Depth-First

Parsing SD Files with Ruby and Rubidium

By Richard L. Apodaca

Reading SD files is a bread-and-butter cheminformatics operation. At a minimum, a cheminformatics toolkit needs to parse the individual entries of an SD file, and provide access to the embedded molfile and data hash for each.

Recent articles have introduced Rubidium, a Ruby cheminformatics scripting environment. The Rubidium team now announces the release of Rubidium-0.1.1, which, among other features, introduces the ability to parse SD files.

Prerequisites

Rubidium is designed to run on JRuby. Installing JRuby is straightforward on unix-like systems. First, download the JRuby-1.1b1 binary release. Then, unpack the archive to your directory of choice. Set $JRUBY\_HOME and $JAVA\_HOME. Finally, add $JRUBY_HOME/bin to your path.

Installing Rubidium-0.1.1

Generally speaking, it should be possible to install Rubidium with a one-line command to RubyGems:

jruby -S gem install rbtk

Unfortunately at the time of this writing, I was receiving the mysterious RubyGems 404 error with the RubyForge remote repository:

jruby -S gem install rbtk
Select which gem to install for your platform (java)
 1. rbtk 0.1.1 (java)
 2. rbtk 0.1.0 (java)
 3. Skip this gem
 4. Cancel installation
> 1
ERROR:  While executing gem ... (OpenURI::HTTPError)
    404 Not Found

This appears to affect only certain RubyGems on RubyForge - possibly only those with multiple versions. It seems to be an error on the RubyForge server that occasionally appears and then disappears.

As a workaround, you can download the Rubidium gem and install it manually:

$ jruby -S gem install tmp/rbtk-0.1.1-jruby.gem

Because Rubidium-0.1.1 introduces an Active Support dependency, you will need to install that library before installing Rubidium:

jruby -S gem install tmp/rbtk-0.1.1-jruby.gem
ERROR:  While executing gem ... (RuntimeError)
    Error instaling tmp/rbtk-0.1.1-jruby.gem:
        rbtk requires activesupport >= 1.4.2
$ jruby -S gem install activesupport
Successfully installed activesupport-1.4.4
Installing ri documentation for activesupport-1.4.4...
Installing RDoc documentation for activesupport-1.4.4...
$ jruby -S gem install tmp/rbtk-0.1.1-jruby.gem
Successfully installed rbtk, version 0.1.1
Installing ri documentation for rbtk-0.1.1-jruby...
Installing RDoc documentation for rbtk-0.1.1-jruby...

It's possible that the RubyForge 404 issue will be resolved by the time you read this article, so jruby -S gem install rbtk should be tried first.

Parsing an SD File

Let's say we'd like to extract all InChIs from a PubChem dataset. If you don't have one handy, a compilation of about 2000 PubChem benzodiazepines has been deposited on RubyForge.

With our unzipped datafile in our working directory, we can now test the SD File parser by saving the following library to a file called parse.rb:

require 'rubygems'
gem 'rbtk'
require 'rubidium/sdf'

def parse_sd filename
  p = Rubidium::SDF::Parser.new File.new(filename)

  p.each do |entry|
    puts "InChI: #{entry['PUBCHEM_NIST_INCHI']}"
  end
end

which can be tested with jirb:

jirb
irb(main):001:0> require 'parse'
=> true
irb(main):002:0> parse_sd 'pubchem_benzodiazepine_20071110.sdf'
InChI: InChI=1/C16H12Cl2N2O/c1-20-14-7-6-12(18)8-13(14)16(19-9-15(20)21)10-2-4-11(17)5-3-10/h2-8H,9H2,1H3

[truncated]

RSpec and Behavior-Driven Development

If you check out the Rubidium source distribution, you'll notice that the SD parser library is tested with RSpec, the BDD framework for Ruby. Ultimately, all components of Rubidium will be tested and documented this way.

Acknowledgments

Rubidium's new SD file parser was written by Moses Hohman. It was kindly donated by Collaborative Drug Discovery, who have built their drug discovery application using Ruby on Rails.

Future Directions

One problem in working with SD files is pinpointing encoding errors. A parser should not only raise an exception, but point to a line number and identify offending text to aid debugging. Rubidium's SD parser will eventually incorporate these enhancements.

Because Rubidium runs on JRuby, performance gains may be achievable by re-writing select portions in Java.

Parsing SD files is only the beginning of the story. Many cheminformatics applications need a convenient, fast, and robust method for writing molfiles. This is also something Rubidium will attempt to provide.

If your company or organization is curious about Ruby and cheminforamatics, give Rubidium a try. Rubidium is licensed under the permissive MIT License to make collaboration as simple as possible.