Sure. I still work with version 2016.03.1.
I will update my installation and try what you suggest.

All the best,

Jean-Marc

Le 17/12/2016 à 14:25, Peter Gedeck a écrit :
Hello

I tried it with the master branch. The function was added August 10, so maybe too late for the current release. That commit added functions to get/set atom specific MDL features (RLabel, atom alias, atom value).

Best

Peter
On Sat, Dec 17, 2016 at 7:47 AM Jean-Marc Nuzillard <jm.nuzill...@univ-reims.fr <mailto:jm.nuzill...@univ-reims.fr>> wrote:

    Dear Peter,

    I got:

    AttributeError: 'module' object has no attribute 'SetAtomAlias'

    with your example code, below.

    Best regards,

    Jean-Marc


    Le 17/12/2016 à 00:44, Peter Gedeck a écrit :
    Hello,

    SetMolAlias is available in Python as a function and not as an
    Atom method:

    from rdkit import Chem
    import sys
    m = Chem.MolFromSmiles('CCC')
    for i, atom in enumerate(m.GetAtoms()):
      Chem.SetAtomAlias(atom, 'C' + str(i + 1))
     w = Chem.SDWriter(sys.stdout)
     w.write(m)
     w.close()

    Best,

    Peter


    On Fri, Dec 16, 2016 at 5:31 PM Paolo Tosco <paolo.to...@unito.it
    <mailto:paolo.to...@unito.it>> wrote:

        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
        >


        
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-- 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/



--
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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