def testDefaultChemicalComposition(self):
edPluginStrategy = self.createPlugin()
from XSDataCommon import XSDataAngle
from XSDataCommon import XSDataLength
from XSDataMXv1 import XSDataSampleCrystalMM
from XSDataMXv1 import XSDataCrystal
from XSDataMXv1 import XSDataCell
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(XSDataAngle(90.0),
XSDataAngle(90.0),
XSDataAngle(90.0),
XSDataLength(78.9),
XSDataLength(95.162),
XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSampleCrystalMM.setCrystal(xsDataCrystal)
inumOperators = 4
xsDataSample2 = edPluginStrategy.getDefaultChemicalComposition(xsDataSampleCrystalMM, inumOperators)
strChainType = xsDataSample2.getStructure().getChain()[0].getType()
EDAssert.equal("protein", strChainType.getValue())
def testDefaultChemicalComposition(self):
edPluginStrategy = self.createPlugin()
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
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)
xsDataSampleCrystalMM.setCrystal(xsDataCrystal)
inumOperators = 4
xsDataSample2 = edPluginStrategy.getDefaultChemicalComposition(xsDataSampleCrystalMM, inumOperators)
pyStrChainType = xsDataSample2.getStructure().getChain()[0].getType()
EDAssert.equal("protein", pyStrChainType.getValue())
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv1_1.preProcess...")
self.__edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if (xsDataSampleCrystalMM is None):
self.__xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self.__xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if (xsDataCrystal is not None):
self.__xsDataSampleCopy.setCrystal(xsDataCrystal)
# Raddose is enabled only if the beam flux is set
if (self.getDataInput().getExperimentalCondition().getBeam().getFlux()
is None):
pyStrWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlStrategyv1_1.preProcess',
self.__strPluginRaddoseName, "Beam Flux not set")
EDVerbose.warning(pyStrWarningMessage)
self.addWarningMessage(pyStrWarningMessage)
else:
self.__edPluginRaddose = self.loadPlugin(
self.__strPluginRaddoseName)
if (self.__edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv1_1.preProcess: " +
self.__strPluginRaddoseName +
" Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput(
).getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
strNumOperators = None
strSpaceGroup = None
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_1.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_1.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self.__xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self.__xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_1.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroupName, strFileSymop)
except Exception, detail:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_1.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self.__xsDataSampleCopy.getCrystal(
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 preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess...")
self._edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if (xsDataSampleCrystalMM is None):
self._xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self._xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if (xsDataCrystal is not None):
self._xsDataSampleCopy.setCrystal(xsDataCrystal)
# Load the Best plugin
self._edPluginBest = self.loadPlugin(self._strPluginBestName)
self._edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self._edPluginBest.setBaseName(self._strPluginBestName)
# Load the plot gle plugin
self._edPluginPlotGle = self.loadPlugin(self._strPluginPlotGleName)
# Check if radiation damage estimation is required or not in the diffraction plan
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.getEstimateRadiationDamage():
if xsDataDiffractionPlan.getEstimateRadiationDamage().getValue(
):
# Yes, is requested
self._bEstimateRadiationDamage = True
else:
# No, is explicitly not requested
self._bEstimateRadiationDamage = False
elif xsDataDiffractionPlan.getStrategyOption() is not None:
if xsDataDiffractionPlan.getStrategyOption().getValue().find(
"-DamPar") != -1:
# The "-DamPar" option requires estimation of radiation damage
self._bEstimateRadiationDamage = True
# Check if we know what to do with radiation damage
if self._bEstimateRadiationDamage is None:
# "Force" the estimation of radiation damage if the flux is present
if self.getDataInput().getExperimentalCondition().getBeam(
).getFlux() is None:
strWarningMessage = "EDPluginControlStrategyv1_2: Missing flux input - cannot estimate radiation damage."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self._bEstimateRadiationDamage = False
else:
self._bEstimateRadiationDamage = True
if self._bEstimateRadiationDamage:
if self.getDataInput().getExperimentalCondition().getBeam(
).getFlux() is None:
strErrorMessage = "EDPluginControlStrategyv1_2: Missing flux input. Cannot estimate radiation damage"
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if not self.isFailure():
self._edPluginRaddose = self.loadPlugin(self._strPluginRaddoseName)
if (self._edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: " +
self._strPluginRaddoseName +
" Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput(
).getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_2.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self._xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self._xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroupName, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_2.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self._xsDataSampleCopy.getCrystal(
).getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Space Group IT Number Found by indexing: %d"
% iSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(iSpaceGroupITNumber), strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_2.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
def buildChildren(self, child_, nodeName_):
if child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'experimentalCondition':
obj_ = XSDataExperimentalCondition()
obj_.build(child_)
self.setExperimentalCondition(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'diffractionPlan':
obj_ = XSDataDiffractionPlan()
obj_.build(child_)
self.setDiffractionPlan(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'sample':
obj_ = XSDataSampleCrystalMM()
obj_.build(child_)
self.setSample(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'imagePath':
obj_ = XSDataFile()
obj_.build(child_)
self.imagePath.append(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'flux':
obj_ = XSDataFloat()
obj_.build(child_)
self.setFlux(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'minExposureTimePerImage':
obj_ = XSDataTime()
obj_.build(child_)
self.setMinExposureTimePerImage(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'beamSize':
obj_ = XSDataLength()
obj_.build(child_)
self.setBeamSize(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'beamSizeX':
obj_ = XSDataLength()
obj_.build(child_)
self.setBeamSizeX(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'beamSizeY':
obj_ = XSDataLength()
obj_.build(child_)
self.setBeamSizeY(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'apertureSize':
obj_ = XSDataLength()
obj_.build(child_)
self.setApertureSize(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'templateMode':
obj_ = XSDataBoolean()
obj_.build(child_)
self.setTemplateMode(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'generatedTemplateFile':
obj_ = XSDataFile()
obj_.build(child_)
self.setGeneratedTemplateFile(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'resultsFilePath':
obj_ = XSDataFile()
obj_.build(child_)
self.setResultsFilePath(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'beamPosX':
obj_ = XSDataFloat()
obj_.build(child_)
self.setBeamPosX(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'beamPosY':
obj_ = XSDataFloat()
obj_.build(child_)
self.setBeamPosY(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'wavelength':
obj_ = XSDataWavelength()
obj_.build(child_)
self.setWavelength(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'transmission':
obj_ = XSDataDouble()
obj_.build(child_)
self.setTransmission(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'dataCollectionId':
obj_ = XSDataInteger()
obj_.build(child_)
self.setDataCollectionId(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'shortComments':
obj_ = XSDataString()
obj_.build(child_)
self.setShortComments(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'comments':
obj_ = XSDataString()
obj_.build(child_)
self.setComments(obj_)
elif child_.nodeType == Node.ELEMENT_NODE and \
nodeName_ == 'inputCharacterisation':
obj_ = XSDataInputCharacterisation()
obj_.build(child_)
self.setInputCharacterisation(obj_)
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))
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 preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlStrategyv1_2.preProcess...")
self._edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if (xsDataSampleCrystalMM is None):
self._xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self._xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if (xsDataCrystal is not None):
self._xsDataSampleCopy.setCrystal(xsDataCrystal)
# Load the Best plugin
self._edPluginBest = self.loadPlugin(self._strPluginBestName)
self._edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self._edPluginBest.setBaseName(self._strPluginBestName)
# Load the plot gle plugin
self._edPluginPlotGle = self.loadPlugin(self._strPluginPlotGleName)
# Check if radiation damage estimation is required or not in the diffraction plan
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.getEstimateRadiationDamage():
if xsDataDiffractionPlan.getEstimateRadiationDamage().getValue(
):
# Yes, is requested
self._bEstimateRadiationDamage = True
else:
# No, is explicitly not requested
self._bEstimateRadiationDamage = False
elif xsDataDiffractionPlan.getStrategyOption() is not None:
if xsDataDiffractionPlan.getStrategyOption().getValue().find(
"-DamPar") != -1:
# The "-DamPar" option requires estimation of radiation damage
self._bEstimateRadiationDamage = True
# Check if we know what to do with radiation damage
if self._bEstimateRadiationDamage is None:
# "Force" the estimation of radiation damage if the flux is present
if self.getDataInput().getExperimentalCondition().getBeam(
).getFlux() is None:
strWarningMessage = "EDPluginControlStrategyv1_2: Missing flux input - cannot estimate radiation damage."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self._bEstimateRadiationDamage = False
else:
self._bEstimateRadiationDamage = True
if self._bEstimateRadiationDamage:
if self.getDataInput().getExperimentalCondition().getBeam(
).getFlux() is None:
strErrorMessage = "EDPluginControlStrategyv1_2: Missing flux input. Cannot estimate radiation damage"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if not self.isFailure():
self._edPluginRaddose = self.loadPlugin(self._strPluginRaddoseName)
if (self._edPluginRaddose is not None):
self.DEBUG("EDPluginControlStrategyv1_2.preProcess: " +
self._strPluginRaddoseName +
" Found... setting Data Input")
xsDataStringSpaceGroup = self.getDataInput(
).getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
bSpaceGroupForced = False
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper(
).replace(" ", "")
if strSpaceGroup != "":
self.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup)
bSpaceGroupForced = True
except Exception as detail:
strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
detail)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
if not bSpaceGroupForced:
# Space Group has NOT been forced
xsDataStringSpaceGroup = self._xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self._xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
self.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroupName)
except Exception as detail:
strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
detail)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self._xsDataSampleCopy.getCrystal(
).getSpaceGroup().getITNumber().getValue()
self.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Space Group IT Number Found by indexing: %d"
% iSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(iSpaceGroupITNumber))
except Exception as detail:
strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
detail)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
if (strNumOperators is not None):
iNumOperators = int(strNumOperators)
else:
strErrorMessage = "EDPluginControlStrategyv1_2: No symmetry operators found for Space Group: {0}".format(
strNumOperators)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
xsDataChemicalComposition = self._xsDataSampleCopy.getChemicalComposition(
)
if (xsDataChemicalComposition is None):
# create a default chemical composition and assign it to the sample
xsDataDefaultChemicalComposition = self.getDefaultChemicalComposition(
self._xsDataSampleCopy, iNumOperators)
self._xsDataSampleCopy.setChemicalComposition(
xsDataDefaultChemicalComposition)
else:
# Check for Sulfur atoms, if none, add native sulfur atoms
xsDataUpdatedChemicalComposition = self.updateChemicalComposition(
xsDataChemicalComposition)
self._xsDataSampleCopy.setChemicalComposition(
xsDataUpdatedChemicalComposition)
# create Data Input for Raddose
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
self._edHandlerXSDataRaddose = EDHandlerXSDataRaddosev10()
xsDataBeam = self.getDataInput().getExperimentalCondition(
).getBeam()
# Calculate number of images (MXSUP-1616):
iNumberOfImages = None
xsDataCollection = self.dataInput.dataCollection
if xsDataCollection is not None:
iNumberOfImages = 0
for xsDataSubWedge in xsDataCollection.subWedge:
xsDataGoniostat = xsDataSubWedge.experimentalCondition.goniostat
iOscStart = xsDataGoniostat.rotationAxisStart.value
iOscEnd = xsDataGoniostat.rotationAxisEnd.value
iOscWidth = xsDataGoniostat.oscillationWidth.value
iNumberOfImages += int(
round((iOscEnd - iOscStart) / iOscWidth, 0))
if iNumberOfImages is None:
iNumberOfImages = 1
self.WARNING(
"No goniostat information, number of images for RADDOSE set to 1"
)
xsDataRaddoseInput = self._edHandlerXSDataRaddose.getXSDataRaddoseInput(
xsDataBeam, self._xsDataSampleCopy, iNumOperators,
iNumberOfImages)
if xsDataRaddoseInput is not None:
self._edPluginRaddose.setDataInput(xsDataRaddoseInput)
self._edPluginRaddose.setBaseDirectory(
self.getWorkingDirectory())
self._edPluginRaddose.setBaseName(
self._strPluginRaddoseName)
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlKappaStrategyv2_0.preProcess...")
self.edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput(
"mxv1InputStrategy")[0].getSample()
if (xsDataSampleCrystalMM is None):
self.xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self.xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput(
"mxv1InputStrategy")[0].getCrystalRefined()
if (xsDataCrystal is not None):
self.xsDataSampleCopy.setCrystal(xsDataCrystal)
# Raddose is enabled only if the beam flux is set
if (self.getDataInput("mxv1InputStrategy")
[0].getExperimentalCondition().getBeam().getFlux() is None):
strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginRaddoseName, "Beam Flux not set")
self.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.edPluginRaddose = self.loadPlugin(self.strPluginRaddoseName)
if (self.edPluginRaddose is not None):
self.DEBUG("EDPluginControlKappaStrategyv2_0.preProcess: " +
self.strPluginRaddoseName +
" Found... setting Data Input")
xsDataStringSpaceGroup = self.getDataInput(
"mxv1InputStrategy")[0].getDiffractionPlan(
).getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
strNumOperators = None
strSpaceGroup = None
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue()
self.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup)
except Exception as detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
self.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup)
except Exception as detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
dSpaceGroupITNumber = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getITNumber().getValue()
self.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Number Found by indexing: %d"
% dSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(dSpaceGroupITNumber))
except Exception as detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
if (strNumOperators is not None):
iNumOperators = int(strNumOperators)
else:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"No symmetry operators found for Space Group: ",
strSpaceGroup)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
xsDataChemicalComposition = self.xsDataSampleCopy.getChemicalComposition(
)
if (xsDataChemicalComposition is None):
# create a default chemical composition and assign it to the sample
xsDataDefaultChemicalComposition = self.getDefaultChemicalComposition(
self.xsDataSampleCopy, iNumOperators)
self.xsDataSampleCopy.setChemicalComposition(
xsDataDefaultChemicalComposition)
else:
# Check for Sulfur atoms, if none, add native sulfur atoms
xsDataUpdatedChemicalComposition = self.updateChemicalComposition(
xsDataChemicalComposition)
self.xsDataSampleCopy.setChemicalComposition(
xsDataUpdatedChemicalComposition)
# create Data Input for Raddose
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
self.edHandlerXSDataRaddose = EDHandlerXSDataRaddosev10()
xsDataBeam = self.getDataInput("mxv1InputStrategy")[
0].getExperimentalCondition().getBeam()
xsDataRaddoseInput = None
iNumberOfImages = 1
self.warning("Number of images for RADDOSE forced to 1")
try:
xsDataRaddoseInput = self.edHandlerXSDataRaddose.getXSDataRaddoseInput(
xsDataBeam, self.xsDataSampleCopy, iNumOperators,
iNumberOfImages)
except Exception as detail:
strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginRaddoseName,
"EDHandlerXSDataRaddose : " + detail)
self.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if (xsDataRaddoseInput is not None):
self.edPluginRaddose.setDataInput(xsDataRaddoseInput)
self.edPluginRaddose.setBaseDirectory(
self.getWorkingDirectory())
self.edPluginRaddose.setBaseName(self.strPluginRaddoseName)
# More checks?
# try:
# self.edPluginRaddose.setDataInput( xsDataRaddoseInput )
# self.edPluginRaddose.setBaseDirectory( self.getWorkingDirectory() )
# self.edPluginRaddose.setBaseName( self.strPluginRaddoseName )
#
# except Exception, detail:
# strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % ('EDPluginControlStrategyv1_1.preProcess', self.strPluginRaddoseName, detail ) )
# self.warning( strWarningMessage )
# self.addWarningMessage( strWarningMessage )
else:
strErrorMessage = EDMessage.ERROR_PLUGIN_NOT_LOADED_02 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginRaddoseName)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
self.edPluginBest = self.loadPlugin(self.strPluginBestName)
if (self.edPluginBest is None):
strErrorMessage = EDMessage.ERROR_PLUGIN_NOT_LOADED_02 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginBestName)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
else:
self.edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self.edPluginBest.setBaseName(self.strPluginBestName)
if (self.KappaStrategy):
# Alignment
self.edPluginAlignment = self.loadPlugin(
self.strPluginAlignmentName)
if (self.edPluginAlignment is None):
errorMessage = EDMessage.ERROR_PLUGIN_NOT_LOADED_02 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginAlignmentName)
self.error(errorMessage)
self.addErrorMessage(errorMessage)
# do not kill the application just because this feature is not available
# raise RuntimeError, errorMessage
else:
self.edPluginAlignment.setBaseDirectory(
self.getWorkingDirectory())
self.edPluginAlignment.setBaseName(self.strPluginAlignmentName)
# KappaStaregy
self.edPluginKappaStrategy = self.loadPlugin(
self.strPluginKappaStrategyName)
if (self.edPluginKappaStrategy is None):
errorMessage = EDMessage.ERROR_PLUGIN_NOT_LOADED_02 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginKappaStrategyName)
self.error(errorMessage)
self.addErrorMessage(errorMessage)
# raise RuntimeError, errorMessage
else:
self.edPluginKappaStrategy.setBaseDirectory(
self.getWorkingDirectory())
self.edPluginKappaStrategy.setBaseName(
self.strPluginKappaStrategyName)
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())