Print molecule "report" as a CSV file

molcsv.py

#!/usr/bin/env python

import sys, os

import pybel
# don't need to reimport openbabel
ob = pybel.ob

for argument in sys.argv[1:]:
    filename, extension = os.path.splitext(argument)

    # read the molecule from the supplied file
    mol = next(pybel.readfile(extension[1:], argument))

    # iterate through all atoms
    for atom in mol.atoms:
        print "Atom %d, %8.4f" % (atom.idx, atom.partialcharge)

    # iterate through all bonds
    for bond in ob.OBMolBondIter(mol.OBMol):
        print "Bond %d-%d, %8.4f" % (bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(), bond.GetLength())

    # iterate through all angles
    for angle in ob.OBMolAngleIter(mol.OBMol):
        a = (angle[0] + 1)
        b = mol.OBMol.GetAtom(angle[1] + 1)
        c = (angle[2] + 1)
        print "Angle %d-%d-%d, %8.3f" % (a, b.GetIdx(), c, b.GetAngle(a, c))

    # iterate through all torsions
    for torsion in ob.OBMolTorsionIter(mol.OBMol):
        a = (torsion[0] + 1)
        b = (torsion[1] + 1)
        c = (torsion[2] + 1)
        d = (torsion[3] + 1)
        print "Torsion %d-%d-%d-%d, %8.3f" % (a, b, c, d, mol.OBMol.GetTorsion(a, b, c, d))