You can not select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
270 lines
6.8 KiB
270 lines
6.8 KiB
2 years ago
|
<!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>
|