tag flexmol

JavaScript for Cheminformatics: Using the Prototype Framework 1

Posted by Rich Apodaca Tue, 26 Aug 2008 14:01:00 GMT

If you want to do the kind of cheminformatics that involves manipulating atoms, bonds, and molecules, object-oriented programming works well as a development paradigm. Although perhaps not readily apparent, JavaScript offers everything needed to create object-oriented models just as intricate at those written in languages like C++ and Java. This article discusses one approach that makes use of the Prototype Framework.

About Prototype

Prototype is a set of extensions to the JavaScript language that make developing in it less painful. Some of the extensions relate to DOM manipulation. Other have to do with the way Strings and Arrays behave. For the purposes of this article, we'll be using Prototype's syntax support for classes and inheritance.

Atoms, Bonds, and Molecules

To start, we'll need classes that define the basic behavior of atoms, bonds, and molecules. Although we may ultimately need to consider issues such as multicentered bonding, for now, we'll stick to a simplified view of chemistry that has bonds connecting two and only two atoms.

Creating the Classes

We could use JavaScript's built-in method for creating objects from class-like structures, but Prototype's approach is cleaner.

In the following library, we define a Molecule as a collection of Atoms and Bonds with useful relationships:

var Molecule = Class.create({
  initialize: function(){
    this.atoms = [];
    this.bonds = [];
  },

  addAtom: function(label){
    var atom = new Atom(label);

    this.atoms.push(atom);

    return atom;
  },

  connect: function(sourceAtom, targetAtom, bondType){
    var bond = new Bond(sourceAtom, targetAtom, bondType);

    sourceAtom.neighbors.push(targetAtom);
    sourceAtom.bonds.push(bond);
    targetAtom.neighbors.push(sourceAtom);
    targetAtom.bonds.push(bond);

    this.bonds.push(bond);

    return bond;
  }
});

var Atom = Class.create({
  initialize: function(label){
    this.label = label;
    this.neighbors = [];
    this.bonds = [];
  }
});

var Bond= Class.create({
  initialize: function(source, target, type){
    this.source = source;
    this.target = target;
    this.type = type;
  },

  getMate: function(atom){
    if (atom == this.source) return this.target;
    if (atom == this.target) return this.source;

    return null;
  },

  contains: function(atom){
    return (atom == this.source || atom == this.target);
  }
});

Testing the Library

We can test the library interactively by saving it in a file called chem.js and creating some simple HTML:

<html>
  <head>
    <script type="text/javascript" src="prototype.js"></script>
    <script type="text/javascript" src="chem.js"></script>
  </head>
  <body></body>
</html>

We can then use the Firebug console to test the library interactively:

>>> m = new Molecule();
Object atoms=[0] bonds=[0]
>>> c = m.addAtom("C");
Object label=C neighbors=[0] bonds=[0]
>>>n = m.addAtom("N");
Object label=N neighbors=[0] bonds=[0]
>>> m.connect(c, n, 3);
>>> c.neighbors.size()
1

Conclusions

Although the cheminformatics library discussed here is far from being useful, it's not difficult to see how to extend it. Prototype offers a several possibilities for doing so.

Posted in Tools
Tags atom, bond, flexmol, javascript, molecule, prototype
Meta 1 comment, permalink, rss, atom

Extending InChI Stereochemistry 6

Posted by Rich Apodaca Wed, 09 Jul 2008 10:18:00 GMT

As covered by Reuters and many other wire services, ArtusLabs and Boston University's CMLD have teamed up to extend InChI's stereochemistry support:

DURHAM, N.C.--(Business Wire)-- ArtusLabs, Inc., a leading provider of life science software tools and data management solutions, has entered into a partnership with Boston University's Center for Chemical Methodology and Library Development (CMLD) to develop a way to standardize and expand the way in which stereochemistry, and ultimately a three-dimensional structures, are represented in the International Chemical Identifier (InChI(TM)).

With the increasing use of molecules containing axial chirality , planar chirality and other forms of non-tetrahedral stereogenicity in chemistry, the move by ArtusLabs and CMLD could be significant.

Put simply, the ability of cheminformatics to represent certain kinds of compounds has fallen way behind the ability of chemistry to make them. While molecules once considered mere oddities 30 years ago continue to pour into corporate compound collections, laboratory notebooks, and product catalogs, cheminformatics has been stuck with a form of molecular representation that hasn't changed significantly in several decades.

InChI isn't alone. All three of the most widely-used molecular representation systems now in use (Molfile, SMILES, and CML) suffer from fundamental limitations in representing axial chirality, planar chirality, and multicenter bonding.

The kind of work being undertaken by ArtusLabs and CMLD is essential if cheminformatics is to continue to keep pace with new developments in chemistry.