def generateDensMap(self,
labelsInit = [],
labelsLater = []):
# run FFT job to generate density map
self.printStepNumber()
if self.densMapType in ('DIFF','SIMPLE'):
tags = ['FP_',
'SIGFP_',
'FOM_']
labelsInit = [i+self.initPDB for i in tags] + ['PHIC_'+self.phaseDataset]
labelsLater = [i+self.laterPDB for i in tags] + ['PHIC_'+self.phaseDataset]
if self.densMapType == '2FOFC':
labelsInit = ['']*4
labelsLater = ['FWT_{}'.format(self.laterPDB),'','','PHIC']
if self.densMapType != 'END':
fft = FFTjob(mapType = self.densMapType,
mapTag = self.mapTag,
FOMweight = self.FOMweight,
pdbFile = self.reorderedPDBFile,
mtzFile = self.densMapMtz,
outputDir = self.outputDir,
axes = self.axes,
gridSamps = self.gridSamps,
labels1 = labelsLater,
labels2 = labelsInit,
runLog = self.runLog)
success = fft.run()
self.densityMap = fft.outputMapFile
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(pdbFile = endInputPDB,
mtzFile = endInputMTZ,
effFile = endInputEFF,
outputDir = self.outputDir,
gridSamps = self.gridSamps,
runLog = self.runLog)
success = end.run()
self.densityMap = end.outputMapFile
return success
def generateFcalcMap(self):
# generate FC map using FFT
self.printStepNumber()
fft_FC = FFTjob(mapType = 'FC',
FOMweight = self.FOMweight,
pdbFile = self.reorderedPDBFile,
mtzFile = self.fcalcMtz,
outputDir = self.outputDir,
axes = self.axes,
gridSamps = self.gridSamps,
labels1 = ['FC_{}'.format(self.phaseDataset),'','','PHIC_'+self.phaseDataset],
runLog = self.runLog)
success = fft_FC.run()
self.FcalcMap = fft_FC.outputMapFile
return success
def generateFcalcMap(self,
method=3):
# generate FC map. Three methods have currently been proposed:
# In 1, the Fcalc map is calculated using the FC and PHIC cols
# in the supplied phase dataset.. due to the order of columns
# in the input mtz file, the map will take the unit cell dims
# of the later dataset.
# In 2, the Fcalc map is also calculated from the phase dataset
# mtz, however is forced to take the cell dims of dataset 1.
# In 3, the Fcalc and PHIC cols are instead generated from a
# pdb file, and so take the cell dims of that pdb file also.
# The important thing here is that the Fcalc map dimensions
# must match those of the atom-map at the same dose. If the PDB
# file is varied between datasets, then only methods 1 and 3
# will allow this. It may be wise to use method 3 as default
# since this does not depend on a separate mtz file for phases
self.printStepNumber()
fft_FC = FFTjob(
FOMweight=self.FOMweight, pdbFile=self.reorderedPDBFile,
outputDir=self.outputDir, axes=self.axes,
gridSamps=self.gridSamps, runLog=self.runLog)
if method == 1:
fcLabels = ['FC_{}'.format(self.Mtz3LabelRename), '', '',
'PHIC_'+self.Mtz3LabelRename]
fft_FC.inputMtzFile = self.fcalcMtz
fft_FC.mapType = 'FC'
fft_FC.labels1 = fcLabels
success = fft_FC.run()
self.FcalcMap = fft_FC.outputMapFile
elif method == 2:
tags = ['FP_', 'SIGFP_', 'FOM_']
labels1 = [i+self.Mtz2LabelRename for i in tags] +\
['PHIC_'+self.Mtz3LabelRename]
labels2 = ['FC_{}'.format(self.Mtz3LabelRename), '', '',
'PHIC_'+self.Mtz3LabelRename]
fft_FC.mapType = 'DIFF'
fft_FC.mapTag = 'FC'
fft_FC.inputMtzFile = self.fcalcMtz
fft_FC.F1Scale = 0.0
fft_FC.labels1 = labels1
fft_FC.labels2 = labels2
success = fft_FC.run()
tmpMap = fft_FC.outputMapFile
if success:
m = self.multiplyMapByFactor(map=tmpMap)
self.FcalcMap = m
elif method == 3:
sfall = SFALLjob(inputPDBfile=self.reorderedPDBFile,
outputDir=self.outputDir, VDWR=self.sfall_VDWR,
symmetrygroup=self.spaceGroup, runLog=self.runLog,
gridDimensions=self.sfallGRIDdims,
task='mtz from pdb')
success = sfall.run()
FcalcMtz = sfall.outputMtzFile
fft_FC.inputMtzFile = FcalcMtz
fft_FC.mapType = 'FC'
fft_FC.labels1 = ['FCalc', '', '', 'PHICalc']
success = fft_FC.run()
self.FcalcMap = fft_FC.outputMapFile
if not success:
error(text='Failure to successfully generate Fcalc map',
log=self.runLog)
def generateCCP4DensMap(self,
labelsInit=[], labelsLater=[]):
# run FFT job to generate density map
self.printStepNumber()
densMap = '{}{}_FFT.map'.format(self.outputDir, self.densMapNaming)
if self.densMapType in ('DIFF', 'HIGHONLY'):
# note that the distinction in these options only comes
# apparent in FFTjob.py. Even though HIGHONLY'
# calculate maps using only the later dataset info, dummy
# information for labelsInit is provided anyway for simplicity
tags = ['FP_', 'SIGFP_', 'FOM_']
labelsInit = [i+self.Mtz1LabelRename for i in tags] +\
['PHIC_'+self.Mtz3LabelRename]
labelsLater = [i+self.Mtz2LabelRename for i in tags] +\
['PHIC_'+self.Mtz3LabelRename]
if self.densMapType == '2FOFC':
if self.useLaterCellDims:
labelsInit = ['']*4
labelsLater = ['FWT{}'.format(self.Mtz2LabelRename),
'', '', 'PHIC']
else:
labelsLater = ['']*4
labelsInit = ['FWT{}'.format(self.Mtz2LabelRename),
'', '', 'PHIC']
if self.densMapType != 'END':
fft = FFTjob(
mapType=self.densMapType, mapTag=self.mapTag,
FOMweight=self.FOMweight, runLog=self.runLog,
pdbFile=self.reorderedPDBFile, outputMapFile=densMap,
mtzFile=self.densMapMtz, useSigLabs=not self.ignoreSIGFs,
outputDir=self.outputDir, axes=self.axes,
gridSamps=self.gridSamps, labels1=labelsLater,
labels2=labelsInit,
lowResCutoff=self.mapResLimits.split(',')[1],
highResCutoff=self.mapResLimits.split(',')[0])
if self.useLaterCellDims:
fft.labels1 = labelsLater
fft.labels2 = labelsInit
else:
fft.labels1 = labelsInit
fft.labels2 = labelsLater
success = fft.run()
self.densityMap = fft.outputMapFile
if success and not self.useLaterCellDims:
m = self.multiplyMapByFactor(map=self.densityMap)
self.densityMap = m
else:
# run END job if required (may take time to run!!)
endInputPDB = self.inputPDBfile
endInputMTZ = ''.join(endInputPDB.split('.')[:-1]+['.mtz'])
endInputEFF = ''.join(endInputPDB.split('.')[:-1]+['.eff'])
end = ENDjob(pdbFile=endInputPDB, mtzFile=endInputMTZ,
effFile=endInputEFF, outputDir=self.outputDir,
gridSamps=self.gridSamps, runLog=self.runLog)
success = end.run()
self.densityMap = end.outputMapFile
if not success:
error(text='Failure to successfully generate density map',
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