Problem Rendering Reaction with Infocom MarvinRenderer

Hi,

I'm using the Knime plug-ins (2.6.0.v0133)  (jp.co.infocom.cheminfo.marvin.renderer.MarvinRenderer) and I'm getting an exception attempting to render reactions.

After some digging it appears that the issue is the format string being sent into the MolImporter.importMol call inside MarvinRenderer.createMol. It's doing this:

mol = MolImporter.importMol(cell.getRxnValue(), MFileFormat.RXN.getName());

which fails. However if I simply emulate this call but WITHOUT the format, it works.

Any ideas ?

Cheers

Luke

Hi,

Is it possible that you post sample data and error message?

Thank you for your cooperation.

Best,
Taka

Hi Taka,

 

Here is the stack trace:

 

012-11-13 14:51:41,564 DEBUG AWT-EventQueue-0 MarvinRenderer : Error while rendering structure

chemaxon.formats.MolFormatException: Can't read molecule from input.

at chemaxon.formats.MolImporter.importMol(MolImporter.java:1296)

at chemaxon.formats.MolImporter.importMol(MolImporter.java:1485)

at jp.co.infocom.cheminfo.marvin.renderer.MarvinRenderer.createMol(MarvinRenderer.java:493)

at jp.co.infocom.cheminfo.marvin.renderer.MarvinRenderer.setValue(MarvinRenderer.java:71)

at org.knime.core.data.renderer.AbstractPainterDataValueRenderer.getTableCellRendererComponent(AbstractPainterDataValueRenderer.java:203)

at org.knime.core.data.renderer.DefaultDataValueRendererFamily.getTableCellRendererComponent(DefaultDataValueRendererFamily.java:220)

at org.knime.core.data.renderer.SetOfRendererFamilies.getTableCellRendererComponent(SetOfRendererFamilies.java:141)

at javax.swing.JTable.prepareRenderer(JTable.java:5720)

at org.knime.core.node.tableview.TableContentView.prepareRenderer(TableContentView.java:286)

at javax.swing.plaf.basic.BasicTableUI.paintCell(BasicTableUI.java:2072)

at javax.swing.plaf.basic.BasicTableUI.paintCells(BasicTableUI.java:1974)

at javax.swing.plaf.basic.BasicTableUI.paint(BasicTableUI.java:1770)

at javax.swing.plaf.ComponentUI.update(ComponentUI.java:143)

at javax.swing.JComponent.paintComponent(JComponent.java:752)

at javax.swing.JComponent.paint(JComponent.java:1029)

at javax.swing.JComponent.paintToOffscreen(JComponent.java:5124)

at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:278)

at javax.swing.RepaintManager.paint(RepaintManager.java:1224)

at javax.swing.JComponent.paintForceDoubleBuffered(JComponent.java:1065)

at javax.swing.JViewport.paintView(JViewport.java:1633)

at javax.swing.JViewport.windowBlitPaint(JViewport.java:1564)

at javax.swing.JViewport.setViewPosition(JViewport.java:1118)

at javax.swing.plaf.basic.BasicScrollPaneUI$Handler.vsbStateChanged(BasicScrollPaneUI.java:1029)

at javax.swing.plaf.basic.BasicScrollPaneUI$Handler.stateChanged(BasicScrollPaneUI.java:1018)

at javax.swing.DefaultBoundedRangeModel.fireStateChanged(DefaultBoundedRangeModel.java:348)

at javax.swing.DefaultBoundedRangeModel.setRangeProperties(DefaultBoundedRangeModel.java:285)

at javax.swing.DefaultBoundedRangeModel.setValue(DefaultBoundedRangeModel.java:151)

at javax.swing.JScrollBar.setValue(JScrollBar.java:446)

at javax.swing.plaf.basic.BasicScrollBarUI$TrackListener.setValueFrom(BasicScrollBarUI.java:1220)

at javax.swing.plaf.basic.BasicScrollBarUI$TrackListener.mouseDragged(BasicScrollBarUI.java:1162)

at java.awt.Component.processMouseMotionEvent(Component.java:6315)

at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3285)

at java.awt.Component.processEvent(Component.java:6036)

at java.awt.Container.processEvent(Container.java:2041)

at java.awt.Component.dispatchEventImpl(Component.java:4630)

at java.awt.Container.dispatchEventImpl(Container.java:2099)

at java.awt.Component.dispatchEvent(Component.java:4460)

at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)

at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4255)

at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)

at java.awt.Container.dispatchEventImpl(Container.java:2085)

at java.awt.Window.dispatchEventImpl(Window.java:2478)

at java.awt.Component.dispatchEvent(Component.java:4460)

at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)

at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)

at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)

at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)

at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)

at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

2012-11-13 14:51:41,580 WARN  AWT-EventQueue-0 MarvinRenderer : Error while rendering structure

When I tested this out by manually calling a trivial example : MolIMporter.importMol("

• C>>
• O"), this worked however using MolIMporter.importMol("
• C>>
• O", MFileFormat.RXN.getName()) failes with the above exception.
  
  

   

  
  

   

  
  

  Hope that helps

  
  

   

  
  

  Luke.

Hi Luke,

Thank you for your updating.
In my understanding, the format of structure you mentioned seems to be smarts format (not rxn format).
Our renderer expects that the RxnCell stores structure as rxn format.
(I'm using expressly format option for the MolIMporter.importMol method. not using automatic recognition.)
Therefore, you should use the SmartsCell for this structure.

Best,
Taka

Hi Taka,

 

Thanks for that. I changed the processing in the node to convert to RXN before creating the RxnCell and it now works perfectly !

 

Cheers

Luke