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<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-->
<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();
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, 2.5 );
light1.position.set( 1, 1, 1 );
scene.add( light1 );
const light2 = new THREE.DirectionalLight( 0xffffff, 1.5 );
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 );
renderer.setAnimationLoop( animate );
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( { color: 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 );
}
} );
}
//
function onWindowResize() {
camera.aspect = window.innerWidth / window.innerHeight;
camera.updateProjectionMatrix();
renderer.setSize( window.innerWidth, window.innerHeight );
labelRenderer.setSize( window.innerWidth, window.innerHeight );
}
function 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>