Add SDFLoader for Molfile support

examples/jsm/Addons.js

@@ -106,6 +106,7 @@ export * from './loaders/NRRDLoader.js';
 export * from './loaders/OBJLoader.js';
 export * from './loaders/PCDLoader.js';
 export * from './loaders/PDBLoader.js';
+export * from './loaders/SDFLoader.js';
 export * from './loaders/PLYLoader.js';
 export * from './loaders/PVRLoader.js';
 export * from './loaders/RGBELoader.js';

examples/jsm/loaders/SDFLoader.js

@@ -0,0 +1,137 @@
+import {
+  Loader,
+  FileLoader,
+  Group,
+  Vector3,
+  Color,
+  SphereGeometry,
+  CylinderGeometry,
+  MeshLambertMaterial,
+  InstancedMesh,
+  Matrix4,
+  Quaternion
+} from 'three';
+
+const DEFAULT_VDW_RADIUS = {
+  H: 0.31, C: 0.76, N: 0.71, O: 0.66, F: 0.57,
+  P: 1.07, S: 1.05, Cl: 1.02, Br: 1.2, I: 1.39
+};
+
+const DEFAULT_ELEMENT_COLOR = {
+  H: 0xffffff, C: 0x909090, N: 0x3050f8, O: 0xff0d0d, F: 0x90e050,
+  P: 0xff8000, S: 0xffff30, Cl: 0x1ff01f, Br: 0xa62929, I: 0x940094
+};
+
+class SDFLoader extends Loader {
+
+  constructor( manager ) {
+    super( manager );
+    this.elementRadii = { ...DEFAULT_VDW_RADIUS };
+    this.elementColors = { ...DEFAULT_ELEMENT_COLOR };
+  }
+
+  setElementData( colors, radii ) {
+    if ( colors ) Object.assign( this.elementColors, colors );
+    if ( radii ) Object.assign( this.elementRadii, radii );
+    return this;
+  }
+
+  load( url, onLoad, onProgress, onError ) {
+    const loader = new FileLoader( this.manager );
+    loader.setPath( this.path );
+    loader.setRequestHeader( this.requestHeader );
+    loader.setWithCredentials( this.withCredentials );
+    loader.setResponseType( 'text' );
+    loader.load( url, text => {
+      try {
+        onLoad( this.parse( text ) );
+      } catch ( e ) {
+        if ( onError ) {
+          onError( e );
+        } else {
+          console.error( e );
+        }
+        this.manager.itemError( url );
+      }
+    }, onProgress, onError );
+  }
+
+  parse( text ) {
+    const lines = text.split( /\r?\n/ );
+    let i = 3; // skip header
+    const counts = lines[ i++ ].trim().split( /\s+/ );
+    const natoms = parseInt( counts[ 0 ] );
+    const nbonds = parseInt( counts[ 1 ] );
+
+    const atoms = [];
+    for ( let k = 0; k < natoms; k ++, i ++ ) {
+      const l = lines[ i ];
+      atoms.push( {
+        position: new Vector3(
+          parseFloat( l.substr( 0, 10 ) ),
+          parseFloat( l.substr( 10, 10 ) ),
+          parseFloat( l.substr( 20, 10 ) )
+        ),
+        element: l.substr( 31, 3 ).trim() || 'C'
+      } );
+    }
+
+    const bonds = [];
+    for ( let k = 0; k < nbonds; k ++, i ++ ) {
+      const l = lines[ i ];
+      bonds.push( [
+        parseInt( l.substr( 0, 3 ) ) - 1,
+        parseInt( l.substr( 3, 3 ) ) - 1
+      ] );
+    }
+
+    return this._buildSceneGraph( atoms, bonds );
+  }
+
+  _buildSceneGraph( atoms, bonds ) {
+    const group = new Group();
+
+    const sphereGeo = new SphereGeometry( 1, 16, 16 );
+    const atomMat = new MeshLambertMaterial();
+    const atomMesh = new InstancedMesh( sphereGeo, atomMat, atoms.length );
+    const m = new Matrix4();
+
+    atoms.forEach( ( atom, idx ) => {
+      const r = ( this.elementRadii[ atom.element ] || 0.75 ) * 0.2;
+      m.makeScale( r, r, r );
+      m.setPosition( atom.position );
+      atomMesh.setMatrixAt( idx, m );
+      const color = this.elementColors[ atom.element ] || 0xcccccc;
+      atomMesh.setColorAt( idx, new Color( color ) );
+    } );
+    atomMesh.instanceMatrix.needsUpdate = true;
+    atomMesh.instanceColor.needsUpdate = true;
+    group.add( atomMesh );
+
+    const cylGeo = new CylinderGeometry( 0.05, 0.05, 1, 8 );
+    const bondMat = new MeshLambertMaterial( { color: 0xaaaaaa } );
+    const bondMesh = new InstancedMesh( cylGeo, bondMat, bonds.length );
+    const up = new Vector3( 0, 1, 0 );
+    const q = new Quaternion();
+
+    bonds.forEach( ( [ a, b ], idx ) => {
+      const v1 = atoms[ a ].position;
+      const v2 = atoms[ b ].position;
+      const mid = v1.clone().add( v2 ).multiplyScalar( 0.5 );
+      const dir = v2.clone().sub( v1 );
+      const len = dir.length();
+      q.setFromUnitVectors( up, dir.clone().normalize() );
+      m.makeRotationFromQuaternion( q );
+      m.setPosition( mid );
+      m.scale( new Vector3( 1, len, 1 ) );
+      bondMesh.setMatrixAt( idx, m );
+    } );
+    bondMesh.instanceMatrix.needsUpdate = true;
+    group.add( bondMesh );
+
+    return group;
+  }
+
+}
+
+export { SDFLoader };