Hi Pablo,
You could loop over the atoms and use SetProp to add a relevant property to
each one. That should survive the embedding.
Cheers,
Dave
On Mon, 29 Mar 2021 at 11:18, Pablo Ramos <pablo.ra...@covestro.com> wrote:
> 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)))
>
> à 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
>
>
>
>
>
> 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
>
> pablo.ra...@covestro.com
>
>
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
--
David Cosgrove
Freelance computational chemistry and chemoinformatics developer
http://cozchemix.co.uk
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
