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 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 createInputCharacterisationFromSubWedges(self):
self.DEBUG("EDPluginControlInterfacev1_3.createInputCharacterisationFromSubWedges")
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSizeX))
xsDataSize.setY(XSDataLength(self.fBeamSizeY))
xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
if (self.fApertureSize is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setApertureSize(XSDataLength(self.fApertureSize))
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
if (self.fWavelength is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
if self.fMinOscillationWidth != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
if self.fMaxOscillationSpeed != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
if (self.strForcedSpaceGroup is not None):
self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if self.xsDataSample is not None:
xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
def createInputCharacterisationFromSubWedges(self):
self.DEBUG("EDPluginControlInterfacev1_2.createInputCharacterisationFromSubWedges")
xsDataResultSubWedgeAssemble = self.edPluginControlSubWedgeAssemble.getDataOutput()
self.xsDataInputCharacterisation = XSDataInputCharacterisation()
xsDataCollection = XSDataCollection()
# Default exposure time (for the moment, this value should be
# possible to read from the command line)
if self.xsDataDiffractionPlan is None:
self.xsDataDiffractionPlan = XSDataDiffractionPlan()
if (not xsDataResultSubWedgeAssemble is None):
pyListSubWedge = xsDataResultSubWedgeAssemble.getSubWedge()
xsDataCollection.setSubWedge(pyListSubWedge)
for xsDataSubWedge in pyListSubWedge:
if (self.strComplexity is not None):
self.xsDataDiffractionPlan.setComplexity(XSDataString(self.strComplexity))
if (self.fFlux is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setFlux(XSDataFlux(self.fFlux))
if (self.fBeamSizeX is not None) and (self.fBeamSizeY is not None):
xsDataSize = XSDataSize()
xsDataSize.setX(XSDataLength(self.fBeamSizeX))
xsDataSize.setY(XSDataLength(self.fBeamSizeY))
xsDataSubWedge.getExperimentalCondition().getBeam().setSize(xsDataSize)
if (self.fBeamPosX is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionX(XSDataLength(self.fBeamPosX))
if (self.fBeamPosY is not None):
xsDataSubWedge.getExperimentalCondition().getDetector().setBeamPositionY(XSDataLength(self.fBeamPosY))
if (self.fMinExposureTimePerImage is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setMinExposureTimePerImage(XSDataTime(self.fMinExposureTimePerImage))
if (self.fTransmission is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setTransmission(XSDataDouble(self.fTransmission))
if (self.fWavelength is not None):
xsDataSubWedge.getExperimentalCondition().getBeam().setWavelength(XSDataWavelength(self.fWavelength))
if self.fMinOscillationWidth != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMinOscillationWidth(XSDataAngle(self.fMinOscillationWidth))
if self.fMaxOscillationSpeed != None:
xsDataSubWedge.getExperimentalCondition().getGoniostat().setMaxOscillationSpeed(XSDataAngularSpeed(self.fMaxOscillationSpeed))
if (self.strForcedSpaceGroup is not None):
self.xsDataDiffractionPlan.setForcedSpaceGroup(XSDataString(self.strForcedSpaceGroup))
self.xsDataDiffractionPlan.setAnomalousData(XSDataBoolean(self.bAnomalousData))
self.xsDataDiffractionPlan.setMaxExposureTimePerDataCollection(XSDataTime(self.fMaxExposureTimePerDataCollection))
if (self.strStrategyOption is not None):
self.xsDataDiffractionPlan.setStrategyOption(XSDataString(self.strStrategyOption))
xsDataCollection.setDiffractionPlan(self.xsDataDiffractionPlan)
if self.xsDataSample is not None:
xsDataCollection.setSample(XSDataSampleCrystalMM.parseString(self.xsDataSample.marshal()))
self.xsDataInputCharacterisation.setDataCollection(xsDataCollection)
self.xsDataInputCharacterisation.setToken(self.xsDataToken)
class EDPluginControlStrategyv1_2(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputStrategy)
self._strPluginRaddoseName = "EDPluginRaddosev10"
self._edPluginRaddose = None
self._edHandlerXSDataRaddose = None
self._strPluginBestName = "EDPluginBestv1_2"
self._edPluginBest = None
self._edHandlerXSDataBest = None
self._strPluginPlotGleName = "EDPluginExecPlotGlev1_0"
self._edPluginPlotGle = None
self._strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self._strSymopHome = None
self._xsDataSampleCopy = None
# For default chemical composition
self._fAverageAminoAcidVolume = 135.49
self._fAverageCrystalSolventContent = 0.47
self._fAverageSulfurContentPerAminoacid = 0.05
self._fAverageSulfurConcentration = 314
# This varaible determines if Raddose should be executed or not
self._bEstimateRadiationDamage = None
# Raddose log file
self.xsDataFileRaddoseLog = None
def setSymopHome(self, _strSymopHome):
self._strSymopHome = _strSymopHome
def getSymopHome(self):
return self._strSymopHome
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
class EDPluginControlKappaStrategyv2_0(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__(self):
EDPluginControl.__init__(self)
#self.setXSDataInputClass(EDList)
self.setRequiredToHaveConfiguration(True)
self.strPluginRaddoseName = "EDPluginRaddosev10"
self.edPluginRaddose = None
self.edHandlerXSDataRaddose = None
self.strPluginBestName = "EDPluginBestv1_2"
self.edPluginBest = None
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self.edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
self.strPluginAlignmentName = "EDPluginSTACAlignmentv2_0"
self.edPluginAlignment = None
self.edHandlerXSDataAlignment = None
self.strPluginKappaStrategyName = "EDPluginSTACStrategyv2_0"
self.edPluginKappaStrategy = None
self.edHandlerXSDataKappaStrategy = None
self.setXSDataInputClass(XSDataInputStrategy, "mxv1InputStrategy")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection,
"mxv2DataCollection")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataIndexingResult,
"mxv1IndexingResult")
#disable kappa by default
self.KappaStrategy = 0
self.strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self.strSymopHome = os.path.normpath("/opt/pxsoft/ccp4-6.0.2/lib/data")
self.xsDataSampleCopy = None
# For default chemical composition
self.fAverageAminoAcidVolume = 135.49
self.fAverageCrystalSolventContent = 0.47
self.fAverageSulfurContentPerAminoacid = 0.05
self.fAverageSulfurConcentration = 314
def setSymopHome(self, _strSymopHome):
self.strSymopHome = _strSymopHome
def getSymopHome(self):
return self.strSymopHome
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.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")
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.edPluginRaddose = self.loadPlugin(self.strPluginRaddoseName)
if (self.edPluginRaddose is not None):
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: " +
self.strPluginRaddoseName + " Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
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()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.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)
strSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.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)
dSpaceGroupITNumber = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Number Found by indexing: %d"
% dSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(dSpaceGroupITNumber), strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
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 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 preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv10.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):
warningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % ('EDPluginControlStrategyv10.preProcess', self.__strPluginRaddoseName, "Beam Flux not set")
EDVerbose.warning(warningMessage)
self.addWarningMessage(warningMessage)
else:
self.__edPluginRaddose = self.loadPlugin(self.__strPluginRaddoseName)
if (self.__edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv10.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()
EDVerbose.DEBUG("EDPluginControlStrategyv10.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv10.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
# 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("EDPluginControlStrategyv10.preProcess: Space Group IT Name found by indexing: " + strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroupName, strFileSymop)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv10.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
strSpaceGroupITNumber = str(self.__xsDataSampleCopy.getCrystal().getSpaceGroup().getITNumber().getValue())
class EDPluginControlKappaStrategyv2_0(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setRequiredToHaveConfiguration(True)
self.strPluginRaddoseName = "EDPluginRaddosev10"
self.edPluginRaddose = None
self.edHandlerXSDataRaddose = None
self.strPluginBestName = "EDPluginBestv1_2"
self.edPluginBest = None
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self.edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
self.strPluginAlignmentName = "EDPluginSTACAlignmentv2_0"
self.edPluginAlignment = None
self.edHandlerXSDataAlignment = None
self.strPluginKappaStrategyName = "EDPluginSTACStrategyv2_0"
self.edPluginKappaStrategy = None
self.edHandlerXSDataKappaStrategy = None
self.setXSDataInputClass(XSDataInputStrategy, "mxv1InputStrategy")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection,
"mxv2DataCollection")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataIndexingResult,
"mxv1IndexingResult")
# disable kappa by default
self.KappaStrategy = 0
self.xsDataSampleCopy = None
# For default chemical composition
self.fAverageAminoAcidVolume = 135.49
self.fAverageCrystalSolventContent = 0.47
self.fAverageSulfurContentPerAminoacid = 0.05
self.fAverageSulfurConcentration = 314
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 configure(self):
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlKappaStrategyv2_0.configure")
bKappaOn = self.config.get("KAPPA")
if bKappaOn:
# self.strPluginStrategyName = "EDPluginControlStrategyv10"
# self.strPluginStrategyName = "EDPluginControlStrategyv2_0"
self.KappaStrategy = 1
else:
self.KappaStrategy = 0
def process(self, _edObject=None):
"""
"""
EDPluginControl.process(self, _edObject)
self.DEBUG("EDPluginControlKappaStrategyv2_0.process...")
# In case Beam Flux has not been set, The plugin Raddose has not been created, so it could be None
# and it won't be launched in this case
if (self.edPluginRaddose is not None):
self.connectProcess(self.edPluginRaddose.executeSynchronous)
self.edPluginRaddose.connectSUCCESS(self.doRaddoseToBestTransition)
self.edPluginRaddose.connectFAILURE(self.doFailureActionRaddose)
else:
# The plugin Best should not be None as this has been checked in the preProcess method... Double check it anyway
if (self.edPluginBest is not None):
self.connectProcess(self.executeBest)
# Launches Best anyway whether Raddose has been launched or not
# The plugin Best should not be None as this has been checked in the preProcess method... Double check it anyway
if (self.edPluginBest is not None):
self.edPluginBest.connectSUCCESS(self.doSuccessActionBest)
self.edPluginBest.connectFAILURE(self.doFailureActionBest)
# Kappa strategy calculation
if self.hasDataInput("mxv2DataCollection"):
if self.edPluginAlignment is not None:
self.connectProcess(self.doBestToAlignmentTransition)
# self.edPluginAlignment.connectSUCCESS( self.doAlignmentToKappaStrategyTransition )
# self.edPluginAlignment.connectFAILURE( self.doFailureActionAlignment )
# self.edPluginKappaStrategy.connectSUCCESS( self.doKappaStrategyMerge )
# self.edPluginKappaStrategy.connectFAILURE( self.doFailureActionKappaStrategy )
# Kappa strategy calculation
if self.edPluginKappaStrategy is not None:
self.connectProcess(self.doAlignmentToStrategyTransition)
# self.edPluginKappaStrategy.connectSUCCESS( self.doKappaStrategyMerge )
# self.edPluginKappaStrategy.connectFAILURE( self.doFailureActionKappaStrategy )
def postProcess(self, _edObject=None):
"""
"""
EDPluginControl.postProcess(self, _edObject)
self.DEBUG("EDPluginControlKappaStrategyv2_0.postProcess...")
xsDataResultBest = self.edPluginBest.getDataOutput()
xsDataResultStrategy = None
if (xsDataResultBest is not None):
xsDataResultStrategy = self.edHandlerXSDataBest.getXSDataResultStrategy(
xsDataResultBest,
self.getDataInput("mxv1InputStrategy")
[0].getExperimentalCondition(), self.xsDataSampleCopy)
self.setDataOutput(xsDataResultStrategy)
# possibleAlignments
try:
self.setDataOutput(self.edPluginAlignment.getDataOutput(),
"possibleOrientations")
except:
self.WARNING("Could not get the list of Possible orientations.")
def doRaddoseToBestTransition(self, _edPlugin):
"""
"""
self.DEBUG(
"EDPluginControlKappaStrategyv2_0.doRaddoseToBestTransition")
self.retrieveSuccessMessages(
_edPlugin,
"EDPluginControlKappaStrategyv2_0.doRaddoseToBestTransition")
xsDataRaddoseOutput = self.edPluginRaddose.getDataOutput()
# update the strategy data with the data coming from Raddose
self.xsDataSampleCopy.setAbsorbedDoseRate(
xsDataRaddoseOutput.getAbsorbedDoseRate())
# Call the Best Translator layer
xsDataInputStrategyCopy = XSDataInputStrategy.parseString(
self.getDataInput("mxv1InputStrategy")[0].marshal())
xsDataInputStrategyCopy.setSample(self.xsDataSampleCopy)
xsDataInputBest = self.edHandlerXSDataBest.getXSDataInputBest(
xsDataInputStrategyCopy)
self.edPluginBest.setDataInput(xsDataInputBest)
self.edPluginBest.executeSynchronous()
def doBestToAlignmentTransition(self, _edPlugin):
"""
"""
self.DEBUG(
"EDPluginControlKappaStrategyv2_0.doBestToAlignmentTransition")
# self.retrieveSuccessMessages( _edPlugin, "EDPluginControlStrategyv01.doRaddoseToBestTransition" )
xsDataInputStrategyCopy = XSDataInputStrategy.parseString(
self.getDataInput("mxv1InputStrategy")[0].marshal())
xsDataInputStrategyCopy.setSample(self.xsDataSampleCopy)
xsDataInputBest = self.edHandlerXSDataBest.getXSDataInputBest(
xsDataInputStrategyCopy)
self.edPluginAlignment.setDataInput(xsDataInputBest, "inputBest")
self.edPluginAlignment.setDataInput(
self.getDataInput("mxv2DataCollection")[0], "dataCollection")
self.edPluginAlignment.setDataInput(
self.getDataInput("mxv1IndexingResult")[0], "indexingResult")
self.edPluginAlignment.executeSynchronous()
def doAlignmentToStrategyTransition(self, _edPlugin):
"""
"""
self.DEBUG("EDPluginControlKappaStrategyv2_0.doAlignmentToStrategy")
# self.retrieveSuccessMessages( _edPlugin, "EDPluginControlStrategyv01.doRaddoseToBestTransition" )
# Call the Best Translator layer
# from XSDataSTACv01 import kappa_alignment_response
# from XSDataSTACv01 import kappa_strategy_request
# from XSDataSTACv01 import strategy_request
self.xsKappaStrategyRequest = kappa_strategy_request()
# self.xsKappaStrategyRequest.build(???)
KappaAlignmentResponse = self.edPluginAlignment.getDataOutput()
xsDataKappaAlignmentList = KappaAlignmentResponse.getPossible_orientation(
)
self.xsKappaStrategyRequest.setDesired_datum(xsDataKappaAlignmentList)
self.xsksreq = strategy_request()
self.xsKappaStrategyRequest.setStandard_request(self.xsksreq)
self.edPluginKappaStrategy.setDataInput(self.xsKappaStrategyRequest,
"kappa_strategy_request")
self.edPluginKappaStrategy.setDataInput(
self.getDataInput("mxv2DataCollection")[0], "dataCollection")
self.edPluginKappaStrategy.setDataInput(
self.getDataInput("mxv1InputStrategy")[0], "inputBest")
# self.edPluginKappaStrategy.m_xsDataBestFileContentPar=self.getDataInput()[0].getBestFileContentPar()
self.edPluginKappaStrategy.executeSynchronous()
def doFailureActionRaddose(self, _edPlugin):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
self.DEBUG("EDPluginControlKappaStrategyv2_0.doFailureActionRaddose")
self.retrieveFailureMessages(
_edPlugin,
"EDPluginControlKappaStrategyv2_0.doFailureActionRaddose")
strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlKappaStrategyv2_0.doFailureActionRaddose',
self.strPluginRaddoseName, "Raddose failure")
self.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self.executeBest(self)
def executeBest(self, _edPlugin):
xsDataInputBest = None
# Call the Best Translator layer
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self.__edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
xsDataInputStrategyCopy = XSDataInputStrategy.parseString(
self.getDataInput("mxv1InputStrategy")[0].marshal())
xsDataInputStrategyCopy.setSample(self.xsDataSampleCopy)
xsDataInputBest = self.__edHandlerXSDataBest.getXSDataInputBest(
xsDataInputStrategyCopy)
self.edPluginBest.setDataInput(xsDataInputBest)
self.edPluginBest.executeSynchronous()
def doSuccessActionBest(self, _edPlugin):
"""
retrieve the potential warning messages
"""
self.DEBUG("EDPluginControlKappaStrategyv2_0.doSuccessActionBest")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlKappaStrategyv2_0.doSuccessActionBest")
def doFailureActionBest(self, _edPlugin):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
self.DEBUG("EDPluginControlKappaStrategyv2_0.doFailureActionBest")
self.retrieveFailureMessages(
_edPlugin, "EDPluginControlKappaStrategyv2_0.doFailureActionBest")
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 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(
XSDataDouble(iNumberOfSulfurAtom))
xsDataAtomicCompositionHeavyAtoms.addAtom(xsDataSulfurAtom)
chain.setHeavyAtoms(xsDataAtomicCompositionHeavyAtoms)
return xsDataChemicalComposition
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG("EDPluginControlKappaStrategyv2_0.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of kappa strategy:")
self.addErrorWarningMessagesToExecutiveSummary()
xsDataResultStrategy = self.getDataOutput()
if (self.edPluginRaddose is not None):
if (self.edPluginRaddose.getDataOutput() is not None):
self.appendExecutiveSummary(self.edPluginRaddose, "Raddose : ")
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine(
"Calculations assuming polymer crystal with:")
self.addExecutiveSummaryLine(
"------------------------------------------")
self.addExecutiveSummaryLine("")
xsDataStructure = xsDataResultStrategy.getCollectionPlan(
)[0].getCollectionStrategy().getSample(
).getChemicalComposition().getStructure()
self.addExecutiveSummaryLine(
"Number of structure copies in asymmetric unit: %.2f" %
xsDataStructure.getNumberOfCopiesInAsymmetricUnit(
).getValue())
self.addExecutiveSummaryLine("")
chains = xsDataStructure.getChain()
self.addExecutiveSummaryLine("Chains:")
for chain in chains:
strChainType = chain.getType().getValue()
self.addExecutiveSummaryLine(
" Type : %s" %
strChainType)
if (strChainType == "protein"):
self.addExecutiveSummaryLine(
" Number of residues : %.2f" %
chain.getNumberOfMonomers().getValue())
elif (strChainType == "dna" or strChainType == "rna"):
self.addExecutiveSummaryLine(
" Number of nucleotides : %.2f" %
chain.getNumberOfMonomers().getValue())
strHeavyAtomsChain = " Number of heavy atoms :"
if (chain.getHeavyAtoms() is not None):
heavyAtomsChain = chain.getHeavyAtoms().getAtom()
for heavyAtomChain in heavyAtomsChain:
strHeavyAtomsChain = strHeavyAtomsChain + " %s=%d" % (
heavyAtomChain.getSymbol().getValue(),
heavyAtomChain.getNumberOf().getValue())
else:
strHeavyAtomsChain = strHeavyAtomsChain + " No heavy atoms"
self.addExecutiveSummaryLine(strHeavyAtomsChain)
self.addExecutiveSummaryLine(
" Number of copies in structure : %.2f" %
chain.getNumberOfCopies().getValue())
self.addExecutiveSummaryLine("")
ligands = xsDataStructure.getLigand()
if (len(ligands) != 0):
self.addExecutiveSummaryLine("Ligands:")
for ligand in ligands:
self.addExecutiveSummaryLine(
" Number of light atoms : %.2f" %
ligand.getNumberOfLightAtoms().getValue())
strHeavyAtomsLigand = " Number of heavy atoms :"
if (ligand.getHeavyAtoms() is not None):
heavyAtomsLigand = ligand.getHeavyAtoms().getAtom()
for heavyAtomLigand in heavyAtomsLigand:
strHeavyAtomsLigand = strHeavyAtomsLigand + " %s=%d" % (
heavyAtomLigand.getSymbol().getValue(),
heavyAtomLigand.getNumberOf().getValue())
else:
strHeavyAtomsChain = strHeavyAtomsChain + " No heavy atoms"
self.addExecutiveSummaryLine(strHeavyAtomsLigand)
self.addExecutiveSummaryLine(
" Number of copies in structure : %.2f" %
chain.getNumberOfCopies().getValue())
self.addExecutiveSummaryLine("")
if (self.edPluginBest is not None):
if (self.edPluginBest.getDataOutput() is not None):
self.appendExecutiveSummary(self.edPluginBest, "Best : ")
self.addExecutiveSummaryLine("")
if (self.edPluginAlignment is not None):
# if ( self.edPluginAlignment.getDataOutput() is not None ):
self.appendExecutiveSummary(self.edPluginAlignment,
"STAC - Alignment : ")
self.addExecutiveSummaryLine("")
if (self.edPluginKappaStrategy is not None):
# if ( self.edPluginAlignment.getDataOutput() is not None ):
self.appendExecutiveSummary(self.edPluginKappaStrategy,
"STAC - Strategy : ")
self.addExecutiveSummaryLine("")
class EDPluginControlStrategyv1_2(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputStrategy)
self._strPluginRaddoseName = "EDPluginRaddosev10"
self._edPluginRaddose = None
self._edHandlerXSDataRaddose = None
self._strPluginBestName = "EDPluginBestv1_2"
self._edPluginBest = None
self._edHandlerXSDataBest = None
self._strPluginPlotGleName = "EDPluginExecPlotGlev1_1"
self._edPluginPlotGle = None
self._strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self._strSymopHome = None
self._xsDataSampleCopy = None
# For default chemical composition
self._fAverageAminoAcidVolume = 135.49
self._fAverageCrystalSolventContent = 0.47
self._fAverageSulfurContentPerAminoacid = 0.05
self._fAverageSulfurConcentration = 314
# This varaible determines if Raddose should be executed or not
self._bEstimateRadiationDamage = None
# Raddose log file
self.xsDataFileRaddoseLog = None
self.roundUpToEven100 = False
def setSymopHome(self, _strSymopHome):
self._strSymopHome = _strSymopHome
def getSymopHome(self):
return self._strSymopHome
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"
)
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)
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, strFileSymop
)
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, strFileSymop
)
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), strFileSymop
)
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 configure(self):
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlStrategyv1_2.configure")
strSymopHome = self.config.get(self._strCONF_SYMOP_HOME)
if strSymopHome is None:
strWarningMessage = "EDPluginControlStrategyv1_2: No configuration parameter found for {0}".format(
self._strCONF_SYMOP_HOME
)
self.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.setSymopHome(strSymopHome)
# Even 100 images?
self.roundUpToEven100 = self.config.get("roundUpToEven100", False)
def process(self, _edObject=None):
EDPluginControl.process(self, _edObject)
self.DEBUG("EDPluginControlStrategyv1_2.process...")
self._edPluginBest.connectSUCCESS(self.doSuccessActionBest)
self._edPluginBest.connectFAILURE(self.doFailureActionBest)
if self._bEstimateRadiationDamage:
self._edPluginRaddose.connectSUCCESS(self.doRaddoseToBestTransition)
self._edPluginRaddose.connectFAILURE(self.doFailureActionRaddose)
self._edPluginRaddose.executeSynchronous()
else:
self.executeBest()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self, _edObject)
self.DEBUG("EDPluginControlStrategyv1_2.postProcess...")
#
# Create the BEST graphs from the plot mtv file
#
# Check if we have GLE files from BEST:
xsDataResultBest = self._edPluginBest.getDataOutput()
xsDataInputPlotGle = XSDataInputPlotGle()
if xsDataResultBest.glePlot != []:
for xsDataBestGlePlot in xsDataResultBest.glePlot:
xsDataGlePlot = XSDataGlePlot()
xsDataGlePlot.script = xsDataBestGlePlot.script
xsDataGlePlot.data = xsDataBestGlePlot.data
xsDataInputPlotGle.addGlePlot(xsDataGlePlot)
else:
xsDataInputPlotGle.filePlotMtv = xsDataResultBest.pathToPlotMtvFile
self._edPluginPlotGle.dataInput = xsDataInputPlotGle
self._edPluginPlotGle.executeSynchronous()
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self, _edObject)
self.DEBUG("EDPluginControlStrategyv1_2.finallyProcess")
xsDataResultStrategy = None
xsDataResultBest = self._edPluginBest.getDataOutput()
if xsDataResultBest is not None and self.getDataInput().getDiffractionPlan().getStrategyOption() is not None:
if self.getDataInput().getDiffractionPlan().getStrategyOption().getValue() != "-Bonly":
xsDataResultStrategy = self._edHandlerXSDataBest.getXSDataResultStrategy(
xsDataResultBest,
self.getDataInput().getExperimentalCondition(),
self._xsDataSampleCopy,
roundUpToEven100=self.roundUpToEven100,
)
else:
xsDataResultStrategy = self._edHandlerXSDataBest.getXSDataResultStrategy(
xsDataResultBest,
self.getDataInput().getExperimentalCondition(),
self._xsDataSampleCopy,
roundUpToEven100=self.roundUpToEven100,
)
if self.xsDataFileRaddoseLog is not None:
xsDataResultStrategy.setRaddoseLogFile(self.xsDataFileRaddoseLog)
# Plots
if not self._edPluginPlotGle.isFailure() and self._edPluginPlotGle.dataOutput is not None:
listFileGraph = self._edPluginPlotGle.dataOutput.fileGraph
xsDataResultStrategy.bestGraphFile = listFileGraph
# Sample
xsDataResultStrategy.setSample(self._xsDataSampleCopy)
# timeToReachHendersonLimit
if self._edPluginRaddose is not None:
xsDataRaddoseOutput = self._edPluginRaddose.dataOutput
if xsDataRaddoseOutput is not None:
xsDataResultStrategy.timeToReachHendersonLimit = xsDataRaddoseOutput.timeToReachHendersonLimit
self.setDataOutput(xsDataResultStrategy)
self.generateStrategyShortSummary(xsDataResultStrategy)
def doRaddoseToBestTransition(self, _edPlugin):
self.DEBUG("EDPluginControlStrategyv1_2.doRaddoseToBestTransition")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlStrategyv1_2.doRaddoseToBestTransition")
xsDataRaddoseOutput = self._edPluginRaddose.getDataOutput()
# update the strategy data with the data coming from Raddose
self._xsDataSampleCopy.setAbsorbedDoseRate(xsDataRaddoseOutput.getAbsorbedDoseRate())
if xsDataRaddoseOutput.getPathToLogFile() != None:
self.xsDataFileRaddoseLog = xsDataRaddoseOutput.getPathToLogFile()
# Call the Best Translator layer
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self._edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
xsDataInputStrategyCopy = XSDataInputStrategy.parseString(self.getDataInput().marshal())
xsDataInputStrategyCopy.setSample(self._xsDataSampleCopy)
xsDataInputBest = self._edHandlerXSDataBest.getXSDataInputBest(xsDataInputStrategyCopy)
self._edPluginBest.setDataInput(xsDataInputBest)
self._edPluginBest.executeSynchronous()
def doFailureActionRaddose(self, _edPlugin=None):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
self.DEBUG("EDPluginControlStrategyv1_2.doFailureActionRaddose")
self.retrieveFailureMessages(_edPlugin, "EDPluginControlStrategyv1_2.doFailureActionRaddose")
strWarningMessage = "EDPluginControlStrategyv1_2: Raddose failure"
self.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self.executeBest(self)
def executeBest(self, _edPlugin=None):
# Call the Best Translator layer
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self._edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
xsDataInputStrategyCopy = XSDataInputStrategy.parseString(self.getDataInput().marshal())
xsDataInputStrategyCopy.setSample(self._xsDataSampleCopy)
xsDataInputBest = self._edHandlerXSDataBest.getXSDataInputBest(xsDataInputStrategyCopy)
self._edPluginBest.setDataInput(xsDataInputBest)
self._edPluginBest.executeSynchronous()
def doSuccessActionBest(self, _edPlugin=None):
"""
retrieve the potential warning messages
"""
self.DEBUG("EDPluginControlStrategyv1_2.doSuccessActionBest")
self.retrieveSuccessMessages(_edPlugin, "EDPluginControlStrategyv1_2.doSuccessActionBest")
def doFailureActionBest(self, _edPlugin):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
self.DEBUG("EDPluginControlStrategyv1_2.doFailureActionBest")
self.retrieveFailureMessages(_edPlugin, "BEST failure:")
self.generateExecutiveSummary(self)
self.setFailure()
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 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(XSDataDouble(iNumberOfSulfurAtom))
xsDataAtomicCompositionHeavyAtoms.addAtom(xsDataSulfurAtom)
chain.setHeavyAtoms(xsDataAtomicCompositionHeavyAtoms)
return xsDataChemicalComposition
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG("EDPluginControlStrategyv1_2.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of Strategy:")
self.addErrorWarningMessagesToExecutiveSummary()
xsDataResultStrategy = self.getDataOutput()
if self._edPluginRaddose is not None:
if self._edPluginRaddose.getDataOutput() is not None:
self.addExecutiveSummaryLine("")
self.appendExecutiveSummary(self._edPluginRaddose, "Raddose : ")
if xsDataResultStrategy is not None:
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine("Calculations assuming polymer crystal with:")
self.addExecutiveSummaryLine("------------------------------------------")
self.addExecutiveSummaryLine("")
xsDataStructure = (
xsDataResultStrategy.getCollectionPlan()[0]
.getCollectionStrategy()
.getSample()
.getChemicalComposition()
.getStructure()
)
self.addExecutiveSummaryLine(
"Number of structure copies in asymmetric unit: %.2f"
% xsDataStructure.getNumberOfCopiesInAsymmetricUnit().getValue()
)
self.addExecutiveSummaryLine("")
chains = xsDataStructure.getChain()
self.addExecutiveSummaryLine("Chains:")
for chain in chains:
strChainType = chain.getType().getValue()
self.addExecutiveSummaryLine(" Type : %s" % strChainType)
if strChainType == "protein":
self.addExecutiveSummaryLine(
" Number of residues : %.2f" % chain.getNumberOfMonomers().getValue()
)
elif strChainType == "dna" or strChainType == "rna":
self.addExecutiveSummaryLine(
" Number of nucleotides : %.2f" % chain.getNumberOfMonomers().getValue()
)
strHeavyAtomsChain = " Number of heavy atoms :"
if chain.getHeavyAtoms() is not None:
heavyAtomsChain = chain.getHeavyAtoms().getAtom()
for heavyAtomChain in heavyAtomsChain:
strHeavyAtomsChain = strHeavyAtomsChain + " %s=%d" % (
heavyAtomChain.getSymbol().getValue(),
heavyAtomChain.getNumberOf().getValue(),
)
else:
strHeavyAtomsChain = strHeavyAtomsChain + " No heavy atoms"
self.addExecutiveSummaryLine(strHeavyAtomsChain)
self.addExecutiveSummaryLine(
" Number of copies in structure : %.2f" % chain.getNumberOfCopies().getValue()
)
self.addExecutiveSummaryLine("")
ligands = xsDataStructure.getLigand()
if len(ligands) != 0:
self.addExecutiveSummaryLine("Ligands:")
for ligand in ligands:
self.addExecutiveSummaryLine(
" Number of light atoms : %.2f" % ligand.getNumberOfLightAtoms().getValue()
)
strHeavyAtomsLigand = " Number of heavy atoms :"
if ligand.getHeavyAtoms() is not None:
heavyAtomsLigand = ligand.getHeavyAtoms().getAtom()
for heavyAtomLigand in heavyAtomsLigand:
strHeavyAtomsLigand = strHeavyAtomsLigand + " %s=%d" % (
heavyAtomLigand.getSymbol().getValue(),
heavyAtomLigand.getNumberOf().getValue(),
)
else:
strHeavyAtomsChain = strHeavyAtomsChain + " No heavy atoms"
self.addExecutiveSummaryLine(strHeavyAtomsLigand)
self.addExecutiveSummaryLine(
" Number of copies in structure : %.2f" % chain.getNumberOfCopies().getValue()
)
self.addExecutiveSummaryLine("")
if self._edPluginBest is not None:
if self._edPluginBest.getDataOutput() is not None:
self.appendExecutiveSummary(self._edPluginBest, "Best : ")
self.addExecutiveSummaryLine("")
def generateStrategyShortSummary(self, _xsDataResultStrategy):
"""
Generates a short summary of the BEST strategy
"""
self.DEBUG("EDPluginControlIntegrationv10.generateIntegrationShortSummary")
strStrategyShortSummary = ""
iTotalNoImages = 0
fTotalExposureTime = 0.0
xsDataDiffractionPlan = None
if self.getDataInput():
if self.getDataInput().getDiffractionPlan():
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if self._bEstimateRadiationDamage:
strStrategyShortSummary += "Strategy: Radiation damage estimated"
if self._edPluginRaddose.getDataOutput().getTimeToReachHendersonLimit():
strStrategyShortSummary += (
", time to reach Henderson limit: %.1f s\n"
% self._edPluginRaddose.getDataOutput().getTimeToReachHendersonLimit().getValue()
)
else:
strStrategyShortSummary += "\n"
else:
strStrategyShortSummary += "Strategy: No radiation damage estimation"
if xsDataDiffractionPlan:
if xsDataDiffractionPlan.getMaxExposureTimePerDataCollection():
strStrategyShortSummary += (
", max exposure time per data collection: %.1f s\n"
% xsDataDiffractionPlan.getMaxExposureTimePerDataCollection().getValue()
)
else:
strStrategyShortSummary += "\n"
else:
strStrategyShortSummary += "\n"
if xsDataDiffractionPlan:
strStrategyShortSummary += "Strategy: Options: "
listStrategyOptions = []
if xsDataDiffractionPlan.getAnomalousData():
if xsDataDiffractionPlan.getAnomalousData().getValue():
listStrategyOptions.append("anomalous data")
if xsDataDiffractionPlan.getAimedCompleteness():
listStrategyOptions.append(
"aimed completeness = %.1f" % xsDataDiffractionPlan.getAimedCompleteness().getValue()
)
if xsDataDiffractionPlan.getAimedMultiplicity():
listStrategyOptions.append(
"aimed multiplicity = %d" % xsDataDiffractionPlan.getAimedMultiplicity().getValue()
)
if xsDataDiffractionPlan.getAimedResolution():
listStrategyOptions.append(
"aimed resolution = %.2f A" % xsDataDiffractionPlan.getAimedResolution().getValue()
)
if xsDataDiffractionPlan.getComplexity():
listStrategyOptions.append("complexity = %s" % xsDataDiffractionPlan.getComplexity().getValue())
if xsDataDiffractionPlan.getStrategyOption():
listStrategyOptions.append(
"extra strategy option(s) = %s" % xsDataDiffractionPlan.getStrategyOption().getValue()
)
if listStrategyOptions != []:
for strStrategyOption in listStrategyOptions[:-1]:
strStrategyShortSummary += strStrategyOption + ", "
strStrategyShortSummary += listStrategyOptions[-1]
strStrategyShortSummary += "\n"
fResolutionMax = None
fRankingResolution = None
for xsDataCollectionPlan in _xsDataResultStrategy.getCollectionPlan():
iNoCollectionPlan = xsDataCollectionPlan.getCollectionPlanNumber().getValue()
strStrategyShortSummary += "Strategy: Collection plan %d" % iNoCollectionPlan
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary()
if xsDataStrategySummary.getResolutionReasoning() != None:
strResolutionResoning = xsDataStrategySummary.getResolutionReasoning().getValue()
strStrategyShortSummary += ": %s\n" % strResolutionResoning
else:
strStrategyShortSummary += "\n"
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy()
if xsDataStrategySummary.getRankingResolution() is not None:
fRankingResolution = xsDataStrategySummary.getRankingResolution().getValue()
strStrategyShortSummary += "Strategy: Ranking resolution: %.2f [A]\n" % fRankingResolution
for xsDataSubWedge in xsDataCollectionStrategy.getSubWedge():
iWedgeNo = xsDataCollectionPlan.getCollectionPlanNumber().getValue()
strStrategyShortSummary += "Strategy: wedge %d: " % iWedgeNo
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary()
fResolution = xsDataStrategySummary.getResolution().getValue()
if (fResolutionMax is None) or (fResolution < fResolutionMax):
fResolutionMax = fResolution
strStrategyShortSummary += "resolution %.2f [A], " % fResolution
xsDataStringAction = xsDataSubWedge.getAction()
if xsDataStringAction is not None:
strStrategyShortSummary += "%s, " % xsDataStringAction.getValue()
iSubWedgeNo = xsDataSubWedge.getSubWedgeNumber().getValue()
strStrategyShortSummary += "sub wedge %d: " % iSubWedgeNo
xsDataExperimentalCondition = xsDataSubWedge.getExperimentalCondition()
xsDataGoniostat = xsDataExperimentalCondition.getGoniostat()
fRotationStart = xsDataGoniostat.getRotationAxisStart().getValue()
strStrategyShortSummary += "start %.2f, " % fRotationStart
fRange = xsDataGoniostat.getOscillationWidth().getValue()
fRotationEnd = xsDataGoniostat.getRotationAxisEnd().getValue()
iNoImages = int((fRotationEnd - fRotationStart) / fRange + 0.1)
strStrategyShortSummary += "images %d, " % iNoImages
strStrategyShortSummary += "width %.2f, " % fRange
xsDataBeam = xsDataExperimentalCondition.getBeam()
fExpTime = xsDataBeam.getExposureTime().getValue()
strStrategyShortSummary += "time %.2f [s], " % fExpTime
fTransmission = xsDataBeam.getTransmission().getValue()
strStrategyShortSummary += "transmission %.2f\n" % fTransmission
iTotalNoImages += iNoImages
fTotalExposureTime += fExpTime * iNoImages
strStrategyShortSummary += "Strategy: total no images %d, total exposure time %.1f [s]\n" % (
iTotalNoImages,
fTotalExposureTime,
)
if fRankingResolution is not None:
if (fRankingResolution < fResolutionMax) and (abs(fRankingResolution - fResolutionMax) > 0.1):
strStrategyShortSummary += "\n"
strStrategyShortSummary += "NOTE! " * 20 + "\n"
strStrategyShortSummary += "\n"
strStrategyShortSummary += (
"BEST has calculated that it should be possible to collect data to %.2f A from this sample.\n"
% fRankingResolution
)
strStrategyShortSummary += (
"If you want to calculate a new strategy for data collection to this resolution you\n"
)
strStrategyShortSummary += "must first recollect reference images at this resolution.\n"
strStrategyShortSummary += "\n"
strStrategyShortSummary += "NOTE! " * 20 + "\n"
strStrategyShortSummary += "\n"
self.setDataOutput(XSDataString(strStrategyShortSummary), "strategyShortSummary")
class EDPluginControlStrategyv1_2(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__ (self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputStrategy)
self._strPluginRaddoseName = "EDPluginRaddosev10"
self._edPluginRaddose = None
self._edHandlerXSDataRaddose = None
self._strPluginBestName = "EDPluginBestv1_2"
self._edPluginBest = None
self._edHandlerXSDataBest = None
self._strPluginPlotGleName = "EDPluginExecPlotGlev1_0"
self._edPluginPlotGle = None
self._strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self._strSymopHome = None
self._xsDataSampleCopy = None
# For default chemical composition
self._fAverageAminoAcidVolume = 135.49
self._fAverageCrystalSolventContent = 0.47
self._fAverageSulfurContentPerAminoacid = 0.05
self._fAverageSulfurConcentration = 314
# This varaible determines if Raddose should be executed or not
self._bEstimateRadiationDamage = None
# Raddose log file
self.xsDataFileRaddoseLog = None
def setSymopHome(self, _strSymopHome):
self._strSymopHome = _strSymopHome
def getSymopHome(self):
return self._strSymopHome
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 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"
)
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)
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, strFileSymop
)
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, strFileSymop
)
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), strFileSymop
)
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)
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)
# 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 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)
class EDPluginControlStrategyv1_2(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__(self):
"""
"""
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputStrategy)
self._strPluginRaddoseName = "EDPluginRaddosev10"
self._edPluginRaddose = None
self._edHandlerXSDataRaddose = None
self._strPluginBestName = "EDPluginBestv1_2"
self._edPluginBest = None
self._edHandlerXSDataBest = None
self._strPluginPlotGleName = "EDPluginExecPlotGlev1_1"
self._edPluginPlotGle = None
self._xsDataSampleCopy = None
# For default chemical composition
self._fAverageAminoAcidVolume = 135.49
self._fAverageCrystalSolventContent = 0.47
self._fAverageSulfurContentPerAminoacid = 0.05
self._fAverageSulfurConcentration = 314
# This varaible determines if Raddose should be executed or not
self._bEstimateRadiationDamage = None
# Raddose log file
self.xsDataFileRaddoseLog = None
self.roundUpToEven100 = False
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 configure(self):
EDPluginControl.configure(self)
self.DEBUG("EDPluginControlStrategyv1_2.configure")
# Even 100 images?
self.roundUpToEven100 = self.config.get("roundUpToEven100", False)
def process(self, _edObject=None):
EDPluginControl.process(self, _edObject)
self.DEBUG("EDPluginControlStrategyv1_2.process...")
self._edPluginBest.connectSUCCESS(self.doSuccessActionBest)
self._edPluginBest.connectFAILURE(self.doFailureActionBest)
if self._bEstimateRadiationDamage:
self._edPluginRaddose.connectSUCCESS(
self.doRaddoseToBestTransition)
self._edPluginRaddose.connectFAILURE(self.doFailureActionRaddose)
self._edPluginRaddose.executeSynchronous()
else:
self.executeBest()
def postProcess(self, _edObject=None):
EDPluginControl.postProcess(self, _edObject)
self.DEBUG("EDPluginControlStrategyv1_2.postProcess...")
#
# Create the BEST graphs from the plot mtv file
#
# Check if we have GLE files from BEST:
xsDataResultBest = self._edPluginBest.getDataOutput()
xsDataInputPlotGle = XSDataInputPlotGle()
if xsDataResultBest.glePlot != []:
for xsDataBestGlePlot in xsDataResultBest.glePlot:
xsDataGlePlot = XSDataGlePlot()
xsDataGlePlot.script = xsDataBestGlePlot.script
xsDataGlePlot.data = xsDataBestGlePlot.data
xsDataInputPlotGle.addGlePlot(xsDataGlePlot)
else:
xsDataInputPlotGle.filePlotMtv = xsDataResultBest.pathToPlotMtvFile
self._edPluginPlotGle.dataInput = xsDataInputPlotGle
self._edPluginPlotGle.executeSynchronous()
def finallyProcess(self, _edObject=None):
EDPluginControl.finallyProcess(self, _edObject)
self.DEBUG("EDPluginControlStrategyv1_2.finallyProcess")
xsDataResultStrategy = None
xsDataResultBest = self._edPluginBest.getDataOutput()
if (xsDataResultBest is not None and
self.getDataInput().getDiffractionPlan().getStrategyOption()
is not None):
if (self.getDataInput().getDiffractionPlan().getStrategyOption().
getValue() != "-Bonly"):
xsDataResultStrategy = self._edHandlerXSDataBest.getXSDataResultStrategy(
xsDataResultBest,
self.getDataInput().getExperimentalCondition(),
self._xsDataSampleCopy,
roundUpToEven100=self.roundUpToEven100)
else:
xsDataResultStrategy = self._edHandlerXSDataBest.getXSDataResultStrategy(
xsDataResultBest,
self.getDataInput().getExperimentalCondition(),
self._xsDataSampleCopy,
roundUpToEven100=self.roundUpToEven100)
if self.xsDataFileRaddoseLog is not None:
xsDataResultStrategy.setRaddoseLogFile(self.xsDataFileRaddoseLog)
# Plots
if not self._edPluginPlotGle.isFailure(
) and self._edPluginPlotGle.dataOutput is not None:
listFileGraph = self._edPluginPlotGle.dataOutput.fileGraph
xsDataResultStrategy.bestGraphFile = listFileGraph
# Sample
xsDataResultStrategy.setSample(self._xsDataSampleCopy)
# timeToReachHendersonLimit
if self._edPluginRaddose is not None:
xsDataRaddoseOutput = self._edPluginRaddose.dataOutput
if xsDataRaddoseOutput is not None:
xsDataResultStrategy.timeToReachHendersonLimit = xsDataRaddoseOutput.timeToReachHendersonLimit
self.setDataOutput(xsDataResultStrategy)
self.generateStrategyShortSummary(xsDataResultStrategy)
def doRaddoseToBestTransition(self, _edPlugin):
self.DEBUG("EDPluginControlStrategyv1_2.doRaddoseToBestTransition")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlStrategyv1_2.doRaddoseToBestTransition")
xsDataRaddoseOutput = self._edPluginRaddose.getDataOutput()
# update the strategy data with the data coming from Raddose
self._xsDataSampleCopy.setAbsorbedDoseRate(
xsDataRaddoseOutput.getAbsorbedDoseRate())
if xsDataRaddoseOutput.getPathToLogFile() != None:
self.xsDataFileRaddoseLog = xsDataRaddoseOutput.getPathToLogFile()
# Call the Best Translator layer
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self._edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
xsDataInputStrategyCopy = XSDataInputStrategy.parseString(
self.getDataInput().marshal())
xsDataInputStrategyCopy.setSample(self._xsDataSampleCopy)
xsDataInputBest = self._edHandlerXSDataBest.getXSDataInputBest(
xsDataInputStrategyCopy)
self._edPluginBest.setDataInput(xsDataInputBest)
self._edPluginBest.executeSynchronous()
def doFailureActionRaddose(self, _edPlugin=None):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
self.DEBUG("EDPluginControlStrategyv1_2.doFailureActionRaddose")
self.retrieveFailureMessages(
_edPlugin, "EDPluginControlStrategyv1_2.doFailureActionRaddose")
strWarningMessage = "EDPluginControlStrategyv1_2: Raddose failure"
self.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self.executeBest(self)
def executeBest(self, _edPlugin=None):
# Call the Best Translator layer
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self._edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
xsDataInputStrategyCopy = XSDataInputStrategy.parseString(
self.getDataInput().marshal())
xsDataInputStrategyCopy.setSample(self._xsDataSampleCopy)
xsDataInputBest = self._edHandlerXSDataBest.getXSDataInputBest(
xsDataInputStrategyCopy)
self._edPluginBest.setDataInput(xsDataInputBest)
self._edPluginBest.executeSynchronous()
def doSuccessActionBest(self, _edPlugin=None):
"""
retrieve the potential warning messages
"""
self.DEBUG("EDPluginControlStrategyv1_2.doSuccessActionBest")
self.retrieveSuccessMessages(
_edPlugin, "EDPluginControlStrategyv1_2.doSuccessActionBest")
def doFailureActionBest(self, _edPlugin):
"""
retrieve the potential warning messages
retrieve the potential error messages
"""
self.DEBUG("EDPluginControlStrategyv1_2.doFailureActionBest")
self.retrieveFailureMessages(_edPlugin, "BEST failure:")
self.generateExecutiveSummary(self)
self.setFailure()
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 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(
XSDataDouble(iNumberOfSulfurAtom))
xsDataAtomicCompositionHeavyAtoms.addAtom(xsDataSulfurAtom)
chain.setHeavyAtoms(xsDataAtomicCompositionHeavyAtoms)
return xsDataChemicalComposition
def generateExecutiveSummary(self, _edPlugin):
"""
Generates a summary of the execution of the plugin.
"""
self.DEBUG("EDPluginControlStrategyv1_2.generateExecutiveSummary")
self.addExecutiveSummaryLine("Summary of Strategy:")
self.addErrorWarningMessagesToExecutiveSummary()
xsDataResultStrategy = self.getDataOutput()
if (self._edPluginRaddose is not None):
if (self._edPluginRaddose.getDataOutput() is not None):
self.addExecutiveSummaryLine("")
self.appendExecutiveSummary(self._edPluginRaddose,
"Raddose : ")
if (xsDataResultStrategy is not None):
self.addExecutiveSummaryLine("")
self.addExecutiveSummaryLine(
"Calculations assuming polymer crystal with:")
self.addExecutiveSummaryLine(
"------------------------------------------")
self.addExecutiveSummaryLine("")
xsDataStructure = xsDataResultStrategy.getCollectionPlan(
)[0].getCollectionStrategy().getSample(
).getChemicalComposition().getStructure()
self.addExecutiveSummaryLine(
"Number of structure copies in asymmetric unit: %.2f" %
xsDataStructure.getNumberOfCopiesInAsymmetricUnit(
).getValue())
self.addExecutiveSummaryLine("")
chains = xsDataStructure.getChain()
self.addExecutiveSummaryLine("Chains:")
for chain in chains:
strChainType = chain.getType().getValue()
self.addExecutiveSummaryLine(
" Type : %s" %
strChainType)
if (strChainType == "protein"):
self.addExecutiveSummaryLine(
" Number of residues : %.2f" %
chain.getNumberOfMonomers().getValue())
elif (strChainType == "dna" or strChainType == "rna"):
self.addExecutiveSummaryLine(
" Number of nucleotides : %.2f" %
chain.getNumberOfMonomers().getValue())
strHeavyAtomsChain = " Number of heavy atoms :"
if (chain.getHeavyAtoms() is not None):
heavyAtomsChain = chain.getHeavyAtoms().getAtom()
for heavyAtomChain in heavyAtomsChain:
strHeavyAtomsChain = strHeavyAtomsChain + " %s=%d" % (
heavyAtomChain.getSymbol().getValue(),
heavyAtomChain.getNumberOf().getValue())
else:
strHeavyAtomsChain = strHeavyAtomsChain + " No heavy atoms"
self.addExecutiveSummaryLine(strHeavyAtomsChain)
self.addExecutiveSummaryLine(
" Number of copies in structure : %.2f" %
chain.getNumberOfCopies().getValue())
self.addExecutiveSummaryLine("")
ligands = xsDataStructure.getLigand()
if (len(ligands) != 0):
self.addExecutiveSummaryLine("Ligands:")
for ligand in ligands:
self.addExecutiveSummaryLine(
" Number of light atoms : %.2f" %
ligand.getNumberOfLightAtoms().getValue())
strHeavyAtomsLigand = " Number of heavy atoms :"
if (ligand.getHeavyAtoms() is not None):
heavyAtomsLigand = ligand.getHeavyAtoms().getAtom()
for heavyAtomLigand in heavyAtomsLigand:
strHeavyAtomsLigand = strHeavyAtomsLigand + " %s=%d" % (
heavyAtomLigand.getSymbol().getValue(),
heavyAtomLigand.getNumberOf().getValue())
else:
strHeavyAtomsChain = strHeavyAtomsChain + " No heavy atoms"
self.addExecutiveSummaryLine(strHeavyAtomsLigand)
self.addExecutiveSummaryLine(
" Number of copies in structure : %.2f" %
chain.getNumberOfCopies().getValue())
self.addExecutiveSummaryLine("")
if (self._edPluginBest is not None):
if (self._edPluginBest.getDataOutput() is not None):
self.appendExecutiveSummary(self._edPluginBest, "Best : ")
self.addExecutiveSummaryLine("")
def generateStrategyShortSummary(self, _xsDataResultStrategy):
"""
Generates a short summary of the BEST strategy
"""
self.DEBUG(
"EDPluginControlIntegrationv10.generateIntegrationShortSummary")
strStrategyShortSummary = ""
iTotalNoImages = 0
fTotalExposureTime = 0.0
xsDataDiffractionPlan = None
if self.getDataInput():
if self.getDataInput().getDiffractionPlan():
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan(
)
if self._bEstimateRadiationDamage:
strStrategyShortSummary += "Strategy: Radiation damage estimated"
if self._edPluginRaddose.getDataOutput(
).getTimeToReachHendersonLimit():
strStrategyShortSummary += ", time to reach Henderson limit: %.1f s\n" % self._edPluginRaddose.getDataOutput(
).getTimeToReachHendersonLimit().getValue()
else:
strStrategyShortSummary += "\n"
else:
strStrategyShortSummary += "Strategy: No radiation damage estimation"
if xsDataDiffractionPlan:
if xsDataDiffractionPlan.getMaxExposureTimePerDataCollection():
strStrategyShortSummary += ", max exposure time per data collection: %.1f s\n" % xsDataDiffractionPlan.getMaxExposureTimePerDataCollection(
).getValue()
else:
strStrategyShortSummary += "\n"
else:
strStrategyShortSummary += "\n"
if xsDataDiffractionPlan:
strStrategyShortSummary += "Strategy: Options: "
listStrategyOptions = []
if xsDataDiffractionPlan.getAnomalousData():
if xsDataDiffractionPlan.getAnomalousData().getValue():
listStrategyOptions.append("anomalous data")
if xsDataDiffractionPlan.getAimedCompleteness():
listStrategyOptions.append(
"aimed completeness = %.1f" %
xsDataDiffractionPlan.getAimedCompleteness().getValue())
if xsDataDiffractionPlan.getAimedMultiplicity():
listStrategyOptions.append(
"aimed multiplicity = %d" %
xsDataDiffractionPlan.getAimedMultiplicity().getValue())
if xsDataDiffractionPlan.getAimedResolution():
listStrategyOptions.append(
"aimed resolution = %.2f A" %
xsDataDiffractionPlan.getAimedResolution().getValue())
if xsDataDiffractionPlan.getComplexity():
listStrategyOptions.append(
"complexity = %s" %
xsDataDiffractionPlan.getComplexity().getValue())
if xsDataDiffractionPlan.getStrategyOption():
listStrategyOptions.append(
"extra strategy option(s) = %s" %
xsDataDiffractionPlan.getStrategyOption().getValue())
if listStrategyOptions != []:
for strStrategyOption in listStrategyOptions[:-1]:
strStrategyShortSummary += strStrategyOption + ", "
strStrategyShortSummary += listStrategyOptions[-1]
strStrategyShortSummary += "\n"
fResolutionMax = None
fRankingResolution = None
for xsDataCollectionPlan in _xsDataResultStrategy.getCollectionPlan():
iNoCollectionPlan = xsDataCollectionPlan.getCollectionPlanNumber(
).getValue()
strStrategyShortSummary += "Strategy: Collection plan %d" % iNoCollectionPlan
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary()
if xsDataStrategySummary.getResolutionReasoning() != None:
strResolutionResoning = xsDataStrategySummary.getResolutionReasoning(
).getValue()
strStrategyShortSummary += ": %s\n" % strResolutionResoning
else:
strStrategyShortSummary += "\n"
xsDataCollectionStrategy = xsDataCollectionPlan.getCollectionStrategy(
)
if xsDataStrategySummary.getRankingResolution() is not None:
fRankingResolution = xsDataStrategySummary.getRankingResolution(
).getValue()
strStrategyShortSummary += "Strategy: Ranking resolution: %.2f [A]\n" % fRankingResolution
for xsDataSubWedge in xsDataCollectionStrategy.getSubWedge():
iWedgeNo = xsDataCollectionPlan.getCollectionPlanNumber(
).getValue()
strStrategyShortSummary += "Strategy: wedge %d: " % iWedgeNo
xsDataStrategySummary = xsDataCollectionPlan.getStrategySummary(
)
fResolution = xsDataStrategySummary.getResolution().getValue()
if (fResolutionMax is None) or (fResolution < fResolutionMax):
fResolutionMax = fResolution
strStrategyShortSummary += "resolution %.2f [A], " % fResolution
xsDataStringAction = xsDataSubWedge.getAction()
if xsDataStringAction is not None:
strStrategyShortSummary += "%s, " % xsDataStringAction.getValue(
)
iSubWedgeNo = xsDataSubWedge.getSubWedgeNumber().getValue()
strStrategyShortSummary += "sub wedge %d: " % iSubWedgeNo
xsDataExperimentalCondition = xsDataSubWedge.getExperimentalCondition(
)
xsDataGoniostat = xsDataExperimentalCondition.getGoniostat()
fRotationStart = xsDataGoniostat.getRotationAxisStart(
).getValue()
strStrategyShortSummary += "start %.2f, " % fRotationStart
fRange = xsDataGoniostat.getOscillationWidth().getValue()
fRotationEnd = xsDataGoniostat.getRotationAxisEnd().getValue()
iNoImages = int((fRotationEnd - fRotationStart) / fRange + 0.1)
strStrategyShortSummary += "images %d, " % iNoImages
strStrategyShortSummary += "width %.2f, " % fRange
xsDataBeam = xsDataExperimentalCondition.getBeam()
fExpTime = xsDataBeam.getExposureTime().getValue()
strStrategyShortSummary += "time %.2f [s], " % fExpTime
fTransmission = xsDataBeam.getTransmission().getValue()
strStrategyShortSummary += "transmission %.2f\n" % fTransmission
iTotalNoImages += iNoImages
fTotalExposureTime += fExpTime * iNoImages
strStrategyShortSummary += "Strategy: total no images %d, total exposure time %.1f [s]\n" % \
(iTotalNoImages, fTotalExposureTime)
if fRankingResolution is not None:
if (fRankingResolution < fResolutionMax) and (
abs(fRankingResolution - fResolutionMax) > 0.1):
strStrategyShortSummary += "\n"
strStrategyShortSummary += "NOTE! " * 20 + "\n"
strStrategyShortSummary += "\n"
strStrategyShortSummary += "BEST has calculated that it should be possible to collect data to %.2f A from this sample.\n" % fRankingResolution
strStrategyShortSummary += "If you want to calculate a new strategy for data collection to this resolution you\n"
strStrategyShortSummary += "must first recollect reference images at this resolution.\n"
strStrategyShortSummary += "\n"
strStrategyShortSummary += "NOTE! " * 20 + "\n"
strStrategyShortSummary += "\n"
self.setDataOutput(XSDataString(strStrategyShortSummary),
"strategyShortSummary")
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())
class EDPluginControlStrategyv1_1(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputStrategy)
self.__strPluginRaddoseName = "EDPluginRaddosev10"
self.__edPluginRaddose = None
self.__edHandlerXSDataRaddose = None
self.__strPluginBestName = "EDPluginBestv1_1"
self.__edPluginBest = None
self.__edHandlerXSDataBest = None
self.__strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self.__strSymopHome = "/opt/pxsoft/ccp4-6.0.2/lib/data"
self.__xsDataSampleCopy = None
# For default chemical composition
self.__fAverageAminoAcidVolume = 135.49
self.__fAverageCrystalSolventContent = 0.47
self.__fAverageSulfurContentPerAminoacid = 0.05
self.__fAverageSulfurConcentration = 314
def setSymopHome(self, _strSymopHome):
self.__strSymopHome = _strSymopHome
def getSymopHome(self):
return self.__strSymopHome
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(
).getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_1.preProcess: Space Group IT Number Found by indexing: "
+ str(iSpaceGroupITNumber))
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(iSpaceGroupITNumber), 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()
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)
bSpaceGroupForced = False
if(xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper().replace(" ", "")
if strSpaceGroup != "":
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
bSpaceGroupForced = True
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
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()
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
class EDPluginControlStrategyv10(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__ (self):
EDPluginControl.__init__(self)
self.__strPluginRaddoseName = "EDPluginRaddosev10"
self.__oedPluginRaddose = None
self.__oedHandlerXSDataRaddose = None
self.__strPluginBestName = "EDPluginBestv10"
self.__edPluginBest = None
self.__edHandlerXSDataBest = None
self.__strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self.__strSymopHome = "/opt/pxsoft/ccp4-6.0.2/lib/data"
self.__xsDataSampleCopy = None
# For default chemical composition
self.__fAverageAminoAcidVolume = 135.49
self.__fAverageCrystalSolventContent = 0.47
self.__fAverageSulfurContentPerAminoacid = 0.05
self.__fAverageSulfurConcentration = 314
self.setXSDataInputClass(XSDataStrategyInput)
def setSymopHome(self, _strSymopHome):
self.__strSymopHome = _strSymopHome
def getSymopHome(self):
return self.__strSymopHome
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv10.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):
warningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % ('EDPluginControlStrategyv10.preProcess', self.__strPluginRaddoseName, "Beam Flux not set")
EDVerbose.warning(warningMessage)
self.addWarningMessage(warningMessage)
else:
self.__edPluginRaddose = self.loadPlugin(self.__strPluginRaddoseName)
if (self.__edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv10.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()
EDVerbose.DEBUG("EDPluginControlStrategyv10.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv10.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
# 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("EDPluginControlStrategyv10.preProcess: Space Group IT Name found by indexing: " + strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroupName, strFileSymop)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv10.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
strSpaceGroupITNumber = str(self.__xsDataSampleCopy.getCrystal().getSpaceGroup().getITNumber().getValue())
EDVerbose.DEBUG("EDPluginControlStrategyv10.preProcess: Space Group IT Number Found by indexing: " + strSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(strSpaceGroupITNumber, strFileSymop)
except Exception, detail:
errorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv10.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(errorMessage)
self.addErrorMessage(errorMessage)
raise RuntimeError, errorMessage
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 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 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(
class EDPluginControlKappaStrategyv2_0(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__ (self):
EDPluginControl.__init__(self)
#self.setXSDataInputClass(EDList)
self.setRequiredToHaveConfiguration(True)
self.strPluginRaddoseName = "EDPluginRaddosev10"
self.edPluginRaddose = None
self.edHandlerXSDataRaddose = None
self.strPluginBestName = "EDPluginBestv1_2"
self.edPluginBest = None
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self.edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
self.strPluginAlignmentName = "EDPluginSTACAlignmentv2_0"
self.edPluginAlignment = None
self.edHandlerXSDataAlignment = None
self.strPluginKappaStrategyName = "EDPluginSTACStrategyv2_0"
self.edPluginKappaStrategy = None
self.edHandlerXSDataKappaStrategy = None
self.setXSDataInputClass(XSDataInputStrategy, "mxv1InputStrategy")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection, "mxv2DataCollection")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataIndexingResult, "mxv1IndexingResult")
#disable kappa by default
self.KappaStrategy = 0
self.strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self.strSymopHome = os.path.normpath("/opt/pxsoft/ccp4-6.0.2/lib/data")
self.xsDataSampleCopy = None
# For default chemical composition
self.fAverageAminoAcidVolume = 135.49
self.fAverageCrystalSolventContent = 0.47
self.fAverageSulfurContentPerAminoacid = 0.05
self.fAverageSulfurConcentration = 314
def setSymopHome(self, _strSymopHome):
self.strSymopHome = _strSymopHome
def getSymopHome(self):
return self.strSymopHome
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.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")
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.edPluginRaddose = self.loadPlugin(self.strPluginRaddoseName)
if (self.edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlKappaStrategyv2_0.preProcess: " + self.strPluginRaddoseName + " Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
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()
EDVerbose.DEBUG("EDPluginControlKappaStrategyv2_0.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlKappaStrategyv2_0.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)
strSpaceGroup = self.xsDataSampleCopy.getCrystal().getSpaceGroup().getName().getValue()
EDVerbose.DEBUG("EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Name found by indexing: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlKappaStrategyv2_0.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)
dSpaceGroupITNumber = self.xsDataSampleCopy.getCrystal().getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG("EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Number Found by indexing: %d" % dSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(str(dSpaceGroupITNumber), strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlKappaStrategyv2_0.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
