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

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

THREE.PDBLoader = function () {};

THREE.PDBLoader.prototype = {

	constructor: THREE.OBJLoader,

	load: function ( url, onLoad ) {

		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 );

		} );

	},

	// 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 );

	}

}