msmbuilder.cfep.VariableCoordinate¶

class msmbuilder.cfep.VariableCoordinate(rxn_coordinate_function, initial_alphas, counts, generators, reactant, product)[source]¶

Class that contains methods for calculating cut-based free energy profiles based on a reaction coordinate mapping that takes variable parameters.

Specifically, a reaction coodinate is formally a map from phase space to the reals. Consider such a map that is dependent on some auxillary parameters alphas. Then we might hope to optimize that reaction coordinate by wisely choosing those weights.

Parameters:

rxn_coordinate_function : function This is a function that represents the reaction coordinate. It takes the arguments of an msm trajectory and an array of weights (floats). It should return an array of floats, specifically the reaction coordinate scalar evaluated for each conformation in the trajectory. Graphically: rxn_coordinate_function(msm_traj, weights) –> array( [float, float, ...] ) An example function of this form is provided, for contact-map based reaction coordinates. initial_alphas : nd_array, float An array representing an initial guess at the optimal alphas. 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__(rxn_coordinate_function, initial_alphas, counts, generators, reactant, product)[source]¶

Methods

__init__(rxn_coordinate_function, ...)
evaluate_partition_functions	Computes the partition function of the cut-based free energy profile based on transition network and reaction coordinate.
optimize([maxiter])	Compute an optimized reaction coordinate, where optimized means the coordinate the maximizes the barrier between two metastable basins.
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.