Hi,Sorry to repost this - I posted it last week but no response and I have not been able to solve it since. The problem is GetReactingAtoms is getting many more atoms than I expected to get - any help would be much appreciated. ------------------------------------------------------------------------------------------------------------ Hi,I have been using rdkit (thank you for creating this!) to get reacting atoms from an rxn but it is getting more atoms than I expected. As a test case I have tried this: tsmi='[cH:1]1[cH:2][c:3]([F:4])[n:5][cH:6][cH:7]1>>[cH:1]1[cH:2][c:3]([Cl:4])[n:5][cH:6][cH:7]1' rxn2 = AllChem.ReactionFromSmarts(tsmi) rdChemReactions.ChemicalReaction.Initialize(rxn2) reacts2=rdChemReactions.ChemicalReaction.GetReactingAtoms(rxn2,mappedAtomsOnly=True) reacts2 ((0, 1, 2, 3, 4, 5, 6),) which is not what I had anticipated. I expected I would get indices for the F atom and c atom to which it is bonded but they all are returned Googling led me to this https://github.com/rdkit/rdkit/issues/2031 but there the problem was different Kekule forms while the atoms are defined as aromatic in this case. Putting the reactant and product strings into a viewer looks OK. why does it not give indices (2,3)? thanks,James
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