Dear Paolo,

Many thanks,
Your solution works.
The key point is to considered an Alias as an atom property:

for i, atom in enumerate(m.GetAtoms()):
     atom.SetProp('molFileAlias', 'C' + str(i + 1))


All the best,

Jean-Marc


Le 16/12/2016 à 23:30, Paolo Tosco a écrit :
> Dear Jean-Marc,
>
> here:
>
> https://gist.github.com/ptosco/6e4468350f0fff183e4507ef24f092a1#file-pdb_atom_names-ipynb
>  
>
>
> there's an example how to use the atom aliases in RDKit.
>
> Cheers,
> p.
>
>
> On 12/16/2016 10:26 PM, Jean-Marc Nuzillard wrote:
>> Hi all,
>>
>> I try add labels to atoms in a molecule, so that lines like
>>
>> A    1
>> C12
>> A    2
>> C3
>>
>> are written when the molecule is written in a SD file.
>>
>> Considering atom a and alias text txt,
>> I expected the function call SetAtomAlias(a, txt) to do the job.
>> I found this function in a documentation page about the rdchem module.
>> So, my script started with
>>
>> from rdkit import Chem
>> from rdkit.Chem import rdchem
>>
>> I got:
>>
>> NameError: name 'SetAtomAlias' is not defined.
>>
>> I guess the solution is trivial.
>> Forgive my ignorance.
>>
>> All the best,
>>
>> Jean-Marc
>>
>
>


-- 
Jean-Marc Nuzillard
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://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/


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