Example #1
0
    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
Example #2
0
    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
Example #3
0
    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)
Example #4
0
    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
Example #5
0
    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)
Example #6
0
    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))
Example #7
0
    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