Visualizing IUPAC Names with ChemNomParse

Rich Apodaca — Mon, 11 Sep 2006 14:29:00 +0000

Nomenclature translation is the process of converting a human-readable chemical name into a machine-readable notational scheme such as a connection table. It plays a key role in linking the older chemical literature to modern information technologies, such as the Internet.

Buried deep within the Chemistry Development Kit (CDK) is a library for nomenclature translation called ChemNomParse. At the heart of ChemNomParse is a remarkable piece of software called the Java Compiler Compiler (JavaCC), a parser generator and lexical analyzer generator for Java. A FAQ on JavaCC is available here.

This tutorial demonstrates how freely-available, open source tools can be used to parse an IUPAC chemical name and generate its corresponding 2-D structure rendering. A closely-related tutorial on generating 2-D structures from SMILES strings may be helpful as background.

Ingredients

This tutorial uses Arton's Ruby Java Bridge, the installation and use of which has been outlined previously. In addition, you'll need to download Structure-CDK v0.1.2, also previously discussed. Be sure to download v0.1.2, as two upgrades have been released since the package was originally described. This tutorial has been tested on Mandriva Linux 2006.

Create a working directory called nom. From the lib directory of the Structure-CDK distribution, copy cdk-20060714.jar and structure-cdk-0.1.2.jar into your depict working directory.

Code

Create a file called depict.rb and copy the following code into it:

ENV['CLASSPATH'] = './cdk-20060714.jar:./structure-cdk-0.1.2.jar'

require 'rubygems'
require_gem 'rjb'
require 'rjb'

NomParser = Rjb::import 'org.openscience.cdk.iupac.parser.NomParser'
StructureDiagramGenerator = Rjb::import 'org.openscience.cdk.layout.StructureDiagramGenerator'
ImageKit = Rjb::import 'net.sf.structure.cdk.util.ImageKit'

class Depictor

  def initialize
    @sdg = StructureDiagramGenerator.new
  end

  def depict_png(nom, width, height, path_to_png)
    ImageKit::writePNG(nom_to_mol(nom), width, height, path_to_png)
  end

  def depict_svg(nom, width, height, path_to_svg)
    ImageKit::writeSVG(nom_to_mol(nom), width, height, path_to_svg)
  end

private

  def nom_to_mol(nom)
    @sdg.setMolecule(NomParser::generate(nom))
    @sdg.generateCoordinates

    @sdg.getMolecule
  end
end

After you save this file, you'll need to set your LD_LIBRARY_PATH on unix (or the equivalent on another OS):

$ export LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/i386:$LD_LIBRARY_PATH

This tells RJB where to find Java's native libraries. Because of RJB's current design, LD_LIBRARY_PATH needs to be set from the command line, rather than from within a Ruby process.

Using the Depictor class is as simple as creating an instance and invoking depict_png or depict_svg on it:

require 'nom'

depictor = Depictor.new

depictor.depict_png('2-phenylcyclohexan-1-ol', 300, 300, 'output.png')

Executing the above code either through the Ruby interpreter (ruby) or via Interactive Ruby (irb) products a PNG image of the chiral auxiliary shown below:

Other names correctly recognized by ChemNomParse include:

phenylhexyne
2-chloro-3-phenyl-4,4-dimethylhexane
3-phenyl-1-aminopropane
1,2-difluoro-3-hydroxycyclohexene

Limitations

Many chemical names, ranging from the simple to the complicated, were not be recognized at all by ChemNomParse. Some examples are:

benzene
piperidine
1-methoxyhexane
2-methyl-5-prop-1-en-2-yl-cyclohex-2-en-1-one (carvone)

Some names were incorrectly interpreted due to misassigned locants. For example, 2-chloro-3-hydroxybutanoic acid produced the incorrectly asssigned structure shown below:

ChemNomParse can accurately recognize chemical names representing simple substitutions on basic hydrocarbon scaffolds. More complicated structures, such as heterocycles, bicyclic systems, and systems involving nested substituents do not appear to be handled at all. It is not clear to what extent these limitations reflect a small dictionary of morphemes (the basic nomenclature building blocks) versus deeper design issues.

Despite its limitations, ChemNomParse is an interesting piece of open source software for working with chemical nomenclature. From this simple tutorial, it can be seen that nomenclature translation, when combined with other capabilities such as 2-D rendering, offers many exciting possibilities.

Depth-First: Tag javacc

Visualizing IUPAC Names with ChemNomParse

Ingredients

Code

Limitations