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- version 11.2.13 of Jmol

    1: ==============================================================================
    2: ===                                  Jmol                                  ===
    3: ==============================================================================
    4: 
    5: 
    6: Jmol is an open-source molecule viewer and editor written in Java.
    7: 
    8: Full information is available at http://www.jmol.org/
    9: 
   10: Usage questions and comments should be posted to jmol-users@lists.sourceforge.net
   11: 
   12: Development questions, suggestions and comments should be posted
   13: to jmol-developers@lists.sf.net
   14: 
   15: 
   16: List of files included:
   17: -------------------
   18: 
   19: - README.txt
   20: 	This file.
   21: 
   22: - COPYRIGHT.txt
   23: 	Copyright informations.
   24: 
   25: - LICENSE.txt
   26: 	GNU LGPL (terms of license for use and distribution of Jmol).
   27: 		
   28: - Jmol.jar
   29: 	  Executable file for the Jmol application (a program written in Java). 
   30: 	This works as any other program: opens in its own window, can be 
   31: 	resized or minimized, admits drag-and-drop, has a top menu bar, 
   32: 	can open and save files, etc. It can be run from the command line 
   33: 	(particulary, using the shell or batch files described below), 
   34: 	but if Java is properly configured in your system, it's usually 
   35: 	enough to double-click on this file.
   36: 
   37: - jmol
   38: 	(Some kind of batch file to start Jmol application)
   39: 	
   40: - jmol.bat
   41: 	A batch file to start Jmol application under Windows. 
   42: 		
   43: - jmol.mac
   44: 	(Some kind of batch file to start Jmol application)
   45: 		
   46: - jmol.sh
   47: 	  A shell script to start Jmol application under Unix-like systems, 
   48: 	like Linux, BSD, Solaris and Cygwin for Windows.
   49: 
   50: - JmolApplet.jar
   51: 	  The applet, i.e. a version of the program that will only run 
   52: 	when embedded in a web page. 
   53: 	  This is an all-in-one (or monolithic) file, kept mainly for 
   54: 	compatibility with old pages that call it explicitly. Current 
   55: 	recommended procedure is to use the split version (JmolApplet0.jar etc.,
   56: 	described below). In particular, Jmol.js uses the split version.
   57: 	  You may wish to use this if you want to keep your website simple or you 
   58: 	just want to upload a single jar file whenever new versions are released. 
   59: 	However, this will load Jmol somewhat slower than the split versions, 
   60: 	as all the program components must get loaded onto a user's machine 
   61: 	before any structure is displayed.
   62: 	  To invoke JmolApplet.jar from Jmol.js, either:
   63: 	a) put it in the folder containing the HTML page requiring it and 
   64: 		do not use jmolInitialize()
   65: 	or
   66: 	b) identify it explicitly in jmolInitialize(), for example:
   67: 		jmolInitialize("folder-containing-jar-files", "JmolApplet.jar")
   68: 
   69: - JmolAppletSigned.jar
   70: 	  An equivalent version of the applet, but this is a "signed" or 
   71: 	"trusted" applet (a term in Java security language). This means it 
   72: 	must be authorized by the web page visitor for it to run, but then 
   73: 	it will have less security restrictions for file access. For example, 
   74: 	it can access files on any part of the user's computer or from any 
   75: 	other web server.
   76: 	  Typically users get a message asking if they want to accept the 
   77: 	"certificate" or if they "trust" the applet, but this security feature 
   78: 	is not always enabled. If you decide to use JmolAppletSigned.jar 
   79: 	you should keep this in mind. 
   80: 	  Other than reading files, Jmol does not currently utilize other capabilities 
   81: 	of signed applets, such as accessing the System clipboard or writing files. 
   82: 	Use only if you know what you are doing and have considered the security issues.
   83: 	  To invoke JmolAppletSigned.jar from Jmol.js, use:
   84: 		jmolInitialize("folder-containing-jar-files", "JmolAppletSigned.jar")
   85: 		                  
   86: - Jmol.js
   87: 	  The utilities library, written in JavaScript language, that assists in 
   88: 	the preparation of web pages that use Jmol applet, without the need to 
   89: 	know and write detailed JmolApplet code.
   90: 	  This library uses by default the split version of the applet (either
   91: 	unsigned or signed).
   92: 	  Fully documented at http://jmol.org/jslibrary/ 
   93: 
   94: - JmolApplet0.jar  and
   95:   JmolApplet0(severalSuffixes).jar
   96: 	  The applet is divided up into several pieces according to their function, 
   97: 	so that if a page does not require a component, that component is 
   98: 	not downloaded from the server. It is still recommended that you put 
   99: 	all JmolApplet0*.jar files on your server, even if your page does not use 
  100: 	the capabilities provided by some of the files, because the pop-up menu 
  101: 	and Jmol console both allow users to access parts of Jmol you might 
  102: 	not have considered.
  103: 	  The set of these files is equivalent to the single JmolApplet.jar.
  104: 	  This split version is the one that will be used by default if you use 
  105: 	Jmol.js. For that, use the simplest form of jmolInitialize(), just 
  106: 	indicating the folder containing the set of jar files:
  107: 		jmolInitialize("folder-containing-jar-files")
  108: 	for example,
  109: 		jmolInitialize(".")  
  110: 			(if jar files are in the same folder as the web page)
  111: 		jmolInitialize("../jmol") 
  112: 			(if jar files are in a parallel folder, named 'jmol')
  113:   
  114: - JmolAppletSigned0.jar  and
  115:   JmolAppletSigned0(severalSuffixes).jar
  116: 	  The signed version of the split applet. This version allows the user 
  117: 	to access files anywhere on the computer and from any location on the web. 
  118: 	Typically, users get a message asking if they want to accept the certificate 
  119: 	for **each** of the (currently 16) loadable jar files. For this reason, this 
  120: 	version may not be of general use.
  121: 	  The set of these files is equivalent to the single JmolAppletSigned.jar.
  122: 	  To use this with Jmol.js, use either:
  123: 	a) jmolInitialize("folder-containing-jar-files", true)
  124: 	or
  125: 	b) jmolInitialize("folder-containing-jar-files", "JmolAppletSigned0.jar")
  126: 
  127: ---------------------------
  128: Given the descriptions, you will realize that the distribution package contains 
  129: 4 full copies of the applet (signed or unsigned, split or not).
  130: ---------------------------