Index

_

__init__() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.MiniBatchKmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.data._base.transformer.StreamingTransformer method) (pyemma.coordinates.data.CustomFeature method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.FragmentedTrajectoryReader method) (pyemma.coordinates.data.MDFeaturizer method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.estimation.covariance.LaggedCovariance method) (pyemma.coordinates.pipelines.Pipeline method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.coordinates.transform.VAMP method) (pyemma.coordinates.transform.VAMPChapmanKolmogorovValidator method) (pyemma.coordinates.transform.VAMPModel method) (pyemma.msm.BayesianHMSM method) (pyemma.msm.BayesianMSM method) (pyemma.msm.ChapmanKolmogorovValidator method) (pyemma.msm.HMSM method) (pyemma.msm.ImpliedTimescales method) (pyemma.msm.MaximumLikelihoodHMSM method) (pyemma.msm.MaximumLikelihoodMSM method) (pyemma.msm.MSM method) (pyemma.msm.OOMReweightedMSM method) (pyemma.msm.PCCA method) (pyemma.msm.ReactiveFlux method) (pyemma.msm.SampledHMSM method) (pyemma.msm.SampledMSM method) (pyemma.plots.NetworkPlot method) (pyemma.thermo.DTRAM method) (pyemma.thermo.MBAR method) (pyemma.thermo.MEMM method) (pyemma.thermo.MultiThermModel method) (pyemma.thermo.StationaryModel method) (pyemma.thermo.TRAM method) (pyemma.thermo.WHAM method)

A

A() (pyemma.msm.models.ReactiveFlux property) active_set() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) 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.Pipeline method), [1] add_group_COM() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer 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_COM() (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) add_sidechain_torsions() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) assign_to_centers() (in module pyemma.coordinates) AssignCenters (class in pyemma.coordinates.clustering) (class in pyemma.coordinates.clustering.assign)

B

B() (pyemma.msm.models.ReactiveFlux property) backward_committor() (pyemma.msm.models.ReactiveFlux property) bayesian_hidden_markov_model() (in module pyemma.msm) bayesian_markov_model() (in module pyemma.msm)

BayesianHMSM (class in pyemma.msm) (class in pyemma.msm.estimators.bayesian_hmsm) BayesianMSM (class in pyemma.msm) (class in pyemma.msm.estimators.bayesian_msm)

C

cfg_dir() (pyemma.util._config.Config property) ChapmanKolmogorovValidator (class in pyemma.msm) check_version() (pyemma.util._config.Config property) chunksize() (pyemma.coordinates.pipelines.Pipeline property), [1] cktest() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM 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) coarse_grain() (pyemma.msm.models.ReactiveFlux method)

combine_sources() (in module pyemma.coordinates) committor() (pyemma.msm.models.ReactiveFlux property) committor_backward() (pyemma.msm.models.msm.MSM method) committor_forward() (pyemma.msm.models.msm.MSM method) Config (class in pyemma.util._config) converged() (pyemma.coordinates.clustering.kmeans.KmeansClustering property) coordinates_check_output() (pyemma.util._config.Config property) correlation() (pyemma.msm.models.msm.MSM method) covariance_lagged() (in module pyemma.coordinates) cumvar() (pyemma.coordinates.transform.pca.PCA property) CustomFeature (class in pyemma.coordinates.data)

D

data_producer() (pyemma.coordinates.clustering.assign.AssignCenters property) (pyemma.coordinates.transform.pca.PCA property) (pyemma.coordinates.transform.tica.TICA property) DataInMemory (class in pyemma.coordinates.data) default_chunksize() (pyemma.util._config.Config property) DEFAULT_CONFIG_DIR (pyemma.util._config.Config attribute) default_config_file() (pyemma.util._config.Config property) DEFAULT_CONFIG_FILE_NAME (pyemma.util._config.Config attribute) default_logging_file() (pyemma.util._config.Config property) DEFAULT_LOGGING_FILE_NAME (pyemma.util._config.Config attribute) describe() (pyemma.coordinates.clustering.assign.AssignCenters method) (pyemma.coordinates.clustering.kmeans.KmeansClustering method) (pyemma.coordinates.clustering.regspace.RegularSpaceClustering method) (pyemma.coordinates.clustering.uniform_time.UniformTimeClustering method) (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method)

dimension() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) (pyemma.coordinates.transform.pca.PCA method) discrete_trajectories_full() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) discrete_trajectories_lagged() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) discrete_trajectories_obs() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) discretizer() (in module pyemma.coordinates) dmin() (pyemma.coordinates.clustering.regspace.RegularSpaceClustering property) dt_model() (pyemma.msm.models.msm.MSM property) (pyemma.msm.models.ReactiveFlux property) dt_traj() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) dtrajs_full() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) dtrajs_lagged() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) dtrajs_obs() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) DTRAM (class in pyemma.thermo) dtram() (in module pyemma.thermo)

E

effective_count_matrix() (pyemma.msm.estimators.maximum_likelihood_msm.MaximumLikelihoodMSM property) eigenvalues() (pyemma.coordinates.transform.pca.PCA property) (pyemma.msm.models.msm.MSM method) eigenvectors() (pyemma.coordinates.transform.pca.PCA property) eigenvectors_left() (pyemma.msm.models.msm.MSM method) eigenvectors_right() (pyemma.msm.models.msm.MSM method) estimate() (pyemma.coordinates.transform.tica.TICA method) (pyemma.msm.estimators.bayesian_msm.BayesianMSM method) (pyemma.msm.estimators.implied_timescales.ImpliedTimescales method), [1], [2]

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) estimators() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales property), [1], [2] expectation() (pyemma.msm.models.msm.MSM method)

F

feature_PC_correlation() (pyemma.coordinates.transform.pca.PCA property) FeatureReader (class in pyemma.coordinates.data) featurizer() (in module pyemma.coordinates) fingerprint_correlation() (pyemma.msm.models.msm.MSM method) fingerprint_relaxation() (pyemma.msm.models.msm.MSM method)

fixed_seed() (pyemma.coordinates.clustering.kmeans.KmeansClustering property) flux() (pyemma.msm.models.ReactiveFlux property) forward_committor() (pyemma.msm.models.ReactiveFlux property) fraction_of_frames() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales property), [1], [2] FragmentedTrajectoryReader (class in pyemma.coordinates.data)

G

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() (pyemma.msm.models.ReactiveFlux property)

H

HMSM (class in pyemma.msm)

I

I() (pyemma.msm.models.ReactiveFlux property) ImpliedTimescales (class in pyemma.msm) (class in pyemma.msm.estimators.implied_timescales), [1], [2] init_hmsm() (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM property)

init_strategy() (pyemma.coordinates.clustering.kmeans.KmeansClustering property) is_reversible() (pyemma.msm.models.msm.MSM property) is_sparse() (pyemma.msm.models.msm.MSM property) its() (in module pyemma.msm)

K

keys() (pyemma.util._config.Config method)

KmeansClustering (class in pyemma.coordinates.clustering) (class in pyemma.coordinates.clustering.kmeans)

L

LaggedCovariance (class in pyemma.coordinates.estimation.covariance) lags() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales property), [1], [2] lagtime() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) lagtimes() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales property), [1], [2]

list_models() (in module pyemma) load() (in module pyemma) (in module pyemma.coordinates) (pyemma.util._config.Config method) logging_config() (pyemma.util._config.Config property)

M

major_flux() (pyemma.msm.models.ReactiveFlux method) markov_model() (in module pyemma.msm) max_centers() (pyemma.coordinates.clustering.regspace.RegularSpaceClustering property) MaximumLikelihoodHMSM (class in pyemma.msm) (class in pyemma.msm.estimators.maximum_likelihood_hmsm) MaximumLikelihoodMSM (class in pyemma.msm) (class in pyemma.msm.estimators.maximum_likelihood_msm) MBAR (class in pyemma.thermo) mbar() (in module pyemma.thermo) MDFeaturizer (class in pyemma.coordinates.data) (class in pyemma.coordinates.data.featurization.featurizer) mean() (pyemma.coordinates.transform.pca.PCA property) MEMM (class in pyemma.thermo) (class in pyemma.thermo.models.memm), [1], [2], [3] metastable_assignments() (pyemma.msm.models.msm.MSM property) metastable_distributions() (pyemma.msm.models.msm.MSM property) metastable_memberships() (pyemma.msm.models.msm.MSM property) metastable_sets() (pyemma.msm.models.msm.MSM property) meval() (pyemma.thermo.models.multi_therm.MultiThermModel method), [1], [2], [3] mfpt() (pyemma.msm.models.msm.MSM method) (pyemma.msm.models.ReactiveFlux property)

MiniBatchKmeansClustering (class in pyemma.coordinates.clustering) (class in pyemma.coordinates.clustering.kmeans) model() (pyemma.coordinates.transform.tica.TICA property) models() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales property), [1], [2] module pyemma.coordinates pyemma.coordinates.clustering pyemma.coordinates.data pyemma.coordinates.pipelines pyemma.coordinates.transform pyemma.msm pyemma.plots pyemma.thermo MSM (class in pyemma.msm) (class in pyemma.msm.models.msm) msm() (pyemma.thermo.models.memm.MEMM property), [1], [2], [3] msm_init() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) mu() (pyemma.msm.models.ReactiveFlux property) MultiThermModel (class in pyemma.thermo) (class in pyemma.thermo.models.multi_therm), [1], [2], [3] mute() (pyemma.util._config.Config property)

N

n_clusters() (pyemma.coordinates.clustering.regspace.RegularSpaceClustering property) n_metastable() (pyemma.msm.models.msm.MSM property) neig() (pyemma.msm.models.msm.MSM property) net_flux() (pyemma.msm.models.ReactiveFlux property) NetworkPlot (class in pyemma.plots) nits() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales property), [1], [2]

nstates() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) (pyemma.msm.models.msm.MSM property) (pyemma.msm.models.ReactiveFlux property) nstates_obs() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) number_of_timescales() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales property), [1], [2] NumPyFileReader (class in pyemma.coordinates.data)

O

observable_set() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property)

observable_state_indexes() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM property) OOMReweightedMSM (class in pyemma.msm)

P

P() (pyemma.msm.models.msm.MSM property) pairs() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer static method) parametrize() (pyemma.coordinates.pipelines.Pipeline method), [1] partial_fit() (pyemma.coordinates.transform.pca.PCA method) (pyemma.coordinates.transform.tica.TICA method) pathways() (pyemma.msm.models.ReactiveFlux method) PCA (class in pyemma.coordinates.transform) (class in pyemma.coordinates.transform.pca) pca() (in module pyemma.coordinates) PCCA (class in pyemma.msm) pcca() (pyemma.msm.models.msm.MSM method) pi() (pyemma.msm.models.msm.MSM property) Pipeline (class in pyemma.coordinates.pipelines), [1], [2] pipeline() (in module pyemma.coordinates) plot_cktest() (in module pyemma.plots) plot_contour() (in module pyemma.plots) plot_density() (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) plot_state_map() (in module pyemma.plots) propagate() (pyemma.msm.models.msm.MSM 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

Q

qminus() (pyemma.msm.models.ReactiveFlux property)

qplus() (pyemma.msm.models.ReactiveFlux property)

R

rate() (pyemma.msm.models.ReactiveFlux property) ReactiveFlux (class in pyemma.msm) (class in pyemma.msm.models) RegularSpaceClustering (class in pyemma.coordinates.clustering) (class in pyemma.coordinates.clustering.regspace)

relaxation() (pyemma.msm.models.msm.MSM method) remove_all_custom_funcs() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) reversible() (pyemma.msm.models.msm.MSM property)

S

sample_by_observation_probabilities() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) sample_mean() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales property), [1], [2] sample_std() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales property), [1], [2] SampledHMSM (class in pyemma.msm) SampledMSM (class in pyemma.msm) samples_available() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales property), [1], [2] save() (pyemma._base.serialization.SerializableMixIn method) (pyemma.util._config.Config 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.Pipeline method), [1]

set_model_params() (pyemma.msm.models.msm.MSM method) (pyemma.msm.models.ReactiveFlux method) (pyemma.thermo.models.multi_therm.MultiThermModel method), [1], [2], [3] show_config_notification() (pyemma.util._config.Config property) show_progress_bars() (pyemma.util._config.Config property) simulate() (pyemma.msm.models.msm.MSM method) source() (in module pyemma.coordinates) sparse() (pyemma.msm.models.msm.MSM property) stationary_distribution() (pyemma.msm.models.msm.MSM property) (pyemma.msm.models.ReactiveFlux property) StationaryModel (class in pyemma.thermo) StreamingTransformer (class in pyemma.coordinates.data._base.transformer) submodel() (pyemma.msm.estimators.bayesian_hmsm.BayesianHMSM method) (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) submodel_disconnect() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) submodel_largest() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) submodel_populous() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method)

T

TICA (class in pyemma.coordinates.transform) (class in pyemma.coordinates.transform.tica) tica() (in module pyemma.coordinates) timescales() (pyemma.msm.estimators.implied_timescales.ImpliedTimescales property), [1], [2] (pyemma.msm.models.msm.MSM method) timescales_hmsm() (in module pyemma.msm) timescales_msm() (in module pyemma.msm) timestep_model() (pyemma.msm.models.msm.MSM property) topologyfile() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer property)

total_flux() (pyemma.msm.models.ReactiveFlux property) tpt() (in module pyemma.msm) traj_info_max_entries() (pyemma.util._config.Config property) traj_info_max_size() (pyemma.util._config.Config property) trajectory_weights() (pyemma.msm.estimators.maximum_likelihood_hmsm.MaximumLikelihoodHMSM method) TRAM (class in pyemma.thermo) tram() (in module pyemma.thermo) transform() (pyemma.coordinates.data.featurization.featurizer.MDFeaturizer method) transition_matrix() (pyemma.msm.models.msm.MSM property)

U

unbiased_state() (pyemma.thermo.models.multi_therm.MultiThermModel property), [1], [2], [3] UniformTimeClustering (class in pyemma.coordinates.clustering) (class in pyemma.coordinates.clustering.uniform_time)

use_trajectory_lengths_cache() (pyemma.util._config.Config property) used_filenames() (pyemma.util._config.Config property)

V

VAMP (class in pyemma.coordinates.transform) vamp() (in module pyemma.coordinates)

VAMPChapmanKolmogorovValidator (class in pyemma.coordinates.transform) VAMPModel (class in pyemma.coordinates.transform)

W

WHAM (class in pyemma.thermo)

wham() (in module pyemma.thermo)