Problem retrieving SMILES from MSketchPane

Hi,


I am getting an error when trying to retrieve SMILES from an MSketchPane:

Code:

String smiles = mSketchPane.getMol("smiles");

which gives the stack trace:


Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException


at chemaxon.marvin.modules.SmilesExport.isNonDefinedRGroup(Unknown Source)


at chemaxon.marvin.modules.SmilesExport.canBeDescribedBySmiles(Unknown Source)


at chemaxon.marvin.modules.SmilesExport.generateSmilesString(Unknown Source)


at chemaxon.marvin.modules.SmilesExport.singleMolToSMILES(Unknown Source)


at chemaxon.marvin.modules.SmilesExport.exportReaction(Unknown Source)


at chemaxon.marvin.modules.SmilesExport.toSMILES(Unknown Source)


at chemaxon.marvin.modules.SmilesExport.convert(Unknown Source)


at chemaxon.struc.Molecule.exportToObject(Unknown Source)


at chemaxon.struc.Molecule.exportToObject(Unknown Source)


at chemaxon.struc.Molecule.exportToFormat(Unknown Source)


at chemaxon.struc.Molecule.toFormat(Unknown Source)


at chemaxon.marvin.beans.MSketchPane.getMol(Unknown Source)


at com.evotec.eln.indexer.ReactionPanel.getReactionPanelValues(ReactionPanel.java:103)


at com.evotec.eln.indexer.IndexingMenuAction.updateCurrentExperiment(IndexingMenuAction.java:273)


at com.evotec.eln.indexer.IndexingMenuAction.actionPerformed(IndexingMenuAction.java:199)


at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)


at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)


at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)


at javax.swing.DefaultButtonModel.setPressed(Unknown Source)


at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)


at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)


at java.awt.Component.processMouseEvent(Unknown Source)


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


at java.awt.Component.processEvent(Unknown Source)


at java.awt.Container.processEvent(Unknown Source)


at java.awt.Component.dispatchEventImpl(Unknown Source)


at java.awt.Container.dispatchEventImpl(Unknown Source)


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


at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)


at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)


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


at java.awt.Container.dispatchEventImpl(Unknown Source)


at java.awt.Window.dispatchEventImpl(Unknown Source)


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


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


at java.awt.EventDispatchThread.pumpOneEventForHierarchy(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)


(sorry I had originally pasted this twice!)





I am using MarvinSketch version 4.1.5 - I have attached the reaction which is causing the problem.


Any help would be appreciated





Cheers


Paul

Could you please update to the latest Marvin version as we fixed numerous bugs since 4.1.5 . Importing undefined R groups works fine for me using 4.1.12 .

Okay I'll try that - thanks for the reply!

This did work by the way, thanks very much