msmbuilder.tpt.net_fluxes¶
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msmbuilder.tpt.
net_fluxes
(sources, sinks, msm, for_committors=None)¶ Computes the transition path theory net 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 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: - net_flux : np.ndarray
The net flux matrix
See also
References
[1] Weinan, E. and Vanden-Eijnden, E. Towards a theory of transition paths. J. Stat. Phys. 123, 503-523 (2006). [2] Metzner, P., Schutte, C. & Vanden-Eijnden, E. Transition path theory for Markov jump processes. Multiscale Model. Simul. 7, 1192-1219 (2009). [3] 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). [4] Noe, Frank, et al. “Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.” PNAS 106.45 (2009): 19011-19016.