MediaWiki/ExtensionV6 - Revision history

AngelHerraez: highlight links to examples

2025-01-18T19:29:01Z

highlight links to examples

AngelHerraez: documenting v6 of the Extension

2025-01-15T19:14:19Z

documenting v6 of the Extension

AngelHerraez: /* Jmol (JSmol) Extension for MediaWiki, version 6 */

2024-05-17T19:24:11Z

‎Jmol (JSmol) Extension for MediaWiki, version 6

AngelHerraez: starting the new page with a duplicate of V5

2024-05-17T19:22:25Z

starting the new page with a duplicate of V5

New page

{{Running_Jmol_Sections}}

= Jmol (JSmol) Extension for MediaWiki, version 6 =

For general information on this Extension and particularly about how to install and set it up, visit the [[MediaWiki]] page.

This version of the Extension has been developed and tested with MediaWiki 1.32.

It will use by default JSmol objects in the HTML5 modality, but configuration may be adjusted to allow the Java modality (signed applet) or the WebGL modality (note that JSmol has limited functionality with the latter). All mentions of either Jmol or JSmol in this documentation are synonyms. Note also that the use of "applet" in names and references is maintained for legacy reasons but Java is not involved any more (unless forced by the user and allowed by the wiki administrator).

:''Please check the version you have installed in your wiki (browse to ''Special pages'', then ''Version''). Documentation for former versions of the Extension may be found in [[MediaWiki/ExtensionV3]], [[MediaWiki/ExtensionV4]] and [[MediaWiki/ExtensionV5]].''

== How to use the Jmol Extension ==
''This applies to version 6 of the Extension''

=== Simple tags ===
There are 4 tags that will render a link in the page that, when clicked by the user,
will open a small window (pop-up) with a JSmol panel that displays a structure. No custom rendering or scripting on the structure is possible.
* <code>jmolFile</code>
* <code>jmolMol</code>
* <code>jmolSmiles</code>
* <code>jmolPdb</code>

See [[MediaWiki/Simple_Tags]] for details and demonstration with examples.

=== Full-featured tag ===
==== First level tag ====
The <code>jmol</code> tag encloses different subtags that offer more flexibility in how and when the model will be displayed,
as well as its rendering or scripting.

==== Second-level subtags that insert a JSmol panel (either inline or in a popup) ====
* Inline JSmol panel:
** <code>jmolApplet</code> inserts the JSmol panel in the page as soon as it is loaded. See [[MediaWiki/Tags for In-page Models]] for details.
** <code>jmolAppletInlineButton</code>
** <code>jmolAppletInlineLink</code> both will, upon user action, insert into the page a JSmol panel displaying a structure. See [[MediaWiki/Tags for Pop-in Models]] for details.
* Pop-up JSmol panel:
** <code>jmolAppletButton</code>
** <code>jmolAppletLink</code> both will, upon user action, open a small window (pop-up) with a JSmol panel displaying the structure. See [[MediaWiki/Tags for Pop-up Models]] for details.

==== Second-level subtags that insert controls to act on one JSmol panel ====
See [[MediaWiki/Tags for Controls]] for details and examples.
* <code>jmolButton</code>
* <code>jmolLink</code>
* <code>jmolCheckbox</code>
* <code>jmolMenu</code>
* <code>jmolRadioGroup</code>

==== Third-level subtags ====
These are relevant for <code>jmolApplet</code>, and some of them also for some other 2nd-level subtags:
* <code>text</code> (displayed in the page or in the UI control)
* <code>script</code> (commands for the molecule display in JSmol)
* <code>uploadedFileContents</code> (model to be loaded)
* <code>urlContents</code>
* <code>wikiPageContents</code>
* <code>inlineContents</code>
* <code>title</code> (either tooltip for the UI control or text to be displayed above the JSmol panel)
* <code>caption</code> (text to be displayed below the JSmol panel)
* <code>color</code> (background color of JSmol panel)
* <code>size</code> (dimensions of JSmol panel)
* <code>controls</code> (display of optional buttons below the JSmol panel; value: any combination of spin | quality | labels | popup)
* <code>frame</code> (border around the JSmol panel)
* <code>image</code> (cover image to be displayed; replaced with the JSmol panel upon click)
* <code>pspeed</code> (performance: higher speed vs. higher quality, relevant for mobile platforms)
* <code>name</code> (applies to <code>jmolApplet</code>, needed when several JSmol panels are presemt in a page)
These are more specific and relevant just for some 2nd-level subtags:
* <code>target</code> applies to <code>jmolButton</code>, <code>jmolLink</code>, <code>jmolCheckbox</code>, <code>jmolMenu</code>, <code>jmolRadioGroup</code>
* <code>scriptWhenChecked</code> applies only to <code>jmolCheckbox</code>
* <code>scriptWhenUnchecked</code> applies only to <code>jmolCheckbox</code>
* <code>checked</code> applies only to <code>jmolMenu</code> and <code>jmolRadioGroup</code>
* <code>item</code> applies only to <code>jmolMenu</code> and <code>jmolRadioGroup</code>
* <code>vertical</code> applies only to <code>jmolRadioGroup</code>
* <code>menuheight</code> applies only to <code>jmolMenu</code>

== How to install the Jmol Extension ==
Please see [[MediaWiki/Installation]]

= Former versions =

For documentation on former versions of the Extension, see [[MediaWiki/ExtensionV3]], [[MediaWiki/ExtensionV4]] or [[MediaWiki/ExtensionV5]].

= Test Pages =

# A few [[MediaWiki/Basic Example|basic examples]] of the {{tag|jmolFile}}, {{tag|jmolPdb}} and {{tag|jmolSmiles}} tags.
# [[Jmol_MediaWiki_Extension | A demo page]] for the {{tag|jmol}} tag
# [[Uploaded XYZ File]] -- includes test of {{tag|jmolCheckbox}}, {{tag|jmolLink}}, {{tag|jmolButton}}, and {{tag|jmolMenu}}
# [[Uploaded MDL Molfile]]
# [[Uploaded CML File]]
# [[Jmol in Pop-up| Uploaded PDB File opening in a pop-up]] -- tests <code>jmolAppletLink</code>
# [[Inlined MDL Molfile]]
# [[Inlined PDB File]]
# [[Inlined CML File]]
# [[Load SMILES]] via script -- Includes test of signed applet and {{tag|jmolMenu}}
# [[User:Bduke#Tests_of_Jmol_incorporated_into_a_MediaWiki_wiki | Test page]] (Brian's)

@@ Line 5: / Line 5: @@
 For general information on this Extension and particularly about how to install and set it up, visit the [[MediaWiki]] page.
-This version of the Extension has been developed and tested with MediaWiki 1.39 and 1.41.
+This version of the Extension has been developed and tested with MediaWiki 1.39, 1.41 and 1.43.
 It will use by default JSmol objects in the HTML5 modality, but configuration may be adjusted to use the WebGL modality (note that JSmol has limited functionality with this). All mentions of either Jmol or JSmol in this documentation are synonyms. Note also that the use of "applet" in names and references is maintained for legacy reasons but Java is not involved any more.

@@ Line 10: / Line 10: @@
 :''Please check the version you have installed in your wiki (browse to ''Special pages'', then ''Version''). Documentation for former versions of the Extension may be found in [[MediaWiki/ExtensionV3]], [[MediaWiki/ExtensionV4]] and [[MediaWiki/ExtensionV5]].''
@@ Line 24: / Line 23: @@
 * <code>jmolPdb</code>
-See [[MediaWiki/Simple_Tags]] for details and demonstration with examples.
+See
 === Full-featured tag ===
@@ Line 33: / Line 33: @@
 ==== Second-level subtags that insert a JSmol panel (either inline or in a popup) ====
 * Inline JSmol panel:
-** <code>jmolApplet</code> inserts the JSmol panel in the page as soon as it is loaded. See [[MediaWiki/Tags for In-page Models]] for details.
+** <code>jmolApplet</code> inserts the JSmol panel in the page as soon as it is loaded. See <span style="font-weight:bold;background:#FFF840;padding:0 0.4ex;">[[MediaWiki/Tags for In-page Models|details and demonstration]]</span> (Tags for In-page Models)
 ** <code>jmolAppletInlineButton</code>
-** <code>jmolAppletInlineLink</code> both will, upon user action, insert into the page a JSmol panel displaying a structure. See [[MediaWiki/Tags for Pop-in Models]] for details.
+** <code>jmolAppletInlineLink</code> both will, upon user action, insert into the page a JSmol panel displaying a structure. See <span style="font-weight:bold;background:#FFF840;padding:0 0.4ex;">[[MediaWiki/Tags for Pop-in Models|details and demonstration]]</span> (Tags for Pop-in Models)
 * Pop-up JSmol panel:
 ** <code>jmolAppletButton</code>
-** <code>jmolAppletLink</code> both will, upon user action, open a small window (pop-up) with a JSmol panel displaying the structure. See [[MediaWiki/Tags for Pop-up Models]] for details.
+** <code>jmolAppletLink</code> both will, upon user action, open a small window (pop-up) with a JSmol panel displaying the structure. See <span style="font-weight:bold;background:#FFF840;padding:0 0.4ex;">[[MediaWiki/Tags for Pop-up Models|details and demonstration]]</span> (Tags for Pop-up Models)
 ==== Second-level subtags that insert controls to act on one JSmol panel ====
-See [[MediaWiki/Tags for Controls]] for details and examples.
+See <span style="font-weight:bold;background:#FFF840;padding:0 0.4ex;">[[MediaWiki/Tags for Controls|details and demonstration]]</span> (Tags for Controls)
 * <code>jmolButton</code>
 * <code>jmolLink</code>