Thanks for the reply but that doesn't seem to be working for me (code below).
If I just want to get a rough set of coordinates, what should I do? I see
that gen3d (see link below) does a weighted rotor search as part of the
process of making 3d coords but I wanted to just get the 3d coords and
specify my own weighted rotor search conditions.
mol = openbabel.OBMol()
cv = openbabel.OBConversion()
cv.SetInAndOutFormats('smi', outfile_type)
cv.ReadString(mol, smiles_string)
mol.AddHydrogens()
ff = openbabel.OBForceField.FindForceField("MMFF94")
ff.GetCoordinates(mol)
gen3d source code:
http://openbabel.svn.sf.net/viewvc/openbabel/openbabel/trunk/src/ops/gen3d.cpp?revision=4307&view=markup
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