NPE during Mview clean + Wedge bond

Hi

 

CCCCCC(=O)OC(CC([O-])=O)C[N+](C)(C)C
http://www.hmdb.ca/metabolites/HMDB00705 />

does not like to be 2D cleaned or wedge bond(ed) in Mview 5.3.8 and 5.3.2

Results in NPE

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
        at sun.font.FontDesignMetrics$MetricsKey.init(Unknown Source)
        at sun.font.FontDesignMetrics.getMetrics(Unknown Source)
        at sun.java2d.SunGraphics2D.getFontMetrics(Unknown Source)
        at chemaxon.marvin.paint.internal.MolPainter.getFontMetrics(Unknown Source)
        at chemaxon.marvin.paint.internal.MolPainter.paintAtomLabel(Unknown Source)
        at chemaxon.marvin.paint.internal.MolPainter.paintAtom(Unknown Source)
        at chemaxon.marvin.paint.internal.MolPainter.paintObjects(Unknown Source)
        at chemaxon.marvin.paint.internal.MolPainter.paintDocument(Unknown Source)
        at chemaxon.marvin.paint.internal.MolPainter.paintDocument(Unknown Source)
        at chemaxon.marvin.view.swing.ViewCanvas.paintGraphics(Unknown Source)
        at chemaxon.marvin.view.swing.ViewCanvas.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.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)

I think none of the 2D methods creates an acceptable (non-overlapping) representation, but 3D and then 2D clean helps a bit and 3.5.8 is better and says bad Clean2D option

Tobias

I have tried to reproduce the problem with the latest online Marvin version:

http://www.chemaxon.com/marvin/sketch/index.php

It generates the 2D coordinates from SMILES without exception.

(See attached screenshot.)

Can you describe the method to generate the exception.

I agree, that the Oxygen and the Carbon ligands are too close for each other.

We try to improve it.

All the best

Andras

Hi,

yes, I think the latest version solves it.

Tobias