Hi Jeff
>If I understand you correctly, you have a PHP filter for Moodle such that if
>this filter is installed on a Moodle server one can create a link on a Moodle
>page to a structure file (pdb, xyz, mol, etc.) and clicking on that link opens
>a page displaying that structure using JSmol.
>Is that something you would be willing to share because I could use something
>like that.
Yes, the code is available on GitHub and will hopefully also be on the
Moodle Plugins database in the near future.
https://github.com/geoffrowland/moodle-filter_jmol
https://moodle.org/plugins/
For convenience, the download includes a fairly recent JSmol bundle
though you may wish to replace the contents of the jsmol folder with
the latest JSmol release.
The Moodle Jmol filter was originally written by Dan Stowell
(University College London) and I have intermittently tinkered with it
over recent years to keep it working with new Moodle versions. There
is somewhat out-of-date documentation at:
http://docs.moodle.org/25/en/Jmol_filter
and some more recent info at:
https://moodle.org/mod/forum/discuss.php?d=227064
and there may be other relevant info scattered around the Moodle forums
The filter should enable you to add JSmol/Jmol anywhere in Moodle that
uses the TinyMCE editor (course topics, label resources, page
resources, HTML blocks, forum postings, glossaries, quizzes etc)
You may also be interested in a JSmol/Jmol plugin for Mahara. Mahara
can function as as stand-alone e-Portfolio system but also integrates
nicely with Moodle (so called 'Mahoodle' SSO). The Mahara Jmol plugin
was originally written by one of my students, James Kerrigan, though,
like the Moodle filter, I have recently updated it to work with JSmol.
It is also available on GitHub.
https://mahara.org
https://wiki.mahara.org/index.php/System_Administrator%27s_Guide/Moodle//Mahara_Integration
https://github.com/geoffrowland/mahara-artefact_file_blocktype_jmol
https://mahara.org/interaction/forum/topic.php?id=5459
Mahara gives considerable flexibility and control of web page layouts
and collections of pages. It enables individual students or
collaborative groups of students to construct content. Moodle courses
are more teacher-owned (not necessarily a bad thing!). So, they are
complementary.
Be aware that both the Moodle filter and Mahara plugins are very much
under development (it's hard to keep up with Jmol/JSmol !!). So, do
install/test on a non-production server in the first instance.
>Incidentally, when I tried your test page in Safari (everything up to date) it
>gave an unrecognized file format error for 1crn.pdb.gz. Also when I tried the
>link to dan.pse it loaded the page but not the structure then the page became
>unresponsive. When I tried the link for 1m19.pdb.gz it also gave an
>unrecognized file format error.
Thanks for the 'heads up' re Safari. I don't have routine access to a
Mac. So, had only tested with the last available Safari version
(5.1.7) for Windows. This does work but is now rather
'long-in-the-tooth'. Perhaps, in the short-term, will be better to
default to Jmol for Safari with binary files with the filter.
Cheers
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