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 – Conditional committors, i.e. the probability of visiting a waypoint when on a path between source and sink.
Return type:

np.ndarray

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.