def updateChemicalComposition(self, _xsDataChemicalComposition):
"""
"""
xsDataChemicalComposition = _xsDataChemicalComposition
for chain in xsDataChemicalComposition.getStructure().getChain():
if(chain.getType().getValue() == "protein"):
bSulfurExists = False
xsDataAtomicCompositionHeavyAtoms = chain.getHeavyAtoms()
if(xsDataAtomicCompositionHeavyAtoms is None):
xsDataAtomicCompositionHeavyAtoms = XSDataAtomicComposition()
else:
for heavyAtom in xsDataAtomicCompositionHeavyAtoms.getAtom():
if(heavyAtom.getSymbol().getValue() == "S" or heavyAtom.getSymbol().getValue() == "s"):
bSulfurExists = True
# all protein chains should contain sulfur atom as a percentage of the number
# of amino acids. Add them if the user did not input them.
if(bSulfurExists == False):
iNumberOfSulfurAtom = int(round(chain.getNumberOfMonomers().getValue() * 0.05))
xsDataSulfurAtom = XSDataAtom()
xsDataSulfurAtom.setSymbol(XSDataString("S"))
xsDataSulfurAtom.setNumberOf(XSDataFloat(iNumberOfSulfurAtom))
xsDataAtomicCompositionHeavyAtoms.addAtom(xsDataSulfurAtom)
chain.setHeavyAtoms(xsDataAtomicCompositionHeavyAtoms)
return xsDataChemicalComposition
def getDefaultChemicalComposition(self, _xsDataSample, _inumOperators):
"""
"""
xsDataCell = _xsDataSample.getCrystal().getCell()
a = xsDataCell.getLength_a().getValue()
b = xsDataCell.getLength_b().getValue()
c = xsDataCell.getLength_c().getValue()
alpha = math.radians(xsDataCell.getAngle_alpha().getValue())
beta = math.radians(xsDataCell.getAngle_beta().getValue())
gamma = math.radians(xsDataCell.getAngle_gamma().getValue())
fUnitCellVolume = (
a
* b
* c
* (
math.sqrt(
1
- math.cos(alpha) * math.cos(alpha)
- math.cos(beta) * math.cos(beta)
- math.cos(gamma) * math.cos(gamma)
+ 2 * math.cos(alpha) * math.cos(beta) * math.cos(gamma)
)
)
)
fPolymerVolume = fUnitCellVolume * (1 - self.fAverageCrystalSolventContent)
fNumberOfMonomersPerUnitCell = fPolymerVolume / self.fAverageAminoAcidVolume
fNumberOfMonomersPerAsymmetricUnit = fNumberOfMonomersPerUnitCell / _inumOperators
iNumberOfSulfurAtom = int(round(fNumberOfMonomersPerAsymmetricUnit * self.fAverageSulfurContentPerAminoacid))
xsDataAtom = XSDataAtom()
xsDataAtom.setSymbol(XSDataString("S"))
xsDataAtom.setNumberOf(XSDataDouble(iNumberOfSulfurAtom))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomicComposition.addAtom(xsDataAtom)
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfMonomers(XSDataDouble(round(fNumberOfMonomersPerAsymmetricUnit)))
xsDataChain.setNumberOfCopies(XSDataDouble(1))
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure = XSDataStructure()
xsDataStructure.addChain(xsDataChain)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(1))
xsDataAtomSolvent = XSDataAtom()
xsDataAtomSolvent.setSymbol(XSDataString("S"))
xsDataAtomSolvent.setConcentration(XSDataDouble(self.fAverageSulfurConcentration))
xsDataAtomicCompositionSolvent = XSDataAtomicComposition()
xsDataAtomicCompositionSolvent.addAtom(xsDataAtomSolvent)
xsDataSolvent = XSDataSolvent()
xsDataSolvent.setAtoms(xsDataAtomicCompositionSolvent)
xsDataChemicalCompositionMM = XSDataChemicalCompositionMM()
xsDataChemicalCompositionMM.setSolvent(xsDataSolvent)
xsDataChemicalCompositionMM.setStructure(xsDataStructure)
return xsDataChemicalCompositionMM
def testUpdateChemicalCompositionWithNativeSulfurAtom(self):
"""
"""
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataString
from XSDataCommon import XSDataInteger
from XSDataCommon import XSDataString
from XSDataCommon import XSDataFloat
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
from XSDataMXv1 import XSDataCell
from XSDataMXv1 import XSDataSpaceGroup
edPluginStrategy = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(os.path.join(self.strDataPath, "XSConfiguration_ESRF.xml"))
edPluginStrategy.setConfiguration(xsPluginItemGood01)
edPluginStrategy.configure()
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataFloat(2))
xsDataChain.setNumberOfMonomers(XSDataFloat(60))
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
EDAssert.equal(3, updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getNumberOf().getValue())
EDAssert.equal("S", updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getSymbol().getValue())
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataFloat(2))
xsDataChain.setNumberOfMonomers(XSDataFloat(60))
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataFloat(4))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
heavyAtoms = updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()
for heavyAtom in heavyAtoms:
EDVerbose.unitTest(heavyAtom.getSymbol().getValue() + " : " + str(heavyAtom.getNumberOf().getValue()))
if(heavyAtom.getSymbol().getValue() == "S"):
EDAssert.equal(3, heavyAtom.getNumberOf().getValue())
def testUpdateChemicalCompositionWithNativeSulfurAtom(self):
edPluginStrategy = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(os.path.join(self.strDataPath, "XSConfiguration_ESRF.xml"))
edPluginStrategy.setConfiguration(xsPluginItemGood01)
edPluginStrategy.configure()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataChain.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
EDAssert.equal(
3,
updatedChemicalComposition.getStructure()
.getChain()[0]
.getHeavyAtoms()
.getAtom()[0]
.getNumberOf()
.getValue(),
)
EDAssert.equal(
"S",
updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getSymbol().getValue(),
)
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataChain.setNumberOfMonomers(XSDataDouble(60))
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
heavyAtoms = updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()
for heavyAtom in heavyAtoms:
EDVerbose.unitTest(heavyAtom.getSymbol().getValue() + " : " + str(heavyAtom.getNumberOf().getValue()))
if heavyAtom.getSymbol().getValue() == "S":
EDAssert.equal(3, heavyAtom.getNumberOf().getValue())
def testUpdateChemicalCompositionWithNativeSulfurAtom(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()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataChain.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
EDAssert.equal(3, updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getNumberOf().getValue())
EDAssert.equal("S", updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getSymbol().getValue())
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataChain.setNumberOfMonomers(XSDataDouble(60))
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
heavyAtoms = updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()
for heavyAtom in heavyAtoms:
self.unitTest(heavyAtom.getSymbol().getValue() + " : " + str(heavyAtom.getNumberOf().getValue()))
if(heavyAtom.getSymbol().getValue() == "S"):
EDAssert.equal(3, heavyAtom.getNumberOf().getValue())
def updateChemicalComposition(self, _xsDataChemicalComposition):
"""
"""
xsDataChemicalComposition = _xsDataChemicalComposition
for chain in xsDataChemicalComposition.getStructure().getChain():
if (chain.getType().getValue() == "protein"):
bSulfurExists = False
xsDataAtomicCompositionHeavyAtoms = chain.getHeavyAtoms()
if (xsDataAtomicCompositionHeavyAtoms is None):
xsDataAtomicCompositionHeavyAtoms = XSDataAtomicComposition(
)
else:
for heavyAtom in xsDataAtomicCompositionHeavyAtoms.getAtom(
):
if (heavyAtom.getSymbol().getValue() == "S"
or heavyAtom.getSymbol().getValue() == "s"):
bSulfurExists = True
# all protein chains should contain sulfur atom as a percentage of the number
# of amino acids. Add them if the user did not input them.
if (bSulfurExists == False):
iNumberOfSulfurAtom = int(
round(chain.getNumberOfMonomers().getValue() * 0.05))
xsDataSulfurAtom = XSDataAtom()
xsDataSulfurAtom.setSymbol(XSDataString("S"))
xsDataSulfurAtom.setNumberOf(
XSDataFloat(iNumberOfSulfurAtom))
xsDataAtomicCompositionHeavyAtoms.addAtom(xsDataSulfurAtom)
chain.setHeavyAtoms(xsDataAtomicCompositionHeavyAtoms)
return xsDataChemicalComposition
def testUpdateChemicalCompositionWithNativeSulfurAtom(self):
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataString
from XSDataCommon import XSDataInteger
from XSDataCommon import XSDataString
from XSDataCommon import XSDataFloat
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
from XSDataMXv1 import XSDataCell
from XSDataMXv1 import XSDataSpaceGroup
edPluginStrategy = self.createPlugin()
xsPluginItemGood01 = self.getPluginConfiguration(os.path.join(self.strDataPath, "XSConfiguration_ESRF.xml"))
edPluginStrategy.setConfiguration(xsPluginItemGood01)
edPluginStrategy.configure()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataFloat(2))
xsDataChain.setNumberOfMonomers(XSDataFloat(60))
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
EDAssert.equal(3, updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getNumberOf().getValue())
EDAssert.equal("S", updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()[0].getSymbol().getValue())
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataFloat(2))
xsDataChain.setNumberOfMonomers(XSDataFloat(60))
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataFloat(4))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(xsDataComposition)
heavyAtoms = updatedChemicalComposition.getStructure().getChain()[0].getHeavyAtoms().getAtom()
for heavyAtom in heavyAtoms:
EDVerbose.unitTest(heavyAtom.getSymbol().getValue() + " : " + str(heavyAtom.getNumberOf().getValue()))
if(heavyAtom.getSymbol().getValue() == "S"):
EDAssert.equal(3, heavyAtom.getNumberOf().getValue())
def testUpdateChemicalCompositionWithNativeSulfurAtom(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()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataChain.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(
xsDataComposition)
EDAssert.equal(
3,
updatedChemicalComposition.getStructure().getChain()
[0].getHeavyAtoms().getAtom()[0].getNumberOf().getValue())
EDAssert.equal(
"S",
updatedChemicalComposition.getStructure().getChain()
[0].getHeavyAtoms().getAtom()[0].getSymbol().getValue())
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataChain.setNumberOfMonomers(XSDataDouble(60))
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addChain(xsDataChain)
xsDataComposition.setStructure(xsDataStructure)
updatedChemicalComposition = edPluginStrategy.updateChemicalComposition(
xsDataComposition)
heavyAtoms = updatedChemicalComposition.getStructure().getChain(
)[0].getHeavyAtoms().getAtom()
for heavyAtom in heavyAtoms:
self.unitTest(heavyAtom.getSymbol().getValue() + " : " +
str(heavyAtom.getNumberOf().getValue()))
if (heavyAtom.getSymbol().getValue() == "S"):
EDAssert.equal(3, heavyAtom.getNumberOf().getValue())
def getDefaultChemicalComposition(self, _xsDataSample, _inumOperators):
"""
"""
xsDataCell = _xsDataSample.getCrystal().getCell()
a = xsDataCell.getLength_a().getValue()
b = xsDataCell.getLength_b().getValue()
c = xsDataCell.getLength_c().getValue()
alpha = math.radians(xsDataCell.getAngle_alpha().getValue())
beta = math.radians(xsDataCell.getAngle_beta().getValue())
gamma = math.radians(xsDataCell.getAngle_gamma().getValue())
fUnitCellVolume = a * b * c * (
math.sqrt(1 - math.cos(alpha) * math.cos(alpha) - math.cos(beta) *
math.cos(beta) - math.cos(gamma) * math.cos(gamma) +
2 * math.cos(alpha) * math.cos(beta) * math.cos(gamma)))
fPolymerVolume = fUnitCellVolume * (
1 - self.__fAverageCrystalSolventContent)
fNumberOfMonomersPerUnitCell = fPolymerVolume / self.__fAverageAminoAcidVolume
fNumberOfMonomersPerAsymmetricUnit = fNumberOfMonomersPerUnitCell / _inumOperators
iNumberOfSulfurAtom = int(
round(fNumberOfMonomersPerAsymmetricUnit *
self.__fAverageSulfurContentPerAminoacid))
xsDataAtom = XSDataAtom()
xsDataAtom.setSymbol(XSDataString("S"))
xsDataAtom.setNumberOf(XSDataFloat(iNumberOfSulfurAtom))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtomicComposition.addAtom(xsDataAtom)
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfMonomers(
XSDataFloat(round(fNumberOfMonomersPerAsymmetricUnit)))
xsDataChain.setNumberOfCopies(XSDataFloat(1))
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure = XSDataStructure()
xsDataStructure.addChain(xsDataChain)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataFloat(1))
xsDataAtomSolvent = XSDataAtom()
xsDataAtomSolvent.setSymbol(XSDataString("S"))
xsDataAtomSolvent.setConcentration(
XSDataFloat(self.__fAverageSulfurConcentration))
xsDataAtomicCompositionSolvent = XSDataAtomicComposition()
xsDataAtomicCompositionSolvent.addAtom(xsDataAtomSolvent)
xsDataSolvent = XSDataSolvent()
xsDataSolvent.setAtoms(xsDataAtomicCompositionSolvent)
xsDataChemicalCompositionMM = XSDataChemicalCompositionMM()
xsDataChemicalCompositionMM.setSolvent(xsDataSolvent)
xsDataChemicalCompositionMM.setStructure(xsDataStructure)
return xsDataChemicalCompositionMM
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)))
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())
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)))
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())
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)
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)
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 testMergeAtomicComposition(self):
from XSDataRaddosev10 import XSDataAtomicComposition
from XSDataRaddosev10 import XSDataAtom
from XSDataCommon import XSDataDouble
from XSDataCommon import XSDataString
from XSDataCommon import XSDataInteger
xsDataAtomicComposition1 = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("S"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition1.addAtom(xsDataAtom1)
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("Se"))
xsDataAtom2.setNumberOf(XSDataDouble(3))
xsDataAtomicComposition1.addAtom(xsDataAtom2)
xsDataAtomicComposition2 = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("S"))
xsDataAtom3.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition2.addAtom(xsDataAtom3)
xsDataAtom4 = XSDataAtom()
xsDataAtom4.setSymbol(XSDataString("Fe"))
xsDataAtom4.setNumberOf(XSDataDouble(5))
xsDataAtomicComposition2.addAtom(xsDataAtom4)
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
xsDataMergedAtomicComposition = EDHandlerXSDataRaddosev10().mergeAtomicComposition(xsDataAtomicComposition1,
xsDataAtomicComposition2)
EDAssert.equal(3, len(xsDataMergedAtomicComposition.getAtom()))
for atom in xsDataMergedAtomicComposition.getAtom():
if(atom.getSymbol().getValue() == "S"):
EDAssert.equal(5, atom.getNumberOf().getValue())
if(atom.getSymbol().getValue() == "Se"):
EDAssert.equal(3, atom.getNumberOf().getValue())
if(atom.getSymbol().getValue() == "Fe"):
EDAssert.equal(5, atom.getNumberOf().getValue())
xsDataMergedAtomicComposition = EDHandlerXSDataRaddosev10().mergeAtomicComposition(XSDataAtomicComposition(),
xsDataAtomicComposition2)
EDAssert.equal(2, len(xsDataMergedAtomicComposition.getAtom()))
for atom in xsDataMergedAtomicComposition.getAtom():
if(atom.getSymbol().getValue() == "S"):
EDAssert.equal(1, atom.getNumberOf().getValue())
if(atom.getSymbol().getValue() == "Fe"):
EDAssert.equal(5, atom.getNumberOf().getValue())
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 testMergeAtomicComposition(self):
from XSDataRaddosev10 import XSDataAtomicComposition
from XSDataRaddosev10 import XSDataAtom
from XSDataCommon import XSDataDouble
from XSDataCommon import XSDataString
from XSDataCommon import XSDataInteger
xsDataAtomicComposition1 = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("S"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition1.addAtom(xsDataAtom1)
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("Se"))
xsDataAtom2.setNumberOf(XSDataDouble(3))
xsDataAtomicComposition1.addAtom(xsDataAtom2)
xsDataAtomicComposition2 = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("S"))
xsDataAtom3.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition2.addAtom(xsDataAtom3)
xsDataAtom4 = XSDataAtom()
xsDataAtom4.setSymbol(XSDataString("Fe"))
xsDataAtom4.setNumberOf(XSDataDouble(5))
xsDataAtomicComposition2.addAtom(xsDataAtom4)
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
xsDataMergedAtomicComposition = EDHandlerXSDataRaddosev10(
).mergeAtomicComposition(xsDataAtomicComposition1,
xsDataAtomicComposition2)
EDAssert.equal(3, len(xsDataMergedAtomicComposition.getAtom()))
for atom in xsDataMergedAtomicComposition.getAtom():
if (atom.getSymbol().getValue() == "S"):
EDAssert.equal(5, atom.getNumberOf().getValue())
if (atom.getSymbol().getValue() == "Se"):
EDAssert.equal(3, atom.getNumberOf().getValue())
if (atom.getSymbol().getValue() == "Fe"):
EDAssert.equal(5, atom.getNumberOf().getValue())
xsDataMergedAtomicComposition = EDHandlerXSDataRaddosev10(
).mergeAtomicComposition(XSDataAtomicComposition(),
xsDataAtomicComposition2)
EDAssert.equal(2, len(xsDataMergedAtomicComposition.getAtom()))
for atom in xsDataMergedAtomicComposition.getAtom():
if (atom.getSymbol().getValue() == "S"):
EDAssert.equal(1, atom.getNumberOf().getValue())
if (atom.getSymbol().getValue() == "Fe"):
EDAssert.equal(5, atom.getNumberOf().getValue())