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 testGenerateXSDataInputBestv1_2(
self, _strFileNameXSDataInputStrategy_reference,
_strFileNameXSDataInputBest_reference):
"""
This method is testing the generation of the XSDataInputBest object given a XSDataIndexingStrategy object.
"""
strReferenceInputFile = os.path.join(
self.strDataPath, _strFileNameXSDataInputStrategy_reference)
strPath = os.path.join(self.strDataPath, strReferenceInputFile)
from XSDataMXv1 import XSDataInputStrategy
xsDataInputStrategy = XSDataInputStrategy.parseFile(strPath)
from EDHandlerXSDataBestv1_2 import EDHandlerXSDataBestv1_2
edHandlerXSDataBestv1_2 = EDHandlerXSDataBestv1_2()
xsDataInputBestv1_2 = edHandlerXSDataBestv1_2.getXSDataInputBest(
xsDataInputStrategy)
strReferencePath = os.path.join(self.strDataPath,
_strFileNameXSDataInputBest_reference)
strXMLInputBestReference = EDUtilsTest.readAndParseFile(
strReferencePath)
EDFactoryPluginStatic.loadModule("XSDataBestv1_2")
from XSDataBestv1_2 import XSDataInputBest
xsDataInputBestReference = XSDataInputBest.parseString(
strXMLInputBestReference)
EDAssert.equal(xsDataInputBestReference.marshal(),
xsDataInputBestv1_2.marshal())
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 __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 __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