Jmol Processor

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.

1. open a source-code section with three curly braces (off", script="JmolScript"

other options are not supported

1. insert the source-code of the molecule
2. 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.

Contributors

NicolasVervelle, AngelHerraez, Pimpim, TylerOderkirk