msm_we
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msm_we
Installation/Usage
Examples
Documentation
TODOs
Credits
History
msm_we
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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M
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N
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O
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P
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R
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S
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U
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W
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)