improved automation#6

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orbeckst wants to merge 82 commits intodevelopfrom

Commits on Aug 23, 2013

Added header to modules with information regarding authorship and licensing
Lennard van der Feltz
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Added header to modules with authorship and licensing information
Lennard van der Feltz
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Added header to scripts and modules with authorship and licensing information
Lennard van der Feltz
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Commits on Aug 25, 2013

Added copyright to modules
Lennard van der Feltz
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Added copyright info to scripts
Lennard van der Feltz
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Added copyright to ez_setup.py
Lennard van der Feltz
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Implemented numpy within apbs-mem-properties.py
Lennard van der Feltz
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Commits on Aug 26, 2013

Updated author information with recent copyrights and Added Lennard van der Feltz's copyright.
Lennard van der Feltz
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Commits on Sep 1, 2013

Altered mem-properties.py to include a try statement which returns an ImportError if MDAnalysis is not present. Also added comments.
Lennard van der Feltz
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Added default title to pdb2dat and improved writing method.
Lennard van der Feltz
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Improved straightpath writing methodology and added title option. Also changed pdb2dat to make use of default from argparse.
Lennard van der Feltz
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Commits on Sep 3, 2013

Fixed typo in mem-potential comment
Lennard van der Feltz
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Commits on Sep 14, 2013

Added option to input local PDB to mem-properties. Allows for finding radii of selections of protein.
Lennard van der Feltz
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Clarified mem-properties output.
Lennard van der Feltz
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Commits on Sep 16, 2013

added no-membrane potential argument handling to io.py
Lennard van der Feltz
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added non-membrane methods to membrane.py for use in potential calculations.
Lennard van der Feltz
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Commits on Sep 17, 2013

Got output from bornprofile-potential.py, a clone of mem-potential with membrane references removed. As a result alterations were made to membrane.py and io.py and a new template was introduced. se…
Lennard van der Feltz
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changed output format from .dat to .pdb
Lennard van der Feltz
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fixed pdb format in straightpath script
Lennard van der Feltz
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Commits on Sep 18, 2013

Renamed membrane file "electrostatics.py" to account for the addition of a membrane-free class. Updated email in init.py
Lennard van der Feltz
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email update
Lennard van der Feltz
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Logging, text file output, and input allowances added to mem-properties.py. Corrected logger name for electrostatics.py(formerly membrane.py)
Lennard van der Feltz
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Commits on Sep 19, 2013

improved wording, flow of mem-properties.
Lennard van der Feltz
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Commits on Sep 20, 2013

Improved error message organization
Lennard van der Feltz
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Commits on Sep 22, 2013

In mem-properties, relocated all sys.exit to main function body.
Lennard van der Feltz
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Commits on Sep 23, 2013

fixed numbering in output of straightpath.
Lennard van der Feltz
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Commits on Oct 1, 2013

Put logger after options in analyze3D.py to allow for easier help access
Lennard van der Feltz
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Commits on Jan 21, 2014

Added graphing, pdb download, and NEBpath scripts. Included these in setup.py.
Lennard van der Feltz
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fixed issues regarding installation of NEBpath.py and treatment of cases where no options are submitted to 1dgraph.py
Lennard van der Feltz
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fixed typo in 1Dgraph.py
Lennard van der Feltz
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Commits on Jan 25, 2014

fixed logging in protein_pdb
Lennard van der Feltz
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Improved logging messages in protein_pdb for use in automation of 1D profiles
Lennard van der Feltz
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Commits on Jan 28, 2014

Updated mem-properties.py to improve logging placement and return values for use in automation.
Lennard van der Feltz
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added graphing section to config file defaults.
Lennard van der Feltz
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Commits on Feb 7, 2014

cleaned up leftover files and added new function library for functions relating to run preparation.
Lennard van der Feltz
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cleaned up leftover perl files and moved functions in scripts relating to run preparation to library in bornprofiler.
Lennard van der Feltz
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actually cleaned up perl files.
Lennard van der Feltz
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Commits on Feb 8, 2014

fixed __init__ function for basemem class
Lennard van der Feltz
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Commits on Feb 24, 2014

introduced plotting library to hold function definitions for 1dgraph script
Lennard van der Feltz
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Moved plotting functions to library in bornprofiler and changed atomnum in NEB.dat to int.
Lennard van der Feltz
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Commits on Feb 25, 2014

First working build of BPauto.py completed.
Lennard van der Feltz
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Commits on Feb 27, 2014

Updated BPauto.py to edit glen and dime to avoid failed calculations
Lennard van der Feltz
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Commits on Mar 13, 2014

Added logging statements to BPauto.py
Lennard van der Feltz
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added scripts to setup.py
Lennard van der Feltz
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added autoanalyze script
Lennard van der Feltz
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Commits on Mar 15, 2014

Added submit command to BPauto
Lennard van der Feltz
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Commits on Mar 19, 2014

Added checking of glen values against points for calculation for placeion and mplaceion in core.py.
Lennard van der Feltz
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Commits on Mar 20, 2014

Improved grid checking algorithm and logging messages in core.py
Lennard van der Feltz
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Commits on Mar 31, 2014

Removed attempted glen automation from Placeion class in core.py
Lennard van der Feltz
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Merged placeion and mplaceion functionalities into new placeion script
Lennard van der Feltz
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Removed reference to mplaceion from setup.py
Lennard van der Feltz
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Commits on Apr 3, 2014

cleanup of placeion classes and improvement of grid checking algorithm.
Lennard van der Feltz
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Removed template option from placeion.
Lennard van der Feltz
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Commits on Apr 5, 2014

Cleanup and renaming of io.py to bpio.py and changing references from io.py to bpio.py in relevant files.
Lennard van der Feltz
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1Dgraph changed to enable submission of cfg file. BPauto minor cleanup.
Lennard van der Feltz
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Commits on Apr 8, 2014

Add cfg_template script which produces a default cfg file under some specifications. Also leaned up some io references(corrected to bpio)
Lennard van der Feltz
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Made changes to allow for template cfg creation to omit certain sections.
Lennard van der Feltz
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Commits on Apr 15, 2014

corrected 'graphing' section of BPauto script to 'plotting'
Lennard van der Feltz
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Corrected naming of graphing functions in 1Dgraph.py
Lennard van der Feltz
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Added protein and membrane plotting, fixed minor typos
Lennard van der Feltz
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Commits on Apr 16, 2014

imrpoved logging in plotting functions regarding cfg reading.
Lennard van der Feltz
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Added documentation,comments, and licensing to 1Dgraph and autoanalyze
Lennard van der Feltz
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Changed legend to loc='best'on all functions in plotting.py
Lennard van der Feltz
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Commits on Apr 20, 2014

added pdf format saving to plotting.py
Lennard van der Feltz
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Commits on Apr 24, 2014

Added fancier formatting to 1Dgraph.py
Lennard van der Feltz
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Commits on Apr 25, 2014

Corrected small formatting mistake in 1Dgraph.py
Lennard van der Feltz
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Commits on May 19, 2014

Fixed more graphing/plotting naming errors, adapted Run_Parameters' _populate_default to work with both placeion and cfg_template scripts.
Lennard van der Feltz
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Commits on May 24, 2014

updated anaylsis to update import io statement to import bpio and RunParameters call to include additional options for compatibility with new populate defaults function.
Lennard van der Feltz
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Commits on Jun 3, 2014

Changed from pyplot to matplotlib in analysis.py plotting and altered backend to AGG to allow for remote use.
Lennard van der Feltz
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Commits on Jun 16, 2014

Added pH option to BPauto script, and changed submission from default to optional.
Lennard van der Feltz
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Commits on Jul 28, 2014

Adapted 1dgraph.py to submit to a single function in bornprofiler/plotting.py with the option to use seaborn to improve plot quality.
Lennard van der Feltz
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Updated placeion.py help info
Lennard van der Feltz
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Added warning message to bpio.RunParameters to alert user if H ion is selected and suggest use of H30 instead
Lennard van der Feltz
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fixed bpio.RunParameters hydrogen warning
Lennard van der Feltz
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Commits on Sep 2, 2014

Finally staged changes that had gone unadded due to negligence. Recent fixes include membraneless bp runs and the addition of support for runs larger than 10k points.
Lennard van der Feltz
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Comments to explain BPauto process for ensuring coarse grids completely enclose all fine grids.
Lennard van der Feltz
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Commits on Oct 22, 2014

Added datalgebra with capacity to take difference between two 1d BP dat files using z interpolation of energies
Lennard van der Feltz
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Commits on Oct 25, 2014

Refactored datalgebra functions into array_alg and bpio. Added average to datalgebra and added object algebra to datarray objects.
Lennard van der Feltz
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Commits on Oct 26, 2014

Added ability to choose axis for operations in array_alg and error messages for when attempting unreasonable manipulations.
Lennard van der Feltz
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Commits on Dec 12, 2014

tweaked NEB cutoff to better value(spacing/10.0 instead of spacing/100.0)
Lennard van der Feltz
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Commits on May 11, 2015

"Prepping for merge with master"
Lennard van der Feltz
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More merge prep
Lennard van der Feltz
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