Working with SDFs using MX and groovy

Rich Apodaca recently introduced MX, a lightweight cheminformatics toolkit. He also recently published a quick demo to demonstrate how easy it was to use MX to read and write SDFiles using jruby to script it.

I wanted to replicate the functionality in groovy, another scripting language that runs on the JVM — one I’ve recently been using quite extensively (in conjunction with its web development framework called, inevitably, grails).

Here’s what I did to get this working

1. Download mx

   $ wget wget http://mx-java.googlecode.com/files/mx-0.107.0.jar

2. Copy to ~/.groovy/lib

   $ cp mx-0.107.0.jar ~/.groovy/lib

3. Test reading an SD file in groovy (this is transliterated from the example provided by Mr Apodaca)

   $ groovysh
   Groovy Shell (1.5.6, JVM: 1.6.0_0-b12)
   Type 'help' or '\h' for help.
   -------------------------------------------------------------------------------
   groovy:000> import com.metamolecular.mx.io.mdl.SDFileReader
   groovy:000> r = new SDFileReader("example.sdf")
   ===> com.metamolecular.mx.io.mdl.SDFileReader@4e2892b
   groovy:000> r.nextRecord()
   ===> null
   groovy:000> m = r.molecule
   ===> com.metamolecular.mx.model.DefaultMolecule@64c272bc
   groovy:000> m.countAtoms()
   ===> 20
   groovy:000> r.keys.each{ key -> println "$key : ${r.getData(key)}" }
   Mol Weight : 275.2203
   Formula : C11H9N5O4
   ===> [Mol Weight, Formula]

There you have it! I am impressed with the relatively straightforward API, though it is rather tempting to wrap it inside a groovy builder to make a mini-DSL. SDFileBuilder has a certain ring to it…

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