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=== Jmol ===
==============================================================================


Jmol is an open-source molecule viewer and editor written in Java.

Full information is available at http://www.jmol.org/

Usage questions and comments should be posted to jmol-users@lists.sourceforge.net

Development questions, suggestions and comments should be posted
to jmol-developers@lists.sf.net


List of files included:
-------------------

- README.txt
This file.

- COPYRIGHT.txt
Copyright informations.

- LICENSE.txt
GNU LGPL (terms of license for use and distribution of Jmol).

- Jmol.jar
Executable file for the Jmol application (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, has a top menu bar,
can open and save files, etc. It can be run 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 this file.

- jmol
(Some kind of batch file to start Jmol application)

- jmol.bat
A batch file to start Jmol application under Windows.

- jmol.mac
(Some kind of batch file to start Jmol application)

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

- 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.,
described below). 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,
as all the program components 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 folder containing the HTML page requiring it and
do not use jmolInitialize()
or
b) identify it explicitly in jmolInitialize(), for example:
jmolInitialize("folder-containing-jar-files", "JmolApplet.jar")

- JmolAppletSigned.jar
An equivalent version of the applet, but this is a "signed" or
"trusted" 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 computer 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. If you decide to use JmolAppletSigned.jar
you should keep 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("folder-containing-jar-files", "JmolAppletSigned.jar")

- Jmol.js
The utilities library, written in JavaScript language, that assists in
the preparation 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 (either
unsigned or signed).
Fully documented at http://jmol.org/jslibrary/

- JmolApplet0.jar and
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 folder containing the set of jar files:
jmolInitialize("folder-containing-jar-files")
for example,
jmolInitialize(".")
(if jar files are in the same folder as the web page)
jmolInitialize("../jmol")
(if jar files are in a parallel folder, named 'jmol')

- JmolAppletSigned0.jar and
JmolAppletSigned0(severalSuffixes).jar
The signed version of the split applet. This version allows the user
to access files anywhere on the computer and from any location on the web.
Typically, users get a message asking if they want to accept the certificate
for **each** of the (currently 16) loadable jar files. For this reason, this
version may not be of general use.
The set of these files is equivalent to the single JmolAppletSigned.jar.
To use this with Jmol.js, use either:
a) jmolInitialize("folder-containing-jar-files", true)
or
b) jmolInitialize("folder-containing-jar-files", "JmolAppletSigned0.jar")

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