Dear Horacio, ---------- Forwarded message ---------- From: Horacio Pérez-Sánchez Date: 2012/3/23 Subject: Molecular flexibility analysis
> I wonder whether Chemistry Development kit tools can be used for, given a > database with thousands of ligands, analyzing each ligand and reporting > which fragments are rigid and which parts or connetors can be modelled as > flexible. Yes, the CDK can do that. Just as an example, there is a Rotatable Bond Count descriptor implemented. There are various approaches you can take, and it depends a bit on what you qualify something as a rigid bond. We have functionality to - identify ring bonds (SpanningTree class) - detect double/triple bonds (simple iteration over all bonds) - detect ring systems (we have at least three algorithms to find ring systems) - classes to do fragmentation, such as the Murcko approach With kind regards, Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
