""" buccaneer.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 from CCP4Modules import PROCESSMANAGER import CCP4ErrorHandling class buccaneer_mr(CPluginScript): TASKMODULE = 'wrappers' # Where this plugin will appear on the gui TASKTITLE = 'Buccaneer_mr' # A short title for gui menu TASKNAME = 'buccaneer_mr' # Task name - should be same as class name TASKCOMMAND = 'cbuccaneer' # The command to execute, should be reachable TASKVERSION = 0.0 # Version of this plugin MAINTAINER = 'jon.agirre@york.ac.uk' def setProgramVersion(self): print 'buccaneer.getProgramVersion' return CPluginScript.setProgramVersion(self,'Buccaneer') def processInputFiles(self): import CCP4XtalData import CCP4Utils import os #print 'taskMakeHklin F_SIGF',self.container.inputData.F_SIGF,type(self.container.inputData.F_SIGF),self.container.inputData.F_SIGF.contentFlag if self.container.inputData.FWT_PHWT_IN.isSet(): if self.container.inputData.FREERFLAG.isSet(): self.hklin,columns,error = self.makeHklin0([['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN], 'ABCD', 'FREERFLAG', 'FWT_PHWT_IN' ]) print 'FREERFLAG is set, so joining all data objects' else : print 'FREERFLAG is not set, so joining the rest of the data objects' self.hklin,columns,error = self.makeHklin0([['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN], 'ABCD', 'FWT_PHWT_IN' ]) if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING: print 'ERROR creating input HKLIN with FWT_PHWT_IN' print error.report() return CPluginScript.FAILED else: if self.container.inputData.FREERFLAG.isSet(): self.hklin,columns,error = self.makeHklin0([['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN],'ABCD','FREERFLAG']) print 'FREERFLAG is set, so joining all data objects' else : print 'FREERFLAG is not set, so joining the rest of the data objects' self.hklin,columns,error = self.makeHklin0([['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN],'ABCD' ]) if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING: print 'ERROR creating input HKLIN' print error.report() return CPluginScript.FAILED if len(self.container.inputData.SEQIN)==1: self.seqin = str(self.container.inputData.SEQIN[0]) else: self.seqin = os.path.join(self.workDirectory,'seqin.fasta') self.container.inputData.SEQIN.mergeFiles(self.seqin) 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 return CPluginScript.SUCCEEDED def processOutputFiles(self): self.container.outputData.XYZOUT.annotation = 'Model built with Buccaneer' self.container.outputData.XYZOUT.subType=1 # self.setPerformanceData() return CPluginScript.SUCCEEDED def makeCommandAndScript(self): import os import CCP4XtalData self.appendCommandLine(['-stdin']) # INPUT DATA self.appendCommandScript("mtzin "+self.hklin) self.appendCommandScript("colin-fo F_SIGF_F,F_SIGF_SIGF") 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") self.appendCommandScript("seqin %s"%(self.seqin)) if self.container.inputData.XYZIN_MODE: if self.container.inputData.XYZIN.isSet(): self.appendCommandScript("pdbin %s"%(str(self.container.inputData.XYZIN.fullPath))) if self.container.controlParameters.KNOWN_STRUCTURE.isSet(): self.appendCommandScript("known-structure %s"%(self.container.controlParameters.KNOWN_STRUCTURE.__str__())) if self.container.inputData.XYZIN_SEQ.isSet(): self.appendCommandScript("pdbin-sequence-prior %s"%(str(self.container.inputData.XYZIN_SEQ.fullPath))) if self.container.inputData.FWT_PHWT_IN.isSet(): self.appendCommandScript( "colin-fc FWT_PHWT_IN_F,FWT_PHWT_IN_PHI" ) # OUTPUT DATA if self.container.outputData.XYZOUT.isSet(): self.appendCommandScript("pdbout %s"%(str(self.container.outputData.XYZOUT.fullPath))) self.appendCommandScript("xmlout %s"%(self.makeFileName('PROGRAMXML'))) # CONTROL PARAMETERS #if self.container.controlParameters.TITLE.isSet(): # self.appendCommandScript("title %s"%(str(self.container.controlParameters.TITLE))) 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.FAST: self.appendCommandScript("fast") if self.container.controlParameters.BUILD_SEMET: self.appendCommandScript("build-semet") if self.container.controlParameters.FIX_POSITION: self.appendCommandScript("fix-position") # if self.container.controlParameters.CORRELATION_MODE: # self.appendCommandScript("correlation-mode") # Kevin said that this option is handled automatically now if self.container.controlParameters.RESOLUTION.isSet(): self.appendCommandScript("resolution %s"%(str(self.container.controlParameters.RESOLUTION))) else: self.appendCommandScript("resolution 2.0") # I've added the default value here if self.container.controlParameters.SEQUENCE_RELIABILITY.isSet(): self.appendCommandScript("sequence-reliability %s"%(str(self.container.controlParameters.SEQUENCE_RELIABILITY))) if self.container.controlParameters.NEW_RESIDUE_NAME.isSet(): self.appendCommandScript("new-residue-name %s"%(str(self.container.controlParameters.NEW_RESIDUE_NAME))) if self.container.controlParameters.JOBS.isSet(): self.appendCommandScript("jobs %s"%(str(self.container.controlParameters.JOBS))) if self.container.controlParameters.VERBOSE.isSet(): self.appendCommandScript("verbose %s"%(str(self.container.controlParameters.VERBOSE))) if self.container.controlParameters.MODEL_SIGMA.isSet(): self.appendCommandScript( "model-filter" ) self.appendCommandScript( "model-filter-sigma %s"%(str(self.container.controlParameters.MODEL_SIGMA))) # Now we're going to determine if we need to trigger MR mode in Buccaneer # pbond and jonesie changed this to make it work like in i1 if self.container.controlParameters.PHSIN_TYPE == "mr": #self.appendCommandScript("mr-model") self.appendCommandScript("pdbin-mr %s"%str(self.container.inputData.MR_MODE_XYZIN.fullPath)) if self.container.controlParameters.MR_MODE_SIGMA.isSet(): self.appendCommandScript("mr-model-filter-sigma %s"%(str(self.container.controlParameters.MR_MODE_SIGMA))) if self.container.controlParameters.MR_MODE == "seed": self.appendCommandScript("mr-model-seed") self.appendCommandScript("mr-model-filter") else: if self.container.controlParameters.MR_MODE == "initialmodel": self.appendCommandScript("mr-model-filter") # REFERENCE DATA if self.refHklin is not None: self.appendCommandScript("colin-ref-fo F_SIGF_REF_F,F_SIGF_REF_SIGF") if self.container.controlParameters.F_SIGF_REF.contentFlag == CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL: self.appendCommandScript("colin-ref-hl ABCD_REF_HLA,ABCD_REF_HLB,ABCD_REF_HLC,ABCD_REF_HLD") else: self.appendCommandScript("colin-ref-phifom PHI,FOM") self.appendCommandScript("pdbin-ref %s"%(str(self.container.controlParameters.XYZIN_REF.fullPath))) return CPluginScript.SUCCEEDED