Convert non-3D molecules to 3D using Open Babel

globalopt.py

#!/usr/bin/env python

import sys, os

import pybel
ob = pybel.ob

# read through multiple files on command-line
for argument in sys.argv[1:]:

    filename, extension = os.path.splitext(argument)

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

        if mol.OBMol.GetDimension() == 3:
            continue

        pybel._builder.Build(mol.OBMol)
        mol.addh()

        ff = pybel._forcefields["mmff94"]
        success = ff.Setup(mol.OBMol)
        if not success:
            ff = pybel._forcefields["uff"]
            success = ff.Setup(mol.OBMol)
            if not success:
                sys.exit("Cannot set up forcefield")

        ff.ConjugateGradients(100, 1.0e-3)
        ff.WeightedRotorSearch(100, 25)
        ff.ConjugateGradients(250, 1.0e-4)

        ff.GetCoordinates(mol.OBMol)
        mol.write("sdf", "test.sdf", overwrite=True)