Jmol on NetBeans Platform

Here's Jmol, an open-source Java viewer for chemical structures in 3D, on the NetBeans Platform, benefiting from its module system, extensibility, loose coupling, windowing management, and ecosystem (e.g., now you can install space invaders from into Jmol). And I imagine that other NetBeans Platform applications, such as Instant JChem, might find it interesting to have Jmol plugged into their application too, which is now completely possible. 

The left hand side, i.e., the list of proteins, is obtained live from the Protein Data Bank, which is what we did during the recent NetBeans Platform course in Amsterdam. Then I continued working on it via the old POV-Ray tutorial, which I am updating to NetBeans Platform 7.1. (It is still currently on Sang Shin's page, but will eventually be removed from there once it has been updated on Then I ended up abandoning that approach since Jmol has embedded POV-Ray, so that the whole process of downloading POV-Ray and running it externally isn't necessary at all. So then it was a question of embedding the JMolPanel in a TopComponent and passing the name of the Node to the Jmol script.

Still a lot of cleaning up to do. Once the architecture is reasonably stable, I'll set up a hacking session in an Amsterdam pub, where all the participants can each work (or in pairs) on various features which can all be contributed via independent modules. For example, Jmol has heaps of export formats and renderers, so each of those could be developed independently once a general architecture has been set up.


You're surprisingly fast. :)

I see you used the Protein Viewer application we started to develop during the course as a base; very nice to see it turned into something useful so quickly! Looking forward to that coding session. Make sure the pub has a good wifi connection we can use :)

Posted by Joris Snellenburg on January 07, 2012 at 11:11 AM PST #

kindly send me the zip file of the project netbeans jmol

Posted by M karthikeyan on February 11, 2014 at 09:12 PM PST #

I want to build an app in Netbeans, which would use Jmol for visualizing and analyzing a structure, can this provide me an api to enable me to do so

Posted by guest on November 08, 2014 at 09:56 AM PST #

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Geertjan Wielenga (@geertjanw) is a Principal Product Manager in the Oracle Developer Tools group living & working in Amsterdam. He is a Java technology enthusiast, evangelist, trainer, speaker, and writer. He blogs here daily.

The focus of this blog is mostly on NetBeans (a development tool primarily for Java programmers), with an occasional reference to NetBeans, and sometimes diverging to topics relating to NetBeans. And then there are days when NetBeans is mentioned, just for a change.


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