test.rb

#!/usr/bin/env ruby

require 'pp'
require 'open3'

entries = File.open('/Users/iehdk/install/src/chem-O-matic/data/mega.sdf').read.split("$$$$")

entries.each do |entry|
  Open3.popen3("obabel -i sdf -o smi") do |stdin, stdout, stderr, wait_thr|
    entries.each do |entry|
      stdin.puts entry
      stdin.close
      stdout.each_line { |line| puts line }
    end

    puts wait_thr.value

  end
end