A Simple and Portable Ruby Interface to InChI

May 29, 2008

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:

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.