예제 #1
0
    def testSetDataInput(self):

        from XSDataRaddosev10 import XSDataRaddoseInput
        edPluginRaddose = self.createPlugin()

        strXMLInputData = self.readAndParseFile(self.strReferenceInputFile)
        edPluginRaddose.setDataInput(strXMLInputData)
        edPluginRaddose.setScriptExecutable("cat")
        edPluginRaddose.preProcess()

        xsDataInput = edPluginRaddose.getDataInput()
        xsDataInput.exportToFile("XSDataInputRaddosev10FromObject.xml")
        strExpectedInput = self.readAndParseFile(self.strReferenceInputFile)
        strObtainedInput = self.readAndParseFile(
            "XSDataInputRaddosev10FromObject.xml")

        xsDataRaddoseInputExpected = XSDataRaddoseInput.parseString(
            strExpectedInput)
        xsDataRaddoseInputObtained = XSDataRaddoseInput.parseString(
            strObtainedInput)

        EDAssert.equal(xsDataRaddoseInputExpected.marshal(),
                       xsDataRaddoseInputObtained.marshal())

        EDAssert.equal("CELL 78.9 95.162 104.087 90.0 90.0 90.0",
                       edPluginRaddose.getCommandCrystalCell())

        EDAssert.equal("NRES 295", edPluginRaddose.getCommandCrystalNRES())
        EDAssert.equal("NMON 8", edPluginRaddose.getCommandCrystalNMON())
        EDAssert.equal(None, edPluginRaddose.getCommandCrystalNDNA())
        EDAssert.equal(None, edPluginRaddose.getCommandCrystalNRNA())
        EDAssert.equal(
            "S",
            xsDataInput.getCrystalPATM().getAtom()[0].getSymbol().getValue())
        EDAssert.equal(
            4,
            xsDataInput.getCrystalPATM().getAtom()[0].getNumberOf().getValue())
        EDAssert.equal(
            "Se",
            xsDataInput.getCrystalPATM().getAtom()[1].getSymbol().getValue())
        EDAssert.equal(
            4,
            xsDataInput.getCrystalPATM().getAtom()[1].getNumberOf().getValue())
        EDAssert.equal("PATM S 4.0 Se 4.0",
                       edPluginRaddose.getCommandCrystalPATM())
        EDAssert.equal(None, xsDataInput.getCrystalSATM())
        EDAssert.equal(None, edPluginRaddose.getCommandCrystalSATM())
        EDAssert.equal("CRYSTAL 0.1 0.1 0.1",
                       edPluginRaddose.getCommandCrystalSize())

        EDAssert.equal("BEAM 0.1 0.1", edPluginRaddose.getCommandBeamSize())
        EDAssert.equal("PHOSEC 1e+12", edPluginRaddose.getCommandBeamFlux())
        EDAssert.equal("WAVELENGTH 2.41",
                       edPluginRaddose.getCommandBeamWavelength())

        EDAssert.equal("EXPOSURE 1.0",
                       edPluginRaddose.getCommandExposureTime())
        EDAssert.equal("IMAGES 1", edPluginRaddose.getCommandImages())

        self.cleanUp(edPluginRaddose)
    def testSetDataInput(self):

        from XSDataRaddosev10 import XSDataRaddoseInput
        edPluginRaddose = self.createPlugin()

        strXMLInputData = self.readAndParseFile (self.strReferenceInputFile)
        edPluginRaddose.setDataInput(strXMLInputData)
        edPluginRaddose.setScriptExecutable("cat")
        edPluginRaddose.preProcess()

        xsDataInput = edPluginRaddose.getDataInput()
        xsDataInput.exportToFile("XSDataInputRaddosev10FromObject.xml")
        strExpectedInput = self.readAndParseFile(self.strReferenceInputFile)
        strObtainedInput = self.readAndParseFile("XSDataInputRaddosev10FromObject.xml")

        xsDataRaddoseInputExpected = XSDataRaddoseInput.parseString(strExpectedInput)
        xsDataRaddoseInputObtained = XSDataRaddoseInput.parseString(strObtainedInput)

        EDAssert.equal(xsDataRaddoseInputExpected.marshal(), xsDataRaddoseInputObtained.marshal())

        EDAssert.equal("CELL 78.9 95.162 104.087 90.0 90.0 90.0", edPluginRaddose.getCommandCrystalCell())

        EDAssert.equal("NRES 295", edPluginRaddose.getCommandCrystalNRES())
        EDAssert.equal("NMON 8", edPluginRaddose.getCommandCrystalNMON())
        EDAssert.equal(None, edPluginRaddose.getCommandCrystalNDNA())
        EDAssert.equal(None, edPluginRaddose.getCommandCrystalNRNA())
        EDAssert.equal("S", xsDataInput.getCrystalPATM().getAtom()[0].getSymbol().getValue())
        EDAssert.equal(4, xsDataInput.getCrystalPATM().getAtom()[0].getNumberOf().getValue())
        EDAssert.equal("Se", xsDataInput.getCrystalPATM().getAtom()[1].getSymbol().getValue())
        EDAssert.equal(4, xsDataInput.getCrystalPATM().getAtom()[1].getNumberOf().getValue())
        EDAssert.equal("PATM S 4.0 Se 4.0", edPluginRaddose.getCommandCrystalPATM())
        EDAssert.equal(None, xsDataInput.getCrystalSATM())
        EDAssert.equal(None, edPluginRaddose.getCommandCrystalSATM())
        EDAssert.equal("CRYSTAL 0.1 0.1 0.1", edPluginRaddose.getCommandCrystalSize())

        EDAssert.equal("BEAM 0.1 0.1", edPluginRaddose.getCommandBeamSize())
        EDAssert.equal("PHOSEC 1e+12", edPluginRaddose.getCommandBeamFlux())
        EDAssert.equal("WAVELENGTH 2.41", edPluginRaddose.getCommandBeamWavelength())

        EDAssert.equal("EXPOSURE 1.0", edPluginRaddose.getCommandExposureTime())
        EDAssert.equal("IMAGES 1", edPluginRaddose.getCommandImages())

        self.cleanUp(edPluginRaddose)
예제 #3
0
    def getXSDataRaddoseInput(self, _xsDataBeam, _xsDataSample, _inumOperators,
                              _iNumberOfImages):

        xsDataRaddoseInput = XSDataRaddoseInput()

        # Beam
        xsDataRaddoseInput.setBeamSize(_xsDataBeam.getSize())
        xsDataRaddoseInput.setBeamFlux(_xsDataBeam.getFlux())
        xsDataRaddoseInput.setBeamWavelength(_xsDataBeam.getWavelength())

        xsDataRaddoseInput.setBeamExposureTime(_xsDataBeam.getExposureTime())
        xsDataRaddoseInput.setNumberOfImages(XSDataInteger(_iNumberOfImages))
        xsDataRaddoseInput.setCrystalCell(_xsDataSample.getCrystal().getCell())

        xsDataRaddoseInput.setCrystalSize(_xsDataSample.getSize())

        xsDataComposition = _xsDataSample.getChemicalComposition()

        xsDataSolvent = xsDataComposition.getSolvent()
        if (xsDataSolvent is not None):
            xsDataRaddoseInput.setCrystalSATM(xsDataSolvent.getAtoms())

        xsDataStructure = xsDataComposition.getStructure()
        if (xsDataStructure is not None):
            xsDataChains = xsDataStructure.getChain()

            totalNRESInStructure = 0
            totalNDNAInStructure = 0
            totalNRNAInStructure = 0
            totalPATM = XSDataAtomicComposition()

            for chain in xsDataChains:
                # heavy atoms of each chain to be added in the PATM
                xsDataAtomicCompositionHeavyAtoms = chain.getHeavyAtoms()
                if (xsDataAtomicCompositionHeavyAtoms is not None):
                    iterator = 1
                    while iterator <= chain.getNumberOfCopies().getValue():
                        totalPATM = self.mergeAtomicComposition(
                            totalPATM, xsDataAtomicCompositionHeavyAtoms)
                        iterator = iterator + 1

                type = chain.getType().getValue()
                numberOfMonomers = chain.getNumberOfMonomers().getValue(
                ) * chain.getNumberOfCopies().getValue()

                if (type == "protein"):
                    totalNRESInStructure = totalNRESInStructure + numberOfMonomers
                elif (type == "dna"):
                    totalNDNAInStructure = totalNDNAInStructure + numberOfMonomers
                elif (type == "rna"):
                    totalNRNAInStructure = totalNRNAInStructure + numberOfMonomers

            xsDataLigands = xsDataStructure.getLigand()
            for ligand in xsDataLigands:

                # Light atoms to be added to the NRES
                nres = ligand.getNumberOfLightAtoms().getValue(
                ) * ligand.getNumberOfCopies().getValue() / 7.85
                totalNRESInStructure = totalNRESInStructure + nres

                # Heavy atoms to be added to the PATM
                if (ligand.getHeavyAtoms() is not None):
                    iterator = 1
                    while iterator <= ligand.getNumberOfCopies().getValue():
                        totalPATM = self.mergeAtomicComposition(
                            totalPATM, ligand.getHeavyAtoms())
                        iterator = iterator + 1

            if (totalNRESInStructure != 0):
                xsDataRaddoseInput.setCrystalNRES(
                    XSDataInteger(int(round(totalNRESInStructure))))
            if (totalNDNAInStructure != 0):
                xsDataRaddoseInput.setCrystalNDNA(
                    XSDataInteger(int(totalNDNAInStructure)))
            if (totalNRNAInStructure != 0):
                xsDataRaddoseInput.setCrystalNRNA(
                    XSDataInteger(int(totalNRNAInStructure)))
            if (len(totalPATM.getAtom()) != 0):
                xsDataRaddoseInput.setCrystalPATM(totalPATM)

            xsDataNumberNumStructInAU = xsDataStructure.getNumberOfCopiesInAsymmetricUnit(
            )
            xsDataNumberNumStructInUC = int(
                xsDataNumberNumStructInAU.getValue() * _inumOperators)
            xsDataRaddoseInput.setCrystalNMON(
                XSDataInteger(xsDataNumberNumStructInUC))

        return xsDataRaddoseInput
    def testSetDataModelInput(self):
        # Crystal
        from XSDataRaddosev10 import XSDataRaddoseInput
        xsDataRaddoseInput = XSDataRaddoseInput()

        from XSDataCommon import XSDataString
        from XSDataCommon import XSDataDouble
        from XSDataCommon import XSDataAngle
        from XSDataCommon import XSDataLength
        from XSDataCommon import XSDataSize
        from XSDataCommon import XSDataInteger
        from XSDataRaddosev10 import XSDataCell
        from XSDataRaddosev10 import XSDataAtom
        from XSDataRaddosev10 import XSDataAtomicComposition

        xsDataAtomSulfur = XSDataAtom()
        xsDataAtomSulfur.setNumberOf(XSDataDouble(4))
        xsDataAtomSulfur.setSymbol(XSDataString("S"))
        xsDataAtomSelenium = XSDataAtom()
        xsDataAtomSelenium.setNumberOf(XSDataDouble(4))
        xsDataAtomSelenium.setSymbol(XSDataString("Se"))

        xsDataAtomicComposition = XSDataAtomicComposition()
        xsDataAtomicComposition.addAtom(xsDataAtomSulfur)
        xsDataAtomicComposition.addAtom(xsDataAtomSelenium)
        xsDataRaddoseInput.setCrystalPATM(xsDataAtomicComposition)
        xsDataRaddoseInput.setCrystalNRES(XSDataInteger(295))
        xsDataRaddoseInput.setCrystalNMON(XSDataInteger(8))
        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))

        xsDataSizeCrystal = XSDataSize(XSDataLength(0.1), XSDataLength(0.1),
                                       XSDataLength(0.1))

        xsDataRaddoseInput.setCrystalCell(xsDataCell)
        xsDataRaddoseInput.setCrystalSize(xsDataSizeCrystal)

        # Beam
        from XSDataCommon import XSDataFlux
        from XSDataCommon import XSDataWavelength
        from XSDataCommon import XSDataTime

        xsDataSize = XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1))

        xsDataRaddoseInput.setBeamSize(xsDataSize)
        xsDataRaddoseInput.setBeamFlux(XSDataFlux(1e+12))
        xsDataRaddoseInput.setBeamWavelength(XSDataWavelength(2.41))
        xsDataRaddoseInput.setBeamExposureTime(XSDataTime(1))

        xsDataRaddoseInput.setNumberOfImages(XSDataInteger(1))

        xsDataRaddoseInput.exportToFile(self.strObtainedInputFile)

        strExpectedInput = self.readAndParseFile(self.strReferenceInputFile)
        strObtainedInput = self.readAndParseFile(self.strObtainedInputFile)

        xsDataRaddoseInputExpected = XSDataRaddoseInput.parseString(
            strExpectedInput)
        xsDataRaddoseInputObtained = XSDataRaddoseInput.parseString(
            strObtainedInput)

        EDAssert.equal(xsDataRaddoseInputExpected.marshal(),
                       xsDataRaddoseInputObtained.marshal())
    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()

        xsDataCrystal.setCell(xsDataCell)

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

        xsDataSample.setCrystal(xsDataCrystal)

        iNumSymOperators = 4


        xsDataRaddosev01Input = EDHandlerXSDataRaddosev10().getXSDataRaddoseInput(xsDataBeam,
                                                                                      xsDataSample,
                                                                                      iNumSymOperators)


        xsDataRaddosev01Input.exportToFile(self.strObtainedInputFile2)
        strExpectedInput = EDUtilsTest.readAndParseFile (self.strReferenceInputFile2)
        strObtainedInput = EDUtilsTest.readAndParseFile (self.strObtainedInputFile2)

        xsDataInputExpected = XSDataRaddoseInput.parseString(strExpectedInput)
        xsDataInputObtained = XSDataRaddoseInput.parseString(strObtainedInput)

        EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())
    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))
        xsDataBeam.setExposureTime(XSDataTime(0.037))

        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()

        xsDataCrystal.setCell(xsDataCell)

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

        xsDataSample.setCrystal(xsDataCrystal)

        iNumSymOperators = 4
        iNumberOfImages = 2

        xsDataRaddosev01Input = EDHandlerXSDataRaddosev10(
        ).getXSDataRaddoseInput(xsDataBeam, xsDataSample, iNumSymOperators,
                                iNumberOfImages)

        xsDataRaddosev01Input.exportToFile(self.strObtainedInputFile2)
        strExpectedInput = EDUtilsTest.readAndParseFile(
            self.strReferenceInputFile2)
        strObtainedInput = EDUtilsTest.readAndParseFile(
            self.strObtainedInputFile2)

        xsDataInputExpected = XSDataRaddoseInput.parseString(strExpectedInput)
        xsDataInputObtained = XSDataRaddoseInput.parseString(strObtainedInput)

        EDAssert.equal(xsDataInputExpected.marshal(),
                       xsDataInputObtained.marshal())
예제 #7
0
    def getXSDataRaddoseInput(self, _xsDataBeam, _xsDataSample, _inumOperators):



        xsDataRaddoseInput = XSDataRaddoseInput()

        # Beam        
        xsDataRaddoseInput.setBeamSize(_xsDataBeam.getSize())
        xsDataRaddoseInput.setBeamFlux(_xsDataBeam.getFlux())
        xsDataRaddoseInput.setBeamWavelength(_xsDataBeam.getWavelength())

        xsDataRaddoseInput.setBeamExposureTime(XSDataTime(1.0))
        xsDataRaddoseInput.setNumberOfImages(XSDataInteger(1))
        xsDataRaddoseInput.setCrystalCell(_xsDataSample.getCrystal().getCell())

        xsDataRaddoseInput.setCrystalSize(_xsDataSample.getSize())

        xsDataComposition = _xsDataSample.getChemicalComposition()

        xsDataSolvent = xsDataComposition.getSolvent()
        if(xsDataSolvent is not None):
            xsDataRaddoseInput.setCrystalSATM(xsDataSolvent.getAtoms())

        xsDataStructure = xsDataComposition.getStructure()
        if(xsDataStructure is not None):
            xsDataChains = xsDataStructure.getChain()

            totalNRESInStructure = 0
            totalNDNAInStructure = 0
            totalNRNAInStructure = 0
            totalPATM = XSDataAtomicComposition()

            for chain in xsDataChains:
                # heavy atoms of each chain to be added in the PATM
                xsDataAtomicCompositionHeavyAtoms = chain.getHeavyAtoms()
                if (xsDataAtomicCompositionHeavyAtoms is not None):
                    iterator = 1
                    while iterator <= chain.getNumberOfCopies().getValue():
                        totalPATM = self.mergeAtomicComposition(totalPATM, xsDataAtomicCompositionHeavyAtoms)
                        iterator = iterator + 1

                type = chain.getType().getValue()
                numberOfMonomers = chain.getNumberOfMonomers().getValue() * chain.getNumberOfCopies().getValue()

                if (type == "protein"):
                    totalNRESInStructure = totalNRESInStructure + numberOfMonomers
                elif(type == "dna"):
                    totalNDNAInStructure = totalNDNAInStructure + numberOfMonomers
                elif(type == "rna"):
                    totalNRNAInStructure = totalNRNAInStructure + numberOfMonomers

            xsDataLigands = xsDataStructure.getLigand()
            for ligand in xsDataLigands:

                # Light atoms to be added to the NRES
                nres = ligand.getNumberOfLightAtoms().getValue() * ligand.getNumberOfCopies().getValue() / 7.85
                totalNRESInStructure = totalNRESInStructure + nres

                # Heavy atoms to be added to the PATM
                if (ligand.getHeavyAtoms() is not None):
                    iterator = 1
                    while iterator <= ligand.getNumberOfCopies().getValue():
                        totalPATM = self.mergeAtomicComposition(totalPATM, ligand.getHeavyAtoms())
                        iterator = iterator + 1

            if(totalNRESInStructure != 0):
                xsDataRaddoseInput.setCrystalNRES(XSDataInteger(int(round(totalNRESInStructure))))
            if(totalNDNAInStructure != 0):
                xsDataRaddoseInput.setCrystalNDNA(XSDataInteger(int(totalNDNAInStructure)))
            if(totalNRNAInStructure != 0):
                xsDataRaddoseInput.setCrystalNRNA(XSDataInteger(int(totalNRNAInStructure)))
            if(len(totalPATM.getAtom()) != 0):
                xsDataRaddoseInput.setCrystalPATM(totalPATM)

            xsDataNumberNumStructInAU = xsDataStructure.getNumberOfCopiesInAsymmetricUnit()
            xsDataNumberNumStructInUC = int(xsDataNumberNumStructInAU.getValue() * _inumOperators)
            xsDataRaddoseInput.setCrystalNMON(XSDataInteger(xsDataNumberNumStructInUC))

        return xsDataRaddoseInput
    def testSetDataModelInput(self):
        # Crystal         
        from XSDataRaddosev10 import XSDataRaddoseInput
        xsDataRaddoseInput = XSDataRaddoseInput()

        from XSDataCommon import XSDataString
        from XSDataCommon import XSDataFloat
        from XSDataCommon import XSDataAngle
        from XSDataCommon import XSDataLength
        from XSDataCommon import XSDataSize
        from XSDataCommon import XSDataInteger
        from XSDataRaddosev10 import XSDataCell
        from XSDataRaddosev10 import XSDataAtom
        from XSDataRaddosev10 import XSDataAtomicComposition

        xsDataAtomSulfur = XSDataAtom()
        xsDataAtomSulfur.setNumberOf(XSDataFloat(4))
        xsDataAtomSulfur.setSymbol(XSDataString("S"))
        xsDataAtomSelenium = XSDataAtom()
        xsDataAtomSelenium.setNumberOf(XSDataFloat(4))
        xsDataAtomSelenium.setSymbol(XSDataString("Se"))

        xsDataAtomicComposition = XSDataAtomicComposition()
        xsDataAtomicComposition.addAtom(xsDataAtomSulfur)
        xsDataAtomicComposition.addAtom(xsDataAtomSelenium)
        xsDataRaddoseInput.setCrystalPATM(xsDataAtomicComposition)
        xsDataRaddoseInput.setCrystalNRES(XSDataInteger(295))
        xsDataRaddoseInput.setCrystalNMON(XSDataInteger(8))
        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))

        xsDataSizeCrystal = XSDataSize(XSDataLength(0.1),
                                        XSDataLength(0.1),
                                        XSDataLength(0.1))

        xsDataRaddoseInput.setCrystalCell(xsDataCell)
        xsDataRaddoseInput.setCrystalSize(xsDataSizeCrystal)

        # Beam
        from XSDataCommon import XSDataFlux
        from XSDataCommon import XSDataWavelength
        from XSDataCommon import XSDataTime

        xsDataSize = XSDataSize(x = XSDataLength(0.1),
                                y = XSDataLength(0.1))

        xsDataRaddoseInput.setBeamSize(xsDataSize)
        xsDataRaddoseInput.setBeamFlux(XSDataFlux(1e+12))
        xsDataRaddoseInput.setBeamWavelength(XSDataWavelength(2.41))
        xsDataRaddoseInput.setBeamExposureTime(XSDataTime(1))

        xsDataRaddoseInput.setNumberOfImages(XSDataInteger(1))

        xsDataRaddoseInput.exportToFile(self.strObtainedInputFile)

        strExpectedInput = self.readAndParseFile (self.strReferenceInputFile)
        strObtainedInput = self.readAndParseFile (self.strObtainedInputFile)

        xsDataRaddoseInputExpected = XSDataRaddoseInput.parseString(strExpectedInput)
        xsDataRaddoseInputObtained = XSDataRaddoseInput.parseString(strObtainedInput)

        EDAssert.equal(xsDataRaddoseInputExpected.marshal(), xsDataRaddoseInputObtained.marshal())