msmbuilder.tpt.hub_scores

msmbuilder.tpt.hub_scores(msm, waypoints=None)

Calculate the hub score for one or more waypoints

The “hub score” is a measure of how well traveled a certain state or set of states is in a network. Specifically, it is the fraction of times that a walker visits a state en route from some state A to another state B, averaged over all combinations of A and B.

Parameters:

msm : msmbuilder.MarkovStateModel

MSM to analyze

waypoints : array_like, int, optional

The index of the intermediate state (or more than one). If None, then all waypoints will be used

Returns:

hub_score : float

The hub score for the waypoint

References

[R62]

Dickson & Brooks (2012), J. Chem. Theory Comput., 8, 3044-3052.