Index

A

adaptive_fpt_distribution() (msm_we.fpt.MatrixFPT static method)

add_trajectory() (msm_we.ensembles.Ensemble method) augment_coordinates() (msm_we.westpa_plugins.augmentation_driver.MDAugmentationDriver method)

B

build_analyze_model() (msm_we.modelWE method)

C

check_tmatrix() (in module msm_we.utils) clean_tmatrix() (in module msm_we.utils) cluster_coordinates() (msm_we.modelWE method) compute_new_pcoord_map() (msm_we.westpa_plugins.optimization_driver.OptimizationDriver method) compute_optimized_allocation() (msm_we.westpa_plugins.optimization_driver.OptimizationDriver method)

compute_optimized_bins() (msm_we.westpa_plugins.optimization_driver.OptimizationDriver method) construct_hamsm() (msm_we.westpa_plugins.hamsm_driver.HAMSMDriver method) corr_function() (msm_we.nmm.NonMarkovModel method) create_new() (msm_we.optimization.OptimizedBinMapper method) cur_iter (msm_we.westpa_plugins.restart_driver.RestartDriver property)

D

default_allocation_optimizer() (msm_we.westpa_plugins.optimization_driver.OptimizationDriver static method) default_bin_optimizer() (msm_we.westpa_plugins.optimization_driver.OptimizationDriver static method) dimReduce() (msm_we.modelWE method) directional_mfpt() (msm_we.fpt.MatrixFPT class method)

DiscreteEnsemble (class in msm_we.ensembles) DiscretePathEnsemble (class in msm_we.ensembles) do_block_validation() (msm_we.modelWE method) do_optimization() (msm_we.westpa_plugins.optimization_driver.OptimizationDriver method)

E

empirical_corr_function() (msm_we.ensembles.Ensemble method) empirical_mfpts() (msm_we.ensembles.Ensemble method) (msm_we.nmm.NonMarkovModel method)

Ensemble (class in msm_we.ensembles)

F

find_connected_sets() (in module msm_we.utils) fit() (msm_we.nmm.MarkovPlusColorModel method) (msm_we.nmm.NonMarkovModel method) fpt_distribution() (msm_we.fpt.MatrixFPT class method) from_ensemble() (msm_we.ensembles.DiscreteEnsemble class method) (msm_we.ensembles.DiscretePathEnsemble class method) (msm_we.ensembles.PathEnsemble class method)

from_nm_tmatrix() (msm_we.nmm.NonMarkovModel class method) from_transition_matrix() (msm_we.ensembles.DiscreteEnsemble class method) (msm_we.ensembles.DiscretePathEnsemble class method)

G

get_cluster_centers() (msm_we.modelWE method) get_clustered_mfpt_bins() (in module msm_we.optimization) get_committor() (msm_we.modelWE method) get_coordSet() (msm_we.modelWE method) get_flux() (msm_we.modelWE method) get_fluxMatrix() (msm_we.modelWE method)

get_original_bins() (msm_we.westpa_plugins.restart_driver.RestartDriver method) get_shape() (in module msm_we.utils) get_steady_state() (msm_we.modelWE method) get_steady_state_target_flux() (msm_we.modelWE method) get_Tmatrix() (msm_we.modelWE method) get_uniform_mfpt_bins() (in module msm_we.optimization)

H

HAMSMDriver (class in msm_we.westpa_plugins.hamsm_driver)

I

initialize() (msm_we.modelWE method) Interval (class in msm_we.utils)

inverse_iteration() (in module msm_we.utils) is_connected() (in module msm_we.utils) is_last_iteration (msm_we.westpa_plugins.restart_driver.RestartDriver property)

M

map_to_integers() (in module msm_we.utils) markov_commute_time() (msm_we.fpt.MarkovFPT class method) MarkovFPT (class in msm_we.fpt) MarkovPlusColorModel (class in msm_we.nmm) MatrixFPT (class in msm_we.fpt) max_commute_time() (msm_we.fpt.MatrixFPT class method) MDAugmentationDriver (class in msm_we.westpa_plugins.augmentation_driver) mean_fpts() (msm_we.fpt.MarkovFPT class method) (msm_we.fpt.MatrixFPT class method) (msm_we.fpt.NonMarkovFPT class method) mfpts_matrix() (msm_we.fpt.MatrixFPT class method) mfpts_to_target_microstate() (msm_we.fpt.MatrixFPT class method) min_commute_time() (msm_we.fpt.MatrixFPT class method) modelWE (class in msm_we) module msm_we.ensembles msm_we.fpt msm_we.nmm msm_we.optimization msm_we.utils msm_we.westpa_plugins.augmentation_driver msm_we.westpa_plugins.hamsm_driver msm_we.westpa_plugins.optimization_driver msm_we.westpa_plugins.restart_driver

msm_we.ensembles module msm_we.fpt module msm_we.nmm module msm_we.optimization module msm_we.utils module msm_we.westpa_plugins.augmentation_driver module msm_we.westpa_plugins.hamsm_driver module msm_we.westpa_plugins.optimization_driver module msm_we.westpa_plugins.restart_driver module

N

n_states (msm_we.nmm.NonMarkovModel attribute) nm_cmatrix (msm_we.nmm.NonMarkovModel attribute) nm_mfpt() (msm_we.ensembles.DiscretePathEnsemble method) NonMarkovFPT (class in msm_we.fpt)

NonMarkovModel (class in msm_we.nmm) normalize() (in module msm_we.utils) normalize_markov_matrix() (in module msm_we.utils) num_of_nonzero_elements() (in module msm_we.utils)

O

OptimizationDriver (class in msm_we.westpa_plugins.optimization_driver)

OptimizedBinMapper (class in msm_we.optimization) organize_fluxMatrix() (msm_we.modelWE method)

P

PathEnsemble (class in msm_we.ensembles) plot_flux() (msm_we.modelWE method) plot_flux_committor() (msm_we.modelWE method) plot_flux_committor_pcoordcolor() (msm_we.modelWE method) pops_from_nm_tmatrix() (in module msm_we.utils)

pops_from_tmatrix() (in module msm_we.utils) populations (msm_we.nmm.NonMarkovModel attribute) prepare_extension_run() (msm_we.westpa_plugins.restart_driver.RestartDriver method) prepare_new_we() (msm_we.westpa_plugins.restart_driver.RestartDriver method) pseudo_nm_tmatrix() (in module msm_we.utils)

R

random_markov_matrix() (in module msm_we.utils)

RestartDriver (class in msm_we.westpa_plugins.restart_driver) reverse_sort_lists() (in module msm_we.utils)

S

solve_discrepancy() (in module msm_we.optimization)

U

update_cluster_structures() (msm_we.modelWE method)

update_westpa_pcoord() (msm_we.westpa_plugins.optimization_driver.OptimizationDriver method)

W

weighted_choice() (in module msm_we.utils)

weighted_fundamental_sequences() (msm_we.ensembles.DiscretePathEnsemble method)