CDK, the Ruby Way: RCDK-0.2.0

Ruby Chemistry Development Kit (RCDK) version 0.2.0 is now available. This version adds built-in support for Structure-CDK, a 2-D rendering framework. Simplifying the use of this library is a convenience layer enabling many common tasks to be accomplished with a single line of Ruby code.

Installing RCDK-0.2.0 is simple. From the command line (as root):

sudo gem install rcdk

Be prepared for a bit of a wait as the large RCDK RubyGem downloads and is installed.

If RCDK-0.1.0 is already installed on your system, version 0.2.0 can peacefully co-exist with it. Ruby will automatically load the most recent version of RCDK, and you can dynamically load the earlier version in your own code. If you'd like to uninstall RCDK-0.1.0 anyway, use the following (also as root):

sudo gem uninstall rcdk

Follow the menu to uninstall RCDK-0.1.0 and you're done.

If you haven't done so already, there is one bit of additional configuration. You'll need to update your LD_LIBRARY_PATH to point to the location of your system's native Java libraries. On Linux with Sun's JDK, this can be done with the following:

export LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/i386:$LD_LIBRARY_PATH

This assumes the JAVA_HOME was already set. If not, it will need to point to your systems Java installation directory.

The whole process can be automated by including the above line at the end of your .bash_profile file (or equivalent).

As a simple demonstration, let's say you'd like to depict the 2-D structure encoded by a SMILES string as a 200x200 pixel PNG image. With RCDK-0.2.0, this can be done with the following Ruby code (which can be entered interactively via irb):

require 'rubygems'
require_gem 'rcdk'
require 'util'

smiles = 'Oc1ccccc1' #phenol
RCDK::Util::Image.smiles_to_png(smiles, 'phenol.png', 200, 200)

This code creates phenol.png in your current directory:

Of course, there's much more to RCDK than just SMILES depiction. Future articles will describe some of the many possibilities.