Hi,
amazing! Thanks for all that effort! I am going to play with it.
Alex
PS:
if you can't wait to try it with a bigger window, execute this in your browser
console (hides all controls but the load/search element, though):
Info.width=1000; Info.height=1000; jmolApplet0 = Jmol.getApplet("jmolApplet0",
Info);
Am 13.10.2012 um 06:21 schrieb Robert Hanson:
> Jmol Developers --
>
> Some of you may know that since the end of August, after coming back from the
> ACS meeting in Philadelphia, I became convinced that we needed to explore
> ways of taking Jmol to the next level -- the JavaScript/HTML5/WebGL level. I
> began experimenting with various ways of doing this -- first with Google's
> web toolkit (a disaster), and then with compiling Jmol into JavaScript using
> the amazing package Java2Script, created by Zhou Renjian. If you have
> followed my code check-ins at all, you know that this has involved a
> substantial amount of refactoring of the Java code, and that was a challenge,
> but it was worth it.
>
> Today I can point you to a not-exactly-fully-functional version of Jmol (we
> are calling it JSmol or maybe J2Smol for now) that uses WebGL for its
> rendering (based on GLmol, by Takanori Nakane). With the help of a St. Olaf
> student, Duncan Blue, we are busy testing this and, of course, finding
> problems daily. But the enormous progress just these last few days prompts me
> to let the cat out of the bag.
>
> http://chemapps.stolaf.edu/jmol/jsmol/test2.htm
>
> Consider it alpha. I do believe we have solved some of the LONG standing
> problems with JavaScript-only molecular visualization. For example:
>
> - All ASCII file readers should work exactly as in Jmol itself (tested so
> far: XYZ, MOL, PDB, CIF)
> - VDW surface and solvent-accessible surface creation is no problem
> - partial charge calculation using MMFF94 is implemented
> - MEP mapping of isosurfaces works beautifully
> - JVXL surface files are read just fine
> - SMILES/SMARTS matching works
> - all database access (RCSB, PubChem, NCI-Cactus) is exactly as in Jmol/Java
> - protein and nucleic acid cartoons work just fine
> - LCAOCartoons work just fine
> - "load append" and multiple file loading/frames are no problem
> - Jmol scripting is fully implemented
> - Jmol math is fully implemented
>
> The list goes on and on. (Though obviously there are bound to be some
> limitations.)
>
> Some of you will recognize that many of these capabilities (all of these
> capabilities?) are completely unheard-of in JavaScript. This goes way, way
> beyond what any currently available JavaScript-only option provides. There
> are no server-side tricks being played here. It is just exactly as
> client-side as the Jmol Java applet itself. Surfaces are being calculated and
> mapped on the fly, and they look and handle almost as well as in Jmol itself.
> I know others have struggled for a long time to do this, and all I can say is
> that Java2Script is amazing. It took a bit of optimizing and adapting, some
> careful coding, but in the end that library just flies. We are fully
> autobonding a protein in 125 ms, creating VDW surfaces for small molecules
> and even proteins in about 1-3 seconds. It's really something to behold.
>
> What's absolutely amazing about this is that I have not created a new program
> at all. "All" I've done is used Zhou's incredible Java-to-JavaScript compiler
> to allow the Jmol trunk Java code to be turned into a JavaScript alternative
> at the click of a button within Eclipse. The Java classes and Jar files are
> all still there. It's one development stream. It's really very bizarre. But,
> wow, does it work. And the code management is a snap -- There are not two
> versions of Jmol here -- there is just the trunk Java version code that can
> be compiled either into class files or their JavaScript alternatives. The
> debugging it totally bizarre -- stepping through the compiled Java/JavaScript
> code using Firebug. Who'd have thought it possible??
>
> What we have is a perfect combinations of efforts -- Zhou's compiler,
> Takanori's GLmol interface, and Jmol. I cannot overemphasize the importance
> of the contributions of these two guys. Perhaps some day we can meet, but
> already I can tell you that none of this would be possible without their
> obviously huge efforts. I have to tell you that this has been perhaps the
> most exciting, rewarding, and at the same time totally weird two months of my
> life. Seriously, two months ago I thought there was absolutely no chance we
> were ever going to see Jmol transcend Java, and, in fact, I argued that it
> couldn't be done, but here we are - surfaces and all! I'm still catching my
> breath.
>
> Go ahead and exercise it some if you want on that test page. Explore the
> code. Don't expect perfection -- this is definitely a work in progress.
>
> I'm off to Washington, D.C., to spread the word...
>
>
> Bob
>
> ps: TODO includes draw, labels, echos, animation, spinning, minimization,
> MOs, binary file loading, and a number of other things.
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> 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
>
>
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