def cropMapToAtomTaggedMap(self,
densMap='untitled.map'):
# crop the density map to exact same dimensions
# as SFALL atom-tagged map
# run MAPMASK job to crop fft density map to asym unit
mapmask2 = MAPMASKjob(mapFile1=densMap, outputDir=self.outputDir,
runLog=self.runLog)
success = mapmask2.crop2AsymUnit()
if not success:
return False
# run MAPMASK job to crop fft density map to same
# grid sampling dimensions as SFALL atom map
mapmask3 = MAPMASKjob(mapFile1=mapmask2.outputMapFile,
mapFile2=self.atomTaggedMap,
outputDir=self.outputDir, runLog=self.runLog)
success = mapmask3.cropMap2Map()
croppedDensityMap = mapmask3.outputMapFile
if not success:
error(text='Failure to successfully crop atom map',
log=self.runLog)
else:
return croppedDensityMap
def multiplyMapByFactor(self,
factor=-1.0, map='./untitled.map'):
# multiply all points in a density map by a value.
# useful to switch positive and negative in a map
mapmask = MAPMASKjob(mapFile1=map, outputDir=self.outputDir,
runLog=self.runLog)
mapmask.multiplyByFactor(factor=factor, symGroup=self.spaceGroup)
return mapmask.outputMapFile
def cropAtmTaggedMapToAsymUnit(self): # crop atom-tagged map to asymmetric unit: self.printStepNumber() mapmask1 = MAPMASKjob(mapFile1 = self.atomTaggedMap, outputDir = self.outputDir, runLog = self.runLog) success = mapmask1.crop2AsymUnit() self.atomTaggedMap = mapmask1.outputMapFile return success
def cropAtmTaggedMapToAsymUnit(self):
# crop atom-tagged map to asymmetric unit:
self.printStepNumber()
mapmask1 = MAPMASKjob(mapFile1=self.atomTaggedMap,
outputDir=self.outputDir, runLog=self.runLog)
success = mapmask1.crop2AsymUnit()
if not success:
error(text='Failure to crop map in MAPMASK',
log=self.runLog)
self.atomTaggedMap = mapmask1.outputMapFile
def ensureSameMapAxesOrder(self): # switch map axes to match SFALL atom-tagged map if # required(only typically required for END maps) mapmask = MAPMASKjob(mapFile1 = self.densityMap, outputDir = self.outputDir, runLog = self.runLog) success = mapmask.switchAxisOrder(order = self.axes, symGroup = self.spaceGroup) self.densityMap = mapmask.outputMapFile return success
def cropMapToModel(self,
map=''):
# crop a map to the input coordinate model
self.printStepNumber()
mapmask1 = MAPMASKjob(
mapFile1=map, pdbFile=self.inputPDBfile,
outputDir=self.outputDir, runLog=self.runLog)
success = mapmask1.crop2model(spaceGroup=self.spaceGroup)
if not success:
error(text='Failure to crop map in MAPMASK',
log=self.runLog)
croppedMap = mapmask1.outputMapFile
return croppedMap
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
