biojs-vis-pdbviewer
Version:
A BioJS 2.0 component to view protein structures
3,143 lines • 104 kB
JavaScript
// JSmoljQueryExt.js
// 9/2/2013 7:43:12 AM BH Opera/Safari fix for binary file reading
// 3/11/2014 6:31:01 AM BH fix for MSIE not working locally
;(function($) {
function createXHR(isMSIE) {
try {
return (isMSIE ? new window.ActiveXObject( "Microsoft.XMLHTTP" ) : new window.XMLHttpRequest());
} catch( e ) {}
}
$.ajaxSettings.xhr = (window.ActiveXObject === undefined ? createXHR :
function() {
return (this.url == document.location || this.url.indexOf("http") == 0 || !this.isLocal) && // BH MSIE fix
/^(get|post|head|put|delete|options)$/i.test( this.type ) &&
createXHR() || createXHR(1);
});
// incorporates jquery.iecors MSIE asynchronous cross-domain request for MSIE < 10
$.extend( $.support, { iecors: !!window.XDomainRequest });
if ($.support.iecors) {
// source: https://github.com/dkastner/jquery.iecors
// author: Derek Kastner dkastner@gmail.com http://dkastner.github.com
$.ajaxTransport(function(s) {
return {
send: function( headers, complete ) {
// Note that xdr is not synchronous.
// This is only being used in JSmol for transport of java code packages.
var xdr = new window.XDomainRequest();
xdr.onload = function() {
var headers = { 'Content-Type': xdr.contentType };
complete(200, 'OK', { text: xdr.responseText }, headers);
};
if ( s.xhrFields ) {
xdr.onerror = s.xhrFields.error;
xdr.ontimeout = s.xhrFields.timeout;
}
xdr.open( s.type, s.url );
xdr.send( ( s.hasContent && s.data ) || null );
},
abort: function() {
xdr.abort();
}
};
});
} else {
// adds support for synchronous binary file reading
$.ajaxSetup({
accepts: { binary: "text/plain; charset=x-user-defined" },
responseFields: { binary: "response" }
})
$.ajaxTransport('binary', function(s) {
var callback;
return {
// synchronous or asynchronous binary transfer only
send: function( headers, complete ) {
var xhr = s.xhr();
xhr.open( s.type, s.url, s.async );
var isOK = false;
try {
if (xhr.hasOwnProperty("responseType")) {
xhr.responseType = "arraybuffer";
isOK = true;
}
} catch(e) {
//
}
try {
if (!isOK && xhr.overrideMimeType) {
xhr.overrideMimeType('text/plain; charset=x-user-defined');
}
} catch(e) {
//
}
if ( !s.crossDomain && !headers["X-Requested-With"] ) {
headers["X-Requested-With"] = "XMLHttpRequest";
}
try {
for (var i in headers )
xhr.setRequestHeader( i, headers[ i ] );
} catch(_) {}
xhr.send( ( s.hasContent && s.data ) || null );
// Listener
callback = function( _, isAbort ) {
var
status = xhr.status,
statusText = "",
responseHeaders = xhr.getAllResponseHeaders(),
responses = {},
xml;
try {
// Firefox throws exceptions when accessing properties
// of an xhr when a network error occured
// http://helpful.knobs-dials.com/index.php/Component_returned_failure_code:_0x80040111_(NS_ERROR_NOT_AVAILABLE)
// Was never called and is aborted or complete
if ( callback && ( xhr.readyState === 4 ) ) {
// Only called once
callback = undefined;
// When requesting binary data, IE6-9 will throw an exception
// on any attempt to access responseText (#11426)
try {
responses.text = (typeof xhr.responseText === "string" ? xhr.responseText : null);
} catch( _ ) {
}
try {
responses.binary = xhr.response;
} catch( _ ) {
}
// Firefox throws an exception when accessing
// statusText for faulty cross-domain requests
try {
statusText = xhr.statusText;
} catch( _ ) {
// We normalize with Webkit giving an empty statusText
statusText = "";
}
// Filter status for non standard behaviors
// If the request is local and we have data: assume a success
// (success with no data won't get notified, that's the best we
// can do given current implementations)
if ( !status && s.isLocal && !s.crossDomain ) {
status = (responses.text ? 200 : 404);
// IE - #1450: sometimes returns 1223 when it should be 204
} else if ( status === 1223 ) {
status = 204;
}
complete( status, statusText, responses, responseHeaders );
}
} catch( e ) {
alert(e)
complete( -1, e );
}
};
if ( !s.async ) {
// if we're in sync mode we fire the callback
callback();
} else if ( xhr.readyState === 4 ) {
// (IE6 & IE7) if it's in cache and has been
// retrieved directly we need to fire the callback
setTimeout( callback );
} else {
// Add to the list of active xhr callbacks
xhr.onreadystatechange = callback;
}
},
abort: function() {}
};
});
}
})( jQuery );
/*
* jQuery outside events - v1.1 - 3/16/2010
* http://benalman.com/projects/jquery-outside-events-plugin/
*
* Copyright (c) 2010 "Cowboy" Ben Alman
* Dual licensed under the MIT and GPL licenses.
* http://benalman.com/about/license/
*
* Modified by Bob Hanson for JSmol-specific events and to add parameter reference to actual jQuery event.
* Used for closing the pop-up menu.
*
*/
;(function($,doc,eventList,id){
// was 'click dblclick mousemove mousedown mouseup mouseover mouseout change select submit keydown keypress keyup'
$.map(
eventList.split(' '),
function( event_name ) { jq_addOutsideEvent( event_name ); }
);
jq_addOutsideEvent( 'focusin', 'focus' + id );
jq_addOutsideEvent( 'focusout', 'blur' + id );
function jq_addOutsideEvent( event_name, outside_event_name ) {
outside_event_name = outside_event_name || event_name + id;
var elems = $(),
event_namespaced = event_name + '.' + outside_event_name + '-special-event';
$.event.special[ outside_event_name ] = {
setup: function(){
elems = elems.add( this );
if ( elems.length === 1 ) {
$(doc).bind( event_namespaced, handle_event );
}
},
teardown: function(){
self.Jmol && Jmol._setMouseOwner(null);
elems = elems.not( this );
if ( elems.length === 0 ) {
$(doc).unbind( event_namespaced );
}
},
add: function( handleObj ) {
var old_handler = handleObj.handler;
handleObj.handler = function( event, elem ) {
event.target = elem;
old_handler.apply( this, arguments );
};
}
};
function handle_event( event ) {
$(elems).each(function(){
self.Jmol && (outside_event_name.indexOf("mouseup") >= 0 || outside_event_name.indexOf("touchend") >= 0) && Jmol._setMouseOwner(null);
var elem = $(this);
if ( this !== event.target && !elem.has(event.target).length ) {
//BH: adds event to pass that along to our handler as well.
elem.triggerHandler( outside_event_name, [ event.target, event ] );
}
});
};
};
})(jQuery,document,"click mousemove mouseup touchmove touchend", "outjsmol");
// JSmolCore.js -- Jmol core capability 7/23/2014 5:34:47 PM
// see JSmolApi.js for public user-interface. All these are private functions
// 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)
// 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
// 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 {
header:z++,
rear: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
monitorZIndex:z+99999 // way way front
}
};
var j = {
_version: 'JSmol 14.2.3 July 23, 2014',
_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)
*/
_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, $) {
// this library is organized into the following sections:
// jQuery interface
// protected variables
// feature detection
// AJAX-related core functionality
// applet start-up functionality
// misc core functionality
// mouse events
////////////////////// jQuery interface ///////////////////////
// hooks to jQuery -- if you have a different AJAX tool, feel free to adapt.
// There should be no other references to jQuery in all the JSmol libraries.
Jmol.$ = function(objectOrId, subdiv) {
// if a subdivv, then return $("#objectOrId_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 $.ajax(info);
}
Jmol._getNCIInfo = function(identifier, what, fCallback) {
if (what == "name")
what = "names"
url = "http://cactus.nci.nih.gov/chemical/structure/"+identifier +"/" + what;
return Jmol._getFileData(url);
}
Jmol.$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 $(what).after(s);
}
Jmol.$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 (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",".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) {
// use host-server PHP relay if not from this host
var type = (Jmol._isBinaryUrl(fileName) ? "binary" : "text");
var isPDB = (fileName.indexOf("pdb.gz") >= 0 && fileName.indexOf("http://www.rcsb.org/pdb/files/") == 0);
var asBase64 = (type == "binary" && !Jmol._canSyncBinary(isPDB));
if (asBase64 && isPDB) {
// avoid unnecessary binary transfer
fileName = fileName.replace(/pdb\.gz/,"pdb");
asBase64 = false;
type = "text";
}
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());
if (!fSuccess || asBase64)
if (cantDoSynchronousLoad || asBase64 || !isMyHost && !isDirectCall)
return Jmol._getRawDataFromServer("_",fileName, fSuccess, fSuccess, asBase64, true);
fileName = fileName.replace(/file:\/\/\/\//, "file://"); // opera
var info = {dataType:type,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(xhr.statusText)};
}
info.xhr = Jmol.$ajax(info);
if (!fSuccess)
return Jmol._xhrReturn(info.xhr);
}
Jmol._xhrReturn = function(xhr){
if (!xhr.responseText || self.Clazz && Clazz.instanceOf(xhr.response, self.ArrayBuffer)) {
// Safari or error
return xhr.response || xhr.statusText;
}
return xhr.responseText;
}
Jmol._isDirectCall = function(url) {
for (var key in Jmol.db._DirectDatabaseCalls) {
if (key.indexOf(".") >= 0 && url.indexOf(key) >= 0)
return true;
}
return false;
}
Jmol._cleanFileData = function(data) {
if (data.indexOf("\r") >= 0 && data.indexOf("\n") >= 0) {
return data.replace(/\r\n/g,"\n");
}
if (data.indexOf("\r") >= 0) {
return data.replace(/\r/g,"\n");
}
return data;
};
Jmol._getFileType = function(name) {
var database = name.substring(0, 1);
if (database == "$" || 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
fileName = Jmol._checkFileName(applet, fileName);
var fSuccess = function(data) {Jmol._setData(fileLoadThread, fileName, data, appData)};
fSuccess = Jmol._checkCache(applet, fileName, fSuccess);
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, 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.$(applet, "localReader"), {display : "none"});
Jmol._setData(fileLoadThread, file.name, evt.target.result, appData);
}
};
reader.readAsArrayBuffer(file);
});
Jmol.$appEvent(applet, "localReader_cancel", "click");
Jmol.$appEvent(applet, "localReader_cancel", "click", function(evt) {
Jmol.$css(Jmol.$(applet, "localReader"), {display: "none"});
fileLoadThread.setData(null, appData);
});
Jmol.$css(Jmol.$(applet, "localReader"), {display : "block"});
}
Jmol._setData = function(fileLoadThread, filename, data, appData) {
data = Jmol._strToBytes(data);
if (filename.indexOf(".jdx") >= 0)
Jmol.Cache.put("cache://" + filename, data);
fileLoadThread.setData(filename, 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;
var data = Jmol._getFileData(url)
return Jmol._processData(data, Jmol._isBinaryUrl(url));
}
// 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(".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._processData = function(data, isBinary) {
if (typeof data == "undefined") {
data = "";
isBinary = false;
}
if (isBinary)
isBinary = Jmol._canSyncBinary();
return (isBinary ? Jmol._strToBytes(data) : JU.SB.newS(data));
};
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,jmolApp) {
appId = appId.split("_object")[0];
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...
Jmol._track(Jmol._applets[appId])._readyCallback(appId, fullId, isReady, jmolApp);
}
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>";
}
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;\">";
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._deferApplet = Info.deferApplet;
obj._deferUncover = Info.deferUncover;
obj._coverImage = !obj._isJava && Info.coverImage;
obj._isCovered = !!obj._coverImage;
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._applet) applet._applet.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();
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.$offset(canvas.id);
var t0 = canvas._touches[0];
var t1 = canvas._touches[1];
t0.push([oe.touches[0].pageX - offsets.left, oe.touches[0].pageY - offsets.top]);
t1.push([oe.touches[1].pageX - offsets.left, oe.touches[1].pageY - offsets.top]);
var n = t0.length;
if (n > 3) {
t0.shift();
t1.shift();
}
if (n >= 2)
canvas.applet._processGesture(canvas._touches);
break;
}
return true;
}
Jmol._jsSetMouse = function(canvas) {
Jmol.$bind(canvas, 'mousedown touchstart', function(ev) {
Jmol._setMouseOwner(canvas, true);
ev.stopPropagation();
ev.preventDefault();
canvas.isDragging = true;
if ((ev.type == "touchstart") && Jmol._gestureUpdate(canvas, ev))
return false;
Jmol._setConsoleDiv(canvas.applet._console);
var xym = Jmol._jsGetXY(canvas, ev);
if(!xym)
return false;
if (ev.button != 2)
Jmol.Swing.hideMenus(canvas.applet);
canvas.applet._processEvent(501, xym); //J.api.Event.MOUSE_DOWN
return false;
});
Jmol.$bind(canvas, 'mouseup touchend', function(ev) {
Jmol._setMouseOwner(null);
ev.stopPropagation();
ev.preventDefault();
canvas.isDragging = false;
if (ev.type == "touchend" && Jmol._gestureUpdate(canvas, ev))
return false;
var xym = Jmol._jsGetXY(canvas, ev);
if(!xym) return false;
canvas.applet._processEvent(502, xym);//J.api.Event.MOUSE_UP
return false;
});
Jmol.$bind(canvas, 'mousemove touchmove', function(ev) { // touchmove
// defer to console or menu when dragging within this canvas
if (Jmol._mouseOwner && Jmol._mouseOwner != canvas && Jmol._mouseOwner.isDragging) {
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;
canvas.applet._processEvent((canvas.isDragging ? 506 : 503), xym); // J.api.Event.MOUSE_DRAG : J.api.Event.MOUSE_MOVE
return false;
}
Jmol.$bind(canvas, 'DOMMouseScroll mousewheel', function(ev) { // Zoom
ev.stopPropagation();
ev.preventDefault();
// Webkit or Firefox
canvas.isDragging = false;
var oe = ev.originalEvent;
var scroll = (oe.detail ? oe.detail : (Jmol.featureDetection.os == "mac" ? 1 : -1) * oe.wheelDelta); // Mac and PC are reverse; but
var modifiers = Jmol._jsGetMouseModifiers(ev);
canvas.applet._processEvent(-1,[scroll < 0 ? -1 : 1,0,modifiers]);
return false;
});
// context menu is fired on mouse down, not up, and it's handled already anyway.
Jmol.$bind(canvas, "contextmenu", function() {return false;});
Jmol.$bind(canvas, 'mouseout', function(ev) {
if (canvas.applet._applet)
canvas.applet._applet.startHoverWatcher(false);
//canvas.isDragging = false;
var xym = Jmol._jsGetXY(canvas, ev);
if (!xym)
return false;
//canvas.applet._processEvent(502, xym);//J.api.Event.MOUSE_UP
//canvas.applet._processEvent(505, xym);//J.api.Event.MOUSE_EXITED
return false;
});
Jmol.$bind(canvas, 'mouseenter', function(ev) {
if (canvas.applet._applet)
canvas.applet._applet.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.$bind(canvas, 'mousemoveoutjsmol', function(evspecial, target, ev) {
if (canvas == Jmol._mouseOwner && canvas.isDragging) {
return Jmol._drag(canvas, ev);
}
});
if (canvas.applet._is2D)
Jmol.$resize(function() {
if (!canvas.applet)
return;
canvas.applet._resize();
});
Jmol.$bind('body', 'mouseup touchend', function(ev) {
if (canvas.applet)
canvas.isDragging = false;
Jmol._setMouseOwner(null);
});
}
Jmol._jsUnsetMouse = function(canvas) {
canvas.applet = null;
Jmol.$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);
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.$getAncestorDiv(element.id, "JDialog").id];
if (dialog.registryKey) {
//System.out.println("JSmolCore.js: windowClosing " + dialog.registryKey);
dialog.manager.processWindowClosing(dialog.registryKey);
} else {
//System.out.println("JSmolCore.js: windowClosing " + dialog.title);
dialog.dispose();
}
}
})(Jmol.Swing);
Jmol._track = function(applet) {
// this function inserts an iFrame that can be used to track your page's applet use.
// By default it tracks to a page at St. Olaf College, but you can change that.
// and you can use
//
// delete Jmol._tracker
//
// yourself to not have you page execute this
//
if (Jmol._tracker){
try {
var url = Jmol._tracker + "&applet=" + applet._jmolType + "&version=" + Jmol._version
+ "&appver=" + self.___JmolVersion + "&url=" + encodeURIComponent(document.location.href);
var s = '<iframe style="display:none" width="0" height="0" frameborder="0" tabindex="-1" src="' + url + '"></iframe>'
Jmol.$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);
me._applet.cacheFileByName("cache://DROP_*",false);
if (me._viewType == "JSV" || cacheName.endsWith(".jdx")) // shared by Jmol and JSV
Jmol.Cache.put(cacheName, bytes);
else
me._applet.cachePut(cacheName, bytes);
var xym = Jmol._jsGetXY(me._canvas, e);
if(xym && (!me._applet.setStatusDragDropped || me._applet.setStatusDragDropped(0, xym[0], xym[1], cacheName))) {
me._applet.openFileAsyncSpecial(cacheName, 1);
}
}
};
reader.readAsArrayBuffer(file);
});
}
})(Jmol, jQuery);
Jmol._debugCode = false;
// JSmolTM.js -- JSmol TwirlyMol implementation
//
// TM for "TwirlyMol" -- which this is derived from.
// Can't say there is much of TwirlyMol left in here, as
// we are not using dojo, there are no shadows, and I use a simpler
// rendering idea. Nonetheless, TwirlyMol is the inspiration.
//
// author: Bob Hanson, hansonr@stolaf.edu 3/23/2012
// This library requires
//
// JSmoljQuery.js
// JSmolCore.js
//
// and is combined with those in JSmol.lite.jq.js
// or packaged without jQuery -- because you are using it already -- in JSmol.lite.js
//
Jmol._grabberOptions = [
["$", "NCI(small molecules)"],
[":", "PubChem(small molecules)"]
];
Jmol.say = function(msg) {
alert(msg);
}
Jmol._TMApplet = function(id, Info, checkOnly){
this._uniqueId = ("" + Math.random()).substring(3);
this._id = id;
this._is2D = true;
this._isJava = false;
this._ready = true;
this._mouseDown = false;
this._jmolType = "Jmol._Canvas2D (TwirlyMol)";
if (checkOnly)
return this;
this._createCanvas(id, Info);
return this;
}
Jmol._TMApplet._getApplet = function(id, Info, checkOnly) {
if (!Jmol.featureDetection.allowHTML5)
return null;
checkOnly || (checkOnly = false);
Info || (Info = {});
var DefaultInfo = {
color: "#FFFFFF",
width: 300,
height: 300,
addSelectionOptions: false,
serverURL: "http://your.server.here/jsmol.php",
defaultModel: "",
readyFunction: null,
use: "HTML5",
bondWidth: 5,
shadeAtoms: false,
zoomScaling: 1.5,
pinchScaling: 2.0,
mouseDragFactor: 0.5,
touchDragFactor: 0.15,
multipleBondSpacing: 4,
spinRateX: 0.0,
spinRateY: 0.5,
spinFPS: 20,
spin: false,
noscript: true,
debug: false
};
Jmol._addDefaultInfo(Info, DefaultInfo);
var applet = new Jmol._TMApplet(id, Info, checkOnly);
if (checkOnly)
return applet;
return Jmol._registerApplet(id, applet);
}
Jmol.getTMApplet = Jmol._TMApplet._getApplet;
;(function(tm){
tm._CPK = ["#FF1493", "#FFFFFF", "#D9FFFF",
"#CC80FF", "#C2FF00", "#FFB5B5", "#909090", "#3050F8", "#FF0D0D", "#90E050", "#B3E3F5",
"#AB5CF2", "#8AFF00", "#BFA6A6", "#F0C8A0", "#FF8000", "#FFFF30", "#1FF01F", "#80D1E3",
"#8F40D4", "#3DFF00", "#E6E6E6", "#BFC2C7", "#A6A6AB", "#8A99C7", "#9C7AC7", "#E06633",
"#F090A0", "#50D050", "#C88033", "#7D80B0", "#C28F8F", "#668F8F", "#BD80E3", "#FFA100", "#A62929", "#5CB8D1",
"#702EB0", "#00FF00", "#94FFFF", "#94E0E0", "#73C2C9", "#54B5B5", "#3B9E9E", "#248F8F",
"#0A7D8C", "#006985", "#C0C0C0", "#FFD98F", "#A67573", "#668080", "#9E63B5", "#D47A00", "#940094", "#429EB0",
"#57178F", "#00C900"] // through barium
// "#70D4FF", "#FFFFC7", "#D9FFC7", "#C7FFC7", "#A3FFC7", "#8FFFC7", "#61FFC7", "#45FFC7", "#30FFC7", "#1FFFC7", "#00FF9C", "#00E675", "#00D452", "#00BF38", "#00AB24", "#4DC2FF", "#4DA6FF", "#2194D6", "#267DAB", "#266696", "#175487", "#D0D0E0", "#FFD123", "#B8B8D0", "#A6544D", "#575961", "#9E4FB5", "#AB5C00", "#754F45", "#428296", "#420066", "#007D00", "#70ABFA", "#00BAFF", "#00A1FF", "#008FFF", "#0080FF", "#006BFF", "#545CF2", "#785CE3", "#8A4FE3", "#A136D4", "#B31FD4", "#B31FBA", "#B30DA6", "#BD0D87", "#C70066", "#CC0059", "#D1004F", "#D90045", "#E00038", "#E6002E", "#EB0026"];
tm._elem = ['X', 'H', 'He',
'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne',
'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar',
'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr',
'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe',
'Cs', 'Ba',
'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb',
'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb','Bi', 'Po', 'At', 'Rn',
'Fr', 'Ra',
'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es'];
tm._elemNo = {};
;(function(proto) {
// A user-available function
proto.spin = function(TF) {
this.__Info.spin = TF;
this._spin(TF);
}
proto._spin = function(TF) {
if (this._spinThread)clearTimeout(this._spinThread);
if (this.spinFPS == 0 || this.spinRateX == 0 && this.spinRateY == 0)
TF = false;
if (!TF) return;
var me = this;
var delay = 1000 / this.spinFPS;
if (!this._mouseDown) {
this._rotate(this.spinRateY, this.spinRateX);
this._draw();
}
this._spinThread = setTimeout(function(){me._spin(true)}, delay);
}
proto._initParams = function() {
this.zoom = this.__Info.defaultZoom || 100;
this.doSpin = this.__Info.spin || false;
this.center2D = [this._canvas.width/2, this._canvas.height/2, 0];
this._getCenterAndRadius();
this.rotation = new tm.M3();
this.shadeAtoms = false;
this._setParams();
}
proto._setParams = function() {
this.bondWidth = this.__Info.bondWidth || 5;
this.zoomScaling = this.__Info.zoomScaling || 1.5;
this.pinchScaling = this.__Info.pinchScaling || 1;
this.mouseDragFactor = this.__Info.mouseDragFactor || 0.5;
this.touchDragFactor = this.__Info.touchDragFactor || 0.15;
this.multipleBondSpacing = this.__Info.multipleBondSpacing || 4;
this.spinRateX = this.__Info.spinRateX || 0;
this.spinRateY = this.__Info.spinRateY || 0;
this.spinFPS = this.__Info.spinFPS || 0;
var p = this.shadeAtoms;
this.shadeAtoms = this.__Info.shadeAtoms || false;
if (this.shadeAtoms && !p)
this._setAtomShades();
}
proto._setAtomShades = function() {
if (!this.atoms)
return;
for (var i = this.atoms.length; --i >= 0;)
this.atoms[i].color50 = this._getColor(this.atoms[i].color, 0.5);
}
proto._createCanvas = function(id, Info) {
Jmol._setObject(this, id, Info);
this._color = this._color.replace(/0x/,"#");
var t = Jmol._getWrapper(this, true);
if (Jmol._document) {
Jmol._documentWrite(t);
this._createCanvas2d(false);
t = "";
} else {
t += '<script type="text/javascript">' + id + '._createCanvas2d(false)</script>';
}
t += Jmol._getWrapper(this, false);
if (Info.addSelectionOptions)
t += Jmol._getGrabberOptions(this, "");
if (Jmol._debugAlert && !Jmol._document)
alert(t);
this._code = Jmol._documentWrite(t);
};
proto._readyCallback = function(id, fullid, isReady, applet) {
if (!isReady)
return; // ignore -- page is closing
var me = this;
Jmol._setDestroy(me);
me._ready = true;
var script = me._readyScript;
me._applet = applet;
if (me._defaultModel)
me._search(me._defaultModel, (script ? ";" + script : ""));
else if (me._src)
me._loadFile(me._src);
me._showInfo(true);
me._showInfo(false);
me._readyFunction && me._readyFunction(me);
Jmol._setReady(this);
};
proto._createCanvas2d = function(doReplace) {
var canvas = document.createElement( 'canvas' );
var container = Jmol.$(this, "appletdiv");
if (doReplace) {
container[0].removeChild(this._canvas);
Jmol._jsUnsetMouse(this._canvas);
}
var w = Math.round(container.width());
var h = Math.round(container.height());
canvas.applet = this;
this._canvas = canvas;
canvas.style.width = "100%";
canvas.style.height = "100%";
canvas.width = w;
canvas.height = h; // w and h used in setScreenDimension
canvas.id = this._id + "_canvas2d";
container.append(canvas);
setTimeout(this._id+"._start()",10);
}
proto._start = function() {
Jmol._jsSetMouse(this._canvas);
if (this._defaultModel)
Jmol._search(this, this._defaultModel);
else if (this._src)
this._loadFile(this._src);
this._showInfo(true);
this._showInfo(false);
}
proto._search = function(query, script){
Jmol._search(this, query, script);
}
proto._searchDatabase = function(query, database, script){
this._showInfo(false);
if (query.indexOf("?") >= 0) {
Jmol._getInfoFromDatabase(this, database, query.split("?")[0]);
return;
}
var dm = database + query;
this._loadFile(dm, script);
}
proto.__loadModel = function(mol) {
this._spin(false);
if (mol == "''")mol = this._mol;
if (!mol) {
alert("No model data.");
return;
}
this._parse(mol);
this._initParams();
this._draw();
this._showInfo(false);
if (this.doSpin)
this._spin(true);
};
proto._showInfo = function(tf) {
Jmol.$html(Jmol.$(this, "infoheaderspan"), this._infoHeader);
if (this._info)
Jmol.$html(Jmol.$(this, "infodiv"), this._info);
if ((!this._isInfoVisible) == (!tf))
return;
this._isInfoVisible = tf;
Jmol.$setVisible(Jmol.$(this, "infotablediv"), tf);
Jmol.$setVisible(Jmol.$(this, "infoheaderdiv"), tf);
this._show(!tf);
}
proto._show = function(tf) {
Jmol.$setVisible(Jmol.$(this, "appletdiv"), tf);
if (tf)
this._draw();
}
proto._resize = function() {
var s = "__resizeTimeout_" + this._id;
// only at end
if (Jmol[s])
clearTimeout(Jmol[s]);
var me = this;
Jmol[s] = setTimeout(function() {me._draw();Jmol[s]=null}, 100);
}
proto._canScript = function(script) {return false};
proto._loadFile = function(fileName){
this._showInfo(false);
this._thisJmolModel = fileName;
var app = this;
Jmol._loadFileData(this, fileName, function(data){app.__loadModel(data)});
}
proto._processEvent = function(type, xym) {
switch(type) {
case 502: // mouse_up
case 503: // mouse_move
this._mouseDown = false;
default:
return;
case 501: // mouse_down
this._mouseX = xym[0];
this._mouseY = xym[1];
this._mouseDown = true;
return;
case 506: // mouse_drag
var dx = xym[0] - this._mouseX;
var dy = xym[1] - this._mouseY;
dx = (dx < 0 ? -1 : dx > 0 ? 1 : 0)
dy = (dy < 0 ? -1 : dy > 0 ? 1 : 0)
switch (xym[2]) {
case 17: // left-shift
this._zoomBy(dy);
break;
case 24: // left-alt
this.center2D[0] += dx;
this.center2D[1] += dy;
break;
default:
this._rotate(dx, dy);
break;
}
this._mouseX = xym[0];
this._mouseY = xym[1];
break;
case -1: // mouse_scroll
this._zoomBy(xym[1])
break;
}
this._draw();
}
proto._processGesture = function (touches) {
if (touches[0].length < 2) return;
var t1 = touches[0];
var t2 = touches[1];
var t10 = t1[0];
var t11 = t1[t2.length - 1];
var x10 = t10[0];
var x11 = t11[0];
var dx1 = x11 - x10;
var y10 = t10[1];
var y11 = t11[1];
var dy1 = y11 - y10;
var v1 = [dx1, dy1, 0];
var d1 = tm._length(v1);
var t20 = t2[0];
var t21 = t2[t2.length - 1];
var x20 = t20[0];
var x21 = t21[0];
var dx2 = x21 - x20;
var y20 = t20[1];
var y21 = t21[1];
var dy2 = y21 - y20;
var v2 = [dx2, dy2, 0];
var d2 = tm._length(v2);
if (d1 < 3 || d2 < 3) return;
tm._scale(v1, 1/d1);
tm._scale(v2, 1/d2);
var cos12 = tm._dot(v1,v2);
if (cos12 > 0.8) {
var deltaX = Math.round(x11 - t1[t1.length - 2][0]);
var deltaY = Math.round(y11 - t1[t1.length - 2][1]);
this.center2D[0] += deltaX;
this.center2D[1] += deltaY;
} else if (cos12 < -0.8) {
v1 = [x20 - x10, y20 - y10, 0]
v2 = [x21 - x11, y21 - y11, 0];
var dx = tm._length(v2) - tm._length(v1);
this.zoom += (dx < 0 ? -1 : 1) * this.pinchScaling;
}
this._draw();
}
proto._zoomBy = function(dz) {
this.zoom += dz * this.zoomScaling;
if (this.zoom < 5) this.zoom = 5;
if (this.zoom > 500) this.zoom = 500;
}
proto._getRotationScaling = function() {
return [1 / Math.max(this._canvas.width, 500) * this.mouseDragFactor * tm.deg_per_radian,
1 / Math.max(this._canvas.height, 500) * this.mouseDragFactor * tm.deg_per_radian];
}
proto._rotate = function(dx, dy) {
var f = this._getRotationScaling();
if (dy) {
tm._m3.rotX(dy * f[1]);
this.rotation.mul(tm._m3);
}
if (dx) {
tm._m3.rotY(dx * f[0]);
this.rotation.mul(tm._m3);
}
}
proto._getCenterAndRadius = function() {
var p = this;
var size = Math.min(p._canvas.width, p._canvas.height);
var min = [999999, 999999, 999999];
var max = [-999999, -999999, -999999];
for (var i= p.atoms.length; --i >= 0;)
for (var j = 3; --j >= 0;) {
var v = p.atoms[i].xyz[j];
if (v < min[j]) min[j]=v;
if (v > max[j]) max[j]=v;
}
var c = [0, 0, 0];
for (var j = 3; --j >= 0;)
c[j] = (max[j] + min[j])/2;
var r = 0;
for (var i= p.atoms.length; --i >= 0;) {
var a = p.atoms[i];
var d = tm._distance(a.xyz, c) + (a.elemNo == 1 ? 1 : 1.5);//a.radius;
if (d > r)
r = d;
}
this.center = c;
this.modelRadius = (r == 0 ? 10 : r);
}
proto._setScreenCoords = function() {
var c = this.center;
var mat = this.rotation;
var sc = this.center2D;
var f = Math.min(this._canvas.width, this._canvas.height) / 2 / this.modelRadius * this.zoom / 100;
for (var i=this.atoms.length; --i >= 0;) {
var a = this.atoms[i];
this._transform(a.xyz, a.sxyz, c, mat, f, sc);
a.srad = f * a.radius;
}
for (var i=this.bonds.length; --i >= 0;) {
var b = this.bonds[i];
this._transform(b.xyz, b.sxyz, c, mat, f, sc);
this._transform(b.pts[0], b.spts[0], c, mat, f, sc);
this._transform(b.pts[1], b.spts[1], c, mat, f, sc);
}
}
proto._transform = function(pt, spt, c, mat, f, sc) {
var a = tm._temp1;
var b = tm._temp2;
for (var i = 3; --i >= 0;)
a[i] = (pt[i] - c[i]) * f;
mat.transform(a, b);
b[1] = -b[1];
b[2] = -b[2];
for (var i = 3; --i >= 0;)
spt[i] = b[i] + sc[i];
}
// adaptable ---
proto._parse = function(data) {
// just MOL data for now
this._parseSDF(data);
}
proto._parseSDF = function(sdf) {
this._mol = sdf;
if (!tm._elemNo["H"])
for (var i = tm._elem.length; --i >= 0;)
tm._elemNo[tm._elem[i]] = i;
var lines = sdf.split("\n");
var pt = 3;
var line = lines[pt++];
this.nAtoms = parseFloat(line.substring(0, 3));
this.nBonds = parseFloat(line.substring(3, 6));
this.atoms = Array(this.nAtoms);
this.bonds = Array(this.nBonds);
this.elements = Array(this.nAtoms + this.nBonds)
var ept = 0;
var x, y, z;
for (var i = 0; i < this.nAtoms; i++) {
line = lines[pt++];
x = parseFloat(line.substring(0, 10));
y = parseFloat(line.substring(10, 20));
z = parseFloat(line.substring(20, 30));
var e = line.substring(31, 34).replace(/\s+/g, '');
var elemNo = tm._elemNo[e] || 0;
var radius = (elemNo == 1 ? 0.23 : 0.35);
var color = tm._CPK[elemNo] || tm._CPK[0];
this.elements[ept++] = this.atoms[i] = {type:0, elemNo: elemNo, xyz:[x, y, z], sxyz:[0, 0, 0], radius: radius, color: color, color50: color};
}
for (var i = 0; i < this.nBonds; i++) {
line = lines[pt++]
var a1 = this.atoms[parseFloat(line.substring(0, 3)) - 1];
var a2 = this.atoms[parseFloat(line.substring(3, 6)) - 1];
var order = Math.abs(parseFloat(line.substring(6, 9)));
switch (order) {
case 4: // JmolAdapter.ORDER_AROMATIC;
case 5: // JmolAdapter.ORDER_PARTIAL12;
case 6: // JmolAdapter.ORDER_AROMATIC_SINGLE;
case 8: // JmolAdapter.ORDER_PARTIAL01;
order = 1;
break;
case 7: // JmolAdapter.ORDER_AROMATIC_DOUBLE;
order = 2;
break;
}
var xyz = tm._getPointAlong(a1.xyz, a2.xyz, 0.5);
var d = tm._distance(a1.xyz, xyz);
var p1 = (a1.radius < d ? tm._getPointAlong(a1.xyz, xyz, a1.radius/d) : [0, 0, 99999]);
var p2 = (a2.radius < d ? tm._getPointAlong(a2.xyz, xyz, a2.radius/d) : [0, 0, 99999]);
this.elements[ept++] = this.bonds[i] = {type:1, atoms: [a1, a2], xyz:xyz, pts:[p1,p2], sxyz:[0, 0, 0], spts:[[0,0,0],[0,0,0]], order: order, color: 0};
}
//alert(this.atoms.length + " atoms " + this.bonds.length + " bonds")
}
proto._getColor = function(c, f) {
if (c == "#FFFFFF") c = "#D0D0D0";
var n = parseInt("0x" + c.substring(1), 16);
var r=(n >> 16) & 0xFF;
var g=(n >> 8) & 0xFF;
var b=(n) & 0xFF;
if (r != 255)
r += Math.floor((255 - r) * f);
if (g != 255)
g += Math.floor((255 - g) * f);
if (b != 255)
b += Math.floor((255 - b) * f);
var s = "000000" + ((r << 16) | (g << 8) | b).toString(16);
return "#"+s.substring(s.length - 6, s.length);
}
proto._draw = function() {
if (!this.atoms)return;
this._setParams();
this._setScreenCoords();
var es = this.elements;
es.sort(tm._zorder);
var ctx=this._canvas.getContext("2d");
ctx.fillStyle=this._color;
ctx.fillRect(0,0,this._canvas.width, this._canvas.height);
for (var i = es.length; --i >= 0;) {
var e = es[i];
if (e.type == 0)
this._drawAtom(ctx, e);
else
this._drawBond(ctx, e);
}
}
///////////////// drawing ///////////////////
proto._drawAtom = function(ctx, a) {
ctx.beginPath();
// context.fillStyle = "rgba(0, 0, 0, 1)";
if (this.shadeAtoms) {
var offset = a.srad / 4;
var grad = ctx.createRadialGradient(a.sxyz[0]-offset,a.sxyz[1]-offset, offset, a.sxyz[0],a.sxyz[1], a.srad);
grad.addColorStop(0.0, a.color50);
grad.addColorStop(1.0, (a.color == "#FFFFFF" ? "#D0D0D0" : a.color));
ctx.fillStyle = grad;
ctx.arc(a.sxyz[0],a.sxyz[1],a.srad,0,tm._pi2);
ctx.fill();
} else {
ctx.fillStyle = a.color;
ctx.arc(a.sxyz[0],a.sxyz[1],a.srad,0,tm._pi2);
ctx.fill();
ctx.strokeStyle = "#000000";
ctx.lineWidth = 1;
ctx.stroke();
}
}
proto._drawBond = function(ctx, b) {
if (b.pts[0][2] != 99999)
this._drawBondLines(ctx, b, b.spts[0], b.atoms[0].color);
if (b.pts[1][2] != 99999)
this._drawBondLines(ctx, b, b.spts[1], b.atoms[1].color);
}
proto._drawBondLines = function(ctx, b, pt, ac) {
var t = tm._temp;
t.width = this.bondWidth;
t.color = (b.color ? b.color : ac);
if (b.order == 1) {
t.pt1 = pt;
t.pt2 = b.sxyz;
this._drawLine(ctx, t);
return;
}
t.pt1 = tm._temp1;
t.pt2 = tm._temp2;
t.pta = pt;
t.ptb = b.sxyz;
t.dx = t.ptb[0] - t.pta[0];
t.dy = t.ptb[1] - t.pta[1];
t.mag2d = Math.round(Math.sqrt(t.dx * t.dx + t.dy * t.dy));
t.bondOrder = b.order;
this._resetAxisCoordinates(t);
while (t.bondOrder > 0) {
this._drawLine(ctx, t);
t.bondOrder--;
this._stepAxisCoordinates(t);
}
}
proto._drawLine = function(ctx, t) {
ctx.beginPath();
ctx.strokeStyle = t.color;
ctx.moveTo(t.pt1[0], t.pt1[1]);
ctx.lineTo(t.pt2[0], t.pt2[1]);
ctx.lineWidth = t.width;
ctx.stroke();
}
proto._resetAxisCoordinates = function(t) {
var space = t.mag2d >> 3;
if (this.multipleBondSpacing != 1) space *= this.multipleBondSpacing;
var step = t.width + space;
t.dxStep = Math.round(step * t.dy / t.mag2d);
t.dyStep = Math.round(step * -t.dx / t.mag2d);
t.pt1[0] = t.pta[0];
t.pt1[1] = t.pta[1];
t.pt2[0] = t.ptb[0];
t.pt2[1] = t.ptb[1];
var f = (t.bondOrder - 1);
t.pt1[0] -= Math.round(t.dxStep * f / 2);
t.pt1[1] -= Math.round(t.dyStep * f / 2);
t.pt2[0] -= Math.round(t.dxStep * f / 2);
t.pt2[1] -= Math.round(t.dyStep * f / 2);
}
proto._stepAxisCoordinates = function(t) {
t.pt1[0] += t.dxStep;
t.pt1[1] += t.dyStep;
t.pt2[0] += t.dxStep;
t.pt2[1] += t.dyStep;
}
})(tm.prototype)
tm._distance = function(a,b){
var d = 0;
for (var i = 3; --i >= 0;) {
var dx = a[i] - b[i];
d += dx * dx;
}
return Math.sqrt(d);
}
tm._dot = function(a,b){
var d = 0;
for (var i = 3; --i >= 0;)
d += a[i] * b[i];
return d;
}
tm._setPt = function(a,b){
for (var i = 3; --i >= 0;)
b[i] = a[i];
return b;
}
tm._scale = function(a, f){
for (var i = 3; --i >= 0;)
a[i] *= f;
}
tm._length = function(a){
var d = 0;
for (var i = 3; --i >= 0;)
d += a[i] * a[i];
return Math.sqrt(d);
}
tm._getPointAlong = function(a, b, f) {
return [(b[0] - a[0]) * f + a[0],
(b[1] - a[1]) * f + a[1],
(b[2] - a[2]) * f + a[2]];
}
tm._zorder = function(a, b) {
var x = a.sxyz[2];
var y = b.sxyz[2];
return (x < y ? -1 : x > y ? 1 : 0);
}
tm.M3 = function() {
this.m00 = 1.0;
this.m01 = 0.0;
this.m02 = 0.0;
this.m10 = 0.0;
this.m11 = 1.0;
this.m12 = 0.0;
this.m20 = 0.0;
this.m21 = 0.0;
this.m22 = 1.0;
}
tm.M3.prototype.set = function (m00, m01, m02, m10, m11, m12, m20, m21, m22) {
this.m00 = m00;
this.m01 = m01;
this.m02 = m02;
this.m10 = m10;
this.m11 = m11;
this.m12 = m12;
this.m20 = m20;
this.m21 = m21;
this.m22 = m22;
}
tm.M3.prototype.transform = function(a, b) {
b[0] = this.m00 * a[0] + this.m01 * a[1] + this.m02 * a[2];
b[1] = this.m10 * a[0] + this.m11 * a[1] + this.m12 * a[2];
b[2] = this.m20 * a[0] + this.m21 * a[1] + this.m22 * a[2];
}
tm.M3.prototype.rotX = function(angle) {
var c = Math.cos(angle);
var s = Math.sin(angle);
this.m00 = 1.0;
this.m01 = 0.0;
this.m02 = 0.0;
this.m10 = 0.0;
this.m11 = c;
this.m12 = -s;
this.m20 = 0.0;
this.m21 = s;
this.m22 = c;
}
tm.M3.prototype.rotY = function(angle) {
var c = Math.cos(angle);
var s = Math.sin(angle);
this.m00 = c;
this.m01 = 0.0;
this.m02 = s;
this.m10 = 0.0;
this.m11 = 1.0;
this.m12 = 0.0;
this.m20 = -s;
this.m21 = 0.0;
this.m22 = c;
}
tm.M3.prototype.mul = function(m) {
var m2 = this;
this.set(m.m00 * m2.m00 + m.m01 * m2.m10 + m.m02 * m2.m20, m.m00 * m2.m01 + m.m01 * m2.m11 + m.m02 * m2.m21, m.m00 * m2.m02 + m.m01 * m2.m12 + m.m02 * m2.m22, m.m10 * m2.m00 + m.m11 * m2.m10 + m.m12 * m2.m20, m.m10 * m2.m01 + m.m11 * m2.m11 + m.m12 * m2.m21, m.m10 * m2.m02 + m.m11 * m2.m12 + m.m12 * m2.m22, m.m20 * m2.m00 + m.m21 * m2.m10 + m.m22 * m2.m20, m.m20 * m2.m01 + m.m21 * m2.m11 + m.m22 * m2.m21, m.m20 * m2.m02 + m.m21 * m2.m12 + m.m22 * m2.m22);
}
tm._pi2 = 2*Math.PI;
tm.deg_per_radian = 180 / Math.PI;
tm._z3 = [0,0,0];
tm._temp1 = [0,0,0];
tm._temp2 = [0,0,0];
tm._temp = {};
tm._m3 = new tm.M3();
})(Jmol._TMApplet);