O.K. Problem solved. Sorry about the spam, folks. I can use GetSubstructMatch, as follows.
# sinput is the input smiles # scanon is the output smiles minput = Chem.MolFromSmiles(sinput) scanon=Chem.MolToSmiles(minput) mcanon=Chem.MolFromSmiles(scanon) map_forward = minput.GetSubstructMatch(mcanon) map_backward = mcanon.GetSubstructMatch(minput) Ling Chan <lingtrek...@gmail.com> 於 2021年11月2日週二 下午3:55寫道： > Dear colleagues, > > Just wonder if I can obtain a mapping of the atom indices upon > canonicalization by MolToSmiles ? I am aware that canonicalization (and > hence atom reordering) can be suppressed in MolToSmiles, but I do want to > canonicalize the output smiles. > > If you are interested, here is a bit more details of my problem. For each > molecule, I want to delete one or two side chains, and obtain a smiles of > what is left. Just that I want to know what are the atoms that bonded to > the deleted side chains. I know, by suppressing canonicalization things > will work. But I would like to canonicalize the smiles so that I can know > if there are duplicates. > > I tried marking the atoms. But I believe that properties that got carried > over to the output smiles, e.g. Isotope, affect the canonicalization, while > properties that do not affect canonicalization, e.g, IntProp, are lost upon > the conversion to smiles. > > Thank you for your insight. > > Ling > > > >
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