Jmol JavaScript Object

From Jmol
Revision as of 16:15, 6 March 2013 by Hansonr (talk | contribs) (getAppletHtml)
Jump to navigation Jump to search


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 File icon.gif 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 (although it requires its own customization of jQuery, File icon.gifJSmoljQuery.js). The library has been W3C and XHTML validated.

Main Features of Jmol-JSO

Non-Java OptionsOptions 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, File icon.gifJSmol.min.js and Folder icon.gifj2s and/or 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() 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 Starts accepting script commands immediately, caching them until Jmol is ready to accept them.


JSmol is the name for the HTML5 canvas version of the Jmol applet. JSmol opens up the use of Jmol to 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 requires 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 (MSIE allows access to non-binary local files only; Opera allows no access to local files; Chrome allows access only after setting a configuration flag).
  • Opening binary files (e.g Spartan files, gzipped files, PNGJ files): binary files can be read, but binary-type files 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).
  • Resizing of HTML5 canvases is not yet supported.
  • The Jmol PROMPT command does not allow more than a simple JavaScript-like response in the HTML5 version.
  • WebGL support is limited.

Reading binary files

These are currently the extensions that make JSmol read a file as binary: File icon.gif.gz File icon.gif.jpg File icon.gif.png File 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. In addition, 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. The demo pages use the jsmol.php script that is included in the JSmol distribution (see below), which does that and considerably more.


As software evolves, it is possible that versions may differ in their compatibility; the Jmol team appreciates all feedback from web page developers in this regard and make every effort to keep the files up to date. Please file a bug report if you find a problem.

The most up-to-date version of JSmol can be found as St. Olaf. Full releases may be obtained at the JSmol Project page.

File contains these files and folders:

  • Major files:
    • File icon.gifJSmol.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 icon.gifjsmol.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
  • Folder icon.gifjava The files for the JmolApplet, the same that have been used for Jmol in previous versions
    • File icon.gifJmolApplet.jar or File icon.gifJmolAppletSigned.jar or File icon.gifJmolApplet0*.jar or File icon.gifJmolAppletSigned0*.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.)
  • Folder icon.gifjs The suite of JavaScript libraries needed for building the Jmol-JSO object (but most of these files are already included in packed form within File icon.gifJSmol.min.js, see below):
    • File icon.gifJSmol.js Primary JSmol libarary
    • File icon.gifJSmolCore.js Primary JSmol library
    • File icon.gifJSmolApplet.js Required applet/canvas prototypes
    • File icon.gifJSmolApi.js All user-intended interface functions
    • File icon.gifJSmoljQuery.js A version of jQuery tweaked to allow synchronous binary file transfer
    • File icon.gifj2sjmol.js Required interface to the Jmol and java classes (translated into JavaScript)
    • File icon.gifJSmolControls.js Required only if any buttons or links or other input methods will be used
    • File icon.gifJSmolJSV.js Needed only for using the JSpecView applet
    • File icon.gifJSmolGLmol.js Needed only for using the WebGL version of JSmol
    • File icon.gifJSmolThree.js Needed only for using the WebGL version of JSmol
  • Folder icon.gifj2s The suite of JavaScript libraries needed for JSmol, which is the non-Java, HTML5-only surrogate with full Jmol functionality
  • Some accessory files, included for your convenience but not required for functionality:
    • File icon.gifjsmol.htm, File icon.gifsimple.htm, File icon.giftest2.htm are demonstration/example pages
    • Folder icon.gifdata Files used by the above demo pages
  • Folder icon.gifmake and Folder icon.giftest are for developers only. (The Folder icon.gifmake directory includes the Google Closure Compiler used to create File icon.gifJsmol.min.js.)

In summary:

  • For pages that use HTML5-only JSmol, you just need File icon.gifJSmol.min.js and Folder icon.gifj2s (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, you just need File icon.gifJSmol.min.js and Folder icon.gifjava (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 icon.gifjs is only important if you want to use the (experimental, not fully functional) WebGL version of JSmol. Specifically, you need File icon.gifjs/JSmolGLmol.js and File icon.gifjs/JSmolThree.js (which are not minimized), since those two libraries are not included in File icon.gifJSmol.min.js.


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: File icon.gif.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
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.

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 an applet or an alternative non-Java viewer is simply:

var myJmol = 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 JmolApplet that is being created. You may wish to have two applets 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 after the equal sign) must be written as such, since it is the internal name and identification of the unique Jmol-JSO constructor.
When you use this method, you must always use as the first parameter the same name, in quotes, of the variable being assigned to the JavaScript Object. This is important, because controls created in relation to the Jmol object and its callback functions need to incorporate the ID of the Jmol JavaScript Object in order to work properly.

Info is an associative array (a set of key/value pairs) indicating all the desired characteristics of the applet. The principal keys and their default values are given below:

var Info = {
  addSelectionOptions: false,
  color: "#FFFFFF",
  debug: false,
  defaultModel: "",
  height: 300,
  isSigned: false,
  jarFile: "JmolApplet0.jar",
  jarPath: ".",
  memoryLimit: 512,
  readyFunction: null,
  script: null,
  serverURL: "",
  src: null,
  use: "Java noWebGL noHTML5 noImage",
  width: 300

Detailed explanation of the parameters of the Info variable.

Functions for creation or display of Jmol Objects

The following functions all relate to applet creation or display. All of them must be applied to the unique Jmol object (this name is literal, cannot be changed) --see syntax and examples below.


Definition: Jmol.getApplet = function(id, Info, checkOnly)

This function creates the JavaScript Object that keeps track of the Jmol applet (or the JSmol surrogate if a non-Java option is active). It should be assigned to a variable with the same name as the id. For example:

myJmol = Jmol.getApplet("myJmol", Info);

checkOnly is an optional true/false flag that allows, when set true, to get a JavaScript Object that can be checked to see what type of applet would be created on this particular platform -- a signed Java applet, an unsigned Java applet, a JSmol canvas, an image, a GLmol canvas, etc.


Definition: Jmol.getAppletHtml = function(id)

Useful for inserting the applet code into the page, in the case when it was generated and stored in a variable (id) after Jmol.setDocument(0). It is particularly useful within the jQuery $(document).ready function. For example:

  Info.deferApplet = false;
  Info.deferUncover = true;
  jmol1 = Jmol.getApplet("jmol1", Info)    
  Info.deferApplet = true;
  Info.deferUncover = true;
  jmol2 = Jmol.getApplet("jmol2", Info)    


Definition: Jmol.getVersion = function()

This function returns the version of Jmol-JSO, like Jmol-JSO 13.0.


var t = Jmol.getVersion(myJmol);


Definition: Jmol.resizeApplet = function(applet,size)

(Untested in the HTML5 version of JSmol.) Used to change the dimensions of the specified applet.

size: a value or a pair of width/height values in an array, either expressed in pixels or as percent.


Jmol.resizeApplet(myJmol, 400);
Jmol.resizeApplet(myJmol, [400,700]);
Jmol.resizeApplet(myJmol, "100%");
Jmol.resizeApplet(myJmol, ["50%","60%"]);


Definition: Jmol.setAppletSync = function(applets, commands, isJmolJSV)


Definition: Jmol.setDocument = function(doc)

doc is the target html context where the Jmol Object must be created.

If using Jmol.setDocument(false) or Jmol.setDocument(0), the Jmol Object may be later inserted using Jmol.getAppletHtml(). What happens is that the HTML code for the object is put into the internal applet._code variable and not written to the page. Then you can still refer to the applet, but place it on the page after the controls are made, or inject ot into the page upon some user action.


myJmol = Jmol.getApplet("myJmol", Info);
document.getElementById('someContainer').innerHTML = Jmol.getAppletHtml(myJmol);

For some situations this may be equivalent to a simpler alternative: Just define the applet variable like var myJmol = "myJmol" and then, "myJmol" will suffice when providing any options or creating buttons and controls. Finally, use myJmol = Jmol.getApplet(myJmol,....) and the Object will work.


Definition: Jmol.setGrabberOptions = function(options)

Jmol._grabberOptions = [
  ["$", "NCI(small molecules)"],
  [":", "PubChem(small molecules)"],
  ["=", "RCSB(macromolecules)"]


Definition: Jmol.showInfo = function(applet, tf)

This displays or hides the information panel (which holds the log console, or maybe an associated JME applet). By default, that panel is located in the same position as the Jmol viewer, so displaying Info will hide Jmol and vice versa.

The tf parameter is a true or false flag.


Definition: Jmol.setInfo = function(applet, info, isShown)


Definition: Jmol.setXHTML = function(id)

Functions for creating controls

These Jmol functions create elements of the page that the page visitor can use to interact with the applet or applet surrogate. Again, all these functions must be applied to the unique Jmol object (this name is literal, cannot be changed) --see syntax and examples below.

The first parameter for nearly all of these functions, appletOrId, must be a reference to the applet that will receive action of the control. Such reference is either the JSO object itself or its name-id (e.g. "myJmol" in the examples above).

In the following descriptions, a colored italic font is used for parameters that are optional.


Inserts in the page a button with a text label.

Definition: Jmol.jmolButton(appletOrId, script, label, id, title)


var myJmol = "myJmol";
var myInfo = {
  color: "#DDDDFF",
  script: "load myMolecule.mol;",
  height: 300,
  width: 300
myJmol = Jmol.getApplet("myJmol", myInfo);
Jmol.jmolButton(myJmol,"spacefill on", "display as vdW spheres");

script is run when the button is pressed. As a special syntax (valid for any other controls as well as the button described here), instead of a Jmol script you can run a JavaScript function that you have defined, by providing this in place of the script: [funcName, param1, param2, param3...] The function must be defined in this way:

function funcName(btn, obj, target) {
    // Entire array object is provided as 2nd argument.
    var param1 = obj[1];
    var param2 = obj[2];
    var param3 = obj[3];
    // JavaScript to execute here.

label is the text in the button; if not specified, it defaults to the first 32 characters of the script.

id (optional) will be set as both the HTML id and HTML name. It will default to jmolButton0, jmolButton1, etc.

In addition, the button will be included in a <span> element that will have an HTML id of "span_" plus the given id, and an HTML title of the given title.
Browsers will hence show title as a tooltip when mouse pointer stays over the button.


Definition: Jmol.jmolCheckbox(appletOrId, scriptWhenChecked, scriptWhenUnchecked, labelHtml, isChecked, id, title)


Definition: Jmol.jmolCommandInput(appletOrId, label, size, id, title)


Definition: Jmol.jmolLink(appletOrId, script, text, id, title)

script is run when the user clicks on the link.

text is written to the page as a link. If it is not specified, it defaults to the first 32 characters of script.

id will be set as both the HTML id and HTML name. It will default to jmolLink0, jmolLink1, etc.

In addition, the link text will be included in a <span> element that will have an HTML id of "span_" plus the given id, and an HTML title of the given title.
Browsers will hence show title as a tooltip when mouse pointer stays over the link.


Definition: Jmol.jmolMenu(appletOrId, arrayOfMenuItems, size, id, title)


Definition: Jmol.jmolRadio(appletOrId, script, labelHtml, isChecked, separatorHtml, groupName, id, title)


Definition: Jmol.jmolRadioGroup(appletOrId, arrayOfRadioButtons, separatorHtml, groupName, id, title)


Definition: Jmol.setCheckboxGroup(chkMaster,chkBox)

Functions that insert HTML

These simple commands just deliver HTML to the page. They are merely convenience functions for use from within the body so as not to have to continually switch in and out of script tags.

Again, all these functions must be applied to the unique Jmol object (this name is literal, cannot be changed) --see syntax and examples below.

Much better practice is to do all control creation in the header of the page, from within jQuery's $(document).ready() function, using Jmol.setDocument(0), appending the HTML to a growing string using the control-specific functions, then setting the code in a predefined div element using the jQuery $('#divId').html() function.


Inserts a soft line break. Its only use is:



Allows to insert in the page any HTML code you may wish. Example:

Jmol.jmolHtml(' <b style="color:red">H<sub>2</sub>O</b> ')

Functions that set CSS rules

These functions, called prior to the creation of the associated object(s), allow the page designer to add specific attributes (usually, but not necessarily CSS style attributes) to the HTML tag(s) that will be created later. This allows setting one or more common style attributes for, for example, all buttons in a certain cell of a table, or all radio buttons of a certain group. Either a class name or an attribute can be given. For example:

  Jmol.setButtonCss(null, "style='width:160px'");

Again, all these functions must be applied to the unique Jmol object (this name is literal, cannot be changed) --see syntax and examples below.


Definition: Jmol.setAppletCss = function(cssClass, text)


Definition: Jmol.setButtonCss = function(cssClass, text)


Definition: Jmol.setCheckboxCss = function(cssClass, text)


Definition: Jmol.setLinkCss = function(cssClass, text)


Definition: Jmol.setMenuCss = function(cssClass, text)


Definition: Jmol.setRadioCss = function(cssClass, text)

Other public methods

All these functions must be applied to the unique Jmol object (this name is literal, cannot be changed) --see syntax and examples below.

(TO-DO -- just transfer text with slight modification from jslibrary)


Jmol.evaluate = function(applet,molecularMath) 
Jmol.getInfo = function(applet) 
Jmol.getPropertyAsArray = function(applet,sKey,sValue)
Jmol.getPropertyAsJavaObject = function(applet,sKey,sValue)
Jmol.getPropertyAsJSON = function(applet,sKey,sValue) 
Jmol.getPropertyAsString = function(applet,sKey,sValue)
Jmol.getStatus = function(applet,strStatus) 
Jmol.loadFile = function(applet, fileName, params)
Jmol.restoreOrientation = function(applet,id) 
Jmol.restoreOrientationDelayed = function(applet,id,delay)
Jmol.saveOrientation = function(applet,id) 
Jmol.say = function(msg) 
Jmol.script = function(applet, script) 
Jmol.scriptEcho = function(applet, script) 
Jmol.scriptMessage = function(applet, script) 
Jmol.scriptWait = function(applet, script) 
Jmol.scriptWaitAsArray = function(applet, script) 
Jmol.scriptWaitOutput = function(applet, script) = function(applet, query, script) 

Methods specific to optional components