On Tue, Oct 23, 2018 at 7:07 PM Chris Earnshaw <cgearns...@gmail.com> wrote:
> > This prompted me to see what happens with azulene, which is another case > where the envelope is aromatic but neither of the individual rings are > based on a simple neutral representation. This ends up being related to > Peter's example; the input SMILES c1ccccc2c1ccc2 gets converted to > c1cc2cccccc-2c1, where the fusion bond is perceived as 'pure single' rather > than aromatic as it should be, so we do indeed end up with two non-aromatic > rings embedded in an aromatic envelope. > > Is there any way to define the aromaticity of an individual ring based on > its mapping to an aromatic envelope? Are there any cases where that > wouldn't be true? > No, there isn't currently a way to do this. In the RDKit's aromaticity model (explained on the page I referenced earlier), the individual rings for azulene are seen as containing 5 and 7 electrons. This is not an aromatic electron count. The 10 electrons of the envelope gets you the aromaticity. If anyone is deeply upset by this well-documented behavior w.r.t. fused rings, it's certainly possible to add your own aromaticity model to the RDKit. -greg
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