Hi, All the steps of ChEMBL's RDKit based standardiser are explained in the recently published manuscript: https://link.springer.com/article/10.1186/s13321-020-00456-1
Hope it helps! Regards, Eloy On Mon, 14 Sep 2020 at 04:32, Francois Berenger <mli...@ligand.eu> wrote: > On 12/09/2020 00:27, Mike Mazanetz wrote: > > Dear Forum, > > > > I'm curious as to how the community standardizes molecules to generate > > unique chemical representations. > > > > Please let me know what are people's referred means to treat: > > > > * Tautomers > > * Protomers > > * Resonance structures > > * Salts when the salt is larger than the ligand > > Here is how ChEMBL does it: > > https://github.com/chembl/ChEMBL_Structure_Pipeline > > Not sure they handle all the cases you listed, though. > > Regards, > F. > > > Particularly when converting between chemical representations SDF to > > smiles, SMARTS to smiles, and one flavour of smiles to another. > > > > And are there any caveats to consider, such as the correct assignment > > of heterocyclic nitrogens as aromatic ? > > > > I look forward to hearing your thoughts. > > > > Regards, > > > > mike > > _______________________________________________ > > Rdkit-discuss mailing list > > Rdkit-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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