Dear community,
I want to embed a molecule. For my personal application, I really need the atom
indices to be respected, even if they are indistinguishable.
The problem is that, because of symmetry, some atoms may be indistinguishable.
This is something you can see by using CanonicalRankAtoms():
mol = Chem.MolFromSmiles('[H]C([H])=O.[H]N([H])[H]')
print("canonical rank atoms for mol:", list(Chem.CanonicalRankAtoms(mol,
breakTies=False)))
--> canonical rank atoms for mol: [6, 5, 7, 0, 0, 2, 2, 2]
In the above example we have one group of two identical atoms (labelled as 0),
and another one of three identical atoms (labelled as 2).
Therefore, the mol object created after embedding may have swapped
indistinguishable atoms, losing the track of the initial indexes I had.
Such problem was discussed in the link bellow. Unfortunately, I cannot find any
solution from it more than understanding where my problem comes from…
Is there, for the new RDKit version, any way to prevent atom labelling changes
when embedding / some available solution to this?
https://github.com/rdkit/rdkit/issues/3219
Thank you, and have a nice day :)
Best regards,
Pablo Ramos
Ph.D. at Covestro Deutschland AG
[cid:[email protected]]
covestro.com<http://www.covestro.com/>
Telephone
+49 214 6009 7356
Covestro Deutschland AG
COVDEAG-Chief Commer-PUR-R&D-EMEA-PMD
B103, R164
51365 Leverkusen, Germany
[email protected]<mailto:[email protected]>
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