Re: [Jmol-users] JmolViewer
Hi Lochana, We embed Jmol and redistribute Jmol.jar in our free StarBiochem application (http://web.mit.edu/star/biochem/). The StarBiochem app has a user interface that drives Jmol with scripts through the JmolViewer interface. Although the scripting interface works and does most things we want, it took us a very long time to understand how to use it properly. As a Java programmer, I would have preferred working with a well documented JmolViewer interface that exposed the complete functionality and architecture of Jmol in a programmer friendly way. StarBiochem uses the SimpleJmolViewer implementation of the JmolViewer interface. We like to use interfaces in StarBiochem to provide some isolation for its various components. StarBiochem required some functionality available in the SimpleJmolViewer but not exposed in the JmolViewer interface. To get to that functionality we extended the JmolViewer interface and implemented a class that uses the new interface and wraps SimpleJmolViewer. Jmol is a wonderful tool. It is very fast in both loading and execution. I would guess that we have had about 20,000 StarBiochem (Jmol) users world wide in the last year. We rarely get a bug report and, when we do, it rarely has anything to do with the behavior of the embedded Jmol. We expect the number StarBiochem users to be significantly higher in 2012, so we are very happy that Jmol is solid. --Chuck - Original Message - From: Nicolas Vervelle To: lochana menikarachchi ; jmol-users@lists.sourceforge.net Sent: Monday, January 30, 2012 2:46 AM Subject: Re: [Jmol-users] JmolViewer Hi, I think you can use Jmol.jar for this purpose. It will probably contain a lot more that you want to use, but it should work. Or maybe JmolData.jar, I'm not sure what's in it. Nico On Sun, Jan 29, 2012 at 3:02 AM, lochana menikarachchi locha...@yahoo.com wrote: Hi All, I was looking for a JmolViewer jar file that I can embed in a stand alone application. I can see JMol application and applet viewer in the downloads but not a jar file that can be used for developing a stand alone application. How do I go about this?? Thanks. Lochana -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JmolViewer
Chuck, question: JmolViewer extends JmolSimpleViewer, so how is it that there is something in JmolSimpleViewer that is not in JmolViewer? Or is SimpleJmolViewer your own class? I regularly add aspects to JmolViewer that people need exposed. Do let me know if that is the case. The point of using JmolViewer is to identify the public methods of Viewer that are actually public and not just necessarily so for inter-package processing within Jmol. Those are the ones that we guarantee will not be changed; others in Viewer may be modified without notice. Can you send me a copy of your SimpleJmolViewer interface? Suggestions for additions to JmolViewer? Bob On Mon, Jan 30, 2012 at 11:05 AM, Charles Shubert cshub...@mit.edu wrote: ** Hi Lochana, StarBiochem required some functionality available in the SimpleJmolViewer but not exposed in the JmolViewer interface. -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JmolViewer
Hi Bob, I wrote my response from my memory of what we do and, unfortunately, I did not look at our current codebase to see what we actually do. Now that I've done my homework, you are absolutely correct in pointing out this flaw in my memory of how to use Jmol. Whatever I was remembering about wanting to expose something that was not available in the JmolViewer interface has either been abandoned in our current code or is now part of the JmolViewer interface. I'll take a look at the JmolViewer interface and see if I can come up with some specific suggestions about what might be helpful. Thanks, --Chuck - Original Message - From: Robert Hanson To: Charles Shubert ; jmol-users@lists.sourceforge.net Sent: Monday, January 30, 2012 11:16 AM Subject: Re: [Jmol-users] JmolViewer Chuck, question: JmolViewer extends JmolSimpleViewer, so how is it that there is something in JmolSimpleViewer that is not in JmolViewer? Or is SimpleJmolViewer your own class? I regularly add aspects to JmolViewer that people need exposed. Do let me know if that is the case. The point of using JmolViewer is to identify the public methods of Viewer that are actually public and not just necessarily so for inter-package processing within Jmol. Those are the ones that we guarantee will not be changed; others in Viewer may be modified without notice. Can you send me a copy of your SimpleJmolViewer interface? Suggestions for additions to JmolViewer? Bob On Mon, Jan 30, 2012 at 11:05 AM, Charles Shubert cshub...@mit.edu wrote: Hi Lochana, StarBiochem required some functionality available in the SimpleJmolViewer but not exposed in the JmolViewer interface. -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JmolViewer
Hi, I think you can use Jmol.jar for this purpose. It will probably contain a lot more that you want to use, but it should work. Or maybe JmolData.jar, I'm not sure what's in it. Nico On Sun, Jan 29, 2012 at 3:02 AM, lochana menikarachchi locha...@yahoo.comwrote: Hi All, I was looking for a JmolViewer jar file that I can embed in a stand alone application. I can see JMol application and applet viewer in the downloads but not a jar file that can be used for developing a stand alone application. How do I go about this?? Thanks. Lochana -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JmolViewer
heavens, yes! http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/examples/basic/Integration.java Very simple. Bob Mir Mohammed Assadullah wrote: Greetings: I want to integrate JMol into a JAVA app that I am writing. I looked at JMol.java source and it looks a bit involved. I am wondering if anyone has a simpler example of integration. I want to use the JmolViewer as a JPanel in my application and be able to pass a molecule coordinates to it. Thanks, Assadullah Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://us.rd.yahoo.com/evt=51733/*http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ%20 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
