Making the Case - Flux-2
… The Flux software makes extensive use of the Chemistry Development Toolkit [sic] (CDK) as a cheminformatics library. Every descriptor that implements the Java interface for CDK descriptors can be utilized for the chemical similarity calculations; this includes the 69 descriptors available in CDK at the time of writing. …
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… CDK is employed as a cheminformatics toolkit (http://cdk.sf.net). The input and output of chemical structures in SDF format and the basic functionality for all structure manipulation are provided by CDK. Compounds are tested for uniqueness by means of canonical SMILES generated by CDK. Our ligand-based fitness function and molecule filter are based on descriptors that implement the Java interface for descriptors defined by CDK.
The number of peer-reviewed publications using the Open Source Java library Chemistry Development Kit (CDK) just keeps growing. The latest addition comes by way of a paper by Fechner and Schneider on ligand-based de novo design. In many areas, Open Source software is used not because it's free, but because it's perceived as superior to alternatives. How long will it be before this is true in cheminformatics?