def runPipeline(self): # read input file success = self.readInputs() if success is False: return 1 # run SIGMAA job sigmaa = SIGMAAjob(self.SIGMAAinputMtz,self.Mtz1LabelName,self.RfreeFlag, self.inputPDBfile,self.outputDir,self.runLog) success = sigmaa.run() if success is False: return 2 self.CADinputMtz1 = sigmaa.outputMtz # run CAD job cad = CADjob(self.CADinputMtz1,self.CADinputMtz2,self.CADinputMtz3, self.Mtz1LabelName,self.Mtz2LabelName,self.Mtz3LabelName, self.Mtz1LabelRename,self.Mtz2LabelRename,self.Mtz3LabelRename, self.CADoutputMtz,self.outputDir,self.runLog) success = cad.run() if success is False: return 3 # run SCALEIT job scaleit = SCALEITjob(self.SCALEITinputMtz,self.SCALEIToutputMtz, self.Mtz1LabelRename,self.Mtz2LabelRename, self.outputDir,self.runLog) success = scaleit.run() if success is False: return 4 # end of pipeline reached return 0
def combineMTZcolumns(self):
# run CAD to combine necessary columns from input mtz files
self.printStepNumber()
cad = CADjob(inputMtz2=self.CADinputMtz2,
inputMtz3=self.CADinputMtz3,
Mtz2FPlabel=self.Mtz2LabelName,
Mtz2SIGFPlabel=self.Mtz2SIGFPlabel,
Mtz2LabelName=self.Mtz2LabelName,
Mtz3phaseLabel=self.Mtz3phaseLabel,
Mtz3FcalcLabel=self.Mtz3FcalcLabel,
Mtz2LabelRename=self.Mtz2LabelRename,
Mtz3LabelRename=self.Mtz3LabelRename,
outputMtz=self.CADoutputMtz,
outputDir=self.outputDir,
runLog=self.runLog,
FOMWeight=self.FOMweight,
ignoreSIGFs=self.ignoreSIGFs)
if self.densMapType != 'HIGHONLY':
cad.inputMtz1 = self.CADinputMtz1
cad.Mtz1FPlabel = self.Mtz1LabelName
cad.Mtz1SIGFPlabel = self.Mtz1SIGFPlabel
cad.Mtz1LabelRename = self.Mtz1LabelRename
else:
cad.ignoreDset1 = True
success = cad.run()
if not success:
error(text='Failure to successfully combine mtz files',
log=self.runLog)
def runPipeline(self):
# run the current subroutine to parse an input
# file and run CAD and SCALEIT to combine the
# mtz information for a low and high dose
# dataset within a damage series
success = self.readInputs()
if not success:
return 1
# copy input mtz files to working directory and rename
self.moveInputMtzs()
# run SIGMAA job if required to generate a new FOM weight column
if self.FFTmapWeight == "recalculate":
if self.densMapType == "2FOFC":
mtzLbls_in = self.Mtz2LabelName
mtzLbls_out = self.Mtz2LabelRename
else:
mtzLbls_in = self.Mtz1LabelName
mtzLbls_out = self.Mtz1LabelName
self.printStepNumber()
sigmaa = SIGMAAjob(
inputMtz=self.SIGMAAinputMtz,
MtzLabelNameIn=mtzLbls_in,
MtzLabelNameOut=mtzLbls_out,
RfreeFlag=self.RfreeFlag1,
inputPDB=self.inputPDBfile,
outputDir=self.outputDir,
runLog=self.runLog,
)
success = sigmaa.run()
if not success:
return 2
# if 2FO-FC map required, use FWT column from sigmaa-output mtz (we are done here)
if self.densMapType == "2FOFC":
self.cleanUpDir()
return 0
self.CADinputMtz1 = sigmaa.outputMtz
else:
self.CADinputMtz1 = self.SIGMAAinputMtz
# run CAD job
self.printStepNumber()
cad = CADjob(
inputMtz1=self.CADinputMtz1,
inputMtz2=self.CADinputMtz2,
inputMtz3=self.CADinputMtz3,
Mtz1LabelName=self.Mtz1LabelName,
Mtz2LabelName=self.Mtz2LabelName,
Mtz3phaseLabel=self.Mtz3phaseLabel,
Mtz3FcalcLabel=self.Mtz3FcalcLabel,
Mtz1LabelRename=self.Mtz1LabelRename,
Mtz2LabelRename=self.Mtz2LabelRename,
Mtz3LabelRename=self.Mtz3LabelRename,
outputMtz=self.CADoutputMtz,
outputDir=self.outputDir,
runLog=self.runLog,
FOMWeight=self.FFTmapWeight,
)
success = cad.run()
if not success:
return 3
# run SCALEIT job
if self.doScaling:
self.printStepNumber()
scaleit = SCALEITjob(
inputMtz=self.SCALEITinputMtz,
outputMtz=self.SCALEIToutputMtz,
Mtz1Label=self.Mtz1LabelRename,
Mtz2Label=self.Mtz2LabelRename,
outputDir=self.outputDir,
runLog=self.runLog,
)
success = scaleit.run()
if not success:
return 4
# end of pipeline reached
self.cleanUpDir()
return 0
