def readIdxrefLp(self, _pathToIdxrefLp, _xsDataResultXDSIndexing=None):
self.DEBUG("EDPluginXDSIndexingv1_0.readIdxrefLp")
if _xsDataResultXDSIndexing is None:
xsDataResultXDSIndexing = XSDataResultXDSIndexing()
else:
xsDataResultXDSIndexing = _xsDataResultXDSIndexing
if os.path.exists(_pathToIdxrefLp):
xsDataResultXDSIndexing.pathToLogFile = XSDataFile(XSDataString(_pathToIdxrefLp))
with open(_pathToIdxrefLp) as f:
listLines = f.readlines()
indexLine = 0
doParseParameters = False
doParseLattice = False
while (indexLine < len(listLines)):
if "DIFFRACTION PARAMETERS USED AT START OF INTEGRATION" in listLines[indexLine]:
doParseParameters = True
doParseLattice = False
elif "DETERMINATION OF LATTICE CHARACTER AND BRAVAIS LATTICE" in listLines[indexLine]:
doParseParameters = False
doParseLattice = True
if doParseParameters:
if "MOSAICITY" in listLines[indexLine]:
mosaicity = float(listLines[indexLine].split()[-1])
xsDataResultXDSIndexing.mosaicity = XSDataAngle(mosaicity)
elif "DETECTOR COORDINATES (PIXELS) OF DIRECT BEAM" in listLines[indexLine]:
xBeam = float(listLines[indexLine].split()[-2])
yBeam = float(listLines[indexLine].split()[-1])
xsDataResultXDSIndexing.beamCentreX = XSDataFloat(xBeam)
xsDataResultXDSIndexing.beamCentreY = XSDataFloat(yBeam)
elif "CRYSTAL TO DETECTOR DISTANCE" in listLines[indexLine]:
distance = float(listLines[indexLine].split()[-1])
xsDataResultXDSIndexing.distance = XSDataLength(distance)
elif doParseLattice:
if listLines[indexLine].startswith(" * ") and not listLines[indexLine + 1].startswith(" * "):
listLine = listLines[indexLine].split()
xsDataResultXDSIndexing.latticeCharacter = XSDataInteger(int(listLine[1]))
bravaisLattice = listLine[2]
xsDataResultXDSIndexing.bravaisLattice = XSDataString(bravaisLattice)
spaceGroup = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(bravaisLattice)
xsDataResultXDSIndexing.spaceGroup = XSDataString(spaceGroup)
spaceGroupNumber = EDUtilsSymmetry.getITNumberFromSpaceGroupName(spaceGroup)
xsDataResultXDSIndexing.spaceGroupNumber = XSDataInteger(spaceGroupNumber)
xsDataResultXDSIndexing.qualityOfFit = XSDataFloat(float(listLine[3]))
xsDataXDSCell = XSDataXDSCell()
xsDataXDSCell.length_a = XSDataLength(float(listLine[4]))
xsDataXDSCell.length_b = XSDataLength(float(listLine[5]))
xsDataXDSCell.length_c = XSDataLength(float(listLine[6]))
xsDataXDSCell.angle_alpha = XSDataAngle(float(listLine[7]))
xsDataXDSCell.angle_beta = XSDataAngle(float(listLine[8]))
xsDataXDSCell.angle_gamma = XSDataAngle(float(listLine[9]))
xsDataResultXDSIndexing.unitCell = xsDataXDSCell
indexLine += 1
return xsDataResultXDSIndexing
def testGetMinimumSymmetrySpaceGroupFromBravaisLattice(self):
"""
Testing retrieving the lowest symmetry space group from all Bravais Lattices
"""
listBravaisLattice = [ "aP", "mP", "mC", "mI", "oP", "oA", "oB", "oC", "oS", "oF", "oI", "tP", "tC", "tI", "tF", "hP", "hR", "cP", "cF", "cI" ]
listSpaceGroup = [ "P1", "P2", "C2", "C2", "P222", "C222", "C222", "C222", "C222", "F222", "I222", "P4", "P4", "I4", "I4", "P3", "H3", "P23", "F23", "I23" ]
for iIndex in range(len(listBravaisLattice)):
EDAssert.equal(listSpaceGroup[ iIndex ], EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(listBravaisLattice[ iIndex]))
def generateXSDataIndexingResult(_xsDataResultXDSIndexing, _xsDataExperimentalCondition=None):
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected()
xsDataCrystalSelected = XSDataCrystal()
# xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
# xsDataCellSelected = xsDataLabelitSolution.getUnitCell()
spaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(_xsDataResultXDSIndexing.bravaisLattice.value)
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(XSDataString(spaceGroupName))
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
# xsDataCrystalSelected.setCell(xsDataCellSelected)
xsDataCrystalSelected.setMosaicity(XSDataDouble(_xsDataResultXDSIndexing.mosaicity.value))
xsDataCrystalSelected.setCell(XSDataCell.parseString(_xsDataResultXDSIndexing.unitCell.marshal()))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(_xsDataResultXDSIndexing.getAMatrix())
xsDataOrientation.setMatrixU(_xsDataResultXDSIndexing.getUMatrix())
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
if (_xsDataExperimentalCondition is not None):
fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionX().getValue()
fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionY().getValue()
fBeamPositionXNew = _xsDataResultXDSIndexing.getBeamCentreX().getValue()
fBeamPositionYNew = _xsDataResultXDSIndexing.getBeamCentreY().getValue()
xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(fBeamPositionXOrig - fBeamPositionXNew))
xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(fBeamPositionYOrig - fBeamPositionYNew))
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(XSDataLength(_xsDataResultXDSIndexing.getBeamCentreX().value))
xsDataDetector.setBeamPositionY(XSDataLength(_xsDataResultXDSIndexing.getBeamCentreY().value))
xsDataDetector.setDistance(_xsDataResultXDSIndexing.getDistance())
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected)
return xsDataIndexingResult
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlXDSAPPv1_0.preProcess")
self.screen("XDSAPP processing started")
if self.dataInput.reprocess is not None:
self.reprocess = self.dataInput.reprocess.value
self.processingCommandLine = ' '.join(sys.argv)
self.processingPrograms = "XDSAPP"
if self.reprocess:
self.processingPrograms += " reprocess"
if self.dataInput.useXdsAsciiToXml is not None:
if self.dataInput.useXdsAsciiToXml.value:
self.useXdsAsciiToXml = True
if self.useXdsAsciiToXml:
self.doAnomAndNonanom = False
elif self.dataInput.doAnomAndNonanom is not None:
self.doAnomAndNonanom = self.dataInput.doAnomAndNonanom.value
if self.doAnomAndNonanom:
self.doAnom = True
self.doNoanom = True
else:
if self.dataInput.doAnom is not None:
self.doAnom = self.dataInput.doAnom.value
self.doNoanom = not self.doAnom
self.strHost = socket.gethostname()
self.screen("Running on {0}".format(self.strHost))
try:
strLoad = os.getloadavg()
self.screen("System load avg: {0}".format(strLoad))
except OSError:
pass
self.edPluginWaitFileFirst = self.loadPlugin("EDPluginMXWaitFilev1_1", "MXWaitFileFirst")
self.edPluginWaitFileLast = self.loadPlugin("EDPluginMXWaitFilev1_1", "MXWaitFileLast")
self.edPluginRetrieveDataCollection = self.loadPlugin("EDPluginISPyBRetrieveDataCollectionv1_4")
if self.doAnom:
self.edPluginExecXDSAPPAnom = self.loadPlugin("EDPluginExecXDSAPPv1_0", "EDPluginExecXDSAPPv1_0_anom")
if self.doNoanom:
self.edPluginExecXDSAPPNoanom = self.loadPlugin("EDPluginExecXDSAPPv1_0", "EDPluginExecXDSAPPv1_0_noanom")
# Check for space group and cell
if self.dataInput.spaceGroup is not None and self.dataInput.unitCell is not None:
spaceGroup = self.dataInput.spaceGroup.value
spaceGroupNumber = EDUtilsSymmetry.getITNumberFromSpaceGroupName(spaceGroup)
self.screen("Forcing space group {0} number {1}".format(spaceGroup, spaceGroupNumber))
unitCell = self.dataInput.unitCell.value
self.screen("Forcing unit cell {0}".format(unitCell))
self.xdsAppSpacegroup = "{0} {1}".format(spaceGroupNumber, unitCell)
def testGetMinimumSymmetrySpaceGroupFromBravaisLattice(self):
"""
Testing retrieving the lowest symmetry space group from all Bravais Lattices
"""
listBravaisLattice = [
"aP", "mP", "mC", "mI", "oP", "oA", "oB", "oC", "oS", "oF", "oI",
"tP", "tC", "tI", "tF", "hP", "hR", "cP", "cF", "cI"
]
listSpaceGroup = [
"P1", "P2", "C2", "C2", "P222", "C222", "C222", "C222", "C222",
"F222", "I222", "P4", "P4", "I4", "I4", "P3", "H3", "P23", "F23",
"I23"
]
for iIndex in range(len(listBravaisLattice)):
EDAssert.equal(
listSpaceGroup[iIndex],
EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(
listBravaisLattice[iIndex]))
def preProcess(self, _edObject=None):
EDPluginControl.preProcess(self)
self.DEBUG("EDPluginControlXDSAPPv1_0.preProcess")
self.screen("XDSAPP processing started")
self.processingCommandLine = ' '.join(sys.argv)
self.processingPrograms = "XDSAPP"
if self.useXdsAsciiToXml:
self.doAnomAndNonanom = False
elif self.dataInput.doAnomAndNonanom is not None:
if self.dataInput.doAnomAndNonanom.value:
self.doAnomAndNonanom = True
else:
self.doAnomAndNonanom = False
self.strHost = socket.gethostname()
self.screen("Running on {0}".format(self.strHost))
try:
strLoad = os.getloadavg()
self.screen("System load avg: {0}".format(strLoad))
except OSError:
pass
self.edPluginWaitFileFirst = self.loadPlugin("EDPluginMXWaitFilev1_1", "MXWaitFileFirst")
self.edPluginWaitFileLast = self.loadPlugin("EDPluginMXWaitFilev1_1", "MXWaitFileLast")
self.edPluginRetrieveDataCollection = self.loadPlugin("EDPluginISPyBRetrieveDataCollectionv1_4")
self.edPluginExecXDSAPPAnom = self.loadPlugin("EDPluginExecXDSAPPv1_0", "EDPluginExecXDSAPPv1_0_anom")
if self.doAnomAndNonanom:
self.edPluginExecXDSAPPNoanom = self.loadPlugin("EDPluginExecXDSAPPv1_0", "EDPluginExecXDSAPPv1_0_noanom")
# Check for space group and cell
if self.dataInput.spaceGroup is not None and self.dataInput.unitCell is not None:
spaceGroup = self.dataInput.spaceGroup.value
spaceGroupNumber = EDUtilsSymmetry.getITNumberFromSpaceGroupName(spaceGroup)
self.screen("Forcing space group {0} number {1}".format(spaceGroup, spaceGroupNumber))
unitCell = self.dataInput.unitCell.value
self.screen("Forcing unit cell {0}".format(unitCell))
self.xdsAppSpacegroup = "{0} {1}".format(spaceGroupNumber, unitCell)
def generateXSDataIndexingResult(_xsDataLabelitScreenOutput, _xsDataLabelitMosflmScriptsOutput, \
_xsDataExperimentalCondition=None):
EDVerbose.DEBUG(
"EDHandlerXSDataLabelitv1_1.generateXSDataIndexingOutput")
iSelectedSolutionNumber = _xsDataLabelitScreenOutput.getSelectedSolutionNumber(
).getValue()
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = None
for xsDataLabelitSolution in _xsDataLabelitScreenOutput.getLabelitScreenSolution(
):
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
edStringSpaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(
xsDataLabelitSolution.getBravaisLattice().getValue())
xsDataSpaceGroup.setName(XSDataString(edStringSpaceGroupName))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataCrystal.setCell(xsDataLabelitSolution.getUnitCell())
xsDataIndexingSolution = XSDataIndexingSolution()
xsDataIndexingSolution.setCrystal(xsDataCrystal)
iIndex = xsDataLabelitSolution.getSolutionNumber().getValue()
xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
xsDataIndexingResult.addSolution(xsDataIndexingSolution)
if (iIndex == iSelectedSolutionNumber):
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected(
)
xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
edStringSelectedSpaceGroupName = edStringSpaceGroupName
xsDataCellSelected = xsDataLabelitSolution.getUnitCell()
fRmsdSelected = xsDataLabelitSolution.getRmsd().getValue()
iNumberOfSpotsSelected = xsDataLabelitSolution.getNumberOfSpots(
).getValue()
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(
XSDataString(edStringSelectedSpaceGroupName))
#xsDataSpaceGroupSelected.setITNumber( XSDataInteger( iSelectedSpaceGroupNumber ) )
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
xsDataCrystalSelected.setCell(xsDataCellSelected)
xsDataCrystalSelected.setMosaicity(
XSDataDouble(_xsDataLabelitScreenOutput.getMosaicity().getValue()))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(
_xsDataLabelitMosflmScriptsOutput.getAMatrix())
xsDataOrientation.setMatrixU(
_xsDataLabelitMosflmScriptsOutput.getUMatrix())
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
if (_xsDataExperimentalCondition is not None):
fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector(
).getBeamPositionX().getValue()
fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector(
).getBeamPositionY().getValue()
fBeamPositionXNew = _xsDataLabelitScreenOutput.getBeamCentreX(
).getValue()
fBeamPositionYNew = _xsDataLabelitScreenOutput.getBeamCentreY(
).getValue()
xsDataStatisticsIndexing.setBeamPositionShiftX(
XSDataLength(fBeamPositionXOrig - fBeamPositionXNew))
xsDataStatisticsIndexing.setBeamPositionShiftY(
XSDataLength(fBeamPositionYOrig - fBeamPositionYNew))
#xsDataStatisticsIndexing.setSpotDeviXSDataLength( dDistanceRefinedationAngular( XSDataAngle( dDeviationAngular ) )
xsDataStatisticsIndexing.setSpotDeviationPositional(
XSDataLength(fRmsdSelected))
xsDataStatisticsIndexing.setSpotsUsed(
XSDataInteger(iNumberOfSpotsSelected))
xsDataStatisticsIndexing.setSpotsTotal(
XSDataInteger(iNumberOfSpotsSelected))
xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(
xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(
_xsDataLabelitScreenOutput.getBeamCentreX())
xsDataDetector.setBeamPositionY(
_xsDataLabelitScreenOutput.getBeamCentreY())
xsDataDetector.setDistance(_xsDataLabelitScreenOutput.getDistance())
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(
xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(
xsDataIndexingSolutionSelected)
xsDataIndexingResult.setIndexingLogFile(
_xsDataLabelitScreenOutput.getPathToLogFile())
return xsDataIndexingResult
def generateXSDataIndexingResult(_xsDataResultLabelitIndexing, _xsDataExperimentalCondition=None):
EDVerbose.DEBUG("EDHandlerXSDataLabelitv1_1.generateXSDataIndexingOutput")
xsDataLabelitScreenOutput = _xsDataResultLabelitIndexing.screenOutput
xsDataLabelitMosflmScriptsOutput = _xsDataResultLabelitIndexing.mosflmScriptsOutput
iSelectedSolutionNumber = xsDataLabelitScreenOutput.getSelectedSolutionNumber().getValue()
xsDataIndexingResult = XSDataIndexingResult()
xsDataIndexingSolutionSelected = None
for xsDataLabelitSolution in xsDataLabelitScreenOutput.getLabelitScreenSolution():
xsDataCrystal = XSDataCrystal()
xsDataSpaceGroup = XSDataSpaceGroup()
edStringSpaceGroupName = EDUtilsSymmetry.getMinimumSymmetrySpaceGroupFromBravaisLattice(xsDataLabelitSolution.getBravaisLattice().getValue())
xsDataSpaceGroup.setName(XSDataString(edStringSpaceGroupName))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataCrystal.setCell(xsDataLabelitSolution.getUnitCell())
xsDataIndexingSolution = XSDataIndexingSolution()
xsDataIndexingSolution.setCrystal(xsDataCrystal)
iIndex = xsDataLabelitSolution.getSolutionNumber().getValue()
xsDataIndexingSolution.setNumber(XSDataInteger(iIndex))
xsDataIndexingResult.addSolution(xsDataIndexingSolution)
if (iIndex == iSelectedSolutionNumber):
xsDataIndexingSolutionSelected = XSDataIndexingSolutionSelected()
xsDataIndexingSolutionSelected.setNumber(XSDataInteger(iIndex))
edStringSelectedSpaceGroupName = edStringSpaceGroupName
xsDataCellSelected = xsDataLabelitSolution.getUnitCell()
fRmsdSelected = xsDataLabelitSolution.getRmsd().getValue()
iNumberOfSpotsSelected = xsDataLabelitSolution.getNumberOfSpots().getValue()
xsDataCrystalSelected = XSDataCrystal()
xsDataSpaceGroupSelected = XSDataSpaceGroup()
xsDataSpaceGroupSelected.setName(XSDataString(edStringSelectedSpaceGroupName))
xsDataSpaceGroupSelected.setITNumber(XSDataInteger(EDUtilsSymmetry.getITNumberFromSpaceGroupName(edStringSelectedSpaceGroupName)))
xsDataCrystalSelected.setSpaceGroup(xsDataSpaceGroupSelected)
xsDataCrystalSelected.setCell(xsDataCellSelected)
xsDataCrystalSelected.setMosaicity(XSDataDouble(xsDataLabelitScreenOutput.getMosaicity().getValue()))
xsDataIndexingSolutionSelected.setCrystal(xsDataCrystalSelected)
xsDataOrientation = XSDataOrientation()
xsDataOrientation.setMatrixA(xsDataLabelitMosflmScriptsOutput.getAMatrix())
xsDataOrientation.setMatrixU(xsDataLabelitMosflmScriptsOutput.getUMatrix())
xsDataIndexingSolutionSelected.setOrientation(xsDataOrientation)
xsDataStatisticsIndexing = XSDataStatisticsIndexing()
if (_xsDataExperimentalCondition is not None):
fBeamPositionXOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionX().getValue()
fBeamPositionYOrig = _xsDataExperimentalCondition.getDetector().getBeamPositionY().getValue()
fBeamPositionXNew = xsDataLabelitScreenOutput.getBeamCentreX().getValue()
fBeamPositionYNew = xsDataLabelitScreenOutput.getBeamCentreY().getValue()
xsDataStatisticsIndexing.setBeamPositionShiftX(XSDataLength(fBeamPositionXOrig - fBeamPositionXNew))
xsDataStatisticsIndexing.setBeamPositionShiftY(XSDataLength(fBeamPositionYOrig - fBeamPositionYNew))
# xsDataStatisticsIndexing.setSpotDeviXSDataLength( dDistanceRefinedationAngular( XSDataAngle( dDeviationAngular ) )
xsDataStatisticsIndexing.setSpotDeviationPositional(XSDataLength(fRmsdSelected))
xsDataStatisticsIndexing.setSpotsUsed(XSDataInteger(iNumberOfSpotsSelected))
xsDataStatisticsIndexing.setSpotsTotal(XSDataInteger(iNumberOfSpotsSelected))
xsDataIndexingSolutionSelected.setStatistics(xsDataStatisticsIndexing)
xsDataExperimentalConditionRefined = None
if (_xsDataExperimentalCondition is None):
xsDataExperimentalConditionRefined = XSDataExperimentalCondition()
else:
# Copy the incoming experimental condition
xmlExperimentalCondition = _xsDataExperimentalCondition.marshal()
xsDataExperimentalConditionRefined = XSDataExperimentalCondition.parseString(xmlExperimentalCondition)
xsDataDetector = xsDataExperimentalConditionRefined.getDetector()
if (xsDataDetector is None):
xsDataDetector = XSDataDetector()
xsDataDetector.setBeamPositionX(xsDataLabelitScreenOutput.getBeamCentreX())
xsDataDetector.setBeamPositionY(xsDataLabelitScreenOutput.getBeamCentreY())
xsDataDetector.setDistance(xsDataLabelitScreenOutput.getDistance())
xsDataExperimentalConditionRefined.setDetector(xsDataDetector)
xsDataIndexingSolutionSelected.setExperimentalConditionRefined(xsDataExperimentalConditionRefined)
xsDataIndexingResult.setSelectedSolution(xsDataIndexingSolutionSelected)
xsDataIndexingResult.setIndexingLogFile(xsDataLabelitScreenOutput.getPathToLogFile())
return xsDataIndexingResult
def testGetITNumberFromSpaceGroupName(self):
strSymopFileName = "/opt/pxsoft/ccp4/v6.3.0/linux-x86_64/lib/data/symop.lib"
if os.path.exists(strSymopFileName):
EDAssert.equal(
1,
EDUtilsSymmetry.getITNumberFromSpaceGroupName(
"P1", strSymopFileName), "ITNumber from space group P1")
EDAssert.equal(
3,
EDUtilsSymmetry.getITNumberFromSpaceGroupName(
"P2", strSymopFileName), "ITNumber from space group P2")
EDAssert.equal(
5,
EDUtilsSymmetry.getITNumberFromSpaceGroupName(
"C2", strSymopFileName), "ITNumber from space group C2")
EDAssert.equal(
16,
EDUtilsSymmetry.getITNumberFromSpaceGroupName(
"P222", strSymopFileName),
"ITNumber from space group P222")
EDAssert.equal(
21,
EDUtilsSymmetry.getITNumberFromSpaceGroupName(
"C222", strSymopFileName),
"ITNumber from space group C222")
EDAssert.equal(
22,
EDUtilsSymmetry.getITNumberFromSpaceGroupName(
"F222", strSymopFileName),
"ITNumber from space group F222")
EDAssert.equal(
75,
EDUtilsSymmetry.getITNumberFromSpaceGroupName(
"P4", strSymopFileName), "ITNumber from space group P4")
EDAssert.equal(
79,
EDUtilsSymmetry.getITNumberFromSpaceGroupName(
"I4", strSymopFileName), "ITNumber from space group I4")
EDAssert.equal(
143,
EDUtilsSymmetry.getITNumberFromSpaceGroupName(
"P3", strSymopFileName), "ITNumber from space group P3")
EDAssert.equal(
146,
EDUtilsSymmetry.getITNumberFromSpaceGroupName(
"H3", strSymopFileName), "ITNumber from space group H3")
EDAssert.equal(
195,
EDUtilsSymmetry.getITNumberFromSpaceGroupName(
"P23", strSymopFileName), "ITNumber from space group P23")
EDAssert.equal(
196,
EDUtilsSymmetry.getITNumberFromSpaceGroupName(
"F23", strSymopFileName), "ITNumber from space group F23")
class EDPluginControlStrategyv1_1(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__(self):
EDPluginControl.__init__(self)
self.setXSDataInputClass(XSDataInputStrategy)
self.__strPluginRaddoseName = "EDPluginRaddosev10"
self.__edPluginRaddose = None
self.__edHandlerXSDataRaddose = None
self.__strPluginBestName = "EDPluginBestv1_1"
self.__edPluginBest = None
self.__edHandlerXSDataBest = None
self.__strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self.__strSymopHome = "/opt/pxsoft/ccp4-6.0.2/lib/data"
self.__xsDataSampleCopy = None
# For default chemical composition
self.__fAverageAminoAcidVolume = 135.49
self.__fAverageCrystalSolventContent = 0.47
self.__fAverageSulfurContentPerAminoacid = 0.05
self.__fAverageSulfurConcentration = 314
def setSymopHome(self, _strSymopHome):
self.__strSymopHome = _strSymopHome
def getSymopHome(self):
return self.__strSymopHome
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv1_1.preProcess...")
self.__edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if (xsDataSampleCrystalMM is None):
self.__xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self.__xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if (xsDataCrystal is not None):
self.__xsDataSampleCopy.setCrystal(xsDataCrystal)
# Raddose is enabled only if the beam flux is set
if (self.getDataInput().getExperimentalCondition().getBeam().getFlux()
is None):
pyStrWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlStrategyv1_1.preProcess',
self.__strPluginRaddoseName, "Beam Flux not set")
EDVerbose.warning(pyStrWarningMessage)
self.addWarningMessage(pyStrWarningMessage)
else:
self.__edPluginRaddose = self.loadPlugin(
self.__strPluginRaddoseName)
if (self.__edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv1_1.preProcess: " +
self.__strPluginRaddoseName +
" Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput(
).getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
strNumOperators = None
strSpaceGroup = None
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_1.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_1.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self.__xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self.__xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_1.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroupName, strFileSymop)
except Exception, detail:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_1.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self.__xsDataSampleCopy.getCrystal(
).getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_1.preProcess: Space Group IT Number Found by indexing: "
+ str(iSpaceGroupITNumber))
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(iSpaceGroupITNumber), strFileSymop)
except Exception, detail:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_1.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlStrategyv1_2.preProcess...")
self._edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if (xsDataSampleCrystalMM is None):
self._xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self._xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if (xsDataCrystal is not None):
self._xsDataSampleCopy.setCrystal(xsDataCrystal)
# Load the Best plugin
self._edPluginBest = self.loadPlugin(self._strPluginBestName)
self._edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self._edPluginBest.setBaseName(self._strPluginBestName)
# Load the plot gle plugin
self._edPluginPlotGle = self.loadPlugin(self._strPluginPlotGleName)
# Check if radiation damage estimation is required or not in the diffraction plan
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.getEstimateRadiationDamage():
if xsDataDiffractionPlan.getEstimateRadiationDamage().getValue(
):
# Yes, is requested
self._bEstimateRadiationDamage = True
else:
# No, is explicitly not requested
self._bEstimateRadiationDamage = False
elif xsDataDiffractionPlan.getStrategyOption() is not None:
if xsDataDiffractionPlan.getStrategyOption().getValue().find(
"-DamPar") != -1:
# The "-DamPar" option requires estimation of radiation damage
self._bEstimateRadiationDamage = True
# Check if we know what to do with radiation damage
if self._bEstimateRadiationDamage is None:
# "Force" the estimation of radiation damage if the flux is present
if self.getDataInput().getExperimentalCondition().getBeam(
).getFlux() is None:
strWarningMessage = "EDPluginControlStrategyv1_2: Missing flux input - cannot estimate radiation damage."
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self._bEstimateRadiationDamage = False
else:
self._bEstimateRadiationDamage = True
if self._bEstimateRadiationDamage:
if self.getDataInput().getExperimentalCondition().getBeam(
).getFlux() is None:
strErrorMessage = "EDPluginControlStrategyv1_2: Missing flux input. Cannot estimate radiation damage"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if not self.isFailure():
self._edPluginRaddose = self.loadPlugin(self._strPluginRaddoseName)
if (self._edPluginRaddose is not None):
self.DEBUG("EDPluginControlStrategyv1_2.preProcess: " +
self._strPluginRaddoseName +
" Found... setting Data Input")
xsDataStringSpaceGroup = self.getDataInput(
).getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
bSpaceGroupForced = False
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper(
).replace(" ", "")
if strSpaceGroup != "":
self.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup)
bSpaceGroupForced = True
except Exception as detail:
strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
detail)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
if not bSpaceGroupForced:
# Space Group has NOT been forced
xsDataStringSpaceGroup = self._xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self._xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
self.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroupName)
except Exception as detail:
strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
detail)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self._xsDataSampleCopy.getCrystal(
).getSpaceGroup().getITNumber().getValue()
self.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Space Group IT Number Found by indexing: %d"
% iSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(iSpaceGroupITNumber))
except Exception as detail:
strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
detail)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
if (strNumOperators is not None):
iNumOperators = int(strNumOperators)
else:
strErrorMessage = "EDPluginControlStrategyv1_2: No symmetry operators found for Space Group: {0}".format(
strNumOperators)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
xsDataChemicalComposition = self._xsDataSampleCopy.getChemicalComposition(
)
if (xsDataChemicalComposition is None):
# create a default chemical composition and assign it to the sample
xsDataDefaultChemicalComposition = self.getDefaultChemicalComposition(
self._xsDataSampleCopy, iNumOperators)
self._xsDataSampleCopy.setChemicalComposition(
xsDataDefaultChemicalComposition)
else:
# Check for Sulfur atoms, if none, add native sulfur atoms
xsDataUpdatedChemicalComposition = self.updateChemicalComposition(
xsDataChemicalComposition)
self._xsDataSampleCopy.setChemicalComposition(
xsDataUpdatedChemicalComposition)
# create Data Input for Raddose
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
self._edHandlerXSDataRaddose = EDHandlerXSDataRaddosev10()
xsDataBeam = self.getDataInput().getExperimentalCondition(
).getBeam()
# Calculate number of images (MXSUP-1616):
iNumberOfImages = None
xsDataCollection = self.dataInput.dataCollection
if xsDataCollection is not None:
iNumberOfImages = 0
for xsDataSubWedge in xsDataCollection.subWedge:
xsDataGoniostat = xsDataSubWedge.experimentalCondition.goniostat
iOscStart = xsDataGoniostat.rotationAxisStart.value
iOscEnd = xsDataGoniostat.rotationAxisEnd.value
iOscWidth = xsDataGoniostat.oscillationWidth.value
iNumberOfImages += int(
round((iOscEnd - iOscStart) / iOscWidth, 0))
if iNumberOfImages is None:
iNumberOfImages = 1
self.WARNING(
"No goniostat information, number of images for RADDOSE set to 1"
)
xsDataRaddoseInput = self._edHandlerXSDataRaddose.getXSDataRaddoseInput(
xsDataBeam, self._xsDataSampleCopy, iNumOperators,
iNumberOfImages)
if xsDataRaddoseInput is not None:
self._edPluginRaddose.setDataInput(xsDataRaddoseInput)
self._edPluginRaddose.setBaseDirectory(
self.getWorkingDirectory())
self._edPluginRaddose.setBaseName(
self._strPluginRaddoseName)
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlKappaStrategyv2_0.preProcess...")
self.edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput(
"mxv1InputStrategy")[0].getSample()
if (xsDataSampleCrystalMM is None):
self.xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self.xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput(
"mxv1InputStrategy")[0].getCrystalRefined()
if (xsDataCrystal is not None):
self.xsDataSampleCopy.setCrystal(xsDataCrystal)
# Raddose is enabled only if the beam flux is set
if (self.getDataInput("mxv1InputStrategy")
[0].getExperimentalCondition().getBeam().getFlux() is None):
strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginRaddoseName, "Beam Flux not set")
self.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.edPluginRaddose = self.loadPlugin(self.strPluginRaddoseName)
if (self.edPluginRaddose is not None):
self.DEBUG("EDPluginControlKappaStrategyv2_0.preProcess: " +
self.strPluginRaddoseName +
" Found... setting Data Input")
xsDataStringSpaceGroup = self.getDataInput(
"mxv1InputStrategy")[0].getDiffractionPlan(
).getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
strNumOperators = None
strSpaceGroup = None
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue()
self.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup)
except Exception as detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
self.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup)
except Exception as detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
dSpaceGroupITNumber = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getITNumber().getValue()
self.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Number Found by indexing: %d"
% dSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(dSpaceGroupITNumber))
except Exception as detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
if (strNumOperators is not None):
iNumOperators = int(strNumOperators)
else:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"No symmetry operators found for Space Group: ",
strSpaceGroup)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
xsDataChemicalComposition = self.xsDataSampleCopy.getChemicalComposition(
)
if (xsDataChemicalComposition is None):
# create a default chemical composition and assign it to the sample
xsDataDefaultChemicalComposition = self.getDefaultChemicalComposition(
self.xsDataSampleCopy, iNumOperators)
self.xsDataSampleCopy.setChemicalComposition(
xsDataDefaultChemicalComposition)
else:
# Check for Sulfur atoms, if none, add native sulfur atoms
xsDataUpdatedChemicalComposition = self.updateChemicalComposition(
xsDataChemicalComposition)
self.xsDataSampleCopy.setChemicalComposition(
xsDataUpdatedChemicalComposition)
# create Data Input for Raddose
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
self.edHandlerXSDataRaddose = EDHandlerXSDataRaddosev10()
xsDataBeam = self.getDataInput("mxv1InputStrategy")[
0].getExperimentalCondition().getBeam()
xsDataRaddoseInput = None
iNumberOfImages = 1
self.warning("Number of images for RADDOSE forced to 1")
try:
xsDataRaddoseInput = self.edHandlerXSDataRaddose.getXSDataRaddoseInput(
xsDataBeam, self.xsDataSampleCopy, iNumOperators,
iNumberOfImages)
except Exception as detail:
strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginRaddoseName,
"EDHandlerXSDataRaddose : " + detail)
self.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
if (xsDataRaddoseInput is not None):
self.edPluginRaddose.setDataInput(xsDataRaddoseInput)
self.edPluginRaddose.setBaseDirectory(
self.getWorkingDirectory())
self.edPluginRaddose.setBaseName(self.strPluginRaddoseName)
# More checks?
# try:
# self.edPluginRaddose.setDataInput( xsDataRaddoseInput )
# self.edPluginRaddose.setBaseDirectory( self.getWorkingDirectory() )
# self.edPluginRaddose.setBaseName( self.strPluginRaddoseName )
#
# except Exception, detail:
# strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % ('EDPluginControlStrategyv1_1.preProcess', self.strPluginRaddoseName, detail ) )
# self.warning( strWarningMessage )
# self.addWarningMessage( strWarningMessage )
else:
strErrorMessage = EDMessage.ERROR_PLUGIN_NOT_LOADED_02 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginRaddoseName)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
self.edPluginBest = self.loadPlugin(self.strPluginBestName)
if (self.edPluginBest is None):
strErrorMessage = EDMessage.ERROR_PLUGIN_NOT_LOADED_02 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginBestName)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
else:
self.edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self.edPluginBest.setBaseName(self.strPluginBestName)
if (self.KappaStrategy):
# Alignment
self.edPluginAlignment = self.loadPlugin(
self.strPluginAlignmentName)
if (self.edPluginAlignment is None):
errorMessage = EDMessage.ERROR_PLUGIN_NOT_LOADED_02 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginAlignmentName)
self.error(errorMessage)
self.addErrorMessage(errorMessage)
# do not kill the application just because this feature is not available
# raise RuntimeError, errorMessage
else:
self.edPluginAlignment.setBaseDirectory(
self.getWorkingDirectory())
self.edPluginAlignment.setBaseName(self.strPluginAlignmentName)
# KappaStaregy
self.edPluginKappaStrategy = self.loadPlugin(
self.strPluginKappaStrategyName)
if (self.edPluginKappaStrategy is None):
errorMessage = EDMessage.ERROR_PLUGIN_NOT_LOADED_02 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginKappaStrategyName)
self.error(errorMessage)
self.addErrorMessage(errorMessage)
# raise RuntimeError, errorMessage
else:
self.edPluginKappaStrategy.setBaseDirectory(
self.getWorkingDirectory())
self.edPluginKappaStrategy.setBaseName(
self.strPluginKappaStrategyName)
class EDPluginControlKappaStrategyv2_0(EDPluginControl):
"""
The Plugin that controls the strategy step
"""
def __init__(self):
EDPluginControl.__init__(self)
#self.setXSDataInputClass(EDList)
self.setRequiredToHaveConfiguration(True)
self.strPluginRaddoseName = "EDPluginRaddosev10"
self.edPluginRaddose = None
self.edHandlerXSDataRaddose = None
self.strPluginBestName = "EDPluginBestv1_2"
self.edPluginBest = None
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
self.edHandlerXSDataBest = EDHandlerXSDataBestv1_2()
self.strPluginAlignmentName = "EDPluginSTACAlignmentv2_0"
self.edPluginAlignment = None
self.edHandlerXSDataAlignment = None
self.strPluginKappaStrategyName = "EDPluginSTACStrategyv2_0"
self.edPluginKappaStrategy = None
self.edHandlerXSDataKappaStrategy = None
self.setXSDataInputClass(XSDataInputStrategy, "mxv1InputStrategy")
EDFactoryPluginStatic.loadModule("XSDataMXv2")
import XSDataMXv2
self.setXSDataInputClass(XSDataMXv2.XSDataCollection,
"mxv2DataCollection")
import XSDataMXv1
self.setXSDataInputClass(XSDataMXv1.XSDataIndexingResult,
"mxv1IndexingResult")
#disable kappa by default
self.KappaStrategy = 0
self.strCONF_SYMOP_HOME = "symopHome"
# Default value for the location of the symop table
self.strSymopHome = os.path.normpath("/opt/pxsoft/ccp4-6.0.2/lib/data")
self.xsDataSampleCopy = None
# For default chemical composition
self.fAverageAminoAcidVolume = 135.49
self.fAverageCrystalSolventContent = 0.47
self.fAverageSulfurContentPerAminoacid = 0.05
self.fAverageSulfurConcentration = 314
def setSymopHome(self, _strSymopHome):
self.strSymopHome = _strSymopHome
def getSymopHome(self):
return self.strSymopHome
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlKappaStrategyv2_0.preProcess...")
self.edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput(
"mxv1InputStrategy")[0].getSample()
if (xsDataSampleCrystalMM is None):
self.xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self.xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput(
"mxv1InputStrategy")[0].getCrystalRefined()
if (xsDataCrystal is not None):
self.xsDataSampleCopy.setCrystal(xsDataCrystal)
# Raddose is enabled only if the beam flux is set
if (self.getDataInput("mxv1InputStrategy")
[0].getExperimentalCondition().getBeam().getFlux() is None):
strWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
self.strPluginRaddoseName, "Beam Flux not set")
EDVerbose.warning(strWarningMessage)
self.addWarningMessage(strWarningMessage)
else:
self.edPluginRaddose = self.loadPlugin(self.strPluginRaddoseName)
if (self.edPluginRaddose is not None):
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: " +
self.strPluginRaddoseName + " Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput(
"mxv1InputStrategy")[0].getDiffractionPlan(
).getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
strNumOperators = None
strSpaceGroup = None
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroup = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
dSpaceGroupITNumber = self.xsDataSampleCopy.getCrystal(
).getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG(
"EDPluginControlKappaStrategyv2_0.preProcess: Space Group IT Number Found by indexing: %d"
% dSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(dSpaceGroupITNumber), strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlKappaStrategyv2_0.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
def testGetSpaceGroupNameFromITNumber(self):
EDAssert.equal("P1", EDUtilsSymmetry.getSpaceGroupNameFromITNumber(1),
"Space group from from it number 1")
EDAssert.equal("P2", EDUtilsSymmetry.getSpaceGroupNameFromITNumber(3),
"Space group from from it number 3")
EDAssert.equal("C2", EDUtilsSymmetry.getSpaceGroupNameFromITNumber(5),
"Space group from from it number 5")
EDAssert.equal("P222",
EDUtilsSymmetry.getSpaceGroupNameFromITNumber(16),
"Space group from from it number 16")
EDAssert.equal("C222",
EDUtilsSymmetry.getSpaceGroupNameFromITNumber(21),
"Space group from from it number 21")
EDAssert.equal("F222",
EDUtilsSymmetry.getSpaceGroupNameFromITNumber(22),
"Space group from from it number 22")
EDAssert.equal("P4", EDUtilsSymmetry.getSpaceGroupNameFromITNumber(75),
"Space group from from it number 75")
EDAssert.equal("I4", EDUtilsSymmetry.getSpaceGroupNameFromITNumber(79),
"Space group from from it number 79")
EDAssert.equal("P3",
EDUtilsSymmetry.getSpaceGroupNameFromITNumber(143),
"Space group from from it number 143")
EDAssert.equal("H3",
EDUtilsSymmetry.getSpaceGroupNameFromITNumber(146),
"Space group from from it number 146")
EDAssert.equal("P23",
EDUtilsSymmetry.getSpaceGroupNameFromITNumber(195),
"Space group from from it number 195")
EDAssert.equal("F23",
EDUtilsSymmetry.getSpaceGroupNameFromITNumber(196),
"Space group from from it number 196")
def testGetITNumberFromSpaceGroupName(self):
EDAssert.equal(1, EDUtilsSymmetry.getITNumberFromSpaceGroupName("P1"),
"ITNumber from space group P1")
EDAssert.equal(3, EDUtilsSymmetry.getITNumberFromSpaceGroupName("P2"),
"ITNumber from space group P2")
EDAssert.equal(5, EDUtilsSymmetry.getITNumberFromSpaceGroupName("C2"),
"ITNumber from space group C2")
EDAssert.equal(16,
EDUtilsSymmetry.getITNumberFromSpaceGroupName("P222"),
"ITNumber from space group P222")
EDAssert.equal(21,
EDUtilsSymmetry.getITNumberFromSpaceGroupName("C222"),
"ITNumber from space group C222")
EDAssert.equal(22,
EDUtilsSymmetry.getITNumberFromSpaceGroupName("F222"),
"ITNumber from space group F222")
EDAssert.equal(75, EDUtilsSymmetry.getITNumberFromSpaceGroupName("P4"),
"ITNumber from space group P4")
EDAssert.equal(79, EDUtilsSymmetry.getITNumberFromSpaceGroupName("I4"),
"ITNumber from space group I4")
EDAssert.equal(143,
EDUtilsSymmetry.getITNumberFromSpaceGroupName("P3"),
"ITNumber from space group P3")
EDAssert.equal(146,
EDUtilsSymmetry.getITNumberFromSpaceGroupName("H3"),
"ITNumber from space group H3")
EDAssert.equal(195,
EDUtilsSymmetry.getITNumberFromSpaceGroupName("P23"),
"ITNumber from space group P23")
EDAssert.equal(196,
EDUtilsSymmetry.getITNumberFromSpaceGroupName("F23"),
"ITNumber from space group F23")
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess...")
self._edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if(xsDataSampleCrystalMM is None):
self._xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self._xsDataSampleCopy = XSDataSampleCrystalMM.parseString(strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if(xsDataCrystal is not None):
self._xsDataSampleCopy.setCrystal(xsDataCrystal)
# Load the Best plugin
self._edPluginBest = self.loadPlugin(self._strPluginBestName)
self._edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self._edPluginBest.setBaseName(self._strPluginBestName)
# Load the plot gle plugin
self._edPluginPlotGle = self.loadPlugin(self._strPluginPlotGleName)
# Check if radiation damage estimation is required or not in the diffraction plan
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.getEstimateRadiationDamage():
if xsDataDiffractionPlan.getEstimateRadiationDamage().getValue():
# Yes, is requested
self._bEstimateRadiationDamage = True
else:
# No, is explicitly not requested
self._bEstimateRadiationDamage = False
elif xsDataDiffractionPlan.getStrategyOption() is not None:
if xsDataDiffractionPlan.getStrategyOption().getValue().find("-DamPar") != -1:
# The "-DamPar" option requires estimation of radiation damage
self._bEstimateRadiationDamage = True
# Check if we know what to do with radiation damage
if self._bEstimateRadiationDamage is None:
# "Force" the estimation of radiation damage if the flux is present
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strWarningMessage = "EDPluginControlStrategyv1_2: Missing flux input - cannot estimate radiation damage."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self._bEstimateRadiationDamage = False
else:
self._bEstimateRadiationDamage = True
if self._bEstimateRadiationDamage:
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strErrorMessage = "EDPluginControlStrategyv1_2: Missing flux input. Cannot estimate radiation damage"
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if not self.isFailure():
self._edPluginRaddose = self.loadPlugin(self._strPluginRaddoseName)
if (self._edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: " + self._strPluginRaddoseName + " Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput().getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
if(xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper()
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName().getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Space Group IT Name found by indexing: " + strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(strSpaceGroupName, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: Space Group IT Number Found by indexing: %d" % iSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(str(iSpaceGroupITNumber), strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % ('EDPluginControlStrategyv1_2.preProcess', "Problem to calculate Number of symmetry operators", detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
self.DEBUG("EDPluginControlStrategyv1_2.preProcess...")
self._edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if xsDataSampleCrystalMM is None:
self._xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self._xsDataSampleCopy = XSDataSampleCrystalMM.parseString(strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if xsDataCrystal is not None:
self._xsDataSampleCopy.setCrystal(xsDataCrystal)
# Load the Best plugin
self._edPluginBest = self.loadPlugin(self._strPluginBestName)
self._edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self._edPluginBest.setBaseName(self._strPluginBestName)
# Load the plot gle plugin
self._edPluginPlotGle = self.loadPlugin(self._strPluginPlotGleName)
# Check if radiation damage estimation is required or not in the diffraction plan
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.getEstimateRadiationDamage():
if xsDataDiffractionPlan.getEstimateRadiationDamage().getValue():
# Yes, is requested
self._bEstimateRadiationDamage = True
else:
# No, is explicitly not requested
self._bEstimateRadiationDamage = False
elif xsDataDiffractionPlan.getStrategyOption() is not None:
if xsDataDiffractionPlan.getStrategyOption().getValue().find("-DamPar") != -1:
# The "-DamPar" option requires estimation of radiation damage
self._bEstimateRadiationDamage = True
# Check if we know what to do with radiation damage
if self._bEstimateRadiationDamage is None:
# "Force" the estimation of radiation damage if the flux is present
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strWarningMessage = (
"EDPluginControlStrategyv1_2: Missing flux input - cannot estimate radiation damage."
)
self.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self._bEstimateRadiationDamage = False
else:
self._bEstimateRadiationDamage = True
if self._bEstimateRadiationDamage:
if self.getDataInput().getExperimentalCondition().getBeam().getFlux() is None:
strErrorMessage = "EDPluginControlStrategyv1_2: Missing flux input. Cannot estimate radiation damage"
self.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if not self.isFailure():
self._edPluginRaddose = self.loadPlugin(self._strPluginRaddoseName)
if self._edPluginRaddose is not None:
self.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: "
+ self._strPluginRaddoseName
+ " Found... setting Data Input"
)
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput().getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
bSpaceGroupForced = False
if xsDataStringSpaceGroup is not None:
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper().replace(" ", "")
if strSpaceGroup != "":
self.DEBUG("EDPluginControlStrategyv1_2.preProcess: Forced Space Group Found: " + strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop
)
bSpaceGroupForced = True
except Exception as detail:
strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
detail
)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
if not bSpaceGroupForced:
# Space Group has NOT been forced
xsDataStringSpaceGroup = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName()
if xsDataStringSpaceGroup is not None:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self._xsDataSampleCopy.getCrystal().getSpaceGroup().getName().getValue()
self.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroupName
)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroupName, strFileSymop
)
except Exception as detail:
strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
detail
)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = (
self._xsDataSampleCopy.getCrystal().getSpaceGroup().getITNumber().getValue()
)
self.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Space Group IT Number Found by indexing: %d"
% iSpaceGroupITNumber
)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(iSpaceGroupITNumber), strFileSymop
)
except Exception as detail:
strErrorMessage = "EDPluginControlStrategyv1_2: Problem to calculate Number of symmetry operators: {0}".format(
detail
)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
if strNumOperators is not None:
iNumOperators = int(strNumOperators)
else:
strErrorMessage = "EDPluginControlStrategyv1_2: No symmetry operators found for Space Group: {0}".format(
strNumOperators
)
self.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError(strErrorMessage)
xsDataChemicalComposition = self._xsDataSampleCopy.getChemicalComposition()
if xsDataChemicalComposition is None:
# create a default chemical composition and assign it to the sample
xsDataDefaultChemicalComposition = self.getDefaultChemicalComposition(
self._xsDataSampleCopy, iNumOperators
)
self._xsDataSampleCopy.setChemicalComposition(xsDataDefaultChemicalComposition)
else:
# Check for Sulfur atoms, if none, add native sulfur atoms
xsDataUpdatedChemicalComposition = self.updateChemicalComposition(xsDataChemicalComposition)
self._xsDataSampleCopy.setChemicalComposition(xsDataUpdatedChemicalComposition)
# create Data Input for Raddose
from EDHandlerXSDataRaddosev10 import EDHandlerXSDataRaddosev10
self._edHandlerXSDataRaddose = EDHandlerXSDataRaddosev10()
xsDataBeam = self.getDataInput().getExperimentalCondition().getBeam()
# Calculate number of images (MXSUP-1616):
iNumberOfImages = None
xsDataCollection = self.dataInput.dataCollection
if xsDataCollection is not None:
iNumberOfImages = 0
for xsDataSubWedge in xsDataCollection.subWedge:
xsDataGoniostat = xsDataSubWedge.experimentalCondition.goniostat
iOscStart = xsDataGoniostat.rotationAxisStart.value
iOscEnd = xsDataGoniostat.rotationAxisEnd.value
iOscWidth = xsDataGoniostat.oscillationWidth.value
iNumberOfImages += int(round((iOscEnd - iOscStart) / iOscWidth, 0))
if iNumberOfImages is None:
iNumberOfImages = 1
self.WARNING("No goniostat information, number of images for RADDOSE set to 1")
xsDataRaddoseInput = self._edHandlerXSDataRaddose.getXSDataRaddoseInput(
xsDataBeam, self._xsDataSampleCopy, iNumOperators, iNumberOfImages
)
if xsDataRaddoseInput is not None:
self._edPluginRaddose.setDataInput(xsDataRaddoseInput)
self._edPluginRaddose.setBaseDirectory(self.getWorkingDirectory())
self._edPluginRaddose.setBaseName(self._strPluginRaddoseName)
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("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())
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess...")
self._edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if (xsDataSampleCrystalMM is None):
self._xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self._xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if (xsDataCrystal is not None):
self._xsDataSampleCopy.setCrystal(xsDataCrystal)
# Load the Best plugin
self._edPluginBest = self.loadPlugin(self._strPluginBestName)
self._edPluginBest.setBaseDirectory(self.getWorkingDirectory())
self._edPluginBest.setBaseName(self._strPluginBestName)
# Load the plot gle plugin
self._edPluginPlotGle = self.loadPlugin(self._strPluginPlotGleName)
# Check if radiation damage estimation is required or not in the diffraction plan
xsDataDiffractionPlan = self.getDataInput().getDiffractionPlan()
if xsDataDiffractionPlan is not None:
if xsDataDiffractionPlan.getEstimateRadiationDamage():
if xsDataDiffractionPlan.getEstimateRadiationDamage().getValue(
):
# Yes, is requested
self._bEstimateRadiationDamage = True
else:
# No, is explicitly not requested
self._bEstimateRadiationDamage = False
elif xsDataDiffractionPlan.getStrategyOption() is not None:
if xsDataDiffractionPlan.getStrategyOption().getValue().find(
"-DamPar") != -1:
# The "-DamPar" option requires estimation of radiation damage
self._bEstimateRadiationDamage = True
# Check if we know what to do with radiation damage
if self._bEstimateRadiationDamage is None:
# "Force" the estimation of radiation damage if the flux is present
if self.getDataInput().getExperimentalCondition().getBeam(
).getFlux() is None:
strWarningMessage = "EDPluginControlStrategyv1_2: Missing flux input - cannot estimate radiation damage."
EDVerbose.WARNING(strWarningMessage)
self.addWarningMessage(strWarningMessage)
self._bEstimateRadiationDamage = False
else:
self._bEstimateRadiationDamage = True
if self._bEstimateRadiationDamage:
if self.getDataInput().getExperimentalCondition().getBeam(
).getFlux() is None:
strErrorMessage = "EDPluginControlStrategyv1_2: Missing flux input. Cannot estimate radiation damage"
EDVerbose.ERROR(strErrorMessage)
self.addErrorMessage(strErrorMessage)
self.setFailure()
if not self.isFailure():
self._edPluginRaddose = self.loadPlugin(self._strPluginRaddoseName)
if (self._edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv1_2.preProcess: " +
self._strPluginRaddoseName +
" Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput(
).getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_2.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self._xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self._xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroupName, strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_2.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self._xsDataSampleCopy.getCrystal(
).getSpaceGroup().getITNumber().getValue()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_2.preProcess: Space Group IT Number Found by indexing: %d"
% iSpaceGroupITNumber)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupITNumber(
str(iSpaceGroupITNumber), strFileSymop)
except Exception, detail:
strErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_2.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(strErrorMessage)
self.addErrorMessage(strErrorMessage)
raise RuntimeError, strErrorMessage
def preProcess(self, _edObject=None):
"""
Gets the Configuration Parameters, if found, overrides default parameters
"""
EDPluginControl.preProcess(self, _edObject)
EDVerbose.DEBUG("EDPluginControlStrategyv1_1.preProcess...")
self.__edPluginRaddose = None
xsDataSampleCrystalMM = self.getDataInput().getSample()
if (xsDataSampleCrystalMM is None):
self.__xsDataSampleCopy = XSDataSampleCrystalMM()
else:
strXmlStringDataSample = xsDataSampleCrystalMM.marshal()
self.__xsDataSampleCopy = XSDataSampleCrystalMM.parseString(
strXmlStringDataSample)
xsDataCrystal = self.getDataInput().getCrystalRefined()
if (xsDataCrystal is not None):
self.__xsDataSampleCopy.setCrystal(xsDataCrystal)
# Raddose is enabled only if the beam flux is set
if (self.getDataInput().getExperimentalCondition().getBeam().getFlux()
is None):
pyStrWarningMessage = EDMessage.WARNING_CANNOT_USE_PLUGIN_03 % (
'EDPluginControlStrategyv1_1.preProcess',
self.__strPluginRaddoseName, "Beam Flux not set")
EDVerbose.warning(pyStrWarningMessage)
self.addWarningMessage(pyStrWarningMessage)
else:
self.__edPluginRaddose = self.loadPlugin(
self.__strPluginRaddoseName)
if (self.__edPluginRaddose is not None):
EDVerbose.DEBUG("EDPluginControlStrategyv1_1.preProcess: " +
self.__strPluginRaddoseName +
" Found... setting Data Input")
strFileSymop = os.path.join(self.getSymopHome(), "symop.lib")
xsDataStringSpaceGroup = self.getDataInput(
).getDiffractionPlan().getForcedSpaceGroup()
# Space Group has been forced
# Prepare chemical composition calculation with the forced Space Group (Space Group Name)
strNumOperators = None
strSpaceGroup = None
if (xsDataStringSpaceGroup is not None):
strSpaceGroup = xsDataStringSpaceGroup.getValue().upper()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_1.preProcess: Forced Space Group Found: "
+ strSpaceGroup)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroup, strFileSymop)
except Exception, detail:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_1.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
# Space Group has NOT been forced
else:
xsDataStringSpaceGroup = self.__xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName()
if (xsDataStringSpaceGroup is not None):
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group Name)
strSpaceGroupName = self.__xsDataSampleCopy.getCrystal(
).getSpaceGroup().getName().getValue()
EDVerbose.DEBUG(
"EDPluginControlStrategyv1_1.preProcess: Space Group IT Name found by indexing: "
+ strSpaceGroupName)
try:
strNumOperators = EDUtilsSymmetry.getNumberOfSymmetryOperatorsFromSpaceGroupName(
strSpaceGroupName, strFileSymop)
except Exception, detail:
pyStrErrorMessage = EDMessage.ERROR_EXECUTION_03 % (
'EDPluginControlStrategyv1_1.preProcess',
"Problem to calculate Number of symmetry operators",
detail)
EDVerbose.error(pyStrErrorMessage)
self.addErrorMessage(pyStrErrorMessage)
self.setFailure()
else:
# Prepare chemical composition calculation with the Space Group calculated by indexing (Space Group IT number)
iSpaceGroupITNumber = self.__xsDataSampleCopy.getCrystal(
def testGetITNumberFromSpaceGroupName(self):
strSymopFileName = "/opt/pxsoft/ccp4/v6.3.0/linux-x86_64/lib/data/symop.lib"
if os.path.exists(strSymopFileName):
EDAssert.equal(1, EDUtilsSymmetry.getITNumberFromSpaceGroupName("P1", strSymopFileName), "ITNumber from space group P1")
EDAssert.equal(3, EDUtilsSymmetry.getITNumberFromSpaceGroupName("P2", strSymopFileName), "ITNumber from space group P2")
EDAssert.equal(5, EDUtilsSymmetry.getITNumberFromSpaceGroupName("C2", strSymopFileName), "ITNumber from space group C2")
EDAssert.equal(16, EDUtilsSymmetry.getITNumberFromSpaceGroupName("P222", strSymopFileName), "ITNumber from space group P222")
EDAssert.equal(21, EDUtilsSymmetry.getITNumberFromSpaceGroupName("C222", strSymopFileName), "ITNumber from space group C222")
EDAssert.equal(22, EDUtilsSymmetry.getITNumberFromSpaceGroupName("F222", strSymopFileName), "ITNumber from space group F222")
EDAssert.equal(75, EDUtilsSymmetry.getITNumberFromSpaceGroupName("P4", strSymopFileName), "ITNumber from space group P4")
EDAssert.equal(79, EDUtilsSymmetry.getITNumberFromSpaceGroupName("I4", strSymopFileName), "ITNumber from space group I4")
EDAssert.equal(143, EDUtilsSymmetry.getITNumberFromSpaceGroupName("P3", strSymopFileName), "ITNumber from space group P3")
EDAssert.equal(146, EDUtilsSymmetry.getITNumberFromSpaceGroupName("H3", strSymopFileName), "ITNumber from space group H3")
EDAssert.equal(195, EDUtilsSymmetry.getITNumberFromSpaceGroupName("P23", strSymopFileName), "ITNumber from space group P23")
EDAssert.equal(196, EDUtilsSymmetry.getITNumberFromSpaceGroupName("F23", strSymopFileName), "ITNumber from space group F23")
