Re: [Rdkit-discuss] unique chemical representation
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 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 > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] unique chemical representation
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
Re: [Rdkit-discuss] unique chemical representation
On 9/11/2020 10:27 AM, Mike Mazanetz wrote: I'm curious as to how the community standardizes molecules to generate unique chemical representations. The first thing you want to do is define "unique". E.g. a sugar in solution forms a mixture of isomers -- is it a "unique" sugar, or is each isomer a "unique" molecule by your definition. Dima ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] unique chemical representation
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 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
