[Rdkit-discuss] Problem generating reduced graphs

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

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