Dear Nils,
thank you for pointing out the existence CXSMILES.
In CXSMILES, the SMILES is written first and is followed by atom data.
This is not what I had in mind first but this is ok for me.
The good point is that the ad hoc reader and writer are already
available through rdkit.
Best regards,
Jean-Marc
Le 13/06/2022 à 17:04, Nils Weskamp a écrit :
Dear Jean-Marc,
I am not entirely sure I understand what you mean with "insert atom
data inside of a chain". There are a number of proprietary extensions
of smiles, such as e.g. CXSMILES
https://docs.chemaxon.com/display/docs/chemaxon-extended-smiles-and-smarts-cxsmiles-and-cxsmarts.md
that offer various additional options. To some extent, CXSMILES are
supported by RDKit:
https://www.rdkit.org/docs/RDKit_Book.html#cxsmiles-cxsmarts-extensions
Hope ths helps,
Nils
Am 13.06.2022 um 14:30 schrieb Jean-Marc Nuzillard:
Dear all,
About mol = Chem.MolFromSmiles(smi), I would like to know
whether the atoms indexes in mol follow always exactly the apparition
order of
the atoms in smi.
Are there extensions of the SMILES format that would allow one to insert
atom data inside of a chain? If yes, where could I find
details about these extensions?
Best,
Jean-Marc Nuzillard
--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS
Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France
ORCID : 0000-0002-5120-2556
Tel : +33 (0)3 26 91 82 10
http://www.univ-reims.fr/icmr
http://eos.univ-reims.fr/LSD/CSNteam.html
https://nuzillard.github.io/PyLSD
http://eos.univ-reims.fr/LSD/JmnSoft
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