def run(self):
inputFiles = [self.inputMtzFile]
if not checkInputsExist(inputFiles, self.runLog):
return False
# can change unique identifier for map type in file name
if self.mapTag == '':
self.mapTag = self.mapType
if self.outputMapFile == '':
self.outputMapFile = '{}-{}_FFT.map'.format(
self.pdbFile.split('.pdb')[0], self.mapTag)
self.runFFT()
if self.jobSuccess:
self.provideFeedback()
self.runLog.writeToLog('Output files:')
self.runLog.writeToLog('{}'.format(self.outputMapFile))
return True
else:
self.runLog.writeToLog('Job did not run successfully, see job ' +
'log file "{}"'.format(self.outputLogfile))
return False
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 run(self):
# a new labelling convention for output files
self.renameLabels = [self.Mtz1LabelRename, self.Mtz2LabelRename,
self.Mtz3LabelRename]
inputFiles = [self.inputMtz2, self.inputMtz3]
if not self.ignoreDset1:
inputFiles += [self.inputMtz1]
if self.FOMWeight.lower() != 'false':
self.FOMtag['out'] = '- \nE3 = FOM_{}'.format(self.renameLabels[0])
self.FOMtag['type'] = '- \nE3 = W'
if self.FOMWeight.lower() == 'recalculate':
self.FOMtag['in'] = '- \nE3 = FOM{}'.format(self.labels[0])
elif 'preset' in self.FOMWeight.lower():
lbl = self.FOMWeight.split(',')[-1]
self.FOMtag['in'] = '- \nE3 = FOM{}'.format(lbl)
if not checkInputsExist(inputFiles, self.runLog):
return False
self.runCAD()
if self.jobSuccess:
self.provideFeedback()
return True
else:
self.runLog.writeToLog('Job did not run successfully, see job' +
'log file "{}"'.format(self.outputLogfile))
return False
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 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 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 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 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 run(self):
inputFiles = [self.inputPDBfile]
if checkInputsExist(inputFiles,self.runLog) is False:
return False
self.runSFALL()
if self.jobSuccess is True:
self.provideFeedback()
return True
else:
ln = 'Job did not run successfully, see job log file "{}"'.format(self.outputLogfile)
self.runLog.writeToLog(ln)
return False
def run(self):
inputFiles = [self.inputMtz]
if checkInputsExist(inputFiles,self.runLog) is False:
return False
self.runSCALEIT()
if self.jobSuccess is True:
self.provideFeedback()
self.runLog.writeToLog('Output files:')
self.runLog.writeToLog('{}'.format(self.outputMtz))
return True
else:
self.runLog.writeToLog('Job did not run successfully, see job log file "{}"'.format(self.outputLogfile))
return False
def run(self):
inputFiles = [self.inputMtz]
if not checkInputsExist(inputFiles,self.runLog):
return False
self.runSCALEIT()
if self.jobSuccess:
self.provideFeedback()
return True
else:
err = 'Job did not run successfully, see job log file "{}"'.format(self.outputLogfile)
self.runLog.writeToLog(err)
return False
def run(self):
inputFiles = [self.inputPDBfile]
if not checkInputsExist(inputFiles, self.runLog):
return False
self.runSFALL()
if self.jobSuccess:
self.provideFeedback()
return True
else:
error(
text='Job did not run successfully, see job log file ' +
'"{}"'.format(self.outputLogfile),
log=self.runLog, type='error')
return False
def run(self):
inputFiles = [self.pdbFile, self.mtzFile, self.effFile]
if not checkInputsExist(inputFiles, self.runLog):
return False
self.runEND()
if self.jobSuccess:
self.provideFeedback()
self.runLog.writeToLog('Output files:')
self.runLog.writeToLog('{}'.format(self.outputMapFile))
return True
else:
self.runLog.writeToLog(
'Job did not run successfully, see job ' +
'log file "{}"'.format(self.outputLogfile))
return False
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 run(self):
inputFiles = [self.inputMtz,self.inputPDB]
if checkInputsExist(inputFiles,self.runLog) is False:
return False
success = self.getSpaceGroup() # get space group from pdb file
if success is False:
return False
self.runSIGMAA()
if self.jobSuccess is True:
self.provideFeedback()
self.runLog.writeToLog('Output files:')
self.runLog.writeToLog('{}'.format(self.outputMtz))
return True
else:
self.runLog.writeToLog('Job did not run successfully, see job log file "{}"'.format(self.outputLogfile))
return False
def run(self):
inputFiles = [self.inputMtz, self.inputPDB]
if not checkInputsExist(inputFiles, self.runLog):
return False
success = self.getSpaceGroup()
if not success:
return False
self.runSIGMAA()
if self.jobSuccess:
self.provideFeedback()
self.runLog.writeToLog('Output files:')
self.runLog.writeToLog('{}'.format(self.outputMtz))
return True
else:
error(text='Job did not run successfully, see job log file ' +
'"{}"'.format(self.outputLogfile),
log=self.runLog, type='error')
return False
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
