Dear Pascal,
To my knowledge, Chem.MolToSmiles exports a molecule to Smiles format using
RDKit's own indexation scheme, so it can be different from the one found in
a SDF file.
A work-around to get the same indexation would be to change the atom ranks
directly in the Mol objects.
To achieve this, you could try to follow the solution suggested by Brian
Kelley (1).
Please find attached a jupyer-notebook for an example (Python 3).
Best regards,
José-Manuel Gally
(1) https://sourceforge.net/p/rdkit/mailman/message/35898962/
2018-08-27 13:15 GMT+02:00 Pascal KREZEL :
>
> Hi,
>
> I remark that the indexation of a molecule extracted of sdf file and the
> molecule created from the smiles of this molecule (even after having
> applied AllChem.Compute2DCoords()) are not the same. Is there a method
> to obtain the same indexation.
>
> Sincerely.
>
>
>
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José-Manuel Gally
PhD Student
Structural Bioinformatics & Chemoinformatics
Institut de Chimie Organique et Analytique (ICOA)
UMR CNRS-Université d'Orléans 7311
Université d'Orléans
Rue de Chartres
F-45067 Orléans
phone: +33 238 494 577
get_same_atom_indexation_sdf_smiles.ipynb
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