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 ==============================================================================  ==============================================================================
 ===                                  Jmol                                  ===  ===                                  Jmol                                  ===
 ==============================================================================  ==============================================================================
         Jmol: an open-source Java viewer for chemical structures in 3D,
        with features for chemicals, crystals, materials and biomolecules.
   ==============================================================================
   
 Jmol is an open-source molecule viewer and editor written in Java.  Jmol is an open-source molecule viewer and editor written in Java.
   
Line 16  to jmol-developers@lists.sf.net Line 18  to jmol-developers@lists.sf.net
 List of files included:  List of files included:
 -------------------  -------------------
   
 - README.txt  
  This file.  
   
 - COPYRIGHT.txt  1 == Files with information ==
  Copyright informations.  
   1.1 === README.txt ===
   This file.
   
   1.2 === LEAME.txt ===
   The Spanish version of README.txt
   
   1.3 === COPYRIGHT.txt ===
   The copyright explanations regarding Jmol and its 3rd-party components.
   
   1.4 === LICENSE.txt ===
   The GNU Lesser General Public License, under which Jmol is released.
   
   1.5 === CHANGES.txt ===
   A list with a history of the feature additions in each version of Jmol.
   
   1.6 === README-CHEMDOODLE.txt ===
   Instructions about using the ChemDoodle plug-in together with Jmol applets,
   and about the license for ChemDoodle (which is different from the Jmol license).
   
   
   2 == Batch and shell files ==
   These can be used to start Jmol application from a command line and,
   particularly, to impose a certain combination of parameters
   (see http://wiki.jmol.org/index.php/Jmol_Application#Command_line_options).
   
   2.1 === jmol ===
   ???? (Some kind of batch file)
   
   2.2 === jmol.bat ===
   A batch file to start Jmol application under Windows.
   
   2.3 === jmol.mac ===
   ??? (Some kind of batch file, for the MacOS)
   
   2.4 === jmol.sh ===
   A shell script to start Jmol application under Unix-like systems, like Linux,
   BSD, Solaris and Cygwin for Windows.
   
   
   3 == Files of Jmol application ==
   This is used as a standalone program.
   
   3.1 === Jmol.jar ===
   The application executable file (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 of files over it, has a top menu bar, can open and save files,
   etc. It can be open from the command line (particulary, using the shell or batch
   files described above), but if Java is properly configured in your system, it's
   usually enough to double-click on the file
   (see http://wiki.jmol.org/index.php/Jmol_Application#Starting_Jmol_Application
   for more details).
   
   3.2 === JmolData.jar ===
   This is a slimmed down version of Jmol.jar that lacks all visualization
   capabilities. So, it betrays the whole (classic) concept of what Jmol is, but
   with JmolData and some clever scripting you can get just about any information
   you want out of a model and output it any way you want.
   
   It operates only from the command line, designed for extracting data from a
   model or set of models. You are limited to commands that don't have to do with
   visualization: there are bonds but no "sticks", atoms but no "dots", helices but
   no "cartoons".
   
   
   4 == Files of Jmol applet ==
   These are used inside web pages, and include:
     Applet files  |  Core Javascript libraries  |  Optional Javascript libraries
   
   4.1 === Applet files ===
   
   4.1.1 ==== JmolApplet0.jar, JmolApplet0(severalSuffixes).jar ====
   The applet, i.e. a version of the program that will only run when embedded in
   a web page.
   
   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.
   
   This split version is the one that will be used by default if you use Jmol.js
   (which is the recommended method).
   For that, use the simplest form of jmolInitialize(), just indicating the
   directory or folder containing the set of jar files:
    jmolInitialize("directory-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')
   
   4.1.2 ==== JmolAppletSigned0.jar, JmolAppletSigned0(severalSuffixes).jar ====
   An equivalent version of the applet, but this is a "signed" 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 hard
    disk 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 (''see notes below''). JmolAppletSigned.jar should
    be used with this in mind. Other than reading files, Jmol does not currently
    use 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 use this with Jmol.js, use the form:
    jmolInitialize("directory-containing-jar-files", true)
   or
    jmolInitialize("directory-containing-jar-files", "JmolAppletSigned0.jar")
   
   Notes:
   * The security feature requesting to trust the applet may not always be enabled
     on users' systems.
   * The message requesting permission will be displayed for each of the 14 (or
     more) loadable files.
   * The user may have the option to trust the applet permanently and so avoid
     having to give permission every time (s)he visits a page that uses Jmol.
   
   4.1.3 ==== JmolApplet.jar ====
   This is an all-in-one or monolithic file, kept mainly for compatibility with old
   pages that call it explicitly.
   This single file is equivalent to the whole set of JmolApplet0*.jar files,
   explained above.
   The recommended procedure is not to use this monolithic file, but the split
   version (JmolApplet0.jar etc.). In particular, Jmol.js uses the split version
   by default.
   
   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 slower than the split versions (described above),
   as all the modules (adding up to 2.4 MB), needed or not, 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 directory containing the HTML page requiring it and do not use
      jmolInitialize(),
   
   or
   
   b) identify it explicitly in jmolInitialize(), for example:
    jmolInitialize("directory-containing-jar-files", "JmolApplet.jar")
   
   4.1.4 ==== JmolAppletSigned.jar ====
   An equivalent version of the monolithic applet, but this is a "signed" 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 hard
    disk 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.
   JmolAppletSigned.jar should be used with 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("directory-containing-jar-files", "JmolAppletSigned.jar")
   
   4.1.5 ==== Notes ====
   # Given the descriptions, you will realize that the distribution package
     contains 4 full copies of the applet (signed or unsigned, split or not).
   
 - 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  4.2 === Core Javascript libraries ===  
   JmolAppletSigned0(severalSuffixes).jar  
   The signed version of the split applet. This version allows the user  4.2.1 ==== Jmol.js ====
  to access files anywhere on the computer and from any location on the web.  The classic library, written in JavaScript language, that assists in the
  Typically, users get a message asking if they want to accept the certificate  programming of web pages that use Jmol applet, without the need to know and
  for **each** of the (currently 16) loadable jar files. For this reason, this  write detailed JmolApplet code.
  version may not be of general use.  
   The set of these files is equivalent to the single JmolAppletSigned.jar.  This library uses by default the split version of the applet (unsigned or
   To use this with Jmol.js, use either:  signed).
  a) jmolInitialize("folder-containing-jar-files", true)  
  or  Fully documented at http://jmol.org/jslibrary/
  b) jmolInitialize("folder-containing-jar-files", "JmolAppletSigned0.jar")  
   Jmol.js is phased out in Jmol v13, in favour of the object-oriented method
 ---------------------------  and set of .js files (described next).
 Given the descriptions, you will realize that the distribution package contains  
 4 full copies of the applet (signed or unsigned, split or not).  4.2.2 ==== JmolApplet.js ====
 ---------------------------  Creates the object for a Jmol applet.
    
   4.2.3 ==== JmolCore.js ====
   Contains functions that make the Jmol applets work but are not to be used by
   the webpage author (private functions).
   
   4.2.4 ==== JmolControls.js ====
   Support for user-interface controls like buttons, links, checkboxes, etc.
   
   4.2.5 ==== JmolApi.js ====
   Contains the Application Programming Interface, that is, functions that may be
   used by the webpage author to interface with the Jmol applets.
   
   
   4.3 === Optional Javascript libraries ===
   
   4.3.1 ==== JmolCD.js ====
   The ChemDoodle extension: provides the means for using ChemDoodle Web Components
   (that uses JavaScript + HTML5 canvas or WebGL) instead of the
   Jmol applets, for systems where Java is not available.
   
   4.3.2 ==== JmolGLmol.js ====
   The GLmol extension: provides the means for using GLmol (that uses WebGL +
   JavaScript) instead of the Jmol applets, for systems where Java is not available.
   
   4.3.3 ==== JmolJME.js ====
   Provides the means for adding a JME applet in the webpage (drawing of 2D chemical
   formulas) and communicate with Jmol applets.
   
   4.3.4 ==== JmolJSV.js ====
   Provides the means for adding a JSpecView applet (viewer for spectral data) in
   the webpage and communicate with Jmol applets.
   
   
   5 == Accessory apps and applets ==
   
   5.1 === ChimeToJmol.jar ===
   Undocumented and experimental.
   An application to convert Chime-using html pages into pages with JmolApplets.
   
   5.2 === JSpecViewApplet, JSpecViewAppletSigned ===
   Unsigned and signed versions of the JSpecView applet, a viewer for spectral data
   that may be intercommunicated with Jmol applets.
   (See supporting .js file above)
   
   5.3 === JmolSmilesApplet.jar ===
   This is currently not included in the distribution, but may be obtained from the
   development site.
   
   This is a lightweight applet, with no visible interface, that allows to check
   SMILES strings. This is particularly useful for comparison of stereochemistry,
   for example from structures drawn using the JME applet.
   
   The same functionality is included in the regular JmolApplet.
Removed from v.1.2  
changed lines
  Added in v.1.3

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