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
[R61] Dickson & Brooks (2012), J. Chem. Theory Comput., 8, 30443052.