From 1a6b06635595e56f67dcdcf4483de93c3621aa05 Mon Sep 17 00:00:00 2001
From: Marco Biasini <mvbiasini@gmail.com>
Date: Sun, 1 Feb 2015 10:54:34 +0100
Subject: [PATCH] port all files to use require.js

---
 demo.js                               |   55 +-
 index.html                            |   69 +-
 js/require.js                         |   36 +
 src/animation.js                      |    7 +-
 src/base-geom.js                      |  292 ++++++
 src/buffer-allocators.js              |   12 +-
 src/cam.js                            |   13 +-
 src/chain-data.js                     |   18 +-
 src/core.js                           |   59 +-
 src/custom-mesh.js                    |   20 +-
 src/framebuffer.js                    |    7 +-
 src/geom-builders.js                  |   14 +-
 src/geom.js                           |   20 +-
 src/indexed-vertex-array.js           |    9 +-
 src/io.js                             |   23 +-
 src/label.js                          |  204 ++++
 src/line-geom.js                      |   99 ++
 src/mesh-geom.js                      |  178 ++++
 src/mol.js                            | 1297 -------------------------
 src/mol/all.js                        |   99 ++
 src/mol/atom.js                       |  110 +++
 src/mol/bond.js                       |   53 +
 src/mol/chain.js                      |  349 +++++++
 src/mol/mol.js                        |  468 +++++++++
 src/mol/residue.js                    |  208 ++++
 src/mol/select.js                     |  171 ++++
 src/pv.js                             |   24 +
 src/render.js                         |   79 +-
 src/scene-node.js                     |   86 ++
 src/scene.js                          |   45 -
 src/shade.js                          |   32 +-
 src/shaders.js                        |   47 +-
 src/slab.js                           |   13 +-
 src/symmetry.js                       |   12 +-
 src/tests/binary-search.js            |   71 ++
 src/tests/colors.js                   |   29 +
 {tests => src/tests}/mol-iterators.js |    6 +
 {tests => src/tests}/mol-select.js    |    6 +-
 {tests => src/tests}/pdb-io.js        |    6 +
 {tests => src/tests}/viewer-render.js |    4 +-
 src/touch.js                          |   18 +-
 src/trace.js                          |   15 +-
 src/unique-object-id-pool.js          |   99 ++
 src/vert-assoc.js                     |   21 +-
 src/vertex-array-base.js              |    8 +-
 src/vertex-array.js                   |   15 +-
 src/viewer.js                         |   52 +-
 src/viewpoint.js                      |   14 +-
 tests/all.html                        |   36 +-
 tests/all.js                          |   78 ++
 tests/binary-search.js                |   64 --
 tests/colors.js                       |   25 -
 52 files changed, 3037 insertions(+), 1758 deletions(-)
 create mode 100644 js/require.js
 create mode 100644 src/base-geom.js
 create mode 100644 src/label.js
 create mode 100644 src/line-geom.js
 create mode 100644 src/mesh-geom.js
 delete mode 100644 src/mol.js
 create mode 100644 src/mol/all.js
 create mode 100644 src/mol/atom.js
 create mode 100644 src/mol/bond.js
 create mode 100644 src/mol/chain.js
 create mode 100644 src/mol/mol.js
 create mode 100644 src/mol/residue.js
 create mode 100644 src/mol/select.js
 create mode 100644 src/pv.js
 create mode 100644 src/scene-node.js
 create mode 100644 src/tests/binary-search.js
 create mode 100644 src/tests/colors.js
 rename {tests => src/tests}/mol-iterators.js (96%)
 rename {tests => src/tests}/mol-select.js (90%)
 rename {tests => src/tests}/pdb-io.js (98%)
 rename {tests => src/tests}/viewer-render.js (98%)
 create mode 100644 src/unique-object-id-pool.js
 create mode 100644 tests/all.js
 delete mode 100644 tests/binary-search.js
 delete mode 100644 tests/colors.js

diff --git a/demo.js b/demo.js
index a6c60c4..269074a 100644
--- a/demo.js
+++ b/demo.js
@@ -1,5 +1,11 @@
-var structure;
+requirejs.config({
+  'baseUrl' : 'src' 
+});
+
+require(['pv', 'mol/all', 'io', 'shade', 'viewpoint'], 
+        function(pv, mol, io, color, viewPoint) {
 
+var structure;
 
 function lines() {
   viewer.clear();
@@ -13,7 +19,7 @@ function cartoon() {
   var go = viewer.cartoon('structure', structure, {
       color : color.ssSuccession(), showRelated : '1',
   });
-  var rotation = principalAxes(go);
+  var rotation = viewPoint.principalAxes(go);
   viewer.setRotation(rotation)
 }
 
@@ -138,3 +144,48 @@ function byChain() {
 function polymerase() {
   load('4UBB');
 };
+
+$(document).foundation();
+$('#1r6a').click(transferase);
+$('#1crn').click(crambin);
+$('#1ake').click(kinase);
+$('#4ubb').click(polymerase);
+$('#4c46').click(longHelices);
+$('#2f8v').click(telethonin);
+$('#style-cartoon').click(cartoon);
+$('#style-tube').click(tube);
+$('#style-line-trace').click(lineTrace);
+$('#style-sline').click(sline);
+$('#style-trace').click(trace);
+$('#style-lines').click(lines);
+$('#style-balls-and-sticks').click(ballsAndSticks);
+$('#style-spheres').click(spheres);
+$('#color-uniform').click(uniform);
+$('#color-element').click(byElement);
+$('#color-chain').click(byChain);
+$('#color-ss-succ').click(ssSuccession);
+$('#color-ss').click(ss);
+$('#color-rainbow').click(rainbow);
+$('#load-from-pdb').change(function() {
+  var pdbId = this.value;
+  this.value = '';
+  this.blur();
+  $.ajax('http://pdb.org/pdb/files/'+pdbId+'.pdb')
+    .done(function(data) {
+      structure = io.pdb(data);
+      cartoon();
+      viewer.autoZoom();
+    })
+});
+var viewer = pv.Viewer(document.getElementById('viewer'), { 
+    width : 'auto', height: 'auto', antialias : true, 
+    outline : true, quality : 'medium',
+    background : '#333'
+});
+viewer.addListener('viewerReady', longHelices);
+
+window.addEventListener('resize', function() {
+      viewer.fitParent();
+});
+
+});
diff --git a/index.html b/index.html
index e24e9f1..423f2d8 100644
--- a/index.html
+++ b/index.html
@@ -7,32 +7,7 @@
     <script src='js/jquery-2.0.2.min.js'></script>
     <script src='js/modernizr.js'></script>
     <script src="js/foundation-5.4.7.min.js"></script>
-    <script src='src/gl-matrix.js'></script>
-    <script src='src/core.js'></script>
-    <script src='src/geom.js'></script>
-    <script src='src/trace.js'></script>
-    <script src='src/symmetry.js'></script>
-    <script src='src/mol.js'></script>
-    <script src='src/io.js'></script>
-    <script src='src/vert-assoc.js'></script>
-    <script src='src/buffer-allocators.js'></script>
-    <script src='src/vertex-array-base.js'></script>
-    <script src='src/indexed-vertex-array.js'></script>
-    <script src='src/vertex-array.js'></script>
-    <script src='src/chain-data.js'></script>
-    <script src='src/geom-builders.js'></script>
-    <script src='src/scene.js'></script>
-    <script src='src/render.js'></script>
-    <script src='src/shade.js'></script>
-    <script src='src/cam.js'></script>
-    <script src='src/shaders.js'></script>
-    <script src='src/framebuffer.js'></script>
-    <script src='src/slab.js'></script>
-    <script src='src/animation.js'></script>
-    <script src='src/touch.js'></script>
-    <script src='src/viewer.js'></script>
-    <script src='src/viewpoint.js'></script>
-    <script src='demo.js'></script>
+    <script data-main='demo' src='js/require.js'></script>
     <link rel='stylesheet' href='css/foundation.css'>
     <style>
       body {
@@ -116,48 +91,6 @@ <h1><a href="#">PV</a></h1>
 </nav>
 </div>
     <script>
-      $(document).foundation();
-      $('#1r6a').click(transferase);
-      $('#1crn').click(crambin);
-      $('#1ake').click(kinase);
-      $('#4ubb').click(polymerase);
-      $('#4c46').click(longHelices);
-      $('#2f8v').click(telethonin);
-      $('#style-cartoon').click(cartoon);
-      $('#style-tube').click(tube);
-      $('#style-line-trace').click(lineTrace);
-      $('#style-sline').click(sline);
-      $('#style-trace').click(trace);
-      $('#style-lines').click(lines);
-      $('#style-balls-and-sticks').click(ballsAndSticks);
-      $('#style-spheres').click(spheres);
-      $('#color-uniform').click(uniform);
-      $('#color-element').click(byElement);
-      $('#color-chain').click(byChain);
-      $('#color-ss-succ').click(ssSuccession);
-      $('#color-ss').click(ss);
-      $('#color-rainbow').click(rainbow);
-      $('#load-from-pdb').change(function() {
-        var pdbId = this.value;
-        this.value = '';
-        this.blur();
-        $.ajax('http://pdb.org/pdb/files/'+pdbId+'.pdb')
-          .done(function(data) {
-            structure = io.pdb(data);
-            cartoon();
-            viewer.autoZoom();
-          })
-      });
-      var viewer = pv.Viewer(document.getElementById('viewer'), { 
-          width : 'auto', height: 'auto', antialias : true, 
-          outline : true, quality : 'medium',
-          background : '#333'
-      });
-      viewer.addListener('viewerReady', longHelices);
-      
-      window.addEventListener('resize', function() {
-        viewer.fitParent();
-      });
     </script>
     </body>
 </html>
diff --git a/js/require.js b/js/require.js
new file mode 100644
index 0000000..be103a7
--- /dev/null
+++ b/js/require.js
@@ -0,0 +1,36 @@
+/*
+ RequireJS 2.1.15 Copyright (c) 2010-2014, The Dojo Foundation All Rights Reserved.
+ Available via the MIT or new BSD license.
+ see: http://github.com/jrburke/requirejs for details
+*/
+var requirejs,require,define;
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+c,d=m(j.shim,a)||{},g=d.exports;for(x();A.length;){c=A.shift();if(null===c[0]){c[0]=a;if(b)break;b=!0}else c[0]===a&&(b=!0);E(c)}c=m(h,a);if(!b&&!t(r,a)&&c&&!c.inited){if(j.enforceDefine&&(!g||!da(g)))return e(a)?void 0:w(C("nodefine","No define call for "+a,null,[a]));E([a,d.deps||[],d.exportsFn])}D()},nameToUrl:function(a,b,c){var d,e,h;(d=m(j.pkgs,a))&&(a=d);if(d=m(aa,a))return i.nameToUrl(d,b,c);if(g.jsExtRegExp.test(a))d=a+(b||"");else{d=j.paths;a=a.split("/");for(e=a.length;0<e;e-=1)if(h=a.slice(0,
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+Y="undefined"!==typeof opera&&"[object Opera]"===opera.toString(),F={},q={},R=[],M=!1;if("undefined"===typeof define){if("undefined"!==typeof requirejs){if(G(requirejs))return;q=requirejs;requirejs=void 0}"undefined"!==typeof require&&!G(require)&&(q=require,require=void 0);g=requirejs=function(b,c,d,e){var n,p="_";!H(b)&&"string"!==typeof b&&(n=b,H(c)?(b=c,c=d,d=e):b=[]);n&&n.context&&(p=n.context);(e=m(F,p))||(e=F[p]=g.s.newContext(p));n&&e.configure(n);return e.require(b,c,d)};g.config=function(b){return g(b)};
+g.nextTick="undefined"!==typeof setTimeout?function(b){setTimeout(b,4)}:function(b){b()};require||(require=g);g.version="2.1.15";g.jsExtRegExp=/^\/|:|\?|\.js$/;g.isBrowser=z;x=g.s={contexts:F,newContext:ga};g({});v(["toUrl","undef","defined","specified"],function(b){g[b]=function(){var c=F._;return c.require[b].apply(c,arguments)}});if(z&&(y=x.head=document.getElementsByTagName("head")[0],D=document.getElementsByTagName("base")[0]))y=x.head=D.parentNode;g.onError=ca;g.createNode=function(b){var c=
+b.xhtml?document.createElementNS("http://www.w3.org/1999/xhtml","html:script"):document.createElement("script");c.type=b.scriptType||"text/javascript";c.charset="utf-8";c.async=!0;return c};g.load=function(b,c,d){var e=b&&b.config||{};if(z)return e=g.createNode(e,c,d),e.setAttribute("data-requirecontext",b.contextName),e.setAttribute("data-requiremodule",c),e.attachEvent&&!(e.attachEvent.toString&&0>e.attachEvent.toString().indexOf("[native code"))&&!Y?(M=!0,e.attachEvent("onreadystatechange",b.onScriptLoad)):
+(e.addEventListener("load",b.onScriptLoad,!1),e.addEventListener("error",b.onScriptError,!1)),e.src=d,J=e,D?y.insertBefore(e,D):y.appendChild(e),J=null,e;if(ea)try{importScripts(d),b.completeLoad(c)}catch(m){b.onError(C("importscripts","importScripts failed for "+c+" at "+d,m,[c]))}};z&&!q.skipDataMain&&T(document.getElementsByTagName("script"),function(b){y||(y=b.parentNode);if(I=b.getAttribute("data-main"))return s=I,q.baseUrl||(E=s.split("/"),s=E.pop(),O=E.length?E.join("/")+"/":"./",q.baseUrl=
+O),s=s.replace(Q,""),g.jsExtRegExp.test(s)&&(s=I),q.deps=q.deps?q.deps.concat(s):[s],!0});define=function(b,c,d){var e,g;"string"!==typeof b&&(d=c,c=b,b=null);H(c)||(d=c,c=null);!c&&G(d)&&(c=[],d.length&&(d.toString().replace(ka,"").replace(la,function(b,d){c.push(d)}),c=(1===d.length?["require"]:["require","exports","module"]).concat(c)));if(M){if(!(e=J))N&&"interactive"===N.readyState||T(document.getElementsByTagName("script"),function(b){if("interactive"===b.readyState)return N=b}),e=N;e&&(b||
+(b=e.getAttribute("data-requiremodule")),g=F[e.getAttribute("data-requirecontext")])}(g?g.defQueue:R).push([b,c,d])};define.amd={jQuery:!0};g.exec=function(b){return eval(b)};g(q)}})(this);
diff --git a/src/animation.js b/src/animation.js
index 1b4e4bf..ae5d8ae 100644
--- a/src/animation.js
+++ b/src/animation.js
@@ -18,9 +18,11 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 // DEALINGS IN THE SOFTWARE.
 
-(function(exports) {
+define(function() {
 "use strict";
 
+var glMatrix = require('./gl-matrix');
+
 // base for all animations, e.g. position transitions, slerping etc.
 function Animation(from, to, duration) {
   this._from = from;
@@ -131,5 +133,4 @@ exports.Move = Move;
 exports.Rotate = Rotate;
 exports.RockAndRoll = RockAndRoll;
 exports.Animation = Animation;
-return true;
-})(this);
+});
diff --git a/src/base-geom.js b/src/base-geom.js
new file mode 100644
index 0000000..824790f
--- /dev/null
+++ b/src/base-geom.js
@@ -0,0 +1,292 @@
+// Copyright (c) 2013-2015 Marco Biasini
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
+define(['core', 'gl-matrix', 'scene-node'], 
+       function(core, glMatrix, SceneNode) {
+
+"use strict";
+
+var vec3 = glMatrix.vec3;
+
+function eachCentralAtomAsym(structure, callback) {
+  structure.eachResidue(function(residue) {
+    var centralAtom = residue.centralAtom();
+    if (centralAtom === null) {
+      return;
+    }
+    callback(centralAtom, centralAtom.pos());
+  });
+}
+
+var eachCentralAtomSym = (function() {
+  var transformedPos = vec3.create();
+  return function(structure, gens, callback) {
+    for (var i = 0; i < gens.length; ++i) {
+      var gen = gens[i];
+      var chains = structure.chainsByName(gen.chains());
+      for (var j = 0; j < gen.matrices().length; ++j) {
+        var matrix = gen.matrix(j);
+        for (var k = 0; k < chains.length; ++k) {
+          var chain = chains[k];
+          for (var l = 0; l < chain.residues().length; ++l) {
+            var centralAtom = chain.residues()[l].centralAtom();
+            if (centralAtom === null) {
+              continue;
+            }
+            vec3.transformMat4(transformedPos, centralAtom.pos(), matrix);
+            callback(centralAtom, transformedPos);
+          }
+        }
+      }
+    }
+  };
+})();
+
+function BaseGeom(gl) {
+  SceneNode.call(this, gl);
+  this._idRanges = [];
+  this._vertAssocs = [];
+  this._showRelated = null;
+}
+
+core.derive(BaseGeom, SceneNode, {
+  setShowRelated : function(rel) {
+    if (rel && rel !== 'asym') {
+      if (this.structure().assembly(rel) === null) {
+        console.error('no assembly with name', rel, 
+                      '. Falling back to asymmetric unit');
+        return;
+      }
+    }
+    this._showRelated = rel;
+    return rel;
+  },
+
+  symWithIndex : function(index) {
+    if (this.showRelated() === 'asym') {
+      return null;
+    }
+    var assembly = this.structure().assembly(this.showRelated());
+    if (!assembly) {
+      return null;
+    }
+    var gen = assembly.generators();
+    for (var i = 0 ; i < gen.length; ++i) {
+      if (gen[i].matrices().length > index) {
+        return gen[i].matrix(index);
+      }
+      index -= gen[i].matrices().length;
+    }
+    return null;
+  },
+
+  showRelated : function() {
+    return this._showRelated;
+  },
+
+  select : function(what) {
+    return this.structure().select(what);
+  },
+
+  structure : function() {
+    return this._vertAssocs[0]._structure;
+  },
+
+
+  getColorForAtom : function(atom, color) {
+    // FIXME: what to do in case there are multiple assocs?
+    return this._vertAssocs[0].getColorForAtom(atom, color);
+  },
+
+  addIdRange : function(range) {
+    this._idRanges.push(range);
+  },
+
+  destroy : function() {
+    SceneNode.prototype.destroy.call(this);
+    for (var i = 0; i < this._idRanges.length; ++i) {
+      this._idRanges[i].recycle();
+    }
+  },
+
+  eachCentralAtom : function(callback) {
+    var go = this;
+    var structure = go.structure();
+    var assembly = structure.assembly(go.showRelated());
+    // in case there is no assembly, just loop over all the atoms contained
+    // in the structure and invoke the callback as is
+    if (assembly === null) {
+      return eachCentralAtomAsym(structure, callback);
+    }
+    return eachCentralAtomSym(structure, assembly.generators(), callback);
+  },
+
+  addVertAssoc : function(assoc) {
+    this._vertAssocs.push(assoc);
+  },
+
+  // returns all vertex arrays that contain geometry for one of the specified
+  // chain names. Typically, there will only be one array for a given chain,
+  // but for larger chains with mesh geometries a single chain may be split
+  // across multiple vertex arrays.
+  _vertArraysInvolving : function(chains) {
+    var vertArrays = this.vertArrays();
+    var selectedArrays = [];
+    var set = {};
+    for (var ci = 0; ci < chains.length; ++ci) {
+      set[chains[ci]] = true;
+    }
+    for (var i = 0; i < vertArrays.length; ++i) {
+      if (set[vertArrays[i].chain()] === true) {
+        selectedArrays.push(vertArrays[i]);
+      }
+    }
+    return selectedArrays;
+  },
+
+
+  // draws vertex arrays by using the symmetry generators contained in assembly
+  _drawSymmetryRelated : function(cam, shader, assembly) {
+    var gens = assembly.generators();
+    for (var i = 0; i < gens.length; ++i) {
+      var gen = gens[i];
+      var affectedVAs = this._vertArraysInvolving(gen.chains());
+      this._drawVertArrays(cam, shader, affectedVAs, gen.matrices());
+    }
+  },
+
+  _updateProjectionIntervalsAsym : 
+      function(xAxis, yAxis, zAxis, xInterval, yInterval, zInterval) {
+      var vertArrays = this.vertArrays();
+      for (var i = 0; i < vertArrays.length; ++i) {
+        vertArrays[i].updateProjectionIntervals(xAxis, yAxis, zAxis, xInterval, 
+                                                yInterval, zInterval);
+      }
+  },
+
+  updateProjectionIntervals :
+      function(xAxis, yAxis, zAxis, xInterval, yInterval, zInterval) {
+    if (!this._visible) {
+      return;
+    }
+    var showRelated = this.showRelated();
+    if (showRelated === 'asym') {
+      return this._updateProjectionIntervalsAsym(xAxis, yAxis, zAxis, 
+                                                 xInterval, yInterval, 
+                                                 zInterval);
+    } 
+    var assembly = this.structure().assembly(showRelated);
+    // in case there is no assembly, fallback to asymmetric unit and bail out.
+    var gens = assembly.generators();
+    for (var i = 0; i < gens.length; ++i) {
+      var gen = gens[i];
+      var affectedVAs = this._vertArraysInvolving(gen.chains());
+      for (var j = 0; j < gen.matrices().length; ++j) {
+        for (var k = 0; k < affectedVAs.length; ++k) {
+          var transform = gen.matrix(j);
+          affectedVAs[k].updateProjectionIntervals(xAxis, yAxis, zAxis, 
+                                                   xInterval, yInterval, 
+                                                   zInterval, transform);
+        }
+      }
+    }
+  },
+
+  // FIXME: investigate the performance cost of sharing code between 
+  // updateSquaredSphereRadius and updateProjectionIntervals 
+  _updateSquaredSphereRadiusAsym : function(center, radius) {
+      var vertArrays = this.vertArrays();
+      for (var i = 0; i < vertArrays.length; ++i) {
+        radius = vertArrays[i].updateSquaredSphereRadius(center, radius);
+      }
+      return radius;
+  },
+
+  updateSquaredSphereRadius : function(center, radius) {
+    if (!this._visible) {
+      return radius;
+    }
+    var showRelated = this.showRelated();
+    if (showRelated === 'asym') {
+      return this._updateSquaredSphereRadiusAsym(center, radius);
+    } 
+    var assembly = this.structure().assembly(showRelated);
+    var gens = assembly.generators();
+    for (var i = 0; i < gens.length; ++i) {
+      var gen = gens[i];
+      var affectedVAs = this._vertArraysInvolving(gen.chains());
+      for (var j = 0; j < gen.matrices().length; ++j) {
+        for (var k = 0; k < affectedVAs.length; ++k) {
+          // FIXME: is this correct?
+          // var transform = gen.matrix(j);
+          radius = affectedVAs[k].updateSquaredSphereRadius(center, radius);
+        }
+      }
+    }
+    return radius;
+  },
+
+  draw : function(cam, shaderCatalog, style, pass) {
+
+    if (!this._visible) {
+      return;
+    }
+
+    var shader = this.shaderForStyleAndPass(shaderCatalog, style, pass);
+
+    if (!shader) {
+      return;
+    }
+    var showRelated = this.showRelated();
+    if (showRelated === 'asym') {
+      return this._drawVertArrays(cam, shader, this.vertArrays(), null);
+    } 
+
+    var assembly = this.structure().assembly(showRelated);
+    return this._drawSymmetryRelated(cam, shader, assembly);
+  },
+
+  colorBy : function(colorFunc, view) {
+    console.time('BaseGeom.colorBy');
+    this._ready = false;
+    view = view || this.structure();
+    for (var i = 0; i < this._vertAssocs.length; ++i) {
+      this._vertAssocs[i].recolor(colorFunc, view);
+    }
+    console.timeEnd('BaseGeom.colorBy');
+  },
+
+  setOpacity : function(val, view) {
+    console.time('BaseGeom.setOpacity');
+    this._ready = false;
+    view = view || this.structure();
+    for (var i = 0; i < this._vertAssocs.length; ++i) {
+      this._vertAssocs[i].setOpacity(val, view);
+    }
+    console.timeEnd('BaseGeom.setOpacity');
+  }
+});
+
+
+return BaseGeom;
+
+});
+
+
diff --git a/src/buffer-allocators.js b/src/buffer-allocators.js
index c04cb6c..e3bf8c5 100644
--- a/src/buffer-allocators.js
+++ b/src/buffer-allocators.js
@@ -18,13 +18,9 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 // DEALINGS IN THE SOFTWARE.
 
-(function(exports) {
+define(function() {
 "use strict";
 
-// contains classes for two kinds of typed array allocation schemes. 
-// PoolAllocator stores every typed array allocation in a list and tries
-// to reuse unused buffers whenever possible. The NativeAllocator just
-// news the typed arrays every time they are used.
 function PoolAllocator(bufferType) {
   this._freeArrays = [];
   this._bufferType = bufferType;
@@ -55,7 +51,5 @@ PoolAllocator.prototype.release = function(buffer) {
   this._freeArrays.push(buffer);
 };
 
-exports.PoolAllocator = PoolAllocator;
-
-return true;
-})(this);
+return PoolAllocator;
+});
diff --git a/src/cam.js b/src/cam.js
index 2228059..4d4b1ab 100644
--- a/src/cam.js
+++ b/src/cam.js
@@ -18,10 +18,16 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 // DEALINGS IN THE SOFTWARE.
 
-(function(exports) {
+define(['gl-matrix'], function(glMatrix) {
 
 "use strict";
 
+var vec3 = glMatrix.vec3;
+var vec4 = glMatrix.vec4;
+var mat3 = glMatrix.mat3;
+var mat4 = glMatrix.mat4;
+var quat = glMatrix.quat;
+
 // A camera, providing us with a view into the 3D worlds. Handles projection,
 // and modelview matrices and controls the global render parameters such as
   // shader and fog.
@@ -296,6 +302,7 @@ Cam.prototype = {
   }
 };
 
-exports.Cam = Cam;
-})(this);
+return Cam;
+
+});
 
diff --git a/src/chain-data.js b/src/chain-data.js
index 82f7a56..b1ac823 100644
--- a/src/chain-data.js
+++ b/src/chain-data.js
@@ -18,7 +18,9 @@
 // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 // SOFTWARE.
 
-(function(exports) {
+define(['core', 'vertex-array', 'indexed-vertex-array'], 
+       function(core, VertexArray, IndexedVertexArray) {
+
 "use strict";
 
 // LineChainData and MeshChainData are two internal classes that add molecule-
@@ -29,7 +31,7 @@ function LineChainData(chain, gl, numVerts, float32Allocator) {
   this._chain = chain;
 }
 
-derive(LineChainData, VertexArray, {
+core.derive(LineChainData, VertexArray, {
   chain : function() { return this._chain; },
 
   drawSymmetryRelated : function(cam, shader, transforms) {
@@ -50,7 +52,7 @@ function MeshChainData(chain, gl, numVerts, numIndices, float32Allocator,
   this._chain = chain;
 }
 
-derive(MeshChainData, IndexedVertexArray, {
+core.derive(MeshChainData, IndexedVertexArray, {
   chain : function() { return this._chain; }
 });
 
@@ -58,8 +60,10 @@ MeshChainData.prototype.drawSymmetryRelated =
   LineChainData.prototype.drawSymmetryRelated;
 
 
-exports.LineChainData = LineChainData;
-exports.MeshChainData = MeshChainData;
+return {
+  LineChainData : LineChainData,
+  MeshChainData : MeshChainData
+};
+
+});
 
-return true;
-})(this);
diff --git a/src/core.js b/src/core.js
index c698b8f..ba40278 100644
--- a/src/core.js
+++ b/src/core.js
@@ -18,9 +18,11 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
 // DEALINGS IN THE SOFTWARE.
 
-(function(exports) {
+define(function() {
+
 "use strict";
 
+var exports = {}
 exports.derive = function(subclass, baseclass, extensions) {
   // jshint forin:false
   for (var prop in baseclass.prototype) {
@@ -158,5 +160,56 @@ exports.indexLastSmallerEqualThan = function(values, value, comp) {
   }
 };
 
-return true;
-})(this);
+function Range(min, max) {
+  if (min === undefined || max === undefined) {
+    this._empty = true;
+    this._min = this._max = null;
+  } else {
+    this._empty = false;
+    this._min = min;
+    this._max = max;
+  }
+}
+
+Range.prototype = {
+  min : function() {
+    return this._min;
+  },
+  max : function() {
+    return this._max;
+  },
+  length : function() {
+    return this._max - this._min;
+  },
+  empty : function() {
+    return this._empty;
+  },
+  center : function() {
+    return (this._max + this._min) * 0.5;
+  },
+
+  extend : function(amount) {
+    this._min -= amount;
+    this._max += amount;
+  },
+
+  update : function(val) {
+    if (!this._empty) {
+      if (val < this._min) {
+        this._min = val;
+      } else if (val > this._max) {
+        this._max = val;
+      }
+      return;
+    }
+    this._min = this._max = val;
+    this._empty = false;
+  }
+};
+
+exports.Range = Range;
+
+return exports;
+
+});
+
diff --git a/src/custom-mesh.js b/src/custom-mesh.js
index 994074a..53a26cb 100644
--- a/src/custom-mesh.js
+++ b/src/custom-mesh.js
@@ -18,10 +18,17 @@
 // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 // SOFTWARE.
 
-(function(exports) {
+define(['gl-matrix', 'core', 'shade', 'geom', 'geom-builders', 'indexed-vertex-array', 
+        'scene-node'], 
+       function(glMatrix, core, color, geom, gb, IndexedVertexArray, SceneNode) {
 
 "use strict";
 
+var vec3 = glMatrix.vec3;
+var mat3 = glMatrix.mat3;
+
+var forceRGB = color.forceRGB;
+
 // small helper with the same interface as IndexedVertexArray that can be used 
 // as a drop-in when the number of vertices/indices is not known in advance.
 function DynamicIndexedVertexArray() {
@@ -60,8 +67,8 @@ function CustomMesh(name, gl, float32Allocator, uint16Allocator) {
   this._float32Allocator = float32Allocator;
   this._uint16Allocator = uint16Allocator;
   this._data = new DynamicIndexedVertexArray();
-  this._protoSphere = new ProtoSphere(8, 8);
-  this._protoCyl = new ProtoCylinder(8);
+  this._protoSphere = new gb.ProtoSphere(8, 8);
+  this._protoCyl = new gb.ProtoCylinder(8);
   this._va = null;
   this._ready = false;
 }
@@ -83,7 +90,7 @@ function capTubeEnd(va, baseIndex, numTubeVerts) {
   va.addTriangle(center, baseIndex, baseIndex + numTubeVerts - 1);
 }
 
-derive(CustomMesh, SceneNode, {
+core.derive(CustomMesh, SceneNode, {
   updateProjectionIntervals : function() {},
   updateSquaredSphereRadius : function(center, radius) { 
     return radius;
@@ -177,6 +184,7 @@ derive(CustomMesh, SceneNode, {
   },
 });
 
-exports.CustomMesh = CustomMesh;
-})(this);
+return CustomMesh;
+
+});
 
diff --git a/src/framebuffer.js b/src/framebuffer.js
index 20cdd99..aa60508 100644
--- a/src/framebuffer.js
+++ b/src/framebuffer.js
@@ -18,7 +18,7 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 // DEALINGS IN THE SOFTWARE.
 
-(function(exports) {
+define(function() {
 
 "use strict";
 
@@ -107,8 +107,7 @@ FrameBuffer.prototype = {
   }
 };
 
+return FrameBuffer;
 
-exports.FrameBuffer = FrameBuffer;
-
-})(this);
+});
 
diff --git a/src/geom-builders.js b/src/geom-builders.js
index 67a4033..2d5f468 100644
--- a/src/geom-builders.js
+++ b/src/geom-builders.js
@@ -19,9 +19,11 @@
 // SOFTWARE.
 
 // contains classes for constructing geometry for spheres, cylinders and tubes.
-(function(exports) {
+define(['gl-matrix', 'geom'], function(glMatrix, geom) {
 "use strict";
 
+var vec3 = glMatrix.vec3;
+
 function ProtoSphere(stacks, arcs) {
   this._arcs = arcs;
   this._stacks = stacks;
@@ -236,9 +238,11 @@ ProtoCylinder.prototype = {
   })()
 };
 
-exports.TubeProfile = TubeProfile;
-exports.ProtoSphere = ProtoSphere;
-exports.ProtoCylinder = ProtoCylinder;
+return {
+  TubeProfile : TubeProfile,
+  ProtoCylinder : ProtoCylinder,
+  ProtoSphere : ProtoSphere
+};
 
-})(this);
+});
 
diff --git a/src/geom.js b/src/geom.js
index 56ed341..901b707 100644
--- a/src/geom.js
+++ b/src/geom.js
@@ -18,10 +18,15 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 // DEALINGS IN THE SOFTWARE.
 
-var geom = (function() {
-  "use strict";
-  // calculates the signed angle of vectors a and b with respect to
-  // the reference normal c. 
+define(['gl-matrix'], function(glMatrix) {
+"use strict";
+
+var vec3 = glMatrix.vec3;
+var mat3 = glMatrix.mat3;
+var quat = glMatrix.quat;
+
+// calculates the signed angle of vectors a and b with respect to
+// the reference normal c. 
 var signedAngle = (function() {
     var tmp = vec3.create();
     return function(a, b, c) {
@@ -253,7 +258,7 @@ var buildRotation = (function() {
   return function(rotation, tangent, left, up, use_left_hint) {
     if (use_left_hint) { vec3.cross(up, tangent, left);
     } else {
-  geom.ortho(up, tangent);
+      ortho(up, tangent);
     }
 
     vec3.cross(left, up, tangent);
@@ -286,8 +291,5 @@ return {
   buildRotation : buildRotation
 };
 
-})();
+});
 
-if(typeof(exports) !== 'undefined') {
-  module.exports = geom;
-}
diff --git a/src/indexed-vertex-array.js b/src/indexed-vertex-array.js
index a09413e..d31573e 100644
--- a/src/indexed-vertex-array.js
+++ b/src/indexed-vertex-array.js
@@ -18,7 +18,7 @@
 // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 // SOFTWARE.
 
-(function(exports) {
+define(['core', 'vertex-array-base'], function(core, VertexArrayBase) {
 "use strict";
 
 function IndexedVertexArray(gl, numVerts, numIndices, 
@@ -32,7 +32,7 @@ function IndexedVertexArray(gl, numVerts, numIndices,
   this._indexData = uint16Allocator.request(numIndices);
 }
 
-derive(IndexedVertexArray, VertexArrayBase, {
+core.derive(IndexedVertexArray, VertexArrayBase, {
 
   destroy : function() {
     VertexArrayBase.prototype.destroy.call(this);
@@ -165,7 +165,6 @@ derive(IndexedVertexArray, VertexArrayBase, {
   }
 });
 
-exports.IndexedVertexArray = IndexedVertexArray;
+return IndexedVertexArray;
 
-return true;
-})(this);
+});
diff --git a/src/io.js b/src/io.js
index bda13d8..2ac562b 100644
--- a/src/io.js
+++ b/src/io.js
@@ -18,10 +18,13 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
 // DEALINGS IN THE SOFTWARE.
 
-(function(exports) {
+define(['gl-matrix', 'mol/all', 'symmetry'], function(glMatrix, mol, symmetry) {
 
 "use strict";
 
+var vec3 = glMatrix.vec3;
+var mat4 = glMatrix.mat4;
+
 function Remark350Reader() {
   this._assemblies = {};
   this._current = null;
@@ -50,7 +53,7 @@ Remark350Reader.prototype = {
     line = line.substr(11);
     if (line[0] === 'B' && line.substr(0, 12) === 'BIOMOLECULE:') {
       var name =  line.substr(13).trim();
-      this._currentAssembly = new Assembly(name); 
+      this._currentAssembly = new symmetry.Assembly(name); 
       this._assemblies[name] =  this._currentAssembly;
       return;
     }
@@ -58,7 +61,7 @@ Remark350Reader.prototype = {
         line.substr(0, 30) === '                   AND CHAINS:') {
       var chains = line.substr(30).split(',');
       if (line[0] === 'A') {
-        this._currentSymGen = new SymGenerator();
+        this._currentSymGen = new symmetry.SymGenerator();
         this._currentAssembly.addGenerator(this._currentSymGen);
       }
       this._currentMatrix = mat4.create();
@@ -339,20 +342,20 @@ function fetchPdb(url, callback, options) {
   oReq.open("GET", url, true);
   oReq.onload = function() {
     if (oReq.response) {
-      var structure= io.pdb(oReq.response, options);
+      var structure= pdb(oReq.response, options);
       callback(structure);
     }
   };
   oReq.send(null);
 }
 
-exports.io = {};
-exports.io.pdb = pdb;
-exports.io.Remark350Reader = Remark350Reader;
-exports.io.fetchPdb = fetchPdb;
-
+return {
+  pdb : pdb,
+  Remark350Reader : Remark350Reader,
+  fetchPdb : fetchPdb
+};
 
-}(this));
+});
 
 
 
diff --git a/src/label.js b/src/label.js
new file mode 100644
index 0000000..49f1605
--- /dev/null
+++ b/src/label.js
@@ -0,0 +1,204 @@
+// Copyright (c) 2013-2015 Marco Biasini
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
+define(['core', 'scene-node'], function(core, SceneNode) {
+
+function TextLabel(gl, canvas, context, pos, text, options) {
+  SceneNode.call(this, gl);
+  var opts = options || {};
+  this._options = {};
+  this._options.fillStyle = opts.fillStyle || '#000';
+  this._options.backgroundAlpha = opts.backgroundAlpha || 0.0;
+  this._options.fontSize = opts.fontSize || 24;
+  this._options.font = opts.font || 'Verdana';
+  this._options.fontStyle = opts.fontStyle || 'normal';
+  this._options.fontColor = opts.fontColor || '#000';
+  this._order = 100;
+  this._pos = pos;
+  this._interleavedBuffer = this._gl.createBuffer();
+  this._interleavedData = new Float32Array(5 * 6);
+
+  this._prepareText(canvas, context, text);
+
+  var halfWidth = 0.5;
+  var halfHeight = 0.5;
+  this._interleavedData[0] = pos[0];
+  this._interleavedData[1] = pos[1];
+  this._interleavedData[2] = pos[2];
+  this._interleavedData[3] = -halfWidth;
+  this._interleavedData[4] = -halfHeight;
+
+  this._interleavedData[5] = pos[0];
+  this._interleavedData[6] = pos[1];
+  this._interleavedData[7] = pos[2];
+  this._interleavedData[8] = halfWidth;
+  this._interleavedData[9] = halfHeight;
+
+  this._interleavedData[10] = pos[0];
+  this._interleavedData[11] = pos[1];
+  this._interleavedData[12] = pos[2];
+  this._interleavedData[13] = halfWidth;
+  this._interleavedData[14] = -halfHeight;
+
+  this._interleavedData[15] = pos[0];
+  this._interleavedData[16] = pos[1];
+  this._interleavedData[17] = pos[2];
+  this._interleavedData[18] = -halfWidth;
+  this._interleavedData[19] = -halfHeight;
+
+  this._interleavedData[20] = pos[0];
+  this._interleavedData[21] = pos[1];
+  this._interleavedData[22] = pos[2];
+  this._interleavedData[23] = -halfWidth;
+  this._interleavedData[24] = halfHeight;
+
+  this._interleavedData[25] = pos[0];
+  this._interleavedData[26] = pos[1];
+  this._interleavedData[27] = pos[2];
+  this._interleavedData[28] = halfWidth;
+  this._interleavedData[29] = halfHeight;
+}
+
+function smallestPowerOfTwo(size) {
+  var s = 1;
+  while (s < size) {
+    s *= 2;
+  }
+  return s;
+}
+
+core.derive(TextLabel, SceneNode, {
+  updateProjectionIntervals : function() {
+    // text labels don't affect the projection interval. Don't do anything.
+  },
+
+  updateSquaredSphereRadius : function(center, radius) { 
+    // text labels don't affect the bounding spheres. 
+    return radius;
+  },
+
+
+  _setupTextParameters : function(ctx) {
+    ctx.fillStyle = this._options.fontColor;
+    ctx.textAlign = 'left';
+    ctx.textBaseline = 'bottom';
+    ctx.font = this._options.fontStyle + ' ' + 
+               this._options.fontSize + 'px '+
+               this._options.font;
+  },
+
+  _prepareText : function(canvas, ctx, text) {
+    this._setupTextParameters(ctx);
+    var estimatedWidth = ctx.measureText(text).width;
+    var estimatedHeight = 24;
+    canvas.width = smallestPowerOfTwo(estimatedWidth);
+    canvas.height = smallestPowerOfTwo(estimatedHeight);
+    ctx.fillStyle = this._options.fillStyle;
+    ctx.globalAlpha = this._options.backgroundAlpha;
+    ctx.fillRect(0, 0, canvas.width, canvas.height);
+    this._setupTextParameters(ctx);
+    ctx.globalAlpha = 1.0;
+    ctx.lineWidth = 0.5;
+    ctx.lineStyle = 'none';
+    ctx.fillText(text, 0, canvas.height);
+    ctx.strokeText(text, 0, canvas.height);
+    /*
+    // use the following code for testing purposes. for optimal visual
+    // results, the pixels of the canvas must match one to one to pixels
+    // in the 3D scene.
+    ctx.fillStyle='black';
+    for (var i = 0; i < canvas.width; i+=2) {
+      for (var j = 0; j < canvas.height; j+=2) {
+        ctx.fillRect(i + j%2, j, 1, 1);
+      }
+    }
+    */
+    this._texture = this._gl.createTexture();
+    this._textureFromCanvas(this._texture, canvas);
+    // these two variables give us the use portion of the canvas.
+    this._xScale = estimatedWidth / canvas.width;
+    this._yScale = estimatedHeight / canvas.height;
+    this._width = estimatedWidth;
+    this._height = estimatedHeight;
+  },
+
+  _textureFromCanvas : function(targetTexture, srcCanvas) {
+    var gl = this._gl;
+    gl.pixelStorei(gl.UNPACK_FLIP_Y_WEBGL, true);
+    gl.bindTexture(gl.TEXTURE_2D, targetTexture);
+    gl.texImage2D(gl.TEXTURE_2D, 0, gl.RGBA, gl.RGBA, 
+                  gl.UNSIGNED_BYTE, srcCanvas);
+    gl.texParameteri(gl.TEXTURE_2D, gl.TEXTURE_MAG_FILTER, gl.NEAREST);
+    gl.texParameteri(gl.TEXTURE_2D, gl.TEXTURE_MIN_FILTER, gl.NEAREST);
+    gl.generateMipmap(gl.TEXTURE_2D);
+    gl.bindTexture(gl.TEXTURE_2D, null);
+  },
+
+  bind : function() {
+    var gl = this._gl;
+    gl.bindBuffer(gl.ARRAY_BUFFER, this._interleavedBuffer);
+    gl.activeTexture(gl.TEXTURE0);
+    gl.bindTexture(gl.TEXTURE_2D, this._texture);
+    if (this._ready) {
+      return;
+    }
+    gl.bufferData(gl.ARRAY_BUFFER, this._interleavedData, gl.STATIC_DRAW);
+    this._ready = true;
+  },
+
+  draw : function(cam, shaderCatalog, style, pass) {
+    if (!this._visible) {
+      return;
+    }
+
+    if (pass !== 'normal') {
+      return;
+    }
+    var shader = shaderCatalog.text;
+    cam.bind(shader);
+    this.bind();
+    var gl = this._gl;
+    var factor = cam.upsamplingFactor();
+    gl.uniform1f(gl.getUniformLocation(shader, 'xScale'), this._xScale);
+    gl.uniform1f(gl.getUniformLocation(shader, 'yScale'), this._yScale);
+    gl.uniform1f(gl.getUniformLocation(shader, 'width'),
+                 factor * 2.0*this._width/cam.viewportWidth());
+    gl.uniform1f(gl.getUniformLocation(shader, 'height'),
+                 factor * 2.0*this._height/cam.viewportHeight());
+    gl.uniform1i(gl.getUniformLocation(shader, 'sampler'), 0);
+    var vertAttrib = gl.getAttribLocation(shader, 'attrCenter');
+    gl.enableVertexAttribArray(vertAttrib);
+    gl.vertexAttribPointer(vertAttrib, 3, gl.FLOAT, false, 5 * 4, 0 * 4);
+    var texAttrib = gl.getAttribLocation(shader, 'attrCorner');
+    gl.vertexAttribPointer(texAttrib, 2, gl.FLOAT, false, 5 * 4, 3 * 4);
+    gl.enableVertexAttribArray(texAttrib);
+    gl.enable(gl.BLEND);
+    gl.blendFunc(gl.SRC_ALPHA, gl.ONE_MINUS_SRC_ALPHA);
+    gl.drawArrays(gl.TRIANGLES, 0, 6);
+    gl.disableVertexAttribArray(vertAttrib);
+    gl.disableVertexAttribArray(texAttrib);
+    gl.disable(gl.BLEND);
+  }
+});
+
+return TextLabel;
+
+});
+
diff --git a/src/line-geom.js b/src/line-geom.js
new file mode 100644
index 0000000..ea25f80
--- /dev/null
+++ b/src/line-geom.js
@@ -0,0 +1,99 @@
+// Copyright (c) 2013-2015 Marco Biasini
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
+define(['core', 'base-geom', 'chain-data'], function(core, BaseGeom, chainData) {
+
+"use strict";
+
+var LineChainData = chainData.LineChainData;
+
+// Holds geometrical data for objects rendered as lines. For each vertex,
+// the color and position is stored in an interleaved format.
+function LineGeom(gl, float32Allocator) {
+  BaseGeom.call(this, gl);
+  this._vertArrays = [];
+  this._float32Allocator = float32Allocator;
+  this._lineWidth = 1.0;
+}
+
+core.derive(LineGeom, BaseGeom, {
+  addChainVertArray : function(chain, numVerts) {
+    var va = new LineChainData(chain.name(), this._gl, numVerts, 
+                              this._float32Allocator);
+    this._vertArrays.push(va);
+    return va;
+  },
+
+
+  setLineWidth : function(width) {
+    this._lineWidth = width;
+  },
+
+  vertArrays : function() {
+    return this._vertArrays;
+  },
+
+  shaderForStyleAndPass :
+      function(shaderCatalog, style, pass) {
+    if (pass === 'outline') {
+      return null;
+    }
+    if (pass === 'select') {
+      return shaderCatalog.select;
+    }
+    if (pass === 'glow') {
+    }
+    return shaderCatalog.lines;
+  },
+
+  destroy : function() {
+    BaseGeom.prototype.destroy.call(this);
+    for (var i = 0; i < this._vertArrays.length; ++i) {
+      this._vertArrays[i].destroy();
+    }
+    this._vertArrays = [];
+  },
+
+  _drawVertArrays : function(cam, shader, vertArrays, 
+                                                additionalTransforms) {
+    this._gl.lineWidth(this._lineWidth * cam.upsamplingFactor());
+    var i;
+    if (additionalTransforms) {
+      for (i = 0; i < vertArrays.length; ++i) {
+        vertArrays[i].drawSymmetryRelated(cam, shader, additionalTransforms);
+      }
+    } else {
+      this._gl.uniform1i(shader.symId, 255);
+      cam.bind(shader);
+      for (i = 0; i < vertArrays.length; ++i) {
+        vertArrays[i].bind(shader);
+        vertArrays[i].draw();
+        vertArrays[i].releaseAttribs(shader);
+      }
+    }
+  },
+
+  vertArray : function() { return this._va; }
+});
+
+return LineGeom;
+
+});
+
diff --git a/src/mesh-geom.js b/src/mesh-geom.js
new file mode 100644
index 0000000..af0ea33
--- /dev/null
+++ b/src/mesh-geom.js
@@ -0,0 +1,178 @@
+// Copyright (c) 2013-2015 Marco Biasini
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
+define(['core', 'base-geom', 'chain-data'], 
+       function(core, BaseGeom, cd) {
+
+"use strict";
+
+var MeshChainData = cd.MeshChainData;
+
+// an (indexed) mesh geometry container
+// ------------------------------------------------------------------------
+//
+// stores the vertex data in interleaved format. not doing so has severe
+// performance penalties in WebGL, and severe means orders of magnitude
+// slower than using an interleaved array.
+//
+// the vertex data is stored in the following format;
+//
+// Px Py Pz Nx Ny Nz Cr Cg Cb Ca Id
+//
+// , where P is the position, N the normal and C the color information
+// of the vertex.
+// 
+// Uint16 index buffer limit
+// -----------------------------------------------------------------------
+//
+// In WebGL, index arrays are restricted to uint16. The largest possible
+// index value is smaller than the number of vertices required to display 
+// larger molecules. To work around this, MeshGeom allows to split the
+// render geometry across multiple indexed vertex arrays. 
+function MeshGeom(gl, float32Allocator, uint16Allocator) {
+  BaseGeom.call(this, gl);
+  this._indexedVAs = [ ];
+  this._float32Allocator = float32Allocator;
+  this._uint16Allocator = uint16Allocator;
+  this._remainingVerts = null;
+  this._remainingIndices = null;
+}
+
+core.derive(MeshGeom, BaseGeom, {
+  _boundedVertArraySize : function(size) {
+    return Math.min(65536, size);
+  },
+
+  addChainVertArray : function(chain, numVerts, numIndices) {
+    this._remainingVerts = numVerts;
+    this._remainingIndices = numIndices;
+    var newVa = new MeshChainData(chain.name(), this._gl, 
+                                  this._boundedVertArraySize(numVerts), 
+                                  numIndices,
+                                  this._float32Allocator, 
+                                  this._uint16Allocator);
+    this._indexedVAs.push(newVa);
+    return newVa;
+  },
+
+  addVertArray : function(numVerts, numIndices) {
+    this._remainingVerts = numVerts;
+    this._remainingIndices = numIndices;
+    var newVa = new IndexedVertexArray(
+      this._gl, this._boundedVertArraySize(numVerts), numIndices,
+      this._float32Allocator, this._uint16Allocator);
+
+    this._indexedVAs.push(newVa);
+    return newVa;
+  },
+
+  vertArrayWithSpaceFor : function(numVerts) {
+    var currentVa = this._indexedVAs[this._indexedVAs.length - 1];
+    var remaining = currentVa.maxVerts() - currentVa.numVerts();
+    if (remaining >= numVerts) {
+      return currentVa;
+    }
+    this._remainingVerts = this._remainingVerts - currentVa.numVerts();
+    this._remainingIndices = this._remainingIndices - currentVa.numIndices();
+    numVerts = this._boundedVertArraySize(this._remainingVerts);
+    var newVa = null;
+    if (currentVa instanceof MeshChainData) {
+      newVa = new MeshChainData(currentVa.chain(), this._gl, numVerts, 
+                                this._remainingIndices,
+                                this._float32Allocator, 
+                                this._uint16Allocator);
+    } else {
+      newVa = new IndexedVertexArray(this._gl, numVerts, this._remainingIndices,
+        this._float32Allocator, this._uint16Allocator);
+    } 
+    this._indexedVAs.push(newVa);
+    return newVa;
+  },
+
+
+
+  vertArray : function(index) {
+    return this._indexedVAs[index];
+  },
+
+  destroy : function() {
+    BaseGeom.prototype.destroy.call(this);
+    for (var i = 0; i < this._indexedVAs.length; ++i) {
+      this._indexedVAs[i].destroy();
+    }
+    this._indexedVAs = [];
+  },
+
+  numVerts : function() {
+    return this._indexedVAs[0].numVerts();
+  },
+
+  shaderForStyleAndPass :
+      function(shaderCatalog, style, pass) {
+    if (pass === 'normal') {
+      return shaderCatalog.hemilight;
+    }
+    if (pass === 'select') {
+      return shaderCatalog.select;
+    }
+    if (pass === 'outline') {
+      return shaderCatalog.outline;
+    }
+    var shader = shaderCatalog[pass];
+    return shader !== undefined ? shader : null;
+  },
+
+  _drawVertArrays : function(cam, shader, indexedVAs, additionalTransforms) {
+    var i;
+    if (additionalTransforms) {
+      for (i = 0; i < indexedVAs.length; ++i) {
+        indexedVAs[i].drawSymmetryRelated(cam, shader, 
+                                                 additionalTransforms);
+      }
+    } else {
+      cam.bind(shader);
+      this._gl.uniform1i(shader.symId, 255);
+      for (i = 0; i < indexedVAs.length; ++i) {
+        indexedVAs[i].bind(shader);
+        indexedVAs[i].draw();
+        indexedVAs[i].releaseAttribs(shader);
+      }
+    }
+  },
+
+  vertArrays : function() {
+    return this._indexedVAs;
+  },
+
+  addVertex : function(pos, normal, color, objId) {
+    var va = this._indexedVAs[0];
+    va.addVertex(pos, normal, color, objId);
+  },
+
+  addTriangle : function(idx1, idx2, idx3) {
+    var va = this._indexedVAs[0];
+    va.addTriangle(idx1, idx2, idx3);
+  },
+
+});
+
+return MeshGeom;
+});
+
diff --git a/src/mol.js b/src/mol.js
deleted file mode 100644
index 1f657fd..0000000
--- a/src/mol.js
+++ /dev/null
@@ -1,1297 +0,0 @@
-// Copyright (c) 2013-2015 Marco Biasini
-// 
-// Permission is hereby granted, free of charge, to any person obtaining a copy
-// of this software and associated documentation files (the "Software"), to 
-// deal in the Software without restriction, including without limitation the 
-// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
-// sell copies of the Software, and to permit persons to whom the Software is 
-// furnished to do so, subject to the following conditions:
-// 
-// The above copyright notice and this permission notice shall be included in 
-// all copies or substantial portions of the Software.
-// 
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
-// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
-// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
-// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 
-// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
-// DEALINGS IN THE SOFTWARE.
-
-(function(exports) {
-"use strict";
-
-// atom covalent radii by element derived from Cambrige Structural Database. 
-// Source: http://profmokeur.ca/chemistry/covalent_radii.htm
-var ELEMENT_COVALENT_RADII = {
- H : 0.31, HE : 0.28, LI : 1.28, BE : 0.96,  B : 0.84,  C : 0.76,  N : 0.71, 
- O : 0.66,  F : 0.57, NE : 0.58, NA : 1.66, MG : 1.41, AL : 1.21, SI : 1.11, 
- P : 1.07,  S : 1.05, CL : 1.02, AR : 1.06,  K : 2.03, CA : 1.76, SC : 1.70, 
-TI : 1.60,  V : 1.53, CR : 1.39, MN : 1.39, FE : 1.32, CO : 1.26, NI : 1.24, 
-CU : 1.32, ZN : 1.22, GA : 1.22, GE : 1.20, AS : 1.19, SE : 1.20, BR : 1.20, 
-KR : 1.16, RB : 2.20, SR : 1.95,  Y : 1.90, ZR : 1.75, NB : 1.64, MO : 1.54, 
-TC : 1.47, RU : 1.46, RH : 1.42, PD : 1.39, AG : 1.45, CD : 1.44, IN : 1.42, 
-SN : 1.39, SB : 1.39, TE : 1.38,  I : 1.39, XE : 1.40, CS : 2.44, BA : 2.15, 
-LA : 2.07, CE : 2.04, PR : 2.03, ND : 2.01, PM : 1.99, SM : 1.98, EU : 1.98, 
-GD : 1.96, TB : 1.94, DY : 1.92, HO : 1.92, ER : 1.89, TM : 1.90, YB : 1.87, 
-LU : 1.87, HF : 1.75, TA : 1.70,  W : 1.62, RE : 1.51, OS : 1.44, IR : 1.41, 
-PT : 1.36, AU : 1.36, HG : 1.32, TL : 1.45, PB : 1.46, BI : 1.48, PO : 1.40, 
-AT : 1.50, RN : 1.50, FR : 2.60, RA : 2.21, AC : 2.15, TH : 2.06, PA : 2.00, 
- U : 1.96, NP : 1.90, PU : 1.87, AM : 1.80, CM : 1.69
-};
-
-function covalentRadius(ele) {
-  var r = ELEMENT_COVALENT_RADII[ele.toUpperCase()];
-  if (r !== undefined) {
-    return r;
-  }
-  return 1.5;
-}
-
-// combines the numeric part of the residue number with the insertion
-// code and returns a single number. Note that this is completely safe
-// and we do not have to worry about overflows, as for PDB files the 
-// range of permitted residue numbers is quite limited anyway.
-function rnumInsCodeHash(num, insCode) {
-  return num << 8 | insCode.charCodeAt(0);
-}
-
-//-----------------------------------------------------------------------------
-// MolBase, ChainBase, ResidueBase, AtomBase
-//-----------------------------------------------------------------------------
-
-function fulfillsPredicates(obj, predicates) {
-  for (var i = 0; i < predicates.length; ++i) {
-    if (!predicates[i](obj)) {
-      return false;
-    }
-  }
-  return true;
-}
-
-function rnumComp(lhs, rhs) {
-  return lhs.num() < rhs.num();
-}
-
-function numify(val) {
-  return { num : function() { return val; }};
-}
-
-function _atomPredicates(dict) {
-  var predicates = [];
-  if (dict.aname !== undefined) {
-    predicates.push(function(a) { return a.name() === dict.aname; });
-  }
-  if (dict.hetatm !== undefined) {
-    predicates.push(function(a) { return a.isHetatm() === dict.hetatm; });
-  }
-  if (dict.anames !== undefined) {
-    predicates.push(function(a) { 
-      var n = a.name();
-      for (var k = 0; k < dict.anames.length; ++k) {
-        if (n === dict.anames[k]) {
-          return true;
-        }
-      }
-      return false;
-    });
-  }
-  return predicates;
-}
-
-// extracts the residue predicates from the dictionary. 
-// ignores rindices, rindexRange because they are handled separately.
-function _residuePredicates(dict) {
-  var predicates = [];
-  if (dict.rname !== undefined) {
-    predicates.push(function(r) { return r.name() === dict.rname; });
-  }
-  if (dict.rnames !== undefined) {
-    predicates.push(function(r) { 
-    var n = r.name();
-    for (var k = 0; k < dict.rnames.length; ++k) {
-      if (n === dict.rnames[k]) {
-          return true;
-        }
-      }
-      return false;
-    });
-  }
-  if (dict.rnums !== undefined) {
-    var num_set = {};
-    for (var i = 0; i < dict.rnums.length; ++i) {
-      num_set[dict.rnums[i]] = true;
-    }
-    predicates.push(function(r) {
-      var n = r.num();
-      return num_set[n] === true;
-    });
-  }
-  return predicates;
-}
-
-function _chainPredicates(dict) {
-  var predicates = [];
-  if (dict.cname !== undefined) {
-    dict.chain = dict.cname;
-  }
-  if (dict.cnames !== undefined) {
-    dict.chains = dict.cnames;
-  }
-  if (dict.chain !== undefined) {
-    predicates.push(function(c) { return c.name() === dict.chain; });
-  }
-  if (dict.chains !== undefined) {
-    predicates.push(function(c) { 
-      var n = c.name();
-      for (var k = 0; k < dict.chains.length; ++k) {
-        if (n === dict.chains[k]) {
-          return true;
-        }
-      }
-      return false;
-    });
-  }
-  return predicates;
-}
-
-
-// handles all residue predicates that can be done through either index-
-// based lookups, or optimized searches of some sorts.
-function _filterResidues(chain, dict) {
-  var residues = chain.residues();
-  if (dict.rnumRange) {
-    residues =
-        chain.residuesInRnumRange(dict.rnumRange[0], dict.rnumRange[1]);
-  }
-  var selResidues = [], i, e;
-  if (dict.rindexRange !== undefined) {
-    for (i = dict.rindexRange[0],
-        e = Math.min(residues.length, dict.rindexRange[1]);
-        i < e; ++i) {
-      selResidues.push(residues[i]);
-    }
-    return selResidues;
-  } 
-  if (dict.rindices) {
-    if (dict.rindices.length !== undefined) {
-      selResidues = [];
-      for (i = 0; i < dict.rindices.length; ++i) {
-        selResidues.push(residues[dict.rindices[i]]);
-      }
-      return selResidues;
-    }
-  }
-  return residues;
-}
-
-// helper function to perform selection by predicates
-function _dictSelect(structure, dict) {
-  var view = new MolView(structure);
-  var residuePredicates = _residuePredicates(dict);
-  var atomPredicates = _atomPredicates(dict);
-  var chainPredicates = _chainPredicates(dict);
-
-  if (dict.rindex) {
-    dict.rindices = [dict.rindex];
-  }
-  for (var ci = 0; ci < structure._chains.length; ++ci) {
-    var chain = structure._chains[ci];
-    if (!fulfillsPredicates(chain, chainPredicates)) {
-      continue;
-    }
-    var residues = _filterResidues(chain, dict);
-    var chainView = null;
-    for (var ri = 0; ri < residues.length; ++ri) {
-      if (!fulfillsPredicates(residues[ri], residuePredicates)) {
-        continue;
-      }
-      if (!chainView) {
-        chainView = view.addChain(chain, false);
-      }
-      var residueView = null;
-      var atoms = residues[ri].atoms();
-      for (var ai = 0; ai < atoms.length; ++ai) {
-        if (!fulfillsPredicates(atoms[ai], atomPredicates)) {
-          continue;
-        }
-        if (!residueView) {
-          residueView = chainView.addResidue(residues[ri], false);
-        }
-        residueView.addAtom(atoms[ai]);
-      }
-    }
-  }
-  return view;
-}
-
-function MolBase() {
-}
-
-MolBase.prototype = {
-  eachResidue : function(callback) {
-    for (var i = 0; i < this._chains.length; i+=1) {
-      if (this._chains[i].eachResidue(callback) === false) {
-        return false;
-      }
-    }
-  },
-
-  eachAtom : function(callback, index) {
-    index |= 0;
-    for (var i = 0; i < this._chains.length; i+=1) {
-      index = this._chains[i].eachAtom(callback, index);
-      if (index === false) {
-        return false;
-      }
-    }
-  },
-
-  residueCount : function () {
-    var chains = this.chains();
-    var count = 0;
-    for (var ci = 0; ci < chains.length; ++ci) {
-      count += chains[ci].residues().length;
-    }
-    return count;
-  },
-
-  eachChain : function(callback) {
-    var chains = this.chains();
-    for (var i = 0; i < chains.length; ++i) {
-      if (callback(chains[i]) === false) {
-        return;
-      }
-    }
-  },
-
-  atomCount : function() {
-    var chains = this.chains();
-    var count = 0;
-    for (var ci = 0; ci < chains.length; ++ci) {
-      count += chains[ci].atomCount();
-    }
-    return count;
-  },
-
-  atoms : function() {
-    var atoms = [];
-    this.eachAtom(function(atom) { atoms.push(atom); });
-    return atoms;
-  },
-
-  atom : function(name) {
-    var parts = name.split('.');
-    var chain = this.chain(parts[0]);
-    if (chain === null) {
-      return null;
-    }
-    var residue = chain.residueByRnum(parseInt(parts[1], 10));
-    if (residue === null) {
-      return null;
-    }
-    return residue.atom(parts[2]);
-  },
-
-  center : function() {
-    var sum = vec3.create();
-    var count = 0;
-    this.eachAtom(function(atom) {
-      vec3.add(sum, sum, atom.pos());
-      count+=1;
-    });
-    if (count) {
-      vec3.scale(sum, sum, 1/count);
-    }
-    return sum;
-  },
-
-  // returns a sphere containing all atoms part of this structure. This will 
-  // not calculate the minimal bounding sphere, just a good-enough 
-  // approximation.
-  boundingSphere : function() {
-    var center = this.center();
-    var radiusSquare = 0.0;
-    this.eachAtom(function(atom) {
-      radiusSquare = Math.max(radiusSquare, vec3.sqrDist(center, atom.pos()));
-    });
-    return new Sphere(center, radiusSquare);
-  },
-
-  // returns all backbone traces of all chains of this structure
-  backboneTraces : function() {
-    var chains = this.chains();
-    var traces = [];
-    for (var i = 0; i < chains.length; ++i) {
-      Array.prototype.push.apply(traces, chains[i].backboneTraces());
-    }
-    return traces;
-  },
-
-
-  select : function(what) {
-
-    if (what === 'protein') {
-      return this.residueSelect(function(r) { return r.isAminoacid(); });
-    }
-    if (what === 'water') {
-      return this.residueSelect(function(r) { return r.isWater(); });
-    }
-    if (what === 'ligand') {
-      return this.residueSelect(function(r) { 
-        return !r.isAminoacid() && !r.isWater();
-      });
-    }
-    // when what is not one of the simple strings above, we assume what
-    // is a dictionary containing predicates which have to be fulfilled.
-    return _dictSelect(this, what || {});
-  },
-
-  selectWithin : (function() {
-    var dist = vec3.create();
-    return function(mol, options) {
-      console.time('Mol.selectWithin');
-      options = options || {};
-      var radius = options.radius || 4.0;
-      var radiusSqr = radius * radius;
-      var matchResidues = !!options.matchResidues;
-      var targetAtoms = [];
-      mol.eachAtom(function(a) { targetAtoms.push(a); });
-
-      var view = new MolView(this.full());
-      var addedRes = null, addedChain = null;
-      var chains = this.chains();
-      var skipResidue = false;
-      for (var ci = 0; ci < chains.length; ++ci) {
-        var residues = chains[ci].residues();
-        addedChain = null;
-        for (var ri = 0; ri < residues.length; ++ri) {
-          addedRes = null;
-          skipResidue = false;
-          var atoms = residues[ri].atoms();
-          for (var ai = 0; ai < atoms.length; ++ai) {
-            if (skipResidue) {
-              break;
-            }
-            skipResidue = addAtomsWithin(view, tagetAtoms, radiusSqr);
-            for (var wi = 0; wi < targetAtoms.length; ++wi) {
-              vec3.sub(dist, atoms[ai].pos(), targetAtoms[wi].pos());
-              if (vec3.sqrLen(dist) > radiusSqr) {
-                continue;
-              }
-              if (!addedChain) {
-                addedChain = view.addChain(chains[ci].full(), false);
-              }
-              if (!addedRes) {
-                addedRes =
-                    addedChain.addResidue(residues[ri].full(), matchResidues);
-              }
-              if (matchResidues) {
-                skipResidue = true;
-                break;
-              } 
-              addedRes.addAtom(atoms[ai].full());
-            }
-          }
-        }
-      }
-      console.timeEnd('Mol.selectWithin');
-      return view;
-    };
-  })(),
-
-  residueSelect : function(predicate) {
-    console.time('Mol.residueSelect');
-    var view = new MolView(this.full());
-    for (var ci = 0; ci < this._chains.length; ++ci) {
-      var chain = this._chains[ci];
-      var chainView = null;
-      var residues = chain.residues();
-      for (var ri = 0; ri < residues.length; ++ri) {
-        if (predicate(residues[ri])) {
-          if (!chainView) {
-            chainView = view.addChain(chain, false);
-          }
-          chainView.addResidue(residues[ri], true);
-        }
-      }
-    }
-    console.timeEnd('Mol.residueSelect');
-    return view;
-  },
-
-
-
-  assembly : function(id) {
-    var assemblies = this.assemblies();
-    for (var i = 0; i < assemblies.length; ++i) {
-      if (assemblies[i].name() === id) {
-        return assemblies[i];
-      }
-    }
-    return null;
-  },
-
-  chainsByName : function(chainNames) {
-    // build a map to avoid O(n^2) behavior. That's overkill when the list 
-    // of names is short but should give better performance when requesting
-    // multiple chains.
-    var chainMap = { };
-    var chains = this.chains();
-    for (var i = 0; i < chains.length; ++i) {
-      chainMap[chains[i].name()] = chains[i];
-    }
-    var filteredChains = [];
-    for (var j = 0; j < chainNames.length; ++j) {
-      var filteredChain = chainMap[chainNames[j]];
-      if (filteredChain !== undefined) {
-        filteredChains.push(filteredChain);
-      }
-    }
-    return filteredChains;
-  }
-};
-
-function ChainBase() {
-
-}
-
-ChainBase.prototype  = {
-  eachAtom : function(callback, index) {
-    index |= 0;
-    for (var i = 0; i< this._residues.length; i+=1) {
-      index = this._residues[i].eachAtom(callback, index);
-      if (index === false) {
-        return false;
-      }
-    }
-    return index;
-  },
-
-
-  atomCount : function() {
-    var count = 0;
-    var residues = this.residues();
-    for (var ri = 0; ri < residues.length; ++ri) {
-      count+= residues[ri].atoms().length;
-    }
-    return count;
-  },
-
-  eachResidue : function(callback) {
-    for (var i = 0; i < this._residues.length; i+=1) {
-      if (callback(this._residues[i]) === false) {
-        return false;
-      }
-    }
-  },
-
-  residues : function() { return this._residues; },
-
-  structure : function() { return this._structure; },
-
-
-  asView : function() {
-    var view = new MolView(this.structure().full());
-    view.addChain(this, true);
-    return view;
-
-  },
-
-  residueByRnum : function(rnum) {
-    var residues = this.residues();
-    if (this._rnumsOrdered) {
-      var index = binarySearch(residues, numify(rnum), rnumComp);
-      if (index === -1) {
-        return null;
-      }
-      return residues[index];
-    } else {
-      for (var i = 0; i < residues.length; ++i) {
-        if (residues[i].num() === rnum) {
-          return residues[i];
-        }
-      }
-      return null;
-    }
-  },
-
-
-  prop : function(propName) { 
-    return this[propName]();
-  }
-};
-
-function ResidueBase() {
-
-}
-
-ResidueBase.prototype = {
-
-  prop : function(propName) { 
-    return this[propName]();
-  },
-
-  isWater : function() {
-    return this.name() === 'HOH' || this.name() === 'DOD';
-  },
-
-  eachAtom : function(callback, index) {
-    index |= 0;
-    for (var i =0; i< this._atoms.length; i+=1) {
-      if (callback(this._atoms[i], index) === false) {
-        return false;
-      }
-      index +=1;
-    }
-    return index;
-  },
-
-  qualifiedName : function() {
-    return this.chain().name()+'.'+this.name()+this.num();
-  },
-
-  atom : function(index_or_name) { 
-    if (typeof index_or_name === 'string') {
-      for (var i =0; i < this._atoms.length; ++i) {
-        if (this._atoms[i].name() === index_or_name) {
-          return this._atoms[i];
-        }
-      }
-      return null;
-    }
-    if (index_or_name >= this._atoms.length && index_or_name < 0) {
-      return null;
-    }
-    return this._atoms[index_or_name]; 
-  },
-
-  // CA for amino acids, P for nucleotides, nucleosides
-  centralAtom : function() {
-    if (this.isAminoacid()) {
-      return this.atom('CA');
-    }
-    if (this.isNucleotide()) {
-      return this.atom('C3\'');
-    }
-    return null;
-  },
-
-
-  center : function() {
-    var count = 0;
-    var c = vec3.create();
-    this.eachAtom(function(atom) {
-      vec3.add(c, c, atom.pos());
-      count += 1;
-    });
-    if (count > 0) {
-      vec3.scale(c, c, 1.0/count);
-    }
-    return c;
-  },
-
-  isAminoacid : function() { 
-    return this._isAminoacid;
-  },
-
-  isNucleotide : function() { 
-    return this._isNucleotide;
-  }
-};
-
-
-function AtomBase() {
-}
-
-
-AtomBase.prototype = {
-  name : function() { return this._name; },
-  pos : function() { return this._pos; },
-  element : function() { return this._element; },
-  index : function() { return this._index; },
-
-  prop : function(propName) { 
-    return this[propName]();
-  },
-
-  bondCount : function() { return this.bonds().length; },
-
-  eachBond : function(callback) {
-    var bonds = this.bonds();
-    for (var i = 0, e = bonds.length; i < e; ++i) {
-      callback(bonds[i]);
-    }
-  }
-};
-
-//-----------------------------------------------------------------------------
-// Mol, Chain, Residue, Atom, Bond
-//-----------------------------------------------------------------------------
-
-function connectPeptides(structure, left, right) {
-  var cAtom = left.atom('C');
-  var nAtom = right.atom('N');
-  if (cAtom && nAtom) {
-    var sqrDist = vec3.sqrDist(cAtom.pos(), nAtom.pos());
-    if (sqrDist < 1.6*1.6) {
-      structure.connect(nAtom, cAtom);
-    }
-  } 
-}
-
-function connectNucleotides(structure, left, right) {
-  var o3Prime = left.atom('O3\'');
-  var pAtom = right.atom('P');
-  if (o3Prime && pAtom) {
-    var sqrDist = vec3.sqrDist(o3Prime.pos(), pAtom.pos());
-    // FIXME: make sure 1.7 is a good threshold here...
-    if (sqrDist < 1.7*1.7) {
-      structure.connect(o3Prime, pAtom);
-    }
-  }
-}
-
-function Mol() {
-  MolBase.call(this);
-  this._chains = [];
-  this._assemblies = [];
-  this._nextAtomIndex = 0;
-}
-
-derive(Mol, MolBase, {
-  addAssembly : function(assembly) { 
-    this._assemblies.push(assembly); 
-  },
-
-  setAssemblies : function(assemblies) { 
-    this._assemblies = assemblies; 
-  },
-
-  assemblies : function() { return this._assemblies; },
-
-  chains : function() { return this._chains; },
-
-  full : function() { return this; },
-
-  containsResidue : function(residue) {
-    return residue.full().structure() === this;
-  },
-
-  chainByName : function(name) { 
-    for (var i = 0; i < this._chains.length; ++i) {
-      if (this._chains[i].name() === name) {
-        return this._chains[i];
-      }
-    }
-    return null;
-  },
-
-  // for backwards compatibility
-  chain : function(name) {
-    return this.chainByName(name);
-  },
-
-  nextAtomIndex : function() {
-    var nextIndex = this._nextAtomIndex; 
-    this._nextAtomIndex+=1; 
-    return nextIndex; 
-  },
-
-  addChain : function(name) {
-    var chain = new Chain(this, name);
-    this._chains.push(chain);
-    return chain;
-  },
-
-
-  connect : function(atom_a, atom_b) {
-    var bond = new Bond(atom_a, atom_b);
-    atom_a.addBond(bond);
-    atom_b.addBond(bond);
-    return bond;
-  },
-
-
-
-  // determine connectivity structure. for simplicity only connects atoms of the
-  // same residue, peptide bonds and nucleotides
-  deriveConnectivity : function() {
-    console.time('Mol.deriveConnectivity');
-    var thisStructure = this;
-    var prevResidue = null;
-    this.eachResidue(function(res) {
-      var sqrDist;
-      var atoms = res.atoms();
-      var numAtoms = atoms.length;
-      for (var i = 0; i < numAtoms; i+=1) {
-        var atomI = atoms[i];
-        var posI = atomI.pos();
-        var covalentI = covalentRadius(atomI.element());
-        for (var j = 0; j < i; j+=1) {
-          var atomJ = atoms[j];
-          var covalentJ = covalentRadius(atomJ.element());
-          sqrDist = vec3.sqrDist(posI, atomJ.pos());
-          var lower = covalentI+covalentJ-0.30;
-          var upper = covalentI+covalentJ+0.30;
-          if (sqrDist < upper*upper && sqrDist > lower*lower) {
-            thisStructure.connect(atomI, atomJ);
-          }
-        }
-      }
-      res._deduceType();
-      if (prevResidue !== null) {
-        if (res.isAminoacid() && prevResidue.isAminoacid()) {
-          connectPeptides(thisStructure, prevResidue, res);
-        }
-        if (res.isNucleotide() && prevResidue.isNucleotide()) {
-          connectNucleotides(thisStructure, prevResidue, res);
-        }
-      }
-      prevResidue = res;
-    });
-    console.timeEnd('Mol.deriveConnectivity');
-  }
-});
-
-
-
-
-function Chain(structure, name) {
-  ChainBase.call(this);
-  this._structure = structure;
-  this._name = name;
-  this._cachedTraces = [];
-  this._residues = [];
-  this._rnumsOrdered = true;
-}
-
-// helper function to determine whether a trace break should be introduced 
-// between two residues of the same type (amino acid, or nucleotides).
-//
-// aaStretch: indicates whether the residues are to be treated as amino 
-//   acids
-function shouldIntroduceTraceBreak(aaStretch, prevResidue, thisResidue) {
-  // these checks are on purpose more relaxed than the checks we use in 
-  // deriveConnectivity(). We don't really care about correctness of bond 
-  // lengths here. The only thing that matters is that the residues are 
-  // more or less close so that they could potentially/ be connected.
-  var prevAtom, thisAtom;
-  if (aaStretch) {
-    prevAtom = prevResidue.atom('C');
-    thisAtom = thisResidue.atom('N');
-  } else {
-    prevAtom = prevResidue.atom('O3\'');
-    thisAtom = thisResidue.atom('P');
-  }
-  var sqrDist = vec3.sqrDist(prevAtom.pos(), thisAtom.pos());
-  return (Math.abs(sqrDist - 1.5*1.5) > 1);
-}
-
-function addNonEmptyTrace(traces, trace) {
-  if (trace.length() < 2) {
-    return;
-  }
-  traces.push(trace);
-}
-
-derive(Chain, ChainBase, {
-
-  name : function() { return this._name; },
-
-  full : function() { return this; },
-
-  addResidue : function(name, num, insCode) {
-    insCode = insCode || '\0';
-    var residue = new Residue(this, name, num, insCode);
-    if (this._residues.length > 0 && this._rnumsOrdered) {
-      var combinedRNum = rnumInsCodeHash(num, insCode);
-      var last = this._residues[this._residues.length-1];
-      var lastCombinedRNum = rnumInsCodeHash(last.num(),last.insCode());
-      this._rnumsOrdered = lastCombinedRNum < combinedRNum;
-    }
-    this._residues.push(residue);
-    return residue;
-  },
-
-
-  residuesInRnumRange : function(start, end) {
-    // FIXME: this currently only works with the numeric part, insertion
-    // codes are not honoured.
-    var matching = [];
-    var i, e;
-    if (this._rnumsOrdered === true) {
-      // binary search our way to heaven
-      var startIdx = indexFirstLargerEqualThan(this._residues, numify(start), 
-                                              rnumComp);
-      if (startIdx === -1) {
-        return matching;
-      }
-      var endIdx = indexLastSmallerEqualThan(this._residues, numify(end), 
-                                            rnumComp);
-      if (endIdx === -1) {
-        return matching;
-      }
-      for (i = startIdx; i <= endIdx; ++i) {
-        matching.push(this._residues[i]);
-      }
-    } else {
-      for (i = 0, e = this._residues.length; i !== e; ++i) {
-        var res = this._residues[i];
-        if (res.num() >= start && res.num() <= end) {
-          matching.push(res);
-        }
-      }
-    }
-    return matching;
-  },
-
-  // assigns secondary structure to residues in range from_num to to_num.
-  assignSS : function(fromNumAndIns, toNumAndIns, ss) {
-    // FIXME: when the chain numbers are completely ordered, perform binary 
-    // search to identify range of residues to assign secondary structure to.
-    var from = rnumInsCodeHash(fromNumAndIns[0], fromNumAndIns[1]);
-    var to = rnumInsCodeHash(toNumAndIns[0], toNumAndIns[1]);
-    for (var i = 1; i < this._residues.length-1; ++i) {
-      var res = this._residues[i];
-      // FIXME: we currently don't set the secondary structure of the first and 
-      // last residue of helices and sheets. that takes care of better 
-      // transitions between coils and helices. ideally, this should be done
-      // in the cartoon renderer, NOT in this function.
-      var combined = rnumInsCodeHash(res.num(), res.insCode());
-      if (combined <=  from || combined >= to) {
-        continue;
-      }
-      res.setSS(ss);
-    }
-  },
-
-  // invokes a callback for each connected stretch of amino acids. these 
-  // stretches are used for all trace-based rendering styles, e.g. sline, 
-  // line_trace, tube, cartoon etc. 
-  eachBackboneTrace : function(callback) {
-    this._cacheBackboneTraces();
-    for (var i=0; i < this._cachedTraces.length; ++i) {
-      callback(this._cachedTraces[i]);
-    }
-  },
-
-  _cacheBackboneTraces : function() {
-    if (this._cachedTraces.length > 0) {
-      return;
-    }
-    var stretch = new BackboneTrace();
-    // true when the stretch consists of amino acid residues, false
-    // if the stretch consists of nucleotides, null otherwise.
-    var aaStretch = null;
-    for (var i = 0; i < this._residues.length; i+=1) {
-      var residue = this._residues[i];
-      var isAminoacid = residue.isAminoacid();
-      var isNucleotide = residue.isNucleotide();
-      if ((aaStretch  === true && !isAminoacid) ||
-          (aaStretch === false && !isNucleotide) ||
-          (aaStretch === null && !isNucleotide && !isAminoacid)) {
-        // a break in the trace: push stretch if there were enough residues
-        // in it and create new backbone trace.
-        addNonEmptyTrace(this._cachedTraces, stretch);
-        aaStretch = null;
-        stretch = new BackboneTrace();
-        continue;
-      }
-      if (stretch.length() === 0) {
-        stretch.push(residue);
-        aaStretch = residue.isAminoacid();
-        continue;
-      }
-      var prevResidue = this._residues[i-1];
-      if (shouldIntroduceTraceBreak(aaStretch, prevResidue, residue)) {
-        addNonEmptyTrace(this._cachedTraces, stretch);
-        stretch = new BackboneTrace();
-      } 
-      stretch.push(residue);
-    }
-    addNonEmptyTrace(this._cachedTraces, stretch);
-  },
-
-
-  // returns all connected stretches of amino acids found in this chain as 
-  // a list.
-  backboneTraces : function() {
-    var traces = [];
-    this.eachBackboneTrace(function(trace) { traces.push(trace); });
-    return traces;
-
-  }
-});
-
-function Residue(chain, name, num, insCode) {
-  ResidueBase.call(this);
-  this._name = name;
-  this._num = num;
-  this._insCode = insCode;
-  this._atoms = [];
-  this._ss = 'C';
-  this._chain = chain;
-  this._isAminoacid = false;
-  this._isNucleotide = false;
-  this._index = chain.residues().length;
-}
-
-derive(Residue, ResidueBase, {
-  _deduceType : function() {
-    this._isNucleotide = this.atom('P')!== null && this.atom('C3\'') !== null;
-    this._isAminoacid = this.atom('N') !== null && this.atom('CA') !== null && 
-                        this.atom('C') !== null && this.atom('O') !== null;
-  },
-
-  name : function() { return this._name; },
-  insCode : function() { return this._insCode; },
-
-  num : function() { return this._num; },
-
-  full : function() { return this; },
-
-  addAtom : function(name, pos, element, isHetatm) {
-    var atom = new Atom(this, name, pos, element, 
-                        this.structure().nextAtomIndex(), 
-                        isHetatm);
-    this._atoms.push(atom);
-    return atom;
-  },
-
-  ss : function() { return this._ss; },
-  setSS : function(ss) { this._ss = ss; },
-  index : function() { return this._index; },
-
-  atoms : function() { return this._atoms; },
-  chain : function() { return this._chain; },
-
-
-  structure : function() { 
-    return this._chain.structure(); 
-  }
-
-});
-
-function Atom(residue, name, pos, element, index, isHetatm) {
-  AtomBase.call(this);
-  this._residue = residue;
-  this._bonds = [];
-  this._isHetatm = !!isHetatm;
-  this._name = name;
-  this._pos = pos;
-  this._index = index;
-  this._element = element;
-}
-
-derive(Atom, AtomBase, {
-  addBond : function(bond) { 
-    this._bonds.push(bond); 
-  },
-  name : function() { return this._name; },
-  bonds : function() { return this._bonds; },
-  residue : function() { return this._residue; },
-  structure : function() { return this._residue.structure(); },
-  full : function() { return this; },
-  qualifiedName : function() {
-    return this.residue().qualifiedName()+'.'+this.name();
-  },
-  isHetatm : function() { 
-    return this._isHetatm; 
-  },
-});
-
-var Bond = function(atom_a, atom_b) {
-  var self = {
-    atom_one : atom_a,
-    atom_two : atom_b
-  };
-  return {
-    atom_one : function() { return self.atom_one; },
-    atom_two : function() { return self.atom_two; },
-
-    // calculates the mid-point between the two atom positions
-    mid_point : function(out) { 
-      if (!out) {
-        out = vec3.create();
-      }
-      vec3.add(out, self.atom_one.pos(), self.atom_two.pos());
-      vec3.scale(out, out, 0.5);
-      return out;
-    }
-  };
-};
-
-//-----------------------------------------------------------------------------
-// MolView, ChainView, ResidueView, AtomView
-//-----------------------------------------------------------------------------
-
-function MolView(mol) {
-  MolBase.call(this);
-  this._mol = mol; 
-  this._chains = [];
-}
-
-derive(MolView, MolBase, {
-
-  full : function() { return this._mol; },
-
-  assemblies : function() { return this._mol.assemblies(); },
-
-  // add chain to view
-  addChain : function(chain, recurse) {
-    var chainView = new ChainView(this, chain.full());
-    this._chains.push(chainView);
-    if (recurse) {
-      var residues = chain.residues();
-      for (var i = 0; i< residues.length; ++i) {
-        chainView.addResidue(residues[i], true);
-      }
-    }
-    return chainView;
-  },
-
-
-  containsResidue : function(residue) {
-    if (!residue) {
-      return false;
-    }
-    var chain = this.chain(residue.chain().name());
-    if (!chain) {
-      return false;
-    }
-    return chain.containsResidue(residue);
-  },
-
-
-  chains : function() { return this._chains; },
-
-  chain : function(name) {
-    for (var i = 0; i < this._chains.length; ++i) {
-      if (this._chains[i].name() === name) {
-        return this._chains[i];
-      }
-    }
-    return null;
-  }
-});
-
-
-function ChainView(molView, chain) {
-  ChainBase.call(this);
-  this._chain = chain;
-  this._residues = [];
-  this._molView = molView;
-  this._residueMap = {};
-}
-
-
-derive(ChainView, ChainBase, {
-
-  addResidue : function(residue, recurse) {
-    var resView = new ResidueView(this, residue.full());
-    this._residues.push(resView);
-    this._residueMap[residue.full().index()] = resView;
-    if (recurse) {
-      var atoms = residue.atoms();
-      for (var i = 0; i < atoms.length; ++i) {
-        resView.addAtom(atoms[i].full());
-      }
-    }
-    return resView;
-  },
-
-  containsResidue : function(residue) {
-    var resView = this._residueMap[residue.full().index()];
-    if (resView === undefined) {
-      return false;
-    }
-    return resView.full() === residue.full();
-  },
-
-
-  eachBackboneTrace : function(callback) {
-    // backbone traces for the view must be based on the the full 
-    // traces for the following reasons:
-    //  - we must be able to display subsets with one residue in length,
-    //    when they are part of a larger trace. 
-    //  - when a trace residue is not at the end, e.g. the C-terminal or
-    //    N-terminal end of the full trace, the trace residue starts
-    //    midway between the residue and the previous, and ends midway
-    //    between the residue and the next.
-    //  - the tangents for the Catmull-Rom spline depend on the residues
-    //    before and after. Thus, to get the same curvature for a 
-    //    trace subset, the residues before and after must be taken
-    //    into account.
-    var fullTraces = this._chain.backboneTraces();
-    for (var i = 0; i < fullTraces.length; ++i) {
-      var subsets = fullTraces[i].subsets(this._residues);
-      for (var j = 0; j < subsets.length; ++j) {
-        callback(subsets[j]);
-      }
-    }
-  },
-
-  backboneTraces : function() {
-    var traces = [];
-    this.eachBackboneTrace(function(trace) { traces.push(trace); });
-    return traces;
-  },
-
-  full : function() { return this._chain; },
-
-  name : function () { return this._chain.name(); },
-
-  structure : function() { return this._molView; }
-});
-
-function ResidueView(chainView, residue) {
-  ResidueBase.call(this);
-  this._chainView = chainView;
-  this._atoms = [];
-  this._residue = residue;
-}
-
-
-derive(ResidueView, ResidueBase, {
-  addAtom : function(atom) {
-    var atomView = new AtomView(this, atom.full());
-    this._atoms.push(atomView);
-  },
-
-  full : function() { return this._residue; },
-  num : function() { return this._residue.num(); },
-
-  insCode : function() { 
-    return this._residue.insCode(); 
-  },
-  ss : function() { return this._residue.ss(); },
-  index : function() { return this._residue.index(); },
-  chain : function() { return this._chainView; },
-  name : function() { return this._residue.name(); },
-
-  atoms : function() { return this._atoms; },
-  qualifiedName : function() {
-    return this._residue.qualifiedName();
-  },
-
-  containsResidue : function(residue) {
-    return this._residue.full() === residue.full();
-  },
-  isAminoacid : function() { 
-    return this._residue.isAminoacid(); 
-  },
-  isNucleotide : function() { 
-    return this._residue.isNucleotide(); 
-  },
-  isWater : function() { 
-    return this._residue.isWater(); 
-  }
-});
-
-
-function AtomView(resView, atom) {
-  AtomBase.call(this);
-  this._resView = resView;
-  this._atom = atom;
-  this._bonds = [];
-}
-
-
-derive(AtomView, AtomBase, {
-  full : function() { return this._atom; },
-  name : function() { return this._atom.name(); },
-  pos : function() { return this._atom.pos(); },
-  element : function() { return this._atom.element(); },
-  residue : function() { return this._resView; },
-  bonds : function() { return this._atom.bonds(); },
-  index : function() { return this._atom.index(); },
-  qualifiedName : function() {
-    return this._atom.qualifiedName();
-  },
-  isHetatm : function() {
-    return this._atom.isHetatm();
-  }
-});
-
-
-
-var zhangSkolnickSS = (function() {
-  var posOne = vec3.create();
-  var posTwo = vec3.create();
-  return function(trace, i, distances, delta) {
-    for (var j = Math.max(0, i-2); j <= i; ++j) {
-      for (var k = 2;  k < 5; ++k) {
-        if (j+k >= trace.length()) {
-          continue;
-        }
-        var d = vec3.dist(trace.posAt(posOne, j), 
-                          trace.posAt(posTwo, j+k));
-        if (Math.abs(d - distances[k-2]) > delta) {
-          return false;
-        }
-      }
-    }
-    return true;
-  };
-})();
-
-var isHelical = function(trace, i) {
-  var helixDistances = [5.45, 5.18, 6.37];
-  var helixDelta = 2.1;
-  return zhangSkolnickSS(trace, i, helixDistances, helixDelta);
-};
-
-var isSheet = function(trace, i) {
-  var sheetDistances = [6.1, 10.4, 13.0];
-  var sheetDelta = 1.42;
-  return zhangSkolnickSS(trace, i, sheetDistances, sheetDelta);
-};
-
-function traceAssignHelixSheet(trace) {
-  for (var i = 0; i < trace.length(); ++i) {
-    if (isHelical(trace, i)) {
-      trace.residueAt(i).setSS('H');
-      continue;
-    } 
-    if (isSheet(trace, i)) {
-      trace.residueAt(i).setSS('E');
-      continue;
-    }
-    trace.residueAt(i).setSS('C');
-  }
-}
-
-
-// assigns secondary structure information based on a simple and very fast 
-// algorithm published by Zhang and Skolnick in their TM-align paper. 
-// Reference:
-//
-// TM-align: a protein structure alignment algorithm based on the Tm-score 
-// (2005) NAR, 33(7) 2302-2309
-function assignHelixSheet(structure) {
-  console.time('mol.assignHelixSheet');
-  var chains = structure.chains();
-  for (var ci = 0; ci < chains.length; ++ci) {
-    var chain = chains[ci];
-    chain.eachBackboneTrace(traceAssignHelixSheet);
-  }
-  console.timeEnd('mol.assignHelixSheet');
-}
-
-exports.mol = {};
-
-exports.mol.Mol = Mol;
-exports.mol.Chain = Chain;
-exports.mol.Residue = Residue;
-exports.mol.Atom = Atom;
-
-exports.mol.MolView = MolView;
-exports.mol.ChainView = ChainView;
-exports.mol.ResidueView = ResidueView;
-exports.mol.AtomView = AtomView;
-exports.mol.assignHelixSheet = assignHelixSheet;
-
-return true;
-
-})(this);
diff --git a/src/mol/all.js b/src/mol/all.js
new file mode 100644
index 0000000..bce9052
--- /dev/null
+++ b/src/mol/all.js
@@ -0,0 +1,99 @@
+// Copyright (c) 2013-2015 Marco Biasini
+// 
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to 
+// deal in the Software without restriction, including without limitation the 
+// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
+// sell copies of the Software, and to permit persons to whom the Software is 
+// furnished to do so, subject to the following conditions:
+// 
+// The above copyright notice and this permission notice shall be included in 
+// all copies or substantial portions of the Software.
+// 
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
+// DEALINGS IN THE SOFTWARE.
+
+define(['gl-matrix', './mol'], function(glMatrix, mol) {
+
+"use strict";
+
+var vec3 = glMatrix.vec3;
+var mat3 = glMatrix.mat3;
+
+
+
+var zhangSkolnickSS = (function() {
+  var posOne = vec3.create();
+  var posTwo = vec3.create();
+  return function(trace, i, distances, delta) {
+    for (var j = Math.max(0, i-2); j <= i; ++j) {
+      for (var k = 2;  k < 5; ++k) {
+        if (j+k >= trace.length()) {
+          continue;
+        }
+        var d = vec3.dist(trace.posAt(posOne, j), 
+                          trace.posAt(posTwo, j+k));
+        if (Math.abs(d - distances[k-2]) > delta) {
+          return false;
+        }
+      }
+    }
+    return true;
+  };
+})();
+
+var isHelical = function(trace, i) {
+  var helixDistances = [5.45, 5.18, 6.37];
+  var helixDelta = 2.1;
+  return zhangSkolnickSS(trace, i, helixDistances, helixDelta);
+};
+
+var isSheet = function(trace, i) {
+  var sheetDistances = [6.1, 10.4, 13.0];
+  var sheetDelta = 1.42;
+  return zhangSkolnickSS(trace, i, sheetDistances, sheetDelta);
+};
+
+function traceAssignHelixSheet(trace) {
+  for (var i = 0; i < trace.length(); ++i) {
+    if (isHelical(trace, i)) {
+      trace.residueAt(i).setSS('H');
+      continue;
+    } 
+    if (isSheet(trace, i)) {
+      trace.residueAt(i).setSS('E');
+      continue;
+    }
+    trace.residueAt(i).setSS('C');
+  }
+}
+
+
+// assigns secondary structure information based on a simple and very fast 
+// algorithm published by Zhang and Skolnick in their TM-align paper. 
+// Reference:
+//
+// TM-align: a protein structure alignment algorithm based on the Tm-score 
+// (2005) NAR, 33(7) 2302-2309
+function assignHelixSheet(structure) {
+  console.time('mol.assignHelixSheet');
+  var chains = structure.chains();
+  for (var ci = 0; ci < chains.length; ++ci) {
+    var chain = chains[ci];
+    chain.eachBackboneTrace(traceAssignHelixSheet);
+  }
+  console.timeEnd('mol.assignHelixSheet');
+}
+
+return {
+  Mol: mol.Mol,
+  assignHelixSheet : assignHelixSheet,
+
+};
+
+});
diff --git a/src/mol/atom.js b/src/mol/atom.js
new file mode 100644
index 0000000..3721834
--- /dev/null
+++ b/src/mol/atom.js
@@ -0,0 +1,110 @@
+// Copyright (c) 2013-2015 Marco Biasini
+// 
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to 
+// deal in the Software without restriction, including without limitation the 
+// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
+// sell copies of the Software, and to permit persons to whom the Software is 
+// furnished to do so, subject to the following conditions:
+// 
+// The above copyright notice and this permission notice shall be included in 
+// all copies or substantial portions of the Software.
+// 
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
+// DEALINGS IN THE SOFTWARE.
+
+define(['gl-matrix', 'core'], function(glMatrix, core) {
+
+"use strict";
+
+var vec3 = glMatrix.vec3;
+var mat3 = glMatrix.mat3;
+
+function AtomBase() {
+}
+
+
+AtomBase.prototype = {
+  name : function() { return this._name; },
+  pos : function() { return this._pos; },
+  element : function() { return this._element; },
+  index : function() { return this._index; },
+
+  prop : function(propName) { 
+    return this[propName]();
+  },
+
+  bondCount : function() { return this.bonds().length; },
+
+  eachBond : function(callback) {
+    var bonds = this.bonds();
+    for (var i = 0, e = bonds.length; i < e; ++i) {
+      callback(bonds[i]);
+    }
+  }
+};
+
+function Atom(residue, name, pos, element, index, isHetatm) {
+  AtomBase.call(this);
+  this._residue = residue;
+  this._bonds = [];
+  this._isHetatm = !!isHetatm;
+  this._name = name;
+  this._pos = pos;
+  this._index = index;
+  this._element = element;
+}
+
+core.derive(Atom, AtomBase, {
+  addBond : function(bond) { 
+    this._bonds.push(bond); 
+  },
+  name : function() { return this._name; },
+  bonds : function() { return this._bonds; },
+  residue : function() { return this._residue; },
+  structure : function() { return this._residue.structure(); },
+  full : function() { return this; },
+  qualifiedName : function() {
+    return this.residue().qualifiedName()+'.'+this.name();
+  },
+  isHetatm : function() { 
+    return this._isHetatm; 
+  },
+});
+
+function AtomView(resView, atom) {
+  AtomBase.call(this);
+  this._resView = resView;
+  this._atom = atom;
+  this._bonds = [];
+}
+
+
+core.derive(AtomView, AtomBase, {
+  full : function() { return this._atom; },
+  name : function() { return this._atom.name(); },
+  pos : function() { return this._atom.pos(); },
+  element : function() { return this._atom.element(); },
+  residue : function() { return this._resView; },
+  bonds : function() { return this._atom.bonds(); },
+  index : function() { return this._atom.index(); },
+  qualifiedName : function() {
+    return this._atom.qualifiedName();
+  },
+  isHetatm : function() {
+    return this._atom.isHetatm();
+  }
+});
+
+return {
+  Atom: Atom,
+  AtomView : AtomView
+};
+
+});
+
diff --git a/src/mol/bond.js b/src/mol/bond.js
new file mode 100644
index 0000000..e324348
--- /dev/null
+++ b/src/mol/bond.js
@@ -0,0 +1,53 @@
+// Copyright (c) 2013-2015 Marco Biasini
+// 
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to 
+// deal in the Software without restriction, including without limitation the 
+// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
+// sell copies of the Software, and to permit persons to whom the Software is 
+// furnished to do so, subject to the following conditions:
+// 
+// The above copyright notice and this permission notice shall be included in 
+// all copies or substantial portions of the Software.
+// 
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
+// DEALINGS IN THE SOFTWARE.
+
+define(['gl-matrix', 'core'], function(glMatrix, core) {
+
+"use strict";
+
+var vec3 = glMatrix.vec3;
+var mat3 = glMatrix.mat3;
+
+var Bond = function(atom_a, atom_b) {
+  var self = {
+    atom_one : atom_a,
+    atom_two : atom_b
+  };
+  return {
+    atom_one : function() { return self.atom_one; },
+    atom_two : function() { return self.atom_two; },
+
+    // calculates the mid-point between the two atom positions
+    mid_point : function(out) { 
+      if (!out) {
+        out = vec3.create();
+      }
+      vec3.add(out, self.atom_one.pos(), self.atom_two.pos());
+      vec3.scale(out, out, 0.5);
+      return out;
+    }
+  };
+};
+
+return {
+  Bond: Bond
+};
+});
+
diff --git a/src/mol/chain.js b/src/mol/chain.js
new file mode 100644
index 0000000..4b9f85a
--- /dev/null
+++ b/src/mol/chain.js
@@ -0,0 +1,349 @@
+// Copyright (c) 2013-2015 Marco Biasini
+// 
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to 
+// deal in the Software without restriction, including without limitation the 
+// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
+// sell copies of the Software, and to permit persons to whom the Software is 
+// furnished to do so, subject to the following conditions:
+// 
+// The above copyright notice and this permission notice shall be included in 
+// all copies or substantial portions of the Software.
+// 
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
+// DEALINGS IN THE SOFTWARE.
+
+define(['gl-matrix', 'core', './residue', 'trace'], 
+       function(glMatrix, core, residue, trace) {
+
+"use strict";
+
+var vec3 = glMatrix.vec3;
+var mat3 = glMatrix.mat3;
+var Residue = residue.Residue;
+var ResidueView = residue.ResidueView;
+
+// combines the numeric part of the residue number with the insertion
+// code and returns a single number. Note that this is completely safe
+// and we do not have to worry about overflows, as for PDB files the 
+// range of permitted residue numbers is quite limited anyway.
+function rnumInsCodeHash(num, insCode) {
+  return num << 8 | insCode.charCodeAt(0);
+}
+
+function ChainBase() {
+}
+
+ChainBase.prototype  = {
+  eachAtom : function(callback, index) {
+    index |= 0;
+    for (var i = 0; i< this._residues.length; i+=1) {
+      index = this._residues[i].eachAtom(callback, index);
+      if (index === false) {
+        return false;
+      }
+    }
+    return index;
+  },
+
+
+  atomCount : function() {
+    var count = 0;
+    var residues = this.residues();
+    for (var ri = 0; ri < residues.length; ++ri) {
+      count+= residues[ri].atoms().length;
+    }
+    return count;
+  },
+
+  eachResidue : function(callback) {
+    for (var i = 0; i < this._residues.length; i+=1) {
+      if (callback(this._residues[i]) === false) {
+        return false;
+      }
+    }
+  },
+
+  residues : function() { return this._residues; },
+
+  structure : function() { return this._structure; },
+
+
+  asView : function() {
+    var view = new MolView(this.structure().full());
+    view.addChain(this, true);
+    return view;
+
+  },
+
+  residueByRnum : function(rnum) {
+    var residues = this.residues();
+    if (this._rnumsOrdered) {
+      var index = binarySearch(residues, numify(rnum), rnumComp);
+      if (index === -1) {
+        return null;
+      }
+      return residues[index];
+    } else {
+      for (var i = 0; i < residues.length; ++i) {
+        if (residues[i].num() === rnum) {
+          return residues[i];
+        }
+      }
+      return null;
+    }
+  },
+
+
+  prop : function(propName) { 
+    return this[propName]();
+  }
+};
+
+function Chain(structure, name) {
+  ChainBase.call(this);
+  this._structure = structure;
+  this._name = name;
+  this._cachedTraces = [];
+  this._residues = [];
+  this._rnumsOrdered = true;
+}
+
+// helper function to determine whether a trace break should be introduced 
+// between two residues of the same type (amino acid, or nucleotides).
+//
+// aaStretch: indicates whether the residues are to be treated as amino 
+//   acids
+function shouldIntroduceTraceBreak(aaStretch, prevResidue, thisResidue) {
+  // these checks are on purpose more relaxed than the checks we use in 
+  // deriveConnectivity(). We don't really care about correctness of bond 
+  // lengths here. The only thing that matters is that the residues are 
+  // more or less close so that they could potentially/ be connected.
+  var prevAtom, thisAtom;
+  if (aaStretch) {
+    prevAtom = prevResidue.atom('C');
+    thisAtom = thisResidue.atom('N');
+  } else {
+    prevAtom = prevResidue.atom('O3\'');
+    thisAtom = thisResidue.atom('P');
+  }
+  var sqrDist = vec3.sqrDist(prevAtom.pos(), thisAtom.pos());
+  return (Math.abs(sqrDist - 1.5*1.5) > 1);
+}
+
+function addNonEmptyTrace(traces, trace) {
+  if (trace.length() < 2) {
+    return;
+  }
+  traces.push(trace);
+}
+
+core.derive(Chain, ChainBase, {
+
+  name : function() { return this._name; },
+
+  full : function() { return this; },
+
+  addResidue : function(name, num, insCode) {
+    insCode = insCode || '\0';
+    var residue = new Residue(this, name, num, insCode);
+    if (this._residues.length > 0 && this._rnumsOrdered) {
+      var combinedRNum = rnumInsCodeHash(num, insCode);
+      var last = this._residues[this._residues.length-1];
+      var lastCombinedRNum = rnumInsCodeHash(last.num(),last.insCode());
+      this._rnumsOrdered = lastCombinedRNum < combinedRNum;
+    }
+    this._residues.push(residue);
+    return residue;
+  },
+
+
+  residuesInRnumRange : function(start, end) {
+    // FIXME: this currently only works with the numeric part, insertion
+    // codes are not honoured.
+    var matching = [];
+    var i, e;
+    if (this._rnumsOrdered === true) {
+      // binary search our way to heaven
+      var startIdx = indexFirstLargerEqualThan(this._residues, numify(start), 
+                                              rnumComp);
+      if (startIdx === -1) {
+        return matching;
+      }
+      var endIdx = indexLastSmallerEqualThan(this._residues, numify(end), 
+                                            rnumComp);
+      if (endIdx === -1) {
+        return matching;
+      }
+      for (i = startIdx; i <= endIdx; ++i) {
+        matching.push(this._residues[i]);
+      }
+    } else {
+      for (i = 0, e = this._residues.length; i !== e; ++i) {
+        var res = this._residues[i];
+        if (res.num() >= start && res.num() <= end) {
+          matching.push(res);
+        }
+      }
+    }
+    return matching;
+  },
+
+  // assigns secondary structure to residues in range from_num to to_num.
+  assignSS : function(fromNumAndIns, toNumAndIns, ss) {
+    // FIXME: when the chain numbers are completely ordered, perform binary 
+    // search to identify range of residues to assign secondary structure to.
+    var from = rnumInsCodeHash(fromNumAndIns[0], fromNumAndIns[1]);
+    var to = rnumInsCodeHash(toNumAndIns[0], toNumAndIns[1]);
+    for (var i = 1; i < this._residues.length-1; ++i) {
+      var res = this._residues[i];
+      // FIXME: we currently don't set the secondary structure of the first and 
+      // last residue of helices and sheets. that takes care of better 
+      // transitions between coils and helices. ideally, this should be done
+      // in the cartoon renderer, NOT in this function.
+      var combined = rnumInsCodeHash(res.num(), res.insCode());
+      if (combined <=  from || combined >= to) {
+        continue;
+      }
+      res.setSS(ss);
+    }
+  },
+
+  // invokes a callback for each connected stretch of amino acids. these 
+  // stretches are used for all trace-based rendering styles, e.g. sline, 
+  // line_trace, tube, cartoon etc. 
+  eachBackboneTrace : function(callback) {
+    this._cacheBackboneTraces();
+    for (var i=0; i < this._cachedTraces.length; ++i) {
+      callback(this._cachedTraces[i]);
+    }
+  },
+
+  _cacheBackboneTraces : function() {
+    if (this._cachedTraces.length > 0) {
+      return;
+    }
+    var stretch = new trace.BackboneTrace();
+    // true when the stretch consists of amino acid residues, false
+    // if the stretch consists of nucleotides, null otherwise.
+    var aaStretch = null;
+    for (var i = 0; i < this._residues.length; i+=1) {
+      var residue = this._residues[i];
+      var isAminoacid = residue.isAminoacid();
+      var isNucleotide = residue.isNucleotide();
+      if ((aaStretch  === true && !isAminoacid) ||
+          (aaStretch === false && !isNucleotide) ||
+          (aaStretch === null && !isNucleotide && !isAminoacid)) {
+        // a break in the trace: push stretch if there were enough residues
+        // in it and create new backbone trace.
+        addNonEmptyTrace(this._cachedTraces, stretch);
+        aaStretch = null;
+        stretch = new trace.BackboneTrace();
+        continue;
+      }
+      if (stretch.length() === 0) {
+        stretch.push(residue);
+        aaStretch = residue.isAminoacid();
+        continue;
+      }
+      var prevResidue = this._residues[i-1];
+      if (shouldIntroduceTraceBreak(aaStretch, prevResidue, residue)) {
+        addNonEmptyTrace(this._cachedTraces, stretch);
+        stretch = new trace.BackboneTrace();
+      } 
+      stretch.push(residue);
+    }
+    addNonEmptyTrace(this._cachedTraces, stretch);
+  },
+
+
+  // returns all connected stretches of amino acids found in this chain as 
+  // a list.
+  backboneTraces : function() {
+    var traces = [];
+    this.eachBackboneTrace(function(trace) { traces.push(trace); });
+    return traces;
+
+  }
+});
+
+function ChainView(molView, chain) {
+  ChainBase.call(this);
+  this._chain = chain;
+  this._residues = [];
+  this._molView = molView;
+  this._residueMap = {};
+}
+
+
+core.derive(ChainView, ChainBase, {
+
+  addResidue : function(residue, recurse) {
+    var resView = new ResidueView(this, residue.full());
+    this._residues.push(resView);
+    this._residueMap[residue.full().index()] = resView;
+    if (recurse) {
+      var atoms = residue.atoms();
+      for (var i = 0; i < atoms.length; ++i) {
+        resView.addAtom(atoms[i].full());
+      }
+    }
+    return resView;
+  },
+
+  containsResidue : function(residue) {
+    var resView = this._residueMap[residue.full().index()];
+    if (resView === undefined) {
+      return false;
+    }
+    return resView.full() === residue.full();
+  },
+
+
+  eachBackboneTrace : function(callback) {
+    // backbone traces for the view must be based on the the full 
+    // traces for the following reasons:
+    //  - we must be able to display subsets with one residue in length,
+    //    when they are part of a larger trace. 
+    //  - when a trace residue is not at the end, e.g. the C-terminal or
+    //    N-terminal end of the full trace, the trace residue starts
+    //    midway between the residue and the previous, and ends midway
+    //    between the residue and the next.
+    //  - the tangents for the Catmull-Rom spline depend on the residues
+    //    before and after. Thus, to get the same curvature for a 
+    //    trace subset, the residues before and after must be taken
+    //    into account.
+    var fullTraces = this._chain.backboneTraces();
+    for (var i = 0; i < fullTraces.length; ++i) {
+      var subsets = fullTraces[i].subsets(this._residues);
+      for (var j = 0; j < subsets.length; ++j) {
+        callback(subsets[j]);
+      }
+    }
+  },
+
+  backboneTraces : function() {
+    var traces = [];
+    this.eachBackboneTrace(function(trace) { traces.push(trace); });
+    return traces;
+  },
+
+  full : function() { return this._chain; },
+
+  name : function () { return this._chain.name(); },
+
+  structure : function() { return this._molView; }
+});
+
+return {
+  Chain : Chain,
+  ChainView : ChainView
+};
+
+});
+
diff --git a/src/mol/mol.js b/src/mol/mol.js
new file mode 100644
index 0000000..79b16ad
--- /dev/null
+++ b/src/mol/mol.js
@@ -0,0 +1,468 @@
+// Copyright (c) 2013-2015 Marco Biasini
+// 
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to 
+// deal in the Software without restriction, including without limitation the 
+// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
+// sell copies of the Software, and to permit persons to whom the Software is 
+// furnished to do so, subject to the following conditions:
+// 
+// The above copyright notice and this permission notice shall be included in 
+// all copies or substantial portions of the Software.
+// 
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
+// DEALINGS IN THE SOFTWARE.
+
+define(['gl-matrix', 'core', './chain', './bond', './select'], 
+       function(glMatrix, core, chain, bond, select) {
+
+"use strict";
+
+var vec3 = glMatrix.vec3;
+var mat3 = glMatrix.mat3;
+
+var Chain = chain.Chain;
+var ChainView = chain.ChainView;
+var Bond = bond.Bond;
+
+// atom covalent radii by element derived from Cambrige Structural Database. 
+// Source: http://profmokeur.ca/chemistry/covalent_radii.htm
+var ELEMENT_COVALENT_RADII = {
+ H : 0.31, HE : 0.28, LI : 1.28, BE : 0.96,  B : 0.84,  C : 0.76,  N : 0.71, 
+ O : 0.66,  F : 0.57, NE : 0.58, NA : 1.66, MG : 1.41, AL : 1.21, SI : 1.11, 
+ P : 1.07,  S : 1.05, CL : 1.02, AR : 1.06,  K : 2.03, CA : 1.76, SC : 1.70, 
+TI : 1.60,  V : 1.53, CR : 1.39, MN : 1.39, FE : 1.32, CO : 1.26, NI : 1.24, 
+CU : 1.32, ZN : 1.22, GA : 1.22, GE : 1.20, AS : 1.19, SE : 1.20, BR : 1.20, 
+KR : 1.16, RB : 2.20, SR : 1.95,  Y : 1.90, ZR : 1.75, NB : 1.64, MO : 1.54, 
+TC : 1.47, RU : 1.46, RH : 1.42, PD : 1.39, AG : 1.45, CD : 1.44, IN : 1.42, 
+SN : 1.39, SB : 1.39, TE : 1.38,  I : 1.39, XE : 1.40, CS : 2.44, BA : 2.15, 
+LA : 2.07, CE : 2.04, PR : 2.03, ND : 2.01, PM : 1.99, SM : 1.98, EU : 1.98, 
+GD : 1.96, TB : 1.94, DY : 1.92, HO : 1.92, ER : 1.89, TM : 1.90, YB : 1.87, 
+LU : 1.87, HF : 1.75, TA : 1.70,  W : 1.62, RE : 1.51, OS : 1.44, IR : 1.41, 
+PT : 1.36, AU : 1.36, HG : 1.32, TL : 1.45, PB : 1.46, BI : 1.48, PO : 1.40, 
+AT : 1.50, RN : 1.50, FR : 2.60, RA : 2.21, AC : 2.15, TH : 2.06, PA : 2.00, 
+ U : 1.96, NP : 1.90, PU : 1.87, AM : 1.80, CM : 1.69
+};
+
+function covalentRadius(ele) {
+  var r = ELEMENT_COVALENT_RADII[ele.toUpperCase()];
+  if (r !== undefined) {
+    return r;
+  }
+  return 1.5;
+}
+
+function connectPeptides(structure, left, right) {
+  var cAtom = left.atom('C');
+  var nAtom = right.atom('N');
+  if (cAtom && nAtom) {
+    var sqrDist = vec3.sqrDist(cAtom.pos(), nAtom.pos());
+    if (sqrDist < 1.6*1.6) {
+      structure.connect(nAtom, cAtom);
+    }
+  } 
+}
+
+function connectNucleotides(structure, left, right) {
+  var o3Prime = left.atom('O3\'');
+  var pAtom = right.atom('P');
+  if (o3Prime && pAtom) {
+    var sqrDist = vec3.sqrDist(o3Prime.pos(), pAtom.pos());
+    // FIXME: make sure 1.7 is a good threshold here...
+    if (sqrDist < 1.7*1.7) {
+      structure.connect(o3Prime, pAtom);
+    }
+  }
+}
+
+function MolBase() {
+}
+
+MolBase.prototype = {
+  eachResidue : function(callback) {
+    for (var i = 0; i < this._chains.length; i+=1) {
+      if (this._chains[i].eachResidue(callback) === false) {
+        return false;
+      }
+    }
+  },
+
+  eachAtom : function(callback, index) {
+    index |= 0;
+    for (var i = 0; i < this._chains.length; i+=1) {
+      index = this._chains[i].eachAtom(callback, index);
+      if (index === false) {
+        return false;
+      }
+    }
+  },
+
+  residueCount : function () {
+    var chains = this.chains();
+    var count = 0;
+    for (var ci = 0; ci < chains.length; ++ci) {
+      count += chains[ci].residues().length;
+    }
+    return count;
+  },
+
+  eachChain : function(callback) {
+    var chains = this.chains();
+    for (var i = 0; i < chains.length; ++i) {
+      if (callback(chains[i]) === false) {
+        return;
+      }
+    }
+  },
+
+  atomCount : function() {
+    var chains = this.chains();
+    var count = 0;
+    for (var ci = 0; ci < chains.length; ++ci) {
+      count += chains[ci].atomCount();
+    }
+    return count;
+  },
+
+  atoms : function() {
+    var atoms = [];
+    this.eachAtom(function(atom) { atoms.push(atom); });
+    return atoms;
+  },
+
+  atom : function(name) {
+    var parts = name.split('.');
+    var chain = this.chain(parts[0]);
+    if (chain === null) {
+      return null;
+    }
+    var residue = chain.residueByRnum(parseInt(parts[1], 10));
+    if (residue === null) {
+      return null;
+    }
+    return residue.atom(parts[2]);
+  },
+
+  center : function() {
+    var sum = vec3.create();
+    var count = 0;
+    this.eachAtom(function(atom) {
+      vec3.add(sum, sum, atom.pos());
+      count+=1;
+    });
+    if (count) {
+      vec3.scale(sum, sum, 1/count);
+    }
+    return sum;
+  },
+
+  // returns a sphere containing all atoms part of this structure. This will 
+  // not calculate the minimal bounding sphere, just a good-enough 
+  // approximation.
+  boundingSphere : function() {
+    var center = this.center();
+    var radiusSquare = 0.0;
+    this.eachAtom(function(atom) {
+      radiusSquare = Math.max(radiusSquare, vec3.sqrDist(center, atom.pos()));
+    });
+    return new Sphere(center, radiusSquare);
+  },
+
+  // returns all backbone traces of all chains of this structure
+  backboneTraces : function() {
+    var chains = this.chains();
+    var traces = [];
+    for (var i = 0; i < chains.length; ++i) {
+      Array.prototype.push.apply(traces, chains[i].backboneTraces());
+    }
+    return traces;
+  },
+
+
+  select : function(what) {
+
+    if (what === 'protein') {
+      return this.residueSelect(function(r) { return r.isAminoacid(); });
+    }
+    if (what === 'water') {
+      return this.residueSelect(function(r) { return r.isWater(); });
+    }
+    if (what === 'ligand') {
+      return this.residueSelect(function(r) { 
+        return !r.isAminoacid() && !r.isWater();
+      });
+    }
+    // when what is not one of the simple strings above, we assume what
+    // is a dictionary containing predicates which have to be fulfilled.
+    return select.dict(this, new MolView(this), what || {});
+  },
+
+  selectWithin : (function() {
+    var dist = vec3.create();
+    return function(mol, options) {
+      console.time('Mol.selectWithin');
+      options = options || {};
+      var radius = options.radius || 4.0;
+      var radiusSqr = radius * radius;
+      var matchResidues = !!options.matchResidues;
+      var targetAtoms = [];
+      mol.eachAtom(function(a) { targetAtoms.push(a); });
+
+      var view = new MolView(this.full());
+      var addedRes = null, addedChain = null;
+      var chains = this.chains();
+      var skipResidue = false;
+      for (var ci = 0; ci < chains.length; ++ci) {
+        var residues = chains[ci].residues();
+        addedChain = null;
+        for (var ri = 0; ri < residues.length; ++ri) {
+          addedRes = null;
+          skipResidue = false;
+          var atoms = residues[ri].atoms();
+          for (var ai = 0; ai < atoms.length; ++ai) {
+            if (skipResidue) {
+              break;
+            }
+            skipResidue = addAtomsWithin(view, tagetAtoms, radiusSqr);
+            for (var wi = 0; wi < targetAtoms.length; ++wi) {
+              vec3.sub(dist, atoms[ai].pos(), targetAtoms[wi].pos());
+              if (vec3.sqrLen(dist) > radiusSqr) {
+                continue;
+              }
+              if (!addedChain) {
+                addedChain = view.addChain(chains[ci].full(), false);
+              }
+              if (!addedRes) {
+                addedRes =
+                    addedChain.addResidue(residues[ri].full(), matchResidues);
+              }
+              if (matchResidues) {
+                skipResidue = true;
+                break;
+              } 
+              addedRes.addAtom(atoms[ai].full());
+            }
+          }
+        }
+      }
+      console.timeEnd('Mol.selectWithin');
+      return view;
+    };
+  })(),
+
+  residueSelect : function(predicate) {
+    console.time('Mol.residueSelect');
+    var view = new MolView(this.full());
+    for (var ci = 0; ci < this._chains.length; ++ci) {
+      var chain = this._chains[ci];
+      var chainView = null;
+      var residues = chain.residues();
+      for (var ri = 0; ri < residues.length; ++ri) {
+        if (predicate(residues[ri])) {
+          if (!chainView) {
+            chainView = view.addChain(chain, false);
+          }
+          chainView.addResidue(residues[ri], true);
+        }
+      }
+    }
+    console.timeEnd('Mol.residueSelect');
+    return view;
+  },
+
+
+
+  assembly : function(id) {
+    var assemblies = this.assemblies();
+    for (var i = 0; i < assemblies.length; ++i) {
+      if (assemblies[i].name() === id) {
+        return assemblies[i];
+      }
+    }
+    return null;
+  },
+
+  chainsByName : function(chainNames) {
+    // build a map to avoid O(n^2) behavior. That's overkill when the list 
+    // of names is short but should give better performance when requesting
+    // multiple chains.
+    var chainMap = { };
+    var chains = this.chains();
+    for (var i = 0; i < chains.length; ++i) {
+      chainMap[chains[i].name()] = chains[i];
+    }
+    var filteredChains = [];
+    for (var j = 0; j < chainNames.length; ++j) {
+      var filteredChain = chainMap[chainNames[j]];
+      if (filteredChain !== undefined) {
+        filteredChains.push(filteredChain);
+      }
+    }
+    return filteredChains;
+  }
+};
+
+function Mol() {
+  MolBase.call(this);
+  this._chains = [];
+  this._assemblies = [];
+  this._nextAtomIndex = 0;
+}
+
+core.derive(Mol, MolBase, {
+  addAssembly : function(assembly) { 
+    this._assemblies.push(assembly); 
+  },
+
+  setAssemblies : function(assemblies) { 
+    this._assemblies = assemblies; 
+  },
+
+  assemblies : function() { return this._assemblies; },
+
+  chains : function() { return this._chains; },
+
+  full : function() { return this; },
+
+  containsResidue : function(residue) {
+    return residue.full().structure() === this;
+  },
+
+  chainByName : function(name) { 
+    for (var i = 0; i < this._chains.length; ++i) {
+      if (this._chains[i].name() === name) {
+        return this._chains[i];
+      }
+    }
+    return null;
+  },
+
+  // for backwards compatibility
+  chain : function(name) {
+    return this.chainByName(name);
+  },
+
+  nextAtomIndex : function() {
+    var nextIndex = this._nextAtomIndex; 
+    this._nextAtomIndex+=1; 
+    return nextIndex; 
+  },
+
+  addChain : function(name) {
+    var chain = new Chain(this, name);
+    this._chains.push(chain);
+    return chain;
+  },
+
+
+  connect : function(atom_a, atom_b) {
+    var bond = new Bond(atom_a, atom_b);
+    atom_a.addBond(bond);
+    atom_b.addBond(bond);
+    return bond;
+  },
+
+
+
+  // determine connectivity structure. for simplicity only connects atoms of the
+  // same residue, peptide bonds and nucleotides
+  deriveConnectivity : function() {
+    console.time('Mol.deriveConnectivity');
+    var thisStructure = this;
+    var prevResidue = null;
+    this.eachResidue(function(res) {
+      var sqrDist;
+      var atoms = res.atoms();
+      var numAtoms = atoms.length;
+      for (var i = 0; i < numAtoms; i+=1) {
+        var atomI = atoms[i];
+        var posI = atomI.pos();
+        var covalentI = covalentRadius(atomI.element());
+        for (var j = 0; j < i; j+=1) {
+          var atomJ = atoms[j];
+          var covalentJ = covalentRadius(atomJ.element());
+          sqrDist = vec3.sqrDist(posI, atomJ.pos());
+          var lower = covalentI+covalentJ-0.30;
+          var upper = covalentI+covalentJ+0.30;
+          if (sqrDist < upper*upper && sqrDist > lower*lower) {
+            thisStructure.connect(atomI, atomJ);
+          }
+        }
+      }
+      res._deduceType();
+      if (prevResidue !== null) {
+        if (res.isAminoacid() && prevResidue.isAminoacid()) {
+          connectPeptides(thisStructure, prevResidue, res);
+        }
+        if (res.isNucleotide() && prevResidue.isNucleotide()) {
+          connectNucleotides(thisStructure, prevResidue, res);
+        }
+      }
+      prevResidue = res;
+    });
+    console.timeEnd('Mol.deriveConnectivity');
+  }
+});
+
+function MolView(mol) {
+  MolBase.call(this);
+  this._mol = mol; 
+  this._chains = [];
+}
+
+core.derive(MolView, MolBase, {
+
+  full : function() { return this._mol; },
+
+  assemblies : function() { return this._mol.assemblies(); },
+
+  // add chain to view
+  addChain : function(chain, recurse) {
+    var chainView = new ChainView(this, chain.full());
+    this._chains.push(chainView);
+    if (recurse) {
+      var residues = chain.residues();
+      for (var i = 0; i< residues.length; ++i) {
+        chainView.addResidue(residues[i], true);
+      }
+    }
+    return chainView;
+  },
+
+
+  containsResidue : function(residue) {
+    if (!residue) {
+      return false;
+    }
+    var chain = this.chain(residue.chain().name());
+    if (!chain) {
+      return false;
+    }
+    return chain.containsResidue(residue);
+  },
+
+
+  chains : function() { return this._chains; },
+
+  chain : function(name) {
+    for (var i = 0; i < this._chains.length; ++i) {
+      if (this._chains[i].name() === name) {
+        return this._chains[i];
+      }
+    }
+    return null;
+  }
+});
+
+return {
+  MolView : MolView,
+  Mol : Mol
+};
+
+});
+
diff --git a/src/mol/residue.js b/src/mol/residue.js
new file mode 100644
index 0000000..095662d
--- /dev/null
+++ b/src/mol/residue.js
@@ -0,0 +1,208 @@
+// Copyright (c) 2013-2015 Marco Biasini
+// 
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to 
+// deal in the Software without restriction, including without limitation the 
+// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or 
+// sell copies of the Software, and to permit persons to whom the Software is 
+// furnished to do so, subject to the following conditions:
+// 
+// The above copyright notice and this permission notice shall be included in 
+// all copies or substantial portions of the Software.
+// 
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
+// DEALINGS IN THE SOFTWARE.
+
+define(['gl-matrix', 'core', './atom'], 
+       function(glMatrix, core, atom) {
+
+"use strict";
+
+var vec3 = glMatrix.vec3;
+var mat3 = glMatrix.mat3;
+var Atom = atom.Atom;
+var AtomView = atom.AtomView;
+
+function ResidueBase() {
+
+}
+
+ResidueBase.prototype = {
+
+  prop : function(propName) { 
+    return this[propName]();
+  },
+
+  isWater : function() {
+    return this.name() === 'HOH' || this.name() === 'DOD';
+  },
+
+  eachAtom : function(callback, index) {
+    index |= 0;
+    for (var i =0; i< this._atoms.length; i+=1) {
+      if (callback(this._atoms[i], index) === false) {
+        return false;
+      }
+      index +=1;
+    }
+    return index;
+  },
+
+  qualifiedName : function() {
+    return this.chain().name()+'.'+this.name()+this.num();
+  },
+
+  atom : function(index_or_name) { 
+    if (typeof index_or_name === 'string') {
+      for (var i =0; i < this._atoms.length; ++i) {
+        if (this._atoms[i].name() === index_or_name) {
+          return this._atoms[i];
+        }
+      }
+      return null;
+    }
+    if (index_or_name >= this._atoms.length && index_or_name < 0) {
+      return null;
+    }
+    return this._atoms[index_or_name]; 
+  },
+
+  // CA for amino acids, P for nucleotides, nucleosides
+  centralAtom : function() {
+    if (this.isAminoacid()) {
+      return this.atom('CA');
+    }
+    if (this.isNucleotide()) {
+      return this.atom('C3\'');
+    }
+    return null;
+  },
+
+
+  center : function() {
+    var count = 0;
+    var c = vec3.create();
+    this.eachAtom(function(atom) {
+      vec3.add(c, c, atom.pos());
+      count += 1;
+    });
+    if (count > 0) {
+      vec3.scale(c, c, 1.0/count);
+    }
+    return c;
+  },
+
+  isAminoacid : function() { 
+    return this._isAminoacid;
+  },
+
+  isNucleotide : function() { 
+    return this._isNucleotide;
+  }
+};
+
+function Residue(chain, name, num, insCode) {
+  ResidueBase.call(this);
+  this._name = name;
+  this._num = num;
+  this._insCode = insCode;
+  this._atoms = [];
+  this._ss = 'C';
+  this._chain = chain;
+  this._isAminoacid = false;
+  this._isNucleotide = false;
+  this._index = chain.residues().length;
+}
+
+core.derive(Residue, ResidueBase, {
+  _deduceType : function() {
+    this._isNucleotide = this.atom('P')!== null && this.atom('C3\'') !== null;
+    this._isAminoacid = this.atom('N') !== null && this.atom('CA') !== null && 
+                        this.atom('C') !== null && this.atom('O') !== null;
+  },
+
+  name : function() { return this._name; },
+  insCode : function() { return this._insCode; },
+
+  num : function() { return this._num; },
+
+  full : function() { return this; },
+
+  addAtom : function(name, pos, element, isHetatm) {
+    var atom = new Atom(this, name, pos, element, 
+                        this.structure().nextAtomIndex(), 
+                        isHetatm);
+    this._atoms.push(atom);
+    return atom;
+  },
+
+  ss : function() { return this._ss; },
+  setSS : function(ss) { this._ss = ss; },
+  index : function() { return this._index; },
+
+  atoms : function() { return this._atoms; },
+  chain : function() { return this._chain; },
+
+
+  structure : function() { 
+    return this._chain.structure(); 
+  }
+
+});
+
+function ResidueView(chainView, residue) {
+  ResidueBase.call(this);
+  this._chainView = chainView;
+  this._atoms = [];
+  this._residue = residue;
+}
+
+
+core.derive(ResidueView, ResidueBase, {
+  addAtom : function(atom) {
+    var atomView = new AtomView(this, atom.full());
+    this._atoms.push(atomView);
+  },
+
+  full : function() { return this._residue; },
+  num : function() { return this._residue.num(); },
+
+  insCode : function() { 
+    return this._residue.insCode(); 
+  },
+  ss : function() { return this._residue.ss(); },
+  index : function() { return this._residue.index(); },
+  chain : function() { return this._chainView; },
+  name : function() { return this._residue.name(); },
+
+  atoms : function() { return this._atoms; },
+  qualifiedName : function() {
+    return this._residue.qualifiedName();
+  },
+
+  containsResidue : function(residue) {
+    return this._residue.full() === residue.full();
+  },
+  isAminoacid : function() { 
+    return this._residue.isAminoacid(); 
+  },
+  isNucleotide : function() { 
+    return this._residue.isNucleotide(); 
+  },
+  isWater : function() { 
+    return this._residue.isWater(); 
+  }
+});
+
+return {
+  ResidueView : ResidueView,
+  Residue : Residue
+};
+
+});
+
diff --git a/src/mol/select.js b/src/mol/select.js
new file mode 100644
index 0000000..b59b259
--- /dev/null
+++ b/src/mol/select.js
@@ -0,0 +1,171 @@
+define(function() {
+
+function fulfillsPredicates(obj, predicates) {
+  for (var i = 0; i < predicates.length; ++i) {
+    if (!predicates[i](obj)) {
+      return false;
+    }
+  }
+  return true;
+}
+
+function rnumComp(lhs, rhs) {
+  return lhs.num() < rhs.num();
+}
+
+function numify(val) {
+  return { num : function() { return val; }};
+}
+
+function _atomPredicates(dict) {
+  var predicates = [];
+  if (dict.aname !== undefined) {
+    predicates.push(function(a) { return a.name() === dict.aname; });
+  }
+  if (dict.hetatm !== undefined) {
+    predicates.push(function(a) { return a.isHetatm() === dict.hetatm; });
+  }
+  if (dict.anames !== undefined) {
+    predicates.push(function(a) { 
+      var n = a.name();
+      for (var k = 0; k < dict.anames.length; ++k) {
+        if (n === dict.anames[k]) {
+          return true;
+        }
+      }
+      return false;
+    });
+  }
+  return predicates;
+}
+
+// extracts the residue predicates from the dictionary. 
+// ignores rindices, rindexRange because they are handled separately.
+function _residuePredicates(dict) {
+  var predicates = [];
+  if (dict.rname !== undefined) {
+    predicates.push(function(r) { return r.name() === dict.rname; });
+  }
+  if (dict.rnames !== undefined) {
+    predicates.push(function(r) { 
+    var n = r.name();
+    for (var k = 0; k < dict.rnames.length; ++k) {
+      if (n === dict.rnames[k]) {
+          return true;
+        }
+      }
+      return false;
+    });
+  }
+  if (dict.rnums !== undefined) {
+    var num_set = {};
+    for (var i = 0; i < dict.rnums.length; ++i) {
+      num_set[dict.rnums[i]] = true;
+    }
+    predicates.push(function(r) {
+      var n = r.num();
+      return num_set[n] === true;
+    });
+  }
+  return predicates;
+}
+
+function _chainPredicates(dict) {
+  var predicates = [];
+  if (dict.cname !== undefined) {
+    dict.chain = dict.cname;
+  }
+  if (dict.cnames !== undefined) {
+    dict.chains = dict.cnames;
+  }
+  if (dict.chain !== undefined) {
+    predicates.push(function(c) { return c.name() === dict.chain; });
+  }
+  if (dict.chains !== undefined) {
+    predicates.push(function(c) { 
+      var n = c.name();
+      for (var k = 0; k < dict.chains.length; ++k) {
+        if (n === dict.chains[k]) {
+          return true;
+        }
+      }
+      return false;
+    });
+  }
+  return predicates;
+}
+
+
+// handles all residue predicates that can be done through either index-
+// based lookups, or optimized searches of some sorts.
+function _filterResidues(chain, dict) {
+  var residues = chain.residues();
+  if (dict.rnumRange) {
+    residues =
+        chain.residuesInRnumRange(dict.rnumRange[0], dict.rnumRange[1]);
+  }
+  var selResidues = [], i, e;
+  if (dict.rindexRange !== undefined) {
+    for (i = dict.rindexRange[0],
+        e = Math.min(residues.length, dict.rindexRange[1]);
+        i < e; ++i) {
+      selResidues.push(residues[i]);
+    }
+    return selResidues;
+  } 
+  if (dict.rindices) {
+    if (dict.rindices.length !== undefined) {
+      selResidues = [];
+      for (i = 0; i < dict.rindices.length; ++i) {
+        selResidues.push(residues[dict.rindices[i]]);
+      }
+      return selResidues;
+    }
+  }
+  return residues;
+}
+
+// helper function to perform selection by predicates
+function dictSelect(structure, view, dict) {
+  var residuePredicates = _residuePredicates(dict);
+  var atomPredicates = _atomPredicates(dict);
+  var chainPredicates = _chainPredicates(dict);
+
+  if (dict.rindex) {
+    dict.rindices = [dict.rindex];
+  }
+  for (var ci = 0; ci < structure._chains.length; ++ci) {
+    var chain = structure._chains[ci];
+    if (!fulfillsPredicates(chain, chainPredicates)) {
+      continue;
+    }
+    var residues = _filterResidues(chain, dict);
+    var chainView = null;
+    for (var ri = 0; ri < residues.length; ++ri) {
+      if (!fulfillsPredicates(residues[ri], residuePredicates)) {
+        continue;
+      }
+      if (!chainView) {
+        chainView = view.addChain(chain, false);
+      }
+      var residueView = null;
+      var atoms = residues[ri].atoms();
+      for (var ai = 0; ai < atoms.length; ++ai) {
+        if (!fulfillsPredicates(atoms[ai], atomPredicates)) {
+          continue;
+        }
+        if (!residueView) {
+          residueView = chainView.addResidue(residues[ri], false);
+        }
+        residueView.addAtom(atoms[ai]);
+      }
+    }
+  }
+  return view;
+}
+
+return {
+  dict : dictSelect
+}
+
+});
diff --git a/src/pv.js b/src/pv.js
new file mode 100644
index 0000000..a168543
--- /dev/null
+++ b/src/pv.js
@@ -0,0 +1,24 @@
+// Copyright (c) 2013-2015 Marco Biasini
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to
+// deal in the Software without restriction, including without limitation the
+// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+// sell copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+// DEALINGS IN THE SOFTWARE.
+
+
+define(['viewer'], function(viewer) {
+  return viewer;
+});
diff --git a/src/render.js b/src/render.js
index 62eb546..80f301d 100644
--- a/src/render.js
+++ b/src/render.js
@@ -18,42 +18,43 @@
 // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 // SOFTWARE.
 
-var render = (function() {
-  "use strict";
-
-  var exports = {};
-
-  var R = 0.7071;
-  var COIL_POINTS = [ -R, -R, 0, R, -R, 0, R, R, 0, -R, R, 0 ];
-
-  var HELIX_POINTS = [
-    -6 * R,
-    -1.0 * R,
-    0,
-    6 * R,
-    -1.0 * R,
-    0,
-    6 * R,
-    1.0 * R,
-    0,
-    -6 * R,
-    1.0 * R,
-    0
-  ];
-  var ARROW_POINTS = [
-    -10 * R,
-    -1.0 * R,
-    0,
-    10 * R,
-    -1.0 * R,
-    0,
-    10 * R,
-    1.0 * R,
-    0,
-    -10 * R,
-    1.0 * R,
-    0
-  ];
+define(['gl-matrix', 'geom', 'geom-builders', 'mesh-geom', 'line-geom', 
+        'vert-assoc', 'shade'], 
+       function(glMatrix, geom, geomBuilders, MeshGeom, LineGeom, 
+                vertAssoc, color) {
+"use strict";
+
+var vec3 = glMatrix.vec3;
+var vec4 = glMatrix.vec4;
+var mat3 = glMatrix.mat3;
+var mat4 = glMatrix.mat4;
+
+var TubeProfile = geomBuilders.TubeProfile;
+var ProtoSphere = geomBuilders.ProtoSphere;
+var ProtoCylinder = geomBuilders.ProtoCylinder;
+
+var TraceVertexAssoc = vertAssoc.TraceVertexAssoc;
+var AtomVertexAssoc = vertAssoc.AtomVertexAssoc;
+var interpolateColor = color.interpolateColor;
+
+var exports = {};
+
+var R = 0.7071;
+var COIL_POINTS = [ -R, -R, 0, R, -R, 0, R, R, 0, -R, R, 0 ];
+
+var HELIX_POINTS = [
+  -6 * R, -1.0 * R, 0,
+   6 * R, -1.0 * R, 0,
+   6 * R,  1.0 * R, 0,
+  -6 * R,  1.0 * R, 0
+];
+
+var ARROW_POINTS = [
+ -10 * R, -1.0 * R, 0,
+  10 * R, -1.0 * R, 0,
+  10 * R,  1.0 * R, 0,
+ -10 * R,  1.0 * R, 0
+];
 
 // performs an in-place smoothing over 3 consecutive positions.
 var smoothStrandInplace = (function() {
@@ -1036,8 +1037,4 @@ var _renderSingleTrace = (function() {
 
 
 return exports;
-})();
-
-if(typeof(exports) !== 'undefined') {
-  module.exports = render;
-}
+});
diff --git a/src/scene-node.js b/src/scene-node.js
new file mode 100644
index 0000000..e48989a
--- /dev/null
+++ b/src/scene-node.js
@@ -0,0 +1,86 @@
+// Copyright (c) 2013-2015 Marco Biasini
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to deal
+// in the Software without restriction, including without limitation the rights
+// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+// copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+// SOFTWARE.
+
+define(function() {
+
+"use strict";
+
+// A scene node holds a set of child nodes to be rendered on screen. Later on,
+// the SceneNode might grow additional functionality commonly found in a scene
+// graph, e.g. coordinate transformations.
+function SceneNode(gl) {
+  this._children = [];
+  this._visible = true;
+  this._name = name || '';
+  this._gl = gl;
+  this._order = 1;
+}
+
+
+SceneNode.prototype = {
+
+  order : function(order) {
+    if (order !== undefined) {
+      this._order = order;
+    }
+    return this._order;
+  },
+
+  add : function(node) {
+    this._children.push(node);
+  },
+
+  draw : function(cam, shaderCatalog, style, pass) {
+    for (var i = 0, e = this._children.length; i !== e; ++i) {
+      this._children[i].draw(cam, shaderCatalog, style, pass);
+    }
+  },
+
+  show : function() {
+    this._visible = true;
+  },
+
+  hide : function() {
+    this._visible = false;
+  },
+
+  name : function(name) {
+    if (name !== undefined) {
+      this._name = name;
+    }
+    return this._name;
+  },
+
+  destroy : function() {
+    for (var i = 0; i < this._children.length; ++i) {
+      this._children[i].destroy();
+    }
+  },
+
+  visible : function() {
+    return this._visible;
+  }
+};
+
+return SceneNode;
+
+});
+
+
diff --git a/src/scene.js b/src/scene.js
index 6e56343..4fa5ba0 100644
--- a/src/scene.js
+++ b/src/scene.js
@@ -807,51 +807,6 @@ ContinuousIdRange.prototype = {
   }
 };
 
-function UniqueObjectIdPool() {
-  this._objects = {};
-  this._unusedRangeStart = 0;
-  this._free = [];
-}
-
-UniqueObjectIdPool.prototype = {
-  getContinuousRange : function(num) {
-    // FIXME: keep the "free" list sorted, so we can binary search it
-    // for a good match
-    var bestIndex = -1;
-    var bestLength = null;
-    for (var i = 0; i < this._free.length; ++i) {
-      var free = this._free[i];
-      var length = free.length();
-      if (length >= num && (bestLength === null || length < bestLength)) {
-        bestLength = length;
-        bestIndex = i;
-      }
-    }
-    if (bestIndex !== -1) {
-      var result = this._free[bestIndex];
-      this._free.splice(bestIndex, 1);
-      return result;
-    }
-    var start = this._unusedRangeStart;
-    var end = start + num;
-    if (end > 65536) {
-      console.log('not enough free object ids.');
-      return null;
-    }
-    this._unusedRangeStart = end;
-    return new ContinuousIdRange(this, start, end);
-  },
-  recycle : function(range) {
-    for (var i = range._start; i < range._next; ++i) {
-      delete this._objects[i];
-    }
-    range._next = range._start;
-    this._free.push(range);
-  },
-  objectForId : function(id) {
-    return this._objects[id];
-  }
-};
 
 function OrientedBoundingBox(gl, center, halfExtents, 
                              float32Allocator, uint16Allocator) {
diff --git a/src/shade.js b/src/shade.js
index 151fcb1..1f46043 100644
--- a/src/shade.js
+++ b/src/shade.js
@@ -18,9 +18,14 @@
 // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 // SOFTWARE.
 
-(function(exports) {
+define(['gl-matrix'], function(glMatrix) {
+
 "use strict";
 
+var vec4 = glMatrix.vec4;
+var vec3 = glMatrix.vec3;
+
+var exports = {};
 exports.rgb = {};
 var rgb = exports.rgb;
 
@@ -209,11 +214,10 @@ ColorOp.prototype = {
   }
 };
 
-exports.color = {};
 
 exports.ColorOp = ColorOp;
 
-exports.color.uniform = function(color) {
+exports.uniform = function(color) {
   color = exports.forceRGB(color || 'white');
   return new ColorOp(function(atom, out, index) {
     out[index+0] = color[0];
@@ -255,7 +259,7 @@ var CPK_TABLE = {
  FE : [0.87, 0.47, 0.00]
 };
 
-exports.color.byElement = function() {
+exports.byElement = function() {
   return new ColorOp(function(atom, out, index) {
     var ele = atom.element();
     var color = CPK_TABLE[ele];
@@ -274,7 +278,7 @@ exports.color.byElement = function() {
   }, null, null);
 };
 
-exports.color.bySS = function() {
+exports.bySS = function() {
 
   return new ColorOp(function(atom, out, index) {
     switch (atom.residue().ss()) {
@@ -294,7 +298,7 @@ exports.color.bySS = function() {
   }, null, null);
 };
 
-exports.color.rainbow = function(grad) {
+exports.rainbow = function(grad) {
   if (!grad) {
     grad = gradient('rainbow');
   }
@@ -337,12 +341,12 @@ exports.color.rainbow = function(grad) {
   return colorFunc;
 };
 
-exports.color.ssSuccession = function(grad, coilColor) {
+exports.ssSuccession = function(grad, coilColor) {
   if (!grad) {
     grad = gradient('rainbow');
   }
   if (!coilColor) {
-    coilColor = forceRGB('lightgrey');
+    coilColor = exports.forceRGB('lightgrey');
   }
   var colorFunc = new ColorOp(function(a, out, index) {
     var idx = a.residue().index();
@@ -401,7 +405,7 @@ exports.color.ssSuccession = function(grad, coilColor) {
   return colorFunc;
 };
 
-exports.color.byChain = function(grad) {
+exports.byChain = function(grad) {
   if (!grad) {
     grad = gradient('rainbow');
   }
@@ -479,12 +483,12 @@ function colorByItemProp(propName, grad, range, iter, item) {
   );
 }
 
-exports.color.byAtomProp = function(propName, grad, range) {
+exports.byAtomProp = function(propName, grad, range) {
   return colorByItemProp(propName, grad, range, 'eachAtom', 
                          function(a) {return a;});
 };
 
-exports.color.byResidueProp = function(propName, grad, range) {
+exports.byResidueProp = function(propName, grad, range) {
   return colorByItemProp(propName, grad, range, 'eachResidue', 
                          function(a) {return a.residue();});
 };
@@ -517,7 +521,7 @@ exports.interpolateColor = function(colors, num) {
 
 
 // initialize gradients with default colors
-initGradients();
+exports.initGradients();
 
-return true;
-})(this);
+return exports;
+});
diff --git a/src/shaders.js b/src/shaders.js
index 6684dc1..e7f0e42 100644
--- a/src/shaders.js
+++ b/src/shaders.js
@@ -18,12 +18,7 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
 // DEALINGS IN THE SOFTWARE.
 
-(function(exports) {
-
-"use strict";
-
-exports.shaders = {};
-
+define({
 // NOTE: The shader code below use the placeholder ${PRECISION} variable 
 // for the shader precision. This values is replaced before compiling 
 // the shader program with highp on iOS and mediump on all other devices. 
@@ -31,7 +26,7 @@ exports.shaders = {};
 // with mediump, but some android devices do not support highp.
 
 // line fragment shader, essentially uses the vertColor and adds some fog.
-exports.shaders.LINES_FS = '\n\
+LINES_FS : '\n\
 precision ${PRECISION} float;\n\
 \n\
 varying vec4 vertColor;\n\
@@ -50,10 +45,10 @@ void main(void) {\n\
     gl_FragColor = mix(gl_FragColor, vec4(fogColor, gl_FragColor.w),\n\
                         fog_factor);\n\
   }\n\
-}';
+}',
 
 // hemilight fragment shader
-exports.shaders.HEMILIGHT_FS = '\n\
+HEMILIGHT_FS : '\n\
 precision ${PRECISION} float;\n\
 \n\
 varying vec4 vertColor;\n\
@@ -75,10 +70,10 @@ void main(void) {\n\
     gl_FragColor = mix(gl_FragColor, vec4(fogColor, gl_FragColor.w),\n\
                         fog_factor);\n\
   }\n\
-}';
+}',
 
 // hemilight vertex shader
-exports.shaders.HEMILIGHT_VS = '\n\
+HEMILIGHT_VS : '\n\
 attribute vec3 attrPos;\n\
 attribute vec4 attrColor;\n\
 attribute vec3 attrNormal;\n\
@@ -92,10 +87,10 @@ void main(void) {\n\
   vec4 n = (modelviewMat * vec4(attrNormal, 0.0));\n\
   vertNormal = n.xyz;\n\
   vertColor = attrColor;\n\
-}';
+}',
 
 // outline shader. mixes outlineColor with fogColor
-exports.shaders.OUTLINE_FS = '\n\
+OUTLINE_FS : '\n\
 precision ${PRECISION} float;\n\
 varying float vertAlpha;\n\
 \n\
@@ -114,11 +109,11 @@ void main() {\n\
     gl_FragColor = mix(gl_FragColor, vec4(fogColor, vertAlpha),\n\
                         fog_factor);\n\
   }\n\
-}';
+}',
 
 // outline vertex shader. Expands vertices along the (in-screen) xy
 // components of the normals.
-exports.shaders.OUTLINE_VS = '\n\
+OUTLINE_VS : '\n\
 precision ${PRECISION} float;\n\
 \n\
 attribute vec3 attrPos;\n\
@@ -135,9 +130,9 @@ void main(void) {\n\
   vec4 normal = modelviewMat * vec4(attrNormal, 0.0);\n\
   vertAlpha = attrColor.a;\n\
   gl_Position.xy += normal.xy*0.200;\n\
-}';
+}',
 
-exports.shaders.TEXT_VS = '\n\
+TEXT_VS : '\n\
 precision ${PRECISION} float;\n\
 \n\
 attribute vec3 attrCenter;\n\
@@ -154,9 +149,9 @@ void main() { \n\
   gl_Position = projectionMat * pos;\n\
   gl_Position.xy += vec2(width,height)*attrCorner*gl_Position.w; \n\
   vertTex = (attrCorner+abs(attrCorner))/(2.0*abs(attrCorner)); \n\
-}';
+}',
 
-exports.shaders.TEXT_FS = '\n\
+TEXT_FS : '\n\
 precision ${PRECISION} float;\n\
 \n\
 uniform mat4 projectionMat;\n\
@@ -169,9 +164,9 @@ void main() { \n\
   vec2 texCoord = vec2(vertTex.x*xScale, vertTex.y*yScale);\n\
   gl_FragColor = texture2D(sampler, texCoord);\n\
   if (gl_FragColor.a == 0.0) { discard; }\n\
-}';
+}',
 
-exports.shaders.SELECT_VS = '\n\
+SELECT_VS : '\n\
 precision ${PRECISION} float;\n\
 uniform mat4 projectionMat;\n\
 uniform mat4 modelviewMat;\n\
@@ -183,9 +178,9 @@ varying float objId;\n\
 void main(void) {\n\
   gl_Position = projectionMat * modelviewMat * vec4(attrPos, 1.0);\n\
   objId = attrObjId;\n\
-}';
+}',
 
-exports.shaders.SELECT_FS = '\n\
+SELECT_FS : '\n\
 precision ${PRECISION} float;\n\
 \n\
 varying float objId;\n\
@@ -204,5 +199,7 @@ void main(void) {\n\
   integralObjId/=256;\n\
   int blue = symId;\n\
   gl_FragColor = vec4(float(red), float(green), float(blue), 255.0)/255.0;\n\
-}';
-})(this);
+}'
+
+});
+
diff --git a/src/slab.js b/src/slab.js
index a09fedb..a97d308 100644
--- a/src/slab.js
+++ b/src/slab.js
@@ -18,7 +18,8 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 // DEALINGS IN THE SOFTWARE.
 
-(function(exports) {
+define(function() {
+
 "use strict";
 
 function Slab(near, far) {
@@ -60,8 +61,10 @@ AutoSlab.prototype.update = function(objects, cam) {
   return new Slab(newNear, newFar);
 };
 
-exports.FixedSlab = FixedSlab;
-exports.AutoSlab = AutoSlab;
-exports.Slab = Slab;
+return {
+  FixedSlab : FixedSlab,
+  AutoSlab : AutoSlab,
+  Slab : Slab
+};
 
-})(this);
+});
diff --git a/src/symmetry.js b/src/symmetry.js
index 930dad9..0da00be 100644
--- a/src/symmetry.js
+++ b/src/symmetry.js
@@ -18,7 +18,8 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
 // DEALINGS IN THE SOFTWARE.
 
-(function(exports) {
+define(function() {
+
 "use strict";
 
 // a list of rotation/translation operators to be applied to certain chains,
@@ -63,10 +64,11 @@ Assembly.prototype = {
   }
 };
 
-exports.SymGenerator = SymGenerator;
-exports.Assembly = Assembly;
+return {
+  SymGenerator : SymGenerator,
+  Assembly : Assembly
+};
 
-return true;
-})(this);
+});
 
 
diff --git a/src/tests/binary-search.js b/src/tests/binary-search.js
new file mode 100644
index 0000000..56641c3
--- /dev/null
+++ b/src/tests/binary-search.js
@@ -0,0 +1,71 @@
+define(['core'], function(core) {
+
+return function() {
+  test("binary search", function() {
+    var VALUES = [1,2,4,6,10,20,21,22,23];
+    strictEqual(0, core.binarySearch(VALUES, 1));
+    strictEqual(1, core.binarySearch(VALUES, 2));
+    strictEqual(2, core.binarySearch(VALUES, 4));
+    strictEqual(3, core.binarySearch(VALUES, 6));
+    strictEqual(4, core.binarySearch(VALUES, 10));
+    strictEqual(5, core.binarySearch(VALUES, 20));
+    strictEqual(6, core.binarySearch(VALUES, 21));
+    strictEqual(7, core.binarySearch(VALUES, 22));
+    strictEqual(8, core.binarySearch(VALUES, 23));
+    strictEqual(-1, core.binarySearch(VALUES, 25));
+    strictEqual(-1, core.binarySearch(VALUES, 0));
+    strictEqual(-1, core.binarySearch(VALUES, 3));
+  });
+
+  test("index of first larger equal than", function() {
+    var VALUES = [0, 1, 2, 4, 5, 5, 6, 7, 8];
+    strictEqual(core.indexFirstLargerEqualThan(VALUES, 0), 0);
+    strictEqual(core.indexFirstLargerEqualThan(VALUES, 1), 1);
+    strictEqual(core.indexFirstLargerEqualThan(VALUES, 2), 2);
+    strictEqual(core.indexFirstLargerEqualThan(VALUES, 3), 2);
+    strictEqual(core.indexFirstLargerEqualThan(VALUES, 4), 3);
+    strictEqual(core.indexFirstLargerEqualThan(VALUES, 5), 4);
+    strictEqual(core.indexFirstLargerEqualThan(VALUES, 6), 6);
+    strictEqual(core.indexFirstLargerEqualThan(VALUES, 7), 7);
+    strictEqual(core.indexFirstLargerEqualThan(VALUES, 8), 8);
+    strictEqual(core.indexFirstLargerEqualThan(VALUES, -1), -1);
+    strictEqual(core.indexFirstLargerEqualThan(VALUES, 9), 8);
+  });
+
+  test("index of last smaller than", function() {
+    var VALUES = [0, 1, 2, 4, 5, 5, 6, 7, 8];
+    strictEqual(core.indexLastSmallerThan(VALUES, 0), -1);
+    strictEqual(core.indexLastSmallerThan(VALUES, 1), 0);
+    strictEqual(core.indexLastSmallerThan(VALUES, 2), 1);
+    strictEqual(core.indexLastSmallerThan(VALUES, 3), 1);
+    strictEqual(core.indexLastSmallerThan(VALUES, 4), 2);
+    strictEqual(core.indexLastSmallerThan(VALUES, 5), 4);
+    strictEqual(core.indexLastSmallerThan(VALUES, 6), 5);
+    strictEqual(core.indexLastSmallerThan(VALUES, 7), 6);
+    strictEqual(core.indexLastSmallerThan(VALUES, 8), 7);
+    strictEqual(core.indexLastSmallerThan(VALUES, -1), -1);
+    strictEqual(core.indexLastSmallerThan(VALUES, -2), -1);
+    strictEqual(core.indexLastSmallerThan(VALUES, 9), 8);
+    strictEqual(core.indexLastSmallerThan(VALUES, 20), 8);
+  });
+
+  test("index of last smaller equal than", function() {
+    var VALUES = [0, 1, 2, 4, 5, 5, 6, 7, 8];
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, 0), 0);
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, 1), 1);
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, 2), 2);
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, 3), 2);
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, 4), 3);
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, 5), 5);
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, 6), 6);
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, 7), 7);
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, 8), 8);
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, -1), -1);
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, -2), -1);
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, -3), -1);
+    strictEqual(core.indexLastSmallerEqualThan(VALUES, 9), 8);
+  });
+
+};
+
+});
diff --git a/src/tests/colors.js b/src/tests/colors.js
new file mode 100644
index 0000000..4964705
--- /dev/null
+++ b/src/tests/colors.js
@@ -0,0 +1,29 @@
+
+define(['shade'], function(color) { return function() {
+
+function compareColor(lhs, rhs) {
+  strictEqual(lhs[0], rhs[0]);
+  strictEqual(lhs[1], rhs[1]);
+  strictEqual(lhs[2], rhs[2]);
+}
+test("force rgb from hex triplet", function() {
+  var red = [1.0, 0.0, 0.0];
+  compareColor([1.0, 0.0, 0.0], color.forceRGB('#f00'));
+  compareColor([1.0, 0.0, 0.0], color.forceRGB('#ff0000'));
+  compareColor([1.0, 1.0, 0.0], color.forceRGB('#ff0'));
+  compareColor([1.0, 1.0, 0.0], color.forceRGB('#ffff00'));
+});
+
+test("force rgb from rgb", function() {
+  var red = [1.0, 0.0, 0.0];
+  compareColor([1.0, 0.0, 0.0], color.forceRGB([1.0, 0.0, 0.0]));
+  compareColor([1.0, 1.0, 0.0], color.forceRGB([1.0, 1.0, 0.0]));
+});
+
+test("force rgb from color names", function() {
+  var red = [1.0, 0.0, 0.0];
+  compareColor([1.0, 0.0, 0.0], color.forceRGB('red'));
+  compareColor([1.0, 1.0, 0.0], color.forceRGB('yellow'));
+});
+
+};});
diff --git a/tests/mol-iterators.js b/src/tests/mol-iterators.js
similarity index 96%
rename from tests/mol-iterators.js
rename to src/tests/mol-iterators.js
index 536f597..4f04105 100644
--- a/tests/mol-iterators.js
+++ b/src/tests/mol-iterators.js
@@ -1,3 +1,6 @@
+define(['mol/all'], function(mol) {
+
+return function() {
 function makeSimpleMolecule() {
   var m = new mol.Mol();
   var chainA = m.addChain("A");
@@ -69,3 +72,6 @@ test("eachResidue breaks when returning false", function() {
     strictEqual(counter, stopAt);
   }
 });
+
+};
+});
diff --git a/tests/mol-select.js b/src/tests/mol-select.js
similarity index 90%
rename from tests/mol-select.js
rename to src/tests/mol-select.js
index 0486e2d..767fcf7 100644
--- a/tests/mol-select.js
+++ b/src/tests/mol-select.js
@@ -1,3 +1,5 @@
+define(['io'], function(io) { return function() {
+
 var SELECT_HETATM='\
 ATOM   3316  C   GLY B 214      24.173   7.911  -3.276  1.00 94.23           C\n\
 ATOM   3317  O   GLY B 214      24.730   8.496  -4.208  1.00 94.94           O\n\
@@ -11,11 +13,11 @@ END\n\
 '
 
 test('dict select select by hetatm flag', function(assert) {
-  var structure = io.pdb(HETATM);
+  var structure = io.pdb(SELECT_HETATM);
   var view = structure.select({ hetatm: true });
   assert.strictEqual(view.atomCount(), 3);
   view = structure.select({ hetatm: false });
   assert.strictEqual(view.atomCount(), 4);
 
+});};
 });
-
diff --git a/tests/pdb-io.js b/src/tests/pdb-io.js
similarity index 98%
rename from tests/pdb-io.js
rename to src/tests/pdb-io.js
index 14038ff..e07e0f8 100644
--- a/tests/pdb-io.js
+++ b/src/tests/pdb-io.js
@@ -1,9 +1,14 @@
+define(['gl-matrix', 'io'], function(glMatrix, io) { return function() {
+
+
+var mat4 = glMatrix.mat4;
 var MULTI_LINE_MT = [
   'REMARK 350 BIOMOLECULE: 1                 \n',
   'REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 55-MERIC       \n',
   'REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, \n',
   'REMARK 350                    AND CHAINS: J, K, L, M, N, O, P, Q, R, \n',
 ];
+
 test("parses remark 350 with multi-line chain definitions", function() {
   var reader = new io.Remark350Reader();
   for (var i = 0; i < MULTI_LINE_MT.length; ++i) {
@@ -149,3 +154,4 @@ test('sets HETATM flag', function(assert) {
 
 });
 
+};});
diff --git a/tests/viewer-render.js b/src/tests/viewer-render.js
similarity index 98%
rename from tests/viewer-render.js
rename to src/tests/viewer-render.js
index 46acab5..393c446 100644
--- a/tests/viewer-render.js
+++ b/src/tests/viewer-render.js
@@ -1,3 +1,5 @@
+define(['pv', 'io', 'shade'], function(pv, io, color) { return function() {
+
 var ALL_STYLES = [
   'cartoon', 'tube', 'lines', 'spheres', 'ballsAndSticks',
   'sline', 'trace', 'lineTrace'
@@ -148,6 +150,6 @@ test('renders custom meshes', function(assert) {
   viewer.destroy();
 });
 
-
+};});
 
 
diff --git a/src/touch.js b/src/touch.js
index 9dfd654..3e71733 100644
--- a/src/touch.js
+++ b/src/touch.js
@@ -18,15 +18,19 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
 // DEALINGS IN THE SOFTWARE.
 
-(function(exports) {
+define(['core'], function(core) {
 "use strict";
 
 function TouchHandler(element, viewer, cam) {
   this._element = element;
-  this._element.addEventListener('touchmove', bind(this, this._touchMove));
-  this._element.addEventListener('touchstart', bind(this, this._touchStart));
-  this._element.addEventListener('touchend', bind(this, this._touchEnd));
-  this._element.addEventListener('touchcancel', bind(this, this._touchEnd));
+  this._element.addEventListener('touchmove', 
+                                 core.bind(this, this._touchMove));
+  this._element.addEventListener('touchstart', 
+                                 core.bind(this, this._touchStart));
+  this._element.addEventListener('touchend', 
+                                 core.bind(this, this._touchEnd));
+  this._element.addEventListener('touchcancel', 
+                                 core.bind(this, this._touchEnd));
   this._touchState = {
     scale : 1.0,
     rotation : 0.0,
@@ -170,5 +174,5 @@ TouchHandler.prototype = {
   },
 };
 
-exports.TouchHandler = TouchHandler;
-})(this);
+return TouchHandler;
+});
diff --git a/src/trace.js b/src/trace.js
index e07a287..e6d6a17 100644
--- a/src/trace.js
+++ b/src/trace.js
@@ -19,15 +19,13 @@
 // DEALINGS IN THE SOFTWARE.
 
 
-(function(exports) {
+define(['gl-matrix', 'geom'], function(glMatrix, geom) {
 
 "use strict";
 
-function BackboneTrace() { this._trace = []; }
+var vec3 = glMatrix.vec3;
 
-if(typeof(exports) !== 'undefined') {
-  exports.BackboneTrace = BackboneTrace;
-}
+function BackboneTrace() { this._trace = []; }
 
 BackboneTrace.prototype = {
   push : function(residue) {
@@ -225,7 +223,10 @@ TraceSubset.prototype = {
   },
 };
 
-exports.TraceSubset = TraceSubset;
+return {
+  TraceSubset : TraceSubset,
+  BackboneTrace : BackboneTrace
+};
 
-})(this);
+});
 
diff --git a/src/unique-object-id-pool.js b/src/unique-object-id-pool.js
new file mode 100644
index 0000000..05b47be
--- /dev/null
+++ b/src/unique-object-id-pool.js
@@ -0,0 +1,99 @@
+// Copyright (c) 2013-2015 Marco Biasini
+//
+// Permission is hereby granted, free of charge, to any person obtaining a copy
+// of this software and associated documentation files (the "Software"), to
+// deal in the Software without restriction, including without limitation the
+// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
+// sell copies of the Software, and to permit persons to whom the Software is
+// furnished to do so, subject to the following conditions:
+//
+// The above copyright notice and this permission notice shall be included in
+// all copies or substantial portions of the Software.
+//
+// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+// FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+// DEALINGS IN THE SOFTWARE.
+
+define(function() {
+
+"use strict";
+
+// A continous range of object identifiers.
+function ContinuousIdRange(pool, start, end) {
+  this._pool = pool;
+  this._start = start;
+  this._next = start;
+  this._end = end;
+}
+
+ContinuousIdRange.prototype = {
+  nextId : function(obj) {
+    var id = this._next;
+    this._next++;
+    this._pool._objects[id] = obj;
+    return id;
+  },
+  recycle : function() {
+    this._pool.recycle(this);
+  },
+  length : function() {
+    return this._end - this._start;
+  }
+};
+
+// simple class that generates unique object identifiers. Identifiers are 
+// requested in sequential groups. 
+// FIXME: describe why!
+function UniqueObjectIdPool() {
+  this._objects = {};
+  this._unusedRangeStart = 0;
+  this._free = [];
+}
+
+UniqueObjectIdPool.prototype = {
+  getContinuousRange : function(num) {
+    // FIXME: keep the "free" list sorted, so we can binary search it
+    // for a good match
+    var bestIndex = -1;
+    var bestLength = null;
+    for (var i = 0; i < this._free.length; ++i) {
+      var free = this._free[i];
+      var length = free.length();
+      if (length >= num && (bestLength === null || length < bestLength)) {
+        bestLength = length;
+        bestIndex = i;
+      }
+    }
+    if (bestIndex !== -1) {
+      var result = this._free[bestIndex];
+      this._free.splice(bestIndex, 1);
+      return result;
+    }
+    var start = this._unusedRangeStart;
+    var end = start + num;
+    if (end > 65536) {
+      console.log('not enough free object ids.');
+      return null;
+    }
+    this._unusedRangeStart = end;
+    return new ContinuousIdRange(this, start, end);
+  },
+  recycle : function(range) {
+    for (var i = range._start; i < range._next; ++i) {
+      delete this._objects[i];
+    }
+    range._next = range._start;
+    this._free.push(range);
+  },
+  objectForId : function(id) {
+    return this._objects[id];
+  }
+};
+
+return UniqueObjectIdPool;
+
+});
diff --git a/src/vert-assoc.js b/src/vert-assoc.js
index 5451f72..41d13bd 100644
--- a/src/vert-assoc.js
+++ b/src/vert-assoc.js
@@ -18,6 +18,9 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
 // DEALINGS IN THE SOFTWARE.
 
+define(['shade'], function(color) {
+
+"use strict";
 
 // During recoloring of a render style, most of the vertex attributes, e.g.
 // normals and positions do not change. Only the color information for each
@@ -38,10 +41,6 @@ function AtomVertexAssoc(structure, callColoringBeginEnd) {
 
 }
 
-if(typeof(exports) !== 'undefined') {
-    exports.AtomVertexAssoc = AtomVertexAssoc;
-}
-
 AtomVertexAssoc.prototype = {
 
   addAssoc : function(atom, va, vertStart, vertEnd)  {
@@ -125,10 +124,6 @@ function TraceVertexAssoc(structure, interpolation, callColoringBeginEnd) {
   this._perResidueColors = {};
 }
 
-if(typeof(exports) !== 'undefined') {
-    exports.TraceVertexAssoc = TraceVertexAssoc;
-}
-
 TraceVertexAssoc.prototype = {
 
   setPerResidueColors : function(traceIndex, colors) {
@@ -168,7 +163,7 @@ TraceVertexAssoc.prototype = {
         index+=4;
       }
       if (this._interpolation > 1) {
-        colorData.push(interpolateColor(data, this._interpolation));
+        colorData.push(color.interpolateColor(data, this._interpolation));
       } else {
         colorData.push(data);
       }
@@ -232,7 +227,7 @@ TraceVertexAssoc.prototype = {
         index+=4;
       }
       if (this._interpolation > 1) {
-        colorData.push(interpolateColor(data, this._interpolation));
+        colorData.push(color.interpolateColor(data, this._interpolation));
       } else {
         colorData.push(data);
       }
@@ -252,3 +247,9 @@ TraceVertexAssoc.prototype = {
   }
 };
 
+return {
+  TraceVertexAssoc : TraceVertexAssoc,
+  AtomVertexAssoc : AtomVertexAssoc
+};
+
+});
diff --git a/src/vertex-array-base.js b/src/vertex-array-base.js
index bd74bf7..7e0cffe 100644
--- a/src/vertex-array-base.js
+++ b/src/vertex-array-base.js
@@ -17,9 +17,11 @@
 // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 // SOFTWARE.
-(function(exports) {
+
+define(['gl-matrix', 'geom'], function(glMatrix, geom) {
 "use strict";
 
+var vec3 = glMatrix.vec3;
 
 function VertexArrayBase(gl, numVerts, float32Allocator) {
   this._gl = gl;
@@ -156,6 +158,6 @@ VertexArrayBase.prototype = {
   })()
 };
 
-exports.VertexArrayBase = VertexArrayBase;
+return VertexArrayBase;
 
-})(this);
+});
diff --git a/src/vertex-array.js b/src/vertex-array.js
index 445663f..267441e 100644
--- a/src/vertex-array.js
+++ b/src/vertex-array.js
@@ -18,7 +18,8 @@
 // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 // SOFTWARE.
 
-(function(exports) {
+define(['core', 'vertex-array-base'], function(core, VertexArrayBase) {
+
 "use strict";
 
 // (unindexed) vertex array for line-based geometries
@@ -27,7 +28,7 @@ function VertexArray(gl, numVerts, float32Allocator)  {
   this._numLines = 0;
 }
 
-derive(VertexArray, VertexArrayBase, {
+core.derive(VertexArray, VertexArrayBase, {
 
   _FLOATS_PER_VERT : 8,
   _POS_OFFSET : 0,
@@ -36,8 +37,7 @@ derive(VertexArray, VertexArrayBase, {
 
   numVerts : function() { return this._numLines * 2; },
 
-  addLine : function(startPos, startColor, endPos, 
-                                          endColor, idOne, idTwo) {
+  addLine : function(startPos, startColor, endPos, endColor, idOne, idTwo) {
     var index = this._FLOATS_PER_VERT * this._numLines * 2;
     this._vertData[index++] = startPos[0];
     this._vertData[index++] = startPos[1];
@@ -102,9 +102,6 @@ derive(VertexArray, VertexArrayBase, {
   }
 });
 
+return VertexArray;
 
-
-exports.VertexArray = VertexArray;
-
-return true;
-})(this);
+});
diff --git a/src/viewer.js b/src/viewer.js
index 9f632f2..7a6e48e 100644
--- a/src/viewer.js
+++ b/src/viewer.js
@@ -18,7 +18,13 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 // DEALINGS IN THE SOFTWARE.
 
-var pv = (function(){
+
+define(['gl-matrix', 'shade', 'slab', 'unique-object-id-pool', 'core', 'framebuffer', 
+        'buffer-allocators', 'cam', 'shaders', 'touch', 'render', 'label',
+        'custom-mesh'], 
+       function(glMatrix, color, slab, UniqueObjectIdPool, core, 
+                FrameBuffer, PoolAllocator, Cam, shaders, 
+                TouchHandler, render, TextLabel, CustomMesh) {
 
 "use strict";
 
@@ -41,6 +47,7 @@ on how to unblock it.\
 </div>';
 
 
+var vec3 = glMatrix.vec3;
 
 function shouldUseHighPrecision() {
   // high precision for shaders is only required on iOS, all the other browsers 
@@ -81,7 +88,7 @@ function slabModeToStrategy(mode, options) {
     return new FixedSlab(options);
   }
   if (mode === 'auto') {
-    return new AutoSlab(options);
+    return new slab.AutoSlab(options);
   }
   return null;
 }
@@ -144,7 +151,8 @@ function PV(domElement, opts) {
       document.readyState === "interactive") {
     this._initPV();
   } else {
-    document.addEventListener('DOMContentLoaded', bind(this, this._initPV));
+    document.addEventListener('DOMContentLoaded', 
+                              core.bind(this, this._initPV));
   }
 }
 
@@ -166,7 +174,7 @@ PV.prototype = {
       antialias : opts.antialias,
       quality : optValue(opts, 'quality', 'low'),
       style : optValue(opts, 'style', 'hemilight'),
-      background : forceRGB(opts.background || 'white'),
+      background : color.forceRGB(opts.background || 'white'),
       slabMode : slabModeToStrategy(opts.slabMode),
       atomClick: opts.atomClicked || opts.atomClick || null,
       outline : optValue(opts, 'outline', true),
@@ -410,8 +418,8 @@ PV.prototype = {
 
     // get vertex attribute location for the shader once to
     // avoid repeated calls to getAttribLocation/getUniformLocation
-    var getAttribLoc = bind(gl, gl.getAttribLocation);
-    var getUniformLoc = bind(gl, gl.getUniformLocation);
+    var getAttribLoc = core.bind(gl, gl.getAttribLocation);
+    var getUniformLoc = core.bind(gl, gl.getUniformLocation);
     shaderProgram.posAttrib = getAttribLoc(shaderProgram, 'attrPos');
     shaderProgram.colorAttrib = getAttribLoc(shaderProgram, 'attrColor');
     shaderProgram.normalAttrib = getAttribLoc(shaderProgram, 'attrNormal');
@@ -462,23 +470,23 @@ PV.prototype = {
       select : this._initShader(shaders.SELECT_VS, shaders.SELECT_FS)
     };
 
-    this._boundDraw = bind(this, this._draw);
+    this._boundDraw = core.bind(this, this._draw);
 
-    this._mousePanListener = bind(this, this._mousePan);
-    this._mouseRotateListener = bind(this, this._mouseRotate);
-    this._mouseUpListener = bind(this, this._mouseUp);
+    this._mousePanListener = core.bind(this, this._mousePan);
+    this._mouseRotateListener = core.bind(this, this._mouseRotate);
+    this._mouseUpListener = core.bind(this, this._mouseUp);
 
     // Firefox responds to the wheel event, whereas other browsers listen to
     // the mousewheel event. Register different event handlers, depending on
     // what properties are available.
-    var addListener = bind(this._canvas, this._canvas.addEventListener);
+    var addListener = core.bind(this._canvas, this._canvas.addEventListener);
     if ('onwheel' in this._canvas) {
-      addListener('wheel', bind(this, this._mouseWheelFF), false);
+      addListener('wheel', core.bind(this, this._mouseWheelFF), false);
     } else {
-      addListener('mousewheel', bind(this, this._mouseWheel), false);
+      addListener('mousewheel', core.bind(this, this._mouseWheel), false);
     }
-    addListener('dblclick', bind(this, this._mouseDoubleClick), false);
-    addListener('mousedown', bind(this, this._mouseDown), false);
+    addListener('dblclick', core.bind(this, this._mouseDoubleClick), false);
+    addListener('mousedown', core.bind(this, this._mouseDown), false);
     this._touchHandler = new TouchHandler(this._canvas, this, this._cam);
 
     if (!this._initialized) {
@@ -659,7 +667,7 @@ PV.prototype = {
       this.listenerMap[eventName] = callbacks;
     }
     if (callback === 'center') {
-      callbacks.push(bind(this, this._centerOnClicked));
+      callbacks.push(core.bind(this, this._centerOnClicked));
     } else {
       callbacks.push(callback);
     }
@@ -781,7 +789,7 @@ PV.prototype = {
   },
 
   _handleStandardOptions : function(opts) {
-    opts = copy(opts);
+    opts = core.copy(opts);
     opts.float32Allocator = this._float32Allocator;
     opts.uint16Allocator = this._uint16Allocator;
     opts.idPool = this._objectIdManager;
@@ -911,7 +919,7 @@ PV.prototype = {
   fitTo : function(what, slabMode) {
     var axes = this._cam.mainAxes();
     slabMode = slabMode || this._options.slabMode;
-    var intervals = [ new Range(), new Range(), new Range() ];
+    var intervals = [ new core.Range(), new core.Range(), new core.Range() ];
     if (what instanceof SceneNode) {
       what.updateProjectionIntervals(axes[0], axes[1], axes[2], intervals[0],
                                     intervals[1], intervals[2]);
@@ -962,7 +970,7 @@ PV.prototype = {
   // adapt the zoom level to fit the viewport to all visible objects.
   autoZoom : function() {
     var axes = this._cam.mainAxes();
-    var intervals = [ new Range(), new Range(), new Range() ];
+    var intervals = [ new core.Range(), new core.Range(), new core.Range() ];
     this.forEach(function(obj) {
       if (!obj.visible()) {
         return;
@@ -1156,8 +1164,4 @@ return {
   isWebGLSupported : isWebGLSupported
 };
 
-})();
-
-if(typeof(exports) !== 'undefined') {
-    module.exports = pv;
-}
+});
diff --git a/src/viewpoint.js b/src/viewpoint.js
index d1d61dc..ffaf48d 100644
--- a/src/viewpoint.js
+++ b/src/viewpoint.js
@@ -18,9 +18,13 @@
 // FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER 
 // DEALINGS IN THE SOFTWARE.
 
-(function(exports) {
+define(['gl-matrix', 'geom'], function(glMatrix, geom) {
+
 "use strict";
 
+var vec3 = glMatrix.vec3;
+var mat3 = glMatrix.mat3;
+
 var calculateCovariance = (function() {
   var center = vec3.create();
   var shiftedPos = vec3.create();
@@ -100,8 +104,8 @@ var principalAxes = (function() {
   };
 })();
 
-exports.principalAxes = principalAxes;
-
-return true;
+return {
+  principalAxes :principalAxes
+}
 
-})(this);
+});
diff --git a/tests/all.html b/tests/all.html
index e4603e1..4a11ce2 100644
--- a/tests/all.html
+++ b/tests/all.html
@@ -26,40 +26,6 @@
   <div id="viewer"></div>
 </td>
 </tr></table>
-  <script src="/js/qunit.js"></script>
-  <script src='/js/blanket.min.js'></script>
-  <script src="/tests/assertions.js"></script>
-  <script src='/src/gl-matrix.js'></script>
-  <script src='/src/core.js' data-cover></script>
-  <script src='/src/geom.js' data-cover></script>
-  <script src='/src/trace.js' data-cover></script>
-  <script src='/src/symmetry.js' data-cover></script>
-  <script src='/src/mol.js' data-cover></script>
-  <script src='/src/io.js' data-cover></script>
-  <script src='/src/vert-assoc.js' data-cover></script>
-  <script src='/src/buffer-allocators.js' data-cover></script>
-  <script src='/src/vertex-array-base.js' data-cover></script>
-  <script src='/src/indexed-vertex-array.js' data-cover></script>
-  <script src='/src/vertex-array.js' data-cover></script>
-  <script src='/src/chain-data.js' data-cover></script>
-  <script src='/src/geom-builders.js' data-cover></script>
-  <script src='/src/scene.js' data-cover></script>
-  <script src='/src/render.js' data-cover></script>
-  <script src='/src/shade.js' data-cover></script>
-  <script src='/src/cam.js' data-cover></script>
-  <script src='/src/shaders.js' data-cover></script>
-  <script src='/src/framebuffer.js' data-cover></script>
-  <script src='/src/slab.js' data-cover></script>
-  <script src='/src/animation.js' data-cover></script>
-  <script src='/src/touch.js' data-cover></script>
-  <script src='/src/custom-mesh.js' data-cover></script>
-  <script src='/src/viewer.js' data-cover></script>
-  <script src='/src/viewpoint.js' data-cover></script>
-  <script src="/tests/binary-search.js"></script>
-  <script src="/tests/mol-iterators.js"></script>
-  <script src="/tests/colors.js"></script>
-  <script src="/tests/pdb-io.js"></script>
-  <script src="/tests/viewer-render.js"></script>
-  <script src="/tests/mol-select.js"></script>
+  <script data-main='all' src='/js/require.js'></script>
 </body>
 </html
diff --git a/tests/all.js b/tests/all.js
new file mode 100644
index 0000000..2de50f0
--- /dev/null
+++ b/tests/all.js
@@ -0,0 +1,78 @@
+"use strict";
+
+function addCustomAssertions(QUnit) {
+  // contains a few assertions we use for testing
+  QUnit.assert.almostEqual = function(actual, expected, epsilon, message) {
+    epsilon = epsilon || 0.000001;
+    var passes = Math.abs(actual -expected) < epsilon;
+    QUnit.push(passes, actual, expected, message);
+  }
+
+  QUnit.assert.mat4Equal = function(actual, expected, epsilon, message) {
+    for (var i = 0; i < 16; ++i) {
+      QUnit.assert.almostEqual(actual[i], expected[i], epsilon, message);
+    }
+  }
+
+  QUnit.assert.mat3Equal = function(actual, expected, epsilon, message) {
+    for (var i = 0; i < 9; ++i) {
+      QUnit.assert.almostEqual(actual[i], expected[i], epsilon, message);
+    }
+  }
+
+  QUnit.assert.vec3Equal = function(actual, expected, epsilon, message) {
+    for (var i = 0; i < 3; ++i) {
+      QUnit.assert.almostEqual(actual[i], expected[i], epsilon, message);
+    }
+  }
+
+  QUnit.assert.vec2Equal = function(actual, expected, epsilon, message) {
+    for (var i = 0; i < 2; ++i) {
+      QUnit.assert.almostEqual(actual[i], expected[i], epsilon, message);
+    }
+  }
+
+  QUnit.assert.vec4Equal = function(actual, expected, epsilon, message) {
+    for (var i = 0; i < 4; ++i) {
+      QUnit.assert.almostEqual(actual[i], expected[i], epsilon, message);
+    }
+  }
+}
+
+require.config({
+    baseUrl : '/src/',
+    paths: {
+        'QUnit': '/js/qunit'
+    },
+    shim: {
+       'QUnit': {
+           exports: 'QUnit',
+           init: function() {
+               QUnit.config.autoload = false;
+               QUnit.config.autostart = false;
+               addCustomAssertions(QUnit);
+           }
+       } 
+    }
+});
+
+var ARGS = [
+  'QUnit',
+  'tests/binary-search',
+  'tests/mol-iterators',
+  'tests/mol-select',
+  'tests/viewer-render',
+  'tests/pdb-io',
+  'tests/colors',
+];
+
+// require the unit tests.
+require(ARGS, function(QUnit) {
+    for (var i = 1; i < arguments.length; ++i) {
+      console.log(i);
+      arguments[i]();
+    }
+    QUnit.load();
+    QUnit.start();
+  }
+);
diff --git a/tests/binary-search.js b/tests/binary-search.js
deleted file mode 100644
index 14c7e93..0000000
--- a/tests/binary-search.js
+++ /dev/null
@@ -1,64 +0,0 @@
-test("binary search", function() {
-  var VALUES = [1,2,4,6,10,20,21,22,23];
-  strictEqual(0, binarySearch(VALUES, 1));
-  strictEqual(1, binarySearch(VALUES, 2));
-  strictEqual(2, binarySearch(VALUES, 4));
-  strictEqual(3, binarySearch(VALUES, 6));
-  strictEqual(4, binarySearch(VALUES, 10));
-  strictEqual(5, binarySearch(VALUES, 20));
-  strictEqual(6, binarySearch(VALUES, 21));
-  strictEqual(7, binarySearch(VALUES, 22));
-  strictEqual(8, binarySearch(VALUES, 23));
-  strictEqual(-1, binarySearch(VALUES, 25));
-  strictEqual(-1, binarySearch(VALUES, 0));
-  strictEqual(-1, binarySearch(VALUES, 3));
-});
-
-test("index of first larger equal than", function() {
-  var VALUES = [0, 1, 2, 4, 5, 5, 6, 7, 8];
-  strictEqual(indexFirstLargerEqualThan(VALUES, 0), 0);
-  strictEqual(indexFirstLargerEqualThan(VALUES, 1), 1);
-  strictEqual(indexFirstLargerEqualThan(VALUES, 2), 2);
-  strictEqual(indexFirstLargerEqualThan(VALUES, 3), 2);
-  strictEqual(indexFirstLargerEqualThan(VALUES, 4), 3);
-  strictEqual(indexFirstLargerEqualThan(VALUES, 5), 4);
-  strictEqual(indexFirstLargerEqualThan(VALUES, 6), 6);
-  strictEqual(indexFirstLargerEqualThan(VALUES, 7), 7);
-  strictEqual(indexFirstLargerEqualThan(VALUES, 8), 8);
-  strictEqual(indexFirstLargerEqualThan(VALUES, -1), -1);
-  strictEqual(indexFirstLargerEqualThan(VALUES, 9), 8);
-});
-
-test("index of last smaller than", function() {
-  var VALUES = [0, 1, 2, 4, 5, 5, 6, 7, 8];
-  strictEqual(indexLastSmallerThan(VALUES, 0), -1);
-  strictEqual(indexLastSmallerThan(VALUES, 1), 0);
-  strictEqual(indexLastSmallerThan(VALUES, 2), 1);
-  strictEqual(indexLastSmallerThan(VALUES, 3), 1);
-  strictEqual(indexLastSmallerThan(VALUES, 4), 2);
-  strictEqual(indexLastSmallerThan(VALUES, 5), 4);
-  strictEqual(indexLastSmallerThan(VALUES, 6), 5);
-  strictEqual(indexLastSmallerThan(VALUES, 7), 6);
-  strictEqual(indexLastSmallerThan(VALUES, 8), 7);
-  strictEqual(indexLastSmallerThan(VALUES, -1), -1);
-  strictEqual(indexLastSmallerThan(VALUES, -2), -1);
-  strictEqual(indexLastSmallerThan(VALUES, 9), 8);
-  strictEqual(indexLastSmallerThan(VALUES, 20), 8);
-});
-
-test("index of last smaller equal than", function() {
-  var VALUES = [0, 1, 2, 4, 5, 5, 6, 7, 8];
-  strictEqual(indexLastSmallerEqualThan(VALUES, 0), 0);
-  strictEqual(indexLastSmallerEqualThan(VALUES, 1), 1);
-  strictEqual(indexLastSmallerEqualThan(VALUES, 2), 2);
-  strictEqual(indexLastSmallerEqualThan(VALUES, 3), 2);
-  strictEqual(indexLastSmallerEqualThan(VALUES, 4), 3);
-  strictEqual(indexLastSmallerEqualThan(VALUES, 5), 5);
-  strictEqual(indexLastSmallerEqualThan(VALUES, 6), 6);
-  strictEqual(indexLastSmallerEqualThan(VALUES, 7), 7);
-  strictEqual(indexLastSmallerEqualThan(VALUES, 8), 8);
-  strictEqual(indexLastSmallerEqualThan(VALUES, -1), -1);
-  strictEqual(indexLastSmallerEqualThan(VALUES, -2), -1);
-  strictEqual(indexLastSmallerEqualThan(VALUES, -3), -1);
-  strictEqual(indexLastSmallerEqualThan(VALUES, 9), 8);
-});
diff --git a/tests/colors.js b/tests/colors.js
deleted file mode 100644
index 9d68aa1..0000000
--- a/tests/colors.js
+++ /dev/null
@@ -1,25 +0,0 @@
-function compareColor(lhs, rhs) {
-  strictEqual(lhs[0], rhs[0]);
-  strictEqual(lhs[1], rhs[1]);
-  strictEqual(lhs[2], rhs[2]);
-}
-test("force rgb from hex triplet", function() {
-  var red = [1.0, 0.0, 0.0];
-  compareColor([1.0, 0.0, 0.0], forceRGB('#f00'));
-  compareColor([1.0, 0.0, 0.0], forceRGB('#ff0000'));
-  compareColor([1.0, 1.0, 0.0], forceRGB('#ff0'));
-  compareColor([1.0, 1.0, 0.0], forceRGB('#ffff00'));
-});
-
-test("force rgb from rgb", function() {
-  var red = [1.0, 0.0, 0.0];
-  compareColor([1.0, 0.0, 0.0], forceRGB([1.0, 0.0, 0.0]));
-  compareColor([1.0, 1.0, 0.0], forceRGB([1.0, 1.0, 0.0]));
-});
-
-test("force rgb from color names", function() {
-  var red = [1.0, 0.0, 0.0];
-  compareColor([1.0, 0.0, 0.0], forceRGB('red'));
-  compareColor([1.0, 1.0, 0.0], forceRGB('yellow'));
-});
-