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
This page provides links for the different versions of jCompoundMapper.
Additionally, it provides a tutorial for the command-line interface.
The different Encodings can easily be accessed by creating a
fingerprinter (they all start with "Encoding") object (e.g.
Encoding2DAllShortestPaths). At the moment, the sources are hosted at
our local repository. It is planned to create a Sourceforge project
after the publication of the library.
Requirements: Java 1.6 runtime
Jar Library API-Doc
Binary Executable (See this tutorial)
- Note: MDL format with attached hydrogens is required as input
format. Additionally, a reasonable geometry for 3D fingerprints is
- You can reproduce the results of the Command-Line Interface Example using the data sets from the environmental toxicity challenge (prepared sd files can be downloaded here: train test). Binaries for LIBSVM can be downloaded from here.