Files Description/Jmol 14

This information is also included in Jmol distribution README file.

Jmol + JSmol Documentation

• Description of files in Jmol+JSmol distribution
• File formats read or written by Jmol
• The Jmol scripting interface
  • Scripting as a programming language
  • Complete reference of scripting commands:
    • at St Olaf (primary site)
    • at Jena3D (mirror)
• Loading models directly from databases
• Mouse manual
• Default colors used by Jmol
• Atom sets predefined in Jmol
• Support for bond orders · isotopes · stereochemistry · hydrogen bonds
• Jmol as editor
• Multi-touch support
• Copying and pasting state scripts between applets.
• Backward compatibility (changes of behavior across versions)
• Features added since version 10
• Users mailing list (and a mirror)

Common files in Jmol distributions

(This refers to both jmol-x.x.x-binary.zip and jmol-x.x.x-binary.tar.gz;
jmol-x.x.x-full.tar.gz contains the full source code)

Jmol.jar

The application executable file (a program written in Java). This works as any other program: opens in its own window, can be resized or minimized, admits drag-and-drop of files over it, has a top menu, can open and save files, etc. It can be open from the command line (particulary, using the shell or batch files described below), but if Java is properly configured in your system, it's usually enough to double-click on the file.

JmolApplet.jar

The applet, i.e. a version of the program that will only run when embedded in a web page.

This is an all-in-one or monolithic file, kept mainly for compatibility with old pages that call it explicitly. Current recommended procedure is to use the split version (JmolApplet0.jar etc.). In particular, Jmol.js uses the split version.

You may wish to use this if you want to keep your website simple or you just want to upload a single jar file whenever new versions are released. However, this will load Jmol somewhat slower than the split versions (described below), as all the modules must get loaded onto a user's machine before any structure is displayed.

To invoke JmolApplet.jar from Jmol.js, either:

a) put it in the directory containing the HTML page requiring it and do not use jmolInitialize(),

or

b) identify it explicitly in jmolInitialize(), for example:

jmolInitialize("directory-containing-jar-files", "JmolApplet.jar")

JmolAppletSigned.jar

An equivalent version of the applet, but this is a "signed" applet (a term in Java security language). This means it must be authorized by the web page visitor for it to run, but then it will have less security restrictions for file access. For example, it can access files on any part of the user's hard disk or from any other web server.

Typically users get a message asking if they want to accept the "certificate" or if they "trust" the applet, but this security feature is not always enabled. JmolAppletSigned.jar should be used with this in mind. Other than reading files, Jmol does not currently utilize other capabilities of signed applets, such as accessing the System clipboard or writing files. Use only if you know what you are doing and have considered the security issues.

To invoke JmolAppletSigned.jar from Jmol.js, use:

jmolInitialize("directory-containing-jar-files", "JmolAppletSigned.jar")

Jmol.js

The library, written in JavaScript language, that assists in the programming of web pages that use Jmol applet, without the need to know and write detailed JmolApplet code.

This library uses by default the split version of the applet (unsigned or signed).

Fully documented at http://jmol.org/jslibrary/

jmol

???? (Some kind of batch file)

jmol.bat

A batch file to start Jmol application under Windows.

jmol.mac

??? (Some kind of batch file)

jmol.sh

A shell script to start Jmol application under Unix-like systems, like Linux, BSD, Solaris and Cygwin for Windows.

COPYRIGHT.txt

The copyright explanations.

LICENSE.txt

The GNU Lesser General Public License, under which Jmol is released.

README.txt

A general description of Jmol package and sources of information, including this file list documentation.

Files in recent Jmol versions

JmolApplet0.jar, JmolApplet0(severalSuffixes).jar

The applet is divided up into several pieces according to their function, so that if a page does not require a component, that component is not downloaded from the server. It is still recommended that you put all JmolApplet0*.jar files on your server even if your page does not use the capabilities provided by some of the files, because the pop-up menu and Jmol console both allow users to access parts of Jmol you might not have considered.

The set of these files is equivalent to the single JmolApplet.jar.

This split version is the one that will be used by default if you use Jmol.js. For that, use the simplest form of jmolInitialize(), just indicating the directory containing the set of jar files:

jmolInitialize("directory-containing-jar-files")

for example,

jmolInitialize(".")  // jar files are in the same folder as the web page 
jmolInitialize("../jmol") // jar files are in a parallel folder, named 'jmol'.

JmolAppletSigned0.jar, JmolAppletSigned0(severalSuffixes).jar

The signed version of the new split applet. This version allows the user to access files anywhere on a hard drive and from any location on the web. Typically users get a message asking if they want to accept the certificate for each of the 16 loadable files. For this reason, this version may not be of general use.

To use this with Jmol.js, use the form:

jmolInitialize("directory-containing-jar-files", true)

or

jmolInitialize("directory-containing-jar-files", "JmolAppletSigned0.jar")

JmolData.jar

This is a slimmed down version of Jmol.jar that lacks all visualization capabilities. So, it betrays the whole (classic) concept of what Jmol is, but with JmolData and some clever scripting you can get just about any information you want out of a model and output it any way you want.

It's a command-line-only operation, designed for extracting data from a model or set of models. You are limited to commands that don't have to do with visualization: there are bonds but no "sticks", atoms but no "dots", helices but no "cartoons".

Files specific to older versions

(up to Jmol 11.1.29)

JmolApplet0.jar, JmolApplet1.jar, ... JmolApplet6.jar, JmolApplet_i18n.jar

The applet divided up into several pieces, hopefully for faster loading. The set of these files is equivalent to the single JmolApplet.jar. This split version is used by default by Jmol.js.

JmolApplet_i18n.jar is the localization module of the applet (i.e., translation of the interface into several languages). This must accompany the JmolApplet#.jar set if you want the interface in a language different from English. (The language shown will depend on the operating system's language.)

JmolAppletSigned0.jar, JmolAppletSigned1.jar, ... JmolAppletSigned6.jar, JmolAppletSigned_i18n.jar

The signed version of the above split applet. (See JmolAppletSigned.jar above for description of what a "signed" applet is.)

Notes

1. Given the descriptions, you will realize that the distribution package contains 4 full copies of the applet (signed or unsigned, split or not).

Contributors

Zhang2010, AngelHerraez, Pimpim, NicolasVervelle