Rubidium: Cheminformatics for Ruby

Project Home Page

RubyForge Project

DESCRIPTION

Rubidium is a full-featured cheminformatics scripting environment for Ruby. It provides a clean, well-documented interface to the best open source cheminformatics software.

Dependencies

• JRuby 1.0.0

Download

Rubidium can be downloaded from RubyForge

Installation

$ jruby -S gem install rbtk

Examples

Convert Benzene SMILES into InChI

require 'rubidium/lang'

c = Rubidium::Converter.new

c.set_formats 'smi', 'inchi'
c.convert 'c1ccccc1' => "InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H"

Create a CDK molecule from a SMILES string and count its atoms.

require 'cdk/lang'

r = CDK::SmilesReader.new
mol = r.read 'c1ccccc1'

mol.atom_count # => 6

Authors

Copyright © 2007 Richard L. Apodaca

Acknowledgments

This library combines capabilities from a variety of open source projects:

• Chemistry Development Kit, distributed under the GNU Lesser GPL

Many thanks to those contributing to these projects.

Rubidium was made possible with the support of Metamolecular, LLC.

License

This library is distributed under the MIT License. Please see the LICENSE file for more details.