Index

_

__init__() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.data.CustomFeature method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.MDFeaturizer method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.pipelines.Pipeline method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) (pyemma.msm.flux.ReactiveFlux method) (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.ImpliedTimescales method) (pyemma.msm.ui.MSM method) (pyemma.plots.NetworkPlot method)

A

A (pyemma.msm.flux.ReactiveFlux attribute) active_count_fraction (pyemma.msm.ui.EstimatedMSM attribute) active_set (pyemma.msm.ui.EstimatedMSM attribute) active_state_fraction (pyemma.msm.ui.EstimatedMSM attribute) active_state_indexes (pyemma.msm.ui.EstimatedMSM attribute) add_all() (pyemma.coordinates.data.MDFeaturizer method) add_angles() (pyemma.coordinates.data.MDFeaturizer method) add_backbone_torsions() (pyemma.coordinates.data.MDFeaturizer method) add_contacts() (pyemma.coordinates.data.MDFeaturizer method) add_custom_feature() (pyemma.coordinates.data.MDFeaturizer method)

add_custom_func() (pyemma.coordinates.data.MDFeaturizer method) add_dihedrals() (pyemma.coordinates.data.MDFeaturizer method) add_distances() (pyemma.coordinates.data.MDFeaturizer method) add_distances_ca() (pyemma.coordinates.data.MDFeaturizer method) add_element() (pyemma.coordinates.pipelines.Discretizer method) (pyemma.coordinates.pipelines.Pipeline method), [1] add_inverse_distances() (pyemma.coordinates.data.MDFeaturizer method) add_selection() (pyemma.coordinates.data.MDFeaturizer method) assign() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) assign_to_centers() (in module pyemma.coordinates) AssignCenters (class in pyemma.coordinates.clustering)

B

B (pyemma.msm.flux.ReactiveFlux attribute) backward_committor (pyemma.msm.flux.ReactiveFlux attribute) bootstrap() (pyemma.msm.ui.ImpliedTimescales method)

bootstrap_counts() (in module pyemma.msm.estimation) bootstrap_trajectories() (in module pyemma.msm.estimation)

C

chunksize (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) cktest() (in module pyemma.msm) cluster_kmeans() (in module pyemma.coordinates) cluster_regspace() (in module pyemma.coordinates) cluster_uniform_time() (in module pyemma.coordinates) cmatrix() (in module pyemma.msm.estimation) coarse_grain() (pyemma.msm.flux.ReactiveFlux method) coarsegrain() (in module pyemma.msm.flux) committor (pyemma.msm.flux.ReactiveFlux attribute) committor() (in module pyemma.msm.analysis) committor_backward() (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method) committor_forward() (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method)

committor_sensitivity() (in module pyemma.msm.analysis) computed (pyemma.msm.ui.EstimatedMSM attribute) conf_values (in module pyemma.util.config) connected_cmatrix() (in module pyemma.msm.estimation) connected_sets (pyemma.msm.ui.EstimatedMSM attribute) connected_sets() (in module pyemma.msm.estimation) correlation() (in module pyemma.msm.analysis) (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method) count_matrix() (in module pyemma.msm.estimation) count_matrix_active (pyemma.msm.ui.EstimatedMSM attribute) count_matrix_full (pyemma.msm.ui.EstimatedMSM attribute) CustomFeature (class in pyemma.coordinates.data)

D

data_producer (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) DataInMemory (class in pyemma.coordinates.data) describe() (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.MDFeaturizer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) dimension() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.MDFeaturizer method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) discrete_trajectories_active (pyemma.msm.ui.EstimatedMSM attribute)

discrete_trajectories_full (pyemma.msm.ui.EstimatedMSM attribute) Discretizer (class in pyemma.coordinates.pipelines) discretizer() (in module pyemma.coordinates) dmin (pyemma.coordinates.clustering.RegularSpaceClustering attribute) dtrajs (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.pipelines.Discretizer attribute)

E

effective_count_matrix (pyemma.msm.ui.EstimatedMSM attribute) eigenvalue_sensitivity() (in module pyemma.msm.analysis) eigenvalues() (in module pyemma.msm.analysis) (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method) eigenvector_sensitivity() (in module pyemma.msm.analysis) eigenvectors() (in module pyemma.msm.analysis) eigenvectors_left() (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method) eigenvectors_right() (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method) error_perturbation() (in module pyemma.msm.estimation)

estimate() (pyemma.msm.ui.EstimatedMSM method) estimate_markov_model() (in module pyemma.msm) EstimatedMSM (class in pyemma.msm.ui) expectation() (in module pyemma.msm.analysis) (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method) expectation_sensitivity() (in module pyemma.msm.analysis) expected_counts() (in module pyemma.msm.analysis) expected_counts_stationary() (in module pyemma.msm.analysis)

F

feature_TIC_correlation (pyemma.coordinates.transform.TICA attribute) FeatureReader (class in pyemma.coordinates.data) featurizer() (in module pyemma.coordinates) fingerprint_correlation() (in module pyemma.msm.analysis) (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method) fingerprint_relaxation() (in module pyemma.msm.analysis) (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method) flux (pyemma.msm.flux.ReactiveFlux attribute)

flux_consumers() (in module pyemma.msm.flux) flux_matrix() (in module pyemma.msm.flux) flux_producers() (in module pyemma.msm.flux) flux_production() (in module pyemma.msm.flux) forward_committor (pyemma.msm.flux.ReactiveFlux attribute)

G

generate_traj() (in module pyemma.msm.generation) (pyemma.msm.ui.EstimatedMSM method) get_lagtimes() (pyemma.msm.ui.ImpliedTimescales method) get_output() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) get_sample_conf() (pyemma.msm.ui.ImpliedTimescales method)

get_sample_mean() (pyemma.msm.ui.ImpliedTimescales method) get_sample_std() (pyemma.msm.ui.ImpliedTimescales method) get_timescales() (pyemma.msm.ui.ImpliedTimescales method) gross_flux (pyemma.msm.flux.ReactiveFlux attribute)

I

I (pyemma.msm.flux.ReactiveFlux attribute) ImpliedTimescales (class in pyemma.msm.ui) in_memory (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute) (pyemma.coordinates.data.DataInMemory attribute) (pyemma.coordinates.data.FeatureReader attribute) (pyemma.coordinates.data.NumPyFileReader attribute) (pyemma.coordinates.data.PyCSVReader attribute) (pyemma.coordinates.transform.PCA attribute) (pyemma.coordinates.transform.TICA attribute) is_connected() (in module pyemma.msm.analysis) (in module pyemma.msm.estimation) is_rate_matrix() (in module pyemma.msm.analysis) is_reversible (pyemma.msm.ui.EstimatedMSM attribute) (pyemma.msm.ui.MSM attribute)

is_reversible() (in module pyemma.msm.analysis) is_sparse (pyemma.msm.ui.EstimatedMSM attribute) (pyemma.msm.ui.MSM attribute) is_tmatrix() (in module pyemma.msm.analysis) is_transition_matrix() (in module pyemma.msm.analysis) iterator() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) its() (in module pyemma.msm)

K

KmeansClustering (class in pyemma.coordinates.clustering)

L

lag (pyemma.coordinates.transform.TICA attribute) lagtime (pyemma.msm.ui.EstimatedMSM attribute) lagtimes (pyemma.msm.ui.ImpliedTimescales attribute) largest_connected_set (pyemma.msm.ui.EstimatedMSM attribute) largest_connected_set() (in module pyemma.msm.estimation) largest_connected_submatrix() (in module pyemma.msm.estimation)

load() (in module pyemma.coordinates) load_discrete_trajectory() (in module pyemma.msm.io) load_dtraj() (in module pyemma.msm.io) load_from_files() (pyemma.coordinates.data.DataInMemory class method) load_matrix() (in module pyemma.msm.io) log_likelihood() (in module pyemma.msm.estimation)

M

major_flux() (pyemma.msm.flux.ReactiveFlux method) map() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.data.MDFeaturizer method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) markov_model() (in module pyemma.msm) max_centers (pyemma.coordinates.clustering.RegularSpaceClustering attribute) MDFeaturizer (class in pyemma.coordinates.data) mean (pyemma.coordinates.transform.TICA attribute) metastable_assignments (pyemma.msm.ui.EstimatedMSM attribute) (pyemma.msm.ui.MSM attribute)

metastable_distributions (pyemma.msm.ui.EstimatedMSM attribute) (pyemma.msm.ui.MSM attribute) metastable_memberships (pyemma.msm.ui.EstimatedMSM attribute) (pyemma.msm.ui.MSM attribute) metastable_sets (pyemma.msm.ui.EstimatedMSM attribute) (pyemma.msm.ui.MSM attribute) mfpt (pyemma.msm.flux.ReactiveFlux attribute) mfpt() (in module pyemma.msm.analysis) (in module pyemma.msm.flux) (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method) mfpt_sensitivity() (in module pyemma.msm.analysis) MSM (class in pyemma.msm.ui)

N

n_frames_total() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) net_flux (pyemma.msm.flux.ReactiveFlux attribute) NetworkPlot (class in pyemma.plots) nstates (pyemma.msm.flux.ReactiveFlux attribute) (pyemma.msm.ui.EstimatedMSM attribute) (pyemma.msm.ui.MSM attribute)

number_of_timescales (pyemma.msm.ui.ImpliedTimescales attribute) number_of_trajectories() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) NumPyFileReader (class in pyemma.coordinates.data)

O

output_type() (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method)

overwrite_dtrajs (pyemma.coordinates.clustering.AssignCenters attribute) (pyemma.coordinates.clustering.KmeansClustering attribute) (pyemma.coordinates.clustering.RegularSpaceClustering attribute) (pyemma.coordinates.clustering.UniformTimeClustering attribute)

P

pairs() (pyemma.coordinates.data.MDFeaturizer static method) parametrize() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.pipelines.Discretizer method) (pyemma.coordinates.pipelines.Pipeline method), [1] (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) pathways() (in module pyemma.msm.flux) (pyemma.msm.flux.ReactiveFlux method) PCA (class in pyemma.coordinates.transform) pca() (in module pyemma.coordinates) pcca() (in module pyemma.msm.analysis) (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method) Pipeline (class in pyemma.coordinates.pipelines), [1] pipeline() (in module pyemma.coordinates) plot_flux() (in module pyemma.plots) plot_implied_timescales() (in module pyemma.plots) plot_markov_model() (in module pyemma.plots) plot_network() (pyemma.plots.NetworkPlot method) prior_const() (in module pyemma.msm.estimation) prior_neighbor() (in module pyemma.msm.estimation) prior_rev() (in module pyemma.msm.estimation)

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.msm.analysis (module) pyemma.msm.estimation (module) pyemma.msm.flux (module) pyemma.msm.generation (module) pyemma.msm.io (module) pyemma.plots (module) pyemma.util.config (module)

R

rate (pyemma.msm.flux.ReactiveFlux attribute) rate() (in module pyemma.msm.flux) rdl_decomposition() (in module pyemma.msm.analysis) ReactiveFlux (class in pyemma.msm.flux) read_discrete_trajectory() (in module pyemma.msm.io)

read_dtraj() (in module pyemma.msm.io) read_matrix() (in module pyemma.msm.io) RegularSpaceClustering (class in pyemma.coordinates.clustering) relaxation() (in module pyemma.msm.analysis) (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method) run() (pyemma.coordinates.pipelines.Discretizer method) (pyemma.coordinates.pipelines.Pipeline method), [1]

S

sample_by_distributions() (pyemma.msm.ui.EstimatedMSM method) sample_by_state() (pyemma.msm.ui.EstimatedMSM method) sample_lagtimes (pyemma.msm.ui.ImpliedTimescales attribute) sample_mean (pyemma.msm.ui.ImpliedTimescales attribute) sample_number_of_timescales (pyemma.msm.ui.ImpliedTimescales attribute) sample_std (pyemma.msm.ui.ImpliedTimescales attribute) samples_available (pyemma.msm.ui.ImpliedTimescales attribute) save_discrete_trajectory() (in module pyemma.msm.io) save_dtraj() (in module pyemma.msm.io) save_dtrajs() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.pipelines.Discretizer method) save_matrix() (in module pyemma.msm.io) save_traj() (in module pyemma.coordinates)

save_trajs() (in module pyemma.coordinates) scatter_contour() (in module pyemma.plots) select() (pyemma.coordinates.data.MDFeaturizer method) select_Backbone() (pyemma.coordinates.data.MDFeaturizer method) select_Ca() (pyemma.coordinates.data.MDFeaturizer method) select_Heavy() (pyemma.coordinates.data.MDFeaturizer method) set_element() (pyemma.coordinates.pipelines.Discretizer method) (pyemma.coordinates.pipelines.Pipeline method), [1] source() (in module pyemma.coordinates) statdist() (in module pyemma.msm.analysis) stationary_distribution (pyemma.msm.flux.ReactiveFlux attribute) (pyemma.msm.ui.EstimatedMSM attribute) (pyemma.msm.ui.MSM attribute) stationary_distribution() (in module pyemma.msm.analysis) stationary_distribution_sensitivity() (in module pyemma.msm.analysis)

T

TICA (class in pyemma.coordinates.transform) tica() (in module pyemma.coordinates) timescale_sensitivity() (in module pyemma.msm.analysis) timescales (pyemma.msm.ui.ImpliedTimescales attribute) timescales() (in module pyemma.msm.analysis) (pyemma.msm.ui.EstimatedMSM method) (pyemma.msm.ui.MSM method) timestep (pyemma.msm.ui.EstimatedMSM attribute) (pyemma.msm.ui.MSM attribute) tmatrix() (in module pyemma.msm.estimation) tmatrix_cov() (in module pyemma.msm.estimation) tmatrix_sampler() (in module pyemma.msm.estimation) to_netflux() (in module pyemma.msm.flux)

total_flux (pyemma.msm.flux.ReactiveFlux attribute) total_flux() (in module pyemma.msm.flux) tpt() (in module pyemma.msm) (in module pyemma.msm.flux) trajectory_length() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) trajectory_lengths() (pyemma.coordinates.clustering.AssignCenters method) (pyemma.coordinates.clustering.KmeansClustering method) (pyemma.coordinates.clustering.RegularSpaceClustering method) (pyemma.coordinates.clustering.UniformTimeClustering method) (pyemma.coordinates.data.DataInMemory method) (pyemma.coordinates.data.FeatureReader method) (pyemma.coordinates.data.NumPyFileReader method) (pyemma.coordinates.data.PyCSVReader method) (pyemma.coordinates.transform.PCA method) (pyemma.coordinates.transform.TICA method) trajectory_weights() (pyemma.msm.ui.EstimatedMSM method) transition_matrix (pyemma.msm.ui.EstimatedMSM attribute) (pyemma.msm.ui.MSM attribute) transition_matrix() (in module pyemma.msm.estimation) transition_matrix_metropolis_1d() (in module pyemma.msm.generation)

U

UniformTimeClustering (class in pyemma.coordinates.clustering)

used_filenames (in module pyemma.util.config)

W

write_discrete_trajectory() (in module pyemma.msm.io) write_dtraj() (in module pyemma.msm.io)

write_matrix() (in module pyemma.msm.io)