Rubidium: Cheminformatics for Ruby

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

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

Extract field named ‘foo’ from an SD File with line numbers.

  require 'rubidium/sdf'

  p=Rubidium::SDF::Parser.new File.new('path/to/sdfile.sdf')

  p.each_with_line_number do |entry, line|
    puts "Entry field 'foo' at line number #{line}: #{entry['foo']}"
  end

Sample Data

For convenience, sample data files can be found at:

rubyforge.org/frs/?group_id=4671

Authors

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 and Collaborative Drug Discovery

Copyright

License

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

README