Bob,
I was aware of the Jmol integration of JSME and JSpecView, but I did not know
that auto sync 2D to 3D was an option - i.e. as the 2d drawing grows the 3d
model is automatically updated with no transfer button click required.
Am I reading you correctly on this:
jmol = Jmol.getApplet("jmol", JmolInfo)
jme = Jmol.getJMEApplet("jme", JMEInfo, jmol);
The above will automatically update any 2d JSME change to 3d Jmol window?
I should have mentioned that JSME has a number of callbacks:
BeforePaste, AfterPaste, AfterStructureModified, AtomHighlight, BondHighlight,
AtomClicked, BondClicked
I was aware of these other JSME callbacks, but I tend to have tunnel vision
when a potential simple “model kit” use is a possibility!
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Apr 28, 2016, at 11:38 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> Oh, and JSmol on that jsv_predict2.htm page is using special "all-atom"
> SMILES calls to find the mapping between JSpecView, JSmol, and JSME, since
> the MOL file coming back from JSpecView is not the mol file sent to it. It's
> critical in this case that every atoms - especially the H atoms -- are
> synchronized.
>
> I am almost done with a C13-NMR predictor that works exactly the same way.
>
> Bob
>
> On Thu, Apr 28, 2016 at 10:34 PM, Robert Hanson <hans...@stolaf.edu
> <mailto:hans...@stolaf.edu>> wrote:
> Otis, that's very interesting. Nice job on that. I think you are forgetting,
> though, that JSME is fully integrated into JSmol already. You do not need to
> add any functions of your own.
> If you look at the code for chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm
> <http://chemapps.stolaf.edu/jmol/jsmol/jsmetest2.htm>, you will see that JSME
> integrates into JSmol very smoothly. It's as simple as this:
>
> <script type="text/javascript" language="javascript"
> src="jsme/jsme/jsme.nocache.js"></script>
> <script type="text/javascript" src="JSmol.min.js"></script>
> <script type="text/javascript" src="js/JSmolJME.js"></script>
>
> var JMEInfo = {
> use: "HTML5",
> visible: true
> ,"options" : "nocanonize"//"query,hydrogens"
> }
> ...
>
> jmol = Jmol.getApplet("jmol", JmolInfo)
> jme = Jmol.getJMEApplet("jme", JMEInfo, jmol);
>
> That last parameter tells JSmol that you want jme to be associated with the
> jmol instance of JSmol.
> You don't need anything more on the page.
> Now you have a 2D and 3D applet linked together with a tab interface.
> Automatic updating.
>
> If you want two separate applets, like you have there, then you just add a
> div to that JMEinfo:
>
> var JMEInfo = {
> use: "HTML5"
> ,visible: true
> ,divId: "jmediv"
> ,options : "autoez;nocanonize"
> }
>
>
> See jsmetest2.htm for something like what you are doing. The two buttons on
> that page are driving:
>
> Jmol.show2d(jmol, false) // to 3D
> Jmol.show2d(jmol, true) // to 2D
>
>
> Note that when JSME is in an environment where JSmol and JSpecView are both
> there -- http://chemapps.stolaf.edu/jmol/jsmol/jsv_predict2.htm
> <http://chemapps.stolaf.edu/jmol/jsmol/jsv_predict2.htm> -- then it doesn't
> use this callback and instead uses an even more interesting one:
>
> app._applet.setAfterStructureModifiedCallback(f);
>
> This sends a detailed message every time you change the structure or click on
> an "atom" in the 2D drawing. JSmol is using this to synchronize the spectrum
> and JSmol window when the JSME applet is clicked or the structure is
> modified. Works like a charm!
>
> That page is actually extraordinarily simple. JSmol automatically senses the
> presence of JSME, Jmol, and JSpecView on the page using a sort of "bus"
> communication system. Robert Lancashire and I worked this out a couple of
> years ago. It's complicated in JSmolCore.js, but it's super simple in terms
> of the page. As the atoms or spectral regions are clicked, registered applets
> are automatically queried for their state, and the signal is passed around
> until all are two or three applets on the page are in sync.
>
> The synchronization is activated by a a call to Jmol.updateView(isJmol ?
> jmol : jme);
>
> "Simple" as that! :)
>
> Bob
>
>
>
>
>
>
>
>
> On Thu, Apr 28, 2016 at 6:15 PM, Otis Rothenberger <osrot...@icloud.com
> <mailto:osrot...@icloud.com>> wrote:
> Maybe someone pointed this out before, but it’s new to me...
>
> The page below is an ongoing test page that I use, so there are some button
> and screen message issues (conflicts). Nevertheless one new JSME point is so
> much fun that I thought I’d point it out:
>
> http://chemagic.org/molecules/mini2.html
> <http://chemagic.org/molecules/mini2.html>
>
> JSME now has a callback function:
> jsmeApplet.setCallBack("AfterStructureModified", sendToJmol);
>
> On the above page, I’ve set the callback sendToJmol to:
>
> function sendToJmol(jsmeEvent) {
> var jsme = jsmeEvent.src;
> var jmefile = jsme.jmeFile();
> window.parent.jms('var molf2 = "' + jmefile + '"; load "@molf2";
> hover off; delete hydrogen;calculate hydrogen;boundbox {*}; centerat
> boundbox; zoom 100;’);
> }
>
> (jms is a run Jmol script function)
>
> On the page, ignore the Jmol window messages and standard Jmol/JSME transfer
> arrow buttons. Just start drawing in the JSME window. Great fun…
>
> There are some loaded Jmol model issues via this route. I’ll try to figure
> them out and then ask Bob!
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org <mailto:o...@chemagic.org>
> http://chemagic.org <http://chemagic.org/>
>
>
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>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr <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
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr <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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> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
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