jCompoundMapper: An Open Source Java Library and Command-Line Tool for Chemical Fingerprints

Georg Hinselmann, Lars Rosenbaum, Andreas Jahn, Nikolas Fechner, and Andreas Zell, University of Tuebingen, Center for Bioinformatics Tuebingen(ZBIT), Sand 1, 72076, Tuebingen, Germany


What is jCompoundMapper?


Getting started



The first lines of code of the jCompoundMapper were written about three years ago as we needed reference approaches for benchmarking new algorithms in the field of cheminformatics. The tool has been extended by exporters to common machine learning tools so that a user can train a model on his data set with a few calls from the command-line. We think that parts of the source code or the tool for itself may be useful for academic users who need alternative fingerprints for the analysis of their data or just reference approaches to test their implementations. A problem with many implementations is that they are closed source and nobody knows what the implementation does exactly. This is extremely bad for the use in academia where the scientist has to state explicitly the tools used for the experiments.

To show that some of the implementations have a performance comparable to the state-of-the-art and to make the methods applicable as methods in scientific papers, we published a study.

Most of the implementations have been already published. The original publications are cited in the paper. Many fingerprint algorithms may be configured so that they may differ from their original implementations.