MRV created in 5.2.4 not recognized by 5.3.7

I have an MRV that was created by MarvinSketch 5.2.4.

 

I can read it in to MarvinSketch 5.3.7, but if I try to save it as a 5.3.7 MRV file, I am told that it is not a valid MRV format, and the application then throws a Stack Trace error:

 

chemaxon.marvin.io.MolExportException: document does not contain MolAtom@11576d7[O] (0) in MAtomSetPoint
    at chemaxon.marvin.io.formats.cml.MrvExport.findMolAtomIds(Unknown Source)
    at chemaxon.marvin.io.formats.cml.MrvExport.appendPoint(Unknown Source)
    at chemaxon.marvin.io.formats.cml.MrvExport.appendMObject(Unknown Source)
    at chemaxon.marvin.io.formats.cml.MrvExport.convert0(Unknown Source)
    at chemaxon.marvin.io.formats.cml.MrvExport.convert(Unknown Source)
    at chemaxon.marvin.common.swing.modules.LoadSave.prepareSaving(Unknown Source)
    at chemaxon.marvin.common.swing.modules.LoadSave.saveAs(Unknown Source)
    at chemaxon.marvin.common.swing.modules.LoadSave.saveAsPerformed(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)

 

 

Any idea what's going on here? I have a huge number of 5.2.4 files that I'm not keen to convert to 5.3.7 if this comes up frequently.

 

Thanks,

 

   Michiel

 

 

UPDATE 1: the incompatibility with 5.2.4 turns out to be a red herring. 5.2.4 can be processed by 5.3.4, but not by 5.3.7. In fact, 5.3.7 cannot write the same information contained in the 5.2.4 file even if drawn in completely from scratch .... there's something flaky about the write-out module in 5.3.7, because the built-in structure checker tells me everything's OK.

 

UPDATE 2: 5.3.6 gives the same error; 5.3.5 seems to work OK so far ...

I have opened the your attached molecule 5.3.7 then save it as. But I have not got any error message. The saved file can be opened without any error.

On which platform do you tested it?

Tamas wrote:

I have opened the your attached molecule 5.3.7 then save it as. But I have not got any error message. The saved file can be opened without any error. On which platform do you tested it?

XP SP3

This is from a local beans installation, not a web service.

 

I can open the 5.2.4 MRV file in 5.3.4, 5.3.5, 5.3.6, and 5.3.7. All will mark the content as "valid" using the structure checker.

Only 5.3.4 and 5.3.5 will, however, write it back out as an MRV file. Both 5.3.6. and 5.3.7 will choke on it and give the stack trace.

Even if I start with a blank slate and simply draw in (not copy) the content of the 5.2.4 file, 5.3.6 and 5.3.7 will throw the stack trace error and refuse to save it.

The only settings I have to modify on a standard GUI are to turn off "auto-calculate lone pairs" and "show lone pairs". The rest is all plain vanilla straight after installation.

This bug may be related to the latest bug I reported here.

Dear Michiel,

I also tried to draw the same, and I confirm that the exception is thrown when I want to save the sketch to Mrv.

Eva, who is responsible for the Electron flow developments is unfortunately ill now, so I ask for your patience until she is back (hopefully early next week).

Thank you and best regards,

Akos