SMILES exception and paste problems - ChemAxon Forum Archive

User 83c8dbce58

06-11-2009 00:46:04

Hi,

One of our users of the SureChem Pro portal (www.surechem.org) has been constantly getting this error message when trying to use the Marvin drawing tool:

"Molfile cannot be loaded because an error occured:

java.io.IOException: Cannot import file in format SMILES

#0"

Any idea what might be causing this?

Lately I have not been able to paste SMILES into our Marvin applet on SureChem either. Any chance this could be related? Please try for yourself by visiting www.surechem.org and trying to paste in a SMILES using either the drop down command on the Edit menu or Ctrl+V

Thanks,

Nicko

ChemAxon 990acf0dec

06-11-2009 09:55:38

Hi Nicko,

I just tried pasting SMILES on surechem.org, and it works smoothly for me, so the problem might be java related then. What is the version of the java plugin in your browser? (Youcan check it in Help > About...)

Thanks and best regards,

Akos

User 83c8dbce58

06-11-2009 15:37:57

Hi Akos,

I'm running Java 1.6.0_13. Perhaps I should roll back to an earlier version? I noticed that the paste functionality stopped working a few weeks ago, so it might indeed be that.

Nicko

User 83c8dbce58

06-11-2009 15:38:46

Any ideas on the .molfile error message I asked about in the original post?

ChemAxon 990acf0dec

06-11-2009 18:22:00

Hi Nicko,

I also use 1.6.0_13, so then it must not be related to that... I pass this topic to an applet specialist, he might help you. (I do not have any idea on the .molfile error either.)

Cheers,

Akos

ChemAxon 5433b8e56b

09-11-2009 17:44:47

Hi Nicko,

i have tried the SureChem site, and it works for me properly. I digg the error messages in Marvin code, and found out the followings: the IOException can be caused by various reasons, but the highly possible reason is that, there is something dirty in the cache of the user and somehow the MolImporter could not be initialized properly. In this case the cache cleaning can solve the problem on the user's machine. The other possibility is that the clipboard is unreachable for the applet due to some security settings.

I hope this can help you, otherwise i will need more information about the error.

Best regards,
Istvan

User 83c8dbce58

09-11-2009 20:14:25

Hi Istvan,

Thank you for your suggestions. Unfortunately, clearing the cache did not work. In addition to that I removed all earlier JRE versions and did a complete removal and reinstall of Firefox and IE. I still can't paste SMILES strings into Marvin. Below is a log from the Java console after I tried using the paste function from the "Edit" drop-down menu. Hopefully this will help:

Exception in thread "AWT-EventQueue-2" java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
    at chemaxon.marvin.util.MarvinModule.load(Unknown Source)
    at chemaxon.marvin.util.ClipboardHandler.getDataFromClipboardOLE(Unknown Source)
    at chemaxon.marvin.util.ClipboardHandler.getObjectFromClipboard(Unknown Source)
    at chemaxon.marvin.common.swing.MolPanel.getMClipboardMol(Unknown Source)
    at chemaxon.marvin.sketch.swing.SketchPanel.d(Unknown Source)
    at chemaxon.marvin.sketch.swing.SketchPanel.doPaste(Unknown Source)
    at chemaxon.marvin.sketch.swing.actions.PasteAction.actionPerformed(Unknown Source)
    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    at javax.swing.AbstractButton.doClick(Unknown Source)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
    at javax.swing.plaf.basic.BasicMenuItemUI$Handler.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.Component.dispatchEvent(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)
Caused by: java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
    at java.lang.reflect.Constructor.newInstance(Unknown Source)
    at chemaxon.marvin.util.MarvinModule.loadClass(Unknown Source)
    at chemaxon.marvin.util.MarvinModule.load(Unknown Source)
    ... 33 more
Caused by: java.lang.UnsatisfiedLinkError: Cannot create CmarvinOLEServerDoc: marvinOLEServer.exe may be not registered
    at chemaxon.marvin.modules.datatransfer.MarvinOLETransfer.<init>(Unknown Source)
    ... 39 more

Koszonom,

Nicko

ChemAxon 5433b8e56b

11-11-2009 11:35:23

Hi Nicko,

finally i have found the cause of the problem. It seems, our applet is unable to paste from clipboard if it runs in a windows environment and the classid of the marvin ole server is present in the windows registry, but marvin ole server is not available in the system.

There are two possible fix of this behaviour:

- clear the marvin oles server related keys form windows registry, they are stored under the HKEY_CLASSES_ROOT\MarvinOLE.Document and HKEY_CLASSES_ROOT\MarvinOLE.LibInfo pathes. The whole contents of those registry pathes should be removed.

- second possible solution is to install the MarvinBeans package on the machine, the MarvinBeans installer will install the ole server, and after that the applet should work correctly.

We will fix this problem in our next release.

Sorry for your inconvenience.

Best regards,
Istvan