javascript
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three.js
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							<!DOCTYPE html>
<html>
	<head>
		<title>three.js css3d - molecules</title>
		<meta charset="utf-8">
		<meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
		<link type="text/css" rel="stylesheet" href="main.css">
		<style>
			body {
				background-color: #050505;
				background: radial-gradient(ellipse at center,  rgba(43,45,48,1) 0%,rgba(0,0,0,1) 100%);
			}

			#topmenu {
				position: absolute;
				top: 50px;
				width: 100%;
				padding: 10px;
				box-sizing: border-box;
				text-align: center;
			}

			#menu {
				position: absolute;
				bottom: 20px;
				width: 100%;
				padding: 10px;
				box-sizing: border-box;
				text-align: center;
			}

			button {
				color: rgb(255,255,255);
				background: rgb(255,255,255,0.1);
				border: 0px;
				padding: 5px 10px;
				margin: 2px;
				font-size: 14px;
				cursor: pointer;
			}

				button:hover {
					background-color: rgba(0,255,255,0.5);
				}

				button:active {
					color: #000000;
					background-color: rgba(0,255,255,1);
				}

			.bond {
				width: 5px;
				height: 10px;
				background: #eee;
				display: block;
			}
		</style>
	</head>
	<body>
		<div id="container"></div>
		<div id="info"><a href="http://threejs.org" target="_blank" rel="noopener">three.js</a> css3d - molecules</div>
		<div id="topmenu">
			<button id="b_a">Atoms</button><button id="b_b">Bonds</button><button id="b_ab">Atoms + Bonds</button>
		</div>
		<div id="menu"></div>

		<script type="module">

			import * as THREE from '../build/three.module.js';

			import { TrackballControls } from './jsm/controls/TrackballControls.js';
			import { PDBLoader } from './jsm/loaders/PDBLoader.js';
			import { CSS3DRenderer, CSS3DObject, CSS3DSprite } from './jsm/renderers/CSS3DRenderer.js';

			var camera, scene, renderer;
			var controls;
			var root;

			var objects = [];
			var tmpVec1 = new THREE.Vector3();
			var tmpVec2 = new THREE.Vector3();
			var tmpVec3 = new THREE.Vector3();
			var tmpVec4 = new THREE.Vector3();
			var offset = new THREE.Vector3();

			var visualizationType = 2;

			var MOLECULES = {
				"Ethanol": "ethanol.pdb",
				"Aspirin": "aspirin.pdb",
				"Caffeine": "caffeine.pdb",
				"Nicotine": "nicotine.pdb",
				"LSD": "lsd.pdb",
				"Cocaine": "cocaine.pdb",
				"Cholesterol": "cholesterol.pdb",
				"Lycopene": "lycopene.pdb",
				"Glucose": "glucose.pdb",
				"Aluminium oxide": "Al2O3.pdb",
				"Cubane": "cubane.pdb",
				"Copper": "cu.pdb",
				"Fluorite": "caf2.pdb",
				"Salt": "nacl.pdb",
				"YBCO superconductor": "ybco.pdb",
				"Buckyball": "buckyball.pdb",
				//"Diamond": "diamond.pdb",
				"Graphite": "graphite.pdb"
			};

			var loader = new PDBLoader();
			var colorSpriteMap = {};
			var baseSprite = document.createElement( 'img' );

			var menu = document.getElementById( "menu" );

			init();
			animate();

			function init() {

				camera = new THREE.PerspectiveCamera( 70, window.innerWidth / window.innerHeight, 1, 5000 );
				camera.position.z = 1500;

				scene = new THREE.Scene();

				root = new THREE.Object3D();
				scene.add( root );

				//

				renderer = new CSS3DRenderer();
				renderer.setSize( window.innerWidth, window.innerHeight );
				document.getElementById( 'container' ).appendChild( renderer.domElement );

				//

				controls = new TrackballControls( camera, renderer.domElement );
				controls.rotateSpeed = 0.5;
				controls.addEventListener( 'change', render );

				//

				baseSprite.onload = function () {

					loadMolecule( "models/molecules/caffeine.pdb" );
					createMenu();

				};

				baseSprite.src = 'textures/sprites/ball.png';

				//

				window.addEventListener( 'resize', onWindowResize, false );

			}

			//

			function generateButtonCallback( url ) {

				return function () {

					loadMolecule( url );

				};

			}

			function createMenu() {

				for ( var m in MOLECULES ) {

					var button = document.createElement( 'button' );
					button.innerHTML = m;
					menu.appendChild( button );

					var url = "models/molecules/" + MOLECULES[ m ];

					button.addEventListener( 'click', generateButtonCallback( url ), false );

				}

				var b_a = document.getElementById( "b_a" );
				var b_b = document.getElementById( "b_b" );
				var b_ab = document.getElementById( "b_ab" );

				b_a.addEventListener( 'click', function () {

					visualizationType = 0;
					showAtoms();

				} );
				b_b.addEventListener( 'click', function () {

					visualizationType = 1;
					showBonds();

				} );
				b_ab.addEventListener( 'click', function () {

					visualizationType = 2;
					showAtomsBonds();

				} );

			}

			//

			function showAtoms() {

				for ( var i = 0; i < objects.length; i ++ ) {

					var object = objects[ i ];

					if ( object instanceof CSS3DSprite ) {

						object.element.style.display = "";
						object.visible = true;

					} else {

						object.element.style.display = "none";
						object.visible = false;

					}

				}

			}

			function showBonds() {

				for ( var i = 0; i < objects.length; i ++ ) {

					var object = objects[ i ];

					if ( object instanceof CSS3DSprite ) {

						object.element.style.display = "none";
						object.visible = false;

					} else {

						object.element.style.display = "";
						object.element.style.height = object.userData.bondLengthFull;
						object.visible = true;

					}

				}

			}

			function showAtomsBonds() {

				for ( var i = 0; i < objects.length; i ++ ) {

					var object = objects[ i ];

					object.element.style.display = "";
					object.visible = true;

					if ( ! ( object instanceof CSS3DSprite ) ) {

						object.element.style.height = object.userData.bondLengthShort;

					}

				}

			}

			//

			function colorify( ctx, width, height, color ) {

				var r = color.r, g = color.g, b = color.b;

				var imageData = ctx.getImageData( 0, 0, width, height );
				var data = imageData.data;

				for ( var i = 0, l = data.length; i < l; i += 4 ) {

					data[ i + 0 ] *= r;
					data[ i + 1 ] *= g;
					data[ i + 2 ] *= b;

				}

				ctx.putImageData( imageData, 0, 0 );

			}

			function imageToCanvas( image ) {

				var width = image.width;
				var height = image.height;

				var canvas = document.createElement( 'canvas' );

				canvas.width = width;
				canvas.height = height;

				var context = canvas.getContext( '2d' );
				context.drawImage( image, 0, 0, width, height );

				return canvas;

			}

			//

			function loadMolecule( url ) {

				for ( var i = 0; i < objects.length; i ++ ) {

					var object = objects[ i ];
					object.parent.remove( object );

				}

				objects = [];

				loader.load( url, function ( pdb ) {

					var geometryAtoms = pdb.geometryAtoms;
					var geometryBonds = pdb.geometryBonds;
					var json = pdb.json;

					geometryAtoms.computeBoundingBox();
					geometryAtoms.boundingBox.getCenter( offset ).negate();

					geometryAtoms.translate( offset.x, offset.y, offset.z );
					geometryBonds.translate( offset.x, offset.y, offset.z );

					var positions = geometryAtoms.getAttribute( 'position' );
					var colors = geometryAtoms.getAttribute( 'color' );

					var position = new THREE.Vector3();
					var color = new THREE.Color();

					for ( var i = 0; i < positions.count; i ++ ) {

						position.x = positions.getX( i );
						position.y = positions.getY( i );
						position.z = positions.getZ( i );

						color.r = colors.getX( i );
						color.g = colors.getY( i );
						color.b = colors.getZ( i );

						var atom = json.atoms[ i ];
						var element = atom[ 4 ];

						if ( ! colorSpriteMap[ element ] ) {

							var canvas = imageToCanvas( baseSprite );
							var context = canvas.getContext( '2d' );

							colorify( context, canvas.width, canvas.height, color );

							var dataUrl = canvas.toDataURL();

							colorSpriteMap[ element ] = dataUrl;

						}

						var colorSprite = colorSpriteMap[ element ];

						var atom = document.createElement( 'img' );
						atom.src = colorSprite;

						var object = new CSS3DSprite( atom );
						object.position.copy( position );
						object.position.multiplyScalar( 75 );

						object.matrixAutoUpdate = false;
						object.updateMatrix();

						root.add( object );

						objects.push( object );

					}

					positions = geometryBonds.getAttribute( 'position' );

					var start = new THREE.Vector3();
					var end = new THREE.Vector3();

					for ( var i = 0; i < positions.count; i += 2 ) {

						start.x = positions.getX( i );
						start.y = positions.getY( i );
						start.z = positions.getZ( i );

						end.x = positions.getX( i + 1 );
						end.y = positions.getY( i + 1 );
						end.z = positions.getZ( i + 1 );

						start.multiplyScalar( 75 );
						end.multiplyScalar( 75 );

						tmpVec1.subVectors( end, start );
						var bondLength = tmpVec1.length() - 50;

						//

						var bond = document.createElement( 'div' );
						bond.className = "bond";
						bond.style.height = bondLength + "px";

						var object = new CSS3DObject( bond );
						object.position.copy( start );
						object.position.lerp( end, 0.5 );

						object.userData.bondLengthShort = bondLength + "px";
						object.userData.bondLengthFull = ( bondLength + 55 ) + "px";

						//

						var axis = tmpVec2.set( 0, 1, 0 ).cross( tmpVec1 );
						var radians = Math.acos( tmpVec3.set( 0, 1, 0 ).dot( tmpVec4.copy( tmpVec1 ).normalize() ) );

						var objMatrix = new THREE.Matrix4().makeRotationAxis( axis.normalize(), radians );
						object.matrix = objMatrix;
						object.quaternion.setFromRotationMatrix( object.matrix );

						object.matrixAutoUpdate = false;
						object.updateMatrix();

						root.add( object );

						objects.push( object );

						//

						var bond = document.createElement( 'div' );
						bond.className = "bond";
						bond.style.height = bondLength + "px";

						var joint = new THREE.Object3D( bond );
						joint.position.copy( start );
						joint.position.lerp( end, 0.5 );

						joint.matrix.copy( objMatrix );
						joint.quaternion.setFromRotationMatrix( joint.matrix );

						joint.matrixAutoUpdate = false;
						joint.updateMatrix();

						var object = new CSS3DObject( bond );
						object.rotation.y = Math.PI / 2;

						object.matrixAutoUpdate = false;
						object.updateMatrix();

						object.userData.bondLengthShort = bondLength + "px";
						object.userData.bondLengthFull = ( bondLength + 55 ) + "px";

						object.userData.joint = joint;

						joint.add( object );
						root.add( joint );

						objects.push( object );

					}

					//console.log( "CSS3DObjects:", objects.length );

					switch ( visualizationType ) {

						case 0:
							showAtoms();
							break;
						case 1:
							showBonds();
							break;
						case 2:
							showAtomsBonds();
							break;

					}

					render();

				} );


			}

			//

			function onWindowResize() {

				camera.aspect = window.innerWidth / window.innerHeight;
				camera.updateProjectionMatrix();

				renderer.setSize( window.innerWidth, window.innerHeight );

				render();

			}

			function animate() {

				requestAnimationFrame( animate );
				controls.update();

				var time = Date.now() * 0.0004;

				root.rotation.x = time;
				root.rotation.y = time * 0.7;

				render();

			}

			function render() {

				renderer.render( scene, camera );

			}

    </script>
  </body>

</html>