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
<[email protected] <mailto:[email protected]>> 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 <[email protected]
<mailto:[email protected]>> 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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