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()