MediaWiki

Description

MediaWiki is an open source wiki engine licensed under the GNU General Public License. It is used by many websites, including this one.

The Jmol Mediawiki Extension enables the use of the Jmol applet inside of Mediawiki pages. This simple page demonstrates how to use the extension.

Note: The Jmol Mediawiki Extension is currently under development. It will go under several changes, different versions will probably be incompatible between each other

Wikis using the Jmol Extension

If you know a Wiki using the Jmol MediaWiki Extension, please add it in the following list:

• This wiki
• Folding@Home wiki

How to use the Jmol Extension

Once the Jmol Extension is installed in the Wiki, you can start adding Jmol applets and controls.

This following documentation is subject to change since the Jmol Extension is currently under development

To add a Jmol applet to a MediaWiki page, just add the following:

<jmol>
  <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>
</jmol>

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>

Installation

Download Jmol and extract all the files in a temporary directory.

Create the directory Jmol in $mediawiki/extensions, and copy the following files in it:

• COPYRIGHT.txt
• Jmol.js
• JmolApplet_i18n.jar
• JmolApplet0.jar
• JmolApplet1.jar
• JmolApplet2.jar
• JmolApplet3.jar
• JmolApplet4.jar
• JmolApplet5.jar
• JmolApplet6.jar
• LICENSE.txt
• README.txt

Add the following line to the end of LocalSettings.php:

require_once('extensions/Jmol/JmolExtension.php');

Copy the following code and paste it into extensions/Jmol/JmolExtension.php:

<?php
$wgExtensionFunctions[] = "wfJmolExtension";
$currentTag = "";
$appletContents = "";
$appletScript = "";
$appletName = "";
$appletSize = "";
$appletColor = "";
$appletText = "";

function wfJmolExtension() {
  global $wgParser;
  $wgParser->setHook( "jmol", "renderJmol" );
  $wgParser->setHook( "jmolButton", "renderJmolButton" );
}

function startElement( $parser, $name, $attrs ) {
  global $currentTag;

  $currentTag = $name;
}

function endElement( $parser, $name ) {
  global $currentTag;

  $currentTag = "";
}

function characterData( $parser, $data ) {
  global $currentTag;
  global $appletContents;
  global $appletScript;
  global $appletName;
  global $appletSize;
  global $appletColor;
  global $appletText;

  switch ($currentTag) {
  case "CONTENTS":
    $data = trim($data);
    if ($data != "") {
      $appletContents = $appletContents . "\n" . $data;
    }
    break;
  case "SCRIPT":
    $appletScript = $data;
    break;
  case "NAME":
    $appletName = $data;
    break;
  case "SIZE":
    $appletSize = $data;
    break;
  case "COLOR":
    $appletColor = $data;
    break;
  case "TEXT":
    $appletText = $data;
    break;
  default:
    break;
  }
}

function renderJmol( $input ) {
  global $appletContents;
  global $appletScript;
  global $appletName;
  global $appletSize;
  global $appletColor;

  resetValues();
  $xmlParser = xml_parser_create();
  xml_set_element_handler($xmlParser, "startElement", "endElement");
  xml_set_character_data_handler($xmlParser, "characterData");
  $input = "<jmolApplet>$input<jmolApplet>";
  if (!xml_parse($xmlParser, $input)) {
    die(sprintf(
      "XML error: %s at line %d",
      xml_error_string(xml_get_error_code($xmlParser)),
      xml_get_current_line_number($xmlParser)));
  }
  xml_parser_free($xmlParser);
  $appletContents = trim($appletContents);
  $appletContents = preg_replace("/\t/", " ", $appletContents);
  $appletContents = preg_replace("/\n/", "\\n'+\n'", $appletContents);
  $output = $output .
    "<script src='/extensions/Jmol/Jmol.js'></script>\n".
    "<script>\n" .
    "jmolInitialize('/extensions/Jmol');\n".
    "jmolCheckBrowser('popup', '/extensions/Jmol/browsercheck', 'onClick');\n".
    "jmolSetAppletColor('$appletColor');\n".
    "jmolAppletInline($appletSize, \n'$appletContents', \n'$appletScript', \n'$appletName');\n" .
    "jmolBr();\n" .
    "</script>\n"
    ;
  return $output;
}

function renderJmolButton( $input ) {
  global $appletScript;
  global $appletName;
  global $appletText;

  resetValues();
  $xmlParser = xml_parser_create();
  xml_set_element_handler($xmlParser, "startElement", "endElement");
  xml_set_character_data_handler($xmlParser, "characterData");
  $input = "<jmolApplet>$input<jmolApplet>";
  if (!xml_parse($xmlParser, $input)) {
    die(sprintf(
      "XML error: %s at line %d",
      xml_error_string(xml_get_error_code($xmlParser)),
      xml_get_current_line_number($xmlParser)));
  }
  xml_parser_free($xmlParser);
  $output = $output .
    "<script>\n" .
    "jmolSetTarget('$appletName');\n" .
    "jmolButton('$appletScript', '$appletText');\n" .
    "</script>\n"
    ;
  return $output;
}

function resetValues() {
  global $currentTag;
  global $appletContents;
  global $appletScript;
  global $appletName;
  global $appletSize;
  global $appletColor;

  $currentTag = "";
  $appletContents = "";
  $appletScript = "set spin Y 10; spin on";
  $appletName = "FahWiki";
  $appletSize = "400";
  $appletColor = "black";
  $appletText = "";
}

?>

External links

• Wikipedia: Using Jmol to display molecular models
• Wikipedia: WikiProject Chemistry

Contributors

AngelHerraez, NicolasVervelle, Rzepa, Mevans86, Ngreeves, Pimpim, SklogWiki, Jacksmind, EricMartz