LIBMCS 05 crash on some NCI smiles

User 677b9c22ff

10-07-2007 06:34:12

LIBMCS 0.5 crash on some files (NCI1000 sort.smi)

Another weird behavior is, sometimes it asks : should I merge into current cluster, sometimes not?


java.lang.ArrayIndexOutOfBoundsException: 9990

at chemaxon.clustering.LibraryMCS.mergeFailed(

at chemaxon.clustering.LibraryMCS.merge(

at chemaxon.clustering.LibraryMCS.clusterOneLevel(


at chemaxon.clustering.gui.JKlustorImport$SearchTask.<init>(

at chemaxon.clustering.gui.JKlustorImport$2.construct(

at chemaxon.clustering.gui.SwingWorker$


Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException

at chemaxon.clustering.gui.component.TreeTableModel.<init>(

at chemaxon.clustering.gui.component.TreeTable.setGraph(

at chemaxon.clustering.gui.component.ClusterViewer.setGraph(

at chemaxon.clustering.gui.JKlustor.setGraph(

at chemaxon.clustering.gui.JKlustorImport$2.finished(

at chemaxon.clustering.gui.SwingWorker$

at java.awt.event.InvocationEvent.dispatch(

at java.awt.EventQueue.dispatchEvent(

at java.awt.EventDispatchThread.pumpOneEventForHierarchy(

at java.awt.EventDispatchThread.pumpEventsForHierarchy(

at java.awt.EventDispatchThread.pumpEvents(

at java.awt.EventDispatchThread.pumpEvents(


User 677b9c22ff

14-07-2007 23:40:08


after hours and hours of testing (in a stupid way) instead

of creating multiple random datasets, I found its due to

several problems.

1) Its good if structures are canonized and duplicates

, although this is not a real problem, because

LibMCS 5.0 clusters all duplicates into the correct branches.

Ok this applies only for standard settings, any changes will also crash libmcs 5.0.


See the three files (all same content, only one without duplicates)

ChemAxon efa1591b5a

26-07-2007 11:53:13

Thanks Tobias, useful as always!!! I'll check these issues and we'll fix them asap.