[LON-CAPA-cvs] cvs: loncom /html/adm/jmol JmolApplet0.jar JmolApplet0_Popup.jar JmolApplet0_ReadersMolXyz.jar JmolApplet0_ReadersMore.jar JmolApplet0_ReadersXml.jar JmolApplet0_ShapeBio.jar JmolApplet0_ShapeSpecial.jar JmolApplet0_Smiles.jar README.txt
raeburn
raeburn at source.lon-capa.org
Fri Aug 22 14:12:59 EDT 2014
raeburn Fri Aug 22 18:12:59 2014 EDT
Modified files:
/loncom/html/adm/jmol JmolApplet0.jar JmolApplet0_Popup.jar
JmolApplet0_ReadersMolXyz.jar
JmolApplet0_ReadersMore.jar
JmolApplet0_ReadersXml.jar
JmolApplet0_ShapeBio.jar
JmolApplet0_ShapeSpecial.jar
JmolApplet0_Smiles.jar README.txt
Log:
- Jmol version 14.2.4
-------------- next part --------------
Index: loncom/html/adm/jmol/JmolApplet0.jar
Index: loncom/html/adm/jmol/JmolApplet0_Popup.jar
Index: loncom/html/adm/jmol/JmolApplet0_ReadersMolXyz.jar
Index: loncom/html/adm/jmol/JmolApplet0_ReadersMore.jar
Index: loncom/html/adm/jmol/JmolApplet0_ReadersXml.jar
Index: loncom/html/adm/jmol/JmolApplet0_ShapeBio.jar
Index: loncom/html/adm/jmol/JmolApplet0_ShapeSpecial.jar
Index: loncom/html/adm/jmol/JmolApplet0_Smiles.jar
Index: loncom/html/adm/jmol/README.txt
diff -u loncom/html/adm/jmol/README.txt:1.2 loncom/html/adm/jmol/README.txt:1.3
--- loncom/html/adm/jmol/README.txt:1.2 Thu Oct 11 00:42:00 2007
+++ loncom/html/adm/jmol/README.txt Fri Aug 22 18:12:59 2014
@@ -1,7 +1,9 @@
==============================================================================
=== 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.
@@ -16,115 +18,243 @@
List of files included:
-------------------
-- README.txt
- This file.
-- COPYRIGHT.txt
- Copyright informations.
+1 == Files with information ==
+
+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
- JmolAppletSigned0(severalSuffixes).jar
- The signed version of the split applet. This version allows the user
- to access files anywhere on the computer and from any location on the web.
- Typically, users get a message asking if they want to accept the certificate
- for **each** of the (currently 16) loadable jar files. For this reason, this
- version may not be of general use.
- The set of these files is equivalent to the single JmolAppletSigned.jar.
- To use this with Jmol.js, use either:
- a) jmolInitialize("folder-containing-jar-files", true)
- or
- b) jmolInitialize("folder-containing-jar-files", "JmolAppletSigned0.jar")
-
----------------------------
-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 === Core Javascript libraries ===
+
+4.2.1 ==== 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).
+
+Fully documented at http://jmol.org/jslibrary/
+
+Jmol.js is phased out in Jmol v13, in favour of the object-oriented method
+and set of .js files (described next).
+
+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.
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