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
