examples/webgl_loader_pdb.html

<!DOCTYPE html>
<html lang="en">
	<head>
		<title>three.js webgl - 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>
			.label {
				text-shadow: -1px 1px 1px rgb(0,0,0);
				margin-left: 25px;
				font-size: 20px;
			}
		</style>
	</head>
	<body>
		<div id="container"></div>
		<div id="info"><a href="https://threejs.org" target="_blank" rel="noopener">three.js webgl</a> - 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 { CSS2DRenderer, CSS2DObject } from 'three/addons/renderers/CSS2DRenderer.js';
			import { GUI } from 'three/addons/libs/lil-gui.module.min.js';

			let camera, scene, renderer, labelRenderer;
			let controls;

			let root;

			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',
				'Graphite': 'graphite.pdb'
			};

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

			const loader = new PDBLoader();
			const offset = new THREE.Vector3();

			init();
			animate();

			function init() {

				scene = new THREE.Scene();
				scene.background = new THREE.Color( 0x050505 );

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

				const light1 = new THREE.DirectionalLight( 0xffffff, 0.8 );
				light1.position.set( 1, 1, 1 );
				scene.add( light1 );

				const light2 = new THREE.DirectionalLight( 0xffffff, 0.5 );
				light2.position.set( - 1, - 1, 1 );
				scene.add( light2 );

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

				//

				renderer = new THREE.WebGLRenderer( { antialias: true } );
				renderer.setPixelRatio( window.devicePixelRatio );
				renderer.setSize( window.innerWidth, window.innerHeight );
				document.getElementById( 'container' ).appendChild( renderer.domElement );

				labelRenderer = new CSS2DRenderer();
				labelRenderer.setSize( window.innerWidth, window.innerHeight );
				labelRenderer.domElement.style.position = 'absolute';
				labelRenderer.domElement.style.top = '0px';
				labelRenderer.domElement.style.pointerEvents = 'none';
				document.getElementById( 'container' ).appendChild( labelRenderer.domElement );

				//

				controls = new TrackballControls( camera, renderer.domElement );
				controls.minDistance = 500;
				controls.maxDistance = 2000;

				//

				loadMolecule( params.molecule );

				//

				window.addEventListener( 'resize', onWindowResize );

				//

				const gui = new GUI();

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

			}

			//

			function loadMolecule( model ) {

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

				while ( root.children.length > 0 ) {

					const object = root.children[ 0 ];
					object.parent.remove( object );

				}

				loader.load( url, function ( pdb ) {

					const geometryAtoms = pdb.geometryAtoms;
					const geometryBonds = pdb.geometryBonds;
					const json = pdb.json;

					const boxGeometry = new THREE.BoxGeometry( 1, 1, 1 );
					const sphereGeometry = new THREE.IcosahedronGeometry( 1, 3 );

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

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

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

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

					for ( let 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 );

						const material = new THREE.MeshPhongMaterial( { color: color } );

						const object = new THREE.Mesh( sphereGeometry, material );
						object.position.copy( position );
						object.position.multiplyScalar( 75 );
						object.scale.multiplyScalar( 25 );
						root.add( object );

						const atom = json.atoms[ i ];

						const text = document.createElement( 'div' );
						text.className = 'label';
						text.style.color = 'rgb(' + atom[ 3 ][ 0 ] + ',' + atom[ 3 ][ 1 ] + ',' + atom[ 3 ][ 2 ] + ')';
						text.textContent = atom[ 4 ];

						const label = new CSS2DObject( text );
						label.position.copy( object.position );
						root.add( label );

					}

					positions = geometryBonds.getAttribute( 'position' );

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

					for ( let 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 );

						const object = new THREE.Mesh( boxGeometry, new THREE.MeshPhongMaterial( 0xffffff ) );
						object.position.copy( start );
						object.position.lerp( end, 0.5 );
						object.scale.set( 5, 5, start.distanceTo( end ) );
						object.lookAt( end );
						root.add( object );

					}

					render();

				} );

			}

			//

			function onWindowResize() {

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

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

				render();

			}

			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 );
				labelRenderer.render( scene, camera );

			}

		</script>
	</body>
</html>