Re: [Rdkit-discuss] Problem generating reduced graphs

[Rafael L <raf...@us...>]

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 <raf...@us...> 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