X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fjs%2FJSmolCore.js;fp=site%2Fjs%2FJSmolCore.js;h=66517bba4771b3b966688ec5b38fa7782c77d92c;hp=b1a06e8d7840b1a865e9e410ad518c77a5e1be5e;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/js/JSmolCore.js b/site/js/JSmolCore.js
index b1a06e8..66517bb 100644
--- a/site/js/JSmolCore.js
+++ b/site/js/JSmolCore.js
@@ -1,2223 +1,2223 @@
-// JSmolCore.js -- Jmol core capability 
-
-// allows Jmol applets to be created on a page with more flexibility and extendability
-// provides an object-oriented interface for JSpecView and syncing of Jmol/JSpecView
-
-// see JSmolApi.js for public user-interface. All these are private functions
-
-// BH 5/30/2015 9:33:12 AM adds class swingjs-ui to ignore 
-// BH 5/9/2015 3:38:52 PM adds data-ignoreMouse attribute for JTextField
-// BH 3/30/2015 9:46:53 PM adds JSAppletPanel for ready callback
-// BH 12/6/2014 3:32:54 PM Jmol.setAppletCss() broken
-// BH 9/13/2014 2:15:51 PM embedded JSME loads from SEARCH when Jmol should 
-// BH 8/14/2014 2:52:38 PM drag-drop cache should not be cleared if SPT file is dropped
-// BH 8/5/2014 6:39:54 AM unnecessary messages about binary for PDB finally removed
-// BH 8/4/2014 5:30:00 AM automatically switch to no document after page loading
-// BH 8/2/2014 5:22:40 PM drag-drop broken in JSmol/HTML5 
-// BH 7/23/2014 5:34:08 PM setting a parameter such as readyFunction to null stops file loading
-// BH 7/3/2014 12:30:28 AM lost drag-drop of models
-// BH 7/2/2014 4:47:55 AM adding pdbe.org to direct database calls
-// BH 5/30/2014 7:20:07 AM better dragging for console and menu
-// BH 4/27/2014 6:31:52 PM allows _USE=SIGNED HTML5 as well as _USE=JAVA HTML5
-// BH 3/8/2014 5:50:51 PM adds support for dataURI download in FF and Chrome
-// BH 3/8/2014 8:43:10 AM moves PubChem access to https
-// BH 3/4/2014 8:40:15 PM adds Jmol.Cache for JSV/Jmol sharing files
-// BH 2/10/2014 10:07:14 AM added Info.z and Info.zIndexBase
-// BH 2/9/2014 9:56:06 PM updated JSmolCore.js with option to extend Viewer with code PRIOR to loading Viewer classes
-// BH 2/6/2014 8:46:25 AM disabled Jmol._tracker for localhost and 127.x.x.x 
-// BH 1/29/2014 8:02:23 AM Jmol.View and Info.viewSet
-// BH 1/21/2014 12:06:59 PM adding Jmol.Info.cacheFiles (applet, true/false) and applet._cacheFiles and Jmol._fileCache
-// BH 1/13/2014 2:12:38 PM adding "http://www.nmrdb.org/tools/jmol/predict.php":"%URL", to _DirectDatabaseCalls
-// BH 12/21/2013 6:38:35 PM applet sync broken
-// BH 12/6/2013 6:18:32 PM cover.htm and coverImage fix
-// BH 12/4/2013 7:44:26 PM fix for JME independent search box
-// BH 12/3/2013 6:30:08 AM fix for ready function returning Boolean instead of boolean in HTML5 version
-// BH 11/30/2013 10:31:37 AM added type:"GET" for jQuery.ajax() requests instead of using defaults
-// BH 11/30/2013 10:31:37 AM added cache:true for jQuery.ajax() requests; can override with cache:"NO", not cache:false
-// BH 11/28/2013 11:09:27 AM added Jmol._alertNoBinary:true
-// BH 11/26/2013 8:19:55 PM fix !xxxx search commmand entry and stop MSIE from duplicating command
-// BH 11/25/2013 7:38:31 AM adds Jmol._tracker: option for GoogleAnalytics tracking
-// BH 11/25/2013 7:39:03 AM adds URL options _J2S=  _JAR=  _USE=
-// BH 11/23/2013 10:51:37 PM  adds JNLP support for local applet
-// BH 11/2/2013 12:05:11 PM JSmolJSME fixes; https access fixed
-// BH 10/31/2013 7:50:06 PM Jmol.Dialog as SwingController; Jmol._mouseOwner added
-// BH 10/19/2013 7:05:04 AM adding Jmol._ajaxCall for Error Contacting Server; database POST method enabled
-// BH 10/17/2013 1:40:51 PM  adding javajs/swing and Jmol.Dialog
-// BH 9/30/2013 6:42:24 PM: pdb.gz switch  pdb should only be for www.rcsb.org
-// BH 9/17/2013 10:17:51 AM: asynchronous file reading and saving
-// BH 8/16/2013 12:02:20 PM: JSmoljQueryExt.js pulled out
-// BH 8/16/2013 12:02:20 PM: Jmol._touching used properly
-
-// BH 3/22/2013 5:53:02 PM: Adds noscript option, JSmol.min.core.js
-// BH 1/17/2013 5:20:44 PM: Fixed problem with console not getting initial position if no first click
-// 1/13/2013 BH: Fixed MSIE not-reading-local-files problem.
-// 11/28/2012 BH: Fixed MacOS Safari binary ArrayBuffer problem
-// 11/21/2012 BH: restructuring of files as JS... instead of J...
-// 11/20/2012 BH: MSIE9 cannot do a synchronous file load cross-domain. See Jmol._getFileData
-// 11/4/2012 BH: RCSB REST format change "<structureId>" to "<dimStructure.structureId>"
-// 9/13/2012 BH: JmolCore.js changes for JSmol doAjax() method -- _3ata()
-// 6/12/2012 BH: JmolApi.js: adds Jmol.setInfo(applet, info, isShown) -- third parameter optional 
-// 6/12/2012 BH: JmolApi.js: adds Jmol.getInfo(applet) 
-// 6/12/2012 BH: JmolApplet.js: Fixes for MSIE 8
-// 6/5/2012  BH: fixes problem with Jmol "javascript" command not working and getPropertyAsArray not working
-// 6/4/2012  BH: corrects problem with MSIE requiring mouse-hover to activate applet
-// 5/31/2012 BH: added JSpecView interface and api -- see JmolJSV.js
-//               also changed "jmolJarPath" to just "jarPath"
-//               jmolJarFile->jarFile, jmolIsSigned->isSigned, jmolReadyFunction->readyFunction
-//               also corrects a double-loading issue
-// 5/14/2012 BH: added AJAX queue for ChemDoodle option with multiple canvases 
-// 8/12/2012 BH: adds support for MSIE xdr cross-domain request (jQuery.iecors.js)
-
-	// BH 4/25 -- added text option. setAppletCss(null, "style=\"xxxx\"")
-	// note that since you must add the style keyword, this can be used to add any attribute to these tags, not just css. 
-
-// required/optional libraries (preferably in the following order):
-
-//    jquery/jquery.js     -- at least jQuery.1.9
-//    js/JSmoljQueryext.js -- required for binary file transfer; otherwise standard jQuery should be OK
-//    js/JSmolCore.js      -- required
-//    js/j2sjmol.js        -- required
-//    js/JSmol.js          -- required
-//    js/JSmolApplet.js    -- required; internal functions for _Applet and _Image; must be after JSmolCore
-//    js/JSmolControls.js  -- optional; internal functions for buttons, links, menus, etc.; must be after JSmolCore
-//    js/JSmolConsole.js   -- optional; for the pop-up console
-//    js/JSmolApi.js       -- required; all user functions; must be after JSmolCore
-//    js/JSmolTHREE.js     -- optional; WebGL library required for JSmolGLmol.js
-//    js/JSmolGLmol.js     -- optional; WebGL version of JSmol.
-//    js/JSmolJME.js       -- optional; JSME (2D editor)
-//    jsme/jsme/jsme.nocache.js   --  required for JSME 
-//    js/JSmolMenu.js      -- optional; required for menuing in JSV
-//    js/JSmolJSV.js       -- optional; for creating and interacting with a JSpecView applet 
-
-// most of these will be loaded automatically, and for most installations, all you need is JSmol.min.js
-
-
-// Allows Jmol-like objects to be displayed on Java-challenged (iPad/iPhone)
-// or applet-challenged (Android/iPhone) platforms, with automatic switching to 
-
-// For your installation, you should consider putting JmolData.jar and jsmol.php 
-// on your own server. Nothing more than these two files is needed on the server, and this 
-// allows more options for MSIE and Chrome when working with cross-domain files (such as RCSB or pubChem) 
-
-// The NCI and RCSB databases are accessed via direct AJAX if available (xhr2/xdr).
-
-
-if(typeof(jQuery)=="undefined") alert ("Note -- JSmoljQuery is required for JSmol, but it's not defined.")
-
-// An example of how to extend Jmol with code PRIOR to JSmolCore.js or JSmol.min.js follows:
-//
-// 
-//	Jmol = {
-//  	z:3000,
-//		extend: function(what, obj) {if (what == "viewer") { obj._testing = true } }
-//	}
-
-self.Jmol || (Jmol = {});
-
-if (!Jmol._version)
-Jmol = (function(document) {
-	var z=Jmol.z || 9000;
-	var getZOrders = function(z) {
-		return {
-			rear:z++,
-			header:z++,
-			main:z++,
-			image:z++,
-			front:z++,
-			fileOpener:z++,
-			coverImage:z++,
-			dialog:z++, // could be several of these, JSV only
-			menu:z+90000, // way front
-			console:z+91000, // even more front
-      consoleImage:z+91001, // bit more front; increments
-			monitorZIndex:z+99999 // way way front
-		}
-	};
-	var j = {
-		_version: "$Date: 2015-04-26 10:57:08 -0500 (Sun, 26 Apr 2015) $", // svn.keywords:lastUpdated
-		_alertNoBinary: true,
-		// this url is used to Google Analytics tracking of Jmol use. You may remove it or modify it if you wish. 
-		_allowedJmolSize: [25, 2048, 300],   // min, max, default (pixels)
-		/*  By setting the Jmol.allowedJmolSize[] variable in the webpage
-				before calling Jmol.getApplet(), limits for applet size can be overriden.
-				2048 standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html)
-		*/
-		_appletCssClass: "",
-		_appletCssText: "",
-		_fileCache: null, // enabled by Jmol.setFileCaching(applet, true/false)
-		_jarFile: null,  // can be set in URL using _JAR=
-		_j2sPath: null,  // can be set in URL using _J2S=
-		_use: null,      // can be set in URL using _USE=
-		_j2sLoadMonitorOpacity: 90, // initial opacity for j2s load monitor message
-		_applets: {},
-		_asynchronous: true,
-		_ajaxQueue: [],
-		_getZOrders: getZOrders,
-		_z:getZOrders(z),
-		_debugCode: true,  // set false in process of minimization
-		db: {
-			_databasePrefixes: "$=:",
-			_fileLoadScript: ";if (_loadScript = '' && defaultLoadScript == '' && _filetype == 'Pdb') { select protein or nucleic;cartoons Only;color structure; select * };",
-			_nciLoadScript: ";n = ({molecule=1}.length < {molecule=2}.length ? 2 : 1); select molecule=n;display selected;center selected;",
-			_pubChemLoadScript: "",
-			_DirectDatabaseCalls:{
-				// these sites are known to implement access-control-allow-origin * 
-				"cactus.nci.nih.gov": "%URL", 
-				"www.rcsb.org": "%URL",
-				"pdbe.org": "%URL", 
-				"www.ebi.ac.uk": "%URL", 
-				"wwwdev.ebi.ac.uk": "%URL", 
-				"pubchem.ncbi.nlm.nih.gov":"%URL",
-				"http://www.nmrdb.org/tools/jmol/predict.php":"%URL",
-				"$": "http://cactus.nci.nih.gov/chemical/structure/%FILENCI/file?format=sdf&get3d=True",
-				"$$": "http://cactus.nci.nih.gov/chemical/structure/%FILENCI/file?format=sdf",
-				"=": "http://www.rcsb.org/pdb/files/%FILE.pdb",
-				"*": "http://www.ebi.ac.uk/pdbe/entry-files/download/%FILE.cif",
-				"==": "http://www.rcsb.org/pdb/files/ligand/%FILE.cif",
-				":": "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d"
-			},
-			_restQueryUrl: "http://www.rcsb.org/pdb/rest/search",
-			_restQueryXml: "<orgPdbQuery><queryType>org.pdb.query.simple.AdvancedKeywordQuery</queryType><description>Text Search</description><keywords>QUERY</keywords></orgPdbQuery>",
-			_restReportUrl: "http://www.pdb.org/pdb/rest/customReport?pdbids=IDLIST&customReportColumns=structureId,structureTitle"
-		},
-		_debugAlert: false,
-		_document: document,
-		_isXHTML: false,
-		_lastAppletID: null,
-		_mousePageX: null,
-		_mouseOwner: null,
-		_serverUrl: "http://your.server.here/jsmol.php",
-		_syncId: ("" + Math.random()).substring(3),
-		_touching: false,
-		_XhtmlElement: null,
-		_XhtmlAppendChild: false
-	}
-	
-	var ref = document.location.href.toLowerCase();
-	j._httpProto = (ref.indexOf("https") == 0 ? "https://" : "http://"); 
-	j._isFile = (ref.indexOf("file:") == 0);
-	j._ajaxTestSite = j._httpProto + "google.com";
-	var isLocal = (j._isFile || ref.indexOf("http://localhost") == 0 || ref.indexOf("http://127.") == 0);
-	j._tracker = (j._httpProto == "http://" && !isLocal && 'http://chemapps.stolaf.edu/jmol/JmolTracker.htm?id=UA-45940799-1');
-	
-	j._isChrome = (navigator.userAgent.toLowerCase().indexOf("chrome") >= 0);
-	j._isSafari = (!j._isChrome && navigator.userAgent.toLowerCase().indexOf("safari") >= 0);
-	j._isMsie = (window.ActiveXObject !== undefined);
-	j._useDataURI = !j._isSafari && !j._isMsie; // safari may be OK here -- untested
-
-	for(var i in Jmol) j[i] = Jmol[i]; // allows pre-definition
-	return j;
-})(document, Jmol);
-
-
-(function (Jmol, $) {
-
-// this library is organized into the following sections:
-
-	// jQuery interface 
-	// protected variables
-	// feature detection
-	// AJAX-related core functionality
-	// applet start-up functionality
-	// misc core functionality
-	// mouse events
-
-
-	////////////////////// jQuery interface ///////////////////////
-
-	// hooks to jQuery -- if you have a different AJAX tool, feel free to adapt.
-	// There should be no other references to jQuery in all the JSmol libraries.
-
-	// automatically switch to returning HTML after the page is loaded
-	$(document).ready(function(){ Jmol._document = null });
-
-	Jmol.$ = function(objectOrId, subdiv) {
-		// if a subdiv, then return $("#objectOrId._id_subdiv") 
-		// or if no subdiv, then just $(objectOrId)
-		if (objectOrId == null)alert (subdiv + arguments.callee.caller.toString());
-			return $(subdiv ? "#" + objectOrId._id + "_" + subdiv : objectOrId);
-	} 
-
-	Jmol._$ = function(id) {
-		// either the object or $("#" + id)
-		return (typeof id == "string" ? $("#" + id) : id);
-	}
-
-	/// special functions:
-
-	Jmol.$ajax = function (info) {
-		Jmol._ajaxCall = info.url;
-		info.cache = (info.cache != "NO");
-		if (info.url.indexOf("http://pubchem.ncbi.nlm.nih") == 0)
-			info.url = "https://" + info.url.substring(7);
-			// fluke at pubchem --- requires https now from all pages 3/8/2014
-		// don't let jQuery add $_=... to URL unless we 
-		// use cache:"NO"; other packages might use $.ajaxSetup() to set this to cache:false
-		return $.ajax(info);
-	}
-
-	Jmol._getNCIInfo = function(identifier, what, fCallback) {
-		return Jmol._getFileData("http://cactus.nci.nih.gov/chemical/structure/"+identifier +"/" + (what == "name" ? "names" : what));
-	}
-	
-
-
-	Jmol.$appEvent = function(app, subdiv, evt, f) {
-		var o = Jmol.$(app, subdiv); 
-		o.off(evt) && f && o.on(evt, f);
-	}   
-
-	Jmol.$resize = function (f) {
-		return $(window).resize(f);
-	}
-
-	//// full identifier expected (could be "body", for example):
-
-	Jmol.$after = function (what, s) {
-		return $(what).after(s);
-	}
-
-	Jmol.$append = function (what, s) {
-		return $(what).append(s);
-	}
-
-	Jmol.$bind = function(what, list, f) {
-		return (f ? $(what).bind(list, f) : $(what).unbind(list));
-	}
-
-	Jmol.$closest = function(what, d) {
-		return $(what).closest(d);
-	}
-	
-	Jmol.$get = function(what, i) {
-	return $(what).get(i);
-	}
- 
-	// element id expected
-			 
-	Jmol.$documentOff = function(evt, id) {
-		return $(document).off(evt, "#" + id);
-	}
-
-	Jmol.$documentOn = function(evt, id, f) {
-		return $(document).on(evt, "#" + id, f);
-	}
-
-	Jmol.$getAncestorDiv = function(id, className) {
-		return $("div." + className + ":has(#" + id + ")")[0];
-	}
-
-	Jmol.$supportsIECrossDomainScripting = function() {
-		return $.support.iecors;
-	}
-
-	//// element id or jQuery object expected:
-
-	Jmol.$attr = function (id, a, val) {
-		return Jmol._$(id).attr(a, val);
-	}
-
-	Jmol.$css = function(id, style) {
-		return Jmol._$(id).css(style);
-	}
-	 
-	Jmol.$find = function(id, d) {
-		return Jmol._$(id).find(d);
-	}
-	
-	Jmol.$focus = function(id) {
-		return Jmol._$(id).focus();
-	}
-
-	Jmol.$html = function(id, html) {
-		return Jmol._$(id).html(html);
-	}
-	 
-	Jmol.$offset = function(id) {
-		return Jmol._$(id).offset();
-	}
-
-	Jmol.$windowOn = function(evt, f) {
-		return $(window).on(evt, f);
-	}
-
-	Jmol.$prop = function(id, p, val) {
-		var o = Jmol._$(id);
-		return (arguments.length == 3 ? o.prop(p, val) : o.prop(p));
-	}
-
-	Jmol.$remove = function(id) {
-		return Jmol._$(id).remove();
-	}
-
-	Jmol.$scrollTo = function (id, n) {
-		var o = Jmol._$(id);
-		return o.scrollTop(n < 0 ? o[0].scrollHeight : n);
-	}
-
-	Jmol.$setEnabled = function(id, b) {
-		return Jmol._$(id).attr("disabled", b ? null : "disabled");  
-	}
-
-	Jmol.$setSize = function(id, w, h) {
-		return Jmol._$(id).width(w).height(h);
-	}
-
-	Jmol.$setVisible = function(id, b) {
-		var o = Jmol._$(id);
-		return (b ? o.show() : o.hide());  
-	}
-
-	Jmol.$submit = function(id) {
-		return Jmol._$(id).submit();
-	}
-
-	Jmol.$val = function (id, v) {
-		var o = Jmol._$(id);
-		return (arguments.length == 1 ? o.val() : o.val(v));
-	}
-
-	////////////// protected variables ///////////
-
-
-	Jmol._clearVars = function() {
-		// only on page closing -- appears to improve garbage collection
-
-		delete jQuery;
-		delete $;
-		delete Jmol;
-		delete SwingController;
-		delete J;
-		delete JM;
-		delete JS;
-		delete JSV;
-		delete JU;
-		delete JV;
-		delete java;
-		delete javajs;
-		delete Clazz;
-		delete c$; // used in p0p; could be gotten rid of
-	}
-
-	////////////// feature detection ///////////////
-
-	Jmol.featureDetection = (function(document, window) {
-
-		var features = {};
-		features.ua = navigator.userAgent.toLowerCase()
-
-		features.os = (function(){
-			var osList = ["linux","unix","mac","win"]
-			var i = osList.length;
-
-			while (i--){
-				if (features.ua.indexOf(osList[i])!=-1) return osList[i]
-			}
-			return "unknown";
-		})();
-
-		features.browser = function(){
-			var ua = features.ua;
-			var browserList = ["konqueror","webkit","omniweb","opera","webtv","icab","msie","mozilla"];
-			for (var i = 0; i < browserList.length; i++)
-			if (ua.indexOf(browserList[i])>=0) 
-				return browserList[i];
-			return "unknown";
-		}
-		features.browserName = features.browser();
-		features.browserVersion= parseFloat(features.ua.substring(features.ua.indexOf(features.browserName)+features.browserName.length+1));
-		features.supportsXhr2 = function() {return ($.support.cors || $.support.iecors)}
-		features.allowDestroy = (features.browserName != "msie");
-		features.allowHTML5 = (features.browserName != "msie" || navigator.appVersion.indexOf("MSIE 8") < 0);
-		features.getDefaultLanguage = function() {
-			return navigator.language || navigator.userLanguage || "en-US";
-		};
-
-		features._webGLtest = 0;
-
-		features.supportsWebGL = function() {
-		if (!Jmol.featureDetection._webGLtest) { 
-			var canvas;
-			Jmol.featureDetection._webGLtest = ( 
-				window.WebGLRenderingContext 
-					&& ((canvas = document.createElement("canvas")).getContext("webgl") 
-				|| canvas.getContext("experimental-webgl")) ? 1 : -1);
-		}
-		return (Jmol.featureDetection._webGLtest > 0);
-	};
-
-	features.supportsLocalization = function() {
-		//<meta charset="utf-8">                                     
-		var metas = document.getElementsByTagName('meta'); 
-		for (var i= metas.length; --i >= 0;) 
-			if (metas[i].outerHTML.toLowerCase().indexOf("utf-8") >= 0) return true;
-		return false;
-		};
-
-	features.supportsJava = function() {
-		if (!Jmol.featureDetection._javaEnabled) {
-			if (Jmol._isMsie) {
-				if (!navigator.javaEnabled()) {
-					Jmol.featureDetection._javaEnabled = -1;
-				} else {
-					//more likely -- would take huge testing
-					Jmol.featureDetection._javaEnabled = 1;
-				}
-			} else {
-				Jmol.featureDetection._javaEnabled = (navigator.javaEnabled() && (!navigator.mimeTypes || navigator.mimeTypes["application/x-java-applet"]) ? 1 : -1);
-			}
-		}
-		return (Jmol.featureDetection._javaEnabled > 0);
-	};
-
-	features.compliantBrowser = function() {
-		var a = !!document.getElementById;
-		var os = features.os;
-		// known exceptions (old browsers):
-		if (features.browserName == "opera" && features.browserVersion <= 7.54 && os == "mac"
-			|| features.browserName == "webkit" && features.browserVersion < 125.12
-			|| features.browserName == "msie" && os == "mac"
-			|| features.browserName == "konqueror" && features.browserVersion <= 3.3
-		) a = false;
-		return a;
-	}
-
-	features.isFullyCompliant = function() {
-		return features.compliantBrowser() && features.supportsJava();
-	}
-
-	features.useIEObject = (features.os == "win" && features.browserName == "msie" && features.browserVersion >= 5.5);
-	features.useHtml4Object = (features.browserName == "mozilla" && features.browserVersion >= 5) ||
-		(features.browserName == "opera" && features.browserVersion >= 8) ||
-		(features.browserName == "webkit"/* && features.browserVersion >= 412.2 && features.browserVersion < 500*/); // 500 is a guess; required for 536.3
-
-	features.hasFileReader = (window.File && window.FileReader);
-
-	return features;
-
-})(document, window);
-
-
-		////////////// AJAX-related core functionality //////////////
-
-	Jmol._ajax = function(info) {
-		if (!info.async) {
-			return Jmol.$ajax(info).responseText;
-		}
-		Jmol._ajaxQueue.push(info)
-		if (Jmol._ajaxQueue.length == 1)
-			Jmol._ajaxDone()
-	}
-	Jmol._ajaxDone = function() {
-		var info = Jmol._ajaxQueue.shift();
-		info && Jmol.$ajax(info);
-	}
-
-	Jmol._grabberOptions = [
-		["$", "NCI(small molecules)"],
-		[":", "PubChem(small molecules)"],
-		["=", "RCSB(macromolecules)"],
-		["*", "PDBe(macromolecules)"]
-	];
-
-	Jmol._getGrabberOptions = function(applet) {
-		// feel free to adjust this look to anything you want
-		if (Jmol._grabberOptions.length == 0)
-			return ""
-
-
-		var s = '<input type="text" id="ID_query" onfocus="jQuery(this).select()" onkeypress="if(13==event.which){Jmol._applets[\'ID\']._search();return false}" size="32" value="" />';
-		var b = '<button id="ID_submit" onclick="Jmol._applets[\'ID\']._search()">Search</button></nobr>'
-		if (Jmol._grabberOptions.length == 1) {
-			s = '<nobr>' + s + '<span style="display:none">';
-			b = '</span>' + b;
-		} else {
-			s += '<br /><nobr>'
-		}
-		s += '<select id="ID_select">'
-		for (var i = 0; i < Jmol._grabberOptions.length; i++) {
-			var opt = Jmol._grabberOptions[i];
-			s += '<option value="' + opt[0] + '" ' + (i == 0 ? 'selected' : '') + '>' + opt[1] + '</option>';
-		}
-		s = (s + '</select>' + b).replace(/ID/g, applet._id);
-		return '<br />' + s;
-	}
-
-	Jmol._getScriptForDatabase = function(database) {
-		return (database == "$" ? Jmol.db._nciLoadScript : database == ":" ? Jmol.db._pubChemLoadScript : Jmol.db._fileLoadScript);
-	}
-
-	 //   <dataset><record><structureId>1BLU</structureId><structureTitle>STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CHROMATIUM VINOSUM</structureTitle></record><record><structureId>3EUN</structureId><structureTitle>Crystal structure of the 2[4Fe-4S] C57A ferredoxin variant from allochromatium vinosum</structureTitle></record></dataset>
-
-	Jmol._setInfo = function(applet, database, data) {
-		var info = [];
-		var header = "";
-		if (data.indexOf("ERROR") == 0)
-			header = data;
-		else
-			switch (database) {
-			case "=":
-				var S = data.split("<dimStructure.structureId>");
-				var info = ["<table>"];
-				for (var i = 1; i < S.length; i++) {
-					info.push("<tr><td valign=top><a href=\"javascript:Jmol.search(" + applet._id + ",'=" + S[i].substring(0, 4) + "')\">" + S[i].substring(0, 4) + "</a></td>");
-					info.push("<td>" + S[i].split("Title>")[1].split("</")[0] + "</td></tr>");
-				}
-				info.push("</table>");
-				header = (S.length - 1) + " matches";
-				break;      
-			case "$": // NCI
-			case ":": // pubChem
-			break;
-			default:
-				return;
-		}
-		applet._infoHeader = header;
-		applet._info = info.join("");
-		applet._showInfo(true);
-	}
-
-	Jmol._loadSuccess = function(a, fSuccess) {
-		if (!fSuccess)
-			return;
-		Jmol._ajaxDone();
-		fSuccess(a);
-	}
-
-	Jmol._loadError = function(fError){
-		Jmol._ajaxDone();
-		Jmol.say("Error connecting to server: " + Jmol._ajaxCall);  
-		null!=fError&&fError()
-	}
-
-	Jmol._isDatabaseCall = function(query) {
-		return (Jmol.db._databasePrefixes.indexOf(query.substring(0, 1)) >= 0);
-	}
-
-	
-	Jmol._getDirectDatabaseCall = function(query, checkXhr2) {
-		if (checkXhr2 && !Jmol.featureDetection.supportsXhr2())
-			return query;
-		var pt = 2;
-		var db;
-		var call = Jmol.db._DirectDatabaseCalls[query.substring(0,pt)];
-		if (!call)
-			call = Jmol.db._DirectDatabaseCalls[db = query.substring(0,--pt)];
-		if (call) {
-			if (db == ":") {
-				var ql = query.toLowerCase();
-				if (!isNaN(parseInt(query.substring(1)))) {
-					query = "cid/" + query.substring(1);
-				} else if (ql.indexOf(":smiles:") == 0) {
-					call += "?POST?smiles=" + query.substring(8);
-					query = "smiles";
-				} else if (ql.indexOf(":cid:") == 0) {
-					query = "cid/" + query.substring(5);
-				} else {
-					if (ql.indexOf(":name:") == 0)
-						query = query.substring(5);
-					else if (ql.indexOf(":cas:") == 0)
-						query = query.substring(4);
-					query = "name/" + encodeURIComponent(query.substring(pt));
-				}
-			} else {
-				query = encodeURIComponent(query.substring(pt));		
-			}
-			if (call.indexOf("FILENCI") >= 0) {
-				query = query.replace(/\%2F/g, "/");				
-				query = call.replace(/\%FILENCI/, query);
-			} else {
-				query = call.replace(/\%FILE/, query);
-			}
-		}		
-		return query;
-	}
-
-	Jmol._getRawDataFromServer = function(database,query,fSuccess,fError,asBase64,noScript){
-	  // note that this method is now only enabled for "_"
-	  // server-side processing of database queries was too slow and only useful for 
-	  // the IMAGE option, which has been abandoned.
-		var s = 
-			"?call=getRawDataFromDatabase&database=" + database + (query.indexOf("?POST?") >= 0 ? "?POST?" : "")
-				+ "&query=" + encodeURIComponent(query)
-				+ (asBase64 ? "&encoding=base64" : "")
-				+ (noScript ? "" : "&script=" + encodeURIComponent(Jmol._getScriptForDatabase(database)));
-		return Jmol._contactServer(s, fSuccess, fError);
-	}
-
-	Jmol._checkFileName = function(applet, fileName, isRawRet) {
-		if (Jmol._isDatabaseCall(fileName)) {
-			if (isRawRet)
-				Jmol._setQueryTerm(applet, fileName);
-			fileName = Jmol._getDirectDatabaseCall(fileName, true);
-			if (Jmol._isDatabaseCall(fileName)) {
-				// xhr2 not supported (MSIE)
-				fileName = Jmol._getDirectDatabaseCall(fileName, false);
-				isRawRet && (isRawRet[0] = true);
-			}
-		}
-		return fileName;
-	}
-	
-	Jmol._checkCache = function(applet, fileName, fSuccess) {
-		if (applet._cacheFiles && Jmol._fileCache && !fileName.endsWith(".js")) {
-			var data = Jmol._fileCache[fileName];
-			if (data) {
-				System.out.println("using "  + data.length + " bytes of cached data for "  + fileName);
-				fSuccess(data);
-				return null;
-			} else {
-				fSuccess = function(fileName, data) { fSuccess(Jmol._fileCache[fileName] = data) };     
-			}
-		}
-		return fSuccess;
-	}
-	
-	Jmol._loadFileData = function(applet, fileName, fSuccess, fError){
-		var isRaw = [];
-		fileName = Jmol._checkFileName(applet, fileName, isRaw);
-		fSuccess = Jmol._checkCache(applet, fileName, fSuccess);
-		if (isRaw[0]) {
-				Jmol._getRawDataFromServer("_",fileName,fSuccess,fError);   
-				return;
-		} 
-		var info = {
-			type: "GET",
-			dataType: "text",
-			url: fileName,
-			async: Jmol._asynchronous,
-			success: function(a) {Jmol._loadSuccess(a, fSuccess)},
-			error: function() {Jmol._loadError(fError)}
-		}
-		Jmol._checkAjaxPost(info);
-		Jmol._ajax(info);
-	}
-
-	Jmol._getInfoFromDatabase = function(applet, database, query){
-		if (database == "====") {
-			var data = Jmol.db._restQueryXml.replace(/QUERY/,query);
-
-			var info = {
-				dataType: "text",
-				type: "POST",
-				contentType:"application/x-www-form-urlencoded",
-				url: Jmol.db._restQueryUrl,
-				data: encodeURIComponent(data) + "&req=browser",
-				success: function(data) {Jmol._ajaxDone();Jmol._extractInfoFromRCSB(applet, database, query, data)},
-				error: function() {Jmol._loadError(null)},
-				async: Jmol._asynchronous
-			}
-			return Jmol._ajax(info);
-		}   
-		query = "?call=getInfoFromDatabase&database=" + database
-				+ "&query=" + encodeURIComponent(query);
-		return Jmol._contactServer(query, function(data) {Jmol._setInfo(applet, database, data)});
-	}
-
-	Jmol._extractInfoFromRCSB = function(applet, database, query, output) {
-		var n = output.length/5;
-		if (n == 0)
-			return; 
-		if (query.length == 4 && n != 1) {
-			var QQQQ = query.toUpperCase();
-			var pt = output.indexOf(QQQQ);
-			if (pt > 0 && "123456789".indexOf(QQQQ.substring(0, 1)) >= 0)
-				output = QQQQ + "," + output.substring(0, pt) + output.substring(pt + 5);
-			if (n > 50)
-				output = output.substring(0, 250);
-			output = output.replace(/\n/g,",");
-			var url = Jmol._restReportUrl.replace(/IDLIST/,output);
-			Jmol._loadFileData(applet, url, function(data) {Jmol._setInfo(applet, database, data) });   
-		}
-	}
-
-	Jmol._checkAjaxPost = function(info) {
-		var pt = info.url.indexOf("?POST?");
-		if (pt > 0) {
-			info.data = info.url.substring(pt + 6);
-			info.url = info.url.substring(0, pt);
-			info.type = "POST";
-			info.contentType = "application/x-www-form-urlencoded";
-		}
-	}
-	Jmol._contactServer = function(data,fSuccess,fError){
-		var info = {
-			dataType: "text",
-			type: "GET",
-			url: Jmol._serverUrl + data,
-			success: function(a) {Jmol._loadSuccess(a, fSuccess)},
-			error:function() { Jmol._loadError(fError) },
-			async:fSuccess ? Jmol._asynchronous : false
-		}
-		Jmol._checkAjaxPost(info);
-		return Jmol._ajax(info);
-	}
-
-	Jmol._setQueryTerm = function(applet, query) {
-		if (!query || !applet._hasOptions || query.substring(0, 7) == "http://")
-			return;
-		if (Jmol._isDatabaseCall(query)) {
-			var database = query.substring(0, 1);
-			query = query.substring(1);
-			if (query.substring(0,1) == database && "=$".indexOf(database) >= 0)
-				query = query.substring(1);
-			var d = Jmol._getElement(applet, "select");
-			if (d && d.options)
-				for (var i = 0; i < d.options.length; i++)
-					if (d[i].value == database)
-						d[i].selected = true;
-		}
-		Jmol.$val(Jmol.$(applet, "query"), query);
-	}
-
-	Jmol._search = function(applet, query, script) {
-		arguments.length > 1 || (query = null);
-		Jmol._setQueryTerm(applet, query);
-		query || (query = Jmol.$val(Jmol.$(applet, "query")))
-		if (query.indexOf("!") == 0) {
-		// command prompt in this box as well
-		// remove exclamation point "immediate" indicator
-			applet._script(query.substring(1));
-			return;
-		} 
-		query && (query = query.replace(/\"/g, ""));
-		applet._showInfo(false);
-		Jmol._searchMol(applet, query, script, true);
-	}
-
-	Jmol._searchMol = function(applet, query, script, checkView) {
-		var database;
-		if (Jmol._isDatabaseCall(query)) {
-			database = query.substring(0, 1);
-			query = query.substring(1);
-		} else {
-			database = (applet._hasOptions ? Jmol.$val(Jmol.$(applet, "select")) : "$");
-		}
-		if (database == "=" && query.length == 3)
-			query = "=" + query; // this is a ligand      
-		var dm = database + query;
-		if (!query || dm.indexOf("?") < 0 && dm == applet._thisJmolModel) {
-			return;    
-		}
-		applet._thisJmolModel = dm;
-		var view;
-		if (checkView && applet._viewSet != null && (view = Jmol.View.__findView(applet._viewSet, {chemID:dm})) != null) {
-			Jmol.View.__setView(view, applet, false);
-			return;
-		}
-
-		if (database == "$" || database == ":")
-			applet._jmolFileType = "MOL";
-		else if (database == "=")
-			applet._jmolFileType = "PDB";
-		applet._searchDatabase(query, database, script);
-	}
-
-	Jmol._searchDatabase = function(applet, query, database, script) {
-		applet._showInfo(false);
-		if (query.indexOf("?") >= 0) {
-			Jmol._getInfoFromDatabase(applet, database, query.split("?")[0]);
-			return true;
-		}
-		if (Jmol.db._DirectDatabaseCalls[database]) {
-			applet._loadFile(database + query, script);
-			return true;
-		}
-		return false;
-	}
-
-	Jmol._syncBinaryOK="?";
-
-	Jmol._canSyncBinary = function(isSilent) {
-		if (Jmol._isAsync) return true;
-		if (self.VBArray) return (Jmol._syncBinaryOK = false);
-		if (Jmol._syncBinaryOK != "?") return Jmol._syncBinaryOK;
-		Jmol._syncBinaryOK = true;
-		try {
-			var xhr = new window.XMLHttpRequest();
-			xhr.open( "text", Jmol._ajaxTestSite, false );
-			if (xhr.hasOwnProperty("responseType")) {
-				xhr.responseType = "arraybuffer";
-			} else if (xhr.overrideMimeType) {
-				xhr.overrideMimeType('text/plain; charset=x-user-defined');
-			}
-		} catch( e ) {
-			var s = "JSmolCore.js: synchronous binary file transfer is requested but not available";
-			System.out.println(s);
-			if (Jmol._alertNoBinary && !isSilent)
-				alert (s)
-			return Jmol._syncBinaryOK = false;
-		}
-		return true;  
-	}
-
-	Jmol._binaryTypes = [".gz",".jpg",".gif",".png",".zip",".jmol",".bin",".smol",".spartan",".mrc",".pse", ".map", ".omap"];
-
-	Jmol._isBinaryUrl = function(url) {
-		for (var i = Jmol._binaryTypes.length; --i >= 0;)
-			if (url.indexOf(Jmol._binaryTypes[i]) >= 0) return true;
-		return false;
-	}
-
-	Jmol._getFileData = function(fileName, fSuccess, doProcess) {
-		// use host-server PHP relay if not from this host
-		var isBinary = Jmol._isBinaryUrl(fileName);
-		var isPDB = (fileName.indexOf("pdb.gz") >= 0 && fileName.indexOf("http://www.rcsb.org/pdb/files/") == 0);
-		var asBase64 = (isBinary && !Jmol._canSyncBinary(isPDB));
-		if (asBase64 && isPDB) {
-			// avoid unnecessary binary transfer
-			fileName = fileName.replace(/pdb\.gz/,"pdb");
-			asBase64 = isBinary = false;
-		}
-		var isPost = (fileName.indexOf("?POST?") >= 0);
-		if (fileName.indexOf("file:/") == 0 && fileName.indexOf("file:///") != 0)
-			fileName = "file://" + fileName.substring(5);      /// fixes IE problem
-		var isMyHost = (fileName.indexOf("://") < 0 || fileName.indexOf(document.location.protocol) == 0 && fileName.indexOf(document.location.host) >= 0);
-		var isDirectCall = Jmol._isDirectCall(fileName);
-		//if (fileName.indexOf("http://pubchem.ncbi.nlm.nih.gov/") == 0)isDirectCall = false;
-
-		var cantDoSynchronousLoad = (!isMyHost && Jmol.$supportsIECrossDomainScripting());
-		var data = null;
-		if ((!fSuccess || asBase64) && (cantDoSynchronousLoad || asBase64 || !isMyHost && !isDirectCall)) {
-				data = Jmol._getRawDataFromServer("_",fileName, fSuccess, fSuccess, asBase64, true);
-		} else {
-			fileName = fileName.replace(/file:\/\/\/\//, "file://"); // opera
-			var info = {dataType:(isBinary ? "binary" : "text"),async:!!fSuccess};
-			if (isPost) {
-				info.type = "POST";
-				info.url = fileName.split("?POST?")[0]
-				info.data = fileName.split("?POST?")[1]
-			} else {
-				info.type = "GET";
-				info.url = fileName;
-			}
-			if (fSuccess) {
-				info.success = function(data) { fSuccess(Jmol._xhrReturn(info.xhr))};
-				info.error = function() { fSuccess(info.xhr.statusText)};
-			}
-			info.xhr = Jmol.$ajax(info);
-			if (!fSuccess) {
-				data = Jmol._xhrReturn(info.xhr);
-			}
-		}
-		if (!doProcess)
-			return data;
-		if (data == null) {
-			data = "";
-			isBinary = false;
-		}
-		isBinary && (isBinary = Jmol._canSyncBinary(true));
-		return (isBinary ? Jmol._strToBytes(data) : JU.SB.newS(data));
-	}
-	
-	Jmol._xhrReturn = function(xhr){
-		if (!xhr.responseText || self.Clazz && Clazz.instanceOf(xhr.response, self.ArrayBuffer)) {
-			// Safari or error 
-			return xhr.response || xhr.statusText;
-		} 
-		return xhr.responseText;
-	}
-
-	Jmol._isDirectCall = function(url) {
-		for (var key in Jmol.db._DirectDatabaseCalls) {
-			if (key.indexOf(".") >= 0 && url.indexOf(key) >= 0)
-				return true;
-		}
-		return false;
-	}
-
-	Jmol._cleanFileData = function(data) {
-		if (data.indexOf("\r") >= 0 && data.indexOf("\n") >= 0) {
-			return data.replace(/\r\n/g,"\n");
-		}
-		if (data.indexOf("\r") >= 0) {
-			return data.replace(/\r/g,"\n");
-		}
-		return data;
-	};
-
-	Jmol._getFileType = function(name) {
-		var database = name.substring(0, 1);
-		if (database == "$" || database == ":")
-			return "MOL";
-		if (database == "=")
-			return (name.substring(1,2) == "=" ? "LCIF" : "PDB");
-		// just the extension, which must be PDB, XYZ..., CIF, or MOL
-		name = name.split('.').pop().toUpperCase();
-		return name.substring(0, Math.min(name.length, 3));
-	};
-
-	Jmol._getZ = function(applet, what) {
-		return applet && applet._z && applet._z[what] || Jmol._z[what];
-	}
-	
-	Jmol._incrZ = function(applet, what) {
-		return applet && applet._z && ++applet._z[what] || ++Jmol._z[what];
-	}
-	
-	Jmol._loadFileAsynchronously = function(fileLoadThread, applet, fileName, appData) {
-		if (fileName.indexOf("?") != 0) {
-			// LOAD ASYNC command
-			var fileName0 = fileName;
-			fileName = Jmol._checkFileName(applet, fileName);
-			var fSuccess = function(data) {Jmol._setData(fileLoadThread, fileName, fileName0, data, appData)};
-			fSuccess = Jmol._checkCache(applet, fileName, fSuccess);
-			if (fileName.indexOf("|") >= 0)
-				fileName = fileName.split("|")[0];
-			return (fSuccess == null ? null : Jmol._getFileData(fileName, fSuccess));		
-		}
-		// we actually cannot suggest a fileName, I believe.
-		if (!Jmol.featureDetection.hasFileReader)
-				return fileLoadThread.setData("Local file reading is not enabled in your browser", null, null, appData);
-		if (!applet._localReader) {
-			var div = '<div id="ID" style="z-index:'+Jmol._getZ(applet, "fileOpener") + ';position:absolute;background:#E0E0E0;left:10px;top:10px"><div style="margin:5px 5px 5px 5px;"><input type="file" id="ID_files" /><button id="ID_loadfile">load</button><button id="ID_cancel">cancel</button></div><div>'
-			Jmol.$after("#" + applet._id + "_appletdiv", div.replace(/ID/g, applet._id + "_localReader"));
-			applet._localReader = Jmol.$(applet, "localReader");
-		}
-		Jmol.$appEvent(applet, "localReader_loadfile", "click");
-		Jmol.$appEvent(applet, "localReader_loadfile", "click", function(evt) {
-			var file = Jmol.$(applet, "localReader_files")[0].files[0];   
-			var reader = new FileReader();
-			reader.onloadend = function(evt) {
-				if (evt.target.readyState == FileReader.DONE) { // DONE == 2
-					Jmol.$css(Jmol.$(applet, "localReader"), {display : "none"});
-					Jmol._setData(fileLoadThread, file.name, file.name, evt.target.result, appData);
-				}
-			};
-			reader.readAsArrayBuffer(file);
-		});
-		Jmol.$appEvent(applet, "localReader_cancel", "click");
-		Jmol.$appEvent(applet, "localReader_cancel", "click", function(evt) {
-			Jmol.$css(Jmol.$(applet, "localReader"), {display: "none"});
-			fileLoadThread.setData(null, null, null, appData);
-		});
-		Jmol.$css(Jmol.$(applet, "localReader"), {display : "block"});
-	}
-
-  Jmol._setData = function(fileLoadThread, filename, filename0, data, appData) {
-  	data = Jmol._strToBytes(data);
-		if (filename.indexOf(".jdx") >= 0)
-			Jmol.Cache.put("cache://" + filename, data);
-		fileLoadThread.setData(filename, filename0, data, appData);
-  }
-  
-	Jmol._toBytes = function(data) {
-	if (typeof data == "string") 
-		return data.getBytes();
-	// ArrayBuffer assumed here
-	data = new Uint8Array(data);
-	var b = Clazz.newByteArray(data.length, 0);
-		for (var i = data.length; --i >= 0;)
-			b[i] = data[i];
-	return b;
-	}
-
-	Jmol._doAjax = function(url, postOut, dataOut) {
-		// called by org.jmol.awtjs2d.JmolURLConnection.doAjax()
-		url = url.toString();
-
-		if (dataOut != null) 
-			return Jmol._saveFile(url, dataOut);
-		if (postOut)
-			url += "?POST?" + postOut;
-		return Jmol._getFileData(url, null, true);
-	}
-
-	// Jmol._localFileSaveFunction --  // do something local here; Maybe try the FileSave interface? return true if successful
-	 
-	Jmol._saveFile = function(filename, data, mimetype, encoding) {
-		if (Jmol._localFileSaveFunction && Jmol._localFileSaveFunction(filename, data))
-			return "OK";
-		var filename = filename.substring(filename.lastIndexOf("/") + 1);
-		mimetype || (mimetype = (filename.indexOf(".pdf") >= 0 ? "application/pdf" 
-			: filename.indexOf(".png") >= 0 ? "image/png" 
-			: filename.indexOf(".gif") >= 0 ? "image/gif" 
-			: filename.indexOf(".jpg") >= 0 ? "image/jpg" : ""));
-		var isString = (typeof data == "string");
-		if (!isString)
-			data = (JU ? JU : J.util).Base64.getBase64(data).toString();
-		encoding || (encoding = (isString ? "" : "base64"));
-		var url = Jmol._serverUrl;
-		url && url.indexOf("your.server") >= 0 && (url = "");
-		if (Jmol._useDataURI || !url) {
-			// Asynchronous output generated using an anchor tag
-			encoding || (data = btoa(data));
-			var a = document.createElement("a");
-			a.href = "data:" + mimetype + ";base64," + data;
-			a.type = mimetype || (mimetype = "text/plain");	
-			a.download = filename;
-			a.target = "_blank";
-				$("body").append(a);
-			a.click();
-			a.remove();		
-		} else {
-		// Asynchronous outputto be reflected as a download
-			if (!Jmol._formdiv) {
-					var sform = '<div id="__jsmolformdiv__" style="display:none">\
-						<form id="__jsmolform__" method="post" target="_blank" action="">\
-						<input name="call" value="saveFile"/>\
-						<input id="__jsmolmimetype__" name="mimetype" value=""/>\
-						<input id="__jsmolencoding__" name="encoding" value=""/>\
-						<input id="__jsmolfilename__" name="filename" value=""/>\
-						<textarea id="__jsmoldata__" name="data"></textarea>\
-						</form>\
-						</div>'
-				Jmol.$after("body", sform);
-				Jmol._formdiv = "__jsmolform__";
-			}
-			Jmol.$attr(Jmol._formdiv, "action", url + "?" + (new Date()).getMilliseconds());
-			Jmol.$val("__jsmoldata__", data);
-			Jmol.$val("__jsmolfilename__", filename);
-			Jmol.$val("__jsmolmimetype__", mimetype);
-			Jmol.$val("__jsmolencoding__", encoding);
-			Jmol.$submit("__jsmolform__");
-			Jmol.$val("__jsmoldata__", "");
-			Jmol.$val("__jsmolfilename__", "");
-		}
-		return "OK";
-	}
-
-	Jmol._strToBytes = function(s) {
-		if (Clazz.instanceOf(s, self.ArrayBuffer))
-			return Jmol._toBytes(s);
-		var b = Clazz.newByteArray(s.length, 0);
-		for (var i = s.length; --i >= 0;)
-			b[i] = s.charCodeAt(i) & 0xFF;
-		return b;
-	}
-
-	////////////// applet start-up functionality //////////////
-
-	Jmol._setConsoleDiv = function (d) {
-		if (!self.Clazz)return;
-		Clazz.setConsoleDiv(d);
-	}
-
-	Jmol._registerApplet = function(id, applet) {
-		return window[id] = Jmol._applets[id] = Jmol._applets[applet] = Jmol._applets[id + "__" + Jmol._syncId + "__"] = applet;
-	} 
-
-	Jmol._readyCallback = function (appId,fullId,isReady,javaApplet,javaAppletPanel) {
-		appId = appId.split("_object")[0];
-    javaAppletPanel || (javaAppletPanel = javaApplet);
-		isReady = (isReady.booleanValue ? isReady.booleanValue() : isReady);
-		// necessary for MSIE in strict mode -- apparently, we can't call 
-		// jmol._readyCallback, but we can call Jmol._readyCallback. Go figure...
-    var applet = Jmol._applets[appId];
-    applet._appletPanel = javaAppletPanel;
-    applet._applet = javaApplet;
-		Jmol._track(applet._readyCallback(appId, fullId, isReady));
-	}
-
-	Jmol._getWrapper = function(applet, isHeader) {
-
-			// id_appletinfotablediv
-			//     id_appletdiv
-			//     id_coverdiv
-			//     id_infotablediv
-			//       id_infoheaderdiv
-			//          id_infoheaderspan
-			//          id_infocheckboxspan
-			//       id_infodiv
-
-
-			// for whatever reason, without DOCTYPE, with MSIE, "height:auto" does not work, 
-			// and the text scrolls off the page.
-			// So I'm using height:95% here.
-			// The table was a fix for MSIE with no DOCTYPE tag to fix the miscalculation
-			// in height of the div when using 95% for height. 
-			// But it turns out the table has problems with DOCTYPE tags, so that's out. 
-			// The 95% is a compromise that we need until the no-DOCTYPE MSIE solution is found. 
-			// (100% does not work with the JME linked applet)
-		var s;
-		// ... here are just for clarification in this code; they are removed immediately
-		if (isHeader) {
-			var img = ""; 
-			if (applet._coverImage){
-				var more = " onclick=\"Jmol.coverApplet(ID, false)\" title=\"" + (applet._coverTitle) + "\"";
-				var play = "<image id=\"ID_coverclickgo\" src=\"" + applet._j2sPath + "/img/play_make_live.jpg\" style=\"width:25px;height:25px;position:absolute;bottom:10px;left:10px;"
-					+ "z-index:" + Jmol._getZ(applet, "coverImage")+";opacity:0.5;\"" + more + " />"  
-				img = "<div id=\"ID_coverdiv\" style=\"background-color:red;z-index:" + Jmol._getZ(applet, "coverImage")+";width:100%;height:100%;display:inline;position:absolute;top:0px;left:0px\"><image id=\"ID_coverimage\" src=\""
-				 + applet._coverImage + "\" style=\"width:100%;height:100%\"" + more + "/>" + play + "</div>";
-			}
-			var css = Jmol._appletCssText.replace(/\'/g,'"');
-			css = (css.indexOf("style=\"") >= 0 ? css.split("style=\"")[1] : "\" " + css);
-			s = "\
-...<div id=\"ID_appletinfotablediv\" style=\"width:Wpx;height:Hpx;position:relative;font-size:14px;text-align:left\">IMG\
-......<div id=\"ID_appletdiv\" style=\"z-index:" + Jmol._getZ(applet, "header") + ";width:100%;height:100%;position:absolute;top:0px;left:0px;" + css + ">";
-			var height = applet._height;
-			var width = applet._width;
-			if (typeof height !== "string" || height.indexOf("%") < 0) 
-				height += "px";
-			if (typeof width !== "string" || width.indexOf("%") < 0)
-				width += "px";
-			s = s.replace(/IMG/, img).replace(/Hpx/g, height).replace(/Wpx/g, width);
-		} else {
-			s = "\
-......</div>\
-......<div id=\"ID_2dappletdiv\" style=\"position:absolute;width:100%;height:100%;overflow:hidden;display:none\"></div>\
-......<div id=\"ID_infotablediv\" style=\"width:100%;height:100%;position:absolute;top:0px;left:0px\">\
-.........<div id=\"ID_infoheaderdiv\" style=\"height:20px;width:100%;background:yellow;display:none\"><span id=\"ID_infoheaderspan\"></span><span id=\"ID_infocheckboxspan\" style=\"position:absolute;text-align:right;right:1px;\"><a href=\"javascript:Jmol.showInfo(ID,false)\">[x]</a></span></div>\
-.........<div id=\"ID_infodiv\" style=\"position:absolute;top:20px;bottom:0px;width:100%;height:100%;overflow:auto\"></div>\
-......</div>\
-...</div>";
-		}
-		return s.replace(/\.\.\./g,"").replace(/[\n\r]/g,"").replace(/ID/g, applet._id);
-	}
-
-	Jmol._documentWrite = function(text) {
-		if (Jmol._document) {
-			if (Jmol._isXHTML && !Jmol._XhtmlElement) {
-				var s = document.getElementsByTagName("script");
-				Jmol._XhtmlElement = s.item(s.length - 1);
-				Jmol._XhtmlAppendChild = false;
-			}
-			if (Jmol._XhtmlElement)
-				Jmol._domWrite(text);
-			else
-				Jmol._document.write(text);
-		}
-		return text;
-	}
-
-	Jmol._domWrite = function(data) {
-		var pt = 0
-		var Ptr = []
-		Ptr[0] = 0
-		while (Ptr[0] < data.length) {
-			var child = Jmol._getDomElement(data, Ptr);
-			if (!child)
-				break;
-			if (Jmol._XhtmlAppendChild)
-				Jmol._XhtmlElement.appendChild(child);
-			else
-				Jmol._XhtmlElement.parentNode.insertBefore(child, _jmol.XhtmlElement);
-		}
-	}
-
-	Jmol._getDomElement = function(data, Ptr, closetag, lvel) {
-
-		// there is no "document.write" in XHTML
-
-		var e = document.createElement("span");
-		e.innerHTML = data;
-		Ptr[0] = data.length;
-
-/*
-	// unnecessary ?  
-
-		closetag || (closetag = "");
-		lvel || (lvel = 0);
-		var pt0 = Ptr[0];
-		var pt = pt0;
-		while (pt < data.length && data.charAt(pt) != "<") 
-			pt++
-		if (pt != pt0) {
-			var text = data.substring(pt0, pt);
-			Ptr[0] = pt;
-			return document.createTextNode(text);
-		}
-		pt0 = ++pt;
-		var ch;
-		while (pt < data.length && "\n\r\t >".indexOf(ch = data.charAt(pt)) < 0) 
-			pt++;
-		var tagname = data.substring(pt0, pt);
-		var e = (tagname == closetag  || tagname == "/" ? ""
-			: document.createElementNS ? document.createElementNS('http://www.w3.org/1999/xhtml', tagname)
-			: document.createElement(tagname));
-		if (ch == ">") {
-			Ptr[0] = ++pt;
-			return e;
-		}
-		while (pt < data.length && (ch = data.charAt(pt)) != ">") {
-			while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) 
-				pt++;
-			pt0 = pt;
-			while (pt < data.length && "\n\r\t =/>".indexOf(ch = data.charAt(pt)) < 0) 
-				pt++;
-			var attrname = data.substring(pt0, pt).toLowerCase();
-			if (attrname && ch != "=")
-				e.setAttribute(attrname, "true");
-			while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) 
-				pt++;
-			if (ch == "/") {
-				Ptr[0] = pt + 2;
-				return e;
-			} else if (ch == "=") {
-				var quote = data.charAt(++pt);
-				pt0 = ++pt;
-				while (pt < data.length && (ch = data.charAt(pt)) != quote) 
-					pt++;
-				var attrvalue = data.substring(pt0, pt);
-				e.setAttribute(attrname, attrvalue);
-				pt++;
-			}
-		}
-		Ptr[0] = ++pt;
-		while (Ptr[0] < data.length) {
-			var child = Jmol._getDomElement(data, Ptr, "/" + tagname, lvel+1);
-			if (!child)
-				break;
-			e.appendChild(child);
-		}
-*/
-		return e;    
-	}
-
-	Jmol._setObject = function(obj, id, Info) {
-		obj._id = id;
-		obj.__Info = {};
-		Info.z && Info.zIndexBase && (Jmol._z = Jmol._getZOrders(Info.zIndexBase));
-		for (var i in Info)
-			obj.__Info[i] = Info[i];
-		(obj._z = Info.z) || Info.zIndexBase && (obj._z = obj.__Info.z = Jmol._getZOrders(Info.zIndexBase));
-		obj._width = Info.width;
-		obj._height = Info.height;
-		obj._noscript = !obj._isJava && Info.noscript;
-		obj._console = Info.console;
-		obj._cacheFiles = !!Info.cacheFiles;
-		obj._viewSet = (Info.viewSet == null || obj._isJava ? null : "Set" + Info.viewSet);
-		if (obj._viewSet != null) {
-			Jmol.View.__init(obj);
-			obj._currentView = null;
-		}
-		!Jmol._fileCache && obj._cacheFiles && (Jmol._fileCache = {});
-		if (!obj._console)
-			obj._console = obj._id + "_infodiv";
-		if (obj._console == "none")
-			obj._console = null;
-
-		obj._color = (Info.color ? Info.color.replace(/0x/,"#") : "#FFFFFF");
-		obj._disableInitialConsole = Info.disableInitialConsole;
-		obj._noMonitor = Info.disableJ2SLoadMonitor;
-		Jmol._j2sPath && (Info.j2sPath = Jmol._j2sPath);
-		obj._j2sPath = Info.j2sPath;
-		obj._coverImage = Info.coverImage;
-		obj._isCovered = !!obj._coverImage; 
-		obj._deferApplet = Info.deferApplet || obj._isCovered && obj._isJava; // must do this if covered in Java
-		obj._deferUncover = Info.deferUncover && !obj._isJava; // can't do this with Java
-		obj._coverScript = Info.coverScript;
-		obj._coverTitle = Info.coverTitle;
-
-		if (!obj._coverTitle)
-			obj._coverTitle = (obj._deferApplet ? "activate 3D model" : "3D model is loading...")
-		obj._containerWidth = obj._width + ((obj._width==parseFloat(obj._width))? "px":"");
-		obj._containerHeight = obj._height + ((obj._height==parseFloat(obj._height))? "px":"");
-		obj._info = "";
-		obj._infoHeader = obj._jmolType + ' "' + obj._id + '"'
-		obj._hasOptions = Info.addSelectionOptions;
-		obj._defaultModel = Info.defaultModel;
-		obj._readyScript = (Info.script ? Info.script : "");
-		obj._readyFunction = Info.readyFunction;
-		if (obj._coverImage && !obj._deferApplet)
-			obj._readyScript += ";javascript " + id + "._displayCoverImage(false)";
-		obj._src = Info.src;
-
-	}
-
-	Jmol._addDefaultInfo = function(Info, DefaultInfo) {
-		for (var x in DefaultInfo)
-			if (typeof Info[x] == "undefined")
-				Info[x] = DefaultInfo[x];
-		Jmol._use && (Info.use = Jmol._use);
-		if (Info.use.indexOf("SIGNED") >= 0) {
-			if (Info.jarFile.indexOf("Signed") < 0)
-				Info.jarFile = Info.jarFile.replace(/Applet/,"AppletSigned");
-			Info.use = Info.use.replace(/SIGNED/, "JAVA");
-			Info.isSigned = true;
-		}
-	}
-
-	Jmol._syncedApplets = [];
-	Jmol._syncedCommands = [];
-	Jmol._syncedReady = [];
-	Jmol._syncReady = false;
-	Jmol._isJmolJSVSync = false;
-
-	Jmol._setReady = function(applet) {
-		Jmol._syncedReady[applet] = 1;
-		var n = 0;
-		for (var i = 0; i < Jmol._syncedApplets.length; i++) {
-			if (Jmol._syncedApplets[i] == applet._id) {
-				Jmol._syncedApplets[i] = applet;
-				Jmol._syncedReady[i] = 1;
-			} else if (!Jmol._syncedReady[i]) {
-				continue;
-			}
-			n++;
-		}
-		if (n != Jmol._syncedApplets.length)
-			return;
-		Jmol._setSyncReady();
-	}
-
-	Jmol._setDestroy = function(applet) {
-		//MSIE bug responds to any link click even if it is just a JavaScript call
-
-		if (Jmol.featureDetection.allowDestroy)
-			Jmol.$windowOn('beforeunload', function () { Jmol._destroy(applet); } );
-	}
-
-	Jmol._destroy = function(applet) {
-		try {
-			if (applet._appletPanel) applet._appletPanel.destroy();
-			applet._applet = null;
-			Jmol._unsetMouse(applet._canvas)
-			applet._canvas = null;
-			var n = 0;
-			for (var i = 0; i < Jmol._syncedApplets.length; i++) {
-				if (Jmol._syncedApplets[i] == applet)
-					Jmol._syncedApplets[i] = null;
-				if (Jmol._syncedApplets[i])
-					n++;
-			}
-			if (n > 0)
-				return;
-			Jmol._clearVars();
-		} catch(e){}
-	}
-
-	////////////// misc core functionality //////////////
-
-	Jmol._setSyncReady = function() {
-		Jmol._syncReady = true;
-		var s = ""
-		for (var i = 0; i < Jmol._syncedApplets.length; i++)
-			if (Jmol._syncedCommands[i])
-				s += "Jmol.script(Jmol._syncedApplets[" + i + "], Jmol._syncedCommands[" + i + "]);"
-		setTimeout(s, 50);  
-	}
-
-	Jmol._mySyncCallback = function(appFullName,msg) {
-		app = Jmol._applets[appFullName];
-		if (app._viewSet) {
-			// when can we do this?
-//			if (app._viewType == "JSV" && !app._currentView.JMOL)
-				Jmol.View.updateFromSync(app, msg);
-			return;
-		}
-		if(!Jmol._syncReady || !Jmol._isJmolJSVSync)
-			return 1; // continue processing and ignore me
-		for (var i = 0; i < Jmol._syncedApplets.length; i++) {
-			if (msg.indexOf(Jmol._syncedApplets[i]._syncKeyword) >= 0)
-				Jmol._syncedApplets[i]._syncScript(msg);
-		}
-		return 0 // prevents further Jmol sync processing 
-	}              
-
-	Jmol._getElement = function(applet, what) {
-		var d = document.getElementById(applet._id + "_" + what);
-		return (d || {});
-	} 
-	 
-	Jmol._evalJSON = function(s,key){
-		s = s + "";
-		if(!s)
-			return [];
-		if(s.charAt(0) != "{") {
-			if(s.indexOf(" | ") >= 0)
-				s = s.replace(/\ \|\ /g, "\n");
-			return s;
-		}
-		var A = (new Function( "return " + s ) )();
-		return (!A ? null : key && A[key] != undefined ? A[key] : A);
-	}
-
-	Jmol._sortMessages = function(A){
-		/*
-		 * private function
-		 */
-		function _sortKey0(a,b){
-			return (a[0]<b[0]?1:a[0]>b[0]?-1:0);
-		}
-
-		if(!A || typeof (A) != "object")
-			return [];
-		var B = [];
-		for(var i = A.length - 1; i >= 0; i--)
-			for(var j = 0, jj= A[i].length; j < jj; j++)
-				B[B.length] = A[i][j];
-		if(B.length == 0)
-			return;
-		B = B.sort(_sortKey0);
-		return B;
-	}
-
-	//////////////////// mouse events //////////////////////
-
-	Jmol._setMouseOwner = function(who, tf) {
-		if (who == null || tf)
-			Jmol._mouseOwner = who;
-		else if (Jmol._mouseOwner == who)
-			Jmol._mouseOwner = null;
-	}
-
-	Jmol._jsGetMouseModifiers = function(ev) {
-		var modifiers = 0;
-		switch (ev.button) {
-		case 0:
-			modifiers = 16;//J.api.Event.MOUSE_LEFT;
-			break;
-		case 1:
-			modifiers = 8;//J.api.Event.MOUSE_MIDDLE;
-			break;
-		case 2:
-			modifiers = 4;//J.api.Event.MOUSE_RIGHT;
-			break;
-		}
-		if (ev.shiftKey)
-			modifiers += 1;//J.api.Event.SHIFT_MASK;
-		if (ev.altKey)
-			modifiers += 8;//J.api.Event.ALT_MASK;
-		if (ev.ctrlKey)
-			modifiers += 2;//J.api.Event.CTRL_MASK;
-		return modifiers;
-	}
-
-	Jmol._jsGetXY = function(canvas, ev) {
-		if (!canvas.applet._ready || Jmol._touching && ev.type.indexOf("touch") < 0)
-			return false;
-		//ev.preventDefault(); // removed 5/9/2015 -- caused loss of focus on text-box clicking in SwingJS
-		var offsets = Jmol.$offset(canvas.id);
-		var x, y;
-		var oe = ev.originalEvent;
-		// drag-drop jQuery event is missing pageX
-		ev.pageX || (ev.pageX = oe.pageX);
-		ev.pageY || (ev.pageY = oe.pageY);
-		Jmol._mousePageX = ev.pageX;
-		Jmol._mousePageY = ev.pageY;
-		if (oe.targetTouches && oe.targetTouches[0]) {
-			x = oe.targetTouches[0].pageX - offsets.left;
-			y = oe.targetTouches[0].pageY - offsets.top;
-		} else if (oe.changedTouches) {
-			x = oe.changedTouches[0].pageX - offsets.left;
-			y = oe.changedTouches[0].pageY - offsets.top;
-		} else {
-			x = ev.pageX - offsets.left;
-			y = ev.pageY - offsets.top;
-		}
-		return (x == undefined ? null : [Math.round(x), Math.round(y), Jmol._jsGetMouseModifiers(ev)]);
-	}
-
-	Jmol._gestureUpdate = function(canvas, ev) {
-		ev.stopPropagation();
-		ev.preventDefault();
-		var oe = ev.originalEvent;
-		switch (ev.type) {
-		case "touchstart":
-			Jmol._touching = true;
-			break;
-		case "touchend":
-			Jmol._touching = false;
-			break;
-		}
-		if (!oe.touches || oe.touches.length != 2) return false;
-		switch (ev.type) {
-		case "touchstart":
-			canvas._touches = [[],[]];
-			break;
-		case "touchmove":
-			var offsets = Jmol.$offset(canvas.id);
-			var t0 = canvas._touches[0];
-			var t1 = canvas._touches[1];
-			t0.push([oe.touches[0].pageX - offsets.left, oe.touches[0].pageY - offsets.top]);
-			t1.push([oe.touches[1].pageX - offsets.left, oe.touches[1].pageY - offsets.top]);
-			var n = t0.length;
-			if (n > 3) {
-				t0.shift();
-				t1.shift();
-			}
-			if (n >= 2)
-				canvas.applet._processGesture(canvas._touches);
-			break;
-		}
-		return true;
-	}  
-
-	Jmol._jsSetMouse = function(canvas) {
-
-    var doIgnore = function(ev) { return (ev.target.className.indexOf("swingjs-ui") >= 0) };
-         
-		Jmol.$bind(canvas, 'mousedown touchstart', function(ev) {
-      if (doIgnore(ev))
-        return true;
-			Jmol._setMouseOwner(canvas, true);
-			ev.stopPropagation();
-      var ui = ev.target["data-UI"];
-      if (!ui || !ui.handleJSEvent(canvas, 501, ev)) 
-  			ev.preventDefault();
-			canvas.isDragging = true;
-			if ((ev.type == "touchstart") && Jmol._gestureUpdate(canvas, ev))
-				return !!ui;
-			Jmol._setConsoleDiv(canvas.applet._console);
-			var xym = Jmol._jsGetXY(canvas, ev);
-			if(xym) {
-		  	if (ev.button != 2)
-          Jmol.Swing.hideMenus(canvas.applet);
-        canvas.applet._processEvent(501, xym); //java.awt.Event.MOUSE_DOWN
-      }
-			return !!ui;
-		});
-    
-		Jmol.$bind(canvas, 'mouseup touchend', function(ev) {
-      if (doIgnore(ev))
-        return true;
-			Jmol._setMouseOwner(null);
-			ev.stopPropagation();
-      var ui = ev.target["data-UI"];
-      if (!ui || !ui.handleJSEvent(canvas, 502, ev))
-  			ev.preventDefault();
-			canvas.isDragging = false;
-			if (ev.type == "touchend" && Jmol._gestureUpdate(canvas, ev))
-				return !!ui;
-			var xym = Jmol._jsGetXY(canvas, ev);
-			if(xym)
-  			canvas.applet._processEvent(502, xym);//java.awt.Event.MOUSE_UP
-			return !!ui;
-		});
-    
-		Jmol.$bind(canvas, 'mousemove touchmove', function(ev) { // touchmove
-      if (doIgnore(ev))
-        return true;
-		  // defer to console or menu when dragging within this canvas
-			if (Jmol._mouseOwner && Jmol._mouseOwner != canvas && Jmol._mouseOwner.isDragging) {
-        if (!Jmol._mouseOwner.mouseMove)
-          return true;
-	   			Jmol._mouseOwner.mouseMove(ev);
-				return false;
-			}
-			return Jmol._drag(canvas, ev);
-		});
-		
-		Jmol._drag = function(canvas, ev) {
-      
-			ev.stopPropagation();
-			ev.preventDefault();
-      
-			var isTouch = (ev.type == "touchmove");
-			if (isTouch && Jmol._gestureUpdate(canvas, ev))
-				return false;
-			var xym = Jmol._jsGetXY(canvas, ev);
-			if(!xym) return false;
-      
-			if (!canvas.isDragging)
-				xym[2] = 0;
-
-      var ui = ev.target["data-UI"];
-      if (canvas.isdragging && (!ui || !ui.handleJSEvent(canvas, 506, ev))) {}
-			canvas.applet._processEvent((canvas.isDragging ? 506 : 503), xym); // java.awt.Event.MOUSE_DRAG : java.awt.Event.MOUSE_MOVE
-			return !!ui;
-		}
-		
-		Jmol.$bind(canvas, 'DOMMouseScroll mousewheel', function(ev) { // Zoom
-      if (doIgnore(ev))
-        return true;
-			ev.stopPropagation();
-			ev.preventDefault();
-			// Webkit or Firefox
-			canvas.isDragging = false;
-			var oe = ev.originalEvent;
-			var scroll = (oe.detail ? oe.detail : (Jmol.featureDetection.os == "mac" ? 1 : -1) * oe.wheelDelta); // Mac and PC are reverse; but 
-			var modifiers = Jmol._jsGetMouseModifiers(ev);
-			canvas.applet._processEvent(-1,[scroll < 0 ? -1 : 1,0,modifiers]);
-			return false;
-		});
-
-		// context menu is fired on mouse down, not up, and it's handled already anyway.
-
-		Jmol.$bind(canvas, "contextmenu", function() {return false;});
-
-		Jmol.$bind(canvas, 'mouseout', function(ev) {
-      if (doIgnore(ev))
-        return true;
-      if (Jmol._mouseOwner && !Jmol._mouseOwner.mouseMove) 
-        Jmol._setMouseOwner(null);
-			if (canvas.applet._appletPanel)
-				canvas.applet._appletPanel.startHoverWatcher(false);
-			//canvas.isDragging = false;
-			var xym = Jmol._jsGetXY(canvas, ev);
-			if (!xym)
-				return false;
-			//canvas.applet._processEvent(502, xym);//J.api.Event.MOUSE_UP
-			//canvas.applet._processEvent(505, xym);//J.api.Event.MOUSE_EXITED
-			return false;
-		});
-
-		Jmol.$bind(canvas, 'mouseenter', function(ev) {
-      if (doIgnore(ev))
-        return true;
-			if (canvas.applet._appletPanel)
-				canvas.applet._appletPanel.startHoverWatcher(true);
-			if (ev.buttons === 0 || ev.which === 0) {
-				canvas.isDragging = false;
-				var xym = Jmol._jsGetXY(canvas, ev);
-				if (!xym)
-					return false;
-				canvas.applet._processEvent(504, xym);//J.api.Event.MOUSE_ENTERED	
-				canvas.applet._processEvent(502, xym);//J.api.Event.MOUSE_UP
-				return false;
-			}
-		});
-
-	Jmol.$bind(canvas, 'mousemoveoutjsmol', function(evspecial, target, ev) {
-      if (doIgnore(ev))
-        return true;
-		if (canvas == Jmol._mouseOwner && canvas.isDragging) {
-			return Jmol._drag(canvas, ev);
-		}
-	});
-
-		if (canvas.applet._is2D)
-			Jmol.$resize(function() {
-				if (!canvas.applet)
-					return;
-				canvas.applet._resize();
-			});
- 
-		Jmol.$bind('body', 'mouseup touchend', function(ev) {
-      if (doIgnore(ev))
-        return true;
-			if (canvas.applet)
-				canvas.isDragging = false;
-			Jmol._setMouseOwner(null);
-		});
-
-	}
-
-	Jmol._jsUnsetMouse = function(canvas) {
-		canvas.applet = null;
-		Jmol.$bind(canvas, 'mousedown touchstart mousemove touchmove mouseup touchend DOMMouseScroll mousewheel contextmenu mouseout mouseenter', null);
-		Jmol._setMouseOwner(null);
-	}
-
-
-////// Jmol.Swing interface  for Javascript implementation of Swing dialogs and menus
-
-Jmol.Swing = {
-	// a static class
-	count:0,
-	menuInitialized:0,
-	menuCounter:0,
-	htDialogs:{}
-};
-
-(function(Swing) {
-
-SwingController = Swing; // see javajs.api.SwingController
-
-Swing.setDraggable = function(Obj) {
-	
-	var proto = Obj.prototype;
-	if (proto.setContainer)
-		return;
-	
-	// for menus, console, and 
-	proto.setContainer = function(container) {
-		this.container = container;
-		container.obj = this;
-		this.isDragging = false;
-		this.ignoreMouse = false;
-		var me = this;
-		container.bind('mousedown touchstart', function(ev) {
-			if (me.ignoreMouse) {
-				me.ignoreMouse = false;
-				return true;
-			}
-			Jmol._setMouseOwner(me, true);
-			me.isDragging = true;
-			me.pageX = ev.pageX;
-			me.pageY = ev.pageY;
-			return false;
-		});
-		container.bind('mousemove touchmove', function(ev) {
-			if (me.isDragging && Jmol._mouseOwner == me) {
-				me.mouseMove(ev);
-				return false;
-			}
-		});
-		container.bind('mouseup touchend', function(ev) {
-			me.mouseUp(ev);
-			Jmol._setMouseOwner(null);
-		});
-	};
-
-	proto.mouseUp = function(ev) {
-		if (this.isDragging && Jmol._mouseOwner == this) {
-			this.pageX0 += (ev.pageX - this.pageX);
-			this.pageY0 += (ev.pageY - this.pageY);
-			this.isDragging = false;
-			return false;
-		}
-		Jmol._setMouseOwner(null);
-	}
-
-	proto.setPosition = function() {
-		if (Jmol._mousePageX === null) {
-			var id = this.applet._id + "_" + (this.applet._is2D ? "canvas2d" : "canvas");
-			var offsets = Jmol.$offset(id);
-			Jmol._mousePageX = offsets.left;
-			Jmol._mousePageY = offsets.top;
-		}
-		this.pageX0 = Jmol._mousePageX;
-		this.pageY0 = Jmol._mousePageY;
-		var pos = { top: Jmol._mousePageY + 'px', left: Jmol._mousePageX + 'px' };
-		this.container.css(pos);
-	};
-
-	proto.mouseMove = function(ev) {
-		if (this.isDragging && Jmol._mouseOwner == this) {
-			this.timestamp = System.currentTimeMillis(); // used for menu closure
-			var x = this.pageX0 + (ev.pageX - this.pageX);
-			var y = this.pageY0 + (ev.pageY - this.pageY);
-      Jmol._mousePageX = x;
-      Jmol._mousePageY = y;
-			this.container.css({ top: y + 'px', left: x + 'px' })
-		}
-	};
-
-	proto.dragBind = function(isBind) {
-		this.applet._ignoreMouse = !isBind;
-		this.container.unbind('mousemoveoutjsmol');
-		this.container.unbind('touchmoveoutjsmol');
-		this.container.unbind('mouseupoutjsmol');
-		this.container.unbind('touchendoutjsmol');
-		Jmol._setMouseOwner(null);
-		if (isBind) {
-			var me = this;
-			this.container.bind('mousemoveoutjsmol touchmoveoutjsmol', function(evspecial, target, ev) {
-				me.mouseMove(ev);
-			});
-			this.container.bind('mouseupoutjsmol touchendoutjsmol', function(evspecial, target, ev) {
-				me.mouseUp(ev);
-			});
-		}
-	};
-}
-
-// Dialog //
-
-Swing.JSDialog = function () {
-}
-
-Swing.setDraggable(Swing.JSDialog);
-
-///// calls from javajs and other Java-derived packages /////
-
-Swing.getScreenDimensions = function(d) {
-	d.width = $(window).width();
-	d.height = $(window).height();
-}
-
-Swing.dispose = function(dialog) {
-	Jmol.$remove(dialog.id + "_mover");
-	delete Swing.htDialogs[dialog.id]
-	dialog.container.obj.dragBind(false);
-//  var btns = $("#" + dialog.id + " *[id^='J']"); // add descendents with id starting with "J"
-//  for (var i = btns.length; --i >= 0;)
-//    delete Dialog.htDialogs[btns[i].id]
-	//System.out.println("JSmolCore.js: dispose " + dialog.id)
-}
- 
-Swing.register = function(dialog, type) {
-	dialog.id = type + (++Swing.count);
-	Swing.htDialogs[dialog.id] = dialog;
-	//System.out.println("JSmolCore.js: register " + dialog.id)
-
-}
-
-Swing.setDialog = function(dialog) {
-	Jmol._setMouseOwner(null);
-	Jmol.$remove(dialog.id);
-	//System.out.println("removed " + dialog.id)
-	var id = dialog.id + "_mover";
-	var container = Jmol._$(id);
-	var jd;
-	//System.out.println("JSmolCore.js: setDialog " + dialog.id);
-	if (container[0]) {
-		container.html(dialog.html);
-		jd = container[0].jd;
-	} else {
-		Jmol.$after("body","<div id='" + id + "' style='position:absolute;left:0px;top:0px;'>" + dialog.html + "</div>");
-		var jd = new Swing.JSDialog();
-		container = Jmol._$(id);
-		dialog.container = container;
-		jd.applet = dialog.manager.vwr.html5Applet;
-		jd.setContainer(container);
-		jd.dialog = dialog;
-		jd.setPosition();  
-		jd.dragBind(true);
-		container[0].jd = jd; 
-	}
-	Jmol.$bind("#" + dialog.id + " .JButton", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
-	Jmol.$bind("#" + dialog.id + " .JComboBox", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
-	Jmol.$bind("#" + dialog.id + " .JCheckBox", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
-	Jmol.$bind("#" + dialog.id + " .JTextField", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
-	Jmol.$bind("#" + dialog.id + " .JTable", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
-	Jmol.$bind("#" + dialog.id + " .JScrollPane", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
-	Jmol.$bind("#" + dialog.id + " .JEditorPane", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
-
-}
- 
-Swing.setSelected = function(chk) {
- Jmol.$prop(chk.id, 'checked', !!chk.selected);
-}
-
-Swing.setSelectedIndex = function(cmb) {
- Jmol.$prop(cmb.id, 'selectedIndex', cmb.selectedIndex);
-}
-
-Swing.setText = function(btn) {
- Jmol.$prop(btn.id, 'value', btn.text);
-}
-
-Swing.setVisible = function(c) {
-	Jmol.$setVisible(c.id, c.visible);
-}
-
-Swing.setEnabled = function(c) {
-	Jmol.$setEnabled(c.id, c.enabled);
-}
-
-/// callbacks from the HTML elements ////
- 
-Swing.click = function(element, keyEvent) {
-	var component = Swing.htDialogs[element.id];
-	if (component) {
-		//System.out.println("click " + element + " " + component)
-		var info = component.toString();
-		// table cells will have an id but are not registered
-		if (info.indexOf("JCheck") >= 0) {
-				component.selected = element.checked;
-		} else if (info.indexOf("JCombo") >= 0) {
-			component.selectedIndex = element.selectedIndex;
-		} else if (component.text != null) {  // JButton, JTextField
-			component.text = element.value;
-			if (keyEvent && ((keyEvent.charCode || keyEvent.keyCode) != 13))
-				return;
-		}    
-	}
-	var dialog = Swing.htDialogs[Jmol.$getAncestorDiv(element.id, "JDialog").id];
-	var key = (component ? component.name :  dialog.registryKey + "/" + element.id);
-	//System.out.println("JSmolCore.js: click " + key); 
-	dialog.manager.actionPerformed(key);
-}
-
-Swing.setFront = function(dialog) {
-  var applet = dialog.manager.vwr.html5Applet;
-	if (dialog.zIndex != Jmol._getZ(applet, "dialog"))
-	 dialog.zIndex = Jmol._incrZ(applet, "dialog");
-	dialog.container && ((dialog.container[0] || dialog.container).style.zIndex = dialog.zIndex);
-}
-
-Swing.hideMenus = function(applet) {
-	// called from LEFT-DOWN mouse event
-	var menus = applet._menus;
-	if (menus)
-		for (var i in menus)
-			if (menus[i].visible)
-				Swing.hideMenu(menus[i]);
-}
-
-Swing.windowClosing = function(element) {
-	var dialog = Swing.htDialogs[Jmol.$getAncestorDiv(element.id, "JDialog").id];
-	if (dialog.registryKey) {
-		//System.out.println("JSmolCore.js: windowClosing " + dialog.registryKey); 
-		dialog.manager.processWindowClosing(dialog.registryKey);
-	} else {
-		//System.out.println("JSmolCore.js: windowClosing " + dialog.title); 
-		dialog.dispose();
-	}
-}
-
-})(Jmol.Swing);
-
-Jmol._track = function(applet) {
-	// this function inserts an iFrame that can be used to track your page's applet use. 
-	// By default it tracks to a page at St. Olaf College, but you can change that. 
-	// and you can use
-	//
-	// delete Jmol._tracker
-	//
-	// yourself to not have you page execute this 
-	//
-	if (Jmol._tracker){
-		try {  
-			var url = Jmol._tracker + "&applet=" + applet._jmolType + "&version=" + Jmol._version 
-				+ "&appver=" + Jmol.___JmolVersion + "&url=" + encodeURIComponent(document.location.href);
-			var s = '<iframe style="display:none" width="0" height="0" frameborder="0" tabindex="-1" src="' + url + '"></iframe>'
-			Jmol.$after("body", s);
-		} catch (e) {
-			// ignore
-		}
-		delete Jmol._tracker;
-	}
-	return applet;
-}
-
-Jmol.getProfile = function() {
-	window["j2s.doProfile"] = true;
-	if (self.Clazz && self.JSON) {
-		Clazz._profile || (Clazz._profile = {});
-		return Clazz.getProfile();
-	}
-}
-
-Jmol._getInChIKey = function(applet, data) {
-	if (data.indexOf("MOL=") >= 0)
-		data = data.split("MOL=")[1].split("\"")[0];
-
-}
-
-Jmol._getAttr = function(s, a) {
-	var pt = s.indexOf(a + "=");
-	return (pt >= 0 && (pt = s.indexOf('"', pt)) >= 0 
-		? s.substring(pt+1, s.indexOf('"', pt+1)) : null);
-}
-
-Jmol.User = {
-	viewUpdatedCallback: null
-}
-
-Jmol.View = {
-
-// The objective of Jmol.View is to coordinate
-// asynchronous applet loading and atom/peak picking
-// among any combination of Jmol, JME, and JSV.
-// 
-// basic element is a view object:
-//   view = {
-//     viewType1: viewRecord1,
-//     viewType2: viewRecord2,
-//     viewType3: viewRecord3
-//   }
-// where viewType is one of (Jmol, JME, JSV)
-// and a viewRecord is an object
-// with elements .chemID, .applet, .data, .script
-//
-// Jmol.View.sets is a list of cached views[0..n]
-// for a given group of applet objects with common Info.viewSet
-//
-// Bob Hanson 1/22/2014 7:05:38 AM
-
-	count: 0,
-	applets: {},
-	sets: {}
-};
-
-(function(View) {
-
-// methods called from other modules have no "_" in their name
-
-View.updateView = function(applet, Info, _View_updateView) {
-	// Info.chemID, Info.data, possibly Info.viewID if no chemID
-	// return from applet after asynchronous download of new data
-	if (applet._viewSet == null)
-		return;
-	Info.chemID || (applet._searchQuery = null);
-	Info.data || (Info.data = "N/A");
-	Info.type = applet._viewType;
-	if((applet._currentView = View.__findView(applet._viewSet, Info)) == null)
-		applet._currentView = View.__createViewSet(applet._viewSet, Info.chemID, Info.viewID || Info.chemID);
-	applet._currentView[Info.type].data = Info.data;
-	applet._currentView[Info.type].smiles = applet._getSmiles();
-	if (Jmol.User.viewUpdatedCallback)
-		Jmol.User.viewUpdatedCallback(applet, "updateView");
-	View.__setView(applet._currentView, applet, false);
-}
-
-View.updateFromSync = function(applet, msg) {
-	applet._updateMsg = msg;
-	var id = Jmol._getAttr(msg, "sourceID") || Jmol._getAttr(msg, "file");
-	if (!id)
-		return;
-	var view = View.__findView(applet._viewSet, {viewID:id});
-	if (view == null)
-		return Jmol.updateView(applet, msg); // JSV has been updated internally
-	if (view != applet._currentView)
-		View.__setView(view, applet, true);
-	var A = ((id = Jmol._getAttr(msg, "atoms")) && msg.indexOf("selectionhalos ON") >= 0  
-		? eval("[" + id + "]") : []);
-	setTimeout(function(){if (applet._currentView == view)View.updateAtomPick(applet, A)}, 10);
-	if (Jmol.User.viewUpdatedCallback)
-		Jmol.User.viewUpdatedCallback(applet, "updateFromSync");
-}
-
-View.updateAtomPick = function(applet, A, _View_updateAtomPick) {
-	var view = applet._currentView;
-	if (view == null)
-		return;
-	for (var viewType in view) {
-		if (viewType != "info" && view[viewType].applet != applet)
-			view[viewType].applet._updateAtomPick(A);
-	}
-	if (Jmol.User.viewUpdatedCallback)
-		Jmol.User.viewUpdatedCallback(applet, "updateAtomPick");
-}
-
-View.dumpViews = function(setID) {
-	var views = View.sets[setID];
-	if (!views)
-	  return;
-	var s = "View set " + setID + ":\n";
-	var applets = View.applets[setID];
-	for (var i in applets)
-		s += "\napplet " + applets[i]._id
-			+ " currentView=" + (applets[i]._currentView ? applets[i]._currentView.info.viewID : null);
-	for (var i = views.length; --i >= 0;) {
-		var view = views[i];
-		s += "\n\n<b>view=" + i 
-			+ " viewID=" + view.info.viewID 
-			+ " chemID=" + view.info.chemID + "</b>\n"
-		var v;
-		for (var viewType in view) 
-			if (viewType != "info")
-				s += "\nview=" + i + " type=" + viewType + " applet=" 
-					+ ((v = view[viewType]).applet ? v.applet._id : null) 
-					+ " SMILES=" + v.smiles + "\n"
-					+ " atomMap=" + JSON.stringify(v.atomMap) + "\n"
-					+ " data=\n" + v.data + "\n"
-	}
-	return s
-}
-
-
-// methods starting with "__" are "private" to JSmolCore.js
-
-View.__init = function(applet) {
-  var set = applet._viewSet;
-	var a = View.applets;
-	a[set] || (a[set] = {});
-	a[set][applet._viewType] = applet;
-}
-
-View.__findView = function(set, Info) {
-	var views = View.sets[set];
-	if (views == null)
-		views = View.sets[set] = [];
-	for (var i = views.length; --i >= 0;) {
-		var view = views[i];
-		if (Info.viewID) {
-			if (view.info.viewID == Info.viewID)
-				return view;
-		} else if (Info.chemID != null && Info.chemID == view.info.chemID) {
-				return view;
-		} else {
-			for (var viewType in view) { 
-				if (viewType != "info") {
-					if (Info.data != null && view[viewType].data != null ? Info.data == view[viewType].data 
-						: Info.type == viewType)
-							return view;
-				}
-			}
-		}
-	}
-	return null;  
-}
-
-View.__createViewSet = function(set, chemID, viewID, _createViewSet) {
-	View.count++;
-	var view = {info:{chemID: chemID, viewID: viewID || "model_" + View.count}};
-
-	for (var id in Jmol._applets) {
-		var a = Jmol._applets[id];
-		if (a._viewSet == set)
-			view[a._viewType] = {applet:a, data: null};
-	}
-	View.sets[set].push(view);
-	return view;
-}
-
-View.__setView = function(view, applet, isSwitch, _setView) {
-	// called from Jmol._searchMol and Jmol.View.setCurrentView 
-	// to notify the applets in the set that there may be new data for them
-	// skip the originating applet itself and cases where the data has not changed.
-	// stop at first null data, because that will initiate some sort of asynchronous
-	// call that will be back here afterward.
-
-	for (var viewType in view) {
-			if (viewType == "info") 
-				continue;
-		var rec = view[viewType];
-		var a = rec.applet;
-		var modified = (isSwitch || a != null && a._molData == "<modified>");
-
-		if (a == null || a == applet && !modified)
-			continue; // may be a mol3d required by JSV but not having a corresponding applet
-		var wasNull = (rec.data == null);
-		var haveView = (a._currentView != null);
-		a._currentView = view; 
-		if (haveView && view[viewType].data == rec.data && !wasNull & !modified)
-			continue;
-		a._loadModelFromView(view);
-		if (wasNull)
-			break;
-	}
-
-	// Either all are taken care of or one was null,
-	// in which case we have started an asynchronous
-	// process to get the data, and we can quit here.
-	// In either case, we are done.
-}
-
-}) (Jmol.View);
-
-Jmol.Cache = {fileCache: {}};
-
-Jmol.Cache.get = function(filename) {
-	return Jmol.Cache.fileCache[filename];
-}
-
-Jmol.Cache.put = function(filename, data) {
-  Jmol.Cache.fileCache[filename] = data;
-}
-
-	Jmol.Cache.setDragDrop = function(me) {
-		Jmol.$appEvent(me, "appletdiv", "dragover", function(e) {
-			e = e.originalEvent;
-			e.stopPropagation();
-			e.preventDefault();
-			e.dataTransfer.dropEffect = 'copy';
-		});
-		Jmol.$appEvent(me, "appletdiv", "drop", function(e) {
-			var oe = e.originalEvent;
-			oe.stopPropagation();
-			oe.preventDefault();
-			var file = oe.dataTransfer.files[0];
-			if (file == null) {
-				// FF and Chrome will drop an image here
-				// but it will be only a URL, not an actual file. 
-				try {
-				  file = "" + oe.dataTransfer.getData("text");
-				  if (file.indexOf("file:/") == 0 || file.indexOf("http:/") == 0) {
-				  	me._scriptLoad(file);
-				  	return;
-			  	}
-				} catch(e) {
-				  return;
-				}
-			  // some other format
-			  return;
-			}
-			// MSIE will drop an image this way, though, and load it!
-			var reader = new FileReader();
-			reader.onloadend = function(evt) {
-				if (evt.target.readyState == FileReader.DONE) {
-					var cacheName = "cache://DROP_" + file.name;
-					var bytes = Jmol._toBytes(evt.target.result);
-					if (!cacheName.endsWith(".spt"))
-						me._appletPanel.cacheFileByName("cache://DROP_*",false);
-					if (me._viewType == "JSV" || cacheName.endsWith(".jdx")) // shared by Jmol and JSV
-						Jmol.Cache.put(cacheName, bytes);
-					else
-						me._appletPanel.cachePut(cacheName, bytes);
-					var xym = Jmol._jsGetXY(me._canvas, e);
-					if(xym && (!me._appletPanel.setStatusDragDropped || me._appletPanel.setStatusDragDropped(0, xym[0], xym[1], cacheName))) {
-						me._appletPanel.openFileAsyncSpecial(cacheName, 1);
-					}
-				}
-			};
-			reader.readAsArrayBuffer(file);
-		});
-	}
-  
-})(Jmol, jQuery);
+// JSmolCore.js -- Jmol core capability 
+
+// allows Jmol applets to be created on a page with more flexibility and extendability
+// provides an object-oriented interface for JSpecView and syncing of Jmol/JSpecView
+
+// see JSmolApi.js for public user-interface. All these are private functions
+
+// BH 5/30/2015 9:33:12 AM adds class swingjs-ui to ignore 
+// BH 5/9/2015 3:38:52 PM adds data-ignoreMouse attribute for JTextField
+// BH 3/30/2015 9:46:53 PM adds JSAppletPanel for ready callback
+// BH 12/6/2014 3:32:54 PM Jmol.setAppletCss() broken
+// BH 9/13/2014 2:15:51 PM embedded JSME loads from SEARCH when Jmol should 
+// BH 8/14/2014 2:52:38 PM drag-drop cache should not be cleared if SPT file is dropped
+// BH 8/5/2014 6:39:54 AM unnecessary messages about binary for PDB finally removed
+// BH 8/4/2014 5:30:00 AM automatically switch to no document after page loading
+// BH 8/2/2014 5:22:40 PM drag-drop broken in JSmol/HTML5 
+// BH 7/23/2014 5:34:08 PM setting a parameter such as readyFunction to null stops file loading
+// BH 7/3/2014 12:30:28 AM lost drag-drop of models
+// BH 7/2/2014 4:47:55 AM adding pdbe.org to direct database calls
+// BH 5/30/2014 7:20:07 AM better dragging for console and menu
+// BH 4/27/2014 6:31:52 PM allows _USE=SIGNED HTML5 as well as _USE=JAVA HTML5
+// BH 3/8/2014 5:50:51 PM adds support for dataURI download in FF and Chrome
+// BH 3/8/2014 8:43:10 AM moves PubChem access to https
+// BH 3/4/2014 8:40:15 PM adds Jmol.Cache for JSV/Jmol sharing files
+// BH 2/10/2014 10:07:14 AM added Info.z and Info.zIndexBase
+// BH 2/9/2014 9:56:06 PM updated JSmolCore.js with option to extend Viewer with code PRIOR to loading Viewer classes
+// BH 2/6/2014 8:46:25 AM disabled Jmol._tracker for localhost and 127.x.x.x 
+// BH 1/29/2014 8:02:23 AM Jmol.View and Info.viewSet
+// BH 1/21/2014 12:06:59 PM adding Jmol.Info.cacheFiles (applet, true/false) and applet._cacheFiles and Jmol._fileCache
+// BH 1/13/2014 2:12:38 PM adding "http://www.nmrdb.org/tools/jmol/predict.php":"%URL", to _DirectDatabaseCalls
+// BH 12/21/2013 6:38:35 PM applet sync broken
+// BH 12/6/2013 6:18:32 PM cover.htm and coverImage fix
+// BH 12/4/2013 7:44:26 PM fix for JME independent search box
+// BH 12/3/2013 6:30:08 AM fix for ready function returning Boolean instead of boolean in HTML5 version
+// BH 11/30/2013 10:31:37 AM added type:"GET" for jQuery.ajax() requests instead of using defaults
+// BH 11/30/2013 10:31:37 AM added cache:true for jQuery.ajax() requests; can override with cache:"NO", not cache:false
+// BH 11/28/2013 11:09:27 AM added Jmol._alertNoBinary:true
+// BH 11/26/2013 8:19:55 PM fix !xxxx search commmand entry and stop MSIE from duplicating command
+// BH 11/25/2013 7:38:31 AM adds Jmol._tracker: option for GoogleAnalytics tracking
+// BH 11/25/2013 7:39:03 AM adds URL options _J2S=  _JAR=  _USE=
+// BH 11/23/2013 10:51:37 PM  adds JNLP support for local applet
+// BH 11/2/2013 12:05:11 PM JSmolJSME fixes; https access fixed
+// BH 10/31/2013 7:50:06 PM Jmol.Dialog as SwingController; Jmol._mouseOwner added
+// BH 10/19/2013 7:05:04 AM adding Jmol._ajaxCall for Error Contacting Server; database POST method enabled
+// BH 10/17/2013 1:40:51 PM  adding javajs/swing and Jmol.Dialog
+// BH 9/30/2013 6:42:24 PM: pdb.gz switch  pdb should only be for www.rcsb.org
+// BH 9/17/2013 10:17:51 AM: asynchronous file reading and saving
+// BH 8/16/2013 12:02:20 PM: JSmoljQueryExt.js pulled out
+// BH 8/16/2013 12:02:20 PM: Jmol._touching used properly
+
+// BH 3/22/2013 5:53:02 PM: Adds noscript option, JSmol.min.core.js
+// BH 1/17/2013 5:20:44 PM: Fixed problem with console not getting initial position if no first click
+// 1/13/2013 BH: Fixed MSIE not-reading-local-files problem.
+// 11/28/2012 BH: Fixed MacOS Safari binary ArrayBuffer problem
+// 11/21/2012 BH: restructuring of files as JS... instead of J...
+// 11/20/2012 BH: MSIE9 cannot do a synchronous file load cross-domain. See Jmol._getFileData
+// 11/4/2012 BH: RCSB REST format change "<structureId>" to "<dimStructure.structureId>"
+// 9/13/2012 BH: JmolCore.js changes for JSmol doAjax() method -- _3ata()
+// 6/12/2012 BH: JmolApi.js: adds Jmol.setInfo(applet, info, isShown) -- third parameter optional 
+// 6/12/2012 BH: JmolApi.js: adds Jmol.getInfo(applet) 
+// 6/12/2012 BH: JmolApplet.js: Fixes for MSIE 8
+// 6/5/2012  BH: fixes problem with Jmol "javascript" command not working and getPropertyAsArray not working
+// 6/4/2012  BH: corrects problem with MSIE requiring mouse-hover to activate applet
+// 5/31/2012 BH: added JSpecView interface and api -- see JmolJSV.js
+//               also changed "jmolJarPath" to just "jarPath"
+//               jmolJarFile->jarFile, jmolIsSigned->isSigned, jmolReadyFunction->readyFunction
+//               also corrects a double-loading issue
+// 5/14/2012 BH: added AJAX queue for ChemDoodle option with multiple canvases 
+// 8/12/2012 BH: adds support for MSIE xdr cross-domain request (jQuery.iecors.js)
+
+	// BH 4/25 -- added text option. setAppletCss(null, "style=\"xxxx\"")
+	// note that since you must add the style keyword, this can be used to add any attribute to these tags, not just css. 
+
+// required/optional libraries (preferably in the following order):
+
+//    jquery/jquery.js     -- at least jQuery.1.9
+//    js/JSmoljQueryext.js -- required for binary file transfer; otherwise standard jQuery should be OK
+//    js/JSmolCore.js      -- required
+//    js/j2sjmol.js        -- required
+//    js/JSmol.js          -- required
+//    js/JSmolApplet.js    -- required; internal functions for _Applet and _Image; must be after JSmolCore
+//    js/JSmolControls.js  -- optional; internal functions for buttons, links, menus, etc.; must be after JSmolCore
+//    js/JSmolConsole.js   -- optional; for the pop-up console
+//    js/JSmolApi.js       -- required; all user functions; must be after JSmolCore
+//    js/JSmolTHREE.js     -- optional; WebGL library required for JSmolGLmol.js
+//    js/JSmolGLmol.js     -- optional; WebGL version of JSmol.
+//    js/JSmolJME.js       -- optional; JSME (2D editor)
+//    jsme/jsme/jsme.nocache.js   --  required for JSME 
+//    js/JSmolMenu.js      -- optional; required for menuing in JSV
+//    js/JSmolJSV.js       -- optional; for creating and interacting with a JSpecView applet 
+
+// most of these will be loaded automatically, and for most installations, all you need is JSmol.min.js
+
+
+// Allows Jmol-like objects to be displayed on Java-challenged (iPad/iPhone)
+// or applet-challenged (Android/iPhone) platforms, with automatic switching to 
+
+// For your installation, you should consider putting JmolData.jar and jsmol.php 
+// on your own server. Nothing more than these two files is needed on the server, and this 
+// allows more options for MSIE and Chrome when working with cross-domain files (such as RCSB or pubChem) 
+
+// The NCI and RCSB databases are accessed via direct AJAX if available (xhr2/xdr).
+
+
+if(typeof(jQuery)=="undefined") alert ("Note -- JSmoljQuery is required for JSmol, but it's not defined.")
+
+// An example of how to extend Jmol with code PRIOR to JSmolCore.js or JSmol.min.js follows:
+//
+// 
+//	Jmol = {
+//  	z:3000,
+//		extend: function(what, obj) {if (what == "viewer") { obj._testing = true } }
+//	}
+
+self.Jmol || (Jmol = {});
+
+if (!Jmol._version)
+Jmol = (function(document) {
+	var z=Jmol.z || 9000;
+	var getZOrders = function(z) {
+		return {
+			rear:z++,
+			header:z++,
+			main:z++,
+			image:z++,
+			front:z++,
+			fileOpener:z++,
+			coverImage:z++,
+			dialog:z++, // could be several of these, JSV only
+			menu:z+90000, // way front
+			console:z+91000, // even more front
+      consoleImage:z+91001, // bit more front; increments
+			monitorZIndex:z+99999 // way way front
+		}
+	};
+	var j = {
+		_version: "$Date: 2015-04-26 10:57:08 -0500 (Sun, 26 Apr 2015) $", // svn.keywords:lastUpdated
+		_alertNoBinary: true,
+		// this url is used to Google Analytics tracking of Jmol use. You may remove it or modify it if you wish. 
+		_allowedJmolSize: [25, 2048, 300],   // min, max, default (pixels)
+		/*  By setting the Jmol.allowedJmolSize[] variable in the webpage
+				before calling Jmol.getApplet(), limits for applet size can be overriden.
+				2048 standard for GeoWall (http://geowall.geo.lsa.umich.edu/home.html)
+		*/
+		_appletCssClass: "",
+		_appletCssText: "",
+		_fileCache: null, // enabled by Jmol.setFileCaching(applet, true/false)
+		_jarFile: null,  // can be set in URL using _JAR=
+		_j2sPath: null,  // can be set in URL using _J2S=
+		_use: null,      // can be set in URL using _USE=
+		_j2sLoadMonitorOpacity: 90, // initial opacity for j2s load monitor message
+		_applets: {},
+		_asynchronous: true,
+		_ajaxQueue: [],
+		_getZOrders: getZOrders,
+		_z:getZOrders(z),
+		_debugCode: true,  // set false in process of minimization
+		db: {
+			_databasePrefixes: "$=:",
+			_fileLoadScript: ";if (_loadScript = '' && defaultLoadScript == '' && _filetype == 'Pdb') { select protein or nucleic;cartoons Only;color structure; select * };",
+			_nciLoadScript: ";n = ({molecule=1}.length < {molecule=2}.length ? 2 : 1); select molecule=n;display selected;center selected;",
+			_pubChemLoadScript: "",
+			_DirectDatabaseCalls:{
+				// these sites are known to implement access-control-allow-origin * 
+				"cactus.nci.nih.gov": "%URL", 
+				"www.rcsb.org": "%URL",
+				"pdbe.org": "%URL", 
+				"www.ebi.ac.uk": "%URL", 
+				"wwwdev.ebi.ac.uk": "%URL", 
+				"pubchem.ncbi.nlm.nih.gov":"%URL",
+				"http://www.nmrdb.org/tools/jmol/predict.php":"%URL",
+				"$": "http://cactus.nci.nih.gov/chemical/structure/%FILENCI/file?format=sdf&get3d=True",
+				"$$": "http://cactus.nci.nih.gov/chemical/structure/%FILENCI/file?format=sdf",
+				"=": "http://www.rcsb.org/pdb/files/%FILE.pdb",
+				"*": "http://www.ebi.ac.uk/pdbe/entry-files/download/%FILE.cif",
+				"==": "http://www.rcsb.org/pdb/files/ligand/%FILE.cif",
+				":": "http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/%FILE/SDF?record_type=3d"
+			},
+			_restQueryUrl: "http://www.rcsb.org/pdb/rest/search",
+			_restQueryXml: "<orgPdbQuery><queryType>org.pdb.query.simple.AdvancedKeywordQuery</queryType><description>Text Search</description><keywords>QUERY</keywords></orgPdbQuery>",
+			_restReportUrl: "http://www.pdb.org/pdb/rest/customReport?pdbids=IDLIST&customReportColumns=structureId,structureTitle"
+		},
+		_debugAlert: false,
+		_document: document,
+		_isXHTML: false,
+		_lastAppletID: null,
+		_mousePageX: null,
+		_mouseOwner: null,
+		_serverUrl: "http://your.server.here/jsmol.php",
+		_syncId: ("" + Math.random()).substring(3),
+		_touching: false,
+		_XhtmlElement: null,
+		_XhtmlAppendChild: false
+	}
+	
+	var ref = document.location.href.toLowerCase();
+	j._httpProto = (ref.indexOf("https") == 0 ? "https://" : "http://"); 
+	j._isFile = (ref.indexOf("file:") == 0);
+	j._ajaxTestSite = j._httpProto + "google.com";
+	var isLocal = (j._isFile || ref.indexOf("http://localhost") == 0 || ref.indexOf("http://127.") == 0);
+	j._tracker = (j._httpProto == "http://" && !isLocal && 'http://chemapps.stolaf.edu/jmol/JmolTracker.htm?id=UA-45940799-1');
+	
+	j._isChrome = (navigator.userAgent.toLowerCase().indexOf("chrome") >= 0);
+	j._isSafari = (!j._isChrome && navigator.userAgent.toLowerCase().indexOf("safari") >= 0);
+	j._isMsie = (window.ActiveXObject !== undefined);
+	j._useDataURI = !j._isSafari && !j._isMsie; // safari may be OK here -- untested
+
+	for(var i in Jmol) j[i] = Jmol[i]; // allows pre-definition
+	return j;
+})(document, Jmol);
+
+
+(function (Jmol, $) {
+
+// this library is organized into the following sections:
+
+	// jQuery interface 
+	// protected variables
+	// feature detection
+	// AJAX-related core functionality
+	// applet start-up functionality
+	// misc core functionality
+	// mouse events
+
+
+	////////////////////// jQuery interface ///////////////////////
+
+	// hooks to jQuery -- if you have a different AJAX tool, feel free to adapt.
+	// There should be no other references to jQuery in all the JSmol libraries.
+
+	// automatically switch to returning HTML after the page is loaded
+	$(document).ready(function(){ Jmol._document = null });
+
+	Jmol.$ = function(objectOrId, subdiv) {
+		// if a subdiv, then return $("#objectOrId._id_subdiv") 
+		// or if no subdiv, then just $(objectOrId)
+		if (objectOrId == null)alert (subdiv + arguments.callee.caller.toString());
+			return $(subdiv ? "#" + objectOrId._id + "_" + subdiv : objectOrId);
+	} 
+
+	Jmol._$ = function(id) {
+		// either the object or $("#" + id)
+		return (typeof id == "string" ? $("#" + id) : id);
+	}
+
+	/// special functions:
+
+	Jmol.$ajax = function (info) {
+		Jmol._ajaxCall = info.url;
+		info.cache = (info.cache != "NO");
+		if (info.url.indexOf("http://pubchem.ncbi.nlm.nih") == 0)
+			info.url = "https://" + info.url.substring(7);
+			// fluke at pubchem --- requires https now from all pages 3/8/2014
+		// don't let jQuery add $_=... to URL unless we 
+		// use cache:"NO"; other packages might use $.ajaxSetup() to set this to cache:false
+		return $.ajax(info);
+	}
+
+	Jmol._getNCIInfo = function(identifier, what, fCallback) {
+		return Jmol._getFileData("http://cactus.nci.nih.gov/chemical/structure/"+identifier +"/" + (what == "name" ? "names" : what));
+	}
+	
+
+
+	Jmol.$appEvent = function(app, subdiv, evt, f) {
+		var o = Jmol.$(app, subdiv); 
+		o.off(evt) && f && o.on(evt, f);
+	}   
+
+	Jmol.$resize = function (f) {
+		return $(window).resize(f);
+	}
+
+	//// full identifier expected (could be "body", for example):
+
+	Jmol.$after = function (what, s) {
+		return $(what).after(s);
+	}
+
+	Jmol.$append = function (what, s) {
+		return $(what).append(s);
+	}
+
+	Jmol.$bind = function(what, list, f) {
+		return (f ? $(what).bind(list, f) : $(what).unbind(list));
+	}
+
+	Jmol.$closest = function(what, d) {
+		return $(what).closest(d);
+	}
+	
+	Jmol.$get = function(what, i) {
+	return $(what).get(i);
+	}
+ 
+	// element id expected
+			 
+	Jmol.$documentOff = function(evt, id) {
+		return $(document).off(evt, "#" + id);
+	}
+
+	Jmol.$documentOn = function(evt, id, f) {
+		return $(document).on(evt, "#" + id, f);
+	}
+
+	Jmol.$getAncestorDiv = function(id, className) {
+		return $("div." + className + ":has(#" + id + ")")[0];
+	}
+
+	Jmol.$supportsIECrossDomainScripting = function() {
+		return $.support.iecors;
+	}
+
+	//// element id or jQuery object expected:
+
+	Jmol.$attr = function (id, a, val) {
+		return Jmol._$(id).attr(a, val);
+	}
+
+	Jmol.$css = function(id, style) {
+		return Jmol._$(id).css(style);
+	}
+	 
+	Jmol.$find = function(id, d) {
+		return Jmol._$(id).find(d);
+	}
+	
+	Jmol.$focus = function(id) {
+		return Jmol._$(id).focus();
+	}
+
+	Jmol.$html = function(id, html) {
+		return Jmol._$(id).html(html);
+	}
+	 
+	Jmol.$offset = function(id) {
+		return Jmol._$(id).offset();
+	}
+
+	Jmol.$windowOn = function(evt, f) {
+		return $(window).on(evt, f);
+	}
+
+	Jmol.$prop = function(id, p, val) {
+		var o = Jmol._$(id);
+		return (arguments.length == 3 ? o.prop(p, val) : o.prop(p));
+	}
+
+	Jmol.$remove = function(id) {
+		return Jmol._$(id).remove();
+	}
+
+	Jmol.$scrollTo = function (id, n) {
+		var o = Jmol._$(id);
+		return o.scrollTop(n < 0 ? o[0].scrollHeight : n);
+	}
+
+	Jmol.$setEnabled = function(id, b) {
+		return Jmol._$(id).attr("disabled", b ? null : "disabled");  
+	}
+
+	Jmol.$setSize = function(id, w, h) {
+		return Jmol._$(id).width(w).height(h);
+	}
+
+	Jmol.$setVisible = function(id, b) {
+		var o = Jmol._$(id);
+		return (b ? o.show() : o.hide());  
+	}
+
+	Jmol.$submit = function(id) {
+		return Jmol._$(id).submit();
+	}
+
+	Jmol.$val = function (id, v) {
+		var o = Jmol._$(id);
+		return (arguments.length == 1 ? o.val() : o.val(v));
+	}
+
+	////////////// protected variables ///////////
+
+
+	Jmol._clearVars = function() {
+		// only on page closing -- appears to improve garbage collection
+
+		delete jQuery;
+		delete $;
+		delete Jmol;
+		delete SwingController;
+		delete J;
+		delete JM;
+		delete JS;
+		delete JSV;
+		delete JU;
+		delete JV;
+		delete java;
+		delete javajs;
+		delete Clazz;
+		delete c$; // used in p0p; could be gotten rid of
+	}
+
+	////////////// feature detection ///////////////
+
+	Jmol.featureDetection = (function(document, window) {
+
+		var features = {};
+		features.ua = navigator.userAgent.toLowerCase()
+
+		features.os = (function(){
+			var osList = ["linux","unix","mac","win"]
+			var i = osList.length;
+
+			while (i--){
+				if (features.ua.indexOf(osList[i])!=-1) return osList[i]
+			}
+			return "unknown";
+		})();
+
+		features.browser = function(){
+			var ua = features.ua;
+			var browserList = ["konqueror","webkit","omniweb","opera","webtv","icab","msie","mozilla"];
+			for (var i = 0; i < browserList.length; i++)
+			if (ua.indexOf(browserList[i])>=0) 
+				return browserList[i];
+			return "unknown";
+		}
+		features.browserName = features.browser();
+		features.browserVersion= parseFloat(features.ua.substring(features.ua.indexOf(features.browserName)+features.browserName.length+1));
+		features.supportsXhr2 = function() {return ($.support.cors || $.support.iecors)}
+		features.allowDestroy = (features.browserName != "msie");
+		features.allowHTML5 = (features.browserName != "msie" || navigator.appVersion.indexOf("MSIE 8") < 0);
+		features.getDefaultLanguage = function() {
+			return navigator.language || navigator.userLanguage || "en-US";
+		};
+
+		features._webGLtest = 0;
+
+		features.supportsWebGL = function() {
+		if (!Jmol.featureDetection._webGLtest) { 
+			var canvas;
+			Jmol.featureDetection._webGLtest = ( 
+				window.WebGLRenderingContext 
+					&& ((canvas = document.createElement("canvas")).getContext("webgl") 
+				|| canvas.getContext("experimental-webgl")) ? 1 : -1);
+		}
+		return (Jmol.featureDetection._webGLtest > 0);
+	};
+
+	features.supportsLocalization = function() {
+		//<meta charset="utf-8">                                     
+		var metas = document.getElementsByTagName('meta'); 
+		for (var i= metas.length; --i >= 0;) 
+			if (metas[i].outerHTML.toLowerCase().indexOf("utf-8") >= 0) return true;
+		return false;
+		};
+
+	features.supportsJava = function() {
+		if (!Jmol.featureDetection._javaEnabled) {
+			if (Jmol._isMsie) {
+				if (!navigator.javaEnabled()) {
+					Jmol.featureDetection._javaEnabled = -1;
+				} else {
+					//more likely -- would take huge testing
+					Jmol.featureDetection._javaEnabled = 1;
+				}
+			} else {
+				Jmol.featureDetection._javaEnabled = (navigator.javaEnabled() && (!navigator.mimeTypes || navigator.mimeTypes["application/x-java-applet"]) ? 1 : -1);
+			}
+		}
+		return (Jmol.featureDetection._javaEnabled > 0);
+	};
+
+	features.compliantBrowser = function() {
+		var a = !!document.getElementById;
+		var os = features.os;
+		// known exceptions (old browsers):
+		if (features.browserName == "opera" && features.browserVersion <= 7.54 && os == "mac"
+			|| features.browserName == "webkit" && features.browserVersion < 125.12
+			|| features.browserName == "msie" && os == "mac"
+			|| features.browserName == "konqueror" && features.browserVersion <= 3.3
+		) a = false;
+		return a;
+	}
+
+	features.isFullyCompliant = function() {
+		return features.compliantBrowser() && features.supportsJava();
+	}
+
+	features.useIEObject = (features.os == "win" && features.browserName == "msie" && features.browserVersion >= 5.5);
+	features.useHtml4Object = (features.browserName == "mozilla" && features.browserVersion >= 5) ||
+		(features.browserName == "opera" && features.browserVersion >= 8) ||
+		(features.browserName == "webkit"/* && features.browserVersion >= 412.2 && features.browserVersion < 500*/); // 500 is a guess; required for 536.3
+
+	features.hasFileReader = (window.File && window.FileReader);
+
+	return features;
+
+})(document, window);
+
+
+		////////////// AJAX-related core functionality //////////////
+
+	Jmol._ajax = function(info) {
+		if (!info.async) {
+			return Jmol.$ajax(info).responseText;
+		}
+		Jmol._ajaxQueue.push(info)
+		if (Jmol._ajaxQueue.length == 1)
+			Jmol._ajaxDone()
+	}
+	Jmol._ajaxDone = function() {
+		var info = Jmol._ajaxQueue.shift();
+		info && Jmol.$ajax(info);
+	}
+
+	Jmol._grabberOptions = [
+		["$", "NCI(small molecules)"],
+		[":", "PubChem(small molecules)"],
+		["=", "RCSB(macromolecules)"],
+		["*", "PDBe(macromolecules)"]
+	];
+
+	Jmol._getGrabberOptions = function(applet) {
+		// feel free to adjust this look to anything you want
+		if (Jmol._grabberOptions.length == 0)
+			return ""
+
+
+		var s = '<input type="text" id="ID_query" onfocus="jQuery(this).select()" onkeypress="if(13==event.which){Jmol._applets[\'ID\']._search();return false}" size="32" value="" />';
+		var b = '<button id="ID_submit" onclick="Jmol._applets[\'ID\']._search()">Search</button></nobr>'
+		if (Jmol._grabberOptions.length == 1) {
+			s = '<nobr>' + s + '<span style="display:none">';
+			b = '</span>' + b;
+		} else {
+			s += '<br /><nobr>'
+		}
+		s += '<select id="ID_select">'
+		for (var i = 0; i < Jmol._grabberOptions.length; i++) {
+			var opt = Jmol._grabberOptions[i];
+			s += '<option value="' + opt[0] + '" ' + (i == 0 ? 'selected' : '') + '>' + opt[1] + '</option>';
+		}
+		s = (s + '</select>' + b).replace(/ID/g, applet._id);
+		return '<br />' + s;
+	}
+
+	Jmol._getScriptForDatabase = function(database) {
+		return (database == "$" ? Jmol.db._nciLoadScript : database == ":" ? Jmol.db._pubChemLoadScript : Jmol.db._fileLoadScript);
+	}
+
+	 //   <dataset><record><structureId>1BLU</structureId><structureTitle>STRUCTURE OF THE 2[4FE-4S] FERREDOXIN FROM CHROMATIUM VINOSUM</structureTitle></record><record><structureId>3EUN</structureId><structureTitle>Crystal structure of the 2[4Fe-4S] C57A ferredoxin variant from allochromatium vinosum</structureTitle></record></dataset>
+
+	Jmol._setInfo = function(applet, database, data) {
+		var info = [];
+		var header = "";
+		if (data.indexOf("ERROR") == 0)
+			header = data;
+		else
+			switch (database) {
+			case "=":
+				var S = data.split("<dimStructure.structureId>");
+				var info = ["<table>"];
+				for (var i = 1; i < S.length; i++) {
+					info.push("<tr><td valign=top><a href=\"javascript:Jmol.search(" + applet._id + ",'=" + S[i].substring(0, 4) + "')\">" + S[i].substring(0, 4) + "</a></td>");
+					info.push("<td>" + S[i].split("Title>")[1].split("</")[0] + "</td></tr>");
+				}
+				info.push("</table>");
+				header = (S.length - 1) + " matches";
+				break;      
+			case "$": // NCI
+			case ":": // pubChem
+			break;
+			default:
+				return;
+		}
+		applet._infoHeader = header;
+		applet._info = info.join("");
+		applet._showInfo(true);
+	}
+
+	Jmol._loadSuccess = function(a, fSuccess) {
+		if (!fSuccess)
+			return;
+		Jmol._ajaxDone();
+		fSuccess(a);
+	}
+
+	Jmol._loadError = function(fError){
+		Jmol._ajaxDone();
+		Jmol.say("Error connecting to server: " + Jmol._ajaxCall);  
+		null!=fError&&fError()
+	}
+
+	Jmol._isDatabaseCall = function(query) {
+		return (Jmol.db._databasePrefixes.indexOf(query.substring(0, 1)) >= 0);
+	}
+
+	
+	Jmol._getDirectDatabaseCall = function(query, checkXhr2) {
+		if (checkXhr2 && !Jmol.featureDetection.supportsXhr2())
+			return query;
+		var pt = 2;
+		var db;
+		var call = Jmol.db._DirectDatabaseCalls[query.substring(0,pt)];
+		if (!call)
+			call = Jmol.db._DirectDatabaseCalls[db = query.substring(0,--pt)];
+		if (call) {
+			if (db == ":") {
+				var ql = query.toLowerCase();
+				if (!isNaN(parseInt(query.substring(1)))) {
+					query = "cid/" + query.substring(1);
+				} else if (ql.indexOf(":smiles:") == 0) {
+					call += "?POST?smiles=" + query.substring(8);
+					query = "smiles";
+				} else if (ql.indexOf(":cid:") == 0) {
+					query = "cid/" + query.substring(5);
+				} else {
+					if (ql.indexOf(":name:") == 0)
+						query = query.substring(5);
+					else if (ql.indexOf(":cas:") == 0)
+						query = query.substring(4);
+					query = "name/" + encodeURIComponent(query.substring(pt));
+				}
+			} else {
+				query = encodeURIComponent(query.substring(pt));		
+			}
+			if (call.indexOf("FILENCI") >= 0) {
+				query = query.replace(/\%2F/g, "/");				
+				query = call.replace(/\%FILENCI/, query);
+			} else {
+				query = call.replace(/\%FILE/, query);
+			}
+		}		
+		return query;
+	}
+
+	Jmol._getRawDataFromServer = function(database,query,fSuccess,fError,asBase64,noScript){
+	  // note that this method is now only enabled for "_"
+	  // server-side processing of database queries was too slow and only useful for 
+	  // the IMAGE option, which has been abandoned.
+		var s = 
+			"?call=getRawDataFromDatabase&database=" + database + (query.indexOf("?POST?") >= 0 ? "?POST?" : "")
+				+ "&query=" + encodeURIComponent(query)
+				+ (asBase64 ? "&encoding=base64" : "")
+				+ (noScript ? "" : "&script=" + encodeURIComponent(Jmol._getScriptForDatabase(database)));
+		return Jmol._contactServer(s, fSuccess, fError);
+	}
+
+	Jmol._checkFileName = function(applet, fileName, isRawRet) {
+		if (Jmol._isDatabaseCall(fileName)) {
+			if (isRawRet)
+				Jmol._setQueryTerm(applet, fileName);
+			fileName = Jmol._getDirectDatabaseCall(fileName, true);
+			if (Jmol._isDatabaseCall(fileName)) {
+				// xhr2 not supported (MSIE)
+				fileName = Jmol._getDirectDatabaseCall(fileName, false);
+				isRawRet && (isRawRet[0] = true);
+			}
+		}
+		return fileName;
+	}
+	
+	Jmol._checkCache = function(applet, fileName, fSuccess) {
+		if (applet._cacheFiles && Jmol._fileCache && !fileName.endsWith(".js")) {
+			var data = Jmol._fileCache[fileName];
+			if (data) {
+				System.out.println("using "  + data.length + " bytes of cached data for "  + fileName);
+				fSuccess(data);
+				return null;
+			} else {
+				fSuccess = function(fileName, data) { fSuccess(Jmol._fileCache[fileName] = data) };     
+			}
+		}
+		return fSuccess;
+	}
+	
+	Jmol._loadFileData = function(applet, fileName, fSuccess, fError){
+		var isRaw = [];
+		fileName = Jmol._checkFileName(applet, fileName, isRaw);
+		fSuccess = Jmol._checkCache(applet, fileName, fSuccess);
+		if (isRaw[0]) {
+				Jmol._getRawDataFromServer("_",fileName,fSuccess,fError);   
+				return;
+		} 
+		var info = {
+			type: "GET",
+			dataType: "text",
+			url: fileName,
+			async: Jmol._asynchronous,
+			success: function(a) {Jmol._loadSuccess(a, fSuccess)},
+			error: function() {Jmol._loadError(fError)}
+		}
+		Jmol._checkAjaxPost(info);
+		Jmol._ajax(info);
+	}
+
+	Jmol._getInfoFromDatabase = function(applet, database, query){
+		if (database == "====") {
+			var data = Jmol.db._restQueryXml.replace(/QUERY/,query);
+
+			var info = {
+				dataType: "text",
+				type: "POST",
+				contentType:"application/x-www-form-urlencoded",
+				url: Jmol.db._restQueryUrl,
+				data: encodeURIComponent(data) + "&req=browser",
+				success: function(data) {Jmol._ajaxDone();Jmol._extractInfoFromRCSB(applet, database, query, data)},
+				error: function() {Jmol._loadError(null)},
+				async: Jmol._asynchronous
+			}
+			return Jmol._ajax(info);
+		}   
+		query = "?call=getInfoFromDatabase&database=" + database
+				+ "&query=" + encodeURIComponent(query);
+		return Jmol._contactServer(query, function(data) {Jmol._setInfo(applet, database, data)});
+	}
+
+	Jmol._extractInfoFromRCSB = function(applet, database, query, output) {
+		var n = output.length/5;
+		if (n == 0)
+			return; 
+		if (query.length == 4 && n != 1) {
+			var QQQQ = query.toUpperCase();
+			var pt = output.indexOf(QQQQ);
+			if (pt > 0 && "123456789".indexOf(QQQQ.substring(0, 1)) >= 0)
+				output = QQQQ + "," + output.substring(0, pt) + output.substring(pt + 5);
+			if (n > 50)
+				output = output.substring(0, 250);
+			output = output.replace(/\n/g,",");
+			var url = Jmol._restReportUrl.replace(/IDLIST/,output);
+			Jmol._loadFileData(applet, url, function(data) {Jmol._setInfo(applet, database, data) });   
+		}
+	}
+
+	Jmol._checkAjaxPost = function(info) {
+		var pt = info.url.indexOf("?POST?");
+		if (pt > 0) {
+			info.data = info.url.substring(pt + 6);
+			info.url = info.url.substring(0, pt);
+			info.type = "POST";
+			info.contentType = "application/x-www-form-urlencoded";
+		}
+	}
+	Jmol._contactServer = function(data,fSuccess,fError){
+		var info = {
+			dataType: "text",
+			type: "GET",
+			url: Jmol._serverUrl + data,
+			success: function(a) {Jmol._loadSuccess(a, fSuccess)},
+			error:function() { Jmol._loadError(fError) },
+			async:fSuccess ? Jmol._asynchronous : false
+		}
+		Jmol._checkAjaxPost(info);
+		return Jmol._ajax(info);
+	}
+
+	Jmol._setQueryTerm = function(applet, query) {
+		if (!query || !applet._hasOptions || query.substring(0, 7) == "http://")
+			return;
+		if (Jmol._isDatabaseCall(query)) {
+			var database = query.substring(0, 1);
+			query = query.substring(1);
+			if (query.substring(0,1) == database && "=$".indexOf(database) >= 0)
+				query = query.substring(1);
+			var d = Jmol._getElement(applet, "select");
+			if (d && d.options)
+				for (var i = 0; i < d.options.length; i++)
+					if (d[i].value == database)
+						d[i].selected = true;
+		}
+		Jmol.$val(Jmol.$(applet, "query"), query);
+	}
+
+	Jmol._search = function(applet, query, script) {
+		arguments.length > 1 || (query = null);
+		Jmol._setQueryTerm(applet, query);
+		query || (query = Jmol.$val(Jmol.$(applet, "query")))
+		if (query.indexOf("!") == 0) {
+		// command prompt in this box as well
+		// remove exclamation point "immediate" indicator
+			applet._script(query.substring(1));
+			return;
+		} 
+		query && (query = query.replace(/\"/g, ""));
+		applet._showInfo(false);
+		Jmol._searchMol(applet, query, script, true);
+	}
+
+	Jmol._searchMol = function(applet, query, script, checkView) {
+		var database;
+		if (Jmol._isDatabaseCall(query)) {
+			database = query.substring(0, 1);
+			query = query.substring(1);
+		} else {
+			database = (applet._hasOptions ? Jmol.$val(Jmol.$(applet, "select")) : "$");
+		}
+		if (database == "=" && query.length == 3)
+			query = "=" + query; // this is a ligand      
+		var dm = database + query;
+		if (!query || dm.indexOf("?") < 0 && dm == applet._thisJmolModel) {
+			return;    
+		}
+		applet._thisJmolModel = dm;
+		var view;
+		if (checkView && applet._viewSet != null && (view = Jmol.View.__findView(applet._viewSet, {chemID:dm})) != null) {
+			Jmol.View.__setView(view, applet, false);
+			return;
+		}
+
+		if (database == "$" || database == ":")
+			applet._jmolFileType = "MOL";
+		else if (database == "=")
+			applet._jmolFileType = "PDB";
+		applet._searchDatabase(query, database, script);
+	}
+
+	Jmol._searchDatabase = function(applet, query, database, script) {
+		applet._showInfo(false);
+		if (query.indexOf("?") >= 0) {
+			Jmol._getInfoFromDatabase(applet, database, query.split("?")[0]);
+			return true;
+		}
+		if (Jmol.db._DirectDatabaseCalls[database]) {
+			applet._loadFile(database + query, script);
+			return true;
+		}
+		return false;
+	}
+
+	Jmol._syncBinaryOK="?";
+
+	Jmol._canSyncBinary = function(isSilent) {
+		if (Jmol._isAsync) return true;
+		if (self.VBArray) return (Jmol._syncBinaryOK = false);
+		if (Jmol._syncBinaryOK != "?") return Jmol._syncBinaryOK;
+		Jmol._syncBinaryOK = true;
+		try {
+			var xhr = new window.XMLHttpRequest();
+			xhr.open( "text", Jmol._ajaxTestSite, false );
+			if (xhr.hasOwnProperty("responseType")) {
+				xhr.responseType = "arraybuffer";
+			} else if (xhr.overrideMimeType) {
+				xhr.overrideMimeType('text/plain; charset=x-user-defined');
+			}
+		} catch( e ) {
+			var s = "JSmolCore.js: synchronous binary file transfer is requested but not available";
+			System.out.println(s);
+			if (Jmol._alertNoBinary && !isSilent)
+				alert (s)
+			return Jmol._syncBinaryOK = false;
+		}
+		return true;  
+	}
+
+	Jmol._binaryTypes = [".gz",".jpg",".gif",".png",".zip",".jmol",".bin",".smol",".spartan",".mrc",".pse", ".map", ".omap"];
+
+	Jmol._isBinaryUrl = function(url) {
+		for (var i = Jmol._binaryTypes.length; --i >= 0;)
+			if (url.indexOf(Jmol._binaryTypes[i]) >= 0) return true;
+		return false;
+	}
+
+	Jmol._getFileData = function(fileName, fSuccess, doProcess) {
+		// use host-server PHP relay if not from this host
+		var isBinary = Jmol._isBinaryUrl(fileName);
+		var isPDB = (fileName.indexOf("pdb.gz") >= 0 && fileName.indexOf("http://www.rcsb.org/pdb/files/") == 0);
+		var asBase64 = (isBinary && !Jmol._canSyncBinary(isPDB));
+		if (asBase64 && isPDB) {
+			// avoid unnecessary binary transfer
+			fileName = fileName.replace(/pdb\.gz/,"pdb");
+			asBase64 = isBinary = false;
+		}
+		var isPost = (fileName.indexOf("?POST?") >= 0);
+		if (fileName.indexOf("file:/") == 0 && fileName.indexOf("file:///") != 0)
+			fileName = "file://" + fileName.substring(5);      /// fixes IE problem
+		var isMyHost = (fileName.indexOf("://") < 0 || fileName.indexOf(document.location.protocol) == 0 && fileName.indexOf(document.location.host) >= 0);
+		var isDirectCall = Jmol._isDirectCall(fileName);
+		//if (fileName.indexOf("http://pubchem.ncbi.nlm.nih.gov/") == 0)isDirectCall = false;
+
+		var cantDoSynchronousLoad = (!isMyHost && Jmol.$supportsIECrossDomainScripting());
+		var data = null;
+		if ((!fSuccess || asBase64) && (cantDoSynchronousLoad || asBase64 || !isMyHost && !isDirectCall)) {
+				data = Jmol._getRawDataFromServer("_",fileName, fSuccess, fSuccess, asBase64, true);
+		} else {
+			fileName = fileName.replace(/file:\/\/\/\//, "file://"); // opera
+			var info = {dataType:(isBinary ? "binary" : "text"),async:!!fSuccess};
+			if (isPost) {
+				info.type = "POST";
+				info.url = fileName.split("?POST?")[0]
+				info.data = fileName.split("?POST?")[1]
+			} else {
+				info.type = "GET";
+				info.url = fileName;
+			}
+			if (fSuccess) {
+				info.success = function(data) { fSuccess(Jmol._xhrReturn(info.xhr))};
+				info.error = function() { fSuccess(info.xhr.statusText)};
+			}
+			info.xhr = Jmol.$ajax(info);
+			if (!fSuccess) {
+				data = Jmol._xhrReturn(info.xhr);
+			}
+		}
+		if (!doProcess)
+			return data;
+		if (data == null) {
+			data = "";
+			isBinary = false;
+		}
+		isBinary && (isBinary = Jmol._canSyncBinary(true));
+		return (isBinary ? Jmol._strToBytes(data) : JU.SB.newS(data));
+	}
+	
+	Jmol._xhrReturn = function(xhr){
+		if (!xhr.responseText || self.Clazz && Clazz.instanceOf(xhr.response, self.ArrayBuffer)) {
+			// Safari or error 
+			return xhr.response || xhr.statusText;
+		} 
+		return xhr.responseText;
+	}
+
+	Jmol._isDirectCall = function(url) {
+		for (var key in Jmol.db._DirectDatabaseCalls) {
+			if (key.indexOf(".") >= 0 && url.indexOf(key) >= 0)
+				return true;
+		}
+		return false;
+	}
+
+	Jmol._cleanFileData = function(data) {
+		if (data.indexOf("\r") >= 0 && data.indexOf("\n") >= 0) {
+			return data.replace(/\r\n/g,"\n");
+		}
+		if (data.indexOf("\r") >= 0) {
+			return data.replace(/\r/g,"\n");
+		}
+		return data;
+	};
+
+	Jmol._getFileType = function(name) {
+		var database = name.substring(0, 1);
+		if (database == "$" || database == ":")
+			return "MOL";
+		if (database == "=")
+			return (name.substring(1,2) == "=" ? "LCIF" : "PDB");
+		// just the extension, which must be PDB, XYZ..., CIF, or MOL
+		name = name.split('.').pop().toUpperCase();
+		return name.substring(0, Math.min(name.length, 3));
+	};
+
+	Jmol._getZ = function(applet, what) {
+		return applet && applet._z && applet._z[what] || Jmol._z[what];
+	}
+	
+	Jmol._incrZ = function(applet, what) {
+		return applet && applet._z && ++applet._z[what] || ++Jmol._z[what];
+	}
+	
+	Jmol._loadFileAsynchronously = function(fileLoadThread, applet, fileName, appData) {
+		if (fileName.indexOf("?") != 0) {
+			// LOAD ASYNC command
+			var fileName0 = fileName;
+			fileName = Jmol._checkFileName(applet, fileName);
+			var fSuccess = function(data) {Jmol._setData(fileLoadThread, fileName, fileName0, data, appData)};
+			fSuccess = Jmol._checkCache(applet, fileName, fSuccess);
+			if (fileName.indexOf("|") >= 0)
+				fileName = fileName.split("|")[0];
+			return (fSuccess == null ? null : Jmol._getFileData(fileName, fSuccess));		
+		}
+		// we actually cannot suggest a fileName, I believe.
+		if (!Jmol.featureDetection.hasFileReader)
+				return fileLoadThread.setData("Local file reading is not enabled in your browser", null, null, appData);
+		if (!applet._localReader) {
+			var div = '<div id="ID" style="z-index:'+Jmol._getZ(applet, "fileOpener") + ';position:absolute;background:#E0E0E0;left:10px;top:10px"><div style="margin:5px 5px 5px 5px;"><input type="file" id="ID_files" /><button id="ID_loadfile">load</button><button id="ID_cancel">cancel</button></div><div>'
+			Jmol.$after("#" + applet._id + "_appletdiv", div.replace(/ID/g, applet._id + "_localReader"));
+			applet._localReader = Jmol.$(applet, "localReader");
+		}
+		Jmol.$appEvent(applet, "localReader_loadfile", "click");
+		Jmol.$appEvent(applet, "localReader_loadfile", "click", function(evt) {
+			var file = Jmol.$(applet, "localReader_files")[0].files[0];   
+			var reader = new FileReader();
+			reader.onloadend = function(evt) {
+				if (evt.target.readyState == FileReader.DONE) { // DONE == 2
+					Jmol.$css(Jmol.$(applet, "localReader"), {display : "none"});
+					Jmol._setData(fileLoadThread, file.name, file.name, evt.target.result, appData);
+				}
+			};
+			reader.readAsArrayBuffer(file);
+		});
+		Jmol.$appEvent(applet, "localReader_cancel", "click");
+		Jmol.$appEvent(applet, "localReader_cancel", "click", function(evt) {
+			Jmol.$css(Jmol.$(applet, "localReader"), {display: "none"});
+			fileLoadThread.setData(null, null, null, appData);
+		});
+		Jmol.$css(Jmol.$(applet, "localReader"), {display : "block"});
+	}
+
+  Jmol._setData = function(fileLoadThread, filename, filename0, data, appData) {
+  	data = Jmol._strToBytes(data);
+		if (filename.indexOf(".jdx") >= 0)
+			Jmol.Cache.put("cache://" + filename, data);
+		fileLoadThread.setData(filename, filename0, data, appData);
+  }
+  
+	Jmol._toBytes = function(data) {
+	if (typeof data == "string") 
+		return data.getBytes();
+	// ArrayBuffer assumed here
+	data = new Uint8Array(data);
+	var b = Clazz.newByteArray(data.length, 0);
+		for (var i = data.length; --i >= 0;)
+			b[i] = data[i];
+	return b;
+	}
+
+	Jmol._doAjax = function(url, postOut, dataOut) {
+		// called by org.jmol.awtjs2d.JmolURLConnection.doAjax()
+		url = url.toString();
+
+		if (dataOut != null) 
+			return Jmol._saveFile(url, dataOut);
+		if (postOut)
+			url += "?POST?" + postOut;
+		return Jmol._getFileData(url, null, true);
+	}
+
+	// Jmol._localFileSaveFunction --  // do something local here; Maybe try the FileSave interface? return true if successful
+	 
+	Jmol._saveFile = function(filename, data, mimetype, encoding) {
+		if (Jmol._localFileSaveFunction && Jmol._localFileSaveFunction(filename, data))
+			return "OK";
+		var filename = filename.substring(filename.lastIndexOf("/") + 1);
+		mimetype || (mimetype = (filename.indexOf(".pdf") >= 0 ? "application/pdf" 
+			: filename.indexOf(".png") >= 0 ? "image/png" 
+			: filename.indexOf(".gif") >= 0 ? "image/gif" 
+			: filename.indexOf(".jpg") >= 0 ? "image/jpg" : ""));
+		var isString = (typeof data == "string");
+		if (!isString)
+			data = (JU ? JU : J.util).Base64.getBase64(data).toString();
+		encoding || (encoding = (isString ? "" : "base64"));
+		var url = Jmol._serverUrl;
+		url && url.indexOf("your.server") >= 0 && (url = "");
+		if (Jmol._useDataURI || !url) {
+			// Asynchronous output generated using an anchor tag
+			encoding || (data = btoa(data));
+			var a = document.createElement("a");
+			a.href = "data:" + mimetype + ";base64," + data;
+			a.type = mimetype || (mimetype = "text/plain");	
+			a.download = filename;
+			a.target = "_blank";
+				$("body").append(a);
+			a.click();
+			a.remove();		
+		} else {
+		// Asynchronous outputto be reflected as a download
+			if (!Jmol._formdiv) {
+					var sform = '<div id="__jsmolformdiv__" style="display:none">\
+						<form id="__jsmolform__" method="post" target="_blank" action="">\
+						<input name="call" value="saveFile"/>\
+						<input id="__jsmolmimetype__" name="mimetype" value=""/>\
+						<input id="__jsmolencoding__" name="encoding" value=""/>\
+						<input id="__jsmolfilename__" name="filename" value=""/>\
+						<textarea id="__jsmoldata__" name="data"></textarea>\
+						</form>\
+						</div>'
+				Jmol.$after("body", sform);
+				Jmol._formdiv = "__jsmolform__";
+			}
+			Jmol.$attr(Jmol._formdiv, "action", url + "?" + (new Date()).getMilliseconds());
+			Jmol.$val("__jsmoldata__", data);
+			Jmol.$val("__jsmolfilename__", filename);
+			Jmol.$val("__jsmolmimetype__", mimetype);
+			Jmol.$val("__jsmolencoding__", encoding);
+			Jmol.$submit("__jsmolform__");
+			Jmol.$val("__jsmoldata__", "");
+			Jmol.$val("__jsmolfilename__", "");
+		}
+		return "OK";
+	}
+
+	Jmol._strToBytes = function(s) {
+		if (Clazz.instanceOf(s, self.ArrayBuffer))
+			return Jmol._toBytes(s);
+		var b = Clazz.newByteArray(s.length, 0);
+		for (var i = s.length; --i >= 0;)
+			b[i] = s.charCodeAt(i) & 0xFF;
+		return b;
+	}
+
+	////////////// applet start-up functionality //////////////
+
+	Jmol._setConsoleDiv = function (d) {
+		if (!self.Clazz)return;
+		Clazz.setConsoleDiv(d);
+	}
+
+	Jmol._registerApplet = function(id, applet) {
+		return window[id] = Jmol._applets[id] = Jmol._applets[applet] = Jmol._applets[id + "__" + Jmol._syncId + "__"] = applet;
+	} 
+
+	Jmol._readyCallback = function (appId,fullId,isReady,javaApplet,javaAppletPanel) {
+		appId = appId.split("_object")[0];
+    javaAppletPanel || (javaAppletPanel = javaApplet);
+		isReady = (isReady.booleanValue ? isReady.booleanValue() : isReady);
+		// necessary for MSIE in strict mode -- apparently, we can't call 
+		// jmol._readyCallback, but we can call Jmol._readyCallback. Go figure...
+    var applet = Jmol._applets[appId];
+    applet._appletPanel = javaAppletPanel;
+    applet._applet = javaApplet;
+		Jmol._track(applet._readyCallback(appId, fullId, isReady));
+	}
+
+	Jmol._getWrapper = function(applet, isHeader) {
+
+			// id_appletinfotablediv
+			//     id_appletdiv
+			//     id_coverdiv
+			//     id_infotablediv
+			//       id_infoheaderdiv
+			//          id_infoheaderspan
+			//          id_infocheckboxspan
+			//       id_infodiv
+
+
+			// for whatever reason, without DOCTYPE, with MSIE, "height:auto" does not work, 
+			// and the text scrolls off the page.
+			// So I'm using height:95% here.
+			// The table was a fix for MSIE with no DOCTYPE tag to fix the miscalculation
+			// in height of the div when using 95% for height. 
+			// But it turns out the table has problems with DOCTYPE tags, so that's out. 
+			// The 95% is a compromise that we need until the no-DOCTYPE MSIE solution is found. 
+			// (100% does not work with the JME linked applet)
+		var s;
+		// ... here are just for clarification in this code; they are removed immediately
+		if (isHeader) {
+			var img = ""; 
+			if (applet._coverImage){
+				var more = " onclick=\"Jmol.coverApplet(ID, false)\" title=\"" + (applet._coverTitle) + "\"";
+				var play = "<image id=\"ID_coverclickgo\" src=\"" + applet._j2sPath + "/img/play_make_live.jpg\" style=\"width:25px;height:25px;position:absolute;bottom:10px;left:10px;"
+					+ "z-index:" + Jmol._getZ(applet, "coverImage")+";opacity:0.5;\"" + more + " />"  
+				img = "<div id=\"ID_coverdiv\" style=\"background-color:red;z-index:" + Jmol._getZ(applet, "coverImage")+";width:100%;height:100%;display:inline;position:absolute;top:0px;left:0px\"><image id=\"ID_coverimage\" src=\""
+				 + applet._coverImage + "\" style=\"width:100%;height:100%\"" + more + "/>" + play + "</div>";
+			}
+			var css = Jmol._appletCssText.replace(/\'/g,'"');
+			css = (css.indexOf("style=\"") >= 0 ? css.split("style=\"")[1] : "\" " + css);
+			s = "\
+...<div id=\"ID_appletinfotablediv\" style=\"width:Wpx;height:Hpx;position:relative;font-size:14px;text-align:left\">IMG\
+......<div id=\"ID_appletdiv\" style=\"z-index:" + Jmol._getZ(applet, "header") + ";width:100%;height:100%;position:absolute;top:0px;left:0px;" + css + ">";
+			var height = applet._height;
+			var width = applet._width;
+			if (typeof height !== "string" || height.indexOf("%") < 0) 
+				height += "px";
+			if (typeof width !== "string" || width.indexOf("%") < 0)
+				width += "px";
+			s = s.replace(/IMG/, img).replace(/Hpx/g, height).replace(/Wpx/g, width);
+		} else {
+			s = "\
+......</div>\
+......<div id=\"ID_2dappletdiv\" style=\"position:absolute;width:100%;height:100%;overflow:hidden;display:none\"></div>\
+......<div id=\"ID_infotablediv\" style=\"width:100%;height:100%;position:absolute;top:0px;left:0px\">\
+.........<div id=\"ID_infoheaderdiv\" style=\"height:20px;width:100%;background:yellow;display:none\"><span id=\"ID_infoheaderspan\"></span><span id=\"ID_infocheckboxspan\" style=\"position:absolute;text-align:right;right:1px;\"><a href=\"javascript:Jmol.showInfo(ID,false)\">[x]</a></span></div>\
+.........<div id=\"ID_infodiv\" style=\"position:absolute;top:20px;bottom:0px;width:100%;height:100%;overflow:auto\"></div>\
+......</div>\
+...</div>";
+		}
+		return s.replace(/\.\.\./g,"").replace(/[\n\r]/g,"").replace(/ID/g, applet._id);
+	}
+
+	Jmol._documentWrite = function(text) {
+		if (Jmol._document) {
+			if (Jmol._isXHTML && !Jmol._XhtmlElement) {
+				var s = document.getElementsByTagName("script");
+				Jmol._XhtmlElement = s.item(s.length - 1);
+				Jmol._XhtmlAppendChild = false;
+			}
+			if (Jmol._XhtmlElement)
+				Jmol._domWrite(text);
+			else
+				Jmol._document.write(text);
+		}
+		return text;
+	}
+
+	Jmol._domWrite = function(data) {
+		var pt = 0
+		var Ptr = []
+		Ptr[0] = 0
+		while (Ptr[0] < data.length) {
+			var child = Jmol._getDomElement(data, Ptr);
+			if (!child)
+				break;
+			if (Jmol._XhtmlAppendChild)
+				Jmol._XhtmlElement.appendChild(child);
+			else
+				Jmol._XhtmlElement.parentNode.insertBefore(child, _jmol.XhtmlElement);
+		}
+	}
+
+	Jmol._getDomElement = function(data, Ptr, closetag, lvel) {
+
+		// there is no "document.write" in XHTML
+
+		var e = document.createElement("span");
+		e.innerHTML = data;
+		Ptr[0] = data.length;
+
+/*
+	// unnecessary ?  
+
+		closetag || (closetag = "");
+		lvel || (lvel = 0);
+		var pt0 = Ptr[0];
+		var pt = pt0;
+		while (pt < data.length && data.charAt(pt) != "<") 
+			pt++
+		if (pt != pt0) {
+			var text = data.substring(pt0, pt);
+			Ptr[0] = pt;
+			return document.createTextNode(text);
+		}
+		pt0 = ++pt;
+		var ch;
+		while (pt < data.length && "\n\r\t >".indexOf(ch = data.charAt(pt)) < 0) 
+			pt++;
+		var tagname = data.substring(pt0, pt);
+		var e = (tagname == closetag  || tagname == "/" ? ""
+			: document.createElementNS ? document.createElementNS('http://www.w3.org/1999/xhtml', tagname)
+			: document.createElement(tagname));
+		if (ch == ">") {
+			Ptr[0] = ++pt;
+			return e;
+		}
+		while (pt < data.length && (ch = data.charAt(pt)) != ">") {
+			while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) 
+				pt++;
+			pt0 = pt;
+			while (pt < data.length && "\n\r\t =/>".indexOf(ch = data.charAt(pt)) < 0) 
+				pt++;
+			var attrname = data.substring(pt0, pt).toLowerCase();
+			if (attrname && ch != "=")
+				e.setAttribute(attrname, "true");
+			while (pt < data.length && "\n\r\t ".indexOf(ch = data.charAt(pt)) >= 0) 
+				pt++;
+			if (ch == "/") {
+				Ptr[0] = pt + 2;
+				return e;
+			} else if (ch == "=") {
+				var quote = data.charAt(++pt);
+				pt0 = ++pt;
+				while (pt < data.length && (ch = data.charAt(pt)) != quote) 
+					pt++;
+				var attrvalue = data.substring(pt0, pt);
+				e.setAttribute(attrname, attrvalue);
+				pt++;
+			}
+		}
+		Ptr[0] = ++pt;
+		while (Ptr[0] < data.length) {
+			var child = Jmol._getDomElement(data, Ptr, "/" + tagname, lvel+1);
+			if (!child)
+				break;
+			e.appendChild(child);
+		}
+*/
+		return e;    
+	}
+
+	Jmol._setObject = function(obj, id, Info) {
+		obj._id = id;
+		obj.__Info = {};
+		Info.z && Info.zIndexBase && (Jmol._z = Jmol._getZOrders(Info.zIndexBase));
+		for (var i in Info)
+			obj.__Info[i] = Info[i];
+		(obj._z = Info.z) || Info.zIndexBase && (obj._z = obj.__Info.z = Jmol._getZOrders(Info.zIndexBase));
+		obj._width = Info.width;
+		obj._height = Info.height;
+		obj._noscript = !obj._isJava && Info.noscript;
+		obj._console = Info.console;
+		obj._cacheFiles = !!Info.cacheFiles;
+		obj._viewSet = (Info.viewSet == null || obj._isJava ? null : "Set" + Info.viewSet);
+		if (obj._viewSet != null) {
+			Jmol.View.__init(obj);
+			obj._currentView = null;
+		}
+		!Jmol._fileCache && obj._cacheFiles && (Jmol._fileCache = {});
+		if (!obj._console)
+			obj._console = obj._id + "_infodiv";
+		if (obj._console == "none")
+			obj._console = null;
+
+		obj._color = (Info.color ? Info.color.replace(/0x/,"#") : "#FFFFFF");
+		obj._disableInitialConsole = Info.disableInitialConsole;
+		obj._noMonitor = Info.disableJ2SLoadMonitor;
+		Jmol._j2sPath && (Info.j2sPath = Jmol._j2sPath);
+		obj._j2sPath = Info.j2sPath;
+		obj._coverImage = Info.coverImage;
+		obj._isCovered = !!obj._coverImage; 
+		obj._deferApplet = Info.deferApplet || obj._isCovered && obj._isJava; // must do this if covered in Java
+		obj._deferUncover = Info.deferUncover && !obj._isJava; // can't do this with Java
+		obj._coverScript = Info.coverScript;
+		obj._coverTitle = Info.coverTitle;
+
+		if (!obj._coverTitle)
+			obj._coverTitle = (obj._deferApplet ? "activate 3D model" : "3D model is loading...")
+		obj._containerWidth = obj._width + ((obj._width==parseFloat(obj._width))? "px":"");
+		obj._containerHeight = obj._height + ((obj._height==parseFloat(obj._height))? "px":"");
+		obj._info = "";
+		obj._infoHeader = obj._jmolType + ' "' + obj._id + '"'
+		obj._hasOptions = Info.addSelectionOptions;
+		obj._defaultModel = Info.defaultModel;
+		obj._readyScript = (Info.script ? Info.script : "");
+		obj._readyFunction = Info.readyFunction;
+		if (obj._coverImage && !obj._deferApplet)
+			obj._readyScript += ";javascript " + id + "._displayCoverImage(false)";
+		obj._src = Info.src;
+
+	}
+
+	Jmol._addDefaultInfo = function(Info, DefaultInfo) {
+		for (var x in DefaultInfo)
+			if (typeof Info[x] == "undefined")
+				Info[x] = DefaultInfo[x];
+		Jmol._use && (Info.use = Jmol._use);
+		if (Info.use.indexOf("SIGNED") >= 0) {
+			if (Info.jarFile.indexOf("Signed") < 0)
+				Info.jarFile = Info.jarFile.replace(/Applet/,"AppletSigned");
+			Info.use = Info.use.replace(/SIGNED/, "JAVA");
+			Info.isSigned = true;
+		}
+	}
+
+	Jmol._syncedApplets = [];
+	Jmol._syncedCommands = [];
+	Jmol._syncedReady = [];
+	Jmol._syncReady = false;
+	Jmol._isJmolJSVSync = false;
+
+	Jmol._setReady = function(applet) {
+		Jmol._syncedReady[applet] = 1;
+		var n = 0;
+		for (var i = 0; i < Jmol._syncedApplets.length; i++) {
+			if (Jmol._syncedApplets[i] == applet._id) {
+				Jmol._syncedApplets[i] = applet;
+				Jmol._syncedReady[i] = 1;
+			} else if (!Jmol._syncedReady[i]) {
+				continue;
+			}
+			n++;
+		}
+		if (n != Jmol._syncedApplets.length)
+			return;
+		Jmol._setSyncReady();
+	}
+
+	Jmol._setDestroy = function(applet) {
+		//MSIE bug responds to any link click even if it is just a JavaScript call
+
+		if (Jmol.featureDetection.allowDestroy)
+			Jmol.$windowOn('beforeunload', function () { Jmol._destroy(applet); } );
+	}
+
+	Jmol._destroy = function(applet) {
+		try {
+			if (applet._appletPanel) applet._appletPanel.destroy();
+			applet._applet = null;
+			Jmol._unsetMouse(applet._canvas)
+			applet._canvas = null;
+			var n = 0;
+			for (var i = 0; i < Jmol._syncedApplets.length; i++) {
+				if (Jmol._syncedApplets[i] == applet)
+					Jmol._syncedApplets[i] = null;
+				if (Jmol._syncedApplets[i])
+					n++;
+			}
+			if (n > 0)
+				return;
+			Jmol._clearVars();
+		} catch(e){}
+	}
+
+	////////////// misc core functionality //////////////
+
+	Jmol._setSyncReady = function() {
+		Jmol._syncReady = true;
+		var s = ""
+		for (var i = 0; i < Jmol._syncedApplets.length; i++)
+			if (Jmol._syncedCommands[i])
+				s += "Jmol.script(Jmol._syncedApplets[" + i + "], Jmol._syncedCommands[" + i + "]);"
+		setTimeout(s, 50);  
+	}
+
+	Jmol._mySyncCallback = function(appFullName,msg) {
+		app = Jmol._applets[appFullName];
+		if (app._viewSet) {
+			// when can we do this?
+//			if (app._viewType == "JSV" && !app._currentView.JMOL)
+				Jmol.View.updateFromSync(app, msg);
+			return;
+		}
+		if(!Jmol._syncReady || !Jmol._isJmolJSVSync)
+			return 1; // continue processing and ignore me
+		for (var i = 0; i < Jmol._syncedApplets.length; i++) {
+			if (msg.indexOf(Jmol._syncedApplets[i]._syncKeyword) >= 0)
+				Jmol._syncedApplets[i]._syncScript(msg);
+		}
+		return 0 // prevents further Jmol sync processing 
+	}              
+
+	Jmol._getElement = function(applet, what) {
+		var d = document.getElementById(applet._id + "_" + what);
+		return (d || {});
+	} 
+	 
+	Jmol._evalJSON = function(s,key){
+		s = s + "";
+		if(!s)
+			return [];
+		if(s.charAt(0) != "{") {
+			if(s.indexOf(" | ") >= 0)
+				s = s.replace(/\ \|\ /g, "\n");
+			return s;
+		}
+		var A = (new Function( "return " + s ) )();
+		return (!A ? null : key && A[key] != undefined ? A[key] : A);
+	}
+
+	Jmol._sortMessages = function(A){
+		/*
+		 * private function
+		 */
+		function _sortKey0(a,b){
+			return (a[0]<b[0]?1:a[0]>b[0]?-1:0);
+		}
+
+		if(!A || typeof (A) != "object")
+			return [];
+		var B = [];
+		for(var i = A.length - 1; i >= 0; i--)
+			for(var j = 0, jj= A[i].length; j < jj; j++)
+				B[B.length] = A[i][j];
+		if(B.length == 0)
+			return;
+		B = B.sort(_sortKey0);
+		return B;
+	}
+
+	//////////////////// mouse events //////////////////////
+
+	Jmol._setMouseOwner = function(who, tf) {
+		if (who == null || tf)
+			Jmol._mouseOwner = who;
+		else if (Jmol._mouseOwner == who)
+			Jmol._mouseOwner = null;
+	}
+
+	Jmol._jsGetMouseModifiers = function(ev) {
+		var modifiers = 0;
+		switch (ev.button) {
+		case 0:
+			modifiers = 16;//J.api.Event.MOUSE_LEFT;
+			break;
+		case 1:
+			modifiers = 8;//J.api.Event.MOUSE_MIDDLE;
+			break;
+		case 2:
+			modifiers = 4;//J.api.Event.MOUSE_RIGHT;
+			break;
+		}
+		if (ev.shiftKey)
+			modifiers += 1;//J.api.Event.SHIFT_MASK;
+		if (ev.altKey)
+			modifiers += 8;//J.api.Event.ALT_MASK;
+		if (ev.ctrlKey)
+			modifiers += 2;//J.api.Event.CTRL_MASK;
+		return modifiers;
+	}
+
+	Jmol._jsGetXY = function(canvas, ev) {
+		if (!canvas.applet._ready || Jmol._touching && ev.type.indexOf("touch") < 0)
+			return false;
+		//ev.preventDefault(); // removed 5/9/2015 -- caused loss of focus on text-box clicking in SwingJS
+		var offsets = Jmol.$offset(canvas.id);
+		var x, y;
+		var oe = ev.originalEvent;
+		// drag-drop jQuery event is missing pageX
+		ev.pageX || (ev.pageX = oe.pageX);
+		ev.pageY || (ev.pageY = oe.pageY);
+		Jmol._mousePageX = ev.pageX;
+		Jmol._mousePageY = ev.pageY;
+		if (oe.targetTouches && oe.targetTouches[0]) {
+			x = oe.targetTouches[0].pageX - offsets.left;
+			y = oe.targetTouches[0].pageY - offsets.top;
+		} else if (oe.changedTouches) {
+			x = oe.changedTouches[0].pageX - offsets.left;
+			y = oe.changedTouches[0].pageY - offsets.top;
+		} else {
+			x = ev.pageX - offsets.left;
+			y = ev.pageY - offsets.top;
+		}
+		return (x == undefined ? null : [Math.round(x), Math.round(y), Jmol._jsGetMouseModifiers(ev)]);
+	}
+
+	Jmol._gestureUpdate = function(canvas, ev) {
+		ev.stopPropagation();
+		ev.preventDefault();
+		var oe = ev.originalEvent;
+		switch (ev.type) {
+		case "touchstart":
+			Jmol._touching = true;
+			break;
+		case "touchend":
+			Jmol._touching = false;
+			break;
+		}
+		if (!oe.touches || oe.touches.length != 2) return false;
+		switch (ev.type) {
+		case "touchstart":
+			canvas._touches = [[],[]];
+			break;
+		case "touchmove":
+			var offsets = Jmol.$offset(canvas.id);
+			var t0 = canvas._touches[0];
+			var t1 = canvas._touches[1];
+			t0.push([oe.touches[0].pageX - offsets.left, oe.touches[0].pageY - offsets.top]);
+			t1.push([oe.touches[1].pageX - offsets.left, oe.touches[1].pageY - offsets.top]);
+			var n = t0.length;
+			if (n > 3) {
+				t0.shift();
+				t1.shift();
+			}
+			if (n >= 2)
+				canvas.applet._processGesture(canvas._touches);
+			break;
+		}
+		return true;
+	}  
+
+	Jmol._jsSetMouse = function(canvas) {
+
+    var doIgnore = function(ev) { return (ev.target.className.indexOf("swingjs-ui") >= 0) };
+         
+		Jmol.$bind(canvas, 'mousedown touchstart', function(ev) {
+      if (doIgnore(ev))
+        return true;
+			Jmol._setMouseOwner(canvas, true);
+			ev.stopPropagation();
+      var ui = ev.target["data-UI"];
+      if (!ui || !ui.handleJSEvent(canvas, 501, ev)) 
+  			ev.preventDefault();
+			canvas.isDragging = true;
+			if ((ev.type == "touchstart") && Jmol._gestureUpdate(canvas, ev))
+				return !!ui;
+			Jmol._setConsoleDiv(canvas.applet._console);
+			var xym = Jmol._jsGetXY(canvas, ev);
+			if(xym) {
+		  	if (ev.button != 2)
+          Jmol.Swing.hideMenus(canvas.applet);
+        canvas.applet._processEvent(501, xym); //java.awt.Event.MOUSE_DOWN
+      }
+			return !!ui;
+		});
+    
+		Jmol.$bind(canvas, 'mouseup touchend', function(ev) {
+      if (doIgnore(ev))
+        return true;
+			Jmol._setMouseOwner(null);
+			ev.stopPropagation();
+      var ui = ev.target["data-UI"];
+      if (!ui || !ui.handleJSEvent(canvas, 502, ev))
+  			ev.preventDefault();
+			canvas.isDragging = false;
+			if (ev.type == "touchend" && Jmol._gestureUpdate(canvas, ev))
+				return !!ui;
+			var xym = Jmol._jsGetXY(canvas, ev);
+			if(xym)
+  			canvas.applet._processEvent(502, xym);//java.awt.Event.MOUSE_UP
+			return !!ui;
+		});
+    
+		Jmol.$bind(canvas, 'mousemove touchmove', function(ev) { // touchmove
+      if (doIgnore(ev))
+        return true;
+		  // defer to console or menu when dragging within this canvas
+			if (Jmol._mouseOwner && Jmol._mouseOwner != canvas && Jmol._mouseOwner.isDragging) {
+        if (!Jmol._mouseOwner.mouseMove)
+          return true;
+	   			Jmol._mouseOwner.mouseMove(ev);
+				return false;
+			}
+			return Jmol._drag(canvas, ev);
+		});
+		
+		Jmol._drag = function(canvas, ev) {
+      
+			ev.stopPropagation();
+			ev.preventDefault();
+      
+			var isTouch = (ev.type == "touchmove");
+			if (isTouch && Jmol._gestureUpdate(canvas, ev))
+				return false;
+			var xym = Jmol._jsGetXY(canvas, ev);
+			if(!xym) return false;
+      
+			if (!canvas.isDragging)
+				xym[2] = 0;
+
+      var ui = ev.target["data-UI"];
+      if (canvas.isdragging && (!ui || !ui.handleJSEvent(canvas, 506, ev))) {}
+			canvas.applet._processEvent((canvas.isDragging ? 506 : 503), xym); // java.awt.Event.MOUSE_DRAG : java.awt.Event.MOUSE_MOVE
+			return !!ui;
+		}
+		
+		Jmol.$bind(canvas, 'DOMMouseScroll mousewheel', function(ev) { // Zoom
+      if (doIgnore(ev))
+        return true;
+			ev.stopPropagation();
+			ev.preventDefault();
+			// Webkit or Firefox
+			canvas.isDragging = false;
+			var oe = ev.originalEvent;
+			var scroll = (oe.detail ? oe.detail : (Jmol.featureDetection.os == "mac" ? 1 : -1) * oe.wheelDelta); // Mac and PC are reverse; but 
+			var modifiers = Jmol._jsGetMouseModifiers(ev);
+			canvas.applet._processEvent(-1,[scroll < 0 ? -1 : 1,0,modifiers]);
+			return false;
+		});
+
+		// context menu is fired on mouse down, not up, and it's handled already anyway.
+
+		Jmol.$bind(canvas, "contextmenu", function() {return false;});
+
+		Jmol.$bind(canvas, 'mouseout', function(ev) {
+      if (doIgnore(ev))
+        return true;
+      if (Jmol._mouseOwner && !Jmol._mouseOwner.mouseMove) 
+        Jmol._setMouseOwner(null);
+			if (canvas.applet._appletPanel)
+				canvas.applet._appletPanel.startHoverWatcher(false);
+			//canvas.isDragging = false;
+			var xym = Jmol._jsGetXY(canvas, ev);
+			if (!xym)
+				return false;
+			//canvas.applet._processEvent(502, xym);//J.api.Event.MOUSE_UP
+			//canvas.applet._processEvent(505, xym);//J.api.Event.MOUSE_EXITED
+			return false;
+		});
+
+		Jmol.$bind(canvas, 'mouseenter', function(ev) {
+      if (doIgnore(ev))
+        return true;
+			if (canvas.applet._appletPanel)
+				canvas.applet._appletPanel.startHoverWatcher(true);
+			if (ev.buttons === 0 || ev.which === 0) {
+				canvas.isDragging = false;
+				var xym = Jmol._jsGetXY(canvas, ev);
+				if (!xym)
+					return false;
+				canvas.applet._processEvent(504, xym);//J.api.Event.MOUSE_ENTERED	
+				canvas.applet._processEvent(502, xym);//J.api.Event.MOUSE_UP
+				return false;
+			}
+		});
+
+	Jmol.$bind(canvas, 'mousemoveoutjsmol', function(evspecial, target, ev) {
+      if (doIgnore(ev))
+        return true;
+		if (canvas == Jmol._mouseOwner && canvas.isDragging) {
+			return Jmol._drag(canvas, ev);
+		}
+	});
+
+		if (canvas.applet._is2D)
+			Jmol.$resize(function() {
+				if (!canvas.applet)
+					return;
+				canvas.applet._resize();
+			});
+ 
+		Jmol.$bind('body', 'mouseup touchend', function(ev) {
+      if (doIgnore(ev))
+        return true;
+			if (canvas.applet)
+				canvas.isDragging = false;
+			Jmol._setMouseOwner(null);
+		});
+
+	}
+
+	Jmol._jsUnsetMouse = function(canvas) {
+		canvas.applet = null;
+		Jmol.$bind(canvas, 'mousedown touchstart mousemove touchmove mouseup touchend DOMMouseScroll mousewheel contextmenu mouseout mouseenter', null);
+		Jmol._setMouseOwner(null);
+	}
+
+
+////// Jmol.Swing interface  for Javascript implementation of Swing dialogs and menus
+
+Jmol.Swing = {
+	// a static class
+	count:0,
+	menuInitialized:0,
+	menuCounter:0,
+	htDialogs:{}
+};
+
+(function(Swing) {
+
+SwingController = Swing; // see javajs.api.SwingController
+
+Swing.setDraggable = function(Obj) {
+	
+	var proto = Obj.prototype;
+	if (proto.setContainer)
+		return;
+	
+	// for menus, console, and 
+	proto.setContainer = function(container) {
+		this.container = container;
+		container.obj = this;
+		this.isDragging = false;
+		this.ignoreMouse = false;
+		var me = this;
+		container.bind('mousedown touchstart', function(ev) {
+			if (me.ignoreMouse) {
+				me.ignoreMouse = false;
+				return true;
+			}
+			Jmol._setMouseOwner(me, true);
+			me.isDragging = true;
+			me.pageX = ev.pageX;
+			me.pageY = ev.pageY;
+			return false;
+		});
+		container.bind('mousemove touchmove', function(ev) {
+			if (me.isDragging && Jmol._mouseOwner == me) {
+				me.mouseMove(ev);
+				return false;
+			}
+		});
+		container.bind('mouseup touchend', function(ev) {
+			me.mouseUp(ev);
+			Jmol._setMouseOwner(null);
+		});
+	};
+
+	proto.mouseUp = function(ev) {
+		if (this.isDragging && Jmol._mouseOwner == this) {
+			this.pageX0 += (ev.pageX - this.pageX);
+			this.pageY0 += (ev.pageY - this.pageY);
+			this.isDragging = false;
+			return false;
+		}
+		Jmol._setMouseOwner(null);
+	}
+
+	proto.setPosition = function() {
+		if (Jmol._mousePageX === null) {
+			var id = this.applet._id + "_" + (this.applet._is2D ? "canvas2d" : "canvas");
+			var offsets = Jmol.$offset(id);
+			Jmol._mousePageX = offsets.left;
+			Jmol._mousePageY = offsets.top;
+		}
+		this.pageX0 = Jmol._mousePageX;
+		this.pageY0 = Jmol._mousePageY;
+		var pos = { top: Jmol._mousePageY + 'px', left: Jmol._mousePageX + 'px' };
+		this.container.css(pos);
+	};
+
+	proto.mouseMove = function(ev) {
+		if (this.isDragging && Jmol._mouseOwner == this) {
+			this.timestamp = System.currentTimeMillis(); // used for menu closure
+			var x = this.pageX0 + (ev.pageX - this.pageX);
+			var y = this.pageY0 + (ev.pageY - this.pageY);
+      Jmol._mousePageX = x;
+      Jmol._mousePageY = y;
+			this.container.css({ top: y + 'px', left: x + 'px' })
+		}
+	};
+
+	proto.dragBind = function(isBind) {
+		this.applet._ignoreMouse = !isBind;
+		this.container.unbind('mousemoveoutjsmol');
+		this.container.unbind('touchmoveoutjsmol');
+		this.container.unbind('mouseupoutjsmol');
+		this.container.unbind('touchendoutjsmol');
+		Jmol._setMouseOwner(null);
+		if (isBind) {
+			var me = this;
+			this.container.bind('mousemoveoutjsmol touchmoveoutjsmol', function(evspecial, target, ev) {
+				me.mouseMove(ev);
+			});
+			this.container.bind('mouseupoutjsmol touchendoutjsmol', function(evspecial, target, ev) {
+				me.mouseUp(ev);
+			});
+		}
+	};
+}
+
+// Dialog //
+
+Swing.JSDialog = function () {
+}
+
+Swing.setDraggable(Swing.JSDialog);
+
+///// calls from javajs and other Java-derived packages /////
+
+Swing.getScreenDimensions = function(d) {
+	d.width = $(window).width();
+	d.height = $(window).height();
+}
+
+Swing.dispose = function(dialog) {
+	Jmol.$remove(dialog.id + "_mover");
+	delete Swing.htDialogs[dialog.id]
+	dialog.container.obj.dragBind(false);
+//  var btns = $("#" + dialog.id + " *[id^='J']"); // add descendents with id starting with "J"
+//  for (var i = btns.length; --i >= 0;)
+//    delete Dialog.htDialogs[btns[i].id]
+	//System.out.println("JSmolCore.js: dispose " + dialog.id)
+}
+ 
+Swing.register = function(dialog, type) {
+	dialog.id = type + (++Swing.count);
+	Swing.htDialogs[dialog.id] = dialog;
+	//System.out.println("JSmolCore.js: register " + dialog.id)
+
+}
+
+Swing.setDialog = function(dialog) {
+	Jmol._setMouseOwner(null);
+	Jmol.$remove(dialog.id);
+	//System.out.println("removed " + dialog.id)
+	var id = dialog.id + "_mover";
+	var container = Jmol._$(id);
+	var jd;
+	//System.out.println("JSmolCore.js: setDialog " + dialog.id);
+	if (container[0]) {
+		container.html(dialog.html);
+		jd = container[0].jd;
+	} else {
+		Jmol.$after("body","<div id='" + id + "' style='position:absolute;left:0px;top:0px;'>" + dialog.html + "</div>");
+		var jd = new Swing.JSDialog();
+		container = Jmol._$(id);
+		dialog.container = container;
+		jd.applet = dialog.manager.vwr.html5Applet;
+		jd.setContainer(container);
+		jd.dialog = dialog;
+		jd.setPosition();  
+		jd.dragBind(true);
+		container[0].jd = jd; 
+	}
+	Jmol.$bind("#" + dialog.id + " .JButton", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
+	Jmol.$bind("#" + dialog.id + " .JComboBox", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
+	Jmol.$bind("#" + dialog.id + " .JCheckBox", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
+	Jmol.$bind("#" + dialog.id + " .JTextField", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
+	Jmol.$bind("#" + dialog.id + " .JTable", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
+	Jmol.$bind("#" + dialog.id + " .JScrollPane", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
+	Jmol.$bind("#" + dialog.id + " .JEditorPane", "mousedown touchstart", function(event) { jd.ignoreMouse=true });
+
+}
+ 
+Swing.setSelected = function(chk) {
+ Jmol.$prop(chk.id, 'checked', !!chk.selected);
+}
+
+Swing.setSelectedIndex = function(cmb) {
+ Jmol.$prop(cmb.id, 'selectedIndex', cmb.selectedIndex);
+}
+
+Swing.setText = function(btn) {
+ Jmol.$prop(btn.id, 'value', btn.text);
+}
+
+Swing.setVisible = function(c) {
+	Jmol.$setVisible(c.id, c.visible);
+}
+
+Swing.setEnabled = function(c) {
+	Jmol.$setEnabled(c.id, c.enabled);
+}
+
+/// callbacks from the HTML elements ////
+ 
+Swing.click = function(element, keyEvent) {
+	var component = Swing.htDialogs[element.id];
+	if (component) {
+		//System.out.println("click " + element + " " + component)
+		var info = component.toString();
+		// table cells will have an id but are not registered
+		if (info.indexOf("JCheck") >= 0) {
+				component.selected = element.checked;
+		} else if (info.indexOf("JCombo") >= 0) {
+			component.selectedIndex = element.selectedIndex;
+		} else if (component.text != null) {  // JButton, JTextField
+			component.text = element.value;
+			if (keyEvent && ((keyEvent.charCode || keyEvent.keyCode) != 13))
+				return;
+		}    
+	}
+	var dialog = Swing.htDialogs[Jmol.$getAncestorDiv(element.id, "JDialog").id];
+	var key = (component ? component.name :  dialog.registryKey + "/" + element.id);
+	//System.out.println("JSmolCore.js: click " + key); 
+	dialog.manager.actionPerformed(key);
+}
+
+Swing.setFront = function(dialog) {
+  var applet = dialog.manager.vwr.html5Applet;
+	if (dialog.zIndex != Jmol._getZ(applet, "dialog"))
+	 dialog.zIndex = Jmol._incrZ(applet, "dialog");
+	dialog.container && ((dialog.container[0] || dialog.container).style.zIndex = dialog.zIndex);
+}
+
+Swing.hideMenus = function(applet) {
+	// called from LEFT-DOWN mouse event
+	var menus = applet._menus;
+	if (menus)
+		for (var i in menus)
+			if (menus[i].visible)
+				Swing.hideMenu(menus[i]);
+}
+
+Swing.windowClosing = function(element) {
+	var dialog = Swing.htDialogs[Jmol.$getAncestorDiv(element.id, "JDialog").id];
+	if (dialog.registryKey) {
+		//System.out.println("JSmolCore.js: windowClosing " + dialog.registryKey); 
+		dialog.manager.processWindowClosing(dialog.registryKey);
+	} else {
+		//System.out.println("JSmolCore.js: windowClosing " + dialog.title); 
+		dialog.dispose();
+	}
+}
+
+})(Jmol.Swing);
+
+Jmol._track = function(applet) {
+	// this function inserts an iFrame that can be used to track your page's applet use. 
+	// By default it tracks to a page at St. Olaf College, but you can change that. 
+	// and you can use
+	//
+	// delete Jmol._tracker
+	//
+	// yourself to not have you page execute this 
+	//
+	if (Jmol._tracker){
+		try {  
+			var url = Jmol._tracker + "&applet=" + applet._jmolType + "&version=" + Jmol._version 
+				+ "&appver=" + Jmol.___JmolVersion + "&url=" + encodeURIComponent(document.location.href);
+			var s = '<iframe style="display:none" width="0" height="0" frameborder="0" tabindex="-1" src="' + url + '"></iframe>'
+			Jmol.$after("body", s);
+		} catch (e) {
+			// ignore
+		}
+		delete Jmol._tracker;
+	}
+	return applet;
+}
+
+Jmol.getProfile = function() {
+	window["j2s.doProfile"] = true;
+	if (self.Clazz && self.JSON) {
+		Clazz._profile || (Clazz._profile = {});
+		return Clazz.getProfile();
+	}
+}
+
+Jmol._getInChIKey = function(applet, data) {
+	if (data.indexOf("MOL=") >= 0)
+		data = data.split("MOL=")[1].split("\"")[0];
+
+}
+
+Jmol._getAttr = function(s, a) {
+	var pt = s.indexOf(a + "=");
+	return (pt >= 0 && (pt = s.indexOf('"', pt)) >= 0 
+		? s.substring(pt+1, s.indexOf('"', pt+1)) : null);
+}
+
+Jmol.User = {
+	viewUpdatedCallback: null
+}
+
+Jmol.View = {
+
+// The objective of Jmol.View is to coordinate
+// asynchronous applet loading and atom/peak picking
+// among any combination of Jmol, JME, and JSV.
+// 
+// basic element is a view object:
+//   view = {
+//     viewType1: viewRecord1,
+//     viewType2: viewRecord2,
+//     viewType3: viewRecord3
+//   }
+// where viewType is one of (Jmol, JME, JSV)
+// and a viewRecord is an object
+// with elements .chemID, .applet, .data, .script
+//
+// Jmol.View.sets is a list of cached views[0..n]
+// for a given group of applet objects with common Info.viewSet
+//
+// Bob Hanson 1/22/2014 7:05:38 AM
+
+	count: 0,
+	applets: {},
+	sets: {}
+};
+
+(function(View) {
+
+// methods called from other modules have no "_" in their name
+
+View.updateView = function(applet, Info, _View_updateView) {
+	// Info.chemID, Info.data, possibly Info.viewID if no chemID
+	// return from applet after asynchronous download of new data
+	if (applet._viewSet == null)
+		return;
+	Info.chemID || (applet._searchQuery = null);
+	Info.data || (Info.data = "N/A");
+	Info.type = applet._viewType;
+	if((applet._currentView = View.__findView(applet._viewSet, Info)) == null)
+		applet._currentView = View.__createViewSet(applet._viewSet, Info.chemID, Info.viewID || Info.chemID);
+	applet._currentView[Info.type].data = Info.data;
+	applet._currentView[Info.type].smiles = applet._getSmiles();
+	if (Jmol.User.viewUpdatedCallback)
+		Jmol.User.viewUpdatedCallback(applet, "updateView");
+	View.__setView(applet._currentView, applet, false);
+}
+
+View.updateFromSync = function(applet, msg) {
+	applet._updateMsg = msg;
+	var id = Jmol._getAttr(msg, "sourceID") || Jmol._getAttr(msg, "file");
+	if (!id)
+		return;
+	var view = View.__findView(applet._viewSet, {viewID:id});
+	if (view == null)
+		return Jmol.updateView(applet, msg); // JSV has been updated internally
+	if (view != applet._currentView)
+		View.__setView(view, applet, true);
+	var A = ((id = Jmol._getAttr(msg, "atoms")) && msg.indexOf("selectionhalos ON") >= 0  
+		? eval("[" + id + "]") : []);
+	setTimeout(function(){if (applet._currentView == view)View.updateAtomPick(applet, A)}, 10);
+	if (Jmol.User.viewUpdatedCallback)
+		Jmol.User.viewUpdatedCallback(applet, "updateFromSync");
+}
+
+View.updateAtomPick = function(applet, A, _View_updateAtomPick) {
+	var view = applet._currentView;
+	if (view == null)
+		return;
+	for (var viewType in view) {
+		if (viewType != "info" && view[viewType].applet != applet)
+			view[viewType].applet._updateAtomPick(A);
+	}
+	if (Jmol.User.viewUpdatedCallback)
+		Jmol.User.viewUpdatedCallback(applet, "updateAtomPick");
+}
+
+View.dumpViews = function(setID) {
+	var views = View.sets[setID];
+	if (!views)
+	  return;
+	var s = "View set " + setID + ":\n";
+	var applets = View.applets[setID];
+	for (var i in applets)
+		s += "\napplet " + applets[i]._id
+			+ " currentView=" + (applets[i]._currentView ? applets[i]._currentView.info.viewID : null);
+	for (var i = views.length; --i >= 0;) {
+		var view = views[i];
+		s += "\n\n<b>view=" + i 
+			+ " viewID=" + view.info.viewID 
+			+ " chemID=" + view.info.chemID + "</b>\n"
+		var v;
+		for (var viewType in view) 
+			if (viewType != "info")
+				s += "\nview=" + i + " type=" + viewType + " applet=" 
+					+ ((v = view[viewType]).applet ? v.applet._id : null) 
+					+ " SMILES=" + v.smiles + "\n"
+					+ " atomMap=" + JSON.stringify(v.atomMap) + "\n"
+					+ " data=\n" + v.data + "\n"
+	}
+	return s
+}
+
+
+// methods starting with "__" are "private" to JSmolCore.js
+
+View.__init = function(applet) {
+  var set = applet._viewSet;
+	var a = View.applets;
+	a[set] || (a[set] = {});
+	a[set][applet._viewType] = applet;
+}
+
+View.__findView = function(set, Info) {
+	var views = View.sets[set];
+	if (views == null)
+		views = View.sets[set] = [];
+	for (var i = views.length; --i >= 0;) {
+		var view = views[i];
+		if (Info.viewID) {
+			if (view.info.viewID == Info.viewID)
+				return view;
+		} else if (Info.chemID != null && Info.chemID == view.info.chemID) {
+				return view;
+		} else {
+			for (var viewType in view) { 
+				if (viewType != "info") {
+					if (Info.data != null && view[viewType].data != null ? Info.data == view[viewType].data 
+						: Info.type == viewType)
+							return view;
+				}
+			}
+		}
+	}
+	return null;  
+}
+
+View.__createViewSet = function(set, chemID, viewID, _createViewSet) {
+	View.count++;
+	var view = {info:{chemID: chemID, viewID: viewID || "model_" + View.count}};
+
+	for (var id in Jmol._applets) {
+		var a = Jmol._applets[id];
+		if (a._viewSet == set)
+			view[a._viewType] = {applet:a, data: null};
+	}
+	View.sets[set].push(view);
+	return view;
+}
+
+View.__setView = function(view, applet, isSwitch, _setView) {
+	// called from Jmol._searchMol and Jmol.View.setCurrentView 
+	// to notify the applets in the set that there may be new data for them
+	// skip the originating applet itself and cases where the data has not changed.
+	// stop at first null data, because that will initiate some sort of asynchronous
+	// call that will be back here afterward.
+
+	for (var viewType in view) {
+			if (viewType == "info") 
+				continue;
+		var rec = view[viewType];
+		var a = rec.applet;
+		var modified = (isSwitch || a != null && a._molData == "<modified>");
+
+		if (a == null || a == applet && !modified)
+			continue; // may be a mol3d required by JSV but not having a corresponding applet
+		var wasNull = (rec.data == null);
+		var haveView = (a._currentView != null);
+		a._currentView = view; 
+		if (haveView && view[viewType].data == rec.data && !wasNull & !modified)
+			continue;
+		a._loadModelFromView(view);
+		if (wasNull)
+			break;
+	}
+
+	// Either all are taken care of or one was null,
+	// in which case we have started an asynchronous
+	// process to get the data, and we can quit here.
+	// In either case, we are done.
+}
+
+}) (Jmol.View);
+
+Jmol.Cache = {fileCache: {}};
+
+Jmol.Cache.get = function(filename) {
+	return Jmol.Cache.fileCache[filename];
+}
+
+Jmol.Cache.put = function(filename, data) {
+  Jmol.Cache.fileCache[filename] = data;
+}
+
+	Jmol.Cache.setDragDrop = function(me) {
+		Jmol.$appEvent(me, "appletdiv", "dragover", function(e) {
+			e = e.originalEvent;
+			e.stopPropagation();
+			e.preventDefault();
+			e.dataTransfer.dropEffect = 'copy';
+		});
+		Jmol.$appEvent(me, "appletdiv", "drop", function(e) {
+			var oe = e.originalEvent;
+			oe.stopPropagation();
+			oe.preventDefault();
+			var file = oe.dataTransfer.files[0];
+			if (file == null) {
+				// FF and Chrome will drop an image here
+				// but it will be only a URL, not an actual file. 
+				try {
+				  file = "" + oe.dataTransfer.getData("text");
+				  if (file.indexOf("file:/") == 0 || file.indexOf("http:/") == 0) {
+				  	me._scriptLoad(file);
+				  	return;
+			  	}
+				} catch(e) {
+				  return;
+				}
+			  // some other format
+			  return;
+			}
+			// MSIE will drop an image this way, though, and load it!
+			var reader = new FileReader();
+			reader.onloadend = function(evt) {
+				if (evt.target.readyState == FileReader.DONE) {
+					var cacheName = "cache://DROP_" + file.name;
+					var bytes = Jmol._toBytes(evt.target.result);
+					if (!cacheName.endsWith(".spt"))
+						me._appletPanel.cacheFileByName("cache://DROP_*",false);
+					if (me._viewType == "JSV" || cacheName.endsWith(".jdx")) // shared by Jmol and JSV
+						Jmol.Cache.put(cacheName, bytes);
+					else
+						me._appletPanel.cachePut(cacheName, bytes);
+					var xym = Jmol._jsGetXY(me._canvas, e);
+					if(xym && (!me._appletPanel.setStatusDragDropped || me._appletPanel.setStatusDragDropped(0, xym[0], xym[1], cacheName))) {
+						me._appletPanel.openFileAsyncSpecial(cacheName, 1);
+					}
+				}
+			};
+			reader.readAsArrayBuffer(file);
+		});
+	}
+  
+})(Jmol, jQuery);