webgl_loader_pdb.html 6.8 KB

123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268
  1. <!DOCTYPE html>
  2. <html lang="en">
  3. <head>
  4. <title>three.js webgl - molecules</title>
  5. <meta charset="utf-8">
  6. <meta name="viewport" content="width=device-width, user-scalable=no, minimum-scale=1.0, maximum-scale=1.0">
  7. <link type="text/css" rel="stylesheet" href="main.css">
  8. <style>
  9. .label {
  10. text-shadow: -1px 1px 1px rgb(0,0,0);
  11. margin-left: 25px;
  12. font-size: 20px;
  13. }
  14. </style>
  15. </head>
  16. <body>
  17. <div id="container"></div>
  18. <div id="info"><a href="https://threejs.org" target="_blank" rel="noopener">three.js webgl</a> - molecules</div>
  19. <!-- Import maps polyfill -->
  20. <!-- Remove this when import maps will be widely supported -->
  21. <script async src="https://unpkg.com/[email protected]/dist/es-module-shims.js"></script>
  22. <script type="importmap">
  23. {
  24. "imports": {
  25. "three": "../build/three.module.js"
  26. }
  27. }
  28. </script>
  29. <script type="module">
  30. import * as THREE from 'three';
  31. import { TrackballControls } from './jsm/controls/TrackballControls.js';
  32. import { PDBLoader } from './jsm/loaders/PDBLoader.js';
  33. import { CSS2DRenderer, CSS2DObject } from './jsm/renderers/CSS2DRenderer.js';
  34. import { GUI } from './jsm/libs/lil-gui.module.min.js';
  35. let camera, scene, renderer, labelRenderer;
  36. let controls;
  37. let root;
  38. const MOLECULES = {
  39. 'Ethanol': 'ethanol.pdb',
  40. 'Aspirin': 'aspirin.pdb',
  41. 'Caffeine': 'caffeine.pdb',
  42. 'Nicotine': 'nicotine.pdb',
  43. 'LSD': 'lsd.pdb',
  44. 'Cocaine': 'cocaine.pdb',
  45. 'Cholesterol': 'cholesterol.pdb',
  46. 'Lycopene': 'lycopene.pdb',
  47. 'Glucose': 'glucose.pdb',
  48. 'Aluminium oxide': 'Al2O3.pdb',
  49. 'Cubane': 'cubane.pdb',
  50. 'Copper': 'cu.pdb',
  51. 'Fluorite': 'caf2.pdb',
  52. 'Salt': 'nacl.pdb',
  53. 'YBCO superconductor': 'ybco.pdb',
  54. 'Buckyball': 'buckyball.pdb',
  55. 'Graphite': 'graphite.pdb'
  56. };
  57. const params = {
  58. molecule: 'caffeine.pdb'
  59. };
  60. const loader = new PDBLoader();
  61. const offset = new THREE.Vector3();
  62. init();
  63. animate();
  64. function init() {
  65. scene = new THREE.Scene();
  66. scene.background = new THREE.Color( 0x050505 );
  67. camera = new THREE.PerspectiveCamera( 70, window.innerWidth / window.innerHeight, 1, 5000 );
  68. camera.position.z = 1000;
  69. scene.add( camera );
  70. const light1 = new THREE.DirectionalLight( 0xffffff, 0.8 );
  71. light1.position.set( 1, 1, 1 );
  72. scene.add( light1 );
  73. const light2 = new THREE.DirectionalLight( 0xffffff, 0.5 );
  74. light2.position.set( - 1, - 1, 1 );
  75. scene.add( light2 );
  76. root = new THREE.Group();
  77. scene.add( root );
  78. //
  79. renderer = new THREE.WebGLRenderer( { antialias: true } );
  80. renderer.setPixelRatio( window.devicePixelRatio );
  81. renderer.setSize( window.innerWidth, window.innerHeight );
  82. document.getElementById( 'container' ).appendChild( renderer.domElement );
  83. labelRenderer = new CSS2DRenderer();
  84. labelRenderer.setSize( window.innerWidth, window.innerHeight );
  85. labelRenderer.domElement.style.position = 'absolute';
  86. labelRenderer.domElement.style.top = '0px';
  87. labelRenderer.domElement.style.pointerEvents = 'none';
  88. document.getElementById( 'container' ).appendChild( labelRenderer.domElement );
  89. //
  90. controls = new TrackballControls( camera, renderer.domElement );
  91. controls.minDistance = 500;
  92. controls.maxDistance = 2000;
  93. //
  94. loadMolecule( params.molecule );
  95. //
  96. window.addEventListener( 'resize', onWindowResize );
  97. //
  98. const gui = new GUI();
  99. gui.add( params, 'molecule', MOLECULES ).onChange( loadMolecule );
  100. gui.open();
  101. }
  102. //
  103. function loadMolecule( model ) {
  104. const url = 'models/pdb/' + model;
  105. while ( root.children.length > 0 ) {
  106. const object = root.children[ 0 ];
  107. object.parent.remove( object );
  108. }
  109. loader.load( url, function ( pdb ) {
  110. const geometryAtoms = pdb.geometryAtoms;
  111. const geometryBonds = pdb.geometryBonds;
  112. const json = pdb.json;
  113. const boxGeometry = new THREE.BoxGeometry( 1, 1, 1 );
  114. const sphereGeometry = new THREE.IcosahedronGeometry( 1, 3 );
  115. geometryAtoms.computeBoundingBox();
  116. geometryAtoms.boundingBox.getCenter( offset ).negate();
  117. geometryAtoms.translate( offset.x, offset.y, offset.z );
  118. geometryBonds.translate( offset.x, offset.y, offset.z );
  119. let positions = geometryAtoms.getAttribute( 'position' );
  120. const colors = geometryAtoms.getAttribute( 'color' );
  121. const position = new THREE.Vector3();
  122. const color = new THREE.Color();
  123. for ( let i = 0; i < positions.count; i ++ ) {
  124. position.x = positions.getX( i );
  125. position.y = positions.getY( i );
  126. position.z = positions.getZ( i );
  127. color.r = colors.getX( i );
  128. color.g = colors.getY( i );
  129. color.b = colors.getZ( i );
  130. const material = new THREE.MeshPhongMaterial( { color: color } );
  131. const object = new THREE.Mesh( sphereGeometry, material );
  132. object.position.copy( position );
  133. object.position.multiplyScalar( 75 );
  134. object.scale.multiplyScalar( 25 );
  135. root.add( object );
  136. const atom = json.atoms[ i ];
  137. const text = document.createElement( 'div' );
  138. text.className = 'label';
  139. text.style.color = 'rgb(' + atom[ 3 ][ 0 ] + ',' + atom[ 3 ][ 1 ] + ',' + atom[ 3 ][ 2 ] + ')';
  140. text.textContent = atom[ 4 ];
  141. const label = new CSS2DObject( text );
  142. label.position.copy( object.position );
  143. root.add( label );
  144. }
  145. positions = geometryBonds.getAttribute( 'position' );
  146. const start = new THREE.Vector3();
  147. const end = new THREE.Vector3();
  148. for ( let i = 0; i < positions.count; i += 2 ) {
  149. start.x = positions.getX( i );
  150. start.y = positions.getY( i );
  151. start.z = positions.getZ( i );
  152. end.x = positions.getX( i + 1 );
  153. end.y = positions.getY( i + 1 );
  154. end.z = positions.getZ( i + 1 );
  155. start.multiplyScalar( 75 );
  156. end.multiplyScalar( 75 );
  157. const object = new THREE.Mesh( boxGeometry, new THREE.MeshPhongMaterial( 0xffffff ) );
  158. object.position.copy( start );
  159. object.position.lerp( end, 0.5 );
  160. object.scale.set( 5, 5, start.distanceTo( end ) );
  161. object.lookAt( end );
  162. root.add( object );
  163. }
  164. render();
  165. } );
  166. }
  167. //
  168. function onWindowResize() {
  169. camera.aspect = window.innerWidth / window.innerHeight;
  170. camera.updateProjectionMatrix();
  171. renderer.setSize( window.innerWidth, window.innerHeight );
  172. labelRenderer.setSize( window.innerWidth, window.innerHeight );
  173. render();
  174. }
  175. function animate() {
  176. requestAnimationFrame( animate );
  177. controls.update();
  178. const time = Date.now() * 0.0004;
  179. root.rotation.x = time;
  180. root.rotation.y = time * 0.7;
  181. render();
  182. }
  183. function render() {
  184. renderer.render( scene, camera );
  185. labelRenderer.render( scene, camera );
  186. }
  187. </script>
  188. </body>
  189. </html>