Hacking PubChem with Ruby

August 30, 2006

PubChem is an increasingly popular, free-access, online molecular database operated by the National Institutes of Health. Web services are a hot topic, with sites such as Flickr, Google, and eBay offering developers the tools to build rich content through "mashups" of several web APIs. Although there is no formal PubChem API, it's possible to roll your own. As a demonstration, this article will show how structural information can be retrieved from PubChem using some simple Ruby code. The inspiration for this article came from the PubChem module that is part of Chemruby.

The only thing you'll need for this tutorial is Ruby, preferably version 1.8.2 or higher. Create a directory called pubchem and make it your working directory. Then create a file called pubchem.rb containing the following code:

require 'net/http'

# A very simple PubChem Web API.
class PubChem

  # Returns a molfile (as a String) for the molecule with PubChem
  # CID matching compound_id.
  def self.get_molfile(compound_id)
    molfile = nil
    path = '/summary/summary.cgi?cid=' + compound_id + '&disopt=DisplaySDF'

    Net::HTTP.start('pubchem.ncbi.nlm.nih.gov') do |http|
      response = http.get(path)
      molfile = response.body


  # Writes a PNG image, for the molecule with PubChem
  # CID matching compound_id, to the file specified by filename.
  def self.write_image(compound_id, filename)
    path = '/image/imgsrv.fcgi?t=l&cid=' + compound_id

    Net::HTTP.start('pubchem.ncbi.nlm.nih.gov') do |http|
      response = http.get(path)
      image = response.body

      File.open(filename, "w") do |file|
        file << image

PubChem references each of its compounds by a unique integer identifier, the PubChem CID. This is very handy because retrieving PubChem resources is as simple as encoding a URL containing the CID of interest. The class above illustrates how this system can be used to get a molfile and write a PNG image using just a few lines of Ruby.

Using the PubChem class is simplicity itself. To get the molfile for Levonorgestrel (Plan B), which has the CID 13109:

require 'pubchem'

molfile = PubChem::get_molfile('13109') #=> returns the molfile for Levonorgestrel as a String

To write the 2-D structure diagram of Levonorgestrel as a PNG:

require 'pubchem'

PubChem::write_png('13109', 'image.png') #=> writes a PNG image of Levonorgestrel

This code saves the image below to your working directory as image.png. The above two code fragments can either be saved as a file and executed by the Ruby interpreter:

$ ruby filename.rb

or it they be entered interactively in your console with irb:

$ irb

As you can see, there's not much to building a PubChem API in Ruby. The same principles discussed here should apply in any programming language. Future articles in this series will show how to build more complex PubChem APIs and integrate them with other software packages and web services.