Python XSDataInputStrategy.setSample方法代码示例

# 需要导入模块: from XSDataMXv1 import XSDataInputStrategy [as 别名]
# 或者: from XSDataMXv1.XSDataInputStrategy import setSample [as 别名]
 def doCharacterisationSuccess(self, _edPlugin=None):
     EDVerbose.DEBUG("EDPluginControlCharForReorientationv2_0.doCharacterisationSuccess")
     self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv2_0.doCharacterisationSuccess")
     self.xsDataResultCharacterisation = self.edPluginControlCharacterisation.getDataOutput()
     # Check if kappa strategy is requested:
     if self.strPluginStrategyName is not None:
         self.edPluginControlStrategy = self.loadPlugin(self.strPluginStrategyName, \
                                                                "MXv2KappaStrategy")
         xsDataInputStrategy = XSDataInputStrategy()
         xsDataSolutionSelected = self.xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
         xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
         xsDataInputStrategy.setSample(self.xsDataResultCharacterisation.getDataCollection().getSample())
         xsDataIntegrationSubWedgeResultList = self.xsDataResultCharacterisation.getIntegrationResult().getIntegrationSubWedgeResult()
         xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
         xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
         xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
         xsDataInputStrategy.setDataCollection(self.mxv1InputCharacterisation.getDataCollection())
         xsDataInputStrategy.setXdsBackgroundImage(self.xsDataResultCharacterisation.getXdsBackgroundImage())
         for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
             xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
         xsDataInputStrategy.setDiffractionPlan(self.xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
         self.edPluginControlStrategy.setDataInput(xsDataInputStrategy, "mxv1InputStrategy")
         self.edPluginControlStrategy.setDataInput(self.mxv2DataCollection, "mxv2DataCollection")
         self.edPluginControlStrategy.setDataInput(self.xsDataResultCharacterisation.getIndexingResult(), "mxv1IndexingResult")
         self.edPluginControlStrategy.connectSUCCESS(self.doStrategySuccess)
         self.edPluginControlStrategy.connectFAILURE(self.doStrategyFailure)
         self.executePluginSynchronous(self.edPluginControlStrategy)

# 需要导入模块: from XSDataMXv1 import XSDataInputStrategy [as 别名]
# 或者: from XSDataMXv1.XSDataInputStrategy import setSample [as 别名]
    def doIntegrationToStrategyTransition(self, _edPlugin=None):
        EDVerbose.DEBUG("EDPluginControlInducedRadiationProcessv10.doIntegrationToStrategyTransition")
        self.retrieveSuccessMessages(_edPlugin, "EDPluginControlInducedRadiationProcessv10.doIntegrationToStrategyTransition")

        xsDataIntegrationOutput = self.__edPluginIntegration.getDataOutput()
        self.__xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
        #EDVerbose.DEBUG( self.__xsDataExperimentCharacterisation.marshal() )
        xsDataInputStrategy = XSDataInputStrategy()

        xsDataSolutionSelected = self.__xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()

        xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
        xsDataInputStrategy.setSample(self.__xsDataResultCharacterisation.getDataCollection().getSample())

        xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()

        xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
        xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
        xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
        xsDataInputStrategy.setDataCollection(self.getDataInput().getDataCollection())
        for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
            xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())

        xsDataInputStrategy.setDiffractionPlan(self.__xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())

        #print xsDataInputStrategy.marshal()
        self.__edPluginStrategy.setDataInput(xsDataInputStrategy)
        self.__edPluginStrategy.executeSynchronous()

# 需要导入模块: from XSDataMXv1 import XSDataInputStrategy [as 别名]
# 或者: from XSDataMXv1.XSDataInputStrategy import setSample [as 别名]
 def doSuccessIntegration(self, _edPlugin=None):
     EDVerbose.DEBUG("EDPluginControlCharacterisationv1_3.doSuccessIntegration")
     self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv1_3.doSuccessIntegration")
     # Wait for XDS plugin if necessary
     self._edPluginControlXDSGenerateBackgroundImage.synchronize()
     self.addStatusMessage("Integration successful.")
     xsDataIntegrationOutput = self._edPluginControlIntegration.getDataOutput()
     self._xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
     # Integration short summary
     if self._edPluginControlIntegration.hasDataOutput("integrationShortSummary"):
         self._strCharacterisationShortSummary += self._edPluginControlIntegration.getDataOutput("integrationShortSummary")[0].getValue()
     #EDVerbose.DEBUG( self._xsDataExperimentCharacterisation.marshal() )
     if self._bDoStrategyCalculation:
         xsDataInputStrategy = XSDataInputStrategy()
         xsDataSolutionSelected = self._xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()
         xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
         xsDataInputStrategy.setSample(self._xsDataResultCharacterisation.getDataCollection().getSample())
         xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()
         xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
         xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
         xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
         xsDataInputStrategy.setXdsBackgroundImage(self._xsDataFileXdsBackgroundImage)
         for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
             xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
         xsDataInputStrategy.setDiffractionPlan(self._xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
         self._edPluginControlStrategy.setDataInput(xsDataInputStrategy)
         self.executePluginSynchronous(self._edPluginControlStrategy)

# 需要导入模块: from XSDataMXv1 import XSDataInputStrategy [as 别名]
# 或者: from XSDataMXv1.XSDataInputStrategy import setSample [as 别名]
    def doIntegrationToStrategyTransition(self, _edPlugin=None):
        self.DEBUG("EDPluginControlCharacterisationv2_0.doIntegrationToStrategyTransition")
        self.retrieveSuccessMessages(_edPlugin, "EDPluginControlCharacterisationv2_0.doIntegrationToStrategyTransition")

        xsDataIntegrationOutput = self.edPluginIntegration.getDataOutput()
        self.xsDataResultCharacterisation.setIntegrationResult(xsDataIntegrationOutput)
        #self.DEBUG( self.xsDataExperimentCharacterisation.marshal() )
        from XSDataMXv1 import XSDataInputStrategy
        xsDataInputStrategyOLD = XSDataInputStrategy()

        xsDataSolutionSelected = self.xsDataResultCharacterisation.getIndexingResult().getSelectedSolution()

        xsDataInputStrategyOLD.setCrystalRefined(xsDataSolutionSelected.getCrystal())
        xsDataInputStrategyOLD.setSample(self.xsDataResultCharacterisation.getDataCollection().getSample())

        xsDataIntegrationSubWedgeResultList = xsDataIntegrationOutput.getIntegrationSubWedgeResult()

        xsDataInputStrategyOLD.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
        xsDataInputStrategyOLD.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
        xsDataInputStrategyOLD.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())

        for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
            xsDataInputStrategyOLD.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())

        xsDataInputStrategyOLD.setDiffractionPlan(self.xsDataResultCharacterisation.getDataCollection().getDiffractionPlan())
        xsDataInputStrategyOLD.setXdsBackgroundImage(self.xsDataResultCharacterisation.getXdsBackgroundImage())

        #print xsDataInputStrategy.marshal()
        self.edPluginStrategy.setDataInput(xsDataInputStrategyOLD, "mxv1InputStrategy")
        if self.hasDataInput("mxv2DataCollection"):
            self.edPluginStrategy.setDataInput(self.getDataInput("mxv2DataCollection")[0], "mxv2DataCollection")
        self.edPluginStrategy.setDataInput(self.xsDataResultCharacterisation.getIndexingResult(), "mxv1IndexingResult")
        self.edPluginStrategy.executeSynchronous()

# 需要导入模块: from XSDataMXv1 import XSDataInputStrategy [as 别名]
# 或者: from XSDataMXv1.XSDataInputStrategy import setSample [as 别名]
 def doSuccessIntegration(self, _edPlugin=None):
     self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIntegration")
     self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessIntegration")
     self.addStatusMessage("Integration successful.")
     self.xsDataIntegrationOutput = self.edPluginControlIntegration.getDataOutput()
     # Integration short summary
     if self.edPluginControlIntegration.hasDataOutput("integrationShortSummary"):
         self.strCharacterisationShortSummary += self.edPluginControlIntegration.getDataOutput("integrationShortSummary")[0].getValue()
     # self.DEBUG( self.xsDataExperimentCharacterisation.marshal() )
     if self.bDoOnlyIntegrationWithXMLOutput:
         # Run mtz2various
         xsDataInputMtz2Various = XSDataInputMtz2Various()
         xsDataInputMtz2Various.setMtzfile(self.edPluginControlIntegration.getDataOutput().getIntegrationSubWedgeResult()[0].getGeneratedMTZFile())
         xsDataInputMtz2Various.addLabin(XSDataString("I=I"))
         xsDataInputMtz2Various.addLabin(XSDataString("SIGI=SIGI"))
         xsDataInputMtz2Various.setOutput(XSDataString("USER '(3I4,2F10.1)'"))
         self.edPluginExecMtz2Various.setDataInput(xsDataInputMtz2Various)
         self.edPluginExecMtz2Various.executeSynchronous()
         strHklFilePath = self.edPluginExecMtz2Various.getDataOutput().getHklfile().getPath().getValue()
         strIntegration = EDUtilsFile.readFile(strHklFilePath)
         # Output the result in XML format
         self.xsDataGridScreeningResultIntegration = XSDataGridScreeningResultIntegration()
         self.xsDataGridScreeningResultIntegration.setFileName(os.path.basename(self.strImageFile))
         self.xsDataGridScreeningResultIntegration.setFileDirectory(os.path.dirname(self.strImageFile))
         self.xsDataGridScreeningResultIntegration.setIntegratedData(strIntegration)
     else:
         # We continue with the strategy calculation
         xsDataInputStrategy = XSDataInputStrategy()
         xsDataSolutionSelected = self.xsDataIndexingResult.getSelectedSolution()
         xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
         xsDataInputStrategy.setSample(self.xsDataCollection.getSample())
         xsDataIntegrationSubWedgeResultList = self.xsDataIntegrationOutput.getIntegrationSubWedgeResult()
         xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
         xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
         xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
         xsDataInputStrategy.setDataCollection(self.xsDataCollection)
         for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
             xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
         xsDataInputStrategy.setDiffractionPlan(self.xsDataDiffractionPlan)
         self.edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
         self.edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
         self.edPluginControlStrategy.setDataInput(xsDataInputStrategy)
         self.executePluginSynchronous(self.edPluginControlStrategy)

# 需要导入模块: from XSDataMXv1 import XSDataInputStrategy [as 别名]
# 或者: from XSDataMXv1.XSDataInputStrategy import setSample [as 别名]
 def doSuccessIntegration(self, _edPlugin=None):
     self.DEBUG("EDPluginControlGridScreeningv1_0.doSuccessIntegration")
     self.retrieveSuccessMessages(_edPlugin, "EDPluginControlGridScreeningv1_0.doSuccessIntegration")
     self.addStatusMessage("Integration successful.")
     self.xsDataIntegrationOutput = self.edPluginControlIntegration.getDataOutput()
     # Integration short summary
     if self.edPluginControlIntegration.hasDataOutput("integrationShortSummary"):
         self.strCharacterisationShortSummary += self.edPluginControlIntegration.getDataOutput("integrationShortSummary")[0].getValue()
     #self.DEBUG( self.xsDataExperimentCharacterisation.marshal() )
     xsDataInputStrategy = XSDataInputStrategy()
     xsDataSolutionSelected = self.xsDataIndexingResult.getSelectedSolution()
     xsDataInputStrategy.setCrystalRefined(xsDataSolutionSelected.getCrystal())
     xsDataInputStrategy.setSample(self.xsDataCollection.getSample())
     xsDataIntegrationSubWedgeResultList = self.xsDataIntegrationOutput.getIntegrationSubWedgeResult()
     xsDataInputStrategy.setBestFileContentDat(xsDataIntegrationSubWedgeResultList[0].getBestfileDat())
     xsDataInputStrategy.setBestFileContentPar(xsDataIntegrationSubWedgeResultList[0].getBestfilePar())
     xsDataInputStrategy.setExperimentalCondition(xsDataIntegrationSubWedgeResultList[0].getExperimentalConditionRefined())
     for xsDataIntegrationSubWedgeResult in xsDataIntegrationSubWedgeResultList:
         xsDataInputStrategy.addBestFileContentHKL(xsDataIntegrationSubWedgeResult.getBestfileHKL())
     xsDataInputStrategy.setDiffractionPlan(self.xsDataDiffractionPlan)
     self.edPluginControlStrategy.connectSUCCESS(self.doSuccessStrategy)
     self.edPluginControlStrategy.connectFAILURE(self.doFailureStrategy)
     self.edPluginControlStrategy.setDataInput(xsDataInputStrategy)
     self.executePluginSynchronous(self.edPluginControlStrategy)

# 需要导入模块: from XSDataMXv1 import XSDataInputStrategy [as 别名]
# 或者: from XSDataMXv1.XSDataInputStrategy import setSample [as 别名]

#.........这里部分代码省略.........
        xsDataGoniostat = XSDataGoniostat()
        xsDataGoniostat.setRotationAxis(XSDataString("phi"))
        xsExperimentalCondition.setGoniostat(xsDataGoniostat)

        xsDataStrategy.setExperimentalCondition(xsExperimentalCondition)


        # Best Files
        bestFileContentDat = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.dat"))
        xsDataStrategy.setBestFileContentDat(XSDataString(bestFileContentDat))
        bestFileContentPar = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.par"))
        xsDataStrategy.setBestFileContentPar(XSDataString(bestFileContentPar))
        bestFileContentHKL = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile1.hkl"))
        xsDataStrategy.addBestFileContentHKL(XSDataString(bestFileContentHKL))

        # Crystal

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

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

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

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

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

        xsDataSolvent = XSDataSolvent()
        xsDataAtomicComposition = XSDataAtomicComposition()

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

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

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

        xsDataSampleCrystalMM.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1), XSDataLength(0.1)))

        xsDataCrystal = XSDataCrystal()
        xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
                                angle_beta=XSDataAngle(90.0),
                                angle_gamma=XSDataAngle(90.0),
                                length_a=XSDataLength(78.9),
                                length_b=XSDataLength(95.162),
                                length_c=XSDataLength(104.087))
        xsDataCrystal.setCell(xsDataCell)

        xsDataSpaceGroup = XSDataSpaceGroup()
        xsDataSpaceGroup.setITNumber(XSDataInteger(16))
        xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)

        xsDataSampleCrystalMM.setSusceptibility(XSDataDouble(1.5))

        xsDataStrategy.setCrystalRefined(xsDataCrystal)

        xsDataStrategy.setSample(xsDataSampleCrystalMM)

        xsDataStrategy.exportToFile(self.strObtainedInputFile)

        pyStrExpectedInput = self.readAndParseFile (self.strReferenceInputFile)
        pyStrObtainedInput = self.readAndParseFile (self.strObtainedInputFile)

        xsDataInputExpected = XSDataInputStrategy.parseString(pyStrExpectedInput)
        xsDataInputObtained = XSDataInputStrategy.parseString(pyStrObtainedInput)

        EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())