal + "_" + self.db_dict["CompoundCode"] + ".cif" + residuePlot = xtal + "_" + ligand + ".png" + pdb = xtal + ".pdb" + event = xtal + "_" + ligand + "_event.ccp4" + thumbNail = xtal + "_" + ligand + "_thumb.png" + resoHigh = self.db_dict["DataProcessingResolutionHigh"] + spg = self.db_dict["RefinementSpaceGroup"] + unitCell = self.db_dict["DataProcessingUnitCell"] + t = "" for ax in unitCell.split(): - t += str(round(float(ax), 1)) + ' ' + t += str(round(float(ax), 1)) + " " unitCell = t[:-1] os.chdir(os.path.join(self.projectDir, xtal)) -# FWT = xtal + '-' + ligand + '_2fofc.ccp4' -# self.cut_and_copy_map(xtal, ligand + '.pdb', '2fofc.map', FWT,'FWT','PHWT') -# DELFWT = xtal + '-' + ligand + '_fofc.ccp4' -# self.cut_and_copy_map(xtal, ligand + '.pdb', 'fofc.map', DELFWT,'DELFWT','PHDELWT') - if os.path.isfile('refine.mtz'): - self.Logfile.insert('%s: found refine.mtz' % xtal) - FWTmap, DELFWTmap = self.prepare_e_density_maps( - xtal, ligand) + # FWT = xtal + '-' + ligand + '_2fofc.ccp4' + # self.cut_and_copy_map(xtal, ligand + '.pdb', '2fofc.map', FWT,'FWT','PHWT') + # DELFWT = xtal + '-' + ligand + '_fofc.ccp4' + # self.cut_and_copy_map(xtal, ligand + '.pdb', 'fofc.map', DELFWT,'DELFWT','PHDELWT') + if os.path.isfile("refine.mtz"): + self.Logfile.insert("%s: found refine.mtz" % xtal) + FWTmap, DELFWTmap = self.prepare_e_density_maps(xtal, ligand) self.copy_electron_density(xtal, ligand, eventMap) ligConfidence = self.db.get_ligand_confidence_for_ligand( - xtal, ligChain, ligNumber, ligName) - if ligConfidence.startswith('0'): - self.Logfile.warning('%s: ligand confidence of %s-%s-%s is %s; ignoring...' % ( - xtal, ligChain, ligNumber, ligName, ligConfidence)) + xtal, ligChain, ligNumber, ligName + ) + if ligConfidence.startswith("0"): + self.Logfile.warning( + "%s: ligand confidence of %s-%s-%s is %s; ignoring..." + % (xtal, ligChain, ligNumber, ligName, ligConfidence) + ) self.Logfile.warning( - '%s: this seems unlikely because this structure is apparently ready for deposition' % xtal) + "%s: this seems unlikely because this structure is apparently ready for deposition" + % xtal + ) self.Logfile.warning( - '%s: will set it to "not assigned" for now, but please update in soakDB' % xtal) - ligConfidence = 'not assigned' - modelStatus = self.db_dict['RefinementOutcome'] + '%s: will set it to "not assigned" for now, but please update in soakDB' + % xtal + ) + ligConfidence = "not assigned" + modelStatus = self.db_dict["RefinementOutcome"] if firstFile: - html += XChemMain.html_ngl(pdb, eventMap.replace( - self.projectDir, ''), FWTmap, DELFWTmap, ligand) + html += XChemMain.html_ngl( + pdb, + eventMap.replace(self.projectDir, ""), + FWTmap, + DELFWTmap, + ligand, + ) html += XChemMain.html_download(self.protein_name) html += XChemMain.html_guide() html += XChemMain.html_table_header() firstFile = False - html += XChemMain.html_table_row(xtal, pdbID, ligand, compoundImage, residuePlot, pdb, event, - thumbNail, resoHigh, spg, unitCell, FWTmap, DELFWTmap, ligConfidence, modelStatus) + html += XChemMain.html_table_row( + xtal, + pdbID, + ligand, + compoundImage, + residuePlot, + pdb, + event, + thumbNail, + resoHigh, + spg, + unitCell, + FWTmap, + DELFWTmap, + ligConfidence, + modelStatus, + ) self.make_thumbnail(xtal, x, y, z, ligand, eventMap) - self.prepare_for_download( - xtal, pdb, event, compoundCIF, ligand) + self.prepare_for_download(xtal, pdb, event, compoundCIF, ligand) self.prepare_zip_archives() -# html = XChemMain.html_download_all_section(html,self.protein_name) + # html = XChemMain.html_download_all_section(html,self.protein_name) self.write_html_file(html) - self.Logfile.insert( - '======== finished preparing HTML summary ========') + self.Logfile.insert("======== finished preparing HTML summary ========") def prepare_e_density_maps(self, xtal, ligand): FWT, PHWT, DELFWT, PHDELWT = XChemUtils.mtztools_gemmi( - 'refine.mtz').get_map_labels() - self.Logfile.insert(xtal + ': calculating 2fofc map...') - XChemUtils.maptools().calculate_map('refine.mtz', FWT, PHWT) - if os.path.isfile('refine.ccp4'): - self.Logfile.insert(xtal + ': 2fofc map successfully calculated') + "refine.mtz" + ).get_map_labels() + self.Logfile.insert(xtal + ": calculating 2fofc map...") + XChemUtils.maptools().calculate_map("refine.mtz", FWT, PHWT) + if os.path.isfile("refine.ccp4"): + self.Logfile.insert(xtal + ": 2fofc map successfully calculated") else: - self.Logfile.error(xtal + ': 2fofc map could not be calculated') - self.Logfile.insert(xtal + ': cutting 2fofc map 7A around ' + ligand) - XChemUtils.maptools().cut_map_around_ligand('refine.ccp4', ligand+'.pdb', '7') - if os.path.isfile('refine_mapmask.ccp4'): - self.Logfile.insert(xtal + ': 2fofc map around ' + - ligand + ' successfully created') + self.Logfile.error(xtal + ": 2fofc map could not be calculated") + self.Logfile.insert(xtal + ": cutting 2fofc map 7A around " + ligand) + XChemUtils.maptools().cut_map_around_ligand("refine.ccp4", ligand + ".pdb", "7") + if os.path.isfile("refine_mapmask.ccp4"): + self.Logfile.insert( + xtal + ": 2fofc map around " + ligand + " successfully created" + ) else: - self.Logfile.error(xtal + ': 2fofc map around ' + - ligand + ' could not be created') - os.system('/bin/mv %s %s_%s_2fofc.ccp4' % - ('refine_mapmask.ccp4', xtal, ligand)) - FWTmap = xtal + '_' + ligand + '_2fofc.ccp4' - self.Logfile.insert(xtal + ': current 2fofc map -> ' + - xtal + '_' + ligand + '_2fofc.ccp4') - XChemUtils.maptools().calculate_map('refine.mtz', DELFWT, PHDELWT) - XChemUtils.maptools().cut_map_around_ligand('refine.ccp4', ligand+'.pdb', '7') - os.system('/bin/mv %s %s_%s_fofc.ccp4' % - ('refine_mapmask.ccp4', xtal, ligand)) - DELFWTmap = xtal + '_' + ligand + '_fofc.ccp4' + self.Logfile.error( + xtal + ": 2fofc map around " + ligand + " could not be created" + ) + os.system("/bin/mv %s %s_%s_2fofc.ccp4" % ("refine_mapmask.ccp4", xtal, ligand)) + FWTmap = xtal + "_" + ligand + "_2fofc.ccp4" + self.Logfile.insert( + xtal + ": current 2fofc map -> " + xtal + "_" + ligand + "_2fofc.ccp4" + ) + XChemUtils.maptools().calculate_map("refine.mtz", DELFWT, PHDELWT) + XChemUtils.maptools().cut_map_around_ligand("refine.ccp4", ligand + ".pdb", "7") + os.system("/bin/mv %s %s_%s_fofc.ccp4" % ("refine_mapmask.ccp4", xtal, ligand)) + DELFWTmap = xtal + "_" + ligand + "_fofc.ccp4" return FWTmap, DELFWTmap def prepare_zip_archives(self): - os.chdir(os.path.join(self.htmlDir, 'files')) + os.chdir(os.path.join(self.htmlDir, "files")) self.Logfile.insert( - '%s: preparing ZIP archive of all PDB files' % self.protein_name) - os.system('zip %s_allPDBs.zip *.pdb' % self.protein_name) + "%s: preparing ZIP archive of all PDB files" % self.protein_name + ) + os.system("zip %s_allPDBs.zip *.pdb" % self.protein_name) self.Logfile.insert( - '%s: preparing ZIP archive of all PanDDA event maps' % self.protein_name) - os.system('zip %s_allEVENTmaps.zip *event.ccp4' % self.protein_name) + "%s: preparing ZIP archive of all PanDDA event maps" % self.protein_name + ) + os.system("zip %s_allEVENTmaps.zip *event.ccp4" % self.protein_name) self.Logfile.insert( - '%s: preparing ZIP archive of all CIF files' % self.protein_name) - os.system('zip %s_allCIFs.zip *.cif' % self.protein_name) + "%s: preparing ZIP archive of all CIF files" % self.protein_name + ) + os.system("zip %s_allCIFs.zip *.cif" % self.protein_name) self.Logfile.insert( - '%s: preparing ZIP archive of all MTZ files' % self.protein_name) - os.system('zip %s_allMTZs.zip *.mtz' % self.protein_name) + "%s: preparing ZIP archive of all MTZ files" % self.protein_name + ) + os.system("zip %s_allMTZs.zip *.mtz" % self.protein_name) def prepare_for_download(self, xtal, pdb, event, compoundCIF, ligID): - os.chdir(os.path.join(self.htmlDir, 'tmp')) - self.Logfile.insert('%s: preparing files for download' % xtal) - zip_in = '' + os.chdir(os.path.join(self.htmlDir, "tmp")) + self.Logfile.insert("%s: preparing files for download" % xtal) + zip_in = "" - if os.path.isfile('../files/%s' % pdb): - os.system('/bin/cp ../files/%s .' % pdb) - zip_in += pdb + ' ' + if os.path.isfile("../files/%s" % pdb): + os.system("/bin/cp ../files/%s ." % pdb) + zip_in += pdb + " " else: - self.Logfile.error('%s: cannot find %s' % (xtal, pdb)) + self.Logfile.error("%s: cannot find %s" % (xtal, pdb)) - if os.path.isfile('../files/%s' % event): - os.system('/bin/cp ../files/%s .' % event) - zip_in += event + ' ' + if os.path.isfile("../files/%s" % event): + os.system("/bin/cp ../files/%s ." % event) + zip_in += event + " " else: - self.Logfile.error('%s: cannot find %s' % (xtal, event)) + self.Logfile.error("%s: cannot find %s" % (xtal, event)) - if os.path.isfile('../files/%s' % compoundCIF): - os.system('/bin/cp ../files/%s .' % compoundCIF) - zip_in += compoundCIF + ' ' + if os.path.isfile("../files/%s" % compoundCIF): + os.system("/bin/cp ../files/%s ." % compoundCIF) + zip_in += compoundCIF + " " else: - self.Logfile.error('%s: cannot find %s' % (xtal, compoundCIF)) + self.Logfile.error("%s: cannot find %s" % (xtal, compoundCIF)) - if zip_in != '': + if zip_in != "": self.Logfile.insert( - '%s: preparing zip file -> zip %s_%s.zip %s' % (xtal, xtal, ligID, zip_in)) - os.system('zip %s_%s.zip %s' % (xtal, ligID, zip_in)) - os.system('/bin/mv %s_%s.zip ../download' % (xtal, ligID)) - os.system('/bin/rm -f *') + "%s: preparing zip file -> zip %s_%s.zip %s" + % (xtal, xtal, ligID, zip_in) + ) + os.system("zip %s_%s.zip %s" % (xtal, ligID, zip_in)) + os.system("/bin/mv %s_%s.zip ../download" % (xtal, ligID)) + os.system("/bin/rm -f *") else: self.Logfile.error( - '%s: cannot find any input files for creating of zip archive of %s_%s' % (xtal, xtal, ligID)) + "%s: cannot find any input files for creating of zip archive of %s_%s" + % (xtal, xtal, ligID) + ) def copy_jscss(self): os.chdir(self.htmlDir) - self.Logfile.insert('copying css and js files to ' + self.htmlDir) - os.system('/bin/cp -r %s/web/jscss/css .' % - os.getenv('XChemExplorer_DIR')) - os.system('/bin/cp -r %s/web/jscss/js .' % - os.getenv('XChemExplorer_DIR')) + self.Logfile.insert("copying css and js files to " + self.htmlDir) + os.system("/bin/cp -r %s/web/jscss/css ." % os.getenv("XChemExplorer_DIR")) + os.system("/bin/cp -r %s/web/jscss/js ." % os.getenv("XChemExplorer_DIR")) def make_thumbnail(self, xtal, x, y, z, ligID, eventMap): self.Logfile.insert( - '%s: making thumbnail of for %s and %s' % (xtal, ligID, eventMap)) + "%s: making thumbnail of for %s and %s" % (xtal, ligID, eventMap) + ) sampleDir = os.path.join(self.projectDir, xtal) os.chdir(sampleDir) - if not os.path.isfile('%s_%s_thumb.png' % (xtal, ligID)): - self.Logfile.insert( - '%s: preparing thumbnail image of %s' % (xtal, ligID)) + if not os.path.isfile("%s_%s_thumb.png" % (xtal, ligID)): + self.Logfile.insert("%s: preparing thumbnail image of %s" % (xtal, ligID)) XChemMain.coot_prepare_input(x, y, z, ligID, sampleDir, eventMap) XChemMain.coot_write_raster_file(ligID, sampleDir) XChemMain.render_scene(xtal, ligID, sampleDir) XChemMain.make_thumbnail(xtal, ligID, sampleDir) - if os.path.isfile('%s_%s_thumb.png' % (xtal, ligID)): + if os.path.isfile("%s_%s_thumb.png" % (xtal, ligID)): self.Logfile.insert( - '%s: managed to prepare %s_%s_thumb.png' % (xtal, xtal, ligID)) + "%s: managed to prepare %s_%s_thumb.png" % (xtal, xtal, ligID) + ) self.copy_thumbnail(xtal, sampleDir, ligID) else: self.Logfile.error( - '%s: could not generate %s_%s_thumb.png' % (xtal, xtal, ligID)) + "%s: could not generate %s_%s_thumb.png" % (xtal, xtal, ligID) + ) def copy_thumbnail(self, xtal, sampleDir, ligID): - os.chdir(os.path.join(self.htmlDir, 'png')) + os.chdir(os.path.join(self.htmlDir, "png")) self.Logfile.insert( - '%s: copying %s_%s_thumb.png to html png' % (xtal, xtal, ligID)) - os.system('/bin/cp %s/%s_%s_thumb.png .' % (sampleDir, xtal, ligID)) + "%s: copying %s_%s_thumb.png to html png" % (xtal, xtal, ligID) + ) + os.system("/bin/cp %s/%s_%s_thumb.png ." % (sampleDir, xtal, ligID)) def makeFolders(self): - self.Logfile.insert('preparing folders in html directory') + self.Logfile.insert("preparing folders in html directory") os.chdir(self.htmlDir) -# if not os.path.isdir('js'): -# os.mkdir('js') - if not os.path.isdir('tmp'): - os.mkdir('tmp') - if not os.path.isdir('png'): - os.mkdir('png') - if not os.path.isdir('files'): - os.mkdir('files') - if not os.path.isdir('download'): - os.mkdir('download') + # if not os.path.isdir('js'): + # os.mkdir('js') + if not os.path.isdir("tmp"): + os.mkdir("tmp") + if not os.path.isdir("png"): + os.mkdir("png") + if not os.path.isdir("files"): + os.mkdir("files") + if not os.path.isdir("download"): + os.mkdir("download") def copy_pdb(self, xtal): - os.chdir(os.path.join(self.htmlDir, 'files')) + os.chdir(os.path.join(self.htmlDir, "files")) self.pdb = None - if os.path.isfile(os.path.join(self.projectDir, xtal, 'refine.split.bound-state.pdb')): - self.pdb = pdbtools(os.path.join( - self.projectDir, xtal, 'refine.split.bound-state.pdb')) + if os.path.isfile( + os.path.join(self.projectDir, xtal, "refine.split.bound-state.pdb") + ): + self.pdb = pdbtools( + os.path.join(self.projectDir, xtal, "refine.split.bound-state.pdb") + ) self.Logfile.insert( - '%s: copying refine.split.bound-state.pdb to html directory' % xtal) - os.system('/bin/cp %s/refine.split.bound-state.pdb %s.pdb' % - (os.path.join(self.projectDir, xtal), xtal)) + "%s: copying refine.split.bound-state.pdb to html directory" % xtal + ) + os.system( + "/bin/cp %s/refine.split.bound-state.pdb %s.pdb" + % (os.path.join(self.projectDir, xtal), xtal) + ) else: - self.Logfile.error( - '%s: cannot find refine.split.bound-state.pdb' % xtal) + self.Logfile.error("%s: cannot find refine.split.bound-state.pdb" % xtal) def copy_mtz(self, xtal): - os.chdir(os.path.join(self.htmlDir, 'files')) - if os.path.isfile(os.path.join(self.projectDir, xtal, xtal+'.free.mtz')): + os.chdir(os.path.join(self.htmlDir, "files")) + if os.path.isfile(os.path.join(self.projectDir, xtal, xtal + ".free.mtz")): self.Logfile.insert( - '%s: copying %s.free.mtz to html directory' % (xtal, xtal)) - os.system('/bin/cp %s/%s.free.mtz .' % - (os.path.join(self.projectDir, xtal), xtal)) + "%s: copying %s.free.mtz to html directory" % (xtal, xtal) + ) + os.system( + "/bin/cp %s/%s.free.mtz ." % (os.path.join(self.projectDir, xtal), xtal) + ) else: - self.Logfile.error('%s: cannot find %s.free.mtz' % (xtal, xtal)) + self.Logfile.error("%s: cannot find %s.free.mtz" % (xtal, xtal)) def copy_electron_density(self, xtal, ligand, eventMap): - os.chdir(os.path.join(self.htmlDir, 'files')) + os.chdir(os.path.join(self.htmlDir, "files")) - emap = xtal+'_'+ligand+'_2fofc.ccp4' + emap = xtal + "_" + ligand + "_2fofc.ccp4" if os.path.isfile(os.path.join(self.projectDir, xtal, emap)): - self.Logfile.insert( - '%s: copying %s to html directory' % (xtal, emap)) - os.system('/bin/cp %s/%s %s' % - (os.path.join(self.projectDir, xtal), emap, emap)) + self.Logfile.insert("%s: copying %s to html directory" % (xtal, emap)) + os.system( + "/bin/cp %s/%s %s" % (os.path.join(self.projectDir, xtal), emap, emap) + ) else: - self.Logfile.error('%s: cannot find %s' % (xtal, emap)) + self.Logfile.error("%s: cannot find %s" % (xtal, emap)) - emap = xtal+'_'+ligand+'_fofc.ccp4' + emap = xtal + "_" + ligand + "_fofc.ccp4" if os.path.isfile(os.path.join(self.projectDir, xtal, emap)): - self.Logfile.insert( - '%s: copying %s to html directory' % (xtal, emap)) - os.system('/bin/cp %s/%s %s' % - (os.path.join(self.projectDir, xtal), emap, emap)) + self.Logfile.insert("%s: copying %s to html directory" % (xtal, emap)) + os.system( + "/bin/cp %s/%s %s" % (os.path.join(self.projectDir, xtal), emap, emap) + ) else: - self.Logfile.error('%s: cannot find %s' % (xtal, emap)) + self.Logfile.error("%s: cannot find %s" % (xtal, emap)) - self.Logfile.insert('%s: looking for %s' % ( - xtal, os.path.join(self.projectDir, xtal, eventMap))) + self.Logfile.insert( + "%s: looking for %s" % (xtal, os.path.join(self.projectDir, xtal, eventMap)) + ) if os.path.isfile(os.path.join(self.projectDir, xtal, eventMap)): - self.Logfile.insert( - '%s: copying %s to html directory' % (xtal, eventMap)) - os.system('/bin/cp %s/%s %s' % - (os.path.join(self.projectDir, xtal), eventMap, eventMap)) + self.Logfile.insert("%s: copying %s to html directory" % (xtal, eventMap)) + os.system( + "/bin/cp %s/%s %s" + % (os.path.join(self.projectDir, xtal), eventMap, eventMap) + ) else: - self.Logfile.error('%s: cannot find %s' % (xtal, eventMap)) + self.Logfile.error("%s: cannot find %s" % (xtal, eventMap)) def copy_ligand_files(self, xtal): - os.chdir(os.path.join(self.htmlDir, 'files')) - - if os.path.isfile(os.path.join(self.projectDir, xtal, self.db_dict['CompoundCode']+'.cif')): - self.Logfile.insert('%s: copying compound cif file' % xtal) - os.system('/bin/cp %s %s_%s' % (os.path.join(self.projectDir, xtal, - self.db_dict['CompoundCode']+'.cif'), xtal, self.db_dict['CompoundCode']+'.cif')) + os.chdir(os.path.join(self.htmlDir, "files")) + + if os.path.isfile( + os.path.join(self.projectDir, xtal, self.db_dict["CompoundCode"] + ".cif") + ): + self.Logfile.insert("%s: copying compound cif file" % xtal) + os.system( + "/bin/cp %s %s_%s" + % ( + os.path.join( + self.projectDir, xtal, self.db_dict["CompoundCode"] + ".cif" + ), + xtal, + self.db_dict["CompoundCode"] + ".cif", + ) + ) else: - self.Logfile.error('%s: cannot find compound cif file -> %s' % - (xtal, self.db_dict['CompoundCode']+'.cif')) - - os.chdir(os.path.join(self.htmlDir, 'png')) - - if os.path.isfile(os.path.join(self.projectDir, xtal, self.db_dict['CompoundCode']+'.png')): - self.Logfile.insert('%s: copying compound png file' % xtal) - os.system('/bin/cp %s %s_%s' % (os.path.join(self.projectDir, xtal, - self.db_dict['CompoundCode']+'.png'), xtal, self.db_dict['CompoundCode']+'.png')) + self.Logfile.error( + "%s: cannot find compound cif file -> %s" + % (xtal, self.db_dict["CompoundCode"] + ".cif") + ) + + os.chdir(os.path.join(self.htmlDir, "png")) + + if os.path.isfile( + os.path.join(self.projectDir, xtal, self.db_dict["CompoundCode"] + ".png") + ): + self.Logfile.insert("%s: copying compound png file" % xtal) + os.system( + "/bin/cp %s %s_%s" + % ( + os.path.join( + self.projectDir, xtal, self.db_dict["CompoundCode"] + ".png" + ), + xtal, + self.db_dict["CompoundCode"] + ".png", + ) + ) else: - self.Logfile.error('%s: cannot find compound png file -> %s' % - (xtal, self.db_dict['CompoundCode']+'.png')) + self.Logfile.error( + "%s: cannot find compound png file -> %s" + % (xtal, self.db_dict["CompoundCode"] + ".png") + ) def copy_spider_plot(self, xtal, ligID): - os.chdir(os.path.join(self.htmlDir, 'png')) - refPDB = os.path.join(self.projectDir, xtal, 'refine.pdb') - self.Logfile.insert('%s: looking for spider plots...' % xtal) + os.chdir(os.path.join(self.htmlDir, "png")) + refPDB = os.path.join(self.projectDir, xtal, "refine.pdb") + self.Logfile.insert("%s: looking for spider plots..." % xtal) if os.path.isfile(refPDB): - refPDBreal = os.path.realpath( - refPDB)[:os.path.realpath(refPDB).rfind('/')] - plot = os.path.join(refPDBreal, 'residue_plots', - ligID.replace('LIG-', '')+'.png') - self.Logfile.insert(xtal + ': looking for ' + plot) + refPDBreal = os.path.realpath(refPDB)[: os.path.realpath(refPDB).rfind("/")] + plot = os.path.join( + refPDBreal, "residue_plots", ligID.replace("LIG-", "") + ".png" + ) + self.Logfile.insert(xtal + ": looking for " + plot) if os.path.isfile(plot): - self.Logfile.insert('%s: found %s' % (xtal, plot)) - self.Logfile.insert('%s: copying spider plot for %s' % ( - xtal, ligID.replace('LIG-', '') + '.png')) - os.system('/bin/cp %s %s_%s.png' % (plot, xtal, ligID)) + self.Logfile.insert("%s: found %s" % (xtal, plot)) + self.Logfile.insert( + "%s: copying spider plot for %s" + % (xtal, ligID.replace("LIG-", "") + ".png") + ) + os.system("/bin/cp %s %s_%s.png" % (plot, xtal, ligID)) else: - self.Logfile.error('%s: cannot find spider plot for %s' % ( - xtal, ligID.replace('LIG-', '')+'.png')) - self.Logfile.warning('%s: using %s instead' % ( - xtal, 'NO_SPIDER_PLOT_AVAILABLE.png')) - os.system('/bin/cp %s %s_%s.png' % (os.path.join(os.getenv( - 'XChemExplorer_DIR'), 'image', 'NO_SPIDER_PLOT_AVAILABLE.png'), xtal, ligID)) + self.Logfile.error( + "%s: cannot find spider plot for %s" + % (xtal, ligID.replace("LIG-", "") + ".png") + ) + self.Logfile.warning( + "%s: using %s instead" % (xtal, "NO_SPIDER_PLOT_AVAILABLE.png") + ) + os.system( + "/bin/cp %s %s_%s.png" + % ( + os.path.join( + os.getenv("XChemExplorer_DIR"), + "image", + "NO_SPIDER_PLOT_AVAILABLE.png", + ), + xtal, + ligID, + ) + ) # else: self.Logfile.error( - '%s: cannot find refine.pdb, i.e. cannot start looking for spider plots...' % xtal) - - -# def ligands_in_pdbFile(self,xtal): -# os.chdir(os.path.join(self.projectDir,xtal)) -# ligPDB = [] -# ligList = [] -# self.Logfile.insert('%s: reading ligands to type LIG in refine.split.bound-state.pdb' %xtal) -# if os.path.isfile('refine.split.bound-state.pdb'): -# ligPDB = self.pdb.save_residues_with_resname(os.path.join(self.projectDir, xtal), 'LIG') -# else: -# self.Logfile.error('%s: cannot find refine.split.bound-state.pdb' %xtal) -# if not ligPDB: -# self.Logfile.error('%s; cannot find any ligands of type LIG in refine.split.bound-state.pdb' %xtal) -# else: -# for lig in sorted(ligPDB): -# ligList.append(lig.replace('.pdb', '')) -# return ligList - - -# def find_matching_event_map_from_database(self,xtal,ligID): -# ligName = ligID.split('-')[0] -# ligChain = ligID.split('-')[1] -# ligNumber = ligID.split('-')[2] -# eventMAP = self.db.get_event_map_for_ligand(xtal, ligChain, ligNumber, ligName) -# self.Logfile.insert('%s: the database thinks the following event map belongs to %s: %s' %(xtal,ligID,eventMAP)) -## print 'event map', eventMAP -# if eventMAP == '' or 'none' in str(eventMAP).lower(): -# self.Logfile.warning('%s: the respective field in the DB is apparently emtpy' %xtal) -# self.Logfile.warning('%s: will try to determine ligand - event map relationship by checking CC...' %xtal) -# eventMAP = self.find_matching_event_map(xtal,ligID) -# elif not os.path.isfile(eventMAP): -# self.Logfile.warning('%s: event map file does not exist!' %xtal) -# self.Logfile.warning('%s: will try to determine ligand - event map relationship by checking CC...' %xtal) -# eventMAP = self.find_matching_event_map(xtal,ligID) -# else: -# self.Logfile.insert('%s: found matching event map!' %xtal) -# return eventMAP - -# def find_matching_event_map(self,xtal,ligID): -# os.chdir(os.path.join(self.projectDir, xtal)) -# eventMAP = [] -# self.Logfile.insert('%s: trying to find fitting event maps for modelled ligands' %xtal) -# if os.path.isfile('no_pandda_analysis_performed'): -# self.Logfile.warning('%s: no pandda analysis performed; skipping this step...' %xtal) -# return -# ligCC = [] -# for mtz in sorted(glob.glob('*event*.native*P1.mtz')): -# self.get_lig_cc(xtal, mtz, ligID+'.pdb') -# cc = self.check_lig_cc(mtz.replace('.mtz', '_CC'+ligID+'.log')) -# self.Logfile.insert('%s: %s -> CC = %s for %s' %(xtal,ligID,cc,mtz)) -# try: -# ligCC.append([mtz,float(cc)]) -# except ValueError: -# ligCC.append([mtz, 0.00]) -# try: -# highestCC = max(ligCC, key=lambda x: x[0])[1] -# except ValueError: -# self.Logfile.error('%s: event maps are not yet converted to mtz files...' %xtal) -# return -# if highestCC == 0.00 or ligCC is []: -# self.Logfile.error('%s: best CC of ligand %s for any event map is 0!' %(xtal,ligID)) -# else: -# self.Logfile.insert('%s: selected event map -> CC(%s) = %s for %s' %(xtal,ligID,highestCC,mtz[mtz.rfind('/')+1:])) -# eventMAP = mtz[mtz.rfind('/')+1:].replace('.P1.mtz','.ccp4') -# if not os.path.isfile(eventMAP): -# eventMAP = [] -# else: -# self.cut_eventMAP(xtal,ligID,eventMAP) -# return eventMAP - -# def cut_and_copy_map(self,xtal,pdbCentre,mapin,mapout,F,PHI): -# os.chdir(os.path.join(self.projectDir, xtal)) -# self.Logfile.insert('%s: cutting density of %s around %s' %(xtal,mapin.replace('.ccp4','.P1.ccp4'),pdbCentre)) -# if os.path.isfile(mapout): -# self.Logfile.warning('%s: removing map -> %s' %(xtal,mapout)) -# os.system('/bin/rm '+mapout) -# else: -# -# if mapin.endswith('.map') or mapin.endswith('.ccp4'): -# cmd = ( -# 'mapmask mapin %s mapout %s xyzin %s << eof\n' %(mapin.replace('.ccp4','.P1.ccp4'),mapout,pdbCentre) + -# ' border 12\n' -# ' end\n' -# 'eof' -# ) - -# cmd = ( -# 'cmapcut -mapin %s -pdbin %s -mapout %s' %(mtzin,pdbCentre,mapout) -# ) - -# cmd = ( -# "phenix.cut_out_density %s %s map_coeff_labels='%s,%s' cutout_model_radius=6 cutout_map_file_name=%s cutout_as_map=True" %(pdbCentre,mtzin,F,PHI,mapout) -# ) -# self.Logfile.insert(xtal+': running command:\n'+cmd) -# os.system(cmd) -# if os.path.isfile(mapout): -# self.Logfile.insert(xtal+': reduced event map successfully created') -# self.Logfile.insert('%s: copying %s to %s/files' % (xtal, mapout, self.htmlDir)) -# os.system('/bin/cp %s %s/files' % (mapout, self.htmlDir)) -# else: -# self.Logfile.error(xtal+': creation of event map failed') - - -# def cut_eventMAP(self,xtal,ligID,eventMAP): -# os.chdir(os.path.join(self.projectDir, xtal)) -# self.Logfile.insert('%s: cutting event map around ligand %s' %(xtal,ligID)) -# ligMAP = xtal + '_' + ligID + '.ccp4' -# cmd = ( -# 'mapmask mapin %s mapout %s xyzin %s << eof\n' %(eventMAP,ligMAP,ligID+'.pdb') + -# ' border 10\n' -# ' end\n' -# 'eof' -# ) -# os.system(cmd) -# self.copy_eventMap(xtal, ligID, eventMAP) - -# def copy_eventMap(self,xtal,ligID,eventMAP): -# os.chdir(os.path.join(self.htmlDir,'files')) -# self.Logfile.insert('%s: copying event map for %s' %(xtal,ligID)) -# os.system('/bin/mv %s/%s_%s.ccp4 .' %(os.path.join(self.projectDir,xtal),xtal,ligID)) - -# def get_lig_cc(self, xtal, mtz, lig): -# ligID = lig.replace('.pdb','') -# ccLog = mtz.replace('.mtz', '_CC'+ligID+'.log') -# self.Logfile.insert('%s: calculating CC for %s in %s' %(xtal,lig,mtz)) -# if os.path.isfile(mtz.replace('.mtz', '_CC'+ligID+'.log')): -# if os.path.isfile(ccLog) and os.path.getsize(ccLog) != 0: -# self.Logfile.warning('logfile of CC analysis exists; skipping...') -# return -# cmd = ( 'module load phenix\n' -# 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log')) ) -# os.system('/bin/rm %s' %mtz.replace('.mtz', '_CC'+ligID+'.log') ) -# cmd = ( 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log')) ) -# os.system(cmd) - -# def check_lig_cc(self,log): -# cc = 'n/a' -# if os.path.isfile(log): -# for line in open(log): -# if line.startswith('local'): -# cc = line.split()[len(line.split()) - 1] -# else: -# self.Logfile.error('logfile does not exist: %s' %log) -# return cc + "%s: cannot find refine.pdb, i.e. cannot start looking for spider plots..." + % xtal + ) + + # def ligands_in_pdbFile(self,xtal): + # os.chdir(os.path.join(self.projectDir,xtal)) + # ligPDB = [] + # ligList = [] + # self.Logfile.insert('%s: reading ligands to type LIG in refine.split.bound-state.pdb' %xtal) + # if os.path.isfile('refine.split.bound-state.pdb'): + # ligPDB = self.pdb.save_residues_with_resname(os.path.join(self.projectDir, xtal), 'LIG') + # else: + # self.Logfile.error('%s: cannot find refine.split.bound-state.pdb' %xtal) + # if not ligPDB: + # self.Logfile.error('%s; cannot find any ligands of type LIG in refine.split.bound-state.pdb' %xtal) + # else: + # for lig in sorted(ligPDB): + # ligList.append(lig.replace('.pdb', '')) + # return ligList + + # def find_matching_event_map_from_database(self,xtal,ligID): + # ligName = ligID.split('-')[0] + # ligChain = ligID.split('-')[1] + # ligNumber = ligID.split('-')[2] + # eventMAP = self.db.get_event_map_for_ligand(xtal, ligChain, ligNumber, ligName) + # self.Logfile.insert('%s: the database thinks the following event map belongs to %s: %s' %(xtal,ligID,eventMAP)) + ## print 'event map', eventMAP + # if eventMAP == '' or 'none' in str(eventMAP).lower(): + # self.Logfile.warning('%s: the respective field in the DB is apparently emtpy' %xtal) + # self.Logfile.warning('%s: will try to determine ligand - event map relationship by checking CC...' %xtal) + # eventMAP = self.find_matching_event_map(xtal,ligID) + # elif not os.path.isfile(eventMAP): + # self.Logfile.warning('%s: event map file does not exist!' %xtal) + # self.Logfile.warning('%s: will try to determine ligand - event map relationship by checking CC...' %xtal) + # eventMAP = self.find_matching_event_map(xtal,ligID) + # else: + # self.Logfile.insert('%s: found matching event map!' %xtal) + # return eventMAP + + # def find_matching_event_map(self,xtal,ligID): + # os.chdir(os.path.join(self.projectDir, xtal)) + # eventMAP = [] + # self.Logfile.insert('%s: trying to find fitting event maps for modelled ligands' %xtal) + # if os.path.isfile('no_pandda_analysis_performed'): + # self.Logfile.warning('%s: no pandda analysis performed; skipping this step...' %xtal) + # return + # ligCC = [] + # for mtz in sorted(glob.glob('*event*.native*P1.mtz')): + # self.get_lig_cc(xtal, mtz, ligID+'.pdb') + # cc = self.check_lig_cc(mtz.replace('.mtz', '_CC'+ligID+'.log')) + # self.Logfile.insert('%s: %s -> CC = %s for %s' %(xtal,ligID,cc,mtz)) + # try: + # ligCC.append([mtz,float(cc)]) + # except ValueError: + # ligCC.append([mtz, 0.00]) + # try: + # highestCC = max(ligCC, key=lambda x: x[0])[1] + # except ValueError: + # self.Logfile.error('%s: event maps are not yet converted to mtz files...' %xtal) + # return + # if highestCC == 0.00 or ligCC is []: + # self.Logfile.error('%s: best CC of ligand %s for any event map is 0!' %(xtal,ligID)) + # else: + # self.Logfile.insert('%s: selected event map -> CC(%s) = %s for %s' %(xtal,ligID,highestCC,mtz[mtz.rfind('/')+1:])) + # eventMAP = mtz[mtz.rfind('/')+1:].replace('.P1.mtz','.ccp4') + # if not os.path.isfile(eventMAP): + # eventMAP = [] + # else: + # self.cut_eventMAP(xtal,ligID,eventMAP) + # return eventMAP + + # def cut_and_copy_map(self,xtal,pdbCentre,mapin,mapout,F,PHI): + # os.chdir(os.path.join(self.projectDir, xtal)) + # self.Logfile.insert('%s: cutting density of %s around %s' %(xtal,mapin.replace('.ccp4','.P1.ccp4'),pdbCentre)) + # if os.path.isfile(mapout): + # self.Logfile.warning('%s: removing map -> %s' %(xtal,mapout)) + # os.system('/bin/rm '+mapout) + # else: + # + # if mapin.endswith('.map') or mapin.endswith('.ccp4'): + # cmd = ( + # 'mapmask mapin %s mapout %s xyzin %s << eof\n' %(mapin.replace('.ccp4','.P1.ccp4'),mapout,pdbCentre) + + # ' border 12\n' + # ' end\n' + # 'eof' + # ) + + # cmd = ( + # 'cmapcut -mapin %s -pdbin %s -mapout %s' %(mtzin,pdbCentre,mapout) + # ) + + # cmd = ( + # "phenix.cut_out_density %s %s map_coeff_labels='%s,%s' cutout_model_radius=6 cutout_map_file_name=%s cutout_as_map=True" %(pdbCentre,mtzin,F,PHI,mapout) + # ) + # self.Logfile.insert(xtal+': running command:\n'+cmd) + # os.system(cmd) + # if os.path.isfile(mapout): + # self.Logfile.insert(xtal+': reduced event map successfully created') + # self.Logfile.insert('%s: copying %s to %s/files' % (xtal, mapout, self.htmlDir)) + # os.system('/bin/cp %s %s/files' % (mapout, self.htmlDir)) + # else: + # self.Logfile.error(xtal+': creation of event map failed') + + # def cut_eventMAP(self,xtal,ligID,eventMAP): + # os.chdir(os.path.join(self.projectDir, xtal)) + # self.Logfile.insert('%s: cutting event map around ligand %s' %(xtal,ligID)) + # ligMAP = xtal + '_' + ligID + '.ccp4' + # cmd = ( + # 'mapmask mapin %s mapout %s xyzin %s << eof\n' %(eventMAP,ligMAP,ligID+'.pdb') + + # ' border 10\n' + # ' end\n' + # 'eof' + # ) + # os.system(cmd) + # self.copy_eventMap(xtal, ligID, eventMAP) + + # def copy_eventMap(self,xtal,ligID,eventMAP): + # os.chdir(os.path.join(self.htmlDir,'files')) + # self.Logfile.insert('%s: copying event map for %s' %(xtal,ligID)) + # os.system('/bin/mv %s/%s_%s.ccp4 .' %(os.path.join(self.projectDir,xtal),xtal,ligID)) + + # def get_lig_cc(self, xtal, mtz, lig): + # ligID = lig.replace('.pdb','') + # ccLog = mtz.replace('.mtz', '_CC'+ligID+'.log') + # self.Logfile.insert('%s: calculating CC for %s in %s' %(xtal,lig,mtz)) + # if os.path.isfile(mtz.replace('.mtz', '_CC'+ligID+'.log')): + # if os.path.isfile(ccLog) and os.path.getsize(ccLog) != 0: + # self.Logfile.warning('logfile of CC analysis exists; skipping...') + # return + # cmd = ( 'module load phenix\n' + # 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log')) ) + # os.system('/bin/rm %s' %mtz.replace('.mtz', '_CC'+ligID+'.log') ) + # cmd = ( 'phenix.get_cc_mtz_pdb %s %s > %s' % (mtz, lig, mtz.replace('.mtz', '_CC'+ligID+'.log')) ) + # os.system(cmd) + + # def check_lig_cc(self,log): + # cc = 'n/a' + # if os.path.isfile(log): + # for line in open(log): + # if line.startswith('local'): + # cc = line.split()[len(line.split()) - 1] + # else: + # self.Logfile.error('logfile does not exist: %s' %log) + # return cc def write_html_file(self, html): os.chdir(self.htmlDir) - self.Logfile.insert('writing index.html') + self.Logfile.insert("writing index.html") html += XChemMain.html_footer() - if os.path.isfile('index.html'): - os.system('/bin/rm -f index.html') - f = open('index.html', 'w') + if os.path.isfile("index.html"): + os.system("/bin/rm -f index.html") + f = open("index.html", "w") f.write(html) f.close() diff --git a/web/process_sqlite.py b/web/process_sqlite.py index c58599d5..02e45f15 100755 --- a/web/process_sqlite.py +++ b/web/process_sqlite.py @@ -17,93 +17,125 @@ import zipfile import glob -sys.path.append(os.path.join(os.getenv('XChemExplorer_DIR'), 'lib')) +sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) -targetID = '' -panddadir = '' +targetID = "" +panddadir = "" def writeTableRow(row, htmlfile): "Write a row of data to the HTML file" htmlfile.write("") - htmlfile.write(""+row['ModelName']+"\n") - htmlfile.write(""+row['CompoundSMILES']+"\n") - htmlfile.write("\n") - htmlfile.write(""+row['PANDDA_site_name']+"\n") - htmlfile.write(""+row['LigandConfidence']+"\n") - htmlfile.write(""+row['ModelStatus']+"\n") - htmlfile.write("\n") - htmlfile.write("
\n") -# htmlfile.write("
\n") - htmlfile.write(""+row['PANDDA_site_comment']+"\n") -# htmlfile.write("TBD\n") -# htmlfile.write("http://www.rcsb.org/pdb/explore/explore.do?structureId=%s\n" %row['Deposition_PDB_ID']) - htmlfile.write('{1!s}\n'.format( - row['Deposition_PDB_ID'], row['Deposition_PDB_ID'])) - htmlfile.write(""+row['DataProcessingResolutionHigh']+"\n") - htmlfile.write(""+row['DataProcessingSpaceGroup']+"\n") - htmlfile.write(""+row['DataProcessingUnitCell']+"\n") - htmlfile.write("Save\n") - htmlfile.write("Save\n") - htmlfile.write("Save\n") + htmlfile.write("" + row["ModelName"] + "\n") + htmlfile.write("" + row["CompoundSMILES"] + "\n") + htmlfile.write( + "\n" + ) + htmlfile.write("" + row["PANDDA_site_name"] + "\n") + htmlfile.write("" + row["LigandConfidence"] + "\n") + htmlfile.write("" + row["ModelStatus"] + "\n") + htmlfile.write( + "\n" + ) + htmlfile.write( + "
\n" + ) + # htmlfile.write("
\n") + htmlfile.write("" + row["PANDDA_site_comment"] + "\n") + # htmlfile.write("TBD\n") + # htmlfile.write("http://www.rcsb.org/pdb/explore/explore.do?structureId=%s\n" %row['Deposition_PDB_ID']) + htmlfile.write( + '{1!s}\n'.format( + row["Deposition_PDB_ID"], row["Deposition_PDB_ID"] + ) + ) + htmlfile.write("" + row["DataProcessingResolutionHigh"] + "\n") + htmlfile.write("" + row["DataProcessingSpaceGroup"] + "\n") + htmlfile.write("" + row["DataProcessingUnitCell"] + "\n") + htmlfile.write("Save\n") + htmlfile.write("Save\n") + htmlfile.write("Save\n") htmlfile.write("\n") return def writeICBPage(row, panddadir): "Write HTML file for ICB visualisation" - icbhtmlfile = open(panddadir+"/icbs/"+row['ModelName']+".html", "w") + icbhtmlfile = open(panddadir + "/icbs/" + row["ModelName"] + ".html", "w") icbhtmlfile.write("\n") icbhtmlfile.write("\n") icbhtmlfile.write( - '\n') - icbhtmlfile.write( - '\n') + '\n' + ) icbhtmlfile.write( - '\n') - icbhtmlfile.write(''+row['ModelName']+'\n') + '\n' + ) + icbhtmlfile.write('\n') + icbhtmlfile.write("" + row["ModelName"] + "\n") icbhtmlfile.write("\n") icbhtmlfile.write("\n") - icbhtmlfile.write("

"+row['CrystalName'] + - " "+row['CompoundCode']+" event

\n") icbhtmlfile.write( - '

Please wait whilst the interactive viewer is loaded!

\n') + "

" + row["CrystalName"] + " " + row["CompoundCode"] + " event

\n" + ) + icbhtmlfile.write( + '

Please wait whilst the interactive viewer is loaded!

\n' + ) icbhtmlfile.write( - '
\n') - icbhtmlfile.write('\n') -# icbhtmlfile.write('\n') - icbhtmlfile.write('
\n') + '
\n' + ) + icbhtmlfile.write( + '\n' + ) + # icbhtmlfile.write('\n') + icbhtmlfile.write("
\n") icbhtmlfile.write('
\n') icbhtmlfile.write("\n") - icbhtmlfile.write("\n") - icbhtmlfile.write("\n") - icbhtmlfile.write("\n") + icbhtmlfile.write("\n") + icbhtmlfile.write( + "\n" + ) + icbhtmlfile.write( + "\n" + ) icbhtmlfile.write("
Protein: "+row['CrystalName']+"
Compound ID: " + - row['CompoundCode']+"
Compound SMILES: "+row['CompoundSMILES']+"
Protein: " + row["CrystalName"] + "
Compound ID: " + + row["CompoundCode"] + + "
Compound SMILES: " + + row["CompoundSMILES"] + + "
\n") icbhtmlfile.write("
\n") - icbhtmlfile.write('\n') + ' act.projectFile = "' + + row["ModelName"] + + "_" + + row["CompoundCode"] + + '.icb";\n' + ) + # icbhtmlfile.write(' act.projectFile = "'+row['ModelName']+'_'+row['CompoundCode']+'.icb.gz";\n') + icbhtmlfile.write(" act.searchBarVisible = false;\n") + icbhtmlfile.write(" act.sequenceViewVisibleAuto = false;\n") + icbhtmlfile.write(" act.tableViewVisibleAuto = false;\n") + icbhtmlfile.write( + ' document.getElementById("wait").style.visibility = "hidden";\n' + ) + icbhtmlfile.write("}\n") + icbhtmlfile.write("\n") icbhtmlfile.write("\n") icbhtmlfile.write("\n") icbhtmlfile.close() @@ -111,22 +143,23 @@ def writeICBPage(row, panddadir): def main(argv): - sqlitefile = '' + sqlitefile = "" # Process command line options try: opts, args = getopt.getopt( - argv, 't:s:d:', ['targetID=', 'sqlitefile=', 'panddadir=']) + argv, "t:s:d:", ["targetID=", "sqlitefile=", "panddadir="] + ) except getopt.GetoptError as err: print(err) - print('process.py -t -s -d ') + print("process.py -t -s -d ") sys.exit(2) if len(opts) < 3: - print('Missing arguments:') - print('process.py -t -s -d ') + print("Missing arguments:") + print("process.py -t -s -d ") sys.exit(2) for opt, arg in opts: - if opt == '-h': - print('process.py -t -s ') + if opt == "-h": + print("process.py -t -s ") sys.exit() elif opt in ("-t", "--targetID"): targetID = arg @@ -136,38 +169,43 @@ def main(argv): panddadir = arg # Create directory structure - if not os.path.exists(panddadir+"/compoundImages"): - os.makedirs(panddadir+"/compoundImages") - if not os.path.exists(panddadir+"/icbs"): - os.makedirs(panddadir+"/icbs") - if not os.path.exists(panddadir+"/pdbs"): - os.makedirs(panddadir+"/pdbs") - if not os.path.exists(panddadir+"/maps"): - os.makedirs(panddadir+"/maps") - if not os.path.exists(panddadir+"/residueplots"): - os.makedirs(panddadir+"/residueplots") - if not os.path.exists(panddadir+"/mapImages"): - os.makedirs(panddadir+"/mapImages") + if not os.path.exists(panddadir + "/compoundImages"): + os.makedirs(panddadir + "/compoundImages") + if not os.path.exists(panddadir + "/icbs"): + os.makedirs(panddadir + "/icbs") + if not os.path.exists(panddadir + "/pdbs"): + os.makedirs(panddadir + "/pdbs") + if not os.path.exists(panddadir + "/maps"): + os.makedirs(panddadir + "/maps") + if not os.path.exists(panddadir + "/residueplots"): + os.makedirs(panddadir + "/residueplots") + if not os.path.exists(panddadir + "/mapImages"): + os.makedirs(panddadir + "/mapImages") # Create HTML file and write header - htmlfile = open(panddadir+"/index.html", "w") + htmlfile = open(panddadir + "/index.html", "w") htmlfile.write("\n") htmlfile.write("\n") htmlfile.write( - '\n') + '\n' + ) htmlfile.write( - '\n') + '\n' + ) htmlfile.write( - '\n') - htmlfile.write(''+targetID+' Fragment Hits\n') + '\n' + ) + htmlfile.write("" + targetID + " Fragment Hits\n") htmlfile.write( - '\n') + '\n") htmlfile.write( - '\n') + '\n") htmlfile.write('\n') + htmlfile.write("} )\n") + htmlfile.write("} );\n") + htmlfile.write("\n") htmlfile.write("\n") htmlfile.write("\n") - htmlfile.write("

Ligand-bound models for "+targetID+"

") - htmlfile.write("""

Interpreting 'Ligand confidence'

+ htmlfile.write("

Ligand-bound models for " + targetID + "

") + htmlfile.write( + """

Interpreting 'Ligand confidence'

4 - High Confidence: The expected ligand was easily interpretable from clear density, and subsequent refinement was well-behaved. This ligand can be trusted.
3 - Clear density, unexpected ligand: Density very clearly showed a well-defined ligand, but that ligand was unexpected in that crystal/dataset. The observed ligand was modelled anyway, because its presence could be explained in some way.
2 - Correct ligand, weak density: Though density was weak, it was possible to model the expected ligand, possibly including other circumstantial evidence (e.g. similar ligand in another model). @@ -209,13 +248,16 @@ def main(argv):
B-factor ratio measures the consistency of the model with surrounding protein, and is calculated from the B factors of respectively the changed atoms and all side-chain atoms within 4Å. Large values (>3) reflect poor evidence for the model, and intermediate values (1.5+) indicate errors in refinement or modelling; for weakly-binding ligands, systematically large ratios may be justifiable.
RMSD compares the positions of all atoms built into event density, with their positions after final refinement, and should be below 1Å.
Precision (RSZO/OCC) measures how clear the density is after refinement. (This is not a quality indicator, but is related to strength of binding but not in a straightforward way.) -

\n""") +

\n""" + ) htmlfile.write("

Download data

\n") htmlfile.write("") htmlfile.write('\n') htmlfile.write("\n") @@ -261,26 +303,26 @@ def main(argv): htmlfile.write("\n") # Now walk through the input data - with open('foricm.csv', 'wb') as f: + with open("foricm.csv", "wb") as f: with sqlite3.connect(sqlitefile) as c: c.row_factory = sqlite3.Row cur = c.cursor() -# sql = ( "select p.ID,p.CrystalName,p.PANDDA_site_event_index,p.CrystalName || '_event'|| p.PANDDA_site_event_index " -# " as ModelName,m.CompoundCode,m.CompoundSMILES,p.PANDDA_site_name,p.PANDDA_site_confidence " -# " as LigandConfidence,p.RefinementOutcome " -# " as ModelStatus,p.PANDDA_site_comment,p.PANDDA_site_x,p.PANDDA_site_y,p.PANDDA_site_z, " -# " p.PANDDA_site_spider_plot,m.DataProcessingResolutionHigh,m.DataProcessingSpaceGroup," -# " m.DataProcessingUnitCell,m.RefinementPDB_latest,m.RefinementMTZ_latest,p.PANDDA_site_event_map " -# " from panddaTable as p, mainTable as m " -# " where p.CrystalName=m.CrystalName and p.PANDDA_site_ligand_placed='True' and " -# " (LigandConfidence like '1%' or LigandConfidence like '2%' or LigandConfidence like '3%' or LigandConfidence like '4%') " -# " order by p.CrystalName,ModelStatus desc,PANDDA_site_event_index" -# ) + # sql = ( "select p.ID,p.CrystalName,p.PANDDA_site_event_index,p.CrystalName || '_event'|| p.PANDDA_site_event_index " + # " as ModelName,m.CompoundCode,m.CompoundSMILES,p.PANDDA_site_name,p.PANDDA_site_confidence " + # " as LigandConfidence,p.RefinementOutcome " + # " as ModelStatus,p.PANDDA_site_comment,p.PANDDA_site_x,p.PANDDA_site_y,p.PANDDA_site_z, " + # " p.PANDDA_site_spider_plot,m.DataProcessingResolutionHigh,m.DataProcessingSpaceGroup," + # " m.DataProcessingUnitCell,m.RefinementPDB_latest,m.RefinementMTZ_latest,p.PANDDA_site_event_map " + # " from panddaTable as p, mainTable as m " + # " where p.CrystalName=m.CrystalName and p.PANDDA_site_ligand_placed='True' and " + # " (LigandConfidence like '1%' or LigandConfidence like '2%' or LigandConfidence like '3%' or LigandConfidence like '4%') " + # " order by p.CrystalName,ModelStatus desc,PANDDA_site_event_index" + # ) # query below is without the LigandConfidence being constrained; this is because some older DBs don't have a starting digit # here we constrain RefinementOutcome of site -# cur.execute("select p.ID,p.CrystalName,p.PANDDA_site_event_index,p.CrystalName || '_event'|| p.PANDDA_site_event_index as ModelName,m.CompoundCode,m.CompoundSMILES,m.Deposition_PDB_ID,p.PANDDA_site_name,p.PANDDA_site_confidence as LigandConfidence,p.RefinementOutcome as ModelStatus,p.PANDDA_site_comment,p.PANDDA_site_x,p.PANDDA_site_y,p.PANDDA_site_z, p.PANDDA_site_spider_plot,m.DataProcessingResolutionHigh,m.DataProcessingSpaceGroup,m.DataProcessingUnitCell,m.RefinementBoundConformation,m.RefinementMTZ_latest,p.PANDDA_site_event_map from panddaTable as p, mainTable as m where p.CrystalName=m.CrystalName and p.PANDDA_site_ligand_placed='True' and (p.RefinementOutcome like '4%' or p.RefinementOutcome like '5%' or p.RefinementOutcome like '6%') order by p.CrystalName,ModelStatus desc,PANDDA_site_event_index") + # cur.execute("select p.ID,p.CrystalName,p.PANDDA_site_event_index,p.CrystalName || '_event'|| p.PANDDA_site_event_index as ModelName,m.CompoundCode,m.CompoundSMILES,m.Deposition_PDB_ID,p.PANDDA_site_name,p.PANDDA_site_confidence as LigandConfidence,p.RefinementOutcome as ModelStatus,p.PANDDA_site_comment,p.PANDDA_site_x,p.PANDDA_site_y,p.PANDDA_site_z, p.PANDDA_site_spider_plot,m.DataProcessingResolutionHigh,m.DataProcessingSpaceGroup,m.DataProcessingUnitCell,m.RefinementBoundConformation,m.RefinementMTZ_latest,p.PANDDA_site_event_map from panddaTable as p, mainTable as m where p.CrystalName=m.CrystalName and p.PANDDA_site_ligand_placed='True' and (p.RefinementOutcome like '4%' or p.RefinementOutcome like '5%' or p.RefinementOutcome like '6%') order by p.CrystalName,ModelStatus desc,PANDDA_site_event_index") sql = ( "select p.ID,p.CrystalName,p.PANDDA_site_event_index,p.CrystalName || '_event'|| p.PANDDA_site_event_index " @@ -316,44 +358,60 @@ def main(argv): rows = cur.fetchall() if not rows: - print('==> WARNING: none of your samples seems to be at least CompChem ready (4)') + print( + "==> WARNING: none of your samples seems to be at least CompChem ready (4)" + ) return None writer = csv.DictWriter(f, fieldnames=list(rows[1].keys())) writer.writeheader() for row in rows: # Make compound structure - print(row['ModelName'], row['PANDDA_site_spider_plot']) - compound = Chem.MolFromSmiles( - row['CompoundSMILES'].encode("ascii")) - Draw.MolToFile(compound, panddadir+'/compoundImages/' + - row['CompoundCode']+'.png', (150, 150)) + print(row["ModelName"], row["PANDDA_site_spider_plot"]) + compound = Chem.MolFromSmiles(row["CompoundSMILES"].encode("ascii")) + Draw.MolToFile( + compound, + panddadir + "/compoundImages/" + row["CompoundCode"] + ".png", + (150, 150), + ) # Write out table information for event - eventID = row['ModelName']+"_"+row['CompoundCode'] - actID = (row['ModelName']+row['CompoundCode'] - ).replace(targetID+'-', '') + eventID = row["ModelName"] + "_" + row["CompoundCode"] + actID = (row["ModelName"] + row["CompoundCode"]).replace( + targetID + "-", "" + ) writeTableRow(row, htmlfile) writeICBPage(row, panddadir) try: - shutil.copy(row['RefinementBoundConformation'], - panddadir+"/pdbs/"+row['ModelName']+".pdb") - shutil.copy(row['RefinementMTZ_latest'], - panddadir+"/maps/"+row['ModelName']+".mtz") - shutil.copy(row['PANDDA_site_event_map'], - panddadir+"/maps/"+row['ModelName']+".ccp4") - if row['PANDDA_site_spider_plot'] is not None: - shutil.copy(row['PANDDA_site_spider_plot'], - panddadir+"/residueplots/"+row['ModelName']+".png") + shutil.copy( + row["RefinementBoundConformation"], + panddadir + "/pdbs/" + row["ModelName"] + ".pdb", + ) + shutil.copy( + row["RefinementMTZ_latest"], + panddadir + "/maps/" + row["ModelName"] + ".mtz", + ) + shutil.copy( + row["PANDDA_site_event_map"], + panddadir + "/maps/" + row["ModelName"] + ".ccp4", + ) + if row["PANDDA_site_spider_plot"] is not None: + shutil.copy( + row["PANDDA_site_spider_plot"], + panddadir + "/residueplots/" + row["ModelName"] + ".png", + ) except (IOError, TypeError): - print('*** WARNING: cannot find PDB and/or MTZ of ' + \ - row['ModelName']+' ***') - print('PDB bound :', row['RefinementBoundConformation']) - print('MTZ :', row['RefinementMTZ_latest']) - print('event map :', row['PANDDA_site_event_map']) - print('spider plot:', row['PANDDA_site_spider_plot']) + print( + "*** WARNING: cannot find PDB and/or MTZ of " + + row["ModelName"] + + " ***" + ) + print("PDB bound :", row["RefinementBoundConformation"]) + print("MTZ :", row["RefinementMTZ_latest"]) + print("event map :", row["PANDDA_site_event_map"]) + print("spider plot:", row["PANDDA_site_spider_plot"]) pass -# shutil.copy(row['RefinementPDB_latest'],panddadir+"/pdbs/"+row['ModelName']+".pdb") -# if row['PANDDA_site_spider_plot'] is not None: -# shutil.copy(row['PANDDA_site_spider_plot'],panddadir+"/residueplots/"+row['ModelName']+".png") + # shutil.copy(row['RefinementPDB_latest'],panddadir+"/pdbs/"+row['ModelName']+".pdb") + # if row['PANDDA_site_spider_plot'] is not None: + # shutil.copy(row['PANDDA_site_spider_plot'],panddadir+"/residueplots/"+row['ModelName']+".png") # Write row to CSV for ICM writer.writerow(dict(row)) @@ -365,20 +423,32 @@ def main(argv): htmlfile.close() # Copy JS & CSS files - if not os.path.exists(panddadir+"/js"): - os.makedirs(panddadir+"/js") - if not os.path.exists(panddadir+"/css"): - os.makedirs(panddadir+"/css") - shutil.copy(os.path.join(os.getenv('XChemExplorer_DIR'), - "web/jscss/css/jquery.dataTables.min.css"), panddadir+"/css/jquery.dataTables.min.css") - shutil.copy(os.path.join(os.getenv('XChemExplorer_DIR'), - "web/jscss/js/jquery-1.12.3.min.js"), panddadir+"/js/jquery-1.12.3.min.js") - shutil.copy(os.path.join(os.getenv('XChemExplorer_DIR'), - "web/jscss/js/jquery.dataTables.min.js"), panddadir+"/js/jquery.dataTables.min.js") + if not os.path.exists(panddadir + "/js"): + os.makedirs(panddadir + "/js") + if not os.path.exists(panddadir + "/css"): + os.makedirs(panddadir + "/css") + shutil.copy( + os.path.join( + os.getenv("XChemExplorer_DIR"), "web/jscss/css/jquery.dataTables.min.css" + ), + panddadir + "/css/jquery.dataTables.min.css", + ) + shutil.copy( + os.path.join( + os.getenv("XChemExplorer_DIR"), "web/jscss/js/jquery-1.12.3.min.js" + ), + panddadir + "/js/jquery-1.12.3.min.js", + ) + shutil.copy( + os.path.join( + os.getenv("XChemExplorer_DIR"), "web/jscss/js/jquery.dataTables.min.js" + ), + panddadir + "/js/jquery.dataTables.min.js", + ) # Create zip files print("Creating zipfile of PDBs...") - os.chdir(panddadir+"/pdbs") + os.chdir(panddadir + "/pdbs") zf = zipfile.ZipFile("allPDBs.zip", "w") for pdb in glob.glob("*.pdb"): zf.write(pdb) @@ -392,7 +462,7 @@ def main(argv): zf.close() # change folder permissions - os.system('chmod -R 775 {0!s}'.format(panddadir)) + os.system("chmod -R 775 {0!s}".format(panddadir)) return From 007a7ae84ef9bd6a8748c7a6cf943a992ecf63b7 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 13:48:11 +0000 Subject: [PATCH 120/358] Use black for autoformatting --- .devcontainer/Dockerfile | 4 ++-- .vscode/settings.json | 5 ++++- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 65233439..123ecb06 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -10,10 +10,10 @@ RUN apt-get update \ libxrender1 libfontconfig libxext6 \ libglib2.0-0 libsm6 libxi6 libxrandr2 libxfixes3 libxcursor1 libxinerama1 \ libgomp1 libxdamage1 libxcb-shm0 libxcb-render0 \ + python3-pip \ && apt-get clean -y && rm -rf /var/lib/apt/lists/* \ && echo . /ccp4-7.1/bin/ccp4.setup-sh | tee ~/.bashrc ~/.zshrc \ - && curl https://bootstrap.pypa.io/pip/2.7/get-pip.py -o /tmp/get-pip.py \ - && /ccp4-7.1/bin/ccp4-python /tmp/get-pip.py + && pip3 install flake8 black[python2] ENV QT_X11_NO_MITSHM=1 \ XChemExplorer_DIR=/workspace/ diff --git a/.vscode/settings.json b/.vscode/settings.json index 30ad8f25..ef076b95 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,4 +1,7 @@ { "python.defaultInterpreterPath": "/ccp4-7.1/bin/ccp4-python", - "python.linting.flake8Enabled": true + "python.linting.flake8Enabled": true, + "python.linting.flake8Path": "/usr/local/bin/flake8", + "python.formatting.provider": "black", + "python.formatting.blackPath": "/usr/local/bin/black" } \ No newline at end of file From 7847ade9258a060d87b9b7e92d077b4143b691e1 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 13:49:16 +0000 Subject: [PATCH 121/358] Add black to CI --- .github/workflows/code.yaml | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/.github/workflows/code.yaml b/.github/workflows/code.yaml index 44063c50..3f54de9d 100644 --- a/.github/workflows/code.yaml +++ b/.github/workflows/code.yaml @@ -23,7 +23,12 @@ jobs: python-version: "2.7" - name: Install linter - run: pip install flake8 + run: pip install flake8 black[python2] - - name: Lint project - run: flake8 . + - name: Lint with flake8 + run: | + flake8 . + + - name: Lint with black + run: | + black --check . From bb66eb03264b688fa1a3beb0bcfcf5f2dab724d0 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 14:06:16 +0000 Subject: [PATCH 122/358] Configure flake8 --- setup.cfg | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 setup.cfg diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 00000000..9f15817e --- /dev/null +++ b/setup.cfg @@ -0,0 +1,5 @@ +[flake8] +# Make flake8 respect black's line length (default 88), +max-line-length = 88 +extend-ignore = + E203, # See https://github.com/PyCQA/pycodestyle/issues/373 \ No newline at end of file From e1b0ac7c186c9d1e31d432696be6ae336d19d326 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 14:07:16 +0000 Subject: [PATCH 123/358] Install CI libraries with pip3 --- .github/workflows/code.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/code.yaml b/.github/workflows/code.yaml index 3f54de9d..747288a8 100644 --- a/.github/workflows/code.yaml +++ b/.github/workflows/code.yaml @@ -23,7 +23,7 @@ jobs: python-version: "2.7" - name: Install linter - run: pip install flake8 black[python2] + run: pip3 install flake8 black[python2] - name: Lint with flake8 run: | From d0882565f27844eb14febbde0a43e204d2c19aff Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 14:17:39 +0000 Subject: [PATCH 124/358] Use python2 flake8 in dev container --- .devcontainer/Dockerfile | 5 ++++- .vscode/settings.json | 5 +++-- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 123ecb06..66866ade 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -13,7 +13,10 @@ RUN apt-get update \ python3-pip \ && apt-get clean -y && rm -rf /var/lib/apt/lists/* \ && echo . /ccp4-7.1/bin/ccp4.setup-sh | tee ~/.bashrc ~/.zshrc \ - && pip3 install flake8 black[python2] + && curl https://bootstrap.pypa.io/pip/2.7/get-pip.py -o /tmp/get-pip.py \ + && /ccp4-7.1/bin/ccp4-python /tmp/get-pip.py \ + && /ccp4-7.1/bin/ccp4-python -m pip install flake8 \ + && pip3 install black[python2] ENV QT_X11_NO_MITSHM=1 \ XChemExplorer_DIR=/workspace/ diff --git a/.vscode/settings.json b/.vscode/settings.json index ef076b95..546d228e 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,7 +1,8 @@ { "python.defaultInterpreterPath": "/ccp4-7.1/bin/ccp4-python", + "python.linting.enabled": true, "python.linting.flake8Enabled": true, - "python.linting.flake8Path": "/usr/local/bin/flake8", + "python.linting.flake8Path": "/ccp4-7.1/bin/flake8", "python.formatting.provider": "black", - "python.formatting.blackPath": "/usr/local/bin/black" + "python.formatting.blackPath": "/usr/local/bin/black", } \ No newline at end of file From edbdcf0421caf4085865d415a03311a57dbdd87a Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 16:22:41 +0000 Subject: [PATCH 125/358] Restructure as python package --- XChemExplorer.py => xce/XChemExplorer.py | 71 ++++-------------- xce/__init__.py | 0 xce/__main__.py | 5 ++ xce/gui_scripts/__init__.py | 0 .../gui_scripts}/datasets_tab.py | 9 +-- .../gui_scripts}/deposition_tab.py | 9 +-- {gui_scripts => xce/gui_scripts}/layout.py | 15 +--- {gui_scripts => xce/gui_scripts}/maps_tab.py | 6 +- .../gui_scripts}/overview_tab.py | 6 +- .../gui_scripts}/pandda_tab.py | 5 -- .../gui_scripts}/refinement_tab.py | 6 +- .../gui_scripts}/settings_preferences.py | 17 ++--- .../gui_scripts}/settings_tab.py | 5 +- .../gui_scripts}/stylesheet.py | 0 xce/helpers/__init__.py | 0 .../helpers}/assign_stereochemistry.py | 4 +- ...ange_residues_in_ground_and_bound-state.py | 0 .../helpers}/create_png_of_compound.py | 2 - .../helpers}/find_best_fitting_ligand.py | 2 - .../make_ligand_links_after_pandda.py | 2 - .../helpers}/merge_ligand_cif_files.py | 0 .../helpers}/phenix_find_TLS_groups.py | 0 .../helpers}/prepare_for_zenodo_upload.py | 2 - .../helpers}/reset_interesting_datasets.py | 2 - .../reset_occupancy_protein_to_one.py | 0 .../reset_to_last_successful_refinement.py | 0 .../helpers}/resort_ligand_atoms.py | 4 - .../helpers}/select_ground_state_dataset.py | 4 - .../update_data_source_after_refinement.py | 4 - .../update_data_source_for_new_cif_files.py | 7 +- .../update_data_source_for_new_dimple_pdb.py | 9 +-- ...ate_data_source_for_new_dimple_twin_pdb.py | 9 +-- .../helpers}/update_pandda_status_flag.py | 7 +- .../helpers}/update_status_flag.py | 7 +- {icons => xce/icons}/001-ducky.png | Bin .../icons}/002-chinese-panda-bear.png | Bin {icons => xce/icons}/003-internet.png | Bin .../icons}/004-database-configuration.png | Bin {icons => xce/icons}/005-sort-down.png | Bin {icons => xce/icons}/006-sort-up.png | Bin .../icons}/drop-down-round-button.png | Bin {icons => xce/icons}/drop-down.png | Bin {image => xce/image}/IMAGE_NOT_AVAILABLE.png | Bin .../image}/NO_COMPOUND_IMAGE_AVAILABLE.png | Bin .../NO_REFINEMENT_HISTORY_AVAILABLE.png | Bin .../image}/NO_SPIDER_PLOT_AVAILABLE.png | Bin .../image}/drag_and_drop_icb_file.png | Bin {image => xce/image}/html_summary_page.png | Bin {image => xce/image}/new_zenodo_upload.png | Bin {image => xce/image}/run_icm_script.png | Bin {image => xce/image}/zenodo_upload_id.png | Bin {lib => xce/lib}/PuckDB.py | 7 -- {lib => xce/lib}/XChemCoot.py | 12 --- {lib => xce/lib}/XChemCootBuster.py | 12 --- {lib => xce/lib}/XChemCootNew.py | 12 --- {lib => xce/lib}/XChemCootOld.py | 12 --- {lib => xce/lib}/XChemCootReference.py | 12 --- {lib => xce/lib}/XChemCootTwin.py | 12 --- {lib => xce/lib}/XChemDB.py | 5 +- {lib => xce/lib}/XChemDeposit.py | 9 +-- {lib => xce/lib}/XChemDialogs.py | 1 - {lib => xce/lib}/XChemLigand.py | 1 - {lib => xce/lib}/XChemLog.py | 15 +--- {lib => xce/lib}/XChemMain.py | 7 +- {lib => xce/lib}/XChemPANDDA.py | 14 +--- {lib => xce/lib}/XChemPlots.py | 8 -- {lib => xce/lib}/XChemProcess.py | 7 +- {lib => xce/lib}/XChemRefine.py | 13 ---- {lib => xce/lib}/XChemThread.py | 20 +---- {lib => xce/lib}/XChemToolTips.py | 2 - {lib => xce/lib}/XChemUtils.py | 21 +----- xce/lib/__init__.py | 0 {lib => xce/lib}/coot_utils_XChem.py | 2 - {web => xce/web}/XChemWeb.py | 18 ++--- xce/web/__init__.py | 0 {web => xce/web}/dsEvent_sqlite.icm | 0 .../web}/jscss/css/custom-fragment.css | 0 .../web}/jscss/css/jquery.dataTables.min.css | 0 {web => xce/web}/jscss/js/create_view.js | 0 .../web}/jscss/js/jquery-1.12.3.min.js | 0 .../web}/jscss/js/jquery.dataTables.min.js | 0 {web => xce/web}/jscss/js/ngl.js | 0 {web => xce/web}/process_sqlite.py | 4 - 83 files changed, 59 insertions(+), 386 deletions(-) rename XChemExplorer.py => xce/XChemExplorer.py (99%) create mode 100644 xce/__init__.py create mode 100644 xce/__main__.py create mode 100644 xce/gui_scripts/__init__.py rename {gui_scripts => xce/gui_scripts}/datasets_tab.py (98%) rename {gui_scripts => xce/gui_scripts}/deposition_tab.py (98%) rename {gui_scripts => xce/gui_scripts}/layout.py (98%) rename {gui_scripts => xce/gui_scripts}/maps_tab.py (95%) rename {gui_scripts => xce/gui_scripts}/overview_tab.py (92%) rename {gui_scripts => xce/gui_scripts}/pandda_tab.py (98%) rename {gui_scripts => xce/gui_scripts}/refinement_tab.py (88%) rename {gui_scripts => xce/gui_scripts}/settings_preferences.py (98%) rename {gui_scripts => xce/gui_scripts}/settings_tab.py (98%) rename {gui_scripts => xce/gui_scripts}/stylesheet.py (100%) create mode 100644 xce/helpers/__init__.py rename {helpers => xce/helpers}/assign_stereochemistry.py (97%) rename {helpers => xce/helpers}/change_residues_in_ground_and_bound-state.py (100%) rename {helpers => xce/helpers}/create_png_of_compound.py (86%) rename {helpers => xce/helpers}/find_best_fitting_ligand.py (98%) rename {helpers => xce/helpers}/make_ligand_links_after_pandda.py (96%) rename {helpers => xce/helpers}/merge_ligand_cif_files.py (100%) rename {helpers => xce/helpers}/phenix_find_TLS_groups.py (100%) rename {helpers => xce/helpers}/prepare_for_zenodo_upload.py (99%) rename {helpers => xce/helpers}/reset_interesting_datasets.py (98%) rename {helpers => xce/helpers}/reset_occupancy_protein_to_one.py (100%) rename {helpers => xce/helpers}/reset_to_last_successful_refinement.py (100%) rename {helpers => xce/helpers}/resort_ligand_atoms.py (94%) rename {helpers => xce/helpers}/select_ground_state_dataset.py (98%) rename {helpers => xce/helpers}/update_data_source_after_refinement.py (99%) rename {helpers => xce/helpers}/update_data_source_for_new_cif_files.py (90%) rename {helpers => xce/helpers}/update_data_source_for_new_dimple_pdb.py (97%) rename {helpers => xce/helpers}/update_data_source_for_new_dimple_twin_pdb.py (97%) rename {helpers => xce/helpers}/update_pandda_status_flag.py (83%) rename {helpers => xce/helpers}/update_status_flag.py (74%) rename {icons => xce/icons}/001-ducky.png (100%) rename {icons => xce/icons}/002-chinese-panda-bear.png (100%) rename {icons => xce/icons}/003-internet.png (100%) rename {icons => xce/icons}/004-database-configuration.png (100%) rename {icons => xce/icons}/005-sort-down.png (100%) rename {icons => xce/icons}/006-sort-up.png (100%) rename {icons => xce/icons}/drop-down-round-button.png (100%) rename {icons => xce/icons}/drop-down.png (100%) rename {image => xce/image}/IMAGE_NOT_AVAILABLE.png (100%) rename {image => xce/image}/NO_COMPOUND_IMAGE_AVAILABLE.png (100%) rename {image => xce/image}/NO_REFINEMENT_HISTORY_AVAILABLE.png (100%) rename {image => xce/image}/NO_SPIDER_PLOT_AVAILABLE.png (100%) rename {image => xce/image}/drag_and_drop_icb_file.png (100%) rename {image => xce/image}/html_summary_page.png (100%) rename {image => xce/image}/new_zenodo_upload.png (100%) rename {image => xce/image}/run_icm_script.png (100%) rename {image => xce/image}/zenodo_upload_id.png (100%) rename {lib => xce/lib}/PuckDB.py (80%) rename {lib => xce/lib}/XChemCoot.py (99%) rename {lib => xce/lib}/XChemCootBuster.py (99%) rename {lib => xce/lib}/XChemCootNew.py (99%) rename {lib => xce/lib}/XChemCootOld.py (99%) mode change 100755 => 100644 rename {lib => xce/lib}/XChemCootReference.py (99%) rename {lib => xce/lib}/XChemCootTwin.py (99%) rename {lib => xce/lib}/XChemDB.py (99%) rename {lib => xce/lib}/XChemDeposit.py (99%) rename {lib => xce/lib}/XChemDialogs.py (96%) rename {lib => xce/lib}/XChemLigand.py (94%) rename {lib => xce/lib}/XChemLog.py (92%) rename {lib => xce/lib}/XChemMain.py (99%) rename {lib => xce/lib}/XChemPANDDA.py (99%) rename {lib => xce/lib}/XChemPlots.py (90%) rename {lib => xce/lib}/XChemProcess.py (99%) rename {lib => xce/lib}/XChemRefine.py (99%) rename {lib => xce/lib}/XChemThread.py (99%) rename {lib => xce/lib}/XChemToolTips.py (99%) rename {lib => xce/lib}/XChemUtils.py (99%) create mode 100644 xce/lib/__init__.py rename {lib => xce/lib}/coot_utils_XChem.py (99%) rename {web => xce/web}/XChemWeb.py (99%) create mode 100644 xce/web/__init__.py rename {web => xce/web}/dsEvent_sqlite.icm (100%) rename {web => xce/web}/jscss/css/custom-fragment.css (100%) rename {web => xce/web}/jscss/css/jquery.dataTables.min.css (100%) rename {web => xce/web}/jscss/js/create_view.js (100%) rename {web => xce/web}/jscss/js/jquery-1.12.3.min.js (100%) rename {web => xce/web}/jscss/js/jquery.dataTables.min.js (100%) rename {web => xce/web}/jscss/js/ngl.js (100%) rename {web => xce/web}/process_sqlite.py (99%) diff --git a/XChemExplorer.py b/xce/XChemExplorer.py similarity index 99% rename from XChemExplorer.py rename to xce/XChemExplorer.py index 879d121c..459a1662 100755 --- a/XChemExplorer.py +++ b/xce/XChemExplorer.py @@ -1,56 +1,26 @@ -######################################################################################################################## -# DEVELOPER README: # -# This is the main script, where the GUI is initialised from. All of the main layout objects live in their own scripts # -# under ./gui_scripts (i.e. the tab content). The settings and preferences script sets up all of the directory paths # -# and contains dictionaries defining the top menu, push buttons and the tables held in the main tabs. The layout # -# script contains functions for performing simple layout tasks, such as adding a combobox, and contains init. # -# functions for all of the main layout functions. # -# # -# In the future, the functions associated with buttons and frames etc. should be moved into the relevant script, but # -# this is a bit more complicated. For now, they are separated out into sections within this script. The only GUI stuff # -# going on in here is calling the initialisation functions. To change the layout of a tab, edit it in it's own script, # -# and add any new functions in this script, in the relevant section. (If there is one yet) # -# # -# There's still a lot of cleaning up to be done in the future... # -######################################################################################################################## - -# solve gtk startup error -# import gtk - -# gtk.set_interactive(False) - -from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas -import matplotlib.pyplot as plt -import XChemWeb -import XChemDeposit -import XChemProcess -import XChemLog -import XChemPlots -import XChemMain -import XChemToolTips -import XChemPANDDA -import XChemDB -import XChemThread -from XChemUtils import parse -from stylesheet import set_stylesheet -from layout import * -from settings_preferences import * -import base64 +from web import XChemWeb +from lib import XChemDeposit +from lib import XChemProcess +from lib import XChemLog +from lib import XChemPlots +from lib import XChemMain +from lib import XChemToolTips +from lib import XChemPANDDA +from lib import XChemDB +from lib import XChemThread +from lib.XChemUtils import parse +from gui_scripts.stylesheet import set_stylesheet +from gui_scripts.layout import * +from gui_scripts.settings_preferences import * import getpass import glob import math -import multiprocessing import pickle -import subprocess import sys import os import webbrowser from datetime import datetime -from PyQt4 import QtGui, QtCore, QtWebKit - -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "web")) -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) +from PyQt4 import QtGui, QtCore class XChemExplorer(QtGui.QApplication): @@ -7179,14 +7149,3 @@ def quit_xce(self): ) self.update_log.insert("quitting XCE... bye,bye!") QtGui.qApp.quit() - - -if __name__ == "__main__": - app = XChemExplorer(sys.argv[1:]) - - -# "Debugging is twice as hard as writing the code in the first -# place. Therefore, if you write the code as cleverly as -# possible, you are, by definition, not smart enough to debug it." -# -- Brian W. Kernighan -# ^^ Who did this? :P diff --git a/xce/__init__.py b/xce/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/xce/__main__.py b/xce/__main__.py new file mode 100644 index 00000000..280468f0 --- /dev/null +++ b/xce/__main__.py @@ -0,0 +1,5 @@ +from XChemExplorer import XChemExplorer +import sys + +if __name__ == "__main__": + app = XChemExplorer(sys.argv[1:]) diff --git a/xce/gui_scripts/__init__.py b/xce/gui_scripts/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/gui_scripts/datasets_tab.py b/xce/gui_scripts/datasets_tab.py similarity index 98% rename from gui_scripts/datasets_tab.py rename to xce/gui_scripts/datasets_tab.py index 1817cd2a..e6c89f9b 100755 --- a/gui_scripts/datasets_tab.py +++ b/xce/gui_scripts/datasets_tab.py @@ -1,11 +1,6 @@ -import XChemMain +from ..lib import XChemMain import layout -import sys -import os -from PyQt4 import QtGui, QtCore, QtWebKit - -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) +from PyQt4 import QtGui, QtCore class DatasetsTab: diff --git a/gui_scripts/deposition_tab.py b/xce/gui_scripts/deposition_tab.py similarity index 98% rename from gui_scripts/deposition_tab.py rename to xce/gui_scripts/deposition_tab.py index 423cfe49..66c38006 100755 --- a/gui_scripts/deposition_tab.py +++ b/xce/gui_scripts/deposition_tab.py @@ -1,11 +1,6 @@ -import XChemToolTips +from ..lib import XChemToolTips import layout -import sys -import os -from PyQt4 import QtGui, QtCore, QtWebKit - -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) +from PyQt4 import QtGui class DepositionTab: diff --git a/gui_scripts/layout.py b/xce/gui_scripts/layout.py similarity index 98% rename from gui_scripts/layout.py rename to xce/gui_scripts/layout.py index a98d140c..f4ff7b7b 100755 --- a/gui_scripts/layout.py +++ b/xce/gui_scripts/layout.py @@ -5,21 +5,10 @@ from maps_tab import MapsTab from datasets_tab import DatasetsTab from overview_tab import OverviewTab -from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas -import matplotlib.pyplot as plt -import XChemMain -import XChemToolTips from settings_preferences import setup -import multiprocessing -import subprocess -import sys import os -from PyQt4 import QtGui, QtCore, QtWebKit -from functools import partial - -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "web")) -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) +from PyQt4 import QtGui, QtCore +from ..lib import XChemToolTips # noqa: F401 class LayoutObjects: diff --git a/gui_scripts/maps_tab.py b/xce/gui_scripts/maps_tab.py similarity index 95% rename from gui_scripts/maps_tab.py rename to xce/gui_scripts/maps_tab.py index 98e8f32f..c581ffb5 100755 --- a/gui_scripts/maps_tab.py +++ b/xce/gui_scripts/maps_tab.py @@ -1,9 +1,5 @@ import layout -import sys -import os -from PyQt4 import QtGui, QtCore, QtWebKit - -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) +from PyQt4 import QtGui, QtCore class MapsTab: diff --git a/gui_scripts/overview_tab.py b/xce/gui_scripts/overview_tab.py similarity index 92% rename from gui_scripts/overview_tab.py rename to xce/gui_scripts/overview_tab.py index bf6fe00c..ebb97c08 100755 --- a/gui_scripts/overview_tab.py +++ b/xce/gui_scripts/overview_tab.py @@ -1,11 +1,7 @@ from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas import matplotlib.pyplot as plt import layout -import sys -import os -from PyQt4 import QtGui, QtCore, QtWebKit - -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) +from PyQt4 import QtGui class OverviewTab: diff --git a/gui_scripts/pandda_tab.py b/xce/gui_scripts/pandda_tab.py similarity index 98% rename from gui_scripts/pandda_tab.py rename to xce/gui_scripts/pandda_tab.py index 5ddaba1e..914797cc 100755 --- a/gui_scripts/pandda_tab.py +++ b/xce/gui_scripts/pandda_tab.py @@ -1,13 +1,8 @@ -import XChemPANDDA import layout -import sys import os import multiprocessing from PyQt4 import QtGui, QtCore, QtWebKit -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - class PanddaTab: def __init__(self): diff --git a/gui_scripts/refinement_tab.py b/xce/gui_scripts/refinement_tab.py similarity index 88% rename from gui_scripts/refinement_tab.py rename to xce/gui_scripts/refinement_tab.py index 6af3c3b0..5f5d0e16 100755 --- a/gui_scripts/refinement_tab.py +++ b/xce/gui_scripts/refinement_tab.py @@ -1,9 +1,5 @@ import layout -import sys -import os -from PyQt4 import QtGui, QtCore, QtWebKit - -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) +from PyQt4 import QtGui class RefinementTab: diff --git a/gui_scripts/settings_preferences.py b/xce/gui_scripts/settings_preferences.py similarity index 98% rename from gui_scripts/settings_preferences.py rename to xce/gui_scripts/settings_preferences.py index 7d9646fc..c24b61c9 100755 --- a/gui_scripts/settings_preferences.py +++ b/xce/gui_scripts/settings_preferences.py @@ -1,18 +1,11 @@ -import XChemDeposit -import XChemLog -import XChemMain -import XChemDB -import XChemUtils +from ..lib import XChemLog +from ..lib import XChemMain +from ..lib import XChemDB +from ..lib import XChemUtils import os import sys import subprocess -from PyQt4 import QtCore, QtGui -from functools import partial -import webbrowser - -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "web")) +from PyQt4 import QtCore class setup: diff --git a/gui_scripts/settings_tab.py b/xce/gui_scripts/settings_tab.py similarity index 98% rename from gui_scripts/settings_tab.py rename to xce/gui_scripts/settings_tab.py index cf4c4a6b..2634302c 100755 --- a/gui_scripts/settings_tab.py +++ b/xce/gui_scripts/settings_tab.py @@ -1,9 +1,6 @@ import layout -import sys import os -from PyQt4 import QtGui, QtCore, QtWebKit - -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "gui_scripts")) +from PyQt4 import QtGui class SettingsTab: diff --git a/gui_scripts/stylesheet.py b/xce/gui_scripts/stylesheet.py similarity index 100% rename from gui_scripts/stylesheet.py rename to xce/gui_scripts/stylesheet.py diff --git a/xce/helpers/__init__.py b/xce/helpers/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/helpers/assign_stereochemistry.py b/xce/helpers/assign_stereochemistry.py similarity index 97% rename from helpers/assign_stereochemistry.py rename to xce/helpers/assign_stereochemistry.py index 2976a241..5c3c5754 100755 --- a/helpers/assign_stereochemistry.py +++ b/xce/helpers/assign_stereochemistry.py @@ -1,4 +1,4 @@ -import XChemDB +from ..lib import XChemDB import os import sys import glob @@ -6,8 +6,6 @@ # from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - def enumerateStereoChem(compoundID, sampleDir, db, xtal): # first need to recreate the original CIF file with phenix.elbow because we cannot be sure diff --git a/helpers/change_residues_in_ground_and_bound-state.py b/xce/helpers/change_residues_in_ground_and_bound-state.py similarity index 100% rename from helpers/change_residues_in_ground_and_bound-state.py rename to xce/helpers/change_residues_in_ground_and_bound-state.py diff --git a/helpers/create_png_of_compound.py b/xce/helpers/create_png_of_compound.py similarity index 86% rename from helpers/create_png_of_compound.py rename to xce/helpers/create_png_of_compound.py index c63c59ed..43ca0d1e 100755 --- a/helpers/create_png_of_compound.py +++ b/xce/helpers/create_png_of_compound.py @@ -4,8 +4,6 @@ import os import sys -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - if __name__ == "__main__": diff --git a/helpers/find_best_fitting_ligand.py b/xce/helpers/find_best_fitting_ligand.py similarity index 98% rename from helpers/find_best_fitting_ligand.py rename to xce/helpers/find_best_fitting_ligand.py index 16f71224..44faf91f 100755 --- a/helpers/find_best_fitting_ligand.py +++ b/xce/helpers/find_best_fitting_ligand.py @@ -3,8 +3,6 @@ import os import glob -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - def parse_autofit_folder(sampleDir, compoundID): filenames = ["best.pdb", "ligand_fit_1.pdb"] diff --git a/helpers/make_ligand_links_after_pandda.py b/xce/helpers/make_ligand_links_after_pandda.py similarity index 96% rename from helpers/make_ligand_links_after_pandda.py rename to xce/helpers/make_ligand_links_after_pandda.py index f7a345d8..1e44953d 100755 --- a/helpers/make_ligand_links_after_pandda.py +++ b/xce/helpers/make_ligand_links_after_pandda.py @@ -1,5 +1,3 @@ -# last edited: 10/08/2017, 15:00 - import os import glob import sys diff --git a/helpers/merge_ligand_cif_files.py b/xce/helpers/merge_ligand_cif_files.py similarity index 100% rename from helpers/merge_ligand_cif_files.py rename to xce/helpers/merge_ligand_cif_files.py diff --git a/helpers/phenix_find_TLS_groups.py b/xce/helpers/phenix_find_TLS_groups.py similarity index 100% rename from helpers/phenix_find_TLS_groups.py rename to xce/helpers/phenix_find_TLS_groups.py diff --git a/helpers/prepare_for_zenodo_upload.py b/xce/helpers/prepare_for_zenodo_upload.py similarity index 99% rename from helpers/prepare_for_zenodo_upload.py rename to xce/helpers/prepare_for_zenodo_upload.py index 4f3a4e2e..45bc00f0 100755 --- a/helpers/prepare_for_zenodo_upload.py +++ b/xce/helpers/prepare_for_zenodo_upload.py @@ -1,5 +1,3 @@ -# last edited: 13/01/2017, 15:00 - import os import sys import glob diff --git a/helpers/reset_interesting_datasets.py b/xce/helpers/reset_interesting_datasets.py similarity index 98% rename from helpers/reset_interesting_datasets.py rename to xce/helpers/reset_interesting_datasets.py index d1d91f08..83efebd9 100755 --- a/helpers/reset_interesting_datasets.py +++ b/xce/helpers/reset_interesting_datasets.py @@ -1,5 +1,3 @@ -# last edited: 01/03/2017, 15:00 - import os import glob import sys diff --git a/helpers/reset_occupancy_protein_to_one.py b/xce/helpers/reset_occupancy_protein_to_one.py similarity index 100% rename from helpers/reset_occupancy_protein_to_one.py rename to xce/helpers/reset_occupancy_protein_to_one.py diff --git a/helpers/reset_to_last_successful_refinement.py b/xce/helpers/reset_to_last_successful_refinement.py similarity index 100% rename from helpers/reset_to_last_successful_refinement.py rename to xce/helpers/reset_to_last_successful_refinement.py diff --git a/helpers/resort_ligand_atoms.py b/xce/helpers/resort_ligand_atoms.py similarity index 94% rename from helpers/resort_ligand_atoms.py rename to xce/helpers/resort_ligand_atoms.py index 9db616fd..6a3be9e2 100755 --- a/helpers/resort_ligand_atoms.py +++ b/xce/helpers/resort_ligand_atoms.py @@ -1,10 +1,6 @@ -# last edited: 07/06/2017, 17:00 - import os import sys -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - def get_atom_order_of_ensemble_model(ensembleModel): diff --git a/helpers/select_ground_state_dataset.py b/xce/helpers/select_ground_state_dataset.py similarity index 98% rename from helpers/select_ground_state_dataset.py rename to xce/helpers/select_ground_state_dataset.py index 07e8be5b..5eb38f47 100755 --- a/helpers/select_ground_state_dataset.py +++ b/xce/helpers/select_ground_state_dataset.py @@ -1,13 +1,9 @@ -# last edited: 03/08/2017, 15:00 - from XChemUtils import mtztools from XChemUtils import parse import os import sys import glob -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - # - select datasets with highest resolution # - select only those without an event map diff --git a/helpers/update_data_source_after_refinement.py b/xce/helpers/update_data_source_after_refinement.py similarity index 99% rename from helpers/update_data_source_after_refinement.py rename to xce/helpers/update_data_source_after_refinement.py index 7ab5af0d..2c93d436 100755 --- a/helpers/update_data_source_after_refinement.py +++ b/xce/helpers/update_data_source_after_refinement.py @@ -1,5 +1,3 @@ -# last edited: 27/07/2016, 17:00 - import csv import XChemDB from XChemUtils import maptools @@ -11,8 +9,6 @@ import sys import glob -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - def parse_pdb(inital_model_directory, xtal, db_dict): if os.path.isfile(os.path.join(inital_model_directory, xtal, "refine.pdb")): diff --git a/helpers/update_data_source_for_new_cif_files.py b/xce/helpers/update_data_source_for_new_cif_files.py similarity index 90% rename from helpers/update_data_source_for_new_cif_files.py rename to xce/helpers/update_data_source_for_new_cif_files.py index ad936e04..2cd39267 100755 --- a/helpers/update_data_source_for_new_cif_files.py +++ b/xce/helpers/update_data_source_for_new_cif_files.py @@ -1,12 +1,7 @@ -# last edited: 22/11/2016, 15:00 - -import XChemDB -from XChemUtils import parse +from ..lib import XChemDB import os import sys -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - if __name__ == "__main__": db_file = sys.argv[1] diff --git a/helpers/update_data_source_for_new_dimple_pdb.py b/xce/helpers/update_data_source_for_new_dimple_pdb.py similarity index 97% rename from helpers/update_data_source_for_new_dimple_pdb.py rename to xce/helpers/update_data_source_for_new_dimple_pdb.py index ff13f109..aed7325e 100755 --- a/helpers/update_data_source_for_new_dimple_pdb.py +++ b/xce/helpers/update_data_source_for_new_dimple_pdb.py @@ -1,14 +1,9 @@ -# last edited: 15/11/2016, 15:00 - -import XChemDB -from XChemUtils import parse +from ..lib import XChemDB +from ..lib.XChemUtils import parse from iotbx import mtz -import glob import os import sys -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - if __name__ == "__main__": db_file = sys.argv[1] diff --git a/helpers/update_data_source_for_new_dimple_twin_pdb.py b/xce/helpers/update_data_source_for_new_dimple_twin_pdb.py similarity index 97% rename from helpers/update_data_source_for_new_dimple_twin_pdb.py rename to xce/helpers/update_data_source_for_new_dimple_twin_pdb.py index af72677e..040831ca 100755 --- a/helpers/update_data_source_for_new_dimple_twin_pdb.py +++ b/xce/helpers/update_data_source_for_new_dimple_twin_pdb.py @@ -1,14 +1,9 @@ -# last edited: 15/11/2016, 15:00 - -import XChemDB -from XChemUtils import parse +from ..lib import XChemDB +from ..lib.XChemUtils import parse from iotbx import mtz -import glob import os import sys -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - if __name__ == "__main__": db_file = sys.argv[1] diff --git a/helpers/update_pandda_status_flag.py b/xce/helpers/update_pandda_status_flag.py similarity index 83% rename from helpers/update_pandda_status_flag.py rename to xce/helpers/update_pandda_status_flag.py index 07a26d5e..649b5324 100755 --- a/helpers/update_pandda_status_flag.py +++ b/xce/helpers/update_pandda_status_flag.py @@ -1,11 +1,6 @@ -# last edited: 18/11/2016, 15:00 - -import XChemDB -import os +from ..lib import XChemDB import sys -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - def update_data_source(db_file, crystalString, status): db = XChemDB.data_source(db_file) diff --git a/helpers/update_status_flag.py b/xce/helpers/update_status_flag.py similarity index 74% rename from helpers/update_status_flag.py rename to xce/helpers/update_status_flag.py index 1ac3b71c..007b1b6c 100755 --- a/helpers/update_status_flag.py +++ b/xce/helpers/update_status_flag.py @@ -1,11 +1,6 @@ -# last edited: 15/11/2016, 15:00 - -import XChemDB -import os +from ..lib import XChemDB import sys -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - def update_data_source(db_file, xtal, db_column, status): db = XChemDB.data_source(db_file) diff --git a/icons/001-ducky.png b/xce/icons/001-ducky.png similarity index 100% rename from icons/001-ducky.png rename to xce/icons/001-ducky.png diff --git a/icons/002-chinese-panda-bear.png b/xce/icons/002-chinese-panda-bear.png similarity index 100% rename from icons/002-chinese-panda-bear.png rename to xce/icons/002-chinese-panda-bear.png diff --git a/icons/003-internet.png b/xce/icons/003-internet.png similarity index 100% rename from icons/003-internet.png rename to xce/icons/003-internet.png diff --git a/icons/004-database-configuration.png b/xce/icons/004-database-configuration.png similarity index 100% rename from icons/004-database-configuration.png rename to xce/icons/004-database-configuration.png diff --git a/icons/005-sort-down.png b/xce/icons/005-sort-down.png similarity index 100% rename from icons/005-sort-down.png rename to xce/icons/005-sort-down.png diff --git a/icons/006-sort-up.png b/xce/icons/006-sort-up.png similarity index 100% rename from icons/006-sort-up.png rename to xce/icons/006-sort-up.png diff --git a/icons/drop-down-round-button.png b/xce/icons/drop-down-round-button.png similarity index 100% rename from icons/drop-down-round-button.png rename to xce/icons/drop-down-round-button.png diff --git a/icons/drop-down.png b/xce/icons/drop-down.png similarity index 100% rename from icons/drop-down.png rename to xce/icons/drop-down.png diff --git a/image/IMAGE_NOT_AVAILABLE.png b/xce/image/IMAGE_NOT_AVAILABLE.png similarity index 100% rename from image/IMAGE_NOT_AVAILABLE.png rename to xce/image/IMAGE_NOT_AVAILABLE.png diff --git a/image/NO_COMPOUND_IMAGE_AVAILABLE.png b/xce/image/NO_COMPOUND_IMAGE_AVAILABLE.png similarity index 100% rename from image/NO_COMPOUND_IMAGE_AVAILABLE.png rename to xce/image/NO_COMPOUND_IMAGE_AVAILABLE.png diff --git a/image/NO_REFINEMENT_HISTORY_AVAILABLE.png b/xce/image/NO_REFINEMENT_HISTORY_AVAILABLE.png similarity index 100% rename from image/NO_REFINEMENT_HISTORY_AVAILABLE.png rename to xce/image/NO_REFINEMENT_HISTORY_AVAILABLE.png diff --git a/image/NO_SPIDER_PLOT_AVAILABLE.png b/xce/image/NO_SPIDER_PLOT_AVAILABLE.png similarity index 100% rename from image/NO_SPIDER_PLOT_AVAILABLE.png rename to xce/image/NO_SPIDER_PLOT_AVAILABLE.png diff --git a/image/drag_and_drop_icb_file.png b/xce/image/drag_and_drop_icb_file.png similarity index 100% rename from image/drag_and_drop_icb_file.png rename to xce/image/drag_and_drop_icb_file.png diff --git a/image/html_summary_page.png b/xce/image/html_summary_page.png similarity index 100% rename from image/html_summary_page.png rename to xce/image/html_summary_page.png diff --git a/image/new_zenodo_upload.png b/xce/image/new_zenodo_upload.png similarity index 100% rename from image/new_zenodo_upload.png rename to xce/image/new_zenodo_upload.png diff --git a/image/run_icm_script.png b/xce/image/run_icm_script.png similarity index 100% rename from image/run_icm_script.png rename to xce/image/run_icm_script.png diff --git a/image/zenodo_upload_id.png b/xce/image/zenodo_upload_id.png similarity index 100% rename from image/zenodo_upload_id.png rename to xce/image/zenodo_upload_id.png diff --git a/lib/PuckDB.py b/xce/lib/PuckDB.py similarity index 80% rename from lib/PuckDB.py rename to xce/lib/PuckDB.py index 5c35ea61..a997f921 100755 --- a/lib/PuckDB.py +++ b/xce/lib/PuckDB.py @@ -1,10 +1,3 @@ -import sqlite3 -import os -import sys - -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") - - class puck_db(object): def __init__(self, data_base): diff --git a/lib/XChemCoot.py b/xce/lib/XChemCoot.py similarity index 99% rename from lib/XChemCoot.py rename to xce/lib/XChemCoot.py index 8acc92e0..74543f39 100755 --- a/lib/XChemCoot.py +++ b/xce/lib/XChemCoot.py @@ -1,8 +1,4 @@ -# last edited: 08/08/2017 - 15:00 - -import pango import gtk -import pygtk import coot_utils_XChem import coot import XChemLog @@ -10,20 +6,12 @@ import XChemRefine import XChemDB import gobject -import sys import os import pickle import glob from matplotlib.figure import Figure -# from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas - -# XCE libraries -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") - -# libraries from COOT - # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. # modified file is now in $XChemExplorer_DIR/lib diff --git a/lib/XChemCootBuster.py b/xce/lib/XChemCootBuster.py similarity index 99% rename from lib/XChemCootBuster.py rename to xce/lib/XChemCootBuster.py index 6298aecb..0d93c7d4 100755 --- a/lib/XChemCootBuster.py +++ b/xce/lib/XChemCootBuster.py @@ -1,8 +1,4 @@ -# last edited: 08/08/2017 - 15:00 - -import pango import gtk -import pygtk import coot_utils_XChem import coot import XChemLog @@ -10,7 +6,6 @@ import XChemRefine import XChemDB import gobject -import sys import os import pickle import glob @@ -20,13 +15,6 @@ from matplotlib.figure import Figure -# from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas - -# XCE libraries -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") - -# libraries from COOT - # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. # modified file is now in $XChemExplorer_DIR/lib diff --git a/lib/XChemCootNew.py b/xce/lib/XChemCootNew.py similarity index 99% rename from lib/XChemCootNew.py rename to xce/lib/XChemCootNew.py index 652b688d..d89b58cb 100755 --- a/lib/XChemCootNew.py +++ b/xce/lib/XChemCootNew.py @@ -1,8 +1,4 @@ -# last edited: 08/08/2017 - 15:00 - -import pango import gtk -import pygtk import coot_utils_XChem import coot import XChemLog @@ -10,7 +6,6 @@ import XChemRefine import XChemDB import gobject -import sys import os import pickle import glob @@ -20,13 +15,6 @@ from matplotlib.figure import Figure -# from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas - -# XCE libraries -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") - -# libraries from COOT - # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. # modified file is now in $XChemExplorer_DIR/lib diff --git a/lib/XChemCootOld.py b/xce/lib/XChemCootOld.py old mode 100755 new mode 100644 similarity index 99% rename from lib/XChemCootOld.py rename to xce/lib/XChemCootOld.py index 8deb0644..1e0b43e5 --- a/lib/XChemCootOld.py +++ b/xce/lib/XChemCootOld.py @@ -1,27 +1,15 @@ -# last edited: 21/07/2017 - 15:00 - -import pango import gtk -import pygtk import coot_utils_XChem import coot import XChemUtils import XChemRefine import XChemDB import gobject -import sys import os import pickle from matplotlib.figure import Figure -# from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas - -# XCE libraries -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") - -# libraries from COOT - # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. # modified file is now in $XChemExplorer_DIR/lib diff --git a/lib/XChemCootReference.py b/xce/lib/XChemCootReference.py similarity index 99% rename from lib/XChemCootReference.py rename to xce/lib/XChemCootReference.py index da710406..381af2d8 100755 --- a/lib/XChemCootReference.py +++ b/xce/lib/XChemCootReference.py @@ -1,30 +1,18 @@ -# last edited: 03/08/2017 - 15:00 - import coot_utils_XChem import coot import XChemLog import XChemUtils import XChemRefine -import sys import glob import os import pickle import time import gtk -# import threading -# import gobject -# gtk.gdk.threads_init() from matplotlib.figure import Figure from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas -# XCE libraries -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") - -# libraries from COOT -# import pygtk, gtk, pango - # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. # modified file is now in $XChemExplorer_DIR/lib diff --git a/lib/XChemCootTwin.py b/xce/lib/XChemCootTwin.py similarity index 99% rename from lib/XChemCootTwin.py rename to xce/lib/XChemCootTwin.py index 691b336c..bf392420 100755 --- a/lib/XChemCootTwin.py +++ b/xce/lib/XChemCootTwin.py @@ -1,8 +1,4 @@ -# last edited: 08/08/2017 - 15:00 - -import pango import gtk -import pygtk import coot_utils_XChem import coot import XChemLog @@ -10,20 +6,12 @@ import XChemRefine import XChemDB import gobject -import sys import os import pickle import glob from matplotlib.figure import Figure -# from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas - -# XCE libraries -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") - -# libraries from COOT - # had to adapt the original coot_utils.py file # otherwise unable to import the original file without complaints about missing modules etc. # modified file is now in $XChemExplorer_DIR/lib diff --git a/lib/XChemDB.py b/xce/lib/XChemDB.py similarity index 99% rename from lib/XChemDB.py rename to xce/lib/XChemDB.py index f68da6e0..c081f05d 100755 --- a/lib/XChemDB.py +++ b/xce/lib/XChemDB.py @@ -1,15 +1,12 @@ -# last edited: 21/07/2017, 15:00 - import XChemLog import sqlite3 import os -import sys import glob import csv from datetime import datetime import getpass -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") + # from XChemUtils import parse diff --git a/lib/XChemDeposit.py b/xce/lib/XChemDeposit.py similarity index 99% rename from lib/XChemDeposit.py rename to xce/lib/XChemDeposit.py index 3bcce791..5c48d05c 100755 --- a/lib/XChemDeposit.py +++ b/xce/lib/XChemDeposit.py @@ -1,11 +1,8 @@ -# last edited: 16/05/2017, 15:00 - from XChemUtils import parse from XChemUtils import smilestools from XChemUtils import mtztools from XChemUtils import pdbtools import XChemMain -import XChemToolTips import XChemDB import XChemLog import sys @@ -13,11 +10,7 @@ import os import glob -from PyQt4 import QtGui, QtCore, QtWebKit - -from lxml import etree - -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") +from PyQt4 import QtCore def create_SF_mmcif(outDir, mtzList): diff --git a/lib/XChemDialogs.py b/xce/lib/XChemDialogs.py similarity index 96% rename from lib/XChemDialogs.py rename to xce/lib/XChemDialogs.py index 5986a356..fdf58fe1 100755 --- a/lib/XChemDialogs.py +++ b/xce/lib/XChemDialogs.py @@ -1,4 +1,3 @@ -import sys from PyQt4 import QtGui, QtCore import XChemDB diff --git a/lib/XChemLigand.py b/xce/lib/XChemLigand.py similarity index 94% rename from lib/XChemLigand.py rename to xce/lib/XChemLigand.py index 9432f2c8..b51aacf6 100755 --- a/lib/XChemLigand.py +++ b/xce/lib/XChemLigand.py @@ -1,4 +1,3 @@ -import rdkit from rdkit import Chem from rdkit.Chem import AllChem diff --git a/lib/XChemLog.py b/xce/lib/XChemLog.py similarity index 92% rename from lib/XChemLog.py rename to xce/lib/XChemLog.py index fa370117..4ec1b2f5 100755 --- a/lib/XChemLog.py +++ b/xce/lib/XChemLog.py @@ -1,13 +1,6 @@ -# last edited: 09/02/2017, 15:00 - - import os -import glob -import sys from datetime import datetime -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - class startLog: def __init__(self, logfile): @@ -124,20 +117,20 @@ def __init__(self, logfile): def insert(self, message): present_time = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S.%f")[:-4] - print(str(present_time) + " ==> XCE: " + message, file=self.logfile) + self.logfile.write(str(present_time) + " ==> XCE: " + message) print("==> XCE: " + message) def warning(self, message): present_time = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S.%f")[:-4] - print(str(present_time) + " ==> XCE: WARNING! " + message, file=self.logfile) + self.logfile.write(str(present_time) + " ==> XCE: WARNING! " + message) print("==> XCE: WARNING! " + message) def error(self, message): present_time = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S.%f")[:-4] - print(str(present_time) + " ==> XCE: ERROR!!! " + message, file=self.logfile) + self.logfile.write(str(present_time) + " ==> XCE: ERROR!!! " + message) print("==> XCE: ERROR!!! " + message) def hint(self, message): present_time = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S.%f")[:-4] - print(str(present_time) + " ==> XCE: HINT -> " + message, file=self.logfile) + self.logfile.write(str(present_time) + " ==> XCE: HINT -> " + message) print("==> XCE: HINT -> " + message) diff --git a/lib/XChemMain.py b/xce/lib/XChemMain.py similarity index 99% rename from lib/XChemMain.py rename to xce/lib/XChemMain.py index 2e6c9d28..8c169ecf 100755 --- a/lib/XChemMain.py +++ b/xce/lib/XChemMain.py @@ -1,17 +1,12 @@ -# last edited: 15/05/2017, 15:00 - import XChemLog import XChemDB import os import glob -import sys import subprocess import getpass import gzip from datetime import datetime -from PyQt4 import QtGui, QtCore - -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) +from PyQt4 import QtCore def space_group_list(): diff --git a/lib/XChemPANDDA.py b/xce/lib/XChemPANDDA.py similarity index 99% rename from lib/XChemPANDDA.py rename to xce/lib/XChemPANDDA.py index feca2f49..be797d59 100755 --- a/lib/XChemPANDDA.py +++ b/xce/lib/XChemPANDDA.py @@ -1,11 +1,8 @@ -# last edited: 10/08/2017, 10:25 - import os -import sys import glob import subprocess from datetime import datetime -from PyQt4 import QtGui, QtCore +from PyQt4 import QtCore import math # from XChemUtils import mtztools @@ -2794,15 +2791,6 @@ def __init__(self, project_directory, xce_logfile, external_software): self.Logfile = XChemLog.updateLog(xce_logfile) self.project_directory = project_directory self.external_software = external_software - try: - import gemmi - - self.Logfile.insert("found gemmi library in ccp4-python") - except ImportError: - self.external_software["gemmi"] = False - self.Logfile.warning( - "cannot import gemmi; will use phenix.map_to_structure_factors instead" - ) def run(self): self.Logfile.insert("======== checking ligand CC in event maps ========") diff --git a/lib/XChemPlots.py b/xce/lib/XChemPlots.py similarity index 90% rename from lib/XChemPlots.py rename to xce/lib/XChemPlots.py index 46f2e568..5ead7f82 100755 --- a/lib/XChemPlots.py +++ b/xce/lib/XChemPlots.py @@ -1,13 +1,5 @@ -# last edited: 29/07/2016, 15:00 - import numpy as np -from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas -import matplotlib.pyplot as plt import XChemMain -import os -import sys - -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) class summary_plot(object): diff --git a/lib/XChemProcess.py b/xce/lib/XChemProcess.py similarity index 99% rename from lib/XChemProcess.py rename to xce/lib/XChemProcess.py index 67c32c8a..a0d1c327 100755 --- a/lib/XChemProcess.py +++ b/xce/lib/XChemProcess.py @@ -1,13 +1,8 @@ -# last edited: 24/03/2017, 15:00 - import XChemDB import XChemLog import os -import sys import glob -from PyQt4 import QtGui, QtCore - -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) +from PyQt4 import QtCore class run_xia2(QtCore.QThread): diff --git a/lib/XChemRefine.py b/xce/lib/XChemRefine.py similarity index 99% rename from lib/XChemRefine.py rename to xce/lib/XChemRefine.py index 08330e09..a3778914 100755 --- a/lib/XChemRefine.py +++ b/xce/lib/XChemRefine.py @@ -1,28 +1,15 @@ -# last edited: 08/08/2017, 15:00 - -import pango import gtk from XChemUtils import mtztools_gemmi from XChemUtils import pdbtools import XChemLog from datetime import datetime -import time -import fileinput import getpass -import sys import glob import os import pygtk pygtk.require("2.0") -# sys.path.append(os.path.join(os.getenv('CCP4'),'lib/python2.7/site-packages')) -# import coot -# sys.path.append('/usr/local/coot/SoakProc/lib') -# import coot_utils_XChem - -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") - def GetSerial(ProjectPath, xtalID): # check if there were already previous refinements diff --git a/lib/XChemThread.py b/xce/lib/XChemThread.py similarity index 99% rename from lib/XChemThread.py rename to xce/lib/XChemThread.py index 4f7e3f0a..0382b709 100755 --- a/lib/XChemThread.py +++ b/xce/lib/XChemThread.py @@ -1,40 +1,22 @@ -# last edited: 31/07/2017, 10:30 - -import iotbx.mtz import XChemMain import XChemLog import XChemDB from XChemUtils import misc -from XChemUtils import reference from XChemUtils import helpers from XChemUtils import pdbtools from XChemUtils import mtztools -from XChemUtils import queue from XChemUtils import parse -from XChemUtils import process import os -import sys import glob from datetime import datetime -from PyQt4 import QtGui, QtCore +from PyQt4 import QtCore -import time -import pickle import pickle -import base64 import math -import subprocess -from datetime import datetime -import time -import getpass import csv -import tarfile -from iotbx import mtz from iotbx.reflection_file_reader import any_reflection_file -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") - class synchronise_db_and_filesystem(QtCore.QThread): diff --git a/lib/XChemToolTips.py b/xce/lib/XChemToolTips.py similarity index 99% rename from lib/XChemToolTips.py rename to xce/lib/XChemToolTips.py index c31f7318..be6763ee 100755 --- a/lib/XChemToolTips.py +++ b/xce/lib/XChemToolTips.py @@ -1,5 +1,3 @@ -# last edited: 03/08/2017, 17:00 - import os import getpass diff --git a/lib/XChemUtils.py b/xce/lib/XChemUtils.py similarity index 99% rename from lib/XChemUtils.py rename to xce/lib/XChemUtils.py index 7ea28363..553e9634 100755 --- a/lib/XChemUtils.py +++ b/xce/lib/XChemUtils.py @@ -1,35 +1,26 @@ import XChemLog import XChemDB -import sys import os import glob import math import subprocess import getpass import shutil -import math -import platform -import tarfile import json import time import gzip import bz2 -from datetime import datetime import gemmi from rdkit import Chem -from rdkit.Chem import AllChem -from rdkit.Chem import Draw import iotbx.pdb from iotbx.reflection_file_reader import any_reflection_file from iotbx import mtz -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") - def open_decompress_file(filename, mode="rb"): """Open file for reading, decompressing silently if necessary.""" @@ -219,17 +210,7 @@ def Run(self, Cmds): class helpers: def __init__(self): - try: - # this sys path append is only meaningful if non-CCP4 python is used to launch XCE - # sys.path.append(os.path.join(os.getenv('CCP4'),'lib','python2.7','site-packages')) - from rdkit import Chem - from rdkit.Chem import AllChem - from rdkit.Chem import Draw - - self.pil_rdkit_present = True - except ImportError: - self.pil_rdkit_present = False - pass + self.pil_rdkit_present = True def pil_rdkit_exist(self): return self.pil_rdkit_present diff --git a/xce/lib/__init__.py b/xce/lib/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/lib/coot_utils_XChem.py b/xce/lib/coot_utils_XChem.py similarity index 99% rename from lib/coot_utils_XChem.py rename to xce/lib/coot_utils_XChem.py index b3319889..cd842518 100755 --- a/lib/coot_utils_XChem.py +++ b/xce/lib/coot_utils_XChem.py @@ -28,8 +28,6 @@ import sys import numbers -sys.path.append("/usr/local/coot/current/lib/python2.7/site-packages") - # 3D annotations - a bit of a hack currently global annotations diff --git a/web/XChemWeb.py b/xce/web/XChemWeb.py similarity index 99% rename from web/XChemWeb.py rename to xce/web/XChemWeb.py index 5b74bb90..91280d10 100755 --- a/web/XChemWeb.py +++ b/xce/web/XChemWeb.py @@ -1,16 +1,8 @@ -# last edited: 05/07/2017, 15:00 - -import XChemUtils -from XChemUtils import mtztools -from XChemUtils import pdbtools -import XChemMain -import XChemDB -import XChemLog +from ..lib import XChemUtils +from ..lib import XChemMain +from ..lib import XChemDB +from ..lib import XChemLog import os -import sys -import glob - -sys.path.append(os.getenv("XChemExplorer_DIR") + "/lib") class export_to_html: @@ -306,7 +298,7 @@ def copy_pdb(self, xtal): if os.path.isfile( os.path.join(self.projectDir, xtal, "refine.split.bound-state.pdb") ): - self.pdb = pdbtools( + self.pdb = XChemUtils.pdbtools( os.path.join(self.projectDir, xtal, "refine.split.bound-state.pdb") ) self.Logfile.insert( diff --git a/xce/web/__init__.py b/xce/web/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/web/dsEvent_sqlite.icm b/xce/web/dsEvent_sqlite.icm similarity index 100% rename from web/dsEvent_sqlite.icm rename to xce/web/dsEvent_sqlite.icm diff --git a/web/jscss/css/custom-fragment.css b/xce/web/jscss/css/custom-fragment.css similarity index 100% rename from web/jscss/css/custom-fragment.css rename to xce/web/jscss/css/custom-fragment.css diff --git a/web/jscss/css/jquery.dataTables.min.css b/xce/web/jscss/css/jquery.dataTables.min.css similarity index 100% rename from web/jscss/css/jquery.dataTables.min.css rename to xce/web/jscss/css/jquery.dataTables.min.css diff --git a/web/jscss/js/create_view.js b/xce/web/jscss/js/create_view.js similarity index 100% rename from web/jscss/js/create_view.js rename to xce/web/jscss/js/create_view.js diff --git a/web/jscss/js/jquery-1.12.3.min.js b/xce/web/jscss/js/jquery-1.12.3.min.js similarity index 100% rename from web/jscss/js/jquery-1.12.3.min.js rename to xce/web/jscss/js/jquery-1.12.3.min.js diff --git a/web/jscss/js/jquery.dataTables.min.js b/xce/web/jscss/js/jquery.dataTables.min.js similarity index 100% rename from web/jscss/js/jquery.dataTables.min.js rename to xce/web/jscss/js/jquery.dataTables.min.js diff --git a/web/jscss/js/ngl.js b/xce/web/jscss/js/ngl.js similarity index 100% rename from web/jscss/js/ngl.js rename to xce/web/jscss/js/ngl.js diff --git a/web/process_sqlite.py b/xce/web/process_sqlite.py similarity index 99% rename from web/process_sqlite.py rename to xce/web/process_sqlite.py index 02e45f15..73c45507 100755 --- a/web/process_sqlite.py +++ b/xce/web/process_sqlite.py @@ -1,5 +1,3 @@ -# last edited: 05/07/2017, 15:00 - #!/usr/local/anaconda/sgc_default/envs/sgc_default/bin/python # Author: Brian Marsden @@ -17,8 +15,6 @@ import zipfile import glob -sys.path.append(os.path.join(os.getenv("XChemExplorer_DIR"), "lib")) - targetID = "" panddadir = "" From 2f287596a03fe4909eddcae72e213e1fba6507a8 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 16:22:51 +0000 Subject: [PATCH 126/358] Set dev container python path --- .vscode/settings.json | 1 + 1 file changed, 1 insertion(+) diff --git a/.vscode/settings.json b/.vscode/settings.json index 546d228e..29bffb55 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,4 +1,5 @@ { + "python.pythonPath": "/ccp4-7.1/bin/ccp4-python", "python.defaultInterpreterPath": "/ccp4-7.1/bin/ccp4-python", "python.linting.enabled": true, "python.linting.flake8Enabled": true, From e35129d8ea931803f577a752269269943900e83c Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 16:28:46 +0000 Subject: [PATCH 127/358] Remove PuckDB --- xce/lib/PuckDB.py | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100755 xce/lib/PuckDB.py diff --git a/xce/lib/PuckDB.py b/xce/lib/PuckDB.py deleted file mode 100755 index a997f921..00000000 --- a/xce/lib/PuckDB.py +++ /dev/null @@ -1,19 +0,0 @@ -class puck_db(object): - def __init__(self, data_base): - - self.data_base = data_base - - def get_all_pucks_from_DB(self): - print("hello") - - def insert_mounted_crystals(self): - print("hello") - - def kill_mounted_cryatsl(self): - print("hello") - - def change_puck_location(self): - print("hello") - - def execute_sqlite(self): - print("hello") From 0c20f0bb94f27189ead7761f9c5a5e3d84296376 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 16:30:35 +0000 Subject: [PATCH 128/358] Use python2 flake8 for CI linting --- .github/workflows/code.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/code.yaml b/.github/workflows/code.yaml index 747288a8..68bfcdba 100644 --- a/.github/workflows/code.yaml +++ b/.github/workflows/code.yaml @@ -22,8 +22,10 @@ jobs: with: python-version: "2.7" - - name: Install linter - run: pip3 install flake8 black[python2] + - name: Install linters + run: | + pip install flake8 + pip3 install black[python2] - name: Lint with flake8 run: | From e8f2214ecdf1a6ffb507c5beec1c0dd851cc9963 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 27 Oct 2022 17:09:56 +0000 Subject: [PATCH 129/358] Update dockerfile entrypoint --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 59bfa419..294dfa51 100755 --- a/Dockerfile +++ b/Dockerfile @@ -20,4 +20,4 @@ RUN apt-get update \ ENV QT_X11_NO_MITSHM=1 \ XChemExplorer_DIR=${XCE_DIR} -ENTRYPOINT /ccp4-7.1/bin/ccp4-python /xce/XChemExplorer.py +ENTRYPOINT /ccp4-7.1/bin/ccp4-python -m xce From 07ed3b5b4dc8c65f111c619dde1ebf07f8274feb Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 13:25:49 +0000 Subject: [PATCH 130/358] Clean up XChemExplorer --- xce/XChemExplorer.py | 730 +++++++++---------------------------------- 1 file changed, 153 insertions(+), 577 deletions(-) diff --git a/xce/XChemExplorer.py b/xce/XChemExplorer.py index 459a1662..30a10ec9 100755 --- a/xce/XChemExplorer.py +++ b/xce/XChemExplorer.py @@ -10,8 +10,7 @@ from lib import XChemThread from lib.XChemUtils import parse from gui_scripts.stylesheet import set_stylesheet -from gui_scripts.layout import * -from gui_scripts.settings_preferences import * +from gui_scripts.layout import setup, LayoutFuncs, LayoutObjects import getpass import glob import math @@ -127,11 +126,11 @@ def create_new_data_source(self): self.data_source_set = True self.datasource_menu_reload_samples() - #################################################################################################################### - # # - # DATASETS TAB # - # # - #################################################################################################################### + #################################################################################### + # # + # DATASETS TAB # + # # + #################################################################################### def continously_check_for_new_data_collection(self, state): self.timer_to_check_for_new_data_collection.timeout.connect( @@ -186,8 +185,6 @@ def search_for_datasets(self): self.work_thread.start() - # self.work_thread = self.update_datasets_reprocess_table(self.diffraction_data_directory) - def translate_datasetID_to_sampleID(self): translate = QtGui.QMessageBox() translateLayout = translate.layout() @@ -218,9 +215,6 @@ def translate_datasetID_to_sampleID(self): dataset_id = str( self.datasets_reprocess_table.item(row, 0).text() ) - sample_id = str( - self.datasets_reprocess_table.item(row, 1).text() - ) if dataset_id in trans_dict: cell_text = QtGui.QTableWidgetItem() cell_text.setText(trans_dict[dataset_id]) @@ -273,7 +267,9 @@ def check_for_new_autoprocessing_or_rescore(self, rescore_only): # first pop up a warning message as this will overwrite all user selections msgBox = QtGui.QMessageBox() msgBox.setText( - "*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?" + "*** WARNING ***\n" + "This will overwrite all your manual selections!\n" + "Do you want to continue?" ) msgBox.addButton(QtGui.QPushButton("Yes"), QtGui.QMessageBox.YesRole) msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.RejectRole) @@ -291,24 +287,15 @@ def check_for_new_autoprocessing_or_rescore(self, rescore_only): warning = ( "*** WARNING ***\n" "Please select a target or\n" - 'select "=== project directory ===" if you want to read reprocessed results\n' - "In case target list is empty, make sure that you have selected the actual\n" + 'select "=== project directory ==="' + " if you want to read reprocessed results\n" + "In case target list is empty," + " make sure that you have selected the actual\n" "data collection visit (e.g. /dls/i04-1/data/2018/lb18145-70)" ) msgBox.setText(warning) start_thread = False - # msgBox.setText(warning) - # msgBox.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) - # msgBox.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) - # reply = msgBox.exec_(); - # if reply == 0: - # start_thread = True - # else: - # start_thread = False - # else: - # start_thread = True - if start_thread: self.work_thread = XChemThread.read_autoprocessing_results_from_disc( self.visit_list, @@ -345,7 +332,7 @@ def check_for_new_autoprocessing_or_rescore(self, rescore_only): ) self.work_thread.start() - ################################################################################################################# + #################################################################################### # # # @@ -398,12 +385,6 @@ def check_for_new_autoprocessing_results(self): elif self.target == "=== project directory ===": processedDir = self.initial_model_directory start_thread = True - # elif self.read_agamemnon.isChecked(): - # tmp = '/'.join(self.beamline_directory.split('/')[:6]) - # processedDir = tmp[:tmp.rfind('-')] - ## processedDir = os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*/processed/agamemnon/'+self.target) - ## processedDir = os.path.join(self.beamline_directory[:self.beamline_directory.rfind('-') + 1] + '*/processed/*/'+self.target) - # start_thread = True else: processedDir = os.path.join( self.beamline_directory, "processed", self.target @@ -411,7 +392,6 @@ def check_for_new_autoprocessing_results(self): start_thread = True if start_thread: - # processedDir=os.path.join(self.beamline_directory,'processed',self.target) self.work_thread = ( XChemThread.read_write_autoprocessing_results_from_to_disc( processedDir, @@ -449,7 +429,9 @@ def select_best_autoprocessing_result(self): # first pop up a warning message as this will overwrite all user selections msgBox = QtGui.QMessageBox() msgBox.setText( - "*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?" + "*** WARNING ***\n" + "This will overwrite all your manual selections!\n" + "Do you want to continue?" ) msgBox.addButton(QtGui.QPushButton("Yes"), QtGui.QMessageBox.YesRole) msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.RejectRole) @@ -521,13 +503,13 @@ def select_best_autoprocessing_result(self): self.work_thread.start() # < end - ################################################################################################################### + #################################################################################### - #################################################################################################################### - # # - # MAPS TAB # - # # - #################################################################################################################### + #################################################################################### + # # + # MAPS TAB # + # # + #################################################################################### def set_new_reference_if_applicable(self): print("hallo") @@ -542,7 +524,8 @@ def set_new_reference_if_applicable(self): break if ucVol_ref == 0.0: self.update_log.insert( - "cannot set reference file since unit cell volume of reference pdb is 0!" + "cannot set reference file" + " since unit cell volume of reference pdb is 0!" ) return @@ -585,11 +568,11 @@ def on_context_menu_initial_model(self, point): # show context menu self.popMenu_for_maps_table.exec_(self.sender().mapToGlobal(point)) - #################################################################################################################### - # # - # PANDDA TAB # - # # - #################################################################################################################### + #################################################################################### + # # + # PANDDA TAB # + # # + #################################################################################### def select_pandda_input_template(self): mtzin = "" filepath_temp = QtGui.QFileDialog.getOpenFileNameAndFilter( @@ -622,14 +605,6 @@ def select_pandda_input_template(self): ) except TypeError: self.update_log.error("directory selection invalid") - # if len(filepath.split('/')) - len(self.initial_model_directory.split('/')) == 2: - # self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*')) - # elif len(filepath.split('/')) - len(self.initial_model_directory.split('/')) > 2: - # subdir = os.path.join( - # *filepath.split('/')[len(self.initial_model_directory.split('/')) + 1:len(filepath.split('/')) - 1]) - # self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*', subdir)) - # else: - # pass self.pandda_pdb_style_entry.setText(pdbin) self.pandda_mtz_style_entry.setText(mtzin) @@ -644,11 +619,11 @@ def on_context_menu_pandda(self, point): # show context menu self.popMenu_for_pandda_table.exec_(self.sender().mapToGlobal(point)) - #################################################################################################################### - # # - # DEPO TAB # - # # - #################################################################################################################### + #################################################################################### + # # + # DEPO TAB # + # # + #################################################################################### def export_to_html(self): XChemWeb.export_to_html( self.html_export_directory, @@ -673,26 +648,6 @@ def export_to_html_deposition_ready(self): self.xce_logfile, ).prepare("5") - # self.update_log.insert('exporting contents of SQLite database into ' + self.html_export_directory) - # os.system( - # 'ccp4-python ' + os.getenv('XChemExplorer_DIR') + '/web/process_sqlite.py -t Summary -s ' + os.path.join( - # self.database_directory, self.data_source_file) + ' -d ' + self.html_export_directory) - # XChemWeb.create_ICM_input_file(self.html_export_directory, - # os.path.join(self.database_directory, self.data_source_file)) - # self.update_log.insert('open ICMpro:') - # self.update_log.insert('/dls/science/groups/i04-1/software/icm-3.8-5/icm64 -g') - # self.update_log.insert('open file browser and navigate to ' + self.html_export_directory) - # self.update_log.insert('drag and drop dsEvent_sqlite.icm into the main window') - # self.update_log.insert('the script will appear in the Workspace Panel') - # self.update_log.insert('right click on the script and select RUN') - # self.update_log.insert('be patient, this may take a while, depending on the number of events') - # self.status_bar.showMessage('please check terminal window for further information') - - # def select_ground_state_pdb(self): - # p = QtGui.QFileDialog.getOpenFileNameAndFilter(self.window, 'Select File', os.getcwd(),'*.pdb') - # pdb = str(tuple(p)[0]) - # self.ground_state_pdb_button_label.setText(pdb) - def select_ground_state_mtz(self): m = QtGui.QFileDialog.getOpenFileNameAndFilter( self.window, "Select File", os.getcwd(), "*.mtz" @@ -702,7 +657,7 @@ def select_ground_state_mtz(self): def add_ground_state_db(self): pdb, mtz = self.auto_select_ground_state_reference_PDB() - if pdb != None: + if pdb is not None: db_dict = { "DimplePANDDApath": self.panddas_directory, "PDB_file": pdb, @@ -738,7 +693,8 @@ def auto_select_ground_state_reference_PDB(self): ) except ValueError: self.update_log.error( - "%s: cannot read Rfree or Resolution from PDB header; skipping..." + "%s: cannot read Rfree or Resolution from PDB header;" + " skipping..." ) pass self.update_log.insert( @@ -820,11 +776,11 @@ def update_html_for_zenodo_upload(self): except ValueError: self.update_log.insert("zenodo upload ID must be an integer!") - #################################################################################################################### - # # - # SETTINGS TAB # - # # - #################################################################################################################### + #################################################################################### + # # + # SETTINGS TAB # + # # + #################################################################################### def settings_button_clicked(self): if self.sender().text() == "Select Project Directory": self.initial_model_directory = str( @@ -954,9 +910,7 @@ def settings_button_clicked(self): self.group_deposition_directory_label.setText(self.group_deposit_directory) self.settings["group_deposit_directory"] = self.group_deposit_directory - # self.datasource_menu_reload_samples() - - ######################################### sort stuff below here #################################################### + # ############################## sort stuff below here ############################# def select_sample_for_dimple(self): indexes = self.maps_table.selectionModel().selectedRows() @@ -1031,7 +985,8 @@ def show_preferences(self): vbox_data = QtGui.QVBoxLayout() vbox_data.addWidget( QtGui.QLabel( - "Select amount of processed data you wish to copy to initial_model directory:" + "Select amount of processed data you wish to copy to initial_model" + " directory:" ) ) self.preferences_data_to_copy_combobox = QtGui.QComboBox() @@ -1058,18 +1013,6 @@ def show_preferences(self): vbox_select.addWidget(self.preferences_selection_mechanism_combobox) vbox.addLayout(vbox_select) - # vbox_inital_refinement = QtGui.QVBoxLayout() - # vbox_inital_refinement.addWidget(QtGui.QLabel('Initial Refinement Pipeline:')) - # self.preferences_initial_refinement_combobox = QtGui.QComboBox() - # for item in self.preferences_initial_refinement_pipeline: - # self.preferences_initial_refinement_combobox.addItem(item) - # self.preferences_initial_refinement_combobox.currentIndexChanged.connect( - # self.preferences_initial_refinement_combobox_changed) - # index = self.preferences_initial_refinement_combobox.findText(self.preferences['initial_refinement_pipeline'], QtCore.Qt.MatchFixedString) - # self.preferences_initial_refinement_combobox.setCurrentIndex(index) - # vbox_inital_refinement.addWidget(self.preferences_initial_refinement_combobox) - # vbox.addLayout(vbox_inital_refinement) - vbox_restraints = QtGui.QVBoxLayout() vbox_restraints.addWidget(QtGui.QLabel("Restraints generation program:")) self.preferences_restraints_generation_combobox = QtGui.QComboBox() @@ -1151,37 +1094,10 @@ def show_preferences(self): hbox.addWidget(button) vbox.addLayout(hbox) - # settings_hbox_max_queue_jobs.addWidget(adjust_max_queue_jobs_label) - # adjust_max_queue_jobs = QtGui.QLineEdit() - # adjust_max_queue_jobs.setFixedWidth(200) - # adjust_max_queue_jobs.setText(str(self.max_queue_jobs)) - # adjust_max_queue_jobs.textChanged[str].connect(self.change_max_queue_jobs) - # settings_hbox_max_queue_jobs.addWidget(adjust_max_queue_jobs) - # vbox.addLayout(settings_hbox_max_queue_jobs) - # - # apply_button = QtGui.QPushButton('Apply') - # apply_button.clicked.connect(self.run_qsub_remotely) - # settings_hbox_remote_qsub.addWidget(apply_button) - preferencesLayout.addLayout(vbox, 0, 0) preferences.exec_() - # def set_second_cif_file(self): - # mb = QtGui.QMessageBox() - # mbLayout = mb.layout() - # vbox = QtGui.QVBoxLayout() - # vbox.addWidget(QtGui.QLabel('CIF file to be merged into ligand CIF files:')) - # self.second_cif_file_label = QtGui.QLabel(self.second_cif_file) - # vbox.addWidget(self.second_cif_file_label) - # button = QtGui.QPushButton("Select") - # button.clicked.connect(self.set_second_cif_file) - # vbox.addWidget(button) - # mbLayout.addLayout(vbox, 0, 0) - # mb.addButton(QtGui.QPushButton('Yes'), QtGui.QMessageBox.YesRole) - # mb.addButton(QtGui.QPushButton('No'), QtGui.QMessageBox.RejectRole) - # reply = mb.exec_(); - def dimple_change_twin_mode(self): if self.preferences["dimple_twin_mode"]: self.update_log.insert( @@ -1293,11 +1209,6 @@ def create_missing_apo_records_in_depositTable(self): self.initial_model_directory, self.xce_logfile ) - # def update_file_information_of_apo_records(self): - # XChemDeposit.update_file_locations_of_apo_structuresin_DB( - # os.path.join(self.database_directory, self.data_source_file), self.initial_model_directory, - # self.xce_logfile) - def prepare_models_for_deposition_ligand_bound(self, structureType): start_thread = True self.update_log.insert("preparing mmcif files for PDB group deposition...") @@ -1331,8 +1242,6 @@ def prepare_models_for_deposition_ligand_bound(self, structureType): if self.deposition_bounnd_state_preparation_ignore_event_map.isChecked(): ignore_event_map = True - # structureType = "ligand_bound" - if start_thread: if ground_state != []: self.update_log.insert("apo PDB: " + ground_state[0]) @@ -1533,7 +1442,6 @@ def deposition_data(self): grid.addWidget(QtGui.QLabel("PI role"), 5, 0) self.contact_author_PI_role = QtGui.QComboBox() - # PIroles = ['group leader', 'principal investigator/group leader', 'investigator'] PIroles = ["principal investigator/group leader"] for item in PIroles: self.contact_author_PI_role.addItem(item) @@ -1757,20 +1665,25 @@ def deposition_data(self): grid = QtGui.QGridLayout() grid.addWidget(QtGui.QLabel("Title & Details"), 0, 0) - note = 'Note: supported wildcards: $ProteinName,$CompoundName; e.g. "Crystal Structure of human JMJD2D in complex with N2317a"' + note = ( + "Note: supported wildcards: $ProteinName,$CompoundName;" + ' e.g. "Crystal Structure of human JMJD2D in complex with N2317a"' + ) grid.addWidget(QtGui.QLabel(note), 1, 0) grid.addWidget(QtGui.QLabel("Group deposition title"), 2, 0) self.group_deposition_title = QtGui.QLineEdit() self.group_deposition_title.setText("PanDDA analysis group deposition") self.group_deposition_title.setFixedWidth(600) - # self.group_deposition_title.setStyleSheet("background-color: rgb(192, 192, 192);") + grid.addWidget(self.group_deposition_title, 2, 1) grid.addWidget(QtGui.QLabel("Description"), 3, 0) self.group_description = QtGui.QLineEdit() self.group_description.setText( - "XDomainX of XOrganismX $ProteinName screened against the XXX Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1" + "XDomainX of XOrganismX $ProteinName screened against the" + " XXX Fragment Library by X-ray Crystallography at the XChem facility of" + " Diamond Light Source beamline I04-1" ) self.group_description.setFixedWidth(600) grid.addWidget(self.group_description, 3, 1) @@ -1944,7 +1857,7 @@ def deposition_data(self): self.molecule_name = QtGui.QLineEdit() self.molecule_name.setText("") self.molecule_name.setFixedWidth(300) - # self.molecule_name.setStyleSheet("background-color: rgb(192, 192, 192);") + grid.addWidget(self.molecule_name, 2, 1) grid.addWidget(QtGui.QLabel("(e.g. RNA Hammerhead Ribozyme)"), 2, 2) @@ -2069,7 +1982,8 @@ def deposition_data(self): grid.addWidget( QtGui.QLabel( - "Entity 2 (IMPORTANT: only fill in if you are working with a protein-protein complex!)" + "Entity 2 (IMPORTANT: only fill in if you are working with a" + " protein-protein complex!)" ), 1, 0, @@ -2079,7 +1993,7 @@ def deposition_data(self): self.molecule_name_two = QtGui.QLineEdit() self.molecule_name_two.setText("") self.molecule_name_two.setFixedWidth(300) - # self.molecule_name_two.setStyleSheet("background-color: rgb(192, 192, 192);") + grid.addWidget(self.molecule_name_two, 2, 1) grid.addWidget(QtGui.QLabel("(e.g. RNA Hammerhead Ribozyme)"), 2, 2) @@ -2227,11 +2141,6 @@ def deposition_data(self): for item in XChemMain.pdbx_keywords(): self.structure_keywords_type.addItem(item) grid.addWidget(self.structure_keywords_type, 2, 1) - # self.structure_keywords = QtGui.QLineEdit() - # self.structure_keywords.setText('SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer') - # self.structure_keywords.setFixedWidth(300) - # grid.addWidget(self.structure_keywords, 1, 1) - # grid.addWidget(QtGui.QLabel('(e.g. beta barrel, protein-DNA complex)'), 1, 2) grid.addWidget(QtGui.QLabel("Biological Assembly"), 3, 0) self.biological_assembly_chain_number = QtGui.QLineEdit() @@ -2252,14 +2161,11 @@ def deposition_data(self): self.molecule_one_letter_sequence.setStyleSheet( "background-color: rgb(255, 255, 255);" ) - # self.molecule_one_letter_sequence.setStyleSheet("background-color: rgb(192, 192, 192);") + self.molecule_one_letter_sequence.setText("") self.molecule_one_letter_sequence.setFixedWidth(300) grid.addWidget(self.molecule_one_letter_sequence, 5, 1, 8, 2) - # grid.addWidget(QtGui.QLabel('Sequence information for entity 2'), 10, 0) - # grid.addWidget(QtGui.QLabel('(Important: only for protein-protein complex'), 10, 1) - grid.addWidget(QtGui.QLabel("Sequence UNIPROT ID (Entity 2) - optional"), 13, 0) self.molecule_one_letter_sequence_uniprot_id_two = QtGui.QLineEdit() self.molecule_one_letter_sequence_uniprot_id_two.setText("") @@ -2595,21 +2501,19 @@ def update_database_with_labelInfo(self): for n, l in enumerate(self.labelList): label = str(l[0].text()) description = str(l[1].text()) - # print "update labelTable set Label='%s',Description='%s' where ID=%s" %(label,description,str(n+1)) + self.db.execute_statement( "update labelTable set Label='%s',Description='%s' where ID=%s" % (label, description, str(n + 1)) ) - # print label,description - def load_deposit_config_file(self): file_name_temp = QtGui.QFileDialog.getOpenFileNameAndFilter( self.window, "Open file", self.current_directory, "*.deposit" ) file_name = tuple(file_name_temp)[0] self.deposit_dict = pickle.load(open(file_name, "rb")) - # print self.deposit_dict + for key in self.get_deposit_dict_template(): if key not in self.deposit_dict: self.update_log.warning("field not in .deposit file: " + str(key)) @@ -2623,7 +2527,9 @@ def save_deposit_to_database(self): self.update_deposit_dict() msgBox = QtGui.QMessageBox() msgBox.setText( - "*** WARNING ***\nAre you sure you want to update the database?\nThis will overwrite previous entries!" + "*** WARNING ***\n" + "Are you sure you want to update the database?\n" + "This will overwrite previous entries!" ) msgBox.addButton(QtGui.QPushButton("Yes"), QtGui.QMessageBox.YesRole) msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.RejectRole) @@ -2827,7 +2733,6 @@ def update_deposit_input(self): self.deposit_dict["Manipulated_source_details"] ) - # try: self.molecule_chain_one.setText(self.deposit_dict["molecule_chain_one"]) # entity 2 self.molecule_name_two.setText(self.deposit_dict["molecule_name_two"]) @@ -2870,24 +2775,6 @@ def update_deposit_input(self): self.molecule_one_letter_sequence_two.setText( self.deposit_dict["molecule_two_letter_sequence"] ) - # except KeyError: - # self.molecule_chain_one.setText('') - # ### entity 2 - # self.molecule_name_two.setText('') - # self.fragment_name_two_specific_mutation.setText('') - # self.Source_organism_scientific_name_two.setCurrentIndex(0) - # self.Source_organism_gene_two.setText('') - # self.Source_organism_strain_two.setText('') - # self.Expression_system_scientific_name_two.setCurrentIndex(0) - # self.Expression_system_strain_two.setText('') - # self.Expression_system_vector_type_two.setText('') - # self.Expression_system_plasmid_name_two.setText('') - # self.Manipulated_source_details_two.setText('') - # self.molecule_chain_two.setText('') - # self.molecule_one_letter_sequence_uniprot_id_two.setText('') - # self.molecule_one_letter_sequence_two.setText('') - - ### self.structure_keywords.setText(self.deposit_dict["structure_keywords"]) self.biological_assembly_chain_number.setText( @@ -2993,7 +2880,6 @@ def update_deposit_input(self): self.pdbx_grant_country_three.setCurrentIndex(index) except ValueError as e: - # self.update_status_bar('Sorry, this is not a XChemExplorer deposit file!') self.update_log.error("file is not a valid .deposit file: " + str(e)) def update_deposit_dict(self): @@ -3427,9 +3313,6 @@ def update_header_and_data_from_datasource(self): self.update_log.insert("load header and data from data source") self.header, self.data = self.db.load_samples_from_data_source() self.update_log.insert("get all samples in data source") - all_samples_in_db = self.db.execute_statement( - "select CrystalName from mainTable where CrystalName is not '';" - ) self.xtal_db_dict = {} sampleID_column = 0 @@ -3595,24 +3478,20 @@ def open_config_file(self): try: pickled_settings = pickle.load(open(file_name, "rb")) - except: print("==> XCE: failed to open config file...") - key_list = { # 'beamline_directory': 'beamline_directory', + key_list = { "initial_model_directory": "initial_model_directory", "panddas_directory": "panddas_directory", "html_export_directory": "html_export_directory", "group_deposit_directory": "group_deposit_directory", "database_directory": "database_directory", "datasets_summary_file": "datasets_summary", - # "'data_source_file': 'data_source', "ccp4_scratch_directory": "ccp4_scratch", "allowed_unitcell_difference_percent": "unitcell_difference", "acceptable_low_resolution_limit_for_data": "too_low_resolution_data", - # 'reference_directory_temp': 'reference_directory' } - # self.pandda_input_data_dir_entry.setText(os.path.join(self.initial_model_directory, '*')) for current_key in key_list: try: @@ -3773,12 +3652,11 @@ def rerun_dimple_on_all_autoprocessing_files(self): def run_dimple_on_selected_autoprocessing_file(self, instruction): job_list = [] for xtal in sorted(self.initial_model_dimple_dict): - # print(xtal) if self.initial_model_dimple_dict[xtal][0].isChecked(): - # print(xtal + ' is checked...') db_dict = self.xtal_db_dict[xtal] - # the if statement below is so convoluted, so that it is compatible with older data source files + # the if statement below is so convoluted, so that it is compatible + # with older data source files if ( os.path.isfile( @@ -3892,7 +3770,8 @@ def run_dimple_on_selected_autoprocessing_file(self, instruction): ( "WARNING: " + xtal - + " has not been submitted to dimple because no files were found: " + + " has not been submitted to dimple" + + " because no files were found: " ) ) if not os.path.isfile( @@ -4246,7 +4125,8 @@ def check_before_running_dimple(self, job_list, instruction): msgBox = QtGui.QMessageBox() msgBox.setText( - "Do you really want to run {0!s} {1!s} jobs?\nNote: we will not run more than {2!s} at once on the cluster!".format( + "Do you really want to run {0!s} {1!s} jobs?\nNote: we will not run more" + " than {2!s} at once on the cluster!".format( len(job_list), self.preferences["initial_refinement_pipeline"], self.preferences["max_queue_jobs"], @@ -4275,12 +4155,12 @@ def check_before_running_dimple(self, job_list, instruction): "we will be running an ARRAY job on the DLS computer cluster" ) self.update_log.insert( - "please note that the maximum number of jobs that will be running at once is {0!s}".format( - self.max_queue_jobs - ) + "please note that the maximum number of jobs that will be running" + " at once is {0!s}".format(self.max_queue_jobs) ) self.update_log.insert( - "you can change this in the PREFERENCES menu, but be warned that to high a number might break the cluster!" + "you can change this in the PREFERENCES menu, but be warned that to" + " high a number might break the cluster!" ) self.update_log.insert("preparing input files for DIMPLE...") self.work_thread = XChemThread.run_dimple_on_all_autoprocessing_files_new( @@ -4418,9 +4298,8 @@ def change_allowed_unitcell_difference_percent(self, text): "unitcell_difference" ] = self.allowed_unitcell_difference_percent self.update_log.insert( - "changing max allowed unit cell difference between reference and xtal to {0!s} percent".format( - self.allowed_unitcell_difference_percent - ) + "changing max allowed unit cell difference between reference and xtal" + " to {0!s} percent".format(self.allowed_unitcell_difference_percent) ) except ValueError: if str(text).find(".") != -1: @@ -4431,7 +4310,8 @@ def change_allowed_unitcell_difference_percent(self, text): "unitcell_difference" ] = self.allowed_unitcell_difference_percent self.update_log.insert( - "changing max allowed unit cell difference between reference and xtal to {0!s} percent".format( + "changing max allowed unit cell difference between reference and" + " xtal to {0!s} percent".format( self.allowed_unitcell_difference_percent ) ) @@ -4443,18 +4323,16 @@ def change_max_queue_jobs(self, text): self.max_queue_jobs = int(text) self.settings["max_queue_jobs"] = self.max_queue_jobs self.update_log.insert( - "changing max number of jobs running simultaneously on DLS cluster to {0!s}".format( - self.max_queue_jobs - ) + "changing max number of jobs running simultaneously on DLS cluster to" + " {0!s}".format(self.max_queue_jobs) ) except ValueError: if str(text).find(".") != -1: self.max_queue_jobs = int(str(text)[: str(text).find(".")]) self.settings["max_queue_jobs"] = self.max_queue_jobs self.update_log.insert( - "changing max number of jobs running simultaneously on DLS cluster to {0!s}".format( - self.max_queue_jobs - ) + "changing max number of jobs running simultaneously on DLS cluster" + " to {0!s}".format(self.max_queue_jobs) ) else: pass @@ -4508,14 +4386,15 @@ def button_clicked(self): for item in self.workflow_widget_dict: for widget in self.workflow_widget_dict[item]: if widget == self.sender(): - # get index of item in self.workflow; Note this index should be the same as the index - # of the self.main_tab_widget which belongs to this task + # get index of item in self.workflow; Note this index should be the + # same as the index of the self.main_tab_widget which belongs to + # this task task_index = self.workflow.index(item) instruction = str(self.workflow_widget_dict[item][0].currentText()) print(instruction) action = str(self.sender().text()) if self.main_tab_widget.currentIndex() == task_index: - if self.explorer_active == 0 and self.data_source_set == True: + if self.explorer_active == 0 and self.data_source_set is True: if action == "Run": print( ( @@ -4523,7 +4402,6 @@ def button_clicked(self): + str(self.using_remote_qsub_submission) ) ) - # print(instruction) self.prepare_and_run_task(instruction) elif action == "Status": self.get_status_of_workflow_milestone(instruction) @@ -4544,7 +4422,10 @@ def button_clicked(self): if os.path.exists( str(self.panddas_directory + "/pandda.errored") ): - self.pandda_status = "Error encountered... please check the log files for pandda!" + self.pandda_status = ( + "Error encountered..." + " please check the log files for pandda!" + ) self.pandda_status_label.setStyleSheet("color: red") self.pandda_status_label.setText( str("STATUS: " + self.pandda_status) @@ -4606,30 +4487,12 @@ def prepare_and_run_task(self, instruction): self.rescore = True self.select_best_autoprocessing_result() - # if instruction == 'Get New Results from Autoprocessing': - # self.check_for_new_autoprocessing_or_rescore(False) - # self.update_header_and_data_from_datasource() - # self.update_all_tables() - # - # elif instruction == 'Rescore Datasets': - # self.check_for_new_autoprocessing_or_rescore(True) - - # elif instruction == "Read PKL file": - # summary = pickle.load(open(self.datasets_summary_file, "rb")) - # self.create_widgets_for_autoprocessing_results_only(summary) - elif instruction == "Run xia2 on selected datasets": self.run_xia2_on_selected_datasets(False) elif instruction == "Run xia2 on selected datasets - overwrite": self.run_xia2_on_selected_datasets(True) - # elif instruction == 'Run DIMPLE on All Autoprocessing MTZ files': - # self.rerun_dimple_on_all_autoprocessing_files() - - # elif instruction == 'Run initial refinement on selected MTZ files': - # self.run_dimple_on_selected_autoprocessing_file() - elif instruction == "Run DIMPLE on selected MTZ files": self.run_dimple_on_selected_autoprocessing_file(instruction) @@ -4639,9 +4502,6 @@ def prepare_and_run_task(self, instruction): elif instruction == "Run PHENIX.LIGAND_PIPELINE on selected MTZ files": self.run_dimple_on_selected_autoprocessing_file(instruction) - # elif instruction == 'Remove selected initial refinement files': - # self.remove_selected_dimple_files() - elif instruction == "Remove selected DIMPLE files": self.remove_selected_dimple_files(instruction) @@ -4651,9 +4511,6 @@ def prepare_and_run_task(self, instruction): elif instruction == "Remove selected PHENIX.LIGAND_PIPELINE files": self.remove_selected_dimple_files(instruction) - # elif instruction == 'Set only results from selected pipeline': - # self.set_results_from_selected_pipeline() - elif instruction == "Set DIMPLE output": self.set_results_from_selected_pipeline(instruction) @@ -4663,12 +4520,6 @@ def prepare_and_run_task(self, instruction): elif instruction == "Set PHENIX.LIGAND_PIPELINE output": self.set_results_from_selected_pipeline(instruction) - # elif instruction == 'Create CIF/PDB/PNG file of ALL compounds': - # self.create_cif_pdb_png_files('ALL') - - # elif instruction == 'Create CIF/PDB/PNG file of NEW compounds': - # self.create_cif_pdb_png_files('NEW') - elif instruction == "Create CIF/PDB/PNG file of SELECTED compounds": self.create_cif_pdb_png_files("SELECTED") @@ -4727,9 +4578,6 @@ def prepare_and_run_task(self, instruction): ): self.run_refine_bound_state_with_buster("newnocheck") - # elif instruction == 'refine NEW bound-state models with BUSTER - NEW': - # self.run_refine_bound_state_with_buster_new('new') - elif instruction == "cluster datasets": self.cluster_datasets_for_pandda() @@ -4772,7 +4620,6 @@ def prepare_and_run_task(self, instruction): interface = "dimple_twin" else: interface = "old" - # print self.settings self.work_thread = XChemThread.start_COOT(self.settings, interface) self.connect( self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished @@ -4823,7 +4670,8 @@ def check_status_create_png_of_soaked_compound(self): "*** WARNING ***\n" "You did not select a target!\n" "In this case we will only parse the project directory!\n" - "Please note that this option is usually only useful in case you reprocessed your data.\n" + "Please note that this option is usually only useful in case you" + " reprocessed your data.\n" "Do you want to continue?" ) msgBox.setText(warning) @@ -4976,8 +4824,6 @@ def run_pandda_analyse(self, run): self.xce_logfile, os.path.join(self.database_directory, self.data_source_file), ) - # self.connect(self.work_thread, QtCore.SIGNAL("datasource_menu_reload_samples"), - # self.datasource_menu_reload_samples) self.connect( self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished ) @@ -5060,10 +4906,6 @@ def convert_event_maps_to_SF(self): self.initial_model_directory ) ) - # self.work_thread = XChemPANDDA.convert_all_event_maps_in_database(self.initial_model_directory, - # self.xce_logfile, - # os.path.join(self.database_directory, - # self.data_source_file)) self.work_thread = XChemPANDDA.find_event_map_for_ligand( self.initial_model_directory, self.xce_logfile, self.external_software ) @@ -5174,17 +5016,21 @@ def run_pandda_export(self, update_datasource_only, which_models): ) else: self.update_log.insert( - "exporting PANDDA models, updating data source and launching inital refinement for new models" + "exporting PANDDA models," + " updating data source and launching inital refinement for new models" ) start_thread = False if which_models == "all": self.update_log.insert( - "exporting ALL models! *** WARNING *** This may overwrite previous refinements!!!" + "exporting ALL models!" + " *** WARNING *** This may overwrite previous refinements!!!" ) msgBox = QtGui.QMessageBox() msgBox.setText( - "*** WARNING ***\nThis will overwrite all your manual selections!\nDo you want to continue?" + "*** WARNING ***\n" + "This will overwrite all your manual selections!\n" + "Do you want to continue?" ) msgBox.addButton(QtGui.QPushButton("Yes"), QtGui.QMessageBox.YesRole) msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.RejectRole) @@ -5216,17 +5062,6 @@ def run_pandda_export(self, update_datasource_only, which_models): ) self.work_thread.start() - # def run_refine_bound_state_with_buster(self,which_models): - # start_thread = True - # if start_thread: - # self.work_thread = XChemPANDDA.refine_bound_state_with_buster(self.panddas_directory, - # os.path.join(self.database_directory, - # self.data_source_file), - # self.initial_model_directory, self.xce_logfile, - # which_models) - # self.connect(self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished) - # self.work_thread.start() - def run_refine_bound_state_with_buster(self, which_models): start_thread = True if start_thread: @@ -5253,7 +5088,9 @@ def show_pandda_html_summary(self): def create_cif_pdb_png_files(self, todo): tmp = self.db.execute_statement( - "select CrystalName,CompoundCode,CompoundSmiles from mainTable where CrystalName is not '' and CompoundSmiles is not '' and CompoundSmiles is not NULL;" + "select CrystalName,CompoundCode,CompoundSmiles from mainTable where" + " CrystalName is not '' and CompoundSmiles is not '' and CompoundSmiles" + " is not NULL;" ) compound_list = [] for item in tmp: @@ -5336,7 +5173,9 @@ def create_cif_pdb_png_files(self, todo): def fit_ligands_into_dimple_maps(self): tmp = self.db.execute_statement( - "select CrystalName,CompoundCode,CompoundSmiles from mainTable where CrystalName is not '' and CompoundSmiles is not '' and CompoundSmiles is not NULL;" + "select CrystalName,CompoundCode,CompoundSmiles from mainTable where" + " CrystalName is not '' and CompoundSmiles is not '' and CompoundSmiles" + " is not NULL;" ) compound_list = [] for item in tmp: @@ -5461,7 +5300,8 @@ def merge_cif_files(self, todo): ) tmp = self.db.execute_statement( - "select CrystalName,CompoundCode from mainTable where CrystalName is not '' and CompoundSmiles is not '' and CompoundSmiles is not NULL;" + "select CrystalName,CompoundCode from mainTable where CrystalName is not ''" + " and CompoundSmiles is not '' and CompoundSmiles is not NULL;" ) compound_list = [] for item in tmp: @@ -5526,7 +5366,8 @@ def update_deposition_table(self): if mismatch != {}: self.update_log.insert( - "The following samples contain ligand that are not ready for deposition:" + "The following samples contain ligand that are not ready for" + " deposition:" ) for entry in mismatch: self.update_log.insert( @@ -5636,33 +5477,26 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): ).translate_xce_column_list_to_sqlite(column_name) for xtal in sorted(self.data_collection_dict): - if os.path.isfile( - os.path.join(self.initial_model_directory, xtal, xtal + ".mtz") - ): - mtz_already_in_inital_model_directory = True - # column 2: data collection date - # this one should always be there; it may need updating in case another run appears - # first find latest run + # this one should always be there; it may need updating in case another run + # appears first find latest run tmp = [] for entry in self.data_collection_dict[xtal]: if entry[0] == "image": tmp.append( [entry[3], datetime.strptime(entry[3], "%Y-%m-%d %H:%M:%S")] ) - latest_run = max(tmp, key=lambda x: x[1])[0] # first check if it does already exist if xtal not in self.data_collection_column_three_dict: - # generate all the widgets which can later be appended and add them to the dictionary - # table with data processing results for each pipeline + # generate all the widgets which can later be appended and add them to + # the dictionary table with data processing results for each pipeline data_collection_table = QtGui.QTableWidget() selection_changed_by_user = False self.data_collection_column_three_dict[xtal] = [ data_collection_table, selection_changed_by_user, ] - xtal_in_table = True else: data_collection_table = self.data_collection_column_three_dict[xtal][0] selection_changed_by_user = self.data_collection_column_three_dict[ @@ -5682,15 +5516,15 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): QtGui.QAbstractItemView.SelectRows ) - ############################################################################# + ############################################################################ # crystal images - # first check there are new images that are not displayed yet; i.e. they are not in the self.data_collection_image_dict + # first check there are new images that are not displayed yet; i.e. they + # are not in the self.data_collection_image_dict if xtal not in self.data_collection_image_dict: # OK this is the first time self.data_collection_image_dict[xtal] = [] # sort crystal images by timestamp - # reminder: ['image',visit,run,timestamp,image_list,diffraction_image,run_number] # a) get only image entries from self.data_collection_dict tmp = [] for entry in self.data_collection_dict[xtal]: @@ -5698,7 +5532,6 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): tmp.append(entry) # b) sort by the previously assigned run number - # note: entry[6]==run_number for entry in sorted(tmp, key=lambda x: x[6]): run_number = entry[6] images_already_in_table = False @@ -5707,27 +5540,25 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): images_already_in_table = True break if not images_already_in_table: - # not if there is a run, but images are for whatever reason not present in self.data_collection_dict - # then use image not available from $XChemExplorer_DIR/image/IMAGE_NOT_AVAILABLE.png - # not sure how to do this at the moment; it will probably trigger an error that I can catch + # not if there is a run, but images are for whatever reason not + # present in self.data_collection_dict then use image not available + # from $XChemExplorer_DIR/image/IMAGE_NOT_AVAILABLE.png self.data_collection_image_dict[xtal].append( [entry[6], entry[1], entry[2], entry[3], entry[5]] ) - ############################################################################# + ############################################################################ # initialize dataset_outcome_dict for xtal if xtal not in self.dataset_outcome_dict: self.dataset_outcome_dict[xtal] = [] # dataset outcome buttons - ############################################################################# + ############################################################################ # table for data processing results - # check if results from particular pipeline are already in table; - # not really looking at the table here, but compare it to self.data_collection_table_dict + # check if results from particular pipeline are already in table row_position = data_collection_table.rowCount() - if not xtal in self.data_collection_table_dict: + if xtal not in self.data_collection_table_dict: self.data_collection_table_dict[xtal] = [] - # reminder: ['logfile',visit,run,timestamp,autoproc,file_name,aimless_results,,False] logfile_list = [] for entry in self.data_collection_dict[xtal]: if entry[0] == "logfile": @@ -5783,17 +5614,18 @@ def create_widgets_for_autoprocessing_results_only(self, data_dict): ) # select best resolution file + set data collection outcome - # the assumption is that index in data_collection_dict and row number are identical - # the assumption for data collection outcome is that as long as a logfile is found, it's a success - logfile_found = False + # the assumption is that index in data_collection_dict and row number are + # identical + # the assumption for data collection outcome is that as long as a logfile + # is found, it's a success for entry in self.data_collection_dict[xtal]: if entry[0] == "logfile": index = entry[7] best_file = entry[8] - logfile_found = True if best_file: - # we change the selection only if the user did not touch it, assuming that he/she knows best - # if not selection_changed_by_user: + # we change the selection only if the user did not touch it, + # assuming that he/she knows best if not + # selection_changed_by_user: data_collection_table.selectRow(index) self.populate_datasets_summary_table() @@ -5802,7 +5634,6 @@ def find_suitable_reference_file(self, db_dict): reference_file = [] dummy = ["...", "", "", "", 0, "0"] reference_file.append([dummy, 999]) - suitable_reference = [] for reference in self.reference_file_list: # first we need one in the same pointgroup if reference[5] == db_dict["DataProcessingPointGroup"]: @@ -5978,7 +5809,6 @@ def preferences_restraints_generation_combobox_changed(self): def refinement_outcome_combobox_changed(self): for xtal in self.refinement_table_dict: if self.sender() == self.refinement_table_dict[xtal]: - # db_dict = {'RefinementOutcome': str(self.sender().currentText())} db_dict = {} db_dict["RefinementOutcome"] = str(self.sender().currentText()) db_dict["RefinementOutcomePerson"] = getpass.getuser() @@ -6023,7 +5853,6 @@ def get_reference_file_list(self, reference_root): if os.path.isfile( os.path.join(self.reference_directory, reference_root + ".pdb") ): - # reference_file = reference_root + '.pdb' pdb_reference = parse().PDBheader( os.path.join( self.reference_directory, reference_root + ".pdb" @@ -6062,19 +5891,7 @@ def dataset_outcome_combobox_change_outcome(self, text): break self.dataset_outcome_dict[xtal] = outcome if xtal != "": - # # need to also update if not yet done - # user_already_changed_selection = False - # for n, entry in enumerate(self.data_collection_dict[xtal]): - # if entry[0] == 'user_changed_selection': - # user_already_changed_selection = True - # if entry[0] == 'logfile': - # db_dict = entry[6] - # db_dict['DataCollectionOutcome'] = outcome - # entry[6] = db_dict - # self.data_collection_dict[xtal][n] = entry - # if not user_already_changed_selection: - # self.data_collection_dict[xtal].append(['user_changed_selection']) - # # finally need to update outcome field in data source accordingly + # need to also update if not yet done self.update_log.insert( "updating dataset outcome in datasource for {0!s}".format(xtal) ) @@ -6119,184 +5936,7 @@ def show_data_collection_details(self, state): # un-check all other ones self.datasets_summary_dict[key][3].setChecked(False) - # def populate_datasets_summary_table(self): - # self.status_bar.showMessage( - # 'Building summary table for data processing results; be patient this may take a while') - # row = self.datasets_summary_table.rowCount() - # column_name = self.db.translate_xce_column_list_to_sqlite(self.datasets_summary_table_columns) - # - # pinList = self.db.execute_statement( - # "Select CrystalName,PinBarcode,DataCollectionPinBarcode from mainTable where CrystalName is not ''") - # pinDict = {} - # for item in pinList: - # pinDict[str(item[0])] = [str(item[1]), str(item[2])] - # - # for xtal in sorted(self.data_collection_dict): - # new_xtal = False - # if xtal not in self.datasets_summary_dict: - # row = self.datasets_summary_table.rowCount() - # self.datasets_summary_table.insertRow(row) - # self.datasets_summary_dict[xtal] = [] - # new_xtal = True - # - # # check for dataset outcome - # outcome = '' - # logfile_found = False - # too_low_resolution = True - # db_dict = {} - # for entry in self.data_collection_dict[xtal]: - # if entry[0] == 'logfile': - # logfile_found = True - # if entry[8]: # if this was auto-selected best resolution file - # db_dict = entry[6] - # try: - # if float(db_dict['DataProcessingResolutionHigh']) <= float( - # self.acceptable_low_resolution_limit_for_data): - # too_low_resolution = False - # except ValueError: - # pass - # - # try: - # outcome = str(self.db.get_value_from_field(xtal, 'DataCollectionOutcome')[0]) - # except TypeError: - # outcome = 'Failed - unknown' - # self.update_log.insert('cannot find DataCollectionOutcome for {0!s}'.format(xtal)) - # self.dataset_outcome_dict[xtal] = outcome - # - # # find latest run for crystal and diffraction images - # tmp = [] - # for entry in self.data_collection_dict[xtal]: - # if entry[0] == 'image': - # tmp.append([entry, datetime.strptime(entry[3], '%Y-%m-%d %H:%M:%S')]) - # latest_run = max(tmp, key=lambda x: x[1])[0] - # - # new_run_for_exisiting_crystal_or_new_sample = True - # if new_xtal: - # self.datasets_summary_dict[xtal] = [outcome, db_dict, latest_run] - # else: - # # check if newer run appeared - # old_run_timestamp = self.datasets_summary_dict[xtal][2][3] - # new_run_timestamp = latest_run[3] - # if old_run_timestamp == new_run_timestamp: - # new_run_for_exisiting_crystal_or_new_sample = False - # else: - # checkbox_for_details = self.datasets_summary_dict[xtal][3] - # self.datasets_summary_dict[xtal] = [outcome, db_dict, latest_run, checkbox_for_details] - # - # if new_xtal: - # current_row = row - # else: - # allRows = self.datasets_summary_table.rowCount() - # for table_row in range(allRows): - # if self.datasets_summary_table.item(table_row, 0).text() == xtal: - # current_row = table_row - # break - # - # image_number = 0 - # for column, header in enumerate(column_name): - # if header[0] == 'Sample ID': - # cell_text = QtGui.QTableWidgetItem() - # cell_text.setText(str(xtal)) - # cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - # self.datasets_summary_table.setItem(current_row, column, cell_text) - # elif header[0] == 'DataCollection\nOutcome': - # if new_xtal: - # dataset_outcome_combobox = QtGui.QComboBox() - # for outcomeItem in self.dataset_outcome: - # dataset_outcome_combobox.addItem(outcomeItem) - # self.datasets_summary_table.setCellWidget(current_row, column, dataset_outcome_combobox) - # dataset_outcome_combobox.activated[str].connect(self.dataset_outcome_combobox_change_outcome) - # self.dataset_outcome_combobox_dict[xtal] = dataset_outcome_combobox - # index = self.dataset_outcome_combobox_dict[xtal].findText(str(outcome), QtCore.Qt.MatchFixedString) - # self.dataset_outcome_combobox_dict[xtal].setCurrentIndex(index) - # continue - # - # elif header[0].startswith('img'): - # if new_run_for_exisiting_crystal_or_new_sample: - # img = latest_run[4] - # pixmap = QtGui.QPixmap() - # # can do this (img[image_number][1]) because made sure in the threading module - # # that there are always exactly 5 images in there - # pixmap.loadFromData(base64.b64decode(img[image_number][1])) - # image = QtGui.QLabel() - # image.resize(128, 80) - # image.setPixmap(pixmap.scaled(image.size(), QtCore.Qt.KeepAspectRatio)) - # self.datasets_summary_table.setCellWidget(current_row, column, image) - # image_number += 1 - # - # elif header[0].startswith('Show Diffraction\nImage'): - # if new_run_for_exisiting_crystal_or_new_sample: - # diffraction_image = latest_run[5] - # diffraction_image_name = diffraction_image[diffraction_image.rfind('/') + 1:] - # try: # need to try because older pkl file may not have this item in list - # html_summary = latest_run[7] - # except IndexError: - # html_summary = '' - # if new_xtal: - # start_albula_button = QtGui.QPushButton('Show: \n' + diffraction_image_name) - # start_albula_button.clicked.connect(self.show_html_summary_and_diffraction_image) - # self.albula_button_dict[xtal] = [start_albula_button, diffraction_image, html_summary] - # self.datasets_summary_table.setCellWidget(current_row, column, start_albula_button) - # else: - # self.albula_button_dict[xtal][1] = diffraction_image - # elif header[0].startswith('Show\nDetails'): - # if new_xtal: - # show_data_collection_details_checkbox = QtGui.QCheckBox() - # show_data_collection_details_checkbox.toggle() - # show_data_collection_details_checkbox.setChecked(False) - # show_data_collection_details_checkbox.stateChanged.connect(self.show_data_collection_details) - # self.datasets_summary_table.setCellWidget(current_row, column, - # show_data_collection_details_checkbox) - # self.datasets_summary_dict[xtal].append(show_data_collection_details_checkbox) - # elif header[0].startswith('SoakDB\nBarcode') or header[0].startswith('GDA\nBarcode'): - # if new_xtal: - # cell_text = QtGui.QTableWidgetItem() - # if xtal in pinDict: - # if header[0].startswith('SoakDB\nBarcode'): - # cell_text.setText(str(pinDict[xtal][0])) - # elif header[0].startswith('GDA\nBarcode'): - # cell_text.setText(str(pinDict[xtal][1])) - # if pinDict[xtal][0] == 'NULL' or pinDict[xtal][1] == 'NULL': - # cell_text.setBackground(QtGui.QColor(255, 215, 0)) - # elif pinDict[xtal][0] != pinDict[xtal][1]: - # cell_text.setBackground(QtGui.QColor(255, 0, 0)) - # else: - # cell_text.setText('') - # cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - # self.datasets_summary_table.setItem(current_row, column, cell_text) - # else: - # cell_text = QtGui.QTableWidgetItem() - # # in case data collection failed for whatever reason - # if logfile_found: - # try: - # cell_text.setText(str(db_dict[header[1]])) - # except KeyError: # older pkl files may not have all the columns - # cell_text.setText('n/a') - # else: - # if header[0].startswith('Resolution\n[Mn = 1.5]'): - # cell_text.setText('999') - # elif header[0].startswith('DataProcessing\nRfree'): - # cell_text.setText('999') - # elif header[0].startswith('Rmerge\nLow'): - # cell_text.setText('999') - # else: - # cell_text.setText('') - # cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - # self.datasets_summary_table.setItem(current_row, column, cell_text) - # - # row += 1 - # - # self.datasets_summary_table.resizeRowsToContents() - # self.datasets_summary_table.resizeColumnsToContents() - # - # self.status_bar.showMessage('updating Overview table') - # - # self.status_bar.showMessage('idle') - # - # self.save_files_to_initial_model_folder() - # - - ################################################################################################################ + #################################################################################### # # # @@ -6378,22 +6018,6 @@ def update_row_in_table(self, sample, row, db_dict, table, columns_to_show): table.setCellWidget(row, column, checkbox) checkbox.setChecked(False) - # elif header[0].startswith('SoakDB\nBarcode') or header[0].startswith('GDA\nBarcode'): - # if new_xtal: - # cell_text = QtGui.QTableWidgetItem() - # if xtal in pinDict: - # if header[0].startswith('SoakDB\nBarcode'): - # cell_text.setText(str(pinDict[xtal][0])) - # elif header[0].startswith('GDA\nBarcode'): - # cell_text.setText(str(pinDict[xtal][1])) - # if pinDict[xtal][0] == 'NULL' or pinDict[xtal][1] == 'NULL': - # cell_text.setBackground(QtGui.QColor(255, 215, 0)) - # elif pinDict[xtal][0] != pinDict[xtal][1]: - # cell_text.setBackground(QtGui.QColor(255, 0, 0)) - # else: - # cell_text.setText('') - # cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - # self.datasets_summary_table.setItem(current_row, column, cell_text) else: cell_text = QtGui.QTableWidgetItem() # in case data collection failed for whatever reason @@ -6401,22 +6025,13 @@ def update_row_in_table(self, sample, row, db_dict, table, columns_to_show): cell_text.setText(str(db_dict[header[1]])) except KeyError: # older pkl files may not have all the columns cell_text.setText("n/a") - # else: - # if header[0].startswith('Resolution\n[Mn = 1.5]'): - # cell_text.setText('999') - # elif header[0].startswith('DataProcessing\nRfree'): - # cell_text.setText('999') - # elif header[0].startswith('Rmerge\nLow'): - # cell_text.setText('999') - # else: - # cell_text.setText('') cell_text.setTextAlignment( QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter ) table.setItem(row, column, cell_text) print( ( - "row: {0!s} column: {1!s} value: {2!s} header: {3!s}".format( + "row: {0!s} column: {1!s} value: {2!s} header: {3!s}".format( row, column, cell_text, header[0] ) ) @@ -6425,7 +6040,8 @@ def update_row_in_table(self, sample, row, db_dict, table, columns_to_show): def populate_datasets_summary_table_NEW(self): self.status_bar.showMessage( - "Building summary table for data processing results; be patient this may take a while" + "Building summary table for data processing results; be patient this may" + " take a while" ) # get information about all samples collected during the current visit @@ -6541,7 +6157,6 @@ def make_data_collection_table(self): ) def data_collection_table_popup(self): - # self.msgBox = QtGui.QMessageBox() msgBoxLayout = self.msgBox.layout() qWid = QtGui.QWidget() qWid.setFixedWidth(3000) @@ -6549,7 +6164,6 @@ def data_collection_table_popup(self): vbox = QtGui.QVBoxLayout() vbox.addWidget(self.data_collection_table) qWid.setLayout(vbox) - # msgBoxLayout.addLayout(vbox, 0, 0) msgBoxLayout.addWidget(qWid) self.msgBox.addButton(QtGui.QPushButton("Cancel"), QtGui.QMessageBox.RejectRole) self.msgBox.resize(1000, 200) @@ -6575,8 +6189,6 @@ def select_different_autoprocessing_result(self): ) except AttributeError: print(("--> {0!s}: None".format(q))) - # get db_dict from collectionTable for visit, run, autoproc - # dbDict = self.db.get_db_dict_for_visit_run_autoproc(xtal,visit,run,autoproc) dbDict = self.db.get_db_dict_for_visit_run_autoproc_score( xtal, visit, run, autoproc, score ) @@ -6608,7 +6220,7 @@ def select_different_autoprocessing_result(self): self.msgBox.done(1) # < end - ################################################################################################################# + #################################################################################### def update_outcome_datasets_summary_table(self, sample, outcome): rows_in_table = self.datasets_summary_table.rowCount() @@ -6631,9 +6243,11 @@ def user_update_selected_autoproc_datasets_summary_table(self): if int(stage) > 2: msgBox = QtGui.QMessageBox() msgBox.setText( - "*** WARNING ***\n%s is currently %s\nIt will disappear from the Refinement table,\n" - "when you refresh it next time.\nDo you want to continue?" - % (key, dbTmp["RefinementOutcome"]) + "*** WARNING ***\n" + "%s is currently %s\n" + "It will disappear from the Refinement table,\n" + "when you refresh it next time.\n" + "Do you want to continue?" % (key, dbTmp["RefinementOutcome"]) ) msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.YesRole) msgBox.addButton( @@ -6659,7 +6273,8 @@ def user_update_selected_autoproc_datasets_summary_table(self): selected_processing_result = 1000000 for index in sorted(indexes): selected_processing_result = index.row() - # the user changed the selection, i.e. no automated selection will update it + # the user changed the selection, i.e. no automated selection will + # update it self.update_log.insert("user changed selection") self.data_collection_column_three_dict[key][1] = True # need to also update if not yet done @@ -6676,8 +6291,8 @@ def user_update_selected_autoproc_datasets_summary_table(self): visit = db_dict["DataCollectionVisit"] run = db_dict["DataCollectionRun"] self.update_log.insert( - "user changed data processing files for {0!s} to visit={1!s}, " - "run={2!s}, program={3!s}".format( + "user changed data processing files for {0!s}" + " to visit={1!s}, run={2!s}, program={3!s}".format( key, visit, run, program ) ) @@ -6750,9 +6365,8 @@ def update_selected_autoproc_datasets_summary_table(self): visit = db_dict["DataCollectionVisit"] run = db_dict["DataCollectionRun"] self.update_log.insert( - "user changed data processing files for {0!s} to visit={1!s}, run={2!s}, program={3!s}".format( - sample, visit, run, program - ) + "user changed data processing files for {0!s} to visit={1!s}," + " run={2!s}, program={3!s}".format(sample, visit, run, program) ) # update datasource self.update_log.insert("updating datasource...") @@ -6791,7 +6405,8 @@ def populate_and_update_datasource_table(self): len(self.overview_datasource_table_columns) ) - # first get a list of all the samples that are already in the table and which will be updated + # first get a list of all the samples that are already in the table and which + # will be updated samples_in_table = [] current_row = self.overview_datasource_table.rowCount() for row in range(current_row): @@ -6803,7 +6418,6 @@ def populate_and_update_datasource_table(self): columns_to_show = self.get_columns_to_show( self.overview_datasource_table_columns ) - n_rows = self.get_rows_with_sample_id_not_null_from_datasource() sample_id_column = self.get_columns_to_show(["Sample ID"]) for row in self.data: @@ -6848,7 +6462,6 @@ def populate_and_update_datasource_table(self): def kill_other_pandda_options(self): for i in range(0, self.pandda_analyse_data_table.rowCount()): - checkbox0 = self.pandda_analyse_data_table.cellWidget(i, 1) checkbox1 = self.pandda_analyse_data_table.cellWidget(i, 7) checkbox2 = self.pandda_analyse_data_table.cellWidget(i, 8) checkbox3 = self.pandda_analyse_data_table.cellWidget(i, 9) @@ -6978,16 +6591,6 @@ def select_sample_for_pandda(self, option): self.kill_other_pandda_options() def populate_and_update_refinement_table(self): - - # panddaList = self.db.execute_statement( - # "select CrystalName,PANDDA_site_index,PANDDA_site_name,RefinementOutcome " - # "from panddaTable where CrystalName is not '' and PANDDA_site_ligand_placed is 'True';") - # panddaDict = {} - # for item in panddaList: - # if str(item[0]) not in panddaDict: - # panddaDict[str(item[0])] = [] - # panddaDict[str(item[0])].append([str(item[1]), str(item[2]), str(item[3])]) - column_name = self.db.translate_xce_column_list_to_sqlite( self.refinement_table_columns ) @@ -7044,8 +6647,6 @@ def populate_and_update_refinement_table(self): ) elif header[0] == "buster-reports": - # "'NAME'".format(db_dict['RefinementBusterReportHTML']) - # db_dict['RefinementBusterReportHTML'] = 'www.google.com' buster_report = db_dict["RefinementBusterReportHTML"] ref_name = buster_report.split("/")[ len(buster_report.split("/")) - 2 @@ -7054,34 +6655,9 @@ def populate_and_update_refinement_table(self): '{1!s}'.format(buster_report, ref_name) ) buster_report_link.setOpenExternalLinks(True) - # buster_report_link.setTextInteractionFlags(QtCore.Qt.TextBrowserInteraction) - # buster_report_link.setTextFormat(QtCore.Qt.RichText) - # self.refinement_table.setItem(current_row, column, buster_report_link) self.refinement_table.setCellWidget( current_row, column, buster_report_link ) - - # elif header[0] == 'PanDDA site details': - # try: - # panddaDict[xtal].insert(0, ['Index', 'Name', 'Status']) - # outerFrame = QtGui.QFrame() - # outerFrame.setFrameShape(QtGui.QFrame.Box) - # grid = QtGui.QGridLayout() - # for y, entry in enumerate(panddaDict[xtal]): - # for x, info in enumerate(entry): - # frame = QtGui.QFrame() - # frame.setFrameShape(QtGui.QFrame.Box) - # vbox = QtGui.QVBoxLayout() - # vbox.addWidget(QtGui.QLabel(str(entry[x]))) - # frame.setLayout(vbox) - # grid.addWidget(frame, y, x) - # outerFrame.setLayout(grid) - # self.refinement_table.setCellWidget(current_row, column, outerFrame) - # except KeyError: - # cell_text = QtGui.QTableWidgetItem() - # cell_text.setText('*** N/A ***') - # cell_text.setTextAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter) - # self.refinement_table.setItem(current_row, column, cell_text) else: cell_text = QtGui.QTableWidgetItem() cell_text.setText(str(db_dict[header[1]])) @@ -7107,9 +6683,9 @@ def populate_and_update_refinement_table(self): self.refinement_table.resizeRowsToContents() def get_columns_to_show(self, column_list): - # maybe I coded some garbage before, but I need to find out which column name in the - # data source corresponds to the actually displayed column name in the table - # reason being that the unique column ID for DB may not be nice to look at + # maybe I coded some garbage before, but I need to find out which column name + # in the data source corresponds to the actually displayed column name in the + # table reason being that the unique column ID for DB may not be nice to look at columns_to_show = [] for column in column_list: # first find out what the column name in the header is: From 6ca38ec8d5812cd0051ddbae21eed34d424f6a43 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 14:05:14 +0000 Subject: [PATCH 131/358] Clean up XChemUtils --- xce/lib/XChemUtils.py | 654 +++++++++++++----------------------------- 1 file changed, 204 insertions(+), 450 deletions(-) diff --git a/xce/lib/XChemUtils.py b/xce/lib/XChemUtils.py index 553e9634..ccda4ee5 100755 --- a/xce/lib/XChemUtils.py +++ b/xce/lib/XChemUtils.py @@ -5,7 +5,6 @@ import math import subprocess import getpass -import shutil import json import time @@ -45,12 +44,8 @@ def __init__(self, dimple): self.fileroot_in = dimple["fileroot_in"] self.mtz_free = self.fileroot_in + ".free.mtz" self.mtz_in = self.fileroot_in + ".mtz" - # need to set $CCP4_SCR, because the default directory in /home/zqr16691/tmp fills up easily - # and then dimple will not run - - # if not os.path.isdir(self.project_directory[:self.project_directory.find('processing')+11]+'/tmp'): - # os.mkdir(self.project_directory[:self.project_directory.find('processing')+11]+'/tmp') - # self.ccp4_scratch=self.project_directory[:self.project_directory.find('processing')+11]+'/tmp' + # need to set $CCP4_SCR, because the default directory in /home/zqr16691/tmp + # fills up easily and then dimple will not run def get_Rfree(self): Cmds = "" @@ -63,54 +58,54 @@ def get_Rfree(self): ) ): Cmds = ( - # '#!'+os.getenv('SHELL')+'\n' "\n" - "cd %s/%s/Dimple\n" % (self.project_directory, self.xtalID) + "\n" - "pointless hklin ../%s hklref %s.mtz hklout %s.reind.mtz << EOF > pointless.log\n" + + "cd %s/%s/Dimple\n" % (self.project_directory, self.xtalID) + + "\n" + + "pointless hklin ../%s hklref %s.mtz hklout %s.reind.mtz" % (self.mtz_in, self.reference, self.xtalID) + + " << EOF > pointless.log\n" + " tolerance 5\n" - "EOF\n" - "\n" - "cad hklin1 %s.reind.mtz hklin2 %s.mtz hklout cad.mtz << EOF > cad.log\n" + + "EOF\n" + + "\n" + + "cad hklin1 %s.reind.mtz hklin2 %s.mtz hklout cad.mtz <<" % (self.xtalID, self.reference) + + " EOF > cad.log\n" + " labin file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" - " labout file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" - " labin file_number 2 E1=FreeR_flag\n" - " labout file_number 2 E1=FreeR_flag\n" - " END\n" - "EOF\n" - "\n" - "freerflag hklin cad.mtz hklout ../%s << EOF > freerflag.log\n" + + " labout file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" + + " labin file_number 2 E1=FreeR_flag\n" + + " labout file_number 2 E1=FreeR_flag\n" + + " END\n" + + "EOF\n" + + "\n" + + "freerflag hklin cad.mtz hklout ../%s << EOF > freerflag.log\n" % self.mtz_free + " COMPLETE FREE=FreeR_flag\n" - " END\n" - "EOF\n" - "#uniqueify -f FreeR_flag cad.mtz ../%s\n" % self.mtz_free + + " END\n" + + "EOF\n" + + "#uniqueify -f FreeR_flag cad.mtz ../%s\n" % self.mtz_free ) else: Cmds = ( - # '#!'+os.getenv('SHELL')+'\n' "\n" - "cd %s/%s/Dimple\n" % (self.project_directory, self.xtalID) + "\n" - "pointless hklin ../%s xyzin %s.pdb hklout %s.reind.mtz << EOF > pointless.log\n" + + "cd %s/%s/Dimple\n" % (self.project_directory, self.xtalID) + + "\n" + + "pointless hklin ../%s xyzin %s.pdb hklout %s.reind.mtz" % (self.mtz_in, self.reference, self.xtalID) + + " << EOF > pointless.log\n" + " tolerance 5\n" - "EOF\n" - "\n" - "cad hklin1 %s.reind.mtz hklout cad.mtz << EOF > cad.log\n" + + "EOF\n" + + "\n" + + "cad hklin1 %s.reind.mtz hklout cad.mtz << EOF > cad.log\n" % self.xtalID + " labin file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" - " labout file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" - " END\n" - "EOF\n" - "\n" - "freerflag hklin cad.mtz hklout ../%s > freerflag.log\n" + + " labout file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" + + " END\n" + + "EOF\n" + + "\n" + + "freerflag hklin cad.mtz hklout ../%s > freerflag.log\n" % self.mtz_free + "#uniqueify cad.mtz ../{0!s}\n".format(self.mtz_free) ) - # os.chdir(os.path.join(self.project_directory,self.xtalID)) - # os.system(Cmds) - # os.symlink(os.path.join('Dimple',self.xtalID+'.free.mtz'),self.xtalID+'.free.mtz') return Cmds def dimple(self): @@ -119,7 +114,8 @@ def dimple(self): if os.path.isdir( "{0!s}/{1!s}/Dimple".format(self.project_directory, self.xtalID) ): - # this 'if not' step is usually not necessary; only if process was stopped in an odd way + # this 'if not' step is usually not necessary + # only if process was stopped in an odd way if not os.path.isfile( self.project_directory + "/" + self.xtalID + "/" + self.mtz_free ): @@ -152,7 +148,8 @@ def dimple(self): # in case additional ligands are present in the reference.pdb file, # the user needs to provide the following files: # - .pdb - # - .cif # this file contains restraints for all the ligands in the respective pdb file + # - .cif - this file contains restraints for all the ligands in the + # respective pdb file if os.path.isfile(self.reference + ".cif"): ref_lib = " --libin " + self.reference + ".cif" @@ -231,7 +228,6 @@ def make_png( ): Logfile = XChemLog.updateLog(xce_logfile) - # if not os.path.isfile(os.path.join(initial_model_directory,sample,'compound','ACEDRG_IN_PROGRESS')): os.system("touch RESTRAINTS_IN_PROGRESS") header = "#!" + os.getenv("SHELL") + "\n" @@ -243,7 +239,8 @@ def make_png( # note: compoundIDs and smiles are semi-colon separated if len(compoundID.split(";")) > 1: Logfile.insert( - "looks like you are working with cocktails; found the following IDs and smiles:" + "looks like you are working with cocktails;" + " found the following IDs and smiles:" ) if len(compoundID.split(";")) != len(smiles.split(";")): Logfile.error("Number of compoundIDs and SMILES does not match:") @@ -272,7 +269,10 @@ def make_png( if os.getcwd().startswith("/dls"): software += "module load ccp4/7.1.018\n" software += "module load buster\n" - software += "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n" + software += ( + "export BDG_TOOL_MOGUL=" + "/dls_sw/apps/ccdc/CSD_2020/bin/mogul\n" + ) software += "export BDG_TOOL_OBABEL='none'\n" for i in range(len(compoundID.split(";"))): @@ -289,27 +289,34 @@ def make_png( compoundID.split(";")[i].replace(" ", ""), ) elif restraints_program == "phenix.elbow": - software += 'phenix.elbow --smiles="{0!s}" --id {1!s}} --output {2!s}\n'.format( - smiles.split(";")[i], - cID, - compoundID.split(";")[i].replace(" ", ""), + software += ( + "phenix.elbow" + + '--smiles="{0!s}" --id {1!s} --output {2!s}\n'.format( + smiles.split(";")[i], + cID, + compoundID.split(";")[i].replace(" ", ""), + ) ) elif restraints_program == "grade": if external_software["mogul"]: mogul = "" else: mogul = "-nomogul" - software += 'grade -resname {0!s} {1!s} "{2!s}" -ocif {3!s}.cif -opdb {4!s}.pdb\n'.format( - cID, - mogul, - smiles.split(";")[i], - compoundID.split(";")[i].replace(" ", ""), - compoundID.split(";")[i].replace(" ", ""), + software += ( + "grade" + + ' -resname {0!s} {1!s} "{2!s}"'.format( + cID, mogul, smiles.split(";")[i] + ) + + " -ocif {0!s}.cif -opdb {1!s}.pdb\n".format( + compoundID.split(";")[i].replace(" ", ""), + compoundID.split(";")[i].replace(" ", ""), + ) ) else: # check if CompoundSMILEScovalent field is not Null - # CompoundSMILESproduct can be used to create only a CIF file for the product to make fitting easier + # CompoundSMILESproduct can be used to create only a CIF file + # for the product to make fitting easier # however, the complete smiles string will be used to make the png file productSmiles = None db = XChemDB.data_source(os.path.join(database_directory, data_source_file)) @@ -349,12 +356,16 @@ def make_png( if os.path.isfile( os.path.join(initial_model_directory, sample, "old.cif") ): - software += "phenix.elbow --file=../old.cif --id LIG --output {0!s}\n".format( - (compoundID.replace(" ", "")) + software += ( + "phenix.elbow --file=../old.cif --id LIG" + + " --output {0!s}\n".format((compoundID.replace(" ", ""))) ) else: - software += 'phenix.elbow --smiles="{0!s}" --id LIG --output {1!s}\n'.format( - productSmiles, compoundID.replace(" ", "") + software += ( + "phenix.elbow" + + ' --smiles="{0!s}" --id LIG --output {1!s}\n'.format( + productSmiles, compoundID.replace(" ", "") + ) ) elif restraints_program == "grade": if os.getcwd().startswith("/dls"): @@ -371,32 +382,36 @@ def make_png( if os.path.isfile( os.path.join(initial_model_directory, sample, "old.cif") ): - software += "grade -resname LIG {0!s} -in ../old.cif -ocif {1!s}.cif -opdb {2!s}.pdb\n".format( - mogul, compoundID.replace(" ", ""), compoundID.replace(" ", "") + software += "grade -resname LIG {0!s}".format( + mogul + ) + " -in ../old.cif -ocif {0!s}.cif -opdb {1!s}.pdb\n".format( + compoundID.replace(" ", ""), compoundID.replace(" ", "") ) else: - software += 'grade -resname LIG {0!s} "{1!s}" -ocif {2!s}.cif -opdb {3!s}.pdb\n'.format( - mogul, - productSmiles, + software += 'grade -resname LIG {0!s} "{1!s}"'.format( + mogul, productSmiles + ) + " -ocif {0!s}.cif -opdb {1!s}.pdb\n".format( compoundID.replace(" ", ""), compoundID.replace(" ", ""), ) # merge all compound CIFs into 1 file called merged.cif - software += "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/merge_ligand_cif_files.py {0!s}\n".format( - os.path.join(initial_model_directory, sample, "compound") + software += ( + "$CCP4/bin/ccp4-python" + "$XChemExplorer_DIR/helpers/merge_ligand_cif_files.py {0!s}\n".format( + os.path.join(initial_model_directory, sample, "compound") + ) ) - # Removal of the hydrogen atoms in PDB files is required for REFMAC 5 run. With hydrogens some ligands fail to - # pass the external restraints in pandda.giant.make_restraints. + # Removal of the hydrogen atoms in PDB files is required for REFMAC 5 run. + # With hydrogens some ligands fail to pass the external restraints in + # pandda.giant.make_restraints. # Copy the file with hydrogens to retain in case needed - - check_stereochemistry = "" - Cmds = ( header + "\n" 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"' + "\n" - "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py {0!s} {1!s} {2!s} {3!s}".format( + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py" + " {0!s} {1!s} {2!s} {3!s}".format( os.path.join(database_directory, data_source_file), sample, "RefinementCIFStatus", @@ -447,8 +462,6 @@ def make_png( sample, compoundID, ccp4_scratch_directory ) ) - # print Cmds - # print 'ccp4_scratch',ccp4_scratch_directory f = open("xce_{0!s}_{1!s}.sh".format(restraints_program, str(counter)), "w") f.write(Cmds) f.close() @@ -457,29 +470,10 @@ def make_png( ) -# if queueing_system_available: -# os.system('qsub acedrg.sh') -# else: -# os.system('chmod +x acedrg.sh') -# os.system('./acedrg.sh') - -# os.chdir(os.path.join(initial_model_directory,sample)) -# if os.path.isfile(os.path.join(initial_model_directory,sample,'compound',compoundID.replace(' ','')+'.pdb'))\ -# and not os.path.isfile(os.path.join(initial_model_directory,sample,compoundID.replace(' ','')+'.pdb')): -# os.symlink(os.path.join(initial_model_directory,sample,'compound',compoundID.replace(' ','')+'.pdb'),compoundID.replace(' ','')+'.pdb') -# if os.path.isfile(os.path.join(initial_model_directory,sample,'compound',compoundID.replace(' ','')+'.cif'))\ -# and not os.path.isfile(os.path.join(initial_model_directory,sample,compoundID.replace(' ','')+'.cif')): -# os.symlink(os.path.join(initial_model_directory,sample,'compound',compoundID.replace(' ','')+'.cif'),compoundID.replace(' ','')+'.cif') -# if os.path.isfile(os.path.join(initial_model_directory,sample,'compound',compoundID.replace(' ','')+'.png'))\ -# and not os.path.isfile(os.path.join(initial_model_directory,sample,compoundID.replace(' ','')+'.png')): -# os.symlink(os.path.join(initial_model_directory,sample,'compound',compoundID.replace(' ','')+'.png'),compoundID.replace(' ','')+'.png') - - class parse: def __init__(self): self.space_group_dict = { "triclinic": ["P1"], - # 'monoclinic': ['P2','P21','C121','P1211','P121'], "monoclinic_P": ["P2", "P21", "P1211", "P121"], "monoclinic_C": ["C2", "C121"], "orthorhombic": [ @@ -620,7 +614,6 @@ def __init__(self): self.aimless = { "DataProcessingProgram": "n/a", - # 'DataCollectionRun': 'n/a', "DataProcessingSpaceGroup": "n/a", "DataProcessingUnitCell": "n/a", "DataProcessingA": "n/a", @@ -690,7 +683,6 @@ def GetAimlessLog(self, Logfile): "Alert": "#FF0000", } - spg = "n/a" a = "n/a" b = "n/a" c = "n/a" @@ -710,9 +702,8 @@ def GetAimlessLog(self, Logfile): Aimless["AutoProc"] = "autoPROC" # get run number from logfile - # Note: only works if file is in original directory, but not once it lifes in 'inital_model' - # print self.Logfile.split('/')[9].split('_')[1] - # if len(self.Logfile.split('/'))>8 and len(self.Logfile.split('/')[9].split('_'))==1: + # only works if file is in original directory, but not once it lifes in + # 'inital_model' try: Aimless["Run"] = self.Logfile.split("/")[9].split("_")[1] except IndexError: @@ -788,12 +779,6 @@ def GetAimlessLog(self, Logfile): + str(gamma) ) - # Hex Color code: - # red: #FF0000 - # orange: #FF9900 - # green: #00FF00 - # gray: #E0E0E0 - if Aimless["ResolutionHigh"] == "n/a" or Aimless["RmergeLow"] == "n/a": Aimless["Alert"] = "#FF0000" else: @@ -821,7 +806,6 @@ def read_aimless_logfile(self, logfile): # essentially same as above, but compatible with datasource # will hopefully supersede function above - spg = "n/a" a = "n/a" b = "n/a" c = "n/a" @@ -847,25 +831,14 @@ def read_aimless_logfile(self, logfile): self.aimless["DataProcessingProgram"] = "aP_staraniso" # get run number from logfile - # Note: only works if file is in original directory, but not once it moved to 'inital_model' folder# - ## print self.Logfile.split('/')[9].split('_')[1] - # if len(self.Logfile.split('/'))>8 and len(self.Logfile.split('/')[9].split('_'))==1: - # try: - # self.aimless['DataCollectionRun']=logfile.split('/')[9].split('_')[1] - # except IndexError: - # pass + # only works if file is in original directory, but not once it moved to + # 'inital_model' folder if logfile.endswith(".log") or logfile.endswith(".table1"): self.aimless_logile(logfile) elif logfile.endswith(".json"): self.json_logfile(logfile) - # Hex Color code: - # red: #FF0000 - # orange: #FF9900 - # green: #00FF00 - # gray: #E0E0E0 - if ( self.aimless["DataProcessingA"] != "n/a" and self.aimless["DataProcessingB"] != "n/a" @@ -902,7 +875,8 @@ def read_aimless_logfile(self, logfile): * high_symmetry_boost * float(self.aimless["DataProcessingIsigOverall"]) ) / float(self.aimless["DataProcessingUnitCellVolume"]) - # When P-6 was accidentally used self.aimless['DataProcessingPointGroup'] through a KeyError, so handling this + # When P-6 was accidentally used self.aimless['DataProcessingPointGroup'] + # through a KeyError, so handling this except (ValueError, KeyError): self.aimless["DataProcessingScore"] = 0.0 self.aimless["DataProcessingUnitCell"] = ( @@ -950,11 +924,7 @@ def read_aimless_logfile(self, logfile): def aimless_logile(self, logfile): resolution_at_15_sigma_line_overall_found = False resolution_at_20_sigma_line_overall_found = False - resolution_at_sigma_line_overall_found = False for line_number, line in enumerate(open(logfile)): - # if 'Wavelength' in line: - # print 'here' - # print line.split() if "Wavelength" in line and len(line.split()) >= 2: self.aimless["DataCollectionWavelength"] = line.split()[1] if "Low resolution limit" in line and len(line.split()) == 6: @@ -1059,29 +1029,6 @@ def aimless_logile(self, logfile): ] = self.get_pointgroup_from_space_group( self.aimless["DataProcessingSpaceGroup"] ) - # print a,b,c,alpha,beta,gamma,self.aimless['DataProcessingLattice'] - - # if a != 'n/a' and b != 'n/a' and c != 'n/a' and \ - # alpha != 'n/a' and beta != 'n/a' and gamma != 'n/a' and self.aimless[ - # 'DataProcessingLattice'] != 'n/a': - # self.aimless['DataProcessingUnitCellVolume'] = str( - # self.calc_unitcell_volume_from_logfile(float(a), float(b), float(c), - # math.radians(float(alpha)), - # math.radians(float(beta)), - # math.radians(float(gamma)), - # self.aimless['DataProcessingLattice'])) - # try: - # high_symmetry_boost = self.nr_asu_in_unitcell_for_point_group[ - # self.aimless['DataProcessingPointGroup']] - # self.aimless['DataProcessingScore'] = (float( - # self.aimless['DataProcessingUniqueReflectionsOverall']) * float(self.aimless['DataProcessingCompletenessOverall']) * high_symmetry_boost * float(self.aimless['DataProcessingIsigOverall'])) / float( - # self.aimless['DataProcessingUnitCellVolume']) - # except ValueError: - # self.aimless['DataProcessingScore'] = 0.0 - # self.aimless['DataProcessingUnitCell'] = str(a) + ' ' + str(b) + ' ' + str(c) + ' ' + str(alpha) + ' ' + str( - # beta) + ' ' + str(gamma) - # self.aimless['DataProcessingResolutionOverall'] = str( - # self.aimless['DataProcessingResolutionLow']) + ' - ' + str(self.aimless['DataProcessingResolutionHigh']) def json_logfile(self, logfile): with open(logfile, "r") as log: @@ -1155,7 +1102,6 @@ def json_logfile(self, logfile): self.aimless["DataProcessingCChalfHigh"] = str( round(obj["cc_one_half"][len(obj["cc_one_half"]) - 1], 2) ) - # self.aimless['DataProcessingResolutionHigh15sigma'] = self.aimless["DataProcessingUniqueReflectionsLow"] = str(obj["n_uniq"][0]) self.aimless["DataProcessingUniqueReflectionsHigh"] = str( @@ -1165,10 +1111,6 @@ def json_logfile(self, logfile): self.aimless["DataProcessingUniqueReflectionsOverall"] = str( obj["overall"]["n_obs"] ) - # self.aimless['DataProcessingPointGroup'] = - # self.aimless['DataProcessingUnitCellVolume'] = - # self.aimless['DataProcessingAlert'] = - # self.aimless['DataProcessingScore'] = json_name = logfile[logfile.rfind("/") + 1 :] mmcif_file = logfile.replace("LogFiles", "DataFiles").replace( json_name, "xia2.mmcif" @@ -1184,26 +1126,34 @@ def make_pseudo_aimless_log_from_json(self, logfile): "==============================================================\n" "\n" " $TEXT:Result: $$ $$\n" - "Summary data for Project: nt11175v63 Crystal: xPHIPAx17245 Dataset: SAD\n" + "Summary data for" + " Project: nt11175v63" + " Crystal: xPHIPAx17245" + " Dataset: SAD\n" "\n" - " Overall InnerShell OuterShell\n" - "Low resolution limit {0!s} {1!s} {2!s}\n".format( + " " + "Overall InnerShell OuterShell\n" + "Low resolution limit" + " {0!s} {1!s} {2!s}\n".format( self.aimless["DataProcessingResolutionLow"], self.aimless["DataProcessingResolutionLow"], self.aimless["DataProcessingResolutionHighOuterShell"], ) - + "High resolution limit {0!s} {1!s} {2!s}\n".format( + + "High resolution limit" + " {0!s} {1!s} {2!s}\n".format( self.aimless["DataProcessingResolutionHigh"], self.aimless["DataProcessingResolutionLowInnerShell"], self.aimless["DataProcessingResolutionHigh"], ) + "\n" - "Rmerge (within I+/I-) {0!s} {1!s} {2!s}\n".format( + "Rmerge (within I+/I-)" + " {0!s} {1!s} {2!s}\n".format( self.aimless["DataProcessingRmergeOverall"], self.aimless["DataProcessingRmergeLow"], self.aimless["DataProcessingRmergeHigh"], ) - + "Rmerge (all I+ and I-) {0!s} {1!s} {2!s}\n".format( + + "Rmerge (all I+ and I-)" + " {0!s} {1!s} {2!s}\n".format( self.aimless["DataProcessingRmergeOverall"], self.aimless["DataProcessingRmergeLow"], self.aimless["DataProcessingRmergeHigh"], @@ -1214,27 +1164,32 @@ def make_pseudo_aimless_log_from_json(self, logfile): "Rpim (all I+ & I-) - - - \n" "Rmerge in top intensity bin - - - \n" "Total number of observations - - - \n" - "Total number unique {0!s} {1!s} {2!s}\n".format( + "Total number unique" + " {0!s} {1!s} {2!s}\n".format( self.aimless["DataProcessingUniqueReflectionsOverall"], self.aimless["DataProcessingUniqueReflectionsLow"], self.aimless["DataProcessingUniqueReflectionsHigh"], ) - + "Mean((I)/sd(I)) {0!s} {1!s} {2!s}\n".format( + + "Mean((I)/sd(I))" + " {0!s} {1!s} {2!s}\n".format( self.aimless["DataProcessingIsigOverall"], self.aimless["DataProcessingIsigLow"], self.aimless["DataProcessingIsigHigh"], ) - + "Mn(I) half-set correlation CC(1/2) {0!s} {1!s} {2!s}\n".format( + + "Mn(I) half-set correlation CC(1/2)" + " {0!s} {1!s} {2!s}\n".format( self.aimless["DataProcessingCChalfOverall"], self.aimless["DataProcessingCChalfLow"], self.aimless["DataProcessingCChalfHigh"], ) - + "Completeness {0!s} {1!s} {2!s}\n".format( + + "Completeness" + " {0!s} {1!s} {2!s}\n".format( self.aimless["DataProcessingCompletenessOverall"], self.aimless["DataProcessingCompletenessLow"], self.aimless["DataProcessingCompletenessHigh"], ) - + "Multiplicity {0!s} {1!s} {2!s}\n".format( + + "Multiplicity" + " {0!s} {1!s} {2!s}\n".format( self.aimless["DataProcessingMultiplicityOverall"], self.aimless["DataProcessingMultiplicityLow"], self.aimless["DataProcessingMultiplicityHigh"], @@ -1310,7 +1265,6 @@ def get_pointgroup_from_space_group(self, logfile_spacegroup): return pointgroup def calc_unitcell_volume_from_logfile(self, a, b, c, alpha, beta, gamma, lattice): - # print '>>>',a,b,c,alpha,beta,gamma,lattice unitcell_volume = 0 if lattice == "triclinic": unitcell_volume = ( @@ -1327,8 +1281,6 @@ def calc_unitcell_volume_from_logfile(self, a, b, c, alpha, beta, gamma, lattice + 2 * (math.cos(alpha) * math.cos(beta) * math.cos(gamma)) ) ) - # print 'unit cell volume',unitcell_volume - # if lattice=='monoclinic': if "monoclinic" in lattice: unitcell_volume = round(a * b * c * math.sin(beta), 1) if lattice == "orthorhombic" or lattice == "tetragonal" or lattice == "cubic": @@ -1337,12 +1289,6 @@ def calc_unitcell_volume_from_logfile(self, a, b, c, alpha, beta, gamma, lattice unitcell_volume = round(a * b * c * (math.sin(math.radians(60))), 1) return unitcell_volume - # def get_all_values_as_dict(self): - # info = { 'unitcell': 'n/a', - # 'spacegroup': 'n/a', - # 'unitcell_volume': 'n/a', - # 'bravais_lattice': 'n/a' } - def PDBheader(self, pdbfile): PDBinfo = { "Rcryst": "n/a", @@ -1468,7 +1414,7 @@ def PDBheader(self, pdbfile): + " " + line.split()[6] ) - # PDBinfo['SpaceGroup']=line[55:len(line)-1].replace(' ','').rstrip('\r') + PDBinfo["SpaceGroup"] = str(line[55:65]).rstrip() PDBinfo["Lattice"] = self.get_lattice_from_space_group( @@ -1594,7 +1540,6 @@ def __init__(self, mtzfile): self.space_group_dict = { "triclinic": [1], - # 'monoclinic': [3,4,5], "monoclinic_P": [3, 4], "monoclinic_C": [5], "orthorhombic": [16, 17, 18, 19, 20, 21, 22, 23, 24], @@ -1750,7 +1695,6 @@ def __init__(self, mtzfile): self.aimless = { "DataProcessingProgram": "n/a", - # 'DataCollectionRun': 'n/a', "DataProcessingSpaceGroup": "n/a", "DataProcessingUnitCell": "n/a", "DataProcessingA": "n/a", @@ -1832,7 +1776,6 @@ def get_point_group_from_spg_number(self, number): return pointgroup def get_unit_cell_from_mtz(self): - unitcell = [] cell_line = 100000 a = 0 b = 0 @@ -1941,12 +1884,12 @@ def get_number_measured_reflections(self): missing_reflections = "0" all_reflections = "0" meassured_reflections = "0" - resolution_line = 1000000 mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) foundTable = False for n, line in enumerate(iter(mtzdmp.stdout.readline, "")): if line.startswith( - " Col Sort Min Max Num % Mean Mean Resolution Type Column" + " Col Sort Min Max Num %" + " Mean Mean Resolution Type Column" ): foundTable = True if foundTable and len(line.split()) == 12: @@ -1965,10 +1908,6 @@ def get_number_measured_reflections(self): def calculate_correlaton_between_intensities_in_mtzfiles(self, mtzin): CC = "0.0" errorMessage = "" - # cmd = ( 'pointless hklin %s hklref %s << eof\n' %(mtzin,self.mtzfile)+ - # 'labref F=F\n' - # 'labin F=F\n' - # 'eof\n' ) cmd = ( "pointless hklin %s hklref %s << eof\n" % (mtzin, self.mtzfile) + "labref I=IMEAN\n" @@ -1988,8 +1927,8 @@ def calculate_correlaton_between_intensities_in_mtzfiles(self, mtzin): errorMessage = "**** Incompatible symmetries ****" break if ( - "Merged test dataset (HKLIN) has different Laue symmetry to reference set" - in line + "Merged test dataset (HKLIN)" + " has different Laue symmetry to reference set" in line ): errorMessage = "%s has different Laue symmetry to %s" % ( mtzin, @@ -2068,7 +2007,6 @@ def get_all_values_as_dict(self): * (math.cos(alpha_rad) * math.cos(beta_rad) * math.cos(gamma_rad)) ) ) - # elif mtz['bravais_lattice']=='monoclinic': elif "monoclinic" in mtz["bravais_lattice"]: mtz["unitcell_volume"] = round(a * b * c * math.sin(beta_rad), 1) elif ( @@ -2144,204 +2082,93 @@ def __init__(self, xce_logfile): self.available_programs = {} self.Logfile = XChemLog.updateLog(xce_logfile) - def check(self): + @staticmethod + def is_available(program): + try: + devnull = open(os.devnull, "w") + subprocess.Popen(program, stdout=devnull, stderr=devnull).communicate() + return True + except OSError as e: + if e.errno == os.errno.ENOENT: + return False + + def log_found_status(self, program_name): + self.Logfile.insert( + "{0:50} {1:10}".format( + "checking for {}:".format(program_name), + "found" if self.available_programs[program_name] else "not found", + ) + ) + def check(self): self.Logfile.insert("Searching for external software...") # default is False; user needs to explicitely set this - self.available_programs["qsub_remote"] = "" + self.available_programs["qsub_remote"] = False - FNULL = open(os.devnull, "w") - - try: - # subprocess.call(['qstat'], stdout=FNULL, stderr=subprocess.STDOUT) - p = subprocess.Popen( - "qstat", - shell=True, - stdin=subprocess.PIPE, - stdout=subprocess.PIPE, - stderr=subprocess.STDOUT, - close_fds=True, - ) - status = "found" - try: - for line in p.stdout: - if ( - "symbol lookup error:" in line - or "command not found" in line - or "error" in line - ): - self.available_programs["qsub"] = False - self.available_programs["qsub_array"] = False - status = "not found" - array_status = "not found" - except IOError: - self.available_programs["qsub"] = False - self.available_programs["qsub_array"] = False - status = "not found" - array_status = "not found" - - if status == "found": - self.available_programs["qsub"] = True - # if os.getcwd().startswith('/dls'): - if os.path.isdir("/dls"): - self.available_programs["qsub_array"] = True - array_status = "found" - else: - self.available_programs["qsub_array"] = False - array_status = "not found" - except OSError: - self.available_programs["qsub"] = False - self.available_programs["qsub_array"] = False - status = "not found" - array_status = "not found" - self.Logfile.insert("{0:50} {1:10}".format("checking for qsub:", status)) - # print '{0:50} {1:10}'.format('-checking for qsub:', status) - # if os.getcwd().startswith('/dls'): - if os.path.isdir("/dls"): - self.Logfile.insert( - "{0:50} {1:10}".format("checking for array qsub:", array_status) - ) + self.available_programs["qsub"] = True if self.is_available("qsub") else False + self.available_programs["qsub_array"] = ( + True if self.is_available("qsub") else False + ) + self.log_found_status("qsub") + self.log_found_status("qsub_array") - try: - subprocess.call(["refmac5", "end"], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs["refmac5"] = True - status = "found" - except OSError: - self.available_programs["refmac5"] = False - status = "not found" - self.Logfile.insert("{0:50} {1:10}".format("checking for refmac5:", status)) + self.available_programs["refmac5"] = ( + True if self.is_available(["refmac5", "end"]) else False + ) + self.log_found_status("refmac5") - try: - subprocess.call( - ["phenix.molprobity"], stdout=FNULL, stderr=subprocess.STDOUT - ) - self.available_programs["phenix.molprobity"] = True - status = "found" - except OSError: - self.available_programs["phenix.molprobity"] = False - status = "not found" - self.Logfile.insert( - "{0:50} {1:10}".format("checking for phenix.molprobity:", status) + self.available_programs["phenix.molprobity"] = ( + True if self.is_available("phenix.molprobity") else False ) + self.log_found_status("phenix.molprobity") - try: - subprocess.call( - ["phenix.find_tls_groups"], stdout=FNULL, stderr=subprocess.STDOUT - ) - self.available_programs["phenix.find_tls_groups"] = True - status = "found" - except OSError: - self.available_programs["phenix.find_tls_groups"] = False - status = "not found" - self.Logfile.insert( - "{0:50} {1:10}".format("checking for phenix.find_tls_groups:", status) + self.available_programs["phenix.find_tls_groups"] = ( + True if self.is_available("phenix.find_tls_groups") else False ) + self.log_found_status("phenix.find_tls_groups") - try: - subprocess.call( - ["mmtbx.validate_ligands"], stdout=FNULL, stderr=subprocess.STDOUT - ) - self.available_programs["mmtbx.validate_ligands"] = True - status = "found" - except OSError: - self.available_programs["mmtbx.validate_ligands"] = False - status = "not found" - self.Logfile.insert( - "{0:50} {1:10}".format("checking for mmtbx.validate_ligands:", status) + self.available_programs["mmtbx.validate_ligands"] = ( + True if self.is_available("mmtbx.validate_ligands") else False ) + self.log_found_status("mmtbx.validate_ligands") - try: - subprocess.call(["acedrg"], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs["acedrg"] = True - shutil.rmtree("AcedrgOut_TMP") - status = "found" - except OSError: - self.available_programs["acedrg"] = False - status = "not found" - self.Logfile.insert("{0:50} {1:10}".format("checking for acedrg:", status)) + self.available_programs["acedrg"] = ( + True if self.is_available(["acedrg", "-h"]) else False + ) + self.log_found_status("acedrg") - try: - subprocess.call(["phenix.elbow"], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs["phenix.elbow"] = True - status = "found" - except OSError: - self.available_programs["phenix.elbow"] = False - status = "not found" - self.Logfile.insert( - "{0:50} {1:10}".format("checking for phenix.elbow:", status) + self.available_programs["phenix.elbow"] = ( + True if self.is_available("phenix.elbow") else False ) + self.log_found_status("phenix.elbow") - try: - subprocess.call(["grade"], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs["grade"] = True - status = "found" - except OSError: - self.available_programs["grade"] = False - status = "not found" - self.Logfile.insert("{0:50} {1:10}".format("checking for grade:", status)) + self.available_programs["grade"] = True if self.is_available("grade") else False + self.log_found_status("grade") - try: - subprocess.call( - ["giant.create_occupancy_params"], - stdout=FNULL, - stderr=subprocess.STDOUT, - ) - self.available_programs["giant.create_occupancy_params"] = True - status = "found" - except OSError: - self.available_programs["giant.create_occupancy_params"] = False - status = "not found" - self.Logfile.insert( - "{0:50} {1:10}".format( - "checking for giant.create_occupancy_params:", status - ) + self.available_programs["giant.create_occupancy_params"] = ( + True if self.is_available("giant.create_occupancy_params") else False ) + self.log_found_status("giant.create_occupancy_params") - self.Logfile.insert("checking if MOGUL is configured...") - self.available_programs["mogul"] = False - if "BDG_TOOL_MOGUL" in os.environ: - self.Logfile.insert( - "BDG_TOOL_MOGUL is set to " + os.environ["BDG_TOOL_MOGUL"] - ) - if str(os.environ["BDG_TOOL_MOGUL"]).lower() == "none": - self.Logfile.warning("BDG_TOOL_MOGUL is not properly configured!") - self.Logfile.hint( - 'try adding "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul" to your .bashrc file' - ) - else: - if os.path.isfile(os.getenv("BDG_TOOL_MOGUL")): - self.available_programs["mogul"] = True - status = "found" - else: - status = "not found" - self.Logfile.hint( - 'try adding "export PATH=/dls_sw/apps/ccdc/CSD_2020/bin:$PATH" to your .bashrc file' - ) - else: - self.Logfile.warning("BDG_TOOL_MOGUL is not set!") - self.Logfile.hint( - 'try adding "export BDG_TOOL_MOGUL=/dls_sw/apps/ccdc/CSD_2020/bin/mogul" to your .bashrc file' - ) - status = "not found" - self.Logfile.insert("{0:50} {1:10}".format("checking for mogul:", status)) + self.available_programs["mogul"] = ( + True + if "BDG_TOOL_MOGUL" in os.environ + and self.is_available(os.environ["BDG_TOOL_MOGUL"]) + else False + ) + self.log_found_status("mogul") - try: - subprocess.call(["gemmi"], stdout=FNULL, stderr=subprocess.STDOUT) - self.available_programs["gemmi"] = True - status = "found" - except OSError: - self.available_programs["gemmi"] = False - status = "not found" - self.Logfile.insert("{0:50} {1:10}".format("checking for gemmi:", status)) + self.available_programs["gemmi"] = True if self.is_available("gemmi") else False + self.log_found_status("gemmi") return self.available_programs class ParseFiles: def __init__(self, DataPath, xtalID): - # probably need to read in compoundID, because for custom projects, need to take newest pdb file - # that has not same root as compoundID + # probably need to read in compoundID, because for custom projects + # need to take newest pdb file that has not same root as compoundID self.DataPath = DataPath self.xtalID = xtalID @@ -2426,8 +2253,6 @@ def UpdateQualityIndicators(self): for line in open( self.DataPath + "/" + self.xtalID + "/validation_summary.txt" ): - # if line.startswith(' Molprobity score ='): - # if line.lower().startswith(' molprobity score'): if "molprobity score" in line.lower(): if len(line.split()) >= 4: QualityIndicators["MolprobityScore"] = line.split()[3] @@ -2440,7 +2265,6 @@ def UpdateQualityIndicators(self): QualityIndicators["MolprobityScoreColor"] = "red" except ValueError: pass - # if line.lower().startswith(' ramachandran outliers ='): if "ramachandran outliers" in line.lower(): if len(line.split()) >= 4: QualityIndicators["RamachandranOutliers"] = line.split()[3] @@ -2455,7 +2279,6 @@ def UpdateQualityIndicators(self): QualityIndicators["RamachandranOutliersColor"] = "red" except ValueError: pass - # if line.startswith(' favored ='): if "favored" in line.lower(): if len(line.split()) >= 3: QualityIndicators["RamachandranFavored"] = line.split()[2] @@ -2474,7 +2297,6 @@ def UpdateQualityIndicators(self): for line in open( self.DataPath + "/" + self.xtalID + "/validate_ligands.txt" ): - # if line.startswith('| LIG'): if "LIG" in line: QualityIndicators["LigandCC"] = line.split()[6] if float(line.split()[6]) < 0.8: @@ -2571,7 +2393,6 @@ def __init__(self, pdb): self.space_group_dict = { "triclinic": [1], - # 'monoclinic': [3,4,5], "monoclinic_P": [3, 4], "monoclinic_C": [5], "orthorhombic": [16, 17, 18, 19, 20, 21, 22, 23, 24], @@ -2757,7 +2578,6 @@ def get_residues_with_resname(self, resname): ) return ligands - # def get_centre_of_gravity_of_residue(self,resname_resseq_chain): def get_centre_of_gravity_of_residue(self, resname_chain_resseq): resname_x = resname_chain_resseq.split("-")[0] chain_x = resname_chain_resseq.split("-")[1] @@ -2789,15 +2609,16 @@ def get_centre_of_gravity_of_residue(self, resname_chain_resseq): def save_residues_with_resname(self, outDir, resname): ligands = self.get_residues_with_resname(resname) ligList = [] - for l in ligands: + for ligand in ligands: sel_cache = self.hierarchy.atom_selection_cache() lig_sel = sel_cache.selection( - "(resname %s and resseq %s and chain %s)" % (l[0], l[1], l[2]) + "(resname %s and resseq %s and chain %s)" + % (ligand[0], ligand[1], ligand[2]) ) hierarchy_lig = self.hierarchy.select(lig_sel) - - # ligName = (l[0] + '-' + l[1] + '-' + l[2] + '.pdb').replace(' ', '') - ligName = (l[0] + "-" + l[2] + "-" + l[1] + ".pdb").replace(" ", "") + ligName = (ligand[0] + "-" + ligand[2] + "-" + ligand[1] + ".pdb").replace( + " ", "" + ) ligList.append(ligName) try: @@ -2854,7 +2675,6 @@ def GetProteinChains(self): return chain def GetSymm(self): - unitcell = [] a = "" b = "" c = "" @@ -2870,7 +2690,6 @@ def GetSymm(self): alpha = line.split()[4] beta = line.split()[5] gamma = line.split()[6] - # spg=line[55:len(line)-1] spg = line[55:65] return [a, b, c, alpha, beta, gamma, spg] @@ -2944,7 +2763,6 @@ def calc_unitcell_volume_from_pdb(self): + 2 * (math.cos(alpha) * math.cos(beta) * math.cos(gamma)) ) ) - # if lattice=='monoclinic': if "monoclinic" in lattice: unitcell_volume = round(a * b * c * math.sin(beta), 1) if lattice == "orthorhombic" or lattice == "tetragonal" or lattice == "cubic": @@ -3001,8 +2819,6 @@ def MatthewsCoefficient(self, sequence): def find_ligands(self): Ligands = [] - # need to count residue numbers in case of alternative conformations - ResiNum = [] for line in open(self.pdb): if (line.startswith("ATOM") or line.startswith("HETATM")) and line[ 17:20 @@ -3214,7 +3030,8 @@ def check_occupancies(self): errorText += ( "ERROR: " + item - + " -> summarised occupanies of alternative conformations are > 1.0 (" + + " -> summarised occupanies of alternative conformations" + + "are > 1.0 (" + str(occupancySumList) + ")\n" ) @@ -3225,7 +3042,8 @@ def get_xyz_coordinated_of_residue(self, chain, number): X = 0.0 Y = 0.0 Z = 0.0 - # pdb definition see: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM + # pdb definition see: + # http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM for line in open(self.pdb): if ( (line.startswith("ATOM") or line.startswith("HETATM")) @@ -3247,9 +3065,9 @@ def get_center_of_gravity_of_residue_ish(self, chain, number): x_list = [] y_list = [] z_list = [] - # pdb definition see: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM + # pdb definition see: + # http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM for line in open(self.pdb): - # print line[21:22],line[22:26] if ( (line.startswith("ATOM") or line.startswith("HETATM")) and line[21:22].replace(" ", "") == chain.replace(" ", "") @@ -3261,7 +3079,8 @@ def get_center_of_gravity_of_residue_ish(self, chain, number): y_list.append(Y) Z = float(line[46:54]) z_list.append(Z) - # 'ish' because it's not really the centre of gravity, but the the middle of the min/max of each x,y,z + # 'ish' because it's not really the centre of gravity + # but the the middle of the min/max of each x,y,z X = ((max(x_list) - min(x_list)) / 2) + min(x_list) Y = ((max(y_list) - min(y_list)) / 2) + min(y_list) Z = ((max(z_list) - min(z_list)) / 2) + min(z_list) @@ -3274,7 +3093,8 @@ def get_center_of_gravity_of_molecule_ish(self): x_list = [] y_list = [] z_list = [] - # pdb definition see: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM + # pdb definition see: + # http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM for line in open(self.pdb): if line.startswith("ATOM") or line.startswith("HETATM"): X = float(line[30:38]) @@ -3283,7 +3103,8 @@ def get_center_of_gravity_of_molecule_ish(self): y_list.append(Y) Z = float(line[46:54]) z_list.append(Z) - # 'ish' because it's not really the centre of gravity, but the the middle of the min/max of each x,y,z + # 'ish' because it's not really the centre of gravity + # but the the middle of the min/max of each x,y,z X = ((max(x_list) - min(x_list)) / 2) + min(x_list) Y = ((max(y_list) - min(y_list)) / 2) + min(y_list) Z = ((max(z_list) - min(z_list)) / 2) + min(z_list) @@ -3322,7 +3143,6 @@ def ElementDict(self, resname, chainID, resseq, altLoc): for line in open(self.pdb): if line.startswith("ATOM") or line.startswith("HETATM"): - atom_line = str(line[12:16]).replace(" ", "") resname_line = str(line[17:20]).replace(" ", "") chainID_line = str(line[21:23]).replace(" ", "") resseq_line = str(line[23:26]).replace(" ", "") @@ -3429,7 +3249,8 @@ def update_residue( def merge_pdb_file(self, pdbin): outPDB = "" - # only merge if residue with same resname, chain and resnumber not already in self.pdb!!! + # only merge if residue with same resname + # chain and resnumber not already in self.pdb!!! residueListReference = self.residue_details_as_list(self.pdb) residueListPDBin = self.residue_details_as_list(pdbin) DuplicateResidue = False @@ -3459,14 +3280,11 @@ def merge_pdb_file(self, pdbin): def get_symmetry_operators(self): symop = [] spg_number = str(self.get_spg_number_from_pdb()) - # print 'spg',spg_number foundSPG = False if os.path.isfile(os.path.join(os.getenv("CCP4"), "lib", "data", "symop.lib")): - # print 'a',os.path.join(os.getenv('CCP4'),'lib','data','symop.lib') for line in open( os.path.join(os.getenv("CCP4"), "lib", "data", "symop.lib") ): - # print line.split()[0] if foundSPG: if line.startswith(" "): tmp = line.replace("\n", "") @@ -3660,7 +3478,6 @@ def phenix_molprobity(self): QualityIndicators["MolprobityScoreColor"] = "red" except ValueError: pass - # if line.lower().startswith(' ramachandran outliers ='): if "ramachandran outliers" in line.lower(): if len(line.split()) >= 4: QualityIndicators["RamachandranOutliers"] = line.split()[3] @@ -3675,7 +3492,6 @@ def phenix_molprobity(self): QualityIndicators["RamachandranOutliersColor"] = "red" except ValueError: pass - # if line.startswith(' favored ='): if "favored" in line.lower(): if len(line.split()) == 4: QualityIndicators["RamachandranFavored"] = line.split()[2] @@ -3708,8 +3524,6 @@ def __init__(self, sample_mtz, reference_file_list): self.sample_mtz = sample_mtz self.reference_file_list = reference_file_list - # print reference_file_list - def find_suitable_reference(self, allowed_unitcell_difference_percent): found_suitable_reference = False unitcell_reference = "n/a" @@ -3728,7 +3542,6 @@ def find_suitable_reference(self, allowed_unitcell_difference_percent): unitcell_volume_autoproc = mtz_autoproc["unitcell_volume"] # check which reference file is most similar for o, reference_file in enumerate(self.reference_file_list): - # print reference_file try: if not reference_file[4] == 0: unitcell_difference = round( @@ -3739,7 +3552,7 @@ def find_suitable_reference(self, allowed_unitcell_difference_percent): * 100, 1, ) - # reference file is accepted when different in unitcell volume < 5% + # reference file accepted when diff in unitcell volume < 5% # and both files have the same lattice type if ( unitcell_difference < allowed_unitcell_difference_percent @@ -3766,7 +3579,6 @@ def find_suitable_reference(self, allowed_unitcell_difference_percent): class misc: def calculate_distance_between_coordinates(self, x1, y1, z1, x2, y2, z2): - # print '==> XCE: calculating distance between two coordinates' distance = 0.0 distance = math.sqrt( math.pow(float(x1) - float(x2), 2) @@ -3810,8 +3622,6 @@ def calculate_map(self, mtz, F, PH): ) os.system(cmd) - # print(cmd) - def cut_map_around_ligand(self, map, ligPDB, border): if map.endswith(".map"): map_extension = ".map" @@ -3830,69 +3640,14 @@ def cut_map_around_ligand(self, map, ligPDB, border): os.system(cmd) -# print(cmd) - -# self.translate_spg_to_number_dict = { -# 'p1': 1, 'p2': 3, 'p121': 4, 'c2': 5, 'c121': 5, 'p222': 16, -# 'p2122': 17, 'p2212': 17, 'p2221': 17, 'p21212': 18, 'p21221': 18, 'p22121': 18, -# 'p212121': 19, 'c2221': 20, 'c222': 21, 'f222': 22, 'i222': 23, 'i212121': 24, -# 'p4': 75, 'p41': 76, 'p42': 77, 'p43': 78, 'i4': 79, 'i41': 80, -# 'p422': 89, 'p4212': 90, 'p4122': 91, 'p41212': 92, 'p4222': 93, 'p42212': 94, -# 'p4322': 95, 'p43212': 96, 'i422': 97, 'i4122': 98, -# 'p3': 143, 'p31': 144, 'p32': 145, 'p312': 149, 'p321': 150, 'p3112': 151, 'p3121': 152, -# 'p3212': 153, 'p3221': 154, 'p6': 168, 'p61': 169, 'p65': 170, 'p62': 171, 'p64': 172, 'p63': 173, -# 'p622': 177, 'p6122': 178, 'p6522': 179, 'p6222': 180, 'p6422': 181, 'p6322': 182, -# 'r3': 146, 'h3': 146, 'r32': 155, 'h32': 155, -# 'p23': 195, 'f23': 196, 'i23': 197, 'p213': 198, 'i213': 199, -# 'p432': 207, 'p4232': 208, 'f432': 209, 'f4132': 210, 'i432': 211, 'p4332': 212, -# 'p4132': 213, 'i4132': 214 } -# -# self.map=map -# cmd = ( 'mapdump mapin {0!s} << eof\n'.format(self.map)+ -# 'end\n' -# 'eof' ) -# mapdump=subprocess.Popen(cmd,shell=True,stdout=subprocess.PIPE) -# self.grid_sampling=[0,0,0] -# self.cell_dimensions=[] -# self.space_group_number=0 -# for line in iter(mapdump.stdout.readline,''): -# if 'Grid sampling on x, y, z' in line: -# if len(line.split()) == 10: -# self.grid_sampling=[line.split()[7],line.split()[8],line.split()[9]] -# if 'Cell dimensions' in line: -# if len(line.split()) == 9: -# self.cell_dimensions=[line.split()[3],line.split()[4],line.split()[5],line.split()[6],line.split()[7],line.split()[8]] -# if 'Space-group' in line: -# if len(line.split()) == 3: -# self.space_group_number=line.split()[2] -# -# def grid_sampling(self): -# return self.grid_sampling -# -# def cell_dimensions(self): -# return self.cell_dimensions -# -# def space_group_number(self): -# return self.space_group_number -# -# def space_group(self): -# space_group='' -# space_group_number=self.space_group_number -# for spg in self.translate_spg_to_number_dict: -# if str(self.translate_spg_to_number_dict[spg]) == str(space_group_number): -# space_group=str(spg) -# return space_group -# - - class mtztools_gemmi: def __init__(self, mtz): self.mtz = gemmi.read_mtz_file(mtz) def get_map_labels(self): labelList = [] - for l in self.mtz.columns: - labelList.append(l.label) + for column in self.mtz.columns: + labelList.append(column.label) FWT = None PHWT = None DELFWT = None @@ -3954,7 +3709,6 @@ def map_to_sf(self, resolution): + self.emap[self.emap.find("BDC") + 4 :].find("_") ] ] - # mtz.write_to_file(self.emtz) else: print("failed to convert event map to SF") From f624fca54b9225827b1ca76e49ae3b935ad98656 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 14:19:46 +0000 Subject: [PATCH 132/358] Clean up update_pandda_status_flag --- xce/helpers/update_pandda_status_flag.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/xce/helpers/update_pandda_status_flag.py b/xce/helpers/update_pandda_status_flag.py index 649b5324..86f089a6 100755 --- a/xce/helpers/update_pandda_status_flag.py +++ b/xce/helpers/update_pandda_status_flag.py @@ -6,13 +6,15 @@ def update_data_source(db_file, crystalString, status): db = XChemDB.data_source(db_file) print( - "update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format( - status, "'" + crystalString.replace(",", "','") + "'" + "update mainTable set PANDDAStatus =" + " '{0!s}' where CrystalName in ('{1!s}')".format( + status, crystalString.replace(",", "','") ) ) db.execute_statement( - "update mainTable set PANDDAStatus = '{0!s}' where CrystalName in ({1!s})".format( - status, "'" + crystalString.replace(",", "','") + "'" + "update mainTable set PANDDAStatus =" + " '{0!s}' where CrystalName in ('{1!s}')".format( + status, crystalString.replace(",", "','") ) ) From 046cec163cc5a622dc5486bafff71da37514fc0e Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 14:21:00 +0000 Subject: [PATCH 133/358] Clean up update_data_source_for_new_dimple_twin_pdb --- ...ate_data_source_for_new_dimple_twin_pdb.py | 33 ++----------------- 1 file changed, 3 insertions(+), 30 deletions(-) diff --git a/xce/helpers/update_data_source_for_new_dimple_twin_pdb.py b/xce/helpers/update_data_source_for_new_dimple_twin_pdb.py index 040831ca..09624fe9 100755 --- a/xce/helpers/update_data_source_for_new_dimple_twin_pdb.py +++ b/xce/helpers/update_data_source_for_new_dimple_twin_pdb.py @@ -38,18 +38,8 @@ db_dict["RefinementOutcome"] = "1 - Analysis Pending" db_dict["RefinementSpaceGroup"] = pdb["SpaceGroup"] db_dict["DimpleTwinFraction"] = pdb["TwinFraction"] - # if not os.path.isfile(xtal+'.free.mtz'): - # os.chdir(os.path.join(inital_model_directory,xtal)) - # os.system('/bin/rm '+xtal+'.free.mtz') - # if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz')): - # os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz'),xtal+'.free.mtz') - # db_dict['RefinementMTZfree']=xtal+'.free.mtz' - # elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz')): - # os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz'),xtal+'.free.mtz') - # db_dict['RefinementMTZfree']=xtal+'.free.mtz' # setting free.mtz file - os.chdir(os.path.join(inital_model_directory, xtal)) os.system("/bin/rm -f %s.free.mtz" % xtal) mtzFree = None @@ -165,30 +155,13 @@ db_dict["RefinementTwinMTZfree"] = xtal + ".free.mtz" - # if no refinement was carried out yet, then we also want to link the dimple files to refine.pdb/refine.log - # so that we can look at them with the COOT plugin - # 15/11/2016: obsolete since COOT will now read dimple.pdb/dimple.mtz if no refine.pdb/refine.mtz is present - # found_previous_refinement=False - # os.chdir(os.path.join(inital_model_directory,xtal)) - # for dirs in glob.glob('*'): - # if os.path.isdir(dirs) and dirs.startswith('Refine_'): - # found_previous_refinement=True - # break - # if not found_previous_refinement: - # # first delete possible old symbolic links - # if os.path.isfile('refine.pdb'): os.system('/bin/rm refine.pdb') - # os.symlink('dimple.pdb','refine.pdb') - # if os.path.isfile('refine.mtz'): os.system('/bin/rm refine.mtz') - # os.symlink('dimple.mtz','refine.mtz') - - # finally, update data source print("==> xce: updating data source after DIMPLE run") db.update_data_source(xtal, db_dict) else: - # the actual dimple script creates symbolic links regardless if dimple was successful or not - # python os.path.isfile is False if symbolic link points to non existing file - # so we remove all of them! + # the actual dimple script creates symbolic links regardless if dimple was + # successful or not python os.path.isfile is False if symbolic link points to + # non existing file so we remove all of them! os.chdir(os.path.join(inital_model_directory, xtal)) os.system("/bin/rm dimple_twin.pdb") os.system("/bin/rm dimple_twin.mtz") From 82fe1f0ccea2d11c87369f7f529ff35d7ba6986d Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 14:21:35 +0000 Subject: [PATCH 134/358] Clean up update_data_source_for_new_dimple_pdb --- .../update_data_source_for_new_dimple_pdb.py | 33 ++----------------- 1 file changed, 3 insertions(+), 30 deletions(-) diff --git a/xce/helpers/update_data_source_for_new_dimple_pdb.py b/xce/helpers/update_data_source_for_new_dimple_pdb.py index aed7325e..9387af9f 100755 --- a/xce/helpers/update_data_source_for_new_dimple_pdb.py +++ b/xce/helpers/update_data_source_for_new_dimple_pdb.py @@ -33,18 +33,8 @@ db_dict["DimpleRfree"] = pdb["Rfree"] db_dict["RefinementOutcome"] = "1 - Analysis Pending" db_dict["RefinementSpaceGroup"] = pdb["SpaceGroup"] - # if not os.path.isfile(xtal+'.free.mtz'): - # os.chdir(os.path.join(inital_model_directory,xtal)) - # os.system('/bin/rm '+xtal+'.free.mtz') - # if os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz')): - # os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared2.mtz'),xtal+'.free.mtz') - # db_dict['RefinementMTZfree']=xtal+'.free.mtz' - # elif os.path.isfile(os.path.join(inital_model_directory,xtal,'dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz')): - # os.symlink(os.path.join('dimple','dimple_rerun_on_selected_file','dimple','prepared.mtz'),xtal+'.free.mtz') - # db_dict['RefinementMTZfree']=xtal+'.free.mtz' # setting free.mtz file - os.chdir(os.path.join(inital_model_directory, xtal)) os.system("/bin/rm -f %s.free.mtz" % xtal) mtzFree = None @@ -142,30 +132,13 @@ db_dict["RefinementMTZfree"] = xtal + ".free.mtz" - # if no refinement was carried out yet, then we also want to link the dimple files to refine.pdb/refine.log - # so that we can look at them with the COOT plugin - # 15/11/2016: obsolete since COOT will now read dimple.pdb/dimple.mtz if no refine.pdb/refine.mtz is present - # found_previous_refinement=False - # os.chdir(os.path.join(inital_model_directory,xtal)) - # for dirs in glob.glob('*'): - # if os.path.isdir(dirs) and dirs.startswith('Refine_'): - # found_previous_refinement=True - # break - # if not found_previous_refinement: - # # first delete possible old symbolic links - # if os.path.isfile('refine.pdb'): os.system('/bin/rm refine.pdb') - # os.symlink('dimple.pdb','refine.pdb') - # if os.path.isfile('refine.mtz'): os.system('/bin/rm refine.mtz') - # os.symlink('dimple.mtz','refine.mtz') - - # finally, update data source print("==> xce: updating data source after DIMPLE run") db.update_data_source(xtal, db_dict) else: - # the actual dimple script creates symbolic links regardless if dimple was successful or not - # python os.path.isfile is False if symbolic link points to non existing file - # so we remove all of them! + # the actual dimple script creates symbolic links regardless if dimple was + # successful or not python os.path.isfile is False if symbolic link points to + # non existing file so we remove all of them! os.chdir(os.path.join(inital_model_directory, xtal)) os.system("/bin/rm dimple.pdb") os.system("/bin/rm dimple.mtz") From 56dd8fb0afbe6eb1e76cfe9cffb4d6e59f12c292 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 14:23:48 +0000 Subject: [PATCH 135/358] Clean up update_data_source_after_refinement --- .../update_data_source_after_refinement.py | 49 ++++++++++--------- 1 file changed, 26 insertions(+), 23 deletions(-) diff --git a/xce/helpers/update_data_source_after_refinement.py b/xce/helpers/update_data_source_after_refinement.py index 2c93d436..e5c0f276 100755 --- a/xce/helpers/update_data_source_after_refinement.py +++ b/xce/helpers/update_data_source_after_refinement.py @@ -87,8 +87,8 @@ def check_refmac_logfile(refinement_directory, db_dict): if os.path.isfile(logFile): for line in open(logFile): if ( - "Your coordinate file has a ligand which has either minimum or no description in the library" - in line + "Your coordinate file has a ligand which has either minimum" + " or no description in the library" in line ): db_dict["RefinementStatus"] = "CIF problem" return db_dict @@ -156,9 +156,11 @@ def parse_ligand_validation(inital_model_directory, refinement_directory, xtal): residue_chain, residue_number ) event = db.execute_statement( - "select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='{0!s}'".format( - xtal - ) + "select PANDDA_site_x," + "PANDDA_site_y," + "PANDDA_site_z," + "PANDDA_site_index" + " from panddaTable where CrystalName='{0!s}'".format(xtal) ) for coord in event: db_pandda_dict = {} @@ -175,7 +177,8 @@ def parse_ligand_validation(inital_model_directory, refinement_directory, xtal): event_z, ) print("distance", distance) - # if coordinate of ligand and event are closer than 7A, then we assume they belong together + # if coordinate of ligand and event are closer than 7A + # then we assume they belong together if distance < 7: db_pandda_dict["PANDDA_site_ligand_id"] = residue db_pandda_dict["PANDDA_site_occupancy"] = line["Occupancy"] @@ -213,15 +216,10 @@ def parse_ligand_validation(inital_model_directory, refinement_directory, xtal): def update_ligand_information_in_panddaTable(inital_model_directory, xtal): if os.path.isfile(os.path.join(inital_model_directory, xtal, "refine.pdb")): - # ligands_in_file=pdbtools(os.path.join(inital_model_directory, xtal, 'refine.pdb')).find_xce_ligand_details() ligands_in_file = pdbtools( os.path.join(inital_model_directory, xtal, "refine.pdb") ).get_residues_with_resname("LIG") for ligand in ligands_in_file: - # residue_name= ligand[0] - # residue_chain= ligand[1] - # residue_number= ligand[2] - # residue_altLoc= ligand[3] residue_name = ligand[0] residue_chain = ligand[2] residue_number = ligand[1] @@ -230,9 +228,11 @@ def update_ligand_information_in_panddaTable(inital_model_directory, xtal): os.path.join(inital_model_directory, xtal, "refine.pdb") ).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) event = db.execute_statement( - "select PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDA_site_index from panddaTable where CrystalName='{0!s}'".format( - xtal - ) + "select PANDDA_site_x," + "PANDDA_site_y," + "PANDDA_site_z," + "PANDDA_site_index" + " from panddaTable where CrystalName='{0!s}'".format(xtal) ) for coord in event: db_pandda_dict = {} @@ -248,7 +248,8 @@ def update_ligand_information_in_panddaTable(inital_model_directory, xtal): event_y, event_z, ) - # if coordinate of ligand and event are closer than 7A, then we assume they belong together + # if coordinate of ligand and event are closer than 7A + # then we assume they belong together if distance < 7: db_pandda_dict["PANDDA_site_ligand_resname"] = residue_name db_pandda_dict["PANDDA_site_ligand_chain"] = residue_chain @@ -268,18 +269,20 @@ def update_data_source(db_dict): db.update_data_source(xtal, db_dict) # update refinement outcome if necessary sqlite = ( - "update mainTable set RefinementOutcome = '3 - In Refinement' where CrystalName is '{0!s}' ".format( - xtal - ) - + "and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending' or RefinementOutcome is '2 - PANDDA model')" + "update mainTable set RefinementOutcome =" + " '3 - In Refinement' where CrystalName is '{0!s}' ".format(xtal) + + "and (RefinementOutcome is null" + " or RefinementOutcome is '1 - Analysis Pending'" + " or RefinementOutcome is '2 - PANDDA model')" ) db.execute_statement(sqlite) # now do the same for each site in the pandda table sqlite = ( - "update panddaTable set RefinementOutcome = '3 - In Refinement' where CrystalName is '{0!s}' ".format( - xtal - ) - + "and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending' or RefinementOutcome is '2 - PANDDA model')" + "update panddaTable set RefinementOutcome =" + " '3 - In Refinement' where CrystalName is '{0!s}' ".format(xtal) + + "and (RefinementOutcome is null" + " or RefinementOutcome is '1 - Analysis Pending'" + " or RefinementOutcome is '2 - PANDDA model')" ) db.execute_statement(sqlite) From 14576d8ab6dbf8349ff9929ef3cf0f7ffa0bd29f Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 14:24:33 +0000 Subject: [PATCH 136/358] Clean up select_ground_state_dataset --- xce/helpers/select_ground_state_dataset.py | 1 - 1 file changed, 1 deletion(-) diff --git a/xce/helpers/select_ground_state_dataset.py b/xce/helpers/select_ground_state_dataset.py index 5eb38f47..c3e0e994 100755 --- a/xce/helpers/select_ground_state_dataset.py +++ b/xce/helpers/select_ground_state_dataset.py @@ -19,7 +19,6 @@ def find_highest_resolution_datasets(panddaDir): line.startswith("Statistical Electron Density Characterisation") and len(line.split()) == 6 ): - resolution = line.split()[5] found = True foundLine = n if found and n >= foundLine + 3: From 0e13773978ba499521139183e65ee83bf0e2b5ae Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 14:25:33 +0000 Subject: [PATCH 137/358] Clean up resort_ligand_atoms --- xce/helpers/resort_ligand_atoms.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/xce/helpers/resort_ligand_atoms.py b/xce/helpers/resort_ligand_atoms.py index 6a3be9e2..15638870 100755 --- a/xce/helpers/resort_ligand_atoms.py +++ b/xce/helpers/resort_ligand_atoms.py @@ -49,7 +49,6 @@ def resort_ligand_atoms_in_refined_model(refinedModel, ensembleLIGdir): out = "" refineLIGDir = {} LIGlineAdditional = "" - LIGlist = [] for line in open(refinedModel): if line.startswith("ATOM") or line.startswith("HETATM"): altLoc_line = str(line[16:17]) @@ -83,7 +82,7 @@ def resort_ligand_atoms_in_refined_model(refinedModel, ensembleLIGdir): atomName = atomLine[0] for line in refineLIGDir[ligand]: atomName_line = str(line[11:16]) - if atomName_line == atom: + if atomName_line == atomName: LIGline += line break From 0abb612e6a838131bf4663360743d326c63683d0 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 14:26:22 +0000 Subject: [PATCH 138/358] Clean up reset_occupancy_protein_to_one --- xce/helpers/reset_occupancy_protein_to_one.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/xce/helpers/reset_occupancy_protein_to_one.py b/xce/helpers/reset_occupancy_protein_to_one.py index 7ddbea30..25c06a9a 100644 --- a/xce/helpers/reset_occupancy_protein_to_one.py +++ b/xce/helpers/reset_occupancy_protein_to_one.py @@ -13,12 +13,8 @@ def reset_residues(projectDir): os.system("/bin/cp %s %s" % (mol, mol + "_original")) print("%s: found %s" % (xtal, mol)) out = "" - changeResi = None for line in open(mol): if line.startswith("ATOM"): - chainID = str(line[21:23]).replace(" ", "") - resseq = str(line[23:26]).replace(" ", "") - occupancy = str(line[56:60]).replace(" ", "") altLoc = str(line[16:17]).replace(" ", "") if altLoc != "": out += line From 99ae3fbd78450f70bc96fed87fb59e81764ce3ee Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 14:26:40 +0000 Subject: [PATCH 139/358] Clean up reset_interesting_datasets --- xce/helpers/reset_interesting_datasets.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/xce/helpers/reset_interesting_datasets.py b/xce/helpers/reset_interesting_datasets.py index 83efebd9..8af25f25 100755 --- a/xce/helpers/reset_interesting_datasets.py +++ b/xce/helpers/reset_interesting_datasets.py @@ -22,8 +22,6 @@ def check_interesting_datasets(panddaDir): os.chdir(os.path.join(panddaDir, "interesting_datasets")) for xtal in sorted(glob.glob("*")): if not os.path.islink(xtal): - # print xtal - # print os.path.join(panddaDir,'interesting_datasets',xtal,'modelled_structures',xtal+'-pandda-model.pdb') if os.path.isfile( os.path.join( panddaDir, From c65cd1baba07d7d80076dd70262deda2e20c4633 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 14:34:12 +0000 Subject: [PATCH 140/358] Remove unused helpers --- xce/helpers/assign_stereochemistry.py | 88 --------- ...ange_residues_in_ground_and_bound-state.py | 63 ------- xce/helpers/reset_interesting_datasets.py | 77 -------- xce/helpers/reset_occupancy_protein_to_one.py | 34 ---- .../reset_to_last_successful_refinement.py | 59 ------ xce/helpers/resort_ligand_atoms.py | 122 ------------- ...ate_data_source_for_new_dimple_twin_pdb.py | 169 ------------------ xce/helpers/update_pandda_status_flag.py | 27 --- 8 files changed, 639 deletions(-) delete mode 100755 xce/helpers/assign_stereochemistry.py delete mode 100755 xce/helpers/change_residues_in_ground_and_bound-state.py delete mode 100755 xce/helpers/reset_interesting_datasets.py delete mode 100644 xce/helpers/reset_occupancy_protein_to_one.py delete mode 100644 xce/helpers/reset_to_last_successful_refinement.py delete mode 100755 xce/helpers/resort_ligand_atoms.py delete mode 100755 xce/helpers/update_data_source_for_new_dimple_twin_pdb.py delete mode 100755 xce/helpers/update_pandda_status_flag.py diff --git a/xce/helpers/assign_stereochemistry.py b/xce/helpers/assign_stereochemistry.py deleted file mode 100755 index 5c3c5754..00000000 --- a/xce/helpers/assign_stereochemistry.py +++ /dev/null @@ -1,88 +0,0 @@ -from ..lib import XChemDB -import os -import sys -import glob -from rdkit import Chem - -# from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions - - -def enumerateStereoChem(compoundID, sampleDir, db, xtal): - # first need to recreate the original CIF file with phenix.elbow because we cannot be sure - # which program was used to create the initial restrains - # this is because funny things happen to aromatic rings in case the file was made with GRADE - os.chdir(os.path.join(sampleDir, "compound")) - sql = "select CompoundSMILES from mainTable where CrystalName = '%s'" % xtal - print("sqlite query:", sql) - query = db.execute_statement(sql) - originalSMILES = query[0][0] - print(originalSMILES) - cmd = 'phenix.elbow --smiles="%s" --id=LIG --output=tmp' % (originalSMILES) - print("current working directory:", os.getcwd()) - print("runnning:", cmd) - os.system(cmd) - - stereosmiles = None - pdb = None - if os.path.isfile(os.path.join(sampleDir, "compound", "tmp.pdb")): - pdb = os.path.join(sampleDir, "compound", "tmp.pdb") - else: - print("cannot find tmp.pdb") - pass - if pdb: - mol = Chem.MolFromPDBFile(pdb) - Chem.AssignStereochemistry( - mol, cleanIt=True, force=True, flagPossibleStereoCenters=True - ) - if Chem.FindMolChiralCenters(mol, includeUnassigned=True) == []: - print("no chiral centres found") - db_dict = {} - db_dict["CompoundStereo"] = "FALSE" - updateDB(db, db_dict, xtal) - else: - stereosmiles = Chem.MolToSmiles(mol, isomericSmiles=True) - generateRestraints(compoundID, sampleDir, db, stereosmiles, xtal) - - -def generateRestraints(compoundID, sampleDir, db, stereosmiles, xtal): - cmd = 'phenix.elbow --smiles="%s" --chiral=enumerate --id=LIG --output=%s' % ( - stereosmiles, - compoundID, - ) - os.system(cmd) - checkFiles(compoundID, sampleDir, db, stereosmiles, xtal) - - -def checkFiles(compoundID, sampleDir, db, stereosmiles, xtal): - foundCIF = False - allCIF = "" - for cif in glob.glob(os.path.join(compoundID + "_*.cif")): - foundCIF = True - allCIF += cif + ";" - print("---", cif, "===", allCIF) - if foundCIF: - db_dict = {} - db_dict["CompoundStereo"] = "TRUE" - db_dict["CompoundStereoSMILES"] = stereosmiles - db_dict["CompoundStereoCIFprogram"] = "phenix.elbow" - db_dict["CompoundStereoCIFs"] = allCIF[:-1] - print(">>>", db_dict) - updateDB(db, db_dict, xtal) - - -def updateDB(db, db_dict, xtal): - # update stereo field - # update restraintsprogram field - # update stereosmiles - db.update_data_source(xtal, db_dict) - - -if __name__ == "__main__": - compoundID = sys.argv[1] - sampleDir = sys.argv[2] - xtal = sampleDir[sampleDir.rfind("/") + 1 :] - print("sampleID:", xtal) - database = sys.argv[3] - print("database:", database) - db = XChemDB.data_source(database) - enumerateStereoChem(compoundID, sampleDir, db, xtal) diff --git a/xce/helpers/change_residues_in_ground_and_bound-state.py b/xce/helpers/change_residues_in_ground_and_bound-state.py deleted file mode 100755 index 1a8d52ca..00000000 --- a/xce/helpers/change_residues_in_ground_and_bound-state.py +++ /dev/null @@ -1,63 +0,0 @@ -import glob -import os -import sys - - -def replace_residues(): - for dirs in glob.glob(os.path.join(projectDir, "*")): - xtal = dirs[dirs.rfind("/") + 1 :] - os.chdir(dirs) - if xtal == test: - continue - for mol in toEdit: - if os.path.isfile(mol): - if not os.path.isfile(mol + "_original"): - os.system("/bin/cp %s %s" % (mol, mol + "_original")) - print("%s: found %s" % (xtal, mol)) - os.system("phenix.superpose_pdbs %s %s" % (mol, newModel)) - out = "" - changeResi = None - for line in open(mol): - if line.startswith("ATOM") or line.startswith("HETATM"): - chainID = str(line[21:23]).replace(" ", "") - resseq = str(line[23:26]).replace(" ", "") - occupancy = str(line[56:60]).replace(" ", "") - resi = chainID + resseq - if changeResi != None: - if resi == changeResi: - print("here", changeResi) - continue - else: - changeResi = None - if resi in residues_to_change: - changeResi = resi - print("changeResi", changeResi) - for line in open(newModelName + "_fitted.pdb"): - if line.startswith("ATOM") or line.startswith("HETATM"): - chainIDFitted = str(line[21:23]).replace(" ", "") - resseqFitted = str(line[23:26]).replace(" ", "") - residFitted = chainIDFitted + resseqFitted - if residFitted == changeResi: - out += line[:56] + occupancy + line[60:] - else: - out += line - else: - out += line - print("saving file", mol, "...") - newFile = open(mol, "w") - newFile.write(out) - newFile.close() - - -if __name__ == "__main__": - # newModel = '/dls/labxchem/data/2019/lb22717-1/processing/INPP5DA/processing/reference/INPP5DA-x0080-ground-state-corrected.pdb' - # residues_to_change = ['A567', 'A812', 'A851'] - # projectDir = '/dls/labxchem/data/2019/lb22717-1/processing/INPP5DA/processing/analysis/model_building' - # toEdit = ['refine.split.ground-state.pdb', 'refine.split.bound-state.pdb'] - # test = 'INPP5DA-x0019' - - newModel = sys.argv[1] - residues_to_change = sys.argv[2] - projectDir = sys.argv[3] - toEdit = ["refine.split.ground-state.pdb", "refine.split.bound-state.pdb"] - newModelName = newModel[newModel.rfind("/") + 1 :] diff --git a/xce/helpers/reset_interesting_datasets.py b/xce/helpers/reset_interesting_datasets.py deleted file mode 100755 index 8af25f25..00000000 --- a/xce/helpers/reset_interesting_datasets.py +++ /dev/null @@ -1,77 +0,0 @@ -import os -import glob -import sys - - -def relink_interesting_datasets(panddaDir): - os.chdir(os.path.join(panddaDir, "interesting_datasets")) - dirList = [] - for dirs in glob.glob("*"): - if os.path.isdir(dirs): - dirList.append(dirs) - - for dirs in dirList: - print("/bin/rm -fr {0!s}".format(dirs)) - os.system("/bin/rm -fr {0!s}".format(dirs)) - print("ln -s ../processed_datasets/{0!s} .".format(dirs)) - os.system("ln -s ../processed_datasets/{0!s} .".format(dirs)) - - -def check_interesting_datasets(panddaDir): - - os.chdir(os.path.join(panddaDir, "interesting_datasets")) - for xtal in sorted(glob.glob("*")): - if not os.path.islink(xtal): - if os.path.isfile( - os.path.join( - panddaDir, - "interesting_datasets", - xtal, - "modelled_structures", - xtal + "-pandda-model.pdb", - ) - ): - print( - "mv --backup=numbered {0!s} {1!s}".format( - os.path.join( - panddaDir, - "interesting_datasets", - xtal, - "modelled_structures", - ), - os.path.join(panddaDir, "processed_datasets", xtal), - ) - ) - os.system( - "mv --backup=numbered {0!s} {1!s}".format( - os.path.join( - panddaDir, - "interesting_datasets", - xtal, - "modelled_structures", - ), - os.path.join(panddaDir, "processed_datasets", xtal), - ) - ) - print( - "cp {0!s} {1!s}".format( - os.path.join( - panddaDir, "interesting_datasets", xtal, "*params" - ), - os.path.join(panddaDir, "processed_datasets", xtal), - ) - ) - os.system( - "cp {0!s} {1!s}".format( - os.path.join( - panddaDir, "interesting_datasets", xtal, "*params" - ), - os.path.join(panddaDir, "processed_datasets", xtal), - ) - ) - - -if __name__ == "__main__": - panddaDir = sys.argv[1] - check_interesting_datasets(panddaDir) - relink_interesting_datasets(panddaDir) diff --git a/xce/helpers/reset_occupancy_protein_to_one.py b/xce/helpers/reset_occupancy_protein_to_one.py deleted file mode 100644 index 25c06a9a..00000000 --- a/xce/helpers/reset_occupancy_protein_to_one.py +++ /dev/null @@ -1,34 +0,0 @@ -import glob -import os -import sys - - -def reset_residues(projectDir): - for dirs in glob.glob(os.path.join(projectDir, "*")): - xtal = dirs[dirs.rfind("/") + 1 :] - os.chdir(dirs) - for mol in toEdit: - if os.path.isfile(mol): - if not os.path.isfile(mol + "_original"): - os.system("/bin/cp %s %s" % (mol, mol + "_original")) - print("%s: found %s" % (xtal, mol)) - out = "" - for line in open(mol): - if line.startswith("ATOM"): - altLoc = str(line[16:17]).replace(" ", "") - if altLoc != "": - out += line - else: - out += line[:56] + "1.00" + line[60:] - else: - out += line - print("saving file", mol, "...") - newFile = open(mol, "w") - newFile.write(out) - newFile.close() - - -if __name__ == "__main__": - projectDir = sys.argv[1] - toEdit = ["refine.split.bound-state.pdb"] - reset_residues(projectDir) diff --git a/xce/helpers/reset_to_last_successful_refinement.py b/xce/helpers/reset_to_last_successful_refinement.py deleted file mode 100644 index ab47ab02..00000000 --- a/xce/helpers/reset_to_last_successful_refinement.py +++ /dev/null @@ -1,59 +0,0 @@ -import os -import glob -import sys - - -def find_refine_folder(projectDir): - for xtalDir in sorted(glob.glob(os.path.join(projectDir, "*"))): - xtal = xtalDir[xtalDir.rfind("/") + 1 :] - os.chdir(xtalDir) - dirList = [] - for dirs in sorted(glob.glob("*")): - if dirs.startswith("Refine_") and os.path.isdir(dirs): - if not os.path.isfile("refine.pdb"): - dirList.append([dirs, os.path.getctime(dirs)]) - if dirList != []: - find_refine_pdb(xtal, dirList) - - -def find_refine_pdb(xtal, dirList): - sorted_list = sorted(dirList, key=lambda x: x[1], reverse=True) - foundRefinePDB = False - for d in sorted_list: - serial = int(d[0].split("_")[1]) - if os.path.isfile(os.path.join(d[0], "refine.pdb")): - print(xtal + ": found refine.pdb in " + d[0]) - pdbLink = os.path.join(d[0], "refine.pdb") - mtzLink = os.path.join(d[0], "refine.mtz") - foundRefinePDB = True - break - elif os.path.isfile(os.path.join(d[0], "refine_%s.pdb" % str(serial))): - print(xtal + ": found refine_%s.pdb in %s" % (str(serial), d[0])) - foundRefinePDB = True - pdbLink = os.path.join(d[0], "refine_%s.pdb" % str(serial)) - mtzLink = os.path.join(d[0], "refine_%s.mtz" % str(serial)) - break - if not foundRefinePDB: - print(xtal + ": ERROR -> cannot find refine.pdb") - else: - print(os.getcwd(), pdbLink, mtzLink) - reset_links(xtal, pdbLink, mtzLink) - - -def find_pandda_refine_pdb(xtal, dirList): - print("hallp") - - -def reset_links(xtal, pdbLink, mtzLink): - print(xtal + ": resetting links...") - os.system("/bin/rm refine.pdb") - os.system("/bin/rm refine.mtz") - os.system("/bin/rm refine.split.bound-state.pdb") - os.system("ln -s %s refine.pdb" % pdbLink) - os.system("ln -s %s refine.mtz" % mtzLink) - os.system("ln -s refine.pdb refine.split.bound-state.pdb") - - -if __name__ == "__main__": - projectDir = sys.argv[1] - find_refine_folder(projectDir) diff --git a/xce/helpers/resort_ligand_atoms.py b/xce/helpers/resort_ligand_atoms.py deleted file mode 100755 index 15638870..00000000 --- a/xce/helpers/resort_ligand_atoms.py +++ /dev/null @@ -1,122 +0,0 @@ -import os -import sys - - -def get_atom_order_of_ensemble_model(ensembleModel): - - ligandResnames = ["LIG", "FRS", "DRG", "UNL"] - - ensembleLIGdir = {} - - for line in open(ensembleModel): - if line.startswith("ATOM") or line.startswith("HETATM"): - atomName_line = str(line[11:16]) - altLoc_line = str(line[16:17]) - resname_line = str(line[17:20]) - chainID_line = str(line[20:23]) - resseq_line = str(line[23:26]) - - residueID = ( - resname_line.replace(" ", "") - + "-" - + chainID_line.replace(" ", "") - + "-" - + resseq_line.replace(" ", "") - + "-" - + chainID_line.replace(" ", "") - + "-" - + altLoc_line - ) - - if resname_line in ligandResnames: - if residueID not in ensembleLIGdir: - ensembleLIGdir[residueID] = [] - ensembleLIGdir[residueID].append( - [ - atomName_line, - altLoc_line, - resname_line, - chainID_line, - resseq_line, - ] - ) - - return ensembleLIGdir - - -def resort_ligand_atoms_in_refined_model(refinedModel, ensembleLIGdir): - ligandResnames = ["LIG", "FRS", "DRG", "UNL"] - out = "" - refineLIGDir = {} - LIGlineAdditional = "" - for line in open(refinedModel): - if line.startswith("ATOM") or line.startswith("HETATM"): - altLoc_line = str(line[16:17]) - resname_line = str(line[17:20]) - chainID_line = str(line[20:23]) - resseq_line = str(line[23:26]) - - residueID = ( - resname_line.replace(" ", "") - + "-" - + chainID_line.replace(" ", "") - + "-" - + resseq_line.replace(" ", "") - + "-" - + chainID_line.replace(" ", "") - + "-" - + altLoc_line - ) - - if residueID in ensembleLIGdir: - if residueID not in refineLIGDir: - refineLIGDir[residueID] = [] - else: - # if a ligand was for modelled after pandda.inspect - LIGlineAdditional += line - refineLIGDir[residueID].append(line) - - LIGline = "" - for ligand in ensembleLIGdir: - for atomLine in ensembleLIGdir[ligand]: - atomName = atomLine[0] - for line in refineLIGDir[ligand]: - atomName_line = str(line[11:16]) - if atomName_line == atomName: - LIGline += line - break - - for line in open(refinedModel): - if line.startswith("ATOM") or line.startswith("HETATM"): - resname_line = str(line[17:20]) - if resname_line in ligandResnames: - continue - else: - out += line - - elif line.startswith("END"): - continue - - elif line.startswith("TER"): - continue - - else: - out += line - - out += LIGline - out += "END\n" - - os.system( - "/bin/mv %s %s" - % (refinedModel, refinedModel.replace(".pdb", "_original_atom_order.pdb")) - ) - f = open(refinedModel, "w") - f.write(out) - f.close() - - -if __name__ == "__main__": - ensembleModel = sys.argv[1] - refinedModel = sys.argv[2] - ensembleLIGdir = get_atom_order_of_ensemble_model(ensembleModel) - resort_ligand_atoms_in_refined_model(refinedModel, ensembleLIGdir) diff --git a/xce/helpers/update_data_source_for_new_dimple_twin_pdb.py b/xce/helpers/update_data_source_for_new_dimple_twin_pdb.py deleted file mode 100755 index 09624fe9..00000000 --- a/xce/helpers/update_data_source_for_new_dimple_twin_pdb.py +++ /dev/null @@ -1,169 +0,0 @@ -from ..lib import XChemDB -from ..lib.XChemUtils import parse -from iotbx import mtz -import os -import sys - - -if __name__ == "__main__": - db_file = sys.argv[1] - xtal = sys.argv[2] - inital_model_directory = sys.argv[3] - - db = XChemDB.data_source(db_file) - if os.path.isfile(os.path.join(inital_model_directory, xtal, "dimple_twin.pdb")): - db_dict = { - "DimpleTwinPathToPDB": os.path.join( - inital_model_directory, xtal, "dimple_twin.pdb" - ) - } - dimple_ran_successfully = False - if os.path.isfile( - os.path.join(inital_model_directory, xtal, "dimple_twin.mtz") - ): - db_dict["DimpleTwinPathToMTZ"] = os.path.join( - inital_model_directory, xtal, "dimple_twin.mtz" - ) - dimple_ran_successfully = True - db_dict["DataProcessingDimpleTwinSuccessful"] = "True" - db_dict["DimpleTwinStatus"] = "finished" - if not dimple_ran_successfully: - db_dict["DataProcessingDimpleTwinSuccessful"] = "False" - db_dict["DimpleTwinStatus"] = "failed" - pdb = parse().PDBheader( - os.path.join(inital_model_directory, xtal, "dimple_twin.pdb") - ) - db_dict["DimpleTwinRcryst"] = pdb["Rcryst"] - db_dict["DimpleTwinRfree"] = pdb["Rfree"] - db_dict["RefinementOutcome"] = "1 - Analysis Pending" - db_dict["RefinementSpaceGroup"] = pdb["SpaceGroup"] - db_dict["DimpleTwinFraction"] = pdb["TwinFraction"] - - # setting free.mtz file - os.chdir(os.path.join(inital_model_directory, xtal)) - os.system("/bin/rm -f %s.free.mtz" % xtal) - mtzFree = None - db_dict["RefinementTwinMTZfree"] = "" - if os.path.isfile( - os.path.join( - inital_model_directory, - xtal, - "dimple_twin", - "dimple_rerun_on_selected_file", - "dimple_twin", - "prepared2.mtz", - ) - ): - mtzFree = os.path.join( - inital_model_directory, - xtal, - "dimple_twin", - "dimple_rerun_on_selected_file", - "dimple_twin", - "prepared2.mtz", - ) - elif os.path.isfile( - os.path.join( - inital_model_directory, - xtal, - "dimple_twin", - "dimple_rerun_on_selected_file", - "dimple_twin", - "prepared.mtz", - ) - ): - mtzFree = os.path.join( - inital_model_directory, - xtal, - "dimple_twin", - "dimple_rerun_on_selected_file", - "dimple_twin", - "prepared.mtz", - ) - elif os.path.isfile( - os.path.join( - inital_model_directory, - xtal, - "dimple_twin", - "dimple_twin", - "prepared.mtz", - ) - ): - mtzFree = os.path.join( - inital_model_directory, - xtal, - "dimple_twin", - "dimple_twin", - "prepared.mtz", - ) - elif os.path.isfile( - os.path.join( - inital_model_directory, - xtal, - "dimple_twin", - "dimple_twin", - "prepared2.mtz", - ) - ): - mtzFree = os.path.join( - inital_model_directory, - xtal, - "dimple_twin", - "dimple_twin", - "prepared2.mtz", - ) - elif os.path.isfile( - os.path.join( - inital_model_directory, - xtal, - "dimple_twin", - "dimple_rerun_on_selected_file", - "dimple_twin", - "free.mtz", - ) - ): - mtzFree = os.path.join( - inital_model_directory, - xtal, - "dimple_twin", - "dimple_rerun_on_selected_file", - "dimple_twin", - "free.mtz", - ) - elif os.path.isfile( - os.path.join( - inital_model_directory, xtal, "dimple_twin", "dimple_twin", "free.mtz" - ) - ): - mtzFree = os.path.join( - inital_model_directory, xtal, "dimple_twin", "dimple_twin", "free.mtz" - ) - - if mtzFree is not None: - if "F_unique" in mtz.object(mtzFree).column_labels(): - cmd = ( - "cad hklin1 %s hklout %s.free.mtz << eof\n" % (mtzFree, xtal) - + " monitor BRIEF\n" - " labin file 1 E1=F E2=SIGF E3=FreeR_flag\n" - " labout file 1 E1=F E2=SIGF E3=FreeR_flag\n" - "eof\n" - ) - - os.system(cmd) - else: - os.symlink(mtzFree, xtal + ".free.mtz") - - db_dict["RefinementTwinMTZfree"] = xtal + ".free.mtz" - - print("==> xce: updating data source after DIMPLE run") - db.update_data_source(xtal, db_dict) - - else: - # the actual dimple script creates symbolic links regardless if dimple was - # successful or not python os.path.isfile is False if symbolic link points to - # non existing file so we remove all of them! - os.chdir(os.path.join(inital_model_directory, xtal)) - os.system("/bin/rm dimple_twin.pdb") - os.system("/bin/rm dimple_twin.mtz") - os.system("/bin/rm 2fofc_twin.map") - os.system("/bin/rm fofc_twin.map") diff --git a/xce/helpers/update_pandda_status_flag.py b/xce/helpers/update_pandda_status_flag.py deleted file mode 100755 index 86f089a6..00000000 --- a/xce/helpers/update_pandda_status_flag.py +++ /dev/null @@ -1,27 +0,0 @@ -from ..lib import XChemDB -import sys - - -def update_data_source(db_file, crystalString, status): - db = XChemDB.data_source(db_file) - - print( - "update mainTable set PANDDAStatus =" - " '{0!s}' where CrystalName in ('{1!s}')".format( - status, crystalString.replace(",", "','") - ) - ) - db.execute_statement( - "update mainTable set PANDDAStatus =" - " '{0!s}' where CrystalName in ('{1!s}')".format( - status, crystalString.replace(",", "','") - ) - ) - - -if __name__ == "__main__": - db_file = sys.argv[1] - crystalString = sys.argv[2] - status = sys.argv[3] - - update_data_source(db_file, crystalString, status) From 59243fedf09fd1cf5c9d0ab8204a3cff830c9e87 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 16:18:29 +0000 Subject: [PATCH 141/358] Clean up pandda_tab --- xce/gui_scripts/pandda_tab.py | 25 ++++++++++++++++--------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/xce/gui_scripts/pandda_tab.py b/xce/gui_scripts/pandda_tab.py index 914797cc..5c6c5b0a 100755 --- a/xce/gui_scripts/pandda_tab.py +++ b/xce/gui_scripts/pandda_tab.py @@ -9,11 +9,11 @@ def __init__(self): self.layout_funcs = layout.LayoutFuncs() def setup(self, xce_object): - ################################################################################################################ - # # - # PANDDA TAB # - # # - ################################################################################################################ + ################################################################################ + # # + # PANDDA TAB # + # # + ################################################################################ # list of subtabs in PanDDA tab pandda_tab_list = [ "pandda.analyse", @@ -132,7 +132,8 @@ def copy_ligands(obj): + data_dir_string + '"/"' + xce_object.panddas_directory - + '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' + + '/processed_datasets/"}| while read line2;+' + " do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; " "done; done;" ) ) @@ -145,7 +146,8 @@ def copy_ligands(obj): + data_dir_string + '"/"' + xce_object.panddas_directory - + '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' + + '/processed_datasets/"}| while read line2;' + + " do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; " "done; done;" ) ) @@ -213,7 +215,11 @@ def copy_ligands(obj): label.setFont(header_font) params_hbox.addWidget(label) - url_html = 'For docs: click here' + url_html = ( + '' + "For docs: click here" + "" + ) label = QtGui.QLabel() label.setText(url_html) label.setOpenExternalLinks(True) @@ -293,7 +299,8 @@ def copy_ligands(obj): # grid spacing label = QtGui.QLabel( - "grid_spacing (default=0.5)\nNote: higher values speed up calculations, but maps might be less pretty)" + "grid_spacing (default=0.5)\n" + "Note: higher values speed up calculations, but maps might be less pretty)" ) xce_object.pandda_analyse_input_params_vbox.addWidget(label) xce_object.pandda_grid_spacing_entry = QtGui.QLineEdit() From 8ba78c2380ef979967a34dc194f81d32b5152750 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 16:25:16 +0000 Subject: [PATCH 142/358] Clean up layout --- xce/gui_scripts/layout.py | 89 +++++++++++++++++++-------------------- 1 file changed, 43 insertions(+), 46 deletions(-) diff --git a/xce/gui_scripts/layout.py b/xce/gui_scripts/layout.py index f4ff7b7b..c6e37db3 100755 --- a/xce/gui_scripts/layout.py +++ b/xce/gui_scripts/layout.py @@ -17,11 +17,11 @@ def __init__(self, xce_object): # function to initialise the top menu bar def initialise_menu_bar(self, xce_object): - ################################################################################################################ - # # - # MENU BAR - TOP OF GUI # - # # - ################################################################################################################ + ################################################################################ + # # + # MENU BAR - TOP OF GUI # + # # + ################################################################################ # initiate menu widget menu_bar = QtGui.QMenuBar() @@ -34,13 +34,8 @@ def initialise_menu_bar(self, xce_object): xce_object, menu_bar, xce_object.menu_dict ) - # END OF MENU BAR - CODE BELOW: stuff removed from apo structure stuff that appears might have a funky - # consequence - work out later. - - # xce_object.prepare_mmcif_files_dict = {} - # xce_object.prepare_mmcif_files_dict['apo'] = prepare_mmcif_files_for_apo_structures - # xce_object.prepare_mmcif_files_dict['ligand_bound'] = prepare_mmcif_files_for_ligand_bound_structures - + # END OF MENU BAR - CODE BELOW: stuff removed from apo structure stuff that + # appears might have a funky consequence - work out later. return menu_bar # function containing setup for bottom boxes @@ -56,11 +51,11 @@ def initialise_bottom_boxes(self, xce_object): xce_object, xce_object.datasource_button_dict ) - ################################################################################################################ - # # - # DATASETS BOX # - # # - ################################################################################################################ + ################################################################################ + # # + # DATASETS BOX # + # # + ################################################################################ # setup the run button with push button function xce_object.dataset_task_run_button = self.layout_funcs.setup_push_button( @@ -105,11 +100,11 @@ def initialise_bottom_boxes(self, xce_object): xce_object.dataset_task_status_button, ] - ################################################################################################################ - # # - # MAPS & RESTRAINTS BOX # - # # - ################################################################################################################ + ################################################################################ + # # + # MAPS & RESTRAINTS BOX # + # # + ################################################################################ # settings for the run button # setup the run button with push button function @@ -157,11 +152,11 @@ def initialise_bottom_boxes(self, xce_object): xce_object.map_cif_file_task_status_button, ] - ################################################################################################################ - # # - # HIT IDENTIFICATION BOX # - # # - ################################################################################################################ + ################################################################################ + # # + # HIT IDENTIFICATION BOX # + # # + ################################################################################ # settings for the run button # setup the run button with push button function @@ -209,11 +204,11 @@ def initialise_bottom_boxes(self, xce_object): xce_object.panddas_file_task_status_button, ] - ################################################################################################################ - # # - # REFINEMENT BOX # - # # - ################################################################################################################ + ################################################################################ + # # + # REFINEMENT BOX # + # # + ################################################################################ # settings for the run button # setup the run button with push button function @@ -315,11 +310,11 @@ def main_layout(self, xce_object): DepositionTab().setup(xce_object) SettingsTab().setup(xce_object) - ################################################################################################################ - # # - # STATUS BAR # - # # - ################################################################################################################ + ################################################################################ + # # + # STATUS BAR # + # # + ################################################################################ xce_object.status_bar = QtGui.QStatusBar() xce_object.progress_bar = QtGui.QProgressBar() xce_object.progress_bar.setMaximum(100) @@ -360,11 +355,11 @@ def main_layout(self, xce_object): xce_object.data_source_set = False def workflow(self, xce_object): - ################################################################################################################ - # # - # ========================================== WORKFLOW TASK CONTAINER ========================================= # - # # - ################################################################################################################ + ################################################################################ + # # + # ========================== WORKFLOW TASK CONTAINER ========================= # + # # + ################################################################################ # workflow task container - order of tabs as they appear for the main window xce_object.workflow = [ @@ -424,10 +419,12 @@ def table_setup(self, table, table_columns, sortingopt=True): def pandda_html(self, xce_object): if os.path.exists(str(xce_object.panddas_directory + "/interesting_datasets")): print( - "WARNING: USING RESULTS FROM OLD PANDDA ANALYSE! THIS IS NOT FULLY SUPPORTED IN XCE2" + "WARNING: USING RESULTS FROM OLD PANDDA ANALYSE!" + " THIS IS NOT FULLY SUPPORTED IN XCE2" ) print( - "PLEASE CHANGE YOUR PANDDA DIRECTORY TO A NEW RUN, OR USE THE OLD VERSION OF XCE!" + "PLEASE CHANGE YOUR PANDDA DIRECTORY TO A NEW RUN," + " OR USE THE OLD VERSION OF XCE!" ) xce_object.pandda_initial_html_file = str( xce_object.panddas_directory + "/results_summareis/pandda_initial.html" @@ -476,13 +473,13 @@ def bottom_box_setup( frame.setFrameShape(QtGui.QFrame.StyledPanel) frame.setStyleSheet( "QFrame { " - "border-radius: 1px; padding: 0px; margin: 0px; background-color: rgb(255, 255, 255); }" + "border-radius: 1px; padding: 0px; margin: 0px;" + " background-color: rgb(255, 255, 255); }" ) vbox = QtGui.QVBoxLayout() label = QtGui.QLabel(label) label.setAlignment(QtCore.Qt.AlignCenter | QtCore.Qt.AlignVCenter) - # label.setFont(xce_object.headlineLabelfont) label.setStyleSheet( str( " QLabel { border: 1px solid rgb(184, 192, 210); border-radius: 1px;" From 46509a677a41d764fd8e6e60f14c57433ce4ac4e Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 16:25:22 +0000 Subject: [PATCH 143/358] Clean up settings_tab --- xce/gui_scripts/settings_tab.py | 29 +++++++---------------------- 1 file changed, 7 insertions(+), 22 deletions(-) diff --git a/xce/gui_scripts/settings_tab.py b/xce/gui_scripts/settings_tab.py index 2634302c..7b065105 100755 --- a/xce/gui_scripts/settings_tab.py +++ b/xce/gui_scripts/settings_tab.py @@ -8,11 +8,11 @@ def __init__(self): self.layout_funcs = layout.LayoutFuncs() def setup(self, xce_object): - ################################################################################################################ - # # - # SETTINGS TAB # - # # - ################################################################################################################ + ################################################################################ + # # + # SETTINGS TAB # + # # + ################################################################################ xce_object.settings_container = QtGui.QWidget() xce_object.buttons_etc = QtGui.QWidget() xce_object.settings_vbox = QtGui.QVBoxLayout() @@ -76,7 +76,8 @@ def setup(self, xce_object): xce_object.data_collection_vbox_for_settings.addWidget( QtGui.QLabel( - "\n\nData Collection Directory: (e.g. /dls/i04-1/data/2017/lb18145-70) -" + "\n\nData Collection Directory:" + " (e.g. /dls/i04-1/data/2017/lb18145-70) -" ) ) @@ -103,21 +104,6 @@ def setup(self, xce_object): xce_object.read_agamemnon = QtGui.QCheckBox("Read Agamemnon data structure") settings_beamline_vbox.addWidget(xce_object.read_agamemnon) - # settings_hbox_datasets_summary_file = QtGui.QHBoxLayout() - # xce_object.datasets_summary_file_label = QtGui.QLabel(xce_object.datasets_summary_file) - # settings_hbox_datasets_summary_file.addWidget(xce_object.datasets_summary_file_label) - # settings_button_datasets_summary_file = QtGui.QPushButton('Select Existing\nCollection Summary File') - # settings_button_datasets_summary_file.setMaximumWidth(247) - # settings_button_datasets_summary_file.clicked.connect(xce_object.settings_button_clicked) - # settings_hbox_datasets_summary_file.addWidget(settings_button_datasets_summary_file) - # - # settings_button_new_datasets_summary_file = QtGui.QPushButton('Assign New\nCollection Summary File') - # settings_button_new_datasets_summary_file.clicked.connect(xce_object.settings_button_clicked) - # settings_button_new_datasets_summary_file.setMaximumWidth(247) - # settings_hbox_datasets_summary_file.addWidget(settings_button_new_datasets_summary_file) - # - # settings_beamline_vbox.addLayout(settings_hbox_datasets_summary_file) - settings_beamline_frame.setLayout(settings_beamline_vbox) xce_object.data_collection_vbox_for_settings.addWidget(settings_beamline_frame) @@ -159,7 +145,6 @@ def setup(self, xce_object): ) ) - # xce_object.data_collection_vbox_for_settings.setSpacing(0) xce_object.data_collection_vbox_for_settings.setContentsMargins(30, 30, 30, 30) xce_object.buttons_etc.resize( From d4734b86b036360c18d508dd26e06d3526014a88 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 16:35:53 +0000 Subject: [PATCH 144/358] Clean up settings_preferences --- xce/gui_scripts/settings_preferences.py | 107 ++++++++---------------- 1 file changed, 36 insertions(+), 71 deletions(-) diff --git a/xce/gui_scripts/settings_preferences.py b/xce/gui_scripts/settings_preferences.py index c24b61c9..d08af629 100755 --- a/xce/gui_scripts/settings_preferences.py +++ b/xce/gui_scripts/settings_preferences.py @@ -52,7 +52,9 @@ def settings(self, xce_object): ) # need splat operator: * xce_object.labxchem_directory_current = "/" + os.path.join( *xce_object.current_directory.split("/")[1:9] - ) # labxchem_directory_current is where they actually have write permission + ) + # labxchem_directory_current is where they actually have write + # permission else: xce_object.labxchem_directory = "/" + os.path.join( *xce_object.current_directory.split("/")[1:6] @@ -60,8 +62,6 @@ def settings(self, xce_object): xce_object.labxchem_directory_current = "/" + os.path.join( *xce_object.current_directory.split("/")[1:7] ) # need splat operator: * - # xce_object.labxchem_directory = '/' + os.path.join( - # *xce_object.current_directory.split('/')[1:6]) # need splat operator: * xce_object.beamline_directory = os.path.join( xce_object.labxchem_directory, "processing", "beamline" ) @@ -97,8 +97,6 @@ def settings(self, xce_object): ) xce_object.datasets_summary_file = None - # xce_object.datasets_summary_file = os.path.join(xce_object.database_directory, - # str(os.getcwd().split('/')[5]) + '_summary.pkl') xce_object.data_source_file = "" xce_object.html_export_directory = os.path.join( xce_object.labxchem_directory, "processing", "html" @@ -242,7 +240,10 @@ def settings(self, xce_object): # external software packages xce_object.using_remote_qsub_submission = False - xce_object.remote_qsub_submission = "/usr/bin/ssh @nx.diamond.ac.uk 'module load global/cluster; qsub'" + xce_object.remote_qsub_submission = ( + "/usr/bin/ssh @nx.diamond.ac.uk" + " 'module load global/cluster; qsub'" + ) xce_object.update_log = XChemLog.updateLog(xce_object.xce_logfile) xce_object.update_log.insert("new session started") @@ -270,7 +271,8 @@ def settings(self, xce_object): else: xce_object.restraints_program = "" xce_object.update_log.warning( - "No program for generation of ligand coordinates and restraints available!" + "No program for generation of ligand coordinates and restraints" + " available!" ) def preferences(self, xce_object): @@ -279,14 +281,12 @@ def preferences(self, xce_object): xce_object.preferences_data_to_copy = [ ["aimless logiles and merged mtz only", "mtz_log_only"], ] - # ['All Files in the respective auto-processing directory','everything'], xce_object.preferences_selection_mechanism = [ "IsigI*Comp*UniqueRefl", "highest_resolution", "lowest_Rfree", "dials - only", - # 'xia2 3d - only', "xia2 3dii - only", "autoProc - only", "autoProc_staraniso - only", @@ -331,7 +331,9 @@ def preferences(self, xce_object): ), "ccp4_scratch": xce_object.ccp4_scratch_directory, "unitcell_difference": xce_object.allowed_unitcell_difference_percent, - "too_low_resolution_data": xce_object.acceptable_low_resolution_limit_for_data, + "too_low_resolution_data": ( + xce_object.acceptable_low_resolution_limit_for_data + ), "filename_root": xce_object.filename_root, "preferences": xce_object.preferences, "xce_logfile": xce_object.xce_logfile, @@ -349,10 +351,13 @@ def tables(self, xce_object): # functions that use tables.overview_datasource_table_columns: # - # - select_datasource_columns_to_display() - dropdown in datasource top menu (select columns to show) - # - populate_data_source_table() - appears to be completely unused, so commented out - # - populate_and_update_datasource_table() - used within select_datasource_columns_to_display and - # update_all_tables() + # select_datasource_columns_to_display() + # - dropdown in datasource top menu (select columns to show) + # populate_data_source_table() + # - appears to be completely unused, so commented out + # populate_and_update_datasource_table() + # - used within select_datasource_columns_to_display and + # update_all_tables() xce_object.overview_datasource_table_columns = [ "Sample ID", @@ -369,13 +374,13 @@ def tables(self, xce_object): # functions that use tables.datasets_summary_table_columns: # - # - populate_datasets_summary_table() - appears in create_widgets_for_autoprocessing_results_only() - # - user_update_selected_autoproc_datasets_summary_table() - # - appears in create_widgets_for_autoprocessing_results_only() + # populate_datasets_summary_table() + # - appears in create_widgets_for_autoprocessing_results_only() + # user_update_selected_autoproc_datasets_summary_table() + # - appears in create_widgets_for_autoprocessing_results_only() xce_object.datasets_summary_table_columns = [ "Sample ID", - # 'Resolution\n[Mn = 2.0]', "Resolution\nHigh", "DataProcessing\nSpaceGroup", "DataProcessing\nRfree", @@ -387,15 +392,13 @@ def tables(self, xce_object): "img1", "img2", "img3", - "img4" - # 'img5', - # 'Show\nDetails', - # 'Show Diffraction\nImage' + "img4", ] # functions that use tables.data_collection_table_columns: # - # - show_results_from_all_pipelines() - appears in populate_datasets_summary_table() + # show_results_from_all_pipelines() + # - appears in populate_datasets_summary_table() xce_object.data_collection_table_columns = [ "Sample ID", @@ -415,13 +418,13 @@ def tables(self, xce_object): # functions that use tables.datasets_reprocess_columns: # - # - update_datasets_reprocess_table() - appears in search_for_datasets() + # update_datasets_reprocess_table() + # - appears in search_for_datasets() xce_object.datasets_reprocess_columns = [ "Dataset ID", "Sample ID", "Run\nxia2", - # 'Resolution\n[Mn = 1.5]', "Resolution\nHigh", "Rmerge\nLow", "Dimple\nRfree", @@ -432,14 +435,14 @@ def tables(self, xce_object): # functions that use tables.maps_table_columns: # - # - update_datasets_reprocess_table() - appears in create_maps_table() + # update_datasets_reprocess_table() + # - appears in create_maps_table() xce_object.maps_table_columns = [ "Sample ID", "Select", "Compound ID", "Smiles", - # 'Resolution\n[Mn = 1.5]', "Resolution\nHigh", "Dimple\nRcryst", "Dimple\nRfree", @@ -455,7 +458,8 @@ def tables(self, xce_object): # functions that use tables.pandda_table_columns: # - # - populate_pandda_analyse_input_table() - appears in update_all_tables() + # populate_pandda_analyse_input_table() + # - appears in update_all_tables() xce_object.pandda_table_columns = [ "Sample ID", @@ -472,7 +476,8 @@ def tables(self, xce_object): # functions that use tables.refinement_table_columns: # - # - populate_and_update_refinement_table() - appears in update_all_tables + # populate_and_update_refinement_table() + # - appears in update_all_tables xce_object.refinement_table_columns = [ "Sample ID", @@ -488,14 +493,6 @@ def tables(self, xce_object): ] def top_menu_dict(self, xce_object): - - # dictionary containing config for top menu setup - # menu dict = { 'order letter: menu_item_name': ["name_in_menu", - # [ - # ['text_in_menu', 'shortcut', 'trigger function']], - # [...], - # ]] - # } xce_object.menu_dict = { "A: file": [ "&File", @@ -565,27 +562,10 @@ def top_menu_dict(self, xce_object): "", xce_object.export_to_html_deposition_ready, ], - # ['Find PanDDA apo structures', '', - # xce_object.create_missing_apo_records_in_depositTable], - # ['Update file info of apo structures', '', - # xce_object.update_file_information_of_apo_records], - # ['Prepare mmcif for apo structures', '', - # xce_object.prepare_models_for_deposition_apo], - # ['Prepare mmcif for ligand bound structures', '', - # xce_object.prepare_models_for_deposition_ligand_bound], - # ['Copy files to group deposition directory (ligand bound)', '', - # xce_object.prepare_for_group_deposition_upload_ligand_bound], - # ['Copy files to group deposition directory (ground state)', '', - # xce_object.prepare_for_group_deposition_upload_ground_state], ["Update DB with PDB codes", "", xce_object.enter_pdb_codes], ["Check SMILES", "", xce_object.check_smiles_in_db_and_pdb], ], ], - # 'E: proasis': ["Proasis", - # [ - # ['Launch Proasis in browser', '', partial(webbrowser.open, - # url='http://cs04r-sc-vserv-137.diamond.ac.uk/Proasis4_2017/')] - # ]], "F: help": [ "&Help", [ @@ -593,7 +573,8 @@ def top_menu_dict(self, xce_object): "Open XCE manual", "", lambda: setup().openFile( - "/dls/science/groups/i04-1/software/XCE_manual_2018-11-09.pdf" + "/dls/science/groups/i04-1/software/" + "XCE_manual_2018-11-09.pdf" ), ], [ @@ -769,21 +750,15 @@ def bottom_box_buttons(self, xce_object): def dropdown_items(self, xce_object): xce_object.dataset_tasks = [ "Get New Results from Autoprocessing", - # 'Run DIMPLE on All Autoprocessing MTZ files', "Rescore Datasets", "Run xia2 on selected datasets", "Run xia2 on selected datasets - overwrite", ] xce_object.map_cif_file_tasks = [ - # 'Run initial refinement on selected MTZ files', - # 'Remove selected initial refinement files', "Run DIMPLE on selected MTZ files", "Remove selected DIMPLE files", "Set DIMPLE output", - # 'Set only results from selected pipeline', - # 'Create CIF/PDB/PNG file of ALL compounds', - # 'Create CIF/PDB/PNG file of NEW compounds', "------------------------------------------", "Create CIF/PDB/PNG file of SELECTED compounds", "Merge ligand CIF file with selected compounds", @@ -809,7 +784,6 @@ def dropdown_items(self, xce_object): "Export SELECTED PANDDA models", "------------------------------------------", "Show HTML summary", - # 'Update datasource with results from pandda.inspect', "cluster datasets", "Event Map -> SF", "apo -> mmcif", @@ -821,7 +795,6 @@ def dropdown_items(self, xce_object): "refine ALL bound-state models with BUSTER (no sanity check)", "refine NEW bound-state models with BUSTER (no sanity check)", "------------------------------------------", - # 'refine NEW bound-state models with BUSTER - NEW', "pre-run for ground state model", "Build ground state model", "------------------------------------------", @@ -832,13 +805,5 @@ def dropdown_items(self, xce_object): "Open COOT - BUSTER refinement -", "Open COOT - REFMAC refinement -", "Open COOT - dimple_twin -", - # '-------------------------------', - # 'Reset to last successful refinement (BUSTER or REFMAC)', "", ] - - -# xce_object.refine_file_tasks = ['Open COOT', -# 'Open COOT for old PanDDA', -# 'Update Deposition Table', -# 'Prepare Group Deposition'] From 3fb5b126d253c9829f9374f9df78640cbbaee4d0 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 16:36:19 +0000 Subject: [PATCH 145/358] Cleanup stylesheet --- xce/gui_scripts/stylesheet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/xce/gui_scripts/stylesheet.py b/xce/gui_scripts/stylesheet.py index 44b217ba..cea23c4d 100755 --- a/xce/gui_scripts/stylesheet.py +++ b/xce/gui_scripts/stylesheet.py @@ -17,7 +17,7 @@ def set_stylesheet(xce_object): } QMenuBar { background-color: rgb(236, 236, 236); - } + } QMenuBar::item { background-color: rgb(236, 236, 236); } From a081eb16310388e975801f9f21184098c33c38c1 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 16:36:53 +0000 Subject: [PATCH 146/358] Clean up refinement_tab --- xce/gui_scripts/refinement_tab.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/xce/gui_scripts/refinement_tab.py b/xce/gui_scripts/refinement_tab.py index 5f5d0e16..57aeca05 100755 --- a/xce/gui_scripts/refinement_tab.py +++ b/xce/gui_scripts/refinement_tab.py @@ -7,11 +7,11 @@ def __init__(self): self.layout_funcs = layout.LayoutFuncs() def setup(self, xce_object): - ################################################################################################################ - # # - # REFINEMENT TAB # - # # - ################################################################################################################ + ################################################################################ + # # + # REFINEMENT TAB # + # # + ################################################################################ xce_object.summary_vbox_for_table = QtGui.QVBoxLayout() # table From 0e6bd3642cba854be54f41e9e1fdf4b540e72419 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 16:37:25 +0000 Subject: [PATCH 147/358] Clean up overview_tab --- xce/gui_scripts/overview_tab.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/xce/gui_scripts/overview_tab.py b/xce/gui_scripts/overview_tab.py index ebb97c08..1cb98c8a 100755 --- a/xce/gui_scripts/overview_tab.py +++ b/xce/gui_scripts/overview_tab.py @@ -9,11 +9,11 @@ def __init__(self): self.layout_funcs = layout.LayoutFuncs() def setup(self, xce_object): - ################################################################################################################ - # # - # OVERVIEW TAB # - # # - ################################################################################################################ + ################################################################################ + # # + # OVERVIEW TAB # + # # + ################################################################################ # define subtab list, widget and dict overview_tab_list = ["Data Source", "Summary"] xce_object.overview_tab_widget = QtGui.QTabWidget() From 991404fde7bf5cbd98e1b7794ea2aa46e62b348f Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 16:38:00 +0000 Subject: [PATCH 148/358] Clean up maps_tab --- xce/gui_scripts/maps_tab.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/xce/gui_scripts/maps_tab.py b/xce/gui_scripts/maps_tab.py index c581ffb5..d65176a9 100755 --- a/xce/gui_scripts/maps_tab.py +++ b/xce/gui_scripts/maps_tab.py @@ -7,11 +7,11 @@ def __init__(self): self.layout_funcs = layout.LayoutFuncs() def setup(self, xce_object): - ################################################################################################################ - # # - # MAPS TAB # - # # - ################################################################################################################ + ################################################################################ + # # + # MAPS TAB # + # # + ################################################################################ # select box for dimple xce_object.select_sample_for_dimple_box = QtGui.QCheckBox( "(de-)select all samples for DIMPLE" From 1075d01dfe6b7dd33fa42a420b958957cab071e4 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 16:39:08 +0000 Subject: [PATCH 149/358] Clean up deposition_tab --- xce/gui_scripts/deposition_tab.py | 65 +++---------------------------- 1 file changed, 6 insertions(+), 59 deletions(-) diff --git a/xce/gui_scripts/deposition_tab.py b/xce/gui_scripts/deposition_tab.py index 66c38006..53d05dcc 100755 --- a/xce/gui_scripts/deposition_tab.py +++ b/xce/gui_scripts/deposition_tab.py @@ -8,11 +8,11 @@ def __init__(self): self.layout_funcs = layout.LayoutFuncs() def setup(self, xce_object): - ################################################################################################################ - # # - # DEPOSITION TAB # - # # - ################################################################################################################ + ################################################################################ + # # + # DEPOSITION TAB # + # # + ################################################################################ xce_object.deposition_vbox = QtGui.QVBoxLayout() scroll = QtGui.QScrollArea() @@ -35,9 +35,7 @@ def setup(self, xce_object): ) deposition_page_introduction_link.setOpenExternalLinks(True) - # # bound-state depostion - # deposition_bound_state_heading = self.layout_funcs.add_depo_heading( "Group deposition of bound-state structures" @@ -113,9 +111,7 @@ def setup(self, xce_object): XChemToolTips.pdb_group_deposition_instruction_two() ) - # # ground-state depostion - # deposition_ground_state_heading = self.layout_funcs.add_depo_heading( "Group deposition of ground-state model" @@ -146,24 +142,6 @@ def setup(self, xce_object): "font: italic bold 17pt Arial " ) - # deposition_ground_state_preparation_step_one_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_one_text()) - - # ground_state_pdb_button = QtGui.QPushButton('Select PDB file') - # ground_state_pdb_button.clicked.connect(xce_object.select_ground_state_pdb) - # ground_state_pdb_button.setMaximumWidth(200) - # xce_object.ground_state_pdb_button_label = QtGui.QLabel('') - # xce_object.ground_state_pdb_button_label.setStyleSheet('color: blue') - # - # deposition_ground_state_log_info = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_log_info()) - # - # deposition_ground_state_preparation_step_two_text = self.layout_funcs.add_depo_text(XChemToolTips.deposition_ground_state_preparation_step_two_text()) - # - # ground_state_mtz_button = QtGui.QPushButton('Select MTZ file') - # ground_state_mtz_button.clicked.connect(xce_object.select_ground_state_mtz) - # ground_state_mtz_button.setMaximumWidth(200) - # xce_object.ground_state_mtz_button_label = QtGui.QLabel('') - # xce_object.ground_state_mtz_button_label.setStyleSheet('color: blue') - deposition_ground_state_preparation_step_three_text = ( self.layout_funcs.add_depo_text( XChemToolTips.deposition_ground_state_preparation_step_three_text() @@ -220,10 +198,7 @@ def setup(self, xce_object): ) ) - # # after ligand_bound depostion - # - after_deposition_heading = self.layout_funcs.add_depo_heading( "After deposition of ligand-bound structures" ) @@ -237,15 +212,6 @@ def setup(self, xce_object): ############################################### - # deposition_html_heading = self.layout_funcs.add_depo_heading('HTML export') - # deposition_html_heading.setStyleSheet("font: 20pt Arial Bold") - # - # introduction_text = self.layout_funcs.add_depo_text(XChemToolTips.html_summary_introduction()) - # - # html_export_button = QtGui.QPushButton('Export to HTML') - # html_export_button.clicked.connect(xce_object.export_to_html) - # html_export_button.setMaximumWidth(200) - deposition_widget_list = [ deposition_page_heading, QtGui.QLabel(" \n "), @@ -280,10 +246,6 @@ def setup(self, xce_object): deposition_ground_state_prerequisites_text, QtGui.QLabel(" \n "), deposition_ground_state_preparation, - # ground_state_pdb_button, xce_object.ground_state_pdb_button_label, - # deposition_ground_state_log_info, - # deposition_ground_state_preparation_step_two_text, - # ground_state_mtz_button,xce_object.ground_state_mtz_button_label, deposition_ground_state_preparation_step_three_text, xce_object.ground_state_pandda_directory_label, deposition_ground_state_preparation_step_four_text, @@ -296,25 +258,10 @@ def setup(self, xce_object): deposition_ground_state_preparation_step_eight_text, pdb_group_deposition_link_two, pdb_group_deposition_instruction_two, - QtGui.QLabel(" \n\n\n ") - # after_deposition_heading, QtGui.QLabel(' \n '), - # after_deposition_preparation, - # after_deposition_preparation_text + QtGui.QLabel(" \n\n\n "), ] - # QtGui.QLabel(' \n\n\n '), - # - # deposition_html_heading, QtGui.QLabel(' \n '), - # introduction_text, - # html_export_button, QtGui.QLabel(' \n\n '), - # s QtGui.QLabel(' \n ')] - # - # deposition_widget_list2 = [update_html_button, QtGui.QLabel(' '), - # upload_html_heading, upload_html_text, QtGui.QLabel(' ')] - self.layout_funcs.add_to_box(scrollLayout, deposition_widget_list) - # scrollLayout.addLayout(hbox_zenodo_upload_id) - # self.layout_funcs.add_to_box(scrollLayout, deposition_widget_list2) # container settings scrollLayout.addStretch(1) From 6d9592583a5adc3a7823cda1c655af21fa91523a Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 16:39:57 +0000 Subject: [PATCH 150/358] Clean up datasets_tab --- xce/gui_scripts/datasets_tab.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/xce/gui_scripts/datasets_tab.py b/xce/gui_scripts/datasets_tab.py index e6c89f9b..3dfca37f 100755 --- a/xce/gui_scripts/datasets_tab.py +++ b/xce/gui_scripts/datasets_tab.py @@ -8,11 +8,11 @@ def __init__(self): self.layout_funcs = layout.LayoutFuncs() def setup(self, xce_object): - ################################################################################################################ - # # - # DATASETS TAB # - # # - ################################################################################################################ + ################################################################################ + # # + # DATASETS TAB # + # # + ################################################################################ # define subtab list, widget and dict datasets_tab_list = ["Summary", "Reprocess"] xce_object.datasets_tab_widget = QtGui.QTabWidget() @@ -248,7 +248,8 @@ def setup(self, xce_object): " QComboBox { padding: 1px; margin: 1px }" ) - # create vertical box to add labels and dropdowns to, create box and put in frame + # create vertical box to add labels and dropdowns to + # create box and put in frame vbox_isigma = QtGui.QVBoxLayout() vbox_isigma_widgets = [label, xce_object.reprocess_isigma_combobox] self.layout_funcs.add_to_box(vbox_isigma, vbox_isigma_widgets) From cf485110b8456ad012b8dd540b920e51c04bf6ca Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 17:06:31 +0000 Subject: [PATCH 151/358] Clean up XChemThread --- xce/lib/XChemThread.py | 976 ++++++----------------------------------- 1 file changed, 141 insertions(+), 835 deletions(-) diff --git a/xce/lib/XChemThread.py b/xce/lib/XChemThread.py index 0382b709..1ec0f404 100755 --- a/xce/lib/XChemThread.py +++ b/xce/lib/XChemThread.py @@ -49,9 +49,7 @@ def run(self): XChemMain.backup_soakDB(self.datasource, self.xce_logfile) - # # get list of xtals - # self.xtal_list = [] progress_step = 1 @@ -77,7 +75,8 @@ def run(self): try: os.chdir(directory) except OSError: - # this could happen if the user accidentaly left a file in the project directory + # this could happen if the user accidentaly left a file in the + # project directory continue if os.listdir(directory) == []: self.Logfile.warning(directory + " is empty; skipping...") @@ -85,9 +84,7 @@ def run(self): xtal = directory[directory.rfind("/") + 1 :] self.xtal_list.append(xtal) - # # go through list - # for xtal in self.xtal_list: self.Logfile.insert("directory name: " + xtal + " = sampleID in database") @@ -124,7 +121,6 @@ def run(self): self.Logfile.insert("database mainTable update finished") self.Logfile.insert("updating panddaTable") self.emit(QtCore.SIGNAL("update_status_bar(QString)"), "updating panddaTable") - # self.sync_pandda_table() self.sync_pandda_table_NEW() self.emit( QtCore.SIGNAL("update_status_bar(QString)"), @@ -181,7 +177,8 @@ def sync_data_processing(self, xtal, db_dict): # AIMLESS logfile - # in case the MTZ file which is used for refinement is different to the one used for refinement + # in case the MTZ file which is used for refinement is different to the one + # used for refinement if os.path.isfile("refine.mtz"): if os.path.isfile(xtal + ".free.mtz"): freeMTZ = mtztools(xtal + ".free.mtz") @@ -196,7 +193,8 @@ def sync_data_processing(self, xtal, db_dict): xtal + ".mtz" ) self.Logfile.insert( - "%s: calculating CC between %s.free.mtz (%s refl) and %s.mtz (%s refl): %s" + "%s: calculating CC between %s.free.mtz" + " (%s refl) and %s.mtz (%s refl): %s" % (xtal, xtal, str(nREFfree), xtal, str(nREF), str(CC)) ) if errorMessage != "": @@ -208,7 +206,9 @@ def sync_data_processing(self, xtal, db_dict): try: if float(CC) < 0.999: self.Logfile.insert( - "correlation coefficient between the two files is below 0.999; will try to understand from dimple.log which one was used for initial map calculation" + "correlation coefficient between the two files is below" + " 0.999; will try to understand from dimple.log which" + " one was used for initial map calculation" ) if os.path.isfile( "dimple/dimple_rerun_on_selected_file/dimple/dimple.log" @@ -216,7 +216,8 @@ def sync_data_processing(self, xtal, db_dict): foundLine = False mtzin = "" for line in open( - "dimple/dimple_rerun_on_selected_file/dimple/dimple.log" + "dimple/dimple_rerun_on_selected_file/dimple/" + "dimple.log" ): if foundLine: mtzin = ( @@ -234,7 +235,8 @@ def sync_data_processing(self, xtal, db_dict): if os.path.isfile(mtzin): self.Logfile.insert( - "%s: mtzfile used for refinement is not the same as the one chosen from autoprocessing" + "%s: mtzfile used for refinement is not the" + " same as the one chosen from autoprocessing" % xtal ) self.Logfile.insert( @@ -266,13 +268,13 @@ def sync_data_processing(self, xtal, db_dict): except ValueError: self.Logfile.insert( - "something went wrong: calculated CC value does not seem to be a floating point number" + "something went wrong: calculated CC value" + " does not seem to be a floating point number" ) found_logfile = False if os.path.isfile(xtal + ".log"): found_logfile = True - # db_dict['DataProcessingPathToLogfile']=os.path.realpath(xtal+'.log').replace(os.getcwd()+'/','') db_dict["DataProcessingPathToLogfile"] = os.path.realpath(xtal + ".log") db_dict["DataProcessingLOGfileName"] = xtal + ".log" if ( @@ -280,7 +282,6 @@ def sync_data_processing(self, xtal, db_dict): or db_dict["DataCollectionOutcome"] == "" ): db_dict["DataCollectionOutcome"] = "success" - # aimless_results=parse().read_aimless_logfile(xtal+'.log') aimless_results = parse().read_aimless_logfile( db_dict["DataProcessingPathToLogfile"] ) @@ -291,11 +292,8 @@ def sync_data_processing(self, xtal, db_dict): # MTZ file - # found_mtzfile=self.find_file(xtal+'.mtz',xtal) - # if found_mtzfile: if os.path.isfile(xtal + ".mtz"): db_dict["DataProcessingPathToMTZfile"] = os.path.realpath(xtal + ".mtz") - # db_dict['DataProcessingPathToMTZfile']=os.path.realpath(xtal+'.mtz').replace(os.getcwd()+'/','') db_dict["DataProcessingMTZfileName"] = xtal + ".mtz" if not found_logfile: mtz_info = mtztools(xtal + ".mtz").get_information_for_datasource() @@ -311,10 +309,7 @@ def sync_dimple_results(self, xtal, db_dict): # DIMPLE pdb - # found_dimple_pdb=self.find_file('dimple.pdb',xtal) - # if found_dimple_pdb: if os.path.isfile("dimple.pdb"): - # db_dict['DimplePathToPDB']=os.path.realpath('dimple.pdb').replace(os.getcwd()+'/','') db_dict["DimplePathToPDB"] = os.path.realpath("dimple.pdb") pdb_info = parse().PDBheader("dimple.pdb") db_dict["DimpleRcryst"] = pdb_info["Rcryst"] @@ -327,13 +322,11 @@ def sync_dimple_results(self, xtal, db_dict): db_dict["DimpleRfree"] = "" db_dict["DimpleResolutionHigh"] = "" db_dict["DimpleStatus"] = "pending" + # DIMPLE mtz dimple_path = "" - # found_dimple_mtz=self.find_file('dimple.mtz',xtal) - # if found_dimple_mtz: if os.path.isfile("dimple.mtz"): - # db_dict['DimplePathToMTZ']=os.path.realpath('dimple.mtz').replace(os.getcwd()+'/','') db_dict["DimplePathToMTZ"] = os.path.realpath("dimple.mtz") dimple_mtz = db_dict["DimplePathToMTZ"] dimple_path = dimple_mtz[: dimple_mtz.rfind("/")] @@ -353,11 +346,8 @@ def sync_dimple_results(self, xtal, db_dict): # MTZ free file - # found_free_mtz=self.find_file(xtal+'.free.mtz',xtal) - # if found_free_mtz: if os.path.isfile(xtal + ".free.mtz"): db_dict["RefinementMTZfree"] = os.path.realpath(xtal + ".free.mtz") - # db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz').replace(os.getcwd()+'/','') else: db_dict["RefinementMTZfree"] = "" os.system("/bin/rm %s.free.mtz 2> /dev/null" % xtal) @@ -366,17 +356,13 @@ def sync_dimple_results(self, xtal, db_dict): os.path.relpath(os.path.join(dimple_path, "prepared2.mtz")), xtal + ".free.mtz", ) - # db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz').replace(os.getcwd()+'/','') db_dict["RefinementMTZfree"] = os.path.realpath(xtal + ".free.mtz") - # db_dict['RefinementMTZfree']=xtal+'.free.mtz' elif os.path.isfile(os.path.join(dimple_path, "prepared.mtz")): os.symlink( os.path.relpath(os.path.join(dimple_path, "prepared.mtz")), xtal + ".free.mtz", ) db_dict["RefinementMTZfree"] = os.path.realpath(xtal + ".free.mtz") - # db_dict['RefinementMTZfree']=os.path.realpath(xtal+'.free.mtz').replace(os.getcwd()+'/','') - # db_dict['RefinementMTZfree']=xtal+'.free.mtz' elif os.path.isfile(os.path.join(dimple_path, "free.mtz")): os.symlink( os.path.relpath(os.path.join(dimple_path, "free.mtz")), @@ -451,17 +437,10 @@ def sync_compound_information(self, db_dict): def sync_refinement_results(self, xtal, db_dict): - # # REFINE pdb - # - - # found_refine_pdb=self.find_file('refine.pdb',xtal) - # if found_refine_pdb and not 'dimple' in os.path.realpath('refine.pdb'): - # if os.path.isfile('refine.pdb') and not 'dimple' in os.path.realpath('refine.pdb'): if os.path.isfile("refine.pdb"): db_dict["RefinementPDB_latest"] = os.path.realpath("refine.pdb") - # db_dict['RefinementPDB_latest']=os.path.realpath('refine.pdb').replace(os.getcwd()+'/','') db_dict["RefinementStatus"] = "finished" pdb_info = parse().dict_for_datasource_update("refine.pdb") db_dict.update(pdb_info) @@ -483,36 +462,19 @@ def sync_refinement_results(self, xtal, db_dict): if os.path.isfile("REFINEMENT_IN_PROGRESS"): db_dict["RefinementStatus"] = "running" - # # REFINE bound pdb - # if os.path.isfile("refine.split.bound-state.pdb"): db_dict["RefinementBoundConformation"] = os.path.realpath( "refine.split.bound-state.pdb" ) - # db_dict['RefinementBoundConformation']='refine.bound.pdb' else: - # if os.path.isfile('refine.pdb'): - # os.system("giant.strip_conformations pdb=refine.pdb suffix='.bound.pdb'") - # if os.path.isfile('refine.bound.pdb'): - # db_dict['RefinementBoundConformation']=os.path.realpath('refine.bound.pdb') - # else: - # db_dict['RefinementBoundConformation']='' - # else: - # db_dict['RefinementBoundConformation']='' db_dict["RefinementBoundConformation"] = "" - # # REFINE mtz - # - # found_refine_mtz=self.find_file('refine.mtz',xtal) - # if found_refine_mtz and not 'dimple' in os.path.realpath('refine.mtz'): - # if os.path.isfile('refine.mtz') and not 'dimple' in os.path.realpath('refine.mtz'): if os.path.isfile("refine.mtz"): db_dict["RefinementMTZ_latest"] = os.path.realpath("refine.mtz") - # db_dict['RefinementMTZ_latest']=os.path.realpath('refine.mtz').replace(os.getcwd()+'/','') else: db_dict["RefinementMTZ_latest"] = "" os.system("/bin/rm refine.mtz 2> /dev/null") @@ -525,7 +487,8 @@ def find_apo_structures_for_PanDDA(self, panddaPATH): # information concur # need to update pandda directory for every exported structure so that - # we know where to look for the pandda.log file that contains the relevant information + # we know where to look for the pandda.log file that contains the relevant + # information # update CrystalName_of_pandda_input in DB @@ -536,22 +499,21 @@ def find_apo_structures_for_PanDDA(self, panddaPATH): panddaLog = glob.glob(os.path.join(panddaPATH, "pandda*log")) panddaLog.sort(key=os.path.getmtime) - panddaVersion = "unknown" readindApoStructures = False apoStructures = [] apoStructureDict = {} apoString = "" for files in panddaLog: for line in open(files): - if line.startswith("- Pandda Version"): - if len(line.split()) >= 4: - panddaVersion = line.split()[3] if "No Statistical Maps Found:" in line: readindApoStructures = True if readindApoStructures: if "Pickling Object: processed_datasets" in line: if line.split() >= 2: - # e.g. line.split() -> ['Pickling', 'Object:', 'processed_datasets/NUDT22A-x0055/pickles/dataset.pickle'] + # e.g. line.split() -> + # ['Pickling', + # 'Object:', + # 'processed_datasets/NUDT22A-x0055/pickles/dataset.pickle'] xtal = line.split()[2].split("/")[1] if os.path.isfile( os.path.join( @@ -564,147 +526,14 @@ def find_apo_structures_for_PanDDA(self, panddaPATH): apoStructures.append(xtal) apoString += xtal + ";" if ( - "Pre-existing statistical maps (from previous runs) have been found and will be reused:" - in line + "Pre-existing statistical maps (from previous runs) have been found" + " and will be reused:" in line ): readindApoStructures = False apoStructureDict[panddaPATH] = apoStructures return apoString[:-1] - # def sync_pandda_table(self): - # progress_step=1 - # progress=0 - # self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - # - # # also need to update PANDDA table... - # pandda_models=self.db.execute_statement("select CrystalName,PANDDA_site_index,PANDDA_site_event_index,PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDApath,ApoStructures from panddaTable") - # if len(pandda_models) > 0: - # progress_step=100/float(len(pandda_models)) - # - # if pandda_models != []: - # for entry in pandda_models: - # db_pandda_dict={} - # xtal=entry[0] - # site_index=entry[1] - # event_index=entry[2] - # panddaPATH=entry[6] - # apoStructures=entry[7] - # self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'checking %s -> site %s -> event %s ' %(xtal,site_index,event_index)) - # try: - # event_x = float(str(entry[3])) - # event_y = float(str(entry[4])) - # event_z = float(str(entry[5])) - # except ValueError: - # pass - # - # # do not update pandda path since this one is updated during pandda export! - # # instead try to get apo semi-colon separated list of apo structures that were used to - # # calculate event maps; but only if field is blank! - # db_pandda_dict['PANDDApath']=self.panddas_directory - # if str(apoStructures)=='None' or apoStructures=='': - # if panddaPATH != 'None' or panddaPATH != '': - # self.Logfile.insert('trying to find which apo structures were used to calculate the event maps in '+panddaPATH) - # db_pandda_dict['ApoStructures']=self.find_apo_structures_for_PanDDA(panddaPATH) - # else: - # self.Logfile.insert('pandda path for '+xtal+' is empty in database') - # - # # event map - # - # found_event_map=False - # db_pandda_dict['PANDDA_site_event_map']='' - # for file in glob.glob(os.path.join(self.initial_model_directory,xtal,'*ccp4')): - # filename=file[file.rfind('/')+1:] - # if filename.startswith(xtal+'-event_'+event_index) and filename.endswith('map.native.ccp4'): - # event_map=file - # db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map) - # db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map).replace(os.getcwd()+'/','') - # found_event_map=True - # break - # if not found_event_map: - # db_pandda_dict['PANDDA_site_event_map']='' - # - # db_pandda_dict['PANDDA_site_initial_model']='' - # for file in glob.glob(os.path.join(self.initial_model_directory,xtal,'*pdb')): - # filename=file[file.rfind('/')+1:] - # if filename.endswith('-ensemble-model.pdb'): - # db_pandda_dict['PANDDA_site_initial_model']=os.path.realpath(file).replace(os.getcwd()+'/','') - # break - # - # db_pandda_dict['PANDDA_site_initial_mtz']='' - # for file in glob.glob(os.path.join(self.initial_model_directory,xtal,'*mtz')): - # filename=file[file.rfind('/')+1:] - # if filename.endswith('pandda-input.mtz'): - # db_pandda_dict['PANDDA_site_initial_mtz']=os.path.realpath(file).replace(os.getcwd()+'/','') - # break - # - # - # db_pandda_dict['PANDDA_site_ligand_resname'] = '' - # db_pandda_dict['PANDDA_site_ligand_chain'] = '' - # db_pandda_dict['PANDDA_site_ligand_sequence_number'] = '' - # db_pandda_dict['PANDDA_site_ligand_altLoc'] = '' - # db_pandda_dict['PANDDA_site_ligand_placed'] = 'False' - # db_pandda_dict['PANDDA_site_spider_plot'] = '' - # db_pandda_dict['PANDDA_site_ligand_id'] = '' - # - # db_pandda_dict['PANDDA_site_occupancy'] = '' - # db_pandda_dict['PANDDA_site_B_average'] = '' - # db_pandda_dict['PANDDA_site_B_ratio_residue_surroundings'] = '' - # db_pandda_dict['PANDDA_site_rmsd'] = '' - # db_pandda_dict['PANDDA_site_RSCC'] = '' - # db_pandda_dict['PANDDA_site_RSR'] = '' - # db_pandda_dict['PANDDA_site_RSZD'] = '' - # - # if os.path.isfile(os.path.join(self.initial_model_directory,xtal,'refine.pdb')): - # ligands_in_file=pdbtools(os.path.join(self.initial_model_directory,xtal,'refine.pdb')).find_xce_ligand_details() - # - # for ligand in ligands_in_file: - # residue_name= ligand[0] - # residue_chain= ligand[1] - # residue_number= ligand[2] - # residue_altLoc= ligand[3] - # residue_xyz = pdbtools(os.path.join(self.initial_model_directory,xtal,'refine.pdb')).get_center_of_gravity_of_residue_ish(residue_chain, residue_number) - # distance = misc().calculate_distance_between_coordinates(residue_xyz[0], residue_xyz[1],residue_xyz[2],event_x, event_y,event_z) - # # if coordinate of ligand and event are closer than 7A, then we assume they belong together - # if distance < 7: - # db_pandda_dict['PANDDA_site_ligand_resname'] = residue_name - # db_pandda_dict['PANDDA_site_ligand_chain'] = residue_chain - # db_pandda_dict['PANDDA_site_ligand_sequence_number'] = residue_number - # db_pandda_dict['PANDDA_site_ligand_altLoc'] = residue_altLoc - # db_pandda_dict['PANDDA_site_ligand_placed'] = 'True' - # db_pandda_dict['PANDDA_site_ligand_id']=residue_name+'-'+residue_chain+'-'+residue_number - # - # if xtal+'/Refine_' in os.path.realpath(os.path.join(self.initial_model_directory,xtal,'refine.pdb')): - # tmp=os.path.realpath(os.path.join(self.initial_model_directory,xtal,'refine.pdb')) - # spider_plot=os.path.join(tmp[:tmp.rfind('/')],'residue_plots',residue_name+'-'+residue_chain+'-'+residue_number+'.png') - # if os.path.isfile(spider_plot): - # db_pandda_dict['PANDDA_site_spider_plot']=os.path.realpath(spider_plot) - # db_pandda_dict['PANDDA_site_spider_plot']=os.path.realpath(spider_plot).replace(os.getcwd()+'/','') - # if os.path.isfile(os.path.join(tmp[:tmp.rfind('/')],'residue_scores.csv')): - # - # with open(os.path.join(tmp[:tmp.rfind('/')],'residue_scores.csv'), 'rb') as csv_import: - # csv_dict = csv.DictReader(csv_import) - # for i, line in enumerate(csv_dict): - # residueNameChainNumber = line[''] - # if residueNameChainNumber == residue_name+'-'+residue_chain+'-'+residue_number: - # db_pandda_dict['PANDDA_site_occupancy'] = line['Occupancy'] - # db_pandda_dict['PANDDA_site_B_average'] = line['Average B-factor (Residue)'] - # db_pandda_dict['PANDDA_site_B_ratio_residue_surroundings'] = line['Surroundings B-factor Ratio'] - # db_pandda_dict['PANDDA_site_rmsd'] = line['Model RMSD'] - # db_pandda_dict['PANDDA_site_RSCC'] = line['RSCC'] - # db_pandda_dict['PANDDA_site_RSR'] = line['RSR'] - # db_pandda_dict['PANDDA_site_RSZD'] = line['RSZD'] - # break - # - # if db_pandda_dict != {}: - ## self.db.update_panddaTable(xtal, site_index, db_pandda_dict) - # self.db.update_site_event_panddaTable(xtal, site_index, event_index, db_pandda_dict) - # self.Logfile.insert('updating panddaTable for xtal: %s, site: %s' %(xtal,site_index)) - # - # progress += progress_step - # self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - # - def sync_pandda_table_NEW(self): progress_step = 1 progress = 0 @@ -712,7 +541,9 @@ def sync_pandda_table_NEW(self): # also need to update PANDDA table... pandda_models = self.db.execute_statement( - "select CrystalName,PANDDA_site_index,PANDDA_site_event_index,PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDApath,ApoStructures from panddaTable" + "select CrystalName,PANDDA_site_index,PANDDA_site_event_index," + "PANDDA_site_x,PANDDA_site_y,PANDDA_site_z,PANDDApath,ApoStructures" + " from panddaTable" ) if len(pandda_models) > 0: progress_step = 100 / float(len(pandda_models)) @@ -743,15 +574,15 @@ def sync_pandda_table_NEW(self): except ValueError: pass - # do not update pandda path since this one is updated during pandda export! - # instead try to get apo semi-colon separated list of apo structures that were used to - # calculate event maps; but only if field is blank! - # db_pandda_dict['PANDDApath']=self.panddas_directory + # do not update pandda path since this one is updated during pandda + # export! instead try to get apo semi-colon separated list of apo + # structures that were used to calculate event maps; but only if field + # is blank! if str(apoStructures) == "None" or apoStructures == "": if panddaPATH != "None" or panddaPATH != "": self.Logfile.insert( - "trying to find which apo structures were used to calculate the event maps in " - + panddaPATH + "trying to find which apo structures were used to calculate" + " the event maps in " + panddaPATH ) db_pandda_dict[ "ApoStructures" @@ -776,7 +607,6 @@ def sync_pandda_table_NEW(self): db_pandda_dict["PANDDA_site_event_map"] = os.path.realpath( event_map ) - # db_pandda_dict['PANDDA_site_event_map']=os.path.realpath(event_map).replace(os.getcwd()+'/','') found_event_map = True break if not found_event_map: @@ -835,9 +665,8 @@ def sync_pandda_table_NEW(self): continue else: self.Logfile.insert( - "{0!s}: found the following ligands in refine.pdb: {1!s}".format( - xtal, str(ligands_in_file) - ) + "{0!s}: found the following ligands in" + " refine.pdb: {1!s}".format(xtal, str(ligands_in_file)) ) distanceList = [] @@ -871,7 +700,8 @@ def sync_pandda_table_NEW(self): ] ) self.Logfile.insert( - "{0!s}: calculating distance between event and ligand ({1!s} {2!s} {3!s}): {4!s}".format( + "{0!s}: calculating distance between event and ligand" + " ({1!s} {2!s} {3!s}): {4!s}".format( xtal, residue_name, residue_chain, @@ -885,7 +715,8 @@ def sync_pandda_table_NEW(self): smallestDistance = min(distanceList, key=lambda x: x[0]) except ValueError: self.Logfile.error( - "could not determine smallest distance between current ligand pandda events" + "could not determine smallest distance between current" + " ligand pandda events" ) continue distance = smallestDistance[0] @@ -894,7 +725,8 @@ def sync_pandda_table_NEW(self): residue_number = smallestDistance[3] residue_altLoc = smallestDistance[4] self.Logfile.insert( - "{0!s}: ligand with the shorted distance ({1!s}A) to the current event (id: {2!s}): {3!s} {4!s} {5!s} {6!s}".format( + "{0!s}: ligand with the shorted distance ({1!s}A) to the" + " current event (id: {2!s}): {3!s} {4!s} {5!s} {6!s}".format( xtal, str(distance), event_index, @@ -967,25 +799,19 @@ def sync_pandda_table_NEW(self): db_pandda_dict["PANDDA_site_RSZD"] = line[ "RSZD" ] - # break - if db_pandda_dict != {}: - # self.db.update_panddaTable(xtal, site_index, db_pandda_dict) self.db.update_site_event_panddaTable( xtal, site_index, event_index, db_pandda_dict ) self.Logfile.insert( - "updating panddaTable for xtal: {0!s}, site: {1!s}, event: {2!s}".format( + "updating panddaTable for" + " xtal: {0!s}, site: {1!s}, event: {2!s}".format( xtal, site_index, event_index ) ) self.Logfile.insert("-> panddaDict: " + str(db_pandda_dict)) -# progress += progress_step -# self.emit(QtCore.SIGNAL('update_progress_bar'), progress) - - class create_png_and_cif_of_compound(QtCore.QThread): def __init__( self, @@ -1060,13 +886,6 @@ def run(self): compoundID.replace(" ", "") + ".pdb", ) ) - # commented this out since people found the presence of the old.cif file interfering with pandda.inspect - # if os.path.isfile(os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.cif')): - # # copy existing CIF file to old.cif so that it can be used as input in - # # restraints generating program - # os.chdir(os.path.join(self.initial_model_directory,sampleID)) - # os.system('/bin/cp %s old.cif' %(compoundID.replace(' ','')+'.cif')) - # os.system('/bin/rm '+os.path.join(self.initial_model_directory,sampleID,compoundID.replace(' ','')+'.cif')) if os.path.isfile( os.path.join( self.initial_model_directory, @@ -1183,7 +1002,6 @@ def run(self): os.chdir(self.ccp4_scratch_directory) self.Logfile.insert("changing directory to " + self.ccp4_scratch_directory) if counter > 1: - # if os.getcwd().startswith('/dls'): if os.path.isdir("/dls"): if self.external_software["qsub_array"]: Cmds = ( @@ -1198,12 +1016,14 @@ def run(self): ) self.Logfile.insert("using the following command:") self.Logfile.insert( - " qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh".format( + " qsub -P labxchem -q medium.q -t 1:{0!s}" + " -tc {1!s} {2!s}_master.sh".format( str(counter), self.max_queue_jobs, self.restraints_program ) ) os.system( - "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} -N {2!s} {3!s}_master.sh".format( + "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s}" + " -N {2!s} {3!s}_master.sh".format( str(counter), self.max_queue_jobs, self.restraints_program, @@ -1212,7 +1032,9 @@ def run(self): ) else: self.Logfile.insert( - "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file" + "cannot start ARRAY job: make sure that" + " 'module load global/cluster'" + " is in your .bashrc or .cshrc file" ) elif self.external_software["qsub"]: self.Logfile.insert( @@ -1253,7 +1075,6 @@ def run(self): ) ) - # self.emit(QtCore.SIGNAL("finished()")) self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) @@ -1288,22 +1109,17 @@ def __init__( def prepareInput(self, cmd, ligList): for cif in ligList: cmd += ( - "rhofit -m ../init.mtz -p ../init.pdb -l ../compound/%s.cif -scanchirals -d %s_rhofit\n" - % (cif, cif) + "rhofit -m ../init.mtz -p ../init.pdb -l ../compound/%s.cif" + " -scanchirals -d %s_rhofit\n" % (cif, cif) ) cmd += ( - "phenix.ligandfit data=../init.mtz model=../init.pdb ligand=../compound/%s.cif clean_up=True\n" - % cif + "phenix.ligandfit data=../init.mtz" + " model=../init.pdb ligand=../compound/%s.cif clean_up=True\n" % cif ) cmd += "/bin/mv LigandFit_run_1_ %s_phenix\n" % cif cmd += "/bin/rm -fr PDS\n\n" return cmd - # rhofit -m refine.mtz -p refine.pdb -l ../compound/NU074105a.cif -d NU074105a_rhofit - # phenix.ligandfit data=refine.mtz model=refine.pdb ligand=../compound/NU074105a.cif - # phenix.get_cc_mtz_pdb LigandFit_run_1_/ligand_fit_1_1.pdb refine.mtz > log - # grep 'local CC:' log - def get_header(self, sampleID): if self.queueing_system_available: top_line = "#PBS -joe -N XCE_dimple\n" @@ -1328,10 +1144,14 @@ def get_header(self, sampleID): return cmd def get_footer(self, cmd, sampleID, compoundID): - cmd += "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/find_best_fitting_ligand.py {0!s} {1!s} {2!s}".format( - compoundID.replace(" ", ""), - os.path.join(self.initial_model_directory, sampleID), - os.path.join(self.database_directory, self.data_source_file), + cmd += ( + "$CCP4/bin/ccp4-python" + " $XChemExplorer_DIR/helpers/" + "find_best_fitting_ligand.py {0!s} {1!s} {2!s}".format( + compoundID.replace(" ", ""), + os.path.join(self.initial_model_directory, sampleID), + os.path.join(self.database_directory, self.data_source_file), + ) ) return cmd @@ -1345,7 +1165,6 @@ def run(self): progress_step = 100 / float(len(self.compound_list)) progress = 0 - counter = 1 for item in self.compound_list: sampleID = item[0] compoundID = item[1] @@ -1390,7 +1209,6 @@ def run(self): progress += progress_step self.emit(QtCore.SIGNAL("update_progress_bar"), progress) - # self.emit(QtCore.SIGNAL("finished()")) self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) def write_script(self, cmd): @@ -1423,18 +1241,19 @@ def run_script(self): ) self.Logfile.insert("using the following command:") self.Logfile.insert( - "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} autofit_ligand_master.sh".format( - str(self.n), self.max_queue_jobs - ) + "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s}" + " autofit_ligand_master.sh".format(str(self.n), self.max_queue_jobs) ) os.system( - "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} autofit_ligand_master.sh".format( + "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s}" + " autofit_ligand_master.sh".format( str(self.n - 1), self.max_queue_jobs ) ) else: self.Logfile.insert( - "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file" + "cannot start ARRAY job: make sure that" + " 'module load global/cluster' is in your .bashrc or .cshrc file" ) elif self.external_software["qsub"]: self.Logfile.insert( @@ -1448,9 +1267,8 @@ def run_script(self): os.system("qsub -q medium.q xce_autofit_ligand_{0!s}.sh".format(str(i))) else: self.Logfile.insert( - "running {0!s} consecutive autofit_ligand jobs on your local machine".format( - str(self.n - 1) - ) + "running {0!s} consecutive autofit_ligand jobs on your" + " local machine".format(str(self.n - 1)) ) for i in range(1, self.n + 1): self.Logfile.insert( @@ -1474,7 +1292,6 @@ def __init__( def run(self): progress_step = 100 / float(len(self.compound_list)) progress = 0 - counter = 1 for item in self.compound_list: sampleID = item[0] @@ -1494,8 +1311,8 @@ def run(self): ) else: self.Logfile.error( - "%s: %s.cif file does not exist in compound sub-directory; skipping..." - % (sampleID, compoundID) + "%s: %s.cif file does not exist in compound sub-directory;" + " skipping..." % (sampleID, compoundID) ) continue @@ -1506,8 +1323,8 @@ def run(self): ) ): self.Logfile.warning( - "%s: removing symbolic link to (or file) %s.cif from sample directory" - % (sampleID, compoundID) + "%s: removing symbolic link to (or file) %s.cif" + " from sample directory" % (sampleID, compoundID) ) os.system("/bin/rm %s.cif 2> /dev/null" % compoundID) @@ -1565,270 +1382,6 @@ def run_libcheck(self, sampleID, compoundID): os.system("ln -s compound/%s.cif ." % compoundID) -# class run_dimple_on_all_autoprocessing_files(QtCore.QThread): -# def __init__(self,sample_list,initial_model_directory,external_software,ccp4_scratch_directory,database_directory, -# data_source_file,max_queue_jobs,xce_logfile, remote_submission, remote_submission_string, -# dimple_twin_mode,pipeline): -# QtCore.QThread.__init__(self) -# self.sample_list=sample_list -# self.initial_model_directory=initial_model_directory -# self.external_software=external_software -# self.queueing_system_available=external_software['qsub'] -# self.ccp4_scratch_directory=ccp4_scratch_directory -# self.database_directory=database_directory -# self.data_source_file=data_source_file -# self.max_queue_jobs=max_queue_jobs -# self.xce_logfile=xce_logfile -# self.Logfile=XChemLog.updateLog(xce_logfile) -# self.pipeline=pipeline -# self.using_remote_qsub_submission = remote_submission -# self.remote_qsub_submission = remote_submission_string -# self.dimple_twin_mode = dimple_twin_mode -# -# -# def run(self): -# progress_step=1 -# if len(self.sample_list) != 0: -# progress_step=100/float(len(self.sample_list)) -# progress=0 -# self.emit(QtCore.SIGNAL('update_progress_bar'), progress) -# -# os.chdir(self.ccp4_scratch_directory) -# os.system('/bin/rm -f xce_dimple*sh') -# -# db=XChemDB.data_source(os.path.join(self.database_directory,self.data_source_file)) -# database=os.path.join(self.database_directory,self.data_source_file) -# -# print(self.sample_list) -# -# for n,item in enumerate(self.sample_list): -# -# xtal = item[0] -# visit_run_autoproc = item[1] -# mtzin = item[2] -# ref_pdb = item[3] -# ref_mtz = item[4] -# ref_cif = item[5] -# -# # check if reference mtzfile has an Rfree column; if not, then ignore -# # DIMPLE assumes an Rfree column and barfs if it is not present -# # note: ref_mtz looks like this: ref mtz -R reference.mtz -# if os.path.isfile(ref_mtz.split()[len(ref_mtz.split())-1]): -# mtz_column_dict=mtztools(ref_mtz.split()[len(ref_mtz.split())-1]).get_all_columns_as_dict() -# if os.path.isfile(ref_mtz): -# if 'FreeR_flag' not in mtz.object(ref_mtz).column_labels(): -# mtz_column_dict=mtztools(ref_mtz).get_all_columns_as_dict() -# if 'FreeR_flag' not in mtz_column_dict['RFREE']: -# self.Logfile.insert('cannot find FreeR_flag in reference mtz file: {0!s} -> ignoring reference mtzfile!!!'.format(ref_mtz)) -# ref_mtz = '' -# if mtz_column_dict['RFREE'] != []: -## self.Logfile.insert('found Rfree set with other column name though: {0!s}'.format(str(mtz_column_dict['RFREE']))) -## self.Logfile.insert('try renaming Rfree column to FreeR_flag with CAD!') -# -## uniqueify = '' -# if 'FreeR_flag' in mtz.object(mtzin).column_labels(): -## uniqueify = 'uniqueify -f FreeR_flag ' + mtzin + ' ' + xtal + '-unique.mtz' + '\n' -# else: -## uniqueify = 'uniqueify ' + mtzin + ' ' + xtal + '-unique.mtz' + '\n' -# -# db_dict= {'DimpleReferencePDB': ref_pdb} -# db.update_data_source(xtal,db_dict) -# -# self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'creating input script for '+xtal+' in '+visit_run_autoproc) -# -# if not os.path.isdir(os.path.join(self.initial_model_directory,xtal)): -# os.mkdir(os.path.join(self.initial_model_directory,xtal)) -# if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'dimple')): -# os.mkdir(os.path.join(self.initial_model_directory,xtal,'dimple')) -# if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc)): -# os.mkdir(os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc)) -# os.chdir(os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc)) -# os.system('touch dimple_run_in_progress') -# os.system('/bin/rm final.mtz 2> /dev/null') -# os.system('/bin/rm final.pdb 2> /dev/null') -# -# if self.queueing_system_available: -# top_line='#PBS -joe -N XCE_dimple\n' -# else: -# top_line='#!'+os.getenv('SHELL')+'\n' -# -# if 'csh' in os.getenv('SHELL'): -# ccp4_scratch='setenv CCP4_SCR '+self.ccp4_scratch_directory+'\n' -# elif 'bash' in os.getenv('SHELL'): -# ccp4_scratch='export CCP4_SCR='+self.ccp4_scratch_directory+'\n' -# else: -# ccp4_scratch='' -# -# if 'dimple_rerun_on_selected_file' in visit_run_autoproc: -# additional_cmds = ( -# 'cd {0!s}\n'.format(os.path.join(self.initial_model_directory,xtal)) + -# '/bin/rm dimple.pdb\n' -# 'ln -s dimple/dimple_rerun_on_selected_file/dimple/final.pdb dimple.pdb\n' -# '/bin/rm dimple.mtz\n' -# 'ln -s dimple/dimple_rerun_on_selected_file/dimple/final.mtz dimple.mtz\n' -# '/bin/rm 2fofc.map\n' -# 'ln -s dimple/dimple_rerun_on_selected_file/dimple/2fofc.map .\n' -# '/bin/rm fofc.map\n' -# 'ln -s dimple/dimple_rerun_on_selected_file/dimple/fofc.map .\n' -# '\n' -# '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_for_new_dimple_pdb.py')+ -# ' {0!s} {1!s} {2!s}\n'.format(os.path.join(self.database_directory,self.data_source_file), xtal, self.initial_model_directory) ) -# -# else: -# additional_cmds='' -# -## resolution_high = 0.1 -## o = iotbx.mtz.object(mtzin) -## low, high = o.max_min_resolution() -# hkl = any_reflection_file(file_name=mtzin) -# miller_arrays = hkl.as_miller_arrays() -# mtzFile = miller_arrays[0] -# -# if mtzFile.space_group_info().symbol_and_number() == 'R 3 :H (No. 146)': -# symNoAbsence = 'H3' -# elif mtzFile.space_group_info().symbol_and_number() == 'R 3 2 :H (No. 155)': -# symNoAbsence = 'H32' -# else: -# symNoAbsence = str([x[0] for x in str(mtzFile.space_group_info().symbol_and_number().split('(')[0]).split()]).replace('[','').replace(']','').replace("'","").replace(',','').replace(' ','') -# if symNoAbsence.replace(' ','') == "R32:": -# symNoAbsence = 'H32' -# -# dls_stuff = '' -# if os.path.isdir('/dls'): -# dls_stuff = ( -# 'module unload ccp4\n' -# 'source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' -# ) -# -# twin = '' -# if self.dimple_twin_mode: -# twin = "--refmac-key 'TWIN'" -# -# Cmds = ( -# '{0!s}\n'.format(top_line)+ -# '\n' -# 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' -# '\n' -# 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc) + -# '\n' -# 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' -# '\n' -# + dls_stuff + -# '\n' -# + ccp4_scratch + -# '\n' -# '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(database,xtal,'DimpleStatus','running') + -# '\n' -# 'unique hklout unique.mtz << eof\n' -# ' cell %s\n' %str([round(float(i),2) for i in mtzFile.unit_cell().parameters()]).replace('[','').replace(']','')+ -# ' symmetry %s\n' %symNoAbsence+ -# ' resolution %s\n' %str(round(float(mtzFile.d_min()),3))+ -# 'eof\n' -# '\n' -## 'freerflag hklin unique.mtz hklout free.mtz > freerflag.log\n' -# '\n' -# 'sftools << eof > sftools.log\n' -# ' read unique.mtz\n' -# ' calc col F = 10.0\n' -# ' calc col SIGF = 1.0\n' -# ' write sftools.mtz\n' -# 'eof\n' -# '\n' -# 'cad hklin1 sftools.mtz hklin2 %s hklout %s.999A.mtz << eof\n' %(mtzin,xtal) + -# ' monitor BRIEF\n' -# ' labin file 1 E1=F E2=SIGF\n' -# ' labout file 1 E1=F_unique E2=SIGF_unique\n' -# ' labin file 2 ALL\n' -# ' resolution file 1 999.0 %s\n' %str(round(float(mtzFile.d_min()),2))+ -# 'eof\n' -# '\n' -# "dimple --no-cleanup %s.999A.mtz %s %s %s %s dimple\n" %(xtal,ref_pdb,ref_mtz,ref_cif,twin) + -# '\n' -# 'cd %s\n' %os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc,'dimple') + -# + uniqueify + -# '\n' -# 'cad hklin1 %s hklout %s < ignoring reference mtzfile!!!' %ref_mtz) - # ref_mtz = '' - # if mtz_column_dict['RFREE'] != []: - # self.Logfile.insert('found Rfree set with other column name though: %s' %str(mtz_column_dict['RFREE'])) - # self.Logfile.insert('try renaming Rfree column to FreeR_flag with CAD!') - # - # db_dict={} - # db_dict['DimpleReferencePDB']=ref_pdb - # self.db.update_data_source(xtal,db_dict) - # - # self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'creating input script for '+xtal+' in '+visit_run_autoproc) - # if not os.path.isdir(os.path.join(self.initial_model_directory, xtal)): os.mkdir(os.path.join(self.initial_model_directory, xtal)) @@ -1979,7 +1517,8 @@ def prepare_phenix_ligand_pipeline_shell_script( + "\n" "source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n" "\n" + ccp4_scratch + "\n" - "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n" + "$CCP4/bin/ccp4-python" + " $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n" % ( os.path.join(self.database_directory, self.data_source_file), xtal, @@ -2007,8 +1546,10 @@ def prepare_phenix_ligand_pipeline_shell_script( "/bin/rm phenix.ligand_pipeline.pdb\n" "/bin/rm phenix.ligand_pipeline.mtz\n" "\n" - "ln -s phenix.ligand_pipeline/pipeline_1/refine_final.pdb phenix.ligand_pipeline.pdb\n" - "ln -s phenix.ligand_pipeline/pipeline_1/refine_final.mtz phenix.ligand_pipeline.mtz\n" + "ln -s phenix.ligand_pipeline/pipeline_1/refine_final.pdb" + " phenix.ligand_pipeline.pdb\n" + "ln -s phenix.ligand_pipeline/pipeline_1/refine_final.mtz" + " phenix.ligand_pipeline.mtz\n" "\n" "/bin/rm init.pdb\n" "/bin/rm init.mtz\n" @@ -2092,7 +1633,8 @@ def prepare_pipedream_shell_script( + "\n" "source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n" "\n" + ccp4_scratch + "\n" - "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py" + " %s %s %s %s\n" % ( os.path.join(self.database_directory, self.data_source_file), xtal, @@ -2100,10 +1642,8 @@ def prepare_pipedream_shell_script( "running", ) + "\n" - "pointless hklin {0!s} xyzin {1!s} hklout pointless.mtz > pointless.log\n".format( - mtzin, ref_pdb - ) - + "\n" + "pointless hklin {0!s} xyzin {1!s} hklout pointless.mtz >" + " pointless.log\n".format(mtzin, ref_pdb) + "\n" "pipedream " " -d pipedreamDir" " -xyzin %s" % ref_pdb + hklref_line + " -hklin pointless.mtz" @@ -2165,8 +1705,6 @@ def prepare_pipedream_shell_script( twin = "" return twin - # pipedream -d pipedreamDir -xyzin $reference.pdb -hklref $referenceDataset.mtz -hklin $mtzFileUnique.mtz -rhofit $inhib.cif -target $reference.pdb -keepwater -nthreads 12 -postquick -allclusters |tee -a pipedream.log - def prepare_dimple_shell_script( self, xtal, visit_run_autoproc, mtzin, ref_pdb, ref_mtz, ref_cif ): @@ -2178,9 +1716,8 @@ def prepare_dimple_shell_script( mtz_column_dict = mtztools(ref_mtz).get_all_columns_as_dict() if "FreeR_flag" not in mtz_column_dict["RFREE"]: self.Logfile.insert( - "cannot find FreeR_flag in reference mtz file: {0!s} -> ignoring reference mtzfile!!!".format( - ref_mtz - ) + "cannot find FreeR_flag in reference mtz file: {0!s} ->" + " ignoring reference mtzfile!!!".format(ref_mtz) ) ref_mtz = "" if mtz_column_dict["RFREE"]: @@ -2275,7 +1812,8 @@ def prepare_dimple_shell_script( + "\n" "source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n" "\n" + ccp4_scratch + "\n" - "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py" + " %s %s %s %s\n" % ( os.path.join(self.database_directory, self.data_source_file), xtal, @@ -2295,7 +1833,6 @@ def prepare_dimple_shell_script( + " resolution %s\n" % str(round(float(mtzFile.d_min()), 3)) + "eof\n" "\n" - # 'freerflag hklin unique.mtz hklout free.mtz > freerflag.log\n' "\n" "sftools << eof > sftools.log\n" " read unique.mtz\n" @@ -2313,9 +1850,8 @@ def prepare_dimple_shell_script( " resolution file 1 999.0 %s\n" % str(round(float(mtzFile.d_min()), 2)) + "eof\n" "\n" - "pointless hklin %s.999A.mtz hklout %s.999A.reind.mtz xyzin %s << eof > pointless.reind.log\n" - % (xtal, xtal, ref_pdb) - + " tolerance 5\n" + "pointless hklin %s.999A.mtz hklout %s.999A.reind.mtz xyzin %s << eof >" + " pointless.reind.log\n" % (xtal, xtal, ref_pdb) + " tolerance 5\n" "eof\n" "\n" "dimple --no-cleanup %s.999A.reind.mtz %s %s %s %s dimple%s\n" @@ -2397,18 +1933,22 @@ def run_script(self, twin): ) self.Logfile.insert("using the following command:") self.Logfile.insert( - "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}_master.sh".format( + "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s}" + " {2!s}_master.sh".format( str(self.n), self.max_queue_jobs, self.pipeline ) ) os.system( - "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s} {2!s}{3!s}_master.sh".format( + "qsub -P labxchem -q medium.q -t 1:{0!s} -tc {1!s}" + " {2!s}{3!s}_master.sh".format( str(self.n - 1), self.max_queue_jobs, self.pipeline, twin ) ) else: self.Logfile.insert( - "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file" + "cannot start ARRAY job: make sure that" + " 'module load global/cluster'" + " is in your .bashrc or .cshrc file" ) elif self.external_software["qsub"]: self.Logfile.insert( @@ -2481,9 +2021,8 @@ def run(self): if os.path.isfile("init.pdb"): if "dimple" in os.path.realpath("init.pdb"): self.Logfile.warning( - "{0!s}: init.pdb & init.mtz is linked to dimple outcome".format( - xtal - ) + "{0!s}: init.pdb & init.mtz is linked to" + " dimple outcome".format(xtal) ) self.Logfile.warning( "{0!s}: removing init.pdb & init.mtz & (2)fofc maps".format( @@ -2504,9 +2043,8 @@ def run(self): if os.path.isfile("init.pdb"): if "dimple" in os.path.realpath("init.pdb"): self.Logfile.warning( - "{0!s}: init.pdb & init.mtz is linked to pipedream outcome".format( - xtal - ) + "{0!s}: init.pdb & init.mtz is linked to" + " pipedream outcome".format(xtal) ) self.Logfile.warning( "{0!s}: removing init.pdb & init.mtz & (2)fofc maps".format( @@ -2517,9 +2055,8 @@ def run(self): else: db_dict = self.remove_init(db_dict) self.Logfile.warning( - "{0!s}: removing pipedream folder & pipedream.pdb/pipedream.mtz".format( - xtal - ) + "{0!s}: removing pipedream folder &" + " pipedream.pdb/pipedream.mtz".format(xtal) ) os.system("/bin/rm pipedream_run_in_progress 2> /dev/null") os.system("/bin/rm pipedream.pdb 2> /dev/null") @@ -2529,9 +2066,8 @@ def run(self): if os.path.isfile("init.pdb"): if "dimple" in os.path.realpath("init.pdb"): self.Logfile.warning( - "{0!s}: init.pdb & init.mtz is linked to phenix.ligand_pipeline outcome".format( - xtal - ) + "{0!s}: init.pdb & init.mtz is linked to" + " phenix.ligand_pipeline outcome".format(xtal) ) self.Logfile.warning( "{0!s}: removing init.pdb & init.mtz & (2)fofc maps".format( @@ -2542,7 +2078,8 @@ def run(self): else: db_dict = self.remove_init(db_dict) self.Logfile.warning( - "{0!s}: removing phenix.ligand_pipeline folder & phenix.ligand_pipeline.pdb/phenix.ligand_pipeline.mtz".format( + "{0!s}: removing phenix.ligand_pipeline folder &" + " phenix.ligand_pipeline.pdb/phenix.ligand_pipeline.mtz".format( xtal ) ) @@ -2719,8 +2256,8 @@ def __init__(self, settings, interface): self.pylib = "XChemCootTwin.py" def run(self): - cwd = os.getcwd() - # coot at Diamond always or sometimes at least open in home directory, so then it won't find the .pkl file + # coot at Diamond always or sometimes at least open in home directory + # so then it won't find the .pkl file pickle.dump( self.settings, open(os.path.join(os.getenv("HOME"), ".xce_settings.pkl"), "wb"), @@ -2741,11 +2278,6 @@ def __init__(self, html_export_directory): def run(self): cwd = os.getcwd() if cwd.startswith("/dls"): - # if not os.path.isfile(os.path.join('/home',getpass.getuser(),'.flexlmrc')): - # os.system('touch '+os.path.join('/home',getpass.getuser(),'.flexlmrc')) - # f=open(os.path.join('/home',getpass.getuser(),'.flexlmrc'),'w') - # f.write('MOLSOFTD_LICENSE_FILE=@diamvicmpro.diamond.ac.uk') - # f.close() os.system("nautilus {0!s} &".format(self.html_export_directory)) os.system("/dls/science/groups/i04-1/software/icm-3.8-5/icm64 -g") @@ -2753,7 +2285,6 @@ def run(self): class start_pandda_inspect(QtCore.QThread): def __init__(self, settings, xce_logfile): QtCore.QThread.__init__(self) - # self.settings=settings self.panddas_directory = settings["panddas_directory"] self.xce_logfile = xce_logfile self.Logfile = XChemLog.updateLog(xce_logfile) @@ -2784,17 +2315,6 @@ def run(self): os.system(Cmds) -# Cmds = ( -# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' -# 'cd '+self.panddas_directory+'\n' -# 'pandda.inspect\n' -# ) -# -# self.Logfile.insert('starting pandda.inspect with the following command:\n/bin/bash\n'+Cmds) -# # need to do this because we're having all sorts of csh bash issues at SGC -# os.system('/bin/bash\n'+Cmds) - - class start_dials_image_viewer(QtCore.QThread): def __init__(self, diffraction_image): QtCore.QThread.__init__(self) @@ -2804,9 +2324,7 @@ def run(self): os.system("dials.image_viewer " + self.diffraction_image) -# -# --- new module from hell ------------------------------------------------------------------------------------------- -# +# --- new module from hell ------------------------------------------------------------- class read_pinIDs_from_gda_logs(QtCore.QThread): @@ -2868,7 +2386,6 @@ def update_database(self, pinDict): ) dbDict = {} dbDict["DataCollectionPinBarcode"] = pinDict[sample] - # self.db.update_data_source(sample,dbDict) self.db.update_specified_table(sample, dbDict, "collectionTable") progress += progress_step self.emit(QtCore.SIGNAL("update_progress_bar"), progress) @@ -2915,9 +2432,6 @@ def __init__( else: self.allSamples = self.db.collected_xtals_during_visit_for_scoring(visit) - # print 'here', self.allSamples - # self.allSamples = self.db.collected_xtals_during_visit_for_scoring(visit,rescore) - def run(self): progress = 0 @@ -2929,16 +2443,14 @@ def run(self): os.path.join(self.projectDir, sample, sample + ".mtz") ): self.Logfile.warning( - "{0!s}: user has manually selected auto-processing result; will NOT auto-select!".format( - sample - ) + "{0!s}: user has manually selected auto-processing result;" + " will NOT auto-select!".format(sample) ) continue else: self.Logfile.warning( - "{0!s}: user has manually selected auto-processing result before, but {1!s}.mtz does not exist".format( - sample, sample - ) + "{0!s}: user has manually selected auto-processing result" + " before, but {1!s}.mtz does not exist".format(sample, sample) ) self.Logfile.insert("%s: selecting autoprocessing result" % sample) elif self.rescore: @@ -2964,11 +2476,12 @@ def run(self): ) continue - # 1.) if posssible, only carry forward samples with similar UCvolume and same point group + # 1.) if posssible, only carry forward samples with similar UCvolume + # and same point group dbList = self.selectResultsSimilarToReference(dbList) - # 2.) if possible, only carry forward samples with low resolution Rmerge smaller than - # specified in perferences + # 2.) if possible, only carry forward samples with low resolution Rmerge + # smaller than specified in perferences dbList = self.selectResultsWithAcceptableLowResoRmerge(dbList) # 3.) Make selection based on speified selection mechanism @@ -3006,11 +2519,13 @@ def report_forward_carried_pipelines(self, dbListOut, dbList): if not dbListOut: dbListOut = dbList self.Logfile.warning( - "none of the MTZ files fulfilled criteria; will carry forward all results:" + "none of the MTZ files fulfilled criteria;" + " will carry forward all results:" ) else: self.Logfile.insert( - "will carry forward the MTZ files from the following auto-processing pipelines:" + "will carry forward the MTZ files from the following auto-processing" + " pipelines:" ) self.Logfile.insert( "{0:30} {1:10} {2:10} {3:10}".format( @@ -3131,12 +2646,14 @@ def selectResultsSimilarToReference(self, dbList): == resultDict["DataProcessingPointGroup"] ): self.Logfile.insert( - "=> passed -> mtz file has same point group as reference file and similar unit cell volume" + "=> passed -> mtz file has same point group" + " as reference file and similar unit cell volume" ) dbListOut.append(resultDict) else: self.Logfile.warning( - "mtz file has different point group/ unit cell volume as reference file" + "mtz file has different point group/" + " unit cell volume as reference file" ) except ValueError: pass @@ -3145,8 +2662,8 @@ def selectResultsSimilarToReference(self, dbList): def selectResultsWithAcceptableLowResoRmerge(self, dbList): self.Logfile.insert( - "checking if MTZ files have acceptable low resolution Rmerge values (currently set to %s)" - % str(self.acceptable_low_resolution_Rmerge) + "checking if MTZ files have acceptable low resolution Rmerge values" + " (currently set to %s)" % str(self.acceptable_low_resolution_Rmerge) ) dbListOut = [] for resultDict in dbList: @@ -3217,7 +2734,7 @@ def selectSpecificPipelineOnly(self, dbList): if ( self.selection_mechanism == "autoProc - only" and "autoPROC" in resultDict["DataProcessingProgram"] - and not "staraniso" in resultDict["DataProcessingProgram"] + and "staraniso" not in resultDict["DataProcessingProgram"] ): tmp.append(resultDict) if ( @@ -3258,14 +2775,15 @@ class read_write_autoprocessing_results_from_to_disc(QtCore.QThread): - results for every autoprocessing result is recorded in new DB table - crystal centring images are copied into project directory - beamline directory in project directory will not be used anymore - - users need to actively select the actual data collection visit as Data Collection Directory in the - settings tab (e.g. /dls/i04-1/data/2017/mx15433-50 + - users need to actively select the actual data collection visit as Data Collection + Directory in the settings tab (e.g. /dls/i04-1/data/2017/mx15433-50 - results from fast_dp are not copied over and included in analysis - DB mainTable gets flag if user updated autoprocessing selection - checking of reprocessed files needs to be explicit - all dictionaries used to store information are retired - - at the moment one can only review/ rescore crystals collected during the selected visit + - at the moment one can only review/ rescore crystals collected during the selected + visit - parsing of pinIDs in gda logfiles is still missing """ @@ -3273,29 +2791,16 @@ def __init__( self, processedDir, database, projectDir, xce_logfile, target, agamemnon ): QtCore.QThread.__init__(self) - # self.target = target self.processedDir = processedDir self.visit, self.beamline = XChemMain.getVisitAndBeamline(self.processedDir) - # print 'visit' self.projectDir = projectDir self.Logfile = XChemLog.updateLog(xce_logfile) self.target = target self.agamemnon = agamemnon - # if self.agamemnon: - ## print 'procDir',self.processedDir - # if len(procDir.split('/')) >= 8: - # if procDir.split('/')[7] == 'agamemnon' - # quit() - # self.visit = 'agamemnon' # this is for trouble-shooting only self.db = XChemDB.data_source(os.path.join(database)) self.exisitingSamples = self.getExistingSamples() - # for xtal in self.exisitingSamples: - # print self.exisitingSamples[xtal] - # break - # quit() - self.toParse = [ [ os.path.join("*"), @@ -3312,12 +2817,6 @@ def __init__( os.path.join("LogFiles", "*aimless.log"), os.path.join("DataFiles", "*free.mtz"), ], - # [ os.path.join('autoPROC', '*'), - # '*aimless.log', - # '*truncate-unique.mtz'], - # [ os.path.join('autoPROC', '*'), - # '*staraniso_alldata-unique.table1', - # '*staraniso_alldata-unique.mtz'], [os.path.join("autoPROC"), "*aimless.log", "*truncate-unique.mtz"], [ os.path.join("autoPROC"), @@ -3331,92 +2830,18 @@ def __init__( "*summary.tar.gz", "*staraniso_alldata-unique.mtz", ], - # [ os.path.join('*'), - # os.path.join('LogFiles', '*aimless.log'), - # os.path.join('DataFiles', '*free.mtz')] ] - # self.toParse = [ - # [ os.path.join('*'), - # os.path.join('LogFiles', '*aimless.log'), - # os.path.join('DataFiles', '*free.mtz')], - # [ os.path.join('*'), - # os.path.join('LogFiles', '*merging-statistics.json'), - # os.path.join('DataFiles', '*free.mtz')], - # [ os.path.join('multi-xia2', '*'), - # os.path.join('LogFiles', '*aimless.log'), - # os.path.join('DataFiles', '*free.mtz')], - # [ os.path.join('autoPROC', '*'), - # '*aimless.log', - # '*truncate-unique.mtz'], - # [ os.path.join('autoPROC', '*'), - # '*staraniso_alldata-unique.table1', - # '*staraniso_alldata-unique.mtz'], - # [ os.path.join('autoPROC'), - # '*aimless.log', - # '*truncate-unique.mtz'], - # [ os.path.join('autoPROC'), - # '*summary.tar.gz', # staraniso_alldata-unique.table1 only available in tar archive - # '*staraniso_alldata-unique.mtz'], - # [ os.path.join('autoPROC-*'), - # '*aimless.log', - # '*truncate-unique.mtz'], - # [ os.path.join('autoPROC-*'), - # '*summary.tar.gz', - # '*staraniso_alldata-unique.mtz'], - # [ os.path.join('*'), - # os.path.join('LogFiles', '*aimless.log'), - # os.path.join('DataFiles', '*free.mtz')] - # ] - - # self.toParse = [ - # [ os.path.join('xia2', '*'), - # os.path.join('LogFiles', '*aimless.log'), - # os.path.join('DataFiles', '*free.mtz')], - # [ os.path.join('xia2-3*'), - # os.path.join('LogFiles', '*aimless.log'), - # os.path.join('DataFiles', '*free.mtz')], - # [ os.path.join('xia2-dials*'), - # os.path.join('LogFiles', '*merging-statistics.json'), - # os.path.join('DataFiles', '*free.mtz')], - # [ os.path.join('multi-xia2', '*'), - # os.path.join('LogFiles', '*aimless.log'), - # os.path.join('DataFiles', '*free.mtz')], - # [ os.path.join('autoPROC', '*'), - # '*aimless.log', - # '*truncate-unique.mtz'], - # [ os.path.join('autoPROC', '*'), - # '*staraniso_alldata-unique.table1', - # '*staraniso_alldata-unique.mtz'], - # [ os.path.join('autoPROC'), - # '*aimless.log', - # '*truncate-unique.mtz'], - # [ os.path.join('autoPROC'), - # '*summary.tar.gz', # staraniso_alldata-unique.table1 only available in tar archive - # '*staraniso_alldata-unique.mtz'], - # [ os.path.join('autoPROC-*'), - # '*aimless.log', - # '*truncate-unique.mtz'], - # [ os.path.join('autoPROC-*'), - # '*summary.tar.gz', - # '*staraniso_alldata-unique.mtz'], - # [ os.path.join('*'), - # os.path.join('LogFiles', '*aimless.log'), - # os.path.join('DataFiles', '*free.mtz')] - # ] - def run(self): - # if self.agamemnon: - # self.parse_agamemnon_file_system() - # else: - # self.parse_file_system() self.parse_file_system() def getExistingSamples(self): existingSamples = {} self.Logfile.insert("reading existing samples from collectionTable") allEntries = self.db.execute_statement( - 'select CrystalName,DataCollectionVisit,DataCollectionRun,DataProcessingProgram, DataCollectionSubdir from collectionTable where DataCollectionOutcome = "success"' + "select CrystalName,DataCollectionVisit,DataCollectionRun," + "DataProcessingProgram, DataCollectionSubdir from collectionTable where" + ' DataCollectionOutcome = "success"' ) for item in allEntries: if str(item[0]) not in existingSamples: @@ -3572,8 +2997,9 @@ def copyMTZandLOGfiles(self, xtal, run, autoproc, mtzfile, logfile, proc_code): self.visit + "-" + run + autoproc + "_" + proc_code, logfile[logfile.rfind("/") + 1 :], ) - # September 2021: xia2 does not also output a xia2.mmcif and json merging statistics file, even if aimless was used - # for scaling, however, the xia2.mmcif file is differently formatted than the one from dials + # September 2021: xia2 does not also output a xia2.mmcif and json merging + # statistics file, even if aimless was used for scaling, however, + # the xia2.mmcif file is differently formatted than the one from dials # hence, if xtal.log file already exists, use this one if "aimless" in os.readlink(xtal + ".log"): logNew = os.path.join( @@ -3595,8 +3021,6 @@ def makeJPGdir(self, xtal, run): os.mkdir(os.path.join(self.projectDir, xtal, "jpg", self.visit + "-" + run)) def copyJPGs(self, xtal, run, auto): - # for img in glob.glob(os.path.join(self.processedDir.replace('processed','jpegs'),xtal,run+'*t.png')): - # for img in glob.glob(os.path.join(self.processedDir.replace('processed', 'jpegs'), run + '*t.png')): self.Logfile.insert("%s: trying to copy crystal snapshots..." % xtal) found = False if self.agamemnon: @@ -3700,7 +3124,6 @@ def copyJPGs(self, xtal, run, auto): def findJPGs(self, xtal, run): jpgDict = {} - # for n,img in enumerate(glob.glob(os.path.join(self.projectDir,xtal,'jpg', self.visit +'-'+ run,'*t.png'))): for n, img in enumerate( glob.glob( os.path.join( @@ -3749,8 +3172,6 @@ def readProcessingUpdateResults( xtal, current_run, autoproc, db_dict, proc_code ) - # return db_dict - def getAutoProc(self, folder_rel, staraniso): self.Logfile.insert("checking name of auto-processing pipeline...") folder = os.path.realpath(folder_rel) @@ -3815,9 +3236,8 @@ def empty_folder(self, xtal, folder): stuff.append(x) if not stuff: self.Logfile.warning( - "{0!s}: {1!s} is empty; probably waiting for autoprocessing to finish; try later!".format( - xtal, folder - ) + "{0!s}: {1!s} is empty; probably waiting for autoprocessing to finish;" + " try later!".format(xtal, folder) ) else: empty = False @@ -3846,7 +3266,6 @@ def parse_file_system(self): ) runList = [] - # for auto in autoDir: self.Logfile.insert("--> " + os.path.join(autoDir, "*")) for nx, collected_xtals in enumerate( sorted(glob.glob(os.path.join(autoDir, "*"))) @@ -3862,9 +3281,6 @@ def parse_file_system(self): if not os.path.isdir(collected_xtals): continue - # for collected_xtals in sorted(glob.glob(os.path.join(self.processedDir,'*'))): - # why is this here? self.visit is derived in init function through XChemMain.getVisitAndBeamline - # self.visit = collected_xtals.split('/')[5] if ( "tmp" in collected_xtals or "results" in collected_xtals @@ -3876,18 +3292,12 @@ def parse_file_system(self): continue xtal = collected_xtals[collected_xtals.rfind("/") + 1 :] - # if self.agamemnon: - # tmp = xtal[:xtal.rfind('_')] - # xtal = tmp[:tmp.rfind('_')] self.Logfile.insert("%s: checking auto-processing results" % xtal) self.createSampleDir(xtal) if self.target == "=== project directory ===": runDir = os.path.join(collected_xtals, "processed", "*") - # elif self.agamemnon: - # tmpDir = collected_xtals[:collected_xtals.rfind('/')] - # runDir = os.path.join(tmpDir,xtal+'_*_') else: runDir = os.path.join(collected_xtals, "*") self.Logfile.insert("current runDir: " + runDir) @@ -3897,8 +3307,6 @@ def parse_file_system(self): for code in glob.glob(os.path.join(run, "*")): if os.path.islink(code): continue - # else: - # proc_code = code[code.rfind('/')+1:] proc_code = code.split("/")[len(code.split("/")) - 1] self.Logfile.insert(xtal + ": processed directory -> " + proc_code) if current_run + proc_code in runList: @@ -3951,8 +3359,6 @@ def parse_file_system(self): proc_code, ) runList.append(current_run + proc_code) - - # quit() progress += progress_step self.emit( QtCore.SIGNAL("update_status_bar(QString)"), @@ -3963,103 +3369,3 @@ def parse_file_system(self): self.Logfile.insert("====== finished parsing beamline directory ======") self.emit(QtCore.SIGNAL("read_pinIDs_from_gda_logs")) self.emit(QtCore.SIGNAL("finished()")) - - -# def parse_agamemnon_file_system(self): -# self.Logfile.insert('checking for new data processing results in '+self.processedDir) -# progress = 0 -# progress_step = 1 -# -# autoDir = ['auto','agamemnon'] -# -# c = 0 -# for auto in autoDir: -# for collected_xtals in sorted(glob.glob(os.path.join(self.processedDir+'-*','processed',auto,self.target,'*'))): -# if 'tmp' in collected_xtals or 'results' in collected_xtals or 'scre' in collected_xtals: -# continue -# c += 1 -# -# if c > 0: -# progress_step = 100/float(c) -# self.Logfile.insert('found %s samples of target %s' %(str(c),self.target)) -# else: -# self.Logfile.warning('found %s samples of target %s' %(str(c),self.target)) -# -# runList = [] -# -# autoDir = ['auto','agamemnon','recollect'] -# -# for auto in autoDir: -# for collected_xtals in sorted(glob.glob(os.path.join(self.processedDir+'-*','processed',auto,self.target,'*'))): -# self.visit = collected_xtals.split('/')[5] -# if 'tmp' in collected_xtals or 'results' in collected_xtals or 'scre' in collected_xtals: -# continue -# if not os.path.isdir(collected_xtals): -# continue -# -# xtal = collected_xtals[collected_xtals.rfind('/')+1:] -# if xtal.endswith('_'): -# continue # happened sometime during testing, but should not happen anymore -# -# self.Logfile.insert('%s: checking auto-processing results in %s %s' %(xtal,self.visit,auto)) -# self.createSampleDir(xtal) -# -# foundRun = False -# self.Logfile.insert('%s: checking for runs in %s' %(xtal,os.path.join(collected_xtals,'*'))) -# for run in sorted(glob.glob(os.path.join(collected_xtals,'*'))): -# foundRun = True -# self.Logfile.insert('%s: current run %s' %(xtal,run)) -# current_run=auto+'_'+run[run.rfind('/')+1:] -# if current_run not in runList: -# self.Logfile.insert('%s: found new run -> %s' %(xtal,current_run)) -# runList.append(self.visit+'_'+auto+'_'+current_run) -# else: -# continue -# self.Logfile.insert('%s -> run: %s -> current run: %s' %(xtal,run,current_run)) -# timestamp=datetime.fromtimestamp(os.path.getmtime(run)).strftime('%Y-%m-%d %H:%M:%S') -# -# # create directory for crystal aligment images in projectDir -# self.makeJPGdir(xtal,current_run) -# self.copyJPGs(xtal, run[run.rfind('/')+1:], auto) -# -# for item in self.toParse: -# procDir = os.path.join(run,item[0]) -# logfile = item[1] -# mtzfile = item[2] -# -# self.Logfile.insert('%s: search template: procDir - logfile - mtzfile' % xtal) -# self.Logfile.insert('%s: procDir = %s' % (xtal, procDir)) -# self.Logfile.insert('%s: logfile = %s' % (xtal, logfile)) -# self.Logfile.insert('%s: mtzfile = %s' % (xtal, mtzfile)) -# -# for folder in glob.glob(procDir): -# for mtz in glob.glob(os.path.join(procDir,mtzfile)): -## print mtz -# -# for folder in glob.glob(procDir): -# staraniso = '' -# self.Logfile.insert('%s: searching %s' % (xtal, folder)) -# if self.junk(folder): -# continue -# if self.empty_folder(xtal,folder): -# continue -# if 'staraniso' in logfile or 'summary.tar.gz' in logfile: -# staraniso = '_staraniso' -# autoproc = self.getAutoProc(folder, staraniso) -# if self.alreadyParsed(xtal,current_run,autoproc): -# continue -# self.readProcessingUpdateResults(xtal,folder,logfile,mtzfile,timestamp,current_run,autoproc) -# -# -# -# -# progress += progress_step -# self.emit(QtCore.SIGNAL('update_status_bar(QString)'), 'parsing auto-processing results for '+collected_xtals) -# self.emit(QtCore.SIGNAL('update_progress_bar'), progress) -# -# if not foundRun: -# self.Logfile.error('%s: could not find run' %xtal) -# -# self.Logfile.insert('====== finished parsing beamline directory ======') -# self.emit(QtCore.SIGNAL('read_pinIDs_from_gda_logs')) -# self.emit(QtCore.SIGNAL("finished()")) From cd3aeb64bab151c03e1f1e7499cc9378bd6f3196 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 17:07:44 +0000 Subject: [PATCH 152/358] Clean up XChemProcess --- xce/lib/XChemProcess.py | 67 +++-------------------------------------- 1 file changed, 5 insertions(+), 62 deletions(-) diff --git a/xce/lib/XChemProcess.py b/xce/lib/XChemProcess.py index a0d1c327..251340af 100755 --- a/xce/lib/XChemProcess.py +++ b/xce/lib/XChemProcess.py @@ -70,13 +70,6 @@ def run(self): if os.getcwd().startswith("/dls"): script += "module load ccp4/7.1.018\n" script += "module load XDS\n" - # script += 'module load phenix\n' - - # 2018-09-19 - removed this for Joe's test - # script += 'module load ccp4\n' - # script += 'module load XDS\n' - # script += 'module load ccp4 xia2\n' - # print 'hallo' if not self.spg: spg_option = "" @@ -114,10 +107,6 @@ def run(self): os.path.join(self.initial_model_directory, xtal, "processed") ): os.mkdir(os.path.join(self.initial_model_directory, xtal, "processed")) - # 2018-09-19 - disabled this for Joe's test - # if os.path.isfile(os.path.join(self.initial_model_directory,xtal,'processed','run_in_progress')): - # self.Logfile.insert('data processing is in progress; skipping...') - # continue f = True if f: print("hallo") @@ -238,8 +227,6 @@ def run(self): ) ) - # 2018-09-19 - changed this for Joe's test - # script+='$CCP4/bin/xia2 pipeline='+pipeline+' '+ref_option+' '+spg_option+' '+reso_limit_option+' '+cc_half_option+' '+image_dir+'\n' script += ( "xia2 pipeline=" + pipeline @@ -307,13 +294,14 @@ def run(self): ) ) os.system( - "qsub -P labxchem -q medium.q -N xia2 -t 1:{0!s} -tc {1!s} xia2_master.sh".format( - str(i + 1), self.max_queue_jobs - ) + "qsub -P labxchem -q medium.q -N xia2 -t 1:{0!s} -tc {1!s}" + " xia2_master.sh".format(str(i + 1), self.max_queue_jobs) ) else: self.Logfile.insert( - "cannot start ARRAY job: make sure that 'module load global/cluster' is in your .bashrc or .cshrc file" + "cannot start ARRAY job: make sure that" + " 'module load global/cluster'" + " is in your .bashrc or .cshrc file" ) elif self.external_software["qsub"]: self.Logfile.insert( @@ -332,48 +320,3 @@ def run(self): for n in range(i + 1): self.Logfile.insert("starting xce_xia2_{0!s}.sh".format((str(n + 1)))) os.system("./xce_xia2_{0!s}.sh".format((str(n + 1)))) - - -# if not os.path.isdir(os.path.join(self.initial_model_directory,xtal)): -# os.mkdir(os.path.join(self.initial_model_directory,xtal)) -# if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'autoprocessing')): -# os.mkdir(os.path.join(self.initial_model_directory,xtal,'autoprocessing')) -# -# -# -# -# if not os.path.isdir(os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc)): -# os.mkdir(os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc)) -# os.chdir(os.path.join(self.initial_model_directory,xtal,'dimple',visit_run_autoproc)) -# os.system('touch dimple_run_in_progress') - - -# header='#!'+os.getenv('SHELL')+'\n' -# if external_software['qsub']: -# if not external_software['qsub_array']: -# header='#PBS -joe -N xce_acedrg\n' -# -# Cmds = ( -# header+ -# '\n' -# 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' -# '\n' -# 'source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n' -# '\n' -# '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','create_png_of_compound.py')+ -# ' "%s" %s %s %s\n' %(smiles,compoundID.replace(' ',''),sample,initial_model_directory)+ -# '\n' -# 'cd '+os.path.join(initial_model_directory,sample,'compound')+'\n' -# '\n' -# 'acedrg --res LIG -i "%s" -o %s\n' %(smiles,compoundID.replace(' ',''))+ -# '\n' -# 'cd '+os.path.join(initial_model_directory,sample)+'\n' -# '\n' -# 'ln -s compound/%s.cif .\n' %compoundID.replace(' ','')+ -# 'ln -s compound/%s.pdb .\n' %compoundID.replace(' ','')+ -# 'ln -s compound/%s.png .\n' %compoundID.replace(' ','')+ -# '\n' -# '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_for_new_cif_files.py')+ -# ' %s %s %s %s\n' %(os.path.join(database_directory,data_source_file),sample,initial_model_directory,compoundID.replace(' ','') )+ -# '\n' -# '/bin/rm compound/ACEDRG_IN_PROGRESS\n' From 0851f43d3fa34803b64c655509ca15f5993b5979 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 17:24:34 +0000 Subject: [PATCH 153/358] Clean up XChemPANDDA --- xce/lib/XChemPANDDA.py | 373 +++++++++++++++++------------------------ 1 file changed, 155 insertions(+), 218 deletions(-) diff --git a/xce/lib/XChemPANDDA.py b/xce/lib/XChemPANDDA.py index be797d59..d69f4ecb 100755 --- a/xce/lib/XChemPANDDA.py +++ b/xce/lib/XChemPANDDA.py @@ -19,24 +19,6 @@ except ImportError: pass -# def get_names_of_current_clusters(xce_logfile,panddas_directory): -# Logfile=XChemLog.updateLog(xce_logfile) -# Logfile.insert('parsing {0!s}/cluster_analysis'.format(panddas_directory)) -# os.chdir('{0!s}/cluster_analysis'.format(panddas_directory)) -# cluster_dict={} -# for out_dir in sorted(glob.glob('*')): -# if os.path.isdir(out_dir): -# cluster_dict[out_dir]=[] -# found_first_pdb=False -# for folder in glob.glob(os.path.join(out_dir,'pdbs','*')): -# xtal=folder[folder.rfind('/')+1:] -# if not found_first_pdb: -# if os.path.isfile(os.path.join(panddas_directory,'cluster_analysis',out_dir,'pdbs',xtal,xtal+'.pdb') ): -# cluster_dict[out_dir].append(os.path.join(panddas_directory,'cluster_analysis',out_dir,'pdbs',xtal,xtal+'.pdb')) -# found_first_pdb=True -# cluster_dict[out_dir].append(xtal) -# return cluster_dict - class export_and_refine_ligand_bound_models(QtCore.QThread): def __init__( @@ -52,14 +34,6 @@ def __init__( self.which_models = which_models self.external_software = XChemUtils.external_software(xce_logfile).check() - # self.initial_model_directory=initial_model_directory - # self.db.create_missing_columns() - # self.db_list=self.db.get_empty_db_dict() - # self.external_software=XChemUtils.external_software(xce_logfile).check() - # self.xce_logfile=xce_logfile - - # self.already_exported_models=[] - def run(self): self.Logfile.warning( @@ -254,10 +228,12 @@ def find_modeled_structures_and_timestamps(self): def find_new_models(self, modelsDict): samples_to_export = {} self.Logfile.hint( - 'XCE will never export/ refine models that are "5-deposition ready" or "6-deposited"' + 'XCE will never export/ refine models that are "5-deposition ready" or' + ' "6-deposited"' ) self.Logfile.hint( - "Please change the RefinementOutcome flag in the Refinement table if you wish to re-export them" + "Please change the RefinementOutcome flag in the Refinement table" + " if you wish to re-export them" ) self.Logfile.insert("checking timestamps of models in database...") for xtal in modelsDict: @@ -271,8 +247,8 @@ def find_new_models(self, modelsDict): timestamp_db = str(db_query[0][0]) except IndexError: self.Logfile.warning( - "%s: database query gave no results for DatePanDDAModelCreated; skipping..." - % xtal + "%s: database query gave no results for DatePanDDAModelCreated;" + " skipping..." % xtal ) self.Logfile.warning( "%s: this might be a brand new model; will continue with export!" @@ -583,8 +559,8 @@ def refine_exported_models(self, samples_to_export): ) else: self.Logfile.error( - "%s: cannot find %s-pandda-model.pdb; cannot start refinement..." - % (xtal, xtal) + "%s: cannot find %s-pandda-model.pdb;" + " cannot start refinement..." % (xtal, xtal) ) elif xtal in samples_to_export and not os.path.isfile( @@ -626,13 +602,16 @@ def export_models(self): # now get these models from the database and compare the datestamps # Note: only get the models that underwent some form of refinement, - # because only if the model was updated in pandda.inspect will it be exported and refined + # because only if the model was updated in pandda.inspect will it be + # exported and refined dbModelsDict = {} if queryModels != "": dbEntries = self.db.execute_statement( - "select CrystalName,DatePanDDAModelCreated from mainTable where CrystalName in (" + "select CrystalName,DatePanDDAModelCreated from mainTable where" + " CrystalName in (" + queryModels[:-1] - + ") and (RefinementOutcome like '3%' or RefinementOutcome like '4%' or RefinementOutcome like '5%')" + + ") and (RefinementOutcome like '3%' or RefinementOutcome like '4%' or" + " RefinementOutcome like '5%')" ) for item in dbEntries: xtal = str(item[0]) @@ -645,7 +624,8 @@ def export_models(self): + str(timestamp) ) - # compare timestamps and only export the ones where the timestamp of the file is newer than the one in the DB + # compare timestamps and only export the ones where the timestamp of the file + # is newer than the one in the DB samples_to_export = {} self.Logfile.insert( "checking which PanDDA models were newly created or updated" @@ -665,23 +645,27 @@ def export_models(self): ) - datetime.strptime(dbModelsDict[sample], "%Y-%m-%d %H:%M:%S") if difference.seconds != 0: self.Logfile.insert( - "exporting " - + sample - + " -> was already refined, but newer PanDDA model available" + "exporting " + sample + " -> was already refined," + " but newer PanDDA model available" ) samples_to_export[sample] = fileModelsDict[sample] except ValueError: # this will be raised if timestamp is not properly formatted; - # which will usually be the case when respective field in database is blank - # these are hopefully legacy cases which are from before this extensive check was introduced (13/01/2017) + # which will usually be the case when respective field in + # database is blank. these are hopefully legacy cases which are + # from before this extensive check was introduced (13/01/2017) advice = ( "The pandda model of " + xtal + " was changed, but it was already refined! " - "This is most likely because this was done with an older version of XCE. " - "If you really want to export and refine this model, you need to open the database " - "with DBbroweser (sqlitebrowser.org); then change the RefinementOutcome field " - 'of the respective sample to "2 - PANDDA model", save the database and repeat the export prodedure.' + "This is most likely because this was done with an older" + " version of XCE. " + "If you really want to export and refine this model," + " you need to open the database " + "with DBbroweser (sqlitebrowser.org);" + " then change the RefinementOutcome field " + 'of the respective sample to "2 - PANDDA model",' + " save the database and repeat the export prodedure." ) self.Logfile.insert(advice) else: @@ -693,7 +677,8 @@ def export_models(self): samples_to_export[sample] = fileModelsDict[sample] # update the DB: - # set timestamp to current timestamp of file and set RefinementOutcome to '2-pandda...' + # set timestamp to current timestamp of file + # and set RefinementOutcome to '2-pandda...' if samples_to_export != {}: select_dir_string = "" @@ -809,23 +794,16 @@ def __init__( } def run(self): - - # v1.3.8.2 - removed option to update database only - # if not self.update_datasource_only: samples_to_export = self.export_models() self.import_samples_into_datasouce(samples_to_export) - # if not self.update_datasource_only: self.refine_exported_models(samples_to_export) def refine_exported_models(self, samples_to_export): self.Logfile.insert("will try to refine the following crystals:") for xtal in samples_to_export: self.Logfile.insert(xtal) - # sample_list=self.db.execute_statement("select CrystalName,CompoundCode from mainTable where RefinementOutcome='2 - PANDDA model';") - # for item in sample_list: - # xtal=str(item[0]) for xtal in sorted(samples_to_export): self.Logfile.insert("%s: getting compound code from database" % xtal) query = self.db.execute_statement( @@ -833,7 +811,6 @@ def refine_exported_models(self, samples_to_export): ) compoundID = str(query[0][0]) self.Logfile.insert("%s: compounds code = %s" % (xtal, compoundID)) - # compoundID=str(item[1]) if os.path.isfile( os.path.join(self.initial_model_directory, xtal, xtal + ".free.mtz") ): @@ -874,7 +851,8 @@ def refine_exported_models(self, samples_to_export): os.system("/bin/rm *-ensemble-model.pdb *restraints*") except: self.Logfile.error( - "Restraint files didn't exist to remove. Will try to continue" + "Restraint files didn't exist to remove." + " Will try to continue" ) else: os.mkdir( @@ -912,17 +890,10 @@ def refine_exported_models(self, samples_to_export): "pandda_refmac", None, ) - - # elif xtal in os.path.join(self.panddas_directory,'processed_datasets',xtal,'modelled_structures', - # '{}-pandda-model.pdb'.format(xtal)): - # self.Logfile.insert('{}: cannot start refinement because {}'.format(xtal,xtal) + - # ' does not have a modelled structure. Check whether you expect this dataset to ' + - # ' have a modelled structure, compare pandda.inspect and datasource,' - # ' then tell XCHEMBB ') else: self.Logfile.error( - "%s: cannot find %s-ensemble-model.pdb; cannot start refinement..." - % (xtal, xtal) + "%s: cannot find %s-ensemble-model.pdb;" + " cannot start refinement..." % (xtal, xtal) ) self.Logfile.error( "Please check terminal window for any PanDDA related tracebacks" @@ -944,9 +915,9 @@ def import_samples_into_datasouce(self, samples_to_export): os.chdir(os.path.join(self.panddas_directory, "processed_datasets")) for xtal in glob.glob("*"): self.db.execute_statement( - "update mainTable set DimplePANDDAwasRun = 'True',DimplePANDDAreject = 'False',DimplePANDDApath='{0!s}' where CrystalName is '{1!s}'".format( - self.panddas_directory, xtal - ) + "update mainTable set DimplePANDDAwasRun = 'True'," + "DimplePANDDAreject = 'False',DimplePANDDApath='{0!s}'" + " where CrystalName is '{1!s}'".format(self.panddas_directory, xtal) ) # do the same as before, but look for rejected datasets @@ -954,7 +925,9 @@ def import_samples_into_datasouce(self, samples_to_export): os.chdir(os.path.join(self.panddas_directory, "rejected_datasets")) for xtal in glob.glob("*"): self.db.execute_statement( - "update mainTable set DimplePANDDAwasRun = 'True',DimplePANDDAreject = 'True',DimplePANDDApath='{0!s}',DimplePANDDAhit = 'False' where CrystalName is '{1!s}'".format( + "update mainTable set DimplePANDDAwasRun = 'True'," + "DimplePANDDAreject = 'True',DimplePANDDApath='{0!s}'," + "DimplePANDDAhit = 'False' where CrystalName is '{1!s}'".format( self.panddas_directory, xtal ) ) @@ -1102,21 +1075,21 @@ def import_samples_into_datasouce(self, samples_to_export): self.db.update_insert_site_event_panddaTable(sampleID, db_dict) - # this is necessary, otherwise RefinementOutcome will be reset for samples that are actually already in refinement + # this is necessary, otherwise RefinementOutcome will be reset for + # samples that are actually already in refinement self.db.execute_statement( - "update panddaTable set RefinementOutcome = '2 - PANDDA model' where CrystalName is '{0!s}' and RefinementOutcome is null".format( - sampleID - ) + "update panddaTable set RefinementOutcome = '2 - PANDDA model'" + " where CrystalName is '{0!s}'" + " and RefinementOutcome is null".format(sampleID) ) self.db.execute_statement( - "update mainTable set RefinementOutcome = '2 - PANDDA model' where CrystalName is '{0!s}' and (RefinementOutcome is null or RefinementOutcome is '1 - Analysis Pending')".format( - sampleID - ) + "update mainTable set RefinementOutcome = '2 - PANDDA model'" + " where CrystalName is '{0!s}' and (RefinementOutcome is null" + " or RefinementOutcome is '1 - Analysis Pending')".format(sampleID) ) self.db.execute_statement( - "update mainTable set DimplePANDDAhit = 'True' where CrystalName is '{0!s}'".format( - sampleID - ) + "update mainTable set DimplePANDDAhit = 'True'" + " where CrystalName is '{0!s}'".format(sampleID) ) progress += progress_step self.emit(QtCore.SIGNAL("update_progress_bar"), progress) @@ -1128,11 +1101,6 @@ def import_samples_into_datasouce(self, samples_to_export): self.Logfile.insert("check which datasets are not interesting") # DimplePANDDAhit - # for xtal in glob.glob('*'): - # if xtal not in pandda_hit_list: - # self.Logfile.insert(xtal+': not in interesting_datasets; updating database...') - # self.db.execute_statement("update mainTable set DimplePANDDAhit = 'False' where CrystalName is '{0!s}'".format(xtal)) - def export_models(self): self.Logfile.insert("finding out which PanDDA models need to be exported") @@ -1162,13 +1130,16 @@ def export_models(self): # now get these models from the database and compare the datestamps # Note: only get the models that underwent some form of refinement, - # because only if the model was updated in pandda.inspect will it be exported and refined + # because only if the model was updated in pandda.inspect will it be + # exported and refined dbModelsDict = {} if queryModels != "": dbEntries = self.db.execute_statement( - "select CrystalName,DatePanDDAModelCreated from mainTable where CrystalName in (" + "select CrystalName,DatePanDDAModelCreated from mainTable" + " where CrystalName in (" + queryModels[:-1] - + ") and (RefinementOutcome like '3%' or RefinementOutcome like '4%' or RefinementOutcome like '5%')" + + ") and (RefinementOutcome like '3%' or RefinementOutcome like '4%'" + " or RefinementOutcome like '5%')" ) for item in dbEntries: xtal = str(item[0]) @@ -1181,7 +1152,8 @@ def export_models(self): + str(timestamp) ) - # compare timestamps and only export the ones where the timestamp of the file is newer than the one in the DB + # compare timestamps and only export the ones where the timestamp of the file + # is newer than the one in the DB samples_to_export = {} self.Logfile.insert( "checking which PanDDA models were newly created or updated" @@ -1210,23 +1182,27 @@ def export_models(self): ) - datetime.strptime(dbModelsDict[sample], "%Y-%m-%d %H:%M:%S") if difference.seconds != 0: self.Logfile.insert( - "exporting " - + sample - + " -> was already refined, but newer PanDDA model available" + "exporting " + sample + " -> was already refined," + " but newer PanDDA model available" ) samples_to_export[sample] = fileModelsDict[sample] except ValueError: # this will be raised if timestamp is not properly formatted; - # which will usually be the case when respective field in database is blank - # these are hopefully legacy cases which are from before this extensive check was introduced (13/01/2017) + # which will usually be the case when respective field in + # database is blank. these are hopefully legacy cases which are + # from before this extensive check was introduced (13/01/2017) advice = ( "The pandda model of " + xtal + " was changed, but it was already refined! " - "This is most likely because this was done with an older version of XCE. " - "If you really want to export and refine this model, you need to open the database " - "with DBbroweser (sqlitebrowser.org); then change the RefinementOutcome field " - 'of the respective sample to "2 - PANDDA model", save the database and repeat the export prodedure.' + "This is most likely because this was done with an older" + " version of XCE. " + "If you really want to export and refine this model," + " you need to open the database " + "with DBbroweser (sqlitebrowser.org);" + " then change the RefinementOutcome field " + 'of the respective sample to "2 - PANDDA model","" save the' + " database and repeat the export prodedure." ) self.Logfile.insert(advice) else: @@ -1238,7 +1214,8 @@ def export_models(self): samples_to_export[sample] = fileModelsDict[sample] # update the DB: - # set timestamp to current timestamp of file and set RefinementOutcome to '2-pandda...' + # set timestamp to current timestamp of file and set RefinementOutcome to + # '2-pandda...' if samples_to_export != {}: select_dir_string = "" @@ -1275,8 +1252,6 @@ def export_models(self): Cmds = ( "module load ccp4/7.1.016\n" - # 'source /dls/science/groups/i04-1/software/pandda-update/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' - # 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' "pandda.export" " pandda_dir=%s" % self.panddas_directory + " export_dir={0!s}".format(self.initial_model_directory) @@ -1351,22 +1326,21 @@ def __init__(self, pandda_params, xce_logfile, datasource): self.make_ligand_links = "" def run(self): - - # print self.reference_dir - # print self.filter_pdb - # how to run pandda.analyse on large datasets # # 1) Run the normal pandda command, with the new setting, e.g. # pandda.analyse data_dirs=... max_new_datasets=500 - # This will do the analysis on the first 500 datasets and build the statistical maps - just as normal. + # This will do the analysis on the first 500 datasets and build the statistical + # maps - just as normal. # # 2) Run pandda with the same command: # pandda.analyse data_dirs=... max_new_datasets=500 - # This will add 500 new datasets, and process them using the existing statistical maps - # (this will be quicker than the original analysis). It will then merge the results of the two analyses. + # This will add 500 new datasets, and process them using the existing + # statistical maps (this will be quicker than the original analysis). + # It will then merge the results of the two analyses. # - # 3) Repeat 2) until you don't add any "new" datasets. Then you can build the models as normal. + # 3) Repeat 2) until you don't add any "new" datasets. + # Then you can build the models as normal. number_of_cyles = int(self.number_of_datasets) / int(self.max_new_datasets) # modulo gives remainder after integer division @@ -1384,24 +1358,17 @@ def run(self): msg = ( "there are three possibilities:\n" "1.) choose another PANDDA directory\n" - "2.) - check if the job is really running either on the cluster (qstat) or on your local machine\n" + "2.) - check if the job is really running either on the cluster (qstat)" + " or on your local machine\n" " - if so, be patient and wait until the job has finished\n" - "3.) same as 2., but instead of waiting, kill the job and remove at least the pandda.running file\n" - " (or all the contents in the directory if you want to start from scratch)\n" + "3.) same as 2., but instead of waiting, kill the job" + " and remove at least the pandda.running file\n" + " (or all the contents in the directory" + " if you want to start from scratch)\n" ) self.Logfile.insert(msg) return None else: - # if os.getenv('SHELL') == '/bin/tcsh' or os.getenv('SHELL') == '/bin/csh': - # source_file=os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh\n') - # elif os.getenv('SHELL') == '/bin/bash' or self.use_remote: - # source_file='export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' - # source_file+='source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') - # else: - # source_file='' - # v1.2.1 - pandda.setup files should be obsolete now that pandda is part of ccp4 - # 08/10/2020 - pandda v0.2.12 installation at DLS is obsolete - # source_file='source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n' source_file = "" source_file += ( 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"\n' @@ -1549,7 +1516,8 @@ def append_to_ignore_string(datasets_list, append_string): + data_dir_string + '"/"' + self.panddas_directory - + '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' + + '/processed_datasets/"}| while read line2;' + " do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; " "done; done;" ) @@ -1562,7 +1530,8 @@ def append_to_ignore_string(datasets_list, append_string): + data_dir_string + '"/"' + self.panddas_directory - + '/processed_datasets/"}| while read line2; do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; ' + + '/processed_datasets/"}| while read line2;' + " do cp $line ${line2//compound/ligand_files} > /dev/null 2>&1; " "done; done;" ) @@ -1574,9 +1543,6 @@ def append_to_ignore_string(datasets_list, append_string): f.write(Cmds) f.close() - # #>>> for testing - # self.submit_mode='local machine' - self.Logfile.insert( "trying to run pandda.analyse on " + str(self.submit_mode) ) @@ -1593,7 +1559,8 @@ def append_to_ignore_string(datasets_list, append_string): "cd " + self.panddas_directory + "; " - + "qsub -P labxchem -q medium.q -N pandda 5 -l exclusive,m_mem_free=100G pandda.sh'" + + "qsub -P labxchem -q medium.q -N pandda 5" + " -l exclusive,m_mem_free=100G pandda.sh'" ), ) os.system(submission_string) @@ -1603,7 +1570,8 @@ def append_to_ignore_string(datasets_list, append_string): else: self.Logfile.insert("running PANDDA on cluster, using qsub...") os.system( - "qsub -P labxchem -q medium.q -N pandda -l exclusive,m_mem_free=100G pandda.sh" + "qsub -P labxchem -q medium.q -N pandda" + " -l exclusive,m_mem_free=100G pandda.sh" ) self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) @@ -1638,7 +1606,6 @@ def __init__(self, pandda_params, xce_logfile, datasource): self.select_ground_state_model = "" def run(self): - if not self.data_directory.startswith("/dls"): self.Logfile.error("Sorry, you need to be at DLS for pandda2 to work!") return None @@ -1650,20 +1617,25 @@ def run(self): "module load ccp4\n" "module load phenix\n" "module load buster\n" - "__conda_setup=\"$('/dls/science/groups/i04-1/conor_dev/conda/anaconda/bin/conda' 'shell.bash' 'hook' 2> /dev/null)\"\n" + "__conda_setup=\"$('/dls/science/groups/i04-1/conor_dev/conda/anaconda/bin/" + "conda' 'shell.bash' 'hook' 2> /dev/null)\"\n" "if [ $? -eq 0 ]; then\n" ' eval "$__conda_setup"\n' "else\n" - ' if [ -f "/dls/science/groups/i04-1/conor_dev/conda/anaconda/etc/profile.d/conda.sh" ]; then\n' - ' . "/dls/science/groups/i04-1/conor_dev/conda/anaconda/etc/profile.d/conda.sh"\n' + ' if [ -f "/dls/science/groups/i04-1/conor_dev/conda/anaconda/etc/' + 'profile.d/conda.sh" ]; then\n' + ' . "/dls/science/groups/i04-1/conor_dev/conda/anaconda/etc/' + 'profile.d/conda.sh"\n' " else\n" - ' export PATH="/dls/science/groups/i04-1/conor_dev/conda/anaconda/bin:$PATH"\n' + " export" + ' PATH="/dls/science/groups/i04-1/conor_dev/conda/anaconda/bin:$PATH"\n' " fi\n" "fi\n" "unset __conda_setup\n" 'export PYTHONPATH=""\n' "conda activate pandda2_ray\n" - "python -u /dls/science/groups/i04-1/conor_dev/pandda_2_gemmi/pandda_gemmi/analyse.py" + "python -u /dls/science/groups/i04-1/conor_dev/pandda_2_gemmi/pandda_gemmi/" + "analyse.py" " --data_dirs={0!s}".format(self.data_directory.replace("/*", "")) + " --out_dir={0!s}".format(self.panddas_directory) + ' --pdb_regex="{0!s}" '.format(self.pdb_style) @@ -1676,7 +1648,8 @@ def run(self): ' --comparison_strategy="hybrid" ' " --min_characterisation_datasets=25 " " {0!s} ".format(self.keyword_arguments) - + ' --debug=True --memory_availability="low" | tee livelog_20220324_event_class_old_score\n' + + ' --debug=True --memory_availability="low"' + " | tee livelog_20220324_event_class_old_score\n" ) self.Logfile.insert( @@ -1691,7 +1664,8 @@ def run(self): self.Logfile.insert("running PANDDA on cluster, using qsub...") os.system( - "qsub -pe smp 6 -l m_mem_free=30G -q medium.q -o log.out -e log.err pandda2.sh" + "qsub -pe smp 6 -l m_mem_free=30G -q medium.q -o log.out -e log.err" + " pandda2.sh" ) self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) @@ -1795,7 +1769,9 @@ def run(self): # 3.) giant.cluster_mtzs_and_pdbs self.Logfile.insert( - "running giant.cluster_mtzs_and_pdbs {0!s}/*/{1!s} pdb_regex='{2!s}/(.*)/{3!s}' out_dir='{4!s}/cluster_analysis'".format( + "running giant.cluster_mtzs_and_pdbs {0!s}/*/{1!s}" + " pdb_regex='{2!s}/(.*)/{3!s}'" + " out_dir='{4!s}/cluster_analysis'".format( self.initial_model_directory, self.pdb_style, self.initial_model_directory, @@ -1823,7 +1799,8 @@ def run(self): "#!" + os.getenv("SHELL") + "\n" "unset PYTHONPATH\n" "source " + source_file + "\n" - "giant.datasets.cluster %s/*/%s pdb_regex='%s/(.*)/%s' out_dir='%s/cluster_analysis'" + "giant.datasets.cluster %s/*/%s pdb_regex='%s/(.*)/%s'" + " out_dir='%s/cluster_analysis'" % ( self.initial_model_directory, self.pdb_style, @@ -1833,7 +1810,6 @@ def run(self): ) ) - # os.system("giant.cluster_mtzs_and_pdbs %s/*/%s pdb_regex='%s/(.*)/%s' out_dir='%s/cluster_analysis'" %(self.initial_model_directory,self.pdb_style,self.initial_model_directory,self.pdb_style,self.panddas_directory)) os.system(Cmds) self.emit(QtCore.SIGNAL("update_progress_bar"), 80) @@ -1914,7 +1890,6 @@ def compare_number_of_atoms_in_reference_vs_all_datasets( ): mismatched_datasets = [] pdbtools = XChemUtils.pdbtools(refData) - refPDB = refData[refData.rfind("/") + 1 :] refPDBlist = pdbtools.get_init_pdb_as_list() n_atom_ref = len(refPDBlist) for n_datasets, dataset in enumerate(dataset_list): @@ -1934,13 +1909,15 @@ def compare_number_of_atoms_in_reference_vs_all_datasets( ) if n_atom_ref == n_atom: self.Logfile.insert( - "{0!s}: atoms in PDB file ({1!s}): {2!s}; atoms in Reference file: {3!s} ===> OK".format( + "{0!s}: atoms in PDB file ({1!s}): {2!s};" + " atoms in Reference file: {3!s} ===> OK".format( dataset, self.pdb_style, str(n_atom), str(n_atom_ref) ) ) if n_atom_ref != n_atom: self.Logfile.insert( - "{0!s}: atoms in PDB file ({1!s}): {2!s}; atoms in Reference file: {3!s} ===> ERROR".format( + "{0!s}: atoms in PDB file ({1!s}): {2!s};" + " atoms in Reference file: {3!s} ===> ERROR".format( dataset, self.pdb_style, str(n_atom), str(n_atom_ref) ) ) @@ -2109,7 +2086,8 @@ def run(self): ): os.chdir(os.path.join(self.initial_model_directory, xtalID)) self.Logfile.insert( - "extracting ligand ({0!s},{1!s},{2!s},{3!s}) from refine.pdb".format( + "extracting ligand ({0!s},{1!s},{2!s},{3!s})" + " from refine.pdb".format( str(resname), str(chainID), str(resseq), str(altLoc) ) ) @@ -2206,10 +2184,11 @@ def run(self): self.Logfile.insert("removing existing " + self.event + ".mtz") os.system("/bin/rm " + self.event + ".mtz") - # event maps generated with pandda v0.2 or higher have the same symmetry as the crystal - # but phenix.map_to_structure_facors only accepts maps in spg P1 - # therefore map is first expanded to full unit cell and spg of map then set tp p1 - # other conversion option like cinvfft give for whatever reason uninterpretable maps + # event maps generated with pandda v0.2 or higher have the same symmetry as the + # crystal but phenix.map_to_structure_facors only accepts maps in spg P1 + # therefore map is first expanded to full unit cell and spg of map then + # set tp p1. other conversion option like cinvfft give for whatever reason + # uninterpretable maps self.convert_map_to_p1() # run phenix.map_to_structure_factors @@ -2275,7 +2254,8 @@ def prepare_conversion_script(self): + " XYZLIM CELL\n" "eof\n" "\n" - "maprot MAPIN onecell_event_map.map MSKIN mask_ligand.msk WRKOUT masked_event_map.map << eof\n" + "maprot MAPIN onecell_event_map.map MSKIN mask_ligand.msk WRKOUT" + " masked_event_map.map << eof\n" " MODE FROM\n" " SYMMETRY WORK %s\n" % self.space_group_numberElectronDensityMap + " AVERAGE\n" @@ -2283,7 +2263,8 @@ def prepare_conversion_script(self): " TRANSLATE 0 0 0\n" "eof\n" "\n" - "mapmask MAPIN masked_event_map.map MAPOUT masked_event_map_fullcell.map << eof\n" + "mapmask MAPIN masked_event_map.map MAPOUT masked_event_map_fullcell.map <<" + " eof\n" " XYZLIM CELL\n" " PAD 0.0\n" "eof\n" @@ -2323,12 +2304,14 @@ def run_phenix_map_to_structure_factors(self): ): # program complains if resolution is 1.2 or higher self.resolution = "1.21" self.Logfile.insert( - "running phenix.map_to_structure_factors {0!s}_p1.map d_min={1!s} output_file_name={2!s}_tmp.mtz".format( + "running phenix.map_to_structure_factors {0!s}_p1.map d_min={1!s}" + " output_file_name={2!s}_tmp.mtz".format( self.event, self.resolution, self.event ) ) os.system( - "phenix.map_to_structure_factors {0!s}_p1.map d_min={1!s} output_file_name={2!s}_tmp.mtz".format( + "phenix.map_to_structure_factors {0!s}_p1.map d_min={1!s}" + " output_file_name={2!s}_tmp.mtz".format( self.event, self.resolution, self.event ) ) @@ -2336,14 +2319,12 @@ def run_phenix_map_to_structure_factors(self): def run_cinvfft(self, mtzin): # mtzin is usually refine.mtz self.Logfile.insert( - "running cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz -colout event".format( - self.event_map, mtzin, self.event - ) + "running cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz" + " -colout event".format(self.event_map, mtzin, self.event) ) os.system( - "cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz -colout event".format( - self.event_map, mtzin, self.event - ) + "cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz" + " -colout event".format(self.event_map, mtzin, self.event) ) def remove_and_rename_column_labels(self): @@ -2522,55 +2503,7 @@ def update_errorDict(self, xtal, message): self.errorDict[xtal] = [] self.errorDict[xtal].append(message) - def insert_new_row_in_panddaTable(self, xtal, ligand, site, dbDict): - resname = site[0] - chain = site[1] - seqnum = site[2] - altLoc = site[3] - x_site = site[5][0] - y_site = site[5][1] - z_site = site[5][2] - - resnameSimilarSite = ligand[0] - chainSimilarSite = ligand[1] - seqnumSimilarSite = ligand[2] - - siteList = [] - for entry in dbDict[xtal]: - siteList.append(str(entry[0])) - if ( - entry[4] == resnameSimilarSite - and entry[5] == chainSimilarSite - and entry[6] == seqnumSimilarSite - ): - eventMap = str(entry[7]) - eventMap_mtz = str(entry[8]) - initialPDB = str(entry[9]) - initialMTZ = str(entry[10]) - event_id = str(entry[12]) - PanDDApath = str(entry[13]) - - db_dict = { - "PANDDA_site_index": str(int(max(siteList)) + 1), - "PANDDApath": PanDDApath, - "PANDDA_site_ligand_id": resname + "-" + chain + "-" + seqnum, - "PANDDA_site_ligand_resname": resname, - "PANDDA_site_ligand_chain": chain, - "PANDDA_site_ligand_sequence_number": seqnum, - "PANDDA_site_ligand_altLoc": "D", - "PANDDA_site_event_index": event_id, - "PANDDA_site_event_map": eventMap, - "PANDDA_site_event_map_mtz": eventMap_mtz, - "PANDDA_site_initial_model": initialPDB, - "PANDDA_site_initial_mtz": initialMTZ, - "PANDDA_site_ligand_placed": "True", - "PANDDA_site_x": x_site, - "PANDDA_site_y": y_site, - "PANDDA_site_z": z_site, - } - def run(self): - self.Logfile.insert("reading modelled ligands from panddaTable") dbDict = {} @@ -2657,13 +2590,11 @@ def run(self): os.mkdir(os.path.join(xtal, "xceTmp")) else: self.Logfile.warning( - "{0!s}: cannot find ligand molecule in refine.pdb; skipping...".format( - xtal - ) + "{0!s}: cannot find ligand molecule in refine.pdb;" + " skipping...".format(xtal) ) continue - made_sym_copies = False ligands_not_in_panddaTable = [] for n, item in enumerate(ligands): resnameLIG = item[0] @@ -2674,9 +2605,8 @@ def run(self): if altLocLIG.replace(" ", "") == "": self.Logfile.insert( xtal - + ": found a ligand not modelled with pandda.inspect -> {0!s} {1!s} {2!s}".format( - resnameLIG, chainLIG, seqnumLIG - ) + + ": found a ligand not modelled with pandda.inspect ->" + " {0!s} {1!s} {2!s}".format(resnameLIG, chainLIG, seqnumLIG) ) residue_xyz = XChemUtils.pdbtools( os.path.join(xtal, "refine.pdb") @@ -2699,14 +2629,16 @@ def run(self): and seqnumLIG == seqnumTable ): self.Logfile.insert( - "{0!s}: found ligand in database -> {1!s} {2!s} {3!s}".format( + "{0!s}: found ligand in database ->" + " {1!s} {2!s} {3!s}".format( xtal, resnameTable, chainTable, seqnumTable ) ) foundLigand = True if not foundLigand: self.Logfile.error( - "{0!s}: did NOT find ligand in database -> {1!s} {2!s} {3!s}".format( + "{0!s}: did NOT find ligand in database ->" + " {1!s} {2!s} {3!s}".format( xtal, resnameLIG, chainLIG, seqnumLIG ) ) @@ -2722,14 +2654,16 @@ def run(self): ) else: self.Logfile.warning( - "ligand in PDB file, but dataset not listed in panddaTable: {0!s} -> {1!s} {2!s} {3!s}".format( + "ligand in PDB file, but dataset not listed in panddaTable:" + " {0!s} -> {1!s} {2!s} {3!s}".format( xtal, item[0], item[1], item[2] ) ) for entry in ligands_not_in_panddaTable: self.Logfile.error( - "{0!s}: refine.pdb contains a ligand that is not assigned in the panddaTable: {1!s} {2!s} {3!s} {4!s}".format( + "{0!s}: refine.pdb contains a ligand that is not assigned in" + " the panddaTable: {1!s} {2!s} {3!s} {4!s}".format( xtal, entry[0], entry[1], entry[2], entry[3] ) ) @@ -2744,7 +2678,8 @@ def run(self): mol_xyz = XChemUtils.pdbtools( files ).get_center_of_gravity_of_molecule_ish() - # now need to check if there is a unassigned entry in panddaTable that is close + # now need to check if there is a unassigned entry in + # panddaTable that is close for entry in dbDict[xtal]: distance = XChemUtils.misc().calculate_distance_between_coordinates( mol_xyz[0], @@ -2755,7 +2690,8 @@ def run(self): entry[3], ) self.Logfile.insert( - "{0!s}: {1!s} {2!s} {3!s} <---> {4!s} {5!s} {6!s}".format( + "{0!s}: {1!s} {2!s} {3!s} <--->" + " {4!s} {5!s} {6!s}".format( xtal, mol_xyz[0], mol_xyz[1], @@ -2780,7 +2716,8 @@ def run(self): if self.errorDict != {}: self.update_errorDict( "General", - "The aforementioned PDB files were automatically changed by XCE!\nPlease check and refine them!!!", + "The aforementioned PDB files were automatically changed by XCE!\n" + "Please check and refine them!!!", ) self.emit(QtCore.SIGNAL("show_error_dict"), self.errorDict) From a4c6acec76957500a45d1489ef9a9dc5c91e7ca9 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 17:38:36 +0000 Subject: [PATCH 154/358] Fix icons dir --- xce/gui_scripts/layout.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/xce/gui_scripts/layout.py b/xce/gui_scripts/layout.py index c6e37db3..ad040a08 100755 --- a/xce/gui_scripts/layout.py +++ b/xce/gui_scripts/layout.py @@ -41,7 +41,7 @@ def initialise_menu_bar(self, xce_object): # function containing setup for bottom boxes def initialise_bottom_boxes(self, xce_object): - icons_directory = os.path.join((os.getenv("XChemExplorer_DIR")), "icons") + icons_directory = os.path.join((os.getenv("XChemExplorer_DIR")), "xce/icons") # import all buttons setup().bottom_box_buttons(xce_object) From 3f6f6dce554f9cb5208554102aa2728cd57195ef Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 17:46:37 +0000 Subject: [PATCH 155/358] Clean up XChemMain --- xce/lib/XChemMain.py | 169 +++++++++++++------------------------------ 1 file changed, 52 insertions(+), 117 deletions(-) diff --git a/xce/lib/XChemMain.py b/xce/lib/XChemMain.py index 8c169ecf..9d90327e 100755 --- a/xce/lib/XChemMain.py +++ b/xce/lib/XChemMain.py @@ -89,29 +89,15 @@ def space_group_list(): def get_target_and_visit_list(beamline_directory, agamemnon): - # target_list=['*'] # always give the option to read in all targets target_list = ["=== SELECT TARGET ===", "=== project directory ==="] visit_list = [] # the beamline directory could be a the real directory or # a directory where the visits are linked into - # if agamemnon: - # # /dls/i03/data/2019/lb18145-136 - # for target in glob.glob(beamline_directory[:beamline_directory.rfind('-') + 1] + '*/agamemnon/*'): - # visit_list.append(beamline_directory[:beamline_directory.rfind('/')].replace('/agamemnon','')) - # if target[target.rfind('/') + 1:] not in ['results', 'README-log', 'edna-latest.html']: - # if target[target.rfind('/') + 1:] not in target_list: - # target_list.append(target[target.rfind('/') + 1:]) - # for target in glob.glob(beamline_directory[:beamline_directory.rfind('-') + 1] + '*/auto/*'): - # visit_list.append(beamline_directory[:beamline_directory.rfind('/')].replace('/auto', '')) - # if target[target.rfind('/') + 1:] not in ['results', 'README-log', 'edna-latest.html']: - # if target[target.rfind('/') + 1:] not in target_list: - # target_list.append(target[target.rfind('/') + 1:]) - # else: if ( len(beamline_directory.split("/")) and beamline_directory.split("/")[1] == "dls" and beamline_directory.split("/")[3] == "data" - and not "labxchem" in beamline_directory + and "labxchem" not in beamline_directory ): visit_list.append(beamline_directory) else: @@ -142,23 +128,6 @@ def get_target_and_visit_list(beamline_directory, agamemnon): return target_list, visit_list -# def get_target_and_visit_list_for_Pietro(beamline_directory): -# target_list=['*'] # always give the option to read in all targets -# target_list=['=== SELECT TARGET ==='] # always give the option to read in all targets -# visit_list=[] -# # the beamline directory could be a the real directory or -# # a directory where the visits are linked into -# for stuff in glob.glob(os.path.join(beamline_directory,'*')): -# visit_list.append(stuff) -# -# for visit in visit_list: -# for target in glob.glob(os.path.join(visit,'processed','*')): -# if target[target.rfind('/')+1:] not in ['results','README-log','edna-latest.html']: -# if target[target.rfind('/')+1:] not in target_list: -# target_list.append(target[target.rfind('/')+1:]) -# return target_list,visit_list - - def get_dewar_configuration(beamline_directory): dewar_sample_configuration_dict = {} # need to do it like this for now until we got a way to query ispyb @@ -231,9 +200,7 @@ def get_jobs_running_on_cluster(): run_time = datetime.now() - datetime.strptime( start, "%Y-%m-%d %H:%M:%S" ) - run_time_seconds = int(run_time.total_seconds()) run_time_minutes = int(run_time.total_seconds() / 60) - run_time_hours = int(run_time.total_seconds() / 3600) ########################################################## # determine run time of each job in minutes @@ -317,7 +284,8 @@ def print_cluster_status_message(program, cluster_dict, xce_logfile): Logfile.insert("average run time " + str(average_runtime) + " minutes") if job_ids: Logfile.insert( - "you can kill them by pasting the following line into a new terminal window:" + "you can kill them by pasting the following line" + " into a new terminal window:" ) out = "qdel " for job in job_ids: @@ -368,53 +336,63 @@ def get_datasource_summary(db_file): out_dict["nr_smiles_for_samples"] = len( db.execute_statement( - "select compoundSMILES from mainTable where compoundSMILES is not (NULL or '')" + "select compoundSMILES from mainTable" + " where compoundSMILES is not (NULL or '')" ) ) out_dict["nr_data_collection_success"] = len( db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'success';" + "select DataCollectionOutcome from mainTable" + " where DataCollectionOutcome is 'success';" ) ) out_dict["nr_data_collection_centring_fail"] = len( db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - centring failed';" + "select DataCollectionOutcome from mainTable" + " where DataCollectionOutcome is 'Failed - centring failed';" ) ) out_dict["nr_data_collection_no-diffraction"] = len( db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - no diffraction';" + "select DataCollectionOutcome from mainTable" + " where DataCollectionOutcome is 'Failed - no diffraction';" ) ) out_dict["nr_data_collection_processing_fail"] = len( db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - processing';" + "select DataCollectionOutcome from mainTable" + " where DataCollectionOutcome is 'Failed - processing';" ) ) out_dict["nr_data_collection_loop-empty"] = len( db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - loop empty';" + "select DataCollectionOutcome from mainTable" + " where DataCollectionOutcome is 'Failed - loop empty';" ) ) out_dict["nr_data_collection_loop-broken"] = len( db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - loop broken';" + "select DataCollectionOutcome from mainTable where" + " DataCollectionOutcome is 'Failed - loop broken';" ) ) out_dict["nr_data_collection_low-resolution"] = len( db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - low resolution';" + "select DataCollectionOutcome from mainTable where" + " DataCollectionOutcome is 'Failed - low resolution';" ) ) out_dict["nr_data_collection_no-X-rays"] = len( db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - no X-rays';" + "select DataCollectionOutcome from mainTable where" + " DataCollectionOutcome is 'Failed - no X-rays';" ) ) out_dict["nr_data_collection_unknown"] = len( db.execute_statement( - "select DataCollectionOutcome from mainTable where DataCollectionOutcome is 'Failed - unknown';" + "select DataCollectionOutcome from mainTable where" + " DataCollectionOutcome is 'Failed - unknown';" ) ) @@ -449,7 +427,8 @@ def get_datasource_summary(db_file): ) out_dict["nr_initial_maps_fail"] = len( db.execute_statement( - "select DataProcessingDimpleSuccessful from mainTable where DataProcessingDimpleSuccessful = 'False';" + "select DataProcessingDimpleSuccessful from mainTable" + " where DataProcessingDimpleSuccessful = 'False';" ) ) out_dict["nr_initial_maps_pending"] = ( @@ -465,13 +444,15 @@ def get_datasource_summary(db_file): ) out_dict["nr_pandda_reject"] = len( db.execute_statement( - "select DimplePANDDAreject from mainTable where DimplePANDDAreject = 'True';" + "select DimplePANDDAreject from mainTable" + " where DimplePANDDAreject = 'True';" ) ) out_dict["nr_pandda_processed"] = ( len( db.execute_statement( - "select DimplePANDDAwasRun from mainTable where DimplePANDDAwasRun = 'True';" + "select DimplePANDDAwasRun from mainTable" + " where DimplePANDDAwasRun = 'True';" ) ) - out_dict["nr_pandda_hits"] @@ -486,33 +467,39 @@ def get_datasource_summary(db_file): out_dict["nr_cif_files"] = len( db.execute_statement( - "select RefinementCIF from mainTable where RefinementCIF is not (Null or '');" + "select RefinementCIF from mainTable" + " where RefinementCIF is not (Null or '');" ) ) out_dict["nr_analysis-pending"] = len( db.execute_statement( - "select RefinementOutcome from mainTable where RefinementOutcome is '1 - Analysis Pending';" + "select RefinementOutcome from mainTable" + " where RefinementOutcome is '1 - Analysis Pending';" ) ) out_dict["nr_pandda-models"] = len( db.execute_statement( - "select RefinementOutcome from mainTable where RefinementOutcome is '2 - PANDDA model';" + "select RefinementOutcome from mainTable" + " where RefinementOutcome is '2 - PANDDA model';" ) ) out_dict["nr_in-refinement"] = len( db.execute_statement( - "select RefinementOutcome from mainTable where RefinementOutcome is '3 - In Refinement';" + "select RefinementOutcome from mainTable" + " where RefinementOutcome is '3 - In Refinement';" ) ) out_dict["nr_comp-chem-ready"] = len( db.execute_statement( - "select RefinementOutcome from mainTable where RefinementOutcome is '4 - ComChem ready';" + "select RefinementOutcome from mainTable" + " where RefinementOutcome is '4 - ComChem ready';" ) ) out_dict["nr_deposition-ready"] = len( db.execute_statement( - "select RefinementOutcome from mainTable where RefinementOutcome is '5 - Deposition ready';" + "select RefinementOutcome from mainTable" + " where RefinementOutcome is '5 - Deposition ready';" ) ) @@ -549,7 +536,6 @@ def change_links_to_selected_data_collection_outcome( run = entry[2] autoproc = entry[4] db_dict = entry[6] - outcome = dataset_outcome_dict[sample] path_to_logfile = db_dict["DataProcessingPathToLogfile"] path_to_mtzfile = db_dict["DataProcessingPathToMTZfile"] mtz_filename = db_dict["DataProcessingMTZfileName"] @@ -591,10 +577,6 @@ def change_links_to_selected_data_collection_outcome( os.system("/bin/rm " + sample + ".mtz 2> /dev/null") os.system("/bin/rm " + sample + ".log 2> /dev/null") # make new links - # Logfile.insert('setting symlink: '+os.path.join(path_to_logfile,log_filename)+' -> '+sample+'.log') - # os.symlink(os.path.join(path_to_logfile,log_filename),sample+'.log') - # Logfile.insert('setting symlink: '+os.path.join(path_to_mtzfile,mtz_filename)+' -> '+sample+'.mtz') - # os.symlink(os.path.join(path_to_mtzfile,mtz_filename),sample+'.mtz') Logfile.insert( "setting relative symlink: " + os.path.join(relative_path_to_logfile, log_filename) @@ -626,25 +608,6 @@ def change_links_to_selected_data_collection_outcome( Logfile.insert("please copy data to PROJECT DIRECTORY first!") -# def find_diffraction_image_directory(diffraction_data_directory): -# data_dict={} -# diffraction_image_extension = ['.img','.cbf','.mccd','.mar2560','.mar2300'] -# os.chdir(diffraction_data_directory) -# for xtal in glob.glob('*'): -# data_dict[xtal]=[] -# for root,dirs,files in os.walk(xtal): -# if 'screening' in root: -# continue -# for n,image_file in enumerate(glob.glob(os.path.join(root,'*'))): -# file_extension=image_file[image_file.rfind('.'):] -# if n > 20 and file_extension in diffraction_image_extension: -# data_dict[xtal].append(os.path.join(diffraction_data_directory,root)) -# break -# if data_dict[xtal]==[]: -# del data_dict[xtal] -# return data_dict - - def get_nr_files_from_gda_log_folder(beamline): n = len(glob.glob(os.path.join("/dls_sw", beamline, "logs", "gda_server*"))) return n @@ -685,8 +648,6 @@ def get_dict_of_gda_barcodes(beamline): def append_dict_of_gda_barcodes(out_dict, files, xce_logfile): - # out_dict={} - # for files in glob.glob(os.path.join('/dls_sw',beamline,'logs','*')): Logfile = XChemLog.updateLog(xce_logfile) found_barcode_entry = False gda_log = files[files.rfind("/") + 1 :] @@ -771,7 +732,8 @@ def get_gda_barcodes( if sampleID in sampleList: pinDict[sampleID] = barcode Logfile.insert( - "found: sample={0!s}, barcode={1!s}, file={2!s}".format( + "found: sample={0!s}, barcode={1!s}," + " file={2!s}".format( sampleID, barcode, gdaLogFile ) ) @@ -794,9 +756,8 @@ def get_gda_barcodes( if sampleID in sampleList: pinDict[sampleID] = barcode Logfile.insert( - "found: sample={0!s}, barcode={1!s}, file={2!s}".format( - sampleID, barcode, gdaLogFile - ) + "found: sample={0!s}, barcode={1!s}," + " file={2!s}".format(sampleID, barcode, gdaLogFile) ) found_barcode_entry = False except IOError: @@ -913,8 +874,8 @@ def getVisitAndBeamline(visitDirectory): except IndexError: pass if not visitDirectory.startswith("/dls"): - # this is all a bit of a fudge in case someone transfers a DLS visit directory back home - # does most certainly not catch all possible scenarios + # this is all a bit of a fudge in case someone transfers a DLS visit directory + # back home does most certainly not catch all possible scenarios if visitDirectory.split("/")[len(visitDirectory.split("/")) - 2] == "processed": visit = visitDirectory.split("/")[len(visitDirectory.split("/")) - 3] else: @@ -1203,7 +1164,6 @@ def pdbx_country(): def html_header(): - header = ( "\n" "\n" @@ -1666,22 +1626,6 @@ def html_table_row( ligChain = ligID.split("-")[1] ligResid = ligID.split("-")[2] - # row = ( - # '\n' - # '\n' %xtalID + - # '\n' %(pdbID,pdbID) + - # '\n' %ligID + - # '\n' % ligConfidence + - # '\n' % modelStatus + - # "\n" %compoundImage + - # "\n" %residuePlot + - # "\n" %(pdbID,pdb,event,FWT,DELFWT,ligChain,ligResid,thumbNail) + - # '\n' %resoHigh + - # '\n' %(spg,unitCell) + - # "\n" %(pdb.replace('.pdb',''),ligID) + - # '\n' - # ) - row = ( " \n" " \n" % xtalID @@ -1722,11 +1666,9 @@ def coot_prepare_input(x, y, z, ligID, sampleDir, eventMap): 'molecule = read_pdb("refine.split.bound-state.pdb")\n' "set_rotation_centre(%s, %s, %s)\n" % (x, y, z) + "set_zoom(30.)\n" "set_view_quaternion(-0.180532, -0.678828, 0, 0.711759)\n" - 'coot.handle_read_ccp4_map(("%s"),0)\n' % eventMap + - # 'mtz = "final.mtz"\n' - # 'map21 = make_and_draw_map(mtz, "FWT", "PHWT", "", 0, 0)\n' - # 'map11 = make_and_draw_map(mtz, "DELFWT", "PHDELWT", "", 0, 1)\n' - 'coot.raster3d("%s.r3d")\n' % ligID + "coot_real_exit(0)\n" + 'coot.handle_read_ccp4_map(("%s"),0)\n' % eventMap + + 'coot.raster3d("%s.r3d")\n' % ligID + + "coot_real_exit(0)\n" ) f = open(ligID + ".py", "w") f.write(cmd) @@ -1778,8 +1720,6 @@ def __init__(self, diffraction_data_directory): ".mar2300", ] - # self.datasetID_to_sampleID_conversion='*' - def run(self): os.chdir(self.diffraction_data_directory) if len(glob.glob(os.path.join(self.diffraction_data_directory, "*"))) != 0: @@ -1814,7 +1754,6 @@ def run(self): self.data_dict[xtal][0].append( os.path.join(self.diffraction_data_directory, root) ) - # break if self.data_dict[xtal][0]: found_new_file_root = False run_list = [] @@ -1859,8 +1798,6 @@ def __init__(self, diffraction_data_directory): ".mar2300", ] - # self.datasetID_to_sampleID_conversion='*' - def run(self): print( ( @@ -1883,14 +1820,14 @@ def run(self): "searching diffraction data directory", ) for xtal in glob.glob("*"): - # print xtal if "screening" in xtal: continue self.data_dict[xtal] = [] rootList = [] imageCounter = 0 - # find image file extension; the assumption is that there is only one file type + # find image file extension; the assumption is that there is only one file + # type imageExtension = "cbf" for files in sorted(glob.glob(os.path.join(xtal, "*"))): fileName = os.path.join(self.diffraction_data_directory, files) @@ -1905,14 +1842,12 @@ def run(self): if file_root not in rootList: rootList.append(file_root) - currentRoot = file_root imageCounter = 0 if imageCounter == 20: self.data_dict[xtal].append( [os.path.join(self.diffraction_data_directory, xtal), file_root] ) - # self.data_dict[xtal][1].append(file_root) imageCounter += 1 From 91b1762d9ea3d63339930c83cd50c192cd5911cb Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 18:15:26 +0000 Subject: [PATCH 156/358] Fix changelog line seperators --- ChangeLog.txt | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/ChangeLog.txt b/ChangeLog.txt index 55980017..fa93cc14 100755 --- a/ChangeLog.txt +++ b/ChangeLog.txt @@ -222,18 +222,18 @@ v1.6.13 (10/05/2020) v1.6.12 (09/05/2020) - capture refinement mmcif file location in DB after refinement (if available) -v1.6.11 (04/05/2020)
 +v1.6.11 (04/05/2020) - added giant.score_model after buster refinement - added field and capture of path to buster-reports in DB -v1.6.10 (04/05/2020)
 +v1.6.10 (04/05/2020) - bug fix: only read (2)fofc_twin.map during dimple_twin map review -v1.6.9 (04/05/2020)
 +v1.6.9 (04/05/2020) - added COOT command to open dimple_twin maps -v1.6.8 (30/04/2020)
 -- enable html export of '4 - CompChem ready' structures only
 +v1.6.8 (30/04/2020) +- enable html export of '4 - CompChem ready' structures only v1.6.7 (29/04/2020) - initial twin refinement with dimple in separate folder and additional fields in XChemDB @@ -247,8 +247,8 @@ v1.6.5 (28/04/2020) v1.6.4 (28/04/2020) - added validation with buster-reports after refinement with buster -v1.6.3 (25/04/2020)
 -- grade will use mogul for restraints generation if program available
 +v1.6.3 (25/04/2020) +- grade will use mogul for restraints generation if program available v1.6.2 (24/04/2020) - restraints generation: use program name in script name for easier trouble-shooting From 1b27f65eb0dcc0939fbe8b203df09108e27b0ed2 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 18:15:38 +0000 Subject: [PATCH 157/358] Launch with xce module --- .vscode/launch.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.vscode/launch.json b/.vscode/launch.json index 93a5a7fb..e5c03dda 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -8,7 +8,7 @@ "name": "XCE", "type": "python", "request": "launch", - "module": "XChemExplorer", + "module": "xce", "justMyCode": true } ] From d3b0617d8188ef32b6b2d02e5c1689d87a2f11e6 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Tue, 8 Nov 2022 18:29:16 +0000 Subject: [PATCH 158/358] Remove unused functions --- xce/XChemExplorer.py | 450 ------ xce/helpers/make_ligand_links_after_pandda.py | 18 - xce/lib/XChemCoot.py | 12 - xce/lib/XChemCootReference.py | 45 - xce/lib/XChemDB.py | 612 -------- xce/lib/XChemDeposit.py | 75 - xce/lib/XChemDialogs.py | 15 - xce/lib/XChemLigand.py | 13 - xce/lib/XChemMain.py | 137 -- xce/lib/XChemPANDDA.py | 310 ---- xce/lib/XChemThread.py | 43 - xce/lib/XChemToolTips.py | 171 --- xce/lib/XChemUtils.py | 1295 ----------------- 13 files changed, 3196 deletions(-) delete mode 100755 xce/lib/XChemLigand.py diff --git a/xce/XChemExplorer.py b/xce/XChemExplorer.py index 30a10ec9..971cc736 100755 --- a/xce/XChemExplorer.py +++ b/xce/XChemExplorer.py @@ -648,13 +648,6 @@ def export_to_html_deposition_ready(self): self.xce_logfile, ).prepare("5") - def select_ground_state_mtz(self): - m = QtGui.QFileDialog.getOpenFileNameAndFilter( - self.window, "Select File", os.getcwd(), "*.mtz" - ) - mtz = str(tuple(m)[0]) - self.ground_state_mtz_button_label.setText(mtz) - def add_ground_state_db(self): pdb, mtz = self.auto_select_ground_state_reference_PDB() if pdb is not None: @@ -744,38 +737,6 @@ def prepare_ground_state_mmcif(self): self.update_log.insert("preparing mmcif file for apo structure deposition") self.prepare_models_for_deposition_ligand_bound("ground_state") - def open_icm(self): - self.update_log.insert("starting ICM...") - self.work_thread = XChemThread.start_ICM(self.html_export_directory) - self.connect( - self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished - ) - self.work_thread.start() - - def prepare_files_for_zenodo_upload(self): - self.update_log.insert("preparing files for ZENODO upload...") - os.system( - "ccp4-python " - + os.getenv("XChemExplorer_DIR") - + "/helpers/prepare_for_zenodo_upload.py " - + self.html_export_directory - ) - - def update_html_for_zenodo_upload(self): - try: - uploadID = int(self.zenodo_upload_id_entry.text()) - self.update_log.insert("updating html files for ZENODO upload,...") - self.update_log.insert("ZENODO upload = " + str(uploadID)) - os.system( - "ccp4-python " - + os.getenv("XChemExplorer_DIR") - + "/helpers/prepare_for_zenodo_upload.py {0!s} {1!s}".format( - self.html_export_directory, uploadID - ) - ) - except ValueError: - self.update_log.insert("zenodo upload ID must be an integer!") - #################################################################################### # # # SETTINGS TAB # @@ -1204,11 +1165,6 @@ def add_label_information(self): label_entryLayout.addLayout(vbox, 0, 0) label_entry.exec_() - def create_missing_apo_records_in_depositTable(self): - self.db.create_missing_apo_records_for_all_structures_in_depositTable( - self.initial_model_directory, self.xce_logfile - ) - def prepare_models_for_deposition_ligand_bound(self, structureType): start_thread = True self.update_log.insert("preparing mmcif files for PDB group deposition...") @@ -1272,34 +1228,6 @@ def prepare_models_for_deposition_ligand_bound(self, structureType): ) self.work_thread.start() - def prepare_models_for_deposition_apo(self): - - structureType = "apo" - - overwrite_existing_mmcif = True - self.work_thread = XChemDeposit.prepare_mmcif_files_for_deposition( - os.path.join(self.database_directory, self.data_source_file), - self.xce_logfile, - overwrite_existing_mmcif, - self.initial_model_directory, - structureType, - ) - self.explorer_active = 1 - self.connect( - self.work_thread, - QtCore.SIGNAL("update_progress_bar"), - self.update_progress_bar, - ) - self.connect( - self.work_thread, - QtCore.SIGNAL("update_status_bar(QString)"), - self.update_status_bar, - ) - self.connect( - self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished - ) - self.work_thread.start() - def prepare_for_group_deposition_upload_ligand_bound(self): self.work_thread = XChemDeposit.prepare_for_group_deposition_upload( @@ -3386,45 +3314,12 @@ def export_data_for_WONKA(self): self.update_log.insert("exporting CSV file for input into WONKA") self.db.export_csv_for_WONKA() - def on_context_menu(self, point): - # show context menu - for key in self.dewar_configuration_dict: - if self.dewar_configuration_dict[key] == self.sender(): - self.dewar_label_active = key - self.popMenu.exec_(self.sender().mapToGlobal(point)) - def on_context_menu_reprocess_data(self, point): # show context menu self.popMenu_for_datasets_reprocess_table.exec_( self.sender().mapToGlobal(point) ) - def flag_sample_for_recollection(self): - self.dewar_configuration_dict[self.dewar_label_active].setStyleSheet( - "background-color: yellow" - ) - - def undo_flag_sample_for_recollection(self): - self.dewar_configuration_dict[self.dewar_label_active].setStyleSheet( - "background-color: gray" - ) - - def show_html_summary_in_firefox(self, xtal): - html_summary = self.albula_button_dict[xtal][2] - print(("html_summary", html_summary)) - new = 2 - webbrowser.open(html_summary, new=new) - - def update_pandda_crystal_from_combobox(self): - self.pandda_analyse_crystal_from_selection_combobox.clear() - self.pandda_analyse_crystal_from_selection_combobox.addItem("use all datasets") - if os.path.isfile(os.path.join(self.database_directory, self.data_source_file)): - self.load_crystal_form_from_datasource() - if self.xtalform_dict != {}: - print((self.xtalform_dict)) - for key in self.xtalform_dict: - self.pandda_analyse_crystal_from_selection_combobox.addItem(key) - def populate_reference_combobox(self, combobox): combobox.clear() for reference_file in self.reference_file_list: @@ -3613,42 +3508,6 @@ def update_reference_files(self, reference_root): self.populate_reference_combobox(self.reference_file_selection_combobox) self.populate_reference_combobox(self.pandda_reference_file_selection_combobox) - def check_status_rerun_dimple_on_all_autoprocessing_files(self): - print("hallo") - - def rerun_dimple_on_all_autoprocessing_files(self): - job_list = [] - self.update_log.insert("preparing to run DIMPLE on all autoprocessing files") - for xtal in self.data_collection_dict: - for entry in self.data_collection_dict[xtal]: - if entry[0] == "logfile": - db_dict = entry[6] - try: - if os.path.isfile( - os.path.join( - db_dict["DataProcessingPathToMTZfile"], - db_dict["DataProcessingMTZfileName"], - ) - ) or os.path.isfile( - os.path.join(db_dict["DataProcessingPathToMTZfile"]) - ): - job_list = self.get_job_list_for_dimple_rerun( - xtal, job_list, db_dict, entry - ) - except KeyError: - try: - if os.path.isfile( - os.path.join(db_dict["DataProcessingPathToMTZfile"]) - ): - job_list = self.get_job_list_for_dimple_rerun( - xtal, job_list, db_dict, entry - ) - except KeyError: - continue - if job_list: - self.update_log.insert("trying to run DIMPLE on ALL auto-processing files") - self.check_before_running_dimple(job_list) - def run_dimple_on_selected_autoprocessing_file(self, instruction): job_list = [] for xtal in sorted(self.initial_model_dimple_dict): @@ -4047,80 +3906,6 @@ def update_reprocessing_table(self): cell_text.setBackground(QtGui.QColor(255, 255, 255)) self.datasets_reprocess_table.setItem(row, 7, cell_text) - def get_job_list_for_dimple_rerun(self, xtal, job_list, db_dict, entry): - self.status_bar.showMessage( - "checking: " - + str( - os.path.join( - db_dict["DataProcessingPathToMTZfile"], - db_dict["DataProcessingMTZfileName"], - ) - ) - ) - suitable_reference = [] - for reference in self.reference_file_list: - # first we need one in the same pointgroup - if reference[5] == db_dict["DataProcessingPointGroup"]: - try: - difference = math.fabs( - 1 - - ( - float(db_dict["DataProcessingUnitCellVolume"]) - / float(reference[4]) - ) - ) - suitable_reference.append([reference[0], difference]) - except ValueError: - continue - if suitable_reference: - reference_file = min(suitable_reference, key=lambda x: x[1])[0] - visit = entry[1] - run = entry[2] - autoproc = entry[4] - - reference_file_pdb = os.path.join( - self.reference_directory, reference_file + ".pdb" - ) - - if os.path.isfile( - os.path.join(self.reference_directory, reference_file + ".mtz") - ): - reference_file_mtz = " -R " + os.path.join( - self.reference_directory, reference_file + ".mtz" - ) - else: - reference_file_mtz = "" - - if os.path.isfile( - os.path.join(self.reference_directory, reference_file + ".cif") - ): - reference_file_cif = " --libin " + os.path.join( - self.reference_directory, reference_file + ".cif" - ) - else: - reference_file_cif = "" - - if os.path.isfile( - os.path.join(self.initial_model_directory, xtal, xtal + ".mtz") - ): - mtzin = os.path.join(self.initial_model_directory, xtal, xtal + ".mtz") - - self.update_log.insert( - "adding " + xtal + visit + "-" + run + autoproc + " to list" - ) - job_list.append( - [ - xtal, - visit + "-" + run + autoproc, - mtzin, - reference_file_pdb, - reference_file_mtz, - reference_file_cif, - ] - ) - self.status_bar.showMessage("idle") - return job_list - def check_before_running_dimple(self, job_list, instruction): msgBox = QtGui.QMessageBox() @@ -4629,129 +4414,6 @@ def prepare_and_run_task(self, instruction): elif instruction == "Update Deposition Table": self.update_deposition_table() - def check_status_create_png_of_soaked_compound(self): - number_of_samples = 0 - running = 0 - timestamp_list = [] - cif_file_generated = 0 - for folder in glob.glob( - os.path.join(self.initial_model_directory, "*", "compound") - ): - number_of_samples += 1 - if os.path.isfile(os.path.join(folder, "RESTRAINTS_IN_PROGRESS")): - running += 1 - timestamp = datetime.fromtimestamp( - os.path.getmtime(os.path.join(folder, "RESTRAINTS_IN_PROGRESS")) - ).strftime("%Y-%m-%d %H:%M:%S") - timestamp_list.append(timestamp) - for cif_file in glob.glob(os.path.join(folder, "*.cif")): - if os.path.isfile(cif_file): - cif_file_generated += 1 - if timestamp_list: - last_timestamp = max(timestamp_list) - else: - last_timestamp = "n/a" - message = ( - "Datasets: " - + str(number_of_samples) - + ", jobs running: " - + str(running) - + ", jobs finished: " - + str(cif_file_generated) - + ", last job submmitted: " - + str(last_timestamp) - ) - self.status_bar.showMessage(message) - - if start_thread: - if self.target == "=== SELECT TARGET ===": - msgBox = QtGui.QMessageBox() - warning = ( - "*** WARNING ***\n" - "You did not select a target!\n" - "In this case we will only parse the project directory!\n" - "Please note that this option is usually only useful in case you" - " reprocessed your data.\n" - "Do you want to continue?" - ) - msgBox.setText(warning) - msgBox.addButton(QtGui.QPushButton("Yes"), QtGui.QMessageBox.YesRole) - msgBox.addButton(QtGui.QPushButton("No"), QtGui.QMessageBox.RejectRole) - reply = msgBox.exec_() - if reply == 0: - start_thread = True - else: - start_thread = False - else: - start_thread = True - - if start_thread: - self.work_thread = XChemThread.read_autoprocessing_results_from_disc( - self.visit_list, - self.target, - self.reference_file_list, - self.database_directory, - self.data_collection_dict, - self.preferences, - self.datasets_summary_file, - self.initial_model_directory, - rescore_only, - self.acceptable_low_resolution_limit_for_data, - os.path.join(self.database_directory, self.data_source_file), - self.xce_logfile, - ) - self.explorer_active = 1 - self.connect( - self.work_thread, - QtCore.SIGNAL("update_progress_bar"), - self.update_progress_bar, - ) - self.connect( - self.work_thread, - QtCore.SIGNAL("update_status_bar(QString)"), - self.update_status_bar, - ) - self.connect( - self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished - ) - self.connect( - self.work_thread, - QtCore.SIGNAL("create_widgets_for_autoprocessing_results_only"), - self.create_widgets_for_autoprocessing_results_only, - ) - self.work_thread.start() - - def save_files_to_initial_model_folder(self): - self.work_thread = XChemThread.save_autoprocessing_results_to_disc( - self.dataset_outcome_dict, - self.data_collection_table_dict, - self.data_collection_column_three_dict, - self.data_collection_dict, - self.database_directory, - self.data_source_file, - self.initial_model_directory, - self.preferences, - self.datasets_summary_file, - ) - self.explorer_active = 1 - self.connect( - self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished - ) - self.connect( - self.work_thread, - QtCore.SIGNAL("update_progress_bar"), - self.update_progress_bar, - ) - self.connect( - self.work_thread, - QtCore.SIGNAL("update_status_bar(QString)"), - self.update_status_bar, - ) - self.connect( - self.work_thread, QtCore.SIGNAL("finished()"), self.thread_finished - ) - self.work_thread.start() - def run_pandda_analyse(self, run): pandda_params = { "data_dir": str(self.pandda_input_data_dir_entry.text()), @@ -5385,12 +5047,6 @@ def update_deposition_table(self): for xtal in toDeposit: self.db.update_insert_depositTable(xtal, {}) - def show_html_summary_and_diffraction_image(self): - for key in self.albula_button_dict: - if self.albula_button_dict[key][0] == self.sender(): - print("==> XCE: showing html summary in firefox") - self.show_html_summary_in_firefox(key) - def need_to_switch_main_tab(self, task_index): msgBox = QtGui.QMessageBox() msgBox.setText("Need to switch main tab before you can launch this job") @@ -5792,11 +5448,6 @@ def preferences_selection_mechanism_combobox_changed(self, i): self.preferences["dataset_selection_mechanism"] = text self.update_log.insert("setting datasets selection mechanism to " + text) - def preferences_initial_refinement_combobox_changed(self, i): - text = str(self.preferences_initial_refinement_combobox.currentText()) - self.preferences["initial_refinement_pipeline"] = text - self.update_log.insert("setting initial refinement pipeline to " + text) - def preferences_restraints_generation_combobox_changed(self): text = str(self.preferences_restraints_generation_combobox.currentText()) self.restraints_program = text @@ -5906,36 +5557,6 @@ def set_run_dimple_flag(self, state): for key in self.initial_model_dimple_dict: self.initial_model_dimple_dict[key][0].setChecked(False) - def show_data_collection_details(self, state): - # first remove currently displayed widget - if self.data_collection_details_currently_on_display is not None: - self.data_collection_details_currently_on_display.hide() - self.data_collection_details_currently_on_display = None - - tmp = [] - allRows = self.datasets_summary_table.rowCount() - for table_row in range(allRows): - tmp.append( - [self.datasets_summary_table.item(table_row, 0).text(), table_row] - ) - - for key in self.datasets_summary_dict: - if self.datasets_summary_dict[key][3] == self.sender(): - if self.sender().isChecked(): - for item in tmp: - if item[0] == key: - self.datasets_summary_table.selectRow(item[1]) - self.data_collection_details_currently_on_display = ( - self.data_collection_column_three_dict[key][0] - ) - self.datasets_summarys_vbox_for_details.addWidget( - self.data_collection_details_currently_on_display - ) - self.data_collection_details_currently_on_display.show() - else: - # un-check all other ones - self.datasets_summary_dict[key][3].setChecked(False) - #################################################################################### # # @@ -6222,14 +5843,6 @@ def select_different_autoprocessing_result(self): # < end #################################################################################### - def update_outcome_datasets_summary_table(self, sample, outcome): - rows_in_table = self.datasets_summary_table.rowCount() - for row in range(rows_in_table): - if self.datasets_summary_table.item(row, 0).text() == sample: - cell_text = QtGui.QTableWidgetItem() - cell_text.setText(outcome) - self.datasets_summary_table.setItem(row, 3, cell_text) - def user_update_selected_autoproc_datasets_summary_table(self): for key in self.data_collection_column_three_dict: if self.data_collection_column_three_dict[key][0] == self.sender(): @@ -6348,58 +5961,6 @@ def user_update_selected_autoproc_datasets_summary_table(self): except KeyError: pass - def update_selected_autoproc_datasets_summary_table(self): - for key in self.data_collection_column_three_dict: - if self.data_collection_column_three_dict[key][0] == self.sender(): - sample = key - break - indexes = self.sender().selectionModel().selectedRows() - for index in sorted(indexes): - selected_processing_result = index.row() - - for n, entry in enumerate(self.data_collection_dict[sample]): - if entry[0] == "logfile": - if entry[7] == selected_processing_result: - db_dict = entry[6] - program = db_dict["DataProcessingProgram"] - visit = db_dict["DataCollectionVisit"] - run = db_dict["DataCollectionRun"] - self.update_log.insert( - "user changed data processing files for {0!s} to visit={1!s}," - " run={2!s}, program={3!s}".format(sample, visit, run, program) - ) - # update datasource - self.update_log.insert("updating datasource...") - self.update_data_source(sample, db_dict) - entry[8] = True - else: - entry[8] = False - self.data_collection_dict[sample][n] = entry - - # update 'Datasets' table - column_name = XChemDB.data_source( - os.path.join(self.database_directory, self.data_source_file) - ).translate_xce_column_list_to_sqlite(self.datasets_summary_table_columns) - rows_in_table = self.datasets_summary_table.rowCount() - for row in range(rows_in_table): - if self.datasets_summary_table.item(row, 0).text() == sample: - for column, header in enumerate(column_name): - if header[0] == "Sample ID": - continue - elif header[0] == "DataCollection\nOutcome": - continue - elif header[0].startswith("img"): - continue - elif header[0].startswith("Show"): - continue - else: - cell_text = QtGui.QTableWidgetItem() - cell_text.setText(str(db_dict[header[1]])) - cell_text.setTextAlignment( - QtCore.Qt.AlignCenter | QtCore.Qt.AlignCenter - ) - self.datasets_summary_table.setItem(row, column, cell_text) - def populate_and_update_datasource_table(self): self.overview_datasource_table.setColumnCount( len(self.overview_datasource_table_columns) @@ -6699,17 +6260,6 @@ def get_columns_to_show(self, column_list): break return columns_to_show - def get_rows_with_sample_id_not_null_from_datasource(self): - sample_id_column = self.get_columns_to_show(["Sample ID"]) - n_rows = 0 - for row in self.data: - if ( - not str(row[sample_id_column[0]]).lower() != "none" - or not str(row[sample_id_column[0]]).replace(" ", "") == "" - ): - n_rows += 1 - return n_rows - def update_data_source(self, sample, db_dict): data_source = XChemDB.data_source( os.path.join(self.database_directory, self.data_source_file) diff --git a/xce/helpers/make_ligand_links_after_pandda.py b/xce/helpers/make_ligand_links_after_pandda.py index 1e44953d..dd748c56 100755 --- a/xce/helpers/make_ligand_links_after_pandda.py +++ b/xce/helpers/make_ligand_links_after_pandda.py @@ -1,27 +1,9 @@ -import os -import glob import sys # projectDir='/dls/labxchem/data/2017/lb13385-109/processing/analysis/initial_model_cov' # panddaDir='/dls/labxchem/data/2017/lb13385-109/processing/analysis/panddas_cov' -def make_links(projectDir, panddaDir): - os.chdir(os.path.join(panddaDir, "processed_datasets")) - for xtal in glob.glob("*"): - # for cif in glob.glob(os.path.join(xtal,'ligand_files','*.cif')): - # print cif - # os.system('/bin/rm %s' %cif) - # for pdb in glob.glob(os.path.join(xtal,'ligand_files','*.pdb')): - # print pdb - # os.system('/bin/rm %s' %pdb) - - for pdb in glob.glob(os.path.join(projectDir, xtal, "compound", "*.pdb")): - os.system("ln -s %s %s/ligand_files" % (pdb, xtal)) - for cif in glob.glob(os.path.join(projectDir, xtal, "compound", "*.cif")): - os.system("ln -s %s %s/ligand_files" % (cif, xtal)) - - if __name__ == "__main__": projectDir = sys.argv[1] panddaDir = sys.argv[2] diff --git a/xce/lib/XChemCoot.py b/xce/lib/XChemCoot.py index 74543f39..e5fde136 100755 --- a/xce/lib/XChemCoot.py +++ b/xce/lib/XChemCoot.py @@ -827,18 +827,6 @@ def update_RefinementOutcome_radiobutton(self): button.set_active(True) break - def update_label_radiobutton(self): - found = False - for button in self.label_button_list: - if button.get_label() == self.label: - button.set_active(True) - found = True - if not found: - for button in self.label_button_list: - if button.get_label() == "not_shown": - button.set_active(True) - break - def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 diff --git a/xce/lib/XChemCootReference.py b/xce/lib/XChemCootReference.py index 381af2d8..687279e2 100755 --- a/xce/lib/XChemCootReference.py +++ b/xce/lib/XChemCootReference.py @@ -843,51 +843,6 @@ def update_plot(self, refinement_cycle, Rfree, Rcryst): ) return fig - def get_ground_state_maps_by_resolution(self): - found = False - mapList = [] - for logFile in glob.glob( - os.path.join( - self.reference_directory, - str(self.cb_select_mean_map.get_active_text()), - "logs", - "*.log", - ) - ): - for n, line in enumerate(open(logFile)): - if ( - line.startswith("Statistical Electron Density Characterisation") - and len(line.split()) == 6 - ): - # try: - # resolution=float(line.split()[5]) - resolution = line.split()[5] - print(resolution) - found = True - foundLine = n - # except ValueError: - # print 'error' - # break - if found and n == foundLine + 3: - xtal = line.split(",")[0].replace(" ", "").replace("\t", "") - meanmap = os.path.join( - self.reference_directory, - self.cb_select_mean_map.get_active_text(), - "processed_datasets", - xtal, - xtal + "-ground-state-mean-map.native.ccp4", - ) - mapList.append([resolution, meanmap]) - found = False - return mapList - - def get_highest_reso_ground_state_map(self): - mapList = self.get_ground_state_maps_by_resolution() - print(mapList) - self.ground_state_map_List = [] - self.ground_state_map_List.append(min(mapList, key=lambda x: x[0])) - return self.ground_state_map_List - if __name__ == "__main__": GUI().StartGUI() diff --git a/xce/lib/XChemDB.py b/xce/lib/XChemDB.py index c081f05d..6ee9e3d2 100755 --- a/xce/lib/XChemDB.py +++ b/xce/lib/XChemDB.py @@ -919,31 +919,6 @@ def get_deposit_dict_for_sample(self, sampleID): pass return db_dict - def get_zenodo_dict_for_pandda_analysis(self, panddaPath): - db_dict = {} - header = [] - data = [] - # creates sqlite file if non existent - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - try: - cursor.execute( - "select * from zenodoTable where DimplePANDDApath='{0!s}';".format( - panddaPath - ) - ) - for column in cursor.description: - header.append(column[0]) - data = cursor.fetchall() - try: - for n, item in enumerate(data[0]): - db_dict[header[n]] = str(item) - except IndexError: - pass - except sqlite3.OperationalError: - db_dict = {} - return db_dict - def get_db_pandda_dict_for_sample_and_site(self, sampleID, site_index): db_dict = {} header = [] @@ -1257,75 +1232,6 @@ def update_insert_data_source(self, sampleID, data_dict): ) connect.commit() - def update_insert_panddaTable(self, sampleID, data_dict): - data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict["LastUpdated_by"] = getpass.getuser() - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - cursor.execute("Select CrystalName,PANDDA_site_index FROM panddaTable") - # available_columns=[] - # cursor.execute("SELECT * FROM panddaTable") - # for column in cursor.description: # only update existing columns in data source - # available_columns.append(column[0]) - samples_sites_in_table = [] - tmp = cursor.fetchall() - for item in tmp: - line = [x.encode("UTF8") for x in list(item)] - samples_sites_in_table.append(line) - - found_sample_site = False - for entry in samples_sites_in_table: - if entry[0] == sampleID and entry[1] == data_dict["PANDDA_site_index"]: - found_sample_site = True - - if found_sample_site: - for key in data_dict: - value = data_dict[key] - if key == "ID" or key == "CrystalName" or key == "PANDDA_site_index": - continue - if not str(value).replace(" ", "") == "": # ignore empty fields - update_string = str(key) + "=" + "'" + str(value) + "'" - # print "UPDATE panddaTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and PANDDA_site_index is '"+data_dict['PANDDA_site_index']+"';" - cursor.execute( - "UPDATE panddaTable SET " - + update_string - + " WHERE CrystalName=" - + "'" - + sampleID - + "' and PANDDA_site_index is '" - + data_dict["PANDDA_site_index"] - + "';" - ) - else: - column_string = "" - value_string = "" - for key in data_dict: - value = data_dict[key] - if key == "ID": - continue - # if key not in available_columns: - # continue - if ( - not str(value).replace(" ", "") == "" - ): # ignore if nothing in csv field - value_string += "'" + str(value) + "'" + "," - column_string += key + "," - print( - "INSERT INTO panddaTable (" - + column_string[:-1] - + ") VALUES (" - + value_string[:-1] - + ");" - ) - cursor.execute( - "INSERT INTO panddaTable (" - + column_string[:-1] - + ") VALUES (" - + value_string[:-1] - + ");" - ) - connect.commit() - def update_insert_any_table(self, table, data_dict, condition_dict): data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) data_dict["LastUpdated_by"] = getpass.getuser() @@ -1540,72 +1446,6 @@ def update_insert_depositTable(self, sampleID, data_dict): ) connect.commit() - def update_insert_not_null_fields_only(self, sampleID, data_dict): - data_dict["LastUpdated"] = str(datetime.now().strftime("%Y-%m-%d %H:%M")) - data_dict["LastUpdated_by"] = getpass.getuser() - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - cursor.execute("Select CrystalName FROM mainTable") - available_columns = [] - cursor.execute("SELECT * FROM mainTable") - for column in cursor.description: # only update existing columns in data source - available_columns.append(column[0]) - if self.check_if_sample_exists_in_data_source(sampleID): - for key in data_dict: - value = data_dict[key] - # print value - if key == "ID" or key == "CrystalName": - continue - if not str(value).replace(" ", "") == "": # ignore empty fields - update_string = str(key) + "=" + "'" + str(value) + "'" - # cursor.execute("UPDATE mainTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and "+str(key)+" is null;") - cursor.execute( - "UPDATE mainTable SET " - + update_string - + " WHERE CrystalName=" - + "'" - + sampleID - + "' and (" - + str(key) - + " is null or " - + str(key) - + "='');" - ) - else: - column_string = "CrystalName" + "," - value_string = "'" + sampleID + "'" + "," - for key in data_dict: - value = data_dict[key] - if key == "ID": - continue - if key not in available_columns: - continue - if ( - not str(value).replace(" ", "") == "" - ): # ignore if nothing in csv field - value_string += "'" + str(value) + "'" + "," - column_string += key + "," - cursor.execute( - "INSERT INTO mainTable (" - + column_string[:-1] - + ") VALUES (" - + value_string[:-1] - + ");" - ) - connect.commit() - - def get_value_from_field(self, sampleID, column): - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - cursor.execute( - "SELECT " - + column - + " FROM mainTable WHERE CrystalName='" - + sampleID - + "';" - ) - return cursor.fetchone() - def export_to_csv_file(self, csv_file): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() @@ -1701,119 +1541,6 @@ def load_samples_from_data_source(self): # # return sample_list_for_coot - def get_pandda_info_for_coot(self, xtalID, pandda_site): - pandda_info_for_coot = [] - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - - sqlite = ( - "select" - " PANDDA_site_event_map," - " PANDDA_site_x," - " PANDDA_site_y," - " PANDDA_site_z," - " PANDDA_site_spider_plot " - "from panddaTable " - "where " - " CrystalName is '%s'" % xtalID - + " and PANDDA_site_index is '{0!s}';".format(pandda_site) - ) - - cursor.execute(sqlite) - - tmp = cursor.fetchall() - for item in tmp: - tmpx = [] - for i in list(item): - if i is None: - tmpx.append("None") - else: - tmpx.append(i) - line = [x.encode("UTF8") for x in tmpx] - pandda_info_for_coot.append(line) - - return pandda_info_for_coot - - def get_todo_list_for_coot(self, RefinementOutcome, pandda_site): - sample_list_for_coot = [] - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - - if RefinementOutcome == "0 - All Datasets": - outcome = " not null " - else: - outcome = " '{0!s}' ".format(RefinementOutcome) - - if int(pandda_site) > 0: - # sqlite = ( - # "select" - # " mainTable.CrystalName," - # " mainTable.CompoundCode," - # " mainTable.RefinementCIF," - # " mainTable.RefinementMTZfree," - # " mainTable.RefinementPathToRefinementFolder," - # " panddaTable.RefinementOutcome, " - # " panddaTable.PANDDA_site_confidence " - # "from mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " - # "where panddaTable.PANDDA_site_index is '%s'" %pandda_site+ - # " and panddaTable.PANDDA_site_ligand_placed is 'True'" - # " and panddaTable.RefinementOutcome is %s;" %outcome - # ) - sqlite = ( - "select" - " mainTable.CrystalName," - " mainTable.CompoundCode," - " mainTable.RefinementCIF," - " mainTable.RefinementMTZfree," - " mainTable.RefinementPathToRefinementFolder," - " panddaTable.RefinementOutcome, " - " panddaTable.PANDDA_site_confidence " - "from mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " - "where panddaTable.PANDDA_site_index is '%s'" % pandda_site - + " and panddaTable.PANDDA_site_ligand_placed is 'True'" - " and panddaTable.RefinementOutcome like " + outcome.split()[0] + "%';" - ) - # sqlite = ( - # "select" - # " mainTable.CrystalName," - # " mainTable.CompoundCode," - # " mainTable.RefinementCIF," - # " mainTable.RefinementMTZfree," - # " mainTable.RefinementPathToRefinementFolder," - # " panddaTable.RefinementOutcome, " - # " panddaTable.PANDDA_site_confidence " - # "from mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " - # "where panddaTable.PANDDA_site_index is '%s'" %pandda_site+ - # " and panddaTable.RefinementOutcome like "+outcome.split()[0]+"%';" - # ) - else: - sqlite = ( - "select" - " CrystalName," - " CompoundCode," - " RefinementCIF," - " RefinementMTZfree," - " RefinementPathToRefinementFolder," - " RefinementOutcome," - " RefinementLigandConfidence " - "from mainTable " - "where RefinementOutcome is %s and DimpleRfree is not Null;" % outcome - ) - cursor.execute(sqlite) - - tmp = cursor.fetchall() - for item in tmp: - tmpx = [] - for i in list(item): - if i is None: - tmpx.append("None") - else: - tmpx.append(i) - line = [x.encode("UTF8") for x in tmpx] - sample_list_for_coot.append(line) - - return sample_list_for_coot - def get_todoList_for_coot(self, RefinementOutcome): sample_list_for_coot = [] connect = sqlite3.connect(self.data_source_file) @@ -2012,146 +1739,6 @@ def export_csv_for_WONKA(self): csvWriter = csv.writer(open("for_wonka.csv", "w")) csvWriter.writerows([header] + rows) - def create_missing_apo_records_in_depositTable(self, xce_logfile): - Logfile = XChemLog.updateLog(xce_logfile) - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - cursor.execute( - "select panddaTable.ApoStructures from panddaTable where panddaTable.ApoStructures is not Null" - ) - tmp = cursor.fetchall() - # print str(tmp) - apoStructureList = [] - for item in tmp: - for xtal in str(item[0]).split(";"): - if xtal not in apoStructureList: - apoStructureList.append(xtal) - if not apoStructureList: - Logfile.insert("no apo structures were assigned to your pandda models") - else: - Logfile.insert( - "the following datasets were at some point used as apo structures for pandda.analyse: " - + str(apoStructureList) - ) - apoInDB = [] - cursor.execute( - "select CrystalName from depositTable where StructureType is 'apo'" - ) - tmp = cursor.fetchall() - for xtal in tmp: - Logfile.insert( - str(xtal[0]) + " exists as entry for apo structure in database" - ) - apoInDB.append(str(xtal[0])) - newEntries = "" - for xtal in apoStructureList: - if xtal not in apoInDB: - Logfile.insert("no entry for " + xtal + " in depositTable") - newEntries += "('{0!s}','apo'),".format(xtal) - if newEntries != "": - sqlite = "insert into depositTable (CrystalName,StructureType) values {0!s};".format( - newEntries[:-1] - ) - Logfile.insert( - "creating new entries with the following SQLite command:\n" + sqlite - ) - cursor.execute(sqlite) - connect.commit() - - def create_missing_apo_records_for_all_structures_in_depositTable( - self, projectDir, xce_logfile - ): - Logfile = XChemLog.updateLog(xce_logfile) - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - cursor.execute( - "select CrystalName from depositTable where StructureType is 'apo'" - ) - tmp = cursor.fetchall() - # print str(tmp) - apoStructureList = [] - for item in tmp: - apoStructureList.append(str(item[0])) - - counter = 0 # there is a SQLite limit which does not allow to insert more than 500 records at once - newEntries = "" - for files in glob.glob(os.path.join(projectDir, "*")): - xtal = files[files.rfind("/") + 1 :] - if xtal not in apoStructureList: - dimple_pdb = False - dimple_mtz = False - aimless_log = False - if os.path.isfile(os.path.join(files, "dimple.pdb")): - dimple_pdb = True - if os.path.isfile(os.path.join(files, "dimple.mtz")): - dimple_mtz = True - if os.path.isfile(os.path.join(files, xtal + ".log")) or os.path.isfile( - os.path.join("aimless.log") - ): - aimless_log = True - - if dimple_mtz == False or dimple_pdb == False or aimless_log == False: - Logfile.insert( - "{0!s}: missing files -> dimple.pdb: {1!s}, dimple.mtz: {2!s}, {3!s}.log: {4!s}".format( - xtal, - str(dimple_pdb), - str(dimple_mtz), - xtal, - str(aimless_log), - ) - ) - else: - newEntries += "('{0!s}','apo'),".format(xtal) - counter += 1 - - if counter == 450: # set to 450 to stay well below 500 records limit - sqlite = "insert into depositTable (CrystalName,StructureType) values {0!s};".format( - newEntries[:-1] - ) - Logfile.insert( - "creating new entries with the following SQLite command:\n" - + sqlite - ) - cursor.execute(sqlite) - connect.commit() - counter = 0 - newEntries = "" - - if newEntries != "": - sqlite = "insert into depositTable (CrystalName,StructureType) values {0!s};".format( - newEntries[:-1] - ) - Logfile.insert( - "creating new entries with the following SQLite command:\n" + sqlite - ) - cursor.execute(sqlite) - connect.commit() - else: - Logfile.insert("did not find any new apo structures") - - # if apoStructureList==[]: - # Logfile.insert('no apo structures were assigned to your pandda models') - # else: - # Logfile.insert('the following datasets were at some point used as apo structures for pandda.analyse: '+str(apoStructureList)) - # apoInDB=[] - # cursor.execute("select CrystalName from depositTable where StructureType is 'apo'") - # tmp = cursor.fetchall() - # for xtal in tmp: - # Logfile.insert(str(xtal[0])+' exists as entry for apo structure in database') - # apoInDB.append(str(xtal[0])) - # newEntries='' - # for xtal in apoStructureList: - # if xtal not in apoInDB: - # Logfile.insert('no entry for '+xtal+' in depositTable') - # newEntries+="('%s','apo')," %xtal - # if newEntries != '': - # sqlite='insert into depositTable (CrystalName,StructureType) values %s;' %newEntries[:-1] - # Logfile.insert('creating new entries with the following SQLite command:\n'+sqlite) - # cursor.execute(sqlite) - # connect.commit() - - # def get_deposit_dict_for_xtal(self,sampleID,structure_type): - def create_or_remove_missing_records_in_depositTable( self, xce_logfile, xtal, type, db_dict ): @@ -2256,54 +1843,6 @@ def create_or_remove_missing_records_in_depositTable( cursor.execute(sqlite) connect.commit() - def remove_selected_apo_structures_from_depositTable(self, xce_logfile, xtalList): - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - - Logfile = XChemLog.updateLog(xce_logfile) - - Logfile.insert("removing the following apo structures from depositTable") - deleteStrg = "(" - for xtal in xtalList: - Logfile.insert(xtal) - deleteStrg += "Crystalname is '" + xtal + "' or " - deleteStrg = deleteStrg[:-4] + ")" - - sqlite = ( - "delete from depositTable where {0!s} and StructureType is 'apo'".format( - deleteStrg - ) - ) - Logfile.insert("executing the following SQLite command:\n" + sqlite) - cursor.execute(sqlite) - connect.commit() - - # for item in tmp: - # print item - # for xtal in str(item[0]).split(';'): - # if xtal not in apoStructureList: apoStructureList.append(xtal) - # if apoStructureList==[]: - # Logfile.insert('no apo structures were assigned to your pandda models') - # else: - # Logfile.insert('the following datasets were at some point used as apo structures for pandda.analyse: '+str(apoStructureList)) - # apoInDB=[] - # cursor.execute("select CrystalName from depositTable where StructureType is 'apo'") - # tmp = cursor.fetchall() - # for xtal in tmp: - # Logfile.insert(str(xtal[0])+' exists as entry for apo structure in database') - # apoInDB.append(str(xtal[0])) - # newEntries='' - # for xtal in apoStructureList: - # if xtal not in apoInDB: - # Logfile.insert('no entry for '+xtal+' in depositTable') - # newEntries+="('%s','apo')," %xtal - # if newEntries != '': - # sqlite='insert into depositTable (CrystalName,StructureType) values %s;' %newEntries[:-1] - # Logfile.insert('creating new entries with the following SQLite command:\n'+sqlite) - # cursor.execute(sqlite) - # connect.commit() - # - def collected_xtals_during_visit(self, visitID): # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) @@ -2364,57 +1903,6 @@ def autoprocessing_result_user_assigned(self, sample): return userassigned - def all_results_of_xtals_collected_during_visit_as_dict(self, visitID): - # first get all collected xtals as list - collectedXtals = self.collected_xtals_during_visit(visitID) - xtalDict = {} - # creates sqlite file if non existent - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - for xtal in sorted(collectedXtals): - if xtal not in xtalDict: - xtalDict[xtal] = [] - sqlite = ( - "select DataCollectionVisit," - " DataCollectionRun," - " DataProcessingProgram," - " DataCollectionDate," - " DataProcessingResolutionHigh," - " DataProcessingRmergeLow," - " DataCollectionCrystalImage1," - " DataCollectionCrystalImage2," - " DataCollectionCrystalImage3," - " DataCollectionCrystalImage4 " - "from collectionTable " - "where CrystalName = '%s'" % xtal - ) - # print sqlite - cursor.execute(sqlite) - sq = cursor.fetchall() - # print sq - for s in sq: - # print s - t = [ - str(s[0]), - str(s[1]), - str(s[2]), - str(s[3]), - str(s[4]), - str(s[5]), - str(s[6]), - str(s[7]), - str(s[8]), - str(s[9]), - ] - inDict = False - for entry in xtalDict[xtal]: - if t[0] == entry[0] and t[1] == entry[1] and t[2] == entry[2]: - inDict = True - break - if not inDict: - xtalDict[xtal].append(t) - return xtalDict - def all_autoprocessing_results_for_xtal_as_dict(self, xtal): dbList = [] header = [] @@ -2434,47 +1922,6 @@ def all_autoprocessing_results_for_xtal_as_dict(self, xtal): dbList.append(db_dict) return dbList - def get_db_list_for_sample_in_panddaTable(self, xtal): - dbList = [] - header = [] - # creates sqlite file if non existent - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - cursor.execute( - "select * from panddaTable where CrystalName='{0!s}';".format(xtal) - ) - for column in cursor.description: - header.append(column[0]) - data = cursor.fetchall() - for result in data: - db_dict = {} - for n, item in enumerate(result): - db_dict[header[n]] = str(item) - dbList.append(db_dict) - return dbList - - def get_db_dict_for_visit_run_autoproc(self, xtal, visit, run, autoproc): - db_dict = {} - header = [] - # creates sqlite file if non existent - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - sqlite = ( - "select * " - "from collectionTable " - "where CrystalName ='%s' and" % xtal - + " DataCollectionVisit = '%s' and" % visit - + " DataCollectionRun = '%s' and" % run - + " DataProcessingProgram = '%s'" % autoproc - ) - cursor.execute(sqlite) - for column in cursor.description: - header.append(column[0]) - data = cursor.fetchall() - for n, item in enumerate(data[0]): - db_dict[header[n]] = str(item) - return db_dict - def get_db_dict_for_visit_run_autoproc_score( self, xtal, visit, run, autoproc, score ): @@ -2521,28 +1968,6 @@ def xtals_collected_during_visit_as_dict(self, visitID): xtalDict[xtal] = db_dict return xtalDict - def getCrystalImageDict(self, visit, xtalList): - # creates sqlite file if non existent - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - imageDict = {} - for xtal in xtalList: - sqlite = ( - "select CrystalName," - " min(DataCollectionDate)," - " DataCollectionCrystalImage1," - " DataCollectionCrystalImage2," - " DataCollectionCrystalImage3," - " DataCollectionCrystalImage4 " - "from collectionTable " - "where DataCollectionVisit = '%s'" % visit - + " and CrystalName = '%s'" % xtal - ) - cursor.execute(sqlite) - img = cursor.fetchall() - imageDict[xtal] = [str(img[1]), str(img[2]), str(img[3]), str(img[4])] - return imageDict - def samples_for_html_summary(self, whichSamples): # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) @@ -2568,32 +1993,6 @@ def samples_for_html_summary(self, whichSamples): xtalList.append(str(sample[0])) return xtalList - def get_event_map_for_ligand(self, xtal, ligChain, ligNumber, ligName): - # creates sqlite file if non existent - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - - sql = ( - "select " - " PANDDA_site_event_map " - "from " - " panddaTable " - "where " - " CrystalName = '%s' and " % xtal - + " PANDDA_site_ligand_chain='%s' and " % ligChain - + " PANDDA_site_ligand_sequence_number='%s' and " % ligNumber - + " PANDDA_site_ligand_resname='%s'" % ligName - ) - - cursor.execute(sql) - - eventMap = "" - maps = cursor.fetchall() - for map in maps: - eventMap = map[0] - - return eventMap - def get_ligand_confidence_for_ligand(self, xtal, ligChain, ligNumber, ligName): # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) @@ -2620,17 +2019,6 @@ def get_ligand_confidence_for_ligand(self, xtal, ligChain, ligNumber, ligName): return ligConfidence - def get_labels_from_db(self): - # creates sqlite file if non existent - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() - cursor.execute("select Label from labelTable") - labels = cursor.fetchall() - labelList = [] - for l in labels: - labelList.append(l[0]) - return labelList - def get_label_info_from_db(self): # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) diff --git a/xce/lib/XChemDeposit.py b/xce/lib/XChemDeposit.py index 5c48d05c..85c4e1ad 100755 --- a/xce/lib/XChemDeposit.py +++ b/xce/lib/XChemDeposit.py @@ -12,40 +12,6 @@ from PyQt4 import QtCore - -def create_SF_mmcif(outDir, mtzList): - print("hallo") - - -def get_protein_sequence(database, xtalID): - print("hallo") - - -def check_depositDict(depositDict): - # check depositDict - for entry in depositDict: - if "middle_name" in depositDict[entry]: - continue - elif "State_or_Province" in depositDict[entry]: - continue - elif depositDict[entry] == "": - print("ERROR") - - -def update_title(depositDict): - - print("hallo") - - -def create_data_template_text(): - - data_template_text = data_template(depositDict, sequence) - - -def create_Model_mmcif(outDir, pdbList): - print("hallo") - - # def update_file_locations_of_apo_structuresin_DB(database,projectDir,xce_logfile): # Logfile=XChemLog.updateLog(xce_logfile) # Logfile.insert('updating file information for apo structures') @@ -651,16 +617,6 @@ def run(self): "======= finished preparing mmcif files for wwPDB deposition =======" ) - def ground_state_mmcif_exists(self): - mmcifStatus = False - for dirs in glob.glob(os.path.join(self.panddaDir, "processed_datasets", "*")): - xtal = dirs[dirs.rfind("/") + 1 :] - if os.path.isfile(os.path.join(dirs, xtal + "_sf.mmcif")): - self.Logfile.insert("%s: found mmcif file for apo structure" % xtal) - mmcifStatus = True - - return mmcifStatus - def data_template_dict_exists(self, xtal): dictStatus = False self.data_template_dict = None @@ -725,37 +681,6 @@ def db_dict_exists(self, xtal): dictStatus = True return dictStatus - def zenodo_dict_exists(self, xtal): - dictStatus = False - self.zenodo_dict = None - if self.ground_state: - self.zenodo_dict = self.db.get_zenodo_dict_for_pandda_analysis( - self.panddaDir - ) - else: - self.Logfile.insert( - "%s: reading information from zenodoTable for pandda run: %s" - % (xtal, self.db_dict["DimplePANDDApath"]) - ) - self.zenodo_dict = self.db.get_zenodo_dict_for_pandda_analysis( - self.db_dict["DimplePANDDApath"] - ) - if self.zenodo_dict == {}: - dictStatus = True - self.zenodo_dict["ZenodoDOI"] = "" - self.Logfile.warning( - "%s: cannot find information about zenodo deposition in zenodoTable!!!" - % xtal - ) - # self.Logfile.error('%s: cannot find information about zenodo deposition in zenodoTable; moving to next dataset...' %xtal) - # self.add_to_errorList(xtal) - else: - self.Logfile.insert( - "%s: found zenodo_dict dictionary in zenodoTable" % xtal - ) - dictStatus = True - return dictStatus - def mmcif_files_can_be_replaced(self, xtal): status = True if self.overwrite_existing_mmcif: diff --git a/xce/lib/XChemDialogs.py b/xce/lib/XChemDialogs.py index fdf58fe1..4938326d 100755 --- a/xce/lib/XChemDialogs.py +++ b/xce/lib/XChemDialogs.py @@ -42,18 +42,3 @@ def __init__(self, data_source_file, parent=None): buttons.accepted.connect(self.accept) buttons.rejected.connect(self.reject) layout.addWidget(buttons) - - def data_source_column_active(self): - columns_to_show = ["Sample ID"] - for key in self.column_dict: - if self.column_dict[key].isChecked(): - columns_to_show.append(self.columns_in_data_source[key][1]) - return columns_to_show - - # static method to create the dialog and return (date, time, accepted) - @staticmethod - def return_selected_columns(parent=None): - dialog = select_columns_to_show(parent) - result = dialog.exec_() - columns = dialog.data_source_column_active() - return (columns, result == QtGui.QDialog.Accepted) diff --git a/xce/lib/XChemLigand.py b/xce/lib/XChemLigand.py deleted file mode 100755 index b51aacf6..00000000 --- a/xce/lib/XChemLigand.py +++ /dev/null @@ -1,13 +0,0 @@ -from rdkit import Chem -from rdkit.Chem import AllChem - - -def generate_steroisomers(input_smiles): - """ - Function to generate all stereoisomers from a SMILES String. Only works on latest version of RDKit. - """ - mol = Chem.MolFromSmiles(input_smiles) - out_mols = AllChem.EnumerateStereoisomers( - mol, AllChem.StereoEnumerationOptions(onlyUnassigned=False, tryEmbedding=True) - ) - return [Chem.MolToSmiles(x, isomericSmiles=True) for x in out_mols] diff --git a/xce/lib/XChemMain.py b/xce/lib/XChemMain.py index 9d90327e..a41c698e 100755 --- a/xce/lib/XChemMain.py +++ b/xce/lib/XChemMain.py @@ -128,28 +128,6 @@ def get_target_and_visit_list(beamline_directory, agamemnon): return target_list, visit_list -def get_dewar_configuration(beamline_directory): - dewar_sample_configuration_dict = {} - # need to do it like this for now until we got a way to query ispyb - for xml in glob.glob( - os.path.join(beamline_directory, "xml", "exptTableParams-*.xml") - ): - prefix = "" - container_reference = "" - sample_location = "" - for line in open(xml): - if "prefix" in line: - prefix = line[line.find(">") + 1 : line.rfind("<")] - if "container_reference" in line: - container_reference = line[line.find(">") + 1 : line.rfind("<")] - if "sample_location" in line: - sample_location = line[line.find(">") + 1 : line.rfind("<")] - dewar_sample_configuration_dict[ - str(container_reference) + "-" + str(sample_location) - ] = prefix - return dewar_sample_configuration_dict - - def get_jobs_running_on_cluster(): out_dict = {} @@ -293,31 +271,6 @@ def print_cluster_status_message(program, cluster_dict, xce_logfile): Logfile.insert(out) -def display_queue_status_in_terminal(in_dict): - # latest_run=max(tmp,key=lambda x: x[1])[0] - max_dimple_runtime = max(in_dict["dimple"], key=lambda x: x[2])[2] - print( - "----------------------------------------------------------------------------" - ) - print( - "| Task | Nr. Jobs | Max. Runtime (minutes) |" - ) - print( - "----------------------------------------------------------------------------" - ) - print( - "{0:24} {1:24} {2:24} {3:1}".format( - "| DIMPLE", - "| {0!s}".format(len(in_dict["dimple"])), - "| %s" & max_dimple_runtime, - "|", - ) - ) - print( - "----------------------------------------------------------------------------" - ) - - def get_datasource_summary(db_file): db = XChemDB.data_source(db_file) @@ -506,10 +459,6 @@ def get_datasource_summary(db_file): return out_dict -def remove_all_refmac_jobs_from_cluster_and_reinstate_last_stable_state(): - print("hallo") - - def change_links_to_selected_data_collection_outcome( sample, data_collection_dict, @@ -608,92 +557,6 @@ def change_links_to_selected_data_collection_outcome( Logfile.insert("please copy data to PROJECT DIRECTORY first!") -def get_nr_files_from_gda_log_folder(beamline): - n = len(glob.glob(os.path.join("/dls_sw", beamline, "logs", "gda_server*"))) - return n - - -def get_dict_of_gda_barcodes(beamline): - out_dict = {} - for files in glob.glob(os.path.join("/dls_sw", beamline, "logs", "*")): - found_barcode_entry = False - gda_log = files[files.rfind("/") + 1 :] - if gda_log.startswith("gda_server.") and gda_log.endswith(".gz"): - with gzip.open(files, "r") as f: - print("parsing", files) - # for line in fin: - for line in f: - if "BART SampleChanger - getBarcode() returning" in line: - barcode = line.split()[len(line.split()) - 1] - found_barcode_entry = True - if found_barcode_entry: - if "Snapshots will be saved" in line: - sampleID = line.split()[len(line.split()) - 1].split("/")[ - -1 - ] - out_dict[sampleID] = barcode - found_barcode_entry = False - elif gda_log.startswith("gda_server.") and gda_log.endswith(".log"): - for line in files: - if "BART SampleChanger - getBarcode() returning" in line: - barcode = line.split()[len(line.split()) - 1] - found_barcode_entry = True - if found_barcode_entry: - if "Snapshots will be saved" in line: - sampleID = line.split()[len(line.split()) - 1].split("/")[-1] - out_dict[sampleID] = barcode - found_barcode_entry = False - - return out_dict - - -def append_dict_of_gda_barcodes(out_dict, files, xce_logfile): - Logfile = XChemLog.updateLog(xce_logfile) - found_barcode_entry = False - gda_log = files[files.rfind("/") + 1 :] - if ( - gda_log.startswith("gda_server.") - or gda_log.startswith("gda-server.") - and gda_log.endswith(".gz") - ): - with gzip.open(files, "r") as f: - for line in f: - if "BART SampleChanger - getBarcode() returning" in line: - barcode = line.split()[len(line.split()) - 1] - found_barcode_entry = True - if found_barcode_entry: - if "Snapshots will be saved" in line: - sampleID = line.split()[len(line.split()) - 1].split("/")[-1] - out_dict[sampleID] = barcode - Logfile.insert( - "found: sample={0!s}, barcode={1!s}, file={2!s}".format( - sampleID, barcode, files - ) - ) - found_barcode_entry = False - elif ( - gda_log.startswith("gda_server") - or gda_log.startswith("gda-server") - and gda_log.endswith("txt") - ): - for line in open(files): - if "BART SampleChanger - getBarcode() returning" in line: - barcode = line.split()[len(line.split()) - 1] - found_barcode_entry = True - if found_barcode_entry: - if "Snapshots will be saved" in line: - sampleID = line.split()[len(line.split()) - 1].split("/")[-1] - out_dict[sampleID] = barcode - Logfile.insert( - "found: sample={0!s}, barcode={1!s}, file={2!s}".format( - sampleID, barcode, files - ) - ) - found_barcode_entry = False - - return out_dict - - def get_gda_barcodes( sampleList, gzipped_logs_parsed, gda_log_start_line, beamline, xce_logfile ): diff --git a/xce/lib/XChemPANDDA.py b/xce/lib/XChemPANDDA.py index d69f4ecb..923864c5 100755 --- a/xce/lib/XChemPANDDA.py +++ b/xce/lib/XChemPANDDA.py @@ -1847,200 +1847,6 @@ def run(self): self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) -class check_if_pandda_can_run: - - # reasons why pandda cannot be run - # - there is currently a job running in the pandda directory - # - min datasets available is too low - # - required input paramters are not complete - # - map amplitude and phase labels don't exist - - def __init__(self, pandda_params, xce_logfile, datasource): - self.data_directory = pandda_params["data_dir"] - self.panddas_directory = pandda_params["out_dir"] - self.min_build_datasets = pandda_params["min_build_datasets"] - self.pdb_style = pandda_params["pdb_style"] - self.mtz_style = pandda_params["mtz_style"] - self.input_dir_structure = pandda_params["pandda_dir_structure"] - self.problem_found = False - self.error_code = -1 - self.Logfile = XChemLog.updateLog(xce_logfile) - self.db = XChemDB.data_source(datasource) - - def number_of_available_datasets(self): - counter = 0 - for file in glob.glob(os.path.join(self.input_dir_structure, self.pdb_style)): - if os.path.isfile(file): - counter += 1 - self.Logfile.insert( - "pandda.analyse: found {0!s} useable datasets".format(counter) - ) - return counter - - def get_first_dataset_in_project_directory(self): - first_dataset = "" - for file in glob.glob(os.path.join(self.input_dir_structure, self.pdb_style)): - if os.path.isfile(file): - first_dataset = file - break - return first_dataset - - def compare_number_of_atoms_in_reference_vs_all_datasets( - self, refData, dataset_list - ): - mismatched_datasets = [] - pdbtools = XChemUtils.pdbtools(refData) - refPDBlist = pdbtools.get_init_pdb_as_list() - n_atom_ref = len(refPDBlist) - for n_datasets, dataset in enumerate(dataset_list): - if os.path.isfile( - os.path.join( - self.data_directory.replace("*", ""), dataset, self.pdb_style - ) - ): - n_atom = len( - pdbtools.get_pdb_as_list( - os.path.join( - self.data_directory.replace("*", ""), - dataset, - self.pdb_style, - ) - ) - ) - if n_atom_ref == n_atom: - self.Logfile.insert( - "{0!s}: atoms in PDB file ({1!s}): {2!s};" - " atoms in Reference file: {3!s} ===> OK".format( - dataset, self.pdb_style, str(n_atom), str(n_atom_ref) - ) - ) - if n_atom_ref != n_atom: - self.Logfile.insert( - "{0!s}: atoms in PDB file ({1!s}): {2!s};" - " atoms in Reference file: {3!s} ===> ERROR".format( - dataset, self.pdb_style, str(n_atom), str(n_atom_ref) - ) - ) - mismatched_datasets.append(dataset) - return n_datasets, mismatched_datasets - - def get_datasets_which_fit_to_reference_file( - self, - ref, - reference_directory, - cluster_dict, - allowed_unitcell_difference_percent, - ): - refStructure = XChemUtils.pdbtools( - os.path.join(reference_directory, ref + ".pdb") - ) - symmRef = refStructure.get_spg_number_from_pdb() - ucVolRef = refStructure.calc_unitcell_volume_from_pdb() - cluster_dict[ref] = [] - cluster_dict[ref].append(os.path.join(reference_directory, ref + ".pdb")) - for dataset in glob.glob(os.path.join(self.data_directory, self.pdb_style)): - datasetStructure = XChemUtils.pdbtools(dataset) - symmDataset = datasetStructure.get_spg_number_from_pdb() - ucVolDataset = datasetStructure.calc_unitcell_volume_from_pdb() - - if symmDataset == symmRef: - try: - difference = ( - math.fabs(1 - (float(ucVolRef) / float(ucVolDataset))) * 100 - ) - if difference < allowed_unitcell_difference_percent: - sampleID = dataset.replace("/" + self.pdb_style, "")[ - dataset.replace("/" + self.pdb_style, "").rfind("/") + 1 : - ] - cluster_dict[ref].append(sampleID) - except ZeroDivisionError: - continue - return cluster_dict - - def remove_dimple_files(self, dataset_list): - for n_datasets, dataset in enumerate(dataset_list): - db_dict = {} - if os.path.isfile( - os.path.join( - self.data_directory.replace("*", ""), dataset, self.pdb_style - ) - ): - os.system( - "/bin/rm " - + os.path.join( - self.data_directory.replace("*", ""), dataset, self.pdb_style - ) - ) - self.Logfile.insert( - "{0!s}: removing {1!s}".format(dataset, self.pdb_style) - ) - db_dict["DimplePathToPDB"] = "" - db_dict["DimpleRcryst"] = "" - db_dict["DimpleRfree"] = "" - db_dict["DimpleResolutionHigh"] = "" - db_dict["DimpleStatus"] = "pending" - if os.path.isfile( - os.path.join( - self.data_directory.replace("*", ""), dataset, self.mtz_style - ) - ): - os.system( - "/bin/rm " - + os.path.join( - self.data_directory.replace("*", ""), dataset, self.mtz_style - ) - ) - self.Logfile.insert( - "{0!s}: removing {1!s}".format(dataset, self.mtz_style) - ) - db_dict["DimplePathToMTZ"] = "" - if db_dict != {}: - self.db.update_data_source(dataset, db_dict) - - def analyse_pdb_style(self): - pdb_found = False - for file in glob.glob(os.path.join(self.data_directory, self.pdb_style)): - if os.path.isfile(file): - pdb_found = True - break - if not pdb_found: - self.error_code = 1 - message = self.warning_messages() - return message - - def analyse_mtz_style(self): - mtz_found = False - for file in glob.glob(os.path.join(self.data_directory, self.mtz_style)): - if os.path.isfile(file): - mtz_found = True - break - if not mtz_found: - self.error_code = 2 - message = self.warning_messages() - return message - - def analyse_min_build_dataset(self): - counter = 0 - for file in glob.glob(os.path.join(self.data_directory, self.mtz_style)): - if os.path.isfile(file): - counter += 1 - if counter <= self.min_build_datasets: - self.error_code = 3 - message = self.warning_messages() - return message - - def warning_messages(self): - message = "" - if self.error_code == 1: - message = "PDB file does not exist" - if self.error_code == 2: - message = "MTZ file does not exist" - if self.error_code == 3: - message = "Not enough datasets available" - - return message - - class convert_all_event_maps_in_database(QtCore.QThread): def __init__(self, initial_model_directory, xce_logfile, datasource): QtCore.QThread.__init__(self) @@ -2206,86 +2012,6 @@ def run(self): # update datasource with event_map_mtz information self.update_database() - def calculate_electron_density_map(self, mtzin): - missing_columns = False - column_dict = XChemUtils.mtztools(mtzin).get_all_columns_as_dict() - if "FWT" in column_dict["F"] and "PHWT" in column_dict["PHS"]: - labin = " labin F1=FWT PHI=PHWT\n" - elif "2FOFCWT" in column_dict["F"] and "PH2FOFCWT" in column_dict["PHS"]: - labin = " labin F1=2FOFCWT PHI=PH2FOFCWT\n" - else: - missing_columns = True - - if not missing_columns: - os.chdir(os.path.join(self.project_directory, self.xtalID)) - cmd = "fft hklin " + mtzin + " mapout 2fofc.map << EOF\n" + labin + "EOF\n" - self.Logfile.insert("calculating 2fofc map from " + mtzin) - os.system(cmd) - else: - self.Logfile.insert("cannot calculate 2fofc.map; missing map coefficients") - - def prepare_conversion_script(self): - - os.chdir(os.path.join(self.project_directory, self.xtalID)) - - # see also: - # http://www.phaser.cimr.cam.ac.uk/index.php/Using_Electron_Density_as_a_Model - - if os.getcwd().startswith("/dls"): - phenix_module = "module_load_phenix\n" - else: - phenix_module = "" - - cmd = ( - "#!" + os.getenv("SHELL") + "\n" - "\n" + phenix_module + "\n" - "pdbset XYZIN %s XYZOUT mask_ligand.pdb << eof\n" % self.ligand_pdb - + " SPACEGROUP {0!s}\n".format(self.space_group) - + " CELL {0!s}\n".format((" ".join(self.unit_cell))) - + " END\n" - "eof\n" - "\n" - "ncsmask XYZIN mask_ligand.pdb MSKOUT mask_ligand.msk << eof\n" - " GRID %s\n" % (" ".join(self.gridElectronDensityMap)) + " RADIUS 10\n" - " PEAK 1\n" - "eof\n" - "\n" - "mapmask MAPIN %s MAPOUT onecell_event_map.map << eof\n" % self.event_map - + " XYZLIM CELL\n" - "eof\n" - "\n" - "maprot MAPIN onecell_event_map.map MSKIN mask_ligand.msk WRKOUT" - " masked_event_map.map << eof\n" - " MODE FROM\n" - " SYMMETRY WORK %s\n" % self.space_group_numberElectronDensityMap - + " AVERAGE\n" - " ROTATE EULER 0 0 0\n" - " TRANSLATE 0 0 0\n" - "eof\n" - "\n" - "mapmask MAPIN masked_event_map.map MAPOUT masked_event_map_fullcell.map <<" - " eof\n" - " XYZLIM CELL\n" - " PAD 0.0\n" - "eof\n" - "\n" - "sfall HKLOUT %s.mtz MAPIN masked_event_map_fullcell.map << eof\n" - % self.event - + " LABOUT FC=FC_event PHIC=PHIC_event\n" - " MODE SFCALC MAPIN\n" - " RESOLUTION %s\n" % self.resolution + " END\n" - ) - - self.Logfile.insert("preparing script for conversion of Event map to SF") - f = open("eventMap2sf.sh", "w") - f.write(cmd) - f.close() - os.system("chmod +x eventMap2sf.sh") - - def run_conversion_script(self): - self.Logfile.insert("running conversion script...") - os.system("./eventMap2sf.sh") - def convert_map_to_p1(self): self.Logfile.insert("running mapmask -> converting map to p1...") cmd = ( @@ -2316,17 +2042,6 @@ def run_phenix_map_to_structure_factors(self): ) ) - def run_cinvfft(self, mtzin): - # mtzin is usually refine.mtz - self.Logfile.insert( - "running cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz" - " -colout event".format(self.event_map, mtzin, self.event) - ) - os.system( - "cinvfft -mapin {0!s} -mtzin {1!s} -mtzout {2!s}_tmp.mtz" - " -colout event".format(self.event_map, mtzin, self.event) - ) - def remove_and_rename_column_labels(self): cmd = ( @@ -2341,22 +2056,6 @@ def remove_and_rename_column_labels(self): self.Logfile.insert("running CAD: new column labels F_ampl,PHIF") os.system(cmd) - def remove_and_rename_column_labels_after_cinvfft(self): - - cmd = ( - "#!" + os.getenv("SHELL") + "\n" - "\n" - "cad hklin1 %s_tmp.mtz hklout %s.mtz << eof\n" % (self.event, self.event) - + " labin file_number 1 E1=event.F_phi.F E2=event.F_phi.phi\n" - " labout file_number 1 E1=F_ampl E2=PHIF\n" - "eof\n" - "\n" - ) - self.Logfile.insert( - "running CAD: renaming event.F_phi.F -> F_ampl and event.F_phi.phi -> PHIF" - ) - os.system(cmd) - def update_database(self): sqlite = ( "update panddaTable set " @@ -2367,15 +2066,6 @@ def update_database(self): self.db.execute_statement(sqlite) self.Logfile.insert("updating data source: " + sqlite) - def clean_output_directory(self): - os.system("/bin/rm mask_targetcell.pdb") - os.system("/bin/rm mask_targetcell.msk") - os.system("/bin/rm onecell.map") - os.system("/bin/rm masked_targetcell.map") - os.system("/bin/rm masked_fullcell.map") - os.system("/bin/rm eventMap2sf.sh") - os.system("/bin/rm " + self.ligand_pdb) - class run_pandda_inspect_at_home(QtCore.QThread): def __init__(self, panddaDir, xce_logfile): diff --git a/xce/lib/XChemThread.py b/xce/lib/XChemThread.py index 1ec0f404..6768313d 100755 --- a/xce/lib/XChemThread.py +++ b/xce/lib/XChemThread.py @@ -130,49 +130,6 @@ def run(self): self.emit(QtCore.SIGNAL("datasource_menu_reload_samples")) - def change_absolute_to_relative_links(self, target, filename): - os.unlink(filename) - os.symlink(os.path.relpath(target), filename) - self.Logfile.insert("{0!s} -> {1!s}".format(os.readlink(filename), target)) - - def find_file(self, filename, xtal): - found_file = False - for files in glob.glob("*"): - if files == filename: - # at this point, this could ba a file or a (broken) symbolic link - try: - link = os.readlink(filename) - if link.startswith("/"): - if os.path.isfile( - link.replace( - link[: link.find(xtal)], - self.initial_model_directory + "/", - ) - ): - target = link.replace( - link[: link.find(xtal)], - self.initial_model_directory + "/", - ) - found_file = True - self.change_absolute_to_relative_links(target, filename) - elif os.path.isfile(files): - # this will leave the absolute path - found_file = True - else: - self.Logfile.insert("removing broken link: " + filename) - os.system("/bin/rm {0!s} 2> /dev/null".format(filename)) - else: - if not os.path.isfile(link): - self.Logfile.insert("removing broken link: " + filename) - os.system("/bin/rm {0!s} 2> /dev/null".format(filename)) - else: - found_file = True - except OSError: - if os.path.isfile(filename): - found_file = True - break - return found_file - def sync_data_processing(self, xtal, db_dict): # AIMLESS logfile diff --git a/xce/lib/XChemToolTips.py b/xce/lib/XChemToolTips.py index be6763ee..bcf8d6a3 100755 --- a/xce/lib/XChemToolTips.py +++ b/xce/lib/XChemToolTips.py @@ -62,55 +62,11 @@ def refine_file_task_status_button_tip(): return tip -def validation_file_task_tip(): - tip = "describes what you can do" - return tip - - -def validation_file_task_run_button_tip(): - tip = "Run validation_file" - return tip - - -def validation_file_task_status_button_tip(): - tip = "Status validation_file" - return tip - - def update_from_datasource_button_tip(): tip = "Status validation_file" return tip -def load_samples_from_datasource(): - tip = "loads all information\n" "which is currently in the\n" "data source" - return tip - - -def save_samples_to_datasource(): - tip = "saves all changes you made\n" "to any of the cells to the\n" "data source" - return tip - - -def create_pdb_cif_png_files(): - tip = ( - "uses ACEDRG to create pdb,cif and png files for all compounds\n" - "that have a smiles string assigned. The compounds ID\n" - "serves as name if available.\n" - "The files are written to initial_model//compound\n" - "data source" - ) - return tip - - -def check_status_create_pdb_cif_png_files(): - tip = ( - "the jobs are sent to a computer cluster if available\n" - "gives you an overview about how it progresses" - ) - return tip - - def run_pandda_inspect_at_home(pandda_directory): # instruction = ( '\n\n' # 'Please follow the instructions below to run pandda.inspect at your home institution:\n\n' @@ -167,114 +123,6 @@ def deposition_interface_note(): return note -def html_summary_introduction(): - - text = ( - "This section describes how to generate an HTML summary page of the current project. \n" - "All you need to do is select the HTML output directory where the html and additional auxiliary files \n" - "and will be written to. " - 'Then press the "Export to HTML" button and \nall bound structures that are labeled as "4 - compchem ready"' - "or higher will be included in the final document. \n" - "Please checkout https://www.thesgc.org/fragment-screening to see what the final pages look like. " - ) - - return text - - -def html_export_directory_background(): - - text = ( - "The HTML export directory will contain all files necessary to generate the summary file.\n" - "It is also makes it easy to share the results with collaborators." - ) - - return text - - -def html_export_step(): - - text = ( - "This step will create an index.html file and it will copy pdb, mtz and cif files\n" - "as well as PanDDA event maps into the html export directory." - ) - - return text - - -def icb_file_background(): - - text = "This step will use ICM-pro to create interactive structure thumbnails in the html file (http://www.molsoft.com/activeicmjs.html)" - - return text - - -def prepare_ICB_files(): - - instruction = ( - "- Open file browser and navigate to HTML export directory.\n" - "- Open ICM (at DLS: select SERVER and enter diamvicmpro.diamond.ac.uk in case ICM asks).\n" - "- Drag-and-drop dsEvent_sqlite.icm file into ICM main window.\n" - '- In ICM workspace panel: right-click on dsEvent_sqlite.icm and select "RUN".' - ) - return instruction - - -def zenodo_upload_start(html_export_directory): - - instruction = ( - "This will copy all files required for ZENODO upload to\n" - "%s" % os.path.join(html_export_directory, "zenodo") - ) - return instruction - - -def zenodo_upload_part_one(html_export_directory): - - instruction = ( - "- Register with ZENODO (www.zenodo.org)\n" - "- Select Upload -> New Upload\n" - "- upload all files from %s/zenodo, BUT NOT any of the .html files!!!" - % html_export_directory - ) - return instruction - - -def zenodo_upload_part_two(): - - instruction = "You might have noticed that once you started uploading files, the address bar in your browser will change to something like this:" - - return instruction - - -def zenodo_upload_part_three(): - - instruction = "Please enter the upload ID, i.e. the number at the end of the line, into the field below" - - return instruction - - -def zenodo_upload_part_four(html_export_directory): - - instruction = ( - "Upload ALL html files in {0!s} to ZENODO and publish the page.".format( - os.path.join(html_export_directory, "zenodo") - ) - ) - - return instruction - - -def deposition_pandda_site_not_ready(xtal): - msg = ( - "Please make sure that all placed ligands in " - + xtal - + " are ready for deposition.\n" - "Go to the Refinement tab -> Open COOT and either delete the ligand or set the site " - ' to "5 - Deposition ready"' - ) - return msg - - def pandda_pre_run(reference_directory): msg = ( "The aim of the pre-run is NOT to identify bound ligands,\n" @@ -374,25 +222,6 @@ def deposition_ground_state_preparation_step_one_text(): return msg -def deposition_ground_state_log_info(): - msg = ( - " IMPORTANT:\n" - " Make sure that a file or symlink to an AIMLESS logile with the same name root as your ground-state PDB file\n" - " is present in the same folder. This is currently not generated automatically! " - ) - return msg - - -def deposition_ground_state_preparation_step_two_text(): - msg = ( - "2. Select ground-state MTZ file.\n" - " Notes: - this is the MTZ file of the ground-state mean map\n" - " - the file should have been created after the pandda pre-run\n" - " - hence, you will usually find it in the reference directory" - ) - return msg - - def deposition_ground_state_preparation_step_three_text(): msg = ( "1. Please check the settings tab that you have selected the correct pandda directory.\n" diff --git a/xce/lib/XChemUtils.py b/xce/lib/XChemUtils.py index ccda4ee5..f44a7896 100755 --- a/xce/lib/XChemUtils.py +++ b/xce/lib/XChemUtils.py @@ -33,185 +33,10 @@ def open_decompress_file(filename, mode="rb"): return open(filename, mode=mode) -class process: - def __init__(self, dimple): - self.project_directory = dimple["project_directory"] - self.delete_old = dimple["delete_old"] - self.xtalID = dimple["xtalID"] - self.reference = dimple["reference"] - self.queueing_system_available = dimple["queueing_system_available"] - self.ccp4_scratch_directory = dimple["ccp4_scratch"] - self.fileroot_in = dimple["fileroot_in"] - self.mtz_free = self.fileroot_in + ".free.mtz" - self.mtz_in = self.fileroot_in + ".mtz" - # need to set $CCP4_SCR, because the default directory in /home/zqr16691/tmp - # fills up easily and then dimple will not run - - def get_Rfree(self): - Cmds = "" - if not os.path.isfile( - os.path.join(self.project_directory, self.xtalID, self.mtz_free) - ): - if os.path.isfile( - os.path.join( - self.project_directory, self.xtalID, self.reference + ".mtz" - ) - ): - Cmds = ( - "\n" - + "cd %s/%s/Dimple\n" % (self.project_directory, self.xtalID) - + "\n" - + "pointless hklin ../%s hklref %s.mtz hklout %s.reind.mtz" - % (self.mtz_in, self.reference, self.xtalID) - + " << EOF > pointless.log\n" - + " tolerance 5\n" - + "EOF\n" - + "\n" - + "cad hklin1 %s.reind.mtz hklin2 %s.mtz hklout cad.mtz <<" - % (self.xtalID, self.reference) - + " EOF > cad.log\n" - + " labin file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" - + " labout file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" - + " labin file_number 2 E1=FreeR_flag\n" - + " labout file_number 2 E1=FreeR_flag\n" - + " END\n" - + "EOF\n" - + "\n" - + "freerflag hklin cad.mtz hklout ../%s << EOF > freerflag.log\n" - % self.mtz_free - + " COMPLETE FREE=FreeR_flag\n" - + " END\n" - + "EOF\n" - + "#uniqueify -f FreeR_flag cad.mtz ../%s\n" % self.mtz_free - ) - else: - Cmds = ( - "\n" - + "cd %s/%s/Dimple\n" % (self.project_directory, self.xtalID) - + "\n" - + "pointless hklin ../%s xyzin %s.pdb hklout %s.reind.mtz" - % (self.mtz_in, self.reference, self.xtalID) - + " << EOF > pointless.log\n" - + " tolerance 5\n" - + "EOF\n" - + "\n" - + "cad hklin1 %s.reind.mtz hklout cad.mtz << EOF > cad.log\n" - % self.xtalID - + " labin file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" - + " labout file_number 1 E1=F E2=SIGF E3=IMEAN E4=SIGIMEAN\n" - + " END\n" - + "EOF\n" - + "\n" - + "freerflag hklin cad.mtz hklout ../%s > freerflag.log\n" - % self.mtz_free - + "#uniqueify cad.mtz ../{0!s}\n".format(self.mtz_free) - ) - return Cmds - - def dimple(self): - os.chdir("{0!s}/{1!s}".format(self.project_directory, self.xtalID)) - generate_Rfree_Cmds = "" - if os.path.isdir( - "{0!s}/{1!s}/Dimple".format(self.project_directory, self.xtalID) - ): - # this 'if not' step is usually not necessary - # only if process was stopped in an odd way - if not os.path.isfile( - self.project_directory + "/" + self.xtalID + "/" + self.mtz_free - ): - generate_Rfree_Cmds = self.get_Rfree() - if self.delete_old: - os.system("rm -fr Dimple") - os.mkdir( - "{0!s}/{1!s}/Dimple".format(self.project_directory, self.xtalID) - ) - else: - return None - else: - os.mkdir("{0!s}/{1!s}/Dimple".format(self.project_directory, self.xtalID)) - generate_Rfree_Cmds = self.get_Rfree() - os.chdir("{0!s}/{1!s}/Dimple".format(self.project_directory, self.xtalID)) - - if self.queueing_system_available: - top_line = "#PBS -joe -N XCE_dimple" - else: - top_line = "#!" + os.getenv("SHELL") - - if "csh" in os.getenv("SHELL"): - ccp4_scratch = "setenv CCP4_SCR " + self.ccp4_scratch_directory + "\n" - elif "bash" in os.getenv("SHELL"): - ccp4_scratch = "export CCP4_SCR=" + self.ccp4_scratch_directory + "\n" - else: - ccp4_scratch = "" - - ################################################################################ - # in case additional ligands are present in the reference.pdb file, - # the user needs to provide the following files: - # - .pdb - # - .cif - this file contains restraints for all the ligands in the - # respective pdb file - - if os.path.isfile(self.reference + ".cif"): - ref_lib = " --libin " + self.reference + ".cif" - else: - ref_lib = "" - - Cmds = ( - "{0!s}\n".format(top_line) + generate_Rfree_Cmds + "\n" - "cd %s/%s/Dimple\n" % (self.project_directory, self.xtalID) - + "\n" - + ccp4_scratch - + "\n" - "dimple %s ../%s %s.pdb dimple" % (ref_lib, self.mtz_free, self.reference) - + "\n" - "cd %s/%s\n" % (self.project_directory, self.xtalID) + "\n" - "/bin/rm refine.pdb\n" - "/bin/rm refine.mtz\n" - "ln -s Dimple/dimple/final.pdb refine.pdb\n" - "ln -s Dimple/dimple/final.mtz refine.mtz\n" - "\n" - "fft hklin refine.mtz mapout 2fofc.map << EOF\n" - " labin F1=2FOFCWT PHI=PH2FOFCWT\n" - "EOF\n" - "\n" - "fft hklin refine.mtz mapout fofc.map << EOF\n" - " labin F1=FOFCWT PHI=PHFOFCWT\n" - "EOF\n" - "\n" - "fft hklin refine.mtz mapout 2fofc.map << EOF\n" - " labin F1=FWT PHI=PHWT\n" - "EOF\n" - "\n" - "fft hklin refine.mtz mapout fofc.map << EOF\n" - " labin F1=DELFWT PHI=PHDELWT\n" - "EOF\n" - "\n" - "/bin/rm dimple_run_in_progress\n" - ) - - self.Run(Cmds) - - def Run(self, Cmds): - os.chdir(self.project_directory + "/" + self.xtalID) - os.system("touch dimple_run_in_progress") - os.chdir(self.project_directory + "/" + self.xtalID + "/Dimple") - f = open("xce_dimple.sh", "w") - f.write(Cmds) - f.close() - if self.queueing_system_available: - os.system("qsub xce_dimple.sh") - else: - os.system("chmod +x xce_dimple.sh") - os.system("./xce_dimple.sh") - - class helpers: def __init__(self): self.pil_rdkit_present = True - def pil_rdkit_exist(self): - return self.pil_rdkit_present - def make_png( self, initial_model_directory, @@ -654,154 +479,6 @@ def __init__(self): "DataProcessingScore": "n/a", } - def GetAimlessLog(self, Logfile): - self.Logfile = Logfile - Aimless = { - "AutoProc": "n/a", - "Run": "n/a", - "SpaceGroup": "n/a", - "UnitCell": "n/a", - "ResolutionLow": "n/a", - "ResolutionLowInnerShell": "n/a", - "ResolutionHigh": "n/a", - "ResolutionHighOuterShell": "n/a", - "RmergeOverall": "n/a", - "RmergeLow": "n/a", - "RmergeHigh": "n/a", - "IsigOverall": "n/a", - "IsigLow": "n/a", - "IsigHigh": "n/a", - "CompletenessOverall": "n/a", - "CompletenessLow": "n/a", - "CompletenessHigh": "n/a", - "MultiplicityOverall": "n/a", - "MultiplicityLow": "n/a", - "MultiplicityHigh": "n/a", - "UniqueReflectionsOverall": "n/a", - "Lattice": "n/a", - "UnitCellVolume": 0, - "Alert": "#FF0000", - } - - a = "n/a" - b = "n/a" - c = "n/a" - alpha = "n/a" - beta = "n/a" - gamma = "n/a" - - if "fast_dp" in self.Logfile: - Aimless["AutoProc"] = "fast_dp" - if "3d-run" in self.Logfile: - Aimless["AutoProc"] = "xia2 3d" - if "3dii-run" in self.Logfile: - Aimless["AutoProc"] = "xia2 3dii" - if "dials-run" in self.Logfile: - Aimless["AutoProc"] = "dials" - if "autoPROC" in self.Logfile: - Aimless["AutoProc"] = "autoPROC" - - # get run number from logfile - # only works if file is in original directory, but not once it lifes in - # 'inital_model' - try: - Aimless["Run"] = self.Logfile.split("/")[9].split("_")[1] - except IndexError: - pass - - for line in open(self.Logfile): - if line.startswith("Low resolution limit") and len(line.split()) == 6: - Aimless["ResolutionLow"] = line.split()[3] - Aimless["ResolutionHighOuterShell"] = line.split()[5] - if line.startswith("High resolution limit") and len(line.split()) == 6: - Aimless["ResolutionHigh"] = line.split()[3] - Aimless["ResolutionLowInnerShell"] = line.split()[4] - if line.startswith("Rmerge (all I+ and I-)") and len(line.split()) == 8: - Aimless["RmergeOverall"] = line.split()[5] - Aimless["RmergeLow"] = line.split()[6] - Aimless["RmergeHigh"] = line.split()[7] - if line.startswith("Mean((I)/sd(I))") and len(line.split()) == 4: - Aimless["IsigOverall"] = line.split()[1] - Aimless["IsigHigh"] = line.split()[3] - Aimless["IsigLow"] = line.split()[2] - if line.startswith("Completeness") and len(line.split()) == 4: - Aimless["CompletenessOverall"] = line.split()[1] - Aimless["CompletenessHigh"] = line.split()[3] - Aimless["CompletenessLow"] = line.split()[2] - if line.startswith("Multiplicity") and len(line.split()) == 4: - Aimless["MultiplicityOverall"] = line.split()[1] - Aimless["MultiplicityHigh"] = line.split()[3] - Aimless["MultiplicityLow"] = line.split()[3] - if line.startswith("Average unit cell:") and len(line.split()) == 9: - tmp = [line.split()] - a = int(float(tmp[0][3])) - b = int(float(tmp[0][4])) - c = int(float(tmp[0][5])) - alpha = int(float(tmp[0][6])) - beta = int(float(tmp[0][7])) - gamma = int(float(tmp[0][8])) - if line.startswith("Total number unique") and len(line.split()) == 6: - Aimless["UniqueReflectionsOverall"] = line.split()[3] - if line.startswith("Space group:"): - Aimless["SpaceGroup"] = line.replace("Space group: ", "")[:-1] - Aimless["Lattice"] = self.get_lattice_from_space_group( - Aimless["SpaceGroup"] - ) - if ( - a != "n/a" - and b != "n/a" - and c != "n/a" - and alpha != "n/a" - and beta != "n/a" - and gamma != "n/a" - and Aimless["Lattice"] != "n/a" - ): - Aimless["UnitCellVolume"] = self.calc_unitcell_volume_from_logfile( - float(a), - float(b), - float(c), - math.radians(float(alpha)), - math.radians(float(beta)), - math.radians(float(gamma)), - Aimless["Lattice"], - ) - Aimless["UnitCell"] = ( - str(a) - + " " - + str(b) - + " " - + str(c) - + " " - + str(alpha) - + " " - + str(beta) - + " " - + str(gamma) - ) - - if Aimless["ResolutionHigh"] == "n/a" or Aimless["RmergeLow"] == "n/a": - Aimless["Alert"] = "#FF0000" - else: - if ( - float(Aimless["ResolutionHigh"]) > 3.5 - or float(Aimless["RmergeLow"]) > 0.1 - ): - Aimless["Alert"] = "#FF0000" - if (3.5 >= float(Aimless["ResolutionHigh"]) > 2.5) or ( - 0.1 >= float(Aimless["RmergeLow"]) > 0.05 - ): - Aimless["Alert"] = "#FF9900" - if ( - float(Aimless["ResolutionHigh"]) <= 2.5 - and float(Aimless["RmergeLow"]) <= 0.05 - ): - Aimless["Alert"] = "#00FF00" - - return Aimless - - def return_empty_aimless_dict_for_db(self): - return self.aimless - def read_aimless_logfile(self, logfile): # essentially same as above, but compatible with datasource # will hopefully supersede function above @@ -1775,27 +1452,6 @@ def get_point_group_from_spg_number(self, number): pointgroup = pg return pointgroup - def get_unit_cell_from_mtz(self): - cell_line = 100000 - a = 0 - b = 0 - c = 0 - alpha = 0 - beta = 0 - gamma = 0 - mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) - for n, line in enumerate(iter(mtzdmp.stdout.readline, "")): - if line.startswith(" * Cell Dimensions :"): - cell_line = n + 2 - if n == cell_line and len(line.split()) == 6: - a = line.split()[0] - b = line.split()[1] - c = line.split()[2] - alpha = line.split()[3] - beta = line.split()[4] - gamma = line.split()[5] - return [a, b, c, alpha, beta, gamma] - def get_spg_number_from_mtz(self): spg_number = 0 mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) @@ -1804,60 +1460,12 @@ def get_spg_number_from_mtz(self): spg_number = int(line[line.rfind(")") - 3 : line.rfind(")")]) return spg_number - def get_spg_from_mtz(self): - spg = "" - mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) - for n, line in enumerate(iter(mtzdmp.stdout.readline, "")): - if line.startswith(" * Space group ="): - spg = line[line.find("'") + 1 : line.rfind("'")] - return spg - - def get_bravais_lattice_from_mtz(self): - bravais_lattice = "" - spg_number = self.get_spg_number_from_mtz() - bravais_lattice = self.get_bravais_lattice_from_spg_number(spg_number) - return bravais_lattice - def get_pointgroup_from_mtz(self): pointgroup = "" spg_number = self.get_spg_number_from_mtz() pointgroup = self.get_point_group_from_spg_number(spg_number) return pointgroup - def calc_unitcell_volume_from_mtz(self): - spg_number = self.get_spg_number_from_mtz() - lattice = self.get_bravais_lattice_from_spg_number(spg_number) - unitcell = self.get_unit_cell_from_mtz() - a = float(unitcell[0]) - b = float(unitcell[1]) - c = float(unitcell[2]) - alpha = math.radians(float(unitcell[3])) - beta = math.radians(float(unitcell[4])) - gamma = math.radians(float(unitcell[5])) - unitcell_volume = 0 - if lattice == "triclinic": - unitcell_volume = ( - a - * b - * c - * math.sqrt( - ( - 1 - - math.cos(alpha) ** 2 - - math.cos(beta) ** 2 - - math.cos(gamma) ** 2 - ) - + 2 * (math.cos(alpha) * math.cos(beta) * math.cos(gamma)) - ) - ) - if "monoclinic" in lattice: - unitcell_volume = round(a * b * c * math.sin(beta), 1) - if lattice == "orthorhombic" or lattice == "tetragonal" or lattice == "cubic": - unitcell_volume = round(a * b * c, 1) - if lattice == "hexagonal" or lattice == "rhombohedral": - unitcell_volume = round(a * b * c * (math.sin(math.radians(60))), 1) - return unitcell_volume - def get_high_resolution_from_mtz(self): resolution_high = "n/a" resolution_line = 1000000 @@ -1869,17 +1477,6 @@ def get_high_resolution_from_mtz(self): resolution_high = line.split()[5] return resolution_high - def get_low_resolution_from_mtz(self): - resolution_low = "n/a" - resolution_line = 1000000 - mtzdmp = subprocess.Popen(["mtzdmp", self.mtzfile], stdout=subprocess.PIPE) - for n, line in enumerate(iter(mtzdmp.stdout.readline, "")): - if line.startswith(" * Resolution Range :"): - resolution_line = n + 2 - if n == resolution_line and len(line.split()) == 8: - resolution_low = line.split()[3] - return resolution_low - def get_number_measured_reflections(self): missing_reflections = "0" all_reflections = "0" @@ -2051,31 +1648,6 @@ def get_all_columns_as_list(self): return column_list -class queue: - def jobs_in_queue(self): - jobs = [] - qstat = subprocess.Popen(["qstat -r"], stdout=subprocess.PIPE) - counter = 0 - for n, line in enumerate(iter(qstat.stdout.readline, "")): - jobID = "" - job_name = "" - user_name = "" - if getpass.getuser() in line: - counter += 1 - jobID = line.split()[0] - user_name = line.split()[3] - if "Full jobname:" in line: - job_name = line.split()[2] - jobs.append([counter, jobID, True, job_name, user_name]) - return jobs - - def remove_all_jobs_from_queue(self): - jobs_in_queue = self.jobs_in_queue() - if jobs_in_queue: - for job in jobs_in_queue: - os.system("qdel " + job[0]) - - class external_software: def __init__(self, xce_logfile): @@ -2180,160 +1752,6 @@ def __init__(self, DataPath, xtalID): else: self.newestPDB = self.DataPath + "/" + self.xtalID + "/refine.pdb" - def UpdateQualityIndicators(self): - - QualityIndicators = { - "R": "-", - "RRfree": "-", - "RRfreeColor": "gray", - "Resolution": "n/a", - "ResolutionColor": "gray", - "MolprobityScore": "n/a", - "MolprobityScoreColor": "gray", - "RamachandranOutliers": "n/a", - "RamachandranOutliersColor": "gray", - "RamachandranFavored": "n/a", - "RamachandranFavoredColor": "gray", - "LigandCCcolor": "gray", - "LigandCC": "n/a", - "rmsdBonds": "n/a", - "rmsdBondsColor": "gray", - "rmsdAngles": "n/a", - "rmsdAnglesColor": "gray", - "MatrixWeight": "n/a", - } - - # R, Rfree, Resolution - found = 0 - if os.path.isfile(self.newestPDB): - for line in open(self.newestPDB): - if line.startswith("REMARK 3 R VALUE (WORKING + TEST SET) :"): - QualityIndicators["R"] = line.split()[9] - if line.startswith("REMARK 3 FREE R VALUE :"): - QualityIndicators["RRfree"] = line.split()[6] - if float(line.split()[6]) < 0.3: - QualityIndicators["RRfreeColor"] = "green" - if float(line.split()[6]) >= 0.3 and float(line.split()[6]): - QualityIndicators["RRfreeColor"] = "orange" - if float(line.split()[6]) >= 0.4: - QualityIndicators["RRfreeColor"] = "red" - if line.startswith("REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) :"): - QualityIndicators["Resolution"] = line.split()[7] - if float(line.split()[7]) < 2.4: - QualityIndicators["ResolutionColor"] = "green" - if 2.4 <= float(line.split()[7]) < 2.8: - QualityIndicators["ResolutionColor"] = "orange" - if float(line.split()[7]) >= 2.8: - QualityIndicators["ResolutionColor"] = "red" - if line.startswith( - "REMARK 3 BOND LENGTHS REFINED ATOMS (A):" - ): - QualityIndicators["rmsdBonds"] = line.split()[9] - if float(line.split()[9]) < 0.02: - QualityIndicators["rmsdBondsColor"] = "green" - if 0.02 <= float(line.split()[9]) < 0.03: - QualityIndicators["rmsdBondsColor"] = "orange" - if float(line.split()[9]) >= 0.03: - QualityIndicators["rmsdBondsColor"] = "red" - if line.startswith( - "REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES):" - ): - QualityIndicators["rmsdAngles"] = line.split()[9] - if float(line.split()[9]) < 2.0: - QualityIndicators["rmsdAnglesColor"] = "green" - if 2.0 <= float(line.split()[9]) < 3.0: - QualityIndicators["rmsdAnglesColor"] = "orange" - if float(line.split()[9]) >= 3.0: - QualityIndicators["rmsdAnglesColor"] = "red" - - # Molprobity - if os.path.isfile( - self.DataPath + "/" + self.xtalID + "/validation_summary.txt" - ): - for line in open( - self.DataPath + "/" + self.xtalID + "/validation_summary.txt" - ): - if "molprobity score" in line.lower(): - if len(line.split()) >= 4: - QualityIndicators["MolprobityScore"] = line.split()[3] - try: - if float(line.split()[3]) < 2: - QualityIndicators["MolprobityScoreColor"] = "green" - if 2 <= float(line.split()[3]) < 3: - QualityIndicators["MolprobityScoreColor"] = "orange" - if float(line.split()[3]) >= 3: - QualityIndicators["MolprobityScoreColor"] = "red" - except ValueError: - pass - if "ramachandran outliers" in line.lower(): - if len(line.split()) >= 4: - QualityIndicators["RamachandranOutliers"] = line.split()[3] - try: - if float(line.split()[3]) < 0.3: - QualityIndicators["RamachandranOutliersColor"] = "green" - if 0.3 <= float(line.split()[3]) < 1: - QualityIndicators[ - "RamachandranOutliersColor" - ] = "orange" - if float(line.split()[3]) >= 1: - QualityIndicators["RamachandranOutliersColor"] = "red" - except ValueError: - pass - if "favored" in line.lower(): - if len(line.split()) >= 3: - QualityIndicators["RamachandranFavored"] = line.split()[2] - try: - if float(line.split()[2]) < 90: - QualityIndicators["RamachandranFavoredColor"] = "red" - if 90 <= float(line.split()[2]) < 98: - QualityIndicators["RamachandranFavoredColor"] = "orange" - if float(line.split()[2]) >= 98: - QualityIndicators["RamachandranFavoredColor"] = "green" - except ValueError: - pass - - # LigandCC - if os.path.isfile(self.DataPath + "/" + self.xtalID + "/validate_ligands.txt"): - for line in open( - self.DataPath + "/" + self.xtalID + "/validate_ligands.txt" - ): - if "LIG" in line: - QualityIndicators["LigandCC"] = line.split()[6] - if float(line.split()[6]) < 0.8: - QualityIndicators["LigandCCcolor"] = "red" - if 0.8 <= float(line.split()[6]) < 0.9: - QualityIndicators["LigandCCcolor"] = "orange" - if float(line.split()[6]) >= 0.9: - QualityIndicators["LigandCCcolor"] = "green" - - # Matrix Weight - temp = [] - found = 0 - if os.path.isdir(os.path.join(self.DataPath, self.xtalID)): - for item in glob.glob(os.path.join(self.DataPath, self.xtalID, "*")): - if item.startswith(os.path.join(self.DataPath, self.xtalID, "Refine_")): - temp.append(int(item[item.rfind("_") + 1 :])) - found = 1 - if found: - Serial = max(temp) - if os.path.isfile( - os.path.join( - self.DataPath, self.xtalID, "Refine_" + str(Serial), "refmac.log" - ) - ): - for line in open( - os.path.join( - self.DataPath, - self.xtalID, - "Refine_" + str(Serial), - "refmac.log", - ) - ): - if line.startswith(" Weight matrix") and len(line.split()) == 3: - QualityIndicators["MatrixWeight"] = line.split()[2] - - return QualityIndicators - class pdbtools(object): def __init__(self, pdb): @@ -2578,34 +1996,6 @@ def get_residues_with_resname(self, resname): ) return ligands - def get_centre_of_gravity_of_residue(self, resname_chain_resseq): - resname_x = resname_chain_resseq.split("-")[0] - chain_x = resname_chain_resseq.split("-")[1] - resseq_x = resname_chain_resseq.split("-")[2] - x = [] - y = [] - z = [] - for model in self.hierarchy.models(): - for chain in model.chains(): - for conformer in chain.conformers(): - for residue in conformer.residues(): - if ( - residue.resname.replace(" ", "") == resname_x - and residue.resseq.replace(" ", "") == resseq_x - and chain.id.replace(" ", "") == chain_x - ): - for atom in residue.atoms(): - x.append(atom.xyz[0]) - y.append(atom.xyz[1]) - z.append(atom.xyz[2]) - - if x != [] and y != [] and z != []: - x = ((max(x) - min(x)) / 2) + min(x) - y = ((max(y) - min(y)) / 2) + min(y) - z = ((max(z) - min(z)) / 2) + min(z) - - return x, y, z - def save_residues_with_resname(self, outDir, resname): ligands = self.get_residues_with_resname(resname) ligList = [] @@ -2634,37 +2024,6 @@ def save_residues_with_resname(self, outDir, resname): return ligList - def GetRefinementProgram(self): - program = "" - for line in open(self.pdb): - if line.startswith("REMARK") and "REFMAC" in line: - program = "REFMAC" - break - if line.startswith("REMARK") and "PHENIX" in line: - program = "PHENIX" - break - if line.startswith("REMARK") and "BUSTER" in line: - program = "BUSTER" - break - - return program - - def GetSequence(self): - chain = [] - Sequence = "" - # need to count residue numbers in case of alternative conformations - ResiNum = [] - for line in open(self.pdb): - if line.startswith("ATOM") and line[17:20] in self.AminoAcids: - if line[21:22] not in chain: - chain.append(line[21:22]) - Sequence = Sequence + "\n>chain{0!s}.\n".format(line[21:22]) - ResiNum = [] - if line[13:15] == "CA" and line[22:27] not in ResiNum: - Sequence = Sequence + self.AAdict[line[17:20]] - ResiNum.append(line[22:27]) - return Sequence - def GetProteinChains(self): chain = [] for line in open(self.pdb): @@ -2674,50 +2033,6 @@ def GetProteinChains(self): chain.append(line[21:22]) return chain - def GetSymm(self): - a = "" - b = "" - c = "" - alpha = "" - beta = "" - gamma = "" - spg = "" - for line in open(self.pdb): - if line.startswith("CRYST1"): - a = line.split()[1] - b = line.split()[2] - c = line.split()[3] - alpha = line.split()[4] - beta = line.split()[5] - gamma = line.split()[6] - spg = line[55:65] - return [a, b, c, alpha, beta, gamma, spg] - - def get_spg_from_pdb(self): - spg = self.GetSymm()[6] - return spg - - def get_spg_number_from_pdb(self): - spg = ( - self.get_spg_from_pdb() - .replace(" ", "") - .lower() - .replace("\n", "") - .replace("\r", "") - ) - spg_number = "0" - for key in self.translate_spg_to_number_dict: - if key == spg: - spg_number = str(self.translate_spg_to_number_dict[key]) - break - return spg_number - - def get_bravais_lattice_from_pdb(self): - bravais_lattice = "" - spg_number = self.get_spg_number_from_pdb() - bravais_lattice = self.get_bravais_lattice_from_spg_number(spg_number) - return bravais_lattice - def get_bravais_lattice_from_spg_number(self, number): lattice = "" for bravaislattice in self.space_group_dict: @@ -2726,97 +2041,6 @@ def get_bravais_lattice_from_spg_number(self, number): lattice = bravaislattice return lattice - def get_pointgroup_from_pdb(self): - pointgroup = "" - spg_number = self.get_spg_number_from_pdb() - pointgroup = self.get_point_group_from_spg_number(spg_number) - return pointgroup - - def get_unit_cell_from_pdb(self): - symm = self.GetSymm() - unit_cell = symm[0:6] - return unit_cell - - def calc_unitcell_volume_from_pdb(self): - spg_number = self.get_spg_number_from_pdb() - lattice = self.get_bravais_lattice_from_spg_number(spg_number) - unitcell = self.get_unit_cell_from_pdb() - a = float(unitcell[0]) - b = float(unitcell[1]) - c = float(unitcell[2]) - alpha = math.radians(float(unitcell[3])) - beta = math.radians(float(unitcell[4])) - gamma = math.radians(float(unitcell[5])) - unitcell_volume = 0 - if lattice == "triclinic": - unitcell_volume = ( - a - * b - * c - * math.sqrt( - ( - 1 - - math.cos(alpha) ** 2 - - math.cos(beta) ** 2 - - math.cos(gamma) ** 2 - ) - + 2 * (math.cos(alpha) * math.cos(beta) * math.cos(gamma)) - ) - ) - if "monoclinic" in lattice: - unitcell_volume = round(a * b * c * math.sin(beta), 1) - if lattice == "orthorhombic" or lattice == "tetragonal" or lattice == "cubic": - unitcell_volume = round(a * b * c, 1) - if lattice == "hexagonal" or lattice == "rhombohedral": - unitcell_volume = round(a * b * c * (math.sin(math.radians(60))), 1) - return unitcell_volume - - def MatthewsCoefficient(self, sequence): - chain = self.GetProteinChains() - symm = self.GetSymm() - nres = 0 - for char in sequence: - if char != " ": - nres += 1 - - cmd = ( - "#!/bin/csh -f\n" - "matthews_coef << eof\n" - " cell %s\n" - % ( - symm[0] - + " " - + symm[1] - + " " - + symm[2] - + " " - + symm[3] - + " " - + symm[4] - + " " - + symm[5] - ) - + " symm {0!s}\n".format(symm[6].replace(" ", "")) - + " nres {0!s}\n".format(nres) - + " auto\n" - " end\n" - "eof\n" - ) - Log = subprocess.check_output(cmd, shell=True) - MatthewsCoeff = "n/a" - Solvent = "n/a" - found = 0 - for line in Log.split(os.linesep): - if found: - if int(line.split()[0]) == len(chain): - MatthewsCoeff = line.split()[1] - Solvent = line.split()[2] - break - if line.startswith("_______________"): - found = 1 - - return [MatthewsCoeff, Solvent] - def find_ligands(self): Ligands = [] for line in open(self.pdb): @@ -2847,46 +2071,6 @@ def save_ligands_to_pdb(self): f.close() return Ligands - def save_ligands_to_pdb_to_directory(self, outDir): - Ligands = self.find_ligands() - if not Ligands == []: - for n, item in enumerate(Ligands): - pdb = "" - for line in open(self.pdb): - if line.startswith("CRYST"): - pdb += line - if ( - (line.startswith("ATOM") or line.startswith("HETATM")) - and line[17:20] == item[0] - and line[21:22] == item[1] - and line[23:26] == item[2] - ): - pdb = pdb + line - f = open(os.path.join(outDir, "ligand_{0!s}.pdb".format(n)), "w") - f.write(pdb) - f.close() - return Ligands - - def save_all_ligands_to_pdb(self, outDir): - Ligands = self.find_ligands() - if not Ligands == []: - pdb = "" - for line in open(self.pdb): - if line.startswith("CRYST"): - pdb += line - for n, item in enumerate(Ligands): - for line in open(self.pdb): - if ( - (line.startswith("ATOM") or line.startswith("HETATM")) - and line[17:20] == item[0] - and line[21:22] == item[1] - and line[23:26] == item[2] - ): - pdb += line - f = open(os.path.join(outDir, "all_ligands.pdb"), "w") - f.write(pdb) - f.close() - def save_specific_ligands_to_pdb(self, resname, chainID, resseq, altLoc): pdb = "" outDir = self.pdb[: self.pdb.rfind("/")] @@ -2941,121 +2125,6 @@ def ligand_details_as_list(self): Ligands.append([resname, chainID, resseq, altLoc, occupancy]) return Ligands - def residue_details_as_list(self, pdbin): - residueList = [] - for line in open(pdbin): - if line.startswith("ATOM") or line.startswith("HETATM"): - resname = str(line[17:20]).replace(" ", "") - chainID = str(line[21:23]).replace(" ", "") - resseq = str(line[23:26]).replace(" ", "") - altLoc = str(line[16:17]).replace(" ", "") - occupancy = str(line[56:60]).replace(" ", "") - if [resname, chainID, resseq, altLoc, occupancy] not in residueList: - residueList.append([resname, chainID, resseq, altLoc, occupancy]) - return residueList - - def check_occupancies(self): - errorText = "" - warningText = "" - residueDict = {} - for line in open(self.pdb): - if line.startswith("ATOM") or line.startswith("HETATM"): - atomname = str(line[12:16]).replace(" ", "") - resname = str(line[17:20]).replace(" ", "") - chainID = str(line[21:22]).replace(" ", "") - resseq = str(line[22:26]).replace(" ", "") - altLoc = str(line[16:17]).replace(" ", "") - occupancy = str(line[56:60]).replace(" ", "") - if resname + "-" + chainID + "-" + resseq not in residueDict: - residueDict[resname + "-" + chainID + "-" + resseq] = [] - if altLoc == "": - altLoc = "0" - residueDict[resname + "-" + chainID + "-" + resseq].append( - [altLoc, occupancy, atomname, resname, chainID, resseq] - ) - for item in residueDict: - altLocDict = {} - for atom in residueDict[item]: - altLoc = atom[0] - occupancy = atom[1] - atomname = atom[2] - resname = atom[3] - chainID = atom[4] - resseq = atom[5] - if altLoc not in altLocDict: - altLocDict[altLoc] = [] - altLocDict[altLoc].append( - [occupancy, atomname, resname, chainID, resseq] - ) - if float(occupancy) > 1: - errorText += "ERROR: %s %s %s (%s) %s: occupancy is %s\n" % ( - chainID, - resname, - resseq, - altLoc, - atomname, - occupancy, - ) - occupancySumList = [] - for altLoc in altLocDict: - occupancySum = 0.0 - nAtom = float(len(altLocDict[altLoc])) - for n, atom in enumerate(altLocDict[altLoc]): - occupancy = atom[0] - occupancySum += float(occupancy) - atomname = atom[1] - resname = atom[2] - chainID = atom[3] - resseq = atom[4] - if n == 0: - occStart = occupancy - else: - if occupancy != occStart: - warningText += ( - "%s %s %s (%s) %s: occupancy differs for altLoc -> %s\n" - % ( - chainID, - resname, - resseq, - altLoc, - atomname, - occupancy, - ) - ) - occupancySumList.append(occupancySum / nAtom) - occAdd = 0.0 - for entry in occupancySumList: - occAdd += entry - if occAdd > 1: - errorText += ( - "ERROR: " - + item - + " -> summarised occupanies of alternative conformations" - + "are > 1.0 (" - + str(occupancySumList) - + ")\n" - ) - - return errorText, warningText - - def get_xyz_coordinated_of_residue(self, chain, number): - X = 0.0 - Y = 0.0 - Z = 0.0 - # pdb definition see: - # http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM - for line in open(self.pdb): - if ( - (line.startswith("ATOM") or line.startswith("HETATM")) - and line[21:22] == chain - and line[22:26].replace(" ", "") == str(number) - ): - X = float(line[30:38]) - Y = float(line[38:46]) - Z = float(line[46:54]) - break - return X, Y, Z - def get_center_of_gravity_of_residue_ish(self, chain, number): print("-> chain:", chain) print("-> number:", number) @@ -3110,23 +2179,6 @@ def get_center_of_gravity_of_molecule_ish(self): Z = ((max(z_list) - min(z_list)) / 2) + min(z_list) return X, Y, Z - def get_init_pdb_as_list(self): - return self.get_pdb_as_list(self.pdb) - - def get_pdb_as_list(self, pdbin): - pdb_list = [] - for line in open(pdbin): - if line.startswith("ATOM") or line.startswith("HETATM"): - atom_line = str(line[12:16]).replace(" ", "") - resname_line = str(line[17:20]).replace(" ", "") - chainID_line = str(line[21:23]).replace(" ", "") - resseq_line = str(line[23:26]).replace(" ", "") - altLoc_line = str(line[16:17]).replace(" ", "") - pdb_list.append( - [atom_line, altLoc_line, resname_line, chainID_line, resseq_line] - ) - return pdb_list - def ElementDict(self, resname, chainID, resseq, altLoc): ElementDict = { @@ -3159,295 +2211,6 @@ def ElementDict(self, resname, chainID, resseq, altLoc): return ElementDict - def update_residue( - self, - resname_old, - chainID_old, - resseq_old, - altLoc_old, - occupancy_old, - resname_new, - chainID_new, - resseq_new, - altLoc_new, - occupancy_new, - ): - outPDB = "" - for line in open(self.pdb): - if line.startswith("ATOM") or line.startswith("HETATM"): - atom_line = str(line[0:6]) - serial_line = str(line[6:11]) - atomName_line = str(line[11:16]) - altLoc_line = str(line[16:17]) - resname_line = str(line[17:20]) - chainID_line = str(line[20:23]) - resseq_line = str(line[23:26]) - insert_line = str(line[26:30]) - x_line = str(line[30:38]) - y_line = str(line[38:46]) - z_line = str(line[46:54]) - occupancy_line = str(line[54:60]) - Bfac_line = str(line[60:66]) - element_line = str(line[66:78]) - charge_line = str(line[78:80]) - if ( - resname_line.replace(" ", "") == resname_old - and chainID_line.replace(" ", "") == chainID_old - and resseq_line.replace(" ", "") == resseq_old - and altLoc_line.replace(" ", "") == altLoc_old - ): - - NewResname = resname_line.replace(resname_old, resname_new) - - NewChain = chainID_line.replace(chainID_old, chainID_new) - - if len(resseq_old) < len(resseq_new): - NewResseq = resseq_line.replace( - resseq_old, - " " * (len(resseq_old) - len(resseq_new)) + resseq_new, - ) - elif len(resseq_old) == len(resseq_new): - NewResseq = resseq_line.replace(resseq_old, resseq_new) - else: - NewResseq = resseq_line[ - len(resseq_new) - len(resseq_old) : - ].replace(resseq_old, resseq_new) - - if altLoc_line == " ": - NewAltloc = altLoc_line.replace(" ", altLoc_new) - else: - NewAltloc = altLoc_line.replace(altLoc_old, altLoc_new) - - NewOccupany = occupancy_line.replace(occupancy_old, occupancy_new) - - outPDB += ( - atom_line - + serial_line - + atomName_line - + NewAltloc - + NewResname - + NewChain - + NewResseq - + insert_line - + x_line - + y_line - + z_line - + NewOccupany - + Bfac_line - + element_line - + charge_line - ) - else: - outPDB += line - else: - outPDB += line - - f = open(self.pdb, "w") - f.write(outPDB) - f.close() - - def merge_pdb_file(self, pdbin): - outPDB = "" - - # only merge if residue with same resname - # chain and resnumber not already in self.pdb!!! - residueListReference = self.residue_details_as_list(self.pdb) - residueListPDBin = self.residue_details_as_list(pdbin) - DuplicateResidue = False - for entry in residueListPDBin: - if entry in residueListReference: - print("residue already exisits in " + self.pdb + ":") - print(str(entry)) - DuplicateResidue = True - - if not DuplicateResidue: - for line in open(self.pdb): - if not line.startswith("END"): - outPDB += line - - for line in open(pdbin): - if not line.startswith("END"): - outPDB += line - - outPDB += "END\n" - - f = open(self.pdb, "w") - f.write(outPDB) - f.close() - else: - print("cannot merge pdb files!") - - def get_symmetry_operators(self): - symop = [] - spg_number = str(self.get_spg_number_from_pdb()) - foundSPG = False - if os.path.isfile(os.path.join(os.getenv("CCP4"), "lib", "data", "symop.lib")): - for line in open( - os.path.join(os.getenv("CCP4"), "lib", "data", "symop.lib") - ): - if foundSPG: - if line.startswith(" "): - tmp = line.replace("\n", "") - symop.append(tmp.split(",")) - else: - break - if line.split()[0] == spg_number: - foundSPG = True - else: - print("CCP4 environmental variable is not set") - - return symop - - def save_sym_equivalents(self): - unit_cell = self.get_unit_cell_from_pdb() - spg = self.get_spg_from_pdb() - symop = self.get_symmetry_operators() - outDir = self.pdb[: self.pdb.rfind("/")] - root = self.pdb[self.pdb.rfind("/") + 1 : self.pdb.rfind(".")] - outPDB = os.path.join(outDir, root + "_sym.pdb") - pdbset = "#!" + os.getenv( - "SHELL" - ) + "\n" "pdbset xyzin %s xyzout %s << eof\n" % ( - self.pdb, - outPDB, - ) + "cell {0!s}\n".format( - (str(",".join(unit_cell))) - ) + "spacegroup {0!s}\n".format( - spg - ) - for op in symop: - pdbset += "SYMGEN " + ",".join(op) + "\n" - pdbset += "eof\n" - os.system(pdbset) - - def save_sym_equivalents_of_ligands_in_pdb(self, pdbIN): - unit_cell = self.get_unit_cell_from_pdb() - spg = self.get_spg_from_pdb() - symop = self.get_symmetry_operators() - outDir = pdbIN[: pdbIN.rfind("/")] - root = pdbIN[pdbIN.rfind("/") + 1 : pdbIN.rfind(".")] - pdbset = "#!" + os.getenv( - "SHELL" - ) + "\n" "pdbset xyzin %s xyzout %s/%s_0.pdb << eof\n" % ( - pdbIN, - outDir, - root, - ) + "cell {0!s}\n".format( - (str(",".join(unit_cell))) - ) + "spacegroup {0!s}\n".format( - spg - ) - for op in symop: - pdbset += "SYMGEN " + ",".join(op) + "\n" - pdbset += "eof\n" - os.system(pdbset) - return os.path.join(outDir, root + "_0.pdb") - - def save_sym_equivalents_of_ligands_in_pdb_as_one_file_per_ligand(self, pdbIN): - nres = 0 - for line in open(pdbIN): - if line.startswith("ATOM") or line.startswith("HETATM"): - nres += 1 - print("NRES", nres) - unit_cell = self.get_unit_cell_from_pdb() - spg = self.get_spg_from_pdb() - symop = self.get_symmetry_operators() - outDir = pdbIN[: pdbIN.rfind("/")] - root = pdbIN[pdbIN.rfind("/") + 1 : pdbIN.rfind(".")] - pdbset = "#!" + os.getenv( - "SHELL" - ) + "\n" "pdbset xyzin %s xyzout %s/out.pdb << eof 2> /dev/null\n" % ( - pdbIN, - outDir, - ) + "cell {0!s}\n".format( - (str(",".join(unit_cell))) - ) + "spacegroup {0!s}\n".format( - spg - ) - for op in symop: - pdbset += "SYMGEN " + ",".join(op) + "\n" - pdbset += "eof\n" - os.system(pdbset) - - pdbList = [] - counter = 0 - out = "" - Cryst = "" - n = 0 - for line in open(os.path.join(outDir, "out.pdb")): - if line.startswith("CRYST"): - Cryst = line - if line.startswith("ATOM") or line.startswith("HETATM"): - if counter < nres - 1: - if counter == 0: - out = Cryst - out += line - counter += 1 - else: - out += line - pdbList.append(os.path.join(outDir, root + "_" + str(n) + ".pdb")) - f = open(os.path.join(outDir, root + "_" + str(n) + ".pdb"), "w") - f.write(out) - f.close() - out = "" - counter = 0 - n += 1 - - return pdbList - - def save_surounding_unit_cells(self, pdbIN): - translations = [ - [0, 1, 0], - [0, 1, 1], - [0, 0, 1], - [0, -1, 1], - [0, -1, 0], - [0, -1, -1], - [0, 0, -1], - [0, 1, -1], - [1, 0, 0], - [1, 1, 0], - [1, 1, 1], - [1, 0, 1], - [1, -1, 1], - [1, -1, 0], - [1, -1, -1], - [1, 0, -1], - [1, 1, -1], - [-1, 0, 0], - [-1, 1, 0], - [-1, 1, 1], - [-1, 0, 1], - [-1, -1, 1], - [-1, -1, 0], - [-1, -1, -1], - [-1, 0, -1], - [-1, 1, -1], - ] - - unit_cell = self.get_unit_cell_from_pdb() - spg = self.get_spg_from_pdb() - outDir = pdbIN[: pdbIN.rfind("/")] - root = pdbIN[pdbIN.rfind("/") + 1 : pdbIN.rfind(".")] - - for n, shift in enumerate(translations): - pdbset = ( - "#!" + os.getenv("SHELL") + "\n" - "pdbset xyzin %s/%s.pdb xyzout %s/%s_%s.pdb << eof 2> /dev/null\n" - % (outDir, root, outDir, root, str(n + 1)) - + "cell {0!s}\n".format((str(",".join(unit_cell)))) - + "spacegroup {0!s}\n".format(spg) - + "shift fractional {0!s}\n".format( - str(shift).replace("[", "").replace("]", "") - ) - + "eof\n" - ) - print("pdinin", pdbIN) - print("outdir", outDir) - print("root", root) - print(pdbset) - os.system(pdbset) - class logtools: def __init__(self, logfile): @@ -3519,64 +2282,6 @@ def refmac_log(self): return QualityIndicators -class reference: - def __init__(self, sample_mtz, reference_file_list): - self.sample_mtz = sample_mtz - self.reference_file_list = reference_file_list - - def find_suitable_reference(self, allowed_unitcell_difference_percent): - found_suitable_reference = False - unitcell_reference = "n/a" - reference = "" - spg_reference = "n/a" - unitcell_difference = "n/a" - resolution_high = "n/a" - spg_autoproc = "n/a" - unitcell_autoproc = "n/a" - if os.path.isfile(self.sample_mtz): - mtz_autoproc = mtztools(self.sample_mtz).get_all_values_as_dict() - resolution_high = mtz_autoproc["resolution_high"] - spg_autoproc = mtz_autoproc["spacegroup"] - unitcell_autoproc = mtz_autoproc["unitcell"] - lattice_autoproc = mtz_autoproc["bravais_lattice"] - unitcell_volume_autoproc = mtz_autoproc["unitcell_volume"] - # check which reference file is most similar - for o, reference_file in enumerate(self.reference_file_list): - try: - if not reference_file[4] == 0: - unitcell_difference = round( - ( - math.fabs(reference_file[4] - unitcell_volume_autoproc) - / reference_file[4] - ) - * 100, - 1, - ) - # reference file accepted when diff in unitcell volume < 5% - # and both files have the same lattice type - if ( - unitcell_difference < allowed_unitcell_difference_percent - and lattice_autoproc == reference_file[3] - ): - spg_reference = reference_file[1] - unitcell_reference = reference_file[2] - reference = reference_file[0] - found_suitable_reference = True - break - except IndexError: - pass - return ( - spg_reference, - unitcell_reference, - reference, - found_suitable_reference, - resolution_high, - spg_autoproc, - unitcell_autoproc, - unitcell_difference, - ) - - class misc: def calculate_distance_between_coordinates(self, x1, y1, z1, x2, y2, z2): distance = 0.0 From cde76b79dc6aa27febc847681014b97d3e315bc3 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 9 Nov 2022 10:12:48 +0000 Subject: [PATCH 159/358] Remove unused import in XChemPANDDA --- xce/lib/XChemPANDDA.py | 1 - 1 file changed, 1 deletion(-) diff --git a/xce/lib/XChemPANDDA.py b/xce/lib/XChemPANDDA.py index 923864c5..44336baf 100755 --- a/xce/lib/XChemPANDDA.py +++ b/xce/lib/XChemPANDDA.py @@ -3,7 +3,6 @@ import subprocess from datetime import datetime from PyQt4 import QtCore -import math # from XChemUtils import mtztools import XChemDB From 6f60e8417b7d0f43d1e2bbf62743a4aa92f03697 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 9 Nov 2022 11:09:16 +0000 Subject: [PATCH 160/358] Move html to independent source files --- xce/lib/XChemMain.py | 493 +++-------------------- xce/lib/html_fragments/download.html | 32 ++ xce/lib/html_fragments/footer.html | 5 + xce/lib/html_fragments/guide.html | 35 ++ xce/lib/html_fragments/header.html | 38 ++ xce/lib/html_fragments/ngl.html | 286 +++++++++++++ xce/lib/html_fragments/table_header.html | 19 + xce/lib/html_fragments/table_row.html | 17 + 8 files changed, 480 insertions(+), 445 deletions(-) create mode 100644 xce/lib/html_fragments/download.html create mode 100644 xce/lib/html_fragments/footer.html create mode 100644 xce/lib/html_fragments/guide.html create mode 100644 xce/lib/html_fragments/header.html create mode 100644 xce/lib/html_fragments/ngl.html create mode 100644 xce/lib/html_fragments/table_header.html create mode 100644 xce/lib/html_fragments/table_row.html diff --git a/xce/lib/XChemMain.py b/xce/lib/XChemMain.py index a41c698e..885eda6c 100755 --- a/xce/lib/XChemMain.py +++ b/xce/lib/XChemMain.py @@ -1026,446 +1026,50 @@ def pdbx_country(): return countries -def html_header(): - header = ( - "\n" - "\n" - ' \n' - ' \n' - ' \n' - ' \n' - " Summary Fragment Hits\n" - ' \n" - ' \n" - ' \n" - ' \n' - "\n" - "\n" +def read_html(file_name): + source_path = os.path.join( + os.path.dirname(os.path.realpath(__file__)), + "html_fragments", + file_name + ".html", ) + with open(source_path) as file: + return file.read() - return header +def html_header(): + return read_html("header") -def html_ngl(firstPDB, firstEvent, firstMap, firstDiffMap, ligID): +def html_ngl(firstPDB, firstEvent, firstMap, firstDiffMap, ligID): ligChain = ligID.split("-")[1] ligResid = ligID.split("-")[2] - ngl = ( - "\n" - " \n" - "\n" + return read_html("ngl") % ( + firstPDB, + firstEvent, + firstMap, + firstDiffMap, + ligChain, + ligResid, ) - return ngl - def html_download(protein_name): - - download = ( - '
\n' - "

%s - XChem results

\n" % protein_name - + " \n" - '
\n' - '

\n' - '

Click event map in table to view a different crystal / compound pair (press SHIFT and scroll mouse wheel to change contour level of event map)

\n' - ' \n" - "
\n" - "\n" + return read_html("download") % ( + protein_name, + protein_name, + protein_name, + protein_name, + protein_name, ) - return download - def html_guide(): - - guide = ( - " \n" - "
\n" - "

Ligand-bound models for Summary

Interpreting 'Ligand confidence'

\n" - "

4 - High Confidence: The expected ligand was easily interpretable from clear density, and subsequent refinement was well-behaved. This ligand can be trusted.\n" - "
3 - Clear density, unexpected ligand: Density very clearly showed a well-defined ligand, but that ligand was unexpected in that crystal/dataset. The observed ligand was modelled anyway, because its presence could be explained in some way.\n" - "
2 - Correct ligand, weak density: Though density was weak, it was possible to model the expected ligand, possibly including other circumstantial evidence (e.g. similar ligand in another model).\n" - "
1 - Low Confidence: The ligand model is to be treated with scepticism, because the evidence (density, identity, pose) were not convincing.\n" - "

Interpreting 'Model status':

\n" - "

6 - Deposited: The model has been deposited in the PDB.\n" - "
5 - Deposition ready: The model is fully error-free, in every residue, and is ready for deposition.\n" - "
4 - CompChem ready: The model is complete and correct in the region of the bound ligand. There may be remaining small errors elsewhere in the structure, but they are far away and unlikely to be relevant to any computational analysis or compound design.\n" - "

Interpreting 'Ligand validation' spider plots:

Each axis represents one of the values described below; small is better, and large values on any axis implies that further investigation is warranted.\n" - "

Quality (RSCC) reflects the fit of the atoms to the experimental density, and should typically be greater than 0.7.\n" - "
Accuracy (RSZD) measures the amount of difference density that is found around these atoms, and should be below 3.\n" - "
B-factor ratio measures the consistency of the model with surrounding protein, and is calculated from the B factors of respectively the changed atoms and all side-chain atoms within 4Å. Large values (>3) reflect poor evidence for the model, and intermediate values (1.5+) indicate errors in refinement or modelling; for weakly-binding ligands, systematically large ratios may be justifiable.\n" - "
RMSD compares the positions of all atoms built into event density, with their positions after final refinement, and should be below 1Å.\n" - "
Precision (RSZO/OCC) measures how clear the density is after refinement. (This is not a quality indicator, but is related to strength of binding but not in a straightforward way.)\n" - "

\n" - "

\n" - "\n" - ) - - return guide + return read_html("guide") def html_table_header(): - - table = ( - "\n" - "\n" - '
%s%s%s%s%s
%s%s
%s		Save
%s
\n' - " \n" - " \n" - " \n" - " \n" - " \n" - " \n" - " \n" - " \n" - " \n" - " \n" - " \n" - " \n" - " \n" - " \n" - " \n" - " \n" - ) - - return table + return read_html("table_header") def html_table_row( @@ -1485,37 +1089,36 @@ def html_table_row( ligConfidence, modelStatus, ): - ligChain = ligID.split("-")[1] ligResid = ligID.split("-")[2] - row = ( - " \n" - " \n" % xtalID - + ' \n' - % (pdbID, pdbID) - + " \n" % ligID - + " \n" % ligConfidence - + " \n" % modelStatus - + " \n" % compoundImage - + " \n" % residuePlot - + " \n" - % (pdbID, pdb, event, FWT, DELFWT, ligChain, ligResid, thumbNail) - + " \n" % resoHigh - + " \n" % (spg, unitCell) - + " \n" - % (pdb.replace(".pdb", ""), ligID) - + " \n" + return read_html("table_row") % ( + xtalID, + pdbID, + pdbID, + ligID, + ligConfidence, + modelStatus, + compoundImage, + residuePlot, + pdbID, + pdb, + event, + FWT, + DELFWT, + ligChain, + ligResid, + thumbNail, + resoHigh, + spg, + unitCell, + pdb.replace(".pdb", ""), + ligID, ) - return row - def html_footer(): - - footer = "\n" "
Crystal IDPDB IDLigand IDLigand confidenceModel statusCompoundLigand ValidationEvent Map 3DResolSPG/ CellFiles
%s%s%s%s%s
%s%s
%s		Save
\n" "\n" "\n" - - return footer + return read_html("footer") def coot_prepare_input(x, y, z, ligID, sampleDir, eventMap): diff --git a/xce/lib/html_fragments/download.html b/xce/lib/html_fragments/download.html new file mode 100644 index 00000000..66222302 --- /dev/null +++ b/xce/lib/html_fragments/download.html @@ -0,0 +1,32 @@ +
+

%s - XChem results

+ + \ No newline at end of file diff --git a/xce/lib/html_fragments/footer.html b/xce/lib/html_fragments/footer.html new file mode 100644 index 00000000..5a752aeb --- /dev/null +++ b/xce/lib/html_fragments/footer.html @@ -0,0 +1,5 @@ + + + + + \ No newline at end of file diff --git a/xce/lib/html_fragments/guide.html b/xce/lib/html_fragments/guide.html new file mode 100644 index 00000000..8199ee96 --- /dev/null +++ b/xce/lib/html_fragments/guide.html @@ -0,0 +1,35 @@ + +
+

Ligand-bound models for Summary

+

Interpreting 'Ligand confidence'

+

4 - High Confidence: The expected ligand was easily interpretable from clear density, and subsequent + refinement was well-behaved. This ligand can be trusted. +
3 - Clear density, unexpected ligand: Density very clearly showed a well-defined ligand, but that + ligand was unexpected in that crystal/dataset. The observed ligand was modelled anyway, because its presence + could be explained in some way. +
2 - Correct ligand, weak density: Though density was weak, it was possible to model the expected + ligand, possibly including other circumstantial evidence (e.g. similar ligand in another model). +
1 - Low Confidence: The ligand model is to be treated with scepticism, because the evidence (density, + identity, pose) were not convincing. +

Interpreting 'Model status':

+

6 - Deposited: The model has been deposited in the PDB. +
5 - Deposition ready: The model is fully error-free, in every residue, and is ready for deposition. +
4 - CompChem ready: The model is complete and correct in the region of the bound ligand. There may be + remaining small errors elsewhere in the structure, but they are far away and unlikely to be relevant to any + computational analysis or compound design. +

Interpreting 'Ligand validation' spider plots:

Each axis represents one of the values described below; + small is better, and large values on any axis implies that further investigation is warranted. +

Quality (RSCC) reflects the fit of the atoms to the experimental density, and should typically be greater + than 0.7. +
Accuracy (RSZD) measures the amount of difference density that is found around these atoms, and + should be below 3. +
B-factor ratio measures the consistency of the model with surrounding protein, and is calculated from + the B factors of respectively the changed atoms and all side-chain atoms within 4Å. Large values (>3) + reflect poor evidence for the model, and intermediate values (1.5+) indicate errors in refinement or modelling; + for weakly-binding ligands, systematically large ratios may be justifiable. +
RMSD compares the positions of all atoms built into event density, with their positions after final + refinement, and should be below 1Å. +
Precision (RSZO/OCC) measures how clear the density is after refinement. (This is not a quality + indicator, but is related to strength of binding but not in a straightforward way.) +

+

\ No newline at end of file diff --git a/xce/lib/html_fragments/header.html b/xce/lib/html_fragments/header.html new file mode 100644 index 00000000..0a7eaef2 --- /dev/null +++ b/xce/lib/html_fragments/header.html @@ -0,0 +1,38 @@ + + + + + + + + Summary Fragment Hits + + + + + \ No newline at end of file diff --git a/xce/lib/html_fragments/ngl.html b/xce/lib/html_fragments/ngl.html new file mode 100644 index 00000000..e41aef97 --- /dev/null +++ b/xce/lib/html_fragments/ngl.html @@ -0,0 +1,286 @@ + + \ No newline at end of file diff --git a/xce/lib/html_fragments/table_header.html b/xce/lib/html_fragments/table_header.html new file mode 100644 index 00000000..87d13c4b --- /dev/null +++ b/xce/lib/html_fragments/table_header.html @@ -0,0 +1,19 @@ +\n" + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/xce/lib/html_fragments/table_row.html b/xce/lib/html_fragments/table_row.html new file mode 100644 index 00000000..e01b6f86 --- /dev/null +++ b/xce/lib/html_fragments/table_row.html @@ -0,0 +1,17 @@ + + + + + + + + + + + + + \ No newline at end of file From a28608079eb6058f7ac1c34d2158d6f345b31a4b Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 9 Nov 2022 11:10:18 +0000 Subject: [PATCH 161/358] Remove unused import in XChemExplorer --- xce/XChemExplorer.py | 1 - 1 file changed, 1 deletion(-) diff --git a/xce/XChemExplorer.py b/xce/XChemExplorer.py index 971cc736..b63d9ad9 100755 --- a/xce/XChemExplorer.py +++ b/xce/XChemExplorer.py @@ -17,7 +17,6 @@ import pickle import sys import os -import webbrowser from datetime import datetime from PyQt4 import QtGui, QtCore From 4b1f6a4028a52aefcc6ab144ec6a3debba2dadc1 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 9 Nov 2022 11:12:04 +0000 Subject: [PATCH 162/358] Clean up XChemLog --- xce/lib/XChemLog.py | 87 +++++++-------------------------------------- 1 file changed, 13 insertions(+), 74 deletions(-) diff --git a/xce/lib/XChemLog.py b/xce/lib/XChemLog.py index 4ec1b2f5..8f40cf02 100755 --- a/xce/lib/XChemLog.py +++ b/xce/lib/XChemLog.py @@ -14,20 +14,19 @@ def create_logfile(self, version): message = ( "\n\n" - " #######################################################################\n" - " # #\n" - " # XCHEMEXPLORER - multi dataset analysis #\n" - " # #\n" - " # Version: %s #\n" - % pasteVersion - + " # #\n" - " # Date: 10/10/2022 #\n" - " # #\n" - " # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n" - " # tobias.krojer@maxiv.lu.se #\n" - " # #\n" - " #######################################################################\n" - "\n" + " ###################################################################\n" + " # #\n" + " # XCHEMEXPLORER - multi dataset analysis #\n" + " # #\n" + " # Version: %s #\n" + " # #\n" + " # Date: 10/10/2022 #\n" + " # #\n" + " # Authors: Tobias Krojer, MAXIV Laboratory, SE #\n" + " # tobias.krojer@maxiv.lu.se #\n" + " # #\n" + " ###################################################################\n" + "\n" % pasteVersion ) if not os.path.isfile(self.logfile): @@ -49,66 +48,6 @@ def create_logfile(self, version): + "\n" ) updateLog(self.logfile).insert(message) - # print(message) - - -# class depositLog: -# -# def __init__(self,logfile): -# self.logfile=logfile -# self.suffixes = ['B', 'KB', 'MB', 'GB', 'TB', 'PB'] -# -# def humansize(self,nbytes): -# if nbytes == 0: return '0 B' -# i = 0 -# while nbytes >= 1024 and i < len(self.suffixes)-1: -# nbytes /= 1024. -# i += 1 -# f = ('{0:.2f}'.format(nbytes)).rstrip('0').rstrip('.') -# return '{0!s} {1!s}'.format(f, self.suffixes[i]) -# -# def modelInfo(self,xtal,structureType): -# message=(xtal+' @ '+structureType) -# updateLog(self.logfile).insert(message) -# -# def nEvents(self,xtal,n_eventMtz): -# updateLog(self.logfile).insert(xtal+' contains '+str(n_eventMtz)+ ' sites which are ready for deposition') -# -# def site_xml(self,xtal,xml): -# updateLog(self.logfile).insert('site description for '+xtal) -# updateLog(self.logfile).insert(xml) -# -# def text(self,message): -# updateLog(self.logfile).insert(message) -# -# def summary(self,n_toDeposit,success,failureDict,structureType,successDict): -# message= ( '\n' -# '==========================================================================\n' -# 'SUMMARY:\n' -# '--------------------------------------------------------------------------\n' -# ' - structure type: %s\n' %structureType+ -# ' - n(structures to deposit): {0!s}\n'.format(str(n_toDeposit))+ -# ' - n(successful mmcif): {0!s}\n'.format(str(success))+ -# '--------------------------------------------------------------------------\n' ) -# -# if successDict != {}: -# message+='\n => the following structures were successfully created:\n' -# message+='--------------------------------------------------------------------------\n' -# for key in sorted(successDict): -# message+='{0:20} {1:5} {2:25} {3:10} {4:25} {5:10}\n'.format(key,'->',successDict[key][0],str(self.humansize(successDict[key][1])),successDict[key][2],str(self.humansize(successDict[key][3]))) -# -# -# if failureDict != {}: -# message+='--------------------------------------------------------------------------\n' -# message+='\n => the following structures had a problem:\n' -# message+='--------------------------------------------------------------------------\n' -# for key in failureDict: -# for entry in failureDict[key]: -# message+='{0!s} -> {1!s}\n'.format(key, entry) -# -# message+='==========================================================================\n\n' -# -# updateLog(self.logfile).insert(message) class updateLog: From 614de17429a0ad4230c102a0aea1b4d7f1e2498f Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 9 Nov 2022 11:19:55 +0000 Subject: [PATCH 163/358] Clean up XChemDeposit --- xce/lib/XChemDeposit.py | 353 +++++++++++----------------------------- 1 file changed, 93 insertions(+), 260 deletions(-) diff --git a/xce/lib/XChemDeposit.py b/xce/lib/XChemDeposit.py index 85c4e1ad..ab54e883 100755 --- a/xce/lib/XChemDeposit.py +++ b/xce/lib/XChemDeposit.py @@ -12,23 +12,6 @@ from PyQt4 import QtCore -# def update_file_locations_of_apo_structuresin_DB(database,projectDir,xce_logfile): -# Logfile=XChemLog.updateLog(xce_logfile) -# Logfile.insert('updating file information for apo structures') -# db=XChemDB.data_source(database) -# apo=db.execute_statement("select CrystalName from depositTable where StructureType is 'apo';") -# for item in apo: -# xtal=str(item[0]) -# db_dict={} -# db_dict['label']=xtal+'-apo' -# db_dict['description']='apo structure for pandda.analyse' -# if os.path.isfile(os.path.join(projectDir,xtal,'dimple.pdb')): -# db_dict['PDB_file']=os.path.realpath(os.path.join(projectDir,xtal,'dimple.pdb')) -# if os.path.isfile(os.path.join(projectDir,xtal,'dimple.mtz')): -# db_dict['MTZ_file']=os.path.realpath(os.path.join(projectDir,xtal,'dimple.mtz')) -# Logfile.insert('updating depositTable for apo structure '+xtal) -# db.update_depositTable(xtal,'apo',db_dict) - class templates: def data_template_cif(self, depositDict): @@ -40,12 +23,9 @@ def data_template_cif(self, depositDict): if taxonomy_dict[key] == depositDict["Expression_system_scientific_name"]: pdbx_host_org_ncbi_taxonomy_id = key - # structure_author_name='' - # for name in depositDict['structure_author_name'].split(';'): - # structure_author_name+='\n' %name - audit_author_name = "" - # one name must be within quotation, last name and first initial must be separated by comma and space + # one name must be within quotation, last name and first initial must be + # separated by comma and space for name in depositDict["structure_author_name"].split(";"): if name.replace(" ", "") == "": continue @@ -54,7 +34,8 @@ def data_template_cif(self, depositDict): audit_author_name += "'{0!s}'\n".format(name) primary_citation_author_name = "" - # one name must be within quotation, last name and first initial must be separated by comma and space + # one name must be within quotation, last name and first initial must be + # separated by comma and space for name in depositDict["primary_citation_author_name"].split(";"): if name.replace(" ", "") == "": continue @@ -123,7 +104,9 @@ def data_template_cif(self, depositDict): ) except UnboundLocalError: print( - "Error: Something went wrong! Please check if you have saved the .deposit file to the database: Menu Deposition -> Edit Information" + "Error: Something went wrong!" + " Please check if you have saved the .deposit file to the database:" + " Menu Deposition -> Edit Information" ) else: molecule_two_letter_sequence = ";" @@ -168,9 +151,9 @@ def data_template_cif(self, depositDict): depositDict["molecule_chain_one"], depositDict["molecule_one_letter_sequence_uniprot_id"], ) - + - # ';\n' - '2 "polypeptide(L)"\n' + molecule_two_letter_sequence + "\n" + + '2 "polypeptide(L)"\n' + + molecule_two_letter_sequence + + "\n" ";\n" "%s %s UNP\n" % ( @@ -268,37 +251,7 @@ def data_template_cif(self, depositDict): "_diffrn_radiation_wavelength.wavelength %s\n" % depositDict["radiation_wavelengths"] + "#\n" - "#\n" + entity + - # 'loop_\n' - # '_entity.id\n' - # '_entity.type\n' - # '_entity.src_method\n' - # '_entity.pdbx_description\n' - # '_entity.pdbx_mutation\n' - # '1 polymer man "%s" %s\n' %(depositDict['Source_organism_gene'],depositDict['fragment_name_one_specific_mutation'])+ - # '#\n' - # 'loop_\n' - # '_entity_poly.entity_id\n' - # '_entity_poly.type\n' - # '_entity_poly.pdbx_seq_one_letter_code\n' - # '_entity_poly.pdbx_strand_id\n' - # '_entity_poly.pdbx_seq_db_id\n' - # '_entity_poly.pdbx_seq_db_name\n' - # '1 "polypeptide(L)"\n' - # +molecule_one_letter_sequence+'\n' - # ';\n' - # '%s %s UNP\n' %(depositDict['protein_chains'],depositDict['molecule_one_letter_sequence_uniprot_id'])+ - # '#\n' - # 'loop_\n' - # '_entity_src_gen.entity_id\n' - # '_entity_src_gen.gene_src_strain\n' - # '_entity_src_gen.pdbx_gene_src_scientific_name\n' - # '_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id\n' - # '_entity_src_gen.pdbx_host_org_scientific_name\n' - # '_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id\n' - # '1 ? "%s" %s "%s" %s\n' %(depositDict['Source_organism_scientific_name'],pdbx_gene_src_ncbi_taxonomy_id,depositDict['Expression_system_scientific_name'],pdbx_host_org_ncbi_taxonomy_id)+ - # '#\n' - "loop_\n" + "#\n" + entity + "loop_\n" "_pdbx_contact_author.id \n" "_pdbx_contact_author.address_1 \n" "_pdbx_contact_author.address_2 \n" @@ -328,7 +281,8 @@ def data_template_cif(self, depositDict): depositDict["contact_author_PI_organization_type"], depositDict["contact_author_PI_ORCID"], ) - + "2 '{0!s}' '{1!s}' '{2!s}' '?' '{3!s}' '{4!s}' {5!s} {6!s} '{7!s}' '{8!s}' '{9!s}' '{10!s}' {11!s}\n".format( + + "2 '{0!s}' '{1!s}' '{2!s}' '?' '{3!s}' '{4!s}' {5!s}" + " {6!s} '{7!s}' '{8!s}' '{9!s}' '{10!s}' {11!s}\n".format( depositDict["contact_author_address"], depositDict["contact_author_organization_name"], depositDict["contact_author_city"], @@ -344,19 +298,14 @@ def data_template_cif(self, depositDict): ) + "#\n" "loop_\n" - "_audit_author.name\n" + audit_author_name + - # "'%s, %s.'\n" %(depositDict['contact_author_last_name'],depositDict['contact_author_first_name'][0])+ - "#\n" + "_audit_author.name\n" + audit_author_name + "#\n" "_citation.id primary\n" "_citation.title '%s'\n" % depositDict["group_title"] + "_citation.journal_abbrev 'To Be Published'\n" "#\n" "loop_\n" "_citation_author.citation_id\n" - "_citation_author.name\n" + primary_citation_author_name + - # "primary 'Krojer, T.'\n" - # "primary 'Von Delft, F.'\n" - "#\n" + "_citation_author.name\n" + primary_citation_author_name + "#\n" "_struct.entry_id UNNAMED\n" "_struct.title\n" ";%s\n" % depositDict["title"] + ";\n" @@ -395,15 +344,15 @@ def run(self): for item in dbEntries: xtal = str(item[0]) type = str(item[1]) - # need to do this because individual fields might need updating for some xtals + # need to do this because individual fields might need updating + # for some xtals db_dict = self.deposit_dict # try to get information about the diffraction experiment try: diffractionExperiment = self.db.execute_statement( - "select DataCollectionBeamline,DataCollectionDate from mainTable where CrystalName is '{0!s}'".format( - xtal - ) + "select DataCollectionBeamline,DataCollectionDate" + " from mainTable where CrystalName is '{0!s}'".format(xtal) ) beamline = str(diffractionExperiment[0][0]) date = str(diffractionExperiment[0][1]) @@ -415,8 +364,8 @@ def run(self): beamline = db_dict["radiation_source"] date = db_dict["data_collection_date"] self.Logfile.warning( - "%s: using values provided in depositTable for beamline and data collection date" - % xtal + "%s: using values provided in depositTable for beamline" + " and data collection date" % xtal ) if beamline.lower() != "none": db_dict = self.tweak_deposit_dict(xtal, db_dict) @@ -481,7 +430,6 @@ def __init__( self.ground_state = False self.ground_state_pdb = "" - # self.ground_state_mean_mtz = '' self.panddaDir = "" self.ignore_event_map = ignore_event_map if ground_state: @@ -494,8 +442,6 @@ def __init__( self.pdb = pdbtools(self.ground_state_pdb) self.mtz = mtztools(self.ground_state_mtz) - # self.mtz = mtztools(self.ground_state_mean_mtz) - def run(self): self.Logfile.insert( @@ -515,18 +461,12 @@ def run(self): "found " + str(len(toDeposit)) + " samples ready for deposition" ) - progress_step = 1 - if len(toDeposit) != 0: - progress_step = 100 / float(len(toDeposit)) - else: - progress_step = 1 progress = 0 self.emit(QtCore.SIGNAL("update_progress_bar"), progress) for item in sorted(toDeposit): xtal = str(item[0]) if self.ground_state: - # projectDir == referenceDir in this case os.chdir(self.projectDir) else: os.chdir(os.path.join(self.projectDir, xtal)) @@ -536,9 +476,6 @@ def run(self): if not self.data_template_dict_exists(xtal): continue - # if not self.zenodo_dict_exists(xtal): - # continue - if not self.save_data_template_dict(xtal): continue @@ -547,9 +484,6 @@ def run(self): self.add_funding_information(xtal) - # if not self.create_sf_mmcif(xtal): - # continue - if not self.apo_mmcif_exists(): continue @@ -569,9 +503,6 @@ def run(self): if not self.db_dict_exists(xtal): continue - # if not self.zenodo_dict_exists(xtal): - # continue - if not self.refine_bound_exists(xtal): continue @@ -626,8 +557,8 @@ def data_template_dict_exists(self, xtal): self.data_template_dict = self.db.get_deposit_dict_for_sample(xtal) if self.data_template_dict == {}: self.Logfile.error( - "%s: cannot find data_template dictionary in depositTable; moving to next dataset..." - % xtal + "%s: cannot find data_template dictionary in depositTable;" + " moving to next dataset..." % xtal ) self.add_to_errorList(xtal) else: @@ -671,8 +602,8 @@ def db_dict_exists(self, xtal): self.db_dict = self.db.get_db_dict_for_sample(xtal) if self.db_dict == {}: self.Logfile.error( - "%s: cannot find db_dict dictionary in mainTable; moving to next dataset..." - % xtal + "%s: cannot find db_dict dictionary in mainTable;" + " moving to next dataset..." % xtal ) self.add_to_errorList(xtal) else: @@ -688,9 +619,8 @@ def mmcif_files_can_be_replaced(self, xtal): "%s: removing existing mmcif files as chosen by user" % xtal ) self.db.execute_statement( - "update depositTable set mmCIF_model_file='',mmCIF_SF_file='' where CrystalName is '{0!s}'".format( - xtal - ) + "update depositTable set mmCIF_model_file='',mmCIF_SF_file=''" + " where CrystalName is '{0!s}'".format(xtal) ) for mmcif in glob.glob("*.mmcif"): self.Logfile.warning("%s: removing %s" % (xtal, mmcif)) @@ -713,8 +643,8 @@ def refine_bound_exists(self, xtal): fileStatus = True else: self.Logfile.error( - "%s: cannot find refine.split.bound-state.pdb; moving to next dataset..." - % xtal + "%s: cannot find refine.split.bound-state.pdb;" + " moving to next dataset..." % xtal ) self.add_to_errorList(xtal) return fileStatus @@ -768,8 +698,6 @@ def aimless_logfile_exists(self, xtal): if "AIMLESS" in line: fileStatus = True break - # if n < 10: - # print line if not fileStatus: if os.path.realpath("%s.log" % xtal).endswith(".table1"): self.Logfile.warning( @@ -813,8 +741,6 @@ def aimless_logfile_exists(self, xtal): "%s: cannot find a suitable AIMLESS logfile" % xtal ) self.add_to_errorList(xtal) - - # fileStatus = True else: self.Logfile.error( "%s: cannot find %s.log; moving to next dataset..." % (xtal, xtal) @@ -846,8 +772,8 @@ def ligand_in_pdb_file(self, xtal): ) if ligList is []: self.Logfile.error( - "%s: refine.split.bound-state.pdb does not contain any modelled ligands of type LIG" - % xtal + "%s: refine.split.bound-state.pdb does not contain any modelled ligands" + " of type LIG" % xtal ) self.add_to_errorList(xtal) else: @@ -863,8 +789,8 @@ def eventMTZ_exists(self, xtal): eventMTZexists = False if os.path.isfile("no_pandda_analysis_performed") or self.ignore_event_map: self.Logfile.warning( - '%s: found empty file named "no_pandda_analysis_performed" which suggests we will ignore event maps for this sample' - % xtal + '%s: found empty file named "no_pandda_analysis_performed"' + " which suggests we will ignore event maps for this sample" % xtal ) eventMTZexists = True elif self.ignore_event_map: @@ -877,8 +803,8 @@ def eventMTZ_exists(self, xtal): eventMTZlist.append(mtz[mtz.rfind("/") + 1 :]) if eventMTZlist is []: self.Logfile.error( - '%s: MTZ files of event maps do not exists! Go to PANDDA tab and run "Event Map -> SF"' - % xtal + "%s: MTZ files of event maps do not exists!" + ' Go to PANDDA tab and run "Event Map -> SF"' % xtal ) self.add_to_errorList(xtal) else: @@ -902,8 +828,8 @@ def find_matching_event_map(self, xtal): foundMatchingMap = None if os.path.isfile("no_pandda_analysis_performed") or self.ignore_event_map: self.Logfile.warning( - '%s: found empty file named "no_pandda_analysis_performed" which suggests we will ignore event maps for this sample' - % xtal + '%s: found empty file named "no_pandda_analysis_performed"' + " which suggests we will ignore event maps for this sample" % xtal ) foundMatchingMap = True ligList = [] @@ -914,14 +840,7 @@ def find_matching_event_map(self, xtal): ) for lig in sorted(ligList): ligID = lig.replace(".pdb", "") - # if os.path.isfile('no_pandda_analysis_performed'): - # self.Logfile.warning('%s: no pandda analysis performed; skipping this step...' %xtal) - # foundMatchingMap = True - # break ligCC = [] - - # for newer BUSTER export - # print '>>>> %s-event_*.native_%s.mtz' %(xtal,lig.replace('.pdb','')) for mtz in glob.glob( ("%s-event_*.native_%s.mtz" % (xtal, lig.replace(".pdb", ""))) ): @@ -953,13 +872,9 @@ def find_matching_event_map(self, xtal): try: for cm in ligCC: self.Logfile.insert("%s: cc = %s - %s" % (xtal, cm[1], cm[0])) - # highestCC = max(ligCC, key=lambda x: x[0])[1] highestCCeventmap = max(ligCC, key=lambda x: float(x[1]))[0] except ValueError: - highestCC = 0.00 highestCCeventmap = None - - # if highestCC == 0.00 or ligCC is []: if highestCCeventmap is None or ligCC is []: self.Logfile.error( "%s: best CC of ligand %s for any event map is 0!" % (xtal, lig) @@ -1076,7 +991,6 @@ def save_data_template_dict(self, xtal): ) if self.ground_state: os.chdir(self.projectDir) - # self.data_template_dict['radiation_wavelengths'] = '1.000' self.data_template_dict["group_type"] = "ground state" self.data_template_dict[ "group_title" @@ -1093,8 +1007,6 @@ def save_data_template_dict(self, xtal): ) else: os.chdir(os.path.join(self.projectDir, xtal)) - # edit wavelength - # self.data_template_dict['radiation_wavelengths'] = self.mtz.get_wavelength() title = ( self.data_template_dict["structure_title"] @@ -1116,8 +1028,6 @@ def save_data_template_dict(self, xtal): .replace("$CompoundName", self.db_dict["CompoundCode"]) ) - # self.data_template_dict[ - # 'group_title'] = 'PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)' self.data_template_dict["group_description"] = self.data_template_dict[ "group_description" ].replace( @@ -1161,8 +1071,6 @@ def save_data_template_dict(self, xtal): ][:-1] data_template = templates().data_template_cif(self.data_template_dict) - # site_details = self.make_site_description(xtal) - # data_template += site_details if self.ground_state: f = open(os.path.join(self.projectDir, "data_template.cif"), "w") else: @@ -1182,10 +1090,6 @@ def create_model_mmcif(self, xtal): refSoft = self.pdb.get_refinement_program() if os.path.isdir("/dls"): - # if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): - # pdb_extract_init = 'source /dls/science/groups/i04-1/software/pdb-extract-v3.26/pdb-extract-v3.26-prod-src/setup.sh\n' - # pdb_extract_init += '/dls/science/groups/i04-1/software/pdb-extract-v3.26/pdb-extract-v3.26-prod-src/bin/pdb_extract' - # else: pdb_extract_init = ( "source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n" ) @@ -1256,18 +1160,7 @@ def create_model_mmcif(self, xtal): parse().make_pseudo_aimless_log_from_json(aimless) aimless = "aimless_dials.log" - # aimless = None - # for n,line in enumerate(open('%s.log' %xtal)): - # if 'AIMLESS' in line: - # aimless = '%s.log' %xtal - # break - # if not aimless: - # if os.path.isfile('aimless_dials.log'): - # aimless = 'aimless_dials.log' - if self.ground_state: - # refXtal = self.ground_state_pdb.split('/')[len(self.ground_state_pdb.split('/')) - 2] - # aimless = os.path.join(self.logDir,refXtal,refXtal+'.log') self.Logfile.insert("aimless.log file: " + aimless) Cmd = ( pdb_extract_init @@ -1279,17 +1172,6 @@ def create_model_mmcif(self, xtal): " -o {0!s}.mmcif > {1!s}.mmcif.log".format(xtal, xtal) ) else: - # if os.path.isfile(self.db_dict['RefinementMMCIFmodel_latest']): - # self.Logfile.insert('%s: found MMCIF file; will use instead of PDB: %s' %(xtal,self.db_dict['RefinementMMCIFmodel_latest'])) - # Cmd = (pdb_extract_init + - # ' -r {0!s}'.format(refSoft) + - # ' -iCIF {0!s}'.format(self.db_dict['RefinementMMCIFmodel_latest']) + - # ' -e MR' - # ' -s AIMLESS' - # ' -iLOG {0!s}.log'.format(xtal) + - # ' -iENT data_template.cif' - # ' -o {0!s}.mmcif > {1!s}.mmcif.log'.format(xtal, xtal)) - # else: Cmd = ( pdb_extract_init + " -r {0!s}".format(refSoft) @@ -1309,15 +1191,16 @@ def create_model_mmcif(self, xtal): self.Logfile.insert("%s: model mmcif file successfully created" % xtal) if self.ground_state: self.db.execute_statement( - "update depositTable set mmCIF_model_file='{0!s}.mmcif' where CrystalName is '{1!s}' and DimplePANDDApath is '{2!s}'".format( + "update depositTable set mmCIF_model_file='{0!s}.mmcif'" + " where CrystalName is '{1!s}'" + " and DimplePANDDApath is '{2!s}'".format( xtal, xtal, self.panddaDir ) ) else: self.db.execute_statement( - "update depositTable set mmCIF_model_file='{0!s}.mmcif' where CrystalName is '{1!s}'".format( - xtal, xtal - ) + "update depositTable set mmCIF_model_file='{0!s}.mmcif'" + " where CrystalName is '{1!s}'".format(xtal, xtal) ) fileStatus = True else: @@ -1332,7 +1215,6 @@ def update_model_mmcif_header(self, xtal): amendSoftwareBlock = False softwareEntry = [] for i, line in enumerate(fileinput.input(xtal + ".mmcif", inplace=1)): - # if i == 4: sys.stdout.write('\n') # write a blank line after the 5th line if "_software.pdbx_ordinal" in line: foundSoftwareBlock = True if foundSoftwareBlock: @@ -1358,11 +1240,10 @@ def update_model_mmcif_header(self, xtal): elif "_refine.pdbx_method_to_determine_struct" in line: sys.stdout.write( - "_refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS'\n" + "_refine.pdbx_method_to_determine_struct" + " 'FOURIER SYNTHESIS'\n" ) elif "_struct.title ---" in line: - # self.Logfile.warning('structure title was not created by pdb_extract; there might be an issue with REFMAC 5.8.0238') - # self.Logfile.insert('trying to get title from data_template.cif file') Title = "" foundTitle = False for li in open("data_template.cif"): @@ -1378,28 +1259,12 @@ def update_model_mmcif_header(self, xtal): Title += li sys.stdout.write(Title) elif amendSoftwareBlock: - cifItem = ( - "{0!s} {1!s} ? ? program ? ? 'data reduction' ? ?\n".format( - str(max(softwareEntry) + 1), - self.data_template_dict["data_integration_software"], - ) - + "{0!s} {1!s} ? ? program ? ? phasing ? ?\n".format( - str(max(softwareEntry) + 2), - self.data_template_dict["phasing_software"], - ) - # '#\n' - # "loop_\n" - # "_pdbx_related_exp_data_set.ordinal\n" - # "_pdbx_related_exp_data_set.data_reference\n" - # "_pdbx_related_exp_data_set.metadata_reference\n" - # "_pdbx_related_exp_data_set.data_set_type\n" - # "_pdbx_related_exp_data_set.details\n" - # " 1 " - # " 'doi:%s' " %self.zenodo_dict['ZenodoDOI']+ - # " 'doi:%s' " %self.zenodo_dict['ZenodoDOI']+ - # " 'other data' " # 'other data' is only thing wwPDB accepts at the moment - # " 'Complete PanDDA analysis'\n" - # "\n" + cifItem = "{0!s} {1!s} ? ? program ? ? 'data reduction' ? ?\n".format( + str(max(softwareEntry) + 1), + self.data_template_dict["data_integration_software"], + ) + "{0!s} {1!s} ? ? program ? ? phasing ? ?\n".format( + str(max(softwareEntry) + 2), + self.data_template_dict["phasing_software"], ) sys.stdout.write(cifItem) @@ -1408,12 +1273,6 @@ def update_model_mmcif_header(self, xtal): else: sys.stdout.write(line) - # elif '_reflns.d_resolution_low' in line and len(line.split()) == 2: - # sys.stdout.write('_reflns.d_resolution_low {0!s}\n'.format(min(low_reso_list))) - # - # elif '_refine.ls_d_res_low' in line and len(line.split()) == 2: - # sys.stdout.write('_refine.ls_d_res_low {0!s}\n'.format(min(low_reso_list))) - def add_funding_information(self, xtal): pdbx_funding_ordinal_one = self.data_template_dict["pdbx_funding_ordinal_one"] if ( @@ -1503,7 +1362,8 @@ def add_ligand_cif_to_model_mmcif(self, xtal): os.chdir(os.path.join(self.projectDir, xtal)) if os.path.isfile(self.db_dict["RefinementMMCIFmodel_latest"]): self.Logfile.insert( - "%s: found %s; assuming that ligand cif dictionary is already included..." + "%s: found %s; assuming that ligand cif dictionary" + " is already included..." % (xtal, self.db_dict["RefinementMMCIFmodel_latest"]) ) filestatus = True @@ -1535,8 +1395,14 @@ def make_table_one(self, xtal): if os.path.isfile(xtal + ".mmcif") and os.path.getsize(xtal + ".mmcif") > 20000: self.Logfile.insert("making table_1 for %s.mmcif" % xtal) if os.path.isdir("/dls"): - extract_table_init = "source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n" - extract_table_init += "/dls/science/groups/i04-1/software/pdb-extract-prod/bin/extract_table" + extract_table_init = ( + "source /dls/science/groups/i04-1/software/" + "pdb-extract-prod/setup.sh\n" + ) + extract_table_init += ( + "/dls/science/groups/i04-1/software/" + "pdb-extract-prod/bin/extract_table" + ) else: extract_table_init = ( "source " @@ -1562,9 +1428,8 @@ def make_table_one(self, xtal): "%s: table_1 successfully created; updating database..." % xtal ) self.db.execute_statement( - "update mainTable set table_one='{0!s}-table-1.txt' where CrystalName is '{1!s}'".format( - xtal, xtal - ) + "update mainTable set table_one='{0!s}-table-1.txt'" + " where CrystalName is '{1!s}'".format(xtal, xtal) ) else: self.Logfile.warning("%s: could not create table_1" % xtal) @@ -1583,9 +1448,6 @@ def create_sf_mmcif(self, xtal): for event in self.eventList: mtzin += event + " " - # if self.ground_state: - # mtzin = self.ground_state_mean_mtz - if os.path.isdir("/dls"): pdb_extract_init = ( "source /dls/science/groups/i04-1/software/pdb-extract-prod/setup.sh\n" @@ -1624,7 +1486,8 @@ def create_sf_mmcif(self, xtal): self.Logfile.insert(xtal + ": running sf_convert: " + Cmd) os.system(Cmd) os.system( - "/bin/rm sf_format_guess.text mtzdmp.log SF_4_validate.cif sf_information.cif" + "/bin/rm sf_format_guess.text mtzdmp.log" + " SF_4_validate.cif sf_information.cif" ) self.update_sf_mmcif_file(xtal) @@ -1636,15 +1499,16 @@ def create_sf_mmcif(self, xtal): self.Logfile.insert("%s: SF mmcif file successfully created" % xtal) if self.ground_state: self.db.execute_statement( - "update depositTable set mmCIF_SF_file='{0!s}_sf.mmcif' where CrystalName is '{1!s}' and DimplePANDDApath is '{2!s}'".format( + "update depositTable set mmCIF_SF_file='{0!s}_sf.mmcif'" + " where CrystalName is '{1!s}'" + " and DimplePANDDApath is '{2!s}'".format( xtal, xtal, self.panddaDir ) ) else: self.db.execute_statement( - "update depositTable set mmCIF_SF_file='{0!s}_sf.mmcif' where CrystalName is '{1!s}'".format( - xtal, xtal - ) + "update depositTable set mmCIF_SF_file='{0!s}_sf.mmcif'" + " where CrystalName is '{1!s}'".format(xtal, xtal) ) fileStatus = True else: @@ -1719,7 +1583,8 @@ def add_apo_sf_mmcif_to_ground_state_mmcif(self): newLine += "#\n" newLine += "_diffrn.id 1\n" newLine += ( - '_diffrn.details "diffraction data from crystal %s; soaked compound: %s"\n' + '_diffrn.details "diffraction data' + ' from crystal %s; soaked compound: %s"\n' % (str(counter), smiles.replace("\n", "").replace("\r", "")) ) f.write(newLine) @@ -1768,7 +1633,6 @@ def add_data_increment_to_apo_mmcif(self): c = 0 foundFirstLine = False - foundCulprit = False datasetCounter = 0 if os.path.isfile(os.path.join(self.panddaDir, "ground_state_sf.mmcif")): f = open("ground_state_sf_tmp.mmcif", "w") @@ -1798,8 +1662,6 @@ def add_data_increment_to_apo_mmcif(self): newLine.replace("\n", "").replace("\r", ""), ) ) - # if datasetCounter % 50 == 0: - # self.Logfile.insert('%s data_rxxxxsf records edited...' %str(datasetCounter)) else: f.write(line) f.close() @@ -1812,9 +1674,9 @@ def add_data_increment_to_apo_mmcif(self): ): self.Logfile.insert("ground_state: SF mmcif file successfully created") self.db.execute_statement( - "update depositTable set mmCIF_SF_file='ground_state_sf.mmcif' where CrystalName is 'ground_state' and DimplePANDDApath is '{0!s}'".format( - self.panddaDir - ) + "update depositTable set mmCIF_SF_file='ground_state_sf.mmcif'" + " where CrystalName is 'ground_state'" + " and DimplePANDDApath is '{0!s}'".format(self.panddaDir) ) else: self.Logfile.error("%s: SF mmcif file was not created successfully") @@ -1933,7 +1795,8 @@ def run(self): xtalString += "CrystalName = '" + xtal + "' or " xtalString = xtalString[:-4] + ")" toDeposit = self.db.execute_statement( - "select CrystalName,mmCIF_model_file,mmCIF_SF_file,DimplePANDDApath from depositTable where StructureType is 'ligand_bound' and %s;" + "select CrystalName,mmCIF_model_file,mmCIF_SF_file,DimplePANDDApath" + " from depositTable where StructureType is 'ligand_bound' and %s;" % xtalString ) elif self.type == "ground_state": @@ -1941,7 +1804,8 @@ def run(self): "checking depositionTable for mmcif files of ground-state structures" ) toDeposit = self.db.execute_statement( - "select CrystalName,mmCIF_model_file,mmCIF_SF_file,DimplePANDDApath from depositTable where StructureType is 'ground_state';" + "select CrystalName,mmCIF_model_file,mmCIF_SF_file,DimplePANDDApath" + " from depositTable where StructureType is 'ground_state';" ) else: return @@ -1977,9 +1841,8 @@ def run(self): os.system("/bin/cp {0!s} .".format(mmcif_sf)) if self.type == "ground_state": os.system( - "/bin/mv ground_state_sf.mmcif ground_state_{0!s}_sf.mmcif".format( - str(n) - ) + "/bin/mv ground_state_sf.mmcif" + " ground_state_{0!s}_sf.mmcif".format(str(n)) ) mmcif_sf = mmcif_sf.replace( "ground_state_sf.mmcif", @@ -2036,41 +1899,6 @@ def run(self): self.Logfile.insert("done!") -# # apo structures -# TextIndex='' -# toDeposit=self.db.execute_statement("select CrystalName,mmCIF_model_file,mmCIF_SF_file from depositTable where StructureType is 'apo';") -# for item in sorted(toDeposit): -# xtal=str(item[0]) -# mmcif=str(item[1]) -# mmcif_sf=str(item[2]) -# if os.path.isfile(mmcif) and os.path.isfile(mmcif_sf): -# self.Logfile.insert('copying {0!s} to {1!s}'.format(mmcif, self.depositDir)) -# os.system('/bin/cp {0!s} .'.format(mmcif)) -# self.Logfile.insert('copying {0!s} to {1!s}'.format(mmcif_sf, self.depositDir)) -# os.system('/bin/cp {0!s} .'.format(mmcif_sf)) -# else: -# self.Logfile.insert('cannot find apo mmcif file for '+xtal+' => ERROR') -# -# text = ( 'label: {0!s}-apo\n'.format(xtal)+ -# 'description: apo structure of {0!s}\n'.format(xtal)+ -# 'model: {0!s}\n'.format(mmcif[mmcif.rfind('/')+1:])+ -# 'sf: {0!s}\n\n'.format(mmcif_sf[mmcif_sf.rfind('/')+1:]) ) -# TextIndex+=text -# -# f = open('index.txt','w') -# f.write(TextIndex) -# f.close() -# -# self.Logfile.insert('preparing tar archive...') -# os.system('tar -cvf apo_structures.tar *apo* index.txt') -# self.Logfile.insert('bzipping archive...') -# os.system('bzip2 apo_structures.tar') -# self.Logfile.insert('removing all apo mmcif files and index.txt file from '+self.depositDir) -# os.system('/bin/rm -f *apo*mmcif index.txt') -# self.Logfile.insert('done!') -# - - class import_PDB_IDs(QtCore.QThread): def __init__(self, pdbCodes, database, xce_logfile): QtCore.QThread.__init__(self) @@ -2086,8 +1914,10 @@ def run(self): xtal = line[: line.rfind("-ligand_bound")].replace(" ", "") pdbID = line.split("/")[1].replace(" ", "") self.Logfile.insert("setting PDB ID for " + xtal + " to " + pdbID) - sqlite = "UPDATE mainTable SET Deposition_PDB_ID='{0!s}',RefinementOutcome='6 - Deposited' where CrystalName is '{1!s}';".format( - pdbID, xtal + sqlite = ( + "UPDATE mainTable SET Deposition_PDB_ID='{0!s}'," + "RefinementOutcome='6 - Deposited'" + " where CrystalName is '{1!s}';".format(pdbID, xtal) ) self.db.execute_statement(sqlite) @@ -2121,9 +1951,8 @@ def run(self): for xtal in sorted(glob.glob("*")): if os.path.isfile(os.path.join(xtal, "refine.pdb")): smiles = self.db.execute_statement( - "select CompoundSmiles,CompoundCode from mainTable where CrystalName is '{0!s}'".format( - xtal - ) + "select CompoundSmiles,CompoundCode from mainTable" + " where CrystalName is '{0!s}'".format(xtal) ) try: LigandSmiles = str(smiles[0][0]) @@ -2131,7 +1960,8 @@ def run(self): elementDict_smiles = smilestools(LigandSmiles).ElementDict() except IndexError: self.Logfile.error( - "{0!s}: something is seems to be wrong with the CompoundCode or SMILES string: {1!s}".format( + "{0!s}: something is seems to be wrong" + " with the CompoundCode or SMILES string: {1!s}".format( xtal, str(smiles) ) ) @@ -2150,7 +1980,9 @@ def run(self): for element in elementDict_ligand: if elementDict_ligand[element] != elementDict_smiles[element]: self.Logfile.error( - "{0!s}: {1!s} {2!s} {3!s} {4!s} contains different number of atoms than smiles in DB: {5!s} -> {6!s}".format( + "{0!s}: {1!s} {2!s} {3!s} {4!s} contains different" + " number of atoms than smiles in DB:" + " {5!s} -> {6!s}".format( xtal, resname, chainID, @@ -2162,7 +1994,8 @@ def run(self): ) self.update_ErrorDict( xtal, - "{0!s} {1!s} {2!s} {3!s} contains different number of atoms than smiles in DB".format( + "{0!s} {1!s} {2!s} {3!s} contains different" + " number of atoms than smiles in DB".format( resname, chainID, resseq, altLoc ), ) From 0850c7c35ee55fb50f8496a48c30fa7c8dbba4e8 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 9 Nov 2022 11:30:25 +0000 Subject: [PATCH 164/358] Clean up XChemDB --- xce/lib/XChemDB.py | 281 ++++++++++++--------------------------------- 1 file changed, 72 insertions(+), 209 deletions(-) diff --git a/xce/lib/XChemDB.py b/xce/lib/XChemDB.py index 6ee9e3d2..fbbce3c3 100755 --- a/xce/lib/XChemDB.py +++ b/xce/lib/XChemDB.py @@ -1,7 +1,5 @@ import XChemLog import sqlite3 -import os -import glob import csv from datetime import datetime import getpass @@ -15,9 +13,9 @@ def __init__(self, data_source_file): self.data_source_file = data_source_file - # [column_name in DB, column_name shown in XCE, SQLite column type (Integer,Text,PKEY...)] + # [column_name in DB, column_name shown in XCE, SQLite column type] self.column_list = [ - # SQLite column name XCE column name SQLite type display in overview tab + # SQLite column name | XCE column name | SQLite type | in overview tab # from Lab36 ["ID", "ID", "INTEGER PRIMARY KEY", 0], ["LabVisit", "LabVisit", "TEXT", 1], @@ -105,8 +103,6 @@ def __init__(self, data_source_file): ["DataProcessingAlpha", "DataProcessing\nAlpha", "TEXT", 0], ["DataProcessingBeta", "DataProcessing\nBeta", "TEXT", 0], ["DataProcessingGamma", "DataProcessing\nGamma", "TEXT", 0], - # True or False depending on whether user changed automatic selection - # ['DataProcessingUserSelected', 'DataProcessingUserSelected', 'TEXT', 0], ["DataProcessingResolutionOverall", "Resolution\nOverall", "TEXT", 0], ["DataProcessingResolutionLow", "Resolution\nLow", "TEXT", 0], [ @@ -150,7 +146,8 @@ def __init__(self, data_source_file): ["DataProcessingCChalfLow", "CC(1/2)\nLow", "TEXT", 1], ["DataProcessingCChalfHigh", "CC(1/2)\nHigh", "TEXT", 1], # the data source is a bit exploding with entries like the ones below, - # but the many different filenames and folder structures of Diamond autoprocessing makes it necessary + # but the many different filenames and folder structures of Diamond + # autoprocessing makes it necessary ["DataProcessingPathToLogfile", "DataProcessingPathToLogfile", "TEXT", 1], ["DataProcessingPathToMTZfile", "DataProcessingPathToMTZfile", "TEXT", 1], ["DataProcessingLOGfileName", "DataProcessingLOGfileName", "TEXT", 0], @@ -783,38 +780,6 @@ def create_missing_columns(self): "insert into labelTable (ID) Values (%s)" % str(idx + 1) ) - # existing_columns=[] - # connect=sqlite3.connect(self.data_source_file) - # connect.row_factory = sqlite3.Row - # cursor = connect.cursor() - # cursor.execute("SELECT * FROM mainTable") - # for column in cursor.description: - # existing_columns.append(column[0]) - # for column in self.column_list: - # if column[0] not in existing_columns: - # cursor.execute("alter table mainTable add column '"+column[0]+"' '"+column[2]+"'") - # connect.commit() - # # create PANDDA table if not exists - # cursor.execute("create table if not exists panddaTable (ID INTEGER);") - # existing_columns=[] - # cursor.execute("SELECT * FROM panddaTable") - # for column in cursor.description: - # existing_columns.append(column[0]) - # for column in self.pandda_table_columns: - # if column[0] not in existing_columns: - # cursor.execute("alter table panddaTable add column '"+column[0]+"' '"+column[2]+"'") - # connect.commit() - # # create DEPOSIT table if not exists - # cursor.execute("create table if not exists depositTable (ID INTEGER);") - # existing_columns=[] - # cursor.execute("SELECT * FROM depositTable") - # for column in cursor.description: - # existing_columns.append(column[0]) - # for column in self.deposition_table_columns: - # if column[0] not in existing_columns: - # cursor.execute("alter table depositTable add column '"+column[0]+"' '"+column[2]+"'") - # connect.commit() - def return_column_list(self): return self.column_list @@ -840,15 +805,9 @@ def create_empty_data_source_file(self): + "'" ) connect.commit() - # Don't need to create panddaTable at this point, because table will be created by create_missing_columns - # which is called the first time a data source in specified in XCE - - # with connect: - # cursor = connect.cursor() - # cursor.execute("CREATE TABLE panddaTable("+self.pandda_table_columns[0][0]+' '+self.pandda_table_columns[0][2]+")") - # for i in range(1,len(self.pandda_table_columns)): - # cursor.execute("alter table mainTable add column '"+self.pandda_table_columns[i][0]+"' '"+self.pandda_table_columns[i][2]+"'") - # connect.commit() + # Don't need to create panddaTable at this point, because table will be created + # by create_missing_columns which is called the first time a data source in + # specified in XCE def get_all_samples_in_data_source_as_list(self): # creates sqlite file if non existent @@ -902,10 +861,6 @@ def get_deposit_dict_for_sample(self, sampleID): # creates sqlite file if non existent connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() - # if sampleID == 'ground-state': # just select first row in depositTable - # cursor.execute("SELECT * FROM depositTable ORDER BY ROWID ASC LIMIT 1;") - # else: - # cursor.execute("select * from depositTable where CrystalName='{0!s}';".format(sampleID)) cursor.execute( "select * from depositTable where CrystalName='{0!s}';".format(sampleID) ) @@ -927,9 +882,8 @@ def get_db_pandda_dict_for_sample_and_site(self, sampleID, site_index): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - "select * from panddaTable where CrystalName='{0!s}' and PANDDA_site_index='{1!s}';".format( - sampleID, site_index - ) + "select * from panddaTable where CrystalName='{0!s}'" + " and PANDDA_site_index='{1!s}';".format(sampleID, site_index) ) for column in cursor.description: header.append(column[0]) @@ -948,7 +902,10 @@ def get_db_pandda_dict_for_sample_and_site_and_event( connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - "select * from panddaTable where CrystalName='{0!s}' and PANDDA_site_index='{1!s}' and PANDDA_site_event_index='{2!s}' and PANDDA_site_ligand_placed='True';".format( + "select * from panddaTable where CrystalName='{0!s}'" + " and PANDDA_site_index='{1!s}'" + " and PANDDA_site_event_index='{2!s}'" + " and PANDDA_site_ligand_placed='True';".format( sampleID, site_index, event_index ) ) @@ -988,16 +945,12 @@ def import_csv_file(self, csv_file): continue if key not in available_columns: continue - # this is how I had it originally, so it would ignore empty fields - # the problem is that if the user wants to set all values to Null, - # if will ignore it and leave the inital value in the datasource - # if not str(value).replace(' ','')=='': # ignore if nothing in csv field - # update_string+=str(key)+'='+"'"+str(value)+"'"+',' - # print "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';" - # cursor.execute("UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';") - # now try this instead; not sure what will break now... + # this is how I had it originally, so it would ignore empty + # fields. the problem is that if the user wants to set all + # values to Null. if will ignore it and leave the inital value + # in the datasource. now try this instead; not sure what will + # break now... update_string += str(key) + "=" + "'" + str(value) + "'" + "," - # print "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"';" cursor.execute( "UPDATE mainTable SET " + update_string[:-1] @@ -1018,8 +971,6 @@ def import_csv_file(self, csv_file): if not str(value).replace(" ", "") == "": value_string += "'" + value + "'" + "," column_string += key + "," - # print sampleID - # print "INSERT INTO mainTable ("+column_string[:-1]+") VALUES ("+value_string[:-1]+");" cursor.execute( "INSERT INTO mainTable (" + column_string[:-1] @@ -1058,7 +1009,6 @@ def update_data_source(self, sampleID, data_dict): else: update_string += str(key) + " = null," if update_string != "": - # print "UPDATE mainTable SET "+update_string[:-1]+" WHERE CrystalName="+"'"+sampleID+"'" cursor.execute( "UPDATE mainTable SET " + update_string[:-1] @@ -1118,7 +1068,8 @@ def update_site_event_panddaTable( cursor.execute( "UPDATE panddaTable SET " + update_string[:-1] - + " WHERE CrystalName='{0!s}' and PANDDA_site_index='{1!s}' and PANDDA_site_event_index='{2!s}'".format( + + " WHERE CrystalName='{0!s}' and PANDDA_site_index='{1!s}'" + " and PANDDA_site_event_index='{2!s}'".format( sampleID, site_index, event_index ) ) @@ -1135,8 +1086,6 @@ def update_depositTable(self, sampleID, structure_type, data_dict): if key == "ID" or key == "CrystalName" or key == "StructureType": continue if not str(value).replace(" ", "") == "": # ignore empty fields - # update_string+=str(key)+'='+"'"+str(value)+"'"+',' - # update_string+=str(key)+'='+'"'+str(value)+'"'+',' update_string += ( str(key) + "=" @@ -1148,8 +1097,6 @@ def update_depositTable(self, sampleID, structure_type, data_dict): else: update_string += str(key) + " = null," if update_string != "": - # print '-->',"UPDATE depositTable SET "+update_string[:-1]+" WHERE CrystalName='{0!s}' and StructureType='{1!s}'".format(sampleID, structure_type) - # cursor.execute("UPDATE depositTable SET "+update_string[:-1]+" WHERE CrystalName='{0!s}' and StructureType='{1!s}'".format(sampleID, structure_type)) cursor.execute( "UPDATE depositTable SET " + update_string[:-1] @@ -1293,12 +1240,9 @@ def update_insert_site_event_panddaTable(self, sampleID, data_dict): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - "Select CrystalName,PANDDA_site_index,PANDDA_site_event_index FROM panddaTable" + "Select CrystalName,PANDDA_site_index,PANDDA_site_event_index" + " FROM panddaTable" ) - # available_columns=[] - # cursor.execute("SELECT * FROM panddaTable") - # for column in cursor.description: # only update existing columns in data source - # available_columns.append(column[0]) samples_sites_in_table = [] tmp = cursor.fetchall() for item in tmp: @@ -1326,7 +1270,6 @@ def update_insert_site_event_panddaTable(self, sampleID, data_dict): continue if not str(value).replace(" ", "") == "": # ignore empty fields update_string = str(key) + "=" + "'" + str(value) + "'" - # print "UPDATE panddaTable SET "+update_string+" WHERE CrystalName="+"'"+sampleID+"' and PANDDA_site_index is '"+data_dict['PANDDA_site_index']+"';" cursor.execute( "UPDATE panddaTable SET " + update_string @@ -1346,8 +1289,6 @@ def update_insert_site_event_panddaTable(self, sampleID, data_dict): value = data_dict[key] if key == "ID": continue - # if key not in available_columns: - # continue if ( not str(value).replace(" ", "") == "" ): # ignore if nothing in csv field @@ -1384,14 +1325,8 @@ def update_insert_depositTable(self, sampleID, data_dict): tmp = cursor.fetchall() for item in tmp: line = [x.encode("UTF8") for x in list(item)] - # print 'a',item - # print 'b',str(item) - # print 'c',line - # print 'd',line[0] - # print 'e',str(line[0]) if str(item) not in samples_in_table: samples_in_table.append(str(line[0])) - # samples_in_table.append(line) if sampleID in samples_in_table: for key in data_dict: @@ -1457,17 +1392,6 @@ def export_to_csv_file(self, csv_file): csvWriter = csv.writer(open(csv_file, "w")) csvWriter.writerows([header] + rows) - # def load_samples_from_data_source(self): - # header=[] - # data=[] - # connect=sqlite3.connect(self.data_source_file) - # cursor = connect.cursor() - # cursor.execute("SELECT * FROM mainTable") - # for column in cursor.description: - # header.append(column[0]) - # data = cursor.fetchall() - # return ([header,data]) - def load_samples_from_data_source(self): header = [] data = [] @@ -1479,68 +1403,6 @@ def load_samples_from_data_source(self): data = cursor.fetchall() return header, data - # def get_samples_for_coot(self,RefinementOutcome,pandda_site): - # sample_list_for_coot=[] - # connect=sqlite3.connect(self.data_source_file) - # cursor = connect.cursor() - # - # if RefinementOutcome=='0 - All Datasets': - # outcome = " not null " - # else: - # outcome = " '%s' " %RefinementOutcome - # - # if int(pandda_site) > 0: - # sqlite = ( - # "select" - # " mainTable.CrystalName," - # " mainTable.CompoundCode," - # " mainTable.RefinementCIF," - # " mainTable.RefinementMTZfree," - # " mainTable.RefinementPathToRefinementFolder," - # " panddaTable.RefinementOutcome, " - # " panddaTable.PANDDA_site_event_map," - # " panddaTable.PANDDA_site_confidence," - # " panddaTable.PANDDA_site_x," - # " panddaTable.PANDDA_site_y," - # " panddaTable.PANDDA_site_z," - # " panddaTable.PANDDA_site_initial_model," - # " panddaTable.PANDDA_site_initial_mtz," - # " panddaTable.PANDDA_site_spider_plot, " - # " panddaTable.PANDDA_site_index " - # "from mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " - # "where panddaTable.PANDDA_site_index is '%s'" %pandda_site+ - # " and panddaTable.PANDDA_site_ligand_placed is 'True'" - # " and panddaTable.RefinementOutcome is %s;" %outcome - # ) - # - # else: - # sqlite = ( - # "select" - # " CrystalName," - # " CompoundCode," - # " RefinementCIF," - # " RefinementMTZfree," - # " RefinementPathToRefinementFolder," - # " RefinementOutcome " - # "from mainTable " - # "where RefinementOutcome is %s;" %outcome - # ) - # - # cursor.execute(sqlite) - # - # tmp = cursor.fetchall() - # for item in tmp: - # tmpx=[] - # for i in list(item): - # if i==None: - # tmpx.append('None') - # else: - # tmpx.append(i) - # line=[x.encode('UTF8') for x in tmpx] - # sample_list_for_coot.append(line) - # - # return sample_list_for_coot - def get_todoList_for_coot(self, RefinementOutcome): sample_list_for_coot = [] connect = sqlite3.connect(self.data_source_file) @@ -1561,8 +1423,9 @@ def get_todoList_for_coot(self, RefinementOutcome): " RefinementOutcome," " RefinementLigandConfidence " "from mainTable " - "where RefinementOutcome is %s and (DimpleRfree is not Null or RefinementRfree is not Null) order by CrystalName ASC;" - % outcome + "where RefinementOutcome is %s" + " and (DimpleRfree is not Null or RefinementRfree is not Null)" + " order by CrystalName ASC;" % outcome ) cursor.execute(sqlite) @@ -1647,11 +1510,7 @@ def translate_xce_column_list_to_sqlite(self, column_list): out_list.append(["Exclude"]) if item.startswith("Ignore"): out_list.append(["Ignore"]) - # if item.startswith('img'): - # out_list.append([item,item]) - # continue if item.startswith("Export"): - # out_list.append('Export') out_list.append(["Export", item]) continue if item.startswith("Show"): @@ -1703,10 +1562,6 @@ def get_list_of_pandda_sites_for_coot(self): cursor.execute(sqlite) tmp = cursor.fetchall() for item in tmp: - # print item - # print str(item[0]) - # print str(item[1]) - # line=[x.encode('UTF8') for x in list(item)] site_list.append([str(item[0]), str(item[1])]) return site_list @@ -1725,9 +1580,11 @@ def export_csv_for_WONKA(self): " panddaTable.CrystalName," " mainTable.CompoundCode " "from" - " mainTable inner join panddaTable on mainTable.CrystalName = panddaTable.CrystalName " - "where" - " (panddaTable.RefinementOutcome like '3%' or panddaTable.RefinementOutcome like '4%' or panddaTable.RefinementOutcome like '5%')" + " mainTable inner join panddaTable" + " on mainTable.CrystalName = panddaTable.CrystalName " + "where (panddaTable.RefinementOutcome like '3%'" + " or panddaTable.RefinementOutcome like '4%'" + " or panddaTable.RefinementOutcome like '5%')" ) connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() @@ -1748,9 +1605,8 @@ def create_or_remove_missing_records_in_depositTable( oldRefiStage = "" if type == "ligand_bound": cursor.execute( - "select RefinementOutcome from mainTable where CrystalName is '{0!s}'".format( - xtal - ) + "select RefinementOutcome" + " from mainTable where CrystalName is '{0!s}'".format(xtal) ) tmp = cursor.fetchall() oldRefiStage = str(tmp[0][0]) @@ -1763,7 +1619,9 @@ def create_or_remove_missing_records_in_depositTable( self.update_insert_data_source(xtal, db_dict) elif type == "ground_state": cursor.execute( - "select DimplePANDDApath from depositTable where StructureType is '{0!s}' and DimplePANDDApath is '{1!s}'".format( + "select DimplePANDDApath from depositTable" + " where StructureType is '{0!s}'" + " and DimplePANDDApath is '{1!s}'".format( type, db_dict["DimplePANDDApath"] ) ) @@ -1780,7 +1638,8 @@ def create_or_remove_missing_records_in_depositTable( "updating PDB, MTZ and DimplePANDDApath for ground-state entry" ) cursor.execute( - "update depositTable set PDB_file='%s', MTZ_file='%s', DimplePANDDApath='%s' where StructureType='ground_state'" + "update depositTable set PDB_file='%s', MTZ_file='%s'," + " DimplePANDDApath='%s' where StructureType='ground_state'" % ( db_dict["PDB_file"], db_dict["MTZ_file"], @@ -1791,15 +1650,17 @@ def create_or_remove_missing_records_in_depositTable( return cursor.execute( - "select CrystalName,StructureType from depositTable where CrystalName is '{0!s}' and StructureType is '{1!s}'".format( + "select CrystalName,StructureType from depositTable" + " where CrystalName is '{0!s}' and StructureType is '{1!s}'".format( xtal, type ) ) tmp = cursor.fetchall() if type == "ligand_bound": if not tmp and int(db_dict["RefinementOutcome"].split()[0]) == 5: - sqlite = "insert into depositTable (CrystalName,StructureType) values ('{0!s}','{1!s}');".format( - xtal, type + sqlite = ( + "insert into depositTable (CrystalName,StructureType)" + " values ('{0!s}','{1!s}');".format(xtal, type) ) Logfile.insert( "creating new entry for " @@ -1812,8 +1673,9 @@ def create_or_remove_missing_records_in_depositTable( connect.commit() else: if int(db_dict["RefinementOutcome"].split()[0]) != 5: - sqlite = "delete from depositTable where CrystalName is '{0!s}' and StructureType is '{1!s}'".format( - xtal, type + sqlite = ( + "delete from depositTable where CrystalName is '{0!s}'" + " and StructureType is '{1!s}'".format(xtal, type) ) if oldRefiStage.startswith("5"): Logfile.insert( @@ -1826,12 +1688,16 @@ def create_or_remove_missing_records_in_depositTable( cursor.execute(sqlite) connect.commit() elif type == "ground_state": - sqlite = "insert into depositTable (CrystalName,StructureType,DimplePANDDApath,PDB_file,MTZ_file) values ('{0!s}','{1!s}','{2!s}','{3!s}','{4!s}');".format( - xtal, - type, - db_dict["DimplePANDDApath"], - db_dict["PDB_file"], - db_dict["MTZ_file"], + sqlite = ( + "insert into depositTable" + " (CrystalName,StructureType,DimplePANDDApath,PDB_file,MTZ_file)" + " values ('{0!s}','{1!s}','{2!s}','{3!s}','{4!s}');".format( + xtal, + type, + db_dict["DimplePANDDApath"], + db_dict["PDB_file"], + db_dict["MTZ_file"], + ) ) Logfile.insert( "creating new entry for " @@ -1848,9 +1714,8 @@ def collected_xtals_during_visit(self, visitID): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() cursor.execute( - "select CrystalName from collectionTable where DataCollectionVisit = '{0!s}'".format( - visitID - ) + "select CrystalName from collectionTable" + " where DataCollectionVisit = '{0!s}'".format(visitID) ) collectedXtals = [] samples = cursor.fetchall() @@ -1864,13 +1729,9 @@ def collected_xtals_during_visit_for_scoring(self, visit): connect = sqlite3.connect(self.data_source_file) cursor = connect.cursor() xtalList = [] - # if rescore == True: - # cursor.execute("select CrystalName from mainTable where DataCollectionVisit = '%s'" %visit) - # else: - # cursor.execute("select CrystalName from mainTable where DataProcessingAutoAssigned = 'True' and DataCollectionVisit = '%s'" %visit) cursor.execute( - "select distinct CrystalName from collectionTable where DataCollectionVisit = '%s'" - % visit + "select distinct CrystalName from collectionTable" + " where DataCollectionVisit = '%s'" % visit ) samples = cursor.fetchall() for sample in samples: @@ -1961,8 +1822,7 @@ def xtals_collected_during_visit_as_dict(self, visitID): collectedXtals = self.collected_xtals_during_visit(visitID) xtalDict = {} # creates sqlite file if non existent - connect = sqlite3.connect(self.data_source_file) - cursor = connect.cursor() + sqlite3.connect(self.data_source_file).cursor() for xtal in sorted(collectedXtals): db_dict = self.get_db_dict_for_sample(xtal) xtalDict[xtal] = db_dict @@ -1974,17 +1834,20 @@ def samples_for_html_summary(self, whichSamples): cursor = connect.cursor() if whichSamples.startswith("4"): cursor.execute( - "select CrystalName from mainTable where RefinementOutcome like '4%' order by CrystalName ASC" + "select CrystalName from mainTable" + " where RefinementOutcome like '4%' order by CrystalName ASC" ) elif whichSamples.startswith("5"): cursor.execute( - "select CrystalName from mainTable where RefinementOutcome like '5%' order by CrystalName ASC" + "select CrystalName from mainTable" + " where RefinementOutcome like '5%' order by CrystalName ASC" ) else: cursor.execute( - "select CrystalName from mainTable where RefinementOutcome like '4%' or " - "RefinementOutcome like '5%' or " - "RefinementOutcome like '6%' order by CrystalName ASC" + "select CrystalName from mainTable" + " where RefinementOutcome like '4%'" + " or RefinementOutcome like '5%'" + " or RefinementOutcome like '6%' order by CrystalName ASC" ) xtalList = [] samples = cursor.fetchall() @@ -2026,8 +1889,8 @@ def get_label_info_from_db(self): cursor.execute("select Label,Description from labelTable") labels = cursor.fetchall() labelList = [] - for l in labels: - labelList.append([str(l[0]), str(l[1])]) + for label in labels: + labelList.append([str(label[0]), str(label[1])]) return labelList def get_label_of_sample(self, xtalID): @@ -2037,7 +1900,7 @@ def get_label_of_sample(self, xtalID): cursor.execute("select label from mainTable where CrystalName is '%s'" % xtalID) label = None lab = cursor.fetchall() - for l in lab: - label = l[0] + for sample in lab: + label = sample[0] break return label From 8371e89c6783868c097792102e9d6fc826aae72d Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 9 Nov 2022 11:47:40 +0000 Subject: [PATCH 165/358] Clean up XChemCootTwin --- xce/lib/XChemCootTwin.py | 477 +++------------------------------------ 1 file changed, 32 insertions(+), 445 deletions(-) diff --git a/xce/lib/XChemCootTwin.py b/xce/lib/XChemCootTwin.py index bf392420..ac3d46c0 100755 --- a/xce/lib/XChemCootTwin.py +++ b/xce/lib/XChemCootTwin.py @@ -13,7 +13,7 @@ from matplotlib.figure import Figure # had to adapt the original coot_utils.py file -# otherwise unable to import the original file without complaints about missing modules etc. +# otherwise unable to import the original file without complaints about missing modules # modified file is now in $XChemExplorer_DIR/lib @@ -24,7 +24,7 @@ class GUI(object): def __init__(self): - ########################################################################################### + ################################################################################ # read in settings file from XChemExplorer to set the relevant paths self.settings = pickle.load(open(".xce_settings.pkl", "rb")) @@ -74,13 +74,12 @@ def __init__(self): # this decides which samples will be looked at self.selection_mode = "" - # self.selected_site='' self.pandda_index = -1 # refers to the number of sites self.site_index = "0" self.event_index = "0" - # the Folder is kind of a legacy thing because my inital idea was to have separate folders - # for Data Processing and Refinement + # the Folder is kind of a legacy thing because my inital idea was to have + # separate folders for Data Processing and Refinement self.project_directory = self.settings["initial_model_directory"] self.Serial = 0 self.panddaSerial = 0 @@ -95,8 +94,6 @@ def __init__(self): self.spider_plot = "" self.ligand_confidence = "" self.refinement_folder = "" - # self.refinementProtocol = 'pandda_refmac' - # self.datasetOutcome='' self.pdb_style = "refine.pdb" self.mtz_style = "refine.mtz" @@ -124,7 +121,7 @@ def __init__(self): self.label_button_list = [] - ########################################################################################### + ################################################################################ # some COOT settings coot.set_map_radius(17) coot.set_colour_map_rotation_for_map(0) @@ -188,13 +185,11 @@ def StartGUI(self): self.window.set_title("XChemExplorer") self.vbox = gtk.VBox() # this is the main container - ################################################################################# + ################################################################################ # --- Sample Selection --- - # self.vbox.add(gtk.Label('Select Samples')) frame = gtk.Frame(label="Select Samples") self.hbox_select_samples = gtk.HBox() - # vbox=gtk.VBox() self.cb_select_samples = gtk.combo_box_new_text() self.cb_select_samples.connect("changed", self.set_selection_mode) @@ -202,48 +197,20 @@ def StartGUI(self): self.cb_select_samples.append_text(citeria) self.hbox_select_samples.add(self.cb_select_samples) - # self.cb_select_sites = gtk.combo_box_new_text() - # self.cb_select_sites.connect("changed", self.set_site) - # for site in self.ligand_site_information: - # self.cb_select_sites.append_text(str(site[0])+' - '+str(site[1])) - # self.hbox_select_samples.add(self.cb_select_sites) - self.select_samples_button = gtk.Button(label="GO") self.select_samples_button.connect("clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) - ################################################################################# + ################################################################################ # --- status window --- frame = gtk.Frame() self.status_label = gtk.Label() frame.add(self.status_label) self.vbox.pack_start(frame) - ################################################################################# - # --- refinement protocol --- - # frame = gtk.Frame() - # self.refinementProtocolcheckbox = gtk.CheckButton('PanDDA model refinement)') - # # callback is defined later - ## self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) - # self.refinementProtocolcheckbox.set_active(True) - # frame.add(self.refinementProtocolcheckbox) - # self.vbox.pack_start(frame) - - ################################################################################# - # --- refinement program --- - # frame = gtk.Frame() - # self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') - # self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) - # self.refinementProgramcheckbox.set_active(False) - # frame.add(self.refinementProgramcheckbox) - # self.vbox.pack_start(frame) - - # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ # --- Refinement Statistics --- # next comes a section which displays some global quality indicators # a combination of labels and textview widgets, arranged in a table @@ -470,15 +437,13 @@ def StartGUI(self): "clicked", self.show_ground_state_mean_map ) hbox.add(self.ground_state_mean_map_button) - # self.vbox.add(self.ground_state_mean_map_button) self.vbox.add(hbox) self.vbox.pack_start(frame) # SPACER - # self.vbox.add(gtk.Label(' ')) - ################################################################################# + ################################################################################ # --- hbox for compound picture & spider_plot (formerly: refinement history) --- frame = gtk.Frame() self.hbox_for_info_graphics = gtk.HBox() @@ -498,11 +463,6 @@ def StartGUI(self): compound_frame.add(self.image) self.hbox_for_info_graphics.add(compound_frame) - # --- Refinement History --- - # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) - # self.canvas.set_size_request(190, 190) - # self.hbox_for_info_graphics.add(self.canvas) - # --- Spider Plot --- spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( @@ -519,55 +479,6 @@ def StartGUI(self): frame.add(self.hbox_for_info_graphics) self.vbox.add(frame) - ################################################################################# - # --- pandda.inspect user comments --- - # outer_frame = gtk.Frame(label='pandda.inspect comments') - # vbox = gtk.VBox() - # ligand_site_name_label_frame = gtk.Frame() - # ligand_site_name_label = gtk.Label('Site Name') - # ligand_site_name_label_frame.add(ligand_site_name_label) - # ligand_inspect_confidence_label_frame = gtk.Frame() - # ligand_inspect_confidence_label = gtk.Label('Confidence') - # ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) - # ligand_inspect_interesting_label_frame = gtk.Frame() - # ligand_inspect_interesting_label = gtk.Label('Interesting') - # ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) - # ligand_inspect_comment_label_frame = gtk.Frame() - # ligand_inspect_comment_label = gtk.Label('Comment') - # ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) - # ligand_site_name_value_frame = gtk.Frame() - # self.ligand_site_name_value = gtk.Label('-') - # ligand_site_name_value_frame.add(self.ligand_site_name_value) - # ligand_inspect_confidence_value_frame = gtk.Frame() - # self.ligand_inspect_confidence_value = gtk.Label('-') - # ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) - # ligand_inspect_interesting_value_frame = gtk.Frame() - # self.ligand_inspect_interesting_value = gtk.Label('-') - # ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) - # ligand_inspect_comment_value_frame = gtk.Frame() - # self.ligand_inspect_comment_value = gtk.Label('-') - # ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) - # - # frame_pandda_inspect_comments_table = gtk.Frame() - # pandda_inspect_comments_table = gtk.Table(2, 6, False) - # pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) - # pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) - # pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) - # - # frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) - # vbox.add(frame_pandda_inspect_comments_table) - # outer_frame.add(vbox) - # self.vbox.pack_start(outer_frame) - - # # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# outer_frame = gtk.Frame(label="Sample Navigator") hboxSample = gtk.HBox() @@ -610,47 +521,7 @@ def StartGUI(self): outer_frame.add(hboxSample) self.vbox.add(outer_frame) - # # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# - # outer_frame = gtk.Frame(label='Label') - # hboxlabel = gtk.HBox() - # - # frame = gtk.Frame() - # hbox = gtk.HBox() - # self.vbox_label = gtk.VBox() - # labels = self.db.get_labels_from_db() - # if len(labels) > 5: - # print '==> sorry, too many labels; cannot display them in panel' - # labels = labels[:5] - # # with radiobuttons, one of them needs to be always on - # # but there will be cases when the user has not assigned a label yet - # # hence, the not_shown button is not shown but gets active - # # if the label has not been set yet - # labels.append('not_shown') - # for n, l in enumerate(labels): - # print n,l - # if n == 0: - # new_button = gtk.RadioButton(None, l) - # else: - # new_button = gtk.RadioButton(new_button, l) - # new_button.connect("toggled", self.label_button_clicked, l) - # if not l == 'not_shown': - # hbox.add(new_button) - # self.label_button_list.append(new_button) - # self.vbox_label.add(hbox) - # frame.add(self.vbox_label) - # - # hboxlabel.add(frame) - # - # outer_frame.add(hboxlabel) - # self.vbox.add(outer_frame) - - # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ # --- current refinement stage --- outer_frame = gtk.Frame() hbox = gtk.HBox() @@ -667,7 +538,6 @@ def StartGUI(self): "toggled", self.experiment_stage_button_clicked, button[1] ) vbox.pack_start(new_button, False, False, 0) - # vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) @@ -685,43 +555,13 @@ def StartGUI(self): "toggled", self.ligand_confidence_button_clicked, criteria ) vbox.pack_start(new_button, False, False, 0) - # vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) - # # label section --> start - # frame = gtk.Frame(label='Label') - # vbox = gtk.VBox() - # labels = self.db.get_labels_from_db() - # if len(labels) > 5: - # print '==> sorry, too many labels; cannot display them in panel' - # labels = labels[:5] - # # with radiobuttons, one of them needs to be always on - # # but there will be cases when the user has not assigned a label yet - # # hence, the not_shown button is not shown but gets active - # # if the label has not been set yet - # labels.append('not_shown') - # for n, l in enumerate(labels): - # print n,l - # if n == 0: - # new_button = gtk.RadioButton(None, l) - # else: - # new_button = gtk.RadioButton(new_button, l) - # new_button.connect("toggled", self.label_button_clicked, l) - # if not l == 'not_shown': - # vbox.add(new_button) - # self.label_button_list.append(new_button) - # frame.add(vbox) - # hbox.pack_start(frame) - # # label section <-- end - outer_frame.add(hbox) self.vbox.pack_start(outer_frame) - # SPACER - # self.vbox.add(gtk.Label(' ')) - # --- ligand modeling --- frame = gtk.Frame(label="Ligand Modeling") self.hbox_for_modeling = gtk.HBox() @@ -737,13 +577,6 @@ def StartGUI(self): frame.add(self.hbox_for_modeling) self.vbox.pack_start(frame) - # # --- ligand confidence --- - # self.cb_ligand_confidence = gtk.combo_box_new_text() - # self.cb_ligand_confidence.connect("changed", self.set_ligand_confidence) - # for citeria in self.ligand_confidence: - # self.cb_ligand_confidence.append_text(citeria) - # self.vbox.add(self.cb_ligand_confidence) - # --- refinement & options --- self.hbox_for_refinement = gtk.HBox() self.REFINEbutton = gtk.Button(label="Refine") @@ -762,13 +595,6 @@ def StartGUI(self): self.hbox_for_refinement.add(self.covalentLinksCreatebutton) self.vbox.add(self.hbox_for_refinement) - # self.VALIDATEbutton = gtk.Button(label="validate structure") - # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") - - # # need to put it here, because attributes within refinementProtocolCallback function - # # are defined after checkbox is defined - # self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) - # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") self.CANCELbutton.connect("clicked", self.CANCEL) @@ -785,7 +611,6 @@ def ChangeXtal(self, widget, data=None): if self.index < 0: self.index = 0 if self.index >= len(self.Todo): - # self.index = len(self.Todo) self.index = 0 self.cb.set_active(self.index) @@ -797,11 +622,6 @@ def ChooseXtal(self, widget): self.merge_ligand_button.set_sensitive(True) self.place_ligand_here_button.set_sensitive(True) - # self.ligand_site_name_value.set_label('-') - # self.ligand_inspect_confidence_value.set_label('-') - # self.ligand_inspect_interesting_value.set_label('-') - # self.ligand_inspect_comment_value.set_label('-') - self.refresh_site_combobox() self.db_dict_mainTable = {} self.db_dict_panddaTable = {} @@ -809,16 +629,11 @@ def ChooseXtal(self, widget): self.compoundID = str(self.Todo[self.index][1]) self.refinement_folder = str(self.Todo[self.index][4]) self.refinement_outcome = str(self.Todo[self.index][5]) - # self.label = self.db.get_label_of_sample(self.xtalID) - # self.update_label_radiobutton() self.update_RefinementOutcome_radiobutton() if ( self.xtalID not in self.siteDict ): # i.e. we are not working with a PanDDA model self.ligand_confidence = str(self.Todo[self.index][6]) - # self.update_LigandConfidence_radiobutton() - # self.label = self.db.get_label_of_sample(self.xtalID) - # self.update_label_radiobutton() self.RefreshData() @@ -876,18 +691,6 @@ def update_RefinementOutcome_radiobutton(self): button.set_active(True) break - # def update_label_radiobutton(self): - # found = False - # for button in self.label_button_list: - # if button.get_label() == self.label: - # button.set_active(True) - # found = True - # if not found: - # for button in self.label_button_list: - # if button.get_label() == 'not_shown': - # button.set_active(True) - # break - def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 @@ -907,7 +710,8 @@ def update_LigandConfidence_radiobutton(self): def refresh_site_combobox(self): # reset self.pandda_index self.pandda_index = -1 - # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites + # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever + # be 100 sites for n in range(-1, 100): self.cb_site.remove_text(0) self.site_index = "0" @@ -953,9 +757,6 @@ def RefreshSiteData(self): if self.compoundID + ".pdb" in coot.molecule_name(imol): coot.close_molecule(imol) - # for w in self.label_button_list: - # w.set_active(False) - print("pandda index", self.pandda_index) self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] print("new spider plot:", self.spider_plot) @@ -969,11 +770,6 @@ def RefreshSiteData(self): print("new site coordinates:", site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) - # self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) - # self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) - # self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) - # self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) - self.spider_plot_data = ( self.db.get_db_pandda_dict_for_sample_and_site_and_event( self.xtalID, self.site_index, self.event_index @@ -1039,14 +835,14 @@ def RefreshSiteData(self): except ValueError: self.ligand_RSZDValue.set_label("-") - ######################################################################################### + ################################################################################ # delete old Event MAPs if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): if "map.native.ccp4" in coot.molecule_name(imol): coot.close_molecule(imol) - ######################################################################################### + ################################################################################ # Spider plot # Note: refinement history was shown instead previously if os.path.isfile(self.spider_plot): @@ -1064,7 +860,7 @@ def RefreshSiteData(self): ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) - ######################################################################################### + ################################################################################ # check for PANDDAs EVENT maps if os.path.isfile(self.event_map): coot.set_colour_map_rotation_on_read_pdb(0) @@ -1072,8 +868,6 @@ def RefreshSiteData(self): for imol in coot_utils_XChem.molecule_number_list(): if self.event_map in coot.molecule_name(imol): coot.set_contour_level_in_sigma(imol, 2) - # coot.set_contour_level_absolute(imol,0.5) - # coot.set_last_map_colour(0.4,0,0.4) coot.set_last_map_colour(0.74, 0.44, 0.02) def experiment_stage_button_clicked(self, widget, data=None): @@ -1085,9 +879,6 @@ def experiment_stage_button_clicked(self, widget, data=None): + str(data) + " in mainTable of datasource" ) - # print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( - # data) + ' in mainTable of datasource' - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.db.create_or_remove_missing_records_in_depositTable( self.xce_logfile, self.xtalID, "ligand_bound", self.db_dict_mainTable ) @@ -1103,8 +894,6 @@ def ligand_confidence_button_clicked(self, widget, data=None): + str(data) + " in mainTable of datasource" ) - # print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( - # data) + ' in mainTable of datasource' self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.Todo[self.index][6] = data else: @@ -1120,36 +909,11 @@ def ligand_confidence_button_clicked(self, widget, data=None): + str(data) + " in panddaTable of datasource" ) - # print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( - # self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( - # data) + ' in panddaTable of datasource' self.db.update_site_event_panddaTable( self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable ) self.siteDict[self.xtalID][self.pandda_index][7] = data - # def update_label(self, widget): - # print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' - # # widget.pressed() - # for w in self.label_button_list: - # print w.get_label(), w.get_active() - # if w != widget: - # w.set_active(False) - # print '<<<<<<<<<<<<<<<<<<<<<<<<<<' - # self.db_dict_mainTable['label'] = widget.get_label() - # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( - # widget.get_label()) + ' in mainTable of datasource' - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - - # def label_button_clicked(self, widget, data=None): - # print '............',data - # if data == 'not_shown': - # self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) - # else: - # self.db_dict_mainTable['label'] = data - # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - def RefreshData(self): # reset spider plot image spider_plot_pic = gtk.gdk.pixbuf_new_from_file( @@ -1181,15 +945,11 @@ def RefreshData(self): ) # initialize Refinement library - # self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) self.Refine = XChemRefine.Refine( self.project_directory, self.xtalID, self.compoundID, self.data_source ) self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) - self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * "0" + str( - self.Serial - ) - # self.Serial=self.Refine.GetSerial() + self.panddaSerial = (4 - len(str(self.Serial))) * "0" + str(self.Serial) if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple if os.path.isfile( @@ -1240,25 +1000,19 @@ def RefreshData(self): self.xtalID, self.data_source, "" ) # '' because file does not exist - # all this information is now updated in the datasource after each refinement cycle + # all this information is now updated in the datasource after each refinement + # cycle self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) - ######################################################################################### + ################################################################################ # history # if the structure was previously refined, try to read the parameters # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) print("==> REFMAC params:", self.RefmacParams) - # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() - # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) - # else: - # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea - # self.canvas.set_size_request(190, 190) - # self.hbox_for_info_graphics.add(self.canvas) - # self.canvas.show() - - ######################################################################################### + + ################################################################################ # ligand files # first remove old samples if present print(">>>", self.mol_dict["ligand_stereo"]) @@ -1267,19 +1021,19 @@ def RefreshData(self): self.select_cpd_cb.remove_text(0) print("done") - ######################################################################################### + ################################################################################ # remove potential generic line which indicates a possible covalent link generic_object_clear(self.covLinkObject) self.covLinkAtomSpec = None - ######################################################################################### + ################################################################################ # reset covalent links self.covLinks = ["X", "X", "X", "X"] - ######################################################################################### + ################################################################################ # update pdb & maps - ######################################################################################### + ################################################################################ # delete old PDB and MAP files # - get a list of all molecules which are currently opened in COOT # - remove all molecules/ maps before loading a new set @@ -1287,7 +1041,7 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): coot.close_molecule(item) - ######################################################################################### + ################################################################################ # read new PDB files # read protein molecule after ligand so that this one is the active molecule coot.set_nomenclature_errors_on_read("ignore") @@ -1350,7 +1104,6 @@ def RefreshData(self): self.select_cpd_cb.set_active(0) else: print("no compound found in sample directory") - # self.select_cpd_cb.append_text('') self.select_cpd_cb.set_sensitive(False) if not os.path.isfile( @@ -1358,59 +1111,6 @@ def RefreshData(self): ): os.chdir(os.path.join(self.project_directory, self.xtalID)) - # if self.refinementProtocol.startswith('pandda'): - # self.Logfile.insert('==> COOT: looking for ground-state model ' + os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.ground-state.pdb')) - # print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.ground-state.pdb') - # if os.path.isfile(os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): - # self.Logfile.insert('==> COOT: found ground-state model') - ## print '=> XCE: found ground-state model' - # os.chdir(os.path.join(self.project_directory, self.xtalID)) - # coot.set_colour_map_rotation_on_read_pdb(0) - # try: - # color_wheel_rotation = 160 / float(imol + 2) - # except UnboundLocalError: - # color_wheel_rotation = 80 - # coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) - # imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.ground-state.pdb'), - # 0) - # coot.set_colour_by_molecule(imol) - # coot.set_mol_active(imol, 0) - # else: - # self.Logfile.error('==> COOT - cannot find ground-state model') - ## print '=> XCE - ERROR: cannot find ground-state model' - # self.Logfile.insert('==> COOT: looking for bound-state model '+ os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.bound-state.pdb')) - # print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.bound-state.pdb') - # if os.path.isfile(os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb')): - # self.Logfile.insert('==> COOT: found bound-state model') - ## print '=> XCE: found bound-state model' - # os.chdir(os.path.join(self.project_directory, self.xtalID)) - # coot.set_colour_map_rotation_on_read_pdb(0) - # color_wheel_rotation = 21 / float(imol + 2) - # coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) - # imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.bound-state.pdb'), - # 0) - # self.mol_dict['protein'] = imol - # else: - # self.Logfile.error('==> COOT: cannot find bound-state model') - ## print '=> XCE - ERROR: cannot find bound-state model' - # self.Logfile.warning('==> COOT: moving to next crystal...') - ## print '=> XCE: moving to next crystal...' - # self.go_to_next_xtal() - # else: if os.path.isfile( os.path.join(self.project_directory, self.xtalID, self.pdb_style) ): @@ -1457,7 +1157,7 @@ def RefreshData(self): coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model - ######################################################################################### + ################################################################################ # read fofc maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level @@ -1477,13 +1177,6 @@ def RefreshData(self): else: # try to open mtz file with same name as pdb file coot.set_default_initial_contour_level_for_map(1) - # if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): - # os.chdir(os.path.join(self.project_directory,self.xtalID)) - # if not os.path.isfile('REFINEMENT_IN_PROGRESS'): - # if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-pandda-input.mtz')): - # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) - # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): - # os.symlink('dimple.mtz',self.mtz_style) if os.path.isfile( os.path.join(self.project_directory, self.xtalID, self.mtz_style) ): @@ -1503,7 +1196,7 @@ def RefreshData(self): os.path.join(self.project_directory, self.xtalID, "dimple_twin.mtz") ) - ######################################################################################### + ################################################################################ # update Quality Indicator table try: self.RRfreeValue.set_label( @@ -1614,62 +1307,6 @@ def REFINE(self, widget): self.start_refinement() def start_refinement(self): - # ####################################################### - # if not os.path.isdir(os.path.join(self.project_directory,self.xtalID,'cootOut')): - # os.mkdir(os.path.join(self.project_directory,self.xtalID,'cootOut')) - # # create folder for new refinement cycle - # os.mkdir(os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial))) - # - # ####################################################### - # # write PDB file - # # now take protein pdb file and write it to newly create Refine_ folder - # # note: the user has to make sure that the ligand file was merged into main file - # for item in coot_utils_XChem.molecule_number_list(): - # if coot.molecule_name(item).endswith(self.pdb_style.replace('.pdb','')+'.split.bound-state.pdb') or coot.molecule_name(item).endswith(self.pdb_style): - # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) - # break - # elif coot.molecule_name(item).endswith('dimple.pdb'): - # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) - # break - # - - ####################################################### - # if self.refinementProtocol.startswith('pandda'): - # - # ####################################################### - # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): - # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) - # # create folder for new refinement cycle - # try: - # self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) - # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) - # except OSError: - # self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') - ## print '==> XCE: WARNING -> folder exists; will overwrite contents!' - # self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') - # - # ####################################################### - # # write PDB file - # # now take protein pdb file and write it to newly create Refine_ folder - # # note: the user has to make sure that the ligand file was merged into main file - # for item in coot_utils_XChem.molecule_number_list(): - # if coot.molecule_name(item).endswith( - # self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( - # item).endswith(self.pdb_style): - # coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', - # 'Refine_' + str(self.Serial), 'refine.modified.pdb')) - # break - # # elif coot.molecule_name(item).endswith('dimple.pdb'): - # # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) - # # break - # - # XChemRefine.panddaRefine(self.project_directory, self.xtalID, self.compoundID, - # self.data_source).RunQuickRefine(self.Serial, self.RefmacParams, - # self.external_software, self.xce_logfile, - # self.refinementProtocol, self.covLinkAtomSpec) - # else: - - ####################################################### if not os.path.isdir( os.path.join(self.project_directory, self.xtalID, "cootOut") ): @@ -1695,18 +1332,11 @@ def start_refinement(self): ) except OSError: self.Logfile.warning("==> COOT: folder exists; will overwrite contents!") - # print '==> XCE: WARNING -> folder exists; will overwrite contents!' self.Logfile.warning( - "==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem" + "==> COOT: it is advised to check the sample directory" + " as this might be a symptom for a PDB file problem" ) - # ####################################################### - # # create folder for new refinement cycle and check if free.mtz exists - # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): - # os.mkdir(os.path.join(self.project_directory, self.xtalID)) - # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): - # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) - ####################################################### # write PDB file # now take protein pdb file and write it to newly create Refine_ folder @@ -1737,7 +1367,6 @@ def start_refinement(self): ), ) - # self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) self.Refine.RunBuster( self.Serial, self.external_software, @@ -1746,7 +1375,6 @@ def start_refinement(self): ) self.index += 1 if self.index >= len(self.Todo): - # self.index = len(self.Todo) self.index = 0 self.cb.set_active(self.index) @@ -1826,7 +1454,8 @@ def show_potential_link(self, *clicks): ] else: print( - "error: both atoms must belong to the same object; did you merge the ligand with your protein?" + "error: both atoms must belong to the same object;" + " did you merge the ligand with your protein?" ) def covalentLinkCreate(self, widget): @@ -1900,11 +1529,6 @@ def place_ligand_here(self, widget): coot_utils_XChem.move_molecule_here(imol) print("LIGAND: ", molName) - # print '===> XCE: moving ligand to pointer' - # # coot.move_molecule_here() - # print 'LIGAND: ', self.mol_dict['ligand'] - # coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) - def merge_ligand_into_protein(self, widget): cpd = str(self.select_cpd_cb.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): @@ -1984,12 +1608,6 @@ def merge_ligand_into_protein(self, widget): self.select_cpd_cb.set_sensitive(False) - # print '===> XCE: merge ligand into protein structure' - # # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) - # coot.merge_molecules_py([self.mol_dict['ligand']], self.mol_dict['protein']) - # print '===> XCE: deleting ligand molecule' - # coot.close_molecule(self.mol_dict['ligand']) - def show_molprobity_to_do(self, widget): print(self.panddaSerial) AdjPanddaSerial = (4 - len(str(self.Serial))) * "0" + str( @@ -2048,37 +1666,6 @@ def show_molprobity_to_do(self, widget): ) ) - # def refinementProtocolCallback(self, widget): - # if widget.get_active(): - # if self.refinementProtocolcheckbox.get_active(): - # self.refinementProtocol = 'pandda_phenix' - # else: - # self.refinementProtocol = 'pandda_refmac' - # self.PREVbuttonSite.set_sensitive(True) - # self.NEXTbuttonSite.set_sensitive(True) - # else: - # self.refinementProtocolcheckbox.set_active(False) - # self.refinementProtocol = 'refmac' - # self.PREVbuttonSite.set_sensitive(False) - # self.NEXTbuttonSite.set_sensitive(False) - # print self.refinementProtocol - - # def refinementProgramCallback(self, widget): - # if widget.get_active(): - # if self.refinementProtocolcheckbox.get_active(): - # self.refinementProtocol = 'pandda_phenix' - # self.RefinementParamsButton.set_sensitive(False) - # else: - # self.refinementProgramcheckbox.set_active(False) - # self.refinementProtocol = 'refmac' - # else: - # self.RefinementParamsButton.set_sensitive(True) - # if self.refinementProtocolcheckbox.get_active(): - # self.refinementProtocol = 'pandda_refmac' - # else: - # self.refinementProtocol = 'refmac' - # print self.refinementProtocol - def show_ground_state_mean_map(self, widget): if widget.get_label().startswith("Show"): loaded = False From a794ebb38bcbfe60ed79ecaf3277e8b027d3f404 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 9 Nov 2022 13:32:10 +0000 Subject: [PATCH 166/358] Fix $XChemExplorer_DIR prefixed paths --- xce/gui_scripts/stylesheet.py | 2 +- xce/lib/XChemPANDDA.py | 2 ++ xce/lib/XChemProcess.py | 6 +++++- xce/lib/XChemRefine.py | 10 +++++++--- xce/lib/XChemThread.py | 13 ++++++++----- xce/lib/XChemUtils.py | 6 ++++-- 6 files changed, 27 insertions(+), 12 deletions(-) diff --git a/xce/gui_scripts/stylesheet.py b/xce/gui_scripts/stylesheet.py index cea23c4d..e5ba64dd 100755 --- a/xce/gui_scripts/stylesheet.py +++ b/xce/gui_scripts/stylesheet.py @@ -8,7 +8,7 @@ def set_stylesheet(xce_object): palette.setColor(QtGui.QPalette.Background, QtGui.QColor("#ececec")) xce_object.setPalette(palette) - icons_directory = os.path.join((os.getenv("XChemExplorer_DIR")), "icons") + icons_directory = os.path.join((os.getenv("XChemExplorer_DIR")), "xce/icons") xce_object.setStyleSheet( """ diff --git a/xce/lib/XChemPANDDA.py b/xce/lib/XChemPANDDA.py index 44336baf..4e507807 100755 --- a/xce/lib/XChemPANDDA.py +++ b/xce/lib/XChemPANDDA.py @@ -1296,6 +1296,7 @@ def __init__(self, pandda_params, xce_logfile, datasource): self.make_ligand_links = "$CCP4/bin/ccp4-python %s %s %s\n" % ( os.path.join( os.getenv("XChemExplorer_DIR"), + "xce", "helpers", "make_ligand_links_after_pandda.py", ), @@ -1317,6 +1318,7 @@ def __init__(self, pandda_params, xce_logfile, datasource): self.select_ground_state_model += "$CCP4/bin/ccp4-python %s %s\n" % ( os.path.join( os.getenv("XChemExplorer_DIR"), + "xce", "helpers", "select_ground_state_dataset.py", ), diff --git a/xce/lib/XChemProcess.py b/xce/lib/XChemProcess.py index 251340af..9eac168e 100755 --- a/xce/lib/XChemProcess.py +++ b/xce/lib/XChemProcess.py @@ -219,6 +219,7 @@ def run(self): "$CCP4/bin/ccp4-python " + os.path.join( os.getenv("XChemExplorer_DIR"), + "xce", "helpers", "update_status_flag.py", ) @@ -246,7 +247,10 @@ def run(self): script += ( "$CCP4/bin/ccp4-python " + os.path.join( - os.getenv("XChemExplorer_DIR"), "helpers", "update_status_flag.py" + os.getenv("XChemExplorer_DIR"), + "xce", + "helpers", + "update_status_flag.py", ) + " {0!s} {1!s} {2!s} {3!s}\n".format( self.database, xtal, "DataProcessingStatus", "finished" diff --git a/xce/lib/XChemRefine.py b/xce/lib/XChemRefine.py index a3778914..ecbe3169 100755 --- a/xce/lib/XChemRefine.py +++ b/xce/lib/XChemRefine.py @@ -542,7 +542,7 @@ def get_source_line(self, cmd): def set_refinement_status(self, cmd): cmd += ( "$CCP4/bin/ccp4-python " - " $XChemExplorer_DIR/helpers/update_status_flag.py " + " $XChemExplorer_DIR/xce/helpers/update_status_flag.py " + self.datasource + " " + self.xtalID @@ -701,6 +701,7 @@ def update_database(self, cmd, Serial): ccp4_module = "module load ccp4/7.1.018" cmd += "\n" + ccp4_module + "\n" "$CCP4/bin/ccp4-python " + os.path.join( os.getenv("XChemExplorer_DIR"), + "xce", "helpers", "update_data_source_after_refinement.py", ) + " %s %s %s %s %s %s\n" % ( @@ -977,6 +978,7 @@ def RunRefmac( findTLS = ( os.path.join( os.getenv("XChemExplorer_DIR"), + "xce", "helpers", "phenix_find_TLS_groups.py", ) @@ -1020,13 +1022,14 @@ def RunRefmac( user = getpass.getuser() if os.path.isfile(self.datasource): refinementStatus = ( - "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/xce/helpers/update_status_flag.py %s %s %s %s\n" % (self.datasource, self.xtalID, "RefinementStatus", "running") ) updateDB = ( "$CCP4/bin/ccp4-python " + os.path.join( os.getenv("XChemExplorer_DIR"), + "xce", "helpers", "update_data_source_after_refinement.py", ) @@ -2134,7 +2137,7 @@ def RunQuickRefine( + self.xtalID + "\n" "\n" - "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/xce/helpers/update_status_flag.py %s %s %s %s\n" % (self.datasource, self.xtalID, "RefinementStatus", "running") + "\n" "giant.quick_refine" @@ -2218,6 +2221,7 @@ def RunQuickRefine( "$CCP4/bin/ccp4-python " + os.path.join( os.getenv("XChemExplorer_DIR"), + "xce", "helpers", "update_data_source_after_refinement.py", ) diff --git a/xce/lib/XChemThread.py b/xce/lib/XChemThread.py index 6768313d..898257fb 100755 --- a/xce/lib/XChemThread.py +++ b/xce/lib/XChemThread.py @@ -1103,7 +1103,7 @@ def get_header(self, sampleID): def get_footer(self, cmd, sampleID, compoundID): cmd += ( "$CCP4/bin/ccp4-python" - " $XChemExplorer_DIR/helpers/" + " $XChemExplorer_DIR/xce/helpers/" "find_best_fitting_ligand.py {0!s} {1!s} {2!s}".format( compoundID.replace(" ", ""), os.path.join(self.initial_model_directory, sampleID), @@ -1475,7 +1475,7 @@ def prepare_phenix_ligand_pipeline_shell_script( "source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n" "\n" + ccp4_scratch + "\n" "$CCP4/bin/ccp4-python" - " $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n" + " $XChemExplorer_DIR/xce/helpers/update_status_flag.py %s %s %s %s\n" % ( os.path.join(self.database_directory, self.data_source_file), xtal, @@ -1523,6 +1523,7 @@ def prepare_phenix_ligand_pipeline_shell_script( "$CCP4/bin/ccp4-python " + os.path.join( os.getenv("XChemExplorer_DIR"), + "xce", "helpers", "update_data_source_for_new_dimple_pdb.py", ) @@ -1590,7 +1591,7 @@ def prepare_pipedream_shell_script( + "\n" "source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n" "\n" + ccp4_scratch + "\n" - "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/xce/helpers/update_status_flag.py" " %s %s %s %s\n" % ( os.path.join(self.database_directory, self.data_source_file), @@ -1636,6 +1637,7 @@ def prepare_pipedream_shell_script( "$CCP4/libexec/python " + os.path.join( os.getenv("XChemExplorer_DIR"), + "xce", "helpers", "update_data_source_for_new_dimple_pdb.py", ) @@ -1769,7 +1771,7 @@ def prepare_dimple_shell_script( + "\n" "source $XChemExplorer_DIR/setup-scripts/xce.setup-sh\n" "\n" + ccp4_scratch + "\n" - "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/xce/helpers/update_status_flag.py" " %s %s %s %s\n" % ( os.path.join(self.database_directory, self.data_source_file), @@ -1838,6 +1840,7 @@ def prepare_dimple_shell_script( "$CCP4/bin/ccp4-python " + os.path.join( os.getenv("XChemExplorer_DIR"), + "xce", "helpers", "update_data_source_for_new_dimple%s_pdb.py" % twin, ) @@ -2222,7 +2225,7 @@ def run(self): os.system( "cd {0!s}\ncoot --no-guano --no-state-script --script {1!s}".format( os.getenv("HOME"), - os.path.join(os.getenv("XChemExplorer_DIR"), "lib", self.pylib), + os.path.join(os.getenv("XChemExplorer_DIR"), "xce", "lib", self.pylib), ) ) diff --git a/xce/lib/XChemUtils.py b/xce/lib/XChemUtils.py index f44a7896..3a209aad 100755 --- a/xce/lib/XChemUtils.py +++ b/xce/lib/XChemUtils.py @@ -223,7 +223,7 @@ def make_png( # merge all compound CIFs into 1 file called merged.cif software += ( "$CCP4/bin/ccp4-python" - "$XChemExplorer_DIR/helpers/merge_ligand_cif_files.py {0!s}\n".format( + "$XChemExplorer_DIR/xce/helpers/merge_ligand_cif_files.py {0!s}\n".format( os.path.join(initial_model_directory, sample, "compound") ) ) @@ -235,7 +235,7 @@ def make_png( Cmds = ( header + "\n" 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"' + "\n" - "$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/xce/helpers/update_status_flag.py" " {0!s} {1!s} {2!s} {3!s}".format( os.path.join(database_directory, data_source_file), sample, @@ -246,6 +246,7 @@ def make_png( '$CCP4/bin/ccp4-python {0!s} "{1!s}" {2!s} {3!s} {4!s}\n'.format( os.path.join( os.getenv("XChemExplorer_DIR"), + "xce", "helpers", "create_png_of_compound.py", ), @@ -268,6 +269,7 @@ def make_png( "$CCP4/bin/ccp4-python " + os.path.join( os.getenv("XChemExplorer_DIR"), + "xce", "helpers", "update_data_source_for_new_cif_files.py", ) From ca55479535f5a097ca85dee911850d5e1d58eacb Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Wed, 9 Nov 2022 17:26:14 +0000 Subject: [PATCH 167/358] Setup dls run script --- XChemExplorer_dls | 12 ++++++++++++ setup.py | 11 +++++++++++ 2 files changed, 23 insertions(+) create mode 100755 XChemExplorer_dls create mode 100644 setup.py diff --git a/XChemExplorer_dls b/XChemExplorer_dls new file mode 100755 index 00000000..2339b393 --- /dev/null +++ b/XChemExplorer_dls @@ -0,0 +1,12 @@ +#!/bin/bash + +module load buster/20211020 +module load phenix/1.20 +module load ccp4/7.1.018 + +export BDG_TOOL_MOGUL="/dls_sw/apps/ccdc/CSD_2020/bin/mogul" +export XChemExplorer_DIR="/dls_sw/i04-1/software/XChemExplorer" + +(cd $XChemExplorer_DIR; ccp4-python setup.py install --user) + +ccp4-python -m xce diff --git a/setup.py b/setup.py new file mode 100644 index 00000000..95213b9f --- /dev/null +++ b/setup.py @@ -0,0 +1,11 @@ +from setuptools import setup, find_packages + +setup( + name="xce", + version="1.5.0", + description="GUI tool for XChem", + author="Tobias Krojer", + packages=find_packages(), + install_requires=[], +) + From e53876eeb4c9477265f0d4608c0409bc2e5d95dd Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 10 Nov 2022 09:47:19 +0000 Subject: [PATCH 168/358] Update git & docker ignore files --- .dockerignore | 16 ++++++++++++++-- .gitignore | 14 +++++++++----- 2 files changed, 23 insertions(+), 7 deletions(-) diff --git a/.dockerignore b/.dockerignore index c4d71aff..69ba180e 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,3 +1,15 @@ -Dockerfile +*.pyc +*.egg-info +/build +/dist + +__pycache__/ +.pytest_cache/ +.mypy_cache/ + +xce.log + /.devcontainer -/.git \ No newline at end of file +/.git + +Dockerfile diff --git a/.gitignore b/.gitignore index ad920278..add26d82 100755 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,10 @@ -**/*.pyc *.pyc -XChemExplorer_dmd.sh -.idea -/libraries -xce.log \ No newline at end of file +*.egg-info +/build +/dist + +__pycache__/ +.pytest_cache/ +.mypy_cache/ + +xce.log From f981b1579f2a2cf513bbffb6a935246ccabd669e Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 10 Nov 2022 10:49:17 +0000 Subject: [PATCH 169/358] Use distutils to check external software --- xce/lib/XChemUtils.py | 49 +++++++++++++++---------------------------- 1 file changed, 17 insertions(+), 32 deletions(-) diff --git a/xce/lib/XChemUtils.py b/xce/lib/XChemUtils.py index 3a209aad..366daec0 100755 --- a/xce/lib/XChemUtils.py +++ b/xce/lib/XChemUtils.py @@ -4,10 +4,11 @@ import glob import math import subprocess -import getpass import json import time +from distutils.spawn import find_executable + import gzip import bz2 @@ -223,7 +224,8 @@ def make_png( # merge all compound CIFs into 1 file called merged.cif software += ( "$CCP4/bin/ccp4-python" - "$XChemExplorer_DIR/xce/helpers/merge_ligand_cif_files.py {0!s}\n".format( + "$XChemExplorer_DIR/xce/helpers/" + "merge_ligand_cif_files.py {0!s}\n".format( os.path.join(initial_model_directory, sample, "compound") ) ) @@ -1656,16 +1658,6 @@ def __init__(self, xce_logfile): self.available_programs = {} self.Logfile = XChemLog.updateLog(xce_logfile) - @staticmethod - def is_available(program): - try: - devnull = open(os.devnull, "w") - subprocess.Popen(program, stdout=devnull, stderr=devnull).communicate() - return True - except OSError as e: - if e.errno == os.errno.ENOENT: - return False - def log_found_status(self, program_name): self.Logfile.insert( "{0:50} {1:10}".format( @@ -1680,60 +1672,53 @@ def check(self): # default is False; user needs to explicitely set this self.available_programs["qsub_remote"] = False - self.available_programs["qsub"] = True if self.is_available("qsub") else False - self.available_programs["qsub_array"] = ( - True if self.is_available("qsub") else False + self.available_programs["qsub"] = self.available_programs["qsub_array"] = ( + find_executable("qsub") is not None ) self.log_found_status("qsub") self.log_found_status("qsub_array") - self.available_programs["refmac5"] = ( - True if self.is_available(["refmac5", "end"]) else False - ) + self.available_programs["refmac5"] = find_executable("refmac5") is not None self.log_found_status("refmac5") self.available_programs["phenix.molprobity"] = ( - True if self.is_available("phenix.molprobity") else False + find_executable("phenix.molprobity") is not None ) self.log_found_status("phenix.molprobity") self.available_programs["phenix.find_tls_groups"] = ( - True if self.is_available("phenix.find_tls_groups") else False + find_executable("phenix.find_tls_groups") is not None ) self.log_found_status("phenix.find_tls_groups") self.available_programs["mmtbx.validate_ligands"] = ( - True if self.is_available("mmtbx.validate_ligands") else False + find_executable("mmtbx.validate_ligands") is not None ) self.log_found_status("mmtbx.validate_ligands") - self.available_programs["acedrg"] = ( - True if self.is_available(["acedrg", "-h"]) else False - ) + self.available_programs["acedrg"] = find_executable("acedrg") is not None self.log_found_status("acedrg") self.available_programs["phenix.elbow"] = ( - True if self.is_available("phenix.elbow") else False + find_executable("phenix.elbow") is not None ) self.log_found_status("phenix.elbow") - self.available_programs["grade"] = True if self.is_available("grade") else False + self.available_programs["grade"] = find_executable("grade") is not None self.log_found_status("grade") self.available_programs["giant.create_occupancy_params"] = ( - True if self.is_available("giant.create_occupancy_params") else False + find_executable("giant.create_occupancy_params") is not None ) self.log_found_status("giant.create_occupancy_params") self.available_programs["mogul"] = ( - True - if "BDG_TOOL_MOGUL" in os.environ - and self.is_available(os.environ["BDG_TOOL_MOGUL"]) - else False + "BDG_TOOL_MOGUL" in os.environ + and find_executable(os.environ["BDG_TOOL_MOGUL"]) is not None ) self.log_found_status("mogul") - self.available_programs["gemmi"] = True if self.is_available("gemmi") else False + self.available_programs["gemmi"] = find_executable("gemmi") is not None self.log_found_status("gemmi") return self.available_programs From 0ba6b7618c3a95a9a93cc26819aaa46c449bcfe7 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 10 Nov 2022 10:58:10 +0000 Subject: [PATCH 170/358] Add setup option to dls run script --- XChemExplorer_dls | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/XChemExplorer_dls b/XChemExplorer_dls index 2339b393..856a87bc 100755 --- a/XChemExplorer_dls +++ b/XChemExplorer_dls @@ -7,6 +7,9 @@ module load ccp4/7.1.018 export BDG_TOOL_MOGUL="/dls_sw/apps/ccdc/CSD_2020/bin/mogul" export XChemExplorer_DIR="/dls_sw/i04-1/software/XChemExplorer" -(cd $XChemExplorer_DIR; ccp4-python setup.py install --user) +if [ $1 = "setup" ]; then + (cd $XChemExplorer_DIR; ccp4-python setup.py install --user) +fi ccp4-python -m xce + From 128617c7fb5eaf8f13e2c45bf7298fdb4128dd26 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 10 Nov 2022 11:12:05 +0000 Subject: [PATCH 171/358] Clean up XChemCootReference --- xce/lib/XChemCootReference.py | 158 +++------------------------------- 1 file changed, 14 insertions(+), 144 deletions(-) diff --git a/xce/lib/XChemCootReference.py b/xce/lib/XChemCootReference.py index 687279e2..4b730a34 100755 --- a/xce/lib/XChemCootReference.py +++ b/xce/lib/XChemCootReference.py @@ -14,7 +14,8 @@ from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureCanvas # had to adapt the original coot_utils.py file -# otherwise unable to import the original file without complaints about missing modules etc. +# otherwise unable to import the original file without complaints about missing modules +# etc. # modified file is now in $XChemExplorer_DIR/lib @@ -26,7 +27,7 @@ class GUI(object): def __init__(self): - ########################################################################################### + ################################################################################ # read in settings file from XChemExplorer to set the relevant paths self.settings = pickle.load(open(".xce_settings.pkl", "rb")) remote_qsub_submission = self.settings["remote_qsub"] @@ -40,8 +41,8 @@ def __init__(self): self.external_software = XChemUtils.external_software(self.xce_logfile).check() self.external_software["qsub_remote"] = remote_qsub_submission - # the Folder is kind of a legacy thing because my inital idea was to have separate folders - # for Data Processing and Refinement + # the Folder is kind of a legacy thing because my inital idea was to have + # separate folders for Data Processing and Refinement self.reference_directory = self.settings["reference_directory"] self.refinementDir = "" self.Serial = 0 @@ -69,11 +70,10 @@ def __init__(self): self.ground_state_map_List = [] self.job_running = False - ########################################################################################### + ################################################################################ # some COOT settings coot.set_map_radius(17) coot.set_colour_map_rotation_for_map(0) - # coot.set_colour_map_rotation_on_read_pdb_flag(21) self.QualityIndicators = { "Rcryst": "-", @@ -122,7 +122,7 @@ def StartGUI(self): self.window.set_title("Reference Model Builder") self.vbox = gtk.VBox() # this is the main container - ################################################################################# + ################################################################################ # --- PDB file selection --- # checking for pdb files in reference directory referenceFiles = [] @@ -134,7 +134,6 @@ def StartGUI(self): frame = gtk.Frame(label="Select PDB file") hbox = gtk.HBox() self.cb_select_pdb = gtk.combo_box_new_text() - # self.cb_select_pdb.connect("changed", self.set_selection_mode) for pdbFile in referenceFiles: self.cb_select_pdb.append_text(pdbFile) hbox.add(self.cb_select_pdb) @@ -142,7 +141,6 @@ def StartGUI(self): self.vbox.pack_start(frame) self.load_pdb_file_button = gtk.Button(label="Load") - # self.load_pdb_file_button.connect("clicked",self.get_samples_to_look_at) self.load_pdb_file_button.connect("clicked", self.load_pdb_file) hbox.add(self.load_pdb_file_button) frame.add(hbox) @@ -172,47 +170,7 @@ def StartGUI(self): # SPACER self.vbox.add(gtk.Label(" \n ")) - ################################################################################# - # --- ground state mean map --- - # checking for ground state mean map in reference folder - # self.meanMaps = {} - # for dirs in glob.glob(os.path.join(self.reference_directory,'pandda_*')): - # panddaDir=dirs.split('/')[len(dirs.split('/'))-1] - # for files in glob.glob(os.path.join(dirs,'processed_datasets','*','*ground-state-mean-map.native.ccp4')): - # if os.path.isfile(files): - # self.meanMaps[panddaDir]=files - # break - - # frame = gtk.Frame(label='Load ground-state-mean-map files') - # hbox=gtk.HBox() - # self.cb_select_mean_map = gtk.combo_box_new_text() - # for item in self.meanMaps: - # self.cb_select_mean_map.append_text(item) - # hbox.add(self.cb_select_mean_map) - # self.load_ground_state_map_button = gtk.Button(label="Load") - # self.load_ground_state_map_button.connect("clicked",self.load_ground_state_map) - # hbox.add(self.load_ground_state_map_button) - # frame.add(hbox) - # self.vbox.pack_start(frame) - - # frame = gtk.Frame() - # hbox=gtk.HBox() - # self.cb_select_mean_map_by_resolution = gtk.combo_box_new_text() - # self.cb_select_mean_map_by_resolution.connect("changed", self.show_selected_mean_map) - # hbox.add(self.cb_select_mean_map_by_resolution) - ## self.show_highres_ground_state_map_button = gtk.Button(label="Show Highest\nResolution Map") - # self.show_highres_ground_state_map_button.connect("clicked",self.show_highres_ground_state_map) - # hbox.add(self.show_highres_ground_state_map_button) - ## self.show_all_ground_state_map_button = gtk.Button(label="Show All Maps") - # self.show_all_ground_state_map_button.connect("clicked",self.show_all_ground_state_map) - # hbox.add(self.show_all_ground_state_map_button) - # frame.add(hbox) - # self.vbox.pack_start(frame) - - # SPACER - # self.vbox.add(gtk.Label(' \n ')) - - ################################################################################# + ################################################################################ # --- Refinement History --- frame = gtk.Frame(label="Refinement History") self.hbox_for_info_graphics = gtk.HBox() @@ -222,23 +180,21 @@ def StartGUI(self): frame.add(self.hbox_for_info_graphics) self.vbox.pack_start(frame) - ################################################################################# + ################################################################################ # --- status window --- frame = gtk.Frame(label="Status") vbox = gtk.VBox() self.spinnerBox = gtk.VBox() self.refinementRunning = gtk.Spinner() vbox.add(self.spinnerBox) - # hbox.add(self.refinementRunning) self.status_label = gtk.Label() vbox.add(self.status_label) frame.add(vbox) self.status_label.set_text("idle") - # frame.add(self.status_label) self.vbox.pack_start(frame) - ################################################################################# + ################################################################################ # --- Refinement Statistics --- # next comes a section which displays some global quality indicators # a combination of labels and textview widgets, arranged in a table @@ -389,7 +345,7 @@ def RefreshData(self): self.Serial = self.Refine.GetSerial() print("====> Serial", self.Serial) - ######################################################################################### + ################################################################################ # history # if the structure was previously refined, try to read the parameters self.hbox_for_info_graphics.remove(self.canvas) @@ -407,7 +363,7 @@ def RefreshData(self): self.hbox_for_info_graphics.add(self.canvas) self.canvas.show() - ######################################################################################### + ################################################################################ # update Quality Indicator table print(self.QualityIndicators) try: @@ -541,8 +497,6 @@ def REFINE(self, widget): self.xce_logfile, None, ) - # self.spinnerBox.add(self.refinementRunning) - # self.refinementRunning.start() self.status_label.set_text("Refinement running...") # waiting 1s to make sure that REFINEMENT_IN_PROGRESS is written @@ -562,28 +516,6 @@ def REFINE(self, widget): snooze += 10 self.update_pdb_mtz_files("") - # launch refinement - - # time.sleep(1) # waiting 1s to make sure that REFINEMENT_IN_PROGRESS is written - # self.source_id = gobject.timeout_add(100, self.wait_for_refined_pdb) - - # def wait_for_refined_pdb(self): - # self.spinnerBox.add(self.refinementRunning) - # self.refinementRunning.show() - # self.refinementRunning.start() - # if not os.path.isfile(os.path.join(self.reference_directory,self.refinementDir,'REFINEMENT_IN_PROGRESS')): - # self.job_running=False - # self.end_thread('update_pdb_mtz') - # return True - - # def end_thread(self,action): - # self.refinementRunning.stop() - # self.spinnerBox.remove(self.refinementRunning) - # self.status_label.set_text('idle') - # gobject.source_remove(self.source_id) - # if action=='update_pdb_mtz': - # self.update_pdb_mtz_files('') - def RefinementParams(self, widget): print("\n==> XCE: changing refinement parameters") self.RefmacParams = self.Refine.RefinementParams(self.RefmacParams) @@ -641,7 +573,6 @@ def update_pdb_mtz_files(self, pdbRoot): self.Logfile.error("cannot find PDB file") if self.pdbFile != "": - # os.chdir(os.path.join(self.reference_directory,self.refinementDir)) coot.set_colour_map_rotation_on_read_pdb(0) imol = coot.handle_read_draw_molecule_with_recentre(self.pdbFile, 0) self.QualityIndicators = XChemUtils.parse().PDBheader( @@ -688,7 +619,8 @@ def update_pdb_mtz_files(self, pdbRoot): else: self.mtzFree_label.set_text("missing file") self.Logfile.error( - "cannot find file with F,SIGF and FreeR_flag; cannot start refinement" + "cannot find file with F,SIGF and FreeR_flag;" + " cannot start refinement" ) self.REFINEbutton.set_sensitive(False) @@ -736,68 +668,6 @@ def update_pdb_mtz_files(self, pdbRoot): self.RefreshData() - # def load_ground_state_map(self,widget): - # self.spinnerBox.add(self.refinementRunning) - # self.refinementRunning.start() - # self.status_label.set_text('loading ground state maps by reso...') - # self.source_id = gobject.timeout_add(100, self.load_ground_state_map_thread) - - # def load_ground_state_map_thread(self): - # self.spinnerBox.add(self.refinementRunning) - # self.refinementRunning.show() - # self.refinementRunning.start() - # - # # first remove all ground state maps files - # if len(coot_utils_XChem.molecule_number_list()) > 0: - # for item in coot_utils_XChem.molecule_number_list(): - # if 'ground-state-mean-map' in coot.molecule_name(item): - # coot.close_molecule(item) - # - # # first remove all entries for self.cb_select_mean_map_by_resolution - # # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 maps - # for n in range(-1,100): - # self.cb_select_mean_map_by_resolution.remove_text(0) - # - # self.status_label.set_text('loading ground state maps') - # self.get_highest_reso_ground_state_map() - # blueStart=0.02 - # for map in self.ground_state_map_List: - # self.cb_select_mean_map_by_resolution.append_text(map[0]) - # imol=coot.handle_read_ccp4_map((map[1]),0) - # coot.set_contour_level_in_sigma(imol,1) - # coot.set_last_map_colour(0.74,0.44,blueStart) - # blueStart+=0.05 - # # show only highest resolution map to start with - # self.show_highres_ground_state_map() - # self.cb_select_mean_map_by_resolution.set_active(0) - # self.end_thread('') - - # def show_highres_ground_state_map(self): - # if len(self.ground_state_map_List) >= 1: - # for imol in coot_utils_XChem.molecule_number_list(): - # if coot.molecule_name(imol) in self.ground_state_map_List[0][1]: - # coot.set_map_displayed(imol,1) - # elif 'ground-state-mean-map' in coot.molecule_name(imol): - # coot.set_map_displayed(imol,0) - - # def show_all_ground_state_map(self): - # if len(self.ground_state_map_List) >= 1: - # for imol in coot_utils_XChem.molecule_number_list(): - # if 'ground-state-mean-map' in coot.molecule_name(imol): - # coot.set_map_displayed(imol,1) - - # def show_selected_mean_map(self,widget): - # reso=str(self.cb_select_mean_map_by_resolution.get_active_text()) - # mapToshow='' - # for maps in self.ground_state_map_List: - # if maps[0]==reso: - # mapToshow=maps[1] - # for imol in coot_utils_XChem.molecule_number_list(): - # if coot.molecule_name(imol) in mapToshow: - # coot.set_map_displayed(imol,1) - # elif 'ground-state-mean-map' in coot.molecule_name(imol): - # coot.set_map_displayed(imol,0) - def show_molprobity_to_do(self, widget): if os.path.isfile( os.path.join( From 29c241e655fe56f7d9fab33a57b28639c9edf0d9 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 10 Nov 2022 11:18:57 +0000 Subject: [PATCH 172/358] Clean up XChemCootNew Clean up XChemCootNew Clean up XChemCootNew --- xce/lib/XChemCootNew.py | 382 +++++----------------------------------- 1 file changed, 45 insertions(+), 337 deletions(-) diff --git a/xce/lib/XChemCootNew.py b/xce/lib/XChemCootNew.py index d89b58cb..bb417c28 100755 --- a/xce/lib/XChemCootNew.py +++ b/xce/lib/XChemCootNew.py @@ -16,7 +16,8 @@ from matplotlib.figure import Figure # had to adapt the original coot_utils.py file -# otherwise unable to import the original file without complaints about missing modules etc. +# otherwise unable to import the original file without complaints about missing modules +# etc. # modified file is now in $XChemExplorer_DIR/lib @@ -27,7 +28,7 @@ class GUI(object): def __init__(self): - ########################################################################################### + ################################################################################ # read in settings file from XChemExplorer to set the relevant paths self.settings = pickle.load(open(".xce_settings.pkl", "rb")) @@ -77,13 +78,12 @@ def __init__(self): # this decides which samples will be looked at self.selection_mode = "" - # self.selected_site='' self.pandda_index = -1 # refers to the number of sites self.site_index = "0" self.event_index = "0" - # the Folder is kind of a legacy thing because my inital idea was to have separate folders - # for Data Processing and Refinement + # the Folder is kind of a legacy thing because my inital idea was to have + # separate folders for Data Processing and Refinement self.project_directory = self.settings["initial_model_directory"] self.Serial = 0 self.panddaSerial = 0 @@ -99,7 +99,6 @@ def __init__(self): self.ligand_confidence = "" self.refinement_folder = "" self.refinementProtocol = "pandda_refmac" - # self.datasetOutcome='' self.pdb_style = "refine.pdb" self.mtz_style = "refine.mtz" @@ -127,11 +126,10 @@ def __init__(self): self.label_button_list = [] - ########################################################################################### + ################################################################################ # some COOT settings coot.set_map_radius(17) coot.set_colour_map_rotation_for_map(0) - # coot.set_colour_map_rotation_on_read_pdb_flag(21) self.QualityIndicators = { "RefinementRcryst": "-", @@ -194,13 +192,11 @@ def StartGUI(self): self.window.set_title("XChemExplorer") self.vbox = gtk.VBox() # this is the main container - ################################################################################# + ################################################################################ # --- Sample Selection --- - # self.vbox.add(gtk.Label('Select Samples')) frame = gtk.Frame(label="Select Samples") self.hbox_select_samples = gtk.HBox() - # vbox=gtk.VBox() self.cb_select_samples = gtk.combo_box_new_text() self.cb_select_samples.connect("changed", self.set_selection_mode) @@ -208,48 +204,29 @@ def StartGUI(self): self.cb_select_samples.append_text(citeria) self.hbox_select_samples.add(self.cb_select_samples) - # self.cb_select_sites = gtk.combo_box_new_text() - # self.cb_select_sites.connect("changed", self.set_site) - # for site in self.ligand_site_information: - # self.cb_select_sites.append_text(str(site[0])+' - '+str(site[1])) - # self.hbox_select_samples.add(self.cb_select_sites) - self.select_samples_button = gtk.Button(label="GO") self.select_samples_button.connect("clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) - ################################################################################# + ################################################################################ # --- status window --- frame = gtk.Frame() self.status_label = gtk.Label() frame.add(self.status_label) self.vbox.pack_start(frame) - ################################################################################# + ################################################################################ # --- refinement protocol --- frame = gtk.Frame() self.refinementProtocolcheckbox = gtk.CheckButton("PanDDA model refinement)") # callback is defined later - # self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) self.refinementProtocolcheckbox.set_active(True) frame.add(self.refinementProtocolcheckbox) self.vbox.pack_start(frame) - ################################################################################# - # --- refinement program --- - # frame = gtk.Frame() - # self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') - # self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) - # self.refinementProgramcheckbox.set_active(False) - # frame.add(self.refinementProgramcheckbox) - # self.vbox.pack_start(frame) - - # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ # --- Refinement Statistics --- # next comes a section which displays some global quality indicators # a combination of labels and textview widgets, arranged in a table @@ -476,15 +453,11 @@ def StartGUI(self): "clicked", self.show_ground_state_mean_map ) hbox.add(self.ground_state_mean_map_button) - # self.vbox.add(self.ground_state_mean_map_button) self.vbox.add(hbox) self.vbox.pack_start(frame) - # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ # --- hbox for compound picture & spider_plot (formerly: refinement history) --- frame = gtk.Frame() self.hbox_for_info_graphics = gtk.HBox() @@ -504,11 +477,6 @@ def StartGUI(self): compound_frame.add(self.image) self.hbox_for_info_graphics.add(compound_frame) - # --- Refinement History --- - # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) - # self.canvas.set_size_request(190, 190) - # self.hbox_for_info_graphics.add(self.canvas) - # --- Spider Plot --- spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( @@ -525,55 +493,7 @@ def StartGUI(self): frame.add(self.hbox_for_info_graphics) self.vbox.add(frame) - ################################################################################# - # --- pandda.inspect user comments --- - # outer_frame = gtk.Frame(label='pandda.inspect comments') - # vbox = gtk.VBox() - # ligand_site_name_label_frame = gtk.Frame() - # ligand_site_name_label = gtk.Label('Site Name') - # ligand_site_name_label_frame.add(ligand_site_name_label) - # ligand_inspect_confidence_label_frame = gtk.Frame() - # ligand_inspect_confidence_label = gtk.Label('Confidence') - # ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) - # ligand_inspect_interesting_label_frame = gtk.Frame() - # ligand_inspect_interesting_label = gtk.Label('Interesting') - # ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) - # ligand_inspect_comment_label_frame = gtk.Frame() - # ligand_inspect_comment_label = gtk.Label('Comment') - # ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) - # ligand_site_name_value_frame = gtk.Frame() - # self.ligand_site_name_value = gtk.Label('-') - # ligand_site_name_value_frame.add(self.ligand_site_name_value) - # ligand_inspect_confidence_value_frame = gtk.Frame() - # self.ligand_inspect_confidence_value = gtk.Label('-') - # ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) - # ligand_inspect_interesting_value_frame = gtk.Frame() - # self.ligand_inspect_interesting_value = gtk.Label('-') - # ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) - # ligand_inspect_comment_value_frame = gtk.Frame() - # self.ligand_inspect_comment_value = gtk.Label('-') - # ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) - # - # frame_pandda_inspect_comments_table = gtk.Frame() - # pandda_inspect_comments_table = gtk.Table(2, 6, False) - # pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) - # pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) - # pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) - # - # frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) - # vbox.add(frame_pandda_inspect_comments_table) - # outer_frame.add(vbox) - # self.vbox.pack_start(outer_frame) - - # # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ outer_frame = gtk.Frame(label="Sample Navigator") hboxSample = gtk.HBox() @@ -616,47 +536,7 @@ def StartGUI(self): outer_frame.add(hboxSample) self.vbox.add(outer_frame) - # # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# - # outer_frame = gtk.Frame(label='Label') - # hboxlabel = gtk.HBox() - # - # frame = gtk.Frame() - # hbox = gtk.HBox() - # self.vbox_label = gtk.VBox() - # labels = self.db.get_labels_from_db() - # if len(labels) > 5: - # print '==> sorry, too many labels; cannot display them in panel' - # labels = labels[:5] - # # with radiobuttons, one of them needs to be always on - # # but there will be cases when the user has not assigned a label yet - # # hence, the not_shown button is not shown but gets active - # # if the label has not been set yet - # labels.append('not_shown') - # for n, l in enumerate(labels): - # print n,l - # if n == 0: - # new_button = gtk.RadioButton(None, l) - # else: - # new_button = gtk.RadioButton(new_button, l) - # new_button.connect("toggled", self.label_button_clicked, l) - # if not l == 'not_shown': - # hbox.add(new_button) - # self.label_button_list.append(new_button) - # self.vbox_label.add(hbox) - # frame.add(self.vbox_label) - # - # hboxlabel.add(frame) - # - # outer_frame.add(hboxlabel) - # self.vbox.add(outer_frame) - - # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ # --- current refinement stage --- outer_frame = gtk.Frame() hbox = gtk.HBox() @@ -673,7 +553,6 @@ def StartGUI(self): "toggled", self.experiment_stage_button_clicked, button[1] ) vbox.pack_start(new_button, False, False, 0) - # vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) @@ -691,43 +570,13 @@ def StartGUI(self): "toggled", self.ligand_confidence_button_clicked, criteria ) vbox.pack_start(new_button, False, False, 0) - # vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) - # # label section --> start - # frame = gtk.Frame(label='Label') - # vbox = gtk.VBox() - # labels = self.db.get_labels_from_db() - # if len(labels) > 5: - # print '==> sorry, too many labels; cannot display them in panel' - # labels = labels[:5] - # # with radiobuttons, one of them needs to be always on - # # but there will be cases when the user has not assigned a label yet - # # hence, the not_shown button is not shown but gets active - # # if the label has not been set yet - # labels.append('not_shown') - # for n, l in enumerate(labels): - # print n,l - # if n == 0: - # new_button = gtk.RadioButton(None, l) - # else: - # new_button = gtk.RadioButton(new_button, l) - # new_button.connect("toggled", self.label_button_clicked, l) - # if not l == 'not_shown': - # vbox.add(new_button) - # self.label_button_list.append(new_button) - # frame.add(vbox) - # hbox.pack_start(frame) - # # label section <-- end - outer_frame.add(hbox) self.vbox.pack_start(outer_frame) - # SPACER - # self.vbox.add(gtk.Label(' ')) - # --- ligand modeling --- frame = gtk.Frame(label="Ligand Modeling") self.hbox_for_modeling = gtk.HBox() @@ -743,13 +592,6 @@ def StartGUI(self): frame.add(self.hbox_for_modeling) self.vbox.pack_start(frame) - # # --- ligand confidence --- - # self.cb_ligand_confidence = gtk.combo_box_new_text() - # self.cb_ligand_confidence.connect("changed", self.set_ligand_confidence) - # for citeria in self.ligand_confidence: - # self.cb_ligand_confidence.append_text(citeria) - # self.vbox.add(self.cb_ligand_confidence) - # --- refinement & options --- self.hbox_for_refinement = gtk.HBox() self.REFINEbutton = gtk.Button(label="Refine") @@ -768,11 +610,8 @@ def StartGUI(self): self.hbox_for_refinement.add(self.covalentLinksCreatebutton) self.vbox.add(self.hbox_for_refinement) - # self.VALIDATEbutton = gtk.Button(label="validate structure") - # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") - - # need to put it here, because attributes within refinementProtocolCallback function - # are defined after checkbox is defined + # need to put it here, because attributes within refinementProtocolCallback + # function are defined after checkbox is defined self.refinementProtocolcheckbox.connect( "toggled", self.refinementProtocolCallback ) @@ -793,7 +632,6 @@ def ChangeXtal(self, widget, data=None): if self.index < 0: self.index = 0 if self.index >= len(self.Todo): - # self.index = len(self.Todo) self.index = 0 self.cb.set_active(self.index) @@ -805,11 +643,6 @@ def ChooseXtal(self, widget): self.merge_ligand_button.set_sensitive(True) self.place_ligand_here_button.set_sensitive(True) - # self.ligand_site_name_value.set_label('-') - # self.ligand_inspect_confidence_value.set_label('-') - # self.ligand_inspect_interesting_value.set_label('-') - # self.ligand_inspect_comment_value.set_label('-') - self.refresh_site_combobox() self.db_dict_mainTable = {} self.db_dict_panddaTable = {} @@ -817,16 +650,11 @@ def ChooseXtal(self, widget): self.compoundID = str(self.Todo[self.index][1]) self.refinement_folder = str(self.Todo[self.index][4]) self.refinement_outcome = str(self.Todo[self.index][5]) - # self.label = self.db.get_label_of_sample(self.xtalID) - # self.update_label_radiobutton() self.update_RefinementOutcome_radiobutton() if ( self.xtalID not in self.siteDict ): # i.e. we are not working with a PanDDA model self.ligand_confidence = str(self.Todo[self.index][6]) - # self.update_LigandConfidence_radiobutton() - # self.label = self.db.get_label_of_sample(self.xtalID) - # self.update_label_radiobutton() self.RefreshData() @@ -884,18 +712,6 @@ def update_RefinementOutcome_radiobutton(self): button.set_active(True) break - # def update_label_radiobutton(self): - # found = False - # for button in self.label_button_list: - # if button.get_label() == self.label: - # button.set_active(True) - # found = True - # if not found: - # for button in self.label_button_list: - # if button.get_label() == 'not_shown': - # button.set_active(True) - # break - def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 @@ -915,7 +731,8 @@ def update_LigandConfidence_radiobutton(self): def refresh_site_combobox(self): # reset self.pandda_index self.pandda_index = -1 - # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites + # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever + # be 100 sites for n in range(-1, 100): self.cb_site.remove_text(0) self.site_index = "0" @@ -961,9 +778,6 @@ def RefreshSiteData(self): if self.compoundID + ".pdb" in coot.molecule_name(imol): coot.close_molecule(imol) - # for w in self.label_button_list: - # w.set_active(False) - print("pandda index", self.pandda_index) self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] print("new spider plot:", self.spider_plot) @@ -977,11 +791,6 @@ def RefreshSiteData(self): print("new site coordinates:", site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) - # self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) - # self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) - # self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) - # self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) - self.spider_plot_data = ( self.db.get_db_pandda_dict_for_sample_and_site_and_event( self.xtalID, self.site_index, self.event_index @@ -1047,14 +856,14 @@ def RefreshSiteData(self): except ValueError: self.ligand_RSZDValue.set_label("-") - ######################################################################################### + ################################################################################ # delete old Event MAPs if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): if "map.native.ccp4" in coot.molecule_name(imol): coot.close_molecule(imol) - ######################################################################################### + ################################################################################ # Spider plot # Note: refinement history was shown instead previously if os.path.isfile(self.spider_plot): @@ -1072,7 +881,7 @@ def RefreshSiteData(self): ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) - ######################################################################################### + ################################################################################ # check for PANDDAs EVENT maps if os.path.isfile(self.event_map): coot.set_colour_map_rotation_on_read_pdb(0) @@ -1080,8 +889,6 @@ def RefreshSiteData(self): for imol in coot_utils_XChem.molecule_number_list(): if self.event_map in coot.molecule_name(imol): coot.set_contour_level_in_sigma(imol, 2) - # coot.set_contour_level_absolute(imol,0.5) - # coot.set_last_map_colour(0.4,0,0.4) coot.set_last_map_colour(0.74, 0.44, 0.02) def experiment_stage_button_clicked(self, widget, data=None): @@ -1097,9 +904,6 @@ def experiment_stage_button_clicked(self, widget, data=None): + str(data) + " in mainTable of datasource" ) - # print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( - # data) + ' in mainTable of datasource' - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.db.create_or_remove_missing_records_in_depositTable( self.xce_logfile, self.xtalID, "ligand_bound", self.db_dict_mainTable ) @@ -1115,8 +919,6 @@ def ligand_confidence_button_clicked(self, widget, data=None): + str(data) + " in mainTable of datasource" ) - # print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( - # data) + ' in mainTable of datasource' self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.Todo[self.index][6] = data else: @@ -1132,36 +934,11 @@ def ligand_confidence_button_clicked(self, widget, data=None): + str(data) + " in panddaTable of datasource" ) - # print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( - # self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( - # data) + ' in panddaTable of datasource' self.db.update_site_event_panddaTable( self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable ) self.siteDict[self.xtalID][self.pandda_index][7] = data - # def update_label(self, widget): - # print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' - # # widget.pressed() - # for w in self.label_button_list: - # print w.get_label(), w.get_active() - # if w != widget: - # w.set_active(False) - # print '<<<<<<<<<<<<<<<<<<<<<<<<<<' - # self.db_dict_mainTable['label'] = widget.get_label() - # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( - # widget.get_label()) + ' in mainTable of datasource' - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - - # def label_button_clicked(self, widget, data=None): - # print '............',data - # if data == 'not_shown': - # self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) - # else: - # self.db_dict_mainTable['label'] = data - # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - def RefreshData(self): # reset spider plot image spider_plot_pic = gtk.gdk.pixbuf_new_from_file( @@ -1197,10 +974,7 @@ def RefreshData(self): self.project_directory, self.xtalID, self.compoundID, self.data_source ) self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) - self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * "0" + str( - self.Serial - ) - # self.Serial=self.Refine.GetSerial() + self.panddaSerial = (4 - len(str(self.Serial))) * "0" + str(self.Serial) if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple if os.path.isfile( @@ -1249,25 +1023,18 @@ def RefreshData(self): self.xtalID, self.data_source, "" ) # '' because file does not exist - # all this information is now updated in the datasource after each refinement cycle + # all this information is now updated in the datasource after each refinement + # cycle self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) - ######################################################################################### + ################################################################################ # history # if the structure was previously refined, try to read the parameters - # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) print("==> REFMAC params:", self.RefmacParams) - # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() - # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) - # else: - # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea - # self.canvas.set_size_request(190, 190) - # self.hbox_for_info_graphics.add(self.canvas) - # self.canvas.show() - - ######################################################################################### + + ################################################################################ # ligand files # first remove old samples if present print(">>>", self.mol_dict["ligand_stereo"]) @@ -1276,19 +1043,19 @@ def RefreshData(self): self.select_cpd_cb.remove_text(0) print("done") - ######################################################################################### + ################################################################################ # remove potential generic line which indicates a possible covalent link generic_object_clear(self.covLinkObject) self.covLinkAtomSpec = None - ######################################################################################### + ################################################################################ # reset covalent links self.covLinks = ["X", "X", "X", "X"] - ######################################################################################### + ################################################################################ # update pdb & maps - ######################################################################################### + ################################################################################ # delete old PDB and MAP files # - get a list of all molecules which are currently opened in COOT # - remove all molecules/ maps before loading a new set @@ -1296,7 +1063,7 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): coot.close_molecule(item) - ######################################################################################### + ################################################################################ # read new PDB files # read protein molecule after ligand so that this one is the active molecule coot.set_nomenclature_errors_on_read("ignore") @@ -1359,7 +1126,6 @@ def RefreshData(self): self.select_cpd_cb.set_active(0) else: print("no compound found in sample directory") - # self.select_cpd_cb.append_text('') self.select_cpd_cb.set_sensitive(False) if not os.path.isfile( @@ -1376,9 +1142,6 @@ def RefreshData(self): self.pdb_style.replace(".pdb", "") + ".split.ground-state.pdb", ) ) - # print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.ground-state.pdb') if os.path.isfile( os.path.join( self.project_directory, @@ -1387,7 +1150,6 @@ def RefreshData(self): ) ): self.Logfile.insert("==> COOT: found ground-state model") - # print '=> XCE: found ground-state model' os.chdir(os.path.join(self.project_directory, self.xtalID)) coot.set_colour_map_rotation_on_read_pdb(0) try: @@ -1407,7 +1169,6 @@ def RefreshData(self): coot.set_mol_active(imol, 0) else: self.Logfile.error("==> COOT - cannot find ground-state model") - # print '=> XCE - ERROR: cannot find ground-state model' self.Logfile.insert( "==> COOT: looking for bound-state model " + os.path.join( @@ -1416,9 +1177,6 @@ def RefreshData(self): self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb", ) ) - # print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.bound-state.pdb') if os.path.isfile( os.path.join( self.project_directory, @@ -1427,7 +1185,6 @@ def RefreshData(self): ) ): self.Logfile.insert("==> COOT: found bound-state model") - # print '=> XCE: found bound-state model' os.chdir(os.path.join(self.project_directory, self.xtalID)) coot.set_colour_map_rotation_on_read_pdb(0) color_wheel_rotation = 21 / float(imol + 2) @@ -1443,9 +1200,7 @@ def RefreshData(self): self.mol_dict["protein"] = imol else: self.Logfile.error("==> COOT: cannot find bound-state model") - # print '=> XCE - ERROR: cannot find bound-state model' self.Logfile.warning("==> COOT: moving to next crystal...") - # print '=> XCE: moving to next crystal...' self.go_to_next_xtal() else: if os.path.isfile( @@ -1494,12 +1249,12 @@ def RefreshData(self): coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model - ######################################################################################### + ################################################################################ # read fofc maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level - # coot 0.9 does not handle P1 maps well, so now looking for non-existent map in order to trigger - # map calculation from mtz file + # coot 0.9 does not handle P1 maps well, so now looking for non-existent map in + # order to trigger map calculation from mtz file if os.path.isfile( os.path.join(self.project_directory, self.xtalID, "2fofc_??????.map") ): @@ -1516,13 +1271,6 @@ def RefreshData(self): else: # try to open mtz file with same name as pdb file coot.set_default_initial_contour_level_for_map(1) - # if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): - # os.chdir(os.path.join(self.project_directory,self.xtalID)) - # if not os.path.isfile('REFINEMENT_IN_PROGRESS'): - # if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-pandda-input.mtz')): - # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) - # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): - # os.symlink('dimple.mtz',self.mtz_style) if os.path.isfile( os.path.join(self.project_directory, self.xtalID, self.mtz_style) ): @@ -1542,7 +1290,7 @@ def RefreshData(self): os.path.join(self.project_directory, self.xtalID, "dimple.mtz") ) - ######################################################################################### + ################################################################################ # update Quality Indicator table try: self.RRfreeValue.set_label( @@ -1653,34 +1401,6 @@ def REFINE(self, widget): self.start_refinement() def start_refinement(self): - # ####################################################### - # if not os.path.isdir(os.path.join(self.project_directory,self.xtalID,'cootOut')): - # os.mkdir(os.path.join(self.project_directory,self.xtalID,'cootOut')) - # # create folder for new refinement cycle - # os.mkdir(os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial))) - # - # ####################################################### - # # write PDB file - # # now take protein pdb file and write it to newly create Refine_ folder - # # note: the user has to make sure that the ligand file was merged into main file - # for item in coot_utils_XChem.molecule_number_list(): - # if coot.molecule_name(item).endswith(self.pdb_style.replace('.pdb','')+'.split.bound-state.pdb') or coot.molecule_name(item).endswith(self.pdb_style): - # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) - # break - # elif coot.molecule_name(item).endswith('dimple.pdb'): - # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) - # break - # - - ####################################################### - - # ####################################################### - # # create folder for new refinement cycle and check if free.mtz exists - # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): - # os.mkdir(os.path.join(self.project_directory, self.xtalID)) - # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): - # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) - if self.refinementProtocol.startswith("pandda"): ####################################################### @@ -1711,15 +1431,16 @@ def start_refinement(self): self.Logfile.warning( "==> COOT: folder exists; will overwrite contents!" ) - # print '==> XCE: WARNING -> folder exists; will overwrite contents!' self.Logfile.warning( - "==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem" + "==> COOT: it is advised to check the sample directory" + " as this might be a symptom for a PDB file problem" ) ####################################################### # write PDB file - # now take protein pdb file and write it to newly create Refine_ folder - # note: the user has to make sure that the ligand file was merged into main file + # now take protein pdb file and write it to newly create Refine_ + # folder. note: the user has to make sure that the ligand file was merged + # into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb" @@ -1735,9 +1456,6 @@ def start_refinement(self): ), ) break - # elif coot.molecule_name(item).endswith('dimple.pdb'): - # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) - # break XChemRefine.panddaRefine( self.project_directory, self.xtalID, self.compoundID, self.data_source @@ -1769,8 +1487,9 @@ def start_refinement(self): ####################################################### # write PDB file - # now take protein pdb file and write it to newly create Refine_ folder - # note: the user has to make sure that the ligand file was merged into main file + # now take protein pdb file and write it to newly create Refine_ + # folder. note: the user has to make sure that the ligand file was merged + # into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith(self.pdb_style): coot.write_pdb_file( @@ -1827,7 +1546,6 @@ def start_refinement(self): self.index += 1 if self.index >= len(self.Todo): - # self.index = len(self.Todo) self.index = 0 self.cb.set_active(self.index) @@ -1907,7 +1625,8 @@ def show_potential_link(self, *clicks): ] else: print( - "error: both atoms must belong to the same object; did you merge the ligand with your protein?" + "error: both atoms must belong to the same object;" + " did you merge the ligand with your protein?" ) def covalentLinkCreate(self, widget): @@ -1981,11 +1700,6 @@ def place_ligand_here(self, widget): coot_utils_XChem.move_molecule_here(imol) print("LIGAND: ", molName) - # print '===> XCE: moving ligand to pointer' - # # coot.move_molecule_here() - # print 'LIGAND: ', self.mol_dict['ligand'] - # coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) - def merge_ligand_into_protein(self, widget): cpd = str(self.select_cpd_cb.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): @@ -2065,12 +1779,6 @@ def merge_ligand_into_protein(self, widget): self.select_cpd_cb.set_sensitive(False) - # print '===> XCE: merge ligand into protein structure' - # # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) - # coot.merge_molecules_py([self.mol_dict['ligand']], self.mol_dict['protein']) - # print '===> XCE: deleting ligand molecule' - # coot.close_molecule(self.mol_dict['ligand']) - def show_molprobity_to_do(self, widget): print(self.panddaSerial) AdjPanddaSerial = (4 - len(str(self.Serial))) * "0" + str( From d57c8f72f094fc7978d6cf6a023d696ae7cbc36d Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 10 Nov 2022 11:25:04 +0000 Subject: [PATCH 173/358] Clean up XChemCootBuster --- xce/lib/XChemCootBuster.py | 495 +++---------------------------------- 1 file changed, 34 insertions(+), 461 deletions(-) diff --git a/xce/lib/XChemCootBuster.py b/xce/lib/XChemCootBuster.py index 0d93c7d4..23431482 100755 --- a/xce/lib/XChemCootBuster.py +++ b/xce/lib/XChemCootBuster.py @@ -16,7 +16,8 @@ from matplotlib.figure import Figure # had to adapt the original coot_utils.py file -# otherwise unable to import the original file without complaints about missing modules etc. +# otherwise unable to import the original file without complaints about missing modules +# etc. # modified file is now in $XChemExplorer_DIR/lib @@ -27,7 +28,7 @@ class GUI(object): def __init__(self): - ########################################################################################### + ################################################################################ # read in settings file from XChemExplorer to set the relevant paths self.settings = pickle.load(open(".xce_settings.pkl", "rb")) @@ -77,13 +78,12 @@ def __init__(self): # this decides which samples will be looked at self.selection_mode = "" - # self.selected_site='' self.pandda_index = -1 # refers to the number of sites self.site_index = "0" self.event_index = "0" - # the Folder is kind of a legacy thing because my inital idea was to have separate folders - # for Data Processing and Refinement + # the Folder is kind of a legacy thing because my inital idea was to have + # separate folders for Data Processing and Refinement self.project_directory = self.settings["initial_model_directory"] self.Serial = 0 self.panddaSerial = 0 @@ -98,8 +98,6 @@ def __init__(self): self.spider_plot = "" self.ligand_confidence = "" self.refinement_folder = "" - # self.refinementProtocol = 'pandda_refmac' - # self.datasetOutcome='' self.pdb_style = "refine.pdb" self.mtz_style = "refine.mtz" @@ -127,7 +125,7 @@ def __init__(self): self.label_button_list = [] - ########################################################################################### + ################################################################################ # some COOT settings coot.set_map_radius(17) coot.set_colour_map_rotation_for_map(0) @@ -194,13 +192,11 @@ def StartGUI(self): self.window.set_title("XChemExplorer") self.vbox = gtk.VBox() # this is the main container - ################################################################################# + ################################################################################ # --- Sample Selection --- - # self.vbox.add(gtk.Label('Select Samples')) frame = gtk.Frame(label="Select Samples") self.hbox_select_samples = gtk.HBox() - # vbox=gtk.VBox() self.cb_select_samples = gtk.combo_box_new_text() self.cb_select_samples.connect("changed", self.set_selection_mode) @@ -208,48 +204,20 @@ def StartGUI(self): self.cb_select_samples.append_text(citeria) self.hbox_select_samples.add(self.cb_select_samples) - # self.cb_select_sites = gtk.combo_box_new_text() - # self.cb_select_sites.connect("changed", self.set_site) - # for site in self.ligand_site_information: - # self.cb_select_sites.append_text(str(site[0])+' - '+str(site[1])) - # self.hbox_select_samples.add(self.cb_select_sites) - self.select_samples_button = gtk.Button(label="GO") self.select_samples_button.connect("clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) - ################################################################################# + ################################################################################ # --- status window --- frame = gtk.Frame() self.status_label = gtk.Label() frame.add(self.status_label) self.vbox.pack_start(frame) - ################################################################################# - # --- refinement protocol --- - # frame = gtk.Frame() - # self.refinementProtocolcheckbox = gtk.CheckButton('PanDDA model refinement)') - # # callback is defined later - ## self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) - # self.refinementProtocolcheckbox.set_active(True) - # frame.add(self.refinementProtocolcheckbox) - # self.vbox.pack_start(frame) - - ################################################################################# - # --- refinement program --- - # frame = gtk.Frame() - # self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') - # self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) - # self.refinementProgramcheckbox.set_active(False) - # frame.add(self.refinementProgramcheckbox) - # self.vbox.pack_start(frame) - - # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ # --- Refinement Statistics --- # next comes a section which displays some global quality indicators # a combination of labels and textview widgets, arranged in a table @@ -476,15 +444,11 @@ def StartGUI(self): "clicked", self.show_ground_state_mean_map ) hbox.add(self.ground_state_mean_map_button) - # self.vbox.add(self.ground_state_mean_map_button) self.vbox.add(hbox) self.vbox.pack_start(frame) - # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ # --- hbox for compound picture & spider_plot (formerly: refinement history) --- frame = gtk.Frame() self.hbox_for_info_graphics = gtk.HBox() @@ -504,11 +468,6 @@ def StartGUI(self): compound_frame.add(self.image) self.hbox_for_info_graphics.add(compound_frame) - # --- Refinement History --- - # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) - # self.canvas.set_size_request(190, 190) - # self.hbox_for_info_graphics.add(self.canvas) - # --- Spider Plot --- spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( @@ -525,55 +484,7 @@ def StartGUI(self): frame.add(self.hbox_for_info_graphics) self.vbox.add(frame) - ################################################################################# - # --- pandda.inspect user comments --- - # outer_frame = gtk.Frame(label='pandda.inspect comments') - # vbox = gtk.VBox() - # ligand_site_name_label_frame = gtk.Frame() - # ligand_site_name_label = gtk.Label('Site Name') - # ligand_site_name_label_frame.add(ligand_site_name_label) - # ligand_inspect_confidence_label_frame = gtk.Frame() - # ligand_inspect_confidence_label = gtk.Label('Confidence') - # ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) - # ligand_inspect_interesting_label_frame = gtk.Frame() - # ligand_inspect_interesting_label = gtk.Label('Interesting') - # ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) - # ligand_inspect_comment_label_frame = gtk.Frame() - # ligand_inspect_comment_label = gtk.Label('Comment') - # ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) - # ligand_site_name_value_frame = gtk.Frame() - # self.ligand_site_name_value = gtk.Label('-') - # ligand_site_name_value_frame.add(self.ligand_site_name_value) - # ligand_inspect_confidence_value_frame = gtk.Frame() - # self.ligand_inspect_confidence_value = gtk.Label('-') - # ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) - # ligand_inspect_interesting_value_frame = gtk.Frame() - # self.ligand_inspect_interesting_value = gtk.Label('-') - # ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) - # ligand_inspect_comment_value_frame = gtk.Frame() - # self.ligand_inspect_comment_value = gtk.Label('-') - # ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) - # - # frame_pandda_inspect_comments_table = gtk.Frame() - # pandda_inspect_comments_table = gtk.Table(2, 6, False) - # pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) - # pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) - # pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) - # - # frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) - # vbox.add(frame_pandda_inspect_comments_table) - # outer_frame.add(vbox) - # self.vbox.pack_start(outer_frame) - - # # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ outer_frame = gtk.Frame(label="Sample Navigator") hboxSample = gtk.HBox() @@ -616,47 +527,7 @@ def StartGUI(self): outer_frame.add(hboxSample) self.vbox.add(outer_frame) - # # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# - # outer_frame = gtk.Frame(label='Label') - # hboxlabel = gtk.HBox() - # - # frame = gtk.Frame() - # hbox = gtk.HBox() - # self.vbox_label = gtk.VBox() - # labels = self.db.get_labels_from_db() - # if len(labels) > 5: - # print '==> sorry, too many labels; cannot display them in panel' - # labels = labels[:5] - # # with radiobuttons, one of them needs to be always on - # # but there will be cases when the user has not assigned a label yet - # # hence, the not_shown button is not shown but gets active - # # if the label has not been set yet - # labels.append('not_shown') - # for n, l in enumerate(labels): - # print n,l - # if n == 0: - # new_button = gtk.RadioButton(None, l) - # else: - # new_button = gtk.RadioButton(new_button, l) - # new_button.connect("toggled", self.label_button_clicked, l) - # if not l == 'not_shown': - # hbox.add(new_button) - # self.label_button_list.append(new_button) - # self.vbox_label.add(hbox) - # frame.add(self.vbox_label) - # - # hboxlabel.add(frame) - # - # outer_frame.add(hboxlabel) - # self.vbox.add(outer_frame) - - # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ # --- current refinement stage --- outer_frame = gtk.Frame() hbox = gtk.HBox() @@ -673,7 +544,6 @@ def StartGUI(self): "toggled", self.experiment_stage_button_clicked, button[1] ) vbox.pack_start(new_button, False, False, 0) - # vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) @@ -691,43 +561,13 @@ def StartGUI(self): "toggled", self.ligand_confidence_button_clicked, criteria ) vbox.pack_start(new_button, False, False, 0) - # vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) - # # label section --> start - # frame = gtk.Frame(label='Label') - # vbox = gtk.VBox() - # labels = self.db.get_labels_from_db() - # if len(labels) > 5: - # print '==> sorry, too many labels; cannot display them in panel' - # labels = labels[:5] - # # with radiobuttons, one of them needs to be always on - # # but there will be cases when the user has not assigned a label yet - # # hence, the not_shown button is not shown but gets active - # # if the label has not been set yet - # labels.append('not_shown') - # for n, l in enumerate(labels): - # print n,l - # if n == 0: - # new_button = gtk.RadioButton(None, l) - # else: - # new_button = gtk.RadioButton(new_button, l) - # new_button.connect("toggled", self.label_button_clicked, l) - # if not l == 'not_shown': - # vbox.add(new_button) - # self.label_button_list.append(new_button) - # frame.add(vbox) - # hbox.pack_start(frame) - # # label section <-- end - outer_frame.add(hbox) self.vbox.pack_start(outer_frame) - # SPACER - # self.vbox.add(gtk.Label(' ')) - # --- ligand modeling --- frame = gtk.Frame(label="Ligand Modeling") self.hbox_for_modeling = gtk.HBox() @@ -743,13 +583,6 @@ def StartGUI(self): frame.add(self.hbox_for_modeling) self.vbox.pack_start(frame) - # # --- ligand confidence --- - # self.cb_ligand_confidence = gtk.combo_box_new_text() - # self.cb_ligand_confidence.connect("changed", self.set_ligand_confidence) - # for citeria in self.ligand_confidence: - # self.cb_ligand_confidence.append_text(citeria) - # self.vbox.add(self.cb_ligand_confidence) - # --- refinement & options --- self.hbox_for_refinement = gtk.HBox() self.REFINEbutton = gtk.Button(label="Refine") @@ -768,13 +601,6 @@ def StartGUI(self): self.hbox_for_refinement.add(self.covalentLinksCreatebutton) self.vbox.add(self.hbox_for_refinement) - # self.VALIDATEbutton = gtk.Button(label="validate structure") - # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") - - # # need to put it here, because attributes within refinementProtocolCallback function - # # are defined after checkbox is defined - # self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) - # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") self.CANCELbutton.connect("clicked", self.CANCEL) @@ -791,7 +617,6 @@ def ChangeXtal(self, widget, data=None): if self.index < 0: self.index = 0 if self.index >= len(self.Todo): - # self.index = len(self.Todo) self.index = 0 self.cb.set_active(self.index) @@ -803,11 +628,6 @@ def ChooseXtal(self, widget): self.merge_ligand_button.set_sensitive(True) self.place_ligand_here_button.set_sensitive(True) - # self.ligand_site_name_value.set_label('-') - # self.ligand_inspect_confidence_value.set_label('-') - # self.ligand_inspect_interesting_value.set_label('-') - # self.ligand_inspect_comment_value.set_label('-') - self.refresh_site_combobox() self.db_dict_mainTable = {} self.db_dict_panddaTable = {} @@ -815,16 +635,11 @@ def ChooseXtal(self, widget): self.compoundID = str(self.Todo[self.index][1]) self.refinement_folder = str(self.Todo[self.index][4]) self.refinement_outcome = str(self.Todo[self.index][5]) - # self.label = self.db.get_label_of_sample(self.xtalID) - # self.update_label_radiobutton() self.update_RefinementOutcome_radiobutton() if ( self.xtalID not in self.siteDict ): # i.e. we are not working with a PanDDA model self.ligand_confidence = str(self.Todo[self.index][6]) - # self.update_LigandConfidence_radiobutton() - # self.label = self.db.get_label_of_sample(self.xtalID) - # self.update_label_radiobutton() self.RefreshData() @@ -882,18 +697,6 @@ def update_RefinementOutcome_radiobutton(self): button.set_active(True) break - # def update_label_radiobutton(self): - # found = False - # for button in self.label_button_list: - # if button.get_label() == self.label: - # button.set_active(True) - # found = True - # if not found: - # for button in self.label_button_list: - # if button.get_label() == 'not_shown': - # button.set_active(True) - # break - def update_LigandConfidence_radiobutton(self): # updating ligand confidence radiobuttons current_stage = 0 @@ -913,7 +716,8 @@ def update_LigandConfidence_radiobutton(self): def refresh_site_combobox(self): # reset self.pandda_index self.pandda_index = -1 - # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites + # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever + # be 100 sites for n in range(-1, 100): self.cb_site.remove_text(0) self.site_index = "0" @@ -959,9 +763,6 @@ def RefreshSiteData(self): if self.compoundID + ".pdb" in coot.molecule_name(imol): coot.close_molecule(imol) - # for w in self.label_button_list: - # w.set_active(False) - print("pandda index", self.pandda_index) self.spider_plot = self.siteDict[self.xtalID][self.pandda_index][4] print("new spider plot:", self.spider_plot) @@ -975,11 +776,6 @@ def RefreshSiteData(self): print("new site coordinates:", site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) - # self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) - # self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) - # self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) - # self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) - self.spider_plot_data = ( self.db.get_db_pandda_dict_for_sample_and_site_and_event( self.xtalID, self.site_index, self.event_index @@ -1045,14 +841,14 @@ def RefreshSiteData(self): except ValueError: self.ligand_RSZDValue.set_label("-") - ######################################################################################### + ################################################################################ # delete old Event MAPs if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): if "map.native.ccp4" in coot.molecule_name(imol): coot.close_molecule(imol) - ######################################################################################### + ################################################################################ # Spider plot # Note: refinement history was shown instead previously if os.path.isfile(self.spider_plot): @@ -1070,16 +866,13 @@ def RefreshSiteData(self): ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) - ######################################################################################### - # check for PANDDAs EVENT maps + ################################################################################ if os.path.isfile(self.event_map): coot.set_colour_map_rotation_on_read_pdb(0) coot.handle_read_ccp4_map((self.event_map), 0) for imol in coot_utils_XChem.molecule_number_list(): if self.event_map in coot.molecule_name(imol): coot.set_contour_level_in_sigma(imol, 2) - # coot.set_contour_level_absolute(imol,0.5) - # coot.set_last_map_colour(0.4,0,0.4) coot.set_last_map_colour(0.74, 0.44, 0.02) def experiment_stage_button_clicked(self, widget, data=None): @@ -1096,9 +889,6 @@ def experiment_stage_button_clicked(self, widget, data=None): + str(data) + " in mainTable of datasource" ) - # print '==> XCE: setting Refinement Outcome for ' + self.xtalID + ' to ' + str( - # data) + ' in mainTable of datasource' - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.db.create_or_remove_missing_records_in_depositTable( self.xce_logfile, self.xtalID, "ligand_bound", self.db_dict_mainTable ) @@ -1114,8 +904,6 @@ def ligand_confidence_button_clicked(self, widget, data=None): + str(data) + " in mainTable of datasource" ) - # print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' to ' + str( - # data) + ' in mainTable of datasource' self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.Todo[self.index][6] = data else: @@ -1131,36 +919,11 @@ def ligand_confidence_button_clicked(self, widget, data=None): + str(data) + " in panddaTable of datasource" ) - # print '==> XCE: setting Ligand Confidence for ' + self.xtalID + ' (site=' + str( - # self.site_index) + ', event=' + str(self.event_index) + ') to ' + str( - # data) + ' in panddaTable of datasource' self.db.update_site_event_panddaTable( self.xtalID, self.site_index, self.event_index, self.db_dict_panddaTable ) self.siteDict[self.xtalID][self.pandda_index][7] = data - # def update_label(self, widget): - # print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' - # # widget.pressed() - # for w in self.label_button_list: - # print w.get_label(), w.get_active() - # if w != widget: - # w.set_active(False) - # print '<<<<<<<<<<<<<<<<<<<<<<<<<<' - # self.db_dict_mainTable['label'] = widget.get_label() - # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( - # widget.get_label()) + ' in mainTable of datasource' - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - - # def label_button_clicked(self, widget, data=None): - # print '............',data - # if data == 'not_shown': - # self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) - # else: - # self.db_dict_mainTable['label'] = data - # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - def RefreshData(self): # reset spider plot image spider_plot_pic = gtk.gdk.pixbuf_new_from_file( @@ -1192,15 +955,11 @@ def RefreshData(self): ) # initialize Refinement library - # self.Refine = XChemRefine.Refine(self.project_directory, self.xtalID, self.compoundID, self.data_source) self.Refine = XChemRefine.Refine( self.project_directory, self.xtalID, self.compoundID, self.data_source ) self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) - self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * "0" + str( - self.Serial - ) - # self.Serial=self.Refine.GetSerial() + self.panddaSerial = (4 - len(str(self.Serial))) * "0" + str(self.Serial) if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple if os.path.isfile( @@ -1249,25 +1008,19 @@ def RefreshData(self): self.xtalID, self.data_source, "" ) # '' because file does not exist - # all this information is now updated in the datasource after each refinement cycle + # all this information is now updated in the datasource after each refinement + # cycle self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) - ######################################################################################### + ################################################################################ # history # if the structure was previously refined, try to read the parameters # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) print("==> REFMAC params:", self.RefmacParams) - # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() - # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) - # else: - # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea - # self.canvas.set_size_request(190, 190) - # self.hbox_for_info_graphics.add(self.canvas) - # self.canvas.show() - - ######################################################################################### + + ################################################################################ # ligand files # first remove old samples if present print(">>>", self.mol_dict["ligand_stereo"]) @@ -1276,19 +1029,19 @@ def RefreshData(self): self.select_cpd_cb.remove_text(0) print("done") - ######################################################################################### + ################################################################################ # remove potential generic line which indicates a possible covalent link generic_object_clear(self.covLinkObject) self.covLinkAtomSpec = None - ######################################################################################### + ################################################################################ # reset covalent links self.covLinks = ["X", "X", "X", "X"] - ######################################################################################### + ################################################################################ # update pdb & maps - ######################################################################################### + ################################################################################ # delete old PDB and MAP files # - get a list of all molecules which are currently opened in COOT # - remove all molecules/ maps before loading a new set @@ -1296,7 +1049,7 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): coot.close_molecule(item) - ######################################################################################### + ################################################################################ # read new PDB files # read protein molecule after ligand so that this one is the active molecule coot.set_nomenclature_errors_on_read("ignore") @@ -1359,7 +1112,6 @@ def RefreshData(self): self.select_cpd_cb.set_active(0) else: print("no compound found in sample directory") - # self.select_cpd_cb.append_text('') self.select_cpd_cb.set_sensitive(False) if not os.path.isfile( @@ -1367,59 +1119,6 @@ def RefreshData(self): ): os.chdir(os.path.join(self.project_directory, self.xtalID)) - # if self.refinementProtocol.startswith('pandda'): - # self.Logfile.insert('==> COOT: looking for ground-state model ' + os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.ground-state.pdb')) - # print '=> XCE: looking for ground-state model', os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.ground-state.pdb') - # if os.path.isfile(os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', '') + '.split.ground-state.pdb')): - # self.Logfile.insert('==> COOT: found ground-state model') - ## print '=> XCE: found ground-state model' - # os.chdir(os.path.join(self.project_directory, self.xtalID)) - # coot.set_colour_map_rotation_on_read_pdb(0) - # try: - # color_wheel_rotation = 160 / float(imol + 2) - # except UnboundLocalError: - # color_wheel_rotation = 80 - # coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) - # imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.ground-state.pdb'), - # 0) - # coot.set_colour_by_molecule(imol) - # coot.set_mol_active(imol, 0) - # else: - # self.Logfile.error('==> COOT - cannot find ground-state model') - ## print '=> XCE - ERROR: cannot find ground-state model' - # self.Logfile.insert('==> COOT: looking for bound-state model '+ os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.bound-state.pdb')) - # print '=> XCE: looking for bound-state model', os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.bound-state.pdb') - # if os.path.isfile(os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb')): - # self.Logfile.insert('==> COOT: found bound-state model') - ## print '=> XCE: found bound-state model' - # os.chdir(os.path.join(self.project_directory, self.xtalID)) - # coot.set_colour_map_rotation_on_read_pdb(0) - # color_wheel_rotation = 21 / float(imol + 2) - # coot.set_colour_map_rotation_on_read_pdb(color_wheel_rotation) - # imol = coot.handle_read_draw_molecule_with_recentre(os.path.join(self.project_directory, self.xtalID, - # self.pdb_style.replace('.pdb', - # '') + '.split.bound-state.pdb'), - # 0) - # self.mol_dict['protein'] = imol - # else: - # self.Logfile.error('==> COOT: cannot find bound-state model') - ## print '=> XCE - ERROR: cannot find bound-state model' - # self.Logfile.warning('==> COOT: moving to next crystal...') - ## print '=> XCE: moving to next crystal...' - # self.go_to_next_xtal() - # else: if os.path.isfile( os.path.join(self.project_directory, self.xtalID, self.pdb_style) ): @@ -1466,13 +1165,12 @@ def RefreshData(self): coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model - ######################################################################################### + ################################################################################ # read fofc maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level - # if os.path.isfile(os.path.join(self.project_directory, self.xtalID, '2fofc.map')): - # coot 0.9 does not handle P1 maps well, so now looking for non-existent map in order to trigger - # map calculation from mtz file + # coot 0.9 does not handle P1 maps well, so now looking for non-existent map in + # order to trigger map calculation from mtz file if os.path.isfile( os.path.join(self.project_directory, self.xtalID, "2fofc_??????.map") ): @@ -1487,16 +1185,7 @@ def RefreshData(self): ) coot.set_last_map_colour(0, 0, 1) else: - # try to open mtz file with same name as pdb file - # coot.set_default_initial_contour_level_for_map(1) coot.set_colour_map_rotation_on_read_pdb(0) - # if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): - # os.chdir(os.path.join(self.project_directory,self.xtalID)) - # if not os.path.isfile('REFINEMENT_IN_PROGRESS'): - # if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-pandda-input.mtz')): - # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) - # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): - # os.symlink('dimple.mtz',self.mtz_style) if os.path.isfile( os.path.join(self.project_directory, self.xtalID, self.mtz_style) ): @@ -1516,7 +1205,7 @@ def RefreshData(self): os.path.join(self.project_directory, self.xtalID, "dimple.mtz") ) - ######################################################################################### + ################################################################################ # update Quality Indicator table try: self.RRfreeValue.set_label( @@ -1627,62 +1316,6 @@ def REFINE(self, widget): self.start_refinement() def start_refinement(self): - # ####################################################### - # if not os.path.isdir(os.path.join(self.project_directory,self.xtalID,'cootOut')): - # os.mkdir(os.path.join(self.project_directory,self.xtalID,'cootOut')) - # # create folder for new refinement cycle - # os.mkdir(os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial))) - # - # ####################################################### - # # write PDB file - # # now take protein pdb file and write it to newly create Refine_ folder - # # note: the user has to make sure that the ligand file was merged into main file - # for item in coot_utils_XChem.molecule_number_list(): - # if coot.molecule_name(item).endswith(self.pdb_style.replace('.pdb','')+'.split.bound-state.pdb') or coot.molecule_name(item).endswith(self.pdb_style): - # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) - # break - # elif coot.molecule_name(item).endswith('dimple.pdb'): - # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) - # break - # - - ####################################################### - # if self.refinementProtocol.startswith('pandda'): - # - # ####################################################### - # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')): - # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut')) - # # create folder for new refinement cycle - # try: - # self.Logfile.insert('==> COOT: trying to make folder: %s' %os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) - # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'cootOut', 'Refine_' + str(self.Serial))) - # except OSError: - # self.Logfile.warning('==> COOT: folder exists; will overwrite contents!') - ## print '==> XCE: WARNING -> folder exists; will overwrite contents!' - # self.Logfile.warning('==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem') - # - # ####################################################### - # # write PDB file - # # now take protein pdb file and write it to newly create Refine_ folder - # # note: the user has to make sure that the ligand file was merged into main file - # for item in coot_utils_XChem.molecule_number_list(): - # if coot.molecule_name(item).endswith( - # self.pdb_style.replace('.pdb', '') + '.split.bound-state.pdb') or coot.molecule_name( - # item).endswith(self.pdb_style): - # coot.write_pdb_file(item, os.path.join(self.project_directory, self.xtalID, 'cootOut', - # 'Refine_' + str(self.Serial), 'refine.modified.pdb')) - # break - # # elif coot.molecule_name(item).endswith('dimple.pdb'): - # # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) - # # break - # - # XChemRefine.panddaRefine(self.project_directory, self.xtalID, self.compoundID, - # self.data_source).RunQuickRefine(self.Serial, self.RefmacParams, - # self.external_software, self.xce_logfile, - # self.refinementProtocol, self.covLinkAtomSpec) - # else: - - ####################################################### if not os.path.isdir( os.path.join(self.project_directory, self.xtalID, "cootOut") ): @@ -1708,18 +1341,11 @@ def start_refinement(self): ) except OSError: self.Logfile.warning("==> COOT: folder exists; will overwrite contents!") - # print '==> XCE: WARNING -> folder exists; will overwrite contents!' self.Logfile.warning( - "==> COOT: it is advised to check the sample directory as this might be a symptom for a PDB file problem" + "==> COOT: it is advised to check the sample directory" + " as this might be a symptom for a PDB file problem" ) - # ####################################################### - # # create folder for new refinement cycle and check if free.mtz exists - # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID)): - # os.mkdir(os.path.join(self.project_directory, self.xtalID)) - # if not os.path.isdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))): - # os.mkdir(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(self.Serial))) - ####################################################### # write PDB file # now take protein pdb file and write it to newly create Refine_ folder @@ -1751,7 +1377,6 @@ def start_refinement(self): ), ) - # self.Refine.RunRefmac(self.Serial, self.RefmacParams, self.external_software, self.xce_logfile, self.covLinkAtomSpec) self.Refine.RunBuster( self.Serial, self.RefmacParams, @@ -1761,7 +1386,6 @@ def start_refinement(self): ) self.index += 1 if self.index >= len(self.Todo): - # self.index = len(self.Todo) self.index = 0 self.cb.set_active(self.index) @@ -1916,11 +1540,6 @@ def place_ligand_here(self, widget): coot_utils_XChem.move_molecule_here(imol) print("LIGAND: ", molName) - # print '===> XCE: moving ligand to pointer' - # # coot.move_molecule_here() - # print 'LIGAND: ', self.mol_dict['ligand'] - # coot_utils_XChem.move_molecule_here(self.mol_dict['ligand']) - def merge_ligand_into_protein(self, widget): cpd = str(self.select_cpd_cb.get_active_text()) for imol in coot_utils_XChem.molecule_number_list(): @@ -2000,18 +1619,8 @@ def merge_ligand_into_protein(self, widget): self.select_cpd_cb.set_sensitive(False) - # print '===> XCE: merge ligand into protein structure' - # # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) - # coot.merge_molecules_py([self.mol_dict['ligand']], self.mol_dict['protein']) - # print '===> XCE: deleting ligand molecule' - # coot.close_molecule(self.mol_dict['ligand']) - def show_molprobity_to_do(self, widget): print(self.panddaSerial) - AdjPanddaSerial = (4 - len(str(self.Serial))) * "0" + str( - int(self.panddaSerial) - 1 - ) - print( "==> XCE COOT: trying to find " + os.path.join( @@ -2041,11 +1650,6 @@ def show_molprobity_to_do(self, widget): + "-report/molprobe/molprobity_coot.py", ) ) - # elif os.path.isfile(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), - # 'molprobity_coot.py')): - # print '==> XCE: running MolProbity Summary for', self.xtalID - # coot.run_script(os.path.join(self.project_directory, self.xtalID, 'Refine_' + str(AdjPanddaSerial), - # 'molprobity_coot.py')) else: print( "==> XCE: cannot find " @@ -2057,37 +1661,6 @@ def show_molprobity_to_do(self, widget): ) ) - # def refinementProtocolCallback(self, widget): - # if widget.get_active(): - # if self.refinementProtocolcheckbox.get_active(): - # self.refinementProtocol = 'pandda_phenix' - # else: - # self.refinementProtocol = 'pandda_refmac' - # self.PREVbuttonSite.set_sensitive(True) - # self.NEXTbuttonSite.set_sensitive(True) - # else: - # self.refinementProtocolcheckbox.set_active(False) - # self.refinementProtocol = 'refmac' - # self.PREVbuttonSite.set_sensitive(False) - # self.NEXTbuttonSite.set_sensitive(False) - # print self.refinementProtocol - - # def refinementProgramCallback(self, widget): - # if widget.get_active(): - # if self.refinementProtocolcheckbox.get_active(): - # self.refinementProtocol = 'pandda_phenix' - # self.RefinementParamsButton.set_sensitive(False) - # else: - # self.refinementProgramcheckbox.set_active(False) - # self.refinementProtocol = 'refmac' - # else: - # self.RefinementParamsButton.set_sensitive(True) - # if self.refinementProtocolcheckbox.get_active(): - # self.refinementProtocol = 'pandda_refmac' - # else: - # self.refinementProtocol = 'refmac' - # print self.refinementProtocol - def show_ground_state_mean_map(self, widget): if widget.get_label().startswith("Show"): loaded = False From f551d947a32bf87ae831e7a52e3bf3bb11ad644f Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 10 Nov 2022 11:45:05 +0000 Subject: [PATCH 174/358] Clean up XChemCoot --- xce/lib/XChemCoot.py | 333 ++++++------------------------------------- 1 file changed, 44 insertions(+), 289 deletions(-) diff --git a/xce/lib/XChemCoot.py b/xce/lib/XChemCoot.py index e5fde136..47b22199 100755 --- a/xce/lib/XChemCoot.py +++ b/xce/lib/XChemCoot.py @@ -13,7 +13,8 @@ from matplotlib.figure import Figure # had to adapt the original coot_utils.py file -# otherwise unable to import the original file without complaints about missing modules etc. +# otherwise unable to import the original file without complaints about missing modules +# etc. # modified file is now in $XChemExplorer_DIR/lib @@ -24,7 +25,7 @@ class GUI(object): def __init__(self): - ########################################################################################### + ################################################################################ # read in settings file from XChemExplorer to set the relevant paths self.settings = pickle.load(open(".xce_settings.pkl", "rb")) @@ -74,13 +75,12 @@ def __init__(self): # this decides which samples will be looked at self.selection_mode = "" - # self.selected_site='' self.pandda_index = -1 # refers to the number of sites self.site_index = "0" self.event_index = "0" - # the Folder is kind of a legacy thing because my inital idea was to have separate folders - # for Data Processing and Refinement + # the Folder is kind of a legacy thing because my inital idea was to have + # separate folders for Data Processing and Refinement self.project_directory = self.settings["initial_model_directory"] self.Serial = 0 self.panddaSerial = 0 @@ -96,7 +96,6 @@ def __init__(self): self.ligand_confidence = "" self.refinement_folder = "" self.refinementProtocol = "pandda_refmac" - # self.datasetOutcome='' self.pdb_style = "refine.pdb" self.mtz_style = "refine.mtz" @@ -119,11 +118,10 @@ def __init__(self): self.label_button_list = [] - ########################################################################################### + ################################################################################ # some COOT settings coot.set_map_radius(17) coot.set_colour_map_rotation_for_map(0) - # coot.set_colour_map_rotation_on_read_pdb_flag(21) self.QualityIndicators = { "RefinementRcryst": "-", @@ -190,13 +188,11 @@ def StartGUI(self): self.window.set_title("XChemExplorer") self.vbox = gtk.VBox() # this is the main container - ################################################################################# + ################################################################################ # --- Sample Selection --- - # self.vbox.add(gtk.Label('Select Samples')) frame = gtk.Frame(label="Select Samples") self.hbox_select_samples = gtk.HBox() - # vbox=gtk.VBox() self.cb_select_samples = gtk.combo_box_new_text() self.cb_select_samples.connect("changed", self.set_selection_mode) @@ -204,48 +200,29 @@ def StartGUI(self): self.cb_select_samples.append_text(citeria) self.hbox_select_samples.add(self.cb_select_samples) - # self.cb_select_sites = gtk.combo_box_new_text() - # self.cb_select_sites.connect("changed", self.set_site) - # for site in self.ligand_site_information: - # self.cb_select_sites.append_text(str(site[0])+' - '+str(site[1])) - # self.hbox_select_samples.add(self.cb_select_sites) - self.select_samples_button = gtk.Button(label="GO") self.select_samples_button.connect("clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) - ################################################################################# + ################################################################################ # --- status window --- frame = gtk.Frame() self.status_label = gtk.Label() frame.add(self.status_label) self.vbox.pack_start(frame) - ################################################################################# + ################################################################################ # --- refinement protocol --- frame = gtk.Frame() self.refinementProtocolcheckbox = gtk.CheckButton("PanDDA model refinement)") # callback is defined later - # self.refinementProtocolcheckbox.connect("toggled", self.refinementProtocolCallback) self.refinementProtocolcheckbox.set_active(True) frame.add(self.refinementProtocolcheckbox) self.vbox.pack_start(frame) - ################################################################################# - # --- refinement program --- - # frame = gtk.Frame() - # self.refinementProgramcheckbox = gtk.CheckButton('use PHENIX for giant.quick_refine') - # self.refinementProgramcheckbox.connect("toggled", self.refinementProgramCallback) - # self.refinementProgramcheckbox.set_active(False) - # frame.add(self.refinementProgramcheckbox) - # self.vbox.pack_start(frame) - - # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ # --- Refinement Statistics --- # next comes a section which displays some global quality indicators # a combination of labels and textview widgets, arranged in a table @@ -472,15 +449,11 @@ def StartGUI(self): "clicked", self.show_ground_state_mean_map ) hbox.add(self.ground_state_mean_map_button) - # self.vbox.add(self.ground_state_mean_map_button) self.vbox.add(hbox) self.vbox.pack_start(frame) - # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ # --- hbox for compound picture & spider_plot (formerly: refinement history) --- frame = gtk.Frame() self.hbox_for_info_graphics = gtk.HBox() @@ -500,11 +473,6 @@ def StartGUI(self): compound_frame.add(self.image) self.hbox_for_info_graphics.add(compound_frame) - # --- Refinement History --- - # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) - # self.canvas.set_size_request(190, 190) - # self.hbox_for_info_graphics.add(self.canvas) - # --- Spider Plot --- spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( @@ -521,55 +489,7 @@ def StartGUI(self): frame.add(self.hbox_for_info_graphics) self.vbox.add(frame) - ################################################################################# - # --- pandda.inspect user comments --- - # outer_frame = gtk.Frame(label='pandda.inspect comments') - # vbox = gtk.VBox() - # ligand_site_name_label_frame = gtk.Frame() - # ligand_site_name_label = gtk.Label('Site Name') - # ligand_site_name_label_frame.add(ligand_site_name_label) - # ligand_inspect_confidence_label_frame = gtk.Frame() - # ligand_inspect_confidence_label = gtk.Label('Confidence') - # ligand_inspect_confidence_label_frame.add(ligand_inspect_confidence_label) - # ligand_inspect_interesting_label_frame = gtk.Frame() - # ligand_inspect_interesting_label = gtk.Label('Interesting') - # ligand_inspect_interesting_label_frame.add(ligand_inspect_interesting_label) - # ligand_inspect_comment_label_frame = gtk.Frame() - # ligand_inspect_comment_label = gtk.Label('Comment') - # ligand_inspect_comment_label_frame.add(ligand_inspect_comment_label) - # ligand_site_name_value_frame = gtk.Frame() - # self.ligand_site_name_value = gtk.Label('-') - # ligand_site_name_value_frame.add(self.ligand_site_name_value) - # ligand_inspect_confidence_value_frame = gtk.Frame() - # self.ligand_inspect_confidence_value = gtk.Label('-') - # ligand_inspect_confidence_value_frame.add(self.ligand_inspect_confidence_value) - # ligand_inspect_interesting_value_frame = gtk.Frame() - # self.ligand_inspect_interesting_value = gtk.Label('-') - # ligand_inspect_interesting_value_frame.add(self.ligand_inspect_interesting_value) - # ligand_inspect_comment_value_frame = gtk.Frame() - # self.ligand_inspect_comment_value = gtk.Label('-') - # ligand_inspect_comment_value_frame.add(self.ligand_inspect_comment_value) - # - # frame_pandda_inspect_comments_table = gtk.Frame() - # pandda_inspect_comments_table = gtk.Table(2, 6, False) - # pandda_inspect_comments_table.attach(ligand_site_name_label_frame, 0, 1, 0, 1) - # pandda_inspect_comments_table.attach(ligand_site_name_value_frame, 1, 2, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_confidence_label_frame, 2, 3, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_confidence_value_frame, 3, 4, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_interesting_label_frame, 4, 5, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_interesting_value_frame, 5, 6, 0, 1) - # pandda_inspect_comments_table.attach(ligand_inspect_comment_label_frame, 0, 1, 1, 2) - # pandda_inspect_comments_table.attach(ligand_inspect_comment_value_frame, 1, 6, 1, 2) - # - # frame_pandda_inspect_comments_table.add(pandda_inspect_comments_table) - # vbox.add(frame_pandda_inspect_comments_table) - # outer_frame.add(vbox) - # self.vbox.pack_start(outer_frame) - - # # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ outer_frame = gtk.Frame(label="Sample Navigator") hboxSample = gtk.HBox() @@ -612,47 +532,7 @@ def StartGUI(self): outer_frame.add(hboxSample) self.vbox.add(outer_frame) - # # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# - # outer_frame = gtk.Frame(label='Label') - # hboxlabel = gtk.HBox() - # - # frame = gtk.Frame() - # hbox = gtk.HBox() - # self.vbox_label = gtk.VBox() - # labels = self.db.get_labels_from_db() - # if len(labels) > 5: - # print '==> sorry, too many labels; cannot display them in panel' - # labels = labels[:5] - # # with radiobuttons, one of them needs to be always on - # # but there will be cases when the user has not assigned a label yet - # # hence, the not_shown button is not shown but gets active - # # if the label has not been set yet - # labels.append('not_shown') - # for n, l in enumerate(labels): - # print n,l - # if n == 0: - # new_button = gtk.RadioButton(None, l) - # else: - # new_button = gtk.RadioButton(new_button, l) - # new_button.connect("toggled", self.label_button_clicked, l) - # if not l == 'not_shown': - # hbox.add(new_button) - # self.label_button_list.append(new_button) - # self.vbox_label.add(hbox) - # frame.add(self.vbox_label) - # - # hboxlabel.add(frame) - # - # outer_frame.add(hboxlabel) - # self.vbox.add(outer_frame) - - # SPACER - # self.vbox.add(gtk.Label(' ')) - - ################################################################################# + ################################################################################ # --- current refinement stage --- outer_frame = gtk.Frame() hbox = gtk.HBox() @@ -669,7 +549,6 @@ def StartGUI(self): "toggled", self.experiment_stage_button_clicked, button[1] ) vbox.pack_start(new_button, False, False, 0) - # vbox.add(new_button) self.experiment_stage_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) @@ -687,43 +566,13 @@ def StartGUI(self): "toggled", self.ligand_confidence_button_clicked, criteria ) vbox.pack_start(new_button, False, False, 0) - # vbox.add(new_button) self.ligand_confidence_button_list.append(new_button) frame.add(vbox) hbox.pack_start(frame) - # label section --> start - # frame = gtk.Frame(label='Label') - # vbox = gtk.VBox() - # labels = self.db.get_labels_from_db() - # if len(labels) > 5: - # print '==> sorry, too many labels; cannot display them in panel' - # labels = labels[:5] - # # with radiobuttons, one of them needs to be always on - # # but there will be cases when the user has not assigned a label yet - # # hence, the not_shown button is not shown but gets active - # # if the label has not been set yet - # labels.append('not_shown') - # for n, l in enumerate(labels): - # print n,l - # if n == 0: - # new_button = gtk.RadioButton(None, l) - # else: - # new_button = gtk.RadioButton(new_button, l) - # new_button.connect("toggled", self.label_button_clicked, l) - # if not l == 'not_shown': - # vbox.add(new_button) - # self.label_button_list.append(new_button) - # frame.add(vbox) - # hbox.pack_start(frame) - # # label section <-- end - outer_frame.add(hbox) self.vbox.pack_start(outer_frame) - # SPACER - # self.vbox.add(gtk.Label(' ')) - # --- ligand modeling --- frame = gtk.Frame(label="Ligand Modeling") self.hbox_for_modeling = gtk.HBox() @@ -736,13 +585,6 @@ def StartGUI(self): frame.add(self.hbox_for_modeling) self.vbox.pack_start(frame) - # # --- ligand confidence --- - # self.cb_ligand_confidence = gtk.combo_box_new_text() - # self.cb_ligand_confidence.connect("changed", self.set_ligand_confidence) - # for citeria in self.ligand_confidence: - # self.cb_ligand_confidence.append_text(citeria) - # self.vbox.add(self.cb_ligand_confidence) - # --- refinement & options --- self.hbox_for_refinement = gtk.HBox() self.REFINEbutton = gtk.Button(label="Refine") @@ -753,11 +595,8 @@ def StartGUI(self): self.hbox_for_refinement.add(self.RefinementParamsButton) self.vbox.add(self.hbox_for_refinement) - # self.VALIDATEbutton = gtk.Button(label="validate structure") - # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") - - # need to put it here, because attributes within refinementProtocolCallback function - # are defined after checkbox is defined + # need to put it here, because attributes within refinementProtocolCallback + # function are defined after checkbox is defined self.refinementProtocolcheckbox.connect( "toggled", self.refinementProtocolCallback ) @@ -778,7 +617,6 @@ def ChangeXtal(self, widget, data=None): if self.index < 0: self.index = 0 if self.index >= len(self.Todo): - # self.index = len(self.Todo) self.index = 0 self.cb.set_active(self.index) @@ -790,11 +628,6 @@ def ChooseXtal(self, widget): self.merge_ligand_button.set_sensitive(True) self.place_ligand_here_button.set_sensitive(True) - # self.ligand_site_name_value.set_label('-') - # self.ligand_inspect_confidence_value.set_label('-') - # self.ligand_inspect_interesting_value.set_label('-') - # self.ligand_inspect_comment_value.set_label('-') - self.refresh_site_combobox() self.db_dict_mainTable = {} self.db_dict_panddaTable = {} @@ -803,7 +636,6 @@ def ChooseXtal(self, widget): self.refinement_folder = str(self.Todo[self.index][4]) self.refinement_outcome = str(self.Todo[self.index][5]) self.label = self.db.get_label_of_sample(self.xtalID) - # self.update_label_radiobutton() self.update_RefinementOutcome_radiobutton() if ( self.xtalID not in self.siteDict @@ -811,7 +643,6 @@ def ChooseXtal(self, widget): self.ligand_confidence = str(self.Todo[self.index][6]) self.update_LigandConfidence_radiobutton() self.label = self.db.get_label_of_sample(self.xtalID) - # self.update_label_radiobutton() self.RefreshData() @@ -846,7 +677,8 @@ def update_LigandConfidence_radiobutton(self): def refresh_site_combobox(self): # reset self.pandda_index self.pandda_index = -1 - # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites + # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever + # be 100 sites for n in range(-1, 100): self.cb_site.remove_text(0) self.site_index = "0" @@ -908,11 +740,6 @@ def RefreshSiteData(self): print("new site coordinates:", site_x, site_y, site_z) coot.set_rotation_centre(site_x, site_y, site_z) - # self.ligand_site_name_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][8])) - # self.ligand_inspect_confidence_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][9])) - # self.ligand_inspect_interesting_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][10])) - # self.ligand_inspect_comment_value.set_label(str(self.siteDict[self.xtalID][self.pandda_index][11])) - self.spider_plot_data = ( self.db.get_db_pandda_dict_for_sample_and_site_and_event( self.xtalID, self.site_index, self.event_index @@ -978,14 +805,14 @@ def RefreshSiteData(self): except ValueError: self.ligand_RSZDValue.set_label("-") - ######################################################################################### + ################################################################################ # delete old Event MAPs if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): if "map.native.ccp4" in coot.molecule_name(imol): coot.close_molecule(imol) - ######################################################################################### + ################################################################################ # Spider plot # Note: refinement history was shown instead previously if os.path.isfile(self.spider_plot): @@ -1003,7 +830,7 @@ def RefreshSiteData(self): ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) - ######################################################################################### + ################################################################################ # check for PANDDAs EVENT maps if os.path.isfile(self.event_map): coot.set_colour_map_rotation_on_read_pdb(0) @@ -1011,8 +838,6 @@ def RefreshSiteData(self): for imol in coot_utils_XChem.molecule_number_list(): if self.event_map in coot.molecule_name(imol): coot.set_contour_level_in_sigma(imol, 2) - # coot.set_contour_level_absolute(imol,0.5) - # coot.set_last_map_colour(0.4,0,0.4) coot.set_last_map_colour(0.74, 0.44, 0.02) def experiment_stage_button_clicked(self, widget, data=None): @@ -1020,7 +845,8 @@ def experiment_stage_button_clicked(self, widget, data=None): "pandda" ): print( - "==> XCE: removing refine.pdb and linking refine_.split.bound-state.pdb to refine.pdb" + "==> XCE: removing refine.pdb and linking" + " refine_.split.bound-state.pdb to refine.pdb" ) os.chdir(os.path.join(self.project_directory, self.xtalID)) if os.path.realpath("refine.pdb").replace(".pdb", ".split.bound-state.pdb"): @@ -1042,7 +868,6 @@ def experiment_stage_button_clicked(self, widget, data=None): + str(data) + " in mainTable of datasource" ) - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) self.db.create_or_remove_missing_records_in_depositTable( self.xce_logfile, self.xtalID, "ligand_bound", self.db_dict_mainTable ) @@ -1078,28 +903,6 @@ def ligand_confidence_button_clicked(self, widget, data=None): ) self.siteDict[self.xtalID][self.pandda_index][7] = data - # def update_label(self, widget): - # print '\n\n\n>>>>>>>>>>>>>>>>>>>>>>>>' - # # widget.pressed() - # for w in self.label_button_list: - # print w.get_label(), w.get_active() - # if w != widget: - # w.set_active(False) - # print '<<<<<<<<<<<<<<<<<<<<<<<<<<' - # self.db_dict_mainTable['label'] = widget.get_label() - # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str( - # widget.get_label()) + ' in mainTable of datasource' - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - - # def label_button_clicked(self, widget, data=None): - # print '............',data - # if data == 'not_shown': - # self.db.execute_statement("update mainTable set label=Null where CrystalName = '%s'" %self.xtalID) - # else: - # self.db_dict_mainTable['label'] = data - # print '==> XCE: setting label for ' + self.xtalID + ' to ' + str(data) + ' in mainTable of datasource' - # self.db.update_data_source(self.xtalID, self.db_dict_mainTable) - def RefreshData(self): # reset spider plot image spider_plot_pic = gtk.gdk.pixbuf_new_from_file( @@ -1135,10 +938,7 @@ def RefreshData(self): self.project_directory, self.xtalID, self.compoundID, self.data_source ) self.Serial = XChemRefine.GetSerial(self.project_directory, self.xtalID) - self.panddaSerial = panddaSerial = m = (4 - len(str(self.Serial))) * "0" + str( - self.Serial - ) - # self.Serial=self.Refine.GetSerial() + self.panddaSerial = (4 - len(str(self.Serial))) * "0" + str(self.Serial) if self.Serial == 1: # i.e. no refinement has been done; data is probably straight out of dimple if os.path.isfile( @@ -1187,28 +987,21 @@ def RefreshData(self): self.xtalID, self.data_source, "" ) # '' because file does not exist - # all this information is now updated in the datasource after each refinement cycle + # all this information is now updated in the datasource after each refinement + # cycle self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) - ######################################################################################### + ################################################################################ # history # if the structure was previously refined, try to read the parameters - # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) print("==> REFMAC params:", self.RefmacParams) - # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() - # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) - # else: - # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea - # self.canvas.set_size_request(190, 190) - # self.hbox_for_info_graphics.add(self.canvas) - # self.canvas.show() - - ######################################################################################### + + ################################################################################ # update pdb & maps - ######################################################################################### + ################################################################################ # delete old PDB and MAP files # - get a list of all molecules which are currently opened in COOT # - remove all molecules/ maps before loading a new set @@ -1216,7 +1009,7 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): coot.close_molecule(item) - ######################################################################################### + ################################################################################ # read new PDB files # read protein molecule after ligand so that this one is the active molecule coot.set_nomenclature_errors_on_read("ignore") @@ -1357,7 +1150,7 @@ def RefreshData(self): coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model - ######################################################################################### + ################################################################################ # read fofc maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level @@ -1377,13 +1170,6 @@ def RefreshData(self): else: # try to open mtz file with same name as pdb file coot.set_default_initial_contour_level_for_map(1) - # if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): - # os.chdir(os.path.join(self.project_directory,self.xtalID)) - # if not os.path.isfile('REFINEMENT_IN_PROGRESS'): - # if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-pandda-input.mtz')): - # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) - # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): - # os.symlink('dimple.mtz',self.mtz_style) if os.path.isfile( os.path.join(self.project_directory, self.xtalID, self.mtz_style) ): @@ -1403,7 +1189,7 @@ def RefreshData(self): os.path.join(self.project_directory, self.xtalID, "dimple.mtz") ) - ######################################################################################### + ################################################################################ # update Quality Indicator table try: self.RRfreeValue.set_label( @@ -1511,27 +1297,6 @@ def go_to_next_xtal(self): self.cb.set_active(self.index) def REFINE(self, widget): - - # ####################################################### - # if not os.path.isdir(os.path.join(self.project_directory,self.xtalID,'cootOut')): - # os.mkdir(os.path.join(self.project_directory,self.xtalID,'cootOut')) - # # create folder for new refinement cycle - # os.mkdir(os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial))) - # - # ####################################################### - # # write PDB file - # # now take protein pdb file and write it to newly create Refine_ folder - # # note: the user has to make sure that the ligand file was merged into main file - # for item in coot_utils_XChem.molecule_number_list(): - # if coot.molecule_name(item).endswith(self.pdb_style.replace('.pdb','')+'.split.bound-state.pdb') or coot.molecule_name(item).endswith(self.pdb_style): - # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) - # break - # elif coot.molecule_name(item).endswith('dimple.pdb'): - # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) - # break - # - - ####################################################### if self.refinementProtocol.startswith("pandda"): ####################################################### @@ -1554,8 +1319,9 @@ def REFINE(self, widget): ####################################################### # write PDB file - # now take protein pdb file and write it to newly create Refine_ folder - # note: the user has to make sure that the ligand file was merged into main file + # now take protein pdb file and write it to newly create Refine_ + # folder. note: the user has to make sure that the ligand file was merged + # into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith( self.pdb_style.replace(".pdb", "") + ".split.bound-state.pdb" @@ -1571,9 +1337,6 @@ def REFINE(self, widget): ), ) break - # elif coot.molecule_name(item).endswith('dimple.pdb'): - # coot.write_pdb_file(item,os.path.join(self.project_directory,self.xtalID,'cootOut','Refine_'+str(self.Serial),'refine.modified.pdb')) - # break XChemRefine.panddaRefine( self.project_directory, self.xtalID, self.compoundID, self.data_source @@ -1604,8 +1367,9 @@ def REFINE(self, widget): ####################################################### # write PDB file - # now take protein pdb file and write it to newly create Refine_ folder - # note: the user has to make sure that the ligand file was merged into main file + # now take protein pdb file and write it to newly create Refine_ + # folder. note: the user has to make sure that the ligand file was merged + # into main file for item in coot_utils_XChem.molecule_number_list(): if coot.molecule_name(item).endswith(self.pdb_style): coot.write_pdb_file( @@ -1658,7 +1422,6 @@ def REFINE(self, widget): self.index += 1 if self.index >= len(self.Todo): - # self.index = len(self.Todo) self.index = 0 self.cb.set_active(self.index) @@ -1683,7 +1446,6 @@ def get_samples_to_look_at(self, widget): self.Todo = [] self.siteDict = {} self.Todo, self.siteDict = self.db.get_todoList_for_coot(self.selection_mode) - # self.status_label.set_text('found {0!s} samples'.format(len(self.Todo))) # refresh sample CB for item in sorted(self.Todo): self.cb.append_text("{0!s}".format(item[0])) @@ -1722,13 +1484,11 @@ def update_plot(self, refinement_cycle, Rfree, Rcryst): def place_ligand_here(self, widget): print("===> XCE: moving ligand to pointer") - # coot.move_molecule_here() print("LIGAND: ", self.mol_dict["ligand"]) coot_utils_XChem.move_molecule_here(self.mol_dict["ligand"]) def merge_ligand_into_protein(self, widget): print("===> XCE: merge ligand into protein structure") - # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) coot.merge_molecules_py([self.mol_dict["ligand"]], self.mol_dict["protein"]) print("===> XCE: deleting ligand molecule") coot.close_molecule(self.mol_dict["ligand"]) @@ -1822,7 +1582,8 @@ def refinementProgramCallback(self, widget): self.refinementProtocol = "refmac" if int(self.refinement_outcome.split()[0]) > 3: print( - "==> XCE: sorry cannot change refinement protocol since you are at a stage when we refine the ligand bound state only" + "==> XCE: sorry cannot change refinement protocol since you are at a" + " stage when we refine the ligand bound state only" ) self.refinementProtocol = "refmac" self.refinementProtocolcheckbox.set_active(False) @@ -1853,7 +1614,8 @@ def reset_occupancy(self): ) if self.refinementProtocol.startswith("pandda"): self.Logfile.warning( - "==> COOT: you cannot reset occupancies while working in PanDDA refine mode" + "==> COOT: you cannot reset occupancies while working in PanDDA" + " refine mode" ) else: for imol in coot_utils_XChem.molecule_number_list(): @@ -1864,10 +1626,9 @@ def reset_occupancy(self): or coot.molecule_name(imol).endswith("dimple.pdb") ): self.Logfile.warning( - "==> COOT: setting occupancies of all protein residues in %s to 1.0" - % coot.molecule_name(imol) + "==> COOT: setting occupancies of all protein residues in %s" + " to 1.0" % coot.molecule_name(imol) ) - # coot.fill_occupancy_residue_range(imol,"A",1,10000) chains = chain_ids(imol) resiDict = {} for chain in chains: @@ -1912,11 +1673,5 @@ def reset_occupancy(self): ) -# -# -# print residues_in_chain(imol, chain) -# for residue in residues_in_chain(imol, chain): -# print residue - if __name__ == "__main__": GUI().StartGUI() From 6d686261ba4bfbe8d0aa58413286eb7bb3e4c28c Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 10 Nov 2022 11:48:32 +0000 Subject: [PATCH 175/358] Clean up XChemCootOld --- xce/lib/XChemCootOld.py | 110 ++++++++++------------------------------ 1 file changed, 27 insertions(+), 83 deletions(-) diff --git a/xce/lib/XChemCootOld.py b/xce/lib/XChemCootOld.py index 1e0b43e5..a50214df 100644 --- a/xce/lib/XChemCootOld.py +++ b/xce/lib/XChemCootOld.py @@ -11,7 +11,8 @@ from matplotlib.figure import Figure # had to adapt the original coot_utils.py file -# otherwise unable to import the original file without complaints about missing modules etc. +# otherwise unable to import the original file without complaints about missing modules +# etc. # modified file is now in $XChemExplorer_DIR/lib @@ -23,13 +24,12 @@ class GUI(object): def __init__(self): - ########################################################################################### + ################################################################################ # read in settings file from XChemExplorer to set the relevant paths print("current dir", os.getcwd()) self.settings = pickle.load(open(".xce_settings.pkl", "rb")) remote_qsub_submission = self.settings["remote_qsub"] print("setting", self.settings) - # self.refine_model_directory=self.settings['refine_model_directory'] self.database_directory = self.settings["database_directory"] self.xce_logfile = self.settings["xce_logfile"] self.data_source = self.settings["data_source"] @@ -69,13 +69,12 @@ def __init__(self): # this decides which samples will be looked at self.selection_mode = "" - # self.selected_site='' self.pandda_index = -1 # refers to the number of sites self.site_index = "0" self.event_index = "0" - # the Folder is kind of a legacy thing because my inital idea was to have separate folders - # for Data Processing and Refinement + # the Folder is kind of a legacy thing because my inital idea was to have + # separate folders for Data Processing and Refinement self.project_directory = self.settings["initial_model_directory"] self.Serial = 0 self.Refine = None @@ -88,7 +87,6 @@ def __init__(self): self.spider_plot = "" self.ligand_confidence = "" self.refinement_folder = "" - # self.datasetOutcome='' self.pdb_style = "refine.pdb" self.mtz_style = "refine.mtz" @@ -107,7 +105,7 @@ def __init__(self): self.db_dict_mainTable = {} self.db_dict_panddaTable = {} - ########################################################################################### + ################################################################################ # some COOT settings coot.set_map_radius(15) coot.set_colour_map_rotation_for_map(0) @@ -171,13 +169,11 @@ def StartGUI(self): self.window.set_title("XChemExplorer") self.vbox = gtk.VBox() # this is the main container - ################################################################################# + ################################################################################ # --- Sample Selection --- - # self.vbox.add(gtk.Label('Select Samples')) frame = gtk.Frame(label="Select Samples") self.hbox_select_samples = gtk.HBox() - # vbox=gtk.VBox() self.cb_select_samples = gtk.combo_box_new_text() self.cb_select_samples.connect("changed", self.set_selection_mode) @@ -185,19 +181,13 @@ def StartGUI(self): self.cb_select_samples.append_text(citeria) self.hbox_select_samples.add(self.cb_select_samples) - # self.cb_select_sites = gtk.combo_box_new_text() - # self.cb_select_sites.connect("changed", self.set_site) - # for site in self.ligand_site_information: - # self.cb_select_sites.append_text(str(site[0])+' - '+str(site[1])) - # self.hbox_select_samples.add(self.cb_select_sites) - self.select_samples_button = gtk.Button(label="GO") self.select_samples_button.connect("clicked", self.get_samples_to_look_at) self.hbox_select_samples.add(self.select_samples_button) frame.add(self.hbox_select_samples) self.vbox.pack_start(frame) - ################################################################################# + ################################################################################ # --- status window --- frame = gtk.Frame() self.status_label = gtk.Label() @@ -207,7 +197,7 @@ def StartGUI(self): # SPACER self.vbox.add(gtk.Label(" ")) - ################################################################################# + ################################################################################ # --- Refinement Statistics --- # next comes a section which displays some global quality indicators # a combination of labels and textview widgets, arranged in a table @@ -430,7 +420,7 @@ def StartGUI(self): # SPACER self.vbox.add(gtk.Label(" ")) - ################################################################################# + ################################################################################ # --- hbox for compound picture & spider_plot (formerly: refinement history) --- frame = gtk.Frame() self.hbox_for_info_graphics = gtk.HBox() @@ -450,11 +440,6 @@ def StartGUI(self): compound_frame.add(self.image) self.hbox_for_info_graphics.add(compound_frame) - # --- Refinement History --- - # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) - # self.canvas.set_size_request(190, 190) - # self.hbox_for_info_graphics.add(self.canvas) - # --- Spider Plot --- spider_plot_frame = gtk.Frame() spider_plot_pic = gtk.gdk.pixbuf_new_from_file( @@ -471,7 +456,7 @@ def StartGUI(self): frame.add(self.hbox_for_info_graphics) self.vbox.add(frame) - ################################################################################# + ################################################################################ # --- pandda.inspect user comments --- outer_frame = gtk.Frame(label="pandda.inspect comments") vbox = gtk.VBox() @@ -533,7 +518,7 @@ def StartGUI(self): # # SPACER self.vbox.add(gtk.Label(" ")) - ################################################################################# + ################################################################################ outer_frame = gtk.Frame(label="Sample Navigator") hboxSample = gtk.HBox() @@ -579,7 +564,7 @@ def StartGUI(self): # SPACER self.vbox.add(gtk.Label(" ")) - ################################################################################# + ################################################################################ # --- current refinement stage --- outer_frame = gtk.Frame() hbox = gtk.HBox() @@ -635,13 +620,6 @@ def StartGUI(self): frame.add(self.hbox_for_modeling) self.vbox.pack_start(frame) - # # --- ligand confidence --- - # self.cb_ligand_confidence = gtk.combo_box_new_text() - # self.cb_ligand_confidence.connect("changed", self.set_ligand_confidence) - # for citeria in self.ligand_confidence: - # self.cb_ligand_confidence.append_text(citeria) - # self.vbox.add(self.cb_ligand_confidence) - # --- refinement & options --- self.hbox_for_refinement = gtk.HBox() self.REFINEbutton = gtk.Button(label="Refine") @@ -652,9 +630,6 @@ def StartGUI(self): self.hbox_for_refinement.add(self.RefinementParamsButton) self.vbox.add(self.hbox_for_refinement) - # self.VALIDATEbutton = gtk.Button(label="validate structure") - # self.DEPOSITbutton = gtk.Button(label="prepare for deposition") - # --- CANCEL button --- self.CANCELbutton = gtk.Button(label="CANCEL") self.CANCELbutton.connect("clicked", self.CANCEL) @@ -671,7 +646,6 @@ def ChangeXtal(self, widget, data=None): if self.index < 0: self.index = 0 if self.index >= len(self.Todo): - # self.index = len(self.Todo) self.index = 0 self.cb.set_active(self.index) @@ -735,7 +709,8 @@ def update_LigandConfidence_radiobutton(self): def refresh_site_combobox(self): # reset self.pandda_index self.pandda_index = -1 - # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever be 100 sites + # clear CB first, 100 is sort of arbitrary since it's unlikely there will ever + # be 100 sites for n in range(-1, 100): self.cb_site.remove_text(0) self.site_index = "0" @@ -868,14 +843,14 @@ def RefreshSiteData(self): except ValueError: self.ligand_RSZDValue.set_label("-") - ######################################################################################### + ################################################################################ # delete old Event MAPs if len(coot_utils_XChem.molecule_number_list()) > 0: for imol in coot_utils_XChem.molecule_number_list(): if "map.native.ccp4" in coot.molecule_name(imol): coot.close_molecule(imol) - ######################################################################################### + ################################################################################ # Spider plot # Note: refinement history was shown instead previously if os.path.isfile(self.spider_plot): @@ -893,15 +868,13 @@ def RefreshSiteData(self): ) self.spider_plot_image.set_from_pixbuf(self.spider_plot_pic) - ######################################################################################### + ################################################################################ # check for PANDDAs EVENT maps if os.path.isfile(self.event_map): coot.handle_read_ccp4_map((self.event_map), 0) for imol in coot_utils_XChem.molecule_number_list(): if self.event_map in coot.molecule_name(imol): coot.set_contour_level_in_sigma(imol, 2) - # coot.set_contour_level_absolute(imol,0.5) - # coot.set_last_map_colour(0.4,0,0.4) coot.set_last_map_colour(0.74, 0.44, 0.02) def experiment_stage_button_clicked(self, widget, data=None): @@ -996,27 +969,20 @@ def RefreshData(self): self.xtalID, self.data_source, "" ) # '' because file does not exist - # all this information is now updated in the datasource after each refinement cycle + # all this information is now updated in the datasource after each refinement + # cycle self.QualityIndicators = self.db.get_db_dict_for_sample(self.xtalID) - ######################################################################################### + ################################################################################ # history # if the structure was previously refined, try to read the parameters - # self.hbox_for_info_graphics.remove(self.canvas) if self.Serial > 1: self.RefmacParams = self.Refine.ParamsFromPreviousCycle(self.Serial - 1) - # refinement_cycle,Rfree,Rcryst=self.Refine.GetRefinementHistory() - # self.canvas = FigureCanvas(self.update_plot(refinement_cycle,Rfree,Rcryst)) - # else: - # self.canvas = FigureCanvas(self.update_plot([0],[0],[0])) # a gtk.DrawingArea - # self.canvas.set_size_request(190, 190) - # self.hbox_for_info_graphics.add(self.canvas) - # self.canvas.show() - - ######################################################################################### + + ################################################################################ # update pdb & maps - ######################################################################################### + ################################################################################ # delete old PDB and MAP files # - get a list of all molecules which are currently opened in COOT # - remove all molecules/ maps before loading a new set @@ -1024,7 +990,7 @@ def RefreshData(self): for item in coot_utils_XChem.molecule_number_list(): coot.close_molecule(item) - ######################################################################################### + ################################################################################ # read new PDB files # read protein molecule after ligand so that this one is the active molecule coot.set_nomenclature_errors_on_read("ignore") @@ -1047,14 +1013,6 @@ def RefreshData(self): os.path.join(self.project_directory, self.xtalID, self.pdb_style) ): os.chdir(os.path.join(self.project_directory, self.xtalID)) - # we want to be able to check dimple results immediately, but don't want to interfere with refinement - # if not os.path.isfile('REFINEMENT_IN_PROGRESS'): - # if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-ensemble-model.pdb')): - # os.symlink(self.xtalID+'-ensemble-model.pdb',self.pdb_style) - # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.pdb')): - # os.symlink('dimple.pdb',self.pdb_style) - # else: - # self.go_to_next_xtal() if os.path.isfile( os.path.join(self.project_directory, self.xtalID, self.pdb_style) ): @@ -1078,7 +1036,7 @@ def RefreshData(self): coot.set_show_symmetry_master(1) coot.set_show_symmetry_molecule(item, 1) # show symm for model - ######################################################################################### + ################################################################################ # read fofo maps # - read ccp4 map: 0 - 2fofc map, 1 - fofc.map # read 2fofc map last so that one can change its contour level @@ -1097,13 +1055,6 @@ def RefreshData(self): else: # try to open mtz file with same name as pdb file coot.set_default_initial_contour_level_for_map(1) - # if not os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.mtz_style)): - # os.chdir(os.path.join(self.project_directory,self.xtalID)) - # if not os.path.isfile('REFINEMENT_IN_PROGRESS'): - # if os.path.isfile(os.path.join(self.project_directory,self.xtalID,self.xtalID+'-pandda-input.mtz')): - # os.symlink(self.xtalID+'-pandda-input.mtz',self.mtz_style) - # elif os.path.isfile(os.path.join(self.project_directory,self.xtalID,'dimple.mtz')): - # os.symlink('dimple.mtz',self.mtz_style) if os.path.isfile( os.path.join(self.project_directory, self.xtalID, self.mtz_style) ): @@ -1117,7 +1068,7 @@ def RefreshData(self): os.path.join(self.project_directory, self.xtalID, "dimple.mtz") ) - ######################################################################################### + ################################################################################ # update Quality Indicator table try: self.RRfreeValue.set_label( @@ -1270,7 +1221,6 @@ def REFINE(self, widget): self.index += 1 if self.index >= len(self.Todo): - # self.index = len(self.Todo) self.index = 0 self.cb.set_active(self.index) @@ -1325,13 +1275,11 @@ def update_plot(self, refinement_cycle, Rfree, Rcryst): def place_ligand_here(self, widget): print("===> XCE: moving ligand to pointer") - # coot.move_molecule_here() print("LIGAND: ", self.mol_dict["ligand"]) coot_utils_XChem.move_molecule_here(self.mol_dict["ligand"]) def merge_ligand_into_protein(self, widget): print("===> XCE: merge ligand into protein structure") - # merge_molecules(list(imols), imol) e.g. merge_molecules([1],0) coot.merge_molecules_py([self.mol_dict["ligand"]], self.mol_dict["protein"]) print("===> XCE: deleting ligand molecule") coot.close_molecule(self.mol_dict["ligand"]) @@ -1366,9 +1314,5 @@ def show_molprobity_to_do(self, widget): ) -# def fit_ligand(self,widget): -# print 'fit' - - if __name__ == "__main__": GUI().StartGUI() From 583ee86e81d06f4aa62ac60f094345fb5331be57 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 10 Nov 2022 13:21:56 +0000 Subject: [PATCH 176/358] Clean up coot_utils_XChem --- xce/lib/coot_utils_XChem.py | 203 ++++++++++++------------------------ 1 file changed, 65 insertions(+), 138 deletions(-) diff --git a/xce/lib/coot_utils_XChem.py b/xce/lib/coot_utils_XChem.py index cd842518..ae6b12ee 100755 --- a/xce/lib/coot_utils_XChem.py +++ b/xce/lib/coot_utils_XChem.py @@ -1,26 +1,3 @@ -# coot-utils.py -# adapted from coot-utils.scm -# -# Copyright 2004, 2005, 2006, 2007 by Bernhard Lohkamp -# Copyright 2008, 2009 by Bernhard Lohkamp, The University of York -# Copyright 2000 by Paul Emsley -# Copyright 2004, 2005, 2006, 2007 by Paul Emsley, The University of York -# -# Copyright (C) -# -# This program is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program. If not, see . - import os import string import re @@ -65,7 +42,6 @@ def with_no_backups(imol, *funcs): for f in funcs: func = f[0] args = f[1 : len(f)] - # print "BL DEBUG:: func %s and args %s" %(func, args) func(*args) if backup_mode == 1: turn_on_backup(imol) @@ -86,7 +62,6 @@ def with_auto_accept(*funcs): for f in funcs: func = f[0] args = f[1 : len(f)] - # print "BL DEBUG:: func %s and args %s" %(func, args) ret = func(*args) accept_regularizement() @@ -100,7 +75,10 @@ def with_auto_accept(*funcs): # funcs is function, active_atom specifiers and extra args # func, args, "aa_imol", "aa_chain_id", ..., args # or list thereof -# [[func1, extra_arg1, ..., "aa_imol", "aa_chain_id",..., extra_arg2, extra arg3, ..], [func2,...]] +# [ +# [func1, extra_arg1, ..., "aa_imol", "aa_chain_id",..., extra_arg2, extra arg3, ..], +# [func2,...] +# ] # returns what? The value from the last function evaluated # @@ -238,7 +216,14 @@ class UsingActiveAtom: use with 'with', e.g.: - > with UsingActiveAtom() as [aa_imol, aa_chain_id, aa_res_no, aa_ins_code, aa_atom_name, aa_alt_conf]: + > with UsingActiveAtom() as [ + aa_imol, + aa_chain_id, + aa_res_no, + aa_ins_code, + aa_atom_name, + aa_alt_conf, + ]: refine_zone(aa_imol, aa_chain_id, aa_res_no-2, aa_res_no+2, aa_ins_code) """ @@ -740,7 +725,6 @@ def command_in_path_qm_old_version(cmd, only_extension="", add_extensions=None): for cmd_name in program_names: for path in string.split(primary_path, os.pathsep): program_exe = os.path.join(path, cmd_name) - # print "BL DEBUG:: program_exe is", program_exe if os.path.isfile(program_exe): return True return False @@ -819,7 +803,6 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): input.write(data + "\n") input.close() - # print "BL DEBUG:: popen command is", cmd_execfile + " " + args_string + " < " + data_list_file + " > " + log_file status = os.popen( cmd_execfile + " " @@ -835,8 +818,6 @@ def popen_command(cmd, args, data_list, log_file, screen_flag=False): print("running command ", cmd, " failed!") return 1 else: - # print "cmd ", cmd ," seems to have run ok!" - # log_file_size = os.stat(log_file)[stat.ST_SIZE] return 0 os.remove(data_list_file) else: @@ -991,7 +972,6 @@ def get_atom_from_residue(atom_name, residue_atoms, alt_conf): for residue_atom in residue_atoms: if residue_atom[0][0] == atom_name and residue_atom[0][1] == alt_conf: return residue_atom - # print "BL WARNING:: no atom name %s found in residue" %atom_name return False # no residue name found fail save @@ -1520,7 +1500,19 @@ def get_first_ncs_master_chain(): # Define a map transformation function that obeys Lapthorn's Law of # NCS Handling Programs # -# typical usage: transform_map_using_lsq_matrix(1, "A", 10, 30, 0, "A", 10, 30, 2, rotation_centre(), 6) +# typical usage: transform_map_using_lsq_matrix( +# 1, +# "A", +# 10, +# 30, +# 0, +# "A", +# 10, +# 30, +# 2, +# rotation_centre(), +# 6 +# ) # # Remember, that now the about-pt is the "to" point, i.e. the maps are brought from # somewhere else and generated about the about-pt. @@ -2056,17 +2048,15 @@ def add_key_binding(name, key, thunk): # def graphics_general_key_press_hook(key, control_flag=0): global key_bindings - # print "graphics_general_key_press_hook(): Key %s was pressed" %key if control_flag: codes = [elem[0] for elem in key_bindings if "Control_" in elem[1]] funcs = [elem[3] for elem in key_bindings if "Control_" in elem[1]] else: - codes = [elem[0] for elem in key_bindings if not "Control_" in elem[1]] - funcs = [elem[3] for elem in key_bindings if not "Control_" in elem[1]] + codes = [elem[0] for elem in key_bindings if "Control_" not in elem[1]] + funcs = [elem[3] for elem in key_bindings if "Control_" not in elem[1]] if key in codes: index = codes.index(key) func = funcs[index] - # print "BL DEBUG:: index and executing:", index, func apply(func) else: if coot_has_guile() and is_windows(): @@ -2197,7 +2187,7 @@ def residue_alt_confs(imol, chain_id, res_no, ins_code): if atom_ls: for i in range(len(atom_ls)): alt_conf_str = atom_ls[i][0][1] - if not alt_conf_str in alt_confs: + if alt_conf_str not in alt_confs: alt_confs.append(alt_conf_str) return alt_confs @@ -2320,7 +2310,6 @@ def update_go_to_atom_from_current_atom(): alt_conf = active_atom[5] go_to_atom_imol_current = go_to_atom_molecule_number() set_go_to_atom_molecule(imol) - # if imol != goto_atom_imol_current update_go_to_atom_window_on_other_molecule_chosen(imol) set_go_to_atom_chain_residue_atom_name(chain_id, resno, atom_name) @@ -2462,13 +2451,13 @@ def mutate_it(): if not map_mols: print("BL WARNING:: no valid maps around! Cannot mutate.") else: - # BL says:: I dunno how to wait for the input from map selection since there is no return - # waiting for mouse/keyboard input may be an option but no curses on windows, maybe - # fix later, for now we use the first map - # show_select_map_dialog() + # BL says:: I dunno how to wait for the input from map selection since + # there is no return waiting for mouse/keyboard input may be an option but + # no curses on windows, maybe fix later, for now we use the first map if len(map_mols) > 1: print( - "BL INFO:: we use the first map! If you wanna use another one, please select from Model/Fit/Refine" + "BL INFO:: we use the first map! If you wanna use another one," + " please select from Model/Fit/Refine" ) else: print("BL INFO:: no refinement map set, will set first one for you!") @@ -2693,7 +2682,8 @@ def dump_positions_to_file(positions, preferences=False): return False port = open(init_file, "w") print( - "BL INFO:: writing dialog positions to .coot-preferences/saved_dialog_positions.py" + "BL INFO:: writing dialog positions to" + " .coot-preferences/saved_dialog_positions.py" ) else: init_file = os.path.join(os.getenv(home), ".coot.py") @@ -2719,9 +2709,8 @@ def dump_positions_to_file(positions, preferences=False): save_state() if not os.path.isfile(state_file): print( - "Ooops {0!s} does not exist (either guile enabled or problem writing the file".format( - state_file - ) + "Ooops {0!s} does not exist (either guile enabled" + " or problem writing the file".format(state_file) ) else: port = open("0-coot.state.py", "r") @@ -2740,7 +2729,7 @@ def dump_positions_to_file(positions, preferences=False): port.close() write_init_status = dump_positions_to_file(positions) - if write_init_status == False: + if not write_init_status: # try to write a file to preferences dump_positions_to_file(positions, preferences=True) @@ -2754,10 +2743,6 @@ def dump_positions_to_file(positions, preferences=False): def save_string_to_file(string, filename, overwrite=False): - - # home = 'HOME' - # if (os.name == 'nt'): - # home = 'COOT_HOME' init_file = filename if os.path.isfile(init_file): # init file exists @@ -2784,11 +2769,6 @@ def save_string_to_file(string, filename, overwrite=False): # removes a line containg all strings of the given list from file def remove_line_containing_from_file(remove_str_ls, filename): - - # home = 'HOME' - # if (os.name == 'nt'): - # home = 'COOT_HOME' - # init_file = os.path.join(os.getenv(home), ".coot.py") init_file = filename if os.path.isfile(init_file): # init file exists @@ -2973,7 +2953,8 @@ def get_ribose_residue_atom_name(imol, residue_spec, pucker_atom): [ pucker_atom, residue_spec, - "Inconsistent phosphate distance for C2' pucker", + "Inconsistent phosphate distance" + " for C2' pucker", ] ) if (abs(pi[0]) < crit_d) and (pucker_atom == " C3'"): @@ -2981,7 +2962,8 @@ def get_ribose_residue_atom_name(imol, residue_spec, pucker_atom): [ pucker_atom, residue_spec, - "Inconsistent phosphate distance for C3' pucker", + "Inconsistent phosphate distance" + " for C3' pucker", ] ) if not ( @@ -3201,10 +3183,6 @@ def add_here(*args): def save_annotations(file_name): global annotations - # if (os.path.isfile(file_name)): - # remove existing file - # print "BL INFO:: overwrite old annotation file", file_name - # os.remove(file_name) save_string_to_file(str(annotations), file_name, True) @@ -3284,7 +3262,6 @@ def match_md5sums(tar_file_name, target_md5sum_file_name): return False else: if not os.path.isfile(target_md5sum_file_name): - # print "OOps! %s does not exist" %target_md5sum_file_name print("OOps! {0!s} does not exist".format(target_md5sum_file_name)) return False else: @@ -3293,22 +3270,17 @@ def match_md5sums(tar_file_name, target_md5sum_file_name): os.remove(target_md5sum_file_name) md5_string = get_md5sum_string(tar_file_name) if not target_md5_string: # need to test if string? - # print "OOps %s is not a string" %target_md5_string print("OOps {0!s} is not a string".format(target_md5_string)) return False else: if not md5_string: # as above - # print "OOps %s is not a string" %md5_string print("OOps {0!s} is not a string".format(md5_string)) return False else: if not (target_md5_string == md5_string): - # print "Oops: md5sums do not match %s %s. Doing nothing" \ - # %(target_md5_string, md5_string) print( - "Oops: md5sums do not match {0!s} {1!s}. Doing nothing".format( - target_md5_string, md5_string - ) + "Oops: md5sums do not match {0!s} {1!s}." + " Doing nothing".format(target_md5_string, md5_string) ) return False else: @@ -3321,17 +3293,14 @@ def install_coot_tar_file(tar_file_name, use_tar=False): prefix_dir = os.getenv("COOT_PREFIX") prefix_dir = os.path.normpath(prefix_dir) # FIXME do we need this? if not prefix_dir: - # print "OOps could not get COOT_PREFIX" return False if not directory_is_modifiable_qm(prefix_dir): - # print "OOps directory %s is not modifiable" %prefix_dir return False else: pending_dir = os.path.join(prefix_dir, "pending-install") if not os.path.isdir(pending_dir): os.mkdir(pending_dir) if not os.path.isdir(pending_dir): - # print "OOps could not create", pending_dir return False else: a_tar_file_name = os.path.abspath(tar_file_name) @@ -3386,9 +3355,6 @@ def get_md5sum_string(file_name): return md5sum # main line - # - # print "::::: run_download_binary_curl.... with revision %s with version_string %s" \ - # %(revision, version_string) prefix = os.getenv("COOT_PREFIX") prefix = os.path.normpath(prefix) # FIXME do we need this? if not prefix: # do we need to check if prefix is string? @@ -3438,9 +3404,6 @@ def get_md5sum_string(file_name): md5_url = url + ".md5sum" md5_tar_file_name = tar_file_name + ".md5sum" - # print "md5sum url for curl:", md5_url - # print "url for curl:", url - if set_file_name_func: set_file_name_func(tar_file_name) @@ -3459,7 +3422,9 @@ def get_md5sum_string(file_name): else: # this is for pythonic urllib # we have graphics here, grrrr, shouldnt - import urllib.request, urllib.parse, urllib.error + import urllib.request + import urllib.parse + import urllib.error def progress_function(count, blockSize, totalSize): global pending_install_in_place @@ -3501,11 +3466,9 @@ def progress_function(count, blockSize, totalSize): return False if not os.path.isfile(tar_file_name): - # print "Ooops: %s does not exist after attempted download" %tar_file_name return False else: if not os.path.isfile(md5_tar_file_name): - # print "Ooops: %s does not exist after attempted download" %md5_tar_file_name return False else: if not match_md5sums(tar_file_name, md5_tar_file_name): @@ -3544,7 +3507,9 @@ def get_revision_from_string(stri): def get_url_as_string(my_url): - import urllib.request, urllib.parse, urllib.error + import urllib.request + import urllib.parse + import urllib.error try: s = urllib.request.urlopen(my_url).read() @@ -3724,7 +3689,9 @@ def square(x): def get_drug_via_wikipedia(drug_name_in): - import urllib.request, urllib.error, urllib.parse + import urllib.request + import urllib.error + import urllib.parse from xml.etree import ElementTree def get_redirected_drug_name(xml): @@ -3740,9 +3707,8 @@ def parse_wiki_drug_xml(tree, key, redirect=False): # seems to be in some strange format!? decode_text = rev_text.encode("ascii", "ignore") for line in decode_text.split("\n"): - # if key in line: # too simple, we need a regular expresssion search if key_re.search(line): - if redirect == False: + if redirect is False: drug_bank_id = line.split(" ")[-1] if not drug_bank_id: # we can get an empty string @@ -3773,7 +3739,8 @@ def parse_wiki_drug_xml(tree, key, redirect=False): if not isinstance(mol_name, str): print( - "BL WARNING:: mol_name not a string (DrugBank entry from wikipedia)", + "BL WARNING:: mol_name not a string" + " (DrugBank entry from wikipedia)", mol_name, ) # try pubchem as fallback @@ -3828,8 +3795,7 @@ def get_SMILES_for_comp_id_from_pdbe(comp_id): make_directory_maybe("coot-download") if os.path.isfile(cif_file_name): # try the filesystem cache - l = os.stat(cif_file_name).st_size - if l > 0: + if os.stat(cif_file_name).st_size > 0: read_cif_dictionary(cif_file_name) s2 = SMILES_for_comp_id(comp_id) if isinstance(s2, str): @@ -3862,14 +3828,6 @@ def get_SMILES_for_comp_id_from_pdbe(comp_id): return False -# # load the redefining functions -# try: -# load_from_search_load_path("redefine_functions.py") -# # import redefine_functions -# except: -# print "load_from_search_load_path() of redefine_functions.py failed" -# pass - # Add file with filename to preferences directory # @@ -3934,13 +3892,13 @@ def using_gui(): return ret -############################################################################################ +######################################################################################## # end of Paul's scripting -############################################################################################ +######################################################################################## # # some BL functions # -############################################################################################ +######################################################################################## # # for easier switching on of GL lighting on surfaces: @@ -4020,8 +3978,8 @@ def reset_b_factor_active_residue(): # # program_name : name of exe to find # -# args (i.e. path_names) : path name to search (usually "PATH", then maybe CCP4_BIN, ..., -# can be a single path as well) +# args (i.e. path_names) : path name to search (usually "PATH", then maybe CCP4_BIN, +# ..., can be a single path as well) # kwargs : for some extra argumentsto # add_extensions=[list] pass extra extensions to be tested # only_extension=str use only this one to test @@ -4146,9 +4104,8 @@ def find_exe(program_name, *args, **kwargs): if info: print( - "BL WARNING:: We cannot find {0!s} anywhere! Program {1!s} won't run!".format( - program_name_noext, program_name_noext - ) + "BL WARNING:: We cannot find {0!s} anywhere!" + " Program {1!s} won't run!".format(program_name_noext, program_name_noext) ) return False @@ -4183,7 +4140,7 @@ def reload_module(name): def printf(*args): for arg in args: - print(arg, end=" ") + print("%s " % arg) # to print elements of a list: @@ -4518,33 +4475,3 @@ def clean_pdb(imol): # acronym merge_water_chains = merge_solvent_chains - -# the python run_thread function if no graphics -# global use_gui_qm -# if not use_gui_qm: -# import threading -# # this has locked, so that no one else can use it -# global python_thread_return -# python_thread_return = False -# -# # function to run a python thread with function using -# # args which is a tuple -# # optionally pass sleep time in ms (default is 20) - usefull -# # for computationally expensive threads which may have run longer -# # N.B. requires gobject hence in coot_gui.py -# # -# def run_python_thread(function, args): -# -# class MyThread(threading.Thread): -# def __init__(self): -# threading.Thread.__init__(self) -# def run(self): -# global python_thread_return -# python_return_lock = threading.Lock() -# python_return_lock.acquire() -# try: -# python_thread_return = function(*args) -# finally: -# python_return_lock.release() -# -# MyThread().start() From b75bd11d30e37cb7bb5b7a08bfb7b5bfb0691425 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 10 Nov 2022 13:34:32 +0000 Subject: [PATCH 177/358] Clean up XChemToolTips --- xce/lib/XChemToolTips.py | 160 +++++++++++++++++++++++---------------- 1 file changed, 93 insertions(+), 67 deletions(-) diff --git a/xce/lib/XChemToolTips.py b/xce/lib/XChemToolTips.py index bcf8d6a3..1dc308cb 100755 --- a/xce/lib/XChemToolTips.py +++ b/xce/lib/XChemToolTips.py @@ -68,38 +68,12 @@ def update_from_datasource_button_tip(): def run_pandda_inspect_at_home(pandda_directory): - # instruction = ( '\n\n' - # 'Please follow the instructions below to run pandda.inspect at your home institution:\n\n' - # ' 1. Make sure that the pandda package is installed at your home institution.\n' - # ' For more details see: http://pandda.bitbucket.org\n\n' - # ' 2. At home: go to the folder where you want the files from pandda.analyse to be;\n' - # ' e.g. cd /home/tkrojer/fragment_screening\n\n' - # ' 3. At home: run the following command:\n' - # ' rsync -av %s@nx.diamond.ac.uk:%s .\n\n' %(getpass.getuser(),pandda_directory)+ - # ' 4. At home: go into the pandda directory\n' - # ' cd %s\n\n' %pandda_directory[pandda_directory.rfind('/')+1:]+ - # ' 5. At home: run pandda.inspect\n' - # ' pandda.inspect\n\n' - # ' 6. Once you finished inspecting your models, close pandda.inspect and copy the data back to DLS\n' - # ' with the following command:\n' - # ' rsync -av * %s@nx.diamond.ac.uk:%s\n\n' %(getpass.getuser(),pandda_directory)+ - # ' 7. At DLS: continue using XChemExplorer; go to the PANDDA tab and run:\n' - # ' "Export PANDDA models"\n' - # ' This will trigger the following steps:\n' - # ' - transform the pandda models back into the crystallographic unit cell\n' - # ' - copy the transformed models into the respective folder of the project directory\n' - # ' - launch an initial round of refinement with REFMAC\n' - # ' Note: All refinement jobs run on the cluster at DLS.\n' - # ' You can check the status of the jobs by typing:\n' - # ' module load global/cluster\n' - # ' qstat\n\n' - # ' 8. At DLS: go to the REFINEMENT tab and run "Open COOT" to review and further refine your models if necessary\n' ) - instruction = ( "\n\n" "Be sure to have pandda installed at home, and go to a clean subdirectory.\n" "From that directory, do the steps below.\n" - "This moves the relevant files to your site so you can do the model building locally, and then moves the files back to Diamond.\n" + "This moves the relevant files to your site so you can do the model building" + " locally, and then moves the files back to Diamond.\n" "1. run: rsync -av %s@nx.diamond.ac.uk:%s .\n" % (getpass.getuser(), pandda_directory) + '2. run: "pandda.inspect", and build all relevant models, etc.\n' @@ -115,9 +89,12 @@ def deposition_interface_note(): note = ( "\n\n" - "Note: you can use this mask to save identical information for ALL structures to be deposited.\n" - "However, this may not be suitable in cases where the information is different for certain samples.\n" - "In such cases, please use for example SQLiteBrowser to edit the relevant fields in the depositTable." + "Note: you can use this mask to save identical information for ALL structures" + " to be deposited.\n" + "However, this may not be suitable in cases where the information is different" + " for certain samples.\n" + "In such cases, please use for example SQLiteBrowser to edit the relevant" + " fields in the depositTable." ) return note @@ -129,13 +106,15 @@ def pandda_pre_run(reference_directory): "but to create mean ground state maps.\n" "Hence, the pre-run will only comprise 100 datasets.\n" "After the pre-run is finished use the resulting ground state mean maps\n" - "to build a suitable reference model for the subsequent PanDDA production run.\n" + "to build a suitable reference model for the subsequent PanDDA production" + " run.\n" "The appendix will determine the name of the folder where the results from\n" "the pre-run will be stored. It is used by the COOT plugin to distinguish\n" "between different pre-runs.\n" "The result from the pre-run will be stored in:\n" "%s/pannda_'https://openlabnotebooks.org/update-on-batch-deposition-of-xchem-structures'" + lnk = ( + "'https://openlabnotebooks.org/update-on-batch-deposition-of-xchem-structures'" + "" + ) return lnk def deposition_bound_state_prerequisites(): msg = ( "1. Event map to MTZ conversion.\n" - " All pandda event maps need to be converted to MTZ format. This is currently not done automatically.\n" - ' If you have not done so, select and run "Event Map -> SF" from the Hit Identification action box.\n' + " All pandda event maps need to be converted to MTZ format." + " This is currently not done automatically.\n" + ' If you have not done so, select and run "Event Map -> SF"' + " from the Hit Identification action box.\n" " This may take a while, but you only need to run this once.\n" "2. Select datasets to be deposited.\n" ' Set crystals to "5-ready for deposition" in XCE refinement tab\n' "3. Enter additional data required for PDB deposition.\n" - ' In the Deposition menu, select "Edit information". Fill out all the required items and press "Save to Database".\n' - " Note: this needs to be done after the datasets have been selected for deposition." + ' In the Deposition menu, select "Edit information".' + ' Fill out all the required items and press "Save to Database".\n' + " Note: this needs to be done after the datasets have been selected" + " for deposition." ) return msg def deposition_bound_state_preparation_step_one_text(): msg = ( - "1. Press the button below to generate structure and structure factor mmcif files of all selected datasets.\n" + "1. Press the button below to generate structure and structure factor mmcif" + " files of all selected datasets.\n" " Note: all previously generated mmcif files will be overwritten." ) return msg @@ -183,19 +172,28 @@ def deposition_bound_state_preparation_step_one_text(): def deposition_bound_state_preparation_step_two_text(): msg = ( - '2. Press the button below to copy all the mmcif files into the "group deposition directory" (see settings tab).\n' - "All mmcif files will be bundled into a single, bzipped tar archive which can be uploaded into via the PDB group deposition website." + "2. Press the button below to copy all the mmcif files into the" + ' "group deposition directory" (see settings tab).\n' + "All mmcif files will be bundled into a single, bzipped tar archive" + " which can be uploaded into via the PDB group deposition website." ) return msg def pdb_group_deposition_instruction_one(): - msg = "3. Go to the group deposition website, create a session and upload the ligand-bound.tar.bz2 file from the group deposition directory." + msg = ( + "3. Go to the group deposition website, create a session and upload the" + " ligand-bound.tar.bz2 file from the group deposition directory." + ) return msg def pdb_group_deposition_link(): - lnk = "'https://deposit-group-1.rcsb.rutgers.edu/groupdeposit'" + lnk = ( + "'https://deposit-group-1.rcsb.rutgers.edu/groupdeposit'" + ) return lnk @@ -207,8 +205,10 @@ def pdb_group_deposition_instruction_two(): def deposition_ground_state_prerequisites(): msg = ( "1. Convert all apo MTZ files to mmcif format.\n" - " Swtich to the pandda tab, select the PanDDA directory which contains the analysis you want to deposit.\n" - ' Then select and run "apo -> mmcif" from the Hit Identification action box.\n' + " Swtich to the pandda tab, select the PanDDA directory which contains the" + " analysis you want to deposit.\n" + ' Then select and run "apo -> mmcif" from the Hit Identification' + " action box.\n" " Note: you only need to do this once." ) return msg @@ -224,7 +224,8 @@ def deposition_ground_state_preparation_step_one_text(): def deposition_ground_state_preparation_step_three_text(): msg = ( - "1. Please check the settings tab that you have selected the correct pandda directory.\n" + "1. Please check the settings tab that you have selected the correct" + " pandda directory.\n" " (Note: we will take all the apo mmcif files from this directory)\n" " Current PanDDA directory:" ) @@ -257,28 +258,39 @@ def deposition_ground_state_preparation_step_six_text(): def deposition_ground_state_preparation_step_seven_text(): msg = ( - '5. Press the button below to copy the structire and structure factor mmcif files into the "group deposition directory" (see settings tab).\n' - "Both mmcif files will be bundled into a single, bzipped tar archive which can be uploaded into via the PDB group deposition website." + "5. Press the button below to copy the structire and structure factor mmcif" + ' files into the "group deposition directory" (see settings tab).\n' + "Both mmcif files will be bundled into a single, bzipped tar archive which can" + " be uploaded into via the PDB group deposition website." ) return msg def deposition_ground_state_preparation_step_eight_text(): - msg = "6. Go to the group deposition website, create a session and upload the ligand-bound.tar.bz2 file from the group deposition directory." + msg = ( + "6. Go to the group deposition website, create a session and upload the" + " ligand-bound.tar.bz2 file from the group deposition directory." + ) return msg def after_deposition_step_one_text(): msg = ( - "After you have successfully submitted the ligand-bound structures via the PDB group deposition interface, you will immediately get\n" - 'an email with the PDB codes. There will be a single line for each PDB submission. Highlight and copy the text! Then go to the "Deposition" menu\n' - 'and select "Update DB with PDB codes". A pop-up window will appear, paste the text into the window and press "Update Database".' + "After you have successfully submitted the ligand-bound structures via the PDB" + " group deposition interface, you will immediately get\n" + "an email with the PDB codes. There will be a single line for each PDB" + ' submission. Highlight and copy the text! Then go to the "Deposition" menu\n' + 'and select "Update DB with PDB codes". A pop-up window will appear, paste the' + ' text into the window and press "Update Database".' ) return msg def deposition_bounnd_state_preparation_ignore_event_map(): - msg = "do NOT include PanDDA event maps (ONLY USE IN CASE IF DATA WERE NOT ANALYSED WITH PANDDA!)" + msg = ( + "do NOT include PanDDA event maps" + " (ONLY USE IN CASE IF DATA WERE NOT ANALYSED WITH PANDDA!)" + ) return msg @@ -289,7 +301,8 @@ def second_cif_file_info(cif_file): "You have selected the following restraints file\n" "for merging into the the ligand CIF files:\n" + second_cif_file + "\n" "Press NO in case you do not want to continue\n" - "In case you want to use another file, open the preferences menu and set it there\n" + "In case you want to use another file, open the preferences menu" + " and set it there\n" "Please check the XCE logfile in case of unexpected behaviour" ) elif second_cif_file.replace(" ", "") == "" or second_cif_file.lower() == "none": @@ -314,16 +327,25 @@ def second_cif_file_not_exists(): def notification_about_changes_to_apo_deposition(): msg = ( "The ground-state deposition procedure has changes in XCE v1.5.0!\n\n" - "Previously, users had to select a specific reference PDB file, which had to have a ground-state mean-map and logfile associated with it.\n" - "However, there were two main problems: (i) the map to mtz conversion did sometimes lead to strange maps or maps in space group P1 only\n" - "and (2) occasionally the resulting MTZ files had missing columns. This lead to errors and delays during deposition, while inclusion of\n" - "ground-state mean maps has little benefit since the mean map can be calculated with the deposited apo datasets. Hence, there is really\n" + "Previously, users had to select a specific reference PDB file," + " which had to have a ground-state mean-map and logfile associated with it.\n" + "However, there were two main problems: (i) the map to mtz conversion" + " did sometimes lead to strange maps or maps in space group P1 only\n" + "and (2) occasionally the resulting MTZ files had missing columns." + " This lead to errors and delays during deposition, while inclusion of\n" + "ground-state mean maps has little benefit since the mean map" + " can be calculated with the deposited apo datasets. Hence, there is really\n" "no need to include it in the deposition.\n\n" - "All you need to do is to select the relevant PanDDA directory and XCE will arbitrarily select a high resolution structure with low Rfree\n" - "as the model for the deposition bundle and then put all structure factor MMCIF files into a single file. Note that it does not matter\n" - "which PDB file gets chosen at this point since the positional modifications during refinement with REFMAC will be minimal.\n" - "If you still want to make the ground-state mean map available, we would recommend to deposit ground-state mean map and \n" - "everything else you think is relevant on ZENODO and ask the PDB annotator to include the respective DOI in the deposition\n" + "All you need to do is to select the relevant PanDDA directory" + " and XCE will arbitrarily select a high resolution structure with low Rfree\n" + "as the model for the deposition bundle and then put all structure factor" + " MMCIF files into a single file. Note that it does not matter\n" + "which PDB file gets chosen at this point since the positional modifications" + " during refinement with REFMAC will be minimal.\n" + "If you still want to make the ground-state mean map available," + " we would recommend to deposit ground-state mean map and \n" + "everything else you think is relevant on ZENODO and ask the PDB annotator to" + " include the respective DOI in the deposition\n" ) return msg @@ -331,10 +353,14 @@ def notification_about_changes_to_apo_deposition(): def pandda_export_ligand_bound_models_only_disclaimer(): msg = ( "You have chosen to export and refine the ligand-bound model only. " - "This is different to the original procedure described by Pearce et al. (doi 10.1107/S2059798317003412), " - "which is based on refinement of an ensemble model consisting of ligand-bound state and confounding ground-state." - "Please note that working with the ligand-bound model only usually works well for reasonably well-defined " - "ligands and conformational changes, but it may not be ideal for weakly bound fragments and corresponding " + "This is different to the original procedure described by" + " Pearce et al. (doi 10.1107/S2059798317003412), " + "which is based on refinement of an ensemble model consisting of ligand-bound" + " state and confounding ground-state." + "Please note that working with the ligand-bound model only usually works well" + " for reasonably well-defined " + "ligands and conformational changes, but it may not be ideal for weakly bound" + " fragments and corresponding " "conformational changes." ) return msg From a11ca6211c59aa23461930879c1300e997e10117 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 10 Nov 2022 13:46:20 +0000 Subject: [PATCH 178/358] Clean up XChemRefine --- xce/lib/XChemRefine.py | 786 ++++++----------------------------------- 1 file changed, 103 insertions(+), 683 deletions(-) diff --git a/xce/lib/XChemRefine.py b/xce/lib/XChemRefine.py index ecbe3169..b4626e87 100755 --- a/xce/lib/XChemRefine.py +++ b/xce/lib/XChemRefine.py @@ -284,7 +284,6 @@ def ParamsFromPreviousCycle(self, Serial): return RefmacParams def GetRefinementHistory(self): - # RefinementHistory='' RefinementCycle = [] RcrystList = [] RfreeList = [] @@ -297,10 +296,6 @@ def GetRefinementHistory(self): found = True if found: for cycle in sorted(RefinementCycle): - # for cycle in RefinementCycle: - # Rcryst=0 - # Rfree=0 - # LigandCC=0 try: found_Rcryst = False found_Rfree = False @@ -334,14 +329,9 @@ def GetRefinementHistory(self): RcrystList.append(0) if not found_Rfree: RfreeList.append(0) - # if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): - # for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): - # if line.startswith('| LIG'): LigandCC = line.split()[6] - # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' except ValueError: RcrystList.append(0) RfreeList.append(0) - # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' else: RefinementCycle = [0] RcrystList = [0] @@ -390,12 +380,14 @@ def make_covalent_link(self, covLinkAtomSpec, Logfile): if residue_2 in residuesToModify: bond_text = ( - "LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s" + "LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2" + " %s ATOM-NAME-2 %s" % (residue_1, self.compoundID, atom1, residue_2, atom2) ) else: bond_text = ( - "LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s" + "LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2" + " %s ATOM-NAME-2 %s" % (residue_2, self.compoundID, atom2, residue_1, atom1) ) @@ -404,7 +396,8 @@ def make_covalent_link(self, covLinkAtomSpec, Logfile): f.write(bond_text) f.close() - # seems somewhat unncessary, but acedrg does not like some certain descriptions generated by phenix.elbow + # seems somewhat unncessary, but acedrg does not like some certain descriptions + # generated by phenix.elbow os.system("acedrg -c %s.cif -o %s_acedrg" % (self.compoundID, self.compoundID)) os.system("acedrg -L covalent_bond.txt -o %s" % self.compoundID) @@ -430,8 +423,6 @@ def get_hklin_hklout(self, Serial): hklin = os.path.join( self.ProjectPath, self.xtalID, self.xtalID + ".free.mtz" ) - # elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): - # RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') else: self.Logfile.error("%s: cannot find HKLIN for refinement" % self.xtalID) self.error = True @@ -515,7 +506,9 @@ def clean_up_before_refinement(self): # and remove all files which will be re-created by current refinement cycle os.chdir(os.path.join(self.ProjectPath, self.xtalID)) os.system( - "/bin/rm refine.pdb refine.mtz refine.split.bound-state.pdb validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log" + "/bin/rm refine.pdb refine.mtz refine.split.bound-state.pdb" + " validation_summary.txt validate_ligands.txt 2fofc.map fofc.map" + " refine_molprobity.log" ) def get_shebang(self, program, qsub): @@ -579,10 +572,14 @@ def add_buster_command( def run_giant_score_model(self, cmd, cycle): old_ccp4 = "" if os.path.isfile( - "/dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh" + "/dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/" + "ccp4.setup-sh" ): # giant.score_model does not work with ccp4 7.1-000 - old_ccp4 = "source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/ccp4-7.0/bin/ccp4.setup-sh\n" + old_ccp4 = ( + "source /dls/science/groups/i04-1/software/pandda_0.2.12/ccp4/" + "ccp4-7.0/bin/ccp4.setup-sh\n" + ) if os.path.isfile( os.path.join( self.ProjectPath, self.xtalID, self.xtalID + "-pandda-model.pdb" @@ -637,11 +634,8 @@ def add_validation(self, cmd, cycle, program): "\n" "phenix.molprobity refine%s.pdb refine%s.mtz\n" % (Serial, Serial) + "/bin/mv molprobity.out refine_molprobity.log\n" - "mmtbx.validate_ligands refine%s.pdb refine%s.mtz LIG > validate_ligands.txt\n" - % (Serial, Serial) - + "\n" - # 'ln -s Refine_%s/validate_ligands.txt .\n' %cycle+ - # 'ln -s Refine_%s/refine_molprobity.log .\n' %cycle+ + "mmtbx.validate_ligands refine%s.pdb refine%s.mtz LIG" + " > validate_ligands.txt\n" % (Serial, Serial) + "\n" "mmtbx.validation_summary refine.pdb > validation_summary.txt\n" "\n" ) @@ -665,29 +659,18 @@ def calculate_maps(self, cmd, program): " labin F1=%s PHI=%s\n" % (FWT, PHWT) + " grid samp 4.5\n" "EOF\n" "\n" - # 'mapmask mapin 2fofc_asu.map xyzin refine.pdb mapout 2fofc.map << EOF\n' - # ' border 5\n' - # 'EOF\n' - # '\n' - # '/bin/rm 2fofc_asu.map\n' - # '\n' "fft hklin refine.mtz mapout fofc.map << EOF\n" " labin F1=%s PHI=%s\n" % (DELFWT, PHDELWT) + " grid samp 4.5\n" "EOF\n" "\n" - # 'mapmask mapin fofc_asu.map xyzin refine.pdb mapout fofc.map << EOF\n' - # ' border 5\n' - # 'EOF\n' - # '\n' - # '/bin/rm fofc_asu.map\n' - "\n" ) return cmd def run_edstats(self, cmd, resh, resl): cmd += ( "\n" - "edstats XYZIN refine.pdb MAPIN1 2fofc.map MAPIN2 fofc.map OUT refine.edstats << eof\n" + "edstats XYZIN refine.pdb MAPIN1 2fofc.map MAPIN2 fofc.map OUT" + " refine.edstats << eof\n" " resl={0!s}\n".format(resl) + " resh={0!s}\n".format(resh) + "eof\n" "\n" ) @@ -696,7 +679,8 @@ def run_edstats(self, cmd, resh, resl): def update_database(self, cmd, Serial): date = datetime.strftime(datetime.now(), "%Y-%m-%d_%H-%M-%S.%f")[:-4] user = getpass.getuser() - ccp4_module = "" # need to source again, because giant.score_model still needs outdated version which does not have gemmi + ccp4_module = "" # need to source again, because giant.score_model still needs + # outdated version which does not have gemmi if self.ProjectPath.startswith("/dls"): ccp4_module = "module load ccp4/7.1.018" cmd += "\n" + ccp4_module + "\n" "$CCP4/bin/ccp4-python " + os.path.join( @@ -758,7 +742,7 @@ def RunBuster( self, Serial, RefmacParams, external_software, xce_logfile, covLinkAtomSpec ): - if RefmacParams == None: + if RefmacParams is None: anisotropic_Bfactor = " -M ADP " update_water = "" else: @@ -803,7 +787,7 @@ def RunBuster( xyzin, xyzout = self.get_xyzin_xyzout(Serial) refine_ligand_occupancy = "" - if RefmacParams != None: + if RefmacParams is not None: if "LIGOCC" in RefmacParams["LIGOCC"]: ligand_info = pdbtools(xyzin).get_residues_with_resname("LIG") if self.prepare_gelly_dat(ligand_info): @@ -875,7 +859,7 @@ def prepare_gelly_dat(self, ligand_info): if "{" in gelly: gelly += "\n" gelly += ( - "NOTE BUSTER_SET NotLigand = \ Ligand\n" + "NOTE BUSTER_SET NotLigand = \\ Ligand\n" "NOTE BUSTER_CONSTANT OCC NotLigand \n" "NOTE BUSTER_COMBINE OCC Ligand \n" "NOTE BUSTER_COMBINE B Ligand \n" @@ -916,8 +900,6 @@ def RunRefmac( RefmacParams["HKLIN"] = "HKLIN " + os.path.join( self.ProjectPath, self.xtalID, self.xtalID + ".free.mtz \\\n" ) - # elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): - # RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') else: Logfile.error( "%s: cannot find HKLIN for refinement; aborting..." % self.xtalID @@ -944,7 +926,6 @@ def RunRefmac( ####################################################### # LIBIN & LIBOUT - found_cif = False if os.path.isfile( os.path.join(self.ProjectPath, self.xtalID, self.compoundID + ".cif") ): @@ -972,7 +953,6 @@ def RunRefmac( ####################################################### # TLSIN & TLSOUT findTLS = "\n" - TLSphenix = "" if RefmacParams["TLS"].startswith("refi"): if external_software["phenix.find_tls_groups"]: findTLS = ( @@ -1002,7 +982,6 @@ def RunRefmac( + Serial + "/refine.tls \\\n" ) - TLSphenix = " phenix.tls " else: RefmacParams["TLS"] = "\n" @@ -1022,7 +1001,8 @@ def RunRefmac( user = getpass.getuser() if os.path.isfile(self.datasource): refinementStatus = ( - "$CCP4/bin/ccp4-python $XChemExplorer_DIR/xce/helpers/update_status_flag.py %s %s %s %s\n" + "$CCP4/bin/ccp4-python" + " $XChemExplorer_DIR/xce/helpers/update_status_flag.py %s %s %s %s\n" % (self.datasource, self.xtalID, "RefinementStatus", "running") ) updateDB = ( @@ -1048,7 +1028,9 @@ def RunRefmac( # clean up! # and remove all files which will be re-created by current refinement cycle os.system( - "/bin/rm refine.pdb refine.mtz refine.split.bound-state.pdb validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log" + "/bin/rm refine.pdb refine.mtz refine.split.bound-state.pdb" + " validation_summary.txt validate_ligands.txt 2fofc.map fofc.map" + " refine_molprobity.log" ) if external_software["qsub"]: @@ -1139,11 +1121,8 @@ def RunRefmac( + Serial + "\n" "\n" - # 'giant.merge_conformations ' - # ' major=../refine.split.ground-state.pdb' - # ' minor=../refine.split.bound-state.pdb' - # ' reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0\n' - "giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n" + "giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s" + " res_names=LIG,UNL,DRG,FRG\n" % (pdb_one, mtz_one, pdb_two, mtz_two) ) @@ -1212,17 +1191,16 @@ def RunRefmac( " rbond 10.0 -\n" " ncsr 10.0\n" "labin FP=F SIGFP=SIGF FREE=FreeR_flag\n" - "labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM\n" - + RefmacParams["TLSADD"] - + "\n" + "labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT" + " FOM=FOM\n" + RefmacParams["TLSADD"] + "\n" "DNAME " + self.xtalID + "\n" "END\n" "EOF\n" "\n" "phenix.molprobity refine_%s.pdb refine_%s.mtz\n" % (Serial, Serial) + "/bin/mv molprobity.out refine_molprobity.log\n" - "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n" - % (Serial, Serial) + "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG" + " > validate_ligands.txt\n" % (Serial, Serial) + "cd " + self.ProjectPath + "/" @@ -1271,7 +1249,6 @@ def RunRefmac( cmd.close() os.chdir(os.path.join(self.ProjectPath, self.xtalID, "Refine_" + Serial)) - # os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) if os.path.isfile(xce_logfile): Logfile.insert( "changing directory to %s" @@ -1291,7 +1268,8 @@ def RunRefmac( elif external_software["qsub"] and os.path.isdir("/dls"): Logfile.insert( - 'starting refinement on cluster with command "qsub -P labxchem -q medium.q refmac.csh"' + 'starting refinement on cluster with command "qsub -P labxchem' + ' -q medium.q refmac.csh"' ) os.system("qsub -P labxchem -q medium.q refmac.csh") elif external_software["qsub"] and not os.path.isdir("/dls"): @@ -1508,7 +1486,6 @@ def ParamsFromPreviousCycle(self, Serial): return RefmacParams def GetRefinementHistory(self): - # RefinementHistory='' RefinementCycle = [] RcrystList = [] RfreeList = [] @@ -1521,10 +1498,6 @@ def GetRefinementHistory(self): found = True if found: for cycle in sorted(RefinementCycle): - # for cycle in RefinementCycle: - # Rcryst=0 - # Rfree=0 - # LigandCC=0 try: found_Rcryst = False found_Rfree = False @@ -1558,14 +1531,9 @@ def GetRefinementHistory(self): RcrystList.append(0) if not found_Rfree: RfreeList.append(0) - # if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): - # for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): - # if line.startswith('| LIG'): LigandCC = line.split()[6] - # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' except ValueError: RcrystList.append(0) RfreeList.append(0) - # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' else: RefinementCycle = [0] RcrystList = [0] @@ -1592,12 +1560,14 @@ def make_covalent_link(self, covLinkAtomSpec, Logfile): if residue_2 in residuesToModify: bond_text = ( - "LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s" + "LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2" + " %s ATOM-NAME-2 %s" % (residue_1, self.compoundID, atom1, residue_2, atom2) ) else: bond_text = ( - "LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2 %s ATOM-NAME-2 %s" + "LINK: RES-NAME-1 %s FILE-1 %s_acedrg.cif ATOM-NAME-1 %s RES-NAME-2" + " %s ATOM-NAME-2 %s" % (residue_2, self.compoundID, atom2, residue_1, atom1) ) @@ -1606,7 +1576,8 @@ def make_covalent_link(self, covLinkAtomSpec, Logfile): f.write(bond_text) f.close() - # seems somewhat unncessary, but acedrg does not like some certain descriptions generated by phenix.elbow + # seems somewhat unncessary, but acedrg does not like some certain descriptions + # generated by phenix.elbow os.system("acedrg -c %s.cif -o %s_acedrg" % (self.compoundID, self.compoundID)) os.system("acedrg -L covalent_bond.txt -o %s" % self.compoundID) @@ -1645,7 +1616,6 @@ def RunQuickRefine( if os.path.isfile( os.path.join(self.ProjectPath, self.xtalID, "REFINEMENT_IN_PROGRESS") ): - # coot.info_dialog('*** REFINEMENT IN PROGRESS ***') Logfile.insert( "cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***" % self.xtalID @@ -1685,10 +1655,11 @@ def RunQuickRefine( self.ProjectPath, self.xtalID, self.compoundID + ".cif" ) if not found_cif: - # this should actually not be necessary, but the following scenario can happen: - # if a new data source is created from a file system, but smiles and compoundID where not updated; - # so the ligand may still be in the structure, but since the compoundID is unknown to the datasource, - # its restraints won't be read in and refmac will fail + # this should actually not be necessary, but the following scenario can + # happen if a new data source is created from a file system, but smiles and + # compoundID where not updated; so the ligand may still be in the structure, + # but since the compoundID is unknown to the datasource its restraints + # won't be read in and refmac will fail for file in glob.glob(os.path.join(self.ProjectPath, self.xtalID, "*")): if file.endswith(".cif"): RefmacParams["LIBIN"] = file @@ -1707,7 +1678,8 @@ def RunQuickRefine( ) ): Logfile.insert( - "seems to be an initial refinement after pandda.export, no need to merge the conformations" + "seems to be an initial refinement after pandda.export," + " no need to merge the conformations" ) os.chdir( os.path.join( @@ -1718,7 +1690,6 @@ def RunQuickRefine( "running giant.make_restraints %s:" % self.xtalID + "-ensemble-model.pdb" ) - # os.system('giant.make_restraints %s' %self.xtalID+'-ensemble-model.pdb') cmd = ( 'export XChemExplorer_DIR="%s"\n' % os.getenv("XChemExplorer_DIR") + "source %s\n" @@ -1768,16 +1739,16 @@ def RunQuickRefine( cmd = ( 'export XChemExplorer_DIR="%s"\n' % os.getenv("XChemExplorer_DIR") - + - # 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') + - "module load ccp4/7.1.018\n" - "giant.merge_conformations major=%s minor=%s reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0" - % (ground_state, bound_state) + + "module load ccp4/7.1.018\n" + "giant.merge_conformations major=%s minor=%s" + " reset_all_occupancies=False options.major_occupancy=1.0" + " options.minor_occupancy=1.0" % (ground_state, bound_state) ) else: cmd = ( - "giant.merge_conformations major=%s minor=%s reset_all_occupancies=False options.major_occupancy=1.0 options.minor_occupancy=1.0" - % (ground_state, bound_state) + "giant.merge_conformations major=%s minor=%s" + " reset_all_occupancies=False options.major_occupancy=1.0" + " options.minor_occupancy=1.0" % (ground_state, bound_state) ) Logfile.insert(cmd + "\n") os.system(cmd) @@ -1832,21 +1803,23 @@ def RunQuickRefine( ) ) Logfile.warning( - "%s: ground-state model does not exist, but refine.modified.pdb does exist" - % self.xtalID + "%s: ground-state model does not exist," + " but refine.modified.pdb does exist" % self.xtalID ) Logfile.warning( - "This may be a case where there are no differences between bound and ground state" + "This may be a case where there are no differences" + " between bound and ground state" ) Logfile.warning( - "creating symbolic link: ln -s refine.modified.pdb %s-ensemble-model.pdb" - % self.xtalID + "creating symbolic link:" + " ln -s refine.modified.pdb %s-ensemble-model.pdb" % self.xtalID ) os.system( "ln -s refine.modified.pdb %s-ensemble-model.pdb" % self.xtalID ) - # note: after first cycle of refinement, REFMAC will remove alternate conformer from the ligand - # i.e. need to link refine.pdb to refine.split.bound-state.pdb + # note: after first cycle of refinement, REFMAC will remove alternate + # conformer from the ligand + # i.e. need to link refine.pdb to refine.split.bound-state.pdb make_all_links = False add_links_line = "ln -s refine.pdb refine.split.bound-state.pdb" Logfile.insert("trying to continue with refinement") @@ -1941,8 +1914,8 @@ def RunQuickRefine( ) ) Logfile.insert( - "checking if %s-ensemble-model.pdb contains residue of type LIG, DRG, FRG, UNK or UNL" - % self.xtalID + "checking if %s-ensemble-model.pdb contains residue of type" + " LIG, DRG, FRG, UNK or UNL" % self.xtalID ) knowLigandIDs = ["LIG", "DRG", "FRG", "UNK", "UNL"] ligandsInFile = pdbtools( @@ -1955,18 +1928,22 @@ def RunQuickRefine( found_lig = True if found_lig: Logfile.warning( - "giant.make_restraints was not able to create multi-state-restraints.refmac.params. " - + "Something may have gone wrong, but it could be that ligand binding did not lead to " - + "displacement of water molecules or rearrangement of protein side-chains. " - + "Hence, there is no difference between the bound-state and the ground-state. " - + "We will create an empty multi-state-restraints.refmac.params which may contain " - + "additional REFMAC keywords and otherwise try to continue with refinement" + "giant.make_restraints was not able to create" + " multi-state-restraints.refmac.params." + " Something may have gone wrong, but it could be that ligand" + " binding did not lead to displacement of water molecules or" + " rearrangement of protein side-chains." + " Hence, there is no difference between the bound-state and" + " the ground-state." + " We will create an empty multi-state-restraints.refmac.params" + " which may contain additional REFMAC keywords and otherwise" + " try to continue with refinement" ) os.system("touch multi-state-restraints.refmac.params") else: Logfile.error( - "%s-ensemble-model.pdb does not contain any modelled ligand; aborting refinement" - % self.xtalID + "%s-ensemble-model.pdb does not contain any modelled ligand;" + " aborting refinement" % self.xtalID ) return None except OSError: @@ -2041,7 +2018,8 @@ def RunQuickRefine( "refine_" + str(Serial) + ".mtz", ) spider_plot += ( - "giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n" + "giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s" + " res_names=LIG,UNL,DRG,FRG\n" % (pdb_one, mtz_one, pdb_two, mtz_two) ) @@ -2052,20 +2030,19 @@ def RunQuickRefine( module_load = "module load ccp4/7.1.018\n" module_load += "module load phenix\n" - # 2017-07-20: for the time being this will explicitly source pandda since version 0.2 really only works at DLS - # 2020-11-02: will start using default ccp4 installation at DLS otherwise gemmi does not work + # 2017-07-20: for the time being this will explicitly source pandda since + # version 0.2 really only works at DLS + # 2020-11-02: will start using default ccp4 installation at DLS otherwise gemmi + # does not work source = "" if "bash" in os.getenv("SHELL"): source = ( 'export XChemExplorer_DIR="' + os.getenv("XChemExplorer_DIR") + '"\n' "\n" - # 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh\n') ) elif "csh" in os.getenv("SHELL"): source = ( - "setenv XChemExplorer_DIR " + os.getenv("XChemExplorer_DIR") + "\n" - "\n" - # 'source %s\n' %os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh\n') + "setenv XChemExplorer_DIR " + os.getenv("XChemExplorer_DIR") + "\n" "\n" ) if refinementProtocol == "pandda_refmac": @@ -2111,12 +2088,18 @@ def RunQuickRefine( if make_all_links: add_links_line = ( - "ln -s Refine_%s/refine_%s.split.bound-state.pdb ./refine.split.bound-state.pdb\n" - % (panddaSerial, Serial) - + "ln -s Refine_%s/refine_%s.split.ground-state.pdb ./refine.split.ground-state.pdb\n" - % (panddaSerial, Serial) - # 'ln -s Refine_%s/refine_%s.output.bound-state.pdb ./refine.output.bound-state.pdb\n' %(panddaSerial,Serial)+ - # 'ln -s Refine_%s/refine_%s.output.ground-state.pdb ./refine.output.ground-state.pdb\n' %(panddaSerial,Serial) + "ln -s Refine_%s/refine_%s.split.bound-state.pdb" + " ./refine.split.bound-state.pdb\n" + % ( + panddaSerial, + Serial, + ) + + "ln -s Refine_%s/refine_%s.split.ground-state.pdb" + " ./refine.split.ground-state.pdb\n" + % ( + panddaSerial, + Serial, + ) ) date = datetime.strftime(datetime.now(), "%Y-%m-%d_%H-%M-%S.%f")[:-4] @@ -2137,7 +2120,8 @@ def RunQuickRefine( + self.xtalID + "\n" "\n" - "$CCP4/bin/ccp4-python $XChemExplorer_DIR/xce/helpers/update_status_flag.py %s %s %s %s\n" + "$CCP4/bin/ccp4-python $XChemExplorer_DIR/xce/helpers/update_status_flag.py" + " %s %s %s %s\n" % (self.datasource, self.xtalID, "RefinementStatus", "running") + "\n" "giant.quick_refine" @@ -2203,8 +2187,8 @@ def RunQuickRefine( "phenix.molprobity refine_%s.pdb refine_%s.mtz\n" % (Serial, Serial) + "/bin/mv molprobity.out refine_molprobity.log\n" "module load phenix\n" - "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n" - % (Serial, Serial) + "mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG" + " > validate_ligands.txt\n" % (Serial, Serial) + "cd " + self.ProjectPath + "/" @@ -2269,7 +2253,6 @@ def RunQuickRefine( self.ProjectPath, self.xtalID, "cootOut", "Refine_" + str(Serial) ) ) - # os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) Logfile.insert( "changing directory to %s" % ( @@ -2299,11 +2282,6 @@ def RunQuickRefine( Logfile.insert("starting refinement on local machine") os.system("./refmac.csh &") - # if '/work/' in os.getcwd(): - # os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) - # else: - # os.system('./refmac.csh &') - def RefinementParams(self, RefmacParams): self.RefmacParams = RefmacParams self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) @@ -2472,7 +2450,6 @@ def ParamsFromPreviousCycle(self, Serial): return RefmacParams def GetRefinementHistory(self): - # RefinementHistory='' RefinementCycle = [] RcrystList = [] RfreeList = [] @@ -2485,10 +2462,6 @@ def GetRefinementHistory(self): found = True if found: for cycle in sorted(RefinementCycle): - # for cycle in RefinementCycle: - # Rcryst=0 - # Rfree=0 - # LigandCC=0 try: found_Rcryst = False found_Rfree = False @@ -2522,565 +2495,12 @@ def GetRefinementHistory(self): RcrystList.append(0) if not found_Rfree: RfreeList.append(0) - # if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): - # for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): - # if line.startswith('| LIG'): LigandCC = line.split()[6] - # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' except ValueError: RcrystList.append(0) RfreeList.append(0) - # RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' else: RefinementCycle = [0] RcrystList = [0] RfreeList = [0] print(RefinementCycle, RcrystList, RfreeList) return (sorted(RefinementCycle), RcrystList, RfreeList) - - -# class RefineOld(object): -# -# def __init__(self,ProjectPath,xtalID,compoundID,datasource): -# self.ProjectPath = ProjectPath -# self.xtalID = xtalID -# self.compoundID = compoundID -# self.prefix = 'refine' -# self.datasource=datasource -# -# def GetSerial(self): -# # check if there were already previous refinements -# # if no: create a folder Refine_1 -# # if yes: create a folder Refine_ -# temp = [] -# found = 0 -# if os.path.isdir(os.path.join(self.ProjectPath,self.xtalID)): -# for item in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): -# if item.startswith(os.path.join(self.ProjectPath,self.xtalID,'Refine_')): -# print int(item[item.rfind('_')+1:]) -# temp.append(int(item[item.rfind('_')+1:])) -# found = 1 -# if found: -# Serial = max(temp) + 1 -# else: -# Serial=1 -# return Serial -# -# -# def RunRefmac(self,Serial,RefmacParams,external_software,xce_logfile): -# Logfile=XChemLog.updateLog(xce_logfile) -# Serial=str(Serial) -# -# # first check if refinement is ongoing and exit if yes -# if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'REFINEMENT_IN_PROGRESS')): -## coot.info_dialog('*** REFINEMENT IN PROGRESS ***') -# Logfile.insert('cannot start new refinement for %s: *** REFINEMENT IN PROGRESS ***' %self.xtalID) -# return None -# -# ####################################################### -# # HKLIN & HKLOUT -# if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz')): -# RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'.free.mtz \\\n') -# elif os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): -# RefmacParams['HKLIN']='HKLIN '+os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz \\\n') -# else: -# Logfile.insert('%s: cannot find HKLIN for refinement; aborting...' %self.xtalID) -# return None -# RefmacParams['HKLOUT']='HKLOUT '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz \\\n') -# -# ####################################################### -# # XYZIN & XYZOUT -# RefmacParams['XYZIN']='XYZIN '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb \\\n') -# RefmacParams['XYZOUT']='XYZOUT '+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.pdb \\\n') -# -# ####################################################### -# # LIBIN & LIBOUT -# found_cif=False -# if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif')): -# found_cif=True -# # in cases where multiple liagnds are present (e.g. NOG, ATP) the user for now needs to put -# # the respective dictionary into the xtalID folder -# # need to think of a better mechanism in the future -# additional_cif=False -# additional_cif_file='' -# for file in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): -# if file.endswith('.cif'): -# if self.compoundID not in file: -# additional_cif_file=file -# additional_cif=True <- should be true, but need to check this part of the code! 16/11/2016 -# additional_cif=False -# if additional_cif: -# Cmds = ( -# '#!'+os.getenv('SHELL')+'\n' -# '\n' -# '$CCP4/bin/libcheck << eof \n' -# '_Y\n' -# '_FILE_L '+os.path.join(self.ProjectPath,self.xtalID,self.compoundID+'.cif')+'\n' -# '_FILE_L2 '+additional_cif_file+'\n' -# '_FILE_O '+os.path.join(self.ProjectPath,self.xtalID,'combined_cif')+'\n' -# '_END\n' -# 'eof\n' -# ) -# os.chdir(os.path.join(self.ProjectPath,self.xtalID)) -# print Cmds -# os.system(Cmds) -# RefmacParams['LIBIN']='LIBIN '+self.ProjectPath+'/'+self.xtalID+'/combined_cif.lib \\\n' -# else: -# RefmacParams['LIBIN']='LIBIN '+self.ProjectPath+'/'+self.xtalID+'/'+self.compoundID+'.cif \\\n' -# RefmacParams['LIBOUT']='LIBOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine_'+Serial+'.cif \\\n' -# if not found_cif: -# # this should actually not be necessary, but the following scenario can happen: -# # if a new data source is created from a file system, but smiles and compoundID where not updated; -# # so the ligand may still be in the structure, but since the compoundID is unknown to the datasource, -# # its restraints won't be read in and refmac will fail -# for file in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): -# if file.endswith('.cif'): -# RefmacParams['LIBIN']='LIBIN '+file+' \\\n' -# RefmacParams['LIBOUT']='LIBOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine_'+Serial+'.cif \\\n' -# break -# -# ####################################################### -# # TLSIN & TLSOUT -# findTLS='\n' -# TLSphenix='' -# if RefmacParams['TLS'].startswith('refi'): -# if external_software['phenix.find_tls_groups']: -# findTLS=os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','phenix_find_TLS_groups.py')+' in.pdb\n' -# RefmacParams['TLSIN']='TLSIN '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refmac.tls \\\n' -# RefmacParams['TLSOUT']='TLSOUT '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'/refine.tls \\\n' -# TLSphenix=' phenix.tls ' -# else: -# RefmacParams['TLS']='\n' -# -# -## ####################################################### -# create folder for new refinement cycle -# os.mkdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) -## -## ####################################################### -# write PDB file -# now take protein pdb file and write it to newly create Refine_ folder -# note: the user has to make sure that the ligand file was merged into main file -# for item in coot_utils_XChem.molecule_number_list(): -# if coot.molecule_name(item).endswith(self.prefix+'.pdb'): -# coot.write_pdb_file(item,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'in.pdb')) -# -# ####################################################### -# # PANDDAs stuff -# # only use occupancy refinement if EVENT map is present -# occupancy_refinement='' -# if external_software['giant.create_occupancy_params']: -# os.chdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) -# cmd = ( '#!'+os.getenv('SHELL')+'\n' -# 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' -# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-sh')+'\n' -# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' -# "giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'\n" ) -## os.system("giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'") -# os.system(cmd) -# print "==> XCE: running giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'" -# os.system("giant.create_occupancy_params pdb=in.pdb refmac_occ_out='refmac_refine.params'") -# # quick fix for the moment; need to talk to Nick since this should not be necessary -# try: -# params_file = fileinput.input('refmac_refine.params',inplace=True) -# for line in params_file: -# if 'incomplete' in line: -# line=line.replace('incomplete','complete') -# print line, -# elif 'occupancy refine' in line: -## line=line.replace('occupancy refine','occupancy refine ncycle 10\noccupancy refine') -## print line, -# else: -# print line, -# params_file.close() -# except OSError: -# # this may happen in case giant.create_occupancy_params did not produce a params output file -# pass -# -# print '==> XCE: waiting 5 seconds for giant.create_occupancy_params to finish...' -# time.sleep(5) -# print '==> XCE: done!' -# -# print '==> XCE: assembling refmac.csh' -# -# create_bound_conformation='' -# if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac_refine.params')): -# occupancy_refinement='@refmac_refine.params\n' -# create_bound_conformation="/bin/rm *bound.pdb\ngiant.strip_conformations pdb=refine.pdb suffix='.bound.pdb'\n" -# -# ####################################################### -# # we write 'REFINEMENT_IN_PROGRESS' immediately to avoid unncessary refiment -# os.chdir(os.path.join(self.ProjectPath,self.xtalID)) -# os.system('touch REFINEMENT_IN_PROGRESS') -# -# ####################################################### -# # clean up! -# # and remove all files which will be re-created by current refinement cycle -# os.system('/bin/rm refine.pdb refine.mtz validation_summary.txt validate_ligands.txt 2fofc.map fofc.map refine_molprobity.log') -# -# if external_software['qsub']: -# pbs_line='#PBS -joe -N XCE_refmac\n' -# else: -# pbs_line='\n' -# -# ####################################################### -# # weight -# if str(RefmacParams['MATRIX_WEIGHT']).lower() == 'auto': -# weight='weight AUTO\n' -# else: -# weight='weight matrix '+str(RefmacParams['MATRIX_WEIGHT'])+'\n' -# -# ####################################################### -# # PANDDA validation @ spider plot -# spider_plot='' -# if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-ensemble-model.pdb')): -# if os.path.isfile(os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz')): -# pdb_two=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-ensemble-model.pdb') -# mtz_two=os.path.join(self.ProjectPath,self.xtalID,self.xtalID+'-pandda-input.mtz') -# pdb_one=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.pdb') -# mtz_one=os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refine_'+Serial+'.mtz') -# spider_plot='$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/resort_ligand_atoms.py %s %s\n\n' %(pdb_two,pdb_one) -# spider_plot+='giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' %(pdb_one,mtz_one,pdb_two,mtz_two) -## spider_plot='giant.score_model pdb1=%s mtz1=%s pdb2=%s mtz2=%s res_names=LIG,UNL,DRG,FRG\n' %(pdb_one,mtz_one,pdb_two,mtz_two) -# -# ####################################################### -# # PHENIX stuff (if working at DLS) -# module_load='' -# if os.getcwd().startswith('/dls'): -# module_load='module load phenix\n' -# -# source ='' -# if 'bash' in os.getenv('SHELL'): -# source = ( -# 'export XChemExplorer_DIR="'+os.getenv('XChemExplorer_DIR')+'"\n' -# '\n' -# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-sh')+'\n' -# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-sh')+'\n' ) -# elif 'csh' in os.getenv('SHELL'): -# source = ( -# 'setenv XChemExplorer_DIR '+os.getenv('XChemExplorer_DIR')+'\n' -# '\n' -# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','xce.setup-csh')+'\n' -# 'source '+os.path.join(os.getenv('XChemExplorer_DIR'),'setup-scripts','pandda.setup-csh')+'\n' ) -# -# -# refmacCmds = ( -# '#!'+os.getenv('SHELL')+'\n' -# +pbs_line+ -# '\n' -# + module_load + -# '\n' -# + source + -# 'cd '+self.ProjectPath+'/'+self.xtalID+'/Refine_'+Serial+'\n' -# '\n' -# '$CCP4/bin/ccp4-python $XChemExplorer_DIR/helpers/update_status_flag.py %s %s %s %s\n' %(self.datasource,self.xtalID,'RefinementStatus','running') + -# '\n' -# +findTLS+ -# 'refmac5 ' -# +RefmacParams['HKLIN'] -# +RefmacParams['HKLOUT'] -# +RefmacParams['XYZIN'] -# +RefmacParams['XYZOUT'] -# +RefmacParams['LIBIN'] -# +RefmacParams['LIBOUT'] -# +RefmacParams['TLSIN'] -# +RefmacParams['TLSOUT']+ -# ' << EOF > refmac.log\n' -# 'make -\n' -# ' hydrogen ALL -\n' -# ' hout NO -\n' -# ' peptide NO -\n' -# ' cispeptide YES -\n' -# ' ssbridge YES -\n' -# ' symmetry YES -\n' -# ' sugar YES -\n' -# ' connectivity NO -\n' -# ' link NO\n' -# +RefmacParams['NCS']+ -# 'refi -\n' -# ' type REST -\n' -# ' resi MLKF -\n' -# ' meth CGMAT -\n' -# +RefmacParams['BREF'] -# +RefmacParams['TLS'] -# +RefmacParams['TWIN']+ -# 'ncyc '+RefmacParams['NCYCLES']+'\n' -# 'scal -\n' -# ' type SIMP -\n' -# ' LSSC -\n' -# ' ANISO -\n' -# ' EXPE\n' -# +weight+ -# 'solvent YES\n' -# +occupancy_refinement+ -# 'monitor MEDIUM -\n' -# ' torsion 10.0 -\n' -# ' distance 10.0 -\n' -# ' angle 10.0 -\n' -# ' plane 10.0 -\n' -# ' chiral 10.0 -\n' -# ' bfactor 10.0 -\n' -# ' bsphere 10.0 -\n' -# ' rbond 10.0 -\n' -# ' ncsr 10.0\n' -# 'labin FP=F SIGFP=SIGF FREE=FreeR_flag\n' -# 'labout FC=FC FWT=FWT PHIC=PHIC PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM\n' -# +RefmacParams['TLSADD']+'\n' -# 'DNAME '+self.xtalID+'\n' -# 'END\n' -# 'EOF\n' -# '\n' -# +spider_plot+ -# '\n' -# 'phenix.molprobity refine_%s.pdb refine_%s.mtz\n' %(Serial,Serial)+ -# '/bin/mv molprobity.out refine_molprobity.log\n' -# 'mmtbx.validate_ligands refine_%s.pdb refine_%s.mtz LIG > validate_ligands.txt\n' %(Serial,Serial)+ -# 'cd '+self.ProjectPath+'/'+self.xtalID+'\n' -# '#ln -s %s/%s/Refine_%s/refine_%s.pdb refine.pdb\n' %(self.ProjectPath,self.xtalID,Serial,Serial)+ -# '#ln -s %s/%s/Refine_%s/refine_%s.mtz refine.mtz\n' %(self.ProjectPath,self.xtalID,Serial,Serial)+ -# 'ln -s ./Refine_%s/refine_%s.pdb refine.pdb\n' %(Serial,Serial)+ -# 'ln -s ./Refine_%s/refine_%s.mtz refine.mtz\n' %(Serial,Serial)+ -# '\n' -# +create_bound_conformation+ -# '\n' -# 'ln -s Refine_%s/validate_ligands.txt .\n' %Serial+ -# 'ln -s Refine_%s/refine_molprobity.log .\n' %Serial+ -# 'mmtbx.validation_summary refine.pdb > validation_summary.txt\n' -# '\n' -# 'fft hklin refine.mtz mapout 2fofc.map << EOF\n' -# 'labin F1=FWT PHI=PHWT\n' -# 'EOF\n' -# '\n' -# 'fft hklin refine.mtz mapout fofc.map << EOF\n' -# 'labin F1=DELFWT PHI=PHDELWT\n' -# 'EOF\n' -# '\n' -# '$CCP4/bin/ccp4-python '+os.path.join(os.getenv('XChemExplorer_DIR'),'helpers','update_data_source_after_refinement.py')+ -# ' %s %s %s %s\n' %(self.datasource,self.xtalID,self.ProjectPath,os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial))+ -# '\n' -# '/bin/rm %s/%s/REFINEMENT_IN_PROGRESS\n' %(self.ProjectPath,self.xtalID)+ -# '\n' -# ) -# -# Logfile.insert('writing refinement shell script to'+os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac.csh')) -# cmd = open(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial,'refmac.csh'),'w') -# cmd.write(refmacCmds) -# cmd.close() -# -# os.chdir(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) -## os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) -# Logfile.insert('changing directory to %s' %(os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial))) -# if external_software['qsub']: -# Logfile.insert('starting refinement on cluster') -# os.system('qsub -P labxchem refmac.csh') -# elif external_software['qsub_remote'] != '': -# Logfile.insert('starting refinement on remote cluster') -# remote_command=external_software['qsub_remote'].replace('qsub','cd %s; qsub' %os.path.join(self.ProjectPath,self.xtalID,'Refine_'+Serial)) -# os.system('%s -P labxchem refmac.csh' %remote_command) -# print '%s -P labxchem refmac.csh' %remote_command -# else: -# Logfile.insert('changing permission of refmac.csh: chmod +x refmac.csh') -# os.system('chmod +x refmac.csh') -# Logfile.insert('starting refinement on local machine') -# os.system('./refmac.csh &') -# if '/work/' in os.getcwd(): -## os.system('ssh artemis "cd %s/%s/Refine_%s; qsub refmac.csh"' %(self.ProjectPath,self.xtalID,Serial)) -# else: -## os.system('./refmac.csh &') -# -# -# -# -# def RefinementParams(self,RefmacParams): -# self.RefmacParams=RefmacParams -# self.window = gtk.Window(gtk.WINDOW_TOPLEVEL) -# self.window.connect("delete_event", gtk.main_quit) -# self.window.set_border_width(10) -# self.window.set_title("Refmac Parameters") -# self.vbox = gtk.VBox() -# -# self.hbox1=gtk.HBox() -# self.hbox1.add(gtk.Label('Refine')) -# self.cb = gtk.combo_box_new_text() -# self.cb.connect("changed", self.ChooseBfacRefinement) -# for item in ['isotropic','anisotropic']: -# self.cb.append_text(item) -# if 'ISOT' in self.RefmacParams['BREF']: -# self.cb.set_active(0) -# if 'ANIS' in self.RefmacParams['BREF']: -# self.cb.set_active(1) -# self.hbox1.add(self.cb) -# self.hbox1.add(gtk.Label('temperature factors')) -# self.vbox.add(self.hbox1) -# -# self.hbox2=gtk.HBox() -# self.hbox2.add(gtk.Label('Number of Cycles: ')) -# self.Ncycles=gtk.Entry() -# self.Ncycles.add_events(gtk.gdk.KEY_RELEASE_MASK) -# self.Ncycles.connect("key-release-event", self.on_key_release_Ncycles) -# self.Ncycles.set_text(self.RefmacParams['NCYCLES']) -# self.hbox2.add(self.Ncycles) -# self.vbox.add(self.hbox2) -# -# self.hbox3=gtk.HBox() -# self.hbox3.add(gtk.Label('MATRIX WEIGHT: ')) -# self.MATRIX_WEIGHT=gtk.Entry() -# self.MATRIX_WEIGHT.add_events(gtk.gdk.KEY_RELEASE_MASK) -# self.MATRIX_WEIGHT.connect("key-release-event", self.on_key_release_MATRIX_WEIGHT) -# self.MATRIX_WEIGHT.set_text(self.RefmacParams['MATRIX_WEIGHT']) -# self.hbox3.add(self.MATRIX_WEIGHT) -# self.vbox.add(self.hbox3) -# -# self.TLS = gtk.CheckButton('TLS (find TLS groups with phenix.find_tls_groups)') -# self.TLS.connect("toggled", self.TLSCallback) -# if self.RefmacParams['TLS']=='refi tlsc 10\n': self.TLS.set_active(True) -# self.vbox.pack_start(self.TLS,False) -# -# self.NCS = gtk.CheckButton('NCS (if applicable') -# self.NCS.connect("toggled", self.NCSCallback) -# if self.RefmacParams['NCS']=='NCSR LOCAL\n': self.NCS.set_active(True) -# self.vbox.pack_start(self.NCS,False) -# -# self.TWIN = gtk.CheckButton('Twin?') -# self.TWIN.connect("toggled", self.TWINCallback) -# if self.RefmacParams['TWIN']=='TWIN\n': self.TWIN.set_active(True) -# self.vbox.pack_start(self.TWIN,False) -# -# self.OKbutton = gtk.Button(label="OK") -# self.OKbutton.connect("clicked",self.OK) -# self.vbox.add(self.OKbutton) -# -# self.window.add(self.vbox) -# self.window.show_all() -# return self.RefmacParams -# -# -# def TLSCallback(self, widget): -# if widget.get_active(): -# self.RefmacParams['TLS']='refi tlsc 10\n' -# self.RefmacParams['TLSIN']='refmac.tls\n' -# self.RefmacParams['TLSOUT']='out.tls\n' -# self.RefmacParams['TLSADD']='TLSO ADDU\n' -# else: -# self.RefmacParams['TLS']='' -# self.RefmacParams['TLSIN']='' -# self.RefmacParams['TLSOUT']='' -# self.RefmacParams['TLSADD']='' -# return self.RefmacParams -# -# def NCSCallback(self, widget): -# if widget.get_active(): -# self.RefmacParams['NCS']='NCSR LOCAL\n' -# else: -# self.RefmacParams['NCS']='' -# return self.RefmacParams -# -# def ChooseBfacRefinement(self,widget): -# if widget.get_active_text()=='isotropic': -# self.RefmacParams['BREF']=' bref ISOT\n' -# if widget.get_active_text()=='anisotropic': -# self.RefmacParams['BREF']=' bref ANIS\n' -# return self.RefmacParams -# -# def on_key_release_Ncycles(self, widget, event): -# print widget.get_text() -# self.RefmacParams['NCYCLES'] = widget.get_text() -# return self.RefmacParams -# -# def on_key_release_MATRIX_WEIGHT(self, widget, event): -# self.RefmacParams['MATRIX_WEIGHT'] = widget.get_text() -# return self.RefmacParams -# -# def TWINCallback(self, widget): -# if widget.get_active(): -# self.RefmacParams['TWIN']='TWIN\n' -# else: -# self.RefmacParams['TWIN']='' -# return self.RefmacParams# -# -# def OK(self,widget): -# self.window.destroy() -# -# -# def ParamsFromPreviousCycle(self,Serial): -# -# RefmacParams={ 'HKLIN': '', 'HKLOUT': '', -# 'XYZIN': '', 'XYZOUT': '', -# 'LIBIN': '', 'LIBOUT': '', -# 'TLSIN': '', 'TLSOUT': '', -# 'TLSADD': '', -# 'NCYCLES': '10', -# 'MATRIX_WEIGHT': 'AUTO', -# 'BREF': ' bref ISOT\n', -# 'TLS': '', -# 'NCS': '', -# 'TWIN': '' } -# -# if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): -# for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(Serial)+'/refmac.csh'): -# if line.startswith('refi tlsc'): -# RefmacParams['TLS']=line -# if line.startswith('TLSO'): -# RefmacParams['TLSADD']=line -# if line.startswith('NCSR LOCAL'): -# RefmacParams['NCS']=line -# if line.startswith(' bref '): -# RefmacParams['BREF']=line -# if line.startswith('ncyc'): -# RefmacParams['Ncycles'] = line.split()[1] -# if line.startswith('weight'): -# RefmacParams['MATRIX_WEIGHT'] = line.split()[len(line.split())-1] -# if line.startswith('TWIN'): -# RefmacParams['TWIN']=line -# -# return RefmacParams -# -# def GetRefinementHistory(self): -# RefinementHistory='' -# RefinementCycle = [] -# RcrystList=[] -# RfreeList=[] -# -# found = False -# for item in glob.glob(os.path.join(self.ProjectPath,self.xtalID,'*')): -# if item.startswith(os.path.join(self.ProjectPath,self.xtalID,'Refine_')): -# print item[item.rfind('_')+1:] -# RefinementCycle.append(int(item[item.rfind('_')+1:])) -# found = True -# if found: -# for cycle in sorted(RefinementCycle): -# for cycle in RefinementCycle: -# Rcryst=0 -# Rfree=0 -# LigandCC=0 -# try: -# found_Rcryst=False -# found_Rfree=False -# newestPDB = max(glob.iglob(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/refine_'+str(cycle)+'.pdb'), key=os.path.getctime) -# for line in open(newestPDB): -# if line.startswith('REMARK 3 R VALUE (WORKING + TEST SET) :'): -# Rcryst = line.split()[9] -# RcrystList.append(float(Rcryst)) -# found_Rcryst=True -# if line.startswith('REMARK 3 FREE R VALUE :'): -# Rfree = line.split()[6] -# RfreeList.append(float(Rfree)) -# found_Rfree=True -# if not found_Rcryst: -# RcrystList.append(0) -# if not found_Rfree: -# RfreeList.append(0) -# if os.path.isfile(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): -# for line in open(self.ProjectPath+'/'+self.xtalID+'/Refine_'+str(cycle)+'/validate_ligands.txt'): -## if line.startswith('| LIG'): LigandCC = line.split()[6] -# RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' -# except ValueError: -# RcrystList.append(0) -# RfreeList.append(0) -# RefinementHistory=RefinementHistory+str(cycle).rjust(10)+str(R).rjust(10)+str(Rfree).rjust(10)+str(LigandCC).rjust(10)+'\n' -# else: -# RefinementCycle = [0] -# RcrystList=[0] -# RfreeList=[0] -# print RefinementCycle,RcrystList,RfreeList -# return(sorted(RefinementCycle),RcrystList,RfreeList) -# From cc0e87fde0a67cf29f68ec1e33584ad4fb276d80 Mon Sep 17 00:00:00 2001 From: Garry O'Donnell Date: Thu, 10 Nov 2022 13:58:42 +0000 Subject: [PATCH 179/358] Clean up process_sqlite --- xce/web/process_sqlite.py | 195 +++++++++++++++++++++++--------------- 1 file changed, 120 insertions(+), 75 deletions(-) diff --git a/xce/web/process_sqlite.py b/xce/web/process_sqlite.py index 73c45507..ba9d4080 100755 --- a/xce/web/process_sqlite.py +++ b/xce/web/process_sqlite.py @@ -1,9 +1,3 @@ -#!/usr/local/anaconda/sgc_default/envs/sgc_default/bin/python - -# Author: Brian Marsden -# -# handover date: 16/12/2016 - from rdkit.Chem import Draw from rdkit import Chem import shutil @@ -45,14 +39,14 @@ def writeTableRow(row, htmlfile): + row["CompoundCode"] + "_small.png'>\n" ) - # htmlfile.write("\n") htmlfile.write("\n") - # htmlfile.write("\n") - # htmlfile.write("\n" %row['Deposition_PDB_ID']) htmlfile.write( - '\n'.format( - row["Deposition_PDB_ID"], row["Deposition_PDB_ID"] - ) + "\n".format(row["Deposition_PDB_ID"], row["Deposition_PDB_ID"]) ) htmlfile.write("\n") htmlfile.write("\n") @@ -83,10 +77,15 @@ def writeICBPage(row, panddadir): "

" + row["CrystalName"] + " " + row["CompoundCode"] + " event

\n" ) icbhtmlfile.write( - '

Please wait whilst the interactive viewer is loaded!

\n' + '
' + '

' + "Please wait whilst the interactive viewer is loaded!" + "

" + "
\n" ) icbhtmlfile.write( - '
\n' + '
\n' ) icbhtmlfile.write( '\n' ) - # icbhtmlfile.write('\n') icbhtmlfile.write("
\n") icbhtmlfile.write('
\n') icbhtmlfile.write("
Crystal IDPDB IDLigand IDLigand confidenceModel statusCompoundLigand ValidationEvent Map 3DResolSPG/ CellFiles
%s%s%s%s%s +
+ 		%s%s
%s		Save
" + row["PANDDA_site_comment"] + "TBDhttp://www.rcsb.org/pdb/explore/explore.do?structureId=%s{1!s}" + '' + "{1!s}" + "" + "" + row["DataProcessingResolutionHigh"] + "" + row["DataProcessingSpaceGroup"] + "
\n") @@ -123,7 +121,6 @@ def writeICBPage(row, panddadir): + row["CompoundCode"] + '.icb";\n' ) - # icbhtmlfile.write(' act.projectFile = "'+row['ModelName']+'_'+row['CompoundCode']+'.icb.gz";\n') icbhtmlfile.write(" act.searchBarVisible = false;\n") icbhtmlfile.write(" act.sequenceViewVisibleAuto = false;\n") icbhtmlfile.write(" act.tableViewVisibleAuto = false;\n") @@ -193,11 +190,13 @@ def main(argv): ) htmlfile.write("" + targetID + " Fragment Hits\n") htmlfile.write( - '\n") htmlfile.write( - '\n") htmlfile.write('