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*
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