No, I didn't realise it existed (or that it could be used like that). I will definitely use that instead.
Thanks, Thomas On Wed, Feb 24, 2010 at 12:42 AM, Egon Willighagen <egon.willigha...@gmail.com> wrote: > Hi Thomas, > > On Sun, Feb 14, 2010 at 9:21 PM, Thomas G. Kristensen <t...@cs.au.dk> 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/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
