Difference between revisions of "Jmol Processor"
(Initialization from JmolWiki) |
m (Fixed formatting) |
||
| Line 11: | Line 11: | ||
To add a Jmol applet to a [[MediaWiki]] page, just add the following: | To add a Jmol applet to a [[MediaWiki]] page, just add the following: | ||
| − | + | <jmolDevelop> | |
<contents>contents of the current.xyz file</contents> | <contents>contents of the current.xyz file</contents> | ||
<script>script to execute</script> | <script>script to execute</script> | ||
| Line 17: | Line 17: | ||
<size>applet size</size> | <size>applet size</size> | ||
<color>applet background color</color> | <color>applet background color</color> | ||
| − | + | </jmolDevelop> | |
To add buttons to send scripts to the applet, just add the following: | To add buttons to send scripts to the applet, just add the following: | ||
| − | + | <jmolButton> | |
<script>script to execute</script> | <script>script to execute</script> | ||
| − | <text>text of the button<text> | + | <text>text of the button</text> |
<name>applet name</name> | <name>applet name</name> | ||
| − | + | </jmolButton> | |
=== Jmol in MoinMoin === | === Jmol in MoinMoin === | ||
Revision as of 07:53, 9 April 2006
Contents
Jmol in Wiki's
The Jmol Applet can be embedded in Wiki pages, like in HTML pages. Below are four processors for four different Wiki engines (MediaWiki, MoinMoin, MoniWiki and UniWakka).
A separate mechanism for MoinMoin is described in MoinMoin Macros.
Jmol in MediaWiki
A small JmolProcessor for MediaWiki is currently under development. The development version can be tested at Jmol MediaWiki Extension. I have only tested it with molecular models coming from Folding@Home, under Windows.
To add a Jmol applet to a MediaWiki page, just add the following:
<jmolDevelop> <contents>contents of the current.xyz file</contents> <script>script to execute</script> <name>applet name</name> <size>applet size</size> <color>applet background color</color> </jmolDevelop>
To add buttons to send scripts to the applet, just add the following:
<jmolButton> <script>script to execute</script> <text>text of the button</text> <name>applet name</name> </jmolButton>
Jmol in MoinMoin
Now we have a small JmolProcessor for MoinMoin, which works similar the JmolProcessor for MoniWiki.
- open a source-code section with three curly braces (off", script="JmolScript"
- other options are not supported
- insert the source-code of the molecule
- close the section with three curly braces ()
Example:
{ { {#!Jmol frank='on'
# height="150" width="150"
# script='cpk 0.3; wireframe 0.1'
ATOM 1 O UNK 1 0.000 0.000 0.000 1.00 0.00
ATOM 2 H UNK 1 0.943 0.000 0.000 1.00 0.00
ATOM 3 H UNK 1 -0.259 0.907 0.000 1.00 0.00
ATOM 4 O UNK 1 3.000 0.000 0.000 1.00 0.00
ATOM 5 H UNK 1 3.568 0.000 0.753 1.00 0.00
ATOM 6 H UNK 1 3.568 0.000 -0.753 1.00 0.00
END
} } }
Jmol in MoniWiki
A processor has been written for MoniWiki (MoniWiki is a PHP clone of the MoinMoin) to embed the JmolPlugin. It use the Processor feature of MoinMoin.
A demo is online: http://chemie.skku.ac.kr/wiki/wiki.php/JmolPlugin
Note that the Jmol Applet is slightly modified to enable Clipboard feature. You can grab a image with a 'Y' key on the applet : type 'y' on the applet and type 'D' to toggle the rendering method. --WkPark
The code that can be embedded in Wiki pages in MoniWiki looks like:
#!jmol (-) ATOM 1 O UNK 1 0.000 0.000 0.000 1.00 0.00 ATOM 2 H UNK 1 0.943 0.000 0.000 1.00 0.00 ATOM 3 H UNK 1 -0.259 0.907 0.000 1.00 0.00 ATOM 4 O UNK 1 3.000 0.000 0.000 1.00 0.00 ATOM 5 H UNK 1 3.568 0.000 0.753 1.00 0.00 ATOM 6 H UNK 1 3.568 0.000 -0.753 1.00 0.00 END
Jmol in UniWakka
A processor has been written for UniWakka, a PHP-powered wiki, to embed the Jmol applet. It uses a customised actions/ feature of UniWakka and accesses data files (.mol, .pdb, whatever) stored within the UniWakka database. The demo is known to work on Mac OSX (Safari, FireFox, Camino, Explorer) and Windoze (Explorer, Opera, FireFox)
A demo is online: http://www.shef.ac.uk/chemistry/uniwakka/
See also Help On Parsers.
