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
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...@
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 Ch
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,
>
> he
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,
Pete
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 t
Hi all,
I try add labels to atoms in a molecule, so that lines like
A1
C12
A2
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 a
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