Marvin & AdvancedMolConverter die ungracefully on this

While importing or pasting the following molecule (from a vendor database)

[H][C@@]12C[C@@]3([H])[C@]4([H])N(c5ccccc5)[C@]5([H])C[C@@]([H])([C@]([H])(N1c1ccccc1)C3(O)O5)C4(O)O2

Both marvin and the AdvancedMolConverter-knime node throw an ArrayIndexOutOfBoundsException.
The funny thing is that IJC can render it just fine.

 

ERROR:
Error in module Clean2D

STACK TRACE:
java.lang.ArrayIndexOutOfBoundsException: 7
    at chemaxon.calculations.clean.Clean2D.setupRingInfo(Clean2D.java:1642)
    at chemaxon.calculations.clean.Clean2D.cleanFragment(Clean2D.java:1388)
    at chemaxon.calculations.clean.Clean2D.cleanMoleculeStructure(Clean2D.java:1137)
    at chemaxon.calculations.clean.Clean2D.clean(Clean2D.java:628)
    at chemaxon.calculations.clean.Clean2D.clean(Clean2D.java:608)
    at chemaxon.calculations.clean.Cleaner.cleanMolGraph(Cleaner.java:205)
    at chemaxon.calculations.clean.Cleaner.cleanMol(Cleaner.java:288)
    at chemaxon.calculations.clean.Cleaner.clean(Cleaner.java:54)
    at chemaxon.calculations.clean.CleanerUtil.clean(CleanerUtil.java:28)
    at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:5434)
    at chemaxon.struc.MoleculeGraph.clean(MoleculeGraph.java:5299)
    at chemaxon.marvin.common.swing.MolPanel.molLoaded(MolPanel.java:4240)
    at chemaxon.marvin.sketch.swing.SketchPanel.molLoaded(SketchPanel.java:4214)
    at chemaxon.marvin.sketch.swing.SketchPanel.clipboardOp(SketchPanel.java:5534)
    at chemaxon.marvin.sketch.swing.SketchPanel.doPaste(SketchPanel.java:2952)
    at chemaxon.marvin.sketch.swing.actions.PasteAction.actionPerformed(PasteAction.java:32)
    at chemaxon.marvin.uif.module.support.ShortcutBinding$DelegatingAction.actionPerformed(ShortcutBinding.java:467)
    at javax.swing.SwingUtilities.notifyAction(SwingUtilities.java:1645)
    at javax.swing.JComponent.processKeyBinding(JComponent.java:2851)
    at javax.swing.JComponent.processKeyBindings(JComponent.java:2897)
    at javax.swing.JComponent.processKeyEvent(JComponent.java:2814)
    at java.awt.Component.processEvent(Component.java:6152)
    at java.awt.Container.processEvent(Container.java:2083)
    at java.awt.Component.dispatchEventImpl(Component.java:4737)
    at java.awt.Container.dispatchEventImpl(Container.java:2141)
    at java.awt.Component.dispatchEvent(Component.java:4565)
    at java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1836)
    at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(DefaultKeyboardFocusManager.java:712)
    at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(DefaultKeyboardFocusManager.java:990)
    at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:855)
    at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:676)
    at java.awt.Component.dispatchEventImpl(Component.java:4609)
    at java.awt.Container.dispatchEventImpl(Container.java:2141)
    at java.awt.Window.dispatchEventImpl(Window.java:2482)
    at java.awt.Component.dispatchEvent(Component.java:4565)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:684)
    at java.awt.EventQueue.access$000(EventQueue.java:85)
    at java.awt.EventQueue$1.run(EventQueue.java:643)
    at java.awt.EventQueue$1.run(EventQueue.java:641)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
    at java.awt.EventQueue$2.run(EventQueue.java:657)
    at java.awt.EventQueue$2.run(EventQueue.java:655)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:654)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

Hi,

I have moved this topic to the Structure representation forum, since this issue is related to a structure level calculation and import. My colleagues will answer you soon.

Regards,
Istvan

Hi,

We've started to investigate the bug, and we will reply you as soon as we've fixed it.

 

Regards, Domi

Hi,

 

We've fixed the bug. It will be available in 5.11.1.

 

Regards, Domi