msmbuilder.tpt.committors

msmbuilder.tpt.committors(sources, sinks, msm)

Get the forward committors of the reaction sources -> sinks.

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 fit to the data.

Returns:

forward_committors : np.ndarray

The forward committors for the reaction sources -> sinks

References

[R56]

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

[R57]

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

[R58]

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).

[R59]

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