from CCP4TaskWidget import CTaskWidget class CRefmacWrk(CTaskWidget): TASKNAME = 'refmac_wrk' TASKVERSION = 0.0 TASKMODULE = 'test' TASKTITLE = 'Refmac Replica' def __init__(self,parent): CTaskWidget.__init__(self,parent) def showFP( self ) : inp = self.container.inputData par = self.container.controlParameters return str(par.INPUT_PHASE) in ['HL','PHASE'] \ or str(par.INPUT_PHASE) == 'NO' and str(par.TWINREF_TYPE) in ['NO','AMPLITUDES'] def showIP( self ) : inp = self.container.inputData par = self.container.controlParameters return str(par.INPUT_PHASE) == 'NO' and str(par.TWINREF_TYPE) == 'INTENSITIES' def drawContents(self): # ---------------------------------------------------------------------- self.openFolder( folderFunction='inputData', title='Input Data') self.createLine([ 'label','Job title', 'widget','TITLE']) self.createLine([ 'label','Do', 'widget','REFINE_TYPE', 'label','using', 'widget','INPUT_PHASE', 'label','input'], toggle=['REFINE_TYPE','hide',['REVIEW','IDEA']]) self.createLine([ 'label','Do', 'widget','REFINE_TYPE'], toggle=['REFINE_TYPE','open',['REVIEW','IDEA']]) self.createLine([ 'widget','IFFIXTLS', 'label','Input fixed TLS parameters'], toggle=['REFINE_TYPE','hide',['REVIEW','IDEA','TLS']]) self.openSubFrame( toggle=['INPUT_PHASE','open',['NO']]) self.createLine([ 'widget','TWINREF_TYPE', 'label','twin refinement']) self.closeSubFrame() self.openSubFrame( toggle=['PROSMART_AVAIL','open',[True]]) self.createLine([ 'widget','IFPROSMART', 'label','Run Prosmart to generate ', 'widget','PROSMART_MODE', 'label','(low resolution refinement)'], toggle=['REFINE_TYPE','open',['REST','TLS']]) self.closeSubFrame() self.openSubFrame( toggle=['COOT_AVAIL','open',[True]]) self.createLine([ 'widget','RUN_COOT_FW', 'label','Run Coot:findwaters to automatically add/remove waters to refined structure'], toggle=['REFINE_TYPE','open',['REST','UNRE']]) self.closeSubFrame() self.openSubFrame( toggle=['REFINE_TYPE','hide',['REVIEW','IDEA']]) self.createLine([ 'label','MTZ in', 'widget','HKLIN']) self.createLine([ 'label','F', 'widget','F_ANO'], toggle=['INPUT_PHASE','open',['SAD']]) self.createLine([ 'label','Wavelength ', 'widget','WAVELENGTH', 'label','Refine substructure occupancy ', 'widget','REF_SUBOCC'], toggle=['INPUT_PHASE','open',['SAD']]) self.createLine([ 'widget', 'ANOMALOUS_ATOMS', '-title','Anomalous form factors'], toggle=['INPUT_PHASE','open',['SAD']]) self.createLine([ 'label','IP ', 'widget','IOBS'], toggleFunction=[self.showIP,['INPUT_PHASE','TWINREF_TYPE']]) self.createLine([ 'label','FP ', 'widget','FOBS'], toggleFunction=[self.showFP,['INPUT_PHASE','TWINREF_TYPE']]) self.createLine([ 'label','PHIB ', 'widget','PHOBS'], toggle=['INPUT_PHASE','open',['PHASE']]) self.createLine([ 'label','HLA', 'widget','ABCD'], toggle=['INPUT_PHASE','open',['HL']]) self.closeSubFrame() self.createLine([ 'label','PDB in', 'widget','XYZIN']) self.createLine([ 'label','LIB in', 'widget','MAKE_LIBRARY'], toggle=['REFINE_TYPE','hide',['RIGID','UNRE']]) # add extra button to launch merge_monomers task self.openSubFrame( toggle=['REFINE_TYPE','open',['TLS']]) self.createLine([ 'label','TLS in (optional) ', 'widget','TLSIN']) # add extra button to launch merge_monomers task self.closeSubFrame() self.openSubFrame( toggle=['IFFIXTLS','open',[True]]) self.createLine([ 'label','TLS in', 'widget','TLSIN']) self.closeSubFrame() self.openSubFrame( toggle=['IFPROSMART','open',[True]]) self.createLine([ 'label','Reference PDB in', 'widget','EXT_XYZIN'], toggle=['PROSMART_MODE','hide',['SECSTR']]) self.createLine([ 'label','Prosmart restraints out', 'widget','RESTRAINTFILE']) self.createLine([ 'label','Prosmart keyword file', 'widget','PROSMART_KEYFILE']) self.closeSubFrame() self.openSubFrame() self.createLine([ 'label','Refmac keyword file', 'widget','INCLUDEFILE']) self.closeSubFrame() # ---------------------------------------------------------------------- self.openFolder( folderFunction='controlParameters', title='Options') # self.drawDataHarvesting() self.drawSetupGeometricRestraints() self.drawSetupGeometricRestraintsReview() self.drawSetupNCSRestraints() self.drawRefinementParametersREST() self.drawRefinementParametersUNRE() self.drawRefinementParametersRIGID() self.drawRefinementParametersTLS() self.drawExternalRestraints() self.drawIdealisationParameters() self.drawCootParameters() self.drawTLSParameters() self.drawMonitoringAndOutputOptions() self.drawScaling() self.drawRigidDomainsDefinition() self.drawGeometricParameters() self.openSubFrame( frame=True) self.closeSubFrame() # ---------------------------------------------------------------------- # def drawDataHarvesting(self): # self.openSubFrame( # frame=True, # toggle=['REFINE_TYPE','hide',['REVIEW','RIGID','IDEA']]) # self.closeSubFrame() # self.openSubFrame( # frame=True, # toggle=['REFINE_TYPE','hide',['REVIEW','RIGID','IDEA']]) # self.createLine([ # 'widget','DATA_HARVESTING', # 'advice','Data Harvesting']) # self.createLine([ # 'label','AAAAAAAAAAAAAAAAAAAAAA 01'], # toggle=['DATA_HARVESTING','open',[True]]) # self.closeSubFrame() # ---------------------------------------------------------------------- def drawSetupGeometricRestraints(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','hide',['REVIEW','RIGID','UNRE']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','hide',['REVIEW','RIGID','UNRE']]) self.createLine([ 'widget','SETUP_GEOMETRIC_RESTRAINTS', 'advice','Setup Geometric Restraints']) self.createLine([ 'label','Checking against dictionary:', 'widget','MAKE_CHECK'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.createLine([ 'label','If the following features are found in coordinate file then make restraints to maintain them:'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.createLine([ 'widget','MAKE_PEPTIDE', 'label','D-peptide ', 'widget','MAKE_CISPEPTIDE', 'label','cis-peptide', 'widget','MAKE_SYMMETRY', 'label','Links between symmetry related atoms'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.createLine([ 'label','Make links between:'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.createLine([ 'label','Amino acids and DNA/RNA if', 'widget','MAKE_CONNECTIVITY'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.createLine([ 'label','Sugar-sugar and sugar-peptide if', 'widget','MAKE_SUGAR'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.createLine([ 'label','All others if', 'widget','MAKE_LINK'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.closeSubFrame() # ---------------------------------------------------------------------- def drawSetupGeometricRestraintsReview(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['REVIEW']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['REVIEW']]) self.createLine([ 'widget','SETUP_GEOMETRIC_RESTRAINTS', 'advice','Setup Geometric Restraints']) self.createLine([ 'label','Checking against dictionary:', 'widget','REVIEW_MAKE_CHECK'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.createLine([ 'label','If the following features are found in coordinate file then make restraints to maintain them:'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.createLine([ 'widget','REVIEW_MAKE_PEPTIDE', 'label','D-peptide ', 'widget','REVIEW_MAKE_CISPEPTIDE', 'label','cis-peptide', 'widget','REVIEW_MAKE_SYMMETRY', 'label','Links between symmetry related atoms'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.createLine([ 'label','Make links between:'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.createLine([ 'label','Amino acids and DNA/RNA if', 'widget','REVIEW_MAKE_CONNECTIVITY'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.createLine([ 'label','Sugar-sugar and sugar-peptide if', 'widget','REVIEW_MAKE_SUGAR'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.createLine([ 'label','All others if', 'widget','REVIEW_MAKE_LINK'], toggle=['SETUP_GEOMETRIC_RESTRAINTS','open',[True]]) self.closeSubFrame() # ---------------------------------------------------------------------- # def show_NCS_GROUP_LIST(self): # par = self.container.controlParameters # gui = self.container.guiParameters # return gui.SETUP_NCS_RESTRAINTS and not par.IFAUTONCS._value # def drawSetupNCSRestraints(self): # self.openSubFrame( # frame=True, # toggle=['REFINE_TYPE','hide',['RIGID','UNRE']]) # self.closeSubFrame() # self.openSubFrame( # frame=True, # toggle=['REFINE_TYPE','hide',['RIGID','UNRE']]) # self.createLine([ # 'widget','SETUP_NCS_RESTRAINTS', # 'advice','Setup Non-Crystallographic Symmetry (NCS) Restraints']) # self.createLine([ # 'widget','IFAUTONCS', # 'label','use automatically generated', # 'widget','AUTONCS_MODE', # 'label','NCS restraints'], # toggle=['SETUP_NCS_RESTRAINTS','open',[True]]) # self.createLine([ # 'widget','NCS_GROUP_LIST'], # toggleFunction=[self.show_NCS_GROUP_LIST,['SETUP_NCS_RESTRAINTS','IFAUTONCS']]) # self.closeSubFrame() # ---------------------------------------------------------------------- def drawSetupNCSRestraints(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','hide',['RIGID','UNRE']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','hide',['RIGID','UNRE']]) self.createLine([ 'widget','SETUP_NCS_RESTRAINTS', 'advice','Setup Non-Crystallographic Symmetry (NCS) Restraints']) self.createLine([ 'widget','IFAUTONCS', 'label','use automatically generated', 'widget','AUTONCS_MODE', 'label','NCS restraints'], toggle=['SETUP_NCS_RESTRAINTS','open',[True]]) self.closeSubFrame() # ---------------------------------------------------------------------- def show_EXTERNAL_NCYCLES(self): par = self.container.controlParameters gui = self.container.guiParameters return gui.REFINEMENT_PARAMETERS and par.RUN_COOT_FW._value def show_MATRIX_WEIGHT(self): par = self.container.controlParameters gui = self.container.guiParameters return gui.REFINEMENT_PARAMETERS and not par.AUTO_WEIGHTING._value def show_PHASE_BBLUR(self): inp = self.container.inputData par = self.container.controlParameters gui = self.container.guiParameters return gui.REFINEMENT_PARAMETERS and str(par.INPUT_PHASE) in ['PHASE','HL'] # ---------------------------------------------------------------------- def drawRefinementParametersREST(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['REST']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['REST']]) self.createLine([ 'widget','REFINEMENT_PARAMETERS', 'advice','Refinement Parameters']) self.createLine([ 'label','Do', 'widget','NCYCLES', 'label','cycles of maximum likelihood restrained refinement'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label',' in each Refmac run and', 'widget','EXTERNAL_NCYCLES', 'label','cycle(s) of Coot:findwaters'], toggleFunction=[self.show_EXTERNAL_NCYCLES,['REFINEMENT_PARAMETERS','RUN_COOT_FW']]) self.createLine([ 'label','Use hydrogen atoms:', 'widget','MAKE_HYDROGEN', 'label','and', 'widget','MAKE_HOUT', 'label','output to coordinate file'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'widget','EXCLUDE_RESOLUTION', 'label','Resolution range from minimum', 'widget','EXCLUDE_RESOLUTION_MIN', 'label',' to ', 'widget','EXCLUDE_RESOLUTION_MAX'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'widget','AUTO_WEIGHTING', 'label','Use automatic weighting', 'widget','EXPERIMENTAL_WEIGHTING', 'label','Use experimental sigmas to weight Xray terms'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label','Use weighting term', 'widget','MATRIX_WEIGHT'], toggleFunction=[self.show_MATRIX_WEIGHT,['REFINEMENT_PARAMETERS','AUTO_WEIGHTING']]) self.createLine([ 'widget','IFJELLY', 'label','use jelly-body refinement with sigma', 'widget','JELLY_SIGMA'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label','Refine', 'widget','B_REFINEMENT_MODE', 'label','temperature factors'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'widget','EXCLUDE_FREER', 'label','Exclude data with freeR label', 'widget','FREERFLAG', 'label','with value of', 'widget','EXCLUDE_FREER_VALUE'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label','Blurring factors for input phase FOM SC', 'widget','PHASE_SCBLUR', 'label','B', 'widget','PHASE_BBLUR'], toggleFunction=[self.show_PHASE_BBLUR,['REFINEMENT_PARAMETERS','INPUT_PHASE']]) self.closeSubFrame() # ---------------------------------------------------------------------- def drawRefinementParametersUNRE(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['UNRE']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['UNRE']]) self.createLine([ 'widget','REFINEMENT_PARAMETERS', 'advice','Refinement Parameters']) self.createLine([ 'label','Do', 'widget','NCYCLES', 'label','cycles of maximum likelihood unrestrained refinement'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label',' in each Refmac run and', 'widget','EXTERNAL_NCYCLES', 'label','cycle(s) of Coot:findwaters'], toggleFunction=[self.show_EXTERNAL_NCYCLES,['REFINEMENT_PARAMETERS','RUN_COOT_FW']]) self.createLine([ 'label','Use hydrogen atoms:', 'widget','MAKE_HYDROGEN', 'label','and', 'widget','MAKE_HOUT', 'label','output to coordinate file'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'widget','EXCLUDE_RESOLUTION', 'label','Resolution range from minimum', 'widget','EXCLUDE_RESOLUTION_MIN', 'label',' to ', 'widget','EXCLUDE_RESOLUTION_MAX'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'widget','AUTO_WEIGHTING', 'label','Use automatic weighting', 'widget','EXPERIMENTAL_WEIGHTING', 'label','Use experimental sigmas to weight Xray terms'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label','Use weighting term', 'widget','MATRIX_WEIGHT'], toggleFunction=[self.show_MATRIX_WEIGHT,['REFINEMENT_PARAMETERS','AUTO_WEIGHTING']]) self.createLine([ 'label','Refine', 'widget','B_REFINEMENT_MODE', 'label','temperature factors'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'widget','EXCLUDE_FREER', 'label','Exclude data with freeR label', 'widget','FREERFLAG', 'label','with value of', 'widget','EXCLUDE_FREER_VALUE'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label','Blurring factors for input phase FOM SC', 'widget','PHASE_SCBLUR', 'label','B', 'widget','PHASE_BBLUR'], toggleFunction=[self.show_PHASE_BBLUR,['REFINEMENT_PARAMETERS','INPUT_PHASE']]) self.closeSubFrame() # ---------------------------------------------------------------------- def drawRefinementParametersRIGID(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['RIGID']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['RIGID']]) self.createLine([ 'widget','REFINEMENT_PARAMETERS', 'advice','Refinement Parameters']) self.createLine([ 'label','Do', 'widget','RIGID_NCYCLES', 'label','cycles of maximum likelihood rigid body refinement'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label','Use hydrogen atoms:', 'widget','MAKE_HYDROGEN', 'label','and', 'widget','MAKE_HOUT', 'label','output to coordinate file'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'widget','EXCLUDE_RESOLUTION', 'label','Resolution range from minimum', 'widget','EXCLUDE_RESOLUTION_MIN', 'label',' to ', 'widget','EXCLUDE_RESOLUTION_MAX'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'widget','AUTO_WEIGHTING', 'label','Use automatic weighting', 'widget','EXPERIMENTAL_WEIGHTING', 'label','Use experimental sigmas to weight Xray terms'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label','Use weighting term', 'widget','MATRIX_WEIGHT'], toggleFunction=[self.show_MATRIX_WEIGHT,['REFINEMENT_PARAMETERS','AUTO_WEIGHTING']]) self.createLine([ 'label','Refine overall B-factor'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'widget','EXCLUDE_FREER', 'label','Exclude data with freeR label', 'widget','FREERFLAG', 'label','with value of', 'widget','EXCLUDE_FREER_VALUE'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label','Blurring factors for input phase FOM SC', 'widget','PHASE_SCBLUR', 'label','B', 'widget','PHASE_BBLUR'], toggleFunction=[self.show_PHASE_BBLUR,['REFINEMENT_PARAMETERS','INPUT_PHASE']]) self.closeSubFrame() # ---------------------------------------------------------------------- def drawRefinementParametersTLS(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['TLS']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['TLS']]) self.createLine([ 'widget','REFINEMENT_PARAMETERS', 'advice','Refinement Parameters']) self.createLine([ 'label','Do', 'widget','NCYCLES', 'label','cycles of maximum likelihood restrained refinement after TLS refinement'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label','Use hydrogen atoms:', 'widget','MAKE_HYDROGEN', 'label','and', 'widget','MAKE_HOUT', 'label','output to coordinate file'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'widget','EXCLUDE_RESOLUTION', 'label','Resolution range from minimum', 'widget','EXCLUDE_RESOLUTION_MIN', 'label',' to ', 'widget','EXCLUDE_RESOLUTION_MAX'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'widget','AUTO_WEIGHTING', 'label','Use automatic weighting', 'widget','EXPERIMENTAL_WEIGHTING', 'label','Use experimental sigmas to weight Xray terms'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label','Use weighting term', 'widget','MATRIX_WEIGHT'], toggleFunction=[self.show_MATRIX_WEIGHT,['REFINEMENT_PARAMETERS','AUTO_WEIGHTING']]) self.createLine([ 'widget','IFJELLY', 'label','use jelly-body refinement with sigma', 'widget','JELLY_SIGMA'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label','Refine', 'widget','B_REFINEMENT_MODE', 'label','temperature factors'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'widget','EXCLUDE_FREER', 'label','Exclude data with freeR label', 'widget','FREERFLAG', 'label','with value of', 'widget','EXCLUDE_FREER_VALUE'], toggle=['REFINEMENT_PARAMETERS','open',[True]]) self.createLine([ 'label','Blurring factors for input phase FOM SC', 'widget','PHASE_SCBLUR', 'label','B', 'widget','PHASE_BBLUR'], toggleFunction=[self.show_PHASE_BBLUR,['REFINEMENT_PARAMETERS','INPUT_PHASE']]) self.closeSubFrame() # ---------------------------------------------------------------------- def show_PROSMART_STRAND(self): par = self.container.controlParameters gui = self.container.guiParameters return gui.EXTERNAL_RESTRAINTS and str(par.PROSMART_MODE) == 'SECSTR' def drawExternalRestraints(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','hide',['RIGID','UNRE']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','hide',['RIGID','UNRE']]) self.createLine([ 'widget','EXTERNAL_RESTRAINTS', 'advice','External Restraints']) self.createLine([ 'widget','PROSMART_HELIX', 'label','Apply Prosmart helix restraints, and', 'widget','PROSMART_STRAND', 'label','Apply Prosmart strand restraints'], toggleFunction=[self.show_PROSMART_STRAND,['EXTERNAL_RESTRAINTS','PROSMART_MODE']]) self.createLine([ 'widget','IFEXTREST_SCALE', 'label','Apply external restraints with weight', 'widget','EXTREST_SCALE', 'label','and', 'widget','IFEXTREST_GMWT', 'label','apply Geman-McClure weight', 'widget','EXTREST_GMWT'], toggle=['EXTERNAL_RESTRAINTS','open',[True]]) self.createLine([ 'widget','IFEXTREST_DMAX', 'label','Apply maximum external restraint distance', 'widget','EXTREST_DMAX', 'label','and', 'widget','IFEXTREST_USEMAIN', 'label',' apply to main chain only'], toggle=['EXTERNAL_RESTRAINTS','open',[True]]) self.closeSubFrame() # ---------------------------------------------------------------------- def drawIdealisationParameters(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['IDEA']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['IDEA']]) self.createLine([ 'widget','IDEALISATION_PARAMETERS', 'advice','Idealisation Parameters']) self.createLine([ 'label','Do', 'widget','NCYCLES', 'label','cycles of idealisation'], toggle=['IDEALISATION_PARAMETERS','open',[True]]) self.createLine([ 'label','Use hydrogen atoms:', 'widget','MAKE_HYDROGEN', 'label','and', 'widget','MAKE_HOUT', 'label','output to coordinate file'], toggle=['IDEALISATION_PARAMETERS','open',[True]]) self.closeSubFrame() # ---------------------------------------------------------------------- def drawCootParameters(self): self.openSubFrame( frame=True, toggle=['RUN_COOT_FW','open',[True]]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['RUN_COOT_FW','open',[True]]) self.createLine([ 'widget','COOT_PARAMETERS', 'advice','Coot Parameters']) self.createLine([ 'label','Add waters where DELFWT map greater than ', 'widget','COOT_SIGMA_ADD', 'label','sigma'], toggle=['COOT_PARAMETERS','open',[True]]) self.createLine([ 'label','Remove waters where FWT map less than ', 'widget','COOT_SIGMA_REMOVE', 'label','sigma'], toggle=['COOT_PARAMETERS','open',[True]]) self.closeSubFrame() # ---------------------------------------------------------------------- def drawTLSParameters(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['TLS']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['TLS']]) self.createLine([ 'widget','TLS_PARAMETERS', 'advice','TLS Parameters']) self.createLine([ 'label','Number of cycles of TLS refinement', 'widget','TLS_NCYCLES'], toggle=['TLS_PARAMETERS','open',[True]]) self.createLine([ 'widget','IFBFAC_SET', 'label','Set initial Bfactors to', 'widget','BFAC_SET', 'label','(numeric value unimportant)'], toggle=['TLS_PARAMETERS','open',[True]]) self.createLine([ 'widget','IFADDU', 'label','Add TLS contribution to XYZOUT (B factors and ANISOU lines)'], toggle=['TLS_PARAMETERS','open',[True]]) self.closeSubFrame() # ---------------------------------------------------------------------- def show_MONI_LEVEL(self): inp = self.container.inputData par = self.container.controlParameters gui = self.container.guiParameters return gui.MONITORING_AND_OUTPUT_OPTIONS and not str(par.REFINE_TYPE) == 'RIGID' def show_MONI_TORSION(self): inp = self.container.inputData par = self.container.controlParameters gui = self.container.guiParameters return gui.MONITORING_AND_OUTPUT_OPTIONS and not str(par.REFINE_TYPE) == 'UNRE' def show_EXTEND_MAP(self): par = self.container.controlParameters gui = self.container.guiParameters return gui.MONITORING_AND_OUTPUT_OPTIONS and par.IF_MAPOUT._value # ---------------------------------------------------------------------- def drawMonitoringAndOutputOptions(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','hide',['REVIEW','IDEA']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','hide',['REVIEW','IDEA']]) self.createLine([ 'widget','MONITORING_AND_OUTPUT_OPTIONS', 'advice','Monitoring and Output Options']) self.createLine([ 'widget','IFSHARP', 'label','Perform map sharpening. Manually set B value', 'widget','B_SHARP', 'label','and/or alpha value', 'widget','AL_SHARP'], toggle=['MONITORING_AND_OUTPUT_OPTIONS','open',[True]]) self.createLine([ 'label','Output', 'widget','MONI_LEVEL', 'label','monitoring statistics'], toggleFunction=[self.show_MONI_LEVEL,['MONITORING_AND_OUTPUT_OPTIONS','REFINE_TYPE']]) self.createLine([ 'label','Sigma cutoffs for monitoring levels..'], toggleFunction=[self.show_MONI_TORSION,['MONITORING_AND_OUTPUT_OPTIONS','REFINE_TYPE']]) self.createLine([ 'label','Torsion', 'label','Distance', 'label','Angle', 'label','Planarity', 'label','vanDerWaals'], toggleFunction=[self.show_MONI_TORSION,['MONITORING_AND_OUTPUT_OPTIONS','REFINE_TYPE']]) self.createLine([ 'widget','MONI_TORSION', 'widget','MONI_DISTANCE', 'widget','MONI_ANGLE', 'widget','MONI_PLANE', 'widget','MONI_VANDERWAALS'], toggleFunction=[self.show_MONI_TORSION,['MONITORING_AND_OUTPUT_OPTIONS','REFINE_TYPE']]) self.createLine([ 'label','Chiral', 'label','Bfactor', 'label','Bsphere', 'label','Rbond', 'label','NCSr'], toggleFunction=[self.show_MONI_TORSION,['MONITORING_AND_OUTPUT_OPTIONS','REFINE_TYPE']]) self.createLine([ 'widget','MONI_CHIRAL', 'widget','MONI_BFACTOR', 'widget','MONI_BSPHERE', 'widget','MONI_RBOND', 'widget','MONI_NCSR'], toggleFunction=[self.show_MONI_TORSION,['MONITORING_AND_OUTPUT_OPTIONS','REFINE_TYPE']]) self.createLine([ 'widget','IF_MAPOUT', 'label','Generate weighted difference maps files in', 'widget','MAPOUT_FORMAT', 'label','format'], toggle=['MONITORING_AND_OUTPUT_OPTIONS','open',[True]]) self.createLine([ 'widget','EXTEND_MAP', 'label','Extend map to cover molecule with border', 'widget','MAP_BORDER'], toggleFunction=[self.show_EXTEND_MAP,['MONITORING_AND_OUTPUT_OPTIONS','IF_MAPOUT']]) self.createLine([ 'label','Fwt map', 'widget','MAPOUT1'], toggleFunction=[self.show_EXTEND_MAP,['MONITORING_AND_OUTPUT_OPTIONS','IF_MAPOUT']]) self.createLine([ 'label','DelFwt map', 'widget','MAPOUT2'], toggleFunction=[self.show_EXTEND_MAP,['MONITORING_AND_OUTPUT_OPTIONS','IF_MAPOUT']]) self.closeSubFrame() # ---------------------------------------------------------------------- def show_BULK_SCALING_RESOLUTION_MIN(self): par = self.container.controlParameters gui = self.container.guiParameters return gui.SCALING and str(par.BULK_SOLVENT_SCALING) == 'BULK' def show_SIMPLE_SCALING_RESOLUTION_MIN(self): par = self.container.controlParameters gui = self.container.guiParameters return gui.SCALING and str(par.BULK_SOLVENT_SCALING) == 'SIMPLE' def show_SOLVENT_VDWPROB(self): par = self.container.controlParameters gui = self.container.guiParameters return gui.SCALING and par.IF_SOLVENT._value # ---------------------------------------------------------------------- def drawScaling(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','hide',['REVIEW','IDEA']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','hide',['REVIEW','IDEA']]) self.createLine([ 'widget','SCALING', 'advice','Scaling']) self.createLine([ 'label','Use', 'widget','BULK_SOLVENT_SCALING', 'label','scaling'], toggle=['SCALING','open',[True]]) self.createLine([ 'label','Bulk solvent scaling for resolution range', 'widget','BULK_SCALING_RESOLUTION_MIN', 'label',' to ', 'widget','BULK_SCALING_RESOLUTION_MAX'], toggleFunction=[self.show_BULK_SCALING_RESOLUTION_MIN,['SCALING','BULK_SOLVENT_SCALING']]) self.createLine([ 'label','Simple solvent scaling for resolution range', 'widget','SIMPLE_SCALING_RESOLUTION_MIN', 'label',' to ', 'widget','SIMPLE_SCALING_RESOLUTION_MAX'], toggleFunction=[self.show_SIMPLE_SCALING_RESOLUTION_MIN,['SCALING','BULK_SOLVENT_SCALING']]) self.createLine([ 'label','Determine scaling using the', 'widget','SCALING_REF_SET', 'label','set of reflections ', 'widget','SCALING_EXPE_SIGMA', 'label','Use experimental sigmas'], toggle=['SCALING','open',[True]]) self.createLine([ 'widget','IF_SOLVENT', 'label','Calculate the contribution from the solvent region'], toggle=['SCALING','open',[True]]) self.createLine([ 'label','For the solvent mask calculation:'], toggleFunction=[self.show_SOLVENT_VDWPROB,['SCALING','IF_SOLVENT']]) self.createLine([ 'label',' Increase VDW radius of non-ion atoms by', 'widget','SOLVENT_VDWPROB'], toggleFunction=[self.show_SOLVENT_VDWPROB,['SCALING','IF_SOLVENT']]) self.createLine([ 'label',' Increase ionic radius of potential ion atoms by', 'widget','SOLVENT_IONPROB'], toggleFunction=[self.show_SOLVENT_VDWPROB,['SCALING','IF_SOLVENT']]) self.createLine([ 'label',' Shrink the area of the mask by', 'widget','SOLVENT_RSHRINK', 'label','after calculation'], toggleFunction=[self.show_SOLVENT_VDWPROB,['SCALING','IF_SOLVENT']]) self.createLine([ 'widget','SCALING_IF_FIXB', 'label','For low resolution structures, fix the B values of Babinet bulk solvent to', 'widget','SCALING_FIXB_BBULK'], toggleFunction=[self.show_BULK_SCALING_RESOLUTION_MIN,['SCALING','BULK_SOLVENT_SCALING']]) self.closeSubFrame() # ---------------------------------------------------------------------- def drawRigidDomainsDefinition(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['RIGID']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','open',['RIGID']]) self.createLine([ 'widget','RIGID_DOMAINS_DEFINITION', 'advice','Rigid Domains Definition']) self.createLine([ 'widget','RIGID_GROUP_LIST'], toggle=['RIGID_DOMAINS_DEFINITION','open',[True]]) self.closeSubFrame() # ---------------------------------------------------------------------- def show_IFISO(self): inp = self.container.inputData par = self.container.controlParameters gui = self.container.guiParameters return gui.GEOMETRIC_PARAMETERS and str(par.REFINE_TYPE) in ['REST','UNRE'] and str(par.B_REFINEMENT_MODE) in ['ANIS','MIXED'] def show_BLIM(self): inp = self.container.inputData par = self.container.controlParameters gui = self.container.guiParameters return gui.GEOMETRIC_PARAMETERS and not str(par.REFINE_TYPE) == 'IDEA' # ---------------------------------------------------------------------- def drawGeometricParameters(self): self.openSubFrame( frame=True, toggle=['REFINE_TYPE','hide',['RIGID','UNRE']]) self.closeSubFrame() self.openSubFrame( frame=True, toggle=['REFINE_TYPE','hide',['RIGID','UNRE']]) self.createLine([ 'widget','GEOMETRIC_PARAMETERS', 'advice','Geometric parameters']) self.createLine([ 'label','Restraint', 'label','Overall wt', 'label','Sigmas'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'widget','IFDIST', 'label','Distance', 'widget','WDSKAL'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'widget','IFANGL', 'label','Angle', 'widget','ANGLE_SCALE'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'label',' ', 'label',' ', 'label','main chain', 'label','main chain', 'label','side chain', 'label','side chain'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'label',' ', 'label',' ', 'label','bond', 'label','angle', 'label','bond', 'label','angle'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'widget','IFTMP', 'label','Bfactor', 'widget','WBSKAL', 'widget','SIGB1', 'widget','SIGB2', 'widget','SIGB3', 'widget','SIGB4'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'label',' ', 'label',' ', 'label','peptide', 'label','aromatic'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'widget','IFPLAN', 'label','Plane', 'widget','WPSKAL', 'widget','SIGPP', 'widget','SIGPA'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'label',' ', 'label',' ', 'label','chiral'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'widget','IFCHIR', 'label','Chiral', 'widget','WCSKAL', 'widget','SIGC'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'widget','IFTORS', 'label','Torsion', 'widget','WTSKAL'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'label',' ', 'label',' ', 'label','tight', 'label','medium', 'label','loose'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'widget','IFNCSR', 'label','NCS position', 'widget','WSSKAL', 'widget','SIGSP1', 'widget','SIGSP2', 'widget','SIGSP3'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'label',' NCS Bfactor ', 'label',' ', 'widget','SIGSB1', 'widget','SIGSB2', 'widget','SIGSB3'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'label','VDW contacts'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'widget','IFVAND', 'label','VDW contacts', 'widget','WVSKAL'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'label','Sigmas for types of non-bonding interaction..'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'label','Non-bonding', 'widget','WAND_SIGMA_VDW', 'label','H-bonding', 'widget','WAND_SIGMA_HBOND', 'label','metal-ion interactions', 'widget','WAND_SIGMA_METAL', 'label','1-4 atoms in torsion', 'widget','WAND_SIGMA_TORS'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'label','Set increments for non-bonded interactions..'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'label','1-4 atoms in torsion', 'widget','WAND_INCR_TORS', 'label','H-bond pair (not hydrogen atom)', 'widget','WAND_INCR_ADHB', 'label','H-bonded pair (one is hydrogen atom)', 'widget','WAND_INCR_AHHB'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'widget','IFISO', 'label','Anisotropic refinement', 'label',' ', 'label','sphericity', 'label','bond projection'], toggleFunction=[self.show_IFISO,['GEOMETRIC_PARAMETERS','REFINE_TYPE','B_REFINEMENT_MODE']]) self.createLine([ 'label',' ', 'label',' ', 'widget','SPHERICITY', 'widget','RBOND'], toggleFunction=[self.show_IFISO,['GEOMETRIC_PARAMETERS','REFINE_TYPE','B_REFINEMENT_MODE']]) self.createLine([ 'label','Set limits for B values..'], toggle=['GEOMETRIC_PARAMETERS','open',[True]]) self.createLine([ 'widget','BLIM', 'label','Limit B value range from', 'widget','BLIM_MIN', 'label','to', 'widget','BLIM_MAX'], toggleFunction=[self.show_BLIM,['GEOMETRIC_PARAMETERS','REFINE_TYPE']]) self.closeSubFrame()