Hi Nikolas, no idea if the Murckofragmenter can do this, but the easiest way should be to get all ring atoms using
org.openscience.cdk.graph.Cycles.markRingAtomsAndBonds(mol); First you need to eat away the peripheral sustituents (recursively delete all atoms with connectivity 1 until no more are found). Then remove all ring atoms and bonds found by Cycles.markRingAtomsAndBonds(mol) from your atomcontainer and get the remaining parts, which should be all the chains. You can get those in individual atomcontainers by IAtomContainerSet parts = ConnectivityChecker.partitionIntoMolecules(mol); Hope this is a) right and b makes sense :) Kind regards, Chris -- Dr. Christoph Steinbeck, Head of Cheminformatics and Metabolism European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Phone +44 1223 49 2640, Email: [email protected], Admin: [email protected] https://www.ebi.ac.uk/about/people/christoph-steinbeck http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. > On 20 Dec 02016, at 13:38, Nikolas Glaser <[email protected]> wrote: > > Hello, > i'm new to mailinglists so i'm not sure if my first mail is received. > I wrote a class which uses the murckofragmenter to create fragments of > molecules. Now I need the possibility to get the chain between to ringsystems > as fragment. > Is it possible to realize it with the murckofragmenter or is there another > class in the cdk which i can use? After hours of research I could not find a > solution. > Does anyone have a idea how it is possible to realize? > I am very new in the bio/cheminformatics and in using the cdk so I am happy > for every advise! > > Thanks. > > Kind regards > Nikolas Glaser > > ------------------------------------------------------------------------------ > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform > today.http://sdm.link/intel_______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------------------ Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today.http://sdm.link/intel _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
