After canonicalization, do the following

d = mol.GetPropsAsDict(True,True)

In the dictionary there will be a key something like _smilesAtomOutputOrder 
which contains a vector of atom indices in output order.

----
Brian Kelley

> On Jun 17, 2017, at 1:42 PM, Jean-Marc Nuzillard <jm.nuzill...@univ-reims.fr> 
> wrote:
> 
> Dear all,
> 
> sorry for asking for something that has certainly been already answered.
> 
> Chem.MolToSmiles(m) produced a SMILES string for the the given molecule m.
> How is it possible to associate the order of atom apparition in the SMILES 
> chain
> to a list of atom indexes in m?
> 
> All the best,
> 
> Jean-Marc
> 
> -- 
> Jean-Marc Nuzillard
> Directeur de Recherches au CNRS
> 
> Institut de Chimie Moléculaire de Reims
> CNRS UMR 7312
> Moulin de la Housse
> CPCBAI, Bâtiment 18
> BP 1039
> 51687 REIMS Cedex 2
> France
> 
> Tel : 03 26 91 82 10
> Fax : 03 26 91 31 66
> http://www.univ-reims.fr/ICMR
> http://eos.univ-reims.fr/LSD/ISgroup.html
> 
> http://www.univ-reims.fr/LSD/
> http://www.univ-reims.fr/LSD/JmnSoft/
> 
> 
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