def runSIGMAA(self):
title = 'run of sigma-a'
fillerLine()
cmd1 = 'sfall ' +\
'HKLIN {} '.format(self.inputMtz) +\
'HKLOUT {} '.format(self.tmpMtz) +\
'XYZIN {}'.format(self.inputPDB)
cmd2 = 'title {}\n'.format(title) +\
'LABIN FP=F{} SIGFP=SIGF{} FREE={}\n'.format(
self.LabelName, self.LabelName, self.RfreeFlag) +\
'labout -\nFC=FC PHIC=PHIC\nMODE SFCALC -\n' +\
'XYZIN -\nHKLIN\nsymmetry {}\n'.format(self.spaceGroup)
if self.noScale is True:
self.commandInput2 += 'NOSCALE\nend'
else:
self.commandInput2 += 'end'
self.outputLogfile = 'SIGMAAlogfile1.txt'
# run SFALL job within SIGMAA routine
job = ccp4Job(jobName='SFALL', commandInput1=cmd1, commandInput2=cmd2,
outputDir=self.outputDir, outputLog=self.outputLogfile,
outputFile=self.tmpMtz)
self.jobSuccess = job.checkJobSuccess(self.runLog)
if not self.jobSuccess:
return
cmd1 = 'sigmaa ' +\
'HKLIN {} '.format(self.tmpMtz) +\
'HKLOUT {} '.format(self.outputMtz)
cmd2 = 'title {}\n'.format(title) +\
'LABIN FP=F{} SIGFP=SIGF{} FC=FC PHIC=PHIC\n'.format(
*([self.LabelName]*2)) +\
'labout -\nDELFWT=DELFWT{} FWT=FWT{} WCMB=FOM{}\n'.format(
*([self.LabelRename]*3)) +\
'ranges 20 -\n1000\nsymmetry "{}"\n'.format(self.spaceGroup) +\
'partial -\ndamp 1.0\nend'
self.outputLogfile = 'SIGMAAlogfile2.txt'
# run SIGMAA next
job = ccp4Job(jobName='SIGMAA', commandInput1=cmd1, commandInput2=cmd2,
outputDir=self.outputDir, outputLog=self.outputLogfile,
outputFile=self.outputMtz)
self.jobSuccess = job.checkJobSuccess()
def switchAxisOrder(self,
order=[], symGroup="", includeDir=False):
# switch the axis order of an input .map file.
# order = [1,2,3] for example
self.defineCorrectOutputMap(switch=True)
xyz = {'1': 'X', '2': 'Y', '3': 'Z'}
axisOrder = [xyz[str(i)] for i in order]
self.printPurpose(mode='switch axes', axisOrder=axisOrder)
inputFiles = [self.inputMapFile]
if not checkInputsExist(inputFiles, self.runLog):
return False
self.defineCommandInput()
self.commandInput2 = 'SYMMETRY {}\nAXIS {}\nEND'.format(
symGroup, ' '.join(axisOrder))
self.outputLogfile = 'MAPMASKlogfile.txt'
# run MAPMASK job
job = ccp4Job(jobName='MAPMASK_switchAxisOrder',
commandInput1=self.commandInput1,
commandInput2=self.commandInput2,
outputDir=self.outputDir,
outputLog=self.outputLogfile,
outputFile=self.outputMapFile)
self.jobSuccess = job.checkJobSuccess(self.runLog)
success = self.provideFeedback()
return success
def multiplyByFactor(self,
includeDir=False, factor=-1.0, symGroup=""):
# multiply all points in a density
# map file by a constant factor
self.printPurpose(mode='Multiply by factor')
self.defineCorrectOutputMap(factorMultiply=True)
inputFiles = [self.inputMapFile]
if not checkInputsExist(inputFiles, self.runLog):
return False
self.defineCommandInput()
self.commandInput2 = 'SYMMETRY {}\nSCALE -\nFACTOR {} 0.0\nEND'.format(
symGroup, factor)
self.outputLogfile = 'MAPMASKlogfile.txt'
# run MAPMASK job
job = ccp4Job(jobName='MAPMASK_multipyByFactor',
commandInput1=self.commandInput1,
commandInput2=self.commandInput2,
outputDir=self.outputDir,
outputLog=self.outputLogfile,
outputFile=self.outputMapFile)
self.jobSuccess = job.checkJobSuccess(self.runLog)
success = self.provideFeedback()
return success
def crop2model(self,
includeDir=False,
spaceGroup='P1'):
# crop map to an input coordinate model
self.printPurpose(mode='crop to model')
self.defineCorrectOutputMap()
inputFiles = [self.inputMapFile, self.inputPdbFile]
if not checkInputsExist(inputFiles, self.runLog):
return False
self.defineCommandInput()
self.commandInput2 = 'SYMMETRY {}\nBORDER 1'.format(spaceGroup)
self.outputLogfile = 'MAPMASKlogfile.txt'
# run MAPMASK job
job = ccp4Job(jobName='MAPMASK_crop2Model',
commandInput1=self.commandInput1,
commandInput2=self.commandInput2,
outputDir=self.outputDir,
outputLog=self.outputLogfile,
outputFile=self.outputMapFile)
self.jobSuccess = job.checkJobSuccess(self.runLog)
success = self.provideFeedback()
return success
def runSCALEIT(self):
# run SCALEIT job to scale 2nd dataset Fs against 1st datasets
title = 'run of scaleit'
# run SCALEIT from command line
self.commandInput1 = 'scaleit '+\
'HKLIN {} '.format(self.inputMtz)+\
'HKLOUT {}'.format(self.outputMtz)
self.commandInput2 = 'title SCALEIT JOB\n'+\
'NOWT\n'+\
'converge NCYC 4\n'+\
'converge ABS 0.001\n'+\
'converge TOLR -7\n'+\
'REFINE ANISOTROPIC\n'+\
'auto\n'+\
'LABIN FP=FP_{} SIGFP=SIGFP_{} -\n'.format(self.Mtz1Label,
self.Mtz1Label)+\
' FPH1=FP_{} SIGFPH1=SIGFP_{}\n'.format(self.Mtz2Label,
self.Mtz2Label)+\
'END'
self.outputLogfile = 'SCALEITlogfile.txt'
# run SCALEIT job
job = ccp4Job('SCALEIT',self.commandInput1,self.commandInput2,self.outputDir,self.outputLogfile,self.outputMtz)
self.jobSuccess = job.checkJobSuccess()
def runFFT(self):
self.commandInput1 = 'fft '+\
'HKLIN {} '.format(self.inputMtzFile)+\
'MAPOUT {} '.format(self.outputMapFile)+\
'SYMINFO syminfo.lib '
# can distinguish here between SIMPLE and DIFFERENCE map types
if self.mapType == 'SIMPLE':
F2Scale = 0.0
else:
F2Scale = 1.0
#if a FOM is specified exists the weighting is applied to the map
if self.FOMweight in ('True','TRUE','true'):
FOMstring = 'W={}'.format(self.FOM2)
FOMstring2 = 'W2={}'.format(self.FOM2)
else:
FOMstring = ''
self.commandInput2 = 'AXIS {} {} {}\n'.format(self.fastAxis,self.medAxis,self.slowAxis)+\
'title FTT DENSITY MAP RUN\n'+\
'grid {} {} {}\n'.format(self.gridSamp1,self.gridSamp2,self.gridSamp3)+\
'xyzlim 0 1 0 1 0 1\n'+\
'LABIN F1={} SIG1={} F2={} SIG2={} '.format(self.F1,self.SIG1,self.F2,self.SIG2)+\
'PHI={} {} PHI2={} {}\n'.format(self.PHI2,FOMstring,self.PHI2,FOMstring2)+\
'SCALE F1 1.0 0.0 F2 {} 0.0\n'.format(F2Scale)+\
'END'
self.outputLogfile = 'FFTlogfile.txt'
# run FFT job
job = ccp4Job('FFT',self.commandInput1,self.commandInput2,self.outputDir,self.outputLogfile,self.outputMapFile)
self.jobSuccess = job.checkJobSuccess()
def cropMap2Map(self,
includeDir = False):
# Crop map 1 to map 2
# fillerLine()
self.printPurpose(mode = 'crop to map')
self.defineCorrectOutputMap(False)
inputFiles = [self.inputMapFile,self.inputMapFile2]
if not checkInputsExist(inputFiles,self.runLog):
return False
maps = [self.inputMapFile,self.inputMapFile2]
if not includeDir:
maps = [m.split('/')[-1] for m in maps]
self.defineCommandInput()
self.commandInput2 = 'EXTEND\nXYZLIM MATCH\nEND'
self.outputLogfile = 'MAPMASKlogfile.txt'
# run MAPMASK job
job = ccp4Job(jobName = 'MAPMASK_cropMap2Map',
commandInput1 = self.commandInput1,
commandInput2 = self.commandInput2,
outputDir = self.outputDir,
outputLog = self.outputLogfile,
outputFile = self.outputMapFile)
self.jobSuccess = job.checkJobSuccess()
success = self.provideFeedback()
return success
def extend2UnitCell(self,
includeDir=False, symGroup=1):
# extend map 1 to the unit cell limits
self.printPurpose(mode='extend to unit cell')
self.defineCorrectOutputMap()
inputFiles = [self.inputMapFile]
if not checkInputsExist(inputFiles, self.runLog):
return False
self.defineCommandInput()
self.commandInput2 = 'SYMMETRY {}\nXYZLIM CELL\nEND'.format(symGroup)
self.outputLogfile = 'MAPMASKlogfile.txt'
# run MAPMASK job
job = ccp4Job(jobName='MAPMASK_extend2UnitCell',
commandInput1=self.commandInput1,
commandInput2=self.commandInput2,
outputDir=self.outputDir,
outputLog=self.outputLogfile,
outputFile=self.outputMapFile)
self.jobSuccess = job.checkJobSuccess(self.runLog)
success = self.provideFeedback()
return success
def runSCALEIT(self):
# run SCALEIT job to scale 2nd dataset Fs against 1st datasets
self.printPurpose()
# run SCALEIT from command line
self.commandInput1 = 'scaleit ' +\
'HKLIN {} '.format(self.inputMtz) +\
'HKLOUT {}'.format(self.outputMtz)
self.commandInput2 = 'title SCALEIT JOB\n' +\
'NOWT\n' +\
'converge NCYC 4\n' +\
'converge ABS 0.001\n' +\
'converge TOLR -7\n' +\
'REFINE {}\n'.format(self.scaling) +\
'auto\n' +\
'LABIN FP=FP_{} SIGFP=SIGFP_{} -\n'.format(
self.Mtz1Label, self.Mtz1Label) +\
' FPH1=FP_{} SIGFPH1=SIGFP_{}\n'.format(
self.Mtz2Label, self.Mtz2Label) +\
'END'
self.outputLogfile = 'SCALEITlogfile.txt'
# run SCALEIT job
job = ccp4Job(jobName='SCALEIT', commandInput1=self.commandInput1,
commandInput2=self.commandInput2,
outputDir=self.outputDir, outputLog=self.outputLogfile,
outputFile=self.outputMtz)
self.jobSuccess = job.checkJobSuccess(self.runLog)
def crop2AsymUnit(self,
includeDir = False):
# Crop map 1 to asymmetric unit
# fillerLine()
self.printPurpose(mode = 'crop to asym')
self.defineCorrectOutputMap(False)
inputFiles = [self.inputMapFile]
if not checkInputsExist(inputFiles,self.runLog):
return False
if not includeDir:
map1 = self.inputMapFile.split('/')[-1]
else:
map1 = self.inputMapFile
self.defineCommandInput()
self.commandInput2 = 'EXTEND\nXYZLIM ASU\nEND'
self.outputLogfile = 'MAPMASKlogfile.txt'
# run MAPMASK job
job = ccp4Job(jobName = 'MAPMASK_crop2AsymUnit',
commandInput1 = self.commandInput1,
commandInput2 = self.commandInput2,
outputDir = self.outputDir,
outputLog = self.outputLogfile,
outputFile = self.outputMapFile)
self.jobSuccess = job.checkJobSuccess()
success = self.provideFeedback()
return success
def runSIGMAA(self):
title = 'run of sigma-a'
self.commandInput1 = 'sfall '+\
'HKLIN {} '.format(self.inputMtz)+\
'HKLOUT {} '.format(self.tmpMtz)+\
'XYZIN {}'.format(self.inputPDB)
self.commandInput2 = 'title {}\n'.format(title)+\
'LABIN FP=F{} SIGFP=SIGF{} FREE={}\n'.format(self.LabelName,self.LabelName,self.RfreeFlag)+\
'labout -\n'+\
'FC=FC PHIC=PHIC\n'+\
'MODE SFCALC -\n'+\
'XYZIN -\n'+\
'HKLIN\n'+\
'symmetry {}\n'.format(self.spaceGroup)+\
'end'
self.outputLogfile = 'SIGMAAlogfile1.txt'
# run SFALL job within SIGMAA routine
job = ccp4Job('SFALL',self.commandInput1,self.commandInput2,self.outputDir,self.outputLogfile,self.tmpMtz)
self.jobSuccess = job.checkJobSuccess()
if self.jobSuccess is False:
return
self.commandInput1 = 'sigmaa '+\
'HKLIN {} '.format(self.tmpMtz)+\
'HKLOUT {} '.format(self.outputMtz)
self.commandInput2 = 'title {}\n'.format(title)+\
'LABIN FP=F{} SIGFP=SIGF{} FC=FC PHIC=PHIC\n'.format(self.LabelName,self.LabelName)+\
'labout -\n'+\
'DELFWT=DELFWT FWT=FWT WCMB=FOM{}\n'.format(self.LabelName)+\
'ranges 20 -\n'+\
'1000\n'+\
'symmetry "{}"\n'.format(self.spaceGroup)+\
'partial -\n'+\
'damp 1.0\n'+\
'end'
self.outputLogfile = 'SIGMAAlogfile2.txt'
# run SIGMAA next
job = ccp4Job('SIGMAA',self.commandInput1,self.commandInput2,self.outputDir,self.outputLogfile,self.outputMtz)
self.jobSuccess = job.checkJobSuccess()
def runCAD(self):
# fillerLine()
self.printPurpose()
title = 'run of cad'
self.commandInput1 = 'cad '+\
'HKLIN1 {} '.format(self.inputMtz1)+\
'HKLIN2 {} '.format(self.inputMtz2)+\
'HKLIN3 {} '.format(self.inputMtz3)+\
'HKLOUT {}'.format(self.outputMtz)
self.commandInput2 = 'title CAD JOB\n'+\
'monitor BRIEF\n'+\
'labin file 1 - \n'+\
'E1 = F{} - \n'.format(self.labels[0])+\
'E2 = SIGF{} '.format(self.labels[0])+\
'{} \n'.format(self.FOMtag['in'])+\
'labout file 1 - \n'+\
'E1 = FP_{} - \n'.format(self.renameLabels[0])+\
'E2 = SIGFP_{} '.format(self.renameLabels[0])+\
'{} \n'.format(self.FOMtag['out'])+\
'ctypin file 1 - \n'+\
'E1 = F - \n'+\
'E2 = Q '+\
'{} \n'.format(self.FOMtag['type'])+\
'labin file 2 - \n'+\
'E1 = F{} - \n'.format(self.labels[1])+\
'E2 = SIGF{} \n'.format(self.labels[1])+\
'labout file 2 - \n'+\
'E1 = FP_{} - \n'.format(self.renameLabels[1])+\
'E2 = SIGFP_{} \n'.format(self.renameLabels[1])+\
'ctypin file 2 - \n'+\
'E1 = F - \n'+\
'E2 = Q \n'+\
'labin file 3 - \n'+\
'E1 = {} -\n'.format(self.labels[2])+\
'E2 = {} \n'.format(self.labels[3])+\
'labout file 3 - \n'+\
'E1 = PHIC_{} - \n'.format(self.renameLabels[2])+\
'E2 = FC_{} \n'.format(self.renameLabels[2])+\
'ctypin file 3 - \n'+\
'E1 = P -\n'+\
'E2 = F \n'
self.outputLogfile = 'CADlogfile.txt'
# run CAD job
job = ccp4Job(jobName = 'CAD',
commandInput1 = self.commandInput1,
commandInput2 = self.commandInput2,
outputDir = self.outputDir,
outputLog = self.outputLogfile,
outputFile = self.outputMtz)
self.jobSuccess = job.checkJobSuccess()
def runNCONT(self):
# the actual running part here
self.commandInput1 = 'ncont ' +\
'XYZIN {} '.format(self.inputPDBfile)
self.commandInput2 = 'source "*"\ntarget "*"\nmindist 0.0\n' +\
'maxdist 4.0\ncells 1\n' +\
'symm {}\nEND'.format(self.symGroup)
self.outputLogfile = '{}-NCONTlogfile.txt'.format(self.seriesName)
# run NCONT job
job = ccp4Job('NCONT', self.commandInput1, self.commandInput2,
self.outputDir, self.outputLogfile,
self.outputDir+'/'+self.outputLogfile)
self.jobSuccess = job.checkJobSuccess(self.runLog)
def cropMap2Map(self):
# Crop map 1 to map 2
self.defineCorrectOutputMap(False)
inputFiles = [self.inputMapFile,self.inputMapFile2]
if checkInputsExist(inputFiles,self.runLog) is False:
return False
self.runLog.writeToLog('Cropping map "{}" to map "{}"'.format(self.inputMapFile,self.inputMapFile2))
self.defineCommandInput()
self.commandInput2 = 'EXTEND\nXYZLIM MATCH\nEND'
self.outputLogfile = 'MAPMASKlogfile.txt'
# run MAPMASK job
job = ccp4Job('MAPMASK_cropMap2Map',self.commandInput1,self.commandInput2,
self.outputDir,self.outputLogfile,self.outputMapFile)
self.jobSuccess = job.checkJobSuccess()
success = self.provideFeedback()
return success
def runCAD(self):
title = 'run of cad'
self.commandInput1 = 'cad '+\
'HKLIN1 {} '.format(self.inputMtz1)+\
'HKLIN2 {} '.format(self.inputMtz2)+\
'HKLIN3 {} '.format(self.inputMtz3)+\
'HKLOUT {}'.format(self.outputMtz)
self.commandInput2 = 'title CAD JOB\n'+\
'monitor BRIEF\n'+\
'labin file 1 - \n'+\
'E1 = F{} - \n'.format(self.labels[0])+\
'E2 = SIGF{} - \n'.format(self.labels[0])+\
'E3 = FOM{} \n'.format(self.labels[0])+\
'labout file 1 - \n'+\
'E1 = FP_{} - \n'.format(self.renameLabels[0])+\
'E2 = SIGFP_{} - \n'.format(self.renameLabels[0])+\
'E3 = FOM_{} \n'.format(self.renameLabels[0])+\
'ctypin file 1 - \n'+\
'E1 = F - \n'+\
'E2 = Q - \n'+\
'E3 = W \n'+\
'labin file 2 - \n'+\
'E1 = F{} - \n'.format(self.labels[1])+\
'E2 = SIGF{} \n'.format(self.labels[1])+\
'labout file 2 - \n'+\
'E1 = FP_{} - \n'.format(self.renameLabels[1])+\
'E2 = SIGFP_{} \n'.format(self.renameLabels[1])+\
'ctypin file 2 - \n'+\
'E1 = F - \n'+\
'E2 = Q \n'+\
'labin file 3 - \n'+\
'E1 = PHI{} \n'.format(self.labels[2])+\
'labout file 3 - \n'+\
'E1 = PHIC_{} \n'.format(self.renameLabels[2])+\
'ctypin file 3 - \n'+\
'E1 = P \n'
self.outputLogfile = 'CADlogfile.txt'
# run CAD job
job = ccp4Job('CAD',self.commandInput1,self.commandInput2,self.outputDir,self.outputLogfile,self.outputMtz)
self.jobSuccess = job.checkJobSuccess()
def switchAxisOrder(self,order,symGroup):
# switch the axis order of an input .map file. order = [1,2,3] for example
self.defineCorrectOutputMap(True)
xyz = {'1':'X','2':'Y','3':'Z'}
axisOrder = [xyz[str(i)] for i in order]
inputFiles = [self.inputMapFile]
if checkInputsExist(inputFiles,self.runLog) is False:
return False
self.runLog.writeToLog('Switching map "{}" axis ordering to {}'.format(self.inputMapFile,axisOrder))
self.defineCommandInput()
self.commandInput2 = 'SYMMETRY {}\nAXIS {}\nEND'.format(symGroup,' '.join(axisOrder))
self.outputLogfile = 'MAPMASKlogfile.txt'
# run MAPMASK job
job = ccp4Job('MAPMASK_switchAxisOrder',self.commandInput1,self.commandInput2,
self.outputDir,self.outputLogfile,self.outputMapFile)
self.jobSuccess = job.checkJobSuccess()
success = self.provideFeedback()
return success
def runSFALL(self):
# run SFALL job using the external ccp4Job class
self.printPurpose()
title = 'run of sfall'
self.commandInput1 = 'sfall '+\
'XYZIN {} '.format(self.inputPDBfile)+\
'ATOMSF atomsf.lib '+\
'MAPOUT {} '.format(self.outputMapFile)+\
'SYMINFO syminfo.lib '
if len(self.gridDims) == 0:
self.commandInput2 = 'MODE ATMMAP {}\n'.format(self.mapoutType)+\
'SYMMETRY {}\n'.format(self.symGroup)+\
'VDWR {}\n'.format(self.VDWR)+\
'title {}\n'.format(title)+\
'END'
else:
self.commandInput2 = 'MODE ATMMAP {}\n'.format(self.mapoutType)+\
'SYMMETRY {}\n'.format(self.symGroup)+\
'VDWR {}\n'.format(self.VDWR)+\
'title {}\n'.format(title)+\
'GRID {} {} {}\n'.format(self.gridDims[0],self.gridDims[1],self.gridDims[2])+\
'END'
self.outputLogfile = 'SFALLlogfile.txt'
# run SFALL job
job = ccp4Job(jobName = 'SFALL',
commandInput1 = self.commandInput1,
commandInput2 = self.commandInput2,
outputDir = self.outputDir,
outputLog = self.outputLogfile,
outputFile = self.outputMapFile)
self.jobSuccess = job.checkJobSuccess()
def runPDBCUR(self):
# PDBcur job to specify to remove hydrogen atoms and pick on the most probably conformation
# (for two conformations with 0.5 occupancy, the first - A is chosen and occupancy
# set to 1.00). Also remove all anisou info from file - since it is not needed for
# current analysis
self.jobName = 'PDBCUR'
# run PDBCUR from command line
self.commandInput1 = 'pdbcur '+\
'XYZIN {} '.format(self.inputPDBfile)+\
'XYZOUT {} '.format(self.outputPDBfile)
self.commandInput2 = 'delhydrogen\n'+\
'mostprob\n'+\
'noanisou\n'+\
'END'
self.outputLogfile = 'PDBCURlogfile.txt'
# run PDBCUR job
job = ccp4Job('PDBCUR',self.commandInput1,self.commandInput2,self.outputDir,self.outputLogfile,self.outputPDBfile)
self.jobSuccess = job.checkJobSuccess()
def runCAD(self):
self.printPurpose()
if not self.ignoreDset1:
cmd1 = 'cad ' +\
'HKLIN1 {} '.format(self.inputMtz1) +\
'HKLIN2 {} '.format(self.inputMtz2) +\
'HKLIN3 {} '.format(self.inputMtz3) +\
'HKLOUT {}'.format(self.outputMtz)
if not self.ignoreSIGFs:
cmd2 = 'title CAD JOB\n' +\
'monitor BRIEF\n' +\
'labin file 1 - \n' +\
'E1 = {} - \n'.format(self.Mtz1FPlabel) +\
'E2 = {} '.format(self.Mtz1SIGFPlabel) +\
'{} \n'.format(self.FOMtag['in']) +\
'labout file 1 - \n' +\
'E1 = FP_{} - \n'.format(self.renameLabels[0]) +\
'E2 = SIGFP_{} '.format(self.renameLabels[0]) +\
'{} \n'.format(self.FOMtag['out']) +\
'ctypin file 1 - \n' +\
'E1 = F - \n' +\
'E2 = Q ' +\
'{} \n'.format(self.FOMtag['type']) +\
'labin file 2 - \n' +\
'E1 = {} - \n'.format(self.Mtz2FPlabel) +\
'E2 = {} \n'.format(self.Mtz2SIGFPlabel) +\
'labout file 2 - \n' +\
'E1 = FP_{} - \n'.format(self.renameLabels[1]) +\
'E2 = SIGFP_{} \n'.format(self.renameLabels[1]) +\
'ctypin file 2 - \n' +\
'E1 = F - \n' +\
'E2 = Q \n' +\
'labin file 3 - \n' +\
'E1 = {} -\n'.format(self.Mtz3phaseLabel) +\
'E2 = {} \n'.format(self.Mtz3FcalcLabel) +\
'labout file 3 - \n' +\
'E1 = PHIC_{} - \n'.format(self.renameLabels[2]) +\
'E2 = FC_{} \n'.format(self.renameLabels[2]) +\
'ctypin file 3 - \n' +\
'E1 = P -\n' +\
'E2 = F \n'
else:
cmd2 = 'title CAD JOB\n' +\
'monitor BRIEF\n' +\
'labin file 1 - \n' +\
'E1 = {} \n'.format(self.Mtz1FPlabel) +\
'{} \n'.format(self.FOMtag['in']) +\
'labout file 1 - \n' +\
'E1 = FP_{} \n'.format(self.renameLabels[0]) +\
'{} \n'.format(self.FOMtag['out']) +\
'ctypin file 1 - \n' +\
'E1 = F \n' +\
'{} \n'.format(self.FOMtag['type']) +\
'labin file 2 - \n' +\
'E1 = {} \n'.format(self.Mtz2FPlabel) +\
'labout file 2 - \n' +\
'E1 = FP_{} \n'.format(self.renameLabels[1]) +\
'ctypin file 2 - \n' +\
'E1 = F \n' +\
'labin file 3 - \n' +\
'E1 = {} -\n'.format(self.Mtz3phaseLabel) +\
'E2 = {} \n'.format(self.Mtz3FcalcLabel) +\
'labout file 3 - \n' +\
'E1 = PHIC_{} - \n'.format(self.renameLabels[2]) +\
'E2 = FC_{} \n'.format(self.renameLabels[2]) +\
'ctypin file 3 - \n' +\
'E1 = P -\n' +\
'E2 = F \n'
else:
cmd1 = 'cad ' +\
'HKLIN1 {} '.format(self.inputMtz2) +\
'HKLIN2 {} '.format(self.inputMtz3) +\
'HKLOUT {}'.format(self.outputMtz)
if not self.ignoreSIGFs:
cmd2 = 'title CAD JOB\n' +\
'monitor BRIEF\n' +\
'labin file 1 - \n' +\
'E1 = {} - \n'.format(self.Mtz2FPlabel) +\
'E2 = {} \n'.format(self.Mtz2SIGFPlabel) +\
'labout file 1 - \n' +\
'E1 = FP_{} - \n'.format(self.renameLabels[1]) +\
'E2 = SIGFP_{} \n'.format(self.renameLabels[1]) +\
'ctypin file 1 - \n' +\
'E1 = F - \n' +\
'E2 = Q \n' +\
'labin file 2 - \n' +\
'E1 = {} -\n'.format(self.Mtz3phaseLabel) +\
'E2 = {} \n'.format(self.Mtz3FcalcLabel) +\
'labout file 2 - \n' +\
'E1 = PHIC_{} - \n'.format(self.renameLabels[2]) +\
'E2 = FC_{} \n'.format(self.renameLabels[2]) +\
'ctypin file 2 - \n' +\
'E1 = P -\n' +\
'E2 = F \n'
else:
cmd2 = 'title CAD JOB\n' +\
'monitor BRIEF\n' +\
'labin file 1 - \n' +\
'E1 = {} \n'.format(self.Mtz2FPlabel) +\
'labout file 1 - \n' +\
'E1 = FP_{} \n'.format(self.renameLabels[1]) +\
'ctypin file 1 - \n' +\
'E1 = F \n' +\
'labin file 2 - \n' +\
'E1 = {} -\n'.format(self.Mtz3phaseLabel) +\
'E2 = {} \n'.format(self.Mtz3FcalcLabel) +\
'labout file 2 - \n' +\
'E1 = PHIC_{} - \n'.format(self.renameLabels[2]) +\
'E2 = FC_{} \n'.format(self.renameLabels[2]) +\
'ctypin file 2 - \n' +\
'E1 = P -\n' +\
'E2 = F \n'
self.outputLogfile = 'CADlogfile.txt'
# run CAD job
job = ccp4Job(jobName='CAD', commandInput1=cmd1,
commandInput2=cmd2, outputDir=self.outputDir,
outputLog=self.outputLogfile,
outputFile=self.outputMtz)
self.jobSuccess = job.checkJobSuccess(self.runLog)
def runFFT(self):
# run FFT job using the external ccp4Job class
F1, F2 = self.labels1[0], self.labels2[0]
SIG1, SIG2 = self.labels1[1], self.labels2[1]
FOM1, FOM2 = self.labels1[2], self.labels2[2]
PHI1, PHI2 = self.labels1[3], self.labels2[3]
self.printPurpose()
cmd1 = 'fft ' +\
'HKLIN {} '.format(self.inputMtzFile) +\
'MAPOUT {} '.format(self.outputMapFile) +\
'SYMINFO syminfo.lib '
# if FOM is specified the weighting is applied to the map
if self.FOMweight.lower() == 'recalculate' or 'preset,' in self.FOMweight.lower():
FOMstring = 'W={}'.format(FOM2)
FOMstring2 = 'W2={}'.format(FOM2)
else:
FOMstring, FOMstring2 = '', ''
# DIFF is the default map option. It calculates a F-F
# difference map between a low and high dataset
if self.mapType == 'DIFF':
if self.useSigLabs:
labinStr = 'LABIN F1={} SIG1={} F2={} SIG2={} '.format(
F1, SIG1, F2, SIG2)
else:
labinStr = 'LABIN F1={} F2={} '.format(F1, F2)
phiStr = 'PHI={} {} PHI2={} {}\n'.format(
PHI2, FOMstring, PHI2, FOMstring2)
scaleStr = 'SCALE F1 {} 0.0 F2 {} 0.0\n'.format(
self.F1Scale, self.F2Scale)
# SIMPLE sets the low dataset weight to 0. This is essentially
# map generated only from the high dataset.
if self.mapType == 'SIMPLE':
if self.useSigLabs:
labinStr = 'LABIN F1={} SIG1={} F2={} SIG2={} '.format(
F1, SIG1, F2, SIG2)
else:
labinStr = 'LABIN F1={} F2={} '.format(F1, F2)
phiStr = 'PHI={} {} PHI2={} {}\n'.format(
PHI2, FOMstring, PHI2, FOMstring2)
scaleStr = 'SCALE F1 {} 0.0 F2 0.0 0.0\n'.format(
self.F1Scale, self.F2Scale)
# this option is very similar to SIMPLE above, however the
# low dataset is neglected entirely.
# It is designed to superseed SIMPLE now and doesn't require
# a valid low dataset F column to be present
if self.mapType == 'HIGHONLY':
if self.useSigLabs:
labinStr = 'LABIN F1={} SIG1={} '.format(F1, SIG1)
else:
labinStr = 'LABIN F1={} '.format(F1)
phiStr = 'PHI={} {}\n'.format(PHI2, FOMstring)
scaleStr = 'SCALE F1 {} 0.0 '.format(self.F1Scale)
# the option below is distinct from DIFF above, since it allows
# a difference map to be generated after SIGF labels have been
# used here to scale datasets, however does NOT use SIGFs in the
# map calculation
if self.mapType == 'DIFF-NO-SIGMA':
labinStr = 'LABIN F1={} F2={} '.format(F1, F2)
phiStr = 'PHI={} {} PHI2={} {}\n'.format(
PHI1, FOMstring, PHI2, FOMstring2)
scaleStr = 'SCALE F1 {} 0.0 F2 {} 0.0\n'.format(
self.F1Scale, self.F2Scale)
# choose sigmaa-derived FWT and PHIC for 2FOFC map setting
if self.mapType == '2FOFC':
labinStr = 'LABIN F1={}'.format(F1)
phiStr = 'PHI={}'.format(PHI1)
scaleStr = 'SCALE F1 1.0 0.0'
# for case of FC map generation
if self.mapType == 'FC':
labinStr = 'LABIN F1={}'.format(F1)
phiStr = 'PHI={}'.format(PHI1)
scaleStr = 'SCALE F1 {} 0.0'.format(self.F1Scale)
# include a resolution cutoff if specified (not used for Fcalc maps)
resStr = ''
if self.mapType != 'FC':
if self.highResCutoff != '':
resStr = 'RESOLUTION {}'.format(self.highResCutoff)
if self.lowResCutoff != '':
resStr += ' {}'.format(self.lowResCutoff)
resStr += '\n'
cmd2 = 'AXIS {} {} {}\n'.format(
self.fastAxis, self.medAxis, self.slowAxis) +\
'title FTT DENSITY MAP RUN\n' +\
'grid {} {} {}\n'.format(
self.gridSamp1, self.gridSamp2, self.gridSamp3) +\
'xyzlim 0 1 0 1 0 1\n' +\
'{}'.format(resStr) +\
'{} {}\n{}\nEND'.format(labinStr, phiStr, scaleStr)
self.outputLogfile = 'FFTlogfile.txt'
# run FFT job
job = ccp4Job(jobName='FFT', commandInput1=cmd1,
commandInput2=cmd2,
outputDir=self.outputDir, outputLog=self.outputLogfile,
outputFile=self.outputMapFile)
self.jobSuccess = job.checkJobSuccess(self.runLog)
def runSFALL(self):
# run SFALL job using the external ccp4Job class
self.printPurpose()
title = 'run of sfall'
if self.task == 'atom map':
# use to make an atom-tagged map from a coordinate model
self.commandInput1 = 'sfall ' +\
'XYZIN {} '.format(self.inputPDBfile) +\
'ATOMSF atomsf.lib ' +\
'MAPOUT {} '.format(self.outputMapFile) +\
'SYMINFO syminfo.lib '
if len(self.gridDims) == 0:
gridDims = ''
else:
gridDims = 'GRID {} {} {}\n'.format(
self.gridDims[0], self.gridDims[1], self.gridDims[2])
self.commandInput2 = 'MODE ATMMAP {}\n'.format(self.mapoutType) +\
'SYMMETRY {}\n'.format(self.symGroup) +\
'VDWR {}\n'.format(self.VDWR) +\
'title {}\n'.format(title) +\
'{}'.format(gridDims) +\
'END'
elif self.task == 'mtz from pdb':
# make a new Fcalc column in a new mtz file
self.commandInput1 = 'sfall ' +\
'XYZIN {} '.format(self.inputPDBfile) +\
'ATOMSF atomsf.lib ' +\
'HKLOUT {} '.format(self.outputMtzFile) +\
'SYMINFO syminfo.lib '
self.commandInput2 = 'title {}\n'.format(title) +\
'labout FC=FCalc PHIC=PHICalc\n' +\
'NAME -\nPROJECT RIDL -\nCRYSTAL RIDL -\n' +\
'DATASET RIDL\nMODE SFCALC -\nXYZIN\n' +\
'SYMMETRY {}\n'.format(self.symGroup) +\
'BADD 0.0\nVDWR 2.5\nEND'
elif self.task == 'mtz from map':
# otherwise make a new Fcalc column in an input map file
self.commandInput1 = 'sfall ' +\
'MAPIN {} '.format(self.inputMapfile) +\
'ATOMSF atomsf.lib ' +\
'HKLOUT {} '.format(self.outputMtzFile) +\
'SYMINFO syminfo.lib '
self.commandInput2 = 'title {}\n'.format(title) +\
'labout FC=FCalc PHIC=PHICalc\n' +\
'NAME -\nPROJECT RIDL -\nCRYSTAL RIDL -\n' +\
'DATASET RIDL\nMODE SFCALC -\MAPIN\n' +\
'SYMMETRY {}\n'.format(self.symGroup) +\
'BADD 0.0\nVDWR 2.5\nEND'
self.outputLogfile = 'SFALLlogfile.txt'
# run SFALL job
job = ccp4Job(jobName='SFALL',
commandInput1=self.commandInput1,
commandInput2=self.commandInput2,
outputDir=self.outputDir,
outputLog=self.outputLogfile,
outputFile=self.outputFile)
self.jobSuccess = job.checkJobSuccess(self.runLog)
def runFFT(self):
# run FFT job using the external ccp4Job class
self.printPurpose()
self.commandInput1 = (
"fft "
+ "HKLIN {} ".format(self.inputMtzFile)
+ "MAPOUT {} ".format(self.outputMapFile)
+ "SYMINFO syminfo.lib "
)
# if FOM is specified the weighting is applied to the map
if self.FOMweight == "recalculate" or "preset," in self.FOMweight:
FOMstring = "W={}".format(self.FOM2)
FOMstring2 = "W2={}".format(self.FOM2)
else:
FOMstring, FOMstring2 = "", ""
# if DIFFERENCE or SIMPLE map types map type chosen
if self.mapType in ("DIFF", "SIMPLE"):
labinStr = "LABIN F1={} SIG1={} F2={} SIG2={} ".format(self.F1, self.SIG1, self.F2, self.SIG2)
phiStr = "PHI={} {} PHI2={} {}\n".format(self.PHI2, FOMstring, self.PHI2, FOMstring2)
# can distinguish here between SIMPLE and DIFFERENCE map types
if self.mapType == "SIMPLE":
self.F2Scale = 0.0
scaleStr = "SCALE F1 {} 0.0 F2 {} 0.0\n".format(self.F1Scale, self.F2Scale)
# choose sigmaa-derived FWT and PHIC for 2FOFC map setting
if self.mapType == "2FOFC":
labinStr = "LABIN F1={}".format(self.F1)
phiStr = "PHI={}".format(self.PHI1)
scaleStr = "SCALE F1 1.0 0.0"
# for case of FC map generation
if self.mapType == "FC":
labinStr = "LABIN F1={}".format(self.F1)
phiStr = "PHI={}".format(self.PHI1)
scaleStr = "SCALE F1 {} 0.0".format(self.F1Scale)
# include a resolution cutoff if specified (not used for Fcalc maps)
resStr = ""
if self.mapType != "FC":
if self.highResCutoff != "":
resStr = "RESOLUTION {}".format(self.highResCutoff)
if self.lowResCutoff != "":
resStr += " {}".format(self.lowResCutoff)
resStr += "\n"
self.commandInput2 = (
"AXIS {} {} {}\n".format(self.fastAxis, self.medAxis, self.slowAxis)
+ "title FTT DENSITY MAP RUN\n"
+ "grid {} {} {}\n".format(self.gridSamp1, self.gridSamp2, self.gridSamp3)
+ "xyzlim 0 1 0 1 0 1\n"
+ "{}".format(resStr)
+ "{} {}\n{}\n".format(labinStr, phiStr, scaleStr)
+ "END"
)
self.outputLogfile = "FFTlogfile.txt"
# run FFT job
job = ccp4Job(
jobName="FFT",
commandInput1=self.commandInput1,
commandInput2=self.commandInput2,
outputDir=self.outputDir,
outputLog=self.outputLogfile,
outputFile=self.outputMapFile,
)
self.jobSuccess = job.checkJobSuccess()
