Difference between revisions of "Files Description"

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This information is also included in Jmol distribution {{File|README}} file.
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'''''For Jmol versions previous to 13.2, see [[Files_Description/Jmol_12]]'''''
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<!--This information is also included in Jmol distribution {{File|README}} file.-->
  
 
The Jmol distribution is available for download as 3 different files:
 
The Jmol distribution is available for download as 3 different files:
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=== jmol.sh ===
 
=== jmol.sh ===
 
A shell script to start Jmol application under Unix-like systems, like Linux, BSD, Solaris and Cygwin for Windows.
 
A shell script to start Jmol application under Unix-like systems, like Linux, BSD, Solaris and Cygwin for Windows.
 +
 +
Under Linux, there are a number of ways to start Jmol as a standalone program using the {{file|jmol.sh}} script:<br>
 +
(1)
 +
sh jmol.sh                      // start Jmol under the jmol-xxx folder
 +
sh yourpath/jmol-xxx/jmol.sh    // start Jmol from anywhere
 +
(2)
 +
chmod +x jmol.sh                // make the ''jmol.sh'' script executable
 +
jmol.sh                        // start Jmol inside the jmol-xxx directory, or 
 +
yourpath/jmol-xxx/jmol.sh      // start Jmol anywhere
 +
(3)
 +
chmod +x jmol.sh                // make the ''jmol.sh'' script executable 
 +
ln -s yourpath/jmol-xxx/jmol.sh /usr/local/bin/jmol.sh //create a symbolic link under /usr/local/bin
 +
Add the following shell variable in the shell script {{file|$HOME/.bash_profile}}
 +
export JMOL_HOME="/yourpath/jmol-xxx/"
 +
Reboot your computer or execute
 +
source $HOME/.bash_profile
 +
Then
 +
jmol.sh                          // start Jmol anywhere
 +
(4) Move the {{file|jmol-xxx}} folder to {{file|/usr/bin/}} or {{file|/usr/local/bin/}}
 +
chmod +x jmol.sh                  // make the ''jmol.sh'' script executable
 +
ln -s /usr/bin/jmol-xxx/jmol.sh /usr/bin/jmol.sh          // or
 +
ln -s /usr/bin/jmol-xxx/jmol.sh /usr/local/bin/jmol.sh    // or
 +
ln -s /usr/local/bin/jmol-xxx/jmol.sh /usr/bin/jmol.sh    //or
 +
ln -s /usr/local/bin/jmol-xxx/jmol.sh /usr/local/bin/jmol.sh
 +
jmol.sh                          // start Jmol from anywhere
  
 
<br>
 
<br>
−
Under Linux, there are a number of ways to start jmol as a standalone program using ''jmol.sh'' script:<br>
 
−
(1) execute
 
−
<code>'''''sh jmol.sh'''''</code>
 
−
inside the jmol-xxx directory
 
−
<code>'''''sh yourpath/jmol-xxx/jmol.sh''''' </code>
 
−
from any other places). 
 
−
 
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(2) execute '''''chmod +x jmol''''' to make the jmol.sh script executable, then execute ''jmol.sh'' inside the jmol-xxx directory (or call the jmol.sh script anywhere with its path name).
 
−
 
−
(3) as (2), make the jmol.sh executable, then create a symbolic link under /usr/local/bin by executing the following command: <br>
 
−
'''''ln -s yourpath/jmol-xxx/jmol.sh /usr/local/bin/jmol.sh'''''<br>
 
−
Then add the following shell varible in your shell script $HOME/.bash_profile <br>
 
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'''''export JMOL_HOME="/yourpath/jmol-xxx/"''''' <br>
 
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reboot your computer or execute: <br>
 
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'''''source $HOME/.bash_profile''''' <br>
 
−
Then you can start jmol by calling ''jmol.sh'' anywhere. <br>
 
−
 
−
(4)As (2), make the jmol.sh executable. Move the jmol program folder jmol-xxx to /usr/bin/ or /usr/local/bin/. Then make a symbolic link of jmol.sh under the /usr/bin/ or /usr/local/bin/ directory:<br>
 
−
'''''ln -s /usr/bin/jmol-xxx/jmol.sh /usr/bin/jmol.sh''''' or '''''ln -s /usr/bin/jmol-xxx/jmol.sh /usr/local/bin/jmol.sh''''' <br>
 
−
or
 
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'''''ln -s /usr/local/bin/jmol-xxx/jmol.sh /usr/bin/jmol.sh''''' or '''''ln -s /usr/local/bin/jmol-xxx/jmol.sh /usr/local/bin/jmol.sh''''' <br>
 
−
Then call the ''jmol.sh'' link from anywhere to start jmol.
 
−
 
 
== Files of Jmol application ==
 
== Files of Jmol application ==
 
This is used as a standalone program.
 
This is used as a standalone program.
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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".
 
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".
  
−
<br>
+
=== JmolLib.jar ===
−
== Files of Jmol applet ==
+
This is a library, meant to make Jmol a module or part of a bigger project, that is, to integrate Jmol viewer inside another software.
−
This is used inside web pages.
 
−
 
 
−
=== Jmol.js ===
 
−
The library, written in JavaScript language, that assists in the programming of web pages that use Jmol applet, without the need to know and write detailed JmolApplet code.
 
−
 
 
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This library uses by default the split version of the applet (unsigned or signed).
 
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Fully documented at http://jmol.org/jslibrary/
 
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=== JmolApplet0.jar, JmolApplet0''(severalSuffixes)''.jar ===
 
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The applet, i.e. a version of the program that will only run when embedded in a web page.
 
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The applet is divided up into several pieces according to their
 
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function, so that if a page does not require a component, that
 
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component is not downloaded from the server.
 
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It is still recommended that you put all JmolApplet0*.jar
 
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files on your server even if your page does not use the capabilities
 
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provided by some of the files, because the pop-up menu and Jmol console
 
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both allow users to access parts of Jmol you might not have considered.
 
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This split version is the one that will be used by default if you use {{File|Jmol.js}} (which is the recommended method).
 
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For that, use the simplest form of jmolInitialize(), just
 
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indicating the directory or folder containing the set of jar files:
 
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jmolInitialize("directory-containing-jar-files")
 
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for example,
 
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jmolInitialize(".")  // jar files are in the same folder as the web page
 
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jmolInitialize("../jmol") // jar files are in a parallel folder, named 'jmol'.
 
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=== JmolAppletSigned0.jar, JmolAppletSigned0''(severalSuffixes)''.jar ===
 
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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.
 
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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 (''see notes below'').
 
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JmolAppletSigned.jar should be used with this in mind. Other than reading
 
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files, Jmol does not currently use other capabilities of signed
 
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applets, such as accessing the system clipboard or writing files. Use only
 
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if you know what you are doing and have considered the security issues.
 
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To use this with Jmol.js, use the form:
 
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jmolInitialize("directory-containing-jar-files", true)
 
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or
 
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jmolInitialize("directory-containing-jar-files", "JmolAppletSigned0.jar")
 
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:''Notes:''
 
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* The security feature requesting to trust the applet may not always be enabled on users' systems.
 
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* The message requesting permission will be displayed for '''each''' of the 14 (or more) loadable files.
 
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* 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.
 
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=== JmolApplet.jar ===
 
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This is an all-in-one or monolithic file, kept mainly for compatibility with old pages that call it explicitly.
 
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This single file is equivalent to the whole set of {{File|JmolApplet0*.jar}} files, explained above.
 
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The recommended procedure is not to use this monolithic file, but the split version ({{File|JmolApplet0.jar}} etc.). In particular, {{File|Jmol.js}} uses the split version by default.
 
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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.
 
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However, this will load Jmol slower than the split versions (described above), as all the modules (adding up to 2 MB), needed or not, must get loaded onto a user's machine 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 directory 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("directory-containing-jar-files", "JmolApplet.jar")
 
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=== 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.
 
−
 
 
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To invoke JmolAppletSigned.jar from Jmol.js, use:
 
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jmolInitialize("directory-containing-jar-files", "JmolAppletSigned.jar")
 
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=== JmolSmilesApplet.jar ===
 
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''This is currently not included in the distribution, but may be obtained from the development site.''
 
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This is a lightweight applet, with no visible interface, that allows
 
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to check SMILES strings. This is particularly useful for comparison of stereochemistry, for example from structures drawn using the [[File_formats/Coordinates#JME|JME applet]].
 
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The same functionality is included in the regular JmolApplet.
 
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<br>
 
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== Files specific to older versions ==
 
−
Versions before Jmol 11.1.30 had a different setup for the split applet files:
 
−
 
 
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=== JmolApplet0.jar, JmolApplet1.jar, ... JmolApplet6.jar, JmolApplet_i18n.jar ===
 
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The applet divided up into several pieces, hopefully for faster loading. The set of these files is equivalent to the single {{File|JmolApplet.jar}}. This split version is used by default by {{File|Jmol.js}}.
 
−
 
 
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{{File|JmolApplet_i18n.jar}} is the localization module of the applet (i.e., translation of the interface into several languages).
 
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This must accompany the {{File|JmolApplet#.jar}} set if you want the interface in a language different from English. (The language shown will depend on the operating system's language.)
 
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=== JmolAppletSigned0.jar, JmolAppletSigned1.jar, ... JmolAppletSigned6.jar, JmolAppletSigned_i18n.jar ===
 
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The signed version of the above split applet. (See JmolAppletSigned0.jar above for description of what a "signed" applet is.)
 
  
 
<br>
 
<br>
−
== Notes ==
+
== Files of the Jmol object ==
 +
=== jsmol.zip ===
 +
This file includes in compressed form all the files for using J(S)mol inside web pages, such as:
 +
* Applet files (for the Java modality of Jmol object)
 +
* Javascript libraries (for the definition of the Jmol object in all cases, and specifically for the HTML5 modality of Jmol object)
  
−
# Given the descriptions, you will realize that the distribution package contains 4 full copies of the applet (signed or unsigned, split or not).
+
For details on the files contained, their purpose and how to use them, please see [[Jmol_JavaScript_Object#Installation]]

Latest revision as of 20:42, 11 January 2014

For Jmol versions previous to 13.2, see Files_Description/Jmol_12


The Jmol distribution is available for download as 3 different files:

  • File icon.gifjmol-x.x.x-binary.zip contains all files needed for using Jmol, compressed using the zip format.
  • File icon.gifjmol-x.x.x-binary.tar.gz contains the same files, in a tar structure and compressed using the gzip format.
  • File icon.gifjmol-x.x.x-full.tar.gz contains the full source code. This will only be useful to developers and programmers wanting to study Jmol programming design or to modify Jmol.

Following is a description of the files contained in any of the first two downloadable files.

Jmol + JSmol Documentation

Files with information

COPYRIGHT.txt

The copyright explanations regarding Jmol and its 3rd-party components.

LICENSE.txt

The GNU Lesser General Public License, under which Jmol is released.

README.txt

A general description of Jmol package and sources of information, including this file list documentation.

LEAME.txt

The Spanish version of README.txt

CHANGES.txt

A list with a history of the feature additions in each version of Jmol.


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 command line options).

jmol

???? (Some kind of batch file)

jmol.bat

A batch file to start Jmol application under Windows.

jmol.mac

??? (Some kind of batch file)

jmol.sh

A shell script to start Jmol application under Unix-like systems, like Linux, BSD, Solaris and Cygwin for Windows.

Under Linux, there are a number of ways to start Jmol as a standalone program using the File icon.gifjmol.sh script:
(1) 

sh jmol.sh                      // start Jmol under the jmol-xxx folder 
sh yourpath/jmol-xxx/jmol.sh    // start Jmol from anywhere

(2) 

chmod +x jmol.sh                // make the jmol.sh script executable 
jmol.sh                         // start Jmol inside the jmol-xxx directory, or  
yourpath/jmol-xxx/jmol.sh       // start Jmol anywhere

(3) 

chmod +x jmol.sh                // make the jmol.sh script executable  
ln -s yourpath/jmol-xxx/jmol.sh /usr/local/bin/jmol.sh //create a symbolic link under /usr/local/bin

Add the following shell variable in the shell script File icon.gif$HOME/.bash_profile 

export JMOL_HOME="/yourpath/jmol-xxx/"

Reboot your computer or execute 

source $HOME/.bash_profile

Then 

jmol.sh                          // start Jmol anywhere

(4) Move the File icon.gifjmol-xxx folder to File icon.gif/usr/bin/ or File icon.gif/usr/local/bin/ 

chmod +x jmol.sh                  // make the jmol.sh script executable 
ln -s /usr/bin/jmol-xxx/jmol.sh /usr/bin/jmol.sh          // or
ln -s /usr/bin/jmol-xxx/jmol.sh /usr/local/bin/jmol.sh    // or
ln -s /usr/local/bin/jmol-xxx/jmol.sh /usr/bin/jmol.sh    //or
ln -s /usr/local/bin/jmol-xxx/jmol.sh /usr/local/bin/jmol.sh
jmol.sh                          // start Jmol from anywhere


Files of Jmol application

This is used as a standalone program.

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 Starting Jmol Application for more details).

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".

JmolLib.jar

This is a library, meant to make Jmol a module or part of a bigger project, that is, to integrate Jmol viewer inside another software.


Files of the Jmol object

jsmol.zip

This file includes in compressed form all the files for using J(S)mol inside web pages, such as:

  • Applet files (for the Java modality of Jmol object)
  • Javascript libraries (for the definition of the Jmol object in all cases, and specifically for the HTML5 modality of Jmol object)

For details on the files contained, their purpose and how to use them, please see Jmol_JavaScript_Object#Installation

Contributors

Zhang2010, AngelHerraez, Pimpim, NicolasVervelle

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