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
Installation
Linux
First of all you should install openbabel with header files.
sudo apt-get install libopenbabel-devThen you can easily install this package using npm
npm install openbabelOS X
Install openbabel using brew
brew install open-babel
npm install openbabelUsage
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 conformerAtom 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'));
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