piezo-distance

piezo-dist.py

#!/usr/bin/env python

import sys
import openbabel as ob
import pybel

for filename in sys.argv[1:]:
    mol = pybel.readfile("g09", filename).next()
    nitro = mol.atoms[0]
    amine = mol.atoms[0]

    # Strip off common extensions
    filename = filename.split('.',1)[0]
    if filename.startswith('line'):
        filename = filename[4:]

    # loop through to find the nitro and amine N atoms
    for atom in mol:
        if atom.OBAtom.IsNitrogen() and atom.OBAtom.CountFreeOxygens() == 2:
#            print "got no2"
            nitro = atom
        if atom.OBAtom.IsNitrogen() and atom.OBAtom.ExplicitHydrogenCount() == 2:
#            print "got nh2"
            amine = atom

    print filename, amine.OBAtom.GetDistance(nitro.OBAtom)