msmbuilder.tpt.calculate_hub_score¶
- msmbuilder.tpt.calculate_hub_score(tprob, waypoint)[source]¶
Calculate the hub score for the states waypoint.
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: tprob : matrix
The transition probability matrix
waypoints : int
The indices of the intermediate state(s)
Returns: Hc : float
The hub score for the state composed of waypoints
See also
- calculate_fraction_visits
- function Calculate the fraction of times a state is visited on pathways going from a set of “sources” to a set of “sinks”.
- calculate_all_hub_scores
- function A more efficient way to compute the hub score for every state in a network.
Notes
- Employs dense linear algebra,
- memory use scales as N^2 cycle use scales as N^5
References
- ..[1] Dickson & Brooks (2012), J. Chem. Theory Comput.,
- Article ASAP DOI: 10.1021/ct300537s