This looks great, I'm very excited. I'm glad we can begin pushing Jmol content
through mobile browsers. And if anyone would like some free advertising, just
send us your links using this and we will add it to the ChemDoodle Web
Components project page.
IE is one of those browsers that just doesn't want to cooperate, but you will
need IE9 for the 2D components. IE6-8 is supported with the Google Chrome Frame
plugin. The Google Chrome Frame plugin will also bring WebGL.
I will take a look at the js file when I get a chance and help you improve it.
I took a quick look, and it looks like you have already mastered the module
pattern.
ChemDoodle has several methods to check for feature support, found in the
featureDetection package: http://web.chemdoodle.com/api#featureDetection
You can use this to easily determine if <canvas> or WebGL is supported.
Bests,
Kevin
On Apr 12, 2012, at 6:39 PM, Robert Hanson wrote:
> Paul, first, check this out now:
>
> http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm
>
> I'd say that was a productive day!
>
> This page is even more interesting. Pending Jmol user reports, it should pull
> up a twiddlable model on all platforms. It's working on my iPhone, my Windows
> laptop, and my MacBook. I can force it into ChemDoodle WebGL mode within
> Chrome; I can force it into ChemDoodle nonWebGL mode in Firefox, Chrome, and
> Safari. Default of Jmol is working on all non-Java-challenged platforms (I
> still can't force it into ChemDoodle for MSIE, but the default is to use Jmol
> anyway for that platform, of course. I don't know if Kevin can get ChemDoodle
> going on MSIE. Doesn't look like my version will, but it looks like a simple
> error that is probably trappable.)
>
> OK, how it works: The key is found in
> http://chemapps.stolaf.edu/jmol/chemdoodle/JmolCD.js This is a very rough
> draft set of extensions to ChemDoodle. Basically a slight modification of
> ChemDoodle.MolGrabberCanvas (for when there is no webGL) and
> ChemDoodle.MolGrabberCanvas3D (when there is), and the addition of
> ChemDoodle.MolGrabberJmol (when you want to use Jmol instead). In addition,
> I've modified some of the transfer methods in ChemDoodle to allow raw data
> transfer -- no need for server-side conversion to JSON, so now you can use it
> with any generic relay server. And if it's the signed applet, of course,
> there's no need to go to the server for anything. The applet itself can
> deliver.
>
> From a Java perspective, it involves an update to JmolData.jar that allows
> for a new command:
>
> write CD
>
> that writes a (crazy! -- sorry, Kevin ;) ) format that involves scaling by
> 20 and inverting the y axis and putting it all in JSON format (that's for the
> WebGL version of ChemDoodle; the scaling is all undone in the browser) and a
> bit of clean-up in JmolData.jar so that the output is clean to sytem.out when
> you use the WRITE command when you use the -i (silent) flag. I'm using the
> exec() command in PHP, and it is working very nicely.
>
> JmolData.jar -- with the fixes I did for Jonathan for Sage involving the
> -Djava.awt.headless flag -- is also used to create static images, if that is
> preferred. That would be good, for example, if the website is serving up
> proteins, because there's a lot there that can't be done with ChemDoodle
> anyway, and maybe just an image would be better. At least for now.
>
>
> Paul, I might even suggest that the object-oriented Jmol.js we were thinking
> of the other day might be this ChemDoodle/Jmol hybrid. That way, we have, for
> example,
>
> c.MolGrabberJmol.prototype.loadMolecule = function(mol) {
> _jmolFindApplet("jmolApplet" + this.id).script('DATA "model"\n' + mol
> + '\nEND "model"');
> };
> c.MolGrabberJmol.prototype.script = function(script) {
> _jmolFindApplet("jmolApplet" + this.id).script(script);
> };
>
> and one could imagine expanding that slowly to allow a higher level interface
> to ChemDoodle in general as well that lets us have essentially a ChemDoodle
> command line like we have in Jmol. I realize that Kevin doesn't see a need
> for that, and if you don't have a popup menu and you don't allow user input
> to a command line or console, that's probably fine. But I think it's well
> demonstrated that those are very useful in Jmol.
>
> This is from test2.htm. The line
>
> molgrabber = new ChemDoodle.MolGrabberJmol('molgrabberJmol', width,
> height, ".",
> (useSigned ? "JmolAppletSigned.jar" : "JmolApplet.jar"));
>
> creates the applet.
>
> So it's all set up via ChemDoodle. From test2.htm we have as below. (I'm sure
> there's a simpler way to check if webGL is working, but that's what I came up
> with, anyway. Kevin can surely clean that up.)
>
> Check it out!
>
> Bob
>
>
> (function(width, height) {
>
> // logic is set as follows:
> // -- if Java is present and have Jmol.js, use Jmol
> // -- otherwise, if WebGL is present and have ChemDoodleWeb.js, use
> ChemDoodle/WebGL
> // -- otherwise, if ChemDoodleWeb.js is present, use ChemDoodle/2D
> // -- otherwise, just display the image
>
> // ?USECD or ?USEIMAGE in the URL can force one or the other of these.
>
> // and, of course, a little tweaking of the logic would let you do anything
>
> myModel = "morphine";
> var dontUseChemDoodle = (document.location.href.indexOf("NOCD") >= 0);
> var useChemDoodle = (!dontUseChemDoodle &&
> document.location.href.indexOf("CD") >= 0);
> var useImage = (document.location.href.indexOf("IMAGE") >= 0);
> var useSigned = (document.location.href.indexOf("SIGNED") >= 0);
>
> if (!useChemDoodle && !useImage && _jmol && navigator.javaEnabled()) {
> molgrabber = new ChemDoodle.MolGrabberJmol('molgrabberJmol', width,
> height, ".",
> (useSigned ? "JmolAppletSigned.jar" : "JmolApplet.jar"));
> molgrabberJmol_isReady = function(app,isReady) {
> if (!isReady) return;
> molgrabber.setSearchTerm(myModel);
> }
> } else if (!dontUseChemDoodle && !useImage && ChemDoodle) {
> document.write("<div id=moldiv style='display:none'>");
> molgrabber = new ChemDoodle.MolGrabberCanvas3D('molgrabber', width,
> height);
> document.write("</div>");
> if (molgrabber.gl) {
> molgrabber.specs.set3DRepresentation('Stick');
> molgrabber.specs.backgroundColor = 'black';
> document.getElementById("moldiv").style.display = "block";
> } else {
> molgrabber = new ChemDoodle.MolGrabberCanvas('molgrabber1', width,
> height, true);
> molgrabber.specs.bonds_useJMOLColors = true;
> molgrabber.specs.bonds_width_2D = 3;
> molgrabber.specs.atoms_display = false;
> molgrabber.specs.backgroundColor = 'black';
> molgrabber.specs.bonds_clearOverlaps_2D = true;
> }
> molgrabber.setSearchTerm(myModel);
> } else {
> var img = "<img width=" + width + " height=" + height + "
> src=http://chemapps.stolaf.edu/jmol/jmolpic.php?model="; + myModel + "&width="
> + width + "&height=" + height + "/>";
> document.write(img);
> }
> })(300, 300);
>
> On Thu, Apr 12, 2012 at 2:44 PM, Paul Pillot
> <paul.pil...@ac-orleans-tours.fr> wrote:
> How does this work ?
> It apparently makes a call to a php script hosted on stolaf's server. Does
> this php script itself calls jmoldata.jar server side ?
> And how does it replies ? by sending back a mol file or a chemdoodle JSON
> object ?
> -Paul
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2
> _______________________________________________
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>
>
>
> --
> 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
> ------------------------------------------------------------------------------
> For Developers, A Lot Can Happen In A Second.
> Boundary is the first to Know...and Tell You.
> Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
> http://p.sf.net/sfu/Boundary-d2dvs2_______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
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