def mergeAtomicComposition(self, _xsDataAtomicComposition1,
_xsDataAtomicComposition2):
EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
mergedAtomicComposition = XSDataAtomicComposition()
dictionary = {}
for atom in _xsDataAtomicComposition2.getAtom():
dictionary[
atom.getSymbol().getValue()] = atom.getNumberOf().getValue()
for atom1 in _xsDataAtomicComposition1.getAtom():
symbol = atom1.getSymbol().getValue()
if (self.exists(symbol, _xsDataAtomicComposition2) == True):
mergedAtom = XSDataAtom()
mergedAtom.setNumberOf(
XSDataDouble(atom1.getNumberOf().getValue() +
dictionary[symbol]))
mergedAtom.setSymbol(XSDataString(symbol))
mergedAtomicComposition.addAtom(mergedAtom)
else:
mergedAtomicComposition.addAtom(atom1)
for atom2 in _xsDataAtomicComposition2.getAtom():
symbol = atom2.getSymbol().getValue()
if (self.exists(symbol, _xsDataAtomicComposition1) == False):
mergedAtomicComposition.addAtom(atom2)
return mergedAtomicComposition
def mergeAtomicComposition(self, _xsDataAtomicComposition1, _xsDataAtomicComposition2):
EDFactoryPluginStatic.loadModule("XSDataRaddosev10")
mergedAtomicComposition = XSDataAtomicComposition()
dictionary = {}
for atom in _xsDataAtomicComposition2.getAtom():
dictionary[atom.getSymbol().getValue()] = atom.getNumberOf().getValue()
for atom1 in _xsDataAtomicComposition1.getAtom():
symbol = atom1.getSymbol().getValue()
if (self.exists(symbol, _xsDataAtomicComposition2) == True):
mergedAtom = XSDataAtom()
mergedAtom.setNumberOf(XSDataDouble(atom1.getNumberOf().getValue() + dictionary[symbol]))
mergedAtom.setSymbol(XSDataString(symbol))
mergedAtomicComposition.addAtom(mergedAtom)
else:
mergedAtomicComposition.addAtom(atom1)
for atom2 in _xsDataAtomicComposition2.getAtom():
symbol = atom2.getSymbol().getValue()
if (self.exists(symbol, _xsDataAtomicComposition1) == False):
mergedAtomicComposition.addAtom(atom2)
return mergedAtomicComposition
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 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())
