Jmol JavaScript Object/Legacy

Converting legacy web pages to JSmol

Overview

It is not hard to convert pages that used the Jmol Applet to use the HTML5 versions of JSmol. The basic sequence includes:

• Switching from Jmol.js to JSmol.min.js
• Adding the j2s folder/directory to your website.
• Setting parameters in the Info variable.
• Modifying function calls from the format jmolXxxx(..., appletExtension) to Jmol.jmolXxxx(appletID, ...) (see below). Depending upon the magnitude of the problem, you may want to write (but read the next section first!) a set of JavaScript functions that allow you to keep your page source code unchanged. For example, if you use the simplest form of jmolButton, the converting function would be:

function jmolButton(script, label) {
  Jmol.jmolButton(myJmol, script, label)
}

Or you can modify your page source code to use the new format. Or, easiest solution, use the 'adapter' library described below.

The main methods formerly implemented in Jmol.js (and more!) have now equivalent functions that can be found in JSmolApi.js -- also included in the distribution: jsmol.zip > js > JSmolApi.js You might consider taking this opportunity to find out how jQuery works, if you are not familiar with it, and work more with those functions.

Table of equivalence old vs. new functions

Legacy (Jmol.js)	New (JSmol.min.js)
jmolInitialize	properties of the Info variable
jmolApplet	Jmol.getApplet or Jmol.getAppletHtml
jmolButton	Jmol.jmolButton
jmolLink	Jmol.jmolLink
jmolCheckbox	Jmol.jmolCheckbox
jmolRadioGroup	Jmol.jmolRadioGroup or Jmol.jmolRadio
jmolMenu	Jmol.jmolMenu
jmolSetAppletColor	color property of the Info variable
jmolResizeApplet	Jmol.resizeApplet
jmolHtml	Jmol.jmolHtml
jmolBr	Jmol.jmolBr
jmolScript	Jmol.script
jmolScriptWait	Jmol.scriptWait, but you should consider using Jmol.evaluateVar instead
jmolScriptWaitAsArray	Jmol.scriptWaitAsArray
jmolCommandInput	Jmol.jmolCommandInput
jmolSaveOrientation	use Jmol.script with save orientation command
jmolRestoreOrientation	use Jmol.script with restore orientation command
jmolRestoreOrientationDelayed	use Jmol.script with restore orientation command
jmolSetDocument	Jmol.setDocument, usually in combination with Jmol.getAppletHtml

Conversion using the Jmol2.js 'adapter' library

What has been just described (i.e., writing custom functions that allow to keep using the old calls as used with Jmol.js) has been implemented in a special new Jmol2.js 'adapter' library. If you use this, you can leave your existing calls to jmolApplet(), jmolButton(), jmolLink() etc. You just need to:

method A:	method B:
Step 1 In all your pages, add a call to JSmol.min.js In all your pages, change the existing call to Jmol.js into Jmol2.js	Step 1 Open in a text editor both JSmol.min.js, Jmol2.js and a new blank document. Combine in this document the contents of JSmol.min.js followed by the contents of Jmol2.js. Save this new document as Jmol.js Do not change your pages, keep the existing call to Jmol.js
Step 2: Add the JSmol files and folders as appropriate †	Step 2: Add the JSmol files and folders as appropriate †

(†) That is described in the Installation and Initialization sections of this page.

For more details, read inside the Jmol2.js file itself.

Locations to get Jmol2.js :

• In the Jmol download, Jmol-14.x.x-binary.zip > jsmol.zip > jsmol\js\Jmol2.js
• In the JSmol repository
• at StOlaf

Upgrading Jmol without using JSmol

If you have a "legacy" site that uses Jmol.js, and you would prefer to stick with Java and just upgrade your site so that it still works, then all you have to do is the following:

• Download the latest Jmol ZIP file distribution.
• Extract all the JmolAppletSigned0*.jar files in the applet directory (you should not be using the JmolApplet0*.jar files any more, unless you are certain what you are doing, since the unsigned applet will be blocked in browsers).
• Use the most recent version of Jmol.js that you have, or retrieve it from St. Olaf.
• Upgrade your site's Jmol.js and your JAR files with the files you have extracted.

Everything should work as before, but users will see a much kinder, more welcoming warning message the first time they access the new applet. Of course they will still have to give permission for the applet to be run, maybe in several dialogs. Please be aware that most users will not be able to see Jmol applets in their browser.

Contributors

AngelHerraez