Difference between revisions of "Jmol JavaScript Object"

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== The Jmol JavaScript Object (JSmol) ==
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{{Lang:Jmol JavaScript Object}}
  
The heart of JSmol is the The Jmol JavaScript object, (<code>window.Jmol</code>), which includes a set of JavaScript functions and utilities.  The initial Jmol object was developed by Bob Hanson and Paul Pillot in early 2012. It was folded into '''JSmol''' later that year. The library {{file| JSmol.min.js}} provides this object and supersedes the [{{Website}}jslibrary/ Jmol.js JavaScript library] formerly used exclusively with the Jmol Java applet, allowing a cleaner, more efficient way to interact with Jmol on a web page, and abstracting the visualization of a molecular model so that the Java applet can be seamlessly and selectively replaced by a non-Java HTML5 canvas element (which might not even be Jmol).
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== JSmol, the Jmol JavaScript Object ==
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<div style="float:right; margin-left:1em;">
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__TOC__
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</div>
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<div style="float:left;">
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[[Image:JSmol_logo13.png]]
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</div>
  
Using '''JSmol''', a web page developer can target Java-challenged (iPad, iPhone) and applet-challenged (Android) platforms using '''a Jmol applet surrogate''' while still implementing the Jmol Java applet on traditional platforms. The wide variety of options available allows Jmol's functionality on all such devices, and there should be no need to ever see a message "Sorry, you don't have Java installed...."
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The heart of JSmol is the Jmol JavaScript object, (<code>window.Jmol</code>), which includes a set of JavaScript functions and utilities.  The initial Jmol object was developed by Bob Hanson and Paul Pillot in early 2012. It was folded into '''JSmol''' later that year. The library {{file| JSmol.min.js}} provides this object and supersedes the Jmol.js JavaScript library formerly used exclusively with the Jmol Java applet, allowing a cleaner, more efficient way to interact with Jmol on a web page, and abstracting the visualization of a molecular model so that the Java applet can be seamlessly and selectively replaced by a non-Java HTML5 canvas element (which might not even be Jmol).  
  
'''JSmol''' also integrates facilities for direct, behind-the-scenes access to public databases such as the [http://rcsb.org RCSB PDB database], the [http://cactus.nci.nih.gov/ National Cancer Institute CACTVS server], and [http://pubchem.ncbi.nlm.nih.gov/ PubChem], even when the user's platform does not allow the Jmol Java applet.
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Using '''JSmol''', a web page developer can target most web browsers that no longer support Java applets, using '''a Jmol applet surrogate''', while still implementing the Jmol Java applet on compatible platforms.
 +
 
 +
'''JSmol''' also integrates facilities for direct, behind-the-scenes access to public databases such as the [https://rcsb.org RCSB PDB database], the [https://cactus.nci.nih.gov/ National Cancer Institute CACTVS server], and [https://pubchem.ncbi.nlm.nih.gov/ PubChem].
  
 
In addition, '''JSmol''' allows easy interaction with
 
In addition, '''JSmol''' allows easy interaction with
* the '''JSpecView Java applet or HTML5 object''', allowing one to tie 3D models to IR, NMR, UV/VIS, GC, and GC/MS spectra (see [[Jmol_JavaScript_Object/JSV|more details]])
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* the '''JSpecView HTML5 object''', allowing one to tie 3D models to IR, NMR, UV/VIS, GC, and GC/MS spectra (see [[Jmol_JavaScript_Object/JSV|more details]])
* the '''JME Java applet or JSME HTML5 object''', so 3D models can be generated by a page visitor using simple chemical 2D drawing (see [[Jmol_JavaScript_Object/JME|more details]])
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* the '''JSME HTML5 object''', so 3D models can be generated by a page visitor using simple chemical 2D drawing (see [[Jmol_JavaScript_Object/JME|more details]])
  
 
'''JSmol''' is fully compatible with [http://jquery.com jQuery] 1.9 or 1.10. (jQuery 2.0 does not and for reasons of principle reportedly will never support MSIE running locally using file://, so if you do not need to run your page in MSIE in a local environment, that should be fine. There is a fix for this, however, if you must do that. In that case you must hack jQuery a bit.) The library has been W3C and XHTML validated.
 
'''JSmol''' is fully compatible with [http://jquery.com jQuery] 1.9 or 1.10. (jQuery 2.0 does not and for reasons of principle reportedly will never support MSIE running locally using file://, so if you do not need to run your page in MSIE in a local environment, that should be fine. There is a fix for this, however, if you must do that. In that case you must hack jQuery a bit.) The library has been W3C and XHTML validated.
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<table class="wikitable">
 
<table class="wikitable">
 
<tr>
 
<tr>
<th>Non-Java Options</th><td>Options for Java, HTML5/WebGL, or HTML5-only. Includes a variety of options, such as initial "deferred-applet" mode, where an initial image is displayed, with a click on the image or link on the page initiating applet/canvas 3D modeling, and "image+loading" mode, in which case the 3D model is loading behind the scenes while an initial image is displayed.</td>
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<th>Non-Java options</th><td>Options for HTML5-only and optionally Java and HTML5/WebGL. Includes a variety of options, such as initial "deferred-applet" mode, where an initial image is displayed, with a click on the image or link on the page initiating applet/canvas 3D modeling, and "image+loading" mode, in which case the 3D model is loading behind the scenes while an initial image is displayed.</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
<th>Library Files</th>
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<th>Library files</th>
<td>Requires at a minimum, {{file|JSmol.min.js}} and {{folder|j2s}} and/or {{folder|java}}.</td>
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<td>Requires at a minimum {{file|JSmol.min.js}} as well as {{folder|j2s}}; for internationalized interface, also {{folder|idioma}}. Also optionally {{folder|java}}.</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
<th>JavaScript Objects</th>
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<th>JavaScript objects</th>
<td>Creates a single JavaScript Object, <code>Jmol</code>, which includes a set of functions and internal objects such as <code>Jmol._Applet</code>, <code>Jmol._Image</code>, and <code>Jmol.controls</code>.</td>
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<td>Creates a single JavaScript object, <code>Jmol</code>, which includes a set of functions and internal objects such as <code>Jmol._Applet</code>, <code>Jmol._Image</code>, and <code>Jmol.controls</code>.</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
<th>JavaScript Prototypes</th>
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<th>JavaScript prototypes</th>
<td>The object you create using <code>Jmol.getApplet()</code> is a JavaScript object that is a subclass of <code>Jmol._Applet</code>. When you use <code>Jmol.getApplet()</code>, you get a reference to a JavaScript object, not the Java applet/canvas itself. The applet or canvas is wrapped in a set of <code>div</code> elements, allowing a richer diversity of options.</td>
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<td>The object you create using <code>Jmol.getApplet()</code> or <code>Jmol.getAppletHtml()</code> is a JavaScript object that is a subclass of <code>Jmol._Applet</code>. When you use <code>Jmol.getApplet()</code>, you get a reference to a JavaScript object, not the applet/canvas itself. The applet or canvas is wrapped in a set of <code>div</code> elements, allowing a richer diversity of options.</td>
 
</tr>
 
</tr>
 
<tr>
 
<tr>
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</div>
 
</div>
  
 
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'''JSmol''' is the name for the HTML5 canvas version of the former Jmol applet. '''JSmol''' opens up the use of Jmol in PC, Mac, and Linux systems, tablets and phones (both iOS and Android) without the need for Java. No hardware-based graphics acceleration is used, allowing '''JSmol''' to run in any web browser that supports HTML5 standards. JSmol runs entirely in the client, needing no server technologies for most of its operation. (Reading binary files in some browsers and saving images and Jmol states in all browsers do require a server-side PHP script, commonly provided as {{file|php/jsmol.php}} &ndash;read details below.)
'''JSmol''' is the name for the HTML5 canvas version of the Jmol applet. '''JSmol''' opens up the use of Jmol in PC, Mac, and Linux systems without Java installed or with Java disabled, as well as tablets and phones (both iOS and Android). No hardware-based graphics acceleration is used, allowing '''JSmol''' to run in any web browser that supports HTML5 standards. JSmol runs entirely in the client, needing no server technologies for most of its operation. (Reading binary files in some browsers and saving images and Jmol states in all browsers do require a server-side PHP script.)
 
  
 
'''JSmol''' was developed by Bob Hanson, Zhou Renjian, and Takanori Nakane.
 
'''JSmol''' was developed by Bob Hanson, Zhou Renjian, and Takanori Nakane.
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** MSIE allows access to local files only if they are not binary.
 
** MSIE allows access to local files only if they are not binary.
 
** Chrome allows access only when Chrome has been started using a special command-line flag (<code>chrome.exe --allow-file-access-from-files</code>).
 
** Chrome allows access only when Chrome has been started using a special command-line flag (<code>chrome.exe --allow-file-access-from-files</code>).
** Firefox allows access only after setting a special about:config flag (<code>security.fileuri.strict_origin_policy = false</code>).
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** Firefox allows access only after setting a special <code>about:config</code> flag (<code>security.fileuri.strict_origin_policy = false</code>).
 
* Opening binary files (e.g Spartan files, gzipped files, {{file|pngj}} files): they can be read but must be identified as such in their file name (see below).  
 
* Opening binary files (e.g Spartan files, gzipped files, {{file|pngj}} files): they can be read but must be identified as such in their file name (see below).  
 
* Writing of {{file|jpg}}, {{file|png}} and {{file|pngj}} (png+zip) data is fully supported, but delivering it to a user may require a server-side piece. (See also [[Recycling_Corner#Exporting_an_image_from_the_applet|Exporting an image]] for alternatives).
 
* Writing of {{file|jpg}}, {{file|png}} and {{file|pngj}} (png+zip) data is fully supported, but delivering it to a user may require a server-side piece. (See also [[Recycling_Corner#Exporting_an_image_from_the_applet|Exporting an image]] for alternatives).
 
* The Jmol <code>prompt</code> command does not allow more than a simple JavaScript-like response in the HTML5 version.
 
* The Jmol <code>prompt</code> command does not allow more than a simple JavaScript-like response in the HTML5 version.
* The WebGL modality of JSmol has not been fully developed and feature support is limited.
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* The [[Jmol_JavaScript_Object/WebGL|WebGL modality]] of JSmol has not been fully developed and feature support is limited.
  
 
=== Reading binary files ===
 
=== Reading binary files ===
Jmol (Java) can open a file and then determine whether the file is binary or not. JSmol (JavaScript) is different, because the AJAX transport mechanism is different for binary and nonbinary files. Thus, JSmol must determine whether a file is binary or not ''prior'' to its loading. JSmol does this by inspection of the file name. JSmol will switch to binary mode for files with any of the following in their file name:  
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Jmol (Java) can open a file and then determine whether the file is binary or not. JSmol (JavaScript) is different, because the AJAX transport mechanism is different for binary and nonbinary files. Thus, JSmol must determine whether a file is binary or not ''prior'' to its loading.  
 +
 
 +
==== File names ====
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JSmol will determine whether a file is binary or not &mdash;before loading it&mdash; by inspection of the file name. JSmol will switch to binary mode for files with any of the following in their file name:  
 
{{file|.bin}}
 
{{file|.bin}}
 
{{file|.gz}}
 
{{file|.gz}}
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These "extensions" can appear anywhere in a file name to trigger the binary access mode. So, for example, if you rename any file to include <code>.bin</code> anywhere in its name, that will instruct JSmol to read it as a binary file.
 
These "extensions" can appear anywhere in a file name to trigger the binary access mode. So, for example, if you rename any file to include <code>.bin</code> anywhere in its name, that will instruct JSmol to read it as a binary file.
  
For binary file reading to be compatible with Chrome and MSIE, you will need to have a base64 server-side piece that will convert the binary data to <code>BASE64</code> format. This is because only Firefox allows clean (reliable) synchronous binary file transfer. (And, so far, we have not figured out how to move all the file loading in Jmol to a fully asynchronous mode.) The [{{StOlaf}}jsmol/jsmol.htm demo pages] use the {{file|jsmol.php}} script that is included in the JSmol distribution (see below), which does that and considerably more. If your page visitors need to read binary files, place a copy of {{file|jsmol.php}} on your server and point to it using the '''serverURL''' item of the Info array.
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:''Advanced'': If you need a different extension to be read as binary, and cannot change the file names to include one of the default extensions, it is possible to extend the set using this code in your JavaScript after the Jmol object has being initialized: <code>Jmol._binaryTypes.push('.myExtension');</code>
  
=== Converting pages from Jmol to JSmol ===
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==== Browser behaviour ====
It is not hard to convert pages that currently use Jmol to use either the Java or the HTML5 versions of JSmol. The basic sequence includes:
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For binary file reading to be compatible with Chrome and MSIE, you will need to have a base64 server-side piece that will convert the binary data to <code>BASE64</code> format. This is because only Firefox allows clean (reliable) synchronous binary file transfer. (And, so far, we have not figured out how to move all the file loading in Jmol to a fully asynchronous mode.)
  
* Switching from {{file|Jmol.js}} to {{file|JSmol.min.js}}
+
If your page visitors need to read binary files, place a copy of the {{file|jsmol.php}} file that is included in the JSmol distribution (see below) on your server and point to it using the [[Jmol_JavaScript_Object/Info#Files_and_paths|'''serverURL''' item of the Info array]].
* Adding the {{folder|java}} or {{folder|j2s}} folders/directories to your website.
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As an example, the [{{StOlaf}}jsmol/jsmol.htm demo pages] use this approach.
* Setting parameters in the <code>Info</code> variable.
 
* Modifying function calls from the format <code>jmolXxxx(..., appletExtension)</code> to <code>Jmol.jmolXxxx(appletID, ...)</code> (see below). Depending upon the magnitude of the problem, you may want to write (''but read the next section first!'') a set of JavaScript functions that allow you to keep your page source code unchanged. For example, if you use the simplest form of jmolButton, the converting function would be:
 
<pre>
 
function jmolButton(script, label) {
 
  Jmol.jmolButton(myJmol, script, label)
 
}
 
</pre>
 
  
Or you can modify your page source code to use the new format. Or, easiest solution, use the 'adapter' library described below.
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For that to work, your server must support PHP. Otherwise, you might "borrow" by pointing to the {{file|jsmol.php}} file in another server that can run PHP (please, ask the owner of that server).
  
The main methods formerly implemented in {{file|Jmol.js}} (and more!) have now [[Jmol_JavaScript_Object/Functions|equivalent functions]] that can be found in [{{SVN JSmol Trunk}}jsmoljs/JSmolApi.js JSmolApi.js]
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In Chrome and also other browsers, you may overcome problems with loading '''''local''''' binary files by running pages through a local web server.
-- also included in the distribution: {{file|jsmol.zip}} > {{folder|js}} > {{file|JSmolApi.js}}
 
You might consider taking this opportunity to find out how jQuery works, if you are not familiar with it, and work more with those functions.
 
  
=== Conversion using the Jmol2.js 'adapter' library ===
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=== Converting legacy web pages to JSmol ===
What has been just described (i.e., writing custom functions that allow to keep using the old calls as used with Jmol.js) has been implemented in a special new Jmol2.js 'adapter' library. If you use this, you can leave your existing calls to jmolApplet(), jmolButton(), jmolLink() etc. You just need to:
 
  
<table>
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It is not hard to convert pages that used the Jmol Applet and the <code>Jmol.js</code> library to use the HTML5 versions of JSmol. See [[Jmol JavaScript Object/Legacy|more details]].
<tr>
 
<th>method A:
 
</th>
 
<th>method B:
 
</th>
 
</tr>
 
<tr>
 
<td>
 
* ''Step 1''
 
** In all your pages, add a call to {{file|JSmol.min.js}}
 
** In all your pages, change the existing call to {{file|Jmol.js}} into {{file|Jmol2.js}}
 
</td>
 
<td>
 
* ''Step 1''
 
** Open in a text editor both {{file|JSmol.min.js}}, {{file|Jmol2.js}} and a new blank document. Combine in this document the contents of {{file|JSmol.min.js}} followed by the contents of {{file|Jmol2.js}}. Save this new document as {{file|Jmol.js}}
 
** Do not change your pages, keep the existing call to {{file|Jmol.js}}
 
</td>
 
</tr>
 
<tr>
 
<td>
 
* ''Step 2:''
 
** Add the JSmol files and folders as appropriate &dagger;
 
</td>
 
<td>
 
* ''Step 2:''
 
** Add the JSmol files and folders as appropriate &dagger;
 
</td>
 
</tr>
 
</table>
 
(&dagger;) That is described in the Installation and Initialization sections of this page.
 
 
 
For more details, read inside the Jmol2.js file itself.
 
 
 
Locations to get {{file|Jmol2.js }}:
 
* In the Jmol download, Jmol-14.x.x-binary.zip > jsmol.zip > jsmol\js\Jmol2.js
 
* In the [{{SVN JSmol Trunk}}jsmoljs/Jmol2.js JSmol repository]
 
* [{{StOlaf}}jsmol/js/Jmol2.js at StOlaf]
 
 
 
=== Upgrading Jmol without using JSmol ===
 
 
 
If you have a "legacy" site that uses Jmol.js, and you would prefer to stick with Java and just upgrade your site so that it still works, then all you have to do is the following:
 
 
 
* Download the latest [http://sourceforge.net/projects/jmol/files Jmol ZIP file distribution]. Inside the ZIP file is a second ZIP file, jsmol.zip. Extract that file.
 
* Open jsmol.zip and extract all the JAR and JNLP files in the jsmol/java directory.
 
* Use the most recent version of Jmol.js that you have, or retrieve it from [http://chemapps.stolaf.edu/jmol/Jmol.js St. Olaf].
 
* Upgrade your site's Jmol.js and your JAR files with the files you have extracted.
 
 
 
Everything should work as before, but users will see a much kinder, more welcoming warning message the first time they access the new applet. Of course they will still have to give permission for the applet to be run, maybe in several dialogs.
 
  
 
==Installation==
 
==Installation==
 
+
See [[Jmol JavaScript Object/Installation]]
:''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===
 
Full releases of J(S)mol may be obtained at [http://sourceforge.net/projects/jmol/files/ the Jmol Project page]. The most up-to-date, development, version can be found as [{{StOlaf}}zip/ St. Olaf].
 
 
 
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 the Jmol Object in a webpage, either in the Jmol/Java or JSmol/HTML5 modalities. Note that usually you don't need all those files, 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 12.6 MB, but only those parts actually needed will be downloaded to the client computer).
 
* For pages that use only the Jmol Java applet modality, you just need {{file|JSmol.min.js}} and {{folder|java}} (A total of 7.9 MB, but may be reduced to 2.2 MB for a single set of signed or unsigned applet files, of which only those parts actually needed will be downloaded to the client computer).
 
* {{folder|js}} is only important if you want to use the (experimental, not fully functional) WebGL version of JSmol. Specifically, you need {{file|js/JSmolGLmol.js}} and {{file|js/JSmolThree.js}} (which are not minimized), since those two libraries are not included in {{file|JSmol.min.js}}.
 
 
 
In detail:
 
{{file|jsmol.zip}} (which is included inside the Jmol distribution zip file) contains 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 {{file|JSmoljQuery.js}}.
 
** {{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).
 
 
 
* {{folder|php}}
 
** {{file|jsmol.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|java}} The files for the Java modality (JmolApplet), the same that have been used for Jmol in previous versions.
 
**  {{file|JmolApplet.jar}} or {{file|JmolAppletSigned.jar}} or {{file|JmolApplet0*.jar}} or {{file|JmolAppletSigned0*.jar}}
 
:: (That is, a set of files, where the * stands for several suffixes. You may need to read about [[Jmol_Applet#Unsigned_vs._Signed_Applet_.26_Data_Access|signed vs. unsigned applet]] if you are unfamiliar with the Jmol jar files.)
 
* {{folder|j2s}} The suite of JavaScript libraries needed for JSmol/HTML5 mode.
 
* {{folder|js}} Non-packed copies of JavaScript libraries needed for the Jmol object (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 pubic 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|JSmoljQuery.js}} A version of jQuery tweaked to allow synchronous binary file transfer and use with MSIE and Safari
 
** {{file|JSmolJSV.js}} Needed only for [[Jmol_JavaScript_Object/JSV|using the JSpecView applet]]
 
** {{file|JSmolGLmol.js}} Needed only when [[Jmol_JavaScript_Object/GLmol|using the WebGL version of JSmol]]
 
** {{file|JSmolThree.js}} Needed only when [[Jmol_JavaScript_Object/GLmol|using the WebGL version of JSmol]]
 
* A few sample pages and files, included for your convenience but not required for functionality:
 
** {{file|jsmol.htm}}, {{file|simple.htm}}, {{file|test2.htm}}, {{file|test3.htm}} , and {{file|cover.htm}} are demonstration/example pages
 
** {{folder|data}} Files used by the above demo pages
 
* {{folder|make}} and {{folder|test}} are for developers only. (The {{folder|make}} directory includes the Google Closure Compiler used to create {{file|Jsmol.min.js}}.)
 
 
 
=== 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]].
 
 
 
==== MSIE/Windows ====
 
 
 
'''Saving files''' from JSmol/HTML5 requires in Internet Explorer to go through the {{file|jsmol.php}} file, so you will need to have that [[Jmol_JavaScript_Object/Info#Customization_or_extras|set-up]]. The user will get a "Save or Open this file" type of dialog, and the file will be usually saved to the browser's default download folder.
 
 
 
==== 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".
 
  
 
==Initialization==
 
==Initialization==
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Please note that there may be restrictions on the folder locations where you can put files for the libraries (js), the page (html), the models and scripts. This is imposed by browser security policies (related to both Java security and AJAX calls in JavaScript) and usually applies only to situations where you are using the pages from local disk (as opposed to a web server).
 
Please note that there may be restrictions on the folder locations where you can put files for the libraries (js), the page (html), the models and scripts. This is imposed by browser security policies (related to both Java security and AJAX calls in JavaScript) and usually applies only to situations where you are using the pages from local disk (as opposed to a web server).
  
: Successful file access by either the signed or unsigned Java applet or the HTML5 version of Jmol/JSmol depends upon whether the page is loaded using "file:" or "http:"
+
: Successful file access by JSmol depends upon whether the page is loaded using "file:" or "http:"
: '''unsigned applet'''
 
:: <code>http:</code> {{file|.jar}} files must be located in the same folder as data files or in a folder above this.
 
:: <code>file:</code> same
 
: '''signed applet'''
 
:: <code>http:</code> no restrictions
 
:: <code>file:</code> same as unsigned applet
 
: '''HTML5 JSmol'''
 
 
:: <code>http:</code> all files should be on the host server or on a server set up to deliver cross-domain AJAX using the "Access-Control-Allow-Origin: *" header.
 
:: <code>http:</code> all files should be on the host server or on a server set up to deliver cross-domain AJAX using the "Access-Control-Allow-Origin: *" header.
 
:: <code>file:</code> all files should be on the local machine within or under the folder containing the {{file|.html}} page.
 
:: <code>file:</code> all files should be on the local machine within or under the folder containing the {{file|.html}} page.
Line 259: Line 139:
  
 
==== Lightweight JSmol ====
 
==== Lightweight JSmol ====
There is an alternative version of Jmol object that, using the HTML5 canvas like JSmol, loads very fast while offering minimal functionality (just a simplified ball and stick rendering, no scripting). It is specially aimed at smartphones and such systems with limited resources. To use this, instead of invoking {{file|JSmol.min.js}} you call:
+
There is an alternative version of Jmol object that, using the HTML5 canvas like JSmol, loads very fast while offering minimal functionality (just a simplified ball and stick rendering, no scripting). It is specially aimed at smartphones and such systems with limited resources.  
  
<code><script type="text/javascript" src="JSmol.lite.js"></script></code>
+
For more details on how to use this, see [[Lightweight JSmol]].
  
and then you use the [[#Jmol.getTMApplet|<code>getTMApplet()</code>]] method.
+
==== Optional components ====
 +
* [[Jmol_JavaScript_Object/JME|Integration with JSME]], an editor to draw 2D chemical structures (Peter Ertl's JavaScript Molecular Editor)
 +
* [[Jmol_JavaScript_Object/JSV|Integration with JSpecView]], a viewer for spectral data.
 +
* [[Jmol_JavaScript_Object/WebGL|WebGL modality]] to render the 3D model using a combination of HTML5 and WebGL graphics (in compatible systems)
 +
* [[Jmol_JavaScript_Object/ChemDoodle|ChemDoodle option]] to render the 3D model using ChemDoodle
  
To partially compensate for the lack of scripting, some [[Jmol_JavaScript_Object/Info#Lightweight_version|specific parameters]] of the Info variable are available.
+
=== Setting parameters ===
 +
The essential and minimal call to create a JSmol object is simply:
  
==== Optional components ====
+
<code>Jmol.getApplet("myJmol")</code>
* [[Jmol_JavaScript_Object/JME|Integration with JME]], a Java-based editor to draw 2D chemical structures (Peter Ertl's Java Molecular Editor)
+
 
* [[Jmol_JavaScript_Object/JSV|Integration with JSpecView]], a Java viewer for spectral data.
+
This will create a <tt>myJmol</tt> global variable in JavaScript that holds the JSmol object and is also the unique ID for that object in all functions and methods described below. ''Note that this simplest syntax will only work when the html file is located in the root JSmol folder.''
* [[Jmol_JavaScript_Object/GLmol|GLmol option]] to render the 3D model using a combination of HTML5 and WebGL graphics (in compatible systems) (does not use Java)  
+
 
* [[Jmol_JavaScript_Object/ChemDoodle|ChemDoodle option]] to render the 3D model using ChemDoodle (does not use Java)
+
However, in most situations you will want to customize some aspects, like the size of the object and the file paths. All of the initialization parameters can be specified.
 +
 
 +
The regular call to create a JSmol object with specified characteristics is
 +
to define an <code>Info</code> variable, which is an associative array (a set of key+value pairs) that indicates all the desired characteristics of the JSmol object.
 +
The JSmol.min.js library will provide a default <code>Info</code> variable, so you only need to specify those keys which values you want to customize.
 +
 
 +
Once <code>Info</code> has been defined, you create and insert the JSmol object in the page using this:
 +
 
 +
<code>'''Jmol'''.getApplet("myJmol", Info)</code>
 +
 
 +
:Note that <tt>myJmol</tt> and <tt>Info</tt> are user-defined variables and may hence have any name you wish. <tt>myJmol</tt> becomes in fact the identifier of the particular JSmol object that is being created. You may wish to have two JSmols in your page and call them e.g. <tt>jmolA</tt> and <tt>jmolB</tt>, and use for them the same set of parameters <tt>Info</tt>, or use two different sets named e.g. <tt>InfoA</tt> and <tt>InfoB</tt>. In contrast, <tt>'''Jmol'''</tt> (right at the beginning) must be written as such, since it is the internal name and identification of the unique JSmol object constructor.
  
=== Setting parameters ===
+
For a start, you may just copy and then adapt this simple example:
 +
<pre>
 +
var Info = {
 +
  color: "#FFFFFF",
 +
  height: 300,
 +
  width: 300,
 +
  script: "load $caffeine",
 +
  use: "HTML5",
 +
  j2sPath: "j2s",
 +
  serverURL: "php/jsmol.php",
 +
};
  
All of the initialization parameters supported in Jmol.js can be implemented in JSmol. However, the method of indicating variables is different. The essential call to create a Jmol object (an applet or an alternative non-Java viewer) is simply:
+
Jmol.getApplet("myJmol", Info);
 +
</pre>
  
<code>Jmol.getApplet("myJmol", Info)</code>
+
What this will do is:
 +
* Create a JavaScript variable (of the object type) named <code>myJmol</code>.
 +
* Insert a JSmol instance at that point in the web page, 300&times;300 pixels in size, with white background.
 +
* Retrieve data for caffeine from the Cactus server and display the molecular structure in the JSmol panel.
  
This will create a <tt>myJmol</tt> global variable in JavaScript that holds the Jmol object and is also the unique ID for that object in all functions and methods described below.
+
If you want more control, keep reading.
:Note that <tt>myJmol</tt> and <tt>Info</tt> are user-defined variables and may hence have any name you wish. <tt>myJmol</tt> becomes in fact the identifier of the particular Jmol object that is being created. You may wish to have two Jmols in your page and call them e.g. <tt>jmolA</tt> and <tt>jmolB</tt>, and use for them the same set of parameters <tt>Info</tt>, or use two different sets named e.g. <tt>InfoA</tt> and <tt>InfoB</tt>. In contrast, <tt>Jmol</tt> (right at the beginning) must be written as such, since it is the internal name and identification of the unique Jmol object constructor.
 
  
<code>Info</code> is an associative array (a set of key+value pairs) indicating all the desired characteristics of the Jmol object. The principal keys and their default values are given below:
+
<span style="font-size:1.2em;">
 +
A '''[[Jmol_JavaScript_Object/Info|detailed explanation]] of the parameters''' included in the <code>Info</code> variable
 +
</span>
 +
is available in a separate page, while the major ones and their default values are given below:
 
<pre>
 
<pre>
 
var Info = {
 
var Info = {
   color: "#FFFFFF", // white background (note this changes legacy default which was black)
+
   color: "#FFFFFF", // white background (note this changes legacy default which was black)
   height: 300,      // pixels (but it may be in percent)
+
   height: 300,      // pixels (but it may be in percent, like "100%")
 
   width: 300,
 
   width: 300,
   use: "HTML5",         // "HTML5" or "Java" (case-insensitive)
+
   use: "HTML5",     // "HTML5" or "Java" (case-insensitive)
   j2sPath: "j2s",           // only used in the HTML5 modality
+
   j2sPath: "j2s",         // only used in the HTML5 modality
   jarPath: "java",             // only used in the Java modality
+
   jarPath: "java",               // only used in the Java modality
   jarFile: "JmolApplet0.jar",   // only used in the Java modality
+
   jarFile: "JmolApplet0.jar",   // only used in the Java modality
   isSigned: false,             // only used in the Java modality
+
   isSigned: false,               // only used in the Java modality
  memoryLimit: 512,            // only used in the Java modality
+
   serverURL: "php/jsmol.php", // this is not applied by default; you should set this value explicitly
   serverURL: "php/jsmol.php", // needed only for some features, but should  
+
   src: null,         // file to load
                              // be in your server for full functionality
+
   script: null,       // script to run
   defaultModel: "",
+
   defaultModel: "",   // name or id of a model to be retrieved from a database
   script: null,
+
   addSelectionOptions: false, // to interface with databases
   src: null,
+
   disableInitialConsole: false, // shows a bunch of messages while the object is being built
   readyFunction: null,
 
   addSelectionOptions: false,
 
 
   debug: false
 
   debug: false
 
};  
 
};  
 
</pre>
 
</pre>
 
A more [[Jmol_JavaScript_Object/Info|detailed explanation]] of the parameters of the <code>Info</code> variable is available in a separate page.
 
  
 
==== Setting parameters from the URL ====
 
==== Setting parameters from the URL ====
 
''Jmol 14.0 or later''
 
''Jmol 14.0 or later''
  
Some values in the <tt>Info</tt> variable defined in the page may be overriden by adding a parameter in the page URL. This may be useful for testing, both own and some else's pages.
+
Some values in the <tt>Info</tt> variable defined in the page may be overriden by the user, by adding a parameter in the page URL. This may be useful for testing, both own and some else's pages.
  
 
The settable options affect  
 
The settable options affect  
Line 335: Line 242:
 
== Functions for Jmol JavaScript Object ==
 
== Functions for Jmol JavaScript Object ==
  
Please see [[Jmol_JavaScript_Object/Functions]].
+
Please see [[Jmol_JavaScript_Object/Functions]] for details about:
 
 
 
* Functions for creation or display of Jmol Objects
 
* Functions for creation or display of Jmol Objects
 
* Functions for creating controls
 
* Functions for creating controls

Latest revision as of 16:00, 18 April 2024


Geographylogo.png

Reference: English – Other: 日本語 ·


JSmol, the Jmol JavaScript Object

JSmol logo13.png

The heart of JSmol is the Jmol JavaScript object, (window.Jmol), which includes a set of JavaScript functions and utilities. The initial Jmol object was developed by Bob Hanson and Paul Pillot in early 2012. It was folded into JSmol later that year. The library File icon.gif JSmol.min.js provides this object and supersedes the Jmol.js JavaScript library formerly used exclusively with the Jmol Java applet, allowing a cleaner, more efficient way to interact with Jmol on a web page, and abstracting the visualization of a molecular model so that the Java applet can be seamlessly and selectively replaced by a non-Java HTML5 canvas element (which might not even be Jmol).

Using JSmol, a web page developer can target most web browsers that no longer support Java applets, using a Jmol applet surrogate, while still implementing the Jmol Java applet on compatible platforms.

JSmol also integrates facilities for direct, behind-the-scenes access to public databases such as the RCSB PDB database, the National Cancer Institute CACTVS server, and PubChem.

In addition, JSmol allows easy interaction with

  • the JSpecView HTML5 object, allowing one to tie 3D models to IR, NMR, UV/VIS, GC, and GC/MS spectra (see more details)
  • the JSME HTML5 object, so 3D models can be generated by a page visitor using simple chemical 2D drawing (see more details)

JSmol is fully compatible with jQuery 1.9 or 1.10. (jQuery 2.0 does not and for reasons of principle reportedly will never support MSIE running locally using file://, so if you do not need to run your page in MSIE in a local environment, that should be fine. There is a fix for this, however, if you must do that. In that case you must hack jQuery a bit.) The library has been W3C and XHTML validated.

Main features of JSmol

Non-Java optionsOptions for HTML5-only and optionally Java and HTML5/WebGL. Includes a variety of options, such as initial "deferred-applet" mode, where an initial image is displayed, with a click on the image or link on the page initiating applet/canvas 3D modeling, and "image+loading" mode, in which case the 3D model is loading behind the scenes while an initial image is displayed.
Library files Requires at a minimum File icon.gifJSmol.min.js as well as Folder icon.gifj2s; for internationalized interface, also Folder icon.gifidioma. Also optionally Folder icon.gifjava.
JavaScript objects Creates a single JavaScript object, Jmol, which includes a set of functions and internal objects such as Jmol._Applet, Jmol._Image, and Jmol.controls.
JavaScript prototypes The object you create using Jmol.getApplet() or Jmol.getAppletHtml() is a JavaScript object that is a subclass of Jmol._Applet. When you use Jmol.getApplet(), you get a reference to a JavaScript object, not the applet/canvas itself. The applet or canvas is wrapped in a set of div elements, allowing a richer diversity of options.
AJAX JSmol includes methods to easily access cross-platform resources using AJAX provided by jQuery.
REST services JSmol lets you access keyword search results from RCSB -- for example, a list of all structures that reference caffeine.
Scripting JSmol provides the same full complement of scripting that Jmol offers. JSmol accepts script commands immediately, before or during applet/canvas creation on the page, caching them until Jmol is ready to accept them.

JSmol

JSmol logo13.png

JSmol is the name for the HTML5 canvas version of the former Jmol applet. JSmol opens up the use of Jmol in PC, Mac, and Linux systems, tablets and phones (both iOS and Android) without the need for Java. No hardware-based graphics acceleration is used, allowing JSmol to run in any web browser that supports HTML5 standards. JSmol runs entirely in the client, needing no server technologies for most of its operation. (Reading binary files in some browsers and saving images and Jmol states in all browsers do require a server-side PHP script, commonly provided as File icon.gifphp/jsmol.php –read details below.)

JSmol was developed by Bob Hanson, Zhou Renjian, and Takanori Nakane.

JSmol allows rendering, scripting and interaction with the models just as Jmol does, since the source code is shared by both. Note that JSmol is not a different program than Jmol: it is Jmol, just compiled into JavaScript instead of Java (thanks to the Java2Script software).

Current limitations of JSmol

  • Using local files (i.e. not in a web server) is not supported on some browsers due to their security policies:
    • Opera allows no access to local files.
    • MSIE allows access to local files only if they are not binary.
    • Chrome allows access only when Chrome has been started using a special command-line flag (chrome.exe --allow-file-access-from-files).
    • Firefox allows access only after setting a special about:config flag (security.fileuri.strict_origin_policy = false).
  • Opening binary files (e.g Spartan files, gzipped files, File icon.gifpngj files): they can be read but must be identified as such in their file name (see below).
  • Writing of File icon.gifjpg, File icon.gifpng and File icon.gifpngj (png+zip) data is fully supported, but delivering it to a user may require a server-side piece. (See also Exporting an image for alternatives).
  • The Jmol prompt command does not allow more than a simple JavaScript-like response in the HTML5 version.
  • The WebGL modality of JSmol has not been fully developed and feature support is limited.

Reading binary files

Jmol (Java) can open a file and then determine whether the file is binary or not. JSmol (JavaScript) is different, because the AJAX transport mechanism is different for binary and nonbinary files. Thus, JSmol must determine whether a file is binary or not prior to its loading.

File names

JSmol will determine whether a file is binary or not —before loading it— by inspection of the file name. JSmol will switch to binary mode for files with any of the following in their file name: File icon.gif.bin File icon.gif.gz File icon.gif.zip File icon.gif.jpg File icon.gif.png File icon.gif.jmol File icon.gif.smol File icon.gif.spartan File icon.gif.mrc File icon.gif.pse

These "extensions" can appear anywhere in a file name to trigger the binary access mode. So, for example, if you rename any file to include .bin anywhere in its name, that will instruct JSmol to read it as a binary file.

Advanced: If you need a different extension to be read as binary, and cannot change the file names to include one of the default extensions, it is possible to extend the set using this code in your JavaScript after the Jmol object has being initialized: Jmol._binaryTypes.push('.myExtension');

Browser behaviour

For binary file reading to be compatible with Chrome and MSIE, you will need to have a base64 server-side piece that will convert the binary data to BASE64 format. This is because only Firefox allows clean (reliable) synchronous binary file transfer. (And, so far, we have not figured out how to move all the file loading in Jmol to a fully asynchronous mode.)

If your page visitors need to read binary files, place a copy of the File icon.gifjsmol.php file that is included in the JSmol distribution (see below) on your server and point to it using the serverURL item of the Info array. As an example, the demo pages use this approach.

For that to work, your server must support PHP. Otherwise, you might "borrow" by pointing to the File icon.gifjsmol.php file in another server that can run PHP (please, ask the owner of that server).

In Chrome and also other browsers, you may overcome problems with loading local binary files by running pages through a local web server.

Converting legacy web pages to JSmol

It is not hard to convert pages that used the Jmol Applet and the Jmol.js library to use the HTML5 versions of JSmol. See more details.

Installation

See Jmol JavaScript Object/Installation

Initialization

Browser issues

JSmol makes strong use of the HTML5 features. Therefore, it is only compatible with modern web browsers. Specifically, Internet Explorer must be version 9 or higher.

In addition, it is important to use a doctype in the header of the html page. The recommended doctype is the simple one, associated to HTML5 standard, as the very first line of your html document.

Also, for full compatibility, particularly for the localization (language translations) of the JSmol pop-up menu, you should declare the charset as UTF-8 and save the html document (and all accessory files) using UTF-8 encoding (usually without BOM, but this needs further confirmation; recent versions of Firefox seem to have problems with non-BOM UTF-8 files, and UTF-8 with BOM looks like a better solution).

Therefore your html documents should start as:

<!DOCTYPE HTML>
<html>
<head>
<meta charset="utf-8">

Loading the library

The web page should have the following in the head section (pointing to appropriate paths if not the same folder as the web page as shown here):

<script type="text/javascript" src="JSmol.min.js"></script>

Please note that there may be restrictions on the folder locations where you can put files for the libraries (js), the page (html), the models and scripts. This is imposed by browser security policies (related to both Java security and AJAX calls in JavaScript) and usually applies only to situations where you are using the pages from local disk (as opposed to a web server).

Successful file access by JSmol depends upon whether the page is loaded using "file:" or "http:"
http: all files should be on the host server or on a server set up to deliver cross-domain AJAX using the "Access-Control-Allow-Origin: *" header.
file: all files should be on the local machine within or under the folder containing the File icon.gif.html page.
All this needs confirmation. See also Java security policy which applies to the Java applet.

Lightweight JSmol

There is an alternative version of Jmol object that, using the HTML5 canvas like JSmol, loads very fast while offering minimal functionality (just a simplified ball and stick rendering, no scripting). It is specially aimed at smartphones and such systems with limited resources.

For more details on how to use this, see Lightweight JSmol.

Optional components

Setting parameters

The essential and minimal call to create a JSmol object is simply:

Jmol.getApplet("myJmol")

This will create a myJmol global variable in JavaScript that holds the JSmol object and is also the unique ID for that object in all functions and methods described below. Note that this simplest syntax will only work when the html file is located in the root JSmol folder.

However, in most situations you will want to customize some aspects, like the size of the object and the file paths. All of the initialization parameters can be specified.

The regular call to create a JSmol object with specified characteristics is to define an Info variable, which is an associative array (a set of key+value pairs) that indicates all the desired characteristics of the JSmol object. The JSmol.min.js library will provide a default Info variable, so you only need to specify those keys which values you want to customize.

Once Info has been defined, you create and insert the JSmol object in the page using this:

Jmol.getApplet("myJmol", Info)

Note that myJmol and Info are user-defined variables and may hence have any name you wish. myJmol becomes in fact the identifier of the particular JSmol object that is being created. You may wish to have two JSmols in your page and call them e.g. jmolA and jmolB, and use for them the same set of parameters Info, or use two different sets named e.g. InfoA and InfoB. In contrast, Jmol (right at the beginning) must be written as such, since it is the internal name and identification of the unique JSmol object constructor.

For a start, you may just copy and then adapt this simple example:

var Info = {
  color: "#FFFFFF",
  height: 300,
  width: 300,
  script: "load $caffeine",
  use: "HTML5",
  j2sPath: "j2s",
  serverURL: "php/jsmol.php",
};

Jmol.getApplet("myJmol", Info);

What this will do is:

  • Create a JavaScript variable (of the object type) named myJmol.
  • Insert a JSmol instance at that point in the web page, 300×300 pixels in size, with white background.
  • Retrieve data for caffeine from the Cactus server and display the molecular structure in the JSmol panel.

If you want more control, keep reading.

A detailed explanation of the parameters included in the Info variable is available in a separate page, while the major ones and their default values are given below:

var Info = {
  color: "#FFFFFF", // white background (note this changes legacy default which was black)
  height: 300,      // pixels (but it may be in percent, like "100%")
  width: 300,
  use: "HTML5",     // "HTML5" or "Java" (case-insensitive)
  j2sPath: "j2s",          // only used in the HTML5 modality
  jarPath: "java",               // only used in the Java modality
  jarFile: "JmolApplet0.jar",    // only used in the Java modality
  isSigned: false,               // only used in the Java modality
  serverURL: "php/jsmol.php",  // this is not applied by default; you should set this value explicitly
  src: null,          // file to load
  script: null,       // script to run
  defaultModel: "",   // name or id of a model to be retrieved from a database
  addSelectionOptions: false,  // to interface with databases
  disableInitialConsole: false, // shows a bunch of messages while the object is being built
  debug: false
};	 

Setting parameters from the URL

Jmol 14.0 or later

Some values in the Info variable defined in the page may be overriden by the user, by adding a parameter in the page URL. This may be useful for testing, both own and some else's pages.

The settable options affect

  • what modality of J(S)mol to use, either Java or HTML5
  • what kind of applet to use, either 'sandboxed' or 'all-permissions' (new terms, more or less equivalent to the formerly called unsigned and signed applets)
  • whether to get the JmolApplet files from some other location (url)
  • whether to get the JavaScript files that build the Jmol Object from some other location (url)

The format for parameters in the url is the standard syntax in so called 'search' part of the url, i.e. ?parameter1=value1&parameter2=value2&...etc.

Examples (you get the meaning, don't you?):

any.htm?_USE=html5
any.htm?_USE=java
any.htm?_USE=signed
any.htm?_JAR=http://some.url.com/some/jsmol/java
any.htm?_J2S=http://some.url.com/some/jsmol/j2s
any.htm?_USE=java&_JAR=http://some.url.com/some/jsmol/java
any.htm?_USE=html5&_J2S=http://some.url.com/some/jsmol/j2s

Note that the names, like _USE, must be uppercase. The values are case-insensitive.

Functions for Jmol JavaScript Object

Please see Jmol_JavaScript_Object/Functions for details about:

  • Functions for creation or display of Jmol Objects
  • Functions for creating controls
  • Functions that insert HTML
  • Functions that set CSS rules
  • Functions that interact with a running Jmol Object
  • Deprecated, unnecessary or not recommended
  • Methods specific to optional components