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version 1.1, 2005/07/01 20:23:42
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version 1.2, 2007/10/11 00:42:00
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| Jmol |
==============================================================================
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=== Jmol ===
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| Jmol is an open-source molecule viewer and editor written in Java. |
==============================================================================
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| Please check out www.jmol.org |
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Jmol is an open-source molecule viewer and editor written in Java.
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| Usage questions/comments should be posted to jmol-users@lists.sourceforge.net |
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Full information is available at http://www.jmol.org/
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| Development questions/suggestions/comments should be posted |
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| to jmol-developers@lists.sf.net |
Usage questions and comments should be posted to jmol-users@lists.sourceforge.net
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Development questions, suggestions and comments should be posted
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to jmol-developers@lists.sf.net
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List of files included:
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-------------------
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- README.txt
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This file.
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- COPYRIGHT.txt
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Copyright informations.
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- LICENSE.txt
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GNU LGPL (terms of license for use and distribution of Jmol).
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- Jmol.jar
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Executable file for the Jmol application (a program written in Java).
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This works as any other program: opens in its own window, can be
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resized or minimized, admits drag-and-drop, has a top menu bar,
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can open and save files, etc. It can be run from the command line
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(particulary, using the shell or batch files described below),
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but if Java is properly configured in your system, it's usually
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enough to double-click on this file.
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- jmol
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(Some kind of batch file to start Jmol application)
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- jmol.bat
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A batch file to start Jmol application under Windows.
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- jmol.mac
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(Some kind of batch file to start Jmol application)
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- jmol.sh
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A shell script to start Jmol application under Unix-like systems,
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like Linux, BSD, Solaris and Cygwin for Windows.
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- JmolApplet.jar
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The applet, i.e. a version of the program that will only run
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when embedded in a web page.
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This is an all-in-one (or monolithic) file, kept mainly for
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compatibility with old pages that call it explicitly. Current
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recommended procedure is to use the split version (JmolApplet0.jar etc.,
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described below). In particular, Jmol.js uses the split version.
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You may wish to use this if you want to keep your website simple or you
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just want to upload a single jar file whenever new versions are released.
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However, this will load Jmol somewhat slower than the split versions,
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as all the program components must get loaded onto a user's machine
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before any structure is displayed.
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To invoke JmolApplet.jar from Jmol.js, either:
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a) put it in the folder containing the HTML page requiring it and
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do not use jmolInitialize()
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or
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b) identify it explicitly in jmolInitialize(), for example:
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jmolInitialize("folder-containing-jar-files", "JmolApplet.jar")
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- JmolAppletSigned.jar
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An equivalent version of the applet, but this is a "signed" or
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"trusted" applet (a term in Java security language). This means it
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must be authorized by the web page visitor for it to run, but then
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it will have less security restrictions for file access. For example,
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it can access files on any part of the user's computer or from any
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other web server.
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Typically users get a message asking if they want to accept the
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"certificate" or if they "trust" the applet, but this security feature
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is not always enabled. If you decide to use JmolAppletSigned.jar
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you should keep this in mind.
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Other than reading files, Jmol does not currently utilize other capabilities
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of signed applets, such as accessing the System clipboard or writing files.
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Use only if you know what you are doing and have considered the security issues.
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To invoke JmolAppletSigned.jar from Jmol.js, use:
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jmolInitialize("folder-containing-jar-files", "JmolAppletSigned.jar")
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- Jmol.js
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The utilities library, written in JavaScript language, that assists in
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the preparation of web pages that use Jmol applet, without the need to
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know and write detailed JmolApplet code.
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This library uses by default the split version of the applet (either
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unsigned or signed).
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Fully documented at http://jmol.org/jslibrary/
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- JmolApplet0.jar and
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JmolApplet0(severalSuffixes).jar
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The applet is divided up into several pieces according to their function,
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so that if a page does not require a component, that component is
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not downloaded from the server. It is still recommended that you put
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all JmolApplet0*.jar files on your server, even if your page does not use
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the capabilities provided by some of the files, because the pop-up menu
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and Jmol console both allow users to access parts of Jmol you might
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not have considered.
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The set of these files is equivalent to the single JmolApplet.jar.
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This split version is the one that will be used by default if you use
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Jmol.js. For that, use the simplest form of jmolInitialize(), just
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indicating the folder containing the set of jar files:
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jmolInitialize("folder-containing-jar-files")
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for example,
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jmolInitialize(".")
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(if jar files are in the same folder as the web page)
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jmolInitialize("../jmol")
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(if jar files are in a parallel folder, named 'jmol')
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- JmolAppletSigned0.jar and
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JmolAppletSigned0(severalSuffixes).jar
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The signed version of the split applet. This version allows the user
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to access files anywhere on the computer and from any location on the web.
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Typically, users get a message asking if they want to accept the certificate
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for **each** of the (currently 16) loadable jar files. For this reason, this
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version may not be of general use.
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The set of these files is equivalent to the single JmolAppletSigned.jar.
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To use this with Jmol.js, use either:
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a) jmolInitialize("folder-containing-jar-files", true)
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or
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b) jmolInitialize("folder-containing-jar-files", "JmolAppletSigned0.jar")
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---------------------------
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Given the descriptions, you will realize that the distribution package contains
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4 full copies of the applet (signed or unsigned, split or not).
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---------------------------
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