Jruby example of using the Chemistry Development Kit (CDK) to parse smiles strings into a canonical format

gistfile1.rb

# Jruby example using the chemistry development kit(CDK) to parse smiles strings into a 
# canonical format
# author : Dana klassen

require 'rubygems'
include Java
# $CLASSPATH << File.join(File.expand_path(File.dirname(__FILE__)),"lib")
Dir.glob(File.join(File.expand_path(File.dirname(__FILE__)),"lib/*.jar")) { |file| require file  }

import 'org.openscience.cdk.smiles.SmilesParser'
import 'org.openscience.cdk.DefaultChemObjectBuilder'
import 'org.openscience.cdk.smiles.SmilesGenerator'

parser    =  SmilesParser.new(DefaultChemObjectBuilder.getInstance())
generator = SmilesGenerator.new()

# examples smiles strings we are going to normalize
# caffeine :)
smiles1 = "CN2C(=O)N(C)C(=O)C1=C2N=CN1C"
smiles2 = "CN1C=NC2=C1C(=O)N(C)C(=O)N2C"

puts "INFO: inputting two smiles strings:"
puts "  #{smiles1}"
puts "	#{smiles2}"

smiles1 = generator.createSMILES(parser.parseSmiles(smiles1))
smiles2 = generator.createSMILES(parser.parseSmiles(smiles2))

puts "INFO: outputting canonical smiles from input:"
puts "	#{smiles1}"
puts "	#{smiles2}"

puts "INFO: asserting these smiles are identical"

puts "true" if (smiles1 == smiles2)