def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.__strCommandBeamSize = None
self.__strCommandBeamFlux = None
self.__strCommandBeamWavelength = None
self.__strCommandCrystalSize = None
self.__strCommandCrystalCell = None
self.__strCommandCrystalNRES = None
self.__strCommandCrystalNMON = None
self.__strCommandCrystalNDNA = None
self.__strCommandCrystalNRNA = None
self.__strCommandCrystalPATM = None
self.__strCommandCrystalSATM = None
self.__strCommandExposureTime = None
self.__strCommandImages = None
self.__listCommandsRaddose = []
self.__dictResults = {}
# ugly workaround while waiting for RADDOSE XML output file
for strAbsorbedDoseKeyword in EDPluginRaddosev10.__listABSORBED_DOSE:
self.__dictResults[strAbsorbedDoseKeyword] = None
self.__dictResults[EDPluginRaddosev10.__strSOLVENT] = None
self.__fSolvent = None
self.__fTimeToReachHendersonLimit = None
self.setXSDataInputClass(XSDataRaddoseInput)
self.dataOutput = XSDataRaddoseOutput()
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputIfeffit)
self.__strOutputSessionFileName = 'session.sav'
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataMinimalXdsIn)
self.setDataOutput(XSDataMinimalXdsOut())
self.dataOutput.succeeded = XSDataBoolean(False)
self.maxNoProcessors = 10
self.pathToNeggiaPlugin = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputIfeffit)
self.__strOutputSessionFileName = 'session.sav'
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.__strCommandBeamSize = None
self.__strCommandBeamFlux = None
self.__strCommandBeamWavelength = None
self.__strCommandCrystalSize = None
self.__strCommandCrystalCell = None
self.__strCommandCrystalNRES = None
self.__strCommandCrystalNMON = None
self.__strCommandCrystalNDNA = None
self.__strCommandCrystalNRNA = None
self.__strCommandCrystalPATM = None
self.__strCommandCrystalSATM = None
self.__strCommandExposureTime = None
self.__strCommandImages = None
self.__listCommandsRaddose = []
self.__dictResults = {}
# ugly workaround while waiting for RADDOSE XML output file
for strAbsorbedDoseKeyword in EDPluginRaddosev10.__listABSORBED_DOSE:
self.__dictResults[ strAbsorbedDoseKeyword ] = None
self.__dictResults[ EDPluginRaddosev10.__strSOLVENT ] = None
self.__fSolvent = None
self.__fTimeToReachHendersonLimit = None
self.setXSDataInputClass(XSDataRaddoseInput)
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputH5ToCBF)
self.setDataOutput(XSDataResultH5ToCBF())
self.CBFFile = None
self.CBFFileTemplate = None
self.tmpCBFFile = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputFIT2DCake)
self.m_strOutputFilePath = None
self.addCompatibleVersion("PROGRAM FIT2D Version: V15.095")
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDozor)
self.setDataOutput(XSDataResultDozor())
self.strImageLinkSubDirectory = "img"
self.defaultFractionPolarization = 0.99
self.defaultImageStep = 1
self.startingAngle = 0.0
self.firstImageNumber = None
self.oscillationRange = None
self.overlap = 0.0
self.ixMin = None
self.iyMin = None
self.ixMax = None
self.iyMax = None
# Default values for ESRF Pilatus6M id23eh1: 1,1230; 1228,1298
self.ixMinPilatus6m = 1
self.ixMaxPilatus6m = 1230
self.iyMinPilatus6m = 1228
self.iyMaxPilatus6m = 1298
# Default values for ESRF Pilatus2M : ID30a1: 1,776; 826,894
self.ixMinPilatus2m = 1
self.ixMaxPilatus2m = 776
self.iyMinPilatus2m = 826
self.iyMaxPilatus2m = 894
# Default values for ESRF Eiger4M : ID30a3: 1,1120; 1025,1140
self.ixMinEiger4m = 1
self.ixMaxEiger4m = 1120
self.iyMinEiger4m = 1025
self.iyMaxEiger4m = 1140
# Bad zones
self.strBad_zona = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputMeasureOffsetSift)
self.inputFiles = []
self.outFile = None
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputBest)
# Version 3.3.0 is deprecated, see bug #532
self.addCompatibleVersion("Version 3.3.0 // 15.11.2009")
self.addCompatibleVersion("Version 3.3.1 // 24.04.2010")
self.addCompatibleVersion("Version 3.3.2 // 25.10.2010")
self.addCompatibleVersion("Version 3.4.0 // 15.11.2010")
self.addCompatibleVersion("Version 3.4.1 // 15.02.2011")
self.addCompatibleVersion("Version 3.4.2 // 05.03.2011")
self.addCompatibleVersion("Version 3.4.3 // 06.05.2011")
self.addCompatibleVersion("Version 3.4.4 // 10.06.2011")
self.addCompatibleVersion("Version 4.1.0 // 02.10.2012")
self.strCONF_BEST_HOME_LABEL = "besthome"
# Default value of strategy complexity
self.strComplexity = "none"
self.strBestHome = None
self.strCommandBestHome = None
self.strCommandBest = None
self.strExposureTime = None
self.strDoseRate = None
self.strDetectorType = None
self.strPathToBestDatFile = None
self.strPathToBestParFile = None
self.listFileBestHKL = []
self.bVersionHigherThan4_0 = False
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.addCompatibleVersion('Version 3.1.0.d // 26.04.2007')
self.addCompatibleVersion('Version 3.1.0.d // 16.07.2007')
self.addCompatibleVersion('Version 3.2.0 // 03.11.2008')
self.strCONF_BEST_HOME_LABEL = "besthome"
# Default value of strategy complexity
self.strComplexity = "none"
self.strBestHome = None
self.strCommandBestHome = None
self.strCommandBest = None
self.strExposureTime = None
self.strDoseRate = None
self.strDetectorType = None
self.strPathToBestDatFile = None
self.strPathToBestParFile = None
self.listFileBestHKL = []
self.setXSDataInputClass(XSDataInputBest)
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDataver)
self.strOutFile = None
self.lstInFiles = []
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setRequiredToHaveConfiguration(True)
self.setXSDataInputClass(XSDataAimless)
self.output_file = None
self.input_file = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDatPorod)
self.gnomFile = None
self.atsasVersion = "2.5.2"
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputCrystFEL)
self.setDataOutput(XSDataResultCrystFEL())
#TODO move to input file
self.partialator_options = "--max-adu=65000 --iterations=1 --model=unity -j 60"
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.addCompatibleVersion('Version 3.1.0.d // 26.04.2007')
self.addCompatibleVersion('Version 3.1.0.d // 16.07.2007')
self.addCompatibleVersion('Version 3.2.0 // 03.11.2008')
self.strCONF_BEST_HOME_LABEL = "besthome"
# Default value of strategy complexity
self.strComplexity = "none"
self.strBestHome = None
self.strCommandBestHome = None
self.strCommandBest = None
self.strExposureTime = None
self.strDoseRate = None
self.strDetectorType = None
self.strPathToBestDatFile = None
self.strPathToBestParFile = None
self.listFileBestHKL = []
self.setXSDataInputClass(XSDataInputBest)
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputBest)
# This version of the Best plugin requires the latest
# version of Best.
self.addCompatibleVersion("Version 4.1.0 // 02.10.2012")
self.strCONF_BEST_HOME_LABEL = "besthome"
# Default value of strategy complexity
self.strComplexity = "none"
self.strBestHome = None
self.strCommandBestHome = None
self.strCommandBest = None
self.strExposureTime = None
self.strDoseRate = None
self.strDetectorType = None
self.strPathToBestDatFile = None
self.strPathToBestParFile = None
self.listFileBestHKL = []
self.bVersionHigherThan4_0 = False
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputBest)
# This version of the Best plugin requires the latest
# version of Best.
self.addCompatibleVersion("Version 4.1.0 // 02.10.2012")
self.strCONF_BEST_HOME_LABEL = "besthome"
# Default value of strategy complexity
self.strComplexity = "none"
self.strBestHome = None
self.strCommandBestHome = None
self.strCommandBest = None
self.strExposureTime = None
self.strDoseRate = None
self.strDetectorType = None
self.strPathToBestDatFile = None
self.strPathToBestParFile = None
self.listFileBestHKL = []
self.bVersionHigherThan4_0 = False
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputSiftDescriptor)
self.strImage = None
self.strKeys = None
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputBest)
# Version 3.3.0 is deprecated, see bug #532
self.addCompatibleVersion("Version 3.3.0 // 15.11.2009")
self.addCompatibleVersion("Version 3.3.1 // 24.04.2010")
self.addCompatibleVersion("Version 3.3.2 // 25.10.2010")
self.addCompatibleVersion("Version 3.4.0 // 15.11.2010")
self.addCompatibleVersion("Version 3.4.1 // 15.02.2011")
self.addCompatibleVersion("Version 3.4.2 // 05.03.2011")
self.addCompatibleVersion("Version 3.4.3 // 06.05.2011")
self.addCompatibleVersion("Version 3.4.4 // 10.06.2011")
self.__strCONF_BEST_HOME_LABEL = "besthome"
# Default value of strategy complexity
self.__strComplexity = "none"
self.__strBestHome = None
self.__strCommandBestHome = None
self.__strCommandBest = None
self.__strExposureTime = None
self.__strDoseRate = None
self.__strDetectorType = None
self.__strPathToBestDatFile = None
self.__strPathToBestParFile = None
self.__listFileBestHKL = []
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataMinimalXdsIn)
self.setDataOutput(XSDataMinimalXdsOut())
self.dataOutput.succeeded = XSDataBoolean(False)
self.maxNoProcessors = 10
self.pathToNeggiaPlugin = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDatPorod)
self.gnomFile = None
self.atsasVersion = "2.5.2"
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDozor)
self.setDataOutput(XSDataResultDozor())
self.strImageLinkSubDirectory = "img"
self.defaultFractionPolarization = 0.99
self.defaultImageStep = 1
self.startingAngle = 0.0
self.firstImageNumber = None
self.oscillationRange = None
self.overlap = 0.0
self.ixMin = None
self.iyMin = None
self.ixMax = None
self.iyMax = None
# Default values for ESRF Pilatus6M
self.ixMinPilatus6m = 1
self.ixMaxPilatus6m = 1270
self.iyMinPilatus6m = 1190
self.iyMaxPilatus6m = 1310
# Default values for ESRF Pilatus2M
self.ixMinPilatus2m = 1
self.ixMaxPilatus2m = 840
self.iyMinPilatus2m = 776
self.iyMaxPilatus2m = 852
# Default values for ESRF Eiger4M
self.ixMinEiger4m = 1
self.ixMaxEiger4m = 840
self.iyMinEiger4m = 776
self.iyMaxEiger4m = 852
# Bad zones
self.strBad_zona = None
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputCrystFEL)
self.setDataOutput(XSDataResultCrystFEL())
self.process_hkl_options = "--max-adu=65000 --scale"
self.process_hkl_type = None
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.addCompatibleVersion(
"Mosflm version 7.0.9 for Image plate and CCD data 14th May 2012")
self.addCompatibleVersion(
"Mosflm version 7.1.2 for Image plate and CCD data 16th June 2014"
)
self.addCompatibleVersion(
"Mosflm version 7.1.3 for Image plate and CCD data 17th February 2015"
)
self.addCompatibleVersion(
"Mosflm version 7.2.0 for IP, CCD and PAD data 5th June 2015")
self.addCompatibleVersion(
"Mosflm version 7.2.1 for IP, CCD and PAD data 10th September 2015"
)
self.addCompatibleVersion(
"Mosflm version 7.3.0 for IP, CCD and PAD data")
self.strMOSFLMNewmatFileName = None
self.strMOSFLMMatrixFileName = None
self.bReversephi = False
self.fPolarization = None
self.iOmega = None
self.strRaster = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputSaxsDelMetadatav1_0)
self.strImage = None
self.strKey = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputSiftDescriptor)
self.strImage = None
self.strKeys = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDataver)
self.strOutFile = None
self.lstInFiles = []
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataString, "paramString")
self.setScriptExecutable(
"/dls_sw/apps/mx-scripts/auto-edna/makeAnEDNAXML-SDA.sh")
def __init__(self):
EDPluginExecProcessScript.__init__(self)
# the 3 regexpes used to parse the output, from max's script
self.start_re = re.compile('Nmol\/asym Matthews Coeff \%solvent P\(tot\)')
self.good_re = re.compile('\S+\s+\S+\s+(\S+)\s+(\S+)')
self.bad_re = re.compile('System')
self.setXSDataInputClass(XSDataMatthewsCoeffIn)
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputCrystFEL)
self.setDataOutput(XSDataResultCrystFEL())
#TODO move to input file
self.partialator_options = "--max-adu=65000 --iterations=1 --model=unity -j 60"
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setRequiredToHaveConfiguration(True)
self.setXSDataInputClass(XSDataAimless)
self.output_file = None
self.input_file = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputMeasureOffsetSift)
self.inputFiles = []
self.outFile = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDamfilt)
self.__strInputPdbFileName = 'input.pdb'
self.__strOutputPdbFileName = 'damfilt.pdb'
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputSaxsAddv1_0)
self.inputImages = []
self.outputImage = None
self.options = None
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputBackground3D)
self.setDataOutput(XSDataResultBackground3D())
self.strImageLinkSubDirectory = "img"
self.defaultFractionPolarization = 0.99
self.defaultImageStep = 1
self.startingAngle = 0.0
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputRsync)
self.strSource = None
self.strDestination = None
self.strOption = None
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(CCP4DataInputFREERFLAG)
self._hklin = None
self._hklout = None
return
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(CCP4DataInputFREERFLAG)
self._hklin = None
self._hklout = None
return
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setRequiredToHaveConfiguration(True)
self.__strXDSInput = None
self.__listJob = None
self.__strImageLinkSubDirectory = "img"
self.__strPathToXGeoCorr = None
self.__strPathToYGeoCorr = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputSaxsAddv1_0)
self.inputImages = []
self.outputImage = None
self.options = None
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setRequiredToHaveConfiguration(True)
self.__strXDSInput = None
self.__listJob = None
self.__strImageLinkSubDirectory = "img"
self.__strPathToXGeoCorr = None
self.__strPathToYGeoCorr = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputFind)
self.__searchPath = None
self.__inputString = None
def __init__(self ):
"""
"""
EDPluginExecProcessScript.__init__(self )
self.setXSDataInputClass(XSDataInputFind)
self.__searchPath = None
self.__inputString = None
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputBackground3D)
self.setDataOutput(XSDataResultBackground3D())
self.strImageLinkSubDirectory = "img"
self.defaultFractionPolarization = 0.99
self.defaultImageStep = 1
self.startingAngle = 0.0
def __init__(self ):
EDPluginExecProcessScript.__init__(self )
self.setXSDataInputClass(XSDataInputRdfit)
self.strScaleIntensityGleFile = self.getBaseName() + "_scaleIntensity.gle"
self.strScaleIntensityPlot = self.strScaleIntensityGleFile.replace(".gle", ".png")
self.strBFactorGleFile = self.getBaseName() + "_bFactor.gle "
self.strBFactorPlot = self.strBFactorGleFile.replace(".gle", ".png")
self.strHtmlPath = self.getBaseName() + ".html"
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputAutoPROC)
self.setDataOutput(XSDataResultAutoPROC())
self.maxNoProcessors = 12
self.pathToNeggiaPlugin = None
self.doScaleWithXscale = False
self.rotationAxis = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputRsync)
self.strSource = None
self.strDestination = None
self.strOption = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDamfilt)
self.__strInputPdbFileName = 'input.pdb'
self.__strOutputPdbFileName = 'damfilt.pdb'
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setRequiredToHaveConfiguration(True)
# from max's script
# start: /Table of resolution bins a/
self.start_re = re.compile('Table of resolution bins a')
# relevant line: /(\S+)\s+--\s+(\S+)/)
self.relevant_re = re.compile('(\S+)\s+--\s+(\S+)')
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDatGnom)
self.datFile = None
self.outFile = None
self.Rg = None
self.skip = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDatGnom)
self.datFile = None
self.outFile = None
self.Rg = None
self.skip = None
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(CCP4DataInputPointlessOrigin)
self._hklin = None
self._xyzin = None
self._hklout = None
return
def __init__(self):
"""
Constructor of EDPluginExecDatcmpv3_0
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDatcmp)
self.listFiles = []
self.fChi = None
self.fFidelity = None
def __init__(self):
"""
Constructor of EDPluginExecDatcmpv2_0
"""
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputDatcmp)
self.listFiles = []
self.fChi = None
self.fFidelity = None
def __init__(self):
"""
"""
EDPluginExecProcessScript.__init__(self)
EDFactoryPluginStatic.loadModule("XSDataMXv1")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
from XSDataMXv2 import XSDataCollection
self.setXSDataInputClass(XSDataCollection, "dataCollection")
self.__pyStrBCMDEF = None
