Python XSDataDiffractionPlan.setForcedSpaceGroup方法代碼示例

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setForcedSpaceGroup [as 別名]
    def setPluginInput(self, _edPlugin):
        xsDataDiffractionPlan = XSDataDiffractionPlan()
        if (not self.__fMaxExposureTimePerDataCollection is None):
            xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.__fMaxExposureTimePerDataCollection))
        if (not self.__strForcedSpaceGroup is None):
            xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.__strForcedSpaceGroup))
        if (not self.__bAnomalousData is None):
            xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.__bAnomalousData))
        if (not self.__strStrategyOption is None):
            xsDataDiffractionPlan.setStrategyOption(XSDataString(self.__strStrategyOption))
        if (not self.__strComplexity is None):
            xsDataDiffractionPlan.setComplexity(XSDataString(self.__strComplexity))
        _edPlugin.setDataInput(xsDataDiffractionPlan, "diffractionPlan")

        if (not self.__listImagePaths is None):
            for strImagePath in self.__listImagePaths:
                _edPlugin.setDataInput(XSDataString(strImagePath), "imagePaths")

        if (not self.__xsDataInputCharacterisation is None):
            _edPlugin.setDataInput(self.__xsDataInputCharacterisation, "inputCharacterisation")
        if (not self.__fFlux is None):
            _edPlugin.setDataInput(XSDataFloat(self.__fFlux), "flux")
        if (not self.__fMinExposureTimePerImage is None):
            _edPlugin.setDataInput(XSDataFloat(self.__fMinExposureTimePerImage), "minExposureTimePerImage")
        if (not self.__fBeamSize is None):
            _edPlugin.setDataInput(XSDataFloat(self.__fBeamSize), "beamSize")
        if (not self.__bTemplateMode is None):
            _edPlugin.setDataInput(XSDataBoolean(self.__bTemplateMode), "templateMode")
        if (not self.__strGeneratedTemplateFile is None):
            _edPlugin.setDataInput(XSDataString(self.__strGeneratedTemplateFile), "generatedTemplateFile")
        if (not self.__strResultsFilePath is None):
            _edPlugin.setDataInput(XSDataString(self.__strResultsFilePath), "resultsFilePath")
        if (not self.__fBeamPosX is None):
            _edPlugin.setDataInput(XSDataFloat(self.__fBeamPosX), "beamPosX")
        if (not self.__fBeamPosY is None):
            _edPlugin.setDataInput(XSDataFloat(self.__fBeamPosY), "beamPosY")
        if (not self.__iDataCollectionId is None):
            _edPlugin.setDataInput(XSDataInteger(self.__iDataCollectionId), "dataCollectionId")
        if (not self.__strShortComments is None):
            _edPlugin.setDataInput(XSDataString(self.__strShortComments), "shortComments")
        if (not self.__strComments is None):
            _edPlugin.setDataInput(XSDataString(self.__strComments), "comments")
        if (not self.__fTransmission is None):
            _edPlugin.setDataInput(XSDataDouble(self.__fTransmission), "transmission")

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setForcedSpaceGroup [as 別名]
 def createInputCharacterisationFromSubWedges(self):
     self.DEBUG("EDPluginControlInterfacev2_0.createInputCharacterisationFromSubWedges")
     xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
     self.xsDataInputCharacterisation = XSDataInputCharacterisation()
     xsDataCollection = XSDataCollection()
     # Default exposure time (for the moment, this value should be
     # possible to read from the command line)
     xsDataDiffractionPlan = XSDataDiffractionPlan()
     if (not xsDataResultSubWedgeAssemble is None):
         pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
         xsDataCollection.setSubWedge(pyListSubWedge)
         for xsDataSubWedge in pyListSubWedge:
             if (self.strComplexity is not None):
                 xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
             if (self.fFlux is not None):
                 xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFloat(self.fFlux))
             if (self.fBeamSize is not None):
                 xsDataSize = XSDataSize()
                 xsDataSize.setX(XSDataLength(self.fBeamSize))
                 xsDataSize.setY(XSDataLength(self.fBeamSize))
                 xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
             if (self.fBeamPosX is not None):
                 xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
             if (self.fBeamPosY is not None):
                 xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
             if (self.fMinExposureTimePerImage is not None):
                 xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataFloat(self.fMinExposureTimePerImage))
             if (self.fTransmission is not None):
                 xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
     if (self.strForcedSpaceGroup is not None):
         xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
     xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
     xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
     if (self.strStrategyOption is not None):
         xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
     xsDataCollection.setDiffractionPlan(xsDataDiffractionPlan)
     self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setForcedSpaceGroup [as 別名]

#.........這裏部分代碼省略.........
        # possible to read from the command line)
        if self.xsDataDiffractionPlan is None:
            self.xsDataDiffractionPlan = XSDataDiffractionPlan()
        if (not xsDataResultSubWedgeAssemble is None):
            pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
            xsDataCollection.setSubWedge(pyListSubWedge)
            for xsDataSubWedge in pyListSubWedge:
                if (self.strComplexity is not None):
                    self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
                if (self.fFlux is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
                if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
                    xsDataSize = XSDataSize()
                    xsDataSize.setX(XSDataLength(self.fBeamSizeX))
                    xsDataSize.setY(XSDataLength(self.fBeamSizeY))
                    xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
                if (self.fApertureSize is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setApertureSize(XSDataLength(self.fApertureSize))
                if (self.fBeamPosX is not None):
                    xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
                if (self.fBeamPosY is not None):
                    xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
                if (self.fMinExposureTimePerImage is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
                if (self.fTransmission is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
                if (self.fWavelength is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
                if self.fMinOscillationWidth != None:
                    xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
                if self.fMaxOscillationSpeed != None:
                    xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
        if (self.strForcedSpaceGroup is not None):
            self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
        self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
        self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
        if (self.strStrategyOption is not None):
            self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
        xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
        if self.xsDataSample is not None:
            xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
        self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)


    def generateTemplateFile(self, _edPlugin):
        self.DEBUG("EDPluginControlInterfacev1_3.generateTemplateFile")
        self.createInputCharacterisationFromSubWedges()
        if(self.strGeneratedTemplateFile is None):
            self.screen("No argument for command line --generateTemplate key word found!")
        elif (self.xsDataInputCharacterisation is None):
            self.screen("ERROR! Cannot generate template file %s, please check the log files." % self.strGeneratedTemplateFile)
        else:
            self.screen("Generating xml template input file for edna: " + self.strGeneratedTemplateFile + "...")
            self.xsDataInputCharacterisation.exportToFile(self.strGeneratedTemplateFile)


    def doSubWedgeAssembleSUCCESS(self, _edPlugin):
        self.DEBUG("EDPluginControlInterfacev1_3.doSubWedgeAssembleSUCCESS")
        self.createInputCharacterisationFromSubWedges()
        self.runCharacterisationPlugin(_edPlugin)

    def doSubWedgeAssembleFAILURE(self, _edPlugin):
        self.DEBUG("EDPluginControlInterfacev1_3.doSubWedgeAssembleFAILURE")
        self.screen("Execution of " + self.strEDPluginControlSubWedgeAssembleName + "  failed.")
        self.screen("Please inspect the log file for further information.")
        self.setFailure()

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setForcedSpaceGroup [as 別名]

#.........這裏部分代碼省略.........

        xsDataGoniostat = XSDataGoniostat()
        xsDataGoniostat.setMaxOscillationSpeed(XSDataSpeed(0.2))
        xsDataGoniostat.setMinOscillationWidth(XSDataAngle(0.1))
        xsExperimentalCondition.setGoniostat(xsDataGoniostat)
        xsDataInputCCP4i.setExperimentalCondition(xsExperimentalCondition)

        # Sample
        from XSDataCommon import XSDataString
        from XSDataCommon import XSDataFloat
        from XSDataCommon import XSDataString

        from XSDataMXv1 import XSDataStructure
        from XSDataMXv1 import XSDataChain
        from XSDataMXv1 import XSDataAtom
        from XSDataMXv1 import XSDataLigand
        from XSDataMXv1 import XSDataSampleCrystalMM
        from XSDataMXv1 import XSDataChemicalCompositionMM
        from XSDataMXv1 import XSDataAtomicComposition
        from XSDataMXv1 import XSDataSolvent

        xsDataSampleCrystalMM = XSDataSampleCrystalMM()
        xsDataStructure = XSDataStructure()
        xsDataComposition = XSDataChemicalCompositionMM()

        xsDataChain = XSDataChain()
        xsDataChain.setType(XSDataString("protein"))
        xsDataChain.setNumberOfCopies(XSDataFloat(2))
        xsDataAtomicComposition = XSDataAtomicComposition()
        xsDataAtom1 = XSDataAtom()
        xsDataAtom1.setSymbol(XSDataString("Se"))
        xsDataAtom1.setNumberOf(XSDataFloat(4))
        xsDataAtomicComposition.addAtom(xsDataAtom1)

        xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
        xsDataChain.setNumberOfMonomers(XSDataFloat(100))
        xsDataStructure.addChain(xsDataChain)

        xsDataChain2 = XSDataChain()
        xsDataChain2.setType(XSDataString("rna"))
        xsDataChain2.setNumberOfCopies(XSDataFloat(1))
        xsDataChain2.setNumberOfMonomers(XSDataFloat(60))
        xsDataStructure.addChain(xsDataChain2)

        xsDataLigand = XSDataLigand()
        xsDataLigand.setNumberOfCopies(XSDataFloat(2))
        xsDataLigand.setNumberOfLightAtoms(XSDataFloat(42))
        xsDataAtomicComposition = XSDataAtomicComposition()
        xsDataAtom2 = XSDataAtom()
        xsDataAtom2.setSymbol(XSDataString("Fe"))
        xsDataAtom2.setNumberOf(XSDataFloat(1))
        xsDataAtomicComposition.addAtom(xsDataAtom2)
        xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
        xsDataStructure.addLigand(xsDataLigand)
        xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataFloat(0.25))

        xsDataSolvent = XSDataSolvent()
        xsDataAtomicComposition = XSDataAtomicComposition()

        xsDataAtom3 = XSDataAtom()
        xsDataAtom3.setSymbol(XSDataString("Na"))
        xsDataAtom3.setConcentration(XSDataFloat(1000))
        xsDataAtom4 = XSDataAtom()
        xsDataAtom4.setSymbol(XSDataString("Cl"))
        xsDataAtom4.setConcentration(XSDataFloat(1000))

        xsDataAtomicComposition.addAtom(xsDataAtom3)
        xsDataAtomicComposition.addAtom(xsDataAtom4)
        xsDataSolvent.setAtoms(xsDataAtomicComposition)

        xsDataComposition.setStructure(xsDataStructure)
        xsDataComposition.setSolvent(xsDataSolvent)
        xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition)

        xsDataSampleCrystalMM.setSize(XSDataSize(XSDataLength(0.2), XSDataLength(0.2), XSDataLength(0.2)))
        xsDataSampleCrystalMM.setSusceptibility(XSDataFloat(1.5))
        xsDataSampleCrystalMM.setShape(XSDataFloat(2))

        xsDataInputCCP4i.setSample(xsDataSampleCrystalMM)

        from XSDataMXv1 import XSDataDiffractionPlan

        xsDataDiffractionPlan = XSDataDiffractionPlan()

        xsDataDiffractionPlan.setAimedCompleteness(XSDataFloat(95.5))
        xsDataDiffractionPlan.setAimedIOverSigmaAtHighestResolution(XSDataFloat(2.5))
        xsDataDiffractionPlan.setAimedMultiplicity(XSDataFloat(95.5))
        xsDataDiffractionPlan.setAimedResolution(XSDataFloat(3))
        xsDataDiffractionPlan.setComplexity(XSDataString("full"))
        xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString("P222"))
        xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataFloat(10000))

        xsDataInputCCP4i.setDiffractionPlan(xsDataDiffractionPlan)

        from XSDataCommon import XSDataFile

        listInputDataFile = []
        xsDataFile = XSDataFile(XSDataString(self.strXSDataGenerateTemplateFile))
        listInputDataFile.append(xsDataFile)
        xsDataInputCCP4i.setDataFile(listInputDataFile)

# 需要導入模塊: from XSDataMXv1 import XSDataDiffractionPlan [as 別名]
# 或者: from XSDataMXv1.XSDataDiffractionPlan import setForcedSpaceGroup [as 別名]

#.........這裏部分代碼省略.........
        xsDataCollection = XSDataCollection()
        # Default exposure time (for the moment, this value should be
        # possible to read from the command line)
        if self.xsDataDiffractionPlan is None:
            self.xsDataDiffractionPlan = XSDataDiffractionPlan()
        if (not xsDataResultSubWedgeAssemble is None):
            pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
            xsDataCollection.setSubWedge(pyListSubWedge)
            for xsDataSubWedge in pyListSubWedge:
                if (self.strComplexity is not None):
                    self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
                if (self.fFlux is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
                if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
                    xsDataSize = XSDataSize()
                    xsDataSize.setX(XSDataLength(self.fBeamSizeX))
                    xsDataSize.setY(XSDataLength(self.fBeamSizeY))
                    xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
                if (self.fBeamPosX is not None):
                    xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
                if (self.fBeamPosY is not None):
                    xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
                if (self.fMinExposureTimePerImage is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
                if (self.fTransmission is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
                if (self.fWavelength is not None):
                    xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
                if self.fMinOscillationWidth != None:
                    xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
                if self.fMaxOscillationSpeed != None:
                    xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
        if (self.strForcedSpaceGroup is not None):
            self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
        self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
        self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
        if (self.strStrategyOption is not None):
            self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
        xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
        if self.xsDataSample is not None:
            xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
        self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)


    def generateTemplateFile(self, _edPlugin):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.generateTemplateFile")
        self.createInputCharacterisationFromSubWedges()
        if(self.strGeneratedTemplateFile is None):
            EDVerbose.screen("No argument for command line --generateTemplate key word found!")
        elif (self.xsDataInputCharacterisation is None):
            EDVerbose.screen("ERROR! Cannot generate template file %s, please check the log files." % self.strGeneratedTemplateFile)
        else:
            EDVerbose.screen("Generating xml template input file for edna: " + self.strGeneratedTemplateFile + "...")
            self.xsDataInputCharacterisation.exportToFile(self.strGeneratedTemplateFile)


    def doSubWedgeAssembleSUCCESS(self, _edPlugin):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doSubWedgeAssembleSUCCESS")
        self.createInputCharacterisationFromSubWedges()
        self.runCharacterisationPlugin(_edPlugin)

    def doSubWedgeAssembleFAILURE(self, _edPlugin):
        EDVerbose.DEBUG("EDPluginControlInterfacev1_2.doSubWedgeAssembleFAILURE")
        EDVerbose.screen("Execution of " + self.strEDPluginControlSubWedgeAssembleName + "  failed.")
        EDVerbose.screen("Please inspect the log file for further information.")
        self.setFailure()