def readAtomMap(self): # read in the atom map logfile = open('{}{}_log.txt'.format(self.filesOut,self.pdbname),'a') self.startTimer() self.fillerLine() print 'Reading in Atom map file...' print 'Atom map name: {}{}'.format(self.filesIn,self.map1['filename']) logfile.write('atom map name: {}{}\n'.format(self.filesOut,self.map1['filename'])) self.atmmap,self.atom_indices = readMap(self.filesIn,self.filesOut,self.pdbname, self.map1['filename'],self.map1['type'],[]) self.success() self.stopTimer() # find number of atoms in structure num_atoms = len(self.PDBarray) # find atom numbers present in list (repeated atom numbers removed) seen = set() seen_add = seen.add uniq_atms = [x for x in self.atmmap.vxls_val if not (x in seen or seen_add(x))] # find set of atoms numbers not present (i.e atoms not assigned to voxels) Atms_notpres = set(range(1,num_atoms+1)) - set(uniq_atms) print 'Number of atoms not assigned to voxels: %s' %str(len(Atms_notpres)) # append to log file for this eTrack run logfile.write('Number of atoms not assigned to voxels: %s\n' %str(len(Atms_notpres)))
def readAtomMap(self): # read in the atom map self.printStepNumber() self.startTimer() self.lgwrite(ln = 'Reading atom-tagged map file...') self.lgwrite(ln = 'Atom map name: {}'.format(self.map1)) self.atmmap,self.atomIndices = readMap(dirIn = self.filesIn, dirOut = self.filesOut, mapName = self.map1, mapType = 'atom_map', log = self.log) self.stopTimer() # find number of atoms in structure num_atoms = len(self.PDBarray) # find atom numbers present in list (repeated atom numbers removed) seen = set() seen_add = seen.add uniq_atms = [x for x in self.atmmap.vxls_val if not (x in seen or seen_add(x))] # find set of atoms numbers not present (i.e atoms not assigned to voxels) Atms_notpres = set(range(1,num_atoms+1)) - set(uniq_atms) self.lgwrite(ln = 'Number of atoms not assigned to voxels: {}'.format(len(Atms_notpres)))
def readDensityMap(self): # read in the density map logfile = open('{}{}_log.txt'.format(self.filesOut,self.pdbname),'a') self.startTimer() self.fillerLine() print 'Reading in Density map file...' print 'Density map name: {}{}'.format(self.filesIn,self.map2['filename']) logfile.write('density map name: {}{}\n'.format(self.filesIn,self.map2['filename'])) self.densmap = readMap(self.filesIn,self.filesOut,self.pdbname, self.map2['filename'],self.map2['type'], self.atom_indices) self.success() self.stopTimer()
def readDensityMap(self): # read in the density map self.printStepNumber() self.startTimer() self.lgwrite(ln = 'Reading density map file...') self.lgwrite(ln = 'Density map name: {}'.format(self.map2)) self.densmap = readMap(dirIn = self.filesIn, dirOut = self.filesOut, mapName = self.map2, mapType = 'density_map', atomInds = self.atomIndices, log = self.log) self.stopTimer()
def readFCMap(self): # read in the FC (calculated structure factor) density map self.printStepNumber() self.startTimer() self.lgwrite(ln = 'Reading Fcalc density map file...') self.lgwrite(ln = 'Density map name: {}'.format(self.map3)) self.FCmap = readMap(dirIn = self.filesIn, dirOut = self.filesOut, mapName = self.map3, mapType = 'density_map', atomInds = self.atomIndices, log = self.log) self.stopTimer()