Hi Martin,
I don’t know about 1.4 but there was DoubleBondAcceptingAromaticityDetector.
which is now deprecated… but does what you need. Perhaps that is in 1.4 I can’t
remember, it’s been in a while.
In 1.5 you pass the model in as an argument along with the ring detection you
want. In your case
> new Aromaticity(ElectronDontation.daylight(),
> Cycles.all())
and to avoid exceptions on bucky balls
> new Aromaticity(ElectronDontation.daylight(),
> Cycles.or(Cycles.all(), Cycles.all(6)))
J
On Jan 20, 2015, at 1:43 PM, Martin Gütlein <guetl...@posteo.de> wrote:
> Hi,
>
> This is yet another question on aromaticity detection. The Hueckel
> detection in 1.4 seems to be rather strict with rings including
> heteroatoms:
> * CCN1CCN(CC1)c1cc2n(cc(C(O)=O)c(=O)c2cc1F)C1CC1 (see
> https://apps.ideaconsult.net/data/depict?search=CCN1CCN%28CC1%29c1cc2n%28cc%28C%28O%29%3DO%29c%28%3DO%29c2cc1F%29C1CC1&smarts=
>
> )
> * CNc1cnn(-c2cccc(c2)C(F)(F)F)c(=O)c1Cl (see
> https://apps.ideaconsult.net/data/depict?search=CNc1cnn%28-c2cccc%28c2%29C%28F%29%28F%29F%29c%28%3DO%29c1Cl&smarts=
>
> )
>
> I know that there is no common algorithm for detecting aromaticity, and
> that there are examples where chemists disagree. However, considering
> these compounds, the chemists in our project (as well as Open Babel,
> PubChem and Cactvs (see above links)) do think that the rings should be
> aromatic.
>
> Can I change the arom detection behaviour? Is there an alternative to
> the CDKHueckelAromaticityDetector?
> The SmilesParser#isPreservingAromaticity() method does not help me, as
> we create new compounds with reactions using the ambit-smarts library,
> and arom detection has to be applied to the products.
>
> Kind regards,
> Martin
>
>
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