I was doing some profiling (YourKit and Eclipse3.4) of the CDK atom typer, and it turns out that most time is spend on the perception of nitrogen atom types, which seems to be caused by the loadClassInternal() method of the JVM (java-1.5.0-sun-1.5.0.16 on Ubuntu Hardy):

This post was originally posted as https://chem-bla-ics.blogspot.com/2008/08/profiling-cdk-atom-typer.html.