msmbuilder.tpt.conditional_committors

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 = C

Parameters:

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

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