Hi Vincent,
for your question, the SSSRFinder is the right choice!
It is fast and reliable. The AllRingsFinder is problematic because
finding all rings in a graph is known to be time consuming while the
smallest set of smallest rings can be computed fast.
Cheers,
Chris
--
Dr. Christoph Steinbeck
Head of Chemoinformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640
Video meliora proboque deteriora sequor.
... Ovid, Metamorphoses VII, 20/21
On 9 Sep 2009, at 16:23, Vincent Le Guilloux wrote:
> Hi,
>
> I need to know if a given Atom is part of any ring in a molecular
> system.
>
> I've checked aCur.getFlag(CDKConstants.ISINRING) but, as all atoms
> have it to false, I guess it has to be set by the programmer itself.
>
> So the fastest (and probably dirtiest) way to do so would be to use
> the AllRingFinder class and check for each atom if it's part of any
> ring detected, but I'm guessing (maybe I'm wrong) there is a faster &
> more specific way to do so.
>
> Well that's my question: is there in the CDK any dedicated method to
> do so?
>
> Thanks in advance.
> Vincent.
>
>
>
> --
> 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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