However, now that I have visualized the graphs generated, I believe this was not an optimal solution, since the graphs do not look reduced at all. Also, the Ac/Ar/D/Hf nomenclature presented on the original ErG paper does not seem to be implemented in RDKit. For now, I believe it's best to stick with the fingerprints and forget about the representations
On Fri, 1 Sept 2023 at 01:13, Rafael L <rafael.lame...@usp.br> wrote: > Using rdReducedGraphs.GenerateMolExtendedReducedGraph() on RDKit > mols obtained from certain SMILES > (e.g. "O=C(OC3c1nccnc1C(=O)N3c2ncc(Cl)cc2)N4CCN(C)CC4") throws the > following error: > getNumImplicitHs() called without preceding call to calcImplicitValence() > > I tried removing sanitization/keeping hydrogens on conversion to mol, > using Kekulized SMILES, mol.UpdatePropertyCache(), Chem.SanitizeMol()... > but all I got were different errors, such as: > - Can't kekulize mol > - RingInfo not initialized > > I was finally able to solve all the errors by calling Chem.AddHs(mol) for > all mols prior to calculation of the reduced graph. > > -- > *Rafael da Fonseca Lameiro* > PhD Student - Medicinal and Biological Chemistry Group (NEQUIMED) > São Carlos Institute of Chemistry - University of São Paulo - Brazil > [image: orcid logo 16px] https://orcid.org/0000-0003-4466-2682 > -- *Rafael da Fonseca Lameiro * PhD Student - Medicinal and Biological Chemistry Group (NEQUIMED) São Carlos Institute of Chemistry - University of São Paulo - Brazil [image: orcid logo 16px] https://orcid.org/0000-0003-4466-2682
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