ChemJS is a bare-bones Chemistry framework built on top of the GraphJS framework. ChemJS uses GraphJS to accomplish low-level representation and search algorithms. ChemJS is intended to be HTML5 WebWorker-compatible and NodeJS-compatible. Algorithms support WebCL computing.

This project was inspired by the ChemDoodle WebComponents project from iChemLabs. ChemJS is a re-purposed version (written from the ground up) designed for more bare-bones, DOM-independent performance with molecular simulation in mind.

ChemJS is currently a work in progress and will share concurrent development with GraphJS, ChemJS, DockJS, and the Social Docking Project.

Step 1: Download the source library (full or minified)

git clone git://github.com/ericjang/chemJS

Step 2: Include the source script in your html, your WebWorker, or NodeJS application.

Step 3: Create and Manipulate Molecules!

var benzene = ChemJS.createMolecule();

ChemJS
└─┬ molecules
  ├── atoms
  ├── bonds
  ├── functional groups (optional)
  └── rings (optional)

The ChemJS object provides the highest level scope.

//example:
var foo = ChemJS.createMolecule();
var bar = ChemJS.createMolecule();
ChemJS.molecules;//returns [foo,bar]

• createMolecule(): creates a new molecule object and appends it to the molecules Array.
• readMOL(string): reads in a MOL file and constructs a molecule.

There are several ways to represent the graph abstract data type. Each vertex stores its incident edges, and each edge stores its incident vertices.

//more code goes here

//more code goes here

//example of DockJS extending ChemJS