MD-jeep: a New Release for Discretizable Distance Geometry Problems with Interval Data

Abstract

With the most recent releases of MD-JEEP, new relevant features have been included to our software tool. MD-JEEP solves instances of the class of Discretizable Distance Geometry Problems (DDGPs), which ask to find possible realizations, in a Euclidean space, of a simple weighted undirected graph for which distance constraints between vertices are given, and for which a discretization of the search space can be supplied. Since its version 0.3.0, MD-JEEP is able to deal with instances containing interval data. We focus in this short paper on the most recent release MD-JEEP 0.3.2: among the new implemented features, we will focus our attention on three features: (i) an improved procedure for the generation and update of the boxes used in the coarse-grained representation (necessary to deal with instances containing interval data); (ii) a new procedure for the selection of the so-called discretization vertices (necessary to perform the discretization of the search space); (iii) the implementation of a general parser which allows the user to easily load DDGP instances in a given specified format. The source code of MD-JEEP 0.3.2 is available on GitHub, where the reader can find all additional details about the implementation of such new features, as well as verify the effectiveness of such features by comparing MD-JEEP 0.3.2 with its previous releases.

A Distance Geometry Procedure Using the Levenberg-Marquardt Algorithm and with Applications in Biology but Not only

“…When the value on the distances is uncertain, however, some nodes of the search domain cannot be associated to singletons, but rather to relatively small portions of the original continuous search domain. This is the reason why, in MDJEEP, the combinatorics is coupled with a refinement step consisting in locally exploring all those small domain portions in the attempt to improve the overall solution quality [14]. The impact of the current work on the future developments of MDJEEP can be two-fold.…”