H Robert, Now you have two possibilities to obtain the fragments. --- In cdk.graph.ConnectivityChecker there is the method partionIntoMolecules(IMolecule) which will return a IMoleculeSet object containing all fragments. But first you muss remove the corresponding bond. Example would be like this:
molecule.removeBond(atom1, atom2); moleculeSet. = ConnectivityChecker.paritonIntoMolecules(molecule); ---- Other possibility is with reactions like we commented. The reaction is called CleavageBondReaction and there is at your service a test = CleavageBondReactionTest as example (make a look please) with your proposal fragmentation. You need to write: bond.setFlag(CDKConstants.REACTIVE_CENTER,true) /*this means this bond is active to react */ and than initiate the reaction. I don't know what is your interest. The first method is a easy to write the other has more means for describing correctly a reaction. I hope that will you help Cheers, Miquel > > I was wondering being new to CDK. Is there a way to generate a library > of fragments of a molecule where want particular bond is not allowed to > be broken. > > so C=O not to be broken so from C-C-C=O > > C-C-C=O > > C=O > > C-C=O > > > > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user -- --- Miguel Rojas Cherto Cologne University BioInformatics Center Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7428 Fax: +49(0)221-470-7786 ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
