Jmol JavaScript Object

Jmol Javascript Object is a set of javascript functions and utilities refactored and reorganized into a single javascript object. It supersedes the former Jmol.js javascript library as it allows for a cleaner, more efficient way to interact with the applet from javascript, and abstracts the view of a molecular model so that the applet could be seamlessly replaced by an image, or a third party visualization method depending on client's browser resources.

Installation

These files must be accessible to the html page. Note that Java scurity policy imposes limitations on the folder location of files. The JavaScript files should be in the following order:

• JmolApplet.jar or JmolAppletSigned.jar or JmolApplet0*.jar or JmolAppletSigned0*.jar

(That is a set of files, where the * stands for several suffixes. You may need to read about signed vs. unsigned applet.)

• JmolCore.js (required)
• JmolApplet.js (required)
• JmolControls.js (optional -- required if any buttons or links or other input methods will be used)
• JmolApi.js (required)

Initialization

Basic

The html page must reference (usually with a script tag in the head section) the javascript libraries:

• JmolCore.js essential
• JmolApplet.js essential, must go after JmolCore
• JmolApi.js essential, must go after JmolCore
• JmolControls.js optional, must go after JmolCore; only needed if you will insert user interface controls like buttons, links, menus, etc.

Using the ChemDoodle alternative

The html page must reference these additional javascript libraries:

• jQuery.min.js required; unrelated to Jmol and not included in Jmol distribution. The jQuery JavaScript Library.
• gl-matrix-min.js required; not included in Jmol distribution. Javascript Matrix and Vector library for High Performance WebGL apps.
• mousewheel.js required; not included in Jmol distribution. jQuery Mouse Wheel Plugin.
• ChemDoodleWeb.js required; from ChemDoodle Web Components; must go after the above three.
• JmolCD.js required; must go after JmolApplet and all those above.

Using the GLmol alternative

The html page must reference these additional javascript libraries:

• jQuery.min.js required; unrelated to Jmol and not included in Jmol distribution. The jQuery JavaScript Library.
• Three49custom.js required; not included in Jmol distribution; available with GLmol, below.
• GLmol.js required; from GLmol - Molecular Viewer on WebGL/Javascript; must go after the above two.
• JmolGlmol.js required; must go after JmolApplet and all those above.

Contributors

AngelHerraez, Hansonr, Hansonrstolaf, Cudo29, Ceroni, Ppillot