[N]1N=NN=C1C2C=CC([N+](=O)[O-])=CC=2 and N1=NN=NC1=C1[CH]C=C([N+](=O)[O-])C=C1 are resonance structures, with the first having the radical site on the N ring and the second having the radial site on the benzene ring.
When generating the resonance structures of this molecule
The first gives 4 resonance structures (the kekulized version of the input molecule + 3 resonance structures with aromatic benzene and radical roaming on the 5-membered ring)
The second gives 6 resonance structures (same as the native RMG results)
It seems that there are still issues with handling aromatic ring molecules.
The difference between the two cases is at least rooted in the different results from analyze_molecule results ("is_aromatic": True for the first, False for the second).
[N]1N=NN=C1C2C=CC([N+](=O)[O-])=CC=2andN1=NN=NC1=C1[CH]C=C([N+](=O)[O-])C=C1are resonance structures, with the first having the radical site on the N ring and the second having the radial site on the benzene ring.When generating the resonance structures of this molecule The first gives 4 resonance structures (the kekulized version of the input molecule + 3 resonance structures with aromatic benzene and radical roaming on the 5-membered ring) The second gives 6 resonance structures (same as the native RMG results)
It seems that there are still issues with handling aromatic ring molecules. The difference between the two cases is at least rooted in the different results from
analyze_moleculeresults ("is_aromatic": True for the first, False for the second).However, even with the differences, the following lines should convert the aromatic form of the molecule to kekulized form... https://github.com/xiaoruiDong/RDMC/blob/a1db373b9ae66c6c5c3f299db8e53b04dc81abde/rdtools/resonance/rmg_backend.py#L316-L329.
Further investigation is needed