msmbuilder.tpt.fraction_visited

msmbuilder.tpt.fraction_visited(source, sink, waypoint, msm)

Calculate the fraction of times a walker on tprob going from sources to sinks will travel through the set of states waypoints en route.

Computes the conditional committors q^{ABC^+} and uses them to find the fraction of paths mentioned above.

Note that in the notation of Dickson et. al. this computes h_c(A,B), with

sources = A sinks = B waypoint = C

Parameters:

source : int

The index of the source state

sink : int

The index of the sink state

waypoint : int

The index of the intermediate state

msm : msmbuilder.MarkovStateModel

MSM to analyze.

Returns:

fraction_visited : float

The fraction of times a walker going from sources -> sinks stops by waypoints on its way.

See also

msmbuilder.tpt.conditional_committors

Calculate the probability of visiting a waypoint while on a path between a source and sink.

msmbuilder.tpt.hub_scores

function Compute the ‘hub score’, the weighted fraction of visits for an entire network.

References

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