def testParsePseudotranslationLogFile(self):
edPluginPhenixXtriagev1_1 = self.createPlugin()
logFilePseudotranslation = os.path.join(self.getPluginTestsDataHome(), "PhenixXtriage_pseudotranslation.log")
xsDataResultPhenixXtriage = edPluginPhenixXtriagev1_1.parseLogFile(logFilePseudotranslation)
# Check log file
EDAssert.equal(True, os.path.exists(xsDataResultPhenixXtriage.logFile.path.value), "Log file")
# Reference data
xmlFile = os.path.join(self.getPluginTestsDataHome(), "XSDataResultPhenixXtriage_pseudotranslation.xml")
xml = self.readAndParseFile(xmlFile)
xsDataResultPhenixXtriageReference = XSDataResultPhenixXtriage.parseString(xml)
# Remove the paths to the log file before comparison
xsDataResultPhenixXtriage.logFile = None
xsDataResultPhenixXtriageReference.logFile = None
EDAssert.equal(xsDataResultPhenixXtriageReference.marshal(),
xsDataResultPhenixXtriage.marshal(), "Output values")
def testParseLogFile(self):
edPluginPhenixXtriagev1_1 = self.createPlugin()
logFile = os.path.join(
self.getPluginTestsDataHome(),
"PhenixXtriage_noTwinning_noPseudotranslation.log")
xsDataResultPhenixXtriage = edPluginPhenixXtriagev1_1.parseLogFile(
logFile)
# Check log file
EDAssert.equal(
True, os.path.exists(xsDataResultPhenixXtriage.logFile.path.value),
"Log file")
# Reference data
xmlFile = os.path.join(self.getPluginTestsDataHome(),
"XSDataResultPhenixXtriage_reference.xml")
xml = self.readAndParseFile(xmlFile)
xsDataResultPhenixXtriageReference = XSDataResultPhenixXtriage.parseString(
xml)
# Remove the paths to the log file before comparison
xsDataResultPhenixXtriage.logFile = None
xsDataResultPhenixXtriageReference.logFile = None
EDAssert.equal(xsDataResultPhenixXtriageReference.marshal(),
xsDataResultPhenixXtriage.marshal(), "Output values")
def __init__(self):
EDPluginExecProcessScript.__init__(self)
self.setXSDataInputClass(XSDataInputPhenixXtriage)
self.setDataOutput(XSDataResultPhenixXtriage())
self.strPathToLocalMtz = None
def parseLogFile(self, _strPathToLogFile):
xsDataResultPhenixXtriage = XSDataResultPhenixXtriage()
hasTwinning = False
hasPseudotranslation = False
if os.path.exists(_strPathToLogFile):
xsDataResultPhenixXtriage.logFile = XSDataFile(XSDataString(_strPathToLogFile))
strLog = EDUtilsFile.readFile(_strPathToLogFile)
iIndex = 0
listLines = strLog.split("\n")
bContinue = True
while bContinue:
if listLines[iIndex].startswith("Statistics depending on twin laws"):
#------------------------------------------------------
#| Operator | type | R obs. | Britton alpha | H alpha |
#------------------------------------------------------
#| k,h,-l | PM | 0.025 | 0.458 | 0.478 |
#| -h,k,-l | PM | 0.017 | 0.459 | 0.487 |
#------------------------------------------------------
iIndex +=4
while not listLines[iIndex].startswith("---------"):
listLine = listLines[iIndex].split("|")
xsDataTwinLawsStatistics =XSDataTwinLawsStatistics()
xsDataTwinLawsStatistics.operator = XSDataString(listLine[1].replace(" ", ""))
xsDataTwinLawsStatistics.twinType = XSDataString(listLine[2].replace(" ", ""))
xsDataTwinLawsStatistics.rObs = XSDataDouble(float(listLine[3]))
xsDataTwinLawsStatistics.brittonAlpha = XSDataDouble(float(listLine[4]))
xsDataTwinLawsStatistics.hAlpha = XSDataDouble(float(listLine[5]))
xsDataTwinLawsStatistics.mlAlpha = XSDataDouble(float(listLine[6]))
xsDataResultPhenixXtriage.addTwinLawStatistics(xsDataTwinLawsStatistics)
iIndex += 1
elif listLines[iIndex].startswith("Patterson analyses"):
# - Largest peak height : 6.089
iIndex += 1
pattersonLargestPeakHeight = float(listLines[iIndex].split(":")[1])
xsDataResultPhenixXtriage.pattersonLargestPeakHeight = XSDataDouble(pattersonLargestPeakHeight)
# (corresponding p value : 6.921e-01)
iIndex += 1
pattersonPValue = float(listLines[iIndex].split(":")[1].split(")")[0])
xsDataResultPhenixXtriage.pattersonPValue = XSDataDouble(pattersonPValue)
elif "indicating pseudo translational symmetry" in listLines[iIndex]:
# The analyses of the Patterson function reveals a significant off-origin
# peak that is 66.43 % of the origin peak, indicating pseudo translational symmetry.
# The chance of finding a peak of this or larger height by random in a
# structure without pseudo translational symmetry is equal to the 6.0553e-06.
# The detected translational NCS is most likely also responsible for the elevated intensity ratio.
# See the relevant section of the logfile for more details.
hasPseudotranslation = True
elif "As there are twin laws possible given the crystal symmetry, twinning could" in listLines[iIndex]:
# The results of the L-test indicate that the intensity statistics
# are significantly different than is expected from good to reasonable,
# untwinned data.
# As there are twin laws possible given the crystal symmetry, twinning could
# be the reason for the departure of the intensity statistics from normality.
hasTwinning = True
iIndex += 1
if iIndex == len(listLines):
bContinue = False
xsDataResultPhenixXtriage.twinning = XSDataBoolean(hasTwinning)
xsDataResultPhenixXtriage.pseudotranslation = XSDataBoolean(hasPseudotranslation)
return xsDataResultPhenixXtriage
