msmbuilder.cfep.CutCoordinate¶

class msmbuilder.cfep.CutCoordinate(counts, generators, reactant, product)[source]¶

Object containing methods for computing the cut-based free energy profiles of reaction coordinates.

Parameters:	counts : matrixs A matrix of the transition counts observed in the MSM generators : msmbuilder trajectory The generators (or a trajectory containing an exemplar structure) for each state. reactant : int Index of the state to use to represent the reactant (unfolded) well product : int Index of the state to use to represent the product (folded) well

__init__(counts, generators, reactant, product)[source]¶

Methods

__init__(counts, generators, reactant, product)
evaluate_partition_functions	Computes the partition function of the cut-based free energy profile based on transition network and reaction coordinate.
plot([num_bins, filename])	Plot the current cut-based free energy profile.
reaction_mfpt([lag_time])	Calculate the MFPT between the reactant and product states, as given by the reaction coordinate.
rescale_to_natural_coordinate	Rescale a cut-based free energy profile along a reaction coordinate such that the diffusion constant is unity for the entire coordinate.
set_coordinate_as_committors([lag_time, ...])	Set the reaction coordinate to be the committors (pfolds).
set_coordinate_as_eigvector2([lag_time, ...])	Set the reaction coordinate to be the second eigenvector of the MSM generated by counts, the provided lag_time, and the provided symmetrization method.
set_coordinate_values(coordinate_values)	Set the reaction coordinate manually, by providing coordinate values that come from some external calculation.