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Python XSDataSampleCrystalMM.setChemicalComposition方法代码示例

本文整理汇总了Python中XSDataMXv1.XSDataSampleCrystalMM.setChemicalComposition方法的典型用法代码示例。如果您正苦于以下问题：Python XSDataSampleCrystalMM.setChemicalComposition方法的具体用法？Python XSDataSampleCrystalMM.setChemicalComposition怎么用？Python XSDataSampleCrystalMM.setChemicalComposition使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类XSDataMXv1.XSDataSampleCrystalMM的用法示例。


在下文中一共展示了XSDataSampleCrystalMM.setChemicalComposition方法的4个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: testSetDataModelInput

# 需要导入模块: from XSDataMXv1 import XSDataSampleCrystalMM [as 别名]
# 或者: from XSDataMXv1.XSDataSampleCrystalMM import setChemicalComposition [as 别名]
    def testSetDataModelInput(self):
        edPluginStrategy = self.createPlugin()
        strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration_ESRF.xml")
        edConfiguration = EDConfiguration(strPathToTestConfigFile)
        dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
        edPluginStrategy.setConfig(dictItem)
        edPluginStrategy.configure()

        xsDataStrategy = XSDataInputStrategy()

        # Beam

        xsExperimentalCondition = XSDataExperimentalCondition()

        xsBeam = XSDataBeam()
        xsBeam.setFlux(XSDataFlux(1e+12))
        xsBeam.setWavelength(XSDataWavelength(2.41))
        xsBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1)))
        xsBeam.setExposureTime(XSDataTime(1))

        xsExperimentalCondition.setBeam(xsBeam)

        # Detector and Exposure Time

        xsDataDetector = XSDataDetector()
        xsDataDetector.setType(XSDataString("q210-2x"))
        xsExperimentalCondition.setDetector(xsDataDetector)

        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)))

#.........这里部分代码省略.........
开发者ID:IvarsKarpics，项目名称:edna-mx，代码行数:103，代码来源:EDTestCasePluginUnitControlStrategyv1_3.py

示例2: testGetXSDataRaddoseInput

# 需要导入模块: from XSDataMXv1 import XSDataSampleCrystalMM [as 别名]
# 或者: from XSDataMXv1.XSDataSampleCrystalMM import setChemicalComposition [as 别名]
    def testGetXSDataRaddoseInput(self):
        """
        """
        from XSDataCommon import XSDataLength
        from XSDataCommon import XSDataWavelength
        from XSDataCommon import XSDataFlux
        from XSDataCommon import XSDataSize
        from XSDataCommon import XSDataDouble
        from XSDataCommon import XSDataString
        from XSDataCommon import XSDataAngle
        from XSDataCommon import XSDataTime
        from XSDataCommon import XSDataInteger

        from XSDataMXv1   import XSDataBeam
        from XSDataMXv1   import XSDataStructure
        from XSDataMXv1   import XSDataChain
        from XSDataMXv1   import XSDataAtom
        from XSDataMXv1   import XSDataLigand
        from XSDataMXv1   import XSDataCrystal
        from XSDataMXv1   import XSDataSpaceGroup
        from XSDataMXv1   import XSDataSampleCrystalMM
        from XSDataMXv1   import XSDataChemicalCompositionMM
        from XSDataMXv1   import XSDataAtomicComposition
        from XSDataMXv1   import XSDataSolvent
        from XSDataMXv1   import XSDataCell

        from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10

        EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
        from XSDataRaddosev10 import XSDataRaddoseInput

        xsDataBeam = XSDataBeam()
        xsDataBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1)))
        xsDataBeam.setWavelength(XSDataWavelength(2.41))
        xsDataBeam.setFlux(XSDataFlux(1e+12))

        xsDataSample = 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)
        xsDataAtom2 = XSDataAtom()
        xsDataAtom2.setSymbol(XSDataString("S"))
        xsDataAtom2.setNumberOf(XSDataDouble(5))
        xsDataAtomicComposition.addAtom(xsDataAtom2)
        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()
        xsDataAtom3 = XSDataAtom()
        xsDataAtom3.setSymbol(XSDataString("Fe"))
        xsDataAtom3.setNumberOf(XSDataDouble(1))
        xsDataAtomicComposition.addAtom(xsDataAtom3)
        xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
        xsDataStructure.addLigand(xsDataLigand)
        xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))

        xsDataSolvent = XSDataSolvent()
        xsDataAtomicComposition = XSDataAtomicComposition()
        xsDataAtomNa = XSDataAtom()
        xsDataAtomNa.setSymbol(XSDataString("Na"))
        xsDataAtomNa.setConcentration(XSDataDouble(1000))
        xsDataAtomicComposition.addAtom(xsDataAtomNa)
        xsDataAtomCl = XSDataAtom()
        xsDataAtomCl.setSymbol(XSDataString("Cl"))
        xsDataAtomCl.setConcentration(XSDataDouble(1000))
        xsDataAtomicComposition.addAtom(xsDataAtomCl)
        xsDataSolvent.setAtoms(xsDataAtomicComposition)

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

        xsDataSample.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1), XSDataLength(0.1)))
        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 = XSDataCrystal()
        xsDataSpaceGroup = XSDataSpaceGroup()
#.........这里部分代码省略.........
开发者ID:antolinos，项目名称:edna，代码行数:103，代码来源:EDTestCaseEDHandlerRaddosev10.py

示例3: testSetDataModelInput

# 需要导入模块: from XSDataMXv1 import XSDataSampleCrystalMM [as 别名]
# 或者: from XSDataMXv1.XSDataSampleCrystalMM import setChemicalComposition [as 别名]
    def testSetDataModelInput(self):
        from XSDataCCP4iv1_1 import XSDataInputCCP4i
        xsDataInputCCP4i = XSDataInputCCP4i()

        # Beam
        from XSDataCommon import XSDataFlux
        from XSDataCommon import XSDataSize
        from XSDataCommon import XSDataLength
        from XSDataCommon import XSDataFloat

        from XSDataMXv1 import XSDataBeam
        from XSDataMXv1 import XSDataExperimentalCondition

        xsExperimentalCondition = XSDataExperimentalCondition()

        xsBeam = XSDataBeam()
        xsBeam.setFlux(XSDataFlux(1e+12))
        xsBeam.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1)))
        xsBeam.setMinExposureTimePerImage(XSDataFloat(0.1))
        xsExperimentalCondition.setBeam(xsBeam)

        # Goniostat
        from XSDataCommon import XSDataSpeed
        from XSDataCommon import XSDataAngle

        from XSDataMXv1 import XSDataGoniostat

        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)

#.........这里部分代码省略.........
开发者ID:IvarsKarpics，项目名称:edna-mx，代码行数:103，代码来源:EDTestCasePluginUnitCCP4iv1_1.py

示例4: EDPluginControlStrategyv1_2

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

#.........这里部分代码省略.........
                        self.DEBUG(
                            "EDPluginControlStrategyv1_2.preProcess: Space Group IT Number Found by indexing: %d"
                            % iSpaceGroupITNumber
                        )
                        try:
                            strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
                                str(iSpaceGroupITNumber), strFileSymop
                            )
                        except Exception as detail:
                            strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
                                detail
                            )
                            self.error(strErrorMessage)
                            self.addErrorMessage(strErrorMessage)
                            raise RuntimeError(strErrorMessage)

                if strNumOperators is not None:
                    iNumOperators = int(strNumOperators)
                else:
                    strErrorMessage = "EDPluginControlStrategyv1_2: No symmetry operators found for Space Group: {0}".format(
                        strNumOperators
                    )
                    self.error(strErrorMessage)
                    self.addErrorMessage(strErrorMessage)
                    raise RuntimeError(strErrorMessage)

                xsDataChemicalComposition = self._xsDataSampleCopy.getChemicalComposition()

                if xsDataChemicalComposition is None:
                    # create a default chemical composition and assign it to the sample
                    xsDataDefaultChemicalComposition = self.getDefaultChemicalComposition(
                        self._xsDataSampleCopy, iNumOperators
                    )
                    self._xsDataSampleCopy.setChemicalComposition(xsDataDefaultChemicalComposition)
                else:
                    # Check for Sulfur atoms, if none, add native sulfur atoms
                    xsDataUpdatedChemicalComposition = self.updateChemicalComposition(xsDataChemicalComposition)
                    self._xsDataSampleCopy.setChemicalComposition(xsDataUpdatedChemicalComposition)

                # create Data Input for Raddose
                from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10

                self._edHandlerXSDataRaddose = EDHandlerXSDataRaddosev10()
                xsDataBeam = self.getDataInput().getExperimentalCondition().getBeam()

                # Calculate number of images (MXSUP-1616):
                iNumberOfImages = None
                xsDataCollection = self.dataInput.dataCollection
                if xsDataCollection is not None:
                    iNumberOfImages = 0
                    for xsDataSubWedge in xsDataCollection.subWedge:
                        xsDataGoniostat = xsDataSubWedge.experimentalCondition.goniostat
                        iOscStart = xsDataGoniostat.rotationAxisStart.value
                        iOscEnd = xsDataGoniostat.rotationAxisEnd.value
                        iOscWidth = xsDataGoniostat.oscillationWidth.value
                        iNumberOfImages += int(round((iOscEnd - iOscStart) / iOscWidth, 0))
                if iNumberOfImages is None:
                    iNumberOfImages = 1
                    self.WARNING("No goniostat information, number of images for RADDOSE set to 1")

                xsDataRaddoseInput = self._edHandlerXSDataRaddose.getXSDataRaddoseInput(
                    xsDataBeam, self._xsDataSampleCopy, iNumOperators, iNumberOfImages
                )
                if xsDataRaddoseInput is not None:
                    self._edPluginRaddose.setDataInput(xsDataRaddoseInput)
                    self._edPluginRaddose.setBaseDirectory(self.getWorkingDirectory())
开发者ID:jordiandreu，项目名称:edna-mx，代码行数:70，代码来源:EDPluginControlStrategyv1_2.py


注：本文中的XSDataMXv1.XSDataSampleCrystalMM.setChemicalComposition方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。