https://github.com/ericjang/dockjs
Molecular Docking framework built on top of ChemJS
https://github.com/ericjang/dockjs
Last synced: 9 months ago
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Molecular Docking framework built on top of ChemJS
- Host: GitHub
- URL: https://github.com/ericjang/dockjs
- Owner: ericjang
- Created: 2012-05-26T19:09:45.000Z (about 14 years ago)
- Default Branch: master
- Last Pushed: 2012-08-02T15:57:12.000Z (almost 14 years ago)
- Last Synced: 2024-12-26T20:42:54.360Z (over 1 year ago)
- Language: JavaScript
- Size: 93.8 KB
- Stars: 1
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# DockJS
DockJS is the underlying code for the next revision of the Social Docking project.
DockJS is currently a work in progress and development will commence after the ChemJS project has been finished.
## Features
- GPU computing via WebCL
- Works in embedded HTML, HTML5 Web Workers, NodeJS
## Usage
Step 1: Download the source library (full or minified)
```bash
git clone git://github.com/ericjang/DockJS
```
Step 2: Include the source script in your html, your WebWorker, or NodeJS application. Make sure that GraphJS and ChemJS (dependencies) are imported beforehand.
```html
```
Step 3: Set up simulation
```JavaScript
var docking_job = new DockJS.simulation({
'ligandOptions': { molecule : caffeine },
'targetOptions': { molecule: adenosineReceptor },
});
```
Step 4: Run the simulation!
```JavaScript
var result = docking_job.start(); //returns a 'result' object
/**
result;
{
'status':'completed',//'aborted'
'optimal ligand pose': {
ligand : Molecule Obj,//ligand molecule with optimal atom positions
receptor : Molecule Obj//receptor molecule with optimal atom positions
}
'score':-1000,//in kJ/mol
'simulationTime': Time difference
}
*/
```
## API
DockJS is designed in a modular fashion, enabling scientists to implement their own algorithms & extend DockJS with minimal effort.
### Simulations and Experiments
In DockJS, a 'simulation' is the simulated interaction between ONE ligand and ONE receptor. An 'experiment' consists of multiple simulations.
See the ChemJS framework on how chemicals are represented.