removeAltLoc.py

The following is listing for removeAltLoc.py.

 1  #!/usr/bin/env python 
 2  "Removes atoms with alternate locations" 
 3  import sys 
 4   
 5  try: 
 6      import MolKit 
 7  except ImportError, inst: 
 8      print inst 
 9      print "Please install MolKit - http://mgltools.scripps.edu" 
10      sys.exit(1) 
11       
12  def usage(): 
13      "Print helpful usage statement to stdout." 
14      print __file__ +": no input file\n" 
15      print "\tUsage: removeAlt.py input molecule supported by MolKit\n" 
16   
17   
18  if len(sys.argv) < 2: 
19         usage() 
20         sys.exit(1) #help(sys.exit) for more info 
21   
22  mol = MolKit.Read(sys.argv[1]) #FIXME: check if file sys.argv[1] exists 
23  for chain in mol.chains: 
24      for residue in chain.residues: 
25          altDict = {} #to keep atoms with  
26          for atom in residue.atoms: 
27              if '@' in atom.name: 
28                  list = atom.name.split('@') #'CB@B'=>['CB', 'B'] 
29                  if list[-1] in altDict: 
30                      altDict[list[-1]].append(atom) 
31                  else: 
32                      altDict[list[-1]] = [atom]          
33          if altDict: 
34              keys = altDict.keys() 
35              print "\nResidue %s altLoc:"%residue.name, 
36              print keys, 
37              print ' Removing ', 
38              for key in keys[1:]: 
39                  for atom in altDict[key]: 
40                      print atom.name, 
41                      residue.remove(atom) 
42   
43  from MolKit.pdbWriter import PdbWriter 
44  writer = PdbWriter() 
45  writer.write('out.pdb',mol) 

Run with 1DM2.pdb as input, for instance, to see it in action.