Choose Java for Speed

O'Boyle and Hutchison offer some interesting comparisons between Open Source cheminformatics toolkits in a recent Chemistry Central article. One of them is contained in the table above, in which the Java cheminformatics library CDK outperforms both the natively-compiled libraries Open Babel and RDKit.

Interestingly, according to Egon Willighagen, a founder of the CDK project, "CDK is hardly optimized for speed" (article).

Benchmarks are always a tricky topic, but at least in this case the measurments come from real tasks likely to be done frequently by users of the respective toolkits: performing a simple molecular weight calculation and iterating over an SD file.