Hello all, I am having some difficulty embedding a few SMILES strings that all correspond to planar structures e.g. ["C1C2OC3C1C23", "C1CC2CCC12", "C1C2C3NC2C13", "O1C2C3OC2C13", "C1C2CC3C1C23", "C1C2CC3C1N23", "N1C2C3OC2C13", "C1OC2CNC12"]
When I embed the SMILES strings without Hs, all is ok: AllChem.EmbedMolecule(mol) 0 but when I add Hs to the SMILES and then embed, it no longer works: mol_H = Chem.AddHs(mol) AllChem.EmbedMolecule(mol_H) -1 Any suggestions as to how to get this to work? Best regards -- *Puck van Gerwen* Doktorandin / PhD candidate Departement Chemie Klingelbergstrasse 80 CH-4056 Basel https://www.chemspacelab.org/
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
