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 postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDamminv0_2.postProcess")
# Create some output data
cwd = self.getWorkingDirectory()
model = XSDataSaxsModel(name=XSDataString("dammin"))
xsDataResult = XSDataResultDammin(model=model)
pathLogFile = os.path.join(cwd, "dammin.log")
pathFitFile = os.path.join(cwd, "dammin.fit")
pathFirFile = os.path.join(cwd, "dammin.fir")
pathMoleculeFile = os.path.join(cwd, "dammin-1.pdb")
pathSolventFile = os.path.join(cwd, "dammin-0.pdb")
try:
res = parse_atsas.parsePDB(pathMoleculeFile, pathMoleculeFile)
except Exception as error:
self.ERROR("EDPluginExecDamminv0_2:parsePDB: %s" % error)
else:
for k in res:
self.__setattr__(k, res[k])
if os.path.exists(pathLogFile):
xsDataResult.logFile = model.logFile = XSDataFile(XSDataString(pathLogFile))
if not self.Rfactor:
self.Rfactor = self.returnDamminRFactor()
if self.Rfactor:
xsDataResult.rfactor = model.rfactor = XSDataDouble(self.Rfactor)
if os.path.exists(pathFitFile):
xsDataResult.fitFile = model.fitFile = XSDataFile(XSDataString(pathFitFile))
if os.path.exists(pathFirFile):
model.firFile = XSDataFile(XSDataString(pathFirFile))
xsDataResult.chiSqrt = model.chiSqrt = self.returnDamminChiSqrt()
if os.path.exists(pathMoleculeFile):
xsDataResult.pdbMoleculeFile = model.pdbFile = XSDataFile(XSDataString(pathMoleculeFile))
if os.path.exists(pathSolventFile):
xsDataResult.pdbSolventFile = XSDataFile(XSDataString(pathSolventFile))
if self.volume:
model.volume = XSDataDouble(self.volume)
if self.Rg:
model.rg = XSDataDouble(self.Rg)
if self.Dmax:
model.dmax = XSDataDouble(self.Dmax)
self.generateExecutiveSummary()
xsDataResult.status = XSDataStatus(message=self.getXSDataMessage(),
executiveSummary=XSDataString(os.linesep.join(self.getListExecutiveSummaryLines())))
self.dataOutput = xsDataResult
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDamstartv0_2.postProcess")
model = XSDataSaxsModel(name=XSDataString("damstart"))
xsDataResult = XSDataResultDamstart(model=model)
xsDataResult.outputPdbFile = model.pdbFile = XSDataFile(XSDataString(os.path.join(self.getWorkingDirectory(), self.__strOutputPdbFileName)))
xsDataResult.status = XSDataStatus(message=self.getXSDataMessage(),
executiveSummary=XSDataString(os.linesep.join(self.getListExecutiveSummaryLines())))
self.setDataOutput(xsDataResult)
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDammifv0_2.postProcess")
# Create some output data
cwd = self.getWorkingDirectory()
model = XSDataSaxsModel(name=XSDataString(self.name))
xsDataResult = XSDataResultDammif(model=model)
pathLogFile = os.path.join(cwd, "dammif.log")
pathFitFile = os.path.join(cwd, "dammif.fit")
pathFirFile = os.path.join(cwd, "dammif.fir")
pathMoleculeFile = os.path.join(cwd, "dammif-1.pdb")
pathSolventFile = os.path.join(cwd, "dammif-0.pdb")
try:
res = parse_atsas.parsePDB(pathMoleculeFile)
except Exception as error:
self.ERROR("EDPluginExecDammifv0_2:parsePDB: %s" % error)
else:
for k in res:
self.__setattr__(k, res[k])
if os.path.exists(pathLogFile):
xsDataResult.logFile = model.logFile = XSDataFile(
XSDataString(pathLogFile))
if self.Rfactor:
xsDataResult.rfactor = model.rfactor = XSDataDouble(
self.Rfactor)
if os.path.exists(pathFitFile):
xsDataResult.fitFile = model.fitfile = XSDataFile(
XSDataString(pathFitFile))
if os.path.exists(pathFirFile):
model.firfile = XSDataFile(XSDataString(pathFirFile))
xsDataResult.chiSqrt = model.chiSqrt = self.returnDammifChiSqrt()
if os.path.exists(pathMoleculeFile):
xsDataResult.pdbMoleculeFile = model.pdbFile = XSDataFile(
XSDataString(pathMoleculeFile))
if os.path.exists(pathSolventFile):
xsDataResult.pdbSolventFile = XSDataFile(
XSDataString(pathSolventFile))
if os.path.exists(pathFirFile):
model.firFile = XSDataFile(XSDataString(pathFirFile))
if self.volume:
model.volume = XSDataDouble(self.volume)
if self.Rg:
model.rg = XSDataDouble(self.Rg)
if self.Dmax:
model.dmax = XSDataDouble(self.Dmax)
self.generateExecutiveSummary()
xsDataResult.status = XSDataStatus(
message=self.getXSDataMessage(),
executiveSummary=XSDataString(
os.linesep.join(self.getListExecutiveSummaryLines())))
self.dataOutput = xsDataResult
def postProcess(self, _edObject=None):
EDPluginExecProcessScript.postProcess(self)
self.DEBUG("EDPluginExecDamfiltv0_3.postProcess")
xsDataResult = XSDataResultDamfilt()
pathOutputFile = os.path.join(self.getWorkingDirectory(), self.__strOutputPdbFileName)
if os.path.exists(pathOutputFile):
xsDataResult.model = XSDataSaxsModel(name=XSDataString("damfilt"))
xsDataResult.outputPdbFile = xsDataResult.model.pdbFile = XSDataFile(XSDataString(pathOutputFile))
res = parse_atsas.parsePDB(pathOutputFile, pathOutputFile)
if "volume" in res:
xsDataResult.model.volume = XSDataDouble(res["volume"])
if "Dmax" in res:
xsDataResult.model.dmax = XSDataDouble(res["Dmax"])
xsDataResult.status = XSDataStatus(message=self.getXSDataMessage(),
executiveSummary=XSDataString(os.linesep.join(self.getListExecutiveSummaryLines())))
self.setDataOutput(xsDataResult)
def outputDamaverPdbFiles(self):
cwd = self.getWorkingDirectory()
damaverPDB = os.path.join(cwd, "damaver.pdb")
if os.path.exists(damaverPDB):
self.__xsDataResult.model = XSDataSaxsModel(
name=XSDataString("damaver"))
self.__xsDataResult.damaverPdbFile = self.__xsDataResult.model.pdbFile = XSDataFile(
XSDataString(damaverPDB))
if self.__bAutomatic:
damfilterFile = os.path.join(cwd, "damfilt.pdb")
if os.path.exists(damfilterFile):
self.__xsDataResult.damfilterPdbFile = XSDataFile(
XSDataString(damfilterFile))
damstartFile = os.path.join(cwd, "damstart.pdb")
if os.path.exists(damstartFile):
self.__xsDataResult.damstartPdbFile = XSDataFile(
XSDataString(damstartFile))
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