> I was wrong, the "F" option retains bonds' order and it even works for
> aromatic atoms.
> For future reference, to generate smiles of fragment by atom indices in
> Python you can do:
> idxs = [1,2,3,4]
> mol.write('smi', opt={'F': ' '.join(map(str, idxs))}).strip()
Yes, this method was from Craig James for fragment-based fingerprints, IIRC. It
would be nice to get it up into OBMol as well.
-Geoff
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