Dear Paolo,
I have asked a very similar question last year. This was what Greg said.
Ling
Re: [Rdkit-discuss] atom equivalence for substructure matching
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From: Paolo Tosco <[email protected]>
To: "[email protected]"
<[email protected]>
Sent: Thursday, October 30, 2014 4:26 PM
Subject: [Rdkit-discuss] GetSubstructMatches() and resonance structures
Dear all,
The following code snippet compares two resonance structures of formate
anion:
import rdkit
from rdkit import Chem
mol1=Chem.MolFromSmiles('C([O-])=O')
mol2=Chem.MolFromSmiles('C(=O)[O-]')
mol1.GetSubstructMatches(mol2, uniquify = False)
((0, 2, 1),)
mol1.GetSubstructMatches(mol1, uniquify = False)
((0, 1, 2),)
I would rather like to get, in both cases, the following output:
((0, 1, 2),(0, 2, 1))
which would account for the carboxylate group symmetry due to resonance.
The same applies to amidinium, guanidinium, etc.
Is that currently feasible within the RDKit API?
Thanks in advance, cheers
Paolo
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