Hi Jean-Marc,

There is a property of the molecule created when it is read that contains
this information.  I forget what it is called, but if you call the
molecule's GetPropNames function you should see something obvious in the
values returned.  You can then call GetProp with that property name to get
a string containing the canonical atom order.  Note that string is a string
representation of the Python list, with '[' at the start, ']' at the end,
and commas in between. You'll need to manipulate it a bit to release the
array of integers you need.

Cheers,
Dave


On Sun, Dec 18, 2016 at 5:19 PM, Jean-Marc Nuzillard <
jm.nuzill...@univ-reims.fr> wrote:

> Hi all,
>
> maybe my question has been already been answered:
> when converting from Mol to a canonical SMILES string,
> is there a way to obtain the mapping between the atom indexes in the
> Mol object and the atom indexes in the SMILES chain?
>
> All the best,
>
> Jean-Marc
>
> --
>
> Dr. Jean-Marc Nuzillard
> Institute of Molecular Chemistry
> CNRS UMR 7312
> Moulin de la Housse
> CPCBAI, B√Ętiment 18
> BP 1039
> 51687 REIMS Cedex 2
> France
>
> Tel : 33 3 26 91 82 10
> Fax :33 3 26 91 31 66
> http://www.univ-reims.fr/ICMR
>
> http://eos.univ-reims.fr/LSD/
> http://eos.univ-reims.fr/LSD/JmnSoft/
>
>
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