Dear All, I am totally novice in java scripting (6 days ago) and I am trying to use the "generatefragments.java" to get, from a molecule, the scaffold, the ringfragments and the linkers. I noticed several points: 1° when I try to generate the scaffold of a molecule (for example, 10 successive trials), I will have 9 trials with the expected scaffold and the remaining one will be a piece of the scaffold. 2° when I try to print out the ring fragment fragments, "generatefragments.java" returns me "null". Could you help me on these issues. I attached the class I named "fragmentor.java" for more informations and also a version of the generatefragments.java Thanks by advance for your precious help. Best regards. Alban
Peter Maas-8 wrote: > > Hi All, > > I'm trying to use the Murcko frameworks which are part of the > org.openscience.cdk.tools.GenerateFragments. > > getMurckoFrameworksAsSmileArray() gives me the expected frameworks. > getLinkerFragmentsAsSmileArray() does NOT give me the expected linkers. > Actually it provides some of the frameworks. It does not give all the > frameworks provided by getMurckoFrameworksAsSmileArray() but it skips a > few. > Apparently it ignores the zero-atom linker fragments. > > Is this intended behavior? > Is anybody planning to add the Murcko side chains as well? > > Thanks, > > Peter > > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user > > http://www.nabble.com/file/p13710999/Fragmentor.java Fragmentor.java http://www.nabble.com/file/p13710999/GenerateFragments.java.txt GenerateFragments.java.txt -- View this message in context: http://www.nabble.com/Murcko-Frameworks-tf4062545.html#a13710999 Sent from the cdk-user mailing list archive at Nabble.com. ------------------------------------------------------------------------- SF.Net email is sponsored by: Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
