def curatePdbFile(self): # run pdbcur job self.printStepNumber() pdbcur = PDBCURjob(inputPDBfile = self.pdbcurPDBinputFile, outputDir = self.outputDir, runLog = self.runLog) success = pdbcur.run() self.PDBCURoutputFile = pdbcur.outputPDBfile return success
def curatePdbFile(self): # run pdbcur job self.printStepNumber() pdbcur = PDBCURjob(inputPDBfile=self.inputPDBfile, outputPDBfile=self.PDBCURoutputFile, outputDir=self.outputDir, runLog=self.runLog) success = pdbcur.run() if not success: error(text='Failure to successfully run PDBCUR', log=self.runLog)
def runPipeline(self): # read input file first success = self.readInputFile() if success is False: return 1 # create log file self.runLog = logFile('{}/{}_runLog_2.txt'.format(self.outputDir,self.jobName)) # run pdbcur job pdbcur = PDBCURjob(self.pdbcurPDBinputFile,self.outputDir,self.runLog) success = pdbcur.run() if success is False: return 2 self.PDBCURoutputFile = pdbcur.outputPDBfile # reorder atoms in PDB file self.renumberPDBFile() # get space group from PDB file success = self.getSpaceGroup() if success is False: return 3 # run SFALL job sfall = SFALLjob(self.reorderedPDBFile,self.outputDir,self.sfall_VDWR, self.spaceGroup,self.sfall_GRID,'ATMMOD',self.runLog) success = sfall.run() if success is False: return 4 # run FFT job sfallMap = mapTools(sfall.outputMapFile) axes = [sfallMap.fastaxis,sfallMap.medaxis,sfallMap.slowaxis] gridSamps = [sfallMap.gridsamp1,sfallMap.gridsamp2,sfallMap.gridsamp3] labelsInit = ['FP_'+self.initPDB,'SIGFP_'+self.initPDB,'FOM_'+self.initPDB,'PHIC_'+self.initPDB] labelsLater = ['FP_'+self.laterPDB,'SIGFP_'+self.laterPDB,'FOM_'+self.laterPDB,'PHIC_'+self.laterPDB] if self.densMapType != 'END': fft = FFTjob(self.densMapType,self.FOMweight,self.reorderedPDBFile,self.inputMtzFile, self.outputDir,axes,gridSamps,labelsLater,labelsInit,self.runLog) success = fft.run() else: # run END job if required (may take time to run!!) endInputPDB = self.pdbcurPDBinputFile endInputMTZ = ''.join(endInputPDB.split('.')[:-1]+['.mtz']) endInputEFF = ''.join(endInputPDB.split('.')[:-1]+['.eff']) end = ENDjob(endInputPDB,endInputMTZ,endInputEFF,self.outputDir,gridSamps,self.runLog) success = end.run() if success is False: return 5 # crop fft and atom-tagged maps to asymmetric unit: mapmask1 = MAPMASKjob(sfall.outputMapFile,'',self.outputDir,self.runLog) success = mapmask1.crop2AsymUnit() if success is False: return 6 # choose correct density map to include in MAPMASK cropping below if self.densMapType != 'END': inputDensMap = fft.outputMapFile else: inputDensMap = end.outputMapFile # switch END map axes to match SFALL atom-tagged map if required if self.densMapType == 'END': mapmask_ENDmap = MAPMASKjob(inputDensMap,'',self.outputDir,self.runLog) success = mapmask_ENDmap.switchAxisOrder(axes,self.spaceGroup) if success is False: return 7.0 else: inputDensMap = mapmask_ENDmap.outputMapFile # run MAPMASK job to crop fft density map to asym unit mapmask2 = MAPMASKjob(inputDensMap,'',self.outputDir,self.runLog) success = mapmask2.crop2AsymUnit() if success is False: return 7.1 # run MAPMASK job to crop fft density map to same grid # sampling dimensions as SFALL atom map mapmask3 = MAPMASKjob(mapmask2.outputMapFile,mapmask1.outputMapFile,self.outputDir,self.runLog) success = mapmask3.cropMap2Map() if success is False: return 8 # perform map consistency check between cropped fft and sfall maps fftMap = mapTools(mapmask3.outputMapFile) fftMap.readHeader() sfallMap = mapTools(mapmask1.outputMapFile) sfallMap.readHeader() success = self.mapConsistencyCheck(sfallMap,fftMap) if success is False: return 9 else: return 0