Open Babel Binding for Node.js

Open Babel is a chemical toolbox designed to speak the many languages of chemical data written in C++. Now you can use the Open Babel features in node.js !

Contents

• Contents
• Installation
  • Linux
  • OS X
• Usage
  • Conversion
    • Read chemical file formats
    • Write chemical file formats
  • ForceField
    • Energy calculation
    • Conformers search
    • Atom types

Installation

Linux

First of all you should install openbabel with header files.

sudo apt-get install libopenbabel-dev

Then you can easily install this package using npm

npm install openbabel

OS X

Install openbabel using brew

brew install open-babel
npm install openbabel

Usage

Check the Documentation API for more details.

Use the openbabel module in your project.

var ob = require('openbabel');

Conversion

Read chemical file formats

Create an instance of ob.Conversion :

var conversion = new ob.Conversion();
var mol = conversion.setInFormat('smiles').read('C1CCCC1');
console.log(mol.atomsCount);

And you can use fs to read chimcal data from files :

var fs = require('fs');
 
var data = readFileSync('methane.smiles');
var conversion = new ob.Conversion();
var mol = conversion.setInFormat('smiles').read(data);
console.log(mol.atomsCount);

Write chemical file formats

Use an ob.Conversion instance :

var str = conversion.setOutFormat('mol').write(mol);
console.log(str);

And also you can export it as a file :

var str = conversion.setOutFormat('mol').write();
fs.writeFileSync('methane.mol', str);

ForceField

Energy Calculation

Create an instance of ob.Conversion using The ob.Conversion.findForceField factory :

var ff = ob.Conversion.findForceField('mmff94');
ff.setup(mol);
console.log(ff.energy);

Conformers search

Call one of systematicRotorSearch, randomRotorSearch, weightedRotorSearch. (Read more in API)

console.log(ff.energy); // Before getting conformer
ff.systematicRotorSearch();
console.log(ff.energy); // After getting conformer

Atom types

You can get data which is set for an atom by calling getData method such as FFAtomType.

ff.prepareAtomTypes();
console.log(mol.atoms[0].getData('FFAtomType'));