Merge pull request #6353 from RosettaCommons/roccomoretti/speed_VDDistanceMatrix Speed up NBR distance calculation. It looks like the slow bit of loading types from the Chemical Components Dictionary is the find_nbr_dist() calc. The slow bit looks to be data structure access in the Floyd-Warshall. Right now we're using a map of maps. If we can use compact data storage (and integer indexes), we can speed this up greatly. The find_nbr_dist() function gets ~50 times faster, though given the total time we spend in it, the overall speedup due to this fix is probably ~1% at most (depending on how many CCD components you have.)