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Atom Mapping with Constraint Programming

Martin Mann, Heinz Ekker, Peter F. Stadler, and Christoph Flamm

submitted to:
Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCB 2012)

The mass ow in a chemical reaction network is determined by the propagation of atoms from educt to product molecules within each of the constituent chemical reactions. The Atom Mapping Problem for a given chemical reaction is the computational task of determining the correspondences of the atoms between educt and product molecules. We propose here a Constraint Programming approach to identify atom mappings for \elementary" reactions. These feature a cyclic imaginary transition state (ITS) imposing an additional strong constraint on the bijection between educt and product atoms. The ongoing work presented here identifies only chemically feasible ITSs by integrating the cyclic structure of the chemical transformation into the search.

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