def writeSummaryFiles(self, csvOnly=False, includeTests=False): # write feedback files for current RIDL job. if csvOnly is True then # ONLY csv files will be output from the run (i.e. no html summary # file and no plots) self.logFile.writeToLog(str='\n**** RIDL FEEDBACK ****\n') # retrieve list of atom objects from .pkl file self.logFile.writeToLog( str='Metric data retrieved from pkl file:\n' + '\t{}'.format(self.pklDataFile)) # retrieve the combinedAtoms object from the pkl file combinedAtoms = retrieveGenericObject(fileName=self.pklDataFile) if not includeTests: outputDir = self.dir + 'RIDL-metrics/' provideFeedback(csvOnly=csvOnly, atmsObjs=combinedAtoms, logFile=self.logFile, outputDir=outputDir, doses=self.getDoses(), pklSeries=self.pklDataFile, inputDir=self.mapProcessDir, densMaps=self.name2.split(','), initialPDB=self.name1, normSet=self.normSet, inclFCmetrics=self.includeFCmaps()) else: furtherAnalysis(csvOnly=csvOnly, atmsObjs=combinedAtoms, logFile=self.logFile, outputDir=outputDir, doses=self.getDoses(), normSet=self.normSet, pklSeries=self.pklDataFile, inputDir=self.mapProcessDir, pdbNames=self.name2, initialPDB=self.name1, inclFCmetrics=self.includeFCmaps())
def PDBmulti_retrieve(self): # retrieve list of atom objects from .pkl file self.fillerLine(blank = True) txt = 'Retrieving per-atom damage metric information from '+\ ' .pkl file for each dataset within damage series.' self.logFile.writeToLog(str = txt) txt = 'Input pkl file for data retrieval chosen from input file:\n'+\ '\t{}'.format(self.pklSeries) self.logFile.writeToLog(str = txt) # retrieve the combinedAtoms object from the pkl file self.combinedAtoms = retrieveGenericObject(fileName = self.outputDir+self.pklSeries)
def PDBmulti_retrieve(self): self.titleCaption('Atom List Retrieval') print 'Input pkl file for data retrieval chosen from input file:' print '\t{}'.format(self.outputDir+self.pklSeries) # retrieve the combinedAtoms object from the pkl file self.combinedAtoms = retrieveGenericObject(self.outputDir+self.pklSeries)