Files Description/Jmol 14 - Revision history

AngelHerraez: separate this legacy info from current one for Jmol 16

2024-04-18T15:14:50Z

separate this legacy info from current one for Jmol 16

AngelHerraez: moving aside old version fileset description

2014-01-11T20:42:21Z

moving aside old version fileset description

Show changes

AngelHerraez: tips to location of applet files and Jmol.js in new distributions

2013-10-25T13:29:47Z

tips to location of applet files and Jmol.js in new distributions

AngelHerraez: info on new fileset in distribution

2013-07-24T16:49:32Z

info on new fileset in distribution

AngelHerraez: /* Optional Javascript libraries */

2012-07-22T16:40:42Z

‎Optional Javascript libraries

AngelHerraez: /* Jmol.js */

2012-07-22T16:26:23Z

‎Jmol.js

AngelHerraez: /* JmolControls.js */

2012-07-22T16:24:46Z

‎JmolControls.js

AngelHerraez: new JS libraries (object-oriented) for v13 and more new files

2012-07-22T16:22:11Z

new JS libraries (object-oriented) for v13 and more new files

AngelHerraez: new JS libraries (object-oriented) for v13

2012-07-22T16:02:59Z

new JS libraries (object-oriented) for v13

AngelHerraez: styling latest contributions by Zhang2010

2010-11-04T21:06:41Z

styling latest contributions by Zhang2010

← Older revision		Revision as of 15:14, 18 April 2024
Line 1:		Line 1:
		+	'''''This is valid up to some Jmol version 14.x; for later versions, see [[Files_Description]]'''''
		+
	'''''For Jmol versions previous to 13.2, see [[Files_Description/Jmol_12]]'''''		'''''For Jmol versions previous to 13.2, see [[Files_Description/Jmol_12]]'''''

@@ Line 95: / Line 95: @@
 === Applet files ===
 ==== JmolApplet0.jar, JmolApplet0''(severalSuffixes)''.jar ====
 The applet, i.e. a version of the program that will only run when embedded in a web page.
@@ Line 173: / Line 176: @@
 ==== Jmol.js ====
 The classic 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.
 This library uses by default the split version of the applet (unsigned or signed).
@@ Line 228: / Line 233: @@
 <br>
 == Accessory apps and applets ==
 === ChimeToJmol.jar ===

← Older revision		Revision as of 16:49, 24 July 2013
Line 1:		Line 1:
		+	'''''Starting in Jmol 13.2, the file set has changed; see [[Files_Description/New]]'''''
		+
		+
		+
	This information is also included in Jmol distribution {{File\|README}} file.		This information is also included in Jmol distribution {{File\|README}} file.

@@ Line 195: / Line 195: @@
 ==== JmolCD.js ====
 The ChemDoodle extension: provides the means for using [http://web.chemdoodle.com/ ChemDoodle Web Components] (that uses JavaScript + HTML5 canvas or WebGL) instead of the
-Jmol applets if Java is not available in the system.
+Jmol applets, for systems where Java is not available.
 ==== JmolGLmol.js ====
 The GLmol extension: provides the means for using [http://webglmol.sourceforge.jp/index-en.html GLmol]  (that uses WebGL + JavaScript) instead of the
-Jmol applets if Java is not available in the system.
+Jmol applets, for systems where Java is not available.
 ==== JmolJME.js ====
@@ Line 210: / Line 210: @@
 <br>
 === Files specific to older versions ===
 Versions before Jmol 11.1.30 had a different setup for the split applet files:

@@ Line 174: / Line 174: @@
 Fully documented at http://jmol.org/jslibrary/
-Jmol.js is phased out in Jmol v.13, in favour of the new set of object-oriented
+{{file|Jmol.js}} is phased out in Jmol v.13, in favour of the new set of object-oriented
-JavaScript method and .js files (described next).
+JavaScript method and {{file|.js}} files (described next).
 ==== JmolApplet.js ====

← Older revision		Revision as of 16:24, 22 July 2012
Line 185:		Line 185:

	==== JmolControls.js ====		==== JmolControls.js ====
		+	Support for user-interface controls like buttons, links, checkboxes, etc.

	==== JmolApi.js ====		==== JmolApi.js ====

@@ Line 82: / Line 82: @@
 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>
@@ Line 197: / Line 193: @@
 ==== JmolCD.js ====
-The ChemDoodle extension: provides the means for using ChemDoodle instead of the
+The ChemDoodle extension: provides the means for using [http://web.chemdoodle.com/ ChemDoodle Web Components] (that uses JavaScript + HTML5 canvas or WebGL) instead of the
 Jmol applets if Java is not available in the system.
 ==== JmolGLmol.js ====
-The GLmol extension: provides the means for using GLmol instead of the
+The GLmol extension: provides the means for using [http://webglmol.sourceforge.jp/index-en.html GLmol]  (that uses WebGL + JavaScript) instead of the
 Jmol applets if Java is not available in the system.
 ==== JmolJME.js ====
-Provides the means for adding JME applet in the webpage (drawing of 2D chemical
+Provides the means for adding a [[File_formats/Chemical_Structure#JME|JME applet]] in the webpage (drawing of 2D chemical
 formulas) and communicate with Jmol applets.
 ==== JmolJSV.js ====
-Provides the means for adding JSpecView applet in the webpage and communicate
+Provides the means for adding a [http://jspecview.sourceforge.net/ JSpecView applet] (viewer for spectral data) in the webpage and communicate
 with Jmol applets.
 <br>
@@ Line 226: / Line 212: @@
 Versions before Jmol 11.1.30 had a different setup for the split applet files:
-==== JmolApplet0.jar, JmolApplet1.jar, ... JmolApplet6.jar, JmolApplet_i18n.jar ====
+==== JmolApplet(number).jar, JmolApplet_i18n.jar ====
 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}}.
@@ Line 232: / Line 218: @@
 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.)
-==== JmolAppletSigned0.jar, JmolAppletSigned1.jar, ... JmolAppletSigned6.jar, JmolAppletSigned_i18n.jar ====
+==== JmolAppletSigned(number).jar, JmolAppletSigned_i18n.jar ====
 The signed version of the above split applet. (See JmolAppletSigned0.jar above for description of what a "signed" applet is.)

@@ Line 26: / Line 26: @@
 === CHANGES.txt ===
 A list with a history of the feature additions in each version of Jmol.
 <br>
@@ Line 78: / Line 82: @@
 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>
 == Files of Jmol applet ==
-This is used inside web pages.
+These are used inside web pages, and include:
+* Applet files
-=== Jmol.js ===
+* Core Javascript libraries
-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.
+* Optional Javascript libraries
-=== JmolApplet0.jar, JmolApplet0''(severalSuffixes)''.jar ===
+=== Applet files ===
 The applet, i.e. a version of the program that will only run when embedded in a web page.
@@ Line 109: / Line 114: @@
   jmolInitialize("../jmol") // jar files are in a parallel folder, named 'jmol'.
-=== JmolAppletSigned0.jar, JmolAppletSigned0''(severalSuffixes)''.jar ===
+==== 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.
@@ Line 129: / Line 134: @@
 * 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.
-=== JmolApplet.jar ===
+==== 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 {{File|JmolApplet0*.jar}} files, explained above.
@@ Line 135: / Line 140: @@
 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 MB), needed or not, must get loaded onto a user's machine before any structure is displayed.
+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:
@@ Line 147: / Line 152: @@
   jmolInitialize("directory-containing-jar-files", "JmolApplet.jar")
-=== JmolAppletSigned.jar ===
+==== 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.
@@ Line 160: / Line 165: @@
   jmolInitialize("directory-containing-jar-files", "JmolAppletSigned.jar")
-=== JmolSmilesApplet.jar ===
+<br>
 ''This is currently not included in the distribution, but may be obtained from the development site.''
@@ Line 169: / Line 223: @@
 <br>
-== Files specific to older versions ==
+=== Files specific to older versions ===
 Versions before Jmol 11.1.30 had a different setup for the split applet files:
-=== JmolApplet0.jar, JmolApplet1.jar, ... JmolApplet6.jar, JmolApplet_i18n.jar ===
+==== JmolApplet0.jar, JmolApplet1.jar, ... JmolApplet6.jar, JmolApplet_i18n.jar ====
 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}}.
@@ Line 178: / Line 232: @@
 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.)
-=== JmolAppletSigned0.jar, JmolAppletSigned1.jar, ... JmolAppletSigned6.jar, JmolAppletSigned_i18n.jar ===
+==== JmolAppletSigned0.jar, JmolAppletSigned1.jar, ... JmolAppletSigned6.jar, JmolAppletSigned_i18n.jar ====
 The signed version of the above split applet. (See JmolAppletSigned0.jar above for description of what a "signed" applet is.)

@@ Line 42: / Line 42: @@
 === jmol.sh ===
 A shell script to start Jmol application under Unix-like systems, like Linux, BSD, Solaris and Cygwin for Windows.
-<br>
-Under Linux, there are a number of ways to start jmol as a standalone program using the ''jmol.sh'' script:<br>
+Under Linux, there are a number of ways to start Jmol as a standalone program using the {{file|jmol.sh}} script:<br>
 (1)
-  <code>sh jmol.sh                      // start jmol under the jmol-xxx folder
+  sh jmol.sh                      // start Jmol under the jmol-xxx folder
-  sh yourpath/jmol-xxx/jmol.sh    // start jmol from anywhere </code>
+  sh yourpath/jmol-xxx/jmol.sh    // start Jmol from anywhere
 (2)
-  <code>chmod +x jmol.sh                //make the ''jmol.sh'' script executable
+  chmod +x jmol.sh                // make the ''jmol.sh'' script executable
-  jmol.sh                         // start jmol inside the jmol-xxx directory, or
+  jmol.sh                         // start Jmol inside the jmol-xxx directory, or
-  yourpath/jmol-xxx/jmol.sh       // start jmol anywhere </code>
+  yourpath/jmol-xxx/jmol.sh       // start Jmol anywhere
 (3)
-  <code>chmod +x jmol.sh                 //make the ''jmol.sh'' script executable
+  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
- </code>
+Add the following shell variable in the shell script {{file|$HOME/.bash_profile}}
-Add the following shell variable in the shell script $HOME/.bash_profile
+  export JMOL_HOME="/yourpath/jmol-xxx/"
 Reboot your computer or execute
-  <code>source $HOME/.bash_profile</code>
+  source $HOME/.bash_profile
 Then
-  <code>jmol.sh                          //start jmol anywhere </code>
+  jmol.sh                          // start Jmol anywhere
-<br>
+(4) Move the {{file|jmol-xxx}} folder to {{file|/usr/bin/}} or {{file|/usr/local/bin/}}
-(4) Move the jmol-xxx folder to /usr/bin/ or /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 </code>
+  jmol.sh                          // start Jmol from anywhere
 == Files of Jmol application ==