Computing Bond Types in Molecule Graphs

Authors:
Sebastian Böcker;Quang B. Bui;Patrick Seeber;Anke Truss
Affiliations:
Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena, Jena, Germany 07743 and Jena Centre for Bioinformatics, Jena, Germany;Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena, Jena, Germany 07743;Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena, Jena, Germany 07743;Lehrstuhl für Bioinformatik, Friedrich-Schiller-Universität Jena, Jena, Germany 07743
Venue:
COCOON '09 Proceedings of the 15th Annual International Conference on Computing and Combinatorics
Year:
2009

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Abstract

In this paper, we deal with restoring missing information in molecule databases: Some data formats only store the atoms' configuration but omit bond multiplicities. As this information is essential for various applications in chemistry, we consider the problem of recovering bond type information using a scoring function for the possible valences of each atom--the Bond Type Assignment problem. We prove the NP-hardness of Bond Type Assignment and give an exact fixed-parameter algorithm for the problem where bond types are computed via dynamic programming on a tree decomposition of the molecule graph. We evaluate our algorithm on a set of real molecule graphs and find that it works fast and accurately.