Dear Greg,
When I read that you did not reproduce the problem,
I updated from rdkit-2016-03.1 to rdkit-2017-03.1
and this solved the problem.
Thank you !
Jean-Marc
Le 19/06/2017 à 11:04, Greg Landrum a écrit :
Hi Jean-Marc,
I can't reproduce that:
In [2]: m = Chem.MolFromSmiles('CN1CCC[C@H]1c1cccnc1')
In [3]: Chem.MolToSmiles(m,isomericSmiles=True)
Out[3]: 'CN1CCC[C@H]1c1cccnc1'
In [4]: Chem.MolToSmiles(m,isomericSmiles=True,allHsExplicit=True)
Out[4]: '[CH3][N]1[CH2][CH2][CH2][C@H]1[c]1[cH][cH][cH][n][cH]1'
Can you send some sample code that shows the problem?
-greg
On Mon, Jun 19, 2017 at 10:59 AM, Jean-Marc Nuzillard
<[email protected] <mailto:[email protected]>> wrote:
Dear All,
Chem.MolToSmiles(m, isomericSmiles=True, allHsExplicit=False) with
m being nicotine downloaded from PubChem returns
CN1CCC[C@H]1c1cccnc1 , which is consistent with the structure of
nicotine.
Chem.MolToSmiles(m, isomericSmiles=True, allHsExplicit=True) returns
[CH3][N]1[CH2][CH2][CH2][CH]1[c]1[cH][cH][cH][n][cH]1 in which
chirality has disappeared.
Would it be possible to get H count and chirality?
All the best,
Jean-Marc
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
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Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR
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<http://eos.univ-reims.fr/LSD/ISgroup.html>
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<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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