Constraint programming approaches for the discretizable molecular distance geometry problem

Abstract

AbstractThe Distance Geometry Problem (DGP) seeks to find positions for a set of points in geometric space when some distances between pairs of these points are known. The so‐called discretization assumptions allow us to discretize the search space of DGP instances. In this paper, we focus on a key subclass of DGP, namely the Discretizable Molecular DGP, and study its associated graph vertex ordering problem, the Contiguous Trilateration Ordering Problem (CTOP), which helps solve DGP. We propose the first constraint programming formulations for CTOP, as well as a set of checks for proving infeasibility, domain reduction techniques, symmetry breaking constraints, and valid inequalities. Our computational results on random and pseudo‐protein instances indicate that our formulations outperform the state‐of‐the‐art integer programming formulations.