Hi,I have been using rdkit (thank you for creating this!) to get reacting atoms
from an rxn but it isn't behaving as I thought it would work. 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 imagined 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
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
