examples/css3d_molecules.html

<!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%);
			}
			.bond {
				width: 5px;
				height: 10px;
				background: #eee;
				display: block;
			}
		</style>
	</head>
	<body>
		<div id="container"></div>
		<div id="info"><a href="https://threejs.org" target="_blank" rel="noopener">three.js</a> css3d - molecules</div>

		<!-- Import maps polyfill -->
		<!-- Remove this when import maps will be widely supported -->
		<script async src="https://unpkg.com/es-module-shims@1.3.6/dist/es-module-shims.js"></script>

		<script type="importmap">
			{
				"imports": {
					"three": "../build/three.module.js",
					"three/addons/": "./jsm/"
				}
			}
		</script>

		<script type="module">

			import * as THREE from 'three';

			import { TrackballControls } from 'three/addons/controls/TrackballControls.js';
			import { PDBLoader } from 'three/addons/loaders/PDBLoader.js';
			import { CSS3DRenderer, CSS3DObject, CSS3DSprite } from 'three/addons/renderers/CSS3DRenderer.js';
			import { GUI } from 'three/addons/libs/lil-gui.module.min.js';

			let camera, scene, renderer;
			let controls;
			let root;

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

			const VIZ_TYPE = {
				'Atoms': 0,
				'Bonds': 1,
				'Atoms + Bonds': 2
			};

			const 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'
			};

			const params = {
				vizType: 2,
				molecule: 'caffeine.pdb'
			};

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

			init();
			animate();

			function init() {

				camera = new THREE.PerspectiveCamera( 70, window.innerWidth / window.innerHeight, 1, 5000 );
				camera.position.z = 1000;

				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;

				//

				baseSprite.onload = function () {

					loadMolecule( params.molecule );

				};

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

				//

				window.addEventListener( 'resize', onWindowResize );

				//

				const gui = new GUI();

				gui.add( params, 'vizType', VIZ_TYPE ).onChange( changeVizType );
				gui.add( params, 'molecule', MOLECULES ).onChange( loadMolecule );
				gui.open();

			}

			function changeVizType( value ) {

				if ( value === 0 ) showAtoms();
				else if ( value === 1 ) showBonds();
				else showAtomsBonds();

			}

			//

			function showAtoms() {

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

					const 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 ( let i = 0; i < objects.length; i ++ ) {

					const 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 ( let i = 0; i < objects.length; i ++ ) {

					const 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 ) {

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

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

				for ( let 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 ) {

				const width = image.width;
				const height = image.height;

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

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

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

				return canvas;

			}

			//

			function loadMolecule( model ) {

				const url = 'models/pdb/' + model;

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

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

				}

				objects.length = 0;

				loader.load( url, function ( pdb ) {

					const geometryAtoms = pdb.geometryAtoms;
					const geometryBonds = pdb.geometryBonds;
					const 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 );

					const positionAtoms = geometryAtoms.getAttribute( 'position' );
					const colorAtoms = geometryAtoms.getAttribute( 'color' );

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

					for ( let i = 0; i < positionAtoms.count; i ++ ) {

						position.fromBufferAttribute( positionAtoms, i );
						color.fromBufferAttribute( colorAtoms, i );

						const atomJSON = json.atoms[ i ];
						const element = atomJSON[ 4 ];

						if ( ! colorSpriteMap[ element ] ) {

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

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

							const dataUrl = canvas.toDataURL();

							colorSpriteMap[ element ] = dataUrl;

						}

						const colorSprite = colorSpriteMap[ element ];

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

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

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

						root.add( object );

						objects.push( object );

					}

					const positionBonds = geometryBonds.getAttribute( 'position' );

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

					for ( let i = 0; i < positionBonds.count; i += 2 ) {

						start.fromBufferAttribute( positionBonds, i );
						end.fromBufferAttribute( positionBonds, i + 1 );

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

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

						//

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

						let 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';

						//

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

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

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

						root.add( object );

						objects.push( object );

						//

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

						const 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();

						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 );

					changeVizType( params.vizType );

				} );


			}

			//

			function onWindowResize() {

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

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

			}

			function animate() {

				requestAnimationFrame( animate );
				controls.update();

				const 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>