Hi Jean-Marc,
You use the molFileAlias property like this:
#-------------------
In [9]: m = Chem.MolFromSmiles('CCO')
In [10]: m.GetAtomWithIdx(0).SetProp('molFileAlias','alias 0')
In [11]: m.GetAtomWithIdx(2).SetProp('molFileAlias','the_oxygen')
In [12]: print(Chem.MolToMolBlock(m))
RDKit
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
A 1
alias 0
A 3
the_oxygen
M END
#-------------------
I hope this helps,
-greg
On Wed, Mar 16, 2016 at 8:23 AM, Jean-Marc Nuzillard <
[email protected]> wrote:
> Dear All,
>
> Is there a way, in Python, to add an alias to an atom in a molecule so
> that is appears
> in an "A" line when the molecule is written in an SD file ?
> Searching the web, I found an atom attribute named molfileAlias
> but how do I practically set/get it?
>
> thanks,
>
> 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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