Пример #1
0
	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
Пример #2
0
	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