Library MCS: ArrayIndexOutofBounds Exception

User c54942f5fd

21-04-2007 03:10:48

When I load a file into Libmcs, after reading it generates the arrayindexoutof bound exception. I have checked the the sdf file and it can be read / write without any problem with mview.

The error goes like this:

[abc@rose bin]$ ./libmcs test/Mol_common_4_3_1t.mrv

java.lang.ArrayIndexOutOfBoundsException: -79

at chemaxon.struc.StaticMolecule.init(

at chemaxon.struc.StaticMolecule.<init>(

at chemaxon.clustering.LibraryMCS.addMolecule(

at chemaxon.clustering.gui.JKlustorImport$1.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( at

ChemAxon efa1591b5a

23-04-2007 07:30:30

Could you provide us your input file - if it's not confidential? Then we can trace back the bug easily....

In order to reduce memory consumption to minimum, LibraryMCs uses a molecule representation different from the one used in MView - this may explain the difference in their behaviour.



User c54942f5fd

25-04-2007 08:43:56

please find attached the data file.

ChemAxon efa1591b5a

26-04-2007 07:50:42

Many thanks for sending the input file, it's a great help. We managed to reproduce the problem you reported. It'll be fixed very soon, I'll let you know when it's ready to try.



ChemAxon efa1591b5a

27-04-2007 14:59:11

LibraryMCS now works with your input file. You may wish to try the Java WebStart version at

This bug fix will be included in the next release of JChem, I'll let you know when it's available for download.