Discretization orders for distance geometry problems

Given a weighted, undirected simple graph G = (V,E, d) (where d : E → R+), the Distance Geometry Problem (DGP) is to determine an embedding x : V → R K such that ∀{i, j} ∈ E ‖xi − xj‖ = dij . Although, in general, the DGP is solved using continuous methods, under certain conditions the search is reduced to a discrete set of points. We give one such condition as a particular order on V . We formalize the decision problem of determining whether such an order exists for a given graph and show that this problem is NP-complete in general and polynomial for fixed dimension K. We present results of computational experiments on a set of protein backbones whose natural atomic order does not satisfy the order requirements and compare our approach with some available continuous space searches.