> Of course, the real question is whether now MOODLE works.. :)
Yes, Moodle (2.4.3 the latest stable version, and 2.5 beta) now works, in
my hands.
JSmol was breaking a few Moodle YUI features. In 'normal' mode the
expanding navigation menus in side blocks (Moodle typically has a 3-panel
layout with blocks in left and right columns and central main content)
failed to work. In 'edit' mode, drag-and-drop upload of files,
drag-and-drop repositioning of blocks, and 'the Add an activity or
resource' link.
With JSmol bundled inside a YUI module and $(document).ready(function(){ },
these now all work. One minor irritation is that on first turning Editing
on, with a JSmol embedded, a page refresh is required before the above
Moodle YUI features start working again, though I can live with that.
I have implemented unique IDs so that multiple independent JSmols can be
inserted on a Moodle page. So far, working fine with a handful of JSmols
inserted in various locations (side blocks and central section). Page load
times, as expected, do increase with additional JSmol instances, though
don't seem unreasonable. If lots of JSmols are required, they can be added
to individual Pages within a Moodle course.
This is all for 'vanilla' Moodle. The M in Moodle stands for Modular, and
folks tend to add additional 3rd-party modules, including additional
JavaScript, which may complicate things. Of course, the Jmol/JSmol filter
is one such example of this. In this context, the decision by Moodle
developers to base JavaScript implementation on the modular YUI 3 framework
(there have been pretty 'heated' jQuery v YUI 3 discussions in the Moodle
forums) may be a good one.
>CDN in what sense, other than SourceForge and
http://chemapps.stolaf.edu/jmol/jsmol ?
Like, amongst many others, MathJax http://www.mathjax.org/download/. So
that JSmol could be invoked without local installation but still load
quickly.
Although, whilst developing/testing things, I have directly linked to
http://chemapps.stolaf.edu/jmol/jsmol, I had assumed you would not
appreciate the traffic generated by doing this in production use ;-)
>Absolutely. JSmol is set to do REST searches, which it does at RCSB, for
example, for protein structures. (See the =caffeine? link at
http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm). But I don't see a usable
API at http://www.crystallography.net
Do they have one?
Not as such (as far as I am aware) though once you have the COD ID (e.g.
from a manual search), you can easily get to the cif file
e.g. for, one of the many, Halite structures COD ID:
9003308<http://www.crystallography.net/information_card.php?cif=9003308>
The cif file is at: http://www.crystallography.net/cif/9/00/33/9003308.cif
May be worth talking to the COD folks about something more sophisticated.
On 11 April 2013 01:23, Robert Hanson <hans...@stolaf.edu> wrote:
>
>
>
> On Wed, Apr 10, 2013 at 4:32 PM, Geoffrey Rowland <rowland.ge...@gmail.com
> > wrote:
>
>> After some trial-and-error and several rereads of Chapter 1 in the YUI 3
>> Cookbook (Evan Goer, 2012; O'Reilly), I think I have got JSmol playing
>> nicely in Moodle. So far tested without problem on recent versions of
>> Firefox, Chrome and Opera browsers.
>>
>> Seems to depend on, both of, two things:
>>
>> 1. JSmol loaded into a 'sandbox' as a YUI module (simple example in my
>> previous post). Moodle uses YUI 3 as the core JavaScript library. The
>> Moodle developers now recommend that any JavaScript is loaded via a YUI
>> module rather than the 'traditional' <script src="..."></script> tags.
>>
>>
> interesting.
>
>
>
>> 2. JSmol is rendered inside a $(document).ready(function(){ }. A simple
>> example is also in the code in my previous post. Without this, JSmol still
>> blocks the function of some Moodle JavaScript/YUI features (e.g. navigation
>> lists and menus) positioned after JSmol on the page. The jQuery
>> $(document).ready(function(){ } seems to result in JSmol being added to the
>> page after everything else, including the other YUI stuff.
>>
>
> That is correct -- at least, it is running its main methods after that.
>
>
>>
>> Hey presto, everything works! In edit mode, can even (YUI) drag-and-drop
>> a block containing a spinning JSmol around a Moodle page. :-)
>>
>>
> Of course, the real question is whether now MOODLE works.. :)
>
>
>
>> I hope to get all thisinto an updated JSmol Moodle filter in the near
>> future. Also, add a few notes to the Jmol Wiki in case it helps anyone else
>> working with JSmol in a YUI context.
>>
>> So, now have JSmol working alongside YUI3 in Moodle and MochiKit in
>> Mahara (though a global swap of $ to $j may still help, if it doesn't break
>> anything else)
>>
>> A couple of very loosely related questions
>>
>> 1. Is there any possibility of a JSmol CDN? Particularly useful given the
>> incredibly rapid development of features over recent years. Its hard to
>> keep up! Would be nice to be 'plumbed' into the latest stable (or
>> development) version.
>>
>>
> CDN in what sense, other than SourceForge and
> http://chemapps.stolaf.edu/jmol/jsmol ?
>
>
>
>
>
>> 2. In addition to the built-in interface to NCI/PubChem and RCSB, would
>> it be possible to have a similar link to the Crystallography Open Database
>> (COD) hosted at http://www.crystallography.net?. Would be nice for an
>> easy showcase of crystal/mineral structures alongside the existing small
>> molecules and biological macromolecules.
>>
>>
> Absolutely. JSmol is set to do REST searches, which it does at RCSB, for
> example, for protein structures. (See the =caffeine? link at
> http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm). But I don't see a
> usable API at http://www.crystallography.net Do they have one?
>
>
>
>
>
>> I continue to be amazed as to what JSmol can do!
>>
>> Cheers
>>
>>
>> On 8 April 2013 23:12, Geoffrey Rowland <rowland.ge...@gmail.com> wrote:
>>
>>> Thanks Bob, that's useful.
>>>
>>> For Mahara, $ is the main (only?) problem. Mahara has both MochiKit
>>> (main library for drag-n-drop editing etc) and jQuery (for a few features,
>>> e.g. image gallery). Both of these (can) use $. By default, Mahara loads
>>> jQuery first, then maps $j to the jQuery global, then loads Mochikit which
>>> 'takes over' ownership of $.
>>>
>>> So, all other things being equal, a swap of $ to $j (or jQuery) in JSmol
>>> (and associated jQuery) should fix things for Mahara. Not sure if this is
>>> more widely useful, though the $ to $j swap is one of the recommended
>>> strategies in http://docs.jquery.com/Using_jQuery_with_Other_Libraries.
>>>
>>> Not yet been brave enough to tackle the global search-replace, and not
>>> entirely sure which files I need to change! As indicated in my earlier
>>> post, my current workaround is to load JSmol.min.js when MochiKit is not
>>> required and switch to JSmol.min.nojq.js when MochiKit is required (in
>>> Mahara edit mode). The only bug I have noticed, is that the right-click
>>> menu does not display and throws up an error pop-up. I have suppressed this
>>> with a 'set disablePopupMenu TRUE'. Since the menu is not essential in
>>> (Mahara) edit view, this is a reasonable compromise, if a bit messy.
>>>
>>> Not made much further progress with Moodle which uses YUI3 as the main
>>> JavaScript library. Have experimented a little with using a YUI module to
>>> load JSmol. As far as I understand it, this should allow the JSMol (and
>>> jQuery) objects to run in a local 'sandbox'. The simple YUI3 loading of
>>> JSmol, listed below, certainly functions, though I have not yet got it all
>>> working with Moodle.
>>>
>>> Hope that makes sense
>>>
>>> Cheers
>>>
>>> Geoff
>>>
>>>
>>> <!DOCTYPE html>
>>>
>>> <head>
>>>
>>> <title>Loading JSmol as a YUI Module</title>
>>>
>>> </head>
>>>
>>> <body>
>>>
>>> <h4>JSmol Plugin</h4>
>>> <div id="panel"></div>
>>>
>>> <script src="http://yui.yahooapis.com/3.5.0/build/yui/yui-min.js
>>> "></script>
>>> <script>
>>> YUI({
>>> groups: {
>>> "jmol": {
>>> base: "http://...path.to.../jmol/jsmol/";,
>>> async: true,
>>> modules: {
>>> "jsmol": {
>>> path: "JSmol.min.js"
>>> }
>>> }
>>> }
>>> }
>>> }).use("jsmol", function (Y) {
>>>
>>> // Start of standard JSmol stuff
>>>
>>> var Info = {
>>> width: 300,
>>> height: 300,
>>> script: 'load ":ethanol"',
>>> use: "HTML5",
>>> j2sPath: "j2s",
>>> addSelectionOptions: true,
>>> serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php";,
>>> readyFunction: null,
>>> console: "jmol_infodiv",
>>> disableInitialConsole: false,
>>> defaultModel: null,
>>> debug: false
>>> }
>>>
>>> var jmol = "jmol"; // the JavaScript applet object
>>>
>>> $(document).ready(function(){
>>> Jmol.setDocument(0);
>>> jmol = Jmol.getApplet("jmol", Info);
>>> $("#panel").html(Jmol.getAppletHtml(jmol));
>>> })
>>>
>>> // End of standard JSmol stuff
>>>
>>> });
>>> </script>
>>> </body>
>>>
>>>
>>>
>>>
>>
>>
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>>
>
>
> --
> 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
>
>
>
> ------------------------------------------------------------------------------
> Precog is a next-generation analytics platform capable of advanced
> analytics on semi-structured data. The platform includes APIs for building
> apps and a phenomenal toolset for data science. Developers can use
> our toolset for easy data analysis & visualization. Get a free account!
> http://www2.precog.com/precogplatform/slashdotnewsletter
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
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