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
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()
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 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 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 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
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")
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_3(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_3"
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
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_3.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_3: 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_3: 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_3.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_3.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
bSpaceGroupForced = True
except Exception, detail:
strErrorMessage = "EDPluginControlStrategyv1_3: 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_3.preProcess: Space Group IT Name found by indexing: " + strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroupName, strFileSymop)
except Exception, detail:
strErrorMessage = "EDPluginControlStrategyv1_3: 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_3.preProcess: Space Group IT Number Found by indexing: %d" % iSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(str(iSpaceGroupITNumber), strFileSymop)
except Exception, detail:
strErrorMessage = "EDPluginControlStrategyv1_3: 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_3: 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 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
class EDPluginControlStrategyv1_3(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_3"
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
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlStrategyv1_3.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_3: 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_3: 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_3.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_3.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup)
bSpaceGroupForced = True
except Exception, detail:
strErrorMessage = "EDPluginControlStrategyv1_3: 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_3.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroupName)
except Exception, detail:
strErrorMessage = "EDPluginControlStrategyv1_3: 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_3.preProcess: Space Group IT Number Found by indexing: %d"
% iSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(iSpaceGroupITNumber))
except Exception, detail:
strErrorMessage = "EDPluginControlStrategyv1_3: 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_3: 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)
