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The code is written to be compiled together with CDK version 1.4.x CDK can be downloaded at http://sourceforge.net/projects/cdk/ usage on commandline: java -jar filename filename should be sdf or smiles file the default code does not generate any output (simple text output is commented out in the code) change it to output whatever results you'd like support: firstname.lastname@example.org The details on the algorithm have been published in Enrichment of True Positives from Structural Alerts Through the Use of Novel Atomic Fragment Based Descriptors Anthony Long, Patrik Rydberg Molecular Informatics, DOI:10.1002/minf.201200092 http://onlinelibrary.wiley.com/doi/10.1002/minf.201200092/abstract