Index

_ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W

_

__init__() (msmtools.flux.ReactiveFlux method)

A

A (msmtools.flux.ReactiveFlux attribute)

active_count_fraction (pyemma.msm.BayesianMSM attribute)

active_set (pyemma.msm.BayesianHMSM attribute)

active_state_fraction (pyemma.msm.BayesianMSM attribute)

active_state_indexes (pyemma.msm.BayesianMSM attribute)

add_all() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_angles() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_backbone_torsions() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_chi1_torsions() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_contacts() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_custom_feature() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_custom_func() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_dihedrals() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_distances() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_distances_ca() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_element() (pyemma.coordinates.pipelines.Discretizer method)

add_group_mindist() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_inverse_distances() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_minrmsd_to_ref() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_residue_mindist() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

add_selection() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

assign() (pyemma.coordinates.clustering.assign.AssignCenters method)

assign_to_centers() (in module pyemma.coordinates)

AssignCenters (class in pyemma.coordinates.clustering)

B

B (msmtools.flux.ReactiveFlux attribute)

backward_committor (msmtools.flux.ReactiveFlux attribute)

bayesian_hidden_markov_model() (in module pyemma.msm)

bayesian_markov_model() (in module pyemma.msm)

BayesianHMSM (class in pyemma.msm)

BayesianMSM (class in pyemma.msm)

bootstrap_counts() (in module msmtools.estimation)

bootstrap_trajectories() (in module msmtools.estimation)

C

ChapmanKolmogorovValidator (class in pyemma.msm)

chunksize (pyemma.coordinates.clustering.assign.AssignCenters attribute)

cktest() (pyemma.msm.BayesianHMSM method)

cluster_kmeans() (in module pyemma.coordinates)

cluster_mini_batch_kmeans() (in module pyemma.coordinates)

cluster_regspace() (in module pyemma.coordinates)

cluster_uniform_time() (in module pyemma.coordinates)

clustercenters (pyemma.coordinates.clustering.assign.AssignCenters attribute)

cmatrix() (in module msmtools.estimation)

coarse_grain() (msmtools.flux.ReactiveFlux method)

coarsegrain() (in module msmtools.flux)

committor (msmtools.flux.ReactiveFlux attribute)

committor() (in module msmtools.analysis)

committor_backward() (pyemma.msm.BayesianHMSM method)

committor_forward() (pyemma.msm.BayesianHMSM method)

committor_sensitivity() (in module msmtools.analysis)

connected_cmatrix() (in module msmtools.estimation)

connected_sets (pyemma.msm.BayesianMSM attribute)

connected_sets() (in module msmtools.estimation)

connectivity (pyemma.msm.BayesianMSM attribute)

correlation() (in module msmtools.analysis)

count_matrix() (in module msmtools.estimation)

count_matrix_active (pyemma.msm.BayesianMSM attribute)

count_matrix_full (pyemma.msm.BayesianMSM attribute)

count_states() (in module msmtools.dtraj)

cov (pyemma.coordinates.transform.TICA attribute)

cov_tau (pyemma.coordinates.transform.TICA attribute)

cumvar (pyemma.coordinates.transform.pca.PCA attribute)

CustomFeature (class in pyemma.coordinates.data)

D

data (pyemma.coordinates.data.DataInMemory attribute)

data_producer (pyemma.coordinates.clustering.assign.AssignCenters attribute)

DataInMemory (class in pyemma.coordinates.data)

default_chunksize (pyemma.coordinates.clustering.assign.AssignCenters attribute)

describe() (pyemma.coordinates.clustering.assign.AssignCenters method)

dimension() (pyemma.coordinates.clustering.assign.AssignCenters method)

discrete_trajectories_active (pyemma.msm.BayesianMSM attribute)

discrete_trajectories_full (pyemma.msm.BayesianHMSM attribute)

discrete_trajectories_lagged (pyemma.msm.BayesianHMSM attribute)

discrete_trajectories_obs (pyemma.msm.BayesianHMSM attribute)

Discretizer (class in pyemma.coordinates.pipelines)

discretizer() (in module pyemma.coordinates)

dmin (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)

dt_model (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)

dtrajs (pyemma.coordinates.clustering.assign.AssignCenters attribute)

dtrajs_active (pyemma.msm.BayesianMSM attribute)

dtrajs_full (pyemma.msm.BayesianHMSM attribute)

dtrajs_lagged (pyemma.msm.BayesianHMSM attribute)

dtrajs_obs (pyemma.msm.BayesianHMSM attribute)

DTRAM (class in pyemma.thermo)

dtram() (in module pyemma.thermo)

E

effective_count_matrix (pyemma.msm.BayesianMSM attribute)

eigenvalue_sensitivity() (in module msmtools.analysis)

eigenvalues (pyemma.coordinates.transform.pca.PCA attribute)

eigenvalues() (in module msmtools.analysis)

eigenvector_sensitivity() (in module msmtools.analysis)

eigenvectors (pyemma.coordinates.transform.pca.PCA attribute)

eigenvectors() (in module msmtools.analysis)

eigenvectors_left() (pyemma.msm.BayesianHMSM method)

eigenvectors_left_obs (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)

eigenvectors_right() (pyemma.msm.BayesianHMSM method)

eigenvectors_right_obs (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)

error_perturbation() (in module msmtools.estimation)

estimate() (pyemma.coordinates.clustering.assign.AssignCenters method)

estimate_hidden_markov_model() (in module pyemma.msm)

estimate_markov_model() (in module pyemma.msm)

estimate_multi_temperature() (in module pyemma.thermo)

estimate_umbrella_sampling() (in module pyemma.thermo)

estimates (pyemma.msm.ChapmanKolmogorovValidator attribute)

estimates_conf (pyemma.msm.ChapmanKolmogorovValidator attribute)

estimators (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]

expectation() (in module msmtools.analysis)

expectation_sensitivity() (in module msmtools.analysis)

expected_counts() (in module msmtools.analysis)

expected_counts_stationary() (in module msmtools.analysis)

F

f_full_state (pyemma.thermo.DTRAM attribute)

feature_PC_correlation (pyemma.coordinates.transform.PCA attribute)

feature_TIC_correlation (pyemma.coordinates.transform.TICA attribute)

FeatureReader (class in pyemma.coordinates.data)

featurizer() (in module pyemma.coordinates)

filenames (pyemma.coordinates.clustering.assign.AssignCenters attribute)

fingerprint_correlation() (in module msmtools.analysis)

fingerprint_relaxation() (in module msmtools.analysis)

fit() (pyemma.coordinates.clustering.assign.AssignCenters method)

fit_predict() (pyemma.coordinates.clustering.assign.AssignCenters method)

fit_transform() (pyemma.coordinates.clustering.assign.AssignCenters method)

flux (msmtools.flux.ReactiveFlux attribute)

flux_consumers() (in module msmtools.flux)

flux_matrix() (in module msmtools.flux)

flux_producers() (in module msmtools.flux)

flux_production() (in module msmtools.flux)

forward_committor (msmtools.flux.ReactiveFlux attribute)

fraction_of_frames (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]

func (pyemma.coordinates.clustering.assign.AssignCenters attribute)

G

generate_traj() (in module msmtools.generation)

get_model_params() (pyemma.coordinates.clustering.assign.AssignCenters method)

get_output() (pyemma.coordinates.clustering.assign.AssignCenters method)

get_params() (pyemma.coordinates.clustering.assign.AssignCenters method)

get_sample_conf() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]

get_sample_mean() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]

get_sample_std() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]

get_timescales() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]

gross_flux (msmtools.flux.ReactiveFlux attribute)

H

hmm() (pyemma.msm.BayesianMSM method)

I

I (msmtools.flux.ReactiveFlux attribute)

ImpliedTimescales (class in pyemma.msm)

in_memory (pyemma.coordinates.clustering.assign.AssignCenters attribute)

index_clusters (pyemma.coordinates.clustering.assign.AssignCenters attribute)

index_states() (in module msmtools.dtraj)

is_connected() (in module msmtools.analysis)

is_random_accessible (pyemma.coordinates.clustering.assign.AssignCenters attribute)

is_rate_matrix() (in module msmtools.analysis)

is_reader (pyemma.coordinates.clustering.assign.AssignCenters attribute)

is_reversible (pyemma.msm.BayesianHMSM attribute)

is_reversible() (in module msmtools.analysis)

is_sparse (pyemma.msm.BayesianHMSM attribute)

is_tmatrix() (in module msmtools.analysis)

is_transition_matrix() (in module msmtools.analysis)

iterator() (pyemma.coordinates.clustering.assign.AssignCenters method)

its() (in module pyemma.msm)

K

KmeansClustering (class in pyemma.coordinates.clustering)

kmeanspp_center_assigned() (pyemma.coordinates.clustering.kmeans.KmeansClustering method)

L

lag (pyemma.coordinates.transform.TICA attribute)

lags (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]

lagtime (pyemma.msm.BayesianHMSM attribute)

lagtimes (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]

largest_connected_set (pyemma.msm.BayesianMSM attribute)

largest_connected_set() (in module msmtools.estimation)

largest_connected_submatrix() (in module msmtools.estimation)

lifetimes (pyemma.msm.BayesianHMSM attribute)

load() (in module pyemma.coordinates)

load_discrete_trajectory() (in module msmtools.dtraj)

load_dtraj() (in module msmtools.dtraj)

load_from_files() (pyemma.coordinates.data.DataInMemory class method)

log_likelihood() (in module msmtools.estimation)

logger (pyemma.coordinates.clustering.assign.AssignCenters attribute)

M

major_flux() (msmtools.flux.ReactiveFlux method)

markov_model() (in module pyemma.msm)

max_centers (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)

MaximumLikelihoodHMSM (class in pyemma.msm)

MaximumLikelihoodMSM (class in pyemma.msm)

MBAR (class in pyemma.thermo)

mbar() (in module pyemma.thermo)

MDFeaturizer (class in pyemma.coordinates.data)

mean (pyemma.coordinates.transform.pca.PCA attribute)

MEMM (class in pyemma.thermo)

metastable_assignment (pyemma.msm.PCCA attribute)

metastable_assignments (pyemma.msm.BayesianHMSM attribute)

metastable_distributions (pyemma.msm.BayesianHMSM attribute)

metastable_memberships (pyemma.msm.BayesianHMSM attribute)

metastable_sets (pyemma.msm.BayesianHMSM attribute)

meval() (pyemma.thermo.DTRAM method)

mfpt (msmtools.flux.ReactiveFlux attribute)

mfpt() (in module msmtools.analysis)

mfpt_sensitivity() (in module msmtools.analysis)

MiniBatchKmeansClustering (class in pyemma.coordinates.clustering)

model (pyemma.coordinates.clustering.assign.AssignCenters attribute)

models (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]

MSM (class in pyemma.msm)

msmtools.analysis (module)

msmtools.dtraj (module)

msmtools.estimation (module)

msmtools.flux (module)

msmtools.generation (module)

mu (pyemma.coordinates.transform.TICA attribute)

MultiThermModel (class in pyemma.thermo)

N

n_clusters (pyemma.coordinates.clustering.regspace.RegularSpaceClustering attribute)

n_frames_total() (pyemma.coordinates.clustering.assign.AssignCenters method)

n_jobs (pyemma.coordinates.clustering.assign.AssignCenters attribute)

name (pyemma.coordinates.clustering.assign.AssignCenters attribute)

ndim (pyemma.coordinates.clustering.assign.AssignCenters attribute)

neig (pyemma.msm.BayesianHMSM attribute)

net_flux (msmtools.flux.ReactiveFlux attribute)

NetworkPlot (class in pyemma.plots)

nstates (msmtools.flux.ReactiveFlux attribute)

nstates_full (pyemma.msm.BayesianMSM attribute)

nstates_obs (pyemma.msm.BayesianHMSM attribute)

ntraj (pyemma.coordinates.clustering.assign.AssignCenters attribute)

number_of_states() (in module msmtools.dtraj)

number_of_timescales (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]

number_of_trajectories() (pyemma.coordinates.clustering.assign.AssignCenters method)

NumPyFileReader (class in pyemma.coordinates.data)

O

observable_set (pyemma.msm.BayesianHMSM attribute)

observable_state_indexes (pyemma.msm.BayesianHMSM attribute)

observation_probabilities (pyemma.msm.BayesianHMSM attribute)

output_type() (pyemma.coordinates.clustering.assign.AssignCenters method)

overwrite_dtrajs (pyemma.coordinates.clustering.assign.AssignCenters attribute)

P

P (pyemma.msm.BayesianHMSM attribute)

pairs() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer static method)

parametrize() (pyemma.coordinates.clustering.assign.AssignCenters method)

partial_fit() (pyemma.coordinates.transform.pca.PCA method)

pathways() (in module msmtools.flux)

PCA (class in pyemma.coordinates.transform)

pca() (in module pyemma.coordinates)

PCCA (class in pyemma.msm)

pcca() (in module msmtools.analysis)

pi (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)

Pipeline (class in pyemma.coordinates.pipelines), [1], [2], [3]

pipeline() (in module pyemma.coordinates)

plot_cktest() (in module pyemma.plots)

plot_flux() (in module pyemma.plots)

plot_free_energy() (in module pyemma.plots)

plot_implied_timescales() (in module pyemma.plots)

plot_markov_model() (in module pyemma.plots)

plot_network() (in module pyemma.plots)

pointwise_free_energies() (pyemma.thermo.TRAM method)

predictions (pyemma.msm.ChapmanKolmogorovValidator attribute)

predictions_conf (pyemma.msm.ChapmanKolmogorovValidator attribute)

prior_const() (in module msmtools.estimation)

prior_neighbor() (in module msmtools.estimation)

prior_rev() (in module msmtools.estimation)

propagate() (pyemma.msm.BayesianHMSM method)

PyCSVReader (class in pyemma.coordinates.data)

pyemma.coordinates (module)

pyemma.coordinates.clustering (module)

pyemma.coordinates.data (module)

pyemma.coordinates.pipelines (module)

pyemma.coordinates.transform (module)

pyemma.msm (module)

pyemma.plots (module)

pyemma.thermo (module)

pyemma.util.config (module)

R

ra_itraj_cuboid (pyemma.coordinates.clustering.assign.AssignCenters attribute)

ra_itraj_jagged (pyemma.coordinates.clustering.assign.AssignCenters attribute)

ra_itraj_linear (pyemma.coordinates.clustering.assign.AssignCenters attribute)

ra_linear (pyemma.coordinates.clustering.assign.AssignCenters attribute)

rate (msmtools.flux.ReactiveFlux attribute)

rate() (in module msmtools.flux)

rdl_decomposition() (in module msmtools.analysis)

ReactiveFlux (class in msmtools.flux)

read_discrete_trajectory() (in module msmtools.dtraj)

read_dtraj() (in module msmtools.dtraj)

register_progress_callback() (pyemma.coordinates.clustering.assign.AssignCenters method)

RegularSpaceClustering (class in pyemma.coordinates.clustering)

relaxation() (in module msmtools.analysis)

reversible (pyemma.msm.BayesianHMSM attribute)

S

sample_by_distributions() (pyemma.msm.BayesianMSM method)

sample_by_observation_probabilities() (pyemma.msm.BayesianHMSM method)

sample_by_state() (pyemma.msm.BayesianMSM method)

sample_conf() (pyemma.msm.BayesianHMSM method)

sample_f() (pyemma.msm.BayesianHMSM method)

sample_indexes_by_cluster() (pyemma.coordinates.clustering.assign.AssignCenters method)

sample_indexes_by_distribution() (in module msmtools.dtraj)

sample_indexes_by_sequence() (in module msmtools.dtraj)

sample_indexes_by_state() (in module msmtools.dtraj)

sample_mean (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]

sample_mean() (pyemma.msm.BayesianHMSM method)

sample_std (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]

sample_std() (pyemma.msm.BayesianHMSM method)

SampledHMSM (class in pyemma.msm)

SampledMSM (class in pyemma.msm)

samples_available (pyemma.msm.estimators.implied_timescales.ImpliedTimescales attribute), [1], [2]

save_discrete_trajectory() (in module msmtools.dtraj)

save_dtraj() (in module msmtools.dtraj)

save_dtrajs() (pyemma.coordinates.clustering.assign.AssignCenters method)

save_traj() (in module pyemma.coordinates)

save_trajs() (in module pyemma.coordinates)

scatter_contour() (in module pyemma.plots)

select() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

select_Backbone() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

select_Ca() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

select_Heavy() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method)

set_element() (pyemma.coordinates.pipelines.Discretizer method)

set_model_params() (pyemma.msm.BayesianHMSM method)

set_params() (pyemma.coordinates.clustering.assign.AssignCenters method)

show_progress (pyemma.coordinates.clustering.assign.AssignCenters attribute)

simulate() (pyemma.msm.BayesianHMSM method)

source() (in module pyemma.coordinates)

sparse (pyemma.msm.BayesianHMSM attribute)

statdist() (in module msmtools.analysis)

stationary_distribution (msmtools.flux.ReactiveFlux attribute)

stationary_distribution() (in module msmtools.analysis)

stationary_distribution_obs (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM attribute)

stationary_distribution_sensitivity() (in module msmtools.analysis)

StationaryModel (class in pyemma.thermo)

StreamingTransformer (class in pyemma.coordinates.transform.transformer)

submodel() (pyemma.msm.BayesianHMSM method)

submodel_disconnect() (pyemma.msm.BayesianHMSM method)

submodel_largest() (pyemma.msm.BayesianHMSM method)

submodel_populous() (pyemma.msm.BayesianHMSM method)

T

TICA (class in pyemma.coordinates.transform)

tica() (in module pyemma.coordinates)

timescale_sensitivity() (in module msmtools.analysis)

timescales (pyemma.coordinates.transform.TICA attribute)

timescales() (in module msmtools.analysis)

timescales_hmsm() (in module pyemma.msm)

timescales_msm() (in module pyemma.msm)

timestep_model (pyemma.msm.BayesianHMSM attribute)

tmatrix() (in module msmtools.estimation)

tmatrix_cov() (in module msmtools.estimation)

tmatrix_sampler() (in module msmtools.estimation)

to_netflux() (in module msmtools.flux)

total_flux (msmtools.flux.ReactiveFlux attribute)

total_flux() (in module msmtools.flux)

tpt() (in module msmtools.flux)

trajectory_length() (pyemma.coordinates.clustering.assign.AssignCenters method)

trajectory_lengths() (pyemma.coordinates.clustering.assign.AssignCenters method)

trajectory_weights() (pyemma.msm.BayesianHMSM method)

TRAM (class in pyemma.thermo)

tram() (in module pyemma.thermo)

transform() (pyemma.coordinates.clustering.assign.AssignCenters method)

transition_matrix (pyemma.msm.BayesianHMSM attribute)

transition_matrix() (in module msmtools.estimation)

transition_matrix_metropolis_1d() (in module msmtools.generation)

transition_matrix_obs() (pyemma.msm.BayesianHMSM method)

U

UniformTimeClustering (class in pyemma.coordinates.clustering)

update_model_params() (pyemma.coordinates.clustering.assign.AssignCenters method)

V

W

write_dtraj() (in module msmtools.dtraj)

write_to_csv() (pyemma.coordinates.clustering.assign.AssignCenters method)