1==============================================================================
2=== Jmol ===
3==============================================================================
4
5
6Jmol is an open-source molecule viewer and editor written in Java.
7
8Full information is available at http://www.jmol.org/
9
10Usage questions and comments should be posted to jmol-users@lists.sourceforge.net
11
12Development questions, suggestions and comments should be posted
13to jmol-developers@lists.sf.net
14
15
16List 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---------------------------
128Given the descriptions, you will realize that the distribution package contains
1294 full copies of the applet (signed or unsigned, split or not).
130---------------------------
131