Pybel/OpenBabel script to determine atomtypes and connectivity for an XYZ file.

atomtypes.py

#!/usr/bin/env python2
#
# The MIT License (MIT)
# 
# Copyright (c) 2015-2016 Anders S. Christensen, University of Wisconsin-Madison
# 
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# 
#     The above copyright notice and this permission notice shall be included in
#     all copies or substantial portions of the Software.
# 
#     THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
#     IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
#     FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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#     OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
#     THE SOFTWARE.

import sys
import pybel
import openbabel

if __name__ == "__main__":

    if len(sys.argv) != 2:
        print "Usage: $ ./atomtypes.py <FILENAME>"

    filename = sys.argv[1]
    mol = pybel.readfile("xyz", filename).next()

    for i, atom in enumerate(mol):

        print "%3i  %-6s  " % (i+1, atom.OBAtom.GetType()),

        bonds = ""
        for obatom in openbabel.OBAtomAtomIter(atom.OBAtom):
            bonds += "%-6s" % obatom.GetType()

        while len(bonds) < 24:
            bonds += "-     "

        print "[ %-24s]" % bonds