The Floyd-Warshall algorithm is crucial in graph theory because it provides an efficient means to compute the shortest paths between all pairs of nodes in a graph. This classic dynamic programming algorithm is widely applicable beyond its traditional use in theoretical network evaluation. It really works by reading in a matrix that describes which pairs of nodes are connected by a single edge, and outputting the minimal variety of edges connecting every possible pair of nodes:
That is precious details about connectivity throughout the graph, that finds tons of applications; for instance in optimizing communication networks, analyzing contacts in social networks, or, as I’ll cover here, in parsing molecular structures — on the core of many tasks in cheminformatics and structural bioinformatics.
On this post I’ll show you the way the Floyd-Warshall algorithm may be employed to compute bond distances between atoms in a molecule, or said otherwise, the minimal variety of bonds separating every possible pair of atoms. Hopefully, my example won’t only showcase the algorithm’s application in chemistry but in addition encourage you to make use of it for other applications in…
