serious error in drawing electron-flow arrows

Marvin 5.6.0.0.  Draw this structure:

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray

          atomID="a1 a2 a3 a4 a5 a6 a7 a8"

          elementType="O C C C C C R H"

          formalCharge="0 0 0 0 0 0 0 1"

          sgroupRef="0 0 0 0 0 0 sg1 0"

          x2="1.058750033378601 -0.2749193076696572 -0.2749193076696572 1.058750033378601 2.3924193744268596 2.3924193744268596 3.7261033865640902 1.5399999618530273"

          y2="2.502533857276223 1.7325169167171826 0.19248303559910152 -0.5775339049599391 0.19248303559910152 1.7325169167171826 2.502508446391074 4.8125"

          />

      <bondArray>

        <bond atomRefs2="a1 a2" order="1" />

        <bond atomRefs2="a2 a3" order="1" />

        <bond atomRefs2="a3 a4" order="1" />

        <bond atomRefs2="a4 a5" order="1" />

        <bond atomRefs2="a5 a6" order="1" />

        <bond atomRefs2="a1 a6" order="1" />

        <bond atomRefs2="a6 a7" order="1" />

      </bondArray>

      <molecule id="sg1" role="SuperatomSgroup" title="OMe" leftName="MeO" molID="m2">

        <atomArray

            atomID="a9 a10"

            elementType="O C"

            attachmentPoint="1 0"

            sgroupAttachmentPoint="1 0"

            x2="3.08158449889003 3.85160143944907"

            y2="-0.5388066895640797 0.7948626514841783"

            />

        <bondArray>

          <bond atomRefs2="a10 a9" order="1" />

        </bondArray>

      </molecule>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

Note draw an electron-flow arrow from the OMe group to the H⁺.  If you try to look at the MRV, you get this error:

ERROR: 

Cannot convert molecule to 'mrv' format



STACK TRACE:

chemaxon.marvin.io.MolExportException: document does not contain MolAtom@279a0eb1[O] in MEFlowBasePoint

	at chemaxon.marvin.io.formats.cml.MrvExport.a(Unknown Source)

	at chemaxon.marvin.io.formats.cml.MrvExport.a(Unknown Source)

	at chemaxon.marvin.io.formats.cml.MrvExport.a(Unknown Source)

	at chemaxon.marvin.io.formats.cml.MrvExport.a(Unknown Source)

	at chemaxon.marvin.io.formats.cml.MrvExport.convert(Unknown Source)

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

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

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

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

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

	at chemaxon.marvin.common.swing.modules.EditMolfileFrame.c(Unknown Source)

	at chemaxon.marvin.common.swing.modules.EditMolfileFrame.setExportFormat(Unknown Source)

	at chemaxon.marvin.common.swing.modules.EditMolfileFrame.callback(Unknown Source)

	at chemaxon.marvin.common.swing.MolPanel.editSource(Unknown Source)

	at chemaxon.marvin.sketch.swing.SketchPanel.c(Unknown Source)

	at chemaxon.marvin.sketch.swing.SketchPanel.doSource(Unknown Source)

	at chemaxon.marvin.sketch.swing.actions.SourceAction.actionPerformed(Unknown Source)

	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)

	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)

	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)

	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)

	at javax.swing.AbstractButton.doClick(AbstractButton.java:389)

	at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)

	at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)

	at java.awt.Component.processMouseEvent(Component.java:6373)

	at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)

	at java.awt.Component.processEvent(Component.java:6138)

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

	at java.awt.Component.dispatchEventImpl(Component.java:4735)

	at java.awt.Container.dispatchEventImpl(Container.java:2143)

	at java.awt.Component.dispatchEvent(Component.java:4565)

	at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)

	at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)

	at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)

	at java.awt.Container.dispatchEventImpl(Container.java:2129)

	at java.awt.Component.dispatchEvent(Component.java:4565)

	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679)

	at java.awt.EventQueue.access$000(EventQueue.java:85)

	at java.awt.EventQueue$1.run(EventQueue.java:638)

	at java.awt.EventQueue$1.run(EventQueue.java:636)

	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:652)

	at java.awt.EventQueue$2.run(EventQueue.java:650)

	at java.security.AccessController.doPrivileged(Native Method)

	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)

	at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)

	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)

I'm using iCab 4.8 applet on MacOS 10.5.  (The only MacOS 10.5 browser that works with Marvin 5.5+.)

I've verified that this bug also exists in Marvin 5.5.1.0.  

I imagine it originates from an effort to fix the problem documented in this discussion.  

Please fix soon.  This bug makes it impossible for us to proceed with an upgrade to JChem 5.6.

Hi Bob,

I have tested this, and fond the same error, if I draw the eflow in the contracted molecule it can not be exported, if I draw it in the expanded state it can be exported. Reverting the changes from the fix You have mentioned do not fix this bug, but it is also about document handling from sgroups.

I have created a task in our bug tracking system, we will fix this.

Best Regards,

Peter

I downloaded a copy of Marvin 5.7.0.0 beta, and this error is still present.  Please, please fix it before you release Marvin 5.7.

Hi Bob,

Marvin 5.7 is in testing phase for a month now, and is in beta phase currently. No more features, or reported bugfixes will be added, only critical bugs found during the testing will be fixed. This issue is currently planned to be fixed in the next release.

Best Regads,

Peter

Now that you are working on Marvin 5.8, let me remind you how important it is to me that you fix this bug.  We're stuck at Marvin 5.5 until you do.

Hi Bob,

We are working on this fix, but it is a bigger problem, than we expected. It was not ready till the commit deadline of 5.8, but it has a big priority now, and we will fix it very soon.

Best Regards,

Peter

So in what version of Marvin do you expect the fix will be released?  We cannot upgrade until it is fixed.

It will be fixed in 5.9, coming out in the beginning of 2012.

I eagerly await it.

We have fixed this issue in 5.8 which is coming out hopefully in a week.

However, we've found other issues with electron flow arrow drawing which we have also fixed so far, but can come out in 5.9.

I'm glad to hear this one has been fixed.  What other errors in drawing electron-flow arrows will remain in Marvin 5.8?

I have checked it again and all fix is in 5.9.

Sorry for misleading. I have somehow mixed up the revisions.

I am happy to confirm that this bug has been fixed in Marvin 5.9.