Add Atom Maps and Electron Flow Arrows kills MRV export

MarvinSketch combination of the "Add Atom Maps" function and insertion of any "Electron Flow" arrows results in error when trying to export to MRV document format.





This can be illustrated with the applet example:


marvin\examples\applets\example-sketch3.4.html





(1) [Import] the molecule into the sketcher applet


(2) Insert > Electron Flow > 2 Electrons and draw a couple arrows on the molecule. It doesn't seem to matter where (I tried drawing some amide bond resonance arrows by drawing arrows from N to C and C to O.


(3) Edit > Add > Atom Maps


(4) Now try to [Export] to "mrv" format


instead of an XML output, just comes out with string "undefined"





Can achieve a similar effect by doing


(5) File > Save As... > some document in mrv format


this yields a failure to export error with the stack trace pasted below.





Whether the arrows are added before or after the atom maps does not seem to make a difference. However, manually adding atom maps (instead of the batch Add Atom Maps menu command) does seem to help.





chemaxon.marvin.util.MolExportException: document does not contain MolAtom@1ecfcd9[C] (0) in MAtomSetPoint


at chemaxon.marvin.modules.MrvExport.a(Unknown Source)


at chemaxon.marvin.modules.MrvExport.c(Unknown Source)


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


at chemaxon.marvin.common.swing.modules.LoadSave.e(Unknown Source)


at chemaxon.marvin.common.swing.modules.LoadSave.a(Unknown Source)


at chemaxon.marvin.common.swing.modules.LoadSave.a(Unknown Source)


at chemaxon.marvin.common.swing.modules.LoadSave.actionPerformed(Unknown Source)


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


at javax.swing.Timer$DoPostEvent.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)

Indeed, it is wrong in the current release but it works fine in the upcoming Marvin release (5.0).


A pre-release is already available from the new Marvin:


http://www.chemaxon.com/shared/alpha/marvin