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 <ghiandon...@gmail.com> wrote: > Hi all, > > Anyone can help with this matter? > > Thanks, > > On Tue, 17 Jan 2023 at 13:03, Gianmarco Ghiandoni <ghiandon...@gmail.com> > 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 > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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