AngelHerraez: /* Access to local files */

2025-08-12T11:31:20Z

‎Access to local files

AngelHerraez: moving to this new independent page what was a section in Jmol_JavaScript_Object and updating info for Jmol 16

2024-04-18T15:58:07Z

moving to this new independent page what was a section in Jmol_JavaScript_Object and updating info for Jmol 16

New page

=Installation of JSmol=

:''The Jmol team appreciates all feedback from web page developers and makes every effort to keep the files up to date. Please file a [http://sourceforge.net/tracker/?atid=379133&group_id=23629&func=browse bug report] if you find a problem.''

==Getting the Files==
JSmol (usual name for the ''Jmol JavaScript Object'') is included as part of the Jmol package.
Full releases of J(S)mol may be obtained at [http://sourceforge.net/projects/jmol/files/ the Jmol Project page].

The distribution is a zipfile, {{file|Jmol-xxx.zip}}, that contains {{file|Jmol.jar}} (the Jmol application) and a {{file|jsmol.zip}} file which in turn contains the whole set of files potentially needed for deploying JSmol in a webpage. Note that usually you don't need the full set of files for operation, as described below.

===In summary===
* For pages that use the HTML5 modality of JSmol, you just need {{file|JSmol.min.js}} and {{folder|j2s}} (A total of about 36 MB, but only those parts actually needed in each occasion will be downloaded to the client computer).
* {{folder|js}} is only important if you want to experiment with the code (advanced).

===In detail===
{{file|jsmol.zip}} (which is included inside the Jmol distribution zip file) contains a {{file|jsmol_dev.htm}} file which is a test an demo page, and a {{folder|jsmol}} folder which holds all these files and folders:

* Major files:
** {{file|JSmol.min.js}} The only library that needs to be called explictly; it will take care of calling any of the other files as needed. (This includes a set of files minimized using the Google Closure Compiler)
*** {{file|JSmol.min.nojq.js}} An alternative version, to be used if you are not loading binary files and you already use jQuery on your page; this one bypasses the {{file|JSmoljQuery.js}} internal component. 
** {{file|JSmol.lite.js}} is a lightweight version of JSmol that will load very fast and offers minimal functionality (just a simplified ball and stick rendering, no scripting). It is specially aimed at phones and systems with limited power, or as a quick first-look option that may be programmatically replaced by a full JSmol at user request.
*** {{file|JSmol.lite.nojq.js}} An equivalent version that does not include jQuery (useful if you are already using jQuery in your page).
** {{file|JSmol.GLmol.min.js}} is a supplementary library addressed at using a [[Jmol_JavaScript_Object/WebGL|WebGL modality]] of the Jmol Object. Note that this does not support the full functionality of Jmol and is not under active development.

* {{folder|php}}
** {{file|jsmol.php}} or {{file|jsmol2.php}} A server-side PHP utility that allows a number of functions that can increase the platform and browser compatibility of JSmol. By default, JSmol will try to use a copy of this file at the St.Olaf server, but you need to put a copy in your own server in order to get full cross-platform compatibility in the following areas:
*** saving images (JPG, PNG) and binary Jmol states (JMOL, PNGJ, ZIP)
*** retrieving RCSB REST XML data services ("load =xxxxxxx?")
*** enabling cross-platform AJAX in MSIE (RCSB, NCI, PubChem)
*** reading binary files synchronously (as in the <code>load</code> command, or when using <code>var x = load(...)</code> in a Jmol script) in some browsers.
:: ''Details'': jsmol.php will be called if you request a binary format file (gz, zip, pse, etc.) from Safari, Chrome, or MSIE. Those browsers can't transfer that sort of file directly and need a server-side piece. But they will have to have that on your server (the same where the webpage is).
:: In addition, jsmol.php processes image creation requests and "turns around" binary data such as {{file|.jpg}} and {{file|.zip}} files created by JSmol on the page and simply returns it. For this functionality, jsmol.php could be anywhere, including the default location at StOlaf.

* {{folder|j2s}} The suite of JavaScript libraries needed for JSmol/HTML5 modality.
* {{folder|js}} Non-packed copies of JavaScript libraries needed for JSmol (most of these files are already included in packed form within {{file|JSmol.min.js}}, see above):
** {{file|j2sjmol.js}} Required interface to the Jmol and java classes (translated into JavaScript and compressed using the Google Closure Compiler.)
** {{file|JSmol.js}} Primary JSmol library, with private methods for creating and interacting with canvases
** {{file|JSmolApi.js}} All public user-intended interface functions
** {{file|JSmolApplet.js}} Required applet prototypes for use with Java or HTML5
** {{file|JSmolControls.js}} Required only if any buttons or links or other input methods will be used
** {{file|JSmolCore.js}} Primary JSmol library, with private methods for file loading, primarily

** {{file|JSmolJSV.js}} Needed only for [[Jmol_JavaScript_Object/JSV|using the JSpecView object]]
** ...and others (undocumented)
** {{folder|core}} (undocumented)
* Some tens of sample pages (htm files) included for your convenience but not required for functionality; among them:
** {{file|supersimple.htm}}, {{file|simple.htm}}, {{file|jsmol.htm}}, {{file|test2.htm}}, {{file|test3.htm}} , and {{file|cover.htm}} are demonstration/example pages
** {{folder|data}}, {{folder|images}} contain files used by the above demo pages
* {{folder|flot}}, {{folder|jcse}}, {{folder|jsme}}, etc. are for specific applications (advanced)

: Note: The {{folder|applet}} folder has been removed from the distribution since the use of Java applets long deprecated in web browsers.

== Specific browser considerations ==

=== Access to local files ===

If you want to load your pages '''from local disk''', some limitations apply depending on the browser. Please see
[[Troubleshooting/Local Files]].

=== Chrome/Windows ===

'''Saving files''' from JSmol/HTML5 will work without accessing {{file|jsmol.php}} file, but any filename and extension that was provided by script will be zapped by Chrome, which insists on offering to save the file with the name "download.txt".

@@ Line 56: / Line 56: @@
 If you want to load your pages '''from local disk''', some limitations apply depending on the browser. Please see
-[[Troubleshooting/Local Files]].
+[[Troubleshooting/Local Files]] and [[JSmol Deployment Local]].
 === Chrome/Windows ===
 '''Saving files''' from JSmol/HTML5 will work without accessing {{file|jsmol.php}} file, but any filename and extension that was provided by script will be zapped by Chrome, which insists on offering to save the file with the name "download.txt".

Jmol JavaScript Object/Installation - Revision history

AngelHerraez: /* Access to local files */

AngelHerraez: moving to this new independent page what was a section in Jmol_JavaScript_Object and updating info for Jmol 16