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
self.logFile.writeToLog(
str='Combining density maps and atom-tagged maps to calculate ' +
'per-atom density metrics for each refined atom.\n')
self.logFile.writeToLog(
str='input directory: {}\n'.format(self.mapDir) +
'output directory: {}'.format(self.outputDir),
strip=False)
# create additional subdirectories
self.makeOutputDir(dirName=self.outputDir)
self.makeOutputDir(dirName=self.outputDataDir)
self.makeOutputDir(dirName=self.pklFileDir)
pklFileNames = []
# set up the class to calculate metrics from maps
maps2DensMets = maps2DensMetrics(
filesIn=self.mapDir, filesOut=self.outputDataDir,
pdbName=self.pdbFileList[0], atomTagMap=self.atomMapList[0],
logFile=self.logFile, calcFCmap=self.inclFCmets)
# only add Fcalc map if it exists. Note, will cause error if
# FcMapList = [] but inclFCmets = True
if self.inclFCmets:
maps2DensMets.FCmapIn = self.FcMapList[0]
for i in range(len(self.densMapList)):
if i == 0:
mapsAlreadyRead = False
else:
mapsAlreadyRead = True
if self.sepPDBperDataset:
maps2DensMets.atomMapIn = self.atomMapList[i]
maps2DensMets.pdbName = self.pdbFileList[i]
if self.inclFCmets:
maps2DensMets.FCmapIn = self.FcMapList[i]
# if new maps per dataset, need to reread them
mapsAlreadyRead = False
self.logFile.writeToLog(
str='\n---------------------------------\n' +
'Higher dose dataset {} starts here'.format(i))
maps2DensMets.densMapIn = self.densMapList[i]
maps2DensMets.maps2atmdensity(mapsAlreadyRead)
# save list of atom objects to a .pkl file
tag = self.densMapList[i].replace('_density.map', '')
pklFileName = save_objectlist(maps2DensMets.PDBarray, tag)
move(pklFileName,
'{}{}'.format(self.pklFileDir, pklFileName))
pklFileNames.append(
'{}{}'.format(self.pklFileDir, pklFileName))
self.pklFiles = pklFileNames
def pickleAtomList(self):
self.pklFileName = save_objectlist(self.PDBarray,self.pdbname)
def pickleAtomList(self):
# save list of atom objects to a .pkl file
self.pklFileName = save_objectlist(self.PDBarray,self.pdbName)
