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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