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
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