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)
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())
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())