from CCP4PluginScript import CPluginScript from CCP4Modules import PROCESSMANAGER import CCP4ErrorHandling import sys class mrbump_basic(CPluginScript): TASKTITLE='MrBUMP Basic' TASKNAME = 'mrbump_basic' TASKMODULE= 'test' TASKCOMMAND = sys.executable TASKVERSION= 0.1 MAINTAINER = 'ronan.keegan@stfc.ac.uk' def processInputFiles(self): import CCP4XtalData error = None self.hklin = None dataObjects = [] #Append Observation with representation dependent on whether we are detwining on Is or not dataObjects += [['F_SIGF',CCP4XtalData.CObsDataFile.CONTENT_FLAG_FMEAN]] #Include FreeRflag if called for if self.container.inputData.FREERFLAG.isSet(): dataObjects += ['FREERFLAG'] self.hklin,error = self.makeHklin(dataObjects) if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING: return CPluginScript.FAILED else: return CPluginScript.SUCCEEDED def makeCommandAndScript(self): inp = self.container.inputData par = self.container.controlParameters gui = self.container.guiParameters out = self.container.outputData import CCP4Utils import os #keyin = "JOBID test_mrbump\n" #keyin += "LABIN F=F SIGF=SIGF FreeR_flag=FREER\n" #keyin += "MAPROGRAM clustalw2\n" #keyin += "MRPROGRAM molrep phaser\n" #keyin += "DOFASTA False\n" #keyin += "DOPHMMER True\n" #keyin += "DOHHPRED False\n" #keyin += "MDLU False\n" #keyin += "MDLD False\n" #keyin += "MDLC True\n" #keyin += "MDLM False\n" #keyin += "MDLP False\n" #keyin += "MDLS True\n" #keyin += "MRNUM 1\n" #keyin += "NCYC 10\n" #keyin += "TRYALL True\n" #keyin += "UPDATE False\n" #keyin += "PDBLOCAL /media/china/pdb\n" #keyin += "END\n" #keyin = "JOBID test_mrbump\n" #keyin += "LABIN F=F SIGF=SIGF FreeR_flag=FREER\n" keyin = "MAPROGRAM clustalw2\n" keyin += "MRPROGRAM phaser\n" keyin += "DOFASTA False\n" keyin += "DOPHMMER True\n" keyin += "DOHHPRED False\n" keyin += "RLEVEL 70\n" keyin += "PICKLE False\n" keyin += "MDLU False\n" keyin += "MDLD False\n" keyin += "MDLC False\n" keyin += "MDLM False\n" keyin += "MDLP False\n" keyin += "MDLS True\n" keyin += "USEPQS False\n" keyin += "MRNUM 5\n" keyin += "NCYC 30\n" keyin += "USEENSEM True\n" keyin += "GESE False\n" keyin += "TRYALL True\n" keyin += "UPDATE False\n" #keyin += "PDBLOCAL /media/china/pdb\n" keyin += "END\n" keyfile=os.path.join(self.getWorkDirectory(), "keywords.txt") kf=open(keyfile, "w") kf.write(keyin) kf.close() self.appendCommandLine( [ '-m', 'mrbump' ] ) self.appendCommandLine( [ 'HKLIN', self.hklin ] ) self.appendCommandLine( [ 'SEQIN', str( inp.SEQIN.fullPath ) ] ) self.appendCommandLine( [ 'KEYIN', str( keyfile ) ] ) #self.appendCommandLine( [ 'HKLOUT', str( out.HKLOUT.fullPath ) ] ) #self.appendCommandLine( [ 'XYZOUT', str( out.XYZOUT.fullPath ) ] ) #self.appendCommandLine(['XYZOUT',self.container.outputData.XYZOUT.fullPath]) #self.appendCommandLine(['HKLOUT',self.container.outputData.HKLOUT.fullPath]) self.appendCommandLine( [ 'XMLOUT', str( self.makeFileName( 'PROGRAMXML' ) ) ] ) # self.appendCommandScript( "JOBID test_mrbump" ) # self.appendCommandScript( "LABIN F=F SIGF=SIGF FreeR_flag=FREER" ) # self.appendCommandScript( "MAPROGRAM clustalw2" ) # self.appendCommandScript( "DOFASTA False" ) # self.appendCommandScript( "DOPHMMER True" ) # self.appendCommandScript( "DOHHPRED False" ) # self.appendCommandScript( "MDLU False" ) # self.appendCommandScript( "MDLD False" ) # self.appendCommandScript( "MDLC False" ) # self.appendCommandScript( "MDLM False" ) # self.appendCommandScript( "MDLP False" ) # self.appendCommandScript( "MDLS True" ) # self.appendCommandScript( "MRNUM 1" ) # self.appendCommandScript( "END" ) self.appendCommandScript( "" ) return CPluginScript.SUCCEEDED # """ # def postProcess( self, processId=-1, data={} ) : # import os # out = self.container.outputData # xmlout = str( self.makeFileName( 'PROGRAMXML' ) ) # self.reportStatus(0) # """ # # process one or more output files # also writes the XML file, previously done by postProcess() def processOutputFiles(self): import os,shutil xyzout = os.path.join(self.getWorkDirectory(), "mrbump_mrbump_1.pdb") if os.path.exists(xyzout): self.container.outputData.XYZOUT=xyzout #self.container.outputData.XYZOUT[-1].annotation = 'Positioned and refined coordinates for solution '+str(i) #self.container.outputData.XYZOUT[-1].subType = 1 hklout = os.path.join(self.getWorkDirectory(), "mrbump_mrbump_1.mtz") if os.path.exists(hklout): self.container.outputData.HKLOUT=hklout import CCP4XtalData import CCP4File import os # Need to set the expected content flag for phases data self.container.outputData.XYZOUT.annotation = 'Model from MrBump refinement' self.container.outputData.FPHIOUT.annotation = 'Weighted map from MrBump refinement' self.container.outputData.DIFFPHIOUT.annotation = 'Weighted difference map from MrBump refinement' #self.container.outputData.ABCDOUT.annotation = 'Calculated phases from refinement' #self.container.outputData.ABCDOUT.contentFlag = CCP4XtalData.CPhsDataFile.CONTENT_FLAG_HL #self.container.outputData.TLSOUT.annotation = 'TLS parameters from refinement' #self.container.outputData.LIBOUT.annotation = 'Generated dictionary from refinement' # Split out data objects that have been generated. Do this after applying the annotation, and flagging # above, since splitHklout needs to know the ABCDOUT contentFlag outputFiles = ['FPHIOUT','DIFFPHIOUT'] outputColumns = ['FWT,PHWT','DELFWT,PHDELWT'] #if self.container.controlParameters.PHOUT: # outputFiles+=['ABCDOUT'] # outputColumns+=['HLACOMB,HLBCOMB,HLCCOMB,HLDCOMB'] error = self.splitHklout(outputFiles,outputColumns,infile=hklout) if error.maxSeverity()>CCP4ErrorHandling.SEVERITY_WARNING: return CPluginScript.FAILED #for indx in range(len(self.container.outputData.MAPOUT)): # self.container.outputData.MAPOUT[indx].annotation = 'Map for solution '+str(indx+1) # self.container.outputData.MAPOUT[indx].subType = 1 # self.container.outputData.DIFMAPOUT[indx].annotation = 'Difference map for solution '+str(indx+1) # self.container.outputData.DIFMAPOUT[indx].subType = 2 # self.container.outputData.PHASEOUT[indx].annotation = 'Phases for solution '+str(indx+1) return CPluginScript.SUCCEEDED #------------------------------------------------------------------------------------ import unittest class testmrbump_basic( unittest.TestCase ) : #- def setUp( self ) : #- def tearDown( self ) : #- def test2( self ) : def test1( self ) : from CCP4Utils import getCCP4I2Dir import os xmlInput = os.path.join( getCCP4I2Dir(), 'wrappers', 'mrbump_basic', 'test_data', 'test1'+'.params.xml' ) self.wrapper = mrbump_basic( name='job' ) self.wrapper.container.loadDataFromXml( xmlInput ) self.wrapper.setWaitForFinished( 1000000 ) pid = self.wrapper.process() self.wrapper.setWaitForFinished( -1 ) if len(self.wrapper.errorReport)>0: print self.wrapper.errorReport.report() def TESTSUITE() : suite = unittest.TestLoader().loadTestsFromTestCase( testmrbump_basic ) return suite def testModule() : suite = TESTSUITE() unittest.TextTestRunner( verbosity=2 ).run( suite )