def map_processing(self): self.titleCaption('Map Processing') # create additional subdirectories for oDir in (self.outputDir,self.outputPlotDir): if not os.path.exists(oDir): os.makedirs(oDir) pklFileNames = [] for dataset in self.pdbNames: # derive per-atom density metrics from maps mapfilname1 = '{}_atoms.map'.format(dataset) mapfilname2 = '{}_density.map'.format(dataset) maps2DensMets = maps2DensMetrics(self.where,self.outputDir,dataset, mapfilname1,'atom_map', mapfilname2,'density_map', self.plot) maps2DensMets.maps2atmdensity() # move pkl file to working output directory pklFileName = maps2DensMets.pklFileName os.system('mv {} {}{}'.format(pklFileName,self.outputDir,pklFileName)) pklFileNames.append(self.outputDir+pklFileName) self.pklFiles = pklFileNames
def map_processing(self): # combine the density map and atom-tagged map for a given dataset, # to calculate per-atom density metrics for each refined atom txt = 'Combining density maps and atom-tagged maps to calculate '+\ 'per-atom density metrics for each refined atom in structure.\n' self.logFile.writeToLog(str = txt) txt = 'input directory: {}\n'.format(self.inDir)+\ 'output directory: {}'.format(self.outputDir) self.logFile.writeToLog(str = txt, strip = False) # create additional subdirectories for oDir in (self.outputDir,self.outputPlotDir): self.makeOutputDir(dirName = oDir) # make pklFiles and dir to move all generated per-dataset pkl files to this pklFileDir = 'pklFiles-perDataset/' self.makeOutputDir(dirName = '{}{}'.format(self.outputDir,pklFileDir)) txt = '{} higher dose datasets located within input file.'.format(len(self.pdbNames))+\ 'Calculating per-atom density metrics for each dataset individually.\n' pklFileNames = [] i = 0 for d,initPDB in zip(self.pdbNames,self.initialPDB): i += 1 # derive per-atom density metrics from maps mapName1 = '{}_atoms.map'.format(d) mapName2 = '{}_density.map'.format(d) mapName3 = initPDB.replace('.pdb','_FC.map') txt = '\n---------------------------------\n'+\ 'Higher dose dataset {} starts here'.format(i) self.logFile.writeToLog(str = txt) maps2DensMets = maps2DensMetrics(filesIn = self.inDir, filesOut = self.outputDir, pdbName = d, atomTagMap = mapName1, densityMap = mapName2, FCmap = mapName3, plotHist = self.plot, logFile = self.logFile, calcFCmap = self.inclFCmets) maps2DensMets.maps2atmdensity() # move pkl file to working output directory pklFileName = maps2DensMets.pklFileName move(pklFileName, '{}{}{}'.format(self.outputDir, pklFileDir, pklFileName)) pklFileNames.append('{}{}{}'.format(self.outputDir, pklFileDir, pklFileName)) self.pklFiles = pklFileNames