Hi Lochana, On Wed, Feb 8, 2012 at 9:36 PM, lochana menikarachchi <[email protected]> wrote: > Is it possible to fragment a molecule based on set of rules using CDK??
Yes, but it requires a bit more work than just SMIRKS, for the fact we don't have that yet. Optionally, you can use Nina's work. > I wonder whether I can achieve the same functionality using CDK?? There is some related work indeed... of course, there are fragmenters already in the CDK, but these hardcode the rules... you can also have a look at the work by Miguel to find possible electron movement, and look for the IReactionMechanism class... he wrote an extensive list of reaction mechanisms specific for fragmentation reactions... I think you will find that interesting reading. 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 ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
