Compatibility

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Known Compatibilities

JSmol is compatible with:

jQuery 1.9+ But see below.
Google Charts
MathJax (but see below)
JSME (JavaScript Molecular Editor
JSpecView

Known jQuery Incompatibilities

A bug/design fault/design decision in jQuery 2.0 prevents MSIE to be used for local pages that access remote files. This issue will reportedly not be fixed. jQuery 1.10 also has this bug, but at least there is a simple fix for that. See [1].

Known Variable Scope Incompatibilities

JSmol will create the following global variables and will be incompatible with any package that does likewise:

our object:

Jmol

primary Java-derived package names:

java javajs  J   JM  JS  JSV   JU   JV 

used by javajs for communication in relation to dialogs and menus:

SwingController

Java2Script globals:

Clazz   c$   "j2s.clazzloaded"  "j2s.doProfile" "j2s.lib" "j2s.object.native"

standard JavaScript classes that have been extended by Java2Script to be compatible with java.lang classes of the same name:

Array Boolean Character Date Error Number String

additional java.lang classes that are made global to be compatible with standard Java usage:

AbstractMethodError AbstractStringBuilder Appendable ArithmeticException ArrayIndexOutOfBoundsException ArrayStoreException AssertionError CharSequence ClassCastException ClassCircularityError ClassFormatError ClassNotFoundException CloneNotSupportedException Cloneable Comparable Enum Exception ExceptionInInitializerError IllegalAccessError IllegalAccessException IllegalArgumentException IllegalMonitorStateException IllegalStateException IllegalThreadStateException IncompatibleClassChangeError IndexOutOfBoundsException InstantiationError InstantiationException InternalError InterruptedException Iterable LinkageError NegativeArraySizeException NoClassDefFoundError NoSuchFieldError NoSuchFieldException NoSuchMethodError NoSuchMethodException NullPointerException NumberFormatException OutOfMemoryError Runnable RuntimeException SecurityException StackOverflowError StackTraceElement StringBuffer StringBuilder StringIndexOutOfBoundsException Thread ThreadDeath ThreadGroup Throwable UnknownError UnsatisfiedLinkError UnsupportedClassVersionError UnsupportedOperationException VerifyError VirtualMachineError Void

Note that Java2Script had to be extensively augmented to work with Jmol. Therefore JSmol will be incompatible with other Java2Script applications using the default implementations of Clazz.

MathJax Compatibility Issues

MathJax works by first loading a web page, then, after that is complete, editing the special mark-up on the page to turn those marks into beautiful math expressions. The problem is that both Jmol and MathJax are competing for the page processing after a page is loaded. Fortunately, MathJax was designed with this issue in mind, and there is a way of monitoring its progress. We need to start creating Jmol objects only after MathJax completes its job.

For compatibility with MathJax, make sure you:

1) are using JSmol (JSmol.min.js, not the older Jmol.js)

2) are using dynamic loading of JSmol

   -- use  $(document).ready() to create all JSmol objects
   -- no <script> tags that use Jmol.getApplet() within the body

3) set the jQuery $(document).ready event to add a hook to start JSmol loading upon the MathJax "End" signal:

$(document).ready(function(){
  MathJax.Hub.Register.StartupHook("End", loadJmol);
});

 loadJmol = function() {
  var Info = {
    width: 300,
    height: 300,
    debug: false,
    color: "0xFFFFFF",
    addSelectionOptions: true,
    use: "HTML5",
    j2sPath: "./j2s",
    jarPath: "./java",
    jarFile: "JmolAppletSigned.jar",
    isSigned: true,
    script: "set antialiasDisplay;load $caffeine",
    serverURL: "http://chemapps.stolaf.edu/jmol/jsmol/php/jsmol.php",
    readyFunction: jmol_isReady,
    disableJ2SLoadMonitor: false,
    disableInitialConsole: true,
    allowJavaScript: true
  }
  $("#appletplace").html(Jmol.getAppletHtml("jmol", Info));
 }
...
 </head>
 <body>
 <div id="appletplace"></div>
...

A demonstration page can be found at [2].(credit goes to David Guichard, Whitman College, for finding this solution)


Other Incompatibilities

Privacy Badger

The Firefox add-on "Privacy Badger" will cause an error with JSmol pages. The error looks like TypeError: getStackTrace(...) is undefined. This is exclusive to the Firefox version of Privacy Badger and does not occur on Chrome.

The add-on must be disabled completely for JSmol to work. Clicking "disable Privacy Badger on this site" will not help.

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