A Simple and Portable Ruby Interface to InChI

Rich Apodaca — Thu, 29 May 2008 12:12:00 +0000

Although the InChI software itself is written in C, it can still be used via Ruby. Rino offers one implementation of a Ruby InChI interface that makes use of a C extension. This article describes a more concise and portable solution.

The Code

The following code will accept a String encoding a molfile and return either its InChI, or an empty String if no InChI could be found:

module InChI
  def inchi_for molfile
    output = %x[echo "#{molfile}" | cInChI-1 -STDIO]

    output.eql?("") ? "" : output.split(/\n/)[1]
  end
end

This code takes advantage of Ruby's built-in support for Command Expansion.

Testing the Code

The code below tests the library:

require 'inchi'
include InChI

molfile =
"http://chempedia.com/compounds/106.mol
  -OEChem-03010811072D

 12 12  0     0  0  0  0  0  0999 V2000
    2.8660    1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000    0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7321    0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0000   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7321   -0.5000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660   -1.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660    1.6200    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4631    0.8100    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690    0.8100    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4631   -0.8100    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2690   -0.8100    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8660   -1.6200    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  7  1  0  0  0  0
  2  4  1  0  0  0  0
  2  8  1  0  0  0  0
  3  5  2  0  0  0  0
  3  9  1  0  0  0  0
  4  6  2  0  0  0  0
  4 10  1  0  0  0  0
  5  6  1  0  0  0  0
  5 11  1  0  0  0  0
  6 12  1  0  0  0  0
M  END"

puts "Found InChI: #{inchi_for(molfile)}"

We can run the test by saving it in a file called test.rb and executing it:

$ ruby test.rb
InChI version 1, Software version 1.02-beta August 2007
Log file not specified. Using standard error output.
Input file not specified. Using standard input.
Output file not specified. Using standard output.
Options: Mobile H Perception ON
Isotopic ON, Absolute Stereo ON
Omit undefined/unknown stereogenic centers and bonds
Full Aux. info
Input format: MOLfile
Output format: Plain text
Timeout per structure: 60.000 sec; Up to 1024 atoms per structure
End of file detected after structure #1.
Finished processing 1 structure: 0 errors, processing time 0:00:00.00
Found InChI: InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H

Prerequisites

The above approach only requires that it be run on a UNIX-like system, and that a copy of the InChI library be present on your path.

Advantages

The approach described here offers some important advantages over Rino:

It works without modification on both the Matz Ruby Interpreter (C-Ruby) and JRuby.
It neither creates nor uses files.

Disadvantages

This approach creates a lot of noisy log output to the console. There must be a way to suppress it, but so far I haven't found out how.

Conclusions

Using Ruby's support for Command Expansions has enabled the creation of a concise and portable Ruby interface to the InChI toolkit. Similar principles would apply to any Unix command-line binary, including for example, Open Babel.