removeHOH.py

The following is listing for removeHOH.py.

 1  #!/usr/bin/env python 
 2  "Removes water (HOH) molecules from a molecule" 
 3  import sys 
 4  try: 
 5      import MolKit 
 6  except ImportError, inst: 
 7      print inst 
 8      print "Please install MolKit - http://mgltools.scripps.edu" 
 9       
10  def usage(): 
11      "Print helpful usage statement to stdout." 
12      print __file__ +": no input file\n" 
13      print "\tUsage: removeHOH.py input molecule supported by MolKit\n" 
14   
15   
16  if len(sys.argv) < 2: 
17         usage() 
18         sys.exit(1) #help(sys.exit) for more info 
19   
20  mol = MolKit.Read(sys.argv[1]) #FIXME: check if file sys.argv[1] exists 
21  chainsToRemove = [] #this is needed to remove chains with no residues. 
22  for chain in mol.chains: 
23      residuesHOH = [] #water residues 
24      for residue in chain.residues: 
25          if "HOH" in residue.name: 
26              #Can't do chain.residues.remove(residue). See for instance http://effbot.org/zone/python-list.htm 
27              residuesHOH.append(residue) 
28      for HOH in residuesHOH: 
29          chain.residues.remove(HOH) 
30      if not chain.residues: 
31          chainsToRemove.append(chain) 
32   
33  for chain in chainsToRemove: 
34      mol.chains.remove(chain) 
35       
36  from MolKit.pdbWriter import PdbWriter 
37  writer = PdbWriter() 
38  writer.write('out.pdb',mol, records=['ATOM', 'CONECT', 'HETATM']) 
39   
40  #TODO: Add an option for choosing output file name 

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