""" pipelines/phaser_simple/phaser_simple_gui.py Copyright (C) 2016 Newcastle University Author: Martin Noble """ from CCP4TaskWidget import CTaskWidget from PyQt4 import QtCore import phaser_pipeline_gui #------------------------------------------------------------------- class phaser_simple_gui(phaser_pipeline_gui.phaser_pipeline_gui): #------------------------------------------------------------------- # Subclass CTaskWidget to give specific task window TASKNAME = 'phaser_simple' TASKVERSION = 0.1 TASKMODULE='molecular_replacement' TASKTITLE='Basic Molecular Replacement - PHASER' SHORTTASKTITLE='Basic MR - PHASER' DESCRIPTION = '''Simple MR with optional refinement and rebuilding (Phaser)''' def __init__(self,*args,**kws): super(phaser_simple_gui,self).__init__(*args, **kws) def drawContents(self): self.setProgramHelpFile('phaser') self.drawPhaserFrontPage() self.openFolder(title='Simple options',drawFolder=self.drawSimpleOptionsFolder) self.openFolder(folderFunction='extraSteps', title='Extra steps',drawFolder=self.drawExtraStepsFolder) self.openFolder(folderFunction='keywords', title='Keywords', drawFolder=self.drawPhaserKeywordsFolder) #Override the phaser_pipeline front page drawer so as not to preent Ensemble List def drawPhaserFrontPage(self): self.openFolder(folderFunction='inputData') self.drawReflectionPanel() self.drawCompositionPanel() self.createLine(['subtitle','Search model']) self.openSubFrame(frame=True) self.createLine(['widget','XYZIN','label','Copies:','widget','NCOPIES']) self.connect(self.container.inputData.XYZIN,QtCore.SIGNAL('dataChanged'),self.XYZINchanged) id_rms = self.createLine( [ 'label', 'Similarity of ensemble to target:', 'widget', 'ID_RMS', 'label'] ) self.createLine( [ 'label', '', 'widget', 'SEARCHSEQUENCEIDENTITY' ], toggle = ['ID_RMS', 'open', [ 'ID' ] ], appendLine=id_rms ) self.createLine( [ 'label', '', 'widget', 'SEARCHRMS' ], toggle = ['ID_RMS', 'open', [ 'RMS' ] ], appendLine=id_rms ) # self.createLine(['label','Sequence identity to target (in range 0.0-1.0)','stretch','widget','SEARCHSEQUENCEIDENTITY']) self.closeSubFrame() self.createLine(['subtitle','Already placed coordinates','widget','INPUT_FIXED']) self.openSubFrame(frame=True,toggle=['INPUT_FIXED','open',[True]]) self.createLine(['widget','XYZIN_FIXED']) self.connect(self.container.inputData.INPUT_FIXED,QtCore.SIGNAL('dataChanged'),self.INPUT_FIXEDchanged) #This line has to come after the creation of the XYZIN_FIXED widget ...Duh ! self.INPUT_FIXEDchanged() id_rms = self.createLine( [ 'label', 'Similarity of fixed ensemble to target:', 'widget', 'FIXED_ID_RMS', 'label'] ) self.createLine( [ 'label', '', 'widget', 'FIXEDSEQUENCEIDENTITY' ], toggle = ['FIXED_ID_RMS', 'open', [ 'ID' ] ], appendLine=id_rms ) self.createLine( [ 'label', '', 'widget', 'FIXEDRMS' ], toggle = ['FIXED_ID_RMS', 'open', [ 'RMS' ] ], appendLine=id_rms ) def drawReflectionPanel(self): self.createLine( ['subtitle', 'Reflections' ]) self.openSubFrame(frame=True) self.drawReflections() self.closeSubFrame() def drawReflections(self): #A simple reflections panel, so that some choices can be moved to the "options" panel self.createLine ( [ 'widget', 'F_SIGF' ] ) self.createLine (['label','Use Intensity (I) or amplitude (F) ML target','stretch','widget', 'F_OR_I']) self.connect(self.container.inputData.F_SIGF,QtCore.SIGNAL('dataChanged'),self.F_SIGFchanged) self.F_SIGFchanged() def drawSimpleOptionsFolder(self): self.createLine( ['subtitle', 'Simple options' ]) self.openSubFrame(frame=True) self.createLine (['label','Resolution','stretch','widget','RESOLUTION_LOW','widget','RESOLUTION_HIGH']) self.createLine (['label', 'Spacegroups','stretch','widget', 'SGALT_SELECT',] ) self.drawSGChoice() self.closeSubFrame() def drawExtraStepsFolder( self ): self.createLine(['subtitle','Reference structure','If you know a structure in a similar crystal form, you may provide a reference structure,']) self.openSubFrame(frame=True) self.createLine(['widget','-browseDb', True, 'XYZIN_TARGET']) self.closeSubFrame() self.createLine(['subtitle','Fit and fill in coot','Optionally run COOT to fill and fit partial residues']) self.openSubFrame(frame=True) self.createLine(['widget','RUNCOOT','label','Run COOT to fill and fit partial residues']) self.closeSubFrame() self.createLine(['subtitle','Run refmac','Run REFMAC on top output solution']) self.openSubFrame(frame=True) self.createLine(['widget','RUNREFMAC','label','Run REFMAC on top output solution']) self.createLine ( [ 'widget', 'FREERFLAG' ],toggle=['RUNREFMAC','open',[True]] ) self.closeSubFrame() def INPUT_FIXEDchanged(self): if self.container.inputData.INPUT_FIXED: self.container.inputData.XYZIN_FIXED.setQualifiers({'allowUndefined':False,'mustExist':True}) else: self.container.inputData.XYZIN_FIXED.setQualifiers({'allowUndefined':True,'mustExist':False}) self.getWidget('XYZIN_FIXED').validate() def XYZINchanged(self): # check for REMARK PHASER cards in XYZIN cardFound = False if self.container.inputData.XYZIN.isSet(): with open (self.container.inputData.XYZIN.__str__(),'r') as pdbFile: for line in pdbFile: if "REMARK PHASER ENSEMBLE MODEL" in line: cardFound = True break elif line[0:4] == "ATOM": break if cardFound: self.container.inputData.ID_RMS.setQualifiers({'enumerators':['ID','RMS','CARD'], 'menuText':['sequence identity (in range 0.0-1.0)','RMS','read from header of PDB']}) self.container.inputData.ID_RMS.set('CARD') else: self.container.inputData.ID_RMS.setQualifiers({'enumerators':['ID','RMS']}) self.container.inputData.ID_RMS.set('ID') self.getWidget('ID_RMS').populateComboBox(self.container.inputData.ID_RMS) self.getWidget('ID_RMS').updateViewFromModel()