Acutally I was wrong with the INRING flag. I checked the sources of
detectAromaticity method in the CDKHueckelAromaticityDetector, and it
makes use of the Spanning tree to detect rings, and take this
opportunity to set INRING flag for atoms included in the resulting
spanning tree.
We just need the aromaticity detection to be performed first & the job
is done.
Two others questions though:
- Is there any notable difference between SpanningTree and SSSR ? In
term of performance & algorithm.
- Just for my curiosity, is there a particular reason why atom type
configuration & aromaticity detection are not performed automatically
when a molecule is loaded ? In a single method that would do the job:
percieve atom types, set all existing flags and so on...
Anyway, thanks all for your rapid answers :)
Vincent
Quoting Egon Willighagen <[email protected]>:
> Hi Vincent,
>
> On Wed, Sep 9, 2009 at 5:23 PM, Vincent Le
> Guilloux<[email protected]> wrote:
>> Well that's my question: is there in the CDK any dedicated method to do so?
>
> Use the SpanningTree class.
>
--
Vincent Le Guilloux
Phd Student - ICOA - UMR CNRS 6005
Div. of chemoinformatic and molecular modeling.
University of Orléans
Phone: ++33 2 38 49 45 77
Fax : ++33 2 38 41 72 81
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