ChemRuby - Cheminformatics Ruby

ChemRuby is a framework for developing cheminformatics applications in Ruby. It will let you retrieve chemical information from variety of data sources in various formats (such as MDL mol, SMILES etc.), fast substructure search based on graph theory, draw a chemical structure in various graphics formats (such as PDF, PNG etc.), and calculate a number of chemical properties.

FOR MORE INFORMATION

ChemRuby’s official website is at ((<URL:www.chemruby.org/>)). You will find links to the related resouces including downloads, Wiki documentations etc. in the top page.

* ((<URL:http://www.chemruby.org/>))

WHERE TO OBTAIN

— WWW

The releases can be obtained at ChemRuby website.

* ((<URL:http://www.chemruby.org/>))

— RubyGems

((<RubyGems|URL:rubyforge.org/projects/rubygems/>)) version of the ChemRuby package is also available for easy installation.

* ((<URL:http://rubyforge.org/projects/chemruby/>))

REQUIREMENTS

• Ruby 1.8.2 or later – ((<URL:www.ruby-lang.org/>))

OPTIONAL REQUIREMENTS

Some optional libraries can be utilized to extend ChemRuby’s functionality. If your needs meets the following conditions, install them from the “Ruby Application Archive” at ((<URL:raa.ruby-lang.org/>)).

For outputting png and jpeg images:

* [RAA:rmagick]

For testing and developing ChemRuby:

* [RAA:rake]

INSTALL

In the chemruby source directory (such as chemruby-x.x.x/), run install.rb as follows:

% ruby setup.rb config
% ruby setup.rb setup
% su
# ruby setup.rb install

If your operating system supports ‘sudo’ command (such as Mac OS X), try the following procedure instead of the above.

% ruby setup.rb config
% ruby setup.rb setup
% sudo ruby setup.rb install

You can run tests by

% rake test

and run

% rake

for more details.

USAGE

You can load all ChemRuby classes just by requiring ‘chem.rb’. All the ChemRuby classes and modules are located under the module name ‘Chem’ to separate the name space.

#!/usr/bin/env ruby
require 'chem'

— RubyGems

In RubyGems, you need to load ‘rubygems’ library before using ‘chem’.

#!/usr/bin/env ruby
require 'rubygems'
require_gem 'chem'

Credits

• GOTO Naohisa, KATAYAMA Toshiaki and NAKAO Mitsuteru (alphabetical order) who are developers of BioRuby, led the design of ChemRuby.

• gSpan parser and PubChem search from KADOWAKI masashi.

LICENSE

ChemRuby can be freely distributed under the Ruby’s license. Note that, setup.rb included in the ChemRuby package comes from <RAA:setup> developed by Minero Aoki.

License of This README file can be also distributed under the Ruby’s license.

Copyright (C) 2006 TANAKA   Nobuya   <tanaka@chemruby.org>
                   KATAYAMA Toshiaki <k@bioruby.org>

CONTACT

Current staffs of the ChemRuby project can be reached by sending e-mail to <staff@chemruby.org>.