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 >
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