msmbuilder.tpt.conditional_committors¶
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msmbuilder.tpt.conditional_committors(source, sink, waypoint, msm)¶ Computes the conditional committors \(q^{ABC^+}\) which are is the probability of starting in one state and visiting state B before A while also visiting state C at some point.
Note that in the notation of Dickson et. al. this computes \(h_c(A,B)\), with
sources = A,sinks = B,waypoint = CParameters: waypoint : int
The index of the intermediate state
source : int
The index of the source state
sink : int
The index of the sink state
msm : msmbuilder.MarkovStateModel
MSM to analyze.
Returns: cond_committors : np.ndarray
Conditional committors, i.e. the probability of visiting a waypoint when on a path between source and sink.
See also
msmbuilder.tpt.fraction_visited- function Calculate the fraction of visits to a waypoint from a given source to a sink.
msmbuilder.tpt.hub_scores- function Compute the ‘hub score’, the weighted fraction of visits for an entire network.
Notes
Employs dense linear algebra, memory use scales as N^2, and cycle use scales as N^3
References
[R56] Dickson & Brooks (2012), J. Chem. Theory Comput., 8, 3044-3052.