Re: [Cdk-user] Getting bonds from a IRingSet

[Egon W. <ego...@gm...>]

Hi Thomas,

On Sun, Feb 14, 2010 at 9:21 PM, Thomas G. Kristensen <tg...@cs...> wrote:
> I'm trying to extract all the bonds that are in some ring in a
> molecule. I'm using the AllRingsFinder to extract a IRingSet. The
> problem is I can't find the prober way to extract the bonds from this
> ring set.

What is it exactly you want to achieve? Are you actually interested in
the rings, or merely want to know if some bond participates in a Ring?

> The only thing I have been able to come up with is iterating
> over all the bonds of the molecule, call getRings(bond) for each bond
> which again return a new IRingSet. As IRingSet implements
> IAtomContainerSet I can call getAtomContainerCount() which should give
> me something reasonable.
>
> This however, does not seem idiomatic. Surely there must be a smarter
> way of extracting the bonds present in any ring of a molecule.

Have a look at the SpanningTree class, which after building will have
flagged atoms and bonds as being ring bonds or not.

Grtz,

Egon

-- 
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
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