Jmol JavaScript Object
JSmol, the Jmol JavaScript Object
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 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
JSmol
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 php/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, 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.
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: .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.
- 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 jsmol.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 jsmol.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
- 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 in the JSmol/HTML5 modality. Note that usually you don't need all those files for operation, 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 21.3 MB, but only those parts actually needed in each occasion will be downloaded to the client computer).
- js is only important if you want to experiment with the code (advanced).
- idioma is no longer available nor needed. In former versions of JSmol it was a sibling folder of j2s, needed so that users of languages other than US English would see the JSmol interface, menu and messages in their own language.
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.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.GLmol.min.js is a supplementary library addressed at using a WebGL modality of the Jmol Object. Note that this is experimental, not under active development, and not fully functional.
- 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 usingvar x = load(...)
in a Jmol script) in some browsers.
- 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:
- 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.
- j2s The suite of JavaScript libraries needed for JSmol/HTML5 modality.
- js Non-packed copies of JavaScript libraries needed for the Jmol 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 public 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
- JSmolJSV.js Needed only for using the JSpecView object
- A few sample pages and files, included for your convenience but not required for functionality:
- make and test are for developers only. (The make directory includes the Google Closure Compiler used to create Jsmol.min.js.) flot, inchi, jcse, jsme, etc. are for specific applications (advanced)
- idioma (deprecated) Support for the interface in languages other than US English. Note: in recent versions, this folder does not exist any more; the functionality is now in files inside the j2s folder.
- applet The files for the Java modality (JmolApplet), the same that have been used for Jmol in previous versions.
- (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.)
- In most cases these are not needed, since Java support has been removed from web browsers.
- In the most recent versions this folder has been removed from the distribution.
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
Use of Internet Explorer (version 9 or higher) may be functional but it is discouraged; compatibility may be reduced and the performance is poor.
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
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".
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:"
- 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
- Integration with JSME, an editor to draw 2D chemical structures (Peter Ertl's JavaScript Molecular Editor)
- Integration with JSpecView, a viewer for spectral data.
- WebGL modality to render the 3D model using a combination of HTML5 and WebGL graphics (in compatible systems)
- ChemDoodle option to render the 3D model using ChemDoodle
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¶meter2=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
Contributors
AngelHerraez, Hansonr, Hansonrstolaf, Cudo29, Ceroni, Ppillot