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css3d_molecules.html
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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%);
}
.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>
<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 );
//
const joint = new THREE.Object3D();
joint.position.copy( start );
joint.position.lerp( end, 0.5 );
joint.matrix.copy( objMatrix );
joint.quaternion.setFromRotationMatrix( joint.matrix );
joint.matrixAutoUpdate = false;
joint.updateMatrix();
bond = document.createElement( 'div' );
bond.className = 'bond';
bond.style.height = bondLength + 'px';
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>