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 – The fraction of times a walker going from sources -> sinks stops by waypoints on its way.
Return type:	float

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.