Displayed customized template structures in MarvinSketch

Hi, 

We customized Marvin Sketch UI using customization xml and user-defined template file and call sketcher.setParams("tmpls0=:Generic:com/.../util/files/marvin.mytemplates"); It works in the earlier version (not sure which version and we are with 6.2 at this point), 

Now when I start it, I got the following exceptions and maybe 4 out 5 times, the template structures are displayed correctly and 1 out of 5 times, no template structures displayed, but every time I got the similar exception below. I know it is caused by setParams call since if I comment that line out, there will be no exception thrown out.

also it is not clear what index and size refers to since I always get 21/20 in the exception whether I remove or add structures in my template file.

Any idea?

Thanks

Hongzhou

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Exception in thread "Thread-16" java.lang.IndexOutOfBoundsException: Index: 21, Size: 20

at java.util.ArrayList.RangeCheck(Unknown Source)

at java.util.ArrayList.get(Unknown Source)

at chemaxon.marvin.sketch.templates.TemplateLibrary.getMyTemplatesSet(TemplateLibrary.java:235)

at chemaxon.marvin.sketch.templates.TemplateLibrary.getMyTemplates(TemplateLibrary.java:243)

at chemaxon.marvin.sketch.swing.templates.TemplateHandler.getMoleculesWithAbbreviations(TemplateHandler.java:700)

at chemaxon.marvin.sketch.swing.SketchPanel$9.run(SketchPanel.java:3627)

Exception in thread "Thread-19" java.lang.IndexOutOfBoundsException: Index: 21, Size: 20

at java.util.ArrayList.RangeCheck(Unknown Source)

at java.util.ArrayList.get(Unknown Source)

at chemaxon.marvin.sketch.templates.TemplateLibrary.getMyTemplatesSet(TemplateLibrary.java:235)

at chemaxon.marvin.sketch.templates.TemplateLibrary.getMyTemplates(TemplateLibrary.java:243)

at chemaxon.marvin.sketch.swing.templates.TemplateHandler.getMoleculesWithAbbreviations(TemplateHandler.java:700)

at chemaxon.marvin.sketch.swing.SketchPanel$9.run(SketchPanel.java:3627)

Hi Hongzhou,

By that time, around 6.2 we introduced a new way of getting template molecules, therefore the template is not location based, but based on a dictionary, provided by us. In the beginning there were some issues with these, since they no longer have a "location" but instead they have "dictionary" property. 

I've tried to find that this was an issue or not, because as I remember, a similar issue has been solved a long time ago, but could not find it. 

What bugs me, that it is not consistent. I could try to reproduce your case, by providing the parameter you use, and the files you used, but I would advise to upgrading to a newer version, and see if the problem exists. 

 

Regards,

Tamas Fazekas-Vigh

Hi Tomas,

 

Thanks for your message. I did upgrade to the latest version and the issue is still here.

Here is my codes. As I said, if I remove last line, no exception.

If I run the same codes many times, I got (no template structure loaded, correctly loaded and double loaded) with similar exceptions. I suspect it is thread issue. I attached the my codes, exception, templates content and screen shot for your review.

Thanks

Hongzhou

Hi Hongzhou

I've been able to reproduce the issue with the code you've provided. Indeed, it seems there is a race condition somewhere inside the code, and it causes this exception, among other exceptions, as I've found.

We've created a ticket in our issue tracking system and will report back, as soon as it is finished. 

Regards, 

Tamas Fazekas-Vígh

Hi Tomas,

Glad you can reproduce the issue. just by any chance, do you have a rough timeline this issue be fixed? an updated jar file would be enough for me.

Thanks

Hongzhou

Hi Hongzhou,

Unfortunately, we cannot give estimation for this problem, we need more time to investigate the possible fixes. 

Regards,

Efi

Hi there, it is almost a year. Do you guys make any progress on this issue? Thanks

Hongzhou

Unfortunately, we were not able to solve this issue yet.

Best regards,

Efi