Agree with Hao above. For the molecules provided, the second example is geometrically inaccessible given the stereochemical constraints. In this case, the expected behavior should be an unsuccessful embedding.
Kangway On Thu, Jan 19, 2023 at 8:49 AM Ling Chan <[email protected]> wrote: > Keep trying with more random seeds? > > On Thu., Jan. 19, 2023, 07:38 Hao, <[email protected]> wrote: > >> Hi Gianmarco, >> >> In my experience, this just means that you have an impossible molecule. I >> haven't found any ways around it besides trying to embed. If it fails, try >> to swap the other stereoisomer. I find this particularly prevalent in large >> scale datasets where data quality is not very good. >> >> Best, >> Hao >> >> On Thu, Jan 19, 2023 at 7:09 AM Gianmarco Ghiandoni < >> [email protected]> wrote: >> >>> Hi all, >>> >>> Anyone can help with this matter? >>> >>> Thanks, >>> >>> On Tue, 17 Jan 2023 at 13:03, Gianmarco Ghiandoni <[email protected]> >>> wrote: >>> >>>> Hi all, >>>> >>>> I have come across an issue while embedding structures with >>>> stereochemistry configurations that presumably lead to clashes between >>>> atoms: >>>> >>>> from rdkit import Chem >>>> from rdkit.Chem import AllChem >>>> >>>> smiles="C1N[C@@H]2CO[C@H]1C2" >>>> m = Chem.MolFromSmiles(smiles) >>>> mh = Chem.AddHs(m) >>>> print(AllChem.EmbedMolecule(mh, randomSeed=11)) >>>> >>>> smiles="C1N[C@@H]2CO[C@@H]1C2" >>>> m = Chem.MolFromSmiles(smiles) >>>> mh = Chem.AddHs(m) >>>> print(AllChem.EmbedMolecule(mh, randomSeed=11)) >>>> >>>> >>>> Produces: >>>> 0 (successful embedding) >>>> -1 (unsuccessful embedding) >>>> >>>> What is in your opinion the best way to deal with this in order to >>>> avoid failures? >>>> >>>> Thanks, >>>> -- >>>> *Gianmarco* >>>> >>> >>> >>> -- >>> *Gianmarco* >>> _______________________________________________ >>> Rdkit-discuss mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >> _______________________________________________ >> Rdkit-discuss mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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