Michael Banck’s research while affiliated with Technical University of Munich and other places

Started in 1993, the Debian project is one of the oldest Free Software projects. Due to its volunteer nature, specialists from all fields contribute to the Debian GNU/Linux distribution, which includes more than 30000 packages. The Debian packaging policy, its advanced package management system and the conservative release process lead to a stable basis which is ideal for customized environments like scientific research. The Debichem project [1] has been packaging and maintaining chemical software compliant with the Debian Free Software Guidelines (DFSG) [2] since 2006. Currently, 35 Free Software package are directly maintained by the Debichem team and 10 more are part of Debichem but maintained by others. At the core of Debichem are the cheminformatics packages OpenBabel [3], CDK [4] and RDKit [5]. They provide file format conversion, 3D coordinate generation, molecular descriptors and fingerprints, stereochemistry prediction, conformation generation and searching, forcefields and more. Besides those, a variety of 2D/3D visualization and molecular modelling programs, as well as ab initio, semi-empirical and molecular dynamics codes are packaged by the Debichem in Debian. Future work will include packaging of cinfony [6], a python module which presents a common API over OpenBabel, CDK and RDKit.

ABSTRACT: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org.