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
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