msmbuilder.tpt.fluxes

msmbuilder.tpt.fluxes(sources, sinks, msm, for_committors=None)

Compute the transition path theory flux matrix.

Parameters:

sources : array_like, int

The set of unfolded/reactant states.

sinks : array_like, int

The set of folded/product states.

msm : msmbuilder.MarkovStateModel

MSM that has been fit to data.

for_committors : np.ndarray, optional

The forward committors associated with sources, sinks, and tprob. If not provided, is calculated from scratch. If provided, sources and sinks are ignored.

Returns:

flux_matrix : np.ndarray

The flux matrix

See also

net_fluxes

References

[R61]

Weinan, E. and Vanden-Eijnden, E. Towards a theory of transition paths. J. Stat. Phys. 123, 503-523 (2006).

[R62]

Metzner, P., Schutte, C. & Vanden-Eijnden, E. Transition path theory for Markov jump processes. Multiscale Model. Simul. 7, 1192-1219 (2009).

[R63]

Berezhkovskii, A., Hummer, G. & Szabo, A. Reactive flux and folding pathways in network models of coarse-grained protein dynamics. J. Chem. Phys. 130, 205102 (2009).

[R64]

Noe, Frank, et al. “Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.” PNAS 106.45 (2009): 19011-19016.