//
// ChemDoodle Web Components 4.2.2
//
// http://web.chemdoodle.com
//
// Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// As a special exception to the GPL, any HTML file in a public website
// or any free web service which merely makes function calls to this
// code, and for that purpose includes it by reference, shall be deemed
// a separate work for copyright law purposes. If you modify this code,
// you may extend this exception to your version of the code, but you
// are not obligated to do so. If you do not wish to do so, delete this
// exception statement from your version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
// Please contact iChemLabs <http://www.ichemlabs.com/contact> for
// alternate licensing options.
//

//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 2934 $
//  $Author: kevin $
//  $LastChangedDate: 2010-12-08 20:53:47 -0500 (Wed, 08 Dec 2010) $
//
var ChemDoodle = (function(q) {

	var c = {};

	c.structures = {};
	c.iChemLabs = {};
	c.informatics = {};
	c.io = {};

	var VERSION = '4.2.2';

	c.getVersion = function(){
		return VERSION;
	};

	return c;

})(jQuery);
//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 2976 $
//  $Author: kevin $
//  $LastChangedDate: 2010-12-29 18:16:10 -0500 (Wed, 29 Dec 2010) $
//

(function(c, iChemLabs, io, structures, q) {

	iChemLabs.SERVER_URL = 'http://ichemlabs.cloud.chemdoodle.com/ICL_servlets/WebHQ1';

	iChemLabs.contactServer = function(call, content, callback, errorback) {
		q.ajax({
			dataType : 'text',
			type : 'POST',
			data : JSON.stringify({
				'call' : call,
				'content' : content,
				'version' : c.getVersion()
			}),
			url : this.SERVER_URL,
			success : function(data) {
				o = JSON.parse(data);
				if (o.message) {
					alert(o.message);
				}
				if (callback != null && o.content && !o.stop) {
					callback(o.content);
				}
				if (o.stop && errorback != null) {
					errorback();
				}
			},
			error : function(xhr, status, error) {
				alert('Server connectivity failed. Please try again or update this browser to the latest version. (XHR2 not supported)');
				if(errorback != null) {
					errorback();
				}
			},
			beforeSend : function(xhr) {
				xhr.withCredentials = true;
			}
		});
	};

	iChemLabs.optimize = function(mol, dimension, callback, errorback) {
		this.contactServer('optimize', {
			'mol' : io.toJSONDummy(mol),
			'dimension' : dimension
		}, function(content) {
			var optimized = io.fromJSONDummy(content.mol);
			if (dimension == 2) {
				for ( var i = 0, ii = optimized.atoms.length; i < ii; i++) {
					mol.atoms[i].x = optimized.atoms[i].x;
					mol.atoms[i].y = optimized.atoms[i].y;
				}
				callback();
			} else if (dimension == 3) {
				for ( var i = 0, ii = optimized.atoms.length; i < ii; i++) {
					optimized.atoms[i].x /= 20;
					optimized.atoms[i].y /= 20;
					optimized.atoms[i].z /= 20;
				}
				callback(optimized);
			}
		}, errorback);
	};

	iChemLabs.readSMILES = function(smiles, callback, errorback) {
		this.contactServer('readSMILES', {
			'smiles' : smiles
		}, function(content) {
			callback(io.fromJSONDummy(content.mol));
		}, errorback);
	};

	iChemLabs.writeSMILES = function(mol, callback, errorback) {
		this.contactServer('writeSMILES', {
			'mol' : io.toJSONDummy(mol)
		}, function(content) {
			callback(content.smiles);
		}, errorback);
	};

	iChemLabs.saveFile = function(mol, ext, callback, errorback) {
		this.contactServer('saveFile', {
			'mol' : io.toJSONDummy(mol),
			'ext' : ext
		}, function(content) {
			callback(content.link);
		}, errorback);
	};

	iChemLabs.getMoleculeFromDatabase = function(database, query, callback, dimension, errorback) {
		this.contactServer('getMoleculeFromDatabase', {
			'database' : database,
			'dimension' : dimension ? dimension : 2,
			'query' : query
		}, function(content) {
			if (dimension == 3) {
				for ( var i = 0, ii = content.mol.a.length; i < ii; i++) {
					content.mol.a[i].x /= 20;
					content.mol.a[i].y /= 20;
					content.mol.a[i].z /= 20;
				}
			}
			callback(io.fromJSONDummy(content.mol));
		}, errorback);
	};

	iChemLabs.calculate = function(mol, descriptors, callback, errorback) {
		this.contactServer('calculate', {
			'mol' : io.toJSONDummy(mol),
			'descriptors' : descriptors
		}, function(content) {
			callback(content);
		}, errorback);
	};

	iChemLabs.simulate1HNMR = function(mol, callback, errorback) {
		this.contactServer('simulateNMR', {
			'mol' : io.toJSONDummy(mol),
			'nucleus' : 'H',
			'isotope' : 1
		}, function(content) {
			callback(c.readJCAMP(content.jcamp));
		}, errorback);
	};

	iChemLabs.simulate13CNMR = function(mol, callback, errorback) {
		this.contactServer('simulateNMR', {
			'mol' : io.toJSONDummy(mol),
			'nucleus' : 'C',
			'isotope' : 13
		}, function(content) {
			callback(c.readJCAMP(content.jcamp));
		}, errorback);
	};

	iChemLabs.simulateMassParentPeak = function(mol, callback, errorback) {
		this.contactServer('simulateMassParentPeak', {
			'mol' : io.toJSONDummy(mol)
		}, function(content) {
			callback(c.readJCAMP(content.jcamp));
		}, errorback);
	};

	iChemLabs.getOptimizedPDBStructure = function(id, withAtoms, callback, errorback) {
		this.contactServer('getOptimizedPDBStructure', {
			'id' : id,
			'withAtoms' : withAtoms
		}, function(content) {
			var mol = null;
			if (content.mol) {
				mol = io.fromJSONDummy(content.mol);
			} else {
				var mol = new structures.Molecule();
			}
			mol.chains = io.fromJSONChains(content.ribbons);
			if (!content.mol) {
				var center = mol.getCenter3D();
				for ( var i = 0, ii = mol.chains.length; i < ii; i++) {
					var chain = mol.chains[i];
					for ( var j = 0, jj = chain.length; j < jj; j++) {
						var residue = chain[j];
						residue.alphaCarbon.x -= center.x;
						residue.alphaCarbon.y -= center.y;
						residue.alphaCarbon.z -= center.z;
						residue.carbonylOxygen.x -= center.x;
						residue.carbonylOxygen.y -= center.y;
						residue.carbonylOxygen.z -= center.z;
					}
				}
			}
			callback(mol);
		}, errorback);
	};

})(ChemDoodle, ChemDoodle.iChemLabs, ChemDoodle.io, ChemDoodle.structures, jQuery);


//
//  Copyright 2006-2010 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
ChemDoodle.extensions = (function(structures, v3, m)
{
	var ext = {};

	ext.stringStartsWith = function(str, match)
	{
		return str.match("^" + match) == match;
	};

	ext.vec3AngleFrom = function(v1, v2)
	{
		var length1 = v3.length(v1);
		var length2 = v3.length(v2);
		var dot = v3.dot(v1, v2);
		var cosine = dot / length1 / length2;
		return m.acos(cosine);
	};

	ext.contextHashTo = function(ctx, xs, ys, xt, yt, width, spacing)
	{
		var travelled = 0;
		var dist = new structures.Point(xs, ys).distance(new structures.Point(xt, yt));
		var space = false;
		var lastX = xs;
		var lastY = ys;
		var difX = xt - xs;
		var difY = yt - ys;
		while (travelled < dist)
		{
			if (space)
			{
				if (travelled + spacing > dist)
				{
					ctx.moveTo(xt, yt);
					break;
				}
				else
				{
					var percent = spacing / dist;
					lastX += percent * difX;
					lastY += percent * difY;
					ctx.moveTo(lastX, lastY);
					travelled += spacing;
				}
			}
			else
			{
				if (travelled + width > dist)
				{
					ctx.lineTo(xt, yt);
					break;
				}
				else
				{
					var percent = width / dist;
					lastX += percent * difX;
					lastY += percent * difY;
					ctx.lineTo(lastX, lastY);
					travelled += width;
				}
			}
			space = !space;
		}
	};

	return ext;

})(ChemDoodle.structures, vec3, Math);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3160 $
//  $Author: kevin $
//  $LastChangedDate: 2011-03-12 18:27:31 -0500 (Sat, 12 Mar 2011) $
//
ChemDoodle.math = (function(extensions, structures, m) {
	var pack = {};

	var namedColors = {
		"aliceblue" : "#f0f8ff",
		"antiquewhite" : "#faebd7",
		"aqua" : "#00ffff",
		"aquamarine" : "#7fffd4",
		"azure" : "#f0ffff",
		"beige" : "#f5f5dc",
		"bisque" : "#ffe4c4",
		"black" : "#000000",
		"blanchedalmond" : "#ffebcd",
		"blue" : "#0000ff",
		"blueviolet" : "#8a2be2",
		"brown" : "#a52a2a",
		"burlywood" : "#deb887",
		"cadetblue" : "#5f9ea0",
		"chartreuse" : "#7fff00",
		"chocolate" : "#d2691e",
		"coral" : "#ff7f50",
		"cornflowerblue" : "#6495ed",
		"cornsilk" : "#fff8dc",
		"crimson" : "#dc143c",
		"cyan" : "#00ffff",
		"darkblue" : "#00008b",
		"darkcyan" : "#008b8b",
		"darkgoldenrod" : "#b8860b",
		"darkgray" : "#a9a9a9",
		"darkgreen" : "#006400",
		"darkkhaki" : "#bdb76b",
		"darkmagenta" : "#8b008b",
		"darkolivegreen" : "#556b2f",
		"darkorange" : "#ff8c00",
		"darkorchid" : "#9932cc",
		"darkred" : "#8b0000",
		"darksalmon" : "#e9967a",
		"darkseagreen" : "#8fbc8f",
		"darkslateblue" : "#483d8b",
		"darkslategray" : "#2f4f4f",
		"darkturquoise" : "#00ced1",
		"darkviolet" : "#9400d3",
		"deeppink" : "#ff1493",
		"deepskyblue" : "#00bfff",
		"dimgray" : "#696969",
		"dodgerblue" : "#1e90ff",
		"firebrick" : "#b22222",
		"floralwhite" : "#fffaf0",
		"forestgreen" : "#228b22",
		"fuchsia" : "#ff00ff",
		"gainsboro" : "#dcdcdc",
		"ghostwhite" : "#f8f8ff",
		"gold" : "#ffd700",
		"goldenrod" : "#daa520",
		"gray" : "#808080",
		"green" : "#008000",
		"greenyellow" : "#adff2f",
		"honeydew" : "#f0fff0",
		"hotpink" : "#ff69b4",
		"indianred " : "#cd5c5c",
		"indigo " : "#4b0082",
		"ivory" : "#fffff0",
		"khaki" : "#f0e68c",
		"lavender" : "#e6e6fa",
		"lavenderblush" : "#fff0f5",
		"lawngreen" : "#7cfc00",
		"lemonchiffon" : "#fffacd",
		"lightblue" : "#add8e6",
		"lightcoral" : "#f08080",
		"lightcyan" : "#e0ffff",
		"lightgoldenrodyellow" : "#fafad2",
		"lightgrey" : "#d3d3d3",
		"lightgreen" : "#90ee90",
		"lightpink" : "#ffb6c1",
		"lightsalmon" : "#ffa07a",
		"lightseagreen" : "#20b2aa",
		"lightskyblue" : "#87cefa",
		"lightslategray" : "#778899",
		"lightsteelblue" : "#b0c4de",
		"lightyellow" : "#ffffe0",
		"lime" : "#00ff00",
		"limegreen" : "#32cd32",
		"linen" : "#faf0e6",
		"magenta" : "#ff00ff",
		"maroon" : "#800000",
		"mediumaquamarine" : "#66cdaa",
		"mediumblue" : "#0000cd",
		"mediumorchid" : "#ba55d3",
		"mediumpurple" : "#9370d8",
		"mediumseagreen" : "#3cb371",
		"mediumslateblue" : "#7b68ee",
		"mediumspringgreen" : "#00fa9a",
		"mediumturquoise" : "#48d1cc",
		"mediumvioletred" : "#c71585",
		"midnightblue" : "#191970",
		"mintcream" : "#f5fffa",
		"mistyrose" : "#ffe4e1",
		"moccasin" : "#ffe4b5",
		"navajowhite" : "#ffdead",
		"navy" : "#000080",
		"oldlace" : "#fdf5e6",
		"olive" : "#808000",
		"olivedrab" : "#6b8e23",
		"orange" : "#ffa500",
		"orangered" : "#ff4500",
		"orchid" : "#da70d6",
		"palegoldenrod" : "#eee8aa",
		"palegreen" : "#98fb98",
		"paleturquoise" : "#afeeee",
		"palevioletred" : "#d87093",
		"papayawhip" : "#ffefd5",
		"peachpuff" : "#ffdab9",
		"peru" : "#cd853f",
		"pink" : "#ffc0cb",
		"plum" : "#dda0dd",
		"powderblue" : "#b0e0e6",
		"purple" : "#800080",
		"red" : "#ff0000",
		"rosybrown" : "#bc8f8f",
		"royalblue" : "#4169e1",
		"saddlebrown" : "#8b4513",
		"salmon" : "#fa8072",
		"sandybrown" : "#f4a460",
		"seagreen" : "#2e8b57",
		"seashell" : "#fff5ee",
		"sienna" : "#a0522d",
		"silver" : "#c0c0c0",
		"skyblue" : "#87ceeb",
		"slateblue" : "#6a5acd",
		"slategray" : "#708090",
		"snow" : "#fffafa",
		"springgreen" : "#00ff7f",
		"steelblue" : "#4682b4",
		"tan" : "#d2b48c",
		"teal" : "#008080",
		"thistle" : "#d8bfd8",
		"tomato" : "#ff6347",
		"turquoise" : "#40e0d0",
		"violet" : "#ee82ee",
		"wheat" : "#f5deb3",
		"white" : "#ffffff",
		"whitesmoke" : "#f5f5f5",
		"yellow" : "#ffff00",
		"yellowgreen" : "#9acd32"
	};

	pack.angleBetweenLargest = function(angles) {
		if (angles.length == 0) {
			return 0;
		}
		if (angles.length == 1) {
			return angles[0] + m.PI;
		}
		var largest = 0;
		var angle = 0;
		var index = -1;
		for ( var i = 0, ii = angles.length - 1; i < ii; i++) {
			var dif = angles[i + 1] - angles[i];
			if (dif > largest) {
				largest = dif;
				angle = (angles[i + 1] + angles[i]) / 2;
				index = i;
			}
		}
		var last = angles[0] + m.PI * 2 - angles[angles.length - 1];
		if (last > largest) {
			angle = angles[0] - last / 2;
			largest = last;
			if (angle < 0) {
				angle += m.PI * 2;
			}
			index = angles.length - 1;
		}
		return angle;
	};

	pack.isBetween = function(x, left, right) {
		return x >= left && x <= right;
	};

	pack.getRGB = function(color, multiplier) {
		var err = [ 0, 0, 0 ];
		if(namedColors[color.toLowerCase()]!=null){
			color = namedColors[color.toLowerCase()];
		}
		if (color.charAt(0) == '#') {
			if(color.length==4){
				color = '#'+color.charAt(1)+color.charAt(1)+color.charAt(2)+color.charAt(2)+color.charAt(3)+color.charAt(3);
			}
			return [ parseInt(color.substring(1, 3), 16) / 255.0 * multiplier, parseInt(color.substring(3, 5), 16) / 255.0 * multiplier, parseInt(color.substring(5, 7), 16) / 255.0 * multiplier ];
		} else if (extensions.stringStartsWith(color, 'rgb')) {
			var cs = color.replace(/rgb\(|\)/g, "").split(",");
			if (cs.length != 3) {
				return err;
			}
			return [ parseInt(cs[0]) / 255.0 * multiplier, parseInt(cs[1]) / 255.0 * multiplier, parseInt(cs[2]) / 255.0 * multiplier ];
		}
		return err;
	};

	pack.distanceFromPointToLineInclusive = function(p, l1, l2) {
		var length = l1.distance(l2);
		var angle = l1.angle(l2);
		var angleDif = m.PI / 2 - angle;
		var pcop = new structures.Point(p.x - l1.x, p.y - l1.x);
		var origin = new structures.Point();
		var newAngleP = l1.angle(p) + angleDif;
		var pDist = l1.distance(p);
		pcopRot = new structures.Point(pDist * m.cos(newAngleP), -pDist * m.sin(newAngleP));
		if (pack.isBetween(-pcopRot.y, 0, length)) {
			return m.abs(pcopRot.x);
		}
		return -1;
	};

	return pack;

})(ChemDoodle.extensions, ChemDoodle.structures, Math);

//
//  Copyright 2006-2010 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3158 $
//  $Author: kevin $
//  $LastChangedDate: 2011-03-10 19:36:21 -0500 (Thu, 10 Mar 2011) $
//

ChemDoodle.featureDetection = (function(iChemLabs, q, document, window) {

	var features = {};

	features.supports_canvas = function() {
		return !!document.createElement('canvas').getContext;
	};

	features.supports_canvas_text = function() {
		if (!features.supports_canvas()) {
			return false;
		}
		var dummy_canvas = document.createElement('canvas');
		var context = dummy_canvas.getContext('2d');
		return typeof context.fillText == 'function';
	};

	features.supports_webgl = function() {
		var dummy_canvas = document.createElement('canvas');
		try {
			if (dummy_canvas.getContext('webgl')) {
				return true;
			}
			if (dummy_canvas.getContext('experimental-webgl')) {
				return true;
			}
		} catch (b) {
		}
		return false;
	};

	features.supports_xhr2 = function() {
		return q.support.cors;
	};

	features.supports_touch = function() {
		return 'ontouchstart' in window;
	};

	return features;

})(ChemDoodle.iChemLabs, jQuery, document, window);

//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3008 $
//  $Author: kevin $
//  $LastChangedDate: 2011-01-07 21:28:00 -0500 (Fri, 07 Jan 2011) $
//
ChemDoodle.ELEMENT = (function() {
	var E = [];

	function Element(symbol, name, atomicNumber) {
		this.symbol = symbol;
		this.name = name;
		this.atomicNumber = atomicNumber;
		return true;
	}

	E['H'] = new Element('H', 'Hydrogen', 1);
	E['He'] = new Element('He', 'Helium', 2);
	E['Li'] = new Element('Li', 'Lithium', 3);
	E['Be'] = new Element('Be', 'Beryllium', 4);
	E['B'] = new Element('B', 'Boron', 5);
	E['C'] = new Element('C', 'Carbon', 6);
	E['N'] = new Element('N', 'Nitrogen', 7);
	E['O'] = new Element('O', 'Oxygen', 8);
	E['F'] = new Element('F', 'Fluorine', 9);
	E['Ne'] = new Element('Ne', 'Neon', 10);
	E['Na'] = new Element('Na', 'Sodium', 11);
	E['Mg'] = new Element('Mg', 'Magnesium', 12);
	E['Al'] = new Element('Al', 'Aluminum', 13);
	E['Si'] = new Element('Si', 'Silicon', 14);
	E['P'] = new Element('P', 'Phosphorus', 15);
	E['S'] = new Element('S', 'Sulfur', 16);
	E['Cl'] = new Element('Cl', 'Chlorine', 17);
	E['Ar'] = new Element('Ar', 'Argon', 18);
	E['K'] = new Element('K', 'Potassium', 19);
	E['Ca'] = new Element('Ca', 'Calcium', 20);
	E['Sc'] = new Element('Sc', 'Scandium', 21);
	E['Ti'] = new Element('Ti', 'Titanium', 22);
	E['V'] = new Element('V', 'Vanadium', 23);
	E['Cr'] = new Element('Cr', 'Chromium', 24);
	E['Mn'] = new Element('Mn', 'Manganese', 25);
	E['Fe'] = new Element('Fe', 'Iron', 26);
	E['Co'] = new Element('Co', 'Cobalt', 27);
	E['Ni'] = new Element('Ni', 'Nickel', 28);
	E['Cu'] = new Element('Cu', 'Copper', 29);
	E['Zn'] = new Element('Zn', 'Zinc', 30);
	E['Ga'] = new Element('Ga', 'Gallium', 31);
	E['Ge'] = new Element('Ge', 'Germanium', 32);
	E['As'] = new Element('As', 'Arsenic', 33);
	E['Se'] = new Element('Se', 'Selenium', 34);
	E['Br'] = new Element('Br', 'Bromine', 35);
	E['Kr'] = new Element('Kr', 'Krypton', 36);
	E['Rb'] = new Element('Rb', 'Rubidium', 37);
	E['Sr'] = new Element('Sr', 'Strontium', 38);
	E['Y'] = new Element('Y', 'Yttrium', 39);
	E['Zr'] = new Element('Zr', 'Zirconium', 40);
	E['Nb'] = new Element('Nb', 'Niobium', 41);
	E['Mo'] = new Element('Mo', 'Molybdenum', 42);
	E['Tc'] = new Element('Tc', 'Technetium', 43);
	E['Ru'] = new Element('Ru', 'Ruthenium', 44);
	E['Rh'] = new Element('Rh', 'Rhodium', 45);
	E['Pd'] = new Element('Pd', 'Palladium', 46);
	E['Ag'] = new Element('Ag', 'Silver', 47);
	E['Cd'] = new Element('Cd', 'Cadmium', 48);
	E['In'] = new Element('In', 'Indium', 49);
	E['Sn'] = new Element('Sn', 'Tin', 50);
	E['Sb'] = new Element('Sb', 'Antimony', 51);
	E['Te'] = new Element('Te', 'Tellurium', 52);
	E['I'] = new Element('I', 'Iodine', 53);
	E['Xe'] = new Element('Xe', 'Xenon', 54);
	E['Cs'] = new Element('Cs', 'Cesium', 55);
	E['Ba'] = new Element('Ba', 'Barium', 56);
	E['La'] = new Element('La', 'Lanthanum', 57);
	E['Ce'] = new Element('Ce', 'Cerium', 58);
	E['Pr'] = new Element('Pr', 'Praseodymium', 59);
	E['Nd'] = new Element('Nd', 'Neodymium', 60);
	E['Pm'] = new Element('Pm', 'Promethium', 61);
	E['Sm'] = new Element('Sm', 'Samarium', 62);
	E['Eu'] = new Element('Eu', 'Europium', 63);
	E['Gd'] = new Element('Gd', 'Gadolinium', 64);
	E['Tb'] = new Element('Tb', 'Terbium', 65);
	E['Dy'] = new Element('Dy', 'Dysprosium', 66);
	E['Ho'] = new Element('Ho', 'Holmium', 67);
	E['Er'] = new Element('Er', 'Erbium', 68);
	E['Tm'] = new Element('Tm', 'Thulium', 69);
	E['Yb'] = new Element('Yb', 'Ytterbium', 70);
	E['Lu'] = new Element('Lu', 'Lutetium', 71);
	E['Hf'] = new Element('Hf', 'Hafnium', 72);
	E['Ta'] = new Element('Ta', 'Tantalum', 73);
	E['W'] = new Element('W', 'Tungsten', 74);
	E['Re'] = new Element('Re', 'Rhenium', 75);
	E['Os'] = new Element('Os', 'Osmium', 76);
	E['Ir'] = new Element('Ir', 'Iridium', 77);
	E['Pt'] = new Element('Pt', 'Platinum', 78);
	E['Au'] = new Element('Au', 'Gold', 79);
	E['Hg'] = new Element('Hg', 'Mercury', 80);
	E['Tl'] = new Element('Tl', 'Thallium', 81);
	E['Pb'] = new Element('Pb', 'Lead', 82);
	E['Bi'] = new Element('Bi', 'Bismuth', 83);
	E['Po'] = new Element('Po', 'Polonium', 84);
	E['At'] = new Element('At', 'Astatine', 85);
	E['Rn'] = new Element('Rn', 'Radon', 86);
	E['Fr'] = new Element('Fr', 'Francium', 87);
	E['Ra'] = new Element('Ra', 'Radium', 88);
	E['Ac'] = new Element('Ac', 'Actinium', 89);
	E['Th'] = new Element('Th', 'Thorium', 90);
	E['Pa'] = new Element('Pa', 'Protactinium', 91);
	E['U'] = new Element('U', 'Uranium', 92);
	E['Np'] = new Element('Np', 'Neptunium', 93);
	E['Pu'] = new Element('Pu', 'Plutonium', 94);
	E['Am'] = new Element('Am', 'Americium', 95);
	E['Cm'] = new Element('Cm', 'Curium', 96);
	E['Bk'] = new Element('Bk', 'Berkelium', 97);
	E['Cf'] = new Element('Cf', 'Californium', 98);
	E['Es'] = new Element('Es', 'Einsteinium', 99);
	E['Fm'] = new Element('Fm', 'Fermium', 100);
	E['Md'] = new Element('Md', 'Mendelevium', 101);
	E['No'] = new Element('No', 'Nobelium', 102);
	E['Lr'] = new Element('Lr', 'Lawrencium', 103);
	E['Rf'] = new Element('Rf', 'Rutherfordium', 104);
	E['Db'] = new Element('Db', 'Dubnium', 105);
	E['Sg'] = new Element('Sg', 'Seaborgium', 106);
	E['Bh'] = new Element('Bh', 'Bohrium', 107);
	E['Hs'] = new Element('Hs', 'Hassium', 108);
	E['Mt'] = new Element('Mt', 'Meitnerium', 109);
	E['Ds'] = new Element('Ds', 'Darmstadtium', 110);
	E['Rg'] = new Element('Rg', 'Roentgenium', 111);
	E['Cn'] = new Element('Cn', 'Copernicium', 112);
	E['Uut'] = new Element('Uut', 'Ununtrium', 113);
	E['Uuq'] = new Element('Uuq', 'Ununquadium', 114);
	E['Uup'] = new Element('Uup', 'Ununpentium', 115);
	E['Uuh'] = new Element('Uuh', 'Ununhexium', 116);
	E['Uus'] = new Element('Uus', 'Ununseptium', 117);
	E['Uuo'] = new Element('Uuo', 'Ununoctium', 118);

	// set up jmol colors
	E['H'].jmolColor = '#656565';
	E['He'].jmolColor = '#D9FFFF';
	E['Li'].jmolColor = '#CC80FF';
	E['Be'].jmolColor = '#C2FF00';
	E['B'].jmolColor = '#FFB5B5';
	E['C'].jmolColor = '#909090';
	E['N'].jmolColor = '#3050F8';
	E['O'].jmolColor = '#FF0D0D';
	E['F'].jmolColor = '#90E050';
	E['Ne'].jmolColor = '#B3E3F5';
	E['Na'].jmolColor = '#AB5CF2';
	E['Mg'].jmolColor = '#8AFF00';
	E['Al'].jmolColor = '#BFA6A6';
	E['Si'].jmolColor = '#F0C8A0';
	E['P'].jmolColor = '#FF8000';
	E['S'].jmolColor = '#B6A43E';
	E['Cl'].jmolColor = '#1FF01F';
	E['Ar'].jmolColor = '#80D1E3';
	E['K'].jmolColor = '#8F40D4';
	E['Ca'].jmolColor = '#3DFF00';
	E['Sc'].jmolColor = '#E6E6E6';
	E['Ti'].jmolColor = '#BFC2C7';
	E['V'].jmolColor = '#A6A6AB';
	E['Cr'].jmolColor = '#8A99C7';
	E['Mn'].jmolColor = '#9C7AC7';
	E['Fe'].jmolColor = '#E06633';
	E['Co'].jmolColor = '#F090A0';
	E['Ni'].jmolColor = '#50D050';
	E['Cu'].jmolColor = '#C88033';
	E['Zn'].jmolColor = '#7D80B0';
	E['Ga'].jmolColor = '#C28F8F';
	E['Ge'].jmolColor = '#668F8F';
	E['As'].jmolColor = '#BD80E3';
	E['Se'].jmolColor = '#FFA100';
	E['Br'].jmolColor = '#A62929';
	E['Kr'].jmolColor = '#5CB8D1';
	E['Rb'].jmolColor = '#702EB0';
	E['Sr'].jmolColor = '#00FF00';
	E['Y'].jmolColor = '#94FFFF';
	E['Zr'].jmolColor = '#94E0E0';
	E['Nb'].jmolColor = '#73C2C9';
	E['Mo'].jmolColor = '#54B5B5';
	E['Tc'].jmolColor = '#3B9E9E';
	E['Ru'].jmolColor = '#248F8F';
	E['Rh'].jmolColor = '#0A7D8C';
	E['Pd'].jmolColor = '#006985';
	E['Ag'].jmolColor = '#C0C0C0';
	E['Cd'].jmolColor = '#FFD98F';
	E['In'].jmolColor = '#A67573';
	E['Sn'].jmolColor = '#668080';
	E['Sb'].jmolColor = '#9E63B5';
	E['Te'].jmolColor = '#D47A00';
	E['I'].jmolColor = '#940094';
	E['Xe'].jmolColor = '#429EB0';
	E['Cs'].jmolColor = '#57178F';
	E['Ba'].jmolColor = '#00C900';
	E['La'].jmolColor = '#70D4FF';
	E['Ce'].jmolColor = '#FFFFC7';
	E['Pr'].jmolColor = '#D9FFC7';
	E['Nd'].jmolColor = '#C7FFC7';
	E['Pm'].jmolColor = '#A3FFC7';
	E['Sm'].jmolColor = '#8FFFC7';
	E['Eu'].jmolColor = '#61FFC7';
	E['Gd'].jmolColor = '#45FFC7';
	E['Tb'].jmolColor = '#30FFC7';
	E['Dy'].jmolColor = '#1FFFC7';
	E['Ho'].jmolColor = '#00FF9C';
	E['Er'].jmolColor = '#00E675';
	E['Tm'].jmolColor = '#00D452';
	E['Yb'].jmolColor = '#00BF38';
	E['Lu'].jmolColor = '#00AB24';
	E['Hf'].jmolColor = '#4DC2FF';
	E['Ta'].jmolColor = '#4DA6FF';
	E['W'].jmolColor = '#2194D6';
	E['Re'].jmolColor = '#267DAB';
	E['Os'].jmolColor = '#266696';
	E['Ir'].jmolColor = '#175487';
	E['Pt'].jmolColor = '#D0D0E0';
	E['Au'].jmolColor = '#FFD123';
	E['Hg'].jmolColor = '#B8B8D0';
	E['Tl'].jmolColor = '#A6544D';
	E['Pb'].jmolColor = '#575961';
	E['Bi'].jmolColor = '#9E4FB5';
	E['Po'].jmolColor = '#AB5C00';
	E['At'].jmolColor = '#754F45';
	E['Rn'].jmolColor = '#428296';
	E['Fr'].jmolColor = '#420066';
	E['Ra'].jmolColor = '#007D00';
	E['Ac'].jmolColor = '#70ABFA';
	E['Th'].jmolColor = '#00BAFF';
	E['Pa'].jmolColor = '#00A1FF';
	E['U'].jmolColor = '#008FFF';
	E['Np'].jmolColor = '#0080FF';
	E['Pu'].jmolColor = '#006BFF';
	E['Am'].jmolColor = '#545CF2';
	E['Cm'].jmolColor = '#785CE3';
	E['Bk'].jmolColor = '#8A4FE3';
	E['Cf'].jmolColor = '#A136D4';
	E['Es'].jmolColor = '#B31FD4';
	E['Fm'].jmolColor = '#B31FBA';
	E['Md'].jmolColor = '#B30DA6';
	E['No'].jmolColor = '#BD0D87';
	E['Lr'].jmolColor = '#C70066';
	E['Rf'].jmolColor = '#CC0059';
	E['Db'].jmolColor = '#D1004F';
	E['Sg'].jmolColor = '#D90045';
	E['Bh'].jmolColor = '#E00038';
	E['Hs'].jmolColor = '#E6002E';
	E['Mt'].jmolColor = '#EB0026';
	E['Ds'].jmolColor = '#000000';
	E['Rg'].jmolColor = '#000000';
	E['Cn'].jmolColor = '#000000';
	E['Uut'].jmolColor = '#000000';
	E['Uuq'].jmolColor = '#000000';
	E['Uup'].jmolColor = '#000000';
	E['Uuh'].jmolColor = '#000000';
	E['Uus'].jmolColor = '#000000';
	E['Uuo'].jmolColor = '#000000';

	// set up covalent radii
	E['H'].covalentRadius = 0.31;
	E['He'].covalentRadius = 0.28;
	E['Li'].covalentRadius = 1.28;
	E['Be'].covalentRadius = 0.96;
	E['B'].covalentRadius = 0.84;
	E['C'].covalentRadius = 0.76;
	E['N'].covalentRadius = 0.71;
	E['O'].covalentRadius = 0.66;
	E['F'].covalentRadius = 0.57;
	E['Ne'].covalentRadius = 0.58;
	E['Na'].covalentRadius = 1.66;
	E['Mg'].covalentRadius = 1.41;
	E['Al'].covalentRadius = 1.21;
	E['Si'].covalentRadius = 1.11;
	E['P'].covalentRadius = 1.07;
	E['S'].covalentRadius = 1.05;
	E['Cl'].covalentRadius = 1.02;
	E['Ar'].covalentRadius = 1.06;
	E['K'].covalentRadius = 2.03;
	E['Ca'].covalentRadius = 1.76;
	E['Sc'].covalentRadius = 1.7;
	E['Ti'].covalentRadius = 1.6;
	E['V'].covalentRadius = 1.53;
	E['Cr'].covalentRadius = 1.39;
	E['Mn'].covalentRadius = 1.39;
	E['Fe'].covalentRadius = 1.32;
	E['Co'].covalentRadius = 1.26;
	E['Ni'].covalentRadius = 1.24;
	E['Cu'].covalentRadius = 1.32;
	E['Zn'].covalentRadius = 1.22;
	E['Ga'].covalentRadius = 1.22;
	E['Ge'].covalentRadius = 1.2;
	E['As'].covalentRadius = 1.19;
	E['Se'].covalentRadius = 1.2;
	E['Br'].covalentRadius = 1.2;
	E['Kr'].covalentRadius = 1.16;
	E['Rb'].covalentRadius = 2.2;
	E['Sr'].covalentRadius = 1.95;
	E['Y'].covalentRadius = 1.9;
	E['Zr'].covalentRadius = 1.75;
	E['Nb'].covalentRadius = 1.64;
	E['Mo'].covalentRadius = 1.54;
	E['Tc'].covalentRadius = 1.47;
	E['Ru'].covalentRadius = 1.46;
	E['Rh'].covalentRadius = 1.42;
	E['Pd'].covalentRadius = 1.39;
	E['Ag'].covalentRadius = 1.45;
	E['Cd'].covalentRadius = 1.44;
	E['In'].covalentRadius = 1.42;
	E['Sn'].covalentRadius = 1.39;
	E['Sb'].covalentRadius = 1.39;
	E['Te'].covalentRadius = 1.38;
	E['I'].covalentRadius = 1.39;
	E['Xe'].covalentRadius = 1.4;
	E['Cs'].covalentRadius = 2.44;
	E['Ba'].covalentRadius = 2.15;
	E['La'].covalentRadius = 2.07;
	E['Ce'].covalentRadius = 2.04;
	E['Pr'].covalentRadius = 2.03;
	E['Nd'].covalentRadius = 2.01;
	E['Pm'].covalentRadius = 1.99;
	E['Sm'].covalentRadius = 1.98;
	E['Eu'].covalentRadius = 1.98;
	E['Gd'].covalentRadius = 1.96;
	E['Tb'].covalentRadius = 1.94;
	E['Dy'].covalentRadius = 1.92;
	E['Ho'].covalentRadius = 1.92;
	E['Er'].covalentRadius = 1.89;
	E['Tm'].covalentRadius = 1.9;
	E['Yb'].covalentRadius = 1.87;
	E['Lu'].covalentRadius = 1.87;
	E['Hf'].covalentRadius = 1.75;
	E['Ta'].covalentRadius = 1.7;
	E['W'].covalentRadius = 1.62;
	E['Re'].covalentRadius = 1.51;
	E['Os'].covalentRadius = 1.44;
	E['Ir'].covalentRadius = 1.41;
	E['Pt'].covalentRadius = 1.36;
	E['Au'].covalentRadius = 1.36;
	E['Hg'].covalentRadius = 1.32;
	E['Tl'].covalentRadius = 1.45;
	E['Pb'].covalentRadius = 1.46;
	E['Bi'].covalentRadius = 1.48;
	E['Po'].covalentRadius = 1.4;
	E['At'].covalentRadius = 1.5;
	E['Rn'].covalentRadius = 1.5;
	E['Fr'].covalentRadius = 2.6;
	E['Ra'].covalentRadius = 2.21;
	E['Ac'].covalentRadius = 2.15;
	E['Th'].covalentRadius = 2.06;
	E['Pa'].covalentRadius = 2.0;
	E['U'].covalentRadius = 1.96;
	E['Np'].covalentRadius = 1.9;
	E['Pu'].covalentRadius = 1.87;
	E['Am'].covalentRadius = 1.8;
	E['Cm'].covalentRadius = 1.69;
	E['Bk'].covalentRadius = 0.0;
	E['Cf'].covalentRadius = 0.0;
	E['Es'].covalentRadius = 0.0;
	E['Fm'].covalentRadius = 0.0;
	E['Md'].covalentRadius = 0.0;
	E['No'].covalentRadius = 0.0;
	E['Lr'].covalentRadius = 0.0;
	E['Rf'].covalentRadius = 0.0;
	E['Db'].covalentRadius = 0.0;
	E['Sg'].covalentRadius = 0.0;
	E['Bh'].covalentRadius = 0.0;
	E['Hs'].covalentRadius = 0.0;
	E['Mt'].covalentRadius = 0.0;
	E['Ds'].covalentRadius = 0.0;
	E['Rg'].covalentRadius = 0.0;
	E['Cn'].covalentRadius = 0.0;
	E['Uut'].covalentRadius = 0.0;
	E['Uuq'].covalentRadius = 0.0;
	E['Uup'].covalentRadius = 0.0;
	E['Uuh'].covalentRadius = 0.0;
	E['Uus'].covalentRadius = 0.0;
	E['Uuo'].covalentRadius = 0.0;

	// set up vdW radii
	E['H'].vdWRadius = 1.2;
	E['He'].vdWRadius = 1.4;
	E['Li'].vdWRadius = 1.82;
	E['Be'].vdWRadius = 0.0;
	E['B'].vdWRadius = 0.0;
	E['C'].vdWRadius = 1.7;
	E['N'].vdWRadius = 1.55;
	E['O'].vdWRadius = 1.52;
	E['F'].vdWRadius = 1.47;
	E['Ne'].vdWRadius = 1.54;
	E['Na'].vdWRadius = 2.27;
	E['Mg'].vdWRadius = 1.73;
	E['Al'].vdWRadius = 0.0;
	E['Si'].vdWRadius = 2.1;
	E['P'].vdWRadius = 1.8;
	E['S'].vdWRadius = 1.8;
	E['Cl'].vdWRadius = 1.75;
	E['Ar'].vdWRadius = 1.88;
	E['K'].vdWRadius = 2.75;
	E['Ca'].vdWRadius = 0.0;
	E['Sc'].vdWRadius = 0.0;
	E['Ti'].vdWRadius = 0.0;
	E['V'].vdWRadius = 0.0;
	E['Cr'].vdWRadius = 0.0;
	E['Mn'].vdWRadius = 0.0;
	E['Fe'].vdWRadius = 0.0;
	E['Co'].vdWRadius = 0.0;
	E['Ni'].vdWRadius = 1.63;
	E['Cu'].vdWRadius = 1.4;
	E['Zn'].vdWRadius = 1.39;
	E['Ga'].vdWRadius = 1.87;
	E['Ge'].vdWRadius = 0.0;
	E['As'].vdWRadius = 1.85;
	E['Se'].vdWRadius = 1.9;
	E['Br'].vdWRadius = 1.85;
	E['Kr'].vdWRadius = 2.02;
	E['Rb'].vdWRadius = 0.0;
	E['Sr'].vdWRadius = 0.0;
	E['Y'].vdWRadius = 0.0;
	E['Zr'].vdWRadius = 0.0;
	E['Nb'].vdWRadius = 0.0;
	E['Mo'].vdWRadius = 0.0;
	E['Tc'].vdWRadius = 0.0;
	E['Ru'].vdWRadius = 0.0;
	E['Rh'].vdWRadius = 0.0;
	E['Pd'].vdWRadius = 1.63;
	E['Ag'].vdWRadius = 1.72;
	E['Cd'].vdWRadius = 1.58;
	E['In'].vdWRadius = 1.93;
	E['Sn'].vdWRadius = 2.17;
	E['Sb'].vdWRadius = 0.0;
	E['Te'].vdWRadius = 2.06;
	E['I'].vdWRadius = 1.98;
	E['Xe'].vdWRadius = 2.16;
	E['Cs'].vdWRadius = 0.0;
	E['Ba'].vdWRadius = 0.0;
	E['La'].vdWRadius = 0.0;
	E['Ce'].vdWRadius = 0.0;
	E['Pr'].vdWRadius = 0.0;
	E['Nd'].vdWRadius = 0.0;
	E['Pm'].vdWRadius = 0.0;
	E['Sm'].vdWRadius = 0.0;
	E['Eu'].vdWRadius = 0.0;
	E['Gd'].vdWRadius = 0.0;
	E['Tb'].vdWRadius = 0.0;
	E['Dy'].vdWRadius = 0.0;
	E['Ho'].vdWRadius = 0.0;
	E['Er'].vdWRadius = 0.0;
	E['Tm'].vdWRadius = 0.0;
	E['Yb'].vdWRadius = 0.0;
	E['Lu'].vdWRadius = 0.0;
	E['Hf'].vdWRadius = 0.0;
	E['Ta'].vdWRadius = 0.0;
	E['W'].vdWRadius = 0.0;
	E['Re'].vdWRadius = 0.0;
	E['Os'].vdWRadius = 0.0;
	E['Ir'].vdWRadius = 0.0;
	E['Pt'].vdWRadius = 1.75;
	E['Au'].vdWRadius = 1.66;
	E['Hg'].vdWRadius = 1.55;
	E['Tl'].vdWRadius = 1.96;
	E['Pb'].vdWRadius = 2.02;
	E['Bi'].vdWRadius = 0.0;
	E['Po'].vdWRadius = 0.0;
	E['At'].vdWRadius = 0.0;
	E['Rn'].vdWRadius = 0.0;
	E['Fr'].vdWRadius = 0.0;
	E['Ra'].vdWRadius = 0.0;
	E['Ac'].vdWRadius = 0.0;
	E['Th'].vdWRadius = 0.0;
	E['Pa'].vdWRadius = 0.0;
	E['U'].vdWRadius = 1.86;
	E['Np'].vdWRadius = 0.0;
	E['Pu'].vdWRadius = 0.0;
	E['Am'].vdWRadius = 0.0;
	E['Cm'].vdWRadius = 0.0;
	E['Bk'].vdWRadius = 0.0;
	E['Cf'].vdWRadius = 0.0;
	E['Es'].vdWRadius = 0.0;
	E['Fm'].vdWRadius = 0.0;
	E['Md'].vdWRadius = 0.0;
	E['No'].vdWRadius = 0.0;
	E['Lr'].vdWRadius = 0.0;
	E['Rf'].vdWRadius = 0.0;
	E['Db'].vdWRadius = 0.0;
	E['Sg'].vdWRadius = 0.0;
	E['Bh'].vdWRadius = 0.0;
	E['Hs'].vdWRadius = 0.0;
	E['Mt'].vdWRadius = 0.0;
	E['Ds'].vdWRadius = 0.0;
	E['Rg'].vdWRadius = 0.0;
	E['Cn'].vdWRadius = 0.0;
	E['Uut'].vdWRadius = 0.0;
	E['Uuq'].vdWRadius = 0.0;
	E['Uup'].vdWRadius = 0.0;
	E['Uuh'].vdWRadius = 0.0;
	E['Uus'].vdWRadius = 0.0;
	E['Uuo'].vdWRadius = 0.0;

	E['H'].valency = 1;
	E['He'].valency = 0;
	E['Li'].valency = 1;
	E['Be'].valency = 2;
	E['B'].valency = 3;
	E['C'].valency = 4;
	E['N'].valency = 3;
	E['O'].valency = 2;
	E['F'].valency = 1;
	E['Ne'].valency = 0;
	E['Na'].valency = 1;
	E['Mg'].valency = 0;
	E['Al'].valency = 0;
	E['Si'].valency = 4;
	E['P'].valency = 3;
	E['S'].valency = 2;
	E['Cl'].valency = 1;
	E['Ar'].valency = 0;
	E['K'].valency = 0;
	E['Ca'].valency = 0;
	E['Sc'].valency = 0;
	E['Ti'].valency = 1;
	E['V'].valency = 1;
	E['Cr'].valency = 2;
	E['Mn'].valency = 3;
	E['Fe'].valency = 2;
	E['Co'].valency = 1;
	E['Ni'].valency = 1;
	E['Cu'].valency = 0;
	E['Zn'].valency = 0;
	E['Ga'].valency = 0;
	E['Ge'].valency = 4;
	E['As'].valency = 3;
	E['Se'].valency = 2;
	E['Br'].valency = 1;
	E['Kr'].valency = 0;
	E['Rb'].valency = 0;
	E['Sr'].valency = 0;
	E['Y'].valency = 0;
	E['Zr'].valency = 0;
	E['Nb'].valency = 1;
	E['Mo'].valency = 2;
	E['Tc'].valency = 3;
	E['Ru'].valency = 2;
	E['Rh'].valency = 1;
	E['Pd'].valency = 0;
	E['Ag'].valency = 0;
	E['Cd'].valency = 0;
	E['In'].valency = 0;
	E['Sn'].valency = 4;
	E['Sb'].valency = 3;
	E['Te'].valency = 2;
	E['I'].valency = 1;
	E['Xe'].valency = 0;
	E['Cs'].valency = 0;
	E['Ba'].valency = 0;
	E['La'].valency = 0;
	E['Ce'].valency = 0;
	E['Pr'].valency = 0;
	E['Nd'].valency = 0;
	E['Pm'].valency = 0;
	E['Sm'].valency = 0;
	E['Eu'].valency = 0;
	E['Gd'].valency = 0;
	E['Tb'].valency = 0;
	E['Dy'].valency = 0;
	E['Ho'].valency = 0;
	E['Er'].valency = 0;
	E['Tm'].valency = 0;
	E['Yb'].valency = 0;
	E['Lu'].valency = 0;
	E['Hf'].valency = 0;
	E['Ta'].valency = 1;
	E['W'].valency = 2;
	E['Re'].valency = 3;
	E['Os'].valency = 2;
	E['Ir'].valency = 3;
	E['Pt'].valency = 0;
	E['Au'].valency = 1;
	E['Hg'].valency = 0;
	E['Tl'].valency = 0;
	E['Pb'].valency = 4;
	E['Bi'].valency = 3;
	E['Po'].valency = 2;
	E['At'].valency = 1;
	E['Rn'].valency = 0;
	E['Fr'].valency = 0;
	E['Ra'].valency = 0;
	E['Ac'].valency = 0;
	E['Th'].valency = 0;
	E['Pa'].valency = 0;
	E['U'].valency = 0;
	E['Np'].valency = 0;
	E['Pu'].valency = 0;
	E['Am'].valency = 0;
	E['Cm'].valency = 0;
	E['Bk'].valency = 0;
	E['Cf'].valency = 0;
	E['Es'].valency = 0;
	E['Fm'].valency = 0;
	E['Md'].valency = 0;
	E['No'].valency = 0;
	E['Lr'].valency = 0;
	E['Rf'].valency = 0;
	E['Db'].valency = 0;
	E['Sg'].valency = 0;
	E['Bh'].valency = 0;
	E['Hs'].valency = 0;
	E['Mt'].valency = 0;
	E['Ds'].valency = 0;
	E['Rg'].valency = 0;
	E['Cn'].valency = 0;
	E['Uut'].valency = 0;
	E['Uuq'].valency = 0;
	E['Uup'].valency = 0;
	E['Uuh'].valency = 0;
	E['Uus'].valency = 0;
	E['Uuo'].valency = 0;

	E['H'].mass = 1;
	E['He'].mass = 4;
	E['Li'].mass = 7;
	E['Be'].mass = 9;
	E['B'].mass = 11;
	E['C'].mass = 12;
	E['N'].mass = 14;
	E['O'].mass = 16;
	E['F'].mass = 19;
	E['Ne'].mass = 20;
	E['Na'].mass = 23;
	E['Mg'].mass = 24;
	E['Al'].mass = 27;
	E['Si'].mass = 28;
	E['P'].mass = 31;
	E['S'].mass = 32;
	E['Cl'].mass = 35;
	E['Ar'].mass = 40;
	E['K'].mass = 39;
	E['Ca'].mass = 40;
	E['Sc'].mass = 45;
	E['Ti'].mass = 48;
	E['V'].mass = 51;
	E['Cr'].mass = 52;
	E['Mn'].mass = 55;
	E['Fe'].mass = 56;
	E['Co'].mass = 59;
	E['Ni'].mass = 58;
	E['Cu'].mass = 63;
	E['Zn'].mass = 64;
	E['Ga'].mass = 69;
	E['Ge'].mass = 74;
	E['As'].mass = 75;
	E['Se'].mass = 80;
	E['Br'].mass = 79;
	E['Kr'].mass = 84;
	E['Rb'].mass = 85;
	E['Sr'].mass = 88;
	E['Y'].mass = 89;
	E['Zr'].mass = 90;
	E['Nb'].mass = 93;
	E['Mo'].mass = 98;
	E['Tc'].mass = 0;
	E['Ru'].mass = 102;
	E['Rh'].mass = 103;
	E['Pd'].mass = 106;
	E['Ag'].mass = 107;
	E['Cd'].mass = 114;
	E['In'].mass = 115;
	E['Sn'].mass = 120;
	E['Sb'].mass = 121;
	E['Te'].mass = 130;
	E['I'].mass = 127;
	E['Xe'].mass = 132;
	E['Cs'].mass = 133;
	E['Ba'].mass = 138;
	E['La'].mass = 139;
	E['Ce'].mass = 140;
	E['Pr'].mass = 141;
	E['Nd'].mass = 142;
	E['Pm'].mass = 0;
	E['Sm'].mass = 152;
	E['Eu'].mass = 153;
	E['Gd'].mass = 158;
	E['Tb'].mass = 159;
	E['Dy'].mass = 164;
	E['Ho'].mass = 165;
	E['Er'].mass = 166;
	E['Tm'].mass = 169;
	E['Yb'].mass = 174;
	E['Lu'].mass = 175;
	E['Hf'].mass = 180;
	E['Ta'].mass = 181;
	E['W'].mass = 184;
	E['Re'].mass = 187;
	E['Os'].mass = 192;
	E['Ir'].mass = 193;
	E['Pt'].mass = 195;
	E['Au'].mass = 197;
	E['Hg'].mass = 202;
	E['Tl'].mass = 205;
	E['Pb'].mass = 208;
	E['Bi'].mass = 209;
	E['Po'].mass = 0;
	E['At'].mass = 0;
	E['Rn'].mass = 0;
	E['Fr'].mass = 0;
	E['Ra'].mass = 0;
	E['Ac'].mass = 0;
	E['Th'].mass = 232;
	E['Pa'].mass = 231;
	E['U'].mass = 238;
	E['Np'].mass = 0;
	E['Pu'].mass = 0;
	E['Am'].mass = 0;
	E['Cm'].mass = 0;
	E['Bk'].mass = 0;
	E['Cf'].mass = 0;
	E['Es'].mass = 0;
	E['Fm'].mass = 0;
	E['Md'].mass = 0;
	E['No'].mass = 0;
	E['Lr'].mass = 0;
	E['Rf'].mass = 0;
	E['Db'].mass = 0;
	E['Sg'].mass = 0;
	E['Bh'].mass = 0;
	E['Hs'].mass = 0;
	E['Mt'].mass = 0;
	E['Ds'].mass = 0;
	E['Rg'].mass = 0;
	E['Cn'].mass = 0;
	E['Uut'].mass = 0;
	E['Uuq'].mass = 0;
	E['Uup'].mass = 0;
	E['Uuh'].mass = 0;
	E['Uus'].mass = 0;
	E['Uuo'].mass = 0;

	return E;

})();

// all symbols
ChemDoodle.SYMBOLS = [ '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', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Uut', 'Uuq', 'Uup', 'Uuh', 'Uus', 'Uuo' ];


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3008 $
//  $Author: kevin $
//  $LastChangedDate: 2011-01-07 21:28:00 -0500 (Fri, 07 Jan 2011) $
//
ChemDoodle.RESIDUE = (function() {

	var R = [];

	function Residue(symbol, name) {
		this.symbol = symbol;
		this.name = name;
		return true;
	}

	R['Ala'] = new Residue('Ala', 'Alanine');
	R['Arg'] = new Residue('Arg', 'Arginine');
	R['Asn'] = new Residue('Asn', 'Asparagine');
	R['Asp'] = new Residue('Asp', 'Aspartic Acid');
	R['Cys'] = new Residue('Cys', 'Cysteine');
	R['Gln'] = new Residue('Gln', 'Glutamine');
	R['Glu'] = new Residue('Glu', 'Glutamic Acid');
	R['Gly'] = new Residue('Gly', 'Glycine');
	R['His'] = new Residue('His', 'Histidine');
	R['Ile'] = new Residue('Ile', 'Isoleucine');
	R['Leu'] = new Residue('Leu', 'Leucine');
	R['Lys'] = new Residue('Lys', 'Lysine');
	R['Met'] = new Residue('Met', 'Methionine');
	R['Phe'] = new Residue('Phe', 'Phenylalanine');
	R['Pro'] = new Residue('Pro', 'Proline');
	R['Ser'] = new Residue('Ser', 'Serine');
	R['Thr'] = new Residue('Thr', 'Threonine');
	R['Trp'] = new Residue('Trp', 'Tryptophan');
	R['Tyr'] = new Residue('Tyr', 'Tyrosine');
	R['Val'] = new Residue('Val', 'Valine');
	R['Asx'] = new Residue('Asx', 'Asparagine/Aspartic Acid');
	R['Glx'] = new Residue('Glx', 'Glutamine/Glutamic Acid');
	R['*'] = new Residue('*', 'Other');
	R['A'] = new Residue('A', 'Adenine');
	R['G'] = new Residue('G', 'Guanine');
	R['I'] = new Residue('I', '');
	R['C'] = new Residue('C', 'Cytosine');
	R['T'] = new Residue('T', 'Thymine');
	R['U'] = new Residue('U', 'Uracil');

	// set up amino colors
	R['Ala'].aminoColor = '#C8C8C8';
	R['Arg'].aminoColor = '#145AFF';
	R['Asn'].aminoColor = '#00DCDC';
	R['Asp'].aminoColor = '#E60A0A';
	R['Cys'].aminoColor = '#E6E600';
	R['Gln'].aminoColor = '#00DCDC';
	R['Glu'].aminoColor = '#E60A0A';
	R['Gly'].aminoColor = '#EBEBEB';
	R['His'].aminoColor = '#8282D2';
	R['Ile'].aminoColor = '#0F820F';
	R['Leu'].aminoColor = '#0F820F';
	R['Lys'].aminoColor = '#145AFF';
	R['Met'].aminoColor = '#E6E600';
	R['Phe'].aminoColor = '#3232AA';
	R['Pro'].aminoColor = '#DC9682';
	R['Ser'].aminoColor = '#FA9600';
	R['Thr'].aminoColor = '#FA9600';
	R['Trp'].aminoColor = '#B45AB4';
	R['Tyr'].aminoColor = '#3232AA';
	R['Val'].aminoColor = '#0F820F';
	R['Asx'].aminoColor = '#FF69B4';
	R['Glx'].aminoColor = '#FF69B4';
	R['*'].aminoColor = '#BEA06E';
	R['A'].aminoColor = '#BEA06E';
	R['G'].aminoColor = '#BEA06E';
	R['I'].aminoColor = '#BEA06E';
	R['C'].aminoColor = '#BEA06E';
	R['T'].aminoColor = '#BEA06E';
	R['U'].aminoColor = '#BEA06E';

	// set up shapely colors
	R['Ala'].shapelyColor = '#8CFF8C';
	R['Arg'].shapelyColor = '#00007C';
	R['Asn'].shapelyColor = '#FF7C70';
	R['Asp'].shapelyColor = '#A00042';
	R['Cys'].shapelyColor = '#FFFF70';
	R['Gln'].shapelyColor = '#FF4C4C';
	R['Glu'].shapelyColor = '#660000';
	R['Gly'].shapelyColor = '#FFFFFF';
	R['His'].shapelyColor = '#7070FF';
	R['Ile'].shapelyColor = '#004C00';
	R['Leu'].shapelyColor = '#455E45';
	R['Lys'].shapelyColor = '#4747B8';
	R['Met'].shapelyColor = '#B8A042';
	R['Phe'].shapelyColor = '#534C52';
	R['Pro'].shapelyColor = '#525252';
	R['Ser'].shapelyColor = '#FF7042';
	R['Thr'].shapelyColor = '#B84C00';
	R['Trp'].shapelyColor = '#4F4600';
	R['Tyr'].shapelyColor = '#8C704C';
	R['Val'].shapelyColor = '#FF8CFF';
	R['Asx'].shapelyColor = '#FF00FF';
	R['Glx'].shapelyColor = '#FF00FF';
	R['*'].shapelyColor = '#FF00FF';
	R['A'].shapelyColor = '#A0A0FF';
	R['G'].shapelyColor = '#FF7070';
	R['I'].shapelyColor = '#80FFFF';
	R['C'].shapelyColor = '#FF8C4B';
	R['T'].shapelyColor = '#A0FFA0';
	R['U'].shapelyColor = '#FF8080';

	return R;

})();
//
//  Copyright 2006-2010 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//


(function(structures){
	/* Creates a new Queue. A Queue is a first-in-first-out (FIFO) data structure.
	 * Functions of the Queue object allow elements to be enqueued and dequeued, the
	 * first element to be obtained without dequeuing, and for the current size of
	 * the Queue and empty/non-empty status to be obtained.
	 */
	structures.Queue = function() {

		// the list of elements, initialised to the empty array
		var queue = [];

		// the amount of space at the front of the queue, initialised to zero
		var queueSpace = 0;

		/*
		 * Returns the size of this Queue. The size of a Queue is equal to the
		 * number of elements that have been enqueued minus the number of elements
		 * that have been dequeued.
		 */
		this.getSize = function() {

			// return the number of elements in the queue
			return queue.length - queueSpace;

		};

		/*
		 * Returns true if this Queue is empty, and false otherwise. A Queue is
		 * empty if the number of elements that have been enqueued equals the number
		 * of elements that have been dequeued.
		 */
		this.isEmpty = function() {
			// return true if the queue is empty, and false otherwise
			return (queue.length == 0);
		};

		/*
		 * Enqueues the specified element in this Queue. The parameter is:
		 *
		 * element - the element to enqueue
		 */
		this.enqueue = function(element) {
			queue.push(element);
		};

		/*
		 * Dequeues an element from this Queue. The oldest element in this Queue is
		 * removed and returned. If this Queue is empty then undefined is returned.
		 */
		this.dequeue = function() {

			// initialise the element to return to be undefined
			var element = undefined;

			// check whether the queue is empty
			if (queue.length) {

				// fetch the oldest element in the queue
				element = queue[queueSpace];

				// update the amount of space and check whether a shift should occur
				if (++queueSpace * 2 >= queue.length)
				{
					// set the queue equal to the non-empty portion of the queue
					queue = queue.slice(queueSpace);

					// reset the amount of space at the front of the queue
					queueSpace = 0;
				}
			}

			// return the removed element
			return element;
		};

		/*
		 * Returns the oldest element in this Queue. If this Queue is empty then
		 * undefined is returned. This function returns the same value as the
		 * dequeue function, but does not remove the returned element from this
		 * Queue.
		 */
		this.getOldestElement = function() {

			// initialise the element to return to be undefined
			var element = undefined;

			// if the queue is not element then fetch the oldest element in the
			// queue
			if (queue.length)
				element = queue[queueSpace];

			// return the oldest element
			return element;
		};
	};
})(ChemDoodle.structures);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(structures, m) {

	structures.Point = function(x, y) {
		this.x = x ? x : 0;
		this.y = y ? y : 0;
		this.sub = function(p) {
			this.x -= p.x;
			this.y -= p.y;
		};
		this.add = function(p) {
			this.x += p.x;
			this.y += p.y;
		};
		this.distance = function(p) {
			return m.sqrt(m.pow(p.x - this.x, 2) + m.pow(p.y - this.y, 2));
		};
		this.angleForStupidCanvasArcs = function(p) {
			var dx = p.x - this.x;
			var dy = p.y - this.y;
			var angle = 0;
			// Calculate angle
			if (dx == 0) {
				if (dy == 0) {
					angle = 0;
				} else if (dy > 0) {
					angle = m.PI / 2;
				} else {
					angle = 3 * m.PI / 2;
				}
			} else if (dy == 0) {
				if (dx > 0) {
					angle = 0;
				} else {
					angle = m.PI;
				}
			} else {
				if (dx < 0) {
					angle = m.atan(dy / dx) + m.PI;
				} else if (dy < 0) {
					angle = m.atan(dy / dx) + 2 * m.PI;
				} else {
					angle = m.atan(dy / dx);
				}
			}
			while (angle < 0) {
				angle += m.PI * 2;
			}
			angle = angle % (m.PI * 2);
			return angle;
		};
		this.angle = function(p) {
			// y is upside down to account for inverted canvas
			var dx = p.x - this.x;
			var dy = this.y - p.y;
			var angle = 0;
			// Calculate angle
			if (dx == 0) {
				if (dy == 0) {
					angle = 0;
				} else if (dy > 0) {
					angle = m.PI / 2;
				} else {
					angle = 3 * m.PI / 2;
				}
			} else if (dy == 0) {
				if (dx > 0) {
					angle = 0;
				} else {
					angle = m.PI;
				}
			} else {
				if (dx < 0) {
					angle = m.atan(dy / dx) + m.PI;
				} else if (dy < 0) {
					angle = m.atan(dy / dx) + 2 * m.PI;
				} else {
					angle = m.atan(dy / dx);
				}
			}
			while (angle < 0) {
				angle += m.PI * 2;
			}
			angle = angle % (m.PI * 2);
			return angle;
		};
		return true;
	};

})(ChemDoodle.structures, Math);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3160 $
//  $Author: kevin $
//  $LastChangedDate: 2011-03-12 18:27:31 -0500 (Sat, 12 Mar 2011) $
//
(function(ELEMENT, extensions, structures, m, m4) {

	structures.Atom = function(label, x, y, z)
	{
		this.x = x ? x : 0;
		this.y = y ? y : 0;
		this.z = z ? z : 0;
		this.charge = 0;
		this.mass = -1;
		this.coordinationNumber = 0;
		this.bondNumber = 0;
		this.angleOfLeastInterference = 0;
		this.isHidden = false;
		this.label = label ? label.replace(/\s/g, '') : 'C';
		if (!ELEMENT[this.label]) {
			this.label = 'C';
		}
		this.isLone = false;
		this.isHover = false;
		this.isSelected = false;
		this.add3D = function(p)
		{
			this.x += p.x;
			this.y += p.y;
			this.z += p.z;
		};
		this.sub3D = function(p)
		{
			this.x -= p.x;
			this.y -= p.y;
			this.z -= p.z;
		};
		this.distance3D = function(p)
		{
			return m.sqrt(m.pow(p.x - this.x, 2) + m.pow(p.y - this.y, 2) + m.pow(p.z - this.z, 2));
		};
		this.draw = function(ctx, specs)
		{
			var font = specs.getFontString(specs.atoms_font_size_2D, specs.atoms_font_families_2D, specs.atoms_font_bold_2D, specs.atoms_font_italic_2D);
			ctx.font = font;
			ctx.fillStyle = specs.atoms_color;

	// ======= For atom rotation =======
			ctx.save();
			ctx.translate(this.x, this.y);
			ctx.rotate(-specs.rotateAngle);
			ctx.translate(-this.x, -this.y);
	// ==================================
			if (specs.atoms_useJMOLColors)
			{
				ctx.fillStyle = ELEMENT[this.label].jmolColor;
			}
			if (this.isLone || specs.atoms_circles_2D)
			{
				ctx.beginPath();
				ctx.arc(this.x, this.y, specs.atoms_circleDiameter_2D / 2, 0, m.PI * 2, false);
				ctx.fill();
				if (specs.atoms_circleBorderWidth_2D > 0)
				{
					ctx.lineWidth = specs.atoms_circleBorderWidth_2D;
					ctx.strokeStyle = 'black';
					ctx.stroke(this.x, this.y, 0, m.PI * 2, specs.atoms_circleDiameter_2D / 2);
				}
			}
			else if (this.isLabelVisible(specs))
			{
				ctx.textAlign = 'center';
				ctx.textBaseline = 'middle';
				ctx.fillText(this.label, this.x, this.y);
				if (this.mass != -1)
				{
					var symbolWidth = ctx.measureText(this.label).width;
					var subFont = specs.getFontString(specs.atoms_font_size_2D * .7, specs.atoms_font_families_2D, specs.atoms_font_bold_2D, specs.atoms_font_italic_2D);
					var fontSave = ctx.font;
					ctx.font = subFont;
					var massWidth = ctx.measureText(this.mass).width;
					ctx.fillText(this.mass, this.x - massWidth - .5, this.y - specs.atoms_font_size_2D * .3);
					ctx.font = fontSave;
				}
				// implicit hydrogens
				var numHs = this.getImplicitHydrogenCount();
				if (specs.atoms_implicitHydrogens_2D && numHs > 0)
				{
					var symbolWidth = ctx.measureText(this.label).width;
					var hWidth = ctx.measureText('H').width;
					if (numHs > 1) {
						var xoffset = symbolWidth / 2 + hWidth / 2;
						var yoffset = 0;
						var subFont = specs.getFontString(specs.atoms_font_size_2D * .8, specs.atoms_font_families_2D, specs.atoms_font_bold_2D, specs.atoms_font_italic_2D);
						ctx.font = subFont;
						var numWidth = ctx.measureText(numHs).width;
						if (this.bondNumber == 1) {
							if (this.angleOfLeastInterference > m.PI / 2 && this.angleOfLeastInterference < 3 * m.PI / 2) {
								xoffset = -symbolWidth / 2 - numWidth - hWidth / 2;
							}
						}
						else
						{
							if (this.angleOfLeastInterference <= m.PI / 4) {
								// default
							} else if (this.angleOfLeastInterference < 3 * m.PI / 4) {
								xoffset = 0;
								yoffset = -specs.atoms_font_size_2D * .9;
							} else if (this.angleOfLeastInterference <= 5 * m.PI / 4) {
								xoffset = -symbolWidth / 2 - numWidth - hWidth / 2;
							} else if (this.angleOfLeastInterference < 7 * m.PI / 4) {
								xoffset = 0;
								yoffset = specs.atoms_font_size_2D * .9;
							}
						}
						ctx.font = font;
						ctx.fillText('H', this.x + xoffset, this.y + yoffset);
						ctx.font = subFont;
						ctx.fillText(numHs, this.x + xoffset + hWidth / 2 + numWidth / 2, this.y + yoffset + specs.atoms_font_size_2D * .3);
					}
					else
					{
						var xoffset = symbolWidth / 2 + hWidth / 2;
						var yoffset = 0;
						if (this.bondNumber == 1)
						{
							if (this.angleOfLeastInterference > m.PI / 2 && this.angleOfLeastInterference < 3 * m.PI / 2) {
								xoffset = -symbolWidth / 2 - hWidth / 2;
							}
						}
						else
						{
							if (this.angleOfLeastInterference <= m.PI / 4)
							{
								// default
							}
							else if (this.angleOfLeastInterference < 3 * m.PI / 4)
							{
								xoffset = 0;
								yoffset = -specs.atoms_font_size_2D * .9;
							}
							else if (this.angleOfLeastInterference <= 5 * m.PI / 4)
							{
								xoffset = -symbolWidth / 2 - hWidth / 2;
							}
							else if (this.angleOfLeastInterference < 7 * m.PI / 4)
							{
								xoffset = 0;
								yoffset = specs.atoms_font_size_2D * .9;
							}
						}
						ctx.fillText('H', this.x + xoffset, this.y + yoffset);
					}
				}
			}
			if (this.charge != null && this.charge != 0) {
				var s = this.charge.toFixed(0);
				if (s == '1') {
					s = '+';
				}
				else if (s == '-1') {
					s = '\u2013';
				}
				else if (extensions.stringStartsWith(s, '-')) {
					s = s.substring(1) + '\u2013';
				}
				else {
					s += '+';
				}
				var angleUse = this.angleOfLeastInterference;
				var distanceUse = specs.atoms_font_size_2D;
				if (this.isLabelVisible(specs) && numHs > 0) {
					angleUse += m.PI / 4;
				}
				ctx.textAlign = 'center';
				ctx.textBaseline = 'middle';
				ctx.fillText(s, this.x + distanceUse * m.cos(angleUse), this.y - distanceUse * m.sin(angleUse));
			}
		// ======= For atom rotation ========
			ctx.restore();
		// ==================================
		};
		this.drawDecorations = function(ctx) {
			if (this.isHover || this.isSelected) {
				ctx.strokeStyle = this.isHover ? '#885110' : '#0060B2';
				ctx.lineWidth = 1.2;
				ctx.beginPath();
				var radius = this.isHover ? 7 : 15;
				ctx.arc(this.x, this.y, radius, 0, m.PI * 2, false);
				ctx.stroke();
			}
		};
		this.render = function(gl, specs) {
			var transform = m4.translate(gl.modelViewMatrix, [ this.x, this.y, this.z ], []);
			var radius = specs.atoms_useVDWDiameters_3D ? ELEMENT[this.label].vdWRadius*specs.atoms_vdwMultiplier_3D : specs.atoms_sphereDiameter_3D / 2;
			m4.scale(transform, [ radius, radius, radius ]);
			// colors
			var color = specs.atoms_useJMOLColors ? ELEMENT[this.label].jmolColor : specs.atoms_color;
			gl.material.setDiffuseColor(gl, color);
			// render
			gl.setMatrixUniforms(transform);
			gl.drawElements(gl.TRIANGLES, gl.sphereBuffer.vertexIndexBuffer.numItems, gl.UNSIGNED_SHORT, 0);
		};
		this.isLabelVisible = function(specs)
		{
			return this.label != 'C' || this.mass != -1 || (this.isHidden && specs.atoms_showHiddenCarbons_2D) || (specs.atoms_displayTerminalCarbonLabels_2D && this.bondNumber == 1);
		};
		this.getImplicitHydrogenCount = function() {
			if (this.label == 'H' || ELEMENT[this.label] == null) {
				return 0;
			}
			var valence = ELEMENT[this.label].valency;
			var dif = valence - this.coordinationNumber;
			if(this.charge>0){
				var vdif = 4-valence;
				if(this.charge<=vdif){
					dif+=this.charge;
				}else{
					dif = 4-this.coordinationNumber-this.charge+vdif;
				}
			}else{
				dif+=this.charge;
			}
			return dif < 0 ? 0 : dif;
		};
		return true;
	};
	structures.Atom.prototype = new structures.Point(0, 0);

})(ChemDoodle.ELEMENT, ChemDoodle.extensions, ChemDoodle.structures, Math, mat4);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3160 $
//  $Author: kevin $
//  $LastChangedDate: 2011-03-12 18:27:31 -0500 (Sat, 12 Mar 2011) $
//
(function(ELEMENT, extensions, structures, m, m4, v3)
{
	structures.Bond = function(a1, a2, bondOrder)
	{
		this.a1 = a1;
		this.a2 = a2;
		this.bondOrder = bondOrder ? bondOrder : 1;
		this.stereo = structures.Bond.STEREO_NONE;
		this.isHover = false;
		this.ring = null;
		this.getCenter = function() {
			return new structures.Point((this.a1.x + this.a2.x) / 2, (this.a1.y + this.a2.y) / 2);
		};
		this.getLength = function() {
			return this.a1.distance(this.a2);
		};
		this.getLength3D = function() {
			return this.a1.distance3D(this.a2);
		};
		this.contains = function(a) {
			return a == this.a1 || a == this.a2;
		};
		this.getNeighbor = function(a) {
			if (a == this.a1) {
				return this.a2;
			} else if (a == this.a2) {
				return this.a1;
			}
			return null;
		};
		this.draw = function(ctx, specs) {
			var x1 = this.a1.x;
			var x2 = this.a2.x;
			var y1 = this.a1.y;
			var y2 = this.a2.y;
			var difX = x2 - x1;
			var difY = y2 - y1;
			if (specs.atoms_display && !specs.atoms_circles_2D && this.a1.isLabelVisible(specs)) {
				x1 += difX * specs.bonds_atomLabelBuffer_2D;
				y1 += difY * specs.bonds_atomLabelBuffer_2D;
			}
			if (specs.atoms_display && !specs.atoms_circles_2D && this.a2.isLabelVisible(specs)) {
				x2 -= difX * specs.bonds_atomLabelBuffer_2D;
				y2 -= difY * specs.bonds_atomLabelBuffer_2D;
			}
			if (specs.bonds_clearOverlaps_2D) {
				var xs = x1 + difX * .15;
				var ys = y1 + difY * .15;
				var xf = x2 - difX * .15;
				var yf = y2 - difY * .15;
				ctx.strokeStyle = specs.backgroundColor;
				ctx.lineWidth = specs.bonds_width_2D + specs.bonds_overlapClearWidth_2D * 2;
				ctx.lineCap = 'round';
				ctx.beginPath();
				ctx.moveTo(xs, ys);
				ctx.lineTo(xf, yf);
				ctx.closePath();
				ctx.stroke();
			}
			ctx.strokeStyle = specs.bonds_color;
			ctx.fillStyle = specs.bonds_color;
			ctx.lineWidth = specs.bonds_width_2D;
			ctx.lineCap = specs.bonds_ends_2D;
			if (specs.bonds_useJMOLColors) {
				var linearGradient = ctx.createLinearGradient(x1, y1, x2, y2);
				linearGradient.addColorStop(0, ELEMENT[this.a1.label].jmolColor);
				linearGradient.addColorStop(1, ELEMENT[this.a2.label].jmolColor);
				ctx.strokeStyle = linearGradient;
				ctx.fillStyle = linearGradient;
			}
			switch (this.bondOrder) {
			case 1:
				if (this.stereo == structures.Bond.STEREO_PROTRUDING || this.stereo == structures.Bond.STEREO_RECESSED) {
					var thinSpread = specs.bonds_width_2D / 2;
					var useDist = this.a1.distance(this.a2) * specs.bonds_wedgeThickness_2D / 2;
					var perpendicular = this.a1.angle(this.a2) + m.PI / 2;
					var mcosp = m.cos(perpendicular);
					var msinp = m.sin(perpendicular);
					var cx1 = x1 - mcosp * thinSpread;
					var cy1 = y1 + msinp * thinSpread;
					var cx2 = x1 + mcosp * thinSpread;
					var cy2 = y1 - msinp * thinSpread;
					var cx3 = x2 + mcosp * useDist;
					var cy3 = y2 - msinp * useDist;
					var cx4 = x2 - mcosp * useDist;
					var cy4 = y2 + msinp * useDist;
					ctx.beginPath();
					ctx.moveTo(cx1, cy1);
					ctx.lineTo(cx2, cy2);
					ctx.lineTo(cx3, cy3);
					ctx.lineTo(cx4, cy4);
					ctx.closePath();
					if (this.stereo == structures.Bond.STEREO_PROTRUDING) {
						ctx.fill();
					} else {
						ctx.save();
						ctx.clip();
						ctx.beginPath();
						ctx.moveTo(x1, y1);
						ctx.lineWidth = useDist * 2;
						ctx.lineCap = 'butt';
						var travelled = 0;
						var dist = this.a1.distance(this.a2);
						var space = false;
						var lastX = x1;
						var lastY = y1;
						while (travelled < dist) {
							if (space) {
								var percent = specs.bonds_hashSpacing_2D / dist;
								lastX += percent * difX;
								lastY += percent * difY;
								ctx.moveTo(lastX, lastY);
								travelled += specs.bonds_hashSpacing_2D;
							} else {
								var percent = specs.bonds_hashWidth_2D / dist;
								lastX += percent * difX;
								lastY += percent * difY;
								ctx.lineTo(lastX, lastY);
								travelled += specs.bonds_hashWidth_2D;
							}
							space = !space;
						}
						ctx.stroke();
						ctx.restore();
					}
				} else {
					ctx.beginPath();
					ctx.moveTo(x1, y1);
					ctx.lineTo(x2, y2);
					ctx.stroke();
				}
				break;
			case 1.5:
				ctx.beginPath();
				ctx.moveTo(x1, y1);
				ctx.lineTo(x2, y2);
				ctx.stroke();
				break;
			case 2:
				if (this.stereo == structures.Bond.STEREO_AMBIGUOUS) {
					var useDist = this.a1.distance(this.a2) * specs.bonds_saturationWidth_2D / 2;
					var perpendicular = this.a1.angle(this.a2) + m.PI / 2;
					var cx1 = x1 - m.cos(perpendicular) * useDist;
					var cy1 = y1 + m.sin(perpendicular) * useDist;
					var cx2 = x1 + m.cos(perpendicular) * useDist;
					var cy2 = y1 - m.sin(perpendicular) * useDist;
					var cx3 = x2 + m.cos(perpendicular) * useDist;
					var cy3 = y2 - m.sin(perpendicular) * useDist;
					var cx4 = x2 - m.cos(perpendicular) * useDist;
					var cy4 = y2 + m.sin(perpendicular) * useDist;
					ctx.beginPath();
					ctx.moveTo(cx1, cy1);
					ctx.lineTo(cx3, cy3);
					ctx.moveTo(cx2, cy2);
					ctx.lineTo(cx4, cy4);
					ctx.stroke();
				} else if (!specs.bonds_symmetrical_2D && (this.ring != null || this.a1.label == 'C' && this.a2.label == 'C')) {
					ctx.beginPath();
					ctx.moveTo(x1, y1);
					ctx.lineTo(x2, y2);
					var clip = 0;
					var dist = this.a1.distance(this.a2);
					var angle = this.a1.angle(this.a2);
					var perpendicular = angle + m.PI / 2;
					var useDist = dist * specs.bonds_saturationWidth_2D;
					var clipAngle = specs.bonds_saturationAngle_2D;
					if (clipAngle < m.PI / 2) {
						clip = -(useDist / m.tan(clipAngle));
					}
					if (m.abs(clip) < dist / 2) {
						var xuse1 = x1 - m.cos(angle) * clip;
						var xuse2 = x2 + m.cos(angle) * clip;
						var yuse1 = y1 + m.sin(angle) * clip;
						var yuse2 = y2 - m.sin(angle) * clip;
						var cx1 = xuse1 - m.cos(perpendicular) * useDist;
						var cy1 = yuse1 + m.sin(perpendicular) * useDist;
						var cx2 = xuse1 + m.cos(perpendicular) * useDist;
						var cy2 = yuse1 - m.sin(perpendicular) * useDist;
						var cx3 = xuse2 - m.cos(perpendicular) * useDist;
						var cy3 = yuse2 + m.sin(perpendicular) * useDist;
						var cx4 = xuse2 + m.cos(perpendicular) * useDist;
						var cy4 = yuse2 - m.sin(perpendicular) * useDist;
						var flip = this.ring == null || (this.ring.center.angle(this.a1) > this.ring.center.angle(this.a2) && !(this.ring.center.angle(this.a1) - this.ring.center.angle(this.a2) > m.PI) || (this.ring.center.angle(this.a1) - this.ring.center.angle(this.a2) < -m.PI));
						if (flip) {
							ctx.moveTo(cx1, cy1);
							ctx.lineTo(cx3, cy3);
						} else {
							ctx.moveTo(cx2, cy2);
							ctx.lineTo(cx4, cy4);
						}
						ctx.stroke();
					}
				} else {
					var useDist = this.a1.distance(this.a2) * specs.bonds_saturationWidth_2D / 2;
					var perpendicular = this.a1.angle(this.a2) + m.PI / 2;
					var cx1 = x1 - m.cos(perpendicular) * useDist;
					var cy1 = y1 + m.sin(perpendicular) * useDist;
					var cx2 = x1 + m.cos(perpendicular) * useDist;
					var cy2 = y1 - m.sin(perpendicular) * useDist;
					var cx3 = x2 + m.cos(perpendicular) * useDist;
					var cy3 = y2 - m.sin(perpendicular) * useDist;
					var cx4 = x2 - m.cos(perpendicular) * useDist;
					var cy4 = y2 + m.sin(perpendicular) * useDist;
					ctx.beginPath();
					ctx.moveTo(cx1, cy1);
					ctx.lineTo(cx4, cy4);
					ctx.moveTo(cx2, cy2);
					ctx.lineTo(cx3, cy3);
					ctx.stroke();
				}
				break;
			case 3:
				var useDist = this.a1.distance(this.a2) * specs.bonds_saturationWidth_2D;
				var perpendicular = this.a1.angle(this.a2) + m.PI / 2;
				var cx1 = x1 - m.cos(perpendicular) * useDist;
				var cy1 = y1 + m.sin(perpendicular) * useDist;
				var cx2 = x1 + m.cos(perpendicular) * useDist;
				var cy2 = y1 - m.sin(perpendicular) * useDist;
				var cx3 = x2 + m.cos(perpendicular) * useDist;
				var cy3 = y2 - m.sin(perpendicular) * useDist;
				var cx4 = x2 - m.cos(perpendicular) * useDist;
				var cy4 = y2 + m.sin(perpendicular) * useDist;
				ctx.beginPath();
				ctx.moveTo(cx1, cy1);
				ctx.lineTo(cx4, cy4);
				ctx.moveTo(cx2, cy2);
				ctx.lineTo(cx3, cy3);
				ctx.moveTo(x1, y1);
				ctx.lineTo(x2, y2);
				ctx.stroke();
				break;
			}
		};
		this.drawDecorations = function(ctx) {
			if (this.isHover || this.isSelected) {
				var pi2 = 2 * m.PI;
				var angle = (this.a1.angleForStupidCanvasArcs(this.a2) + m.PI / 2) % pi2;
				ctx.strokeStyle = this.isHover ? '#885110' : '#0060B2';
				ctx.lineWidth = 1.2;
				ctx.beginPath();
				var angleTo = (angle + m.PI) % pi2;
				angleTo = angleTo % (m.PI * 2);
				ctx.arc(this.a1.x, this.a1.y, 7, angle, angleTo, false);
				ctx.stroke();
				ctx.beginPath();
				angle += m.PI;
				angleTo = (angle + m.PI) % pi2;
				ctx.arc(this.a2.x, this.a2.y, 7, angle, angleTo, false);
				ctx.stroke();
			}
		};
		this.render = function(gl, specs)
		{
			// this is the elongation vector for the cylinder
			var height = 1.001 * this.a1.distance3D(this.a2) / (specs.bonds_useJMOLColors ? 2 : 1);
			if (height == 0) {
				// if there is no height, then no point in rendering this bond,
				// just return
				return false;
			}
			var scaleVector = [ specs.bonds_cylinderDiameter_3D / 2, height, specs.bonds_cylinderDiameter_3D / 2 ];
			// transform to the atom as well as the opposite atom (for JMol
			// color splits)
			var transform = m4.translate(gl.modelViewMatrix, [ this.a1.x, this.a1.y, this.a1.z ], []);
			var transformOpposite = null;
			// align bond
			var a2b = [ this.a2.x - this.a1.x, this.a2.y - this.a1.y, this.a2.z - this.a1.z ];
			if (specs.bonds_useJMOLColors) {
				v3.scale(a2b, .5);
				transformOpposite = m4.translate(gl.modelViewMatrix, [ this.a2.x, this.a2.y, this.a2.z ], []);
			}
			// calculate the translations for unsaturated bonds
			var others = [ 0 ];
			var saturatedCross = null;
			if (specs.bonds_showBondOrders_3D) {
				switch (this.bondOrder) {
				case 2:
					others = [ -specs.bonds_cylinderDiameter_3D, specs.bonds_cylinderDiameter_3D ];
					break;
				case 3:
					others = [ -1.2 * specs.bonds_cylinderDiameter_3D, 0, 1.2 * specs.bonds_cylinderDiameter_3D ];
					break;
				}
				if (others.length > 1) {
					var z = [ 0, 0, 1 ];
					var inverse = m4.inverse(gl.rotationMatrix, []);
					m4.multiplyVec3(inverse, z);
					saturatedCross = v3.cross(a2b, z, []);
					v3.normalize(saturatedCross);
				}
			}
			// calculate the rotation
			var y = [ 0, 1, 0 ];
			var ang = 0;
			var axis = null;
			if (this.a1.x == this.a2.x && this.a1.z == this.a2.z) {
				axis = [ 0, 0, 1 ];
				if (this.a2.y < this.a1.y) {
					ang = m.PI;
				}
			} else {
				ang = extensions.vec3AngleFrom(y, a2b);
				axis = v3.cross(y, a2b, []);
			}
			// render bonds
			for ( var i = 0, ii = others.length; i < ii; i++) {
				var transformUse = m4.set(transform, []);
				if (others[i] != 0) {
					m4.translate(transformUse, v3.scale(saturatedCross, others[i], []));
				}
				if (ang != 0) {
					m4.rotate(transformUse, ang, axis);
				}
				m4.scale(transformUse, scaleVector);
				// colors
				var color = specs.bonds_useJMOLColors ? ELEMENT[this.a1.label].jmolColor : specs.bonds_color;
				gl.material.setDiffuseColor(gl, color);
				// render
				gl.setMatrixUniforms(transformUse);
				gl.drawArrays(gl.TRIANGLE_STRIP, 0, gl.cylinderBuffer.vertexPositionBuffer.numItems);
				if (specs.bonds_useJMOLColors) {
					m4.set(transformOpposite, transformUse);
					if (others[i] != 0) {
						m4.translate(transformUse, v3.scale(saturatedCross, others[i], []));
					}
					// don't check for 0 here as that means it should be rotated
					// by PI, but PI will be negated
					m4.rotate(transformUse, ang + m.PI, axis);
					m4.scale(transformUse, scaleVector);
					// colors
					gl.material.setDiffuseColor(gl, ELEMENT[this.a2.label].jmolColor);
					// render
					gl.setMatrixUniforms(transformUse);
					gl.drawArrays(gl.TRIANGLE_STRIP, 0, gl.cylinderBuffer.vertexPositionBuffer.numItems);
				}
			}
		};
		return true;
	};
	structures.Bond.STEREO_NONE = 'none';
	structures.Bond.STEREO_PROTRUDING = 'protruding';
	structures.Bond.STEREO_RECESSED = 'recessed';
	structures.Bond.STEREO_AMBIGUOUS = 'ambiguous';

})(ChemDoodle.ELEMENT, ChemDoodle.extensions, ChemDoodle.structures, Math, mat4, vec3);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(structures, m) {
	structures.Ring = function()
	{
		this.atoms = [];
		this.bonds = [];
		this.center = null;
		this.setupBonds = function()
		{
			for ( var i = 0, ii = this.bonds.length; i < ii; i++)
			{
				this.bonds[i].ring = this;
			}
			this.center = this.getCenter();
		};
		this.getCenter = function()
		{
			var minX = minY = Infinity;
			var maxX = maxY = -Infinity;
			for ( var i = 0, ii = this.atoms.length; i < ii; i++)
			{
				minX = m.min(this.atoms[i].x, minX);
				minY = m.min(this.atoms[i].y, minY);
				maxX = m.max(this.atoms[i].x, maxX);
				maxY = m.max(this.atoms[i].y, maxY);
			}
			return new structures.Point((maxX + minX) / 2, (maxY + minY) / 2);
		};
		return true;
	};
})(ChemDoodle.structures, Math);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3149 $
//  $Author: kevin $
//  $LastChangedDate: 2011-03-04 07:17:59 -0500 (Fri, 04 Mar 2011) $
//
(function(c, structures, m) {
	structures.Molecule = function()
	{
		this.atoms = [];
		this.bonds = [];
		this.rings = [];
		// this can be an extensive algorithm for large molecules, you may want
		// to turn this off
		this.findRings = true;
		this.draw = function(ctx, specs)
		{
			// draw
			if (specs.bonds_display)
			{
				for ( var i = 0, ii = this.bonds.length; i < ii; i++)
				{
					this.bonds[i].draw(ctx, specs);
				}
			}
			if (specs.atoms_display)
			{
				for ( var i = 0, ii = this.atoms.length; i < ii; i++)
				{
					this.atoms[i].draw(ctx, specs);
				}
			}
		};
		this.render = function(gl, specs)
		{
			if (specs.bonds_display) {
				if (this.bonds.length > 0) {
					// positions
					gl.bindBuffer(gl.ARRAY_BUFFER, gl.cylinderBuffer.vertexPositionBuffer);
					gl.vertexAttribPointer(gl.shader.vertexPositionAttribute, gl.cylinderBuffer.vertexPositionBuffer.itemSize, gl.FLOAT, false, 0, 0);
					// normals
					gl.bindBuffer(gl.ARRAY_BUFFER, gl.cylinderBuffer.vertexNormalBuffer);
					gl.vertexAttribPointer(gl.shader.vertexNormalAttribute, gl.cylinderBuffer.vertexNormalBuffer.itemSize, gl.FLOAT, false, 0, 0);
					//colors
					gl.material.setTempColors(gl, specs.bonds_materialAmbientColor_3D, null, specs.bonds_materialSpecularColor_3D, specs.bonds_materialShininess_3D);
				}
				for ( var i = 0, ii = this.bonds.length; i < ii; i++) {
					this.bonds[i].render(gl, specs);
				}
			}
			if (specs.atoms_display) {
				if (this.atoms.length > 0) {
					// positions
					gl.bindBuffer(gl.ARRAY_BUFFER, gl.sphereBuffer.vertexPositionBuffer);
					gl.vertexAttribPointer(gl.shader.vertexPositionAttribute, gl.sphereBuffer.vertexPositionBuffer.itemSize, gl.FLOAT, false, 0, 0);
					// normals
					gl.bindBuffer(gl.ARRAY_BUFFER, gl.sphereBuffer.vertexNormalBuffer);
					gl.vertexAttribPointer(gl.shader.vertexNormalAttribute, gl.sphereBuffer.vertexNormalBuffer.itemSize, gl.FLOAT, false, 0, 0);
					// indexes
					gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, gl.sphereBuffer.vertexIndexBuffer);
					// colors
					gl.material.setTempColors(gl, specs.atoms_materialAmbientColor_3D, null, specs.atoms_materialSpecularColor_3D, specs.atoms_materialShininess_3D);
				}
				for ( var i = 0, ii = this.atoms.length; i < ii; i++) {
					this.atoms[i].render(gl, specs);
				}
			}
			if (specs.ribbons_display && this.chains) {
				//set up the model view matrix, since it won't be modified for ribbons
				gl.setMatrixUniforms(gl.modelViewMatrix);
				// colors
				gl.material.setTempColors(gl, specs.ribbons_materialAmbientColor_3D, null, specs.ribbons_materialSpecularColor_3D, specs.bonds_materialShininess_3D);
				for ( var j = 0, jj = this.chains.length; j < jj; j++) {
					if (specs.ribbons_useShapelyColors||specs.ribbons_useAminoColors) {
						var use = specs.ribbons_cartoonize ? this.cartoons[j] : this.ribbons[j];
						// positions
						gl.bindBuffer(gl.ARRAY_BUFFER, use.front.vertexPositionBuffer);
						gl.vertexAttribPointer(gl.shader.vertexPositionAttribute, use.front.vertexPositionBuffer.itemSize, gl.FLOAT, false, 0, 0);
						// normals
						gl.bindBuffer(gl.ARRAY_BUFFER, use.front.vertexNormalBuffer);
						gl.vertexAttribPointer(gl.shader.vertexNormalAttribute, use.front.vertexNormalBuffer.itemSize, gl.FLOAT, false, 0, 0);
						for ( var i = 0, ii = use.front.segments.length; i < ii; i++) {
							use.front.segments[i].render(gl, specs);
						}
						// positions
						gl.bindBuffer(gl.ARRAY_BUFFER, use.back.vertexPositionBuffer);
						gl.vertexAttribPointer(gl.shader.vertexPositionAttribute, use.back.vertexPositionBuffer.itemSize, gl.FLOAT, false, 0, 0);
						// normals
						gl.bindBuffer(gl.ARRAY_BUFFER, use.back.vertexNormalBuffer);
						gl.vertexAttribPointer(gl.shader.vertexNormalAttribute, use.back.vertexNormalBuffer.itemSize, gl.FLOAT, false, 0, 0);
						for ( var i = 0, ii = use.back.segments.length; i < ii; i++) {
							use.back.segments[i].render(gl, specs);
						}
					} else {
						if (specs.ribbons_cartoonize) {
							var use = this.cartoons[j];
							// positions
							gl.bindBuffer(gl.ARRAY_BUFFER, use.front.vertexPositionBuffer);
							gl.vertexAttribPointer(gl.shader.vertexPositionAttribute, use.front.vertexPositionBuffer.itemSize, gl.FLOAT, false, 0, 0);
							// normals
							gl.bindBuffer(gl.ARRAY_BUFFER, use.front.vertexNormalBuffer);
							gl.vertexAttribPointer(gl.shader.vertexNormalAttribute, use.front.vertexNormalBuffer.itemSize, gl.FLOAT, false, 0, 0);
							for ( var i = 0, ii = use.front.cartoonSegments.length; i < ii; i++) {
								use.front.cartoonSegments[i].render(gl, specs);
							}
							// positions
							gl.bindBuffer(gl.ARRAY_BUFFER, use.back.vertexPositionBuffer);
							gl.vertexAttribPointer(gl.shader.vertexPositionAttribute, use.back.vertexPositionBuffer.itemSize, gl.FLOAT, false, 0, 0);
							// normals
							gl.bindBuffer(gl.ARRAY_BUFFER, use.back.vertexNormalBuffer);
							gl.vertexAttribPointer(gl.shader.vertexNormalAttribute, use.back.vertexNormalBuffer.itemSize, gl.FLOAT, false, 0, 0);
							for ( var i = 0, ii = use.back.cartoonSegments.length; i < ii; i++) {
								use.back.cartoonSegments[i].render(gl, specs);
							}
						} else {
							var use = this.ribbons[j];
							use.front.render(gl, specs);
							use.back.render(gl, specs);
						}
					}
				}
			}
		};
		this.getCenter3D = function()
		{
			if (this.atoms.length == 1)
			{
				return new structures.Atom('C', this.atoms[0].x, this.atoms[0].y, this.atoms[0].z);
			}
			var minX = minY = minZ = Infinity;
			var maxX = maxY = maxZ = -Infinity;
			if(this.atoms.length==0 && this.chains.length>0)
			{
				//only ribbons
				for(var i = 0, ii = this.chains.length; i<ii; i++){
					var chain = this.chains[i];
					for(var j = 0, jj = chain.length; j<jj; j++){
						var residue = chain[j];
						minX = m.min(residue.alphaCarbon.x, minX);
						minY = m.min(residue.alphaCarbon.y, minY);
						minZ = m.min(residue.alphaCarbon.z, minZ);
						maxX = m.max(residue.alphaCarbon.x, maxX);
						maxY = m.max(residue.alphaCarbon.y, maxY);
						maxZ = m.max(residue.alphaCarbon.z, maxZ);
						minX = m.min(residue.carbonylOxygen.x, minX);
						minY = m.min(residue.carbonylOxygen.y, minY);
						minZ = m.min(residue.carbonylOxygen.z, minZ);
						maxX = m.max(residue.carbonylOxygen.x, maxX);
						maxY = m.max(residue.carbonylOxygen.y, maxY);
						maxZ = m.max(residue.carbonylOxygen.z, maxZ);
					}
				}
			}
			else
			{
				for ( var i = 0, ii = this.atoms.length; i < ii; i++)
				{
					minX = m.min(this.atoms[i].x, minX);
					minY = m.min(this.atoms[i].y, minY);
					minZ = m.min(this.atoms[i].z, minZ);
					maxX = m.max(this.atoms[i].x, maxX);
					maxY = m.max(this.atoms[i].y, maxY);
					maxZ = m.max(this.atoms[i].z, maxZ);
				}
			}
			return new structures.Atom('C', (maxX + minX) / 2, (maxY + minY) / 2, (maxZ + minZ) / 2);
		};
		this.getCenter = function()
		{
			if (this.atoms.length == 1)
			{
				return new structures.Point(this.atoms[0].x, this.atoms[0].y);
			}
			var minX = minY = Infinity;
			var maxX = maxY = -Infinity;
			for ( var i = 0, ii = this.atoms.length; i < ii; i++)
			{
				minX = m.min(this.atoms[i].x, minX);
				minY = m.min(this.atoms[i].y, minY);
				maxX = m.max(this.atoms[i].x, maxX);
				maxY = m.max(this.atoms[i].y, maxY);
			}
			return new structures.Point((maxX + minX) / 2, (maxY + minY) / 2);
		};
		this.getDimension = function()
		{
			if (this.atoms.length == 1)
			{
				return new structures.Point(0, 0);
			}
			var minX = minY = Infinity;
			var maxX = maxY = -Infinity;
			if(this.atoms.length==0 && this.chains.length>0){
				//only ribbons
				for(var i = 0, ii = this.chains.length; i<ii; i++){
					var chain = this.chains[i];
					for(var j = 0, jj = chain.length; j<jj; j++){
						var residue = chain[j];
						minX = m.min(residue.alphaCarbon.x, minX);
						minY = m.min(residue.alphaCarbon.y, minY);
						maxX = m.max(residue.alphaCarbon.x, maxX);
						maxY = m.max(residue.alphaCarbon.y, maxY);
						minX = m.min(residue.carbonylOxygen.x, minX);
						minY = m.min(residue.carbonylOxygen.y, minY);
						maxX = m.max(residue.carbonylOxygen.x, maxX);
						maxY = m.max(residue.carbonylOxygen.y, maxY);
					}
				}
			}
			else
			{
				for ( var i = 0, ii = this.atoms.length; i < ii; i++) {
					minX = m.min(this.atoms[i].x, minX);
					minY = m.min(this.atoms[i].y, minY);
					maxX = m.max(this.atoms[i].x, maxX);
					maxY = m.max(this.atoms[i].y, maxY);
				}
			}
			return new structures.Point(maxX - minX, maxY - minY);
		};
		this.check = function()
		{
			// find lones
			for ( var i = 0, ii = this.atoms.length; i < ii; i++) {
				this.atoms[i].isLone = false;
				if (this.atoms[i].label == 'C') {
					var counter = 0;
					for ( var j = 0, jj = this.bonds.length; j < jj; j++) {
						if (this.bonds[j].a1 == this.atoms[i] || this.bonds[j].a2 == this.atoms[i]) {
							counter++;
						}
					}
					if (counter == 0) {
						this.atoms[i].isLone = true;
					}
				}
			}
			if (this.findRings)
			{
				// find rings
				this.rings = new c.informatics.SSSRFinder(this).rings;
				for ( var i = 0, ii = this.bonds.length; i < ii; i++) {
					this.bonds[i].ring = null;
				}
				for ( var i = 0, ii = this.rings.length; i < ii; i++) {
					this.rings[i].setupBonds();
				}
			}
			// sort
			var sort = false;
			for ( var i = 0, ii = this.atoms.length; i < ii; i++) {
				if (this.atoms[i].z != 0) {
					sort = true;
				}
			}
			if (sort) {
				this.sortAtomsByZ();
				this.sortBondsByZ();
			}
			// setup metadata
			this.setupMetaData();
		};
		this.getAngles = function(a)
		{
			var angles = [];
			for ( var i = 0, ii = this.bonds.length; i < ii; i++) {
				if (this.bonds[i].contains(a)) {
					angles.push(a.angle(this.bonds[i].getNeighbor(a)));
				}
			}
			angles.sort();
			return angles;
		};
		this.getCoordinationNumber = function(bs)
		{
			var coordinationNumber = 0;
			for ( var i = 0, ii = bs.length; i < ii; i++) {
				coordinationNumber += bs[i].bondOrder;
			}
			return coordinationNumber;
		};
		this.getBonds = function(a)
		{
			var bonds = [];
			for ( var i = 0, ii = this.bonds.length; i < ii; i++) {
				if (this.bonds[i].contains(a)) {
					bonds.push(this.bonds[i]);
				}
			}
			return bonds;
		};
		this.sortAtomsByZ = function()
		{
			for ( var i = 1, ii = this.atoms.length; i < ii; i++) {
				var index = i;
				while (index > 0 && this.atoms[index].z < this.atoms[index - 1].z) {
					var hold = this.atoms[index];
					this.atoms[index] = this.atoms[index - 1];
					this.atoms[index - 1] = hold;
					index--;
				}
			}
		};
		this.sortBondsByZ = function()
		{
			for ( var i = 1, ii = this.bonds.length; i < ii; i++) {
				var index = i;
				while (index > 0 && (this.bonds[index].a1.z + this.bonds[index].a2.z) < (this.bonds[index - 1].a1.z + this.bonds[index - 1].a2.z)) {
					var hold = this.bonds[index];
					this.bonds[index] = this.bonds[index - 1];
					this.bonds[index - 1] = hold;
					index--;
				}
			}
		};
		this.setupMetaData = function()
		{
			for ( var i = 0, ii = this.atoms.length; i < ii; i++) {
				var a = this.atoms[i];
				var bonds = this.getBonds(a);
				var angles = this.getAngles(a);
				a.isHidden = bonds.length == 2 && m.abs(m.abs(angles[1] - angles[0]) - m.PI) < m.PI / 30 && bonds[0].bondOrder == bonds[1].bondOrder;
				a.angleOfLeastInterference = c.math.angleBetweenLargest(angles) % (m.PI * 2);
				a.coordinationNumber = this.getCoordinationNumber(bonds);
				a.bondNumber = bonds.length;
			}
		};
		this.scaleToAverageBondLength = function(length)
		{
			var avBondLength = this.getAverageBondLength();
			if (avBondLength != 0) {
				var scale = length / avBondLength;
				for ( var i = 0, ii = this.atoms.length; i < ii; i++) {
					this.atoms[i].x *= scale;
					this.atoms[i].y *= scale;
				}
			}
		};
		this.getAverageBondLength = function()
		{
			if (this.bonds.length == 0) {
				return 0;
			}
			var tot = 0;
			for ( var i = 0, ii = this.bonds.length; i < ii; i++) {
				tot += this.bonds[i].getLength();
			}
			tot /= this.bonds.length;
			return tot;
		};
		return true;
	};
})(ChemDoodle, ChemDoodle.structures, Math);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(structures, m, m4, v3)
{
	var Ns = 9;
	var N = 10;
	var S = [ 6 / m.pow(N, 3), 0, 0, 0, 6 / m.pow(N, 3), 2 / m.pow(N, 2), 0, 0, 1 / m.pow(N, 3), 1 / m.pow(N, 2), 1 / N, 0, 0, 0, 0, 1 ];
	var Bm = [ -1 / 6, 1 / 2, -1 / 2, 1 / 6, 1 / 2, -1, 1 / 2, 0, -1 / 2, 0, 1 / 2, 0, 1 / 6, 2 / 3, 1 / 6, 0 ];
	var SB = m4.multiply(Bm, S, []);

	structures.Residue = function(alphaCarbon) {
		this.alphaCarbon = alphaCarbon;
		this.setup = function(nextAlpha) {
			// define plane
			var A = [ nextAlpha.x - this.alphaCarbon.x, nextAlpha.y - this.alphaCarbon.y, nextAlpha.z - this.alphaCarbon.z ];
			var B = [ this.carbonylOxygen.x - this.alphaCarbon.x, this.carbonylOxygen.y - this.alphaCarbon.y, this.carbonylOxygen.z - this.alphaCarbon.z ];
			var C = v3.cross(A, B, []);
			this.D = v3.cross(C, A, []);
			v3.normalize(C);
			v3.normalize(this.D);
			// generate guide coordinates
			this.guidePointsSmall = [];
			this.guidePointsLarge = [];
			var P = [ (nextAlpha.x + this.alphaCarbon.x) / 2, (nextAlpha.y + this.alphaCarbon.y) / 2, (nextAlpha.z + this.alphaCarbon.z) / 2 ];
			if (this.helix) {
				// expand helices
				v3.scale(C, 1.5);
				v3.add(P, C);
			}
			this.guidePointsSmall[0] = new structures.Atom('', P[0] - this.D[0] / 2, P[1] - this.D[1] / 2, P[2] - this.D[2] / 2);
			for ( var i = 1; i < Ns; i++) {
				this.guidePointsSmall[i] = new structures.Atom('', this.guidePointsSmall[0].x + this.D[0] * i / Ns, this.guidePointsSmall[0].y + this.D[1] * i / Ns, this.guidePointsSmall[0].z + this.D[2] * i / Ns);
			}
			v3.scale(this.D, 4);
			this.guidePointsLarge[0] = new structures.Atom('', P[0] - this.D[0] / 2, P[1] - this.D[1] / 2, P[2] - this.D[2] / 2);
			for ( var i = 1; i < Ns; i++) {
				this.guidePointsLarge[i] = new structures.Atom('', this.guidePointsLarge[0].x + this.D[0] * i / Ns, this.guidePointsLarge[0].y + this.D[1] * i / Ns, this.guidePointsLarge[0].z + this.D[2] * i / Ns);
			}
		};
		this.getGuidePointSet = function(type) {
			if (type == 0) {
				return this.helix || this.sheet ? this.guidePointsLarge : this.guidePointsSmall;
			} else if (type == 1) {
				return this.guidePointsSmall;
			} else if (type == 2) {
				return this.guidePointsLarge;
			}
		};
		this.computeLineSegments = function(b1, a3, a4) {
			this.split = a3.helix != this.helix || a3.sheet != this.sheet;
			this.lineSegments = this.innerCompute(0, b1, a3, a4, false);
			this.lineSegmentsCartoon = this.innerCompute(a3.helix || a3.sheet ? 2 : 1, b1, a3, a4, true);
		};
		this.innerCompute = function(set, b1, a3, a4, useArrows) {
			var segments = [];
			var use = this.getGuidePointSet(set);
			var useb1 = b1.getGuidePointSet(set);
			var usea3 = a3.getGuidePointSet(set);
			var usea4 = a4.getGuidePointSet(set);
			for ( var l = 0, ll = this.guidePointsLarge.length; l < ll; l++) {
				var G = [ useb1[l].x, useb1[l].y, useb1[l].z, 1, use[l].x, use[l].y, use[l].z, 1, usea3[l].x, usea3[l].y, usea3[l].z, 1, usea4[l].x, usea4[l].y, usea4[l].z, 1 ];
				var M = m4.multiply(G, SB, []);
				var strand = [];
				for ( var k = 0; k < N; k++) {
					for ( var i = 3; i > 0; i--) {
						for ( var j = 0; j < 4; j++) {
							M[i * 4 + j] += M[(i - 1) * 4 + j];
						}
					}
					strand[k] = new structures.Atom('', M[12] / M[15], M[13] / M[15], M[14] / M[15]);
				}
				segments[l] = strand;
			}
			if (useArrows && this.arrow) {
				for ( var i = 0, ii = N; i < ii; i++) {
					var mult = 1.5 - 1.3 * i / N;
					var mid = m.floor(Ns / 2);
					var center = segments[mid];
					for ( var j = 0, jj = segments.length; j < jj; j++) {
						if (j != mid) {
							var o = center[i];
							var f = segments[j][i];
							var vec = [ f.x - o.x, f.y - o.y, f.z - o.z ];
							v3.scale(vec, mult);
							f.x = o.x + vec[0];
							f.y = o.y + vec[1];
							f.z = o.z + vec[2];
						}
					}
				}
			}
			return segments;
		};
	};

})(ChemDoodle.structures, Math, mat4, vec3);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3103 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-20 12:58:08 -0500 (Sun, 20 Feb 2011) $
//
(function(extensions, structures, math, q, m) {

	structures.Spectrum = function() {
		this.data = [];
		this.metadata = [];
		this.dataDisplay = [];
		this.title = null;
		this.xUnit = null;
		this.yUnit = null;
		this.continuous = true;
		this.integrationSensitivity = 0.01;
		var memoryOffsetLeft = 0;
		var memoryFlipXAxis = false;
		this.draw = function(ctx, specs, width, height) {
			var offsetTop = 5;
			var offsetLeft = 0;
			var offsetBottom = 0;
			// draw decorations
			ctx.fillStyle = specs.text_color;
			ctx.textAlign = 'center';
			ctx.textBaseline = 'alphabetic';
			ctx.font = specs.getFontString(specs.text_font_size, specs.text_font_families);
			if (this.xUnit) {
				offsetBottom += specs.text_font_size;
				ctx.fillText(this.xUnit, width / 2, height - 2);
			}
			if (this.yUnit && specs.plots_showYAxis)
			{
				offsetLeft += specs.text_font_size;
				ctx.save();
				ctx.translate(specs.text_font_size, height / 2);
				ctx.rotate(-m.PI / 2);
				ctx.fillText(this.yUnit, 0, 0);
				ctx.restore();
			}
			if (this.title != null) {
				offsetTop += specs.text_font_size;
				ctx.fillText(this.title, width / 2, specs.text_font_size);
			}
			// draw ticks
			offsetBottom += 5 + specs.text_font_size;
			if (specs.plots_showYAxis) {
				offsetLeft += 5 + ctx.measureText('1000').width;
			}
			if (specs.plots_showGrid) {
				ctx.strokeStyle = specs.plots_gridColor;
				ctx.lineWidth = specs.plots_gridLineWidth;
				ctx.strokeRect(offsetLeft, offsetTop, width - offsetLeft, height - offsetBottom - offsetTop);
			}
			ctx.textAlign = 'center';
			ctx.textBaseline = 'top';
			var span = this.maxX - this.minX;
			var t = span / 100;
			var major = .001;
			while (major < t || span / major > 25) {
				major *= 10;
			}
			var counter = 0;
			for ( var i = m.round(this.minX / major) * major; i <= this.maxX; i += major / 2) {
				var x = this.getTransformedX(i, specs, width, offsetLeft);
				if (x > offsetLeft) {
					ctx.strokeStyle = 'black';
					ctx.lineWidth = 1;
					if (counter % 2 == 0) {
						ctx.beginPath();
						ctx.moveTo(x, height - offsetBottom);
						ctx.lineTo(x, height - offsetBottom + 2);
						ctx.stroke();
						var s = i.toFixed(5);
						while (s.charAt(s.length - 1) == '0') {
							s = s.substring(0, s.length - 1);
						}
						if (s.charAt(s.length - 1) == '.') {
							s = s.substring(0, s.length - 1);
						}
						ctx.fillText(s, x, height - offsetBottom + 2);
						if (specs.plots_showGrid) {
							ctx.strokeStyle = specs.plots_gridColor;
							ctx.lineWidth = specs.plots_gridLineWidth;
							ctx.beginPath();
							ctx.moveTo(x, height - offsetBottom);
							ctx.lineTo(x, offsetTop);
							ctx.stroke();
						}
					} else {
						ctx.beginPath();
						ctx.moveTo(x, height - offsetBottom);
						ctx.lineTo(x, height - offsetBottom + 2);
						ctx.stroke();
					}
				}
				counter++;
			}
			if (specs.plots_showYAxis) {
				var spany = 1 / specs.scale;
				var counter = 0;
				ctx.textAlign = 'right';
				ctx.textBaseline = 'middle';
				for ( var i = 0; i <= 10; i++) {
					var yval = spany / 10 * i;
					var y = offsetTop + (height - offsetBottom - offsetTop) * (1 - yval * specs.scale);
					ctx.strokeStyle = 'black';
					ctx.lineWidth = 1;
					ctx.beginPath();
					ctx.moveTo(offsetLeft, y);
					ctx.lineTo(offsetLeft - 3, y);
					ctx.stroke();
					if (specs.plots_showGrid) {
						ctx.strokeStyle = specs.plots_gridColor;
						ctx.lineWidth = specs.plots_gridLineWidth;
						ctx.beginPath();
						ctx.moveTo(offsetLeft, y);
						ctx.lineTo(width, y);
						ctx.stroke();
					}
					var val = yval * 100;
					var cutoff = m.max(0,3-m.floor(val).toString().length);
					var s = val.toFixed(cutoff);
					if(cutoff>0){
						while (s.charAt(s.length - 1) == '0') {
							s = s.substring(0, s.length - 1);
						}
					}
					if (s.charAt(s.length - 1) == '.') {
						s = s.substring(0, s.length - 1);
					}
					ctx.fillText(s, offsetLeft - 3, y);
				}
			}
			// draw axes
			ctx.strokeStyle = 'black';
			ctx.lineWidth = 1;
			ctx.beginPath();
			// draw x axis
			ctx.moveTo(width, height - offsetBottom);
			ctx.lineTo(offsetLeft, height - offsetBottom);
			// draw y axis
			if (specs.plots_showYAxis) {
				ctx.lineTo(offsetLeft, offsetTop);
			}
			ctx.stroke();
			//draw metadata
			if(this.dataDisplay.length>0){
				ctx.textAlign = 'left';
				ctx.textBaseline = 'top';
				var mcount = 0;
				for ( var i = 0, ii = this.dataDisplay.length; i < ii; i++) {
					if(this.dataDisplay[i].value){
						ctx.fillText([this.dataDisplay[i].display, ': ', this.dataDisplay[i].value].join(''), offsetLeft + 10, offsetTop+10+mcount*(specs.text_font_size+5));
						mcount++;
					}else if(this.dataDisplay[i].tag){
						for ( var j = 0, jj = this.metadata.length; j < jj; j++) {
							if(extensions.stringStartsWith(this.metadata[j], this.dataDisplay[i].tag)){
								var draw = this.metadata[j];
								if(this.dataDisplay[i].display){
									var index = q.inArray('=', this.metadata[j]);
									draw = [this.dataDisplay[i].display, ': ', index>-1?this.metadata[j].substring(index+2):this.metadata[j]].join('');
								}
								ctx.fillText(draw, offsetLeft + 10, offsetTop+10+mcount*(specs.text_font_size+5));
								mcount++;
								break;
							}
						}
					}
				}
			}
			// draw plot
			ctx.strokeStyle = specs.plots_color;
			ctx.lineWidth = specs.plots_width;
			var integration = [];
			ctx.beginPath();
			if (this.continuous) {
				var started = false;
				for ( var i = 0, ii = this.data.length; i < ii; i++) {
					var x = this.getTransformedX(this.data[i].x, specs, width, offsetLeft);
					if (x >= offsetLeft && x < width) {
						var y = this.getTransformedY(this.data[i].y, specs, height, offsetBottom, offsetTop);
						if (specs.plots_showIntegration && m.abs(this.data[i].y)>this.integrationSensitivity) {
							integration.push(new structures.Point(this.data[i].x, this.data[i].y));
						}
						if (!started) {
							ctx.moveTo(x, y);
							started = true;
						}
						ctx.lineTo(x, y);
					} else if (started) {
						break;
					}
				}
			} else {
				for ( var i = 0, ii = this.data.length; i < ii; i++) {
					var x = this.getTransformedX(this.data[i].x, specs, width, offsetLeft);
					if (x >= offsetLeft && x < width) {
						ctx.moveTo(x, height - offsetBottom);
						ctx.lineTo(x, this.getTransformedY(this.data[i].y, specs, height, offsetBottom, offsetTop));
					}
				}
			}
			ctx.stroke();
			if (specs.plots_showIntegration && integration.length > 1) {
				ctx.strokeStyle = specs.plots_integrationColor;
				ctx.lineWidth = specs.plots_integrationLineWidth;
				ctx.beginPath();
				var ascending = integration[1].x > integration[0].x;
				var max;
				if (this.flipXAxis && !ascending || !this.flipXAxis && ascending) {
					for ( var i = integration.length - 2; i >= 0; i--) {
						integration[i].y = integration[i].y + integration[i + 1].y;
					}
					max = integration[0].y;
				} else {
					for ( var i = 1, ii = integration.length; i < ii; i++) {
						integration[i].y = integration[i].y + integration[i - 1].y;
					}
					max = integration[integration.length - 1].y;
				}
				for ( var i = 0, ii = integration.length; i < ii; i++) {
					var x = this.getTransformedX(integration[i].x, specs, width, offsetLeft);
					var y = this.getTransformedY(integration[i].y / specs.scale / max, specs, height, offsetBottom, offsetTop);
					if (i == 0) {
						ctx.moveTo(x, y);
					} else {
						ctx.lineTo(x, y);
					}
				}
				ctx.stroke();
			}
			memoryOffsetLeft = offsetLeft;
			memoryFlipXAxis = specs.plots_flipXAxis;
		};
		this.getTransformedY = function(y, specs, height, offsetBottom, offsetTop) {
			return offsetTop + (height - offsetBottom - offsetTop) * (1 - y * specs.scale);
		};
		this.getTransformedX = function(x, specs, width, offsetLeft) {
			var returning = offsetLeft + (x - this.minX) / (this.maxX - this.minX) * (width - offsetLeft);
			if (specs.plots_flipXAxis) {
				returning = width + offsetLeft - returning;
			}
			return returning;
		};
		this.getInverseTransformedX = function(x, width, offsetLeft) {
			if (memoryFlipXAxis) {
				x = width + offsetLeft - x;
			}
			return ((x - offsetLeft) * (this.maxX - this.minX) / (width - offsetLeft)) + this.minX;
		};
		this.setup = function() {
			var xmin = Number.MAX_VALUE;
			var xmax = Number.MIN_VALUE;
			var ymax = Number.MIN_VALUE;
			for ( var i = 0, ii = this.data.length; i < ii; i++) {
				xmin = m.min(xmin, this.data[i].x);
				xmax = m.max(xmax, this.data[i].x);
				ymax = m.max(ymax, this.data[i].y);
			}
			if (this.continuous) {
				this.minX = xmin;
				this.maxX = xmax;
			} else {
				this.minX = xmin - 1;
				this.maxX = xmax + 1;
			}
			for ( var i = 0, ii = this.data.length; i < ii; i++) {
				this.data[i].y /= ymax;
			}
		};
		this.zoom = function(pixel1, pixel2, width, rescaleY) {
			var p1 = this.getInverseTransformedX(pixel1, width, memoryOffsetLeft);
			var p2 = this.getInverseTransformedX(pixel2, width, memoryOffsetLeft);
			this.minX = m.min(p1, p2);
			this.maxX = m.max(p1, p2);
			if(rescaleY){
				var ymax = Number.MIN_VALUE;
				for ( var i = 0, ii = this.data.length; i < ii; i++) {
					if(math.isBetween(this.data[i].x, this.minX, this.maxX)){
						ymax = m.max(ymax, this.data[i].y);
					}
				}
				return 1/ymax;
			}
		};
		this.translate = function(dif, width) {
			var dist = dif / (width - memoryOffsetLeft) * (this.maxX - this.minX) * (memoryFlipXAxis ? 1 : -1);
			this.minX += dist;
			this.maxX += dist;
		};
		this.alertMetadata = function() {
			alert(this.metadata.join('\n'));
		};
		return true;
	};

})(ChemDoodle.extensions, ChemDoodle.structures, ChemDoodle.math, jQuery, Math);

//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3100 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-17 07:35:56 -0500 (Thu, 17 Feb 2011) $
//

(function(structures)
{
	structures.Cube = function(gl)
	{
		this.vertexPositionBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ARRAY_BUFFER, this.vertexPositionBuffer);
		vertices = [ // Front face
		-1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, 1.0, // Back
																		// face
		-1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0, -1.0, // Top
		// face
		-1.0, 1.0, -1.0, -1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, -1.0, // Bottom
		// face
		-1.0, -1.0, -1.0, 1.0, -1.0, -1.0, 1.0, -1.0, 1.0, -1.0, -1.0, 1.0, // Right
		// face
		1.0, -1.0, -1.0, 1.0, 1.0, -1.0, 1.0, 1.0, 1.0, 1.0, -1.0, 1.0, // Left
																		// face
		-1.0, -1.0, -1.0, -1.0, -1.0, 1.0, -1.0, 1.0, 1.0, -1.0, 1.0, -1.0 ];
		gl.bufferData(gl.ARRAY_BUFFER, new Float32Array(vertices), gl.STATIC_DRAW);
		this.vertexPositionBuffer.itemSize = 3;
		this.vertexPositionBuffer.numItems = 24;

		this.vertexColorBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ARRAY_BUFFER, this.vertexColorBuffer);
		var colors = [ [ 1.0, 0.0, 0.0, 1.0 ], // Front face
		[ 1.0, 1.0, 0.0, 1.0 ], // Back face
		[ 0.0, 1.0, 0.0, 1.0 ], // Top face
		[ 1.0, 0.5, 0.5, 1.0 ], // Bottom face
		[ 1.0, 0.0, 1.0, 1.0 ], // Right face
		[ 0.0, 0.0, 1.0, 1.0 ] // Left face
		];
		var unpackedColors = [];
		for ( var i in colors) {
			var color = colors[i];
			for ( var j = 0; j < 4; j++) {
				unpackedColors = unpackedColors.concat(color);
			}
		}
		gl.bufferData(gl.ARRAY_BUFFER, new Float32Array(unpackedColors), gl.STATIC_DRAW);
		this.vertexColorBuffer.itemSize = 4;
		this.vertexColorBuffer.numItems = 24;

		this.vertexNormalBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ARRAY_BUFFER, this.vertexNormalBuffer);
		var vertexNormals = [ // Front face
		0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, // Back face
		0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, // Top
																		// face
		0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, // Bottom
																	// face
		0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, // Right
		// face
		1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, 1.0, 0.0, 0.0, // Left face
		-1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0, -1.0, 0.0, 0.0 ];
		gl.bufferData(gl.ARRAY_BUFFER, new Float32Array(vertexNormals), gl.STATIC_DRAW);
		this.vertexNormalBuffer.itemSize = 3;
		this.vertexNormalBuffer.numItems = 24;

		this.vertexIndexBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, this.vertexIndexBuffer);
		var cubeVertexIndices = [ 0, 1, 2, 0, 2, 3, // Front face
		4, 5, 6, 4, 6, 7, // Back face
		8, 9, 10, 8, 10, 11, // Top face
		12, 13, 14, 12, 14, 15, // Bottom face
		16, 17, 18, 16, 18, 19, // Right face
		20, 21, 22, 20, 22, 23 // Left face
		];
		gl.bufferData(gl.ELEMENT_ARRAY_BUFFER, new Uint16Array(cubeVertexIndices), gl.STATIC_DRAW);
		this.vertexIndexBuffer.itemSize = 1;
		this.vertexIndexBuffer.numItems = 36;
		return true;
	};
})(ChemDoodle.structures);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3100 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-17 07:35:56 -0500 (Thu, 17 Feb 2011) $
//
(function(structures, m)
{
	structures.Cylinder = function(gl, radius, height, bands)
	{
		var vertexPositionData = [];
		var normalData = [];
		for ( var i = 0; i < bands; i++) {
			var theta = i * 2 * m.PI / bands;
			var cosTheta = m.cos(theta);
			var sinTheta = m.sin(theta);
			normalData.push(cosTheta, 0, sinTheta);
			vertexPositionData.push(radius * cosTheta, 0, radius * sinTheta);
			normalData.push(cosTheta, 0, sinTheta);
			vertexPositionData.push(radius * cosTheta, height, radius * sinTheta);
		}
		normalData.push(1, 0, 0);
		vertexPositionData.push(radius, 0, 0);
		normalData.push(1, 0, 0);
		vertexPositionData.push(radius, height, 0);

		this.vertexNormalBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ARRAY_BUFFER, this.vertexNormalBuffer);
		gl.bufferData(gl.ARRAY_BUFFER, new Float32Array(normalData), gl.STATIC_DRAW);
		this.vertexNormalBuffer.itemSize = 3;
		this.vertexNormalBuffer.numItems = normalData.length / 3;

		this.vertexPositionBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ARRAY_BUFFER, this.vertexPositionBuffer);
		gl.bufferData(gl.ARRAY_BUFFER, new Float32Array(vertexPositionData), gl.STATIC_DRAW);
		this.vertexPositionBuffer.itemSize = 3;
		this.vertexPositionBuffer.numItems = vertexPositionData.length / 3;
		return true;
	};
})(ChemDoodle.structures, Math);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3100 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-17 07:35:56 -0500 (Thu, 17 Feb 2011) $
//
(function(structures, m)
{
	structures.Sphere = function(gl, radius, latitudeBands, longitudeBands) {
		var vertexPositionData = [];
		var normalData = [];
		for ( var latNumber = 0; latNumber <= latitudeBands; latNumber++) {
			var theta = latNumber * m.PI / latitudeBands;
			var sinTheta = m.sin(theta);
			var cosTheta = m.cos(theta);

			for ( var longNumber = 0; longNumber <= longitudeBands; longNumber++) {
				var phi = longNumber * 2 * m.PI / longitudeBands;
				var sinPhi = m.sin(phi);
				var cosPhi = m.cos(phi);

				var x = cosPhi * sinTheta;
				var y = cosTheta;
				var z = sinPhi * sinTheta;

				normalData.push(x);
				normalData.push(y);
				normalData.push(z);
				vertexPositionData.push(radius * x);
				vertexPositionData.push(radius * y);
				vertexPositionData.push(radius * z);
			}
		}

		var indexData = [];
		longitudeBands += 1;
		for ( var latNumber = 0; latNumber < latitudeBands; latNumber++) {
			for ( var longNumber = 0; longNumber < longitudeBands; longNumber++) {
				var first = (latNumber * longitudeBands) + (longNumber % longitudeBands);
				var second = first + longitudeBands;
				indexData.push(first);
				indexData.push(second);
				indexData.push(first + 1);

				if (longNumber < longitudeBands - 1) {
					indexData.push(second);
					indexData.push(second + 1);
					indexData.push(first + 1);
				}
			}
		}

		this.vertexNormalBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ARRAY_BUFFER, this.vertexNormalBuffer);
		gl.bufferData(gl.ARRAY_BUFFER, new Float32Array(normalData), gl.STATIC_DRAW);
		this.vertexNormalBuffer.itemSize = 3;
		this.vertexNormalBuffer.numItems = normalData.length / 3;

		this.vertexPositionBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ARRAY_BUFFER, this.vertexPositionBuffer);
		gl.bufferData(gl.ARRAY_BUFFER, new Float32Array(vertexPositionData), gl.STATIC_DRAW);
		this.vertexPositionBuffer.itemSize = 3;
		this.vertexPositionBuffer.numItems = vertexPositionData.length / 3;

		this.vertexIndexBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, this.vertexIndexBuffer);
		gl.bufferData(gl.ELEMENT_ARRAY_BUFFER, new Uint16Array(indexData), gl.STATIC_DRAW);
		this.vertexIndexBuffer.itemSize = 1;
		this.vertexIndexBuffer.numItems = indexData.length;
		return true;
	};
})(ChemDoodle.structures, Math);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//

(function(RESIDUE, structures, m, v3)
{
	function SubRibbon(gl, entire, name, indexes){
		this.name = name;
		this.entire = entire;

		this.vertexIndexBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, this.vertexIndexBuffer);
		gl.bufferData(gl.ELEMENT_ARRAY_BUFFER, new Uint16Array(indexes), gl.STATIC_DRAW);
		this.vertexIndexBuffer.itemSize = 1;
		this.vertexIndexBuffer.numItems = indexes.length;

		this.getColor = function(specs){
			if(this.name){
				if(RESIDUE[this.name]==null){
					return specs.ribbons_useShapelyColors?RESIDUE['*'].shapelyColor:RESIDUE['*'].aminoColor;
				}else{
					return specs.ribbons_useShapelyColors?RESIDUE[this.name].shapelyColor:RESIDUE[this.name].aminoColor;
				}
			}else if(this.helix){
				return entire.front?specs.ribbons_cartoonHelixFrontColor:specs.ribbons_cartoonHelixBackColor;
			}else if(this.sheet){
				return specs.ribbons_cartoonSheetColor;
			}else{
				return entire.front?specs.ribbons_frontColor:specs.ribbons_backColor;
			}
		};
		this.render = function(gl, specs){
			// indexes
			gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, this.vertexIndexBuffer);
			// colors
			gl.material.setDiffuseColor(gl, this.getColor(specs));
			// render
			gl.drawElements(gl.TRIANGLES, this.vertexIndexBuffer.numItems, gl.UNSIGNED_SHORT, 0);
		};
	}

	structures.Ribbon = function(gl, chain, offset, cartoon) {
		var lineSegmentNum = chain[0].lineSegments.length;
		var lineSegmentLength = chain[0].lineSegments[0].length;
		var vertexPositionData = [];
		var normalData = [];
		this.front = true;
		for ( var i = 0, ii = chain.length - 1; i < ii; i++) {
			var residue = chain[i];
			for ( var j = 0; j < lineSegmentNum; j++) {
				var lineSegment = cartoon?residue.lineSegmentsCartoon[j]:residue.lineSegments[j];
				for ( var k = 0; k < lineSegmentLength; k++) {
					var a = lineSegment[k];
					// normals
					var abovei = i;
					var abovek = k+1;
					if(i == chain.length - 2&&k==lineSegmentLength-1){
						abovek--;
					}else if(k==lineSegmentLength-1){
						abovei++;
						abovek = 0;
					}
					var above = cartoon?chain[abovei].lineSegmentsCartoon[j][abovek]:chain[abovei].lineSegments[j][abovek];
					var negate = false;
					var nextj = j + 1;
					if(j == lineSegmentNum - 1){
						nextj-=2;
						negate = true;
					}
					var side = cartoon?residue.lineSegmentsCartoon[nextj][k]:residue.lineSegments[nextj][k];
					var toAbove = [ above.x - a.x, above.y - a.y, above.z - a.z ];
					var toSide = [ side.x - a.x, side.y - a.y, side.z - a.z ];
					var normal = v3.cross(toAbove, toSide, []);
					v3.normalize(normal);
					if(negate){
						v3.scale(normal, -1);
					}
					if(offset<0){
						this.front = false;
						v3.scale(normal, -1);
					}
					normalData.push(normal[0]);
					normalData.push(normal[1]);
					normalData.push(normal[2]);
					//positions
					v3.scale(normal, m.abs(offset));
					vertexPositionData.push(a.x+normal[0]);
					vertexPositionData.push(a.y+normal[1]);
					vertexPositionData.push(a.z+normal[2]);
				}
			}
		}

		this.segments = [];
		var cartoonSegmentIndexData;
		if(cartoon){
			this.cartoonSegments = [];
			cartoonSegmentIndexData = [];
		}
		var indexData = [];
		for ( var i = 0, ii = chain.length - 1; i < ii; i++) {
			if(i>0 && cartoonSegmentIndexData){
				var b4 = chain[i-1];
				if(chain[i].split){
					var sr = new SubRibbon(gl, this, null, cartoonSegmentIndexData);
					if(chain[i].helix){
						sr.helix = true;
					}
					if(chain[i].sheet){
						sr.sheet = true;
					}
					this.cartoonSegments.push(sr);
					cartoonSegmentIndexData = [];
				}
			}
			var residueIndexStart = i * lineSegmentNum * lineSegmentLength;
			var individualIndexData = [];
			for ( var j = 0, jj=lineSegmentNum - 1; j < jj; j++) {
				var segmentIndexStart = residueIndexStart + j * lineSegmentLength;
				for ( var k = 0; k < lineSegmentLength; k++) {
					var nextRes = 1;
					if(i == chain.length - 2){
						nextRes = 0;
					}else if(k==lineSegmentLength-1){
						nextRes = lineSegmentNum * lineSegmentLength-k;
					}
					var add = [segmentIndexStart + k, segmentIndexStart + lineSegmentLength + k, segmentIndexStart + lineSegmentLength + k + nextRes,
					           segmentIndexStart + k, segmentIndexStart + k + nextRes, segmentIndexStart + lineSegmentLength + k + nextRes];
					for(var l=0; l<6; l++){
						indexData.push(add[l]);
					}
					if(k!=lineSegmentLength-1){
						for(var l=0; l<6; l++){
							individualIndexData.push(add[l]);
						}
					}
					if(cartoonSegmentIndexData){
						for(var l=0; l<6; l++){
							cartoonSegmentIndexData.push(add[l]);
						}
					}
				}
			}
			var resName = chain[i+1].name;
			this.segments.push(new SubRibbon(gl, this, resName, individualIndexData));
		}
		if(cartoonSegmentIndexData){
			this.cartoonSegments.push(new SubRibbon(gl, this, null, cartoonSegmentIndexData));
		}

		this.vertexNormalBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ARRAY_BUFFER, this.vertexNormalBuffer);
		gl.bufferData(gl.ARRAY_BUFFER, new Float32Array(normalData), gl.STATIC_DRAW);
		this.vertexNormalBuffer.itemSize = 3;
		this.vertexNormalBuffer.numItems = normalData.length / 3;

		this.vertexPositionBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ARRAY_BUFFER, this.vertexPositionBuffer);
		gl.bufferData(gl.ARRAY_BUFFER, new Float32Array(vertexPositionData), gl.STATIC_DRAW);
		this.vertexPositionBuffer.itemSize = 3;
		this.vertexPositionBuffer.numItems = vertexPositionData.length / 3;

		this.vertexIndexBuffer = gl.createBuffer();
		gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, this.vertexIndexBuffer);
		gl.bufferData(gl.ELEMENT_ARRAY_BUFFER, new Uint16Array(indexData), gl.STATIC_DRAW);
		this.vertexIndexBuffer.itemSize = 1;
		this.vertexIndexBuffer.numItems = indexData.length;

		this.render = function(gl, specs){
			// positions
			gl.bindBuffer(gl.ARRAY_BUFFER, this.vertexPositionBuffer);
			gl.vertexAttribPointer(gl.shader.vertexPositionAttribute, this.vertexPositionBuffer.itemSize, gl.FLOAT, false, 0, 0);
			// normals
			gl.bindBuffer(gl.ARRAY_BUFFER, this.vertexNormalBuffer);
			gl.vertexAttribPointer(gl.shader.vertexNormalAttribute, this.vertexNormalBuffer.itemSize, gl.FLOAT, false, 0, 0);
			// indexes
			gl.bindBuffer(gl.ELEMENT_ARRAY_BUFFER, this.vertexIndexBuffer);
			// colors
			gl.material.setDiffuseColor(gl, this.front?specs.ribbons_frontColor:specs.ribbons_backColor);
			// render
			gl.drawElements(gl.TRIANGLES, this.vertexIndexBuffer.numItems, gl.UNSIGNED_SHORT, 0);
		};

		return true;
	};
})(ChemDoodle.RESIDUE, ChemDoodle.structures, Math, vec3);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3160 $
//  $Author: kevin $
//  $LastChangedDate: 2011-03-12 18:27:31 -0500 (Sat, 12 Mar 2011) $
//
(function(math, structures, v3)
{
	structures.Light = function(diffuseColor, specularColor, direction) {
		this.diffuseRGB = math.getRGB(diffuseColor, 1);
		this.specularRGB = math.getRGB(specularColor, 1);
		this.direction = direction;
		this.lightScene = function(gl) {
			var prefix = 'u_light.';
			gl.uniform3f(gl.getUniformLocation(gl.program, prefix + 'diffuse_color'), this.diffuseRGB[0], this.diffuseRGB[1], this.diffuseRGB[2]);
			gl.uniform3f(gl.getUniformLocation(gl.program, prefix + 'specular_color'), this.specularRGB[0], this.specularRGB[1], this.specularRGB[2]);

			var lightingDirection = v3.create(this.direction);
			v3.normalize(lightingDirection);
			v3.negate(lightingDirection);
			gl.uniform3f(gl.getUniformLocation(gl.program, prefix + 'direction'), lightingDirection[0], lightingDirection[1], lightingDirection[2]);

			// compute the half vector
			var eyeVector = [ 0, 0, 0 ];
			var halfVector = [ eyeVector[0] + lightingDirection[0], eyeVector[1] + lightingDirection[1], eyeVector[2] + lightingDirection[2] ];
			var length = v3.length(halfVector);
			if (length == 0)
				halfVector = [ 0, 0, 1 ];
			else {
				v3.scale(1 / length);
			}
			gl.uniform3f(gl.getUniformLocation(gl.program, prefix + "half_vector"), halfVector[0], halfVector[1], halfVector[2]);
		};
		return true;
	};

})(ChemDoodle.math, ChemDoodle.structures, vec3);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3163 $
//  $Author: kevin $
//  $LastChangedDate: 2011-03-12 18:47:17 -0500 (Sat, 12 Mar 2011) $
//
(function(math, structures)
{
	structures.Material = function(gl)
	{
		var prefix = 'u_material.';
		var aUL = gl.getUniformLocation(gl.program, prefix + 'ambient_color');
		var dUL = gl.getUniformLocation(gl.program, prefix + 'diffuse_color');
		var sUL = gl.getUniformLocation(gl.program, prefix + 'specular_color');
		var snUL = gl.getUniformLocation(gl.program, prefix + 'shininess');
		this.setTempColors = function(gl, ambientColor, diffuseColor, specularColor, shininess) {
			if(!this.aCache || this.aCache!=ambientColor){
				this.aCache = ambientColor;
				var cs = math.getRGB(ambientColor, 1);
				gl.uniform3f(aUL, cs[0], cs[1], cs[2]);
			}
			if(diffuseColor!=null && (!this.dCache || this.dCache!=diffuseColor)){
				this.dCache = diffuseColor;
				var cs = math.getRGB(diffuseColor, 1);
				gl.uniform3f(dUL, cs[0], cs[1], cs[2]);
			}
			if(!this.sCache || this.sCache!=specularColor){
				this.sCache = specularColor;
				var cs = math.getRGB(specularColor, 1);
				gl.uniform3f(sUL, cs[0], cs[1], cs[2]);
			}
			if(!this.snCache || this.snCache!=shininess){
				this.snCache = shininess;
				gl.uniform1f(snUL, shininess);
			}
		};
		this.setDiffuseColor = function(gl, diffuseColor) {
			if(!this.dCache || this.dCache!=diffuseColor){
				this.dCache = diffuseColor;
				var cs = math.getRGB(diffuseColor, 1);
				gl.uniform3f(dUL, cs[0], cs[1], cs[2]);
			}
		};
		return true;
	};
})(ChemDoodle.math, ChemDoodle.structures);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3149 $
//  $Author: kevin $
//  $LastChangedDate: 2011-03-04 07:17:59 -0500 (Fri, 04 Mar 2011) $
//
(function(structures, document)
{
	structures.Shader = function() {
		this.init = function(gl) {
			var vertexShader = this.getShader(gl, "vertex-shader");
			if (vertexShader == null) {
				vertexShader = this.loadDefaultVertexShader(gl);
			}
			var fragmentShader = this.getShader(gl, "fragment-shader");
			if (fragmentShader == null) {
				fragmentShader = this.loadDefaultFragmentShader(gl);
			}

			gl.attachShader(gl.program, vertexShader);
			gl.attachShader(gl.program, fragmentShader);
			gl.linkProgram(gl.program);

			if (!gl.getProgramParameter(gl.program, gl.LINK_STATUS)) {
				alert("Could not initialize shaders!");
			}

			gl.useProgram(gl.program);

			this.vertexPositionAttribute = gl.getAttribLocation(gl.program, "a_vertex_position");
			gl.enableVertexAttribArray(this.vertexPositionAttribute);

			this.vertexNormalAttribute = gl.getAttribLocation(gl.program, "a_vertex_normal");
			gl.enableVertexAttribArray(this.vertexNormalAttribute);
		};
		this.getShader = function(gl, id) {
			var shaderScript = document.getElementById(id);
			if (!shaderScript) {
				return null;
			}
			var sb = [];
			var k = shaderScript.firstChild;
			while (k) {
				if (k.nodeType == 3)
					sb.push(k.textContent);
				k = k.nextSibling;
			}
			var shader;
			if (shaderScript.type == "x-shader/x-fragment") {
				shader = gl.createShader(gl.FRAGMENT_SHADER);
			} else if (shaderScript.type == "x-shader/x-vertex") {
				shader = gl.createShader(gl.VERTEX_SHADER);
			} else {
				return null;
			}
			gl.shaderSource(shader, sb.join(''));
			gl.compileShader(shader);
			if (!gl.getShaderParameter(shader, gl.COMPILE_STATUS)) {
				alert(gl.getShaderInfoLog(shader));
				return null;
			}
			return shader;
		};
		this.loadDefaultVertexShader = function(gl) {
			var sb = [];
			// set precision
			sb.push("#ifdef GL_ES\n");
			sb.push("precision highp float;\n");
			sb.push("#endif\n");
			// phong shader
			sb.push("struct Light");
			sb.push("{");
			sb.push("vec3 diffuse_color;");
			sb.push("vec3 specular_color;");
			sb.push("vec3 direction;");
			sb.push("vec3 half_vector;");
			sb.push("};");
			sb.push("struct Material");
			sb.push("{");
			sb.push("vec3 ambient_color;");
			sb.push("vec3 diffuse_color;");
			sb.push("vec3 specular_color;");
			sb.push("float shininess;");
			sb.push("};");
			// attributes set when rendering objects
			sb.push("attribute vec3 a_vertex_position;");
			sb.push("attribute vec3 a_vertex_normal;");
			// scene structs
			sb.push("uniform Light u_light;");
			sb.push("uniform Material u_material;");
			// matrices set by gl.setMatrixUniforms
			sb.push("uniform mat4 u_model_view_matrix;");
			sb.push("uniform mat4 u_projection_matrix;");
			sb.push("uniform mat3 u_normal_matrix;");
			// sent to the fragment shader
			sb.push("varying vec4 v_diffuse;");
			sb.push("varying vec4 v_ambient;");
			sb.push("varying vec3 v_normal;");
			sb.push("varying vec3 v_light_direction;");
			sb.push("void main(void)");
			sb.push("{");
			sb.push("v_normal = normalize(u_normal_matrix * a_vertex_normal);");

			sb.push("vec4 diffuse = vec4(u_light.diffuse_color, 1.0);");
			sb.push("v_light_direction = u_light.direction;");

			sb.push("v_ambient = vec4(u_material.ambient_color, 1.0);");
			sb.push("v_diffuse = vec4(u_material.diffuse_color, 1.0) * diffuse;");

			sb.push("gl_Position = u_projection_matrix * u_model_view_matrix * vec4(a_vertex_position, 1.0);");
			sb.push("}");
			var shader = gl.createShader(gl.VERTEX_SHADER);
			gl.shaderSource(shader, sb.join(''));
			gl.compileShader(shader);
			if (!gl.getShaderParameter(shader, gl.COMPILE_STATUS)) {
				alert(gl.getShaderInfoLog(shader));
				return null;
			}
			return shader;
		};
		this.loadDefaultFragmentShader = function(gl) {
			var sb = [];
			// set precision
			sb.push("#ifdef GL_ES\n");
			sb.push("precision highp float;\n");
			sb.push("#endif\n");
			sb.push("struct Light");
			sb.push("{");
			sb.push("vec3 diffuse_color;");
			sb.push("vec3 specular_color;");
			sb.push("vec3 direction;");
			sb.push("vec3 half_vector;");
			sb.push("};");
			sb.push("struct Material");
			sb.push("{");
			sb.push("vec3 ambient_color;");
			sb.push("vec3 diffuse_color;");
			sb.push("vec3 specular_color;");
			sb.push("float shininess;");
			sb.push("};");
			// scene structs
			sb.push("uniform Light u_light;");
			sb.push("uniform Material u_material;");
			// from the vertex shader
			sb.push("varying vec4 v_diffuse;");
			sb.push("varying vec4 v_ambient;");
			sb.push("varying vec3 v_normal;");
			sb.push("varying vec3 v_light_direction;");
			sb.push("void main(void)");
			sb.push("{");
			sb.push("float nDotL = max(dot(v_normal, v_light_direction), 0.0);");
			sb.push("vec4 color = vec4(v_diffuse.rgb*nDotL, v_diffuse.a);");
			sb.push("float nDotHV = max(dot(v_normal, u_light.half_vector), 0.0);");
			sb.push("vec4 specular = vec4(u_material.specular_color * u_light.specular_color, 1.0);");
			sb.push("color+=vec4(specular.rgb * pow(nDotHV, u_material.shininess), specular.a);");
			sb.push("gl_FragColor = color+v_ambient;");
			sb.push("}");
			var shader = gl.createShader(gl.FRAGMENT_SHADER);
			gl.shaderSource(shader, sb.join(''));
			gl.compileShader(shader);
			if (!gl.getShaderParameter(shader, gl.COMPILE_STATUS)) {
				alert(gl.getShaderInfoLog(shader));
				return null;
			}
			return shader;
		};
		return true;
	};
})(ChemDoodle.structures, document);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3160 $
//  $Author: kevin $
//  $LastChangedDate: 2011-03-12 18:27:31 -0500 (Sat, 12 Mar 2011) $
//
(function(c, structures, m)
{
	// default canvas properties
	c.default_backgroundColor = '#FFFFFF';
	c.default_scale = 1;
	c.default_rotateAngle = 0;
	c.default_bondLength_2D = 20;
	c.default_angstromsPerBondLength = 1.25;
	c.default_lightDirection_3D = [ -.1, -.1, -1 ];
	c.default_lightDiffuseColor_3D = '#FFFFFF';
	c.default_lightSpecularColor_3D = '#FFFFFF';
	c.default_projectionVerticalFieldOfView_3D = 45;
	c.default_projectionWidthHeightRatio_3D = 1;
	c.default_projectionFrontCulling_3D = .1;
	c.default_projectionBackCulling_3D = 10000;

	// default atom properties
	c.default_atoms_display = true;
	c.default_atoms_color = '#000000';
	c.default_atoms_font_size_2D = 12;
	c.default_atoms_font_families_2D = [ 'Helvetica', 'Arial', 'Dialog' ];
	c.default_atoms_font_bold_2D = false;
	c.default_atoms_font_italic_2D = false;
	c.default_atoms_circles_2D = false;
	c.default_atoms_circleDiameter_2D = 10;
	c.default_atoms_circleBorderWidth_2D = 1;
	c.default_atoms_useJMOLColors = false;
	c.default_atoms_resolution_3D = 60;
	c.default_atoms_sphereDiameter_3D = .8;
	c.default_atoms_useVDWDiameters_3D = false;
	c.default_atoms_vdwMultiplier_3D = 1;
	c.default_atoms_materialAmbientColor_3D = '#000000';
	c.default_atoms_materialSpecularColor_3D = '#555555';
	c.default_atoms_materialShininess_3D = 32;
	c.default_atoms_implicitHydrogens_2D = true;
	c.default_atoms_displayTerminalCarbonLabels_2D = false;
	c.default_atoms_showHiddenCarbons_2D = true;

	// default bond properties
	c.default_bonds_display = true;
	c.default_bonds_color = '#000000';
	c.default_bonds_width_2D = 1;
	c.default_bonds_saturationWidth_2D = .2;
	c.default_bonds_ends_2D = 'round';
	c.default_bonds_useJMOLColors = false;
	c.default_bonds_saturationAngle_2D = m.PI / 3;
	c.default_bonds_symmetrical_2D = false;
	c.default_bonds_clearOverlaps_2D = false;
	c.default_bonds_overlapClearWidth_2D = .5;
	c.default_bonds_atomLabelBuffer_2D = .25;
	c.default_bonds_wedgeThickness_2D = .22;
	c.default_bonds_hashWidth_2D = 1;
	c.default_bonds_hashSpacing_2D = 2.5;
	c.default_bonds_showBondOrders_3D = false;
	c.default_bonds_resolution_3D = 60;
	c.default_bonds_cylinderDiameter_3D = .3;
	c.default_bonds_materialAmbientColor_3D = '#222222';
	c.default_bonds_materialSpecularColor_3D = '#555555';
	c.default_bonds_materialShininess_3D = 32;

	// default macromolecular properties
	c.default_ribbons_display = true;
	c.default_ribbons_cartoonize = false;
	c.default_ribbons_useShapelyColors = false;
	c.default_ribbons_useAminoColors = false;
	c.default_ribbons_frontColor = '#FF0D0D';
	c.default_ribbons_backColor = '#FFFF30';
	c.default_ribbons_cartoonHelixFrontColor = '#00E740';
	c.default_ribbons_cartoonHelixBackColor = '#9905FF';
	c.default_ribbons_cartoonSheetColor = '#E8BB99';
	c.default_ribbons_materialAmbientColor_3D = '#222222';
	c.default_ribbons_materialSpecularColor_3D = '#555555';
	c.default_ribbons_materialShininess_3D = 32;

	// default spectrum properties
	c.default_plots_color = '#000000';
	c.default_plots_width = 1;
	c.default_plots_showIntegration = false;
	c.default_plots_integrationColor = '#c10000';
	c.default_plots_integrationLineWidth = 1;
	c.default_plots_showGrid = false;
	c.default_plots_gridColor = 'gray';
	c.default_plots_gridLineWidth = .5;
	c.default_plots_showYAxis = true;
	c.default_plots_flipXAxis = false;
	c.default_text_font_size = 12;
	c.default_text_font_families = [ 'Helvetica', 'Arial', 'Dialog' ];
	c.default_text_color = '#000000';

	structures.VisualSpecifications = function()
	{
		// canvas properties
		this.backgroundColor = c.default_backgroundColor;
		this.scale = c.default_scale;
		this.rotateAngle = c.default_rotateAngle;
		this.bondLength = c.default_bondLength_2D;
		this.angstromsPerBondLength = c.default_angstromsPerBondLength;
		this.lightDirection_3D = c.default_lightDirection_3D;
		this.lightDiffuseColor_3D = c.default_lightDiffuseColor_3D;
		this.lightSpecularColor_3D = c.default_lightSpecularColor_3D;
		this.projectionVerticalFieldOfView_3D = c.default_projectionVerticalFieldOfView_3D;
		this.projectionWidthHeightRatio_3D = c.default_projectionWidthHeightRatio_3D;
		this.projectionFrontCulling_3D = c.default_projectionFrontCulling_3D;
		this.projectionBackCulling_3D = c.default_projectionBackCulling_3D;

		// atom properties
		this.atoms_display = c.default_atoms_display;
		this.atoms_color = c.default_atoms_color;
		this.atoms_font_size_2D = c.default_atoms_font_size_2D;
		this.atoms_font_families_2D = [];
		for ( var i = 0, ii = c.default_atoms_font_families_2D.length; i < ii; i++) {
			this.atoms_font_families_2D[i] = c.default_atoms_font_families_2D[i];
		}
		this.atoms_font_bold_2D = c.default_atoms_font_bold_2D;
		this.atoms_font_italic_2D = c.default_atoms_font_italic_2D;
		this.atoms_circles_2D = c.default_atoms_circles_2D;
		this.atoms_circleDiameter_2D = c.default_atoms_circleDiameter_2D;
		this.atoms_circleBorderWidth_2D = c.default_atoms_circleBorderWidth_2D;
		this.atoms_useJMOLColors = c.default_atoms_useJMOLColors;
		this.atoms_resolution_3D = c.default_atoms_resolution_3D;
		this.atoms_sphereDiameter_3D = c.default_atoms_sphereDiameter_3D;
		this.atoms_useVDWDiameters_3D = c.default_atoms_useVDWDiameters_3D;
		this.atoms_vdwMultiplier_3D = c.default_atoms_vdwMultiplier_3D;
		this.atoms_materialAmbientColor_3D = c.default_atoms_materialAmbientColor_3D;
		this.atoms_materialSpecularColor_3D = c.default_atoms_materialSpecularColor_3D;
		this.atoms_materialShininess_3D = c.default_atoms_materialShininess_3D;
		this.atoms_implicitHydrogens_2D = c.default_atoms_implicitHydrogens_2D;
		this.atoms_displayTerminalCarbonLabels_2D = c.default_atoms_displayTerminalCarbonLabels_2D;
		this.atoms_showHiddenCarbons_2D = c.default_atoms_showHiddenCarbons_2D;

		// bond properties
		this.bonds_display = c.default_bonds_display;
		this.bonds_color = c.default_bonds_color;
		this.bonds_width_2D = c.default_bonds_width_2D;
		this.bonds_saturationWidth_2D = c.default_bonds_saturationWidth_2D;
		this.bonds_ends_2D = c.default_bonds_ends_2D;
		this.bonds_useJMOLColors = c.default_bonds_useJMOLColors;
		this.bonds_saturationAngle_2D = c.default_bonds_saturationAngle_2D;
		this.bonds_symmetrical_2D = c.default_bonds_symmetrical_2D;
		this.bonds_clearOverlaps_2D = c.default_bonds_clearOverlaps_2D;
		this.bonds_overlapClearWidth_2D = c.default_bonds_overlapClearWidth_2D;
		this.bonds_atomLabelBuffer_2D = c.default_bonds_atomLabelBuffer_2D;
		this.bonds_wedgeThickness_2D = c.default_bonds_wedgeThickness_2D;
		this.bonds_hashWidth_2D = c.default_bonds_hashWidth_2D;
		this.bonds_hashSpacing_2D = c.default_bonds_hashSpacing_2D;
		this.bonds_showBondOrders_3D = c.default_bonds_showBondOrders_3D;
		this.bonds_resolution_3D = c.default_bonds_resolution_3D;
		this.bonds_cylinderDiameter_3D = c.default_bonds_cylinderDiameter_3D;
		this.bonds_materialAmbientColor_3D = c.default_bonds_materialAmbientColor_3D;
		this.bonds_materialSpecularColor_3D = c.default_bonds_materialSpecularColor_3D;
		this.bonds_materialShininess_3D = c.default_bonds_materialShininess_3D;

		// macromolecular properties
		this.ribbons_display = c.default_ribbons_display;
		this.ribbons_cartoonize = c.default_ribbons_cartoonize;
		this.ribbons_useShapelyColors = c.default_ribbons_useShapelyColors;
		this.ribbons_useAminoColors = c.default_ribbons_useAminoColors;
		this.ribbons_frontColor = c.default_ribbons_frontColor;
		this.ribbons_backColor = c.default_ribbons_backColor;
		this.ribbons_cartoonHelixFrontColor = c.default_ribbons_cartoonHelixFrontColor;
		this.ribbons_cartoonHelixBackColor = c.default_ribbons_cartoonHelixBackColor;
		this.ribbons_cartoonSheetColor = c.default_ribbons_cartoonSheetColor;
		this.ribbons_materialAmbientColor_3D = c.default_ribbons_materialAmbientColor_3D;
		this.ribbons_materialSpecularColor_3D = c.default_ribbons_materialSpecularColor_3D;
		this.ribbons_materialShininess_3D = c.default_ribbons_materialShininess_3D;

		// spectrum properties
		this.plots_color = c.default_plots_color;
		this.plots_width = c.default_plots_width;
		this.plots_showIntegration = c.default_plots_showIntegration;
		this.plots_integrationColor = c.default_plots_integrationColor;
		this.plots_integrationLineWidth = c.default_plots_integrationLineWidth;
		this.plots_showGrid = c.default_plots_showGrid;
		this.plots_gridColor = c.default_plots_gridColor;
		this.plots_gridLineWidth = c.default_plots_gridLineWidth;
		this.plots_showYAxis = c.default_plots_showYAxis;
		this.plots_flipXAxis = c.default_plots_flipXAxis;
		this.text_font_size = c.default_text_font_size;
		this.text_font_families = [];
		for ( var i = 0, ii = c.default_text_font_families.length; i < ii; i++) {
			this.text_font_families[i] = c.default_text_font_families[i];
		}
		this.text_color = c.default_text_color;

		this.set3DRepresentation = function(representation)
		{
			this.atoms_display = true;
			this.bonds_display = true;
			this.bonds_color = '#777777';
			this.atoms_useVDWDiameters_3D = true;
			this.atoms_useJMOLColors = true;
			this.bonds_useJMOLColors = true;
			this.bonds_showBondOrders_3D = true;
			if (representation == 'Ball and Stick') {
				this.atoms_vdwMultiplier_3D = .3;
				this.bonds_useJMOLColors = false;
				this.bonds_cylinderDiameter_3D = .3;
				this.bonds_materialAmbientColor_3D = c.default_atoms_materialAmbientColor_3D;
			} else if (representation == 'van der Waals Spheres') {
				this.bonds_display = false;
				this.atoms_vdwMultiplier_3D = 1;
			} else if (representation == 'Stick') {
				this.atoms_useVDWDiameters_3D = false;
				this.bonds_showBondOrders_3D = false;
				this.bonds_cylinderDiameter_3D = this.atoms_sphereDiameter_3D = .8;
				this.bonds_materialAmbientColor_3D = this.atoms_materialAmbientColor_3D;
			} else if (representation == 'Wireframe') {
				this.atoms_useVDWDiameters_3D = false;
				this.bonds_cylinderDiameter_3D = .05;
				this.atoms_sphereDiameter_3D = .15;
				this.bonds_materialAmbientColor_3D = c.default_atoms_materialAmbientColor_3D;
			} else {
				alert('"' + representation + '" is not recognized. Use one of the following strings:\n\n' + '1. Ball and Stick\n' + '2. van der Waals Spheres\n' + '3. Stick\n' + '4. Wireframe\n');
			}
		};
		this.getFontString = function(size, families, bold, italic) {
			var sb = [];
			if(bold){
				sb.push('bold ');
			}
			if(italic){
				sb.push('italic ');
			}
			sb.push(size + 'px ');
			for ( var i = 0, ii = families.length; i < ii; i++) {
				var use = families[i];
				if (use.indexOf(' ') != -1) {
					use = '"' + use + '"';
				}
				sb.push((i != 0 ? ',' : '') + use);
			}
			return sb.join('');
		};
	};
})(ChemDoodle, ChemDoodle.structures, Math);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3103 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-20 12:58:08 -0500 (Sun, 20 Feb 2011) $
//
(function(c, ELEMENT, informatics, structures)
{
	informatics.getPointsPerAngstrom = function()
	{
		return c.default_bondLength_2D / c.default_angstromsPerBondLength;
	};

	informatics.BondDeducer = function()
	{
		this.margin = 1.1;
		this.deduceCovalentBonds = function(molecule, customPointsPerAngstrom) {
			var pointsPerAngstrom = informatics.getPointsPerAngstrom();
			if (customPointsPerAngstrom) {
				pointsPerAngstrom = customPointsPerAngstrom;
			}
			for ( var i = 0, ii = molecule.atoms.length; i < ii; i++) {
				for ( var j = i + 1; j < ii; j++) {
					var first = molecule.atoms[i];
					var second = molecule.atoms[j];
					if (first.distance3D(second) < (ELEMENT[first.label].covalentRadius + ELEMENT[second.label].covalentRadius) * pointsPerAngstrom * this.margin) {
						molecule.bonds.push(new structures.Bond(first, second, 1));
					}
				}
			}
		};
		return true;
	};
})(ChemDoodle, ChemDoodle.ELEMENT, ChemDoodle.informatics, ChemDoodle.structures);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3103 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-20 12:58:08 -0500 (Sun, 20 Feb 2011) $
//
(function(informatics)
{
	informatics.HydrogenDeducer = function() {
		this.removeHydrogens = function(molecule)
		{
			var atoms = [];
			var bonds = [];
			for ( var i = 0, ii = molecule.bonds.length; i < ii; i++) {
				if (molecule.bonds[i].a1.label != 'H' && molecule.bonds[i].a2.label != 'H') {
					bonds.push(molecule.bonds[i]);
				}
			}
			for ( var i = 0, ii = molecule.atoms.length; i < ii; i++) {
				if (molecule.atoms[i].label != 'H') {
					atoms.push(molecule.atoms[i]);
				}
			}
			molecule.atoms = atoms;
			molecule.bonds = bonds;
		};
		return true;
	};
})(ChemDoodle.informatics);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(informatics, structures)
{
	informatics.StructureBuilder = function() {
		this.copy = function(molecule) {
			for ( var i = 0, ii = molecule.atoms.length; i < ii; i++) {
				molecule.atoms[i].metaID = i;
			}
			var newMol = new structures.Molecule();
			for ( var i = 0, ii = molecule.atoms.length; i < ii; i++) {
				newMol.atoms[i] = new structures.Atom(molecule.atoms[i].label, molecule.atoms[i].x, molecule.atoms[i].y, molecule.atoms[i].z);
			}
			for ( var i = 0, ii = molecule.bonds.length; i < ii; i++) {
				newMol.bonds[i] = new structures.Bond(newMol.atoms[molecule.bonds[i].a1.metaID], newMol.atoms[molecule.bonds[i].a2.metaID], molecule.bonds[i].bondOrder);
			}
			return newMol;
		};
		return true;
	};
})(ChemDoodle.informatics, ChemDoodle.structures);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(informatics)
{
	informatics._Counter = function() {
		this.value = 0;
		this.molecule = null;
		this.setMolecule = function(molecule) {
			this.value = 0;
			this.molecule = molecule;
			if (this.innerCalculate) {
				this.innerCalculate();
			}
		};
		return true;
	};
})(ChemDoodle.informatics);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(informatics)
{
	informatics.FrerejacqueNumberCounter = function(molecule) {
		this.setMolecule(molecule);
		return true;
	};
	informatics.FrerejacqueNumberCounter.prototype = new informatics._Counter();
	informatics.FrerejacqueNumberCounter.prototype.innerCalculate = function() {
		this.value = this.molecule.bonds.length - this.molecule.atoms.length + new informatics.NumberOfMoleculesCounter(this.molecule).value;
	};
})(ChemDoodle.informatics);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(structures, informatics)
{
	informatics.NumberOfMoleculesCounter = function(molecule) {
		this.setMolecule(molecule);
		return true;
	};
	informatics.NumberOfMoleculesCounter.prototype = new informatics._Counter();
	informatics.NumberOfMoleculesCounter.prototype.innerCalculate = function() {
		for ( var i = 0, ii = this.molecule.atoms.length; i < ii; i++) {
			this.molecule.atoms[i].visited = false;
		}
		for ( var i = 0, ii = this.molecule.atoms.length; i < ii; i++) {
			if (!this.molecule.atoms[i].visited) {
				this.value++;
				var q = new structures.Queue();
				this.molecule.atoms[i].visited = true;
				q.enqueue(this.molecule.atoms[i]);
				while (!q.isEmpty()) {
					var atom = q.dequeue();
					for ( var j = 0, jj = this.molecule.bonds.length; j < jj; j++) {
						if (this.molecule.bonds[j].contains(atom)) {
							var neigh = this.molecule.bonds[j].getNeighbor(atom);
							if (!neigh.visited) {
								neigh.visited = true;
								q.enqueue(neigh);
							}
						}
					}
				}
			}
		}
	};
})(ChemDoodle.structures, ChemDoodle.informatics);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3103 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-20 12:58:08 -0500 (Sun, 20 Feb 2011) $
//
(function(informatics, inArray)
{
	informatics._RingFinder = function() {
		this.atoms = null;
		this.bonds = null;
		this.rings = null;
		this.reduce = function(molecule) {
			for ( var i = 0, ii = molecule.atoms.length; i < ii; i++) {
				molecule.atoms[i].visited = false;
			}
			for ( var i = 0, ii = molecule.bonds.length; i < ii; i++) {
				molecule.bonds[i].visited = false;
			}
			var cont = true;
			while (cont) {
				cont = false;
				for ( var i = 0, ii = molecule.atoms.length; i < ii; i++) {
					var count = 0;
					var bond = null;
					for ( var j = 0, jj = molecule.bonds.length; j < jj; j++) {
						if (molecule.bonds[j].contains(molecule.atoms[i]) && !molecule.bonds[j].visited) {
							count++;
							if (count == 2) {
								break;
							}
							bond = molecule.bonds[j];
						}
					}
					if (count == 1) {
						cont = true;
						bond.visited = true;
						molecule.atoms[i].visited = true;
					}
				}
			}
			for ( var i = 0, ii = molecule.atoms.length; i < ii; i++) {
				if (!molecule.atoms[i].visited) {
					this.atoms.push(molecule.atoms[i]);
				}
			}
			for ( var i = 0, ii = molecule.bonds.length; i < ii; i++) {
				if (!molecule.bonds[i].visited) {
					this.bonds.push(molecule.bonds[i]);
				}
			}
			if (this.bonds.length == 0 && this.atoms.length != 0) {
				this.atoms = [];
			}
		};
		this.setMolecule = function(molecule) {
			this.atoms = [];
			this.bonds = [];
			this.rings = [];
			this.reduce(molecule);
			if (this.atoms.length > 2 && this.innerGetRings) {
				this.innerGetRings();
			}
		};
		this.fuse = function() {
			for ( var i = 0, ii = this.rings.length; i < ii; i++) {
				for ( var j = 0, jj = this.bonds.length; j < jj; j++) {
					if (inArray(this.bonds[j].a1, this.rings[i].atoms) != -1 && inArray(this.bonds[j].a2, this.rings[i].atoms) != -1) {
						this.rings[i].bonds.push(this.bonds[j]);
					}
				}
			}
		};
		return true;
	};
})(ChemDoodle.informatics, jQuery.inArray);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3103 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-20 12:58:08 -0500 (Sun, 20 Feb 2011) $
//
(function(informatics, structures, inArray)
{
	function Finger(a, from) {
		this.atoms = [];
		if (from) {
			for ( var i = 0, ii = from.atoms.length; i < ii; i++) {
				this.atoms[i] = from.atoms[i];
			}
		}
		this.atoms.push(a);
		this.grow = function(bonds, blockers) {
			var last = this.atoms[this.atoms.length - 1];
			var neighs = [];
			for ( var i = 0, ii = bonds.length; i < ii; i++) {
				if (bonds[i].contains(last)) {
					var neigh = bonds[i].getNeighbor(last);
					if (inArray(neigh, blockers) == -1) {
						neighs.push(neigh);
					}
				}
			}
			var returning = [];
			for ( var i = 0, ii = neighs.length; i < ii; i++) {
				returning.push(new Finger(neighs[i], this));
			}
			return returning;
		};
		this.check = function(bonds, finger, a) {
			// check that they dont contain similar parts
			for ( var i = 0, ii = finger.atoms.length - 1; i < ii; i++) {
				if (inArray(finger.atoms[i], this.atoms) != -1) {
					return null;
				}
			}
			var ring = null;
			// check if fingers meet at tips
			if (finger.atoms[finger.atoms.length - 1] == this.atoms[this.atoms.length - 1]) {
				ring = new structures.Ring();
				ring.atoms[0] = a;
				for ( var i = 0, ii = this.atoms.length; i < ii; i++) {
					ring.atoms.push(this.atoms[i]);
				}
				for ( var i = finger.atoms.length - 2; i >= 0; i--) {
					ring.atoms.push(finger.atoms[i]);
				}
			} else {
				// check if fingers meet at bond
				var endbonds = [];
				for ( var i = 0, ii = bonds.length; i < ii; i++) {
					if (bonds[i].contains(finger.atoms[finger.atoms.length - 1])) {
						endbonds.push(bonds[i]);
					}
				}
				for ( var i = 0, ii = endbonds.length; i < ii; i++) {
					if ((finger.atoms.length == 1 || !endbonds[i].contains(finger.atoms[finger.atoms.length - 2])) && endbonds[i].contains(this.atoms[this.atoms.length - 1])) {
						ring = new structures.Ring();
						ring.atoms[0] = a;
						for ( var j = 0, jj = this.atoms.length; j < jj; j++) {
							ring.atoms.push(this.atoms[j]);
						}
						for ( var j = finger.atoms.length - 1; j >= 0; j--) {
							ring.atoms.push(finger.atoms[j]);
						}
						break;
					}
				}
			}
			return ring;
		};
		return true;
	}

	informatics.EulerFacetRingFinder = function(molecule) {
		this.fingerBreak = 5;
		this.setMolecule(molecule);
		return true;
	};
	informatics.EulerFacetRingFinder.prototype = new informatics._RingFinder();
	informatics.EulerFacetRingFinder.prototype.innerGetRings = function() {
		for ( var i = 0, ii = this.atoms.length; i < ii; i++) {
			var neigh = [];
			for ( var j = 0, jj = this.bonds.length; j < jj; j++) {
				if (this.bonds[j].contains(this.atoms[i])) {
					neigh.push(this.bonds[j].getNeighbor(this.atoms[i]));
				}
			}
			for ( var j = 0, jj = neigh.length; j < jj; j++) {
				// weird that i can't optimize this loop without breaking a test
				// case...
				for ( var k = j + 1; k < neigh.length; k++) {
					var fingers = [];
					fingers[0] = new Finger(neigh[j]);
					fingers[1] = new Finger(neigh[k]);
					var blockers = [];
					blockers[0] = this.atoms[i];
					for ( var l = 0, ll = neigh.length; l < ll; l++) {
						if (l != j && l != k) {
							blockers.push(neigh[l]);
						}
					}
					var found = [];
					// check for 3 membered ring
					var three = fingers[0].check(this.bonds, fingers[1], this.atoms[i]);
					if (three) {
						found[0] = three;
					}
					while (found.length == 0 && fingers.length > 0 && fingers[0].atoms.length < this.fingerBreak) {
						var newfingers = [];
						for ( var l = 0, ll = fingers.length; l < ll; l++) {
							var adding = fingers[l].grow(this.bonds, blockers);
							for ( var m = 0, mm = adding.length; m < mm; m++) {
								newfingers.push(adding[m]);
							}
						}
						fingers = newfingers;
						for ( var l = 0, ll = fingers.length; l < ll; l++) {
							for ( var m = l + 1; m < ll; m++) {
								var r = fingers[l].check(this.bonds, fingers[m], this.atoms[i]);
								if (r) {
									found.push(r);
								}
							}
						}
						if (found.length == 0) {
							var newBlockers = [];
							for ( var l = 0, ll = blockers.length; l < ll; l++) {
								for ( var m = 0, mm = this.bonds.length; m < mm; m++) {
									if (this.bonds[m].contains(blockers[l])) {
										var neigh = this.bonds[m].getNeighbor(blockers[l]);
										if (inArray(neigh, blockers) == -1 && inArray(neigh, newBlockers) == -1) {
											newBlockers.push(neigh);
										}
									}
								}
							}
							for ( var l = 0, ll = newBlockers.length; l < ll; l++) {
								blockers.push(newBlockers[l]);
							}
						}
					}
					if (found.length > 0) {
						var use = null;
						for ( var l = 0, ll = found.length; l < ll; l++) {
							if (!use || use.atoms.length > found[l].atoms.length) {
								use = found[l];
							}
						}
						var already = false;
						for ( var l = 0, ll = this.rings.length; l < ll; l++) {
							var all = true;
							for ( var m = 0, mm = use.atoms.length; m < mm; m++) {
								if (inArray(use.atoms[m], this.rings[l].atoms) == -1) {
									all = false;
									break;
								}
							}
							if (all) {
								already = true;
								break;
							}
						}
						if (!already) {
							this.rings.push(use);
						}
					}
				}
			}
		}
		this.fuse();
	};
})(ChemDoodle.informatics, ChemDoodle.structures, jQuery.inArray);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3103 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-20 12:58:08 -0500 (Sun, 20 Feb 2011) $
//
(function(informatics)
{
	informatics.SSSRFinder = function(molecule) {
		this.rings = [];
		if (molecule.atoms.length > 0) {
			var frerejacqueNumber = new informatics.FrerejacqueNumberCounter(molecule).value;
			var all = new informatics.EulerFacetRingFinder(molecule).rings;
			all.sort(function(a, b) {
				return a.atoms.length - b.atoms.length;
			});
			for ( var i = 0, ii = molecule.bonds.length; i < ii; i++) {
				molecule.bonds[i].visited = false;
			}
			for ( var i = 0, ii = all.length; i < ii; i++) {
				var use = false;
				for ( var j = 0, jj = all[i].bonds.length; j < jj; j++) {
					if (!all[i].bonds[j].visited) {
						use = true;
						break;
					}
				}
				if (use) {
					for ( var j = 0, jj = all[i].bonds.length; j < jj; j++) {
						all[i].bonds[j].visited = true;
					}
					this.rings.push(all[i]);
				}
				if (this.rings.length == frerejacqueNumber) {
					break;
				}
			}
		}
		return true;
	};
})(ChemDoodle.informatics);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(c, ELEMENT, io, structures, inArray)
{
	function fit(data, length)
	{
		var size = data.length;
		var padding = '';
		for ( var i = 0; i < length - size; i++) {
			padding = padding + ' ';
		}
		return padding + data;
	}

	io.MOLInterpreter = function()
	{
		this.read = function(content, multiplier) {
			var save = c.default_bondLength_2D;
			if (multiplier) {
				c.default_bondLength_2D = multiplier;
			}
			var molecule = new structures.Molecule();
			if (content == null || content.length == 0) {
				return molecule;
			}
			var currentTagTokens = content.split("\n");

			var counts = currentTagTokens[3];
			var numAtoms = parseInt(counts.substring(0, 3));
			var numBonds = parseInt(counts.substring(3, 6));

			for ( var i = 0; i < numAtoms; i++) {
				var line = currentTagTokens[4 + i];
				molecule.atoms[i] = new structures.Atom(line.substring(31, 34), parseFloat(line.substring(0, 10)) * c.default_bondLength_2D, -parseFloat(line.substring(10, 20)) * c.default_bondLength_2D, parseFloat(line.substring(20, 30)) * c.default_bondLength_2D);
				var massDif = parseInt(line.substring(34, 36));
				if (massDif != 0 && ELEMENT[molecule.atoms[i].label] != null) {
					molecule.atoms[i].mass = ELEMENT[molecule.atoms[i].label].mass + massDif;
				}
				switch (parseInt(line.substring(36, 39))) {
				case 1:
					molecule.atoms[i].charge = 3;
					break;
				case 2:
					molecule.atoms[i].charge = 2;
					break;
				case 3:
					molecule.atoms[i].charge = 1;
					break;
				case 5:
					molecule.atoms[i].charge = -1;
					break;
				case 6:
					molecule.atoms[i].charge = -2;
					break;
				case 7:
					molecule.atoms[i].charge = -3;
					break;
				}
			}
			for ( var i = 0; i < numBonds; i++) {
				var line = currentTagTokens[4 + numAtoms + i];
				var bondOrder = parseInt(line.substring(6, 9));
				var stereo = parseInt(line.substring(9, 12));
				if (bondOrder > 3) {
					switch (bondOrder) {
					case 4:
						bondOrder = 1.5;
						break;
					default:
						bondOrder = 1;
						break;
					}
				}
				var b = new structures.Bond(molecule.atoms[parseInt(line.substring(0, 3)) - 1], molecule.atoms[parseInt(line.substring(3, 6)) - 1], bondOrder);
				switch (stereo) {
				case 3:
					b.stereo = structures.Bond.STEREO_AMBIGUOUS;
					break;
				case 1:
					b.stereo = structures.Bond.STEREO_PROTRUDING;
					break;
				case 6:
					b.stereo = structures.Bond.STEREO_RECESSED;
					break;
				}
				molecule.bonds[i] = b;
			}
			if (multiplier) {
				c.default_bondLength_2D = save;
			}
			return molecule;
		};

		this.write = function(molecule)
		{
			var content = 'Molecule from ChemDoodle Web Components\n\nhttp://www.ichemlabs.com\n';
			content = content + fit(molecule.atoms.length.toString(), 3) + fit(molecule.bonds.length.toString(), 3) + '  0  0  0  0            999 v2000\n';
			var p = molecule.getCenter();
			for ( var i = 0, ii = molecule.atoms.length; i < ii; i++) {
				var a = molecule.atoms[i];
				var mass = ' 0';
				if (a.mass != -1 && ELEMENT[a.label] != null) {
					var dif = a.mass - ELEMENT[a.label].mass;
					if (dif < 5 && dif > -4) {
						mass = (dif > -1 ? ' ' : '') + dif;
					}
				}
				var charge = '  0';
				if (a.charge != 0) {
					switch (a.charge) {
					case 3:
						charge = '  1';
						break;
					case 2:
						charge = '  2';
						break;
					case 1:
						charge = '  3';
						break;
					case -1:
						charge = '  5';
						break;
					case -2:
						charge = '  6';
						break;
					case -3:
						charge = '  7';
						break;
					}
				}
				content = content + fit(((a.x - p.x) / c.default_bondLength_2D).toFixed(4), 10) + fit((-(a.y - p.y) / c.default_bondLength_2D).toFixed(4), 10) + fit((a.z / c.default_bondLength_2D).toFixed(4), 10) + ' ' + fit(a.label, 3) + mass + charge + '  0  0  0  0\n';
			}
			for ( var i = 0, ii = molecule.bonds.length; i < ii; i++) {
				var b = molecule.bonds[i];
				var stereo = 0;
				if (b.stereo == structures.Bond.STEREO_AMBIGUOUS) {
					stereo = 3;
				} else if (b.stereo == structures.Bond.STEREO_PROTRUDING) {
					stereo = 1;
				} else if (b.stereo == structures.Bond.STEREO_RECESSED) {
					stereo = 6;
				}
				content = content + fit((inArray(b.a1, molecule.atoms) + 1).toString(), 3) + fit((inArray(b.a2, molecule.atoms) + 1).toString(), 3) + fit(b.bondOrder.toString(), 3) + '  ' + stereo + '     0  0\n';
			}
			content = content + 'M  END';
			return content;
		};
	};

	// shortcuts
	var interpreter = new io.MOLInterpreter();
	c.readMOL = function(content, multiplier) {
		return interpreter.read(content, multiplier);
	};
	c.writeMOL = function(mol) {
		return interpreter.write(mol);
	};

})(ChemDoodle, ChemDoodle.ELEMENT, ChemDoodle.io, ChemDoodle.structures, jQuery.inArray);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3155 $
//  $Author: kevin $
//  $LastChangedDate: 2011-03-10 10:16:04 -0500 (Thu, 10 Mar 2011) $
//
(function(c, extensions, io, structures, trim)
{
	io.PDBInterpreter = function()
	{
		function checkContained(residue, set, chainID, index, helix) {
			for ( var j = 0, jj = set.length; j < jj; j++) {
				var check = set[j];
				if (check.id == chainID && index >= check.start && index <= check.end) {
					if (helix) {
						residue.helix = true;
					} else {
						residue.sheet = true;
					}
					if (index + 1 == check.end) {
						residue.arrow = true;
					}
					return;
				}
			}
		}

		this.read = function(content, multiplier) {
			var molecule = new structures.Molecule();
			molecule.chains = [];
			if (content == null || content.length == 0) {
				return molecule;
			}
			var currentTagTokens = content.split('\n');
			if (!multiplier) {
				multiplier = 1;
			}
			var helices = [];
			var sheets = [];
			var firstN = null;
			var lastC = null;
			var unclaimedCarbonyl = null;
			var currentChain = [];
			for ( var i = 0, ii = currentTagTokens.length; i < ii; i++) {
				var line = currentTagTokens[i];
				if (extensions.stringStartsWith(line, 'HELIX')) {
					helices.push({
						id : line.substring(19, 20),
						start : parseInt(line.substring(21, 25)),
						end : parseInt(line.substring(33, 37))
					});
				} else if (extensions.stringStartsWith(line, 'SHEET')) {
					sheets.push({
						id : line.substring(21, 22),
						start : parseInt(line.substring(22, 26)),
						end : parseInt(line.substring(33, 37))
					});
				} else if (extensions.stringStartsWith(line, 'ATOM')) {
					var altLoc = line.substring(16, 17);
					if (altLoc == ' ' || altLoc == 'A') {
						var a = new structures.Atom(line.substring(76, 78), parseFloat(line.substring(30, 38)) * multiplier, -parseFloat(line.substring(46, 54)) * multiplier, parseFloat(line.substring(38, 46) * multiplier));
						a.resSeq = parseInt(line.substring(22, 26));
						molecule.atoms.push(a);
						var residueName = trim(line.substring(12, 16));
						if (residueName == 'CA' || residueName == 'C3\'') {
							if (residueName == 'C3\'') {
								firstN = a;
							}
							if (currentChain.length == 0) {
								for ( var j = 0; j < 2; j++) {
									var dummyFront = new structures.Residue(firstN);
									dummyFront.carbonylOxygen = a;
									currentChain.push(dummyFront);
								}
							}
							var r = new structures.Residue(a);
							r.name = trim(line.substring(17, 20));
							if (r.name.length == 3) {
								r.name = r.name.substring(0, 1) + r.name.substring(1).toLowerCase();
							} else {
								if (r.name.length == 2 && r.name.charAt(0) == 'D') {
									r.name = r.name.substring(1);
								}
							}
							if(unclaimedCarbonyl!=null && unclaimedCarbonyl.resSeq==a.resSeq){
								r.carbonylOxygen = a;
							}
							unclaimedCarbonyl = null;
							currentChain.push(r);
							// need to subtract 1 to ignore first dummy in
							// front,
							// second dummy represents start, indexing starts at
							// 1,
							// not 0
							var chainID = line.substring(21, 22);
							checkContained(r, helices, chainID, a.resSeq, true);
							checkContained(r, sheets, chainID, a.resSeq, false);
						} else if (residueName == 'O' || residueName == 'C1\'') {
							if (residueName == 'C1\'') {
								lastC = a;
							}
							var lastRes = currentChain[currentChain.length - 1];
							if(lastRes.alphaCarbon.resSeq==a.resSeq){
								currentChain[currentChain.length - 1].carbonylOxygen = a;
							}else{
								unclaimedCarbonyl = a;
							}
						} else if (residueName == 'N' && !firstN) {
							firstN = a;
						} else if (residueName == 'C') {
							lastC = a;
						}
					}
				} else if (extensions.stringStartsWith(line, 'HETATM')) {
					var symbol = trim(line.substring(76, 78));
					if(symbol.length>1){
						symbol = symbol.substring(0,1)+symbol.substring(1).toLowerCase();
					}
					molecule.atoms.push(new structures.Atom(symbol, parseFloat(line.substring(30, 38)) * multiplier, -parseFloat(line.substring(46, 54)) * multiplier, parseFloat(line.substring(38, 46) * multiplier)));
				} else if (extensions.stringStartsWith(line, 'TER')) {
					this.endChain(molecule, currentChain, lastC);
					currentChain = [];
					firstN = null;
				} else if (extensions.stringStartsWith(line, 'ENDMDL')) {
					break;
				}
			}
			this.endChain(molecule, currentChain, lastC);
			new c.informatics.BondDeducer().deduceCovalentBonds(molecule, multiplier);
			return molecule;
		};
		this.endChain = function(molecule, chain, lastC) {
			if (chain.length > 0) {
				if (!chain[chain.length - 1].carbonylOxygen) {
					chain[chain.length - 1].carbonylOxygen = chain[chain.length - 1];
				}
				for ( var i = 0; i < 4; i++) {
					var dummyEnd = new structures.Residue(lastC);
					dummyEnd.carbonylOxygen = chain[chain.length - 1].carbonylOxygen;
					chain.push(dummyEnd);
				}
				molecule.chains.push(chain);
			}
		};
	};

	// shortcuts
	var interpreter = new io.PDBInterpreter();
	c.readPDB = function(content, multiplier) {
		return interpreter.read(content, multiplier);
	};

})(ChemDoodle, ChemDoodle.extensions, ChemDoodle.io, ChemDoodle.structures, jQuery.trim);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3160 $
//  $Author: kevin $
//  $LastChangedDate: 2011-03-12 18:27:31 -0500 (Sat, 12 Mar 2011) $
//
(function(c, extensions, io, structures, q, trim)
{
	var SQZ_HASH = {
		'@' : 0,
		'A' : 1,
		'B' : 2,
		'C' : 3,
		'D' : 4,
		'E' : 5,
		'F' : 6,
		'G' : 7,
		'H' : 8,
		'I' : 9,
		'a' : -1,
		'b' : -2,
		'c' : -3,
		'd' : -4,
		'e' : -5,
		'f' : -6,
		'g' : -7,
		'h' : -8,
		'i' : -9
	}, DIF_HASH = {
		'%' : 0,
		'J' : 1,
		'K' : 2,
		'L' : 3,
		'M' : 4,
		'N' : 5,
		'O' : 6,
		'P' : 7,
		'Q' : 8,
		'R' : 9,
		'j' : -1,
		'k' : -2,
		'l' : -3,
		'm' : -4,
		'n' : -5,
		'o' : -6,
		'p' : -7,
		'q' : -8,
		'r' : -9
	}, DUP_HASH = {
		'S' : 1,
		'T' : 2,
		'U' : 3,
		'V' : 4,
		'W' : 5,
		'X' : 6,
		'Y' : 7,
		'Z' : 8,
		's' : 9
	};

	io.JCAMPInterpreter = function() {
		this.convertHZ2PPM = false;
		this.read = function(content) {
			this.isBreak = function(c) {
				return SQZ_HASH[c] != null || DIF_HASH[c] != null || DUP_HASH[c] != null || c == ' ' || c == '-' || c == '+';
			};
			this.getValue = function(decipher, lastDif) {
				var first = decipher.charAt(0);
				var rest = decipher.substring(1);
				if (SQZ_HASH[first] != null) {
					return parseFloat(SQZ_HASH[first] + rest);
				} else if (DIF_HASH[first] != null) {
					return parseFloat(DIF_HASH[first] + rest) + lastDif;
				}
				return parseFloat(rest);
			};
			var spectrum = new structures.Spectrum();
			if (content == null || content.length == 0) {
				return spectrum;
			}
			var lines = content.split('\n');
			var sb = [];
			var xLast, xFirst, yFirst, nPoints, xFactor = 1, yFactor = 1, observeFrequency = 1, deltaX = -1;
			var recordMeta = true, divideByFrequency = false;
			for ( var i = 0, ii = lines.length; i < ii; i++) {
				var use = trim(lines[i]);
				var index = q.inArray('$$', use);
				if (index != -1) {
					use = use.substring(0, index);
				}
				if (sb.length == 0 || !extensions.stringStartsWith(lines[i], '##')) {
					if (sb.length != 0) {
						sb.push('\n');
					}
					sb.push(trim(use));
				} else {
					var currentRecord = sb.join('');
					if (recordMeta && currentRecord.length < 100) {
						spectrum.metadata.push(currentRecord);
					}
					sb = [ use ];
					if (extensions.stringStartsWith(currentRecord, '##TITLE=')) {
						spectrum.title = trim(currentRecord.substring(8));
					} else if (extensions.stringStartsWith(currentRecord, '##XUNITS=')) {
						spectrum.xUnit = trim(currentRecord.substring(9));
						if (this.convertHZ2PPM && spectrum.xUnit.toUpperCase() == 'HZ') {
							spectrum.xUnit = 'PPM';
							divideByFrequency = true;
						}
					} else if (extensions.stringStartsWith(currentRecord, '##YUNITS=')) {
						spectrum.yUnit = trim(currentRecord.substring(9));
					} else if (extensions.stringStartsWith(currentRecord, '##XYPAIRS=')) {
						// spectrum.yUnit =
						// trim(currentRecord.substring(9));
					} else if (extensions.stringStartsWith(currentRecord, '##FIRSTX=')) {
						xFirst = parseFloat(trim(currentRecord.substring(9)));
					} else if (extensions.stringStartsWith(currentRecord, '##LASTX=')) {
						xLast = parseFloat(trim(currentRecord.substring(8)));
					} else if (extensions.stringStartsWith(currentRecord, '##FIRSTY=')) {
						yFirst = parseFloat(trim(currentRecord.substring(9)));
					} else if (extensions.stringStartsWith(currentRecord, '##NPOINTS=')) {
						nPoints = parseFloat(trim(currentRecord.substring(10)));
					} else if (extensions.stringStartsWith(currentRecord, '##XFACTOR=')) {
						xFactor = parseFloat(trim(currentRecord.substring(10)));
					} else if (extensions.stringStartsWith(currentRecord, '##YFACTOR=')) {
						yFactor = parseFloat(trim(currentRecord.substring(10)));
					} else if (extensions.stringStartsWith(currentRecord, '##DELTAX=')) {
						deltaX = parseFloat(trim(currentRecord.substring(9)));
					} else if (extensions.stringStartsWith(currentRecord, '##.OBSERVE FREQUENCY=')) {
						if (this.convertHZ2PPM) {
							observeFrequency = parseFloat(trim(currentRecord.substring(21)));
						}
					} else if (extensions.stringStartsWith(currentRecord, '##XYDATA=')) {
						if (!divideByFrequency) {
							observeFrequency = 1;
						}
						recordMeta = false;
						var lastWasDif = false;
						var innerLines = currentRecord.split('\n');
						var abscissaSpacing = (xLast - xFirst) / (nPoints - 1);
						// use provided deltaX if determined to be compressed and discontinuous
						if (deltaX != -1) {
							for ( var j = 1, jj = innerLines.length; j < jj; j++) {
								if (innerLines[j].charAt(0) == '|') {
									abscissaSpacing = deltaX;
									break;
								}
							}
						}
						var lastX = xFirst - abscissaSpacing;
						var lastY = yFirst;
						var lastDif = 0;
						var lastOrdinate;
						for ( var j = 1, jj = innerLines.length; j < jj; j++) {
							var data = [];
							var read = trim(innerLines[j]);
							var sb = [];
							var isCompressedDiscontinuous = false;
							for ( var k = 0, kk = read.length; k < kk; k++) {
								if (this.isBreak(read.charAt(k))) {
									if (sb.length > 0 && !(sb.length == 1 && sb[0] == ' ')) {
										data.push(sb.join(''));
									}
									sb = [ read.charAt(k) ];
								} else {
									if (read.charAt(k) == '|') {
										isCompressedDiscontinuous = true;
									} else {
										sb.push(read.charAt(k));
									}
								}
							}
							data.push(sb.join(''));
							lastX = parseFloat(data[0]) * xFactor - abscissaSpacing;
							for ( var k = 1, kk = data.length; k < kk; k++) {
								var decipher = data[k];
								if (DUP_HASH[decipher.charAt(0)] != null) {
									// be careful when reading this, to keep
									// spectra efficient, DUPS are actually
									// discarded, except the last y!
									var dup = parseInt(DUP_HASH[decipher.charAt(0)] + decipher.substring(1)) - 1;
									for ( var l = 0; l < dup; l++) {
										lastX += abscissaSpacing;
										lastDif = this.getValue(lastOrdinate, lastDif);
										lastY = lastDif * yFactor;
										count++;
										spectrum.data[spectrum.data.length - 1] = new structures.Point(lastX / observeFrequency, lastY);
									}
								} else {
									if (!(SQZ_HASH[decipher.charAt(0)] != null && lastWasDif)) {
										lastWasDif = DIF_HASH[decipher.charAt(0)] != null;
										lastOrdinate = decipher;
										lastX += abscissaSpacing;
										lastDif = this.getValue(decipher, lastDif);
										lastY = lastDif * yFactor;
										count++;
										spectrum.data.push(new structures.Point(lastX / observeFrequency, lastY));
									} else {
										lastY = this.getValue(decipher, lastDif) * yFactor;
										if (isCompressedDiscontinuous) {
											lastX += abscissaSpacing;
											spectrum.data.push(new structures.Point(lastX / observeFrequency, lastY));
										}
									}
								}
							}
						}
					} else if (extensions.stringStartsWith(currentRecord, '##PEAK TABLE=')) {
						recordMeta = false;
						spectrum.continuous = false;
						var innerLines = currentRecord.split('\n');
						var count = 0;
						for ( var j = 1, jj = innerLines.length; j < jj; j++) {
							var items = innerLines[j].split(/[\s,]+/);
							count += items.length / 2;
							for ( var k = 0, kk = items.length; k + 1 < kk; k += 2) {
								spectrum.data.push(new structures.Point(parseFloat(trim(items[k])), parseFloat(trim(items[k + 1]))));
							}
						}
					}
				}
			}
			spectrum.setup();
			return spectrum;
		};
	};

	// shortcuts
	var interpreter = new io.JCAMPInterpreter();
	interpreter.convertHZ2PPM = true;
	c.readJCAMP = function(content) {
		return interpreter.read(content);
	};
})(ChemDoodle, ChemDoodle.extensions, ChemDoodle.io, ChemDoodle.structures, jQuery, jQuery.trim);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 2934 $
//  $Author: kevin $
//  $LastChangedDate: 2010-12-08 20:53:47 -0500 (Wed, 08 Dec 2010) $
//
(function(io, structures, inArray)
{
	io.fromJSONChains = function(content) {
		var chains = [];
		for ( var i = 0, ii = content.cs.length; i < ii; i++) {
			var chain = content.cs[i];
			var c = [];
			for ( var j = 0, jj = chain.length; j < jj; j++) {
				var convert = chain[j];
				var r = new structures.Residue();
				r.name = convert.n;
				r.alphaCarbon = {x:convert.x1,y:convert.y1,z:convert.z1};
				r.carbonylOxygen = {x:convert.x2,y:convert.y2,z:convert.z2};
				r.helix = convert.h;
				r.sheet = convert.s;
				r.arrow = convert.a;
				c.push(r);
			}
			chains.push(c);
		}
		return chains;
	};

	io.fromJSONDummy = function(content) {
		var molecule = new structures.Molecule();
		for ( var i = 0, ii = content.a.length; i < ii; i++) {
			var c = content.a[i];
			var a = new structures.Atom(c.l?c.l:'C', c.x, c.y);
			if (c.z) {
				a.z = c.z;
			}
			if (c.c) {
				a.charge = c.c;
			}
			if (c.m) {
				a.mass = c.m;
			}
			molecule.atoms.push(a);
		}
		for ( var i = 0, ii = content.b.length; i < ii; i++) {
			var c = content.b[i];
			var b = new structures.Bond(molecule.atoms[c.b], molecule.atoms[c.e], c.o?c.o:1);
			if (c.s) {
				b.stereo = c.s;
			}
			molecule.bonds.push(b);
		}
		return molecule;
	};

	io.toJSONDummy = function(molecule) {
		var dummy = {
			a : [],
			b : []
		};
		for ( var i = 0, ii = molecule.atoms.length; i < ii; i++) {
			var a = molecule.atoms[i];
			dummy.a[i] = {
				x : a.x,
				y : a.y
			};
			if(a.label!='C'){
				dummy.a[i].l = a.label;
			}
			if (a.z != 0) {
				dummy.a[i].z = a.z;
			}
			if (a.charge != 0) {
				dummy.a[i].c = a.charge;
			}
			if (a.mass != -1) {
				dummy.a[i].m = a.mass;
			}
		}
		for ( var i = 0, ii = molecule.bonds.length; i < ii; i++) {
			var b = molecule.bonds[i];
			dummy.b[i] = {
				b : inArray(b.a1, molecule.atoms),
				e : inArray(b.a2, molecule.atoms)
			};
			if (b.bondOrder != 1) {
				dummy.b[i].o = b.bondOrder;
			}
			if (b.stereo != structures.Bond.STEREO_NONE) {
				dummy.b[i].s = b.stereo;
			}
		}
		return dummy;
	};

})(ChemDoodle.io, ChemDoodle.structures, jQuery.inArray);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 2974 $
//  $Author: kevin $
//  $LastChangedDate: 2010-12-29 11:07:06 -0500 (Wed, 29 Dec 2010) $
//
ChemDoodle.monitor = (function(q, document)
{
	var m = {};

	m.CANVAS_DRAGGING = null;
	m.CANVAS_OVER = null;
	m.ALT = false;
	m.SHIFT = false;
	m.META = false;

	q(document).ready(function() {
		// handles dragging beyond the canvas bounds
		q(document).mousemove(function(e) {
			if (m.CANVAS_DRAGGING != null) {
				if (m.CANVAS_DRAGGING.drag) {
					m.CANVAS_DRAGGING.prehandleEvent(e);
					m.CANVAS_DRAGGING.drag(e);
				}
			}
		});
		q(document).mouseup(function(e) {
			if (m.CANVAS_DRAGGING != null && m.CANVAS_DRAGGING!=m.CANVAS_OVER) {
				if (m.CANVAS_DRAGGING.mouseup) {
					m.CANVAS_DRAGGING.prehandleEvent(e);
					m.CANVAS_DRAGGING.mouseup(e);
				}
			}
			m.CANVAS_DRAGGING = null;
		});
		// handles modifier keys from a single keyboard
		q(document).keydown(function(e) {
			m.SHIFT = e.shiftKey;
			m.ALT = e.altKey;
			m.META = e.metaKey;
			var affecting = m.CANVAS_OVER;
			if (m.CANVAS_DRAGGING != null) {
				affecting = m.CANVAS_DRAGGING;
			}
			if (affecting != null) {
				if (affecting.keydown) {
					affecting.prehandleEvent(e);
					affecting.keydown(e);
				}
			}
		});
		q(document).keypress(function(e) {
			var affecting = m.CANVAS_OVER;
			if (m.CANVAS_DRAGGING != null) {
				affecting = m.CANVAS_DRAGGING;
			}
			if (affecting != null) {
				if (affecting.keypress) {
					affecting.prehandleEvent(e);
					affecting.keypress(e);
				}
			}
		});
		q(document).keyup(function(e) {
			m.SHIFT = e.shiftKey;
			m.ALT = e.altKey;
			m.META = e.metaKey;
			var affecting = m.CANVAS_OVER;
			if (m.CANVAS_DRAGGING != null) {
				affecting = m.CANVAS_DRAGGING;
			}
			if (affecting != null) {
				if (affecting.keyup) {
					affecting.prehandleEvent(e);
					affecting.keyup(e);
				}
			}
		});
	});

	return m;
})(jQuery, document);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3099 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-15 19:47:54 -0500 (Tue, 15 Feb 2011) $
//
(function(c, monitor, structures, q, browser, m, document)
{
	c._Canvas = function()
	{
		this.molecule = null;
		this.emptyMessage = null;
		this.image = null;
		return true;
	};
	c._Canvas.prototype.repaint = function()
	{
		var canvas = document.getElementById(this.id);
		if (canvas.getContext) {
			var ctx = canvas.getContext('2d');
			if (this.image == null) {
				if (this.specs.backgroundColor != null)
				{
					ctx.fillStyle = this.specs.backgroundColor;
					ctx.fillRect(0, 0, this.width, this.height);
				}
			}
			else
			{
				ctx.drawImage(this.image, 0, 0);
			}
			if (this.molecule != null && this.molecule.atoms.length > 0)
			{
				ctx.save();
				ctx.translate(this.width / 2, this.height / 2);
				ctx.rotate(this.specs.rotateAngle);
				ctx.scale(this.specs.scale, this.specs.scale);
				ctx.translate(-this.width / 2, -this.height / 2);
				this.molecule.draw(ctx, this.specs);
				ctx.restore();
			}
			else if (this.emptyMessage != null)
			{
				ctx.fillStyle = '#737683';
				ctx.textAlign = 'center';
				ctx.textBaseline = 'middle';
				ctx.font = '18px Helvetica, Verdana, Arial, Sans-serif';
				ctx.fillText(this.emptyMessage, this.width / 2, this.height / 2);
			}
			if (this.drawChildExtras) {
				this.drawChildExtras(ctx);
			}
		}
	};
	c._Canvas.prototype.setBackgroundImage = function(path)
	{
		this.image = new Image(); // Create new Image object
		var me = this;
		this.image.onload = function() {
			me.repaint();
		};
		this.image.src = path; // Set source path
	};
	c._Canvas.prototype.loadMolecule = function(molecule)
	{
		this.molecule = molecule;
		this.center();
		this.molecule.check();
		if (this.afterLoadMolecule) {
			this.afterLoadMolecule();
		}
		this.repaint();
	};
	c._Canvas.prototype.center = function()
	{
		var canvas = document.getElementById(this.id);
		var p = this.molecule.getCenter3D();
		var center = new structures.Atom('C', this.width / 2, this.height / 2, 0);
		center.sub3D(p);
		for ( var i = 0, ii = this.molecule.atoms.length; i < ii; i++) {
			this.molecule.atoms[i].add3D(center);
		}
		var dim = this.molecule.getDimension();
		this.specs.scale = 1;
		if (dim.x > this.width || dim.y > this.height) {
			this.specs.scale = m.min(this.width / dim.x, this.height / dim.y) * .85;
		}
	};
	c._Canvas.prototype.create = function(id, width, height)
	{
		this.id = id;
		this.width = width;
		this.height = height;
// *** MODIF SB : ENLEVE LE WRITELN CAR MARCHE PAS AVEC AJAX ***
		if (!c.featureDetection.supports_canvas_text() && browser.msie && browser.version >= '6') {
			// Install Google Chrome Frame
			//~ document.writeln('<div style="border: 1px solid black;" width="' + width + '" height="' + height + '">Please install <a href="http://code.google.com/chrome/chromeframe/">Google Chrome Frame</a>, then restart Internet Explorer.</div>');
		} else {
			//~ document.writeln('<canvas class="ChemDoodleWebComponent" id="' + id + '" width="' + width + '" height="' + height + '">This browser does not support HTML5/Canvas.</canvas>');
		}
// *************************************************************
		this.specs = new structures.VisualSpecifications();
		// setup input events
		// make sure prehandle events are only in if statements if handled, so
		// as not to block browser events
		var me = this;
		// for iPhone OS and Android devices
		q('#' + id).bind('touchstart', function(e) {
			var time = new Date().getTime();
			if (me.lastTouch && e.originalEvent.touches.length==1 && (time - me.lastTouch) < 500) {
				if (me.dbltap) {
					me.prehandleEvent(e);
					me.dbltap(e);
				} else if (me.dblclick) {
					me.prehandleEvent(e);
					me.dblclick(e);
				} else if (me.touchstart) {
					me.prehandleEvent(e);
					me.touchstart(e);
				} else if (me.mousedown) {
					me.prehandleEvent(e);
					me.mousedown(e);
				}
			} else if (me.touchstart) {
				me.prehandleEvent(e);
				me.touchstart(e);
			} else if (me.mousedown) {
				me.prehandleEvent(e);
				me.mousedown(e);
			}
			me.lastTouch = time;
		});
		q('#' + id).bind('touchmove', function(e) {
			if (e.originalEvent.touches.length > 1 && me.multitouchmove) {
				var numFingers = e.originalEvent.touches.length;
				me.prehandleEvent(e);
				var center = new structures.Point(-e.offset.left * numFingers, -e.offset.top * numFingers);
				for ( var i = 0; i < numFingers; i++) {
					center.x += e.originalEvent.changedTouches[i].pageX;
					center.y += e.originalEvent.changedTouches[i].pageY;
				}
				center.x /= numFingers;
				center.y /= numFingers;
				e.p = center;
				me.multitouchmove(e, numFingers);
			} else if (me.touchmove) {
				me.prehandleEvent(e);
				me.touchmove(e);
			} else if (me.drag) {
				me.prehandleEvent(e);
				me.drag(e);
			}
		});
		q('#' + id).bind('touchend', function(e) {
			if (me.touchend) {
				me.prehandleEvent(e);
				me.touchend(e);
			} else if (me.mouseup) {
				me.prehandleEvent(e);
				me.mouseup(e);
			}
		});
		q('#' + id).bind('gesturestart', function(e) {
			if (me.gesturestart) {
				me.prehandleEvent(e);
				me.gesturestart(e);
			}
		});
		q('#' + id).bind('gesturechange', function(e) {
			if (me.gesturechange) {
				me.prehandleEvent(e);
				me.gesturechange(e);
			}
		});
		q('#' + id).bind('gestureend', function(e) {
			if (me.gestureend) {
				me.prehandleEvent(e);
				me.gestureend(e);
			}
		});
		// normal events
		q('#' + id).click(function(e) {
			switch (e.which) {
			case 1:
				// left mouse button pressed
				if (me.click) {
					me.prehandleEvent(e);
					me.click(e);
				}
				break;
			case 2:
				// middle mouse button pressed
				if (me.middleclick) {
					me.prehandleEvent(e);
					me.middleclick(e);
				}
				break;
			case 3:
				// right mouse button pressed
				if (me.rightclick) {
					me.prehandleEvent(e);
					me.rightclick(e);
				}
				break;
			}
		});
		q('#' + id).dblclick(function(e) {
			if (me.dblclick) {
				me.prehandleEvent(e);
				me.dblclick(e);
			}
		});
		q('#' + id).mousedown(function(e) {
			switch (e.which) {
			case 1:
				// left mouse button pressed
				monitor.CANVAS_DRAGGING = me;
				if (me.mousedown) {
					me.prehandleEvent(e);
					me.mousedown(e);
				}
				break;
			case 2:
				// middle mouse button pressed
				if (me.middlemousedown) {
					me.prehandleEvent(e);
					me.middlemousedown(e);
				}
				break;
			case 3:
				// right mouse button pressed
				if (me.rightmousedown) {
					me.prehandleEvent(e);
					me.rightmousedown(e);
				}
				break;
			}
		});
		q('#' + id).mousemove(function(e) {
			if (monitor.CANVAS_DRAGGING == null && me.mousemove) {
				me.prehandleEvent(e);
				me.mousemove(e);
			}
		});
		q('#' + id).mouseout(function(e) {
			monitor.CANVAS_OVER = null;
			if (me.mouseout) {
				me.prehandleEvent(e);
				me.mouseout(e);
			}
		});
		q('#' + id).mouseover(function(e) {
			monitor.CANVAS_OVER = me;
			if (me.mouseover) {
				me.prehandleEvent(e);
				me.mouseover(e);
			}
		});
		q('#' + id).mouseup(function(e) {
			switch (e.which) {
			case 1:
				// left mouse button pressed
				if (me.mouseup) {
					me.prehandleEvent(e);
					me.mouseup(e);
				}
				break;
			case 2:
				// middle mouse button pressed
				if (me.middlemouseup) {
					me.prehandleEvent(e);
					me.middlemouseup(e);
				}
				break;
			case 3:
				// right mouse button pressed
				if (me.rightmouseup) {
					me.prehandleEvent(e);
					me.rightmouseup(e);
				}
				break;
			}
		});
		q('#' + id).mousewheel(function(e, delta) {
			if (me.mousewheel) {
				me.prehandleEvent(e);
				me.mousewheel(e, delta);
			}
		});
		if (this.subCreate) {
			this.subCreate();
		}
	};
	c._Canvas.prototype.getMolecule = function() {
		return this.molecule;
	};
	c._Canvas.prototype.prehandleEvent = function(e) {
		if (e.originalEvent.changedTouches) {
			e.pageX = e.originalEvent.changedTouches[0].pageX;
			e.pageY = e.originalEvent.changedTouches[0].pageY;
		}
		e.preventDefault();
		e.offset = q('#' + this.id).offset();
		e.p = new structures.Point(e.pageX - e.offset.left, e.pageY - e.offset.top);
	};
})(ChemDoodle, ChemDoodle.monitor, ChemDoodle.structures, jQuery, jQuery.browser, Math, document);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(c)
{
	c._AnimatorCanvas = function(id, width, height)
	{
		if (id) {
			this.create(id, width, height);
		}
		this.timeout = 33;
		return true;
	};
	c._AnimatorCanvas.prototype = new c._Canvas();
	c._AnimatorCanvas.prototype.startAnimation = function()
	{
		this.stopAnimation();
		this.lastTime = new Date().getTime();
		var me = this;
		if (this.nextFrame) {
			this.handle = setInterval(function() {
				//advance clock
				var timeNow = new Date().getTime();
				//update and repaint
				me.nextFrame(timeNow - me.lastTime);
				me.repaint();
				me.lastTime = timeNow;
			}, this.timeout);
		}
	};
	c._AnimatorCanvas.prototype.stopAnimation = function()
	{
		if (this.handle != null) {
			clearInterval(this.handle);
			this.handle = null;
		}
	};
	c._AnimatorCanvas.prototype.isRunning = function()
	{
		return this.handle != null;
	};
})(ChemDoodle);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(c, document)
{
	c.FileCanvas = function(id, width, height, action)
	{
		if (id) {
			this.create(id, width, height);
		}
		form = '<br><form name="FileForm" enctype="multipart/form-data" method="POST" action="' + action + '" target="HiddenFileFrame"><input type="file" name="f" /><input type="submit" name="submitbutton" value="Show File" /></form><iframe id="HFF-' + id + '" name="HiddenFileFrame" height="0" width="0" style="display:none;" onLoad="GetMolFromFrame(\'HFF-' + id + '\', ' + id + ')"></iframe>';
		document.writeln(form);
		this.emptyMessage = 'Click below to load file';
		this.repaint();
		return true;
	};
	c.FileCanvas.prototype = new c._Canvas();
})(ChemDoodle, document);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(c)
{
	c.HyperlinkCanvas = function(id, width, height, urlOrFunction, color, size) {
		if (id) {
			this.create(id, width, height);
		}
		this.urlOrFunction = urlOrFunction;
		this.color = color ? color : 'blue';
		this.size = size ? size : 2;
		this.openInNewWindow = true;
		this.hoverImage = null;
		this.e = null;
		return true;
	};
	c.HyperlinkCanvas.prototype = new c._Canvas();
	c.HyperlinkCanvas.prototype.drawChildExtras = function(ctx) {
		if (this.e != null) {
			if (this.hoverImage == null) {
				ctx.strokeStyle = this.color;
				ctx.lineWidth = this.size * 2;
				ctx.strokeRect(0, 0, this.width, this.height);
			} else {
				ctx.drawImage(this.hoverImage, 0, 0);
			}
		}
	};
	c.HyperlinkCanvas.prototype.setHoverImage = function(url) {
		this.hoverImage = new Image();
		this.hoverImage.src = url;
	};
	c.HyperlinkCanvas.prototype.click = function(p) {
		this.e = null;
		this.repaint();
		if (this.urlOrFunction instanceof Function) {
			this.urlOrFunction();
		} else {
			if (this.openInNewWindow) {
				window.open(this.urlOrFunction);
			} else {
				location.href = this.urlOrFunction;
			}
		}
	};
	c.HyperlinkCanvas.prototype.mouseout = function(e) {
		this.e = null;
		this.repaint();
	};
	c.HyperlinkCanvas.prototype.mouseover = function(e) {
		this.e = e;
		this.repaint();
	};

})(ChemDoodle);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(c, iChemLabs, q, document)
{
	c.MolGrabberCanvas = function(id, width, height)
	{
		if (id) {
			this.create(id, width, height);
		}
		var sb = [];
		sb.push('<br><input type="text" id="');
		sb.push(id);
		sb.push('_query" size="32" value="" />');
		sb.push('<br><nobr>');
		sb.push('<select id="');
		sb.push(id);
		sb.push('_select">');
		sb.push('<option value="chemexper">ChemExper');
		sb.push('<option value="chemspider">ChemSpider');
		sb.push('<option value="pubchem" selected>PubChem');
		sb.push('</select>');
		sb.push('<button id="');
		sb.push(id);
		sb.push('_submit">Show Molecule</button>');
		sb.push('</nobr>');
		document.writeln(sb.join(''));
		var self = this;
		q('#' + id + '_submit').click(function() {
			self.search();
		});
		q('#' + id + '_query').keypress(function(e) {
	        if(e.which == 13) {
	        	self.search();
	        }
	    });
		this.emptyMessage = 'Enter search term below';
		this.repaint();
		return true;
	};
	c.MolGrabberCanvas.prototype = new c._Canvas();
	c.MolGrabberCanvas.prototype.setSearchTerm = function(term)
	{
		q('#' + this.id + '_query').val(term);
		this.search();
	};
	c.MolGrabberCanvas.prototype.search = function()
	{
		this.emptyMessage = 'Searching...';
		this.molecule = null;
		this.repaint();
		var self = this;
		iChemLabs.getMoleculeFromDatabase(q('#' + this.id + '_select').val(), q('#' + this.id + '_query').val(), function(mol) {
			self.loadMolecule(mol);
		});
	};

})(ChemDoodle, ChemDoodle.iChemLabs, jQuery, document);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3099 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-15 19:47:54 -0500 (Tue, 15 Feb 2011) $
//
(function(c, m, m4)
{
	c.RotatorCanvas = function(id, width, height, rotate3D)
	{
		if (id) {
			this.create(id, width, height);
		}
		this.rotate3D = rotate3D;
		var increment = m.PI / 15;
		this.xIncrement = increment;
		this.yIncrement = increment;
		this.zIncrement = increment;
		return true;
	};
	c.RotatorCanvas.prototype = new c._AnimatorCanvas();
	c.RotatorCanvas.prototype.nextFrame = function(delta)
	{
		if (this.molecule == null)
		{
			this.stopAnimation();
			return;
		}
		var change = delta / 1000;
		if (this.rotate3D) {
			var matrix = [];
			m4.identity(matrix);
			m4.rotate(matrix, this.xIncrement * change, [ 1, 0, 0 ]);
			m4.rotate(matrix, this.yIncrement * change, [ 0, 1, 0 ]);
			m4.rotate(matrix, this.zIncrement * change, [ 0, 0, 1 ]);
			for ( var i = 0, ii = this.molecule.atoms.length; i < ii; i++)
			{
				var a = this.molecule.atoms[i];
				var p = [ a.x - this.width / 2, a.y - this.height / 2, a.z ];
				m4.multiplyVec3(matrix, p);
				a.x = p[0] + this.width / 2;
				a.y = p[1] + this.height / 2;
				a.z = p[2];
			}
			for ( var i = 0, ii = this.molecule.rings.length; i < ii; i++)
			{
				this.molecule.rings[i].center = this.molecule.rings[i].getCenter();
			}
			if (this.specs.atoms_display && this.specs.atoms_circles_2D)
			{
				this.molecule.sortAtomsByZ();
			}
			if (this.specs.bonds_display && this.specs.bonds_clearOverlaps_2D)
			{
				this.molecule.sortBondsByZ();
			}
		}
		else
		{
			this.specs.rotateAngle += this.zIncrement * change;
		}
	};
	c.RotatorCanvas.prototype.dblclick = function(e)
	{
		if (this.isRunning()) {
			this.stopAnimation();
		} else {
			this.startAnimation();
		}
	};
})(ChemDoodle, Math, mat4);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3103 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-20 12:58:08 -0500 (Sun, 20 Feb 2011) $
//
(function(c)
{
	c.SlideshowCanvas = function(id, width, height)
	{
		if (id)
		{
			this.create(id, width, height);
		}
		this.molecules = [];
		this.curIndex = 0;
		this.timeout = 5000;
		this.alpha = 0;
		this.innerHandle = null;
		this.phase = 0;
		return true;
	};
	c.SlideshowCanvas.prototype = new c._AnimatorCanvas();
	c.SlideshowCanvas.prototype.drawChildExtras = function(ctx)
	{
		ctx.fillStyle = 'rgba(' + parseInt(this.specs.backgroundColor.substring(1, 3), 16) + ', ' + parseInt(this.specs.backgroundColor.substring(3, 5), 16) + ', ' + parseInt(this.specs.backgroundColor.substring(5, 7), 16) + ', ' + this.alpha + ')';
		ctx.fillRect(0, 0, this.width, this.height);
	};
	c.SlideshowCanvas.prototype.nextFrame = function(delta)
	{
		if (this.molecules.length == 0) {
			this.stopAnimation();
			return;
		}
		this.phase = 0;
		var me = this;
		var count = 1;
		this.innerHandle = setInterval(function() {
			me.alpha = count / 15;
			me.repaint();
			if (count == 15) {
				me.breakInnerHandle();
			}
			count++;
		}, 33);
	};
	c.SlideshowCanvas.prototype.breakInnerHandle = function()
	{
		if (this.innerHandle != null) {
			clearInterval(this.innerHandle);
			this.innerHandle = null;
		}
		if (this.phase == 0) {
			this.curIndex++;
			if (this.curIndex > this.molecules.length - 1) {
				this.curIndex = 0;
			}
			this.alpha = 1;
			this.loadMolecule(this.molecules[this.curIndex]);
			this.phase = 1;
			var me = this;
			var count = 1;
			this.innerHandle = setInterval(function() {
				me.alpha = (15 - count) / 15;
				me.repaint();
				if (count == 15) {
					me.breakInnerHandle();
				}
				count++;
			}, 33);
		} else if (this.phase == 1) {
			this.alpha = 0;
			this.repaint();
		}
	};
	c.SlideshowCanvas.prototype.addMolecule = function(molecule) {
		if (this.molecules.length == 0) {
			this.loadMolecule(molecule);
		}
		this.molecules.push(molecule);
	};
})(ChemDoodle);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3099 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-15 19:47:54 -0500 (Tue, 15 Feb 2011) $
//
(function(c, monitor, structures, m, m4)
{
	c.TransformCanvas = function(id, width, height, rotate3D)
	{
		if (id)
		{
			this.create(id, width, height);
		}
		this.lastPoint = null;
		this.rotate3D = rotate3D;
		this.rotationMultMod = 1.3;
		this.lastPinchScale = 1;
		this.lastGestureRotate = 0;
		return true;
	};

	c.TransformCanvas.prototype = new c._Canvas();

	c.TransformCanvas.prototype.mousedown = function(e)
	{
		this.lastPoint = e.p;
	};

	c.TransformCanvas.prototype.dblclick = function(e)
	{
		// center structure
		var dif = new structures.Point(this.width / 2, this.height / 2);
		dif.sub(this.molecule.getCenter());
		for ( var i = 0, ii = this.molecule.atoms.length; i < ii; i++)
		{
			this.molecule.atoms[i].add(dif);
		}
		this.molecule.check();
		this.repaint();
	};

	c.TransformCanvas.prototype.drag = function(e)
	{
		if (!this.lastPoint.multi)
		{
			if (monitor.ALT)
			{
				var t = new structures.Point(e.p.x, e.p.y);
				t.sub(this.lastPoint);
				for ( var i = 0, ii = this.molecule.atoms.length; i < ii; i++)
				{
					this.molecule.atoms[i].add(t);
				}
				this.lastPoint = e.p;
				this.molecule.check();
				this.repaint();
			}
			else
			{
				if (this.rotate3D == true)
				{
					var diameter = m.max(this.width / 4, this.height / 4);
					var difx = e.p.x - this.lastPoint.x;
					var dify = e.p.y - this.lastPoint.y;
					var yIncrement = difx / diameter * this.rotationMultMod;
					var xIncrement = -dify / diameter * this.rotationMultMod;
					var matrix = [];
					m4.identity(matrix);
					m4.rotate(matrix, xIncrement, [ 1, 0, 0 ]);
					m4.rotate(matrix, yIncrement, [ 0, 1, 0 ]);
					for ( var i = 0, ii = this.molecule.atoms.length; i < ii; i++)
					{
						var a = this.molecule.atoms[i];
						var p = [ a.x - this.width / 2, a.y - this.height / 2, a.z ];
						m4.multiplyVec3(matrix, p);
						a.x = p[0] + this.width / 2;
						a.y = p[1] + this.height / 2;
						a.z = p[2];
					}
					for ( var i = 0, ii = this.molecule.rings.length; i < ii; i++)
					{
						this.molecule.rings[i].center = this.molecule.rings[i].getCenter();
					}
					this.lastPoint = e.p;
					if (this.specs.atoms_display && this.specs.atoms_circles_2D)
					{
						this.molecule.sortAtomsByZ();
					}
					if (this.specs.bonds_display && this.specs.bonds_clearOverlaps_2D)
					{
						this.molecule.sortBondsByZ();
					}
					this.repaint();
				}
				else
				{
					var center = new structures.Point(this.width / 2, this.height / 2);
					var before = center.angle(this.lastPoint);
					var after = center.angle(e.p);
					this.specs.rotateAngle -= (after - before);
					this.lastPoint = e.p;
					this.repaint();
				}
			}
		}
	};

	c.TransformCanvas.prototype.mousewheel = function(e, delta)
	{
		this.specs.scale += delta / 10;
		if (this.specs.scale < .01) {
			this.specs.scale = .01;
		}
		this.repaint();
	};
	c.TransformCanvas.prototype.multitouchmove = function(e, numFingers)
	{
		if (numFingers == 2) {
			if (this.lastPoint.multi) {
				var t = new structures.Point(e.p.x, e.p.y);
				t.sub(this.lastPoint);
				for ( var i = 0, ii = this.molecule.atoms.length; i < ii; i++)
				{
					this.molecule.atoms[i].add(t);
				}
				this.lastPoint = e.p;
				this.lastPoint.multi = true;
				this.molecule.check();
				this.repaint();
			} else {
				this.lastPoint = e.p;
				this.lastPoint.multi = true;
			}
		}
	};
	c.TransformCanvas.prototype.gesturechange = function(e)
	{
		if (e.originalEvent.scale - this.lastPinchScale != 0)
		{
			this.specs.scale *= e.originalEvent.scale / this.lastPinchScale;
			if (this.specs.scale < .01) {
				this.specs.scale = .01;
			}
			this.lastPinchScale = e.originalEvent.scale;
		}
		if (this.lastGestureRotate - e.originalEvent.rotation != 0)
		{
			var rot = (this.lastGestureRotate - e.originalEvent.rotation) / 180 * m.PI;
			var center = new structures.Point(this.width / 2, this.height / 2);
			for ( var i = 0, ii = this.molecule.atoms.length; i < ii; i++)
			{
				var dist = center.distance(this.molecule.atoms[i]);
				var angle = center.angle(this.molecule.atoms[i]) + rot;
				this.molecule.atoms[i].x = center.x + dist * m.cos(angle);
				this.molecule.atoms[i].y = center.y - dist * m.sin(angle);
			}
			this.lastGestureRotate = e.originalEvent.rotation;
			this.molecule.check();
		}
		this.repaint();
	};

	c.TransformCanvas.prototype.gestureend = function(e)
	{
		this.lastPinchScale = 1;
		this.lastGestureRotate = 0;
	};
})(ChemDoodle, ChemDoodle.monitor, ChemDoodle.structures, Math, mat4);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(c)
{
	c.ViewerCanvas = function(id, width, height) {
		if (id) {
			this.create(id, width, height);
		}
		return true;
	};
	c.ViewerCanvas.prototype = new c._Canvas();
})(ChemDoodle);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(c, document)
{
	c._SpectrumCanvas = function(id, width, height) {
		if (id) {
			this.create(id, width, height);
		}
		this.spectrum = null;
		this.emptyMessage = 'No Spectrum Loaded or Recognized';
		return true;
	};
	c._SpectrumCanvas.prototype = new c._Canvas();
	c._SpectrumCanvas.prototype.repaint = function() {
		var canvas = document.getElementById(this.id);
		if (canvas.getContext) {
			var ctx = canvas.getContext('2d');
			if (this.image == null) {
				if (this.specs.backgroundColor != null) {
					ctx.fillStyle = this.specs.backgroundColor;
					ctx.fillRect(0, 0, this.width, this.height);
				}
			} else {
				ctx.drawImage(this.image, 0, 0);
			}
			if (this.spectrum != null && this.spectrum.data.length > 0) {
				this.spectrum.draw(ctx, this.specs, this.width, this.height);
			} else if (this.emptyMessage != null) {
				ctx.fillStyle = '#737683';
				ctx.textAlign = 'center';
				ctx.textBaseline = 'middle';
				ctx.font = '18px Helvetica, Verdana, Arial, Sans-serif';
				ctx.fillText(this.emptyMessage, this.width / 2, this.height / 2);
			}
			if (this.drawChildExtras) {
				this.drawChildExtras(ctx);
			}
		}
	};
	c._SpectrumCanvas.prototype.loadSpectrum = function(spectrum) {
		this.spectrum = spectrum;
		this.repaint();
	};
	c._SpectrumCanvas.prototype.getSpectrum = function() {
		return this.spectrum;
	};

})(ChemDoodle, document);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(c)
{
	c.ObserverCanvas = function(id, width, height) {
		if (id) {
			this.create(id, width, height);
		}
		return true;
	};
	c.ObserverCanvas.prototype = new c._SpectrumCanvas();

})(ChemDoodle);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3099 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-15 19:47:54 -0500 (Tue, 15 Feb 2011) $
//
(function(c, monitor, m)
{

	c.PerspectiveCanvas = function(id, width, height) {
		if (id) {
			this.create(id, width, height);
		}
		this.dragRange = null;
		this.rescaleYAxisOnZoom = true;
		this.lastPinchScale = 1;
		return true;
	};
	c.PerspectiveCanvas.prototype = new c._SpectrumCanvas();
	c.PerspectiveCanvas.prototype.mousedown = function(e) {
		this.dragRange = new c.structures.Point(e.p.x, e.p.x);
	};
	c.PerspectiveCanvas.prototype.mouseup = function(e) {
		if (this.dragRange != null && this.dragRange.x != this.dragRange.y) {
			if(!this.dragRange.multi){
				var newScale = this.spectrum.zoom(this.dragRange.x, e.p.x, this.width, this.rescaleYAxisOnZoom);
				if (this.rescaleYAxisOnZoom) {
					this.specs.scale = newScale;
				}
			}
			this.dragRange = null;
			this.repaint();
		}
	};
	c.PerspectiveCanvas.prototype.drag = function(e) {
		if (this.dragRange != null) {
			if(this.dragRange.multi){
				this.dragRange = null;
			}else if (monitor.SHIFT) {
				this.spectrum.translate(e.p.x - this.dragRange.x, this.width);
				this.dragRange.x = e.p.x;
				this.dragRange.y = e.p.x;
			} else {
				this.dragRange.y = e.p.x;
			}
			this.repaint();
		}
	};
	c.PerspectiveCanvas.prototype.drawChildExtras = function(ctx) {
		if (this.dragRange != null) {
			var xs = m.min(this.dragRange.x, this.dragRange.y);
			var xe = m.max(this.dragRange.x, this.dragRange.y);
			ctx.strokeStyle = 'gray';
			ctx.lineStyle = 1;
			ctx.beginPath();
			ctx.moveTo(xs, this.height / 2);
			for ( var i = xs; i <= xe; i++) {
				if (i % 10 < 5) {
					ctx.lineTo(i, m.round(this.height / 2));
				} else {
					ctx.moveTo(i, m.round(this.height / 2));
				}
			}
			ctx.stroke();
		}
	};
	c.PerspectiveCanvas.prototype.mousewheel = function(e, delta) {
		this.specs.scale += delta / 10;
		if (this.specs.scale < .01) {
			this.specs.scale = .01;
		}
		this.repaint();
	};
	c.PerspectiveCanvas.prototype.dblclick = function(e) {
		this.spectrum.setup();
		this.specs.scale = 1;
		this.repaint();
	};
	c.PerspectiveCanvas.prototype.multitouchmove = function(e, numFingers) {
		if (numFingers == 2) {
			if (this.dragRange == null || !this.dragRange.multi) {
				this.dragRange = new c.structures.Point(e.p.x, e.p.x);
				this.dragRange.multi = true;
			} else {
				this.spectrum.translate(e.p.x - this.dragRange.x, this.width);
				this.dragRange.x = e.p.x;
				this.dragRange.y = e.p.x;
				this.repaint();
			}
		}
	};
	c.PerspectiveCanvas.prototype.gesturechange = function(e) {
		this.specs.scale *= e.originalEvent.scale / this.lastPinchScale;
		if (this.specs.scale < .01) {
			this.specs.scale = .01;
		}
		this.lastPinchScale = e.originalEvent.scale;
		this.repaint();
	};
	c.PerspectiveCanvas.prototype.gestureend = function(e) {
		this.lastPinchScale = 1;
	};

})(ChemDoodle, ChemDoodle.monitor, Math);

//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3163 $
//  $Author: kevin $
//  $LastChangedDate: 2011-03-12 18:47:17 -0500 (Sat, 12 Mar 2011) $

(function(c, extensions, math, structures, m, document, m4, m3, v3) {

	c._Canvas3D = function(id, width, height) {
		if (id) {
			this.create(id, width, height);
		}
		this.rotationMatrix = m4.identity([]);
		this.translationMatrix = m4.identity([]);
		this.lastPoint = null;
		this.emptyMessage = "WebGL is Unavailable!";
		return true;
	};
	c._Canvas3D.prototype = new c._Canvas();
	c._Canvas3D.prototype.afterLoadMolecule = function() {
		var d = this.molecule.getDimension();
		this.translationMatrix = m4.translate(m4.identity([]), [ 0, 0, -m.max(d.x, d.y) - 10 ]);
		this.setupScene();
	};
	c._Canvas3D.prototype.setViewDistance = function(distance) {
		this.translationMatrix = m4.translate(m4.identity([]), [ 0, 0, -distance ]);
	};
	c._Canvas3D.prototype.repaint = function() {
		if (this.gl) {
			// ready the bits for rendering
			this.gl.clear(this.gl.COLOR_BUFFER_BIT | this.gl.DEPTH_BUFFER_BIT);

			// set up the model view matrix to the specified transformations
			this.gl.modelViewMatrix = m4.multiply(this.translationMatrix, this.rotationMatrix, []);
			this.gl.rotationMatrix = this.rotationMatrix;

			if (this.molecule != null) {
				// render molecule
				this.molecule.render(this.gl, this.specs);
			}

			// flush as this is seen in documentation
			this.gl.flush();
		}
	};
	c._Canvas3D.prototype.center = function() {
		var canvas = document.getElementById(this.id);
		var p = this.molecule.getCenter3D();
		var center = new structures.Atom('C', 0, 0, 0);
		center.sub3D(p);
		for ( var i = 0, ii = this.molecule.atoms.length; i < ii; i++) {
			this.molecule.atoms[i].add3D(center);
		}
	};
	c._Canvas3D.prototype.subCreate = function() {
		// setup gl object
		try {
			this.gl = document.getElementById(this.id).getContext("webgl");
			if (!this.gl) {
				this.gl = document.getElementById(this.id).getContext("experimental-webgl");
			}
		} catch (e) {
		}
		if (this.gl) {
			this.gl.viewport(0, 0, this.width, this.height);
			this.gl.program = this.gl.createProgram();
			// this is the shader
			this.gl.shader = new structures.Shader();
			this.gl.shader.init(this.gl);
			this.setupScene();
		} else {
			this.molecule = null;
			this.displayMessage();
		}
	};
	c._Canvas.prototype.displayMessage = function() {
		var canvas = document.getElementById(this.id);
		if (canvas.getContext) {
			var ctx = canvas.getContext('2d');
			if (this.specs.backgroundColor != null) {
				ctx.fillStyle = this.specs.backgroundColor;
				ctx.fillRect(0, 0, this.width, this.height);
			}
			if (this.emptyMessage != null) {
				ctx.fillStyle = '#737683';
				ctx.textAlign = 'center';
				ctx.textBaseline = 'middle';
				ctx.font = '18px Helvetica, Verdana, Arial, Sans-serif';
				ctx.fillText(this.emptyMessage, this.width / 2, this.height / 2);
			}
		}
	};
	c._Canvas3D.prototype.setupScene = function() {
		if (this.gl) {
			// clear the canvas
			var cs = math.getRGB(this.specs.backgroundColor, 1);
			this.gl.clearColor(cs[0], cs[1], cs[2], 1.0);
			this.gl.clearDepth(1.0);
			this.gl.enable(this.gl.DEPTH_TEST);
			this.gl.depthFunc(this.gl.LEQUAL);
			// here is the sphere buffer to be drawn, make it once, then scale
			// and
			// translate to draw atoms
			this.gl.sphereBuffer = new structures.Sphere(this.gl, 1, this.specs.atoms_resolution_3D, this.specs.atoms_resolution_3D);
			this.gl.cylinderBuffer = new structures.Cylinder(this.gl, 1, 1, this.specs.bonds_resolution_3D);
			if (this.molecule && this.molecule.chains) {
				this.molecule.ribbons = [];
				this.molecule.cartoons = [];
				// set up ribbon diagram if available and not already setup
				for ( var j = 0, jj = this.molecule.chains.length; j < jj; j++) {
					var rs = this.molecule.chains[j];
					if (rs.length > 0 && !rs[0].lineSegments) {
						for ( var i = 0, ii = rs.length - 1; i < ii; i++) {
							rs[i].setup(rs[i + 1].alphaCarbon);
							// uncomment to show guide points
							/*
							 * molecule.atoms.push(rs.guidePointsSmall[0]);
							 * molecule.atoms.push(rs.guidePointsSmall[8]);
							 * molecule.atoms[molecule.atoms.length-1].label =
							 * 'N';
							 * molecule.atoms[molecule.atoms.length-2].label =
							 * 'N';
							 */
						}
						for ( var i = 1, ii = rs.length - 1; i < ii; i++) {
							// reverse guide points if carbonyl orientation
							// flips
							if (extensions.vec3AngleFrom(rs[i - 1].D, rs[i].D) > m.PI / 2) {
								rs[i].guidePointsSmall.reverse();
								rs[i].guidePointsLarge.reverse();
								v3.scale(rs[i].D, -1);
							}
						}
						for ( var i = 1, ii = rs.length - 3; i < ii; i++) {
							// compute line segments
							rs[i].computeLineSegments(rs[i - 1], rs[i + 1], rs[i + 2]);
						}
						// remove unneeded dummies
						rs.pop();
						rs.pop();
						rs.pop();
						rs.shift();
					}
					this.molecule.ribbons.push({
						front : new structures.Ribbon(this.gl, rs, .02, false),
						back : new structures.Ribbon(this.gl, rs, -.02, false)
					});
					this.molecule.cartoons.push({
						front : new structures.Ribbon(this.gl, rs, .02, true),
						back : new structures.Ribbon(this.gl, rs, -.02, true)
					});
				}
			}
			// set up lighting
			this.gl.lighting = new structures.Light(this.specs.lightDiffuseColor_3D, this.specs.lightSpecularColor_3D, this.specs.lightDirection_3D);
			this.gl.lighting.lightScene(this.gl);
			// set up material
			this.gl.material = new structures.Material(this.gl);
			// projection matrix
			// arg1: vertical field of view (degrees)
			// arg2: width to height ratio
			// arg3: front culling
			// arg4: back culling
			this.gl.projectionMatrix = m4.perspective(this.specs.projectionVerticalFieldOfView_3D, this.specs.projectionWidthHeightRatio_3D, this.specs.projectionFrontCulling_3D, this.specs.projectionBackCulling_3D);
			// push the projection matrix to the graphics card
			var pUniform = this.gl.getUniformLocation(this.gl.program, "u_projection_matrix");
			this.gl.uniformMatrix4fv(pUniform, false, this.gl.projectionMatrix);
			// matrix setup functions
			var mvUL = this.gl.getUniformLocation(this.gl.program, "u_model_view_matrix");
			var nUL = this.gl.getUniformLocation(this.gl.program, "u_normal_matrix");
			this.gl.setMatrixUniforms = function(mvMatrix) {
				// push the model-view matrix to the graphics card
				this.uniformMatrix4fv(mvUL, false, mvMatrix);
				// create the normal matrix and push it to the graphics card
				var normalMatrix = m3.transpose(m4.toInverseMat3(mvMatrix, []));
				this.uniformMatrix3fv(nUL, false, normalMatrix);
			};
		}
	};
	c._Canvas3D.prototype.mousedown = function(e) {
		this.lastPoint = e.p;
	};
	c._Canvas3D.prototype.rightmousedown = function(e) {
		this.lastPoint = e.p;
	};
	c._Canvas3D.prototype.drag = function(e) {
		if (c.monitor.ALT) {
			var t = new structures.Point(e.p.x, e.p.y);
			t.sub(this.lastPoint);
			m4.translate(this.translationMatrix, [ t.x / 20, -t.y / 20, 0 ]);
			this.lastPoint = e.p;
			this.repaint();
		} else {
			var diameter = m.max(this.width / 4, this.height / 4);
			var difx = e.p.x - this.lastPoint.x;
			var dify = e.p.y - this.lastPoint.y;
			var rotation = m4.rotate(m4.identity([]), difx * m.PI / 180.0, [ 0, 1, 0 ]);
			m4.rotate(rotation, dify * m.PI / 180.0, [ 1, 0, 0 ]);
			this.rotationMatrix = m4.multiply(rotation, this.rotationMatrix);
			this.lastPoint = e.p;
			this.repaint();
		}
	};
	c._Canvas3D.prototype.mousewheel = function(e, delta) {
		m4.translate(this.translationMatrix, [ 0, 0, delta * 2 ]);
		this.repaint();
	};

})(ChemDoodle, ChemDoodle.extensions, ChemDoodle.math, ChemDoodle.structures, Math, document, mat4, mat3, vec3);

//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//

(function(c, iChemLabs, q, document) {

	c.MolGrabberCanvas3D = function(id, width, height) {
		if (id) {
			this.create(id, width, height);
		}
		var sb = [];
		sb.push('<br><input type="text" id="');
		sb.push(id);
		sb.push('_query" size="32" value="" />');
		sb.push('<br><nobr>');
		sb.push('<select id="');
		sb.push(id);
		sb.push('_select">');
		//sb.push('<option value="chemexper">ChemExper');
		//sb.push('<option value="chemspider">ChemSpider');
		sb.push('<option value="pubchem" selected>PubChem');
		sb.push('</select>');
		sb.push('<button id="');
		sb.push(id);
		sb.push('_submit">Show Molecule</button>');
		sb.push('</nobr>');
		document.writeln(sb.join(''));
		var self = this;
		q('#' + id + '_submit').click(function() {
			self.search();
		});
		q('#' + id + '_query').keypress(function(e) {
	        if(e.which == 13) {
	        	self.search();
	        }
	    });
		return true;
	};
	c.MolGrabberCanvas3D.prototype = new c._Canvas3D();
	c.MolGrabberCanvas3D.prototype.setSearchTerm = function(term) {
		q('#'+this.id+'_query').val(term);
		this.search();
	};
	c.MolGrabberCanvas3D.prototype.search = function() {
		var self = this;
		iChemLabs.getMoleculeFromDatabase(q('#'+this.id+'_select').val(), q('#'+this.id+'_query').val(), function(mol){
			self.loadMolecule(mol);
		}, 3);
	};
})(ChemDoodle, ChemDoodle.iChemLabs, jQuery, document);


//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3099 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-15 19:47:54 -0500 (Tue, 15 Feb 2011) $
//
(function(c, m, m4)
{
	c.RotatorCanvas3D = function(id, width, height) {
		if (id) {
			this.create(id, width, height);
		}
		this.timeout = 33;
		var increment = m.PI / 15;
		this.xIncrement = increment;
		this.yIncrement = increment;
		this.zIncrement = increment;
		return true;
	};
	c.RotatorCanvas3D.prototype = new c._Canvas3D();
	c.RotatorCanvas3D.prototype.startAnimation = c._AnimatorCanvas.prototype.startAnimation;
	c.RotatorCanvas3D.prototype.stopAnimation = c._AnimatorCanvas.prototype.stopAnimation;
	c.RotatorCanvas3D.prototype.isRunning = c._AnimatorCanvas.prototype.isRunning;
	c.RotatorCanvas3D.prototype.dblclick = c.RotatorCanvas.prototype.dblclick;
	c.RotatorCanvas3D.prototype.mousedown = null;
	c.RotatorCanvas3D.prototype.rightmousedown = null;
	c.RotatorCanvas3D.prototype.drag = null;
	c.RotatorCanvas3D.prototype.mousewheel = null;
	c.RotatorCanvas3D.prototype.nextFrame = function(delta) {
		if (this.molecule == null) {
			this.stopAnimation();
			return;
		}
		var matrix = [];
		m4.identity(matrix);
		var change = delta / 1000;
		m4.rotate(matrix, this.xIncrement * change, [ 1, 0, 0 ]);
		m4.rotate(matrix, this.yIncrement * change, [ 0, 1, 0 ]);
		m4.rotate(matrix, this.zIncrement * change, [ 0, 0, 1 ]);
		m4.multiply(this.rotationMatrix, matrix);
	};

})(ChemDoodle, Math, mat4);

//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(c) {

	c.TransformCanvas3D = function(id, width, height) {
		if (id) {
			this.create(id, width, height);
		}
		return true;
	};
	c.TransformCanvas3D.prototype = new c._Canvas3D();

})(ChemDoodle);

//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//
(function(c) {

	c.ViewerCanvas3D = function(id, width, height) {
		if (id) {
			this.create(id, width, height);
		}
		return true;
	};
	c.ViewerCanvas3D.prototype = new c._Canvas3D();
	c.ViewerCanvas3D.prototype.mousedown = null;
	c.ViewerCanvas3D.prototype.rightmousedown = null;
	c.ViewerCanvas3D.prototype.drag = null;
	c.ViewerCanvas3D.prototype.mousewheel = null;

})(ChemDoodle);

//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3078 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-06 18:27:15 -0500 (Sun, 06 Feb 2011) $
//

(function(c, structures) {

	c._Layout = function() {
		return true;
	};
	c._Layout.prototype.layout = function() {
		if (this.innerLayout) {
			this.innerLayout();
		}
	};
	c._Layout.prototype.create = function(name) {
		this.name = name;
		this.specs = new structures.VisualSpecifications();
	};

})(ChemDoodle, ChemDoodle.structures);

//
//  Copyright 2009 iChemLabs, LLC.  All rights reserved.
//
//  $Revision: 3103 $
//  $Author: kevin $
//  $LastChangedDate: 2011-02-20 12:58:08 -0500 (Sun, 20 Feb 2011) $
//

(function(c, q, document) {

	c.SimpleReactionLayout = function(name) {
		this.reactants = [];
		this.products = [];
		this.textAbove = null;
		this.textBelow = null;
		this.arrow = '&rarr;';
		this.plus = '+';
		this.create(name);
		return true;
	};
	c.SimpleReactionLayout.prototype = new c._Layout();
	c.SimpleReactionLayout.prototype.addReactant = function(reactant) {
		this.reactants.push(reactant);
	};
	c.SimpleReactionLayout.prototype.addProduct = function(product) {
		this.products.push(product);
	};
	c.SimpleReactionLayout.prototype.innerLayout = function() {
		var glyphStyle = '<span style="font-size:25px;">';
		document.writeln("<table><tr>");
		// reactants
		for ( var i = 0, ii = this.reactants.length; i < ii; i++) {
			if (i > 0) {
				document.writeln("<td>" + glyphStyle + this.plus + "</span></td>");
			}
			document.writeln("<td>");
			var dim = this.reactants[i].getDimension();
			var view = new c.ViewerCanvas(this.name + '_reactant' + i, dim.x + 60, dim.y + 60);
			if (this.specs.backgroundColor == null) {
				q('#' + this.name + '_reactant' + i).css("border", "0px");
			}
			view.specs = this.specs;
			view.loadMolecule(this.reactants[i]);
			document.writeln("</td>");
		}
		// arrow
		document.writeln("<td>");
		document.writeln("<table>");
		document.writeln("<tr><td>");
		if (this.textAbove != null) {
			document.writeln("<center>" + this.textAbove + "</center>");
		} else {
			document.writeln("&nbsp;");
		}
		document.writeln("</td></tr>");
		document.writeln("<tr><td><center>" + glyphStyle + this.arrow + "</span></center></td></tr>");
		document.writeln("<tr><td>");
		if (this.textBelow != null) {
			document.writeln("<center>" + this.textBelow + "</center>");
		} else {
			document.writeln("&nbsp;");
		}
		document.writeln("</td></tr>");
		document.writeln("</table>");
		document.writeln("</td>");
		// products
		for ( var i = 0, ii = this.products.length; i < ii; i++) {
			if (i > 0) {
				document.writeln("<td>" + glyphStyle + this.plus + "</td>");
			}
			document.writeln("<td>");
			var dim = this.products[i].getDimension();
			var view = new c.ViewerCanvas(this.name + '_product' + i, dim.x + 60, dim.y + 60);
			if (this.specs.backgroundColor == null) {
				q('#' + this.name + '_product' + i).css("border", "0px");
			}
			view.specs = this.specs;
			view.loadMolecule(this.products[i]);
			document.writeln("</td>");
		}
		document.writeln("</tr></table>");
	};

})(ChemDoodle, jQuery, document);