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- #!/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)
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