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> 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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