""" parrot.py: CCP4 GUI Project Copyright (C) 2010 University of York This library is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License version 3, modified in accordance with the provisions of the license to address the requirements of UK law. You should have received a copy of the modified GNU Lesser General Public License along with this library. If not, copies may be downloaded from http://www.ccp4.ac.uk/ccp4license.php 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 Lesser General Public License for more details. """ from CCP4PluginScript import CPluginScript import CCP4Utils import CCP4ErrorHandling, CCP4XtalData class parrot(CPluginScript): TASKMODULE = 'model_building' # Where this plugin will appear on the gui TASKTITLE = 'Parrot' # A short title for gui menu TASKNAME = 'parrot' # Task name - should be same as class name TASKCOMMAND = 'cparrot' # The command to run the executable TASKVERSION= 0.0 # Version of this plugin COMTEMPLATE = None # The program com file template COMTEMPLATEFILE = None # Name of file containing com file template PERFORMANCECLASS = 'CExpPhasPerformance' # Only FOM is relevent MAINTAINER = 'kevin.cowtan@york.ac.uk' def processInputFiles(self): import CCP4XtalData cols = [['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN],'ABCD'] if self.container.inputData.FREERFLAG.isSet(): cols.append('FREERFLAG') if self.container.inputData.F_PHI.isSet(): cols.append('F_PHI') self.hklin,columns,error = self.makeHklin0(cols) if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING: return CPluginScript.FAILED self.refHklin = None conPars = self.container.controlParameters if conPars.F_SIGF_REF.isSet() and conPars.ABCD_REF.isSet() and conPars.XYZIN_REF.isSet() and \ conPars.F_SIGF_REF.exists() and conPars.ABCD_REF.exists() and conPars.XYZIN_REF.exists(): self.refHklin,error = self.makeHklin([['F_SIGF_REF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN],'ABCD_REF']) if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING: self.refHklin = None if len(self.container.inputData.SEQIN)==1: self.seqin = str(self.container.inputData.SEQIN[0]) else: import os self.seqin = os.path.join(self.workDirectory,'seqin.fasta') self.container.inputData.SEQIN.mergeFiles(self.seqin) return CPluginScript.SUCCEEDED def processOutputFiles(self): import CCP4XtalData # Need to set the expected content flag for phases data self.container.outputData.ABCDOUT.contentFlag.set(CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL) print 'parrot.processOutputFiles jobNumberString',self.jobNumberString() self.container.outputData.ABCDOUT.annotation = self.jobNumberString() + ' Phases from density modification' self.container.outputData.FPHIOUT.contentFlag.set(1) self.container.outputData.FPHIOUT.subType.set(1) self.container.outputData.FPHIOUT.annotation = self.jobNumberString() + ' Map coefficients from density modification' # extend XML output from lxml import etree rootNode = etree.Element("ParrotResult") with open(self.xmlout,'r') as xmlFile: rootNode = etree.fromstring(xmlFile.read()) smartieNode = etree.SubElement(rootNode,'SmartieGraphs') self.scrapeSmartieGraphs(smartieNode) with open(self.xmlout,'w') as xmlFile: xmlFile.write(etree.tostring(rootNode,pretty_print=True)) # performance data final_fom = float(rootNode.xpath('//ParrotResult/Final/MeanFOM')[0].text) self.container.outputData.PERFORMANCE.FOM = final_fom # error checking error = self.splitHklout(['FPHIOUT','ABCDOUT'],['parrot.F_phi.F,parrot.F_phi.phi','parrot.ABCD.A,parrot.ABCD.B,parrot.ABCD.C,parrot.ABCD.D']) if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING: return CPluginScript.FAILED else: return CPluginScript.SUCCEEDED def scrapeSmartieGraphs(self, smartieNode): import sys, os import CCP4Utils smartiePath = os.path.join(CCP4Utils.getCCP4I2Dir(),'smartie') sys.path.append(smartiePath) import smartie from lxml import etree logfile = smartie.parselog(self.makeFileName('LOG')) for smartieTable in logfile.tables(): if smartieTable.ngraphs() > 0: tableelement = self.xmlForSmartieTable(smartieTable, smartieNode) return def xmlForSmartieTable(self, table, parent): import MGQTmatplotlib tableetree = MGQTmatplotlib.CCP4LogToEtree(table.rawtable()) parent.append(tableetree) return tableetree def makeCommandAndScript(self): import os import CCP4XtalData self.hklout = os.path.join(self.workDirectory,"hklout.mtz") self.appendCommandLine(['-stdin']) # INPUT DATA self.appendCommandScript("mtzin "+self.hklin) self.appendCommandScript("colin-fo F_SIGF_F,F_SIGF_SIGF") self.container.inputData.ABCD.setContentFlag() if self.container.inputData.ABCD.contentFlag == CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL: self.appendCommandScript("colin-hl ABCD_HLA,ABCD_HLB,ABCD_HLC,ABCD_HLD") else: self.appendCommandScript("colin-phifom ABCD_PHI,ABCD_FOM") if self.container.inputData.FREERFLAG.isSet(): self.appendCommandScript("colin-free FREERFLAG_FREER") if self.container.inputData.F_PHI.isSet(): self.appendCommandScript("colin-fc F_PHI_F,F_PHI_PHI") self.appendCommandScript("seqin %s"%(self.seqin)) if self.container.inputData.XYZIN_MODE=='ha' and self.container.inputData.XYZIN_HA.isSet(): self.appendCommandScript("pdbin-ha %s"%(str(self.container.inputData.XYZIN_HA.fullPath))) elif self.container.inputData.XYZIN_MODE=='mr' and self.container.inputData.XYZIN_MR.isSet(): self.appendCommandScript("pdbin-mr %s"%(str(self.container.inputData.XYZIN_MR.fullPath))) # OUTPUT DATA self.xmlout = self.makeFileName('PROGRAMXML') self.appendCommandScript("mtzout "+self.hklout) self.appendCommandScript("xmlout "+self.xmlout) # CONTROL PARAMETERS if self.container.controlParameters.CYCLES.isSet(): self.appendCommandScript("cycles %s"%(str(self.container.controlParameters.CYCLES))) if self.container.controlParameters.ANISOTROPY_CORRECTION: self.appendCommandScript("anisotropy-correction") if self.container.controlParameters.RESOLUTION.isSet(): self.appendCommandScript("resolution %s"%(str(self.container.controlParameters.RESOLUTION))) if self.container.controlParameters.SOLVENT_CONTENT.isSet(): self.appendCommandScript("solvent-content %s"%(str(self.container.controlParameters.SOLVENT_CONTENT))) if self.container.controlParameters.NCS_MASK_FILTER_RADIUS.isSet(): self.appendCommandScript("ncs-mask-filter-radius %s"%(str(self.container.controlParameters.NCS_MASK_FILTER_RADIUS))) if self.container.controlParameters.VERBOSE.isSet(): self.appendCommandScript("verbose %s"%(str(self.container.controlParameters.VERBOSE))) # REFERENCE DATA if self.refHklin is not None: self.appendCommandScript("colin-ref-fo F,SIGF") if self.container.controlParameters.F_SIGF_REF.contentFlag == CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL: self.appendCommandScript("colin-ref-hl HLA,HLB,HLC,HLD") else: self.appendCommandScript("colin-ref-phifom PHI,FOM") self.appendCommandScript("pdbin-ref %s"%(str(self.container.controlParameters.XYZIN_REF.fullPath))) return CPluginScript.SUCCEEDED # ---------------------------------------------------------------------- # Function to return list of names of exportable MTZ(s) ''' def exportJobFile(jobId=None,mode=None): import os import CCP4Modules import CCP4XtalData # Devise name for the merged file and check if it has already been created jobDir = CCP4Modules.PROJECTSMANAGER().jobDirectory(jobId=jobId,create=False) exportFile = os.path.join(jobDir,'exportMtz.mtz') if os.path.exists(exportFile): return exportFile # Get the source reflection data either from aimless or an imported file # getSourceReflectionFile() returns a dict with elements: fileName, source, jobNumber reflnInfo = CCP4Modules.PROJECTSMANAGER().getSourceReflectionFile(jobId = jobId, jobParamName='F_SIGF') print 'parrot.exportJobFile getSourceReflectionFile',reflnInfo if reflnInfo['fileName'] is None: return None # Query database for filenames and job info for the input and ouptput phase objects db = CCP4Modules.PROJECTSMANAGER().db() abcdInfo = db.getJobFilesInfo(jobId=jobId,jobParamName='ABCD',input=True) jN2 = abcdInfo[0]['jobnumber']+'_'+abcdInfo[0]['taskname'] abcdOutInfo = db.getJobFilesInfo(jobId=jobId,jobParamName='ABCDOUT') jN3 = abcdOutInfo[0]['jobnumber']+'_'+abcdOutInfo[0]['taskname'] print 'parrot.exportJobFile abcdInfo',abcdInfo print 'parrot.exportJobFile abcdOutInfo',abcdOutInfo print 'parrot.exportJobFile runCad:',exportFile,abcdInfo[0]['fullPath'], abcdOutInfo[0]['fullPath'] # Custom input to runCad to set output column names comLines = [ ] # Beware the input phases not necessarilly HL if abcdInfo[0].get('fileContent',None) is not None: fC = abcdInfo[0]['fileContent'] else: p = CCP4XtalData.CPhsDataFile(abcdInfo[0]['fullPath']) p.setContentFlag() fC = int(p.contentFlag) # Use CAD LABOUT line to set column labels in export file if fC == 1: comLines.append ( 'LABOUT FILENUMBER 2 E1=HLA_'+jN2+' E2=HLB_'+jN2+' E3=HLC_'+jN2+' E4=HLD_'+jN2 ) else: comLines.append ( 'LABOUT FILENUMBER 2 E1=PHI_'+jN2+' E2=FOM_'+jN2 ) # Parrot output is always HLs? comLines.append ( 'LABOUT FILENUMBER 3 E1=HLA_'+jN3+' E2=HLB_'+jN3+' E3=HLC_'+jN3+' E4=HLD_'+jN3 ) # Create an CMtzDataFile object and initialise with the refln data file m = CCP4XtalData.CMtzDataFile(reflnInfo['fileName']) #print m.runCad.__doc__ #Print out docs for the function outfile,err = m.runCad(exportFile,[ abcdInfo[0]['fullPath'], abcdOutInfo[0]['fullPath'] ] ,comLines ) print 'aimless_pipe.exportJobFile',outfile,err.report() return outfile ''' def exportJobFileMenu(jobId=None): # Return a list of items to appear on the 'Export' menu - each has three subitems: # [ unique identifier - will be mode argument to exportJobFile() , menu item , mime type (see CCP4CustomMimeTypes module) ] return [ [ 'complete_mtz' ,'MTZ file' , 'application/CCP4-mtz' ] ]