Dear Geun, currently the resonance structure enumerator does not take into account radical species. I hope I can find the time to take into account radical species as well in the near future.
Cheers, p. > On 19 Aug 2016, at 10:06, Geun Ho Gu <googh...@hotmail.com> wrote: > > Hello RDkitters, > > > I'm a user interested in the more of the catalytic side of the chemistry > involving radical chemistry. I found a couple deficiency in RDkit > functionality regarding this. > > > 1. rdqueries module in python wrapper lacks a query for number of radical > electrons. > > I can work around this if I know the atomic number of the species and use the > default valence with total valence queries, but it's not possible for atom > query where atomic number is not well-defined. > > > 2. ResonanceMolSupplier module in python wrapper does not enumerate the > radical resonance structure. For example, > > > > mol = Chem.MolFromSmiles('[CH2]C=CC') > > resmols = ResonanceMolSupplier(mol) > > for resmol in resmols: > > print Chem.MolToSmiles(resmol) > > > should produce two molecules: [CH2]C=CC and C=C[CH]C. But only produce the > original molecule. > > It seems that the enumerator only looks at the resonance structure of charged > species, because when I do the same procedure with charged species, (i.e. > replace the smiles of the code above to [CH2+]C=CC), it produces [CH2+]C=CC > and C=C[CH+]C just fine. > > > > I apologize for not working on these issues myself. I'm not very familiar > with C++, and do not have much time in my hand.. > > > > Thank you very much, > > Geun Ho Gu > > > ------------------------------------------------------------------------------ > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
------------------------------------------------------------------------------
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss