Actually… remembering now. Don’t use DoubleBondAcceptingAromaticityDetector is
gives a contribution of 1 from ketones in you case you want it to contribute 0.
This is only possible in 1.5.
J
On Jan 20, 2015, at 7:06 PM, John May <john.wilkinson...@gmail.com> wrote:
> 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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New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
GigeNET is offering a free month of service with a new server in Ashburn.
Choose from 2 high performing configs, both with 100TB of bandwidth.
Higher redundancy.Lower latency.Increased capacity.Completely compliant.
http://p.sf.net/sfu/gigenet
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