Ruby CDK for Newbies

October 04, 2007

Scripting languages and cheminformatics can be a highly-effective combination. With their relaxed syntax, compilation-free execution, and interactive testing environments, scripting languages offer fast development iteration cycles. And scripting languages' support for manipulating libraries written in other languages can be key in today's heterogeneous cheminformatics software environment.

Although there are many cheminformatics scripting environments to choose from, Ruby offers some important advantages. Number one on the list is the wildly-popular Ruby on Rails Web development framework. Others worth mentioning include interactive ruby (irb), the RubyGems package manager, the Rake build system, the JRuby Ruby implementation, RubyForge, and a host of other productivity-boosters.

A major focus of Depth-First over the last few months has been Ruby CDK. This library consists of a thin Ruby wrapper around the open source Chemistry Development Kit (CDK), Structure-CDK, an open source 2D rendering toolkit, and OPSIN, an open source chemical nomenclature parser. A recent comment on Depth-First by Egon Willighagen, one of CDK's creators, got me thinking about centralizing this documentation. The following collection of links is a step in that direction.

Overview and Installation

Ruby CDK in Its Environment

Using Ruby CDK

Image Generation Credit: txt2pic.com