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.

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 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 constructor (this name is literal, cannot be changed) --see syntax and examples below.

getApplet

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

This function creates in JavaScript space of the webpage the Jmol object (either a Jmol/Java applet or a JSmol object). For example:

Jmol.getApplet("myJmol", Info);

The above example will create a myJmol variable that holds the Jmol Object, and the object will be inserted in the page (unless Jmol.setDocument() has been set false, see below).

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 Jmol Object would be created on this particular platform -- a signed Java applet, an unsigned Java applet, a JSmol canvas, an image, a WebGL canvas, etc.

getTMApplet

This function creates and inserts the lightweight variety of JSmol object. For example:

Jmol.getTMApplet("myJmol", Info);

Note: the reason for the name is that this lightweight alternative was inspired on a viewer named TwirlyMol.

getAppletHtml

Definition: Jmol.getAppletHtml = function(JmolObject)

or: Jmol.getAppletHtml = function(id, Info)

Useful for inserting the Jmol object code into the page, either after page has loaded or in the case when the object was generated and stored in a variable, e.g. after Jmol.setDocument(0). It is particularly useful with .innerHTML inside window.onload or in a function fired by user action (or the jQuery equivalents .html() and $(document).ready). Some examples:

window.onload = function(){
  Jmol.setDocument(0);
  Jmol.getApplet("jmol1", Info); // creates the object but does not insert it
  Jmol.getApplet("jmol2", Info);
  [...] // other actions, that may affect the Jmol objects
  // now, let's insert the objects in the page:
  document.getElementById("place1").innerHTML = Jmol.getAppletHtml(jmol1);
  document.getElementById("place2").innerHTML = Jmol.getAppletHtml(jmol2);
});

jQuery equivalent syntax:

$(document).ready(function(){
  Jmol.setDocument(0);
  Jmol.getApplet("jmol1", Info); // creates the object but does not insert it
  Jmol.getApplet("jmol2", Info);
  [...] // other actions, that may affect the Jmol objects
  // now, let's insert the objects in the page:
  $("#place1").html(Jmol.getAppletHtml(jmol1));
  $("#place2").html(Jmol.getAppletHtml(jmol2));
});

Or a simpler syntax that creates the object and inserts it at the same time:

window.onload = function(){
  document.getElementById("place1").innerHTML = Jmol.getAppletHtml("jmol1", Info);
  document.getElementById("place2").innerHTML = Jmol.getAppletHtml("jmol2", Info);
});

See also under Jmol.setDocument()

getVersion

Definition: Jmol.getVersion = function()

This function returns the version of Jmol-JSO, like Jmol-JSO 13.1.12.

Example:

var t = Jmol.getVersion(myJmol);
alert(t);

resizeApplet

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

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

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

Examples:

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

setAppletSync

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

setDocument

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.

Example:

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

or, using jQuery syntax;

Jmol.setDocument(false);
Jmol.getApplet("myJmol", Info);
(...)
$("#someContainer").html(Jmol.getAppletHtml(myJmol));

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

setGrabberOptions

Definition: Jmol.setGrabberOptions = function(options)

Allows to customize the items offered in the drop-down menu that fetches molecules from databases, when using addSelectionOptions:true. Example:

Jmol.setGrabberOptions([
  ["$", "small molecules at NCI"],
  [":", "small molecules at PubChem"],
  ["==", "ligands at PDB"],
  ["=", "macromolecules at PDB"]
])

The first value in each element is the JmolScript prefix to direct the request to the database (this cannot be customized). The second value is the text that is displayed in the drop-down menu in the page, below the Jmol object.

showInfo

Definition: Jmol.showInfo = function(JmolObject, 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.

setInfo

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

Sets the information div for the Jmol object to be info (HTML) and optionally displays it.

setXHTML

Definition: Jmol.setXHTML = function(id)

Indicates id of the DOM node into which the Jmol object will be inserted, following XHTML format when creating page elements. Largely untested.

Example:

<!doctype html>
<head>
<meta charset="UTF-8" />
<title>test XHTML</title>
<script type="text/javascript" src="JSmol.min.js"></script>
<script type="text/javascript">
$(document).ready(function(){
  var Info = {
    height: 300,
    width: 300,
    j2sPath: "j2s",
    use: "HTML5"
  };
  Jmol.setXHTML('myContainer');
  Jmol.getApplet(myJmol, Info);
});
</script>
</head>
<body>
<p>Some text</p>
<div id="myContainer"></div>
<p>Some more text</p>
</body>
</html>

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 constructor (this name is literal, cannot be changed) --see syntax and examples below.

The first parameter for nearly all of these functions, JmolObject, must be a reference to the object 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.

jmolButton

Inserts in the page a button with a text content.

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

Example:

var myInfo = {
  color: "#DDDDFF",
  script: "load myMolecule.mol;",
  height: 300,
  width: 300
};
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.

Advanced:

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.

jmolCheckbox

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

Inserts a checkbox into the page, followed immediately by labelHtml.

scriptWhenChecked is run when the checkbox is checked by the user.

scriptWhenUnchecked is run when the user unchecks the checkbox.

isChecked should be set to a non-false value (e.g.: true) if you want the checkbox to be checked or marked upon page loading (default: unchecked).

id will be set as both the HTML id and HTML name. It will default to jmolCheckbox0, jmolCheckbox1, etc.

Browsers will show title as a tooltip when mouse pointer stays over the checkbox or over its accompanying labelHtml.

Example:

Jmol.jmolCheckbox(myJmol,"spacefill on","spacefill off","toggle display as spheres");

setCheckboxGroup

Definition: Jmol.setCheckboxGroup(chkMaster,chkBoxes)

Starting with previously inserted checkboxes (using Jmol.jmolCheckbox()), this allows to establish a relation between one "parent" or "leader" checkbox and one or more "child" or "follower" checkboxes, according to these rules:

• Whenever the leader is checked, all its followers get automatically checked.
• Whenever the leader is unchecked, all its followers get automatically unchecked.
• Whenever one of the followers is checked or unchecked, its siblings are examined; if all have the same state, the leader will be checked or unchecked accordingly.

The Jmol scripts associated to each checkbox when it was inserted/defined will be executed when its state changes due to action on another checkbox.

chkMaster is the ID given to the checkbox that will act as leader. This ID may have been specified in its Jmol.jmolCheckbox()) definition, or may be a number (if ID was not specified, sequential numeric IDs are assigned by default, starting from zero).

chkBoxes is an array of one or more IDs or numbers, pointing to the checkboxes that will act as followers.

Any number of groups can be set in a page, with any number of component checkboxes. Nesting groups within other groups is also possible (i.e., a follower in one group may be the leader for an inner group).

jmolCommandInput

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

jmolLink

Definition: Jmol.jmolLink(JmolObject, 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.

Example:

Jmol.jmolLink(myJmol,"load adenine.mol","adenine");

Advanced:

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.

jmolMenu

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

jmolRadio

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

Inserts a single radio button into the page, followed immediately by labelHtml.

script is run when the user checks the radio button.

labelHtml is written to the page right after the radio button. Note that it must be a text string (if you wanted to use a number, wrap it in quotes).

isChecked should be set to a non-false value (e.g.: true) if you want the radio button to be marked upon page loading (default: not checked).

Radio buttons will be assigned to the group specified by groupName. In other words, linked radio buttons (those mutually exclusive in their checked state) will be those that share the same value of groupName. If you don't want to use a groupName, all buttons will be assigned to the same group (with an automatically assigned name).

separatorHtml is used to specify HTML code that should be placed after the radio button and its labelHtml. For example, to put the radio buttons on separate lines you should pass in <br> as the actual parameter. If separatorHtml is not specified, it defaults to a non-breaking space.

id will be set as the HTML id. If not provided, a default name is made up automatically.

The radio button label will be surrounded by <label> tags; the effect is that clicking on the label text will have the same effect as clicking on the radio button itself.

Example:

Jmol.jmolRadio(myJmol,"spacefill 23%; wireframe 0.15;","ball and stick",true);

jmolRadioGroup

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

Inserts a group of mutually-exclusive radio buttons into the page.

arrayOfRadioButtons is usually specified using the JavaScript square brackets [ entryA, entryB, ... ] notation. Each entry is generally another array which contains a script, a label (text displayed in the page after the radio button), and an optional isChecked flag. If an entry is a single string instead of an array, then that string is used for both the script and the label.

separatorHtml is used to specify HTML code that should be placed after each radio button and its label, but before the next radio button. For example, to put the radio buttons on separate lines you should pass in <br> as the actual parameter. If separatorHtml is not specified, it defaults to a non-breaking space.

Radio buttons will all belong to a group with an HTML name of groupName. If you don't specify one, it will be automatically made up.

The whole group of radio buttons will be included in a <span> element that will have as its HTML id the value of id or, if this is not given, the value of groupName. In turn, each radio button + label will have as its HTML id span_ plus the group's id plus an underscore plus a sequential number (starting at zero), and as its HTML title, the common title. Each radio button label will be surrounded by <label> tags; the effect is that clicking on the label text will have the same effect as clicking on the radio button itself.

Example:

 var r = [
    ["spacefill 23%; wireframe 0.15;","ball and stick",true],
    ["spacefill off; wireframe 0.15;","sticks"],
    ["spacefill on; wireframe off;","spheres"]
 ];
 Jmol.jmolRadioGroup(myJmol, r, "<br>", "atomstyle");

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 constructor (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.

jmolBr

Inserts a soft line break. Its only use is:

Jmol.jmolBr()

jmolHtml

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 constructor (this name is literal, cannot be changed) --see syntax and examples below.

setAppletCss

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

setButtonCss

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

setCheckboxCss

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

setLinkCss

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

setMenuCss

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

setRadioCss

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

Function that interact with a running applet

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

evaluateVar

Allows to extract to JavaScript (e.g. to a variable) information from a variable set in the Jmol scripting language, a Jmol math expression, or some model information. Examples:

Definition: Jmol.evaluateVar = function(applet,molecularMath)

Examples:

   	alert( Jmol.evaluateVar(jmolApplet0, "a") );
   	// Displays the value of the 'a' variable if set in Jmol script.
   	alert( Jmol.evaluateVar(jmolApplet0, "{*}.xyz") );
   	// Displays the coordinates of the geometric center of the model.
   	alert( Jmol.evaluateVar(jmolApplet0, "{*}.length") );
   	// Displays the total number of atoms in the model.
   	alert( Jmol.evaluateVar(jmolApplet0, "{carbon}.bonds.length.min") );
   	// Displays the minimum bond length between carbon atoms.
   	alert( Jmol.evaluateVar(jmolApplet0, "_atomPicked") );
   	// Displays the index of the atom that was most recently picked.

Note: An older version of this method, Jmol.evaluate(), is deprecated, as it only returns String, Integer, or Float values.

getPropertyAsArray

Returns applet information in the form of a JavaScript array, when applicable, or other appropriate JavaScript variable type such as boolean, number, or string.

Definition: Jmol.getPropertyAsArray = function(JmolObject,sKey,sValue)

Example:

   	var atoms = Jmol.getPropertyAsArray(jmolApplet0, "atomInfo","all");
   	var atom1 = atoms[0];
   	var x = atom1.x;
   	var info = atom1.info; 

getPropertyAsJavaObject

Returns the property as a Java (not JavaScript) object. This function is for advanced users only and is not generally recommended, as it delivers a pointer to the Java object itself, not a copy of it. This pointer may or may not be valid indefinitely and may or may not be properly garbage-collected by all browsers. The principal use of this function is for access to public Viewer methods that are not generally available via the applet interface.

Note that even the HTML5 version of JSmol returns objects that for all practical purposes are "Java Objects" using this method. The only difference is that the JavaScript implementations have no aspect of "private" or "public" -- all methods are effectively public.

Definition: Jmol.getPropertyAsJavaObject = function(JmolObject,sKey,sValue)

Example:

   	var viewer = jmolGetPropertyAsJavaObject("jmolViewer")
   	var radius = viewer.getRotationRadius() 

Many of these public methods are listed in http://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/api/JmolViewer.java

getPropertyAsJSON

Returns data as per jmolGetPropertyAsArray, but always as a JavaScript string in JavaScript Object Notation. This string can then be surrounded by parentheses and evaluated to create array content.

Definition: Jmol.getPropertyAsJSON = function(JmolObject,sKey,sValue)

Example:

   var info = Jmol.getPropertyAsJSON(jmolApplet0, "filename") // {"filename": "file:/C:/data/caffeine.xyz"}

getPropertyAsString

Returns data as per jmolGetPropertyAsArray, but always as a JavaScript string. In the case of arrayed data, this string is formatted for easier reading.

Definition: Jmol.getPropertyAsString = function(JmolObject,sKey,sValue)

Examples:

var s = Jmol.getPropertyAsString(myJmol,'stateInfo');
img.src = 'data:image/jpeg;base64,' + Jmol.getPropertyAsString(JmolObject,'image');

script

Runs a Jmol script asynchronously, meaning the script is put into a queue and most likely not processed before the function call is returned. This call can be made any time after applet creation; one does not have to wait until the applet is ready for receiving scripts (as was the case with Jmol/java utilizing Jmol.js).

Definition: Jmol.script = function(JmolObject, myScript)

myScript (a text string containing one or several Jmol commands) is placed on the script queue.

Examples:

Jmol.script(myJmol,"spacefill off; wireframe 0.3;");
Jmol.script(myJmol,"script someScript.spt;");

scriptEcho

Runs a script synchronously, returning the text that might have gone to the console

Definition: Jmol.scriptEcho = function(JmolObject, myScript)

Example:

alert(Jmol.scriptEcho(jmolApplet0,"show file")) 

scriptWait

Runs a script synchronously, similarly to ScriptEcho, but returns a string including messages.

Definition: Jmol.scriptWait = function(JmolObject, myScript)

Example:

 Jmol.scriptWait(jmolApplet0, "backgroundred")

returns:

 2,scriptStatus,0,script 15 started
 3,scriptStatus,0,script ERROR: command expected
 ----
         >> backgroundred <<
 4,scriptStatus,0,Script completed
 5,scriptTerminated,1,Jmol script terminated successfully
 7,scriptTerminated,1,Jmol script terminated unsuccessfully: Jmol script terminated
 1,scriptStarted,15,backgroundred
 6,scriptError,0,Jmol script terminated

Deprecated/Unnecessary/Not Recommended

The following methods are retained for JSmol from Jmol but are not recommended. Most have simple scriptable alternatives.

Jmol.getInfo = function(applet) // Jmol.getPropertyAsArray(jmolApplet0, "appletInfo")
Jmol.getStatus = function(applet,strStatus)  // deprecated
Jmol.loadFile = function(applet, fileName, params) // Jmol.script(jmolApplet0, "load '" + fileName + "'....")
Jmol.restoreOrientation = function(applet,id) // Jmol.script(jmolApplet0, "restore orientation " + id)
Jmol.restoreOrientationDelayed = function(applet,id,delay)  // Jmol.script(jmolApplet0, "delay " + delay  + "; restore orientation " + id)
Jmol.say = function(msg)  // alert(msg)
Jmol.saveOrientation = function(applet,id) // Jmol.script(jmolApplet0, "saveOrientation " + id) 
Jmol.scriptMessage = function(applet, script) // Jmol.scriptWait(....)
Jmol.scriptWaitAsArray = function(applet, script) // deprecated
Jmol.scriptWaitOutput = function(applet, script)  // same as Jmol.scriptWait; deprecated; see Jmol.scriptEcho
Jmol.search = function(applet, query, script) // Jmol.script(jmolApplet0, "load $caffeine") for example

Methods specific to optional components

• Methods specific to the JME applet
• Methods specific to the JSpecView applet

Contributors

AngelHerraez, Hansonr, Hansonrstolaf, Cudo29, Ceroni, Ppillot