Jmol Processor - Revision history

AngelHerraez: merging content from Jmol Processor page

2025-08-12T10:39:30Z

merging content from Jmol Processor page

AngelHerraez: DokuWiki plugin

2009-01-26T10:40:41Z

DokuWiki plugin

TylerOderkirk: /* Jmol in MoinMoin */ added nowiki tag to escape triple-open-curlies

2007-09-23T16:59:48Z

‎Jmol in MoinMoin: added nowiki tag to escape triple-open-curlies

Pimpim: adding the running jmol template

2007-05-30T15:24:08Z

adding the running jmol template

NicolasVervelle: Mediawiki extension

2006-05-08T15:43:30Z

Mediawiki extension

NicolasVervelle: Moved to MediaWiki page

2006-04-09T08:05:43Z

Moved to MediaWiki page

NicolasVervelle: Fixed formatting

2006-04-09T07:53:34Z

Fixed formatting

NicolasVervelle: Initialization from JmolWiki

2006-03-28T21:09:42Z

Initialization from JmolWiki

New page

== 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 [http://fahwiki.fahstats.com/index.php?title=Jmol_MediaWiki_Extension Jmol MediaWiki Extension]. I have only tested it with molecular models coming from [http://folding.stanford.edu/ 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 (<tt>{{{</tt>) followed by <tt>#!Jmol</tt> (note the capital J).
# this and all following lines beginning with a "#" character may include the following options:
:: <tt>height="pixel", width="pixel", frank="on|off", script="JmolScript"</tt>
:: other options are not supported
# insert the source-code of the molecule
# close the section with three curly braces (<tt>}}}</tt>)

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 [http://uniwakka.sourceforge.net/ UniWakka], a PHP-powered wiki, to embed the Jmol applet. It uses a customised actions/ feature of [http://uniwakka.sourceforge.net/ UniWakka] and accesses data files (.mol, .pdb, whatever) stored within the [http://uniwakka.sourceforge.net/ 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 [http://moinmoin.wikiwikiweb.de/HelpOnParsers Help On Parsers].

← Older revision		Revision as of 10:39, 12 August 2025
Line 1:		Line 1:
−	~~{{Running_Jmol_Sections}}~~	+	Content moved to [[Jmol in Wikis and Blogs]]
−	~~== 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).~~
−
−	~~=== Jmol in DokuWiki ===~~
−
−	~~A [http://wiki.symplus.co.jp/doku.php/computer/en/jmol_plugin DokuWiki plugin] allows to display Jmol applets with files from the 'pdb' namespace.~~
−
−	~~Once the wiki is properly configured, the code for inserting Jmol looks like this:~~
−	~~<nowiki><jmol (filename) (width) (height) (button)>~~
−	~~... Jmol scripts ...~~
−	~~</jmol></nowiki>~~
−
−	~~It is possible to put a button so the model is loaded later, as well as~~ to ~~use <tt>Jmol.js</tt> functions.~~
−
−	~~=== Jmol in MediaWiki ===~~
−
−	~~A fully functional JmolProcessor has been written for MediaWiki. Check the~~ [[~~MediaWiki]] page.~~
−	~~It has been installed on this Wiki.~~
−
−	~~===~~ 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 <tt>(<nowiki>{{{</nowiki>)</tt> followed by <tt>#!Jmol</tt> (note the capital J).~~
−	~~# this~~ and ~~all following lines beginning with a "#" character may include the following options:~~
−	~~:: <tt>height="pixel", width="pixel", frank="on\|off", script="JmolScript"</tt>~~
−	~~:: other options are not supported~~
−	~~# insert the source-code of the molecule~~
−	~~# close the section with three curly braces (<tt>}}}</tt>)~~
−
−	~~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~~
−	~~} } }~~
−
−	~~A separate mechanism for MoinMoin is described in [[MoinMoin Macros]].~~
−
−	~~=== 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 [http://uniwakka.sourceforge.net/ UniWakka~~], a PHP-powered wiki, to embed the Jmol applet. It uses a customised actions/ feature of [http://uniwakka.sourceforge.net/ UniWakka] and accesses data files (.mol, .pdb, whatever) stored within the [http://uniwakka.sourceforge.net/ 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 [http://moinmoin.wikiwikiweb.de/HelpOnParsers Help On Parsers~~].

← Older revision		Revision as of 15:24, 30 May 2007
Line 1:		Line 1:
		+	{{Running_Jmol_Sections}}
	== Jmol in Wiki's ==		== Jmol in Wiki's ==

@@ Line 7: / Line 7: @@
 === Jmol in MediaWiki ===
-A small JmolProcessor for [[MediaWiki]] is currently under development. Check [[MediaWiki]].
+A fully functional JmolProcessor has been written for MediaWiki. Check the [[MediaWiki]] page.
 === Jmol in MoinMoin ===

@@ Line 4: / Line 4: @@
 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 DokuWiki ===
 === Jmol in MediaWiki ===
@@ Line 34: / Line 43: @@
   END
   } } }
 === Jmol in MoniWiki ===

@@ Line 14: / Line 14: @@
 Now we have a small JmolProcessor for MoinMoin, which works similar the JmolProcessor for MoniWiki.
-# open a source-code section with three curly braces (<tt>{{{</tt>) followed by <tt>#!Jmol</tt> (note the capital J).
+# open a source-code section with three curly braces <tt>(<nowiki>{{{</nowiki>)</tt> followed by <tt>#!Jmol</tt> (note the capital J).
 # this and all following lines beginning with a "#" character may include the following options:
 :: <tt>height="pixel", width="pixel", frank="on|off", script="JmolScript"</tt>
@@ Line 33: / Line 33: @@
   ATOM      6  H   UNK     1       3.568   0.000  -0.753  1.00  0.00
   END
   } } }
 === Jmol in MoniWiki ===

@@ Line 11: / Line 11: @@
 To add a Jmol applet to a [[MediaWiki]] page, just add the following:
-  <jmolDevelop>
+  &lt;jmolDevelop&gt;
     <contents>contents of the current.xyz file</contents>
     <script>script to execute</script>
@@ Line 17: / Line 17: @@
     <size>applet size</size>
     <color>applet background color</color>
-  </jmolDevelop>
+  &lt;/jmolDevelop&gt;
 To add buttons to send scripts to the applet, just add the following:
-  <jmolButton>
+  &lt;jmolButton&gt;
     <script>script to execute</script>
-    <text>text of the button<text>
+    <text>text of the button</text>
     <name>applet name</name>
-  </jmolButton>
+  &lt;/jmolButton&gt;
 === Jmol in MoinMoin ===