Enable to run tortoize within prosmart_refmac and servalcat_pipe

CHANGELOG.md

@@ -7,6 +7,7 @@
 - Fix for reflection CIF files containing both merged and unmerged data
 - New Pointless options to remove lattice centering reflections
 - Fix to Servalcat report type handling
+- Added option to do Tortoize Rama-Z calculation in Refmac & Servalcat pipelines
 
 ## [2.4.1] - 2025-10-07
 

pipelines/prosmart_refmac/script/prosmart_refmac.def.xml

@@ -474,6 +474,12 @@
                   <default>True</default>
                </qualifiers>
             </content>
+            <content id="VALIDATE_TORTOIZE">
+               <className>CBoolean</className>
+               <qualifiers>
+                  <default>False</default>
+               </qualifiers>
+            </content>
             <content id="VALIDATE_MOLPROBITY">
                <className>CBoolean</className>
                <qualifiers>

pipelines/prosmart_refmac/script/prosmart_refmac.py

@@ -639,11 +639,15 @@ def finishUp(self, refmacJob):
            if hasattr(self.container.controlParameters,"VALIDATE_RAMACHANDRAN"):
               validate_ramachandran = self.container.controlParameters.VALIDATE_RAMACHANDRAN
 
+           validate_tortoize = False
+           if hasattr(self.container.controlParameters,"VALIDATE_TORTOIZE"):
+               validate_tortoize = self.container.controlParameters.VALIDATE_TORTOIZE
+
            validate_molprobity = False
            if hasattr(self.container.controlParameters,"VALIDATE_MOLPROBITY"):
               validate_molprobity = self.container.controlParameters.VALIDATE_MOLPROBITY
 
-           if validate_baverage or validate_molprobity or validate_ramachandran or validate_iris:
+           if validate_baverage or validate_molprobity or validate_ramachandran or validate_tortoize or validate_iris:
              xml_validation = etree.SubElement(self.xmlroot,"Validation")
              xml_validation_status = etree.SubElement(xml_validation,"Success")
              try:
@@ -670,6 +674,7 @@ def finishUp(self, refmacJob):
                 self.validate.container.controlParameters.DO_IRIS = validate_iris
                 self.validate.container.controlParameters.DO_BFACT = validate_baverage
                 self.validate.container.controlParameters.DO_RAMA = validate_ramachandran
+                self.validate.container.controlParameters.DO_TORTOIZE = validate_tortoize
                 self.validate.container.controlParameters.DO_MOLPROBITY = validate_molprobity
 
                 self.validate.doAsync = False

pipelines/prosmart_refmac/script/prosmart_refmac_gui.py

@@ -533,9 +533,10 @@ def drawOutput( self ):
 
     self.createLine( [ 'subtitle', 'Validation and Analysis' ] )
     self.openSubFrame(frame=[True], toggleFunction=[self.ToggleRigidModeOff,['REFINEMENT_MODE']])
-    self.createLine( [ 'widget', 'VALIDATE_IRIS', 'label', 'Generate Iris report' ] )
+    self.createLine( [ 'widget', 'VALIDATE_IRIS', 'label', 'Generate Iris validation report' ] )
     self.createLine( [ 'widget', 'VALIDATE_BAVERAGE', 'label', 'Analyse B-factor distributions' ] )
     self.createLine( [ 'widget', 'VALIDATE_RAMACHANDRAN', 'label', 'Generate Ramachandran plots' ] )
+    self.createLine( [ 'widget', 'VALIDATE_TORTOIZE', 'label', 'Calculate Rama-Z score using <i>tortoize</i>' ] )
     self.createLine( [ 'widget', 'VALIDATE_MOLPROBITY', 'label', 'Run MolProbity to analyse geometry' ] )
     #self.createLine( [ 'widget', 'RUN_MOLPROBITY', 'label', 'Run standalone MolProbity (to be deprecated)' ] )
     self.closeSubFrame()

pipelines/servalcat_pipe/script/servalcat_pipe.def.xml

@@ -584,6 +584,12 @@
                   <default>True</default>
                </qualifiers>
             </content>
+            <content id="VALIDATE_TORTOIZE">
+               <className>CBoolean</className>
+               <qualifiers>
+                  <default>True</default>
+               </qualifiers>
+            </content>
             <content id="VALIDATE_MOLPROBITY">
                <className>CBoolean</className>
                <qualifiers>

pipelines/servalcat_pipe/script/servalcat_pipe.py

@@ -331,11 +331,15 @@ def multimericValidation(self):
         if hasattr(self.container.controlParameters,"VALIDATE_RAMACHANDRAN"):
             validate_ramachandran = self.container.controlParameters.VALIDATE_RAMACHANDRAN
 
+        validate_tortoize = False
+        if hasattr(self.container.controlParameters,"VALIDATE_TORTOIZE"):
+            validate_tortoize = self.container.controlParameters.VALIDATE_TORTOIZE
+
         validate_molprobity = False
         if hasattr(self.container.controlParameters,"VALIDATE_MOLPROBITY"):
             validate_molprobity = self.container.controlParameters.VALIDATE_MOLPROBITY
 
-        if validate_iris or validate_baverage or validate_molprobity or validate_ramachandran:
+        if validate_iris or validate_baverage or validate_molprobity or validate_ramachandran or validate_tortoize:
             self.validate = self.makePluginObject('validate_protein')
             self.validate.container.inputData.XYZIN_2.set(self.container.outputData.CIFFILE)
             self.validate.container.inputData.XYZIN_1.set(self.container.inputData.XYZIN)
@@ -355,6 +359,7 @@ def multimericValidation(self):
             self.validate.container.controlParameters.DO_IRIS.set(validate_iris)
             self.validate.container.controlParameters.DO_BFACT.set(validate_baverage)
             self.validate.container.controlParameters.DO_RAMA.set(validate_ramachandran)
+            self.validate.container.controlParameters.DO_TORTOIZE.set(validate_tortoize)
             self.validate.container.controlParameters.DO_MOLPROBITY.set(validate_molprobity)
 
             self.validate.doAsync = False

pipelines/servalcat_pipe/script/servalcat_pipe_gui.py

@@ -459,6 +459,7 @@ def drawAdvanced( self ):
     self.openSubFrame(frame=[True])
     self.createLine( [ 'widget', 'VALIDATE_IRIS', 'label', 'Generate Iris validation report' ] )
     self.createLine( [ 'widget', 'VALIDATE_RAMACHANDRAN', 'label', 'Generate Ramachandran plots' ] )
+    self.createLine( [ 'widget', 'VALIDATE_TORTOIZE', 'label', 'Calculate Rama-Z score using <i>tortoize</i>' ] )
     self.createLine( [ 'widget', 'VALIDATE_MOLPROBITY', 'label', 'Run MolProbity to analyse geometry' ] )
 
     self.createLine( [ 'widget', 'RUN_ADP_ANALYSIS', 'label', 'Run ADP analysis' ] )