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.FileLoader( scope.manager );
		loader.load( url, function ( text ) {

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

		}, onProgress, onError );

	},

	// 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 );

	}

};