flux - Reactive flux an transition pathways (msmtools.flux)¶
This module contains functions to compute reactive flux networks and find dominant reaction pathways in such networks.
TPT-object¶
tpt(T, A, B[, mu, qminus, qplus, rate_matrix]) |
Computes the A->B reactive flux using transition path theory (TPT) |
ReactiveFlux(A, B, flux[, mu, qminus, ...]) |
A->B reactive flux from transition path theory (TPT) |
Reactive flux¶
flux_matrix(T, pi, qminus, qplus[, netflux]) |
Compute the TPT flux network for the reaction A–>B. |
to_netflux(flux) |
Compute the netflux from the gross flux. |
flux_production(F) |
Returns the net flux production for all states |
flux_producers(F[, rtol, atol]) |
Return indexes of states that are net flux producers. |
flux_consumers(F[, rtol, atol]) |
Return indexes of states that are net flux producers. |
coarsegrain(F, sets) |
Coarse-grains the flux to the given sets. |
Reaction rates and fluxes¶
total_flux(F[, A]) |
Compute the total flux, or turnover flux, that is produced by the flux sources and consumed by the flux sinks. |
rate(totflux, pi, qminus) |
Transition rate for reaction A to B. |
mfpt(totflux, pi, qminus) |
Mean first passage time for reaction A to B. |