Re: [Rdkit-discuss] Canonical order in SMILES

2017-06-18 Thread Jean-Marc Nuzillard 

Dear Brian,

thank you! This is exactly what I needed.

All the best,

Jean-Marc

Le 17/06/2017 à 15:05, Brian Kelley a écrit :

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  
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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--
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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Re: [Rdkit-discuss] Canonical order in SMILES

2017-06-17 Thread Brian Kelley 
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  
> 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/
> 
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

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[Rdkit-discuss] Canonical order in SMILES

2017-06-17 Thread Jean-Marc Nuzillard 

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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