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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: ---------------------------
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