three.js/examples/js/loaders/PDBLoader.js

/**
 * @author alteredq / http://alteredqualia.com/
 */

THREE.PDBLoader = function ( manager ) {

	this.manager = ( manager !== undefined ) ? manager : THREE.DefaultLoadingManager;

};

THREE.PDBLoader.prototype = {

	constructor: THREE.PDBLoader,

	load: function ( url, onLoad, onProgress, onError ) {

		var scope = this;

		var loader = new THREE.XHRLoader( scope.manager );
		loader.setCrossOrigin( this.crossOrigin );
		loader.load( url, function ( text ) {

			var json = scope.parsePDB( text );
			scope.createModel( json, onLoad );

		}, onProgress, onError );

	},

	setCrossOrigin: function ( value ) {

		this.crossOrigin = value;

	},

	// Based on CanvasMol PDB parser

	parsePDB: function ( text ) {

		function trim( text ) {

			return text.replace( /^\s\s*/, '' ).replace( /\s\s*$/, '' );

		}

		function capitalize( text ) {

			return text.charAt( 0 ).toUpperCase() + text.substr( 1 ).toLowerCase();

		}

		function hash( s, e ) {

			return "s" + Math.min( s, e ) + "e" + Math.max( s, e );

		}

		function parseBond( start, length ) {

			var eatom = parseInt( lines[ i ].substr( start, length ) );

			if ( eatom ) {

				var h = hash( satom, eatom );

				if ( bhash[ h ] == undefined ) {

					bonds.push( [ satom - 1, eatom - 1, 1 ] );
					bhash[ h ] = bonds.length - 1;

				} else {

					// doesn't really work as almost all PDBs
					// have just normal bonds appearing multiple
					// times instead of being double/triple bonds
					// bonds[bhash[h]][2] += 1;

				}

			}

		}

		var CPK = { "h": [ 255,255,255 ],"he": [ 217,255,255 ],"li": [ 204,128,255 ],"be": [ 194,255,0 ],"b": [ 255,181,181 ],"c": [ 144,144,144 ],"n": [ 48,80,248 ],"o": [ 255,13,13 ],"f": [ 144,224,80 ],"ne": [ 179,227,245 ],"na": [ 171,92,242 ],"mg": [ 138,255,0 ],"al": [ 191,166,166 ],"si": [ 240,200,160 ],"p": [ 255,128,0 ],"s": [ 255,255,48 ],"cl": [ 31,240,31 ],"ar": [ 128,209,227 ],"k": [ 143,64,212 ],"ca": [ 61,255,0 ],"sc": [ 230,230,230 ],"ti": [ 191,194,199 ],"v": [ 166,166,171 ],"cr": [ 138,153,199 ],"mn": [ 156,122,199 ],"fe": [ 224,102,51 ],"co": [ 240,144,160 ],"ni": [ 80,208,80 ],"cu": [ 200,128,51 ],"zn": [ 125,128,176 ],"ga": [ 194,143,143 ],"ge": [ 102,143,143 ],"as": [ 189,128,227 ],"se": [ 255,161,0 ],"br": [ 166,41,41 ],"kr": [ 92,184,209 ],"rb": [ 112,46,176 ],"sr": [ 0,255,0 ],"y": [ 148,255,255 ],"zr": [ 148,224,224 ],"nb": [ 115,194,201 ],"mo": [ 84,181,181 ],"tc": [ 59,158,158 ],"ru": [ 36,143,143 ],"rh": [ 10,125,140 ],"pd": [ 0,105,133 ],"ag": [ 192,192,192 ],"cd": [ 255,217,143 ],"in": [ 166,117,115 ],"sn": [ 102,128,128 ],"sb": [ 158,99,181 ],"te": [ 212,122,0 ],"i": [ 148,0,148 ],"xe": [ 66,158,176 ],"cs": [ 87,23,143 ],"ba": [ 0,201,0 ],"la": [ 112,212,255 ],"ce": [ 255,255,199 ],"pr": [ 217,255,199 ],"nd": [ 199,255,199 ],"pm": [ 163,255,199 ],"sm": [ 143,255,199 ],"eu": [ 97,255,199 ],"gd": [ 69,255,199 ],"tb": [ 48,255,199 ],"dy": [ 31,255,199 ],"ho": [ 0,255,156 ],"er": [ 0,230,117 ],"tm": [ 0,212,82 ],"yb": [ 0,191,56 ],"lu": [ 0,171,36 ],"hf": [ 77,194,255 ],"ta": [ 77,166,255 ],"w": [ 33,148,214 ],"re": [ 38,125,171 ],"os": [ 38,102,150 ],"ir": [ 23,84,135 ],"pt": [ 208,208,224 ],"au": [ 255,209,35 ],"hg": [ 184,184,208 ],"tl": [ 166,84,77 ],"pb": [ 87,89,97 ],"bi": [ 158,79,181 ],"po": [ 171,92,0 ],"at": [ 117,79,69 ],"rn": [ 66,130,150 ],"fr": [ 66,0,102 ],"ra": [ 0,125,0 ],"ac": [ 112,171,250 ],"th": [ 0,186,255 ],"pa": [ 0,161,255 ],"u": [ 0,143,255 ],"np": [ 0,128,255 ],"pu": [ 0,107,255 ],"am": [ 84,92,242 ],"cm": [ 120,92,227 ],"bk": [ 138,79,227 ],"cf": [ 161,54,212 ],"es": [ 179,31,212 ],"fm": [ 179,31,186 ],"md": [ 179,13,166 ],"no": [ 189,13,135 ],"lr": [ 199,0,102 ],"rf": [ 204,0,89 ],"db": [ 209,0,79 ],"sg": [ 217,0,69 ],"bh": [ 224,0,56 ],"hs": [ 230,0,46 ],"mt": [ 235,0,38 ],
			   "ds": [ 235,0,38 ],"rg": [ 235,0,38 ],"cn": [ 235,0,38 ],"uut": [ 235,0,38 ],"uuq": [ 235,0,38 ],"uup": [ 235,0,38 ],"uuh": [ 235,0,38 ],"uus": [ 235,0,38 ],"uuo": [ 235,0,38 ] };


		var atoms = [];
		var bonds = [];
		var histogram = {};

		var bhash = {};

		var lines = text.split( "\n" );

		var x, y, z, e;

		for ( var i = 0, il = lines.length; i < il; ++ i ) {

			if ( lines[ i ].substr( 0, 4 ) == "ATOM" || lines[ i ].substr( 0, 6 ) == "HETATM" ) {

				x = parseFloat( lines[ i ].substr( 30, 7 ) );
				y = parseFloat( lines[ i ].substr( 38, 7 ) );
				z = parseFloat( lines[ i ].substr( 46, 7 ) );

				e = trim( lines[ i ].substr( 76, 2 ) ).toLowerCase();

				if ( e == "" ) e = trim( lines[ i ].substr( 12, 2 ) ).toLowerCase();
				atoms.push( [ x,y,z, CPK[ e ], capitalize( e ) ] );

				if ( histogram[ e ] == undefined ) histogram[ e ] = 1;
				else histogram[ e ] += 1;

			} else if ( lines[ i ].substr( 0, 6 ) == "CONECT" ) {

				var satom = parseInt( lines[ i ].substr( 6, 5 ) );

				parseBond( 11, 5 );
				parseBond( 16, 5 );
				parseBond( 21, 5 );
				parseBond( 26, 5 );

			}

		}

		return { "ok": true, "atoms": atoms, "bonds": bonds, "histogram": histogram };

	},

	createModel: function ( json, callback ) {

		var scope = this,
		geometryAtoms = new THREE.Geometry(),
		geometryBonds = new THREE.Geometry();

		geometryAtoms.elements = [];

		var atoms = json.atoms;
		var bonds = json.bonds;

		for ( var i = 0; i < atoms.length; i ++ ) {

			var atom = atoms[ i ];

			var x = atom[ 0 ];
			var y = atom[ 1 ];
			var z = atom[ 2 ];

			var position = new THREE.Vector3( x, y, z );
			geometryAtoms.vertices.push( position );

			var r = atom[ 3 ][ 0 ] / 255;
			var g = atom[ 3 ][ 1 ] / 255;
			var b = atom[ 3 ][ 2 ] / 255;

			var color = new THREE.Color();
			color.setRGB( r, g, b );

			geometryAtoms.colors.push( color );

			geometryAtoms.elements.push( atom[ 4 ] );

		}

		for ( var i = 0; i < bonds.length; i ++ ) {

			var bond = bonds[ i ];

			var start = bond[ 0 ];
			var end = bond[ 1 ];

			var vertex1 = geometryAtoms.vertices[ start ];
			var vertex2 = geometryAtoms.vertices[ end ];

			geometryBonds.vertices.push( vertex1.clone() );
			geometryBonds.vertices.push( vertex2.clone() );

		}

		callback( geometryAtoms, geometryBonds, json );

	}

};