def __init__(self, root, conf_param, activ_code):
CommonFunctions.__init__(self, root, conf_param, activ_code)
self.root = root
self.logFile = logFile()
self.conf_param = conf_param
self.type = "GDB"
self.activ_code = activ_code
self.ds = ""
def __init__(self,root,conf_param,activ_code):
CommonFunctions.__init__(self,root,conf_param,activ_code)
self.root = root
self.logFile = logFile()
self.conf_param = conf_param
self.activ_code = activ_code
self.logs_text = conf_param["logsText"]["report"]
self.ds =""
def __init__(self,where,inputFile,jobName):
# specify where output files should be written
self.outputDir = where
self.makeOutputDir()
self.txtInputFile = inputFile
self.jobName = jobName
self.runLog = logFile('{}/{}_runLog_1.txt'.format(self.outputDir,jobName))
# specify output files for parts of pipeline
self.CADoutputMtz = '{}/{}_CADcombined.mtz'.format(self.outputDir,self.jobName)
self.SCALEITinputMtz = self.CADoutputMtz
self.SCALEIToutputMtz = '{}/{}_SCALEITcombined.mtz'.format(self.outputDir,self.jobName)
def __init__(self, root, conf_param):
"""
Description: Init function
----------
conf_param : Dictionary
the config file
root: string
the folder path
"""
self.file = ""
self.root = root
self.logFile = logFile()
self.conf_param = conf_param
def __init__(self, root, conf_param, activ_cod):
"""
Description: Init function
----------
conf_param : Dictionary
the config file
root: string
the folder path
"""
self.file = ""
self.root = root
self.driver = ''
self.ds = None
self.logFile = logFile()
self.conf_param = conf_param
self.activ_cod = activ_cod
self.nameConvention = True
def startLogFile(self):
# create log file for the current job
self.quickParseInputFile()
self.checkOutputDirExists(printToScreen = self.printOutput)
name = '{}RIDLjob.log'.format(self.outputDir)
logName = lambda x: name.replace('.log','_{}{}'.format(x,'.log'))
i = 1
while os.path.isfile(logName(i)):
i += 1
uniqLogName = logName(i)
log = logFile(fileName = uniqLogName,
fileDir = self.outputDir,
printToScreen = self.printOutput)
self.logFile = log
def __init__(self, outputDir="", inputFile="", jobName="untitled-job", doScaling=True, log=""):
# specify where output files should be written
self.outputDir = outputDir
self.makeOutputDir(dirName=self.outputDir)
self.findFilesInDir()
self.txtInputFile = inputFile
self.jobName = jobName
self.doScaling = doScaling
if log == "":
f = "{}{}_runLog1.log".format(self.outputDir, jobName)
self.runLog = logFile(fileName=f, fileDir=self.outputDir)
else:
self.runLog = log
# specify output files for parts of pipeline
self.CADoutputMtz = "{}{}_CADcombined.mtz".format(self.outputDir, self.jobName)
self.SCALEITinputMtz = self.CADoutputMtz
self.SCALEIToutputMtz = "{}{}_SCALEITcombined.mtz".format(self.outputDir, self.jobName)
def __init__(self,
outputDir = '',
inputFile = '',
jobName = 'untitled-job',
log = '',
useUnscaledMtz = False):
self.outputDir = outputDir
self.inputFile = inputFile
self.jobName = jobName
self.findFilesInDir() # find files initially in working dir
# create log file
if log == '':
f = '{}{}_runLog1.log'.format(self.outputDir,jobName)
self.runLog = logFile(fileName = f,
fileDir = self.outputDir)
else:
self.runLog = log
# provide option to use non-scaleit scaled Fobs(n) for
# density map calculations (retrieved directly from CAD instead)
self.useUnscaledMtz = useUnscaledMtz
def __init__(self,
outputDir='', log='', densMapNaming='', atomMapNaming='',
mtzIn1='./untitled.mtz', Mtz1LabelName='FP',
Mtz1SIGFPlabel='SIGFP', RfreeFlag1='FREE',
Mtz1LabelRename='D1', mtzIn2='./untitled2.mtz',
Mtz2LabelName='FP', Mtz2SIGFPlabel='SIGFP',
Mtz2LabelRename='D2', mtzIn3='./untitled3.mtz',
Mtz3phaseLabel='PHIC', Mtz3FcalcLabel='FC', ignoreSIGFs=False,
Mtz3LabelRename='DP', inputPDBfile='./untitled.pdb',
densMapType='DIFF', scaleType='anisotropic',
deleteIntermediateFiles=True, FOMweight='none',
sfall_VDWR=1, mapResLimits=',', includeFCmaps=True,
useLaterCellDims=True, sfallGRIDdims=[], mapAxisOrder=[],
firstTimeRun=True, premadeAtomMap='', spaceGroup='',
gridSampBeforeCropping=[], cropToModel=False):
# specify where output files should be written
self.outputDir = outputDir
self.makeOutputDir(dirName=self.outputDir)
self.findFilesInDir()
self.densMapNaming = densMapNaming
if atomMapNaming == '':
atomMapNaming = densMapNaming
self.atomMapNaming = atomMapNaming
self.scaleType = scaleType
self.mtzIn1 = mtzIn1
self.Mtz1LabelName = Mtz1LabelName
self.RfreeFlag1 = RfreeFlag1
self.Mtz1LabelRename = Mtz1LabelRename
self.Mtz1SIGFPlabel = Mtz1SIGFPlabel
self.mtzIn2 = mtzIn2
self.Mtz2LabelName = Mtz2LabelName
self.Mtz2LabelRename = Mtz2LabelRename
self.Mtz2SIGFPlabel = Mtz2SIGFPlabel
# Provide option to ignore SIGFs during map calculations.
# Must ensure scaling set to NONE if this chosen
self.ignoreSIGFs = ignoreSIGFs
if ignoreSIGFs:
if scaleType.lower() != 'none':
error(text='Cross-dataset scaling specified, but user has ' +
'specified to ignore all SIGF terms. Incompatible!',
log=self.runLog, type='error')
if densMapType == 'HIGHONLY':
if scaleType.lower() != 'none':
error(text='Cross-dataset scaling specified, but user has ' +
'specified densMapType as "HIGHONLY". Incompatible!',
log=self.runLog, type='error')
self.mtzIn3 = mtzIn3
self.Mtz3phaseLabel = Mtz3phaseLabel
self.Mtz3FcalcLabel = Mtz3FcalcLabel
self.Mtz3LabelRename = Mtz3LabelRename
self.inputPDBfile = inputPDBfile
self.densMapType = densMapType
self.deleteIntermediateFiles = deleteIntermediateFiles
self.FOMweight = FOMweight
self.sfall_VDWR = sfall_VDWR
self.mapResLimits = mapResLimits
self.includeFCmaps = includeFCmaps
self.useLaterCellDims = useLaterCellDims
self.sfallGRIDdims = sfallGRIDdims
self.firstTimeRun = firstTimeRun
self.spaceGroup = spaceGroup
self.axes = mapAxisOrder
self.gridSamps = gridSampBeforeCropping
# usually not crop to model, but crop to asym unit
# to get a smaller output map file
self.cropToModel = cropToModel
self.findFilesInDir()
# create log file
if log == '':
f = '{}{}_runLog1.log'.format(
self.outputDir+'RIDL-log', densMapNaming)
self.runLog = logFile(fileName=f, fileDir=self.outputDir)
else:
self.runLog = log
self.CADoutputMtz = '{}{}_CADcombined.mtz'.format(
self.outputDir, densMapNaming)
self.SCALEIToutputMtz = '{}{}_SCALEITcombined.mtz'.format(
self.outputDir, densMapNaming)
self.PDBCURoutputFile = '{}{}_PDBCUR.pdb'.format(
self.outputDir, atomMapNaming)
self.reorderedPDBFile = '{}{}_curated.pdb'.format(
self.outputDir, atomMapNaming)
if premadeAtomMap == '':
self.atomTaggedMap = '{}{}_SFALL.map'.format(
self.outputDir, atomMapNaming)
else:
self.atomTaggedMap = premadeAtomMap
def __init__(self, root, conf_param, activ_code):
self.root = root
self.conf_param = conf_param
self.activ_code = activ_code
self.logFile = logFile()
elif lyr in dirs:
root2 = os.path.join(path, lyr)
for root3, dirs_lyr, files in os.walk(root2):
VectorLayer = globals()[attri["VectorFormats"]["symbology"]["className"]]
vectortype = VectorLayer(root3,attri,activation_code)
vectortype.checkextension(files)
elif report in dirs:
root2 = os.path.join(path, report)
for root3, dirs_lyr, files in os.walk(root2):
VectorLayer = globals()[attri["VectorFormats"]["report"]["className"]]
vectortype = VectorLayer(root3,attri,activation_code)
vectortype.checkextension(files)
time = logs_text["time"]
#shutil.rmtree(attri["Temp_root"])
time.append(str(datetime.now() - startTime))
#logFile.writelogs(time)
#print("FINISH")
except Exception as ex:
e = logs_text["e"]
e.append(str(ex))
logFile.writelogs(e)
time = logs_text["time"]
time.append(str(datetime.now() - startTime))
logFile.writelogs(time)
logFile = logFile()
main(sys.argv[1],logFile)
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
