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 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): 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 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 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 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 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(XSDataInteger(4)) xsDataAtomicComposition1.addAtom(xsDataAtom1) xsDataAtom2 = XSDataAtom() xsDataAtom2.setSymbol(XSDataString("Se")) xsDataAtom2.setNumberOf(XSDataInteger(3)) xsDataAtomicComposition1.addAtom(xsDataAtom2) xsDataAtomicComposition2 = XSDataAtomicComposition() xsDataAtom3 = XSDataAtom() xsDataAtom3.setSymbol(XSDataString("S")) xsDataAtom3.setNumberOf(XSDataInteger(1)) xsDataAtomicComposition2.addAtom(xsDataAtom3) xsDataAtom4 = XSDataAtom() xsDataAtom4.setSymbol(XSDataString("Fe")) xsDataAtom4.setNumberOf(XSDataInteger(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 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 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 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 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())