Extension:Jmol

Jmol extension is an extension for allowing inclusion of Jmol applets inside MediaWiki articles.

Current documentation can be found on the Jmol wiki.

Usage
The Jmol extension can be used in several ways:
 * directly in the media pages of molecular files,
 * as a "custom tag" to display a molecule in 3d in-line (or in a popup window) on a wiki page.

Media pages
Not yet implemented

Tag &lt;jmolFile&gt;
The &lt;jmolFile&gt; tag can be used to display in 3d a molecule file that has been previously uploaded into Wikipedia. Some examples of its usage are available in the Jmol wiki.

A few examples:
 *  Chair.cml  will add a link named Chair.cml to the article. When this link is clicked on, a popup window is displayed containing a Jmol applet with the molecular file File:Chair.cml.
 *  Chair.cml  will add a link named Chair to the article. When this link is clicked on, a popup window is displayed containing a Jmol applet with the molecular file File:Chair.cml.

The following attributes are available for the &lt;jmolFile&gt;</tt> tag:
 * text: To configure the text used for the link. By default, the file name is used for the link.

Tag &lt;jmolSmiles&gt;</tt>
The &lt;jmolSmiles&gt;</tt> tag can be used to display in 3d a molecule file using its SMILES notation. Some examples of its usage are available in the Jmol wiki.

A few examples:
 *  <jmolSmiles>CCCNC</jmolSmiles> </tt> will add a link named CCCNC to the article. When this link is clicked on, a popup window is displayed containing a Jmol applet with a molecular file matching the SMILES string CCCNC.
 *  <jmolFile text="Smiles">CCCNC</jmolSmiles> </tt> will add a link named Smiles to the article. When this link is clicked on, a popup window is displayed containing a Jmol applet with a molecular file matching the SMILES string CCCNC.

The following attributes are available for the &lt;jmolSmiles&gt;</tt> tag:
 * text: To configure the text used for the link. By default, the SMILES string is used for the link.

Installing Jmol extension
Note: The latest version of the Jmol extension has been tested against MediaWiki 1.16. It probably works also with some earlier versions but this has not been tested.

To install the Jmol extension:
 * Create a Jmol</tt> folder in the extensions</tt> folder of your MediaWiki installation.
 * Download the latest stable release of Jmol (or the latest development release).
 * Extract into the Jmol</tt> folder the following files from the Jmol release :
 * all the *.txt</tt> files,
 * the Jmol.js</tt> file,
 * all the JmolApplet0*.jar</tt>,
 * all the JmolAppletSigned0*.jar</tt> files, if you want to be able to use the signed applet (this is necessary for some tags, see description in the following chapters). The certificate used to sign the files is auto-signed, so you may wish to resign them with an authentic certificate.
 * Download all the source files of the Jmol extension and place them in the Jmol</tt> folder.
 * Add the following line to your LocalSettings.php file (near the end):

Note: This description needs to be completed, especially for managing file uploads.

Molecular file types
MediaWiki authorizes the uploading of a very limited set of types, based on file extensions and MIME types. By default, molecular files are not authorized, so you need to change the configuration if you want to take advantage of all the Jmol extension features.

First, you need to authorize new file extensions being uploaded in the wiki, using $wgFileExtensions. For example, if you want to authorize uploading of CML files (*.cml</tt>), you can add the following line in your LocalSettings.php file: You can check what file extensions are authorized in the Special:Upload page.

Note: This description needs to be completed, especially for dealing with MIME types which is quite complex and depends on your server configuration.

Now that new file extensions being uploaded have been authorized, you can do a last modification so that molecular files are shown with a specific icon in categories (see example on the Jmol wiki). You can add an icon in the skins/common/images/icons</tt> folder for each extension for molecular files (for example <tt>fileicon-cml.png</tt>). You can use.

Configuration
There are some options you can specify in your LocalSettings.php file (after the <tt>require_once</tt> line you've already added): Note: This list is not complete.
 * wgJmolAuthorizeJmolTag: Authorize the use of the <tt> </tt> tag. Default is <tt>true</tt>.
 * wgJmolAuthorizeJmolFileTag: Authorize the use of the <tt> <jmolFile/> </tt> tag. Default is <tt>true</tt>.
 * wgJmolAuthorizeJmolPdbTag: Authorize the use of the <tt> <jmolPdb/> </tt> tag. Default is <tt>true</tt>. Note: this tag requires the signed applet to be installed.
 * wgJmolAuthorizeJmolSmilesTag: Authorize the use of the <tt> <jmolSmiles/> </tt> tag. Default is <tt>true</tt>. Note: this tag requires the signed applet to be installed.

Options in LocalSettings.php have no effect

 * Make sure you specify the options after including the extension.

Weblinks

 * Jmol official web site
 * Jmol official Wiki
 * Browse extension source code
 * Extension documentation in Jmol Wiki