def parseSupcombOutputFile(self):
logFile = self.readProcessLogFile()
logLines = logFile.splitlines()
xsRot = self.returnRotation(logLines[-3:])
xsTrns = self.returnTranslation(logLines[-6:-3])
xsNSD = XSDataDouble(float(logLines[-8].split()[-1]))
pdb = os.path.join(self.getWorkingDirectory(), self.__strOutputFileName)
try:
res = parse_atsas.parsePDB(pdb, pdb)
except Exception as error:
self.ERROR("in parsePDB: %s" % error)
model = XSDataSaxsModel(name=XSDataString(self.name),
logFile=XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName()))))
if "Rfactor" in res:
model.rfactor = XSDataDouble(res["Rfactor"])
if "volume" in res:
model.volume = XSDataDouble(res["volume"])
if "Rg" in res:
model.rg = XSDataDouble(res["Rg"])
if "Dmax" in res :
model.dmax = XSDataDouble(res["Dmax"])
xsDataResult = XSDataResultSupcomb(NSD=xsNSD,
rot=xsRot,
trns=xsTrns,
model=model)
xsDataResult.outputFilename = model.pdbFile = XSDataFile(XSDataString(pdb))
xsDataResult.status = XSDataStatus(message=self.getXSDataMessage(),
executiveSummary=XSDataString(os.linesep.join(self.getListExecutiveSummaryLines())))
return xsDataResult
def parseSupcombOutputFile(self):
logFile = self.readProcessLogFile()
logLines = logFile.splitlines()
line = -1
for l, ln in enumerate( logLines):
if "Transformation matrix" in ln:
line = l
if line>=0:
xsRot = self.returnRotation(logLines[line+1:line+4], 1)
xsTrns = self.returnTranslation(logLines[line+1:line+4])
xsNSD = None
else:
xsRot = self.returnRotation(logLines[-3:])
xsTrns = self.returnTranslation(logLines[-6:-3])
xsNSD = XSDataDouble(float(logLines[-8].split()[-1]))
pdb = os.path.join(self.getWorkingDirectory(), self.__strOutputFileName)
try:
res = parse_atsas.parsePDB(pdb, pdb)
except Exception as error:
self.ERROR("in parsePDB: %s" % error)
if "NSD" in res:
xsNSD = XSDataDouble(res["NSD"])
model = XSDataSaxsModel(name=XSDataString(self.name),
logFile=XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), self.getScriptLogFileName()))))
if "Rfactor" in res:
model.rfactor = XSDataDouble(res["Rfactor"])
if "volume" in res:
model.volume = XSDataDouble(res["volume"])
if "Rg" in res:
model.rg = XSDataDouble(res["Rg"])
if "Dmax" in res :
model.dmax = XSDataDouble(res["Dmax"])
xsDataResult = XSDataResultSupcomb(NSD=xsNSD,
rot=xsRot,
trns=xsTrns,
model=model)
xsDataResult.outputFilename = model.pdbFile = XSDataFile(XSDataString(pdb))
xsDataResult.status = XSDataStatus(message=self.getXSDataMessage(),
executiveSummary=XSDataString(os.linesep.join(self.getListExecutiveSummaryLines())))
return xsDataResult
def parseSupcombOutputFile(self):
logFile = self.readProcessLogFile()
logLines = logFile.splitlines()
xsRot = self.returnRotation(logLines[-3:])
xsTrns = self.returnTranslation(logLines[-6:-3])
xsNSD = XSDataDouble(float(logLines[-8].split()[-1]))
xsDataResult = XSDataResultSupcomb()
xsDataResult.setNSD(xsNSD)
xsDataResult.setRot(xsRot)
xsDataResult.setTrns(xsTrns)
EDPDBFilter.filterPDBFile(os.path.join(self.getWorkingDirectory(), self.__strOutputFileNameRaw), \
os.path.join(self.getWorkingDirectory(), self.__strOutputFileName))
pathOutputFile = XSDataString(os.path.join(self.getWorkingDirectory(), self.__strOutputFileName))
xsDataResult.setOutputFilename(XSDataFile(pathOutputFile))
return xsDataResult
def parseSupcombOutputFile(self):
logFile = self.readProcessLogFile()
logLines = logFile.splitlines()
xsRot = self.returnRotation(logLines[-3:])
xsTrns = self.returnTranslation(logLines[-6:-3])
xsNSD = XSDataDouble(float(logLines[-8].split()[-1]))
xsDataResult = XSDataResultSupcomb()
xsDataResult.setNSD(xsNSD)
xsDataResult.setRot(xsRot)
xsDataResult.setTrns(xsTrns)
EDPDBFilter.filterPDBFile(os.path.join(self.getWorkingDirectory(), self.__strOutputFileNameRaw), \
os.path.join(self.getWorkingDirectory(), self.__strOutputFileName))
pathOutputFile = XSDataString(os.path.join(self.getWorkingDirectory(), self.__strOutputFileName))
xsDataResult.setOutputFilename(XSDataFile(pathOutputFile))
return xsDataResult
