Jmol JavaScript Object

Jmol-JSO

The Jmol JavaScript Object (Jmol-JSO) is a set of JavaScript functions and utilities refactored and reorganized for Jmol 13.0 into a single JavaScript object (window.Jmol). The library JSmol.min.js supersedes the Jmol.js JavaScript library, 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 replaced by a non-Java HTML5 canvas element (which might not even be Jmol) or even an image, depending on client platform's resources.

Jmol-JSO was initially developed by Bob Hanson and Paul Pillot in early 2012. It was folded into JSmol in late 2012.

Using Jmol-JSO, a web page developer can target Java-challenged (iPad, iPhone) and applet-challenged (Android) platforms using a Jmol applet surrogate while still implementing Jmol/Java 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...."

Jmol-JSO 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, even when the user's platform does not allow the Jmol Java applet.

In addition, Jmol-JSO allows easy interaction with

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

Jmol-JSO 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 Jmol-JSO

Non-Java Options	Options for Java, HTML5/WebGL, HTML5-only, and image-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.
Library Files	Requires at a minimum, `JSmol.min.js` and `j2s` and/or `java`.
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()` 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 Java applet/canvas itself. The applet or canvas is wrapped in a set of `div` elements, allowing a richer diversity of options.
AJAX	Jmol-JSO includes methods to easily access cross-platform resources using AJAX provided by jQuery.
REST services	Jmol-JSO lets you access keyword search results from RCSB -- for example, a list of all structures that reference caffeine.
Scripting	Jmol-JSO in conjunction with JSmol provides the same full complement of scripting that Jmol offers. Jmol-JSO accepts script commands immediately, before or during applet/canvas creation on the page, caching them until Jmol is ready to accept them.

JSmol

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 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, pngj files): they can be read but must be identified as such in their file name (see below).
Writing of jpg, png and pngj (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. 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: .bin .gz .zip .jpg .png .jmol .smol .spartan .mrc .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.

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.) The demo pages use the 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 jsmol.php on your server and point to it using the serverURL item of the Info array.

Converting pages from Jmol to JSmol

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:

Switching from Jmol.js to JSmol.min.js
Adding the java or j2s folders/directories to your website.
Setting parameters in the Info variable.
Modifying function calls from the format jmolXxxx(..., appletExtension) to Jmol.jmolXxxx(appletID, ...) (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:

function jmolButton(script, label) {
  Jmol.jmolButton(myJmol, script, label)
}

Or you can modify your page source code to use the new format. Or, easiest solution, use the 'adapter' library described below.

The main methods formerly implemented in Jmol.js (and more!) have now equivalents that can be found in [[[:Template:WebsiteJSmolCode]]jsmoljs/JSmolApi.js JSmolApi.js] -- also included in the distribution: jsmol.zip > js > 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

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:

Step 1, method A:
- In all your pages, add a call to JSmol.min.js
- In all your pages, change the existing call to Jmol.js into Jmol2.js
Step 1, method B:
- Open in a text editor both JSmol.min.js, Jmol2.js and a new blank document. Combine in this document the contents of JSmol.min.js followed by the contents of Jmol2.js. Save this new document as Jmol.js
- Keep in your pages the existing call to Jmol.js
Step 2:
- Add the JSmol files and folders as appropriate (described in the Installation and Initialization sections of this page).

For more details, read inside the Jmol2.js file itself.

Locations to get Jmol2.js :

In the Jmol download, Jmol-14.x.x-binary.zip > jsmol.zip > jsmol\js\Jmol2.js
In the JSmol repository
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 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 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

The Jmol team appreciates all feedback from web page developers and makes every effort to keep the files up to date. Please file a bug report if you find a problem.

Getting the Files

Full releases of J(S)mol may be obtained at the Jmol Project page. The most up-to-date, development, version can be found as St. Olaf.

The distribution is a zipfile, Jmol-xxx.zip, that contains Jmol.jar (the Jmol application) and a 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 JSmol.min.js and 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 JSmol.min.js and 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).
js is only important if you want to use the (experimental, not fully functional) WebGL version of JSmol. Specifically, you need js/JSmolGLmol.js and js/JSmolThree.js (which are not minimized), since those two libraries are not included in JSmol.min.js.

In detail: jsmol.zip (which is included inside the Jmol distribution zip file) contains these files and folders:

Major files:
- 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)
  - 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 JSmoljQuery.js.
- 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.
  - JSmol.lite.nojq.js An equivalent version that does not include jQuery (useful if you are already using jQuery in your page).

php
- 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 load command, or when using var x = load(...) 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

.jpg and

.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.

java The files for the Java modality (JmolApplet), the same that have been used for Jmol in previous versions.
- JmolApplet.jar or JmolAppletSigned.jar or JmolApplet0*.jar or JmolAppletSigned0*.jar

(That is, a set of files, where the * stands for several suffixes. You may need to read about signed vs. unsigned applet if you are unfamiliar with the Jmol jar files.)

j2s The suite of JavaScript libraries needed for the HTML5 modality (JSmol).
js Non-packed copies of JavaScript libraries needed for the Jmol-JSO object (most of these files are already included in packed form within JSmol.min.js, see above):
- j2sjmol.js Required interface to the Jmol and java classes (translated into JavaScript and compressed using the Google Closure Compiler.)
- JSmol.js Primary JSmol library, with private methods for creating and interacting with canvases
- JSmolApi.js All pubic user-intended interface functions
- JSmolApplet.js Required applet prototypes for use with Java or HTML5
- JSmolControls.js Required only if any buttons or links or other input methods will be used
- JSmolCore.js Primary JSmol library, with private methods for file loading, primarily
- JSmoljQuery.js A version of jQuery tweaked to allow synchronous binary file transfer and use with MSIE and Safari
- JSmolJSV.js Needed only for using the JSpecView applet
- JSmolGLmol.js Needed only when using the WebGL version of JSmol
- JSmolThree.js Needed only when using the WebGL version of JSmol
A few sample pages and files, included for your convenience but not required for functionality:
- jsmol.htm, simple.htm, test2.htm, test3.htm , and cover.htm are demonstration/example pages
- data Files used by the above demo pages
make and test are for developers only. (The make directory includes the Google Closure Compiler used to create Jsmol.min.js.)

Specific browser considerations

Firefox/Windows

You will be able to read both binary and text files locally. Navigate to about:config and set security.fileuri.strict_origin_policy false.

MSIE/Windows

No local binary file access in JSmol/HTML5 from standard script commands. That is, no direct file reading with any of the following in their names:

 .bin .gz .jmol .jpg .map .mrc .omap .png .pse .smol .spartan .zip

This does not apply to files drag-dropped onto the applet or files loaded using "?", which use the HTML5 FileReader object. That method reads binary files without a problem.

Saving files from JSmol/HTML5 requires in Internet Explorer to go through the jsmol.php file, so you will need to have that 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

If you need to open local files, start Chrome using the command-line flag --allow-file-access-from-files. Beyond that, same as for MSIE/Windows.

Saving files from JSmol/HTML5 will work without accessing 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".

Opera/Windows

TODO

Firefox/Mac

TODO

Chrome/Mac

TODO

Safari/Mac

TODO

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 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:"

unsigned applet

http:

.jar files must be located in the same folder as data files or in a folder above this.

file: same

signed applet

http: no restrictions

file: same as unsigned applet

HTML5 JSmol

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

.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. To use this, instead of invoking JSmol.min.js you call:

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

and then you use the getTMApplet() method.

To partially compensate for the lack of scripting, some specific parameters of the Info variable are available.

Optional components

Integration with JME, a Java-based editor to draw 2D chemical structures (Peter Ertl's Java Molecular Editor)
Integration with JSpecView, a Java viewer for spectral data.
GLmol option to render the 3D model using a combination of HTML5 and WebGL graphics (in compatible systems) (does not use Java)
ChemDoodle option to render the 3D model using ChemDoodle (does not use Java)

Setting parameters

All of the initialization parameters supported in Jmol.js can be implemented in Jmol-JSO. 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)

This will create a myJmol 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.

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 Jmol object that is being created. You may wish to have two Jmols 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. To the contrary, Jmol (right at the beginning) must be written as such, since it is the internal name and identification of the unique Jmol-JSO constructor.

Info 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:

var Info = {
  color: "#FFFFFF",  // white background (note this changes legacy default which was black)
  height: 300,      // pixels (but it may be in percent)
  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
  memoryLimit: 512,             // only used in the Java modality
  serverURL: "php/jsmol.php", // needed only for some features, but should 
                              // be in your server for full functionality
  defaultModel: "",
  script: null,
  src: null,
  readyFunction: null,
  addSelectionOptions: false,
  debug: false
};

A more detailed explanation of the parameters of the Info variable is available in a separate page.

Setting parameters from the URL

Jmol 14.0 or later

Some values in the Info 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.

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.

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

Contributors

AngelHerraez, Hansonr, Hansonrstolaf, Cudo29, Ceroni, Ppillot

Jmol JavaScript Object

Contents

Jmol-JSO

Main features of Jmol-JSO

JSmol

Current limitations of JSmol

Reading binary files

Converting pages from Jmol to JSmol

Conversion using the Jmol2.js 'adapter' library

Upgrading Jmol without using JSmol

Installation

Getting the Files

Specific browser considerations

Firefox/Windows

MSIE/Windows

Chrome/Windows

Opera/Windows

Firefox/Mac

Chrome/Mac

Safari/Mac

Initialization

Browser issues

Loading the library

Lightweight JSmol

Optional components

Setting parameters

Setting parameters from the URL

Functions for Jmol JavaScript Object

Contributors

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