I'm using mol.RemoveAtom(atom) to remove atoms from a molecule, and then calling Chem.SanitizeMol(mol) at the end to clean up the molecule. Mostly this works fine. But when I delete atoms in an aromatic ring but leave a single ring atom remaining in the molecule then the sanitize function fails:
rdkit.Chem.rdchem.AtomKekulizeException: non-ring atom 0 marked aromatic I'm using SanitizeMol() with default options so SanitizeFlags.SANITIZE_ALL should be in place. What do I need to do to have sanitize to fix the atom type in the general case? Tim
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
