def doRaddoseToBestTransition(self, _edPlugin):
EDVerbose.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 doBestToAlignmentTransition(self, _edPlugin):
"""
"""
EDVerbose.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)
#xsDataAlignmentInput=EDList()
#xsDataAlignmentInput.add(xsDataBestInput)
##data collection descriptor
#xsDataAlignmentInput.add(self.getDataInput("mxv2DataCollection")[0])
##indexing result
#xsDataAlignmentInput.add(self.getDataInput("mxv1Indexingresult")[0])
#self.edPluginAlignment.setDataInput( xsDataAlignmentInput )
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 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):
"""
"""
EDVerbose.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)
#xsDataAlignmentInput=EDList()
#xsDataAlignmentInput.add(xsDataBestInput)
##data collection descriptor
#xsDataAlignmentInput.add(self.getDataInput("mxv2DataCollection")[0])
##indexing result
#xsDataAlignmentInput.add(self.getDataInput("mxv1Indexingresult")[0])
#self.edPluginAlignment.setDataInput( xsDataAlignmentInput )
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 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 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 doRaddoseToBestTransition(self, _edPlugin):
"""
"""
EDVerbose.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 doRaddoseToBestTransition(self, _edPlugin):
EDVerbose.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 testSetDataModelInput(self):
edPluginStrategy = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(),
"XSConfiguration_ESRF.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
edPluginStrategy.setConfig(dictItem)
edPluginStrategy.configure()
xsDataStrategy = XSDataInputStrategy()
# Beam
xsExperimentalCondition = XSDataExperimentalCondition()
xsBeam = XSDataBeam()
xsBeam.setFlux(XSDataFlux(1e+12))
xsBeam.setWavelength(XSDataWavelength(2.41))
xsBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1)))
xsBeam.setExposureTime(XSDataTime(1))
xsExperimentalCondition.setBeam(xsBeam)
# Detector and Exposure Time
xsDataDetector = XSDataDetector()
xsDataDetector.setType(XSDataString("q210-2x"))
xsExperimentalCondition.setDetector(xsDataDetector)
xsDataGoniostat = XSDataGoniostat()
xsDataGoniostat.setRotationAxis(XSDataString("phi"))
xsExperimentalCondition.setGoniostat(xsDataGoniostat)
xsDataStrategy.setExperimentalCondition(xsExperimentalCondition)
# Best Files
bestFileContentDat = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile.dat"))
xsDataStrategy.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile.par"))
xsDataStrategy.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(
os.path.join(self.strDataPath, "bestfile1.hkl"))
xsDataStrategy.addBestFileContentHKL(XSDataString(bestFileContentHKL))
# Crystal
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataDouble(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataDouble(1))
xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataDouble(2))
xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("Fe"))
xsDataAtom2.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Na"))
xsDataAtom3.setConcentration(XSDataDouble(1000))
xsDataAtom4 = XSDataAtom()
xsDataAtom4.setSymbol(XSDataString("Cl"))
xsDataAtom4.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataAtomicComposition.addAtom(xsDataAtom4)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition)
xsDataSampleCrystalMM.setSize(
XSDataSize(XSDataLength(0.1), XSDataLength(0.1),
XSDataLength(0.1)))
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setITNumber(XSDataInteger(16))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataSampleCrystalMM.setSusceptibility(XSDataDouble(1.5))
xsDataStrategy.setCrystalRefined(xsDataCrystal)
xsDataStrategy.setSample(xsDataSampleCrystalMM)
xsDataStrategy.exportToFile(self.strObtainedInputFile)
pyStrExpectedInput = self.readAndParseFile(self.strReferenceInputFile)
pyStrObtainedInput = self.readAndParseFile(self.strObtainedInputFile)
xsDataInputExpected = XSDataInputStrategy.parseString(
pyStrExpectedInput)
xsDataInputObtained = XSDataInputStrategy.parseString(
pyStrObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(),
xsDataInputObtained.marshal())
def testSetDataModelInput(self):
edPluginStrategy = self.createPlugin()
strPathToTestConfigFile = os.path.join(self.getPluginTestsDataHome(), "XSConfiguration_ESRF.xml")
edConfiguration = EDConfiguration(strPathToTestConfigFile)
dictItem = edConfiguration.get(edPluginStrategy.getPluginName())
edPluginStrategy.setConfig(dictItem)
edPluginStrategy.configure()
xsDataStrategy = XSDataInputStrategy()
# Beam
xsExperimentalCondition = XSDataExperimentalCondition()
xsBeam = XSDataBeam()
xsBeam.setFlux(XSDataFlux(1e+12))
xsBeam.setWavelength(XSDataWavelength(2.41))
xsBeam.setSize(XSDataSize(x=XSDataLength(0.1), y=XSDataLength(0.1)))
xsBeam.setExposureTime(XSDataTime(1))
xsExperimentalCondition.setBeam(xsBeam)
# Detector and Exposure Time
xsDataDetector = XSDataDetector()
xsDataDetector.setType(XSDataString("q210-2x"))
xsExperimentalCondition.setDetector(xsDataDetector)
xsDataGoniostat = XSDataGoniostat()
xsDataGoniostat.setRotationAxis(XSDataString("phi"))
xsExperimentalCondition.setGoniostat(xsDataGoniostat)
xsDataStrategy.setExperimentalCondition(xsExperimentalCondition)
# Best Files
bestFileContentDat = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.dat"))
xsDataStrategy.setBestFileContentDat(XSDataString(bestFileContentDat))
bestFileContentPar = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile.par"))
xsDataStrategy.setBestFileContentPar(XSDataString(bestFileContentPar))
bestFileContentHKL = EDUtilsFile.readFile(os.path.join(self.strDataPath, "bestfile1.hkl"))
xsDataStrategy.addBestFileContentHKL(XSDataString(bestFileContentHKL))
# Crystal
xsDataSampleCrystalMM = XSDataSampleCrystalMM()
xsDataStructure = XSDataStructure()
xsDataComposition = XSDataChemicalCompositionMM()
xsDataChain = XSDataChain()
xsDataChain.setType(XSDataString("protein"))
xsDataChain.setNumberOfCopies(XSDataDouble(2))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom1 = XSDataAtom()
xsDataAtom1.setSymbol(XSDataString("Se"))
xsDataAtom1.setNumberOf(XSDataDouble(4))
xsDataAtomicComposition.addAtom(xsDataAtom1)
xsDataChain.setHeavyAtoms(xsDataAtomicComposition)
xsDataChain.setNumberOfMonomers(XSDataDouble(100))
xsDataStructure.addChain(xsDataChain)
xsDataChain2 = XSDataChain()
xsDataChain2.setType(XSDataString("rna"))
xsDataChain2.setNumberOfCopies(XSDataDouble(1))
xsDataChain2.setNumberOfMonomers(XSDataDouble(60))
xsDataStructure.addChain(xsDataChain2)
xsDataLigand = XSDataLigand()
xsDataLigand.setNumberOfCopies(XSDataDouble(2))
xsDataLigand.setNumberOfLightAtoms(XSDataDouble(42))
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom2 = XSDataAtom()
xsDataAtom2.setSymbol(XSDataString("Fe"))
xsDataAtom2.setNumberOf(XSDataDouble(1))
xsDataAtomicComposition.addAtom(xsDataAtom2)
xsDataLigand.setHeavyAtoms(xsDataAtomicComposition)
xsDataStructure.addLigand(xsDataLigand)
xsDataStructure.setNumberOfCopiesInAsymmetricUnit(XSDataDouble(0.25))
xsDataSolvent = XSDataSolvent()
xsDataAtomicComposition = XSDataAtomicComposition()
xsDataAtom3 = XSDataAtom()
xsDataAtom3.setSymbol(XSDataString("Na"))
xsDataAtom3.setConcentration(XSDataDouble(1000))
xsDataAtom4 = XSDataAtom()
xsDataAtom4.setSymbol(XSDataString("Cl"))
xsDataAtom4.setConcentration(XSDataDouble(1000))
xsDataAtomicComposition.addAtom(xsDataAtom3)
xsDataAtomicComposition.addAtom(xsDataAtom4)
xsDataSolvent.setAtoms(xsDataAtomicComposition)
xsDataComposition.setStructure(xsDataStructure)
xsDataComposition.setSolvent(xsDataSolvent)
xsDataSampleCrystalMM.setChemicalComposition(xsDataComposition)
xsDataSampleCrystalMM.setSize(XSDataSize(XSDataLength(0.1), XSDataLength(0.1), XSDataLength(0.1)))
xsDataCrystal = XSDataCrystal()
xsDataCell = XSDataCell(angle_alpha=XSDataAngle(90.0),
angle_beta=XSDataAngle(90.0),
angle_gamma=XSDataAngle(90.0),
length_a=XSDataLength(78.9),
length_b=XSDataLength(95.162),
length_c=XSDataLength(104.087))
xsDataCrystal.setCell(xsDataCell)
xsDataSpaceGroup = XSDataSpaceGroup()
xsDataSpaceGroup.setITNumber(XSDataInteger(16))
xsDataCrystal.setSpaceGroup(xsDataSpaceGroup)
xsDataSampleCrystalMM.setSusceptibility(XSDataDouble(1.5))
xsDataStrategy.setCrystalRefined(xsDataCrystal)
xsDataStrategy.setSample(xsDataSampleCrystalMM)
xsDataStrategy.exportToFile(self.strObtainedInputFile)
pyStrExpectedInput = self.readAndParseFile (self.strReferenceInputFile)
pyStrObtainedInput = self.readAndParseFile (self.strObtainedInputFile)
xsDataInputExpected = XSDataInputStrategy.parseString(pyStrExpectedInput)
xsDataInputObtained = XSDataInputStrategy.parseString(pyStrObtainedInput)
EDAssert.equal(xsDataInputExpected.marshal(), xsDataInputObtained.marshal())