On Wed, Sep 21, 2016 at 4:31 PM, Guillaume GODIN < guillaume.go...@firmenich.com> wrote:
> After testing the code, It works perfectly, thanks! > Well, there's at least that. ;-) > Unfortunatly, I discovered that it's still not compatible with the > aromaticity method used in the article i mention in another post from > Rudolf Naef. > Before going further with this I have a question for you (note that I still haven't had time to read the paper in detail): I understand that in order to exactly reproduce the results from that paper you do need to reproduce the aromaticity model used. However, if you were to borrow the methods and data from the paper, you could theoretically build your own models based on RDKit aromaticity. This would likely be more efficient at runtime than re-perceiving aromaticity. > I need to keep aromaticity of all 6 rings (having C or N which is > possible using your function), but also keep info of aromaticity of fused 6 > rings (aka. naphthalene, ...) + convert/keep guanidium moieties aromatic > too. > > So, I would be more interesting to fine a fast process to > revoke aromaticity on rings that are not 6 members rings only, which should > preserve all 6 rings + fused aromatic rings and also set guanidium salt as > aromatic. > "Revoking" aromaticity is tricky because you really need to also kekulize the rings that you remove aromaticity from. I think you're going to be better off just describing the features that are aromatic and applying the method I described in the previous message. The SMARTS I sent to you should certainly work for fused rings like naphthalene and could be adapted to support heteroatoms. Guanidinium is a different problem though... the RDKit does not tolerate aromatic bonds/atoms that aren't in rings. What exactly do you want to do there? -greg
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