ArrayIndexOutOfBoundsException during 3D clean

Hi,


if I try to clean the following structure I get sometimes


an ArrayIndexOutOfBoundsException during 3D clean.


SMILES: [H]\C([H])=C1\[C@@]2([H])[C@@]3([H])[C@@]4([H])[C@]1([H])[C@@]1([H])[C@]2([H])[C@]3([H])[C@@]41[H]





3D clean is successful.


This is Marvin 5.0.1





I added the C10H10 isomers to another forum post maybe it helps during error finding.





Cheers


Tobias





Tobias


Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 12


at chemaxon.marvin.paint.internal.AromatiCalc.calc(AromatiCalc.java:115)


at chemaxon.marvin.paint.internal.MolPainter.bondLine(MolPainter.java:3750)


at chemaxon.marvin.paint.internal.MolPainter.bondLine(MolPainter.java:3477)


at chemaxon.marvin.paint.internal.MolPainter.paintBond(MolPainter.java:4596)


at chemaxon.marvin.paint.internal.MolPainter.paintObjects(MolPainter.java:2613)


at chemaxon.marvin.paint.internal.MolPainter.paintDocument(MolPainter.java:618)


at chemaxon.marvin.view.swing.ViewCanvas.paintGraphics(ViewCanvas.java:315)


at chemaxon.marvin.view.swing.ViewCanvas.paint(ViewCanvas.java:215)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JLayeredPane.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JLayeredPane.paint(Unknown Source)


at javax.swing.JComponent.paintChildren(Unknown Source)


at javax.swing.JComponent.paint(Unknown Source)


at javax.swing.JComponent.paintToOffscreen(Unknown Source)


at javax.swing.BufferStrategyPaintManager.paint(Unknown Source)


at javax.swing.RepaintManager.paint(Unknown Source)


at javax.swing.JComponent._paintImmediately(Unknown Source)


at javax.swing.JComponent.paintImmediately(Unknown Source)


at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)


at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)


at javax.swing.RepaintManager.seqPaintDirtyRegions(Unknown Source)


at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(Unknown Source)


at java.awt.event.InvocationEvent.dispatch(Unknown Source)


at java.awt.EventQueue.dispatchEvent(Unknown Source)


at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)


at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)


at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)


at java.awt.EventDispatchThread.pumpEvents(Unknown Source)


at java.awt.EventDispatchThread.pumpEvents(Unknown Source)


at java.awt.EventDispatchThread.run(Unknown Source)

Dear Tobias,





Thank You for the error report. In the current version your structure results in failed clean, the exception seems to be fixed.





It is interesting that removing all chirality criteria will lead to a valid 3D structure, while it can not be cleaned back to 3D after a clean2D.


SMILES: [H]\C([H])=C1/C2([H])C3([H])C4([H])C1([H])C1([H])C2([H])C3([H])C41[H]





We will check this and notify you in this topic.





Regards,


Gabor

Dear Tobias,

 

It seems that 3D coordinate generation now handles well the attached structure. Thanks again for the report!

 

Regards,

Gabor